Pseudomonas: Volume 4: Molecular Biology of Emerging Issues

Pseudomonas

Pseudomonas Edited by Juan-Luis Ramos, CSIC, Granada, Spain Volume 1: Genomics, Life Style and Molecular Architecture Volume 2: Virulence and Gene Regulation Volume 3: Biosynthesis of Macromolecules and Molecular Metabolism Volume 4: Molecular Biology of Emerging Issues

Pseudomonas Volume 4 Molecular Biology of Emerging Issues

Edited by

Juan-Luis Ramos CSIC Granada, Spain

and

Roger C. Levesque Universit´e Laval Qu´ebec, Canada

Library of Congress Cataloging-in-Publication Data Pseudomonas / edited by Juan-Luis Ramos. p. cm. Includes bibliographical references and index. ISBN 0-306-48375-0 (v. 1) – ISBN 0-306-48376-9 (v. 2) – ISBN 0-306-48377-7 (v. 3) – ISBN 0-306-48378-5 (set) 1. Pseudomonas. I. Ramos, Juan-Luis, 1956– QR82.P78P772 2004 579.3 32 – dc22 2004043811

ISBN-10 0-306-48375-0 (Vol. 1) ISBN-13 978-0-306-48375-2 (Vol. 1) ISBN-10 0-306-48376-9 (Vol. 2) ISBN-13 978-0-306-48376-9 (Vol. 2) ISBN-10 0-306-48377-7 (Vol. 3) ISBN-13 978-0-306-48377-6 (Vol. 3) ISBN-10 0-387-28834-1 (Vol. 4) ISBN-13 978-0-387-28834-5 (Vol. 4) Also available as part of an indivisible set of all 3 volumes 0-306-48378-5 C 2006 Springer

www.springer.com 10 9 8 7 6 5 4 3 2 1 A C.I.P. record for this book is available from the Library of Congress. All rights reserved. No part of this work may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microﬁlming, recording or otherwise, without written permission from the Publisher, with the exception of any material supplied speciﬁcally for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Printed in the Netherlands.

PREFACE

Twenty years have gone by since Jack Sokatch ﬁrst published his outstanding The Biology of Pseudomonas back in 1986. This was followed by two books published by the ASM that contained the presentations of the Pseudomonas meetings held in Chicago in 1989 and Trieste in 1991. The earlier volume of these two was edited by Simon Silver, Al Chakrabarty, Barbara Iglewski, and Sam Kaplan, and the later one by Enrica Galli, Simon Silver, and Bernard Witholt. The time was ripe for a series of books on Pseudomonas because of its importance in human and plant pathogenesis, bioﬁlms, soil and rhizosphere colonization, etc. Efforts were devoted to produce the ﬁrst three volumes of the series on the biology of Pseudomonas after a meeting with Kluwer staff members in August 2002 during the XI IUMS conference in Paris (France). In less than a year a group of outstanding scientists in the ﬁeld, after devoting much of their valuable time, managed to complete their chapters for the three volumes of the series. To ensure the high standard of each chapter, renowned scientists participated in the reviewing process. The three books collected part of the “explosion” of new vital information on the genus Pseudomonas. A rapid search for articles containing the word “Pseudomonas” in the title in the last 10 years produces more than 6000 articles! Consequently, not all possible topics relevant to this genus were covered in the three previous volumes. This new volume, Pseudomonas volume IV edited by Roger Levesque from Universit´e Laval in Canada and Juan L. Ramos from the CSIC in Spain, is intended to collect some of the most relevant emerging new issues. This fourth volume on Pseudomonas is organized in various topics grouped under a common heading: “Pseudomonas: Molecular Biology of Emerging Issues” and the chapters are organized in three sections: Virulence and Pathogens, Genomics and Proteomics, and Physiology, Metabolism and Biotechnology. The section “Virulence and Pathogens” comprises a series of fascinating chapters on relevant issues that make bacteria of the species Pseudomonas aeruginosa pathogenic for humans and animals. Typing of strain collections using different molecular approaches have revealed that the current P. aeruginosa population is in linkage equilibrium and consists of a network of equivalent

Preface

genotypes. How these bacteria colonize the host tissues, which genes are specifically induced, cloning of pathogenesis determinants, how bacteria acquire iron or the role of phospholipases are some of the issues that are treated in this section. The section “Genomics and proteomics” covers in two chapters issue related to how a genome-wide mutant library of P. aeruginosa is created, together with an update of the genome database of the PAO1 strain. This information is of an extremely high value not only for those working in P. aeruginosa but also for scientists working with other species of the genus Pseudomonas, an even to those working in other more general ﬁelds. This section also includes an authoritative review of type IV pili in species of the genus Pseudomonas and their role in twitching motility, bacteriophage sensitivity, attachment to surfaces and DNA uptake. Finally the section on Physiology, Metabolism and Biotechnology covers the characteristics of a set of extremely important proteins in the metabolism of Pseudomonas: The oxygenases. The chapters included in this section cover structure, mechanisms of reaction and biotechnological potential of the enzymes that make Pseudomonas key in mineralization of many chemicals and in biotransformation processes. The chapter on the evolution of catabolic pathways explores some of the catabolic specialties of bacteria of this genus and how the information is spread in nature. This fourth volume would never have seen the light if it were not for a group of outstanding scientists in the ﬁeld, who after devoting much of their valuable time, have produced enlightening chapters to try to complete the story that began with the three previous volumes of the series. It has been an honor for us to work with them and we truly thank them. The review process has also been of great importance to ensure the high standard of each chapter. Renowned scientists have participated in the review, correction, and editing of the chapters. Their assistance is immensely appreciated. We would like to express my most sincere gratitude to: Arie Ben-Bassat Lori Burrows Pierre Cornelis Eduardo D´ıaz Estrella Duque Kensuke Furukawa

Jos´e-Luis Garc´ıa Bob Hanco*ck Karl-Erich Jaeger Jos´e-Luis Mart´ınez Soeren Molin George O’Toole

Keith Poole Burkhard Tuemmler Paolo Visca Rolf-Michael Wittich Thomas K. Wood

We would also like to thank Carmen Lorente for her assistance and enthusiasm in the preparation of this fourth volume. Juan L. Ramos and Roger C. Levesque

CONTENTS

List of Contributors ................................................................

1. New Insights on Iron Acquisition Mechanisms in Pathogenic Pseudomonas................................................................... Isabelle J. Schalk

2. Clonal Variations in Pseudomonas aeruginosa.......................... Burkhard T¨ummler

3. Pseudomonas aeruginosa Phospholipases and Phospholipids ........ Michael L. Vasil

4. In Vivo Functional Genomics of Pseudomonas: PCR-Based Signature-Tagged Mutagenesis ............................................. Roger C. Levesque 5. A Genome-Wide Mutant Library of Pseudomonas aeruginosa ...... Michael A. Jacobs and Colin Manoil

99 121

6. Biogenesis and Function of Type IV Pili in Pseudomonas Species .......................................................................... Cynthia B. Whitchurch

139

7. Evolution of Catabolic Pathways in Pseudomonas Through Gene Transfer .................................................................. Jan Roelof van der Meer

189

8. Controlling Regiospeciﬁc Oxidation of Aromatics and the Degradation of Chlorinated Aliphatics via Active Site Engineering of Toluene Monooxygenases................................ 237 Ayelet Fishman, Ying Tao, G¨on¨ulvardar, Linfyun Rui, and Thomas Wood 9. Aromatic Ring Hydroxylating Dioxygenases ............................ Rebecca E. Parales and Sol M. Resnick

287

vii

viii

Contents

10. The Pseudomonas Genome Database ..................................... Fiona S. L. Brinkman

341

Index ..................................................................................

363

LIST OF CONTRIBUTORS

Dr. Fiona Brinkman Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, B.C., Canada, [emailprotected] Dr. Ayelet Fischman Department of Biotechnology and Food Engineering, Technion—Israel Institute of Technology, Haifa, 32000, Israel Dr. Michael A. Jacobs Department of Genome Sciences, Box 357730, University of Washington, Seattle, WA 98195, USA Dr. Roger C. Levesque* Microbiologie mol´eculaire et g´enie des prot´eines, D´epartement de Biologie M´edicale, et Pavillon Charles-Eug`ene Marchand, Facult´e de M´edecine Universit´e Laval, Sainte-Foy, Qu´ebec, Canada G1K 7P4 E-mail: [emailprotected] Dr. Colin Manoil* Department of Genome Sciences, Box 357730, University of Washington, Seattle, WA 98195, USA, E-mail: [emailprotected] Dr. Rebecca Parales* Section of Microbiology, 226 Briggs Hall, 1 Shields Avenue, University of California, Davis, CA 95616, USA, E-mail: [emailprotected] Dr. Sol M. Resnick Biotechnology R&D. The DOW Chemical Company, San Diego CA 92121, USA

List of Contributors

Dr. Lingyun Rui Departments of Chemical Engineering and Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3222, USA Dr. Isabelle Schalk* D´epartement des R´ecepteurs et Prot´eines Membranaires, UMR 7176 – LC1 CNRS – Universit´e Louis Pasteur Bld S´ebastien Brant, F-67 413 Illkirc, Strasbourg, France, E-mail: [emailprotected] Dr. Ying Tao Departments of Chemical Engineering and Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3222, USA Dr. Burkhard Tummler* ¨ Klinische Forschergruppe, OE 6711, Medizinische Hochschule Hannover, D-30625 Hannover, Germany, E-mail: [emailprotected] Dr. Jan Roelof van der Meer* Department of Fundamental Microbiology, Bˆatiment de Biologie, University of Lausanne, 1015 Lausanne, Switzerland, E-mail: [emailprotected] Dr. G¨onul ¨ Vardar Departments of Chemical Engineering and Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3222, USA Dr. Michael L. Vasil* University of Colorado at Denver and Health Sciences Center, Aurora, CO 80045, USA, E-mail: [emailprotected] Dr. Cynthia B. Whitchurch* Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia, E-mail: [emailprotected] Dr. Thomas K. Wood* Departments of Chemical Engineering and Biology, TEXAS A&M University, College Station, TX 77843–3122 USA E-mail: [emailprotected] Marked with an asterisk are the corresponding authors of each chapter.

NEW INSIGHTS ON IRON ACQUISITION MECHANISMS IN PATHOGENIC PSEUDOMONAS Isabelle J. Schalk

D´epartement des R´ecepteurs et Prot´eines Membranaires UMR 7176 – LC1 CNRS, Universit´e Louis Pasteur ESBS, Bld S´ebastien Brant F-67 413 Illkirch, Strasbourg, France

Key Words: iron uptake, iron uptake regulation, siderophore, hemophore, outer membrane transporter

1. INTRODUCTION Almost all bacteria require iron for growth and survival. Iron is a constituent of enzymes crucial in oxygen metabolism, electron transfer, and RNA synthesis. Despite its abundance in the earth’s crust, the availability of iron is severely limited by the very high insolubility of iron(III) at physiological pH. In the presence of oxygen, iron(II) is rapidly oxidized to iron(III) which precipitates as a polymeric oxyhydroxide. The solubility of ferric hydroxide is extremely low (10−38 M) such that, at physiological pH, the concentration of free iron(III) is <10−18 M. This value is far too low for sufﬁcient iron to be acquired by passive diffusion of ions into the cells and to allow growth of aerobic microorganisms. In humans and animals, intracellular iron is mostly bound to ferritin or heme and the extracellular iron found in body ﬂuids is attached to high-afﬁnity iron-binding proteins, such as transferrin found in serum Pseudomonas, Volume 4, edited by Juan-Luis Ramos and Roger C. Levesque C 2006 Springer. Printed in the Netherlands.

Isabelle J. Schalk

Figure 1. Iron uptake in Gram-negative bacteria. Iron is delivered by either lactoferrin or transferrin, heme or heme-hemophore, and hom*ologous or heterologous siderophores to speciﬁc OMTs located in the outer membrane. The OMTs transport iron/iron ligand across the outer membrane and the transport is energized by the pmf of the cytoplasmic membrane via a complex formed of three proteins, TonB–ExbB–ExbD. In the periplasm, Fe3+ , heme, or siderophore-Fe3+ bind to periplasmic binding proteins (PBPs) that are speciﬁc for either Fe3+ , heme or ferric-siderophore. The PBPs deliver the iron compounds to an ABC transporter for the transport across the cytoplasmic membrane. The energy required for transport across the cytoplasmic membrane is provided by the hydrolysis of ATP.

and lymph and lactoferrin in secretions. The level of free iron in body ﬂuids is therefore in the order of 10−18 M, which is far too low to support the growth of microorganisms. The infected host can therefore be considered as an irondepleted environment. In order to gain access to iron, bacteria have developed several strategies for the acquisition, solubilization, and transportation of iron (Figure 1). One of the most common methods of iron acquisition involves the synthesis and the secretion of low molecular weight iron ligands that are called siderophores.20–22 After secretion, siderophores chelate iron in the extracellular environment with high afﬁnity (K d = 10−49 M in some cases) and transport it back into the bacteria. This siderophore-mediated iron acquisition plays an important role in the virulence of pathogenic bacteria19,128 including Pseudomonas.102,151,166,167 It has been shown that siderophores are produced by clinical isolates during infection62 and in the case of Pseudomonas aeruginosa in animal models of infection.63 In parallel to the iron uptake via siderophores, certain bacteria (many of them pathogens) are able to use heme bound iron from hemoglobin,

Iron Acquisition Mechanism in Pathogenic Pseudomonas

hemopexin, and haptoglobin.58,157,164 At last, some species can acquire iron from transferrins or lactoferrins also involving speciﬁc uptake systems in the cell envelope.38,139 All iron uptake mechanisms involve a speciﬁc outer membrane transporter (OMT) and an ABC transporter for the transport across the outer and the inner membrane, respectively (Figure 1). The energy required is provided by the hydrolysis of ATP for the inner membrane transport and by the proton motive force (pmf) of the inner membrane for the transport through the OMT. In the case of the OMT, the energy is transferred from the inner membrane to the receptor located in the outer membrane by the TonB–ExbB–ExbD complex. The different iron uptake systems of Pseudomonas have recently been reviewed in details120 and will be summarized here. The major objective of this review is to address current information about the mechanism of the iron uptake at the molecular level in Pseudomonas and more speciﬁcally in P. aeruginosa, the best-studied member of this family of bacteria. The ﬂuorescent properties of the siderophore pyoverdine (Pvd) of this bacterium have been used as a powerful tool to unfold the mechanism of interaction of the ferric-Pvd complex with its OMT FpvA. New insights on the iron uptake in the Burkholderia (formerly Pseudomonas) cepacia complex will be also presented. The different regulators of these iron uptake activities in Pseudomonas have been the topic of a chapter in Pseudomonas Vol III52 and will be just summarized here.

2. IRON UPTAKE VIA SIDEROPHORES 2.1. Siderophores In the last 40 years, structural studies have shown a great diversity of siderophore structures (for recent review on siderophores see refs [17,36,165]). But despite their great diversity, siderophore structures are always characterized by the presence of one, two, and in most cases, three bidentate chelating groups, which are generally oxygenated and crucial for the formation of very stable hexacoordinated octahedral complexes between the siderophore and iron(III). The chelating groups are generally either catecholates, hydroxamates or hydroxyacids, but can also be any other bidentate groups. Siderophores show strong afﬁnity for only the higher oxidation state of iron, and the association constant for iron(III) for typical molecules containing three bidentate ligands is around 1030 M−1 , or greater. The afﬁnity for gallium is also high, but the attraction for aluminum and for divalent ions is substantially less. Thus, among all naturally occurring metal ions of abundance, Fe(III) is the speciﬁc ion for the siderophore ligand.

Isabelle J. Schalk

Under iron deﬁcient conditions, all ﬂuorescent Pseudomonas are characterized by the production of yellow-green, water-soluble siderophores called Pvds. Pvds form a wide class of mixed siderophores with a great variety of structures and a high afﬁnity for iron, with association constants as high as 1032 M−1 .5 These siderophores are effective at acquiring iron from transferrin102,166,167 and lactoferrin167 and this has obvious implications vis-`a-vis in vivo growth and pathogenesis. Mutants with deﬁciencies in Pvd biosynthesis or transport are effectively avirulent in animal models of infection.102,151 In addition to their high-afﬁnity iron chelators, ﬂuorescent pseudomonads are known to produce lower-afﬁnity siderophores, such as pyochelin, a derivative of salicylic acid, salicylic acid itself,99,161 and quinolobactin.111 These compounds can be considered as secondary siderophores since they are usually produced in much lower amounts than Pvds (a few mg/l vs. 100–200 mg/l for the Pvds, unpublished data) and are less efﬁcient in iron binding and uptake. They can also be considered as compounds that provide rescue iron uptake systems, since their production (in the case of salicylic acid) and their role in iron uptake (in the case of pyochelin) have been shown to be greater in Pvd-deﬁcient mutants than in wild-type cells.59,98 Fluorescent Pseudomonas are also characterized by their capacity to take up heterologous siderophores like citrate, enterobactin,122 ferrioxamine,157 or Pvds produced by other pseudomonads,37,98,122 which explains the large number of ferric-siderophore receptor hom*ologs identiﬁed in the recently completed genome sequence150 of P. aeruginosa (23 putative siderophore OMTs, http:// www.pseudomonas.com/). The B. cepacia complex has been shown to produce four siderophores: ornibactins, salicylic acid, pyochelin, and cepabactin.101,104,144,145,161 Ornibactins and salicylic acid are the predominant siderophores found in cystic ﬁbrosis isolates, but there is species and strain variation.42 2.1.1. Pyoverdine Pvds, the main siderophores produced by all ﬂuorescent pseudomonads, are constituted of a chromophore derived from 2,3-diamino-6,7dihydroxyquinoline, a peptidic moiety bound to the chromophore and a side chain bound to the nitrogen atom at position C-3 of the chromophore. The side chain bound to the chromophore is most frequently a diacid of the Krebs cycle such as succinic, malic, or α-ketoglutaric acid or one of their respective amide derivatives. The composition and length of the peptide are unique to each strain. Based on the determination of about 30 primary structures of Pvd, the peptidic moiety is usually composed of 6–12 amino acids and can be either linear, partially cyclic or completely cyclic.1 In the P. aeruginosa strain, three structurally different Pvds (with different peptide chains) have been identiﬁed (Pvd type I, II, and III), each recognized at the level of the outer membrane by a speciﬁc receptor, called FpvAI-III.35,45,103 Since the chromophore is common

Iron Acquisition Mechanism in Pathogenic Pseudomonas

to each Pvd among ﬂuorescent pseudomonads, the speciﬁcity of siderophore recognition by its OMT is attributed to the peptide region. Moreover, this diversity of Pvd structure among ﬂuorescent Pseudomonas forms the basis of a novel typing scheme called siderotyping.56,100 The iron is chelated with a 1:1 stoichiometry by the chromophore, which forms the ﬁrst bidentate group and by the peptide moiety, which contains the two other bidentate chelating groups, creating a complete and efﬁcient iron(III) complexation. Three-dimensional structures of only three Pvds have been solved: the crystal structure of pseudobactin A from Pseudomonas B10 and the NMR structure of gallium(III) complexes of Pvd GM-II and Pvd G4R from Pseudomonas ﬂuorescens and Pseudomonas putida G4R, respectively.12,109,152,153 Comparison of these three Pvd structures shows that the coordination is not achieved in the same manner in all Pvds. Pseudobactin B10-Fe(III) and PvdGa(III) have conﬁgurations around the metal ion, while Pvd G4R-Ga(III) has a conﬁguration. The diversity in the Pvd primary structures indicates that a large variety of enzymes are likely to be required for their synthesis. For all Pvds, the peptide and the chromophore are thought to be derived from amino acid precursors that are assembled by nonribosomal peptide synthetases (NRPSs) with other enzymes catalyzing additional reactions to complete the mature Pvds.2,13,41,83,84,86,94,95,97,106,148,160 NRPSs are multimodular enzymes, with each module governing the insertion of a single amino acid into the peptide product. The synthesis of the chromophore, which is a condensation product of D-tyrosine and L-2,4-diaminobutyrate,47 seems to involve the PvdL NRPS in P. aeruginosa.112 PvdL is indeed, the only NRPS, which is highly conserved in all genomes analyzed. Another conserved enzyme among ﬂuorescent Pseudomonas is PvdH. This enzyme, required also for the chromophore synthesis, is an aminotransferase that catalyzes the formation of L-2,4-diaminobutyrate from aspartate β-semialdehyde.156 These enzymes involved in the synthesis of the chromophore probably work in concert with the other NRPS found in P. aeruginosa (PvdI, PvdJ, and PvdD97 ) to synthesize the entire Pvd backbone. The pvc genes have been described previously as being also involved in the synthesis of the chromophore of Pvd in P. aeruginosa.147,148 These genes are however, not present in the genomes of the other ﬂuorescent pseudomonads, suggesting that these genes play a role in Pvd biosynthesis only in the case of P. aeruginosa strains. It is likely that most of the genes required for the biosynthesis of Pvd in P. aeruginosa PAO1 have now been identiﬁed, however, more studies will be needed to clearly understand the complete enzymatic pathway of Pvd synthesis. A limited number of Pvd biosynthetic genes have also been reported in other ﬂuorescent pseudomonads.3,6,46,112 They show hom*ology to known P. aeruginosa pvd genes and this is consistent with the presence of a conserved pathway for Pvd biosynthesis.

Isabelle J. Schalk

2.1.2. Ornibactin Ornibactins are linear hydroxamate/hydroxycarboxylate siderophores similar in structure to the Pvds produced by ﬂuorescent pseudomonads, yet they lack a chromophore. They are composed of a conserved tetrapeptide L-Orn1 (N δ-OH,N δ-acyl)-D-threo-Asp(β-OH)-L-Ser-L-Orn4 (N δ-OH,N δ-formyl)1,4-diaminobutane to which is attached one of three possible acyl groups. These acyl groups, linked to Orn,1 vary in length and include 3-hydroxybutanoic acid, 3-hydroxyhexanoic acid, and 3-hydroxyoctanoic acid, forming the three different ornibactins, which are designated ornibactin-C4 , ornibactin-C6 , and ornibactin-C8 according to they acyl chain length.145 Two genes (pvdA and pvdD) involved in the synthesis of ornibactin have been identiﬁed in B. cepacia. The pvdA gene encodes the enzyme L-ornithine N 5 -oxygenase, which is responsible for catalyzing the hydroxylation of Lornithine and for the formation of the hydroxamate ligands.143 The identiﬁcation of the B. cepacia pvdA gene was based on its hom*ology to the P. aeruginosa pvdA gene, which codes for the same enzyme and which is required for the synthesis of the siderophore.160 A pvdD hom*olog that demonstrate hom*ology to NRPSs, was also identiﬁed.143 2.1.3. Pyochelin Pyochelin is a structurally unique phenolate siderophore which has neither hydroxamate nor cathecolate character. Pyochelin has been assigned the structure 2-[2-(o-hydroxyphenyl)-2-thiazolin-4-yl]-3-methyl-4thiazolidinecarboxylic acid and apparently chelates Fe(III) in a 2:1 pyochelinFe(III) stoichiometry, with an afﬁnity in the range of 2 × 105 M−1 in methanol.8,39 The coordination site of pyochelin to ferric iron is not yet fully described but probably involves the phenolic-OH, the thiazoline, and perhaps the thiazolidine nitrogens. Pyochelin also binds other transition metals [e.g. Mo(IV), Ni(II), and Co(II)] with appreciable afﬁnities and might be implicated in the delivery of both Co(II) and Mo(IV) to P. aeruginosa cells.162 Pyochelin is a condensation product of salicylic acid and two cysteins and its synthesis involves the pchDEFG genes.57,129,130 The biosynthesis of this siderophore has recently been reviewed.40

2.2. Siderophore Outer Membrane Transporters Once formed in the extracellular medium, the ferric-siderophore complexes are captured by their cognate OMT (MW between 75 and 90 kDa) at the bacterial cell surface, with K d in the range of 0.3–50 nM. Twenty-three putative TonB-dependent OMT genes potentially involved in iron uptake were retrieved from the complete genome sequence of P. aeruginosa PAO1.150 Only a few of these transporters have been identiﬁed: FptA,9 PfeA,122 FiuA,157 FpvA,121 and FpvB60 for the iron uptake via pyochelin, enterobactine, ferrioxamine, and

Iron Acquisition Mechanism in Pathogenic Pseudomonas

Pvd, respectively. Recent studies have identiﬁed FpvB (gene PA4168) as being an alternative type of Pvd-Fe receptor of P. aeruginosa. Functional studies are available mostly on FpvA (PA2398), the OMT involved in the iron uptake via type I Pvd in P. aeruginosa. Three structurally different Pvds (with different peptide chains) have been identiﬁed (Pvd type I, II, and III) from P. aeruginosa strains, each recognized at the level of the outer membrane by a speciﬁc receptor, called FpvAI-III.35,45,103 Each P. aeruginosa strain produces only one single receptor and uses one type of Pvd.44 The receptor for P. aeruginosa PAO1 Pvd (type I Pvd, Figure 2) has been intensively characterized using physiological, immunological, molecular biology approaches, and also using the intrinsic ﬂuorescence of Pvd. The spectral characteristics of iron-free Pvd or Pvd loaded with Ga or Al and FpvA are almost ideal to observe Fluorescence Resonance Energy Transfer (FRET) between Pvd and Trps of FpvA (Figure 2b), when they are at a short distance from each other, i.e. when Pvd is bound to its receptor.53,136 FRET is one of the most powerful techniques to monitor protein ligand interactions as a function of time. It has been largely used to study the FpvA receptor generating many data that were used to deﬁne the ﬁrst steps of the iron uptake mechanism via the siderophore Pvd. The different steps of FpvA dependent Pvd uptake will be discussed here after. Hybridization studies suggest that hom*ologs of fpvA are present in a variety of P. aeruginosa strains as well as in P. aureofaciens, P. putida, and P. ﬂuorescens,154 and receptors for ferric-pseudobactin have been cloned and sequenced from P. putida WCS368 (pupA)15 and P. ﬂuorescens M114 (pbuA).110 A receptor for Pvd/pseudobactin has also been described in P. syringae143 although the gene has not been cloned. In B. cepacia, only the gene for the ferric-ornibactin receptor, orbA, has been cloned. Until recently, only the crystal structures of OMTs of E. coli have been solved. The structure of FhuA,52,92 the ferrichrome OMTs has been published in 1998, followed in 1999 by the structure of FepA, the ferric-enterobactin receptor24 and in 2002 the structure of FecA, the ferric-citrate OMT.51,168 Finally, recently the crystal structure of an OMT of P. aeruginosa, FpvA, has been solved32,33 (Figure 3). Crystals of the FptA receptor have been also obtained and the crystal structure should be available soon.34 2.2.1. Structure of Siderophore OMTs Based on sequence alignment,54 all the siderophore OMTs of Gramnegative bacteria should have the same kind of structure as those described previously for the E. coli transporters and more recently for the FpvA receptor (Figure 3) of P. aeruginosa.33 All these receptors are composed of a COOHterminal β-barrel domain (22 β-strands) occluded by a N-terminal domain containing a mixed 4-stranded β-sheet, called plug (Figure 3). The globular N-terminal domain is ﬁrmly held in place by many hydrogen bonds made with the β-strands of the barrel (70 in the case of FecA168 ), blocking completely the

Isabelle J. Schalk

Lys Ser2

Arg

HO-Orn1

Thr1

Thr2

Ser1 +

HO-Orn2

B. Figure 2. (a) Structure of Pvd. (b) Spectral properties of Pvd. UV spectrum of iron-free Pvd (thin line), ﬂuorescent spectra of puriﬁed FpvA (dotted line), and iron-free Pvd (thick line). For the UV spectrum of iron-free Pvd (thin line), Pvd was dissolved in pyridine–acetic acid buffer pH 5.0. For the ﬂuorescent spectra of puriﬁed FpvA (dotted line) and iron-free Pvd (thick line) the excitation wavelength was set at 290 and 380 nm, respectively. The protein and iron-free Pvd were dissolved in Tris–HCl buffer pH 8.0 and 1% (v/v) octyl-POE.

access to the periplasm. The major differences between all these structures are the sequence and the conformation of the extracellular loops of the β-barrel, which are speciﬁc to each OMT. In all the OMT structures solved, the ferric-siderophore-binding site is located above the plug, well outside the membrane and is composed of residues of the plug and of the β-barrel domain. The electrostatic properties of the

Iron Acquisition Mechanism in Pathogenic Pseudomonas

Figure 3. The FpvA-Pvd structure33 . (a) Ribbon representation of the FpvA-Pvd. The plug domain and the transmembrane β-barrel domains are colored in purple and gray, respectively. The Pvd is depicted in space ﬁlling representation. (b) View along the β-barrel axis of the FpvA-Pvd structure drawn in ribbon. The Pvd is drawn in space ﬁlling representation.

siderophore-binding pocket confers speciﬁcity related to the chemical features of the siderophore. The binding pocket of iron-free Pvd on FpvA in P. aeruginosa, is mainly composed of aromatic residues.33 In the FhuA-ferrichrome structure,50,92 eight aromatic and two hydrophilic residues form the ferrichromebinding site of FhuA. The ferric-citrate-binding pocket of FecA is composed of positively charged residues (5 Arg) interacting with the negatively charged ferric-citrate.51,168 In the FepA structure, disorder in the electron density map in the region of the putative iron sites did not allow to model the ferricenterobactin-binding site unambiguously.24 However, the presence of two Fe density peaks and their relative weakness suggest both partial occupancy and multiple binding sites or ligand orientations for ferric-enterobactin. Sequence alignment studies of all known siderophore OMTs showed the existence of a siderophore OMTs subfamily having an additional domain of around 70 amino acids at the N-terminus.54,137,159 This region, of so far unknown structure, is localized in the periplasm and is involved in the regulation of the expression of the genes necessary for iron uptake in the bacteria.163 Among others, belong to this subfamily the Pvd OMT FpvA of P. aeruginosa, the ferriccitrate OMT FecA of E. coli18,83 and the hemophore OMT HasR of Serratia marcescens.131 This subfamily and their special features have recently been reviewed.137

2.2.2. Binding Properties of Siderophore OMTs The siderophore OMT subfamily characterized by an additional Nterminal end seem to have another special feature. At least two members of

Isabelle J. Schalk

the siderophore OMT family (FpvA and FecA, the archetypes of this subfamily) are able to bind with close afﬁnities to a common or overlapping binding site, their iron-loaded and iron-free siderophore.136,168 This ability of a siderophore OMT to bind its iron-free siderophore has been shown for the ﬁrst time on FpvA (the Pvd receptor in P. aeruginosa).136 The ﬂuorescent properties of the Pvd clearly showed that under iron limiting conditions, all the FpvA receptors at the cell surface of P. aeruginosa ATCC15692 are loaded with iron-free Pvd.135,136 When the cells are iron starved, the FpvAPvd complex seems to be the normal state of this transporter. Based on binding assays, it was shown that iron-free and iron-loaded Pvd bind to a common or overlapping binding site on FpvA, with unexpected similar afﬁnities of 3 and 0.5 nM, respectively.31,135,136 A larger difference in afﬁnity was expected to explain the efﬁciency in the iron uptake mechanism observed under iron-limited conditions, where the concentration of iron-free siderophore is higher than the concentration of ferric-siderophore. More recently, the crystal structures of the three different forms of FecA, e.g. FecA, FecA-cit, and FecA-cit-Fe, have shown that this receptor, like FpvA, is able to bind its apo- and ferric-siderophore, dicitrate and diferric-dicitrate, at a common binding site.168 Although the binding site is common, the interaction of the apo- and ferric-siderophore with the residues of the binding site in FecA and FpvA is quite different.53,168 Only the ferric form of the siderophore will be transported inside the cells, since the FecA-cit or FpvA-Pvd complexes are not capable of transport the apo-siderophore. Therefore, the OMT must be able to distinguish between iron-free and ferric-siderophores. In the FecA-cit-Fe complex, the two citrate ions are in planar orientation, which allows their carboxyl groups to coordinate the two ferric ions. In the FecA-cit complex, the iron-free dicitrate are in orthogonal orientation. Comparison of the binding pocket for diferricdicitrate and iron-free dicitrate shows two Arg residues of the β-barrel involved in ligand binding via hydrogen bonds. In addition, diferric-dicitrate accepts hydrogen bonds from three other residues that do not participate in the binding of iron-free dicitrate by FecA and van der Waals contacts are provided by residues from the β-barrel. However, the most important feature is that only the binding of the diferric-dicitrate to FecA is accompanied by signiﬁcant conformational changes in two extracellular loops, L7 and L8. The binding of diferric-dicitrate generates a large rearrangement of these loops, which closes the binding pockets, sequestering the ligand in the binding site. When iron-free dicitrate binds to FecA, no binding pocket closure is observed and the iron-free dicitrate remains accessible from the extracellular medium. Although, apo- and Pvd-Fe bind to a common binding site, time resolved ﬂuorescent spectroscopy studies, using the ﬂuorescent properties of Pvd and Pvd-Ga, have shown a different proteic environment for both forms of Pvd.53 When loaded with metal, the binding site of the siderophore is not as ﬂexible and solvent accessible and its environment is not as polar as in the FpvA-Pvd complex, suggesting that some extracellular

Iron Acquisition Mechanism in Pathogenic Pseudomonas

kon2 = 0.0004 s-1

kon1

Recept + Sid

Recept*-Sid

Recept-Sid

koff1

kon1 = 9.6 x 105 M-1 s-1

Recept + Sid-metal

kon2 = 0.0024 s-1

Recept*-Sid-metal

koff1 = 0.0056 s-1

Recept-Sid-metal koff2

Figure 4. Kinetic model for the binding of Pvd-metal and apo-Pvd to FpvA. The equilibriums represent a minimal kinetic binding model, derived from in vivo and in vitro binding data.31 Receptor (recept) stands for FpvA and Sid for Pvd.

loops could form a lid and trap the Pvd-metal in its binding site as observed in FecA-citrate-Fe. While the FecA structures and FpvA-binding assays both suggest a single binding pocket for the iron-free or ferric-siderophore in the transporter, it seems that the binding of either form of siderophore to the pocket may occur in more than one kinetically distinct step. Kinetic studies using the ﬂuorescent properties of Pvd have shown that both Pvd and Pvd-Ga bind in two kinetic steps to the FpvA transporter31 (Figure 4). For the ﬁrst step, the binding process is in the range of seconds for Ga-Pvd (kon1 = 9.6 × 10−5 M−1 s−1 , t1/2 = 7 s for [Pvd-Ga] = 100 nM) and on the same timescale for iron-free Pvd. The second step is slower, in the range of minutes for Ga-Pvd (kon2 = 0.0024 s−1 , t1/2 = 5 min) and half an hour for iron-free Pvd (kon2 = 0.0004 s−1 , t1/2 = 29 min) (Figure 4). A reasonable explanation may be that the two kinetically distinct steps represent ﬁrst, the recognition and capture of the ligand (iron-free or ferricsiderophore) at the cell surface by the extracellular loops of FpvA and second, a stabilization of the ligand within the binding pocket. Mutagenesis studies27 and experiments using ﬂuorescent-labeled FepA,118 the ferric-enterobactin receptor in E. coli, suggested the existence of dual ligand-binding sites for this receptor. The initial site located in the extracellular loops contains aromatic residues and probably functions through hydrophobic interactions. The secondary site, located deeper in the protein, contains both charged and aromatic residues.27 Deletion of loop 3 or 11 of the E. coli FhuA receptor inactivated the ferrichrome transport activity, suggesting the existence of a second binding site for this transporter located in the extracellular loops.48 However, the crystal structure of FpvA, FecA, FhuA, and FepA24,51,92,168 shows a single binding pocket for the corresponding ferric-siderophore. The Pvd and metal-Pvd kinetic data can be interpreted as follows: iron-free or Fe-Pvd ﬁrst binds to the single binding site, and then induces a change in the conformation of FpvA. This hypothesis is fully consistent with the time resolved ﬂuorescent spectroscopy data on the FpvA-Pvd

Isabelle J. Schalk

and FpvA-Pvd-Ga complexes.53 When the siderophore is metal loaded, the Pvd is less solvent accessible and less mobile, like trapped in its binding site. Moreover, cross-linking reactions141 and spectroscopic observations28 on FepA suggest loop conformational changes during ligand binding and transport. All these data raise the possibility that such conformational changes in some of the extracellular loops of the transporter are a general facet of siderophore transport dynamics. In the crystal structure of FhuA, these changes were not observed,52,92 but according molecular dynamics simulations of FhuA, loop L8 appears to be also involved in a mechanism whereby the binding site is gated closed upon ligand binding.49 Of course, all the data presented here are also consistent with a mechanism in which a binding site at the level of the extracellular loops ﬁrst recognizes the ferric-siderophore. As a second step, the ligand migrates deeper into the protein and associates with a secondary binding site localized on the plug domain. This induces a conformation change of some extracellular loops and traps the ferric-siderophore in its secondary binding site. So far, it is not known if the binding of apo- and ferric-siderophore to a common binding site is a feature reserved to the subfamily of signal transducing siderophore receptors or a common feature to all siderophore OMTs in Gram-negative bacteria. Further investigations will be necessary to answer this question, especially on receptors lacking the N-terminus extension.

2.3. Ferric-Siderophore Transport by the Outer Membrane Transporters The transport of ferric-siderophore across the outer membrane via the OMT consumes energy. There is no known energy source in the outer membrane or in the adjacent periplasmic space. The energy is provided by the electrochemical potential across the cytoplasmic membrane and ﬂows from the cytoplasmic membrane into the OMT via the TonB machinery. This is a protein complex anchored to the cytoplasmic membrane and composed of TonB, ExbB, and ExbD.85,107,149 2.3.1. Structure and Stoichiometry of the TonB–ExbB–ExbD Complex Three tonB genes (tonB1,123 tonB2,169 and tonB368 ) have been identiﬁed in P. aeruginosa. A fourth gene (PA0695)150 codes for a protein showing weak similarity to the known TonB proteins. Whereas hom*olog sets of exbB and exbD have been found linked to tonB2169 and PA0695,150 in an apparent operon structure, no exbB and exbD set have been found near the tonB1 gene. TonB1 works with so far unidentiﬁed ExbB and ExbD proteins. Disruption of the tonB1 gene abrogates siderophore-mediated iron uptake123 and heme uptake,169 but

Iron Acquisition Mechanism in Pathogenic Pseudomonas

inactivation of tonB2, exbB, or exbD has no adverse effect on iron or heme acquisition in this organism,169 suggesting that TonB1 is more important for high-afﬁnity iron uptake than TonB2. The involvement of tonB3 and PA0695 in iron acquisition in P. aeruginosa has not yet been tested. Although TonB1 displays sequence signiﬁcant hom*ology to E. coli TonB, the TonB1 protein is the largest TonB protein with an additional 90 amino acid residues at it Nterminus.123 In B. cepacia, tonB–exbB–exbD genes have been identiﬁed and their involvement in iron acquisition conﬁrmed.11 The organization of TonB–ExbB–ExbD complex in the inner membrane and its stoichiometry has been mostly studied in E. coli (for review see ref [126]). TonB is anchored to the cytoplasmic membrane by an uncleaved signal peptide and contains a distinctive proline-rich region, which extends the C-terminus of TonB out of the cytoplasmic membrane. ExbD is also N-terminally anchored in the cytoplasmic membrane and extends into the periplasm.77 ExbB, on the other hand, spans the cytoplasmic membrane three times and is mostly located in the cytoplasm.76 ExbB and ExbD are therefore topologically partitioned to opposite sides of the cytoplasmic membrane and cross-linking experiments suggest that ExbB and ExbD may exist in a complex with the following ratio: 1 TonB:2 ExbD:7 ExbB.67 The crystal structure of the C-terminal-soluble domain of TonB of E. coli has been solved. The structure shows tight intertwined dimers,30 suggesting that TonB might be active as a dimer, which is in good agreement with many biochemical data.25,78,80,115 If it is assumed that TonB is active under a dimeric form, the TonB machinery will be a complex of 520 kDa (2 TonB:4 ExbD:14 ExbB). In this quite huge structure, ExbB and ExbD proteins probably interact through transmembrane segments and together may provide a protein channel for the transmembrane segment of TonB. The process by which the TonB machinery, composed of several ExbB and ExbD proteins, transfers the energy from the inner membrane to the receptor located in the outer membrane remains unknown. Sequence alignment has shown some hom*ologies between ExbB and MotA and has suggested a similar topology for ExbD and MotB.29,30 MotA and MotB are believed to form the stator of the motor in bacterial ﬂagellum and the TonB–ExbB–ExbD complex may have common features with molecular machines such as the ﬂagellum or ATP synthetases. In the TonB–ExbB–ExbD complex the pmf might cause as well a torsion motion, which is transduced to the TonB C-terminal domain via the stiff proline-rich region. Then, TonB physically contacts a TonB-dependent OMT, triggering a conformational change in the OMT such that ligand is pumped into the periplasmic space. Clearly, the mechanism of energy transfer from the cytoplasmic membrane into the outer membrane via the TonB machinery is still unclear at the molecular level, and remains a major question in the ﬁeld of ferric-siderophore uptake in Gram-negative bacteria.

Isabelle J. Schalk

Figure 5. Three different mechanisms describing the formation of the receptor-siderophore-Fe complex in Gram-negative bacteria. In the ﬁrst mechanism (a), the ferric-siderophore binds to the OMT, which has an empty binding site, and is transported as such across the outer membrane. In the second mechanism (b), the OMT has its binding site loaded with a molecule of iron-free siderophore. The extracellular ferric-siderophore acts as an iron donor for the already bound siderophore on the OMT. In this mechanism, different ferric-siderophores may supply iron to the siderophore bound to the OMT.146 In the third mechanism (c), the OMT is also loaded with a molecule of iron-free siderophore. However, in this case the extracellular siderophore is able to bind to its binding site on the OMT only after dissociation of the already bound apo-siderophore from the receptor.31,135

2.3.2. Formation of the Receptor-Siderophore-Iron Complex The ﬁrst step for iron uptake across the outer membrane via siderophores is the formation of an OMT-siderophore-iron complex. Three different mechanisms have been described in the literature for the formation of this complex in Gram-negative bacteria134 (Figure 5). The ﬁrst mechanism (Figure 5A) has been described for FhuA and FepA, the ferrichrome and the ferric-enterobactin receptor in E. coli, respectively. In this case, the binding site of the receptor is free, and the ferric-siderophore formed in the extracellular medium, binds to it in a TonB and pmf independent way. In a second mechanism (Figure 5B), the extracellular ferric-siderophore acts as an iron donor and brings the iron to the apo-siderophore already bound to the membrane receptor. This mechanism is proposed to work out in Aeromonas hydrophila.146 The third mechanism (Figure 5C) has been described in P. aeruginosa for the Pvd pathway and is a mechanism of siderophore displacement on the FpvA receptor, in a two step process: dissociation of the bound Pvd from FpvA followed by subsequent binding of Pvd-Fe.31,135 Kinetic studies showed that the FpvA-Pvd complex, which is the normal state of the receptor under iron limitation (see Section 2.2.2), is extremely

Iron Acquisition Mechanism in Pathogenic Pseudomonas

stable and needs to be activated by the TonB machinery and the pmf of the inner membrane to get a fast dissociation of the bound iron-free Pvd.31,135 In vitro or in the absence of TonB and pmf, this FpvA-Pvd complex dissociates in the presence of an excess of Pvd-Fe, with a half life time of 25 h.31,136 In vivo, the FpvA receptor is highly activated in the presence of TonB and pmf and dissociates by a so far unknown mechanism with a half life time of 4 min.31 Such a regulating function of the binding properties of an OMT by the TonB machinery and the pmf has been described only for FpvA and the hemophore receptor HasR in S. marcescens87 (see below in Iron uptake via hemophores). It is possible that TonB and pmf regulate the afﬁnity of FpvA for its apo-siderophore but this regulation cannot be seen under the experimental conditions used. Experiments using the ﬂuorescent properties of Pvd clearly showed that during iron uptake, TonB activates only a few FpvA-Pvd complexes to get a fast release of the apo-siderophore.31 TonB levels in the cells are indeed likely to be much lower than the number of transport proteins.124,125,127 Only a few OMTs are activated by the TonB machinery and most likely during a short time.31,74 Once the FpvA receptor binding site is empty, Pvd-Fe or another molecule of Pvd can bind. 2.3.3. Ligand Transport by the OMT Binding of the ferric-siderophore to the OMT is not enough to start the translocation process of the iron-loaded ligand across the outer membrane. It is an energy consuming process, which involves the pmf of the inner membrane, the TonB machinery and a conserved N-terminal motif of the OMTs called the TonB box. This region is important for the interaction between the OMT and the TonB protein. Many studies in the literature emphasize the importance of the TonB box in ferric-siderophore uptake and as a mediator of some physical interaction between TonB and TonB-dependent receptors.26,73,108,142 Full length FhuA or BtuB (E. coli vitamin B12 OMT), mutants carrying an inactive TonB box show no iron or vitamin B12 uptake.14,66,138 Site-directed spin labeling and EPR experiments on BtuB have shown that in the absence of substrate the TonB box exists in a structured helical conformation that contacts the barrel of the transporter.96 Addition of substrate converts this segment into an extended structure that is highly dynamic, disordered, and probably extended into the periplasm, where it associates with TonB. The TonB box is disordered in the crystals structure of FhuA, but a conformational change occurs when the ironsiderophore binds to the receptor. Moreover, an unfolding of the N-terminal helix (H1 ) in the central hatch near the N-terminus was observed in the presence of ferrichrome.52,92 In FecA bound to ferric-citrate, electron density for the Nterminal residues was not seen.51,168 The ﬂexibility of the TonB box and the increased ﬂexibility of the N-terminal part in the cork domain upon binding of the ferric-siderophore through an allosteric mechanism, are probably crucial for interactions with the TonB protein.

Isabelle J. Schalk

The mechanism of the siderophore-mediated iron translocation across the outer membrane itself remains unsolved despite the structural information available for FpvA and for four E. coli OMTs. It seems unlikely that the cork domain of the OMT is removed during iron uptake and ﬂoats freely in the periplasm. The energy needed to break each of the 70 hydrogen bounds (in the case of FecA) that position the globular domain into the lumen of the β-barrel would be too high (>100 kcal/mol). It is more likely that a conformational change in the cork domain allows the formation of a passage for the ferricsiderophore between the barrel and the cork. The only experiment showing conformational changes during iron uptake has been done by Klebba and coworkers on FepA, using site-directed spin labeling and electron spin resonance spectroscopy.91 They observed conformational changes in the FepA receptor during iron uptake in vivo72 that were TonB, energy and temperature dependent. The crystal structures of FpvA, FhuA, FecA, and FepA show a continuous water ﬁlled channel, which is going from the extracellular face to the periplasm, but which is too small to allow the iron-siderophore transport across the outer membrane because of the amino acid side chains. This channel, under the activation of the TonB machinery, may be widened and could be a pathway for the ferric-siderophores to reach the periplasm. Usher et al. showed that the over-expressed cork domain of FepA is unfolded in solution but still able to bind the ferric-siderophore.155 These observations support a structural change of the plug domain for the transport of the ferric-siderophore along the channel. However, more investigation is needed to clarify the translocation mechanism of ferric-siderophore across the outer membrane via these OMTs.

2.4. Proposed Pvd-Fe Uptake Mechanism Via FpvA in P. aeruginosa Among all possible iron uptake pathway in P. aeruginosa, the Pvd-Fe uptake mechanism is the best known at the molecular level and is summarized in Figure 6. In this mechanism, the normal state of the FpvA receptor in the outer membrane, under iron-limited conditions, is the FpvA-Pvd complex.135,136 This complex is extremely stable and activation of the transporter by the pmf and the TonB machinery is needed to get a fast dissociation of the ligand and generate an OMT with a binding site ready for Pvd-Fe binding and uptake.31 Binding assays have shown that both, Pvd and Pvd-Fe, have similar afﬁnities (a 10-fold difference only) for FpvA and are in competition for a common or overlapping binding site.31,136 Nonetheless, the binding kinetics for the apo form are appreciably slower than for the ferric form.31 In the case of binding of apoPvd, the TonB machinery will activate again the receptor for a new cycle until Pvd-Fe binding. The binding of Pvd-Fe is a two-step process: the bimolecular step (association of the ligand with the receptor) is followed by a slower step that

Iron Acquisition Mechanism in Pathogenic Pseudomonas

FpvA-Pvd complex 1 Fe uptake and recycling of the Pvd on FpvA TonB machinery

Free FpvA

uptake of Pvd-Fe by FpvA

FpvA*-Pvd complex apo Pvd 1a

activated TonB machinery

FpvA-Pvd complex 1

TonB machinery

Pvd-Fe closed FpvA-Pvd-Fe 1a

TonB machinery

FpvA-Pvd-Fe

TonB machinery

Figure 6. Mechanism of iron uptake by the Pvd pathway in P. aeruginosa. In this proposed mechanism (based on the FecA structures and the functional data for FpvA), the FpvA receptors at the cell surface are loaded with iron-free Pvd, under iron-limited conditions (1). Release of the iron-free Pvd occurs only after activation of the FpvA receptor by the TonB machinery. Once the receptor has an empty binding site (2), two events may occur: either an iron-free Pvd binds again to the transporter with formation of an FpvA-Pvd complex (1) or the Pvd-Fe binds to the transporter (3). In the ﬁrst case, TonB will activate the FpvA receptor until there is binding of ferric-siderophore. In the second case, the binding of ferric-siderophore (3) induces a change of conformation in the receptor, which traps the ferric-siderophore in its binding site (4). The FpvA-Pvd-Fe complex is then ready for transport. The translocation of ferric-siderophore is induced by TonB activation of the transporter (5). Afterward, the ferric-siderophore is in most cases transported into the cytoplasm by an ABC transporter, where iron is released from the siderophore, and the iron-free siderophore is recycled again to the extracellular surface, where it can bind an empty receptor (1) and a new cycle can start.

presumably corresponds to a change of conformation of FpvA.31 Time resolved ﬂuorescence spectroscopy studies have shown a Pvd, which is less solvent accessible and less mobile in the FpvA-Pvd-Ga complex than in the FpvAPvd complex.53 The binding of the ferric-siderophore may induce a change of conformation of some extracellular loops, as described for FecA,51,168 which traps the ferric-siderophore in its binding site. This conformation of the OMT can be considered as competent for ferric-siderophore uptake after activation of the transporter by the TonB machinery. The mechanism of translocation of the Pvd-Fe through the FpvA structure and the mechanism of iron release

Isabelle J. Schalk

from Pvd remain unknown. Based on the ﬂuorescent properties of Pvd it could be shown that the iron-free Pvd is recycled on the FpvA receptor and in the extracellular medium after iron release.133 It is not clear whether iron-free Pvd is recycled ﬁrst through a step involving the formation of a FpvA-Pvd complex and subsequent released into the medium or whether the Pvd is ﬁrst released into the medium and then binds to FpvA in the outer membranes. This proposed mechanism is consistent with the turnovers usually observed for ferric-siderophore uptake in Gram-negative bacteria (1 PvdFe/min/FpvA and 6.4 enterobactin-Fe/min/FepA140 ). Such iron uptake rates are more than sufﬁcient to satisfy the iron requirement of a cell, which is in the order of 105 iron ion per generation, through approximately 1000 receptor molecules present in the outer membrane under iron limitation conditions.20 The biological function of the binding of apo-Pvd to FpvA remains unknown. At ﬁrst sight, this binding does not seem to play a key role in the iron uptake mechanism, except in the case the Pvd is recycled in the extracellular medium via FpvA. The binding of iron-free siderophore to an OMT may be involved in the regulation of iron uptake, which must be strictly controlled to avoid the deleterious effects of excessive or insufﬁcient iron levels. In P. aeruginosa, the loading status of FpvA (iron-free Pvd vs. Pvd-Fe) depends on the relative concentrations of the two Pvd forms in the medium, and this property may be linked to a regulatory role. This idea is discussed in the paragraph below, describing the iron uptake regulation.

3. HEME ACQUISITION Heme uptake has also been suggested to play an important role in P. aeruginosa infections.151 Two distinct heme uptake systems, Fur-repressible, encoded by the phu and has loci, have been described in this bacterium.113 The phu genes include phuR, which encodes an outer membrane heme receptor, and phuSTUVW, which encodes a typical ABC transporter. The heme uptake in other Gram-negative bacteria involves the same proteic partner as ferric-siderophore uptake, e.g. a speciﬁc OMT that is activated by a TonB machinery and an ABC transporter (Figure 1). The second heme uptake system is composed of a hemeOMT gene, hasR, in an operon with hasA a heme-binding extracellular protein. This uptake system was identiﬁed as a hom*olog of the well characterized Has system in S. marcescens.90 In S. marcescens and several Gram-negative bacteria, heme acquisition involves a secreted heme-binding protein called hemophore, which extracts heme from various hemoproteins and delivers it to a speciﬁc TonB-dependent OMT.164 Extracellular release of HasA in S. marcescens and P. ﬂuorescens requires a type I secretion apparatus of the ABC family (hasDEF operon).70,89 The well characterized S. marcescens hemophore is a monomer, which binds

Iron Acquisition Mechanism in Pathogenic Pseudomonas

heme with a stoichiometry of one to one (1:1) and an afﬁnity lower than 10−9 M71 . The crystal structure of the holoprotein has been solved and found to consist of a single module with two residues interacting with the heme.10 The hemophore receptor HasR in the outer membrane of S. marcescens recognizes the heme-free and heme-loaded hemophores with similar afﬁnities (10−10 M) and at a unique or overlapping sites. It also recognizes the free or hemoglobinbound heme.88 Two tonB genes, tonB and hasB, have been identiﬁed in S. marcescens.117 Though TonB and HasB are signiﬁcantly similar and can replace each other for heme acquisition, only TonB mediates iron acquisition from iron sources other than heme and hemoproteins.117 For the two tonB genes characterized in P. aeruginosa, iron and heme acquisition appear to depend on the TonB1 protein.170 The function of the HasB machinery is to activate the HasR receptor for the uptake of the heme moiety (apo-HasA stays bound to the receptor at the extracellular side) and then subsequently to activate HasR to get dissociation of the hemophore HasA. Over-expression of the HasB machinery (HasB plus corresponding ExbB and ExbD proteins) in S. marcescens speeds up the release of empty hemophores from HasR.87 The mechanism by which HasB complex in the inner membrane causes heme uptake and hemophore release at the cell surface remains unclear. The heme uptake mechanism of S. marcescens clearly shows hom*ology with the Pvd-Fe uptake in P. aeruginosa and is summarized in Figure 7. The ﬁrst major hom*ology is a similar binding afﬁnity of the apo and ferric ligand to a common binding site on the OMT. The second hom*ology between heme uptake via HasA and iron uptake via Pvd is the activation of the release of the apo ligand from the receptor by the TonB machinery. This parallel between these two different iron uptake mechanisms suggests that the mechanism described in Figure 6 for FpvA may be not only speciﬁc for FpvA but may be a more general iron uptake mechanism among Gram-negative bacteria. Sequence alignment studies showed also that HasR of P. aeruginosa and S. marcescens have both, like FpvA and FecA, an additional N-terminal extension.54,137,159 Like FpvA and FecA, the HasR receptor belongs to a subfamily of OMTs, with dual function: (i) speciﬁc ligand transport across the outer membrane and (ii) sensing of the presence of the loaded ligand to trigger transcription induction.18 Binding of the heme-loaded hemophore to HasR was shown to be the stimulus for the HasR-mediated signal transduction.131 In the case of Pvd, it has not yet been determined if apo- or Pvd-Fe were the inducers.83

4. TRANSPORT ACROSS THE INNER MEMBRANE After transport across the outer membrane, the ferric-siderophore complex binds to a periplasmic binding protein that delivers the iron compounds to the integral cytoplasmic membrane proteins of an ABC transporter. This step

Isabelle J. Schalk OMT outer membrane

hemophore-heme

periplasm hemophore

inner membrane OMT-hemophore-heme

TonB machinery

OM 2

TonB machinery

TonB machinery OMT-hemophore

OMT hemophore

4 TonB machinery activates the transport of heme

5 TonB machinery activates the release of hemophore

Figure 7. Mechanism of heme uptake in S. marcescens. In this mechanism, the HasR receptor binds with the same afﬁnity and to a common binding site both apo- and holo-hemophore (HasA). Two events may occur after step (1): either an heme-free HasA binds to the transporter with formation of a HasR–HasA complex (2), or the holo-HasA binds to the transporter (3). In the case of the binding of holo-HasA (3), the translocation of heme is induced by TonB activation of the transporter (4). Only the heme is transported into the periplasm, HasA stays bound to HasR until the TonB machinery activates HasR to get a fast release of the hemophore.

of the iron acquisition in pseudomonads has received little if any attention and almost no data are available. In general, ABC transporters involved in iron uptake are composed of: (i) one or several periplasmic substrate binding proteins, (ii) one or two different (hom*odimer or heterodimer) integral membrane proteins, and (iii) one or two different ATP hydrolases that face the cytoplasm and supply the system with energy.82 Often there are more different TonB-dependent OMTs in a bacterial cell than corresponding ABC transporters. In E. coli, the siderophore receptor

Iron Acquisition Mechanism in Pathogenic Pseudomonas

displays higher substrate speciﬁcity than the proteins of the ABC transporter.20 This difference can be most striking, as for instance in P. aeruginosa: 23 putative TonB-dependent receptors were identiﬁed in the P. aeruginosa genome150 and only four iron-related ABC transporters were found to exist in this organism. The FepBCDG hom*ologs of the ABC transporter involved in the uptake of ferricenterobactin in E. coli could be found in the P. aeruginosa genome sequence. hom*ologs of the E. coli FeoAB Fe(II) transporter (PA4359–PA4358),75 of the S. marcescens SfuABC7 (PA5216–PA5217), and of the Hemophilus inﬂuenzae HitABC4 (PA4687–PA4688) Fe(III) uptake systems have also been found. But no ABC transporter involved in metal uptake could be localized in the pch-fptA locus of pyochelin synthesis and uptake, in the vicinity of fecA-fecIR genes involved in the ferric-dicitrate uptake. An ABC transporter can be found in the pvd locus (PA2407–PA2408–PA2409), but the periplasmic binding protein (PA2407) of this transporter seems not to be involved in Pvd-Fe uptake.114 According the genome of P. aeruginosa, there is clearly a lack of ABC transporter compared to the number of OMTs present. It is unlikely that the ABC transporters involved in the iron uptake in P. aeruginosa have a very large speciﬁcity and are able to transport ferric-siderophore complexes with different structures. It is probably more reasonable to think that for most of the ferric-siderophore complexes used by P. aeruginosa, the dissociation of iron from the siderophore occurs in the periplasm, and only iron is transported in the cytoplasm by one or two of the ABC transporters. Such a mechanism would probably involve the reduction of Fe(III) into Fe(II), in order to facilitate the dissociation step of the iron from its siderophore in the periplasm. The decrease in transport observed in the presence of dipyridyl suggests indeed involvement of siderophore reduction in the process of iron dissociation.132 Moreover, studies using cells osmotically shocked after incubating with [55 Fe]ferri[14 C]Pvd132 and M¨ossbauer spectroscopy studies105 suggest a separation of metal and ligand in the periplasmic space for the Pvd iron uptake pathway. These different data are consistent with a mechanism where iron is released from the siderophore by a reduction process in the periplasm, then transported by an ABC transporter into the cytoplasm, but more studies are necessary to demonstrate this hypothesis.

5. IRON TRANSPORT REGULATION The iron content of the cells must be regulated to conserve energy and substrates, and to avoid iron toxicity. In Gram-negative bacteria, iron regulation is mediated by the Fur protein, which represses the transcription of numerous genes involved in the synthesis of siderophores and in the iron uptake (for a review see refs [64,157]). Fur requires iron (corepressor) in order to bind to a

Isabelle J. Schalk

target sequence (“Fur box”) in the promoter region of iron-regulated genes and block their transcription when the level of intracellular iron (Fe2+ ) reaches a threshold. By contrast, when the cells are iron starved, the apo form of Fur loses its ability to bind DNA and gene transcription occurs. The crystal structure of P. aeruginosa Fur protein has been solved.119 The protein is composed of two domains, the N-terminal domain implicated in DNA binding and the C-terminal domain responsible for hom*odimerization. The fur gene of B. cepacia and P. putida have been identiﬁed and also cloned.93,158 The Fur protein is not the only regulator of iron acquisition. Additional regulatory devices, acting positively on the expression of iron uptake genes, have been identiﬁed in Pseudomonas. Expression of the ferripyochelin receptor FptA in P. aeruginosa is pyochelin inducible, with induction involving an AraC-type transcriptional activator (PchR) as well as pyochelin and the FptA transporter itself.65 The expression of the ferric-enterobactin receptor in P. aeruginosa (PfeA) relies on a sensor protein PfeS, belonging to the histidine protein kinase superfamily, and a response regulator PfeR that activates pfeA expression following phosphorylation by PfeS.43 A similar mode of signal transduction has also been reported for PirA, a low afﬁnity receptor for ferricenterobactin that responds to the iron-regulated PirR–PirS system.157 At last, a regulatory cascade involving extracytoplasmic function (ECF) sigma factor has been best characterized for the ferric-citrate uptake system of E.coli (for a review see ref [23]), the Pvd-Fe uptake system in P. aeruginosa (for reviews see refs [157,163]) and the heme uptake system via HasR in S. marcescens.16 Transcription induction is initiated at the cell surface, and a signal is transmitted to the cytoplasm by a signaling mechanism involving three components: an OMT bound with its ferric ligand, an inner membrane regulator protein (also referred to as an anti-sigma factor), and a cytoplasmic sigma factor belonging to the ECF family. The interaction of ferric ligand with its cognate transporter is thought to induce a conformational change in the OMT that is transmitted by an energy-driven, TonB-dependent mechanism and via the N-terminal domain of the OMT, to the inner membrane regulator.79 Once the OMT has signaled that a ferric-siderophore is bound, the inner membrane regulator modulates the activity of a speciﬁc ECF sigma factor, which in turn binds to an RNA polymerase core enzyme and initiates transcription of the iron transport operon. In the E. coli Fec system, the anti-sigma factor is FecR and the sigma factor, FecI. In P. aeruginosa, the anti-sigma factor FpvR regulates two ECF sigma factors, FpvI and PvdS.13,163 This is the ﬁrst example of an anti-sigma factor (FpvR) that directly regulates the activities of two different ECF sigma factors, involving branched signaling system. FpvI binds RNA polymerase and initiates transcription of fpvA. PvdS initiates transcription of genes required for the production of Pvd, as well as for the secreted proteins, exotoxin A and PrL endoprotease. This signaling pathway has also clear parallels with the PupB/PupR/PupI system in P. putida WCS358.81

Iron Acquisition Mechanism in Pathogenic Pseudomonas

In the case of the FecA receptor, it seems that ferric-citrate induces the signal transduction via FecR and FecI.69 In P. aeruginosa, the presence of Pvd in the extracellular medium positively regulates the expression of fpvA,59 suggesting that the binding of apo-Pvd to FpvA may be involved in this regulation process. Moreover, the loading status of FpvA (iron-free Pvd vs. Pvd-Fe) depends on the relative concentrations of the two Pvd forms in the medium, and this property may be linked to a regulatory role in P. aeruginosa. FpvA may sense iron availability and then either interacts or not with the signal transduction machinery, depending on its loading status with iron-free Pvd or Pvd-Fe. For species like P. aeruginosa that possess multiple endogenous siderophore systems, autoinduction of siderophore synthesis and expression of the corresponding OMT, following siderophore interaction with the cognate OMT, could represent a convenient strategy for ensuring selective expression of the most effective iron carrier under particular environmental conditions. Here also further studies are necessary to understand if the binding of an apo-siderophore to its OMT may be involved in the activation of the signal transduction.

6. CONCLUSIONS The presence in the genome of P. aeruginosa of a number of genes encoding putative siderophores OMTs, the ability to use multiple sources of iron for survival and the regulation of known virulence factors by iron highlight the importance of iron for this bacterium and, more in general, for Pseudomonas. Until recently, research on siderophore-mediated iron uptake in Pseudomonas was mostly focused on diverse Pvds, and more speciﬁcally, on the Pvd uptake pathway in P. aeruginosa. The ﬂuorescent properties of Pvd were crucial in providing valuable insights into the understanding of the ferric-siderophore uptake process across the membranes of P. aeruginosa (Figure 6). The mechanism proposed from these studies has interesting similarities with the heme uptake via the HasR receptor in S. marcescens (Figure 7). In both mechanisms, the ligand (siderophore or hemophore) loaded or not with iron (or heme) binds with close afﬁnities to a common site or to an overlapping binding site on the receptor. Additionally, in both cases the receptor loaded with the apo ligand (apo-siderophore or apo-hemophore) is a very stable complex. An activation of the receptor by the pmf and the TonB machinery is necessary to get a fast dissociation of the apo ligand from the OMT. These similarities in the binding properties of FpvA, HasR, and also FecA and in the iron uptake mechanisms proposed for these receptors suggest that the iron uptake mechanism in Figure 6 is probably not only speciﬁc for FpvA but may be a more general mechanism among Gram-negative bacteria. Despite the determination of the crystal structure of FpvA, FhuA, FepA, and FecA many questions remain unanswered. For instance, the mechanism of

Isabelle J. Schalk

translocation of the ferric-siderophore through a structure composed of a βbarrel domain with the lumen closed by a plug remains unsolved. It is also not yet known how OMTs receive and respond to the pmf and how the TonB machinery transduces energy from the proton gradient of the cytoplasmic membrane to the OMTs. Another challenge for the future will be to go beyond genomic analysis of all iron putative uptake systems present in the genomes of Pseudomonas and characterize them. Transcriptome and proteome approaches are certainly interesting tools to reach these goals. The last 2 years, P. aeruginosa proteomic and transcriptome proﬁling data were reviewed for different environment conditions, among other iron starvation conditions.61,114,116 Under such conditions, transcriptome analysis conﬁrmed the iron-responsive expression of known genes, but also the identiﬁcation of many novel iron-regulated genes of unknown function, suggesting that they are involved directly or indirectly in iron metabolism or metabolic adaptation to different iron-availability conditions.114,116 More recently, the transcription proﬁle of P. aeruginosa after interactions with primary normal human airway epithelial cells was determined using Affymetrix GeneChip technology. Surprisingly, the gene expression proﬁles indicated repression of iron acquisition genes.55 The number of genes showing these trends increased over time, suggesting that P. aeruginosa may be able to acquire ample iron for growth from the epithelial cells during infection. The recent completion of the Pseudomonas Genome Project, in conjunction with the Pseudomonas Community Annotation Project (PseudoCAP) has fast-tracked the ability to apply the tools encompassed under the term proteomics or transcriptome to this pathogen. Such global approaches combined with biochemistry, molecular biology, and microbiology studies will allow the research community to answer long-standing questions regarding the ability of P. aeruginosa to survive diverse habitats, its pathogenic nature toward humans, and concerning iron metabolism identiﬁcation of all iron uptake pathways and the regulations involved.

ACKNOWLEDGMENTS I am very grateful to Dr D. Cobessi (ESBS, Illkirch) for having provided the ﬁgure showing the crystal structure of FpvA. I also acknowledge Drs C. Hihi and D. Cobessi for critical reading the manuscript. This work was supported by Vaincre la Mucoviscidose, by the ACI Physique et Chimie du Vivant program from the Minist`ere de l’Enseignement Sup´erieur de la Recherche et de la Technologie and by the Center National de la Recherche Scientiﬁque (CNRS).

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CLONAL VARIATIONS IN PSEUDOMONAS AERUGINOSA

Burkhard T¨ummler

Klinische Forschergruppe, OE 6711 Medizinische Hochschule Hannover D-30625 Hannover, Germany

1. INTRODUCTION The genetic diversity within a bacterial species is determined by the number and size of chromosomal and extrachromosomal elements, rates of nucleotide substitution, recombination, genome rearrangements and gene ﬂow, and both the size and growth of the bacterial population. Most species of bacteria that were initially analyzed, were of a clonal nature.77 The structural characteristics of a clonal population are the paucity of genotypes, linkage disequilibrium among gene loci, and recovery of closely related genotypes over large geographic areas and/or over long periods of time. The accumulation of molecular data during the last 15 years and the growing evidence of the occurrence of horizontal gene transfer among bacteria in nature, however, have led to consideration that bacterial populations are not invariably clonal but range from the highly sexual Neisseria gonorrhoeae to the almost strictly clonal Salmonella.80 The metabolically versatile Pseudomonas aeruginosa is present in soil and aquatic habitats, but it is also an important opportunistic pathogen for humans, animals, and plants. Typing of strain collections in single nucleotide polymorphisms (SNPs), DNA fragment length polymorphisms and phenotypic traits indicated that the current P. aeruginosa population is in linkage equilibrium and consists of a net of equivalent genotypes (termed clones), whereby a subset of clones is overrepresented due to epidemic spread.36,60 Isolates from the Pseudomonas, Volume 4, edited by Juan-Luis Ramos and Roger C. Levesque C 2006 Springer. Printed in the Netherlands.

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inanimate environment and clinical habitats have been shown to share the same chemotaxonomic proﬁle23 and repertoire of metabolic and virulence traits.1 Irrespective of their origin, isolates from disease and environment were similarly proﬁcient in the degradation of environmental pollutants and secretion of virulence factors.1 In other words, there are no disease- or habitat-associated clones. However, we do observe adaptation of P. aeruginosa to a particular niche. Most data exists of how P. aeruginosa colonizes and persists in the atypical habitat of the cystic ﬁbrosis (CF) lung where independent of the genetic background of the clone a convergent evolution towards common phenotypes takes place.89 This chapter summarizes our current knowledge about the inter- and intraclonal diversity of genotype and phenotype of P. aeruginosa.

2. INTRA- AND INTERCLONAL GENOME DIVERSITY Physical mapping and sequencing and Southern hybridization data indicate that the P. aeruginosa genome is made up of a mosaic of a conserved core and variable accessory segments.20,31,36,66,84 The core genome is characterized by a conserved synteny of genes and a low average nucleotide substitution rate. Clone- or strain-speciﬁc genome islands and genome islets deﬁne the accessory part of the chromosome and lead to ﬂuctuations in the genome size, which can range from 5.2 to 7 Mbp.73

2.1. Clonal Variation of the Core Genome The complete genome sequence of strain PAO185 is the genetic blueprint for P. aeruginosa. Genomic DNA hybridization of in total 39 P. aeruginosa strains of diverse origin onto PAO1 microarrays20,95 detected the presence of almost 90% of the 5570 predicted PAO1 protein coding sequences in all strains. Hence, the core genome is made up of about 5000 highly conserved genes. Interclonal sequence variation is low in the P. aeruginosa core genome. Comparative sequencing of housekeeping genes in strain collections revealed an average rate of sequence polymorphism of 0.3%, which is about one order of magnitude lower than in comparable housekeeping genes of Salmonella enterica.36 The ratio of non-synonymous to synonymous nucleotide substitutions is about 1:6. Sequence variation within clones is substantially lower than the already low sequence diversity amongst unrelated clones: Within 300 kb of bulk sequence, just a single synonymous nucleotide substitution was detected in one of four analyzed strains.36,43 In other words, members of a clone are characterized by virtually identical core genome sequence in all segments with low sequence diversity. Figure 1 shows the comparison of 49 single nucleotide substitutions (SNPs) of P. aeruginosa detected in oriC, ampC, citS, ﬂiC, oprI with 500 SNPs of S. enterica detected in gapA, putP, and mdh.37 In contrast to the high GC

Clonal Variations in Pseudomonas aeruginosa

P. aeruginosa (n=49) G>C

T>A

C>G A>C

C>T

T>G

Salmonella (n=500) T>A A>T G>C C>G A>C C>T

T>G

C>A

C>A G>T

A>G

T>C G>A

T>C

G>A

Figure 1. Pie charts showing all single base substitutions detected in oriC, citS, ampC, oprI, and ﬂiC sequences of 18 P. aeruginosa strains and in gapA, putP, and mdh of 16 Salmonella strains.

content of the bulk P. aeruginosa chromosome (67%), the phylogenetically closely related but ecologically distinct S. enterica exhibits a much lower GC content (50–53% GC) and a less pronounced codon usage bias.93 The quantitative distribution of nucleotide substitution types is similar in both bacterial species except for the more frequent G→C transversion in the GC rich P. aeruginosa. In spite of their dissimilar GC content and codon usage bias, about 75% of nucleotide substitutions are transitions. C→T is the most abundant substitution, followed by G→A, T→C, and A→G (Figure 1). Both nucleotide substitution proﬁle and transition-to-transversion ratio are non-randomly distributed. The observed bias probably reﬂects ﬁrst, the thermodynamic stability and geometric selection of the mismatches; and second, evolutionarily conserved errorcorrection mechanisms, i.e. the preferential repair of lesions on the transcribed strand.37 This argument that nucleotide sequence variation is not governed by chromosomal GC content and codon usage but by DNA structure and repair is substantiated by the ﬁnding that the same proﬁles seen in bacteria were also observed for sequence variants and disease-causing mutations in phylogenetically distant mammalian genomes.37 Twenty-ﬁve regions of signiﬁcantly elevated sequence variation were uncovered in pairwise comparisons between PAO1 and three other partially sequenced strains (Table 1).84 There were no obvious sequence features unique to these regions that ﬂag them relative to the rest of the genomic sequence, albeit a lower average GC contents and an underutilization of the most frequently used codons were noted. The genome segments with the highest level of sequence diversity are the genes whose products are involved in ﬂagellar biosynthesis and genes whose products are involved in the biosynthesis of the siderophore pyoverdine and the receptor for ferripyoverdines.84 Pyoverdine is the primary siderophore of

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Table 1. PAO1 sequence coordinates for regions of high sequence diversitya (modiﬁed from Table 3 in ref [84] by permission of the authors and the American Society for Microbiology).

Start

End

Length PAO1 (bp)c

290,000 320,000 515,000 530,000 555,000 652,500 685,000 695,000 790,000 1,060,000 1,170,000 2,150,000 2,550,000 2,635,000 2,660,000 2,672,500 2,682,500 3,647,500 4,060,000 5,037,500 5,070,000 5,097,500 5,187,500 5,722,500 6,090,000

294,999 324,999 519,999 534,999 559,999 657,499 689,999 699,999 799,999 1,064,999 1,174,999 2,154,999 2,554,999 2,654,999 2,664,999 2,677,499 2,692,499 3,652,499 4,064,999 5,042,499 5,074,999 5,102,499 5,192,499 5,727,499 6,094,999

5000 5000 5000 5000 5000 5000 5000 5000 10,000 5000 5000 5000 5000 20,000 5000 5000 10,000 5000 5000 5000 5000 5000 5000 5000 5000

Coordinatesb of PAO1

No. of SNPsd

No. of bases availablee

%SNPs f

PAO1 ORFsg

83 97 143 111 66 76 44 84 274 57 224 88 59 451 115 186 139 81 85 98 162 119 91 162 93

1488 1754 2103 2288 1252 1171 789 1436 2535 926 1881 842 1346 5787 551 1132 1723 1417 1695 1923 2030 1825 1561 1966 618

5.58 5.53 6.80 4.85 5.27 6.49 5.58 5.85 10.81 6.16 11.91 10.45 4.38 7.79 20.87 16.43 8.07 5.72 5.01 5.10 7.98 6.52 5.83 8.24 15.05

PA0259–PA0262 PA0285–PA0289 PA0457–PA0459 PA0470–PA0473 PA0495–PA0500 PA0594–PA0596 PA0625–PA0633 PA0640–PA0643 PA0719–PA0731 PA0976–PA0982 PA1084–PA1087h PA1967–PA1972 PA2312–PA2317 PA2383–PA2397i PA2399i PA2402i PA2402–PA2409i PA3260–PA3264 PA3624–PA3629 PA4500–PA4503 PA4526–PA4532 PA4549–PA4554 j PA4625 PA5084–PA5089 PA5412–PA5415

Sequencing data for all three strains that had been subjected to whole genome shot-gun sequencing was compared to the PAO1 reference in 5000-bp sliding windows that were sequentially offset by 2500 bp. Regions with at least 500 bp of alignable sequence that exhibited nucleotide diversity values greater than three standard deviations (>4.35% sequence differences) from the mean value of 0.5% are shown. b Sequence coordinates of the PAO1 reference sequence, accessible at www.pseudomonas.com. c Overall span of the PAO1 region encompassed by high sequence variation. d Number of SNPs detected. e Total number of alignable bases in which SNPs were detected. f Percent SNPs among alignable bases. g Annotated ORFs within high-diversity regions. A more comprehensive description of these genes is available at www.genome.washington.edu/UWGC and at www.pseudomonas.com. h Flagellar biogenesis genes. i Pyoverdine locus. j Minor type IV pili prepilin.

Clonal Variations in Pseudomonas aeruginosa

P. aeruginosa. Each strain makes one of three pyoverdine types, each type with a distinct peptide chain that is synthesized non-ribosomally. The pyoverdine region spans an interval of approximately 50 kb in PAO1. The three divergent sequence types correspond to the three structural types of pyoverdines.79 The outer-membrane pyoverdine receptor, FvpA (PA2398), is also type-speciﬁc, transporting only its corresponding pyoverdine. FvpA exhibits the largest variations with about 50% mismatch of amino acid pairwise alignment between genes of each pyoverdine type.15,42,63 FpvA moreover shows substantial intratype variation and apparently accumulated non-synonymous changes at a elevated rate which has been interpreted as strong evidence of positive selection.25,79 The next most divergent genes with 15–40% mismatch of amino acid pairwise alignment are immediately adjacent to fpvA, and include the ABC transporter pvdE (PA2397) and the non-ribosomal peptide synthetase genes pvdD, pvdJ, and pvdI (PA2399–PA2402). Besides fvpA 10 further hotspots of elevated intratype sequence divergence were identiﬁed. Since these islands of about 100 bp in length are located within regions that are divergent between pyoverdine types and since intratype differences are very similar to those between pyoverdine types, the sequence divergence probably arose from recombinations.79 The ﬂagellin biosynthesis genes encode the elements for the serologically distinct a- and b-type ﬂagellae. The ﬂagellum confers motility and chemotaxis, facilitates adherence to cells and inanimate surfaces and contributes to the colonization and invasion of hosts during infection. Flagellins, a- and b-type, are 74% identical in the nucleotide sequence and 63–65% identical in the amino acid sequence.7,82,94 They share nearly identical N- and C-terminal sequences, whereas the central region is variable in size and primary structure. This central part is also the major region of intratype sequence variation among a-type ﬂiC genes. Based on the amino acid sequences of ﬂagellins from 24 a-type P. aeruginosa strains, two subtypes, A1 and A2 were recognized that differ in the central regions by 13 amino acid substitutions and two small deletions of threeand four- amino acids.7 Although a-type and b-type ﬂagellins differ by 37– 38% in their primary structure, the impact of sequence diversity on secondary and tertiary structure is low. A1, A2, and b-type ﬂagellins match perfectly in their proﬁles for hydrophobicity, ﬂexibility of the peptide backbone, antigenic index, and probability of surface exposure.83 The constraints for the efﬁcient multimerization of subunits to a functional ﬂagellum are probably so tight that the polymorphic proteins fold into a similar three-dimensional structure. a-type ﬂagellins are glycosylated.12 a-type strains carry a polymorphic genomic island that is essential for glycosylation of ﬂagellin.4 An a-type strain either harbors the long version of the island of 14 open reading frames (orfA to orfN) or an abbreviated version (short island) in which orfD, -E, and -H are polymorphic and orfI, -J , -K , -L, and -M are absent.7 The glycosylation island is located upstream of ﬂiC. Comparative sequencing between strains PAK and PAO1 as representatives for a- and b-type ﬂagella revealed that the polymorphic region

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of the ﬂagellar regulon encompasses the region from ﬂgK (PA1086) at the 5 end up to amino acid 88 of ﬂeP (PA1096) at the 3 end: 5 -ﬂgKL – glycosylation island – ﬂiC – ﬂeL – ﬂiDSS – ﬂeP.4,84 Correspondingly, there are two types of ﬂagellar cap proteins, FliD, which are only 58% identical at the nucleotide level and 43% identical at the amino acid level.5 These genes are co-inherited with their cognate ﬂagellin gene types, a or b. The most substantial interclonal sequence variation for a single gene common to all P. aeruginosa is observed for the pilA gene (PA4525) encoding the type IV pili that play a major role in mediating the adhesion of the bacterial cell to host tissue. All classic pilin subunits share characteristic features, including a six- or seven-amino acid leader peptide, an N -methylated phenylalanine as the ﬁrst residue of the mature protein and a highly conserved N-terminus with 25–30 hydrophobic amino acids, but otherwise the primary sequence is highly variable. The published pilA sequences segregate into ﬁve groups exhibiting less than 30% nucleotide identity that provide fewer hom*ologies between themselves than with pilins of different species.36,81 Each group carries a speciﬁc sequence insertion downstream of pilA. Group I members share about 85%, group II members about 65% nucleotide identity amongst themselves.13 The type IV pili of P. aeruginosa are no more closely related to each other or to other γ-Proteobacteria genera Escherichia, Aeromonas, Vibrio, and Moraxella than they are to the pili of the β-Proteobacteria Neisseria and Eikenella, the genus Dichelobacter, representative of the deepest branching γ-Proteobacteria, or the phylogenetically distant δ-Proteobacterium Myxococcus.81 P. aeruginosa probably acquired its pilin genes from the Moraxella lineage, because the pilA genes still retain the GC and codon usage characteristics of Moraxella pilin genes.48 The type III secretion system as one of the major virulence determinants of P. aeruginosa transports four known effector proteins: ExoS, ExoT, ExoU, and ExoY. The bifunctional ExoS exerts its cytotoxic activities by a GTPase-activating domain and a ADP-ribosyltransferase activity.8 ExoT is also an ADP-ribosyltransferase but has only 0.2% of the catalytic activity of ExoS. Like ExoS, it is a GTPase-activating protein for Rho GTPases. ExoU is a potent patatin-like phospholipase that causes rapid cell death following its injection into host cells.71 ExoY is an adenylate cyclase that elevates the intracellular cAMP levels in eukaryotic cells and causes rounding of certain cell types.90 The genes encoding the secretion, translocation, and regulatory machinery of the type III secretion system are clustered together in the P. aeruginosa chromosome. The genes encoding the type III effector proteins, however, are scattered throughout the chromosome. In an epidemiological study on 115 P. aeruginosa isolates22 the large chromosomal locus and exoT (PA0044) were present in all isolates. In contrast, the exoS (PA3841), exoU, and exoY (PA2191) genes were variable traits. Overall, 72% of examined isolates contained the exoS gene, 28% contained the exoU gene, and 89% contained the exoY gene. An inverse correlation was noted between the presence of the exoS and exoU genes in that all isolates except two, one containing both genes and another containing neither

Clonal Variations in Pseudomonas aeruginosa

of them, contained either exoS or exoU but not both. No signiﬁcant difference in exoS, exoU, or exoY prevalence was observed between clinical and environmental isolates or between isolates cultured from different disease sites except for respiratory isolates from patients with CF. CF isolates harbored the exoU gene less frequently and the exoS gene more frequently than did isolates from some of the other sites of infection, including the respiratory tract of patients without CF. These results suggest that the P. aeruginosa type III secretion system is present in nearly all clinical and environmental isolates but that individual isolates differ in their effector genotypes. P. aeruginosa lipopolysaccharide (LPS) is composed of lipid A, the core oligosaccharide, and the long chain polysaccharides (O-antigen) (detailed information in the article by Lam et al., volume 3, Chapter 1 of this monograph series). In short, the majority of P. aeruginosa produces two distinct forms of O-antigens called A-band and B-band. Differences in the chemical structure of the B-band LPS are responsible for the serogroup speciﬁcity of the respective strains and has been employed for many years for serotyping of P. aeruginosa isolates. The major set of enzymes responsible for O-antigen B-band synthesis and assembly are encoded in a single, large gene cluster (PA3160–PA3141 in strain PAO1). Raymond et al.64 sequenced this B-band gene island in all 20 IATS reference serotype strains. Eleven groups of gene clusters were identiﬁed that are highly divergent from one another at the DNA sequence level. Within each group a high degree of sequence conservation was observed. The B-band gene islands of serotypes O1, O4, O6, O9, and O12 constitute each a distinct gene cluster. Groups with two members include O3 and O15 (Lory), O7 and O8, O10 and O19, O11 and O17, and O13 and O14. The largest group with 98% sequence identity contains strains of serotypes O2, O5, O16, O18, and O20, consequently the variations in the structures among these serotypes are not conferred by the B-band gene island. This argument also applies to the O10–O19 group, for which no DNA sequence differences were found in 16 kbp of sequence, and to the O7–O8 group, in which only two conservative amino acid changes were identiﬁed. In summary, to date the following genes and gene clusters exhibit the largest interclonal genetic diversity in the core genome: the pyoverdine locus, the ﬂagellar regulon, pilA, the type III secretion effector proteins and the Oantigen biosynthesis locus. Each locus is present in all strains, but the genes in each locus are highly divergent between strains. This “replacement island” phenomenon presumably results from diversifying selection, a type of selection that maintains multiple alleles in the population.79 Mosaic genes are a further source of genetic diversity. Evidence for a mosaic gene structure is drawn from SNP haplotype36,83 or the detection of cassettes.82 Our current knowledge about mosaic genes in P. aeruginosa is restricted to ampC (PA4110),83 ﬂeP (PA1096),4 ﬂiC (PA1092),36,83 mucABCD (PA0763–PA0766),11 and oprD (PA0958).61 The ampC sequences of 18 strains were compiled into 12 groups by their diagnostic SNP patterns.83 No

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hom*ology (% nt) 95 100

n 9

4 1

24° 1 (mutator) 3

C1 C

1(PAO1) C2 Base pairs 0

12 500

1000

1330

Figure 2. Graphical representation of the mosaic structure of the oprD gene in 55 unbiased P. aeruginosa strains. Including 10 clone C isolates; n, number of isolates belonging to a subgroup. Reproduced from the article by Pirnay et al.61 by permission of the authors and Blackwell Publishing.

linkage of dimorphisms was observed which indicated repetitive intragenic recombination events. However, the low nucleotide substitution rate and the low number of analyzed strains did not allow statistical evidence of a putative mosaic structure of ampC. ﬂeP is a mosaic gene because the 3 end of the polymorphic region of the ﬂagellar regulon is located within ﬂeP.4 The ﬁrst 264 nucleotide of ﬂeP were only 56% identical between strains PAK and PAO1 but the last 31 nucleotides of ﬂeP were 100% identical. a-Type ﬂiC genes contain a variable 141-bp central cassette showing 28% nucleotide and 40% amino acid diversity.82 Signiﬁcant non-random clustering of polymorphic sites within this cassette indicated an intragenic recombination event and a mosaic gene structure.36 Sequencing of 37 CF P. aeruginosa isolates in the mucABD operon uncovered 16 SNP genotypes. The non-random distribution of conserved SNP blocks visualized the mosaic structure of the muc operon.11 Sequence analysis of oprD in 55 P. aeruginosa isolates, collected over a period of 15 years from various, spatially separated, clinical and environmental habitats, uncovered a microscale mosaic structure of oprD.61 All sequences fell into three main groups, which differ by 7–9% of nucleotides. Several recombinational exchanges of DNA blocks of 100–300 bp led to a mosaic gene structure and caused a further divergence into subgroups (Figure 2). Our knowledge about sequence variation resides on the complete genome sequence of two strains, whole genome shot-gun sequencing in another three strains and comparative sequencing of strain collections in 11 loci. Considering this rather limited body of comparative sequence data the proportion of ﬁve genes with intragenic mosaicism is substantial. In other words, intragenic recombination may be a major driving force for genetic diversity of P. aeruginosa.

Clonal Variations in Pseudomonas aeruginosa

2.2. Clonal Variation of the Accessory Genome Genome diversity is accomplished by sequence variation in coding and non-coding regions of the core genome and by a differential repertoire of the accessory genome the latter being made up of genome islands and genome islets and of mobile genetic elements such as phages, plasmids, and transposons. The reader is referred to volume 1, Chapters 6–8 to get comprehensive information about the features of phages, plasmids, and transposons in Pseudomonas. This chapter focuses on the variation of chromosomal contents. Diversity of the P. aeruginosa chromosome was ﬁrst studied by Southern hybridization analysis.31,66 SpeI macrorestriction fragment length diversity was scanned in 60 unrelated clones for using probes of known map position of the PAO1 chromosome. The oriC-containing SpeI fragment was the most conserved SpeI fragment on the chromosome. Small insertions or deletions lead to a variation of ±10% of chromosomal contents in this region of the origin of replication (Figure 3). Few fragment length classes were seen for most analyzed segments indicating an intermediate range of diversity. In contrast, extensive genomic diversity was detected around the pilA and lipH loci that later turned out to be hotspots for the integration of genome islands (see below). In other words, the gene contig of the core genome is interrupted by few islets around oriC as one extreme and by large segments around pilA and lipA. Heuer et al.31 studied the same strain collection by probing the chromosome in four regions with 40–114 kb large PAO1 SpeI fragments cloned into yeast artiﬁcial chromosomes (YACs). In one region the broad distribution of hybridizing SpeI fragment size indicated substantial genome plasticity, but otherwise only few bands within narrow fragment length classes reacted with the probe. The low complexity of the hybridization pattern indicates that conserved PAO1 coding and non-coding sequence is maintained as contigs in P. aeruginosa. Intrachromosomal shufﬂing of sequence is rare. In other words, gene order established for strain PAO1 should be valid for most P. aeruginosa. YAC hybridizations compare genomes at low resolution so that the disruption of the sequence contig by small genome islets is not resolved. Indirect evidence for the presence of such small insertions and deletions was provided by the strain-to-strain variation of up to 10% in macrorestriction fragment size. Information about the PAO1 accessory genome in terms of genome islets and genome islands has meanwhile been obtained by hybridization of genomic DNA from strain collections onto PAO1 microarrays. Wolfgang et al.95 analyzed 18 strains of diverse origin. Strain-speciﬁc genes were localized to 90 discrete regions relative to the PAO1 genome. Many of these regions are composed of small gene blocks (one to four genes) that showed variability in one or more strains. These variable blocks likely contain genes that are highly polymorphic at the nucleotide sequence level or are gained or lost through local recombination events. A second pattern, which was more readily apparent, is characterized by large clusters of tandem genes that show varying levels of

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Figure 3. Southern analysis of P. aeruginosa clones: size variation of hybridizing SpeI fragments. The number of fragments detected by one probe is given as a function of size. Fragment length was counted in 5 kbp increments. Fragment size variation within a clone is indicated by identical open symbols.

polymorphism between strains. Twenty-four of these regions (termed variable segments) were identiﬁed. These variable segments are scattered throughout the genome; however, nine segments are immediately adjacent to tRNA or tmRNA genes. Ernst et al.20 detected 38 PAO1 gene islands to be absent or divergent in at least 2 out of 14 examined clones. Besides the pyoverdine cluster, the ﬂagellar regulon and the O-antigen biosynthetic gene cluster described above, a further not yet characterized exopolysaccharide is encoded by a gene island (PA1383–PA1393). Numerous islands in P. aeruginosa encode pyocins or phage proteins.20 Six further islands were each adjacent to 1 of the 10 members of the vgr gene family, genes associated with rearrangement hotspots in the E. coli

Clonal Variations in Pseudomonas aeruginosa

chromosome. Seven of these 38 islands belong to the subset of 10 chromosomal regions whose low G + C content suggested that they were sites of recent horizontal transfer in PAO1.85,95 The hotspots for gene island replacement are apparently the regions where most intra- and interclonal genome diversity takes place. Intraclonal genome diversity has so far been studied in 21 P. aeruginosa isolates of clone C.67 Clone C is one of the major clones in the P. aeruginosa population and has frequently been isolated from inanimate and disease habitats.18,68 Clone C consists of closely related genotypes (also called clonal variants), each of which is characterized by a unique macrorestriction fragment pattern. Within clone C the total genome size varies at maximum by 300 kb. In total 34 different insertions or deletions were mapped that each were present in 1 to 13 strains. The acquisition and loss of DNA occurred preferentially around the terminus of replication but was not observed around the origin of replication, from about rrnC to rrnA (Figure 4). Three regions close to the phnAB, pilA, and lipH loci were subject to extensive variation processes. These hypervariable regions of the clone C chromosomes match with the hotspots of variation in the Southern and PAO1 microarray hybridization experiments. Subsequent sequencing revealed that most larger genome islands are located in these regions. The ca. 110 kb large hypervariable region located near the lipH gene was sequenced in two clone C strains, strain C and strain SG17M.43 In both strains the region consists of an individual strain-speciﬁc genome island of 111 (strain C) or 106 (SG17M) open reading frames (ORFs) and of a 7 kb stretch of clone C-speciﬁc sequence of nine ORFs. The left boundary of the islands is a cluster of tRNA genes comprising one tRNAGlu gene followed by two identical tRNAGly genes separated by 84 bp, one serving as the integration site for the P. aeruginosa genome island PAGI-2 in strain C, the other for PAGI-3 in SG17M. PAGI-2 and PAGI-3 terminate at the right end with the terminal 16 and 24 nucleotides of the 3 end of the tRNAGly gene, respectively. The same organization is seen for the Pseudomonas clc genome island that contains the genes encoding the degradation of 3-chlorobenzoate (see Chapter 16 by J.R. van der Meer in this volume for more information). In all three islands the ﬁrst ORF adjacent to the tRNAGly gene encodes a bacteriophage P4related multidomain integrase with an unusual transposase-like C-terminus. PAGI-2 and PAGI-3 have a bipartite structure. The ﬁrst part adjacent to the tRNA gene consists of strain-speciﬁc ORFs encoding metabolic functions and transporters, the majority of which has hom*ologs of known function in other eubacteria. The second part is made up of a syntenic set of ORFs the majority of which is classiﬁed as conserved hypotheticals. Forty-seven of these ORFs are arranged in the same order in both islands with a pairwise amino acid identity of 35–88% (Figure 5). Interestingly, PAGI-2 is also found with 100% sequence identity in the Ralstonia metallidurans CH34 chromosome43 indicating that ﬁrst, the genome island is also present in other phylogenetically distant taxa,

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rrnD oriC

6 rrn

1 2 11 1 2 9 Q 13 1 L 5 1

P. aeruginosa C

1 3 R

S E

2 50

30 2

2 3

1 B

rrn A

100 %

rrnB

3 2 2 6

6.5 Mb

H W V X 2 83 3 P2 1 1 2 1 13 1 21 2

1 2

Figure 4. SpeI restriction map of P. aeruginosa C summarizing all chromosomal changes that occurred within the 21 analyzed clone C strains. Open triangles represent deletions, ﬁlled triangles represent insertions, open circles indicate deletion of a SpeI site, and ﬁlled circles indicate additional SpeI sites. Crosses indicate endpoints of recombination. Numbers in the symbols refer to the frequency of an additional genome alteration. Shaded regions indicate additional genetic material in strain C in comparison to PAO1. The hotspots of gene replacement around the pilA and lipH loci are indicated by the large circles.

and second, this type of island may have closer hom*ologs in other clones and taxa than within the same clone. Subsequent hybridization analyses revealed that additional copies of PAGI-2 that ﬁrst had been sequenced in a P. aeruginosa isolate from a German CF patient’s lung, were present in the majority of tested R. metallidurans and R. campiniensis isolates from wastewater and polluted habitats in Europe and North America.38 PAGI-2 and PAGI-3 are prototypes for tRNA-associated gene islands that are causative for the genetic make-up of one of the hypervariable areas of the P. aeruginosa chromosome. The other two hypervariable regions in the P. aeruginosa chromosome with pronounced genomic variability reside in the

Clonal Variations in Pseudomonas aeruginosa

75% G+C-content 65% 55% 45% 35%

100

105

100

105

SG17M C kb 0

75%

65% 55% 45%

G+C-content

Figure 5. Comparison of the strain-speciﬁc gene islands in the P. aeruginosa clone C strains SG17M (upper line) and C (lower line). Gene are represented by arrows. hom*ologous ORFs are linked by light bars. Genes with hom*ologs in the Xylella fastidiosa genome island78 are highlighted with a dark background. Gray boxes above and below the gene maps mark the syntenic set of core genes that are characteristic for this type of island.51 Reproduced from the article by Larbig et al.43 with permission by the authors and the American Society for Microbiology.

vicinity to the pilA and oprL – phnAB loci. The duplicated copies of a tRNALys gene were identiﬁed as the hotspots for the integration and excision of DNA in these regions. The large plasmid pKLK106 sequentially recombined with either of the two tRNALys genes in P. aeruginosa clone K strains, giving rise to reversible rearrangement of a 106 kb genome island in sequential isolates from CF patients35 (Figure 9). In all investigated clone K strains, both episomal and chromosomal copies were detected. During the propagation of single colonies on agar plates in vitro, progeny that had retargeted pKLK106 into the other tRNALys locus were regularly observed, indicating that pKLK106 is mobilized and reintegrated into the clone K chromosomes at high frequency. In strain PAO1 the tRNALys (1) gene close to oprL–phnAB is located between coding sequences PA0976 and PA0977. The 8.9 kb DNA block 3 of tRNALys from PA0977 to PA0987 represents a non-conserved insertion that terminates with duplicated 22 bp of the 3 end of the tRNALys (1) gene, presumably the former attP-site of the integrated element. This 8.9 kb block of PAO1-speciﬁc DNA is absent in clone K strains, harboring PA0988 as their ﬁrst PAO1 hom*olog downstream of tRNALys (1).35 In strain C a 23.4 kb large gene island termed PAGI-4 is integrated at this tRNALys (1) site.39 PAGI-4 substitutes PA0977 to PA0994 and consists of two blocks of non-PAO1 sequence that each are ﬂanked by short stretches of PAO1hom*ologous sequence. The ﬁrst block of 9.5 kb of non-PAO1 sequence ﬂanked by truncated versions of PA0977 and PA0980, shares conserved synteny and 87–99% amino acid sequence with ORFs of PAGI-2, PAGI-3, and pKLC102 (see below). The second 12.7 kb DNA segment ﬂanked by truncated versions of PA0981 and PA0994 encodes the typical elements of a transposon similar to Tn4652 from Pseudomonas putida.

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Strain PA14 carries the 10.7 kb island PAPI-2 at this location that shares substantial sequence similarity with the PAO1 genome island.30 The PAO1 pyocin genes PA0984-85 are replaced in PAPI-2 by the cytotoxin exoU gene and its chaperone spcU, and accordingly PAPI-2 has termed a pathogenicity island. In two clinical isolates another 81 kb island that also contains the exoU gene has been identiﬁed to again reside at the very same genomic position.95 In summary, ﬁve different genome islands varying of 8.9–106 kb in size have yet been identiﬁed to integrate into the tRNALys (1) gene close to oprL–phnAB. Three different genome islands PAPI-1, pKLK106, and pKLC102 are known to insert into the tRNALys (2) gene close to pilA. pKLK106 and pKLC102 are highly hom*ologous plasmids. Clone K and clone C strains from the environment harbored chromosomal and episomal copies of this mobile genetic element.39 PAPI-1, pKLK106, and pKLC102 share numerous features: approximate size (108, 106, 102 kb), a tRNAAsp , tRNAPro , and tRNALys gene cluster at their leftward PAO1 junction, and a direct repeat of the 3 half of the tRNALys gene at their right border, and the integrase and the chromosome partitioning genes at the ends of the island, similar to PAGI-2 and PAGI-3.30,39 PAPI-1 is a pathogenicity island because it carries at least 19 virulence factors that occur on genomic islands found in a wide spectrum of other pathogenic bacteria.30 pKLC102 contains the 8.5 kb chvB gene hom*ologs of which are known to confer host tropism and virulence and to be essential for the interaction of the bacterium with its eukaryotic host. PAPI-1 and pKLC102 encode type IV group B pili and type IV thin sex pili, respectively, and share a set of hom*ologs found as island-speciﬁc genes in PAGI-2, PAGI-3 (see above), and numerous genome islands in other proteobacteria (Figure 6). Fifteen of 33 core genes common to 15 genome islands from β- and γ-Proteobacteria were congruent with the phylogenetic relationships of each of the individual genes indicating that all ﬁve large genome islands known so far in P. aeruginosa belong to one family of related syntenic genomic islands with a deep evolutionary origin.51 The mobile pKLC102 shares with PAPI-1 the phage module that conferred integrase, the att element and the syntenic set of genes, but it differs from PAPI-1 in carrying a plasmid module that conferred oriV and genes for replication, partitioning, and conjugation.39 The only large genome island known so far that is not associated with a tRNA gene is the 49 kbp PAGI-1. This ﬁrst described genome island in P. aeruginosa is widely distributed in the population.45 The island was probably assembled from two ancestral components of different G + C content. 35 kb of the higher G + C content portion is also found in the P. putida KT2440 genome.53 PAGI-1 contains genes potentially involved in oxidative stress resistance, and replaced PAO1 genes PA2218 to PA2222. Furthermore, in other P. aeruginosa strains, this region contains an insertion of 3 kbp of DNA unrelated to PAGI-1.

Clonal Variations in Pseudomonas aeruginosa

49 = XerC/D int = P4 int = Type IV secretion

P. aeruginosa PA14 (PAP1)

P. aeruginosa C (pKLC102)

R. metallidurans CH34

P. fluorescens SBW25

Pseudomonas sp. B13 (clc)

100

P. fluorescens Pf O-1

P. aeruginosa SG17M (PAGI-3)

98 100

100

X. axonopodis 306

100

S. typhi CT18 (SPI-7)

100 100 100 H. influenzae 1056 (ICEHin1056) P. luminescens TT01

80 100 H. ducreyi 35000 HP

Y. enterocolitica 8081 H. somnus 2336

H. somnus 129PT

0.1

Figure 6. The amino acid sequences of the 15 predicted sequences common to 15 genome islands were concatenated and aligned by ClustalX. The alignment of each of the genes alone was consistent with the alignment illustrated. Reproduced from the article by Mohd-Zain et al.51 with permission by the authors and the American Society for Microbiology.

In summary, the accessory genome of P. aeruginosa is made up of numerous genome islets and islands. Most genome islands analyzed so far are integrated into tRNA genes and share a signature of syntenic genes that are widespread among proteobacteria. Accessory genes are nestled among these core genes and confer a diverse repertoire of strain-speciﬁc features.

2.3. Population Biology of P. aeruginosa Bacteria can have population structures ranging from the fully sexual to the highly clonal. Several independent studies in the last years demonstrated that P. aeruginosa has a nonclonal population structure punctuated by highly successful epidemic clones or clonal complexes.14,36,52,60,76 By applying multilocus SNP typing on two unrelated strain collections, the index of association was consistently calculated in two independent studies to be 0.2914 and 0.3136 indicating that P. aeruginosa has a nonclonal population

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structure. The index of association is a measure of the extent of linkage equilibrium within a population by quantifying the amount of recombination among a set of sequences and detecting associations between alleles at different loci. Comparisons of the topologies of neighbor-joining trees for the nucleotide sequences of individual loci revealed in both studies that there was little, if any, congruence between the trees. Strains, which belong to the same genotype, are characterized by non-random association of alleles that is not disrupted by recombination. In contrast, the recombination frequency of large chromosomal segments between genotypes is high enough to break up clonal associations and have all genotypes in linkage equilibrium to each other. Hence, the P. aeruginosa genotypes are equivalent biovars that form a net-like population structure. Each genotype represents a cluster of closely related strains (clonal variants) that share identical alleles.36 When typing a strain, the core genome can be represented by the multilocus SNP genotype of conserved genes whereas both core and accessory genome can be represented by the PFGE-separated macrorestriction fragment proﬁle. By comparative SNP and SpeI PFGE genotyping52 numerous cases were resolved whereby strains shared the SNP genotype but had different SpeI macrorestriction proﬁles. Interestingly, this ﬁnding applied to the most abundant SpeI genotypes. Further examples were the completely sequenced strains PAO1 and PA14 isolated in Australia and the US, respectively, which shared their SNP genotype with numerous clinical and environmental isolates from Europe. This data indicate the high proportion of dominant epidemic clones in the P. aeruginosa population. These epidemic clones such as the European clone C, the Australian, and the UK epidemic clones have unrelated genotypes, suggesting that they have evolved independently.14,76 RFLP analysis of the chromosome and SNP analysis of individual genes measure different evolutionary forces. The conservation of the SNP genotypes and the divergence of SpeI macrorestriction patterns in strains sharing the same SNP proﬁle agree with the idea that the core genome of P. aeruginosa is highly conserved and that its evolution and structure rely more on acquisition, loss, and rearrangements of genome islands and genome islets than on point mutations. In other words, horizontal gene transfer has a more important role than point mutations on the evolution of P. aeruginosa in most habitats. The only known exception seems to be the uncommon habitat of the human respiratory tract where a high proportion of hypermutable P. aeruginosa strains emerges over time.56 In enterobacteria a single genotype predominates one habitat (Figure 7). Genotypes are associated with particular pathogenicity islands which result in disease-associated clones. In contrast, there is no correlation between P. aeruginosa clones and habitats (Figure 7). Dominant clones are ubiquitously distributed in both disease and environmental habitats: for example, members of the same clone were recovered from oil shale and from the lungs of patients

Clonal Variations in Pseudomonas aeruginosa

Figure 7. Clonal population structure of E. coli and P. aeruginosa differing in spatio-temporal distribution. The related disease habitats of E. coli are designated A1, A2, A3, and A4; the diverse disease and environmental habitats of P. aeruginosa are symbolized by A, B, C, and D. Whereas E. coli shows a clear correlation between clone and habitat (disease-associated clones), being only occasionally interrupted by horizontal gene transfer, the same spectrum of P. aeruginosa clones colonizes even unrelated habitats. Individual variants of a certain clone may predominate in several niches. Variants of P. aeruginosa clones undergo adaptive genetic changes, suggested by the shading. Reproduced from the article by Kiewitz and T¨ummler36 with permission by the authors and the American Society for Microbiology.

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Upregulation

Downregulation 892

TB 204

892

TB 206

317

126 141

300 10

13 36

54 PAO1

119 PAO1

Figure 8. Transcriptome analyses in strain PAO1 and the two clone TB strains TB and 892: PAO1 genes with signiﬁcantly changed expression levels in hydrogen peroxide treated P. aeruginosa TB, 892, and PAO1. Genes that were found to be up- or down-regulated in two or three strains are indicated in the intersections.

with CF.23,52 Disease and environmental isolates of P. aeruginosa clones are indistinguishable in their genotypic and chemotaxonomic properties14,23,52 and are functionally equivalent in several traits relevant for their virulence and environmental properties.1 In summary, P. aeruginosa appears to be so versatile that it can colonize a variety of different ecological niches without specialization (Figure 7).

3. CLONAL VARIATIONS OF PHENOTYPE The polymorphic loci in the P. aeruginosa core genome lead to a clonespeciﬁc repertoire of pyoverdines, LPS, pili, and ﬂagella, whereby the latter two do not only vary in the primary amino acid sequence, but also in the posttranslational glycosylation pattern. Most interclonal variations are conferred by the genome islets and islands of the accessory genome, but their impact on phenotype has yet not been resolved. The differential sets of O-antigens, pyocins, and phage receptors have been exploited for decades for strain typing, but the ﬁrst systematic comparisons of global mRNA transcript and protein proﬁles in genetically typed strains have only reported recently. Salunkhe et al.69,70 compared the inter- and intraclonal diversity of the PAO1 transcriptome between strain PAO1 and the two clone TB strains TB and 892 under different environmental conditions. The number of expressed genes differed by clone. The PAO1 strain expressed 64% of its genes in LB medium, whereas the TB and 892 strains expressed more than 70% of genes. When the strains were exposed to the stressor hydrogen peroxide, 24, 17, 12% of the 5900 ORFs were signiﬁcantly differentially regulated in P. aeruginosa TB, 892 and PAO1, respectively. Only 441 genes were consistently differentially expressed in the three strains. 729 genes showed strain-speciﬁc responses and 501 genes

Clonal Variations in Pseudomonas aeruginosa

were similarly regulated in two strains (Figure 8). The expression proﬁle was signiﬁcantly more related between the two members of the TB clone than between either strain with PAO1. The 892 strain shared 84% and 88% of up- and down-regulated genes with its more virulent clonal variant TB that exhibited a more strain-speciﬁc expression proﬁle with 50% and 76% of up- and downregulated genes being in common with 892. It is noteworthy that strains TB and 892 exhibit identical SNP and SpeI genotypes52 and that the DNA sequence was 100% identical in more than 100 kb of randomly selected loci of the core genome.36 Nevertheless the global mRNA expression proﬁles of the two clonal variants were divergent when the strains were cultivated simultaneously in LB medium in the presence or absence of oxidative stress. Apparently there are a few sequence variations in some key genes that account for the divergent phenotypes. In other words, genetically very closely related P. aeruginosa strains present a strain-speciﬁc mRNA expression proﬁle that under carefully controlled identical conditions is highly reproducible, but distinct from members of the same clone. The proteome of the two clonal variants TB and 892 has also been compared by two-dimensional polyacrylamide gel electrophoresis coupled to mass spectrometry to map the extracellular, intracellular, and surface sub-proteomes and to identify differentially expressed proteins.3 About 4% of all detected protein spots were differentially expressed between both strains including absent or present spots and spots with a more than two-fold changed intensity. Nineteen of 78 differentially expressed spots were identiﬁed by mass spectrometry on the basis of a predicted gene product in the genome database for P. aeruginosa PAO1, for 13 additional spots mass ﬁngerprints were obtained which most likely represent clone-speciﬁc proteins of the TB lineage. Many of the protein spots in TB that were missing or expressed at lower levels in the less virulent 892 strain were identiﬁed as quorum-sensing regulated virulence factors. Strains of P. aeruginosa can be phenotypically classiﬁed by their mode of pathogenicity as either invasive, where the bacterium is internalized by host cells, or cytotoxic, where the host cell is killed without internalization through the expression of cytotoxicity factors. These phenotypes are thought to depend primarily on the interactions of pseudomonal membrane and secreted proteins with host cells. Nouwens et al.54 compared the proteomes of the outer membrane and extracellular protein-enriched fractions from the invasive strain PAO1 and the cytotoxic strains 6206. Membrane protein strain differences were typically the result of minor amino acid sequence variations resulting in small mass and isoelectric point shifts visible on two-dimensional gels. Analysis of extracellular proteins from stationary phase growth, however, revealed signiﬁcantly different protein proﬁles between the two unrelated clones. Extracellular fractions from the invasive PAO1 strain were dominated by extracellular proteases including elastase (LasB), LasA protease, and chitin-binding protein, as well as several previously designated ,conserved hypotheticals’ of unknown function. Conversely, extracellular fractions from strain 6206 consisted mainly of

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cellular and membrane exposed proteins including GroEL, DnaK, and ﬂagellar subunits. These are thought to result from cellular turnover during growth and the reliance on the secretory mechanisms of this strain to produce high levels of cytotoxicity factors, such as ExoU, which may be produced only upon speciﬁc interactions with host cells. Wehmh¨oner et al.92 compared the proteome proﬁles of six P. aeruginosa clones grown in modiﬁed minimal Vogel-Bonner medium. The proteome analysis revealed almost identical patterns for the cellular extracts, whereas interclonal diversity were demonstrated for the secretomes of cultured P. aeruginosa. The diversity was even greater for the immunogenic protein patterns expressed in vivo. The observed interclonal variability of the secretome may reﬂect the differential, clone-speciﬁc regulation of gene expression and/or the utilization of genes that are not encoded by the core genome but are encoded by the highly dynamic accessory genome. To differentiate between the two mechanisms, Wehmh¨oner et al.92 also analyzed the proteomes of sequential clonal variants with diverse morphotypes. A P. aeruginosa isolate that formed irregularly shaped colonies was compared with a hyperpiliated and autoaggregative P. aeruginosa small colony variant. The expression proﬁles of cellular extracts of the two morphotypes exhibited only minor differences, in contrast to the marked differences in the expression proﬁles of the extracellular fractions. Mass spectrometry revealed that the small colony variant overexpressed proteins secreted by the type I and type III secretion systems. This ﬁnding implies that the variability of the secretome is due to differential regulation of protein expression, possibly as a consequence of small adaptational mutations. These observations were backed up by genome-wide transcriptional proﬁles of the two clonal morphotypes.91 Of the more than 300 differentially expressed genes, the upregulation of the type III secretion system and the respective effector proteins in the small colony variant was the most striking ﬁnding. The conserved intracellular proteome of strains grown in vitro probably reﬂects the fact that the need for adaptation under these conditions is low, and inter- and intraclonal differences that reﬂect the versatility of niche specialists are not likely to be detected. Moreover, the cellular proteome comprises mostly proteinaceous cell constituents that are expected to be species-speciﬁc but not clone- or strain-speciﬁc. However, the secretome expression is strongly strain and morphotype-speciﬁc. Since the secreted P. aeruginosa proteins come into direct contact with their environment, they could be especially important and thus be essential for bacterial adaptation. Moreover, the secretome includes important virulence factors essential for establishment of an infection within the human host. In summary, the secretome is a sensitive measure of P. aeruginosa strain variation. A special case of intraclonal diversity are the strain variations that occur during subculturing in vitro. A timely and important example is the completely sequenced reference strain PAO1. The sequenced strain85 differs from the ancestor strain that had been independently physically mapped in Australia and Germany,33 by a 1.7 Mbp inversion between the rrnA and rrnB loci and an about

Clonal Variations in Pseudomonas aeruginosa

20 kbp deletion close to the rrnC locus. Moreover, PAO1 stocks maintained at different laboratories are not identical in phenotypic traits, a spectacular example being the differential virulence in infection models even though the strain had been originally obtained from the same public collection (own unpublished data). During storage and subculturing the PAO1-derived isolates apparently diversiﬁed by inversion, deletion, and point mutation.

4. INTRACLONAL EVOLUTION AND DIVERSITY IN CLINICAL HABITATS 4.1. Hospital-Acquired Infections P. aeruginosa is resistant to many antimicrobial agents and a major source for nosocomial infections in predisposed individuals. Hence, the major practical issue to assess clonality and intraclonal evolution are infection control measures to determine epidemic clonality amongst multidrug-resistant strains or to document outbreaks of (drug-resistant) clones (as examples see refs [34,50,58,59]). A few groups combined the molecular epidemiology of hospital-acquired infection with the characterization of intraclonal diversity. Hocquet et al.32 retrospectively analyzed the intraclonal variation of drug resistance of a serotype O:6 multidrug-resistant P. aeruginosa clone during a 4-year long outbreak at a French University Hospital. This clone was initially recognized because of its particular susceptibility proﬁle to aminoglycosides [conferred by an ANT (2”)-I enzyme] and ﬂuoroquinolones (caused by mutations in the QRDR of gyrA and parC) and because of its elevated resistance to many β-lactams. The susceptibility proﬁle of this epidemic clone to ﬂuoroquinolones and aminoglycosides was relatively stable during the outbreak but showed important isolate-to-isolate variations in the susceptibility to β-lactams. Analysis of 18 genotypically related isolates selected on a quarterly basis demonstrated alterations in DNA topoisomerases, constitutive overexpression of the MexXY efﬂux system, derepression of intrinsic AmpC β-lactamase and sporadic deﬁciency in the carbapenem-selective porin OprD. Of the 18 isolates, 14 were also found to overproduce the efﬂux system MexAB-OprM as a result of alteration of the repressor protein MexR. Of the four isolates exhibiting wild-type MexAB-OprM expression despite the MexR alteration, two appeared to harbor secondary mutations in the mexA-mexR intergenic region and one harbored secondary mutations in the putative ribosome binding site located upstream of the mexAB-oprM operon. In conclusion, many mechanisms were involved in the multiresistance phenotype and the clone sporadically underwent substantial genetic and phenotypic variations during the course of the outbreak. P. aeruginosa is responsible for severe nosocomial pneumonia in mechanically ventilated patients. Denervaud et al.16 collected 442 P. aeruginosa isolates during the ﬁrst 3 days of documented colonization of 13 intubated

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patients in order to study quorum-sensing dependent phenotypic traits. The 442 isolates belonged to nine different clones. Eighty-one percent of the isolates produced hom*oserine lactones and quorum-sensing dependent extracellular virulence factors, including total exoprotease, elastase, HCN, pyocyanin, and rhamnolipids, at levels equivalent to those of the reference strain PAO1, but 19% of the isolates were deﬁcient in cell-to-cell signaling, because the lasR gene encoding the LasR transcriptional regulator was inactivated by various mutations. A subset of these isolates also had mutations in the rhlR gene, probably explaining the defect in both hom*oserine lactone and extracellular virulence factor production. Since the hom*oserine lactone production of these strains was complemented by the chromosomal insertion of the wild-type lasR and rhlR genes, additional mutations are unlikely. Three of the 13 patients presented a P. aeruginosa pneumonia as a complication of their respiratory colonization of whom two subsequently developed a P. aeruginosa bacteremia. These bacteremic isolates were clonal variants carrying the lasR or lasR/rhlR mutants. This is the ﬁrst report on clinical isolates that are unable to produce cell-to-cell signals as a result of both lasR and rhlR mutations, and it is interesting to note that the intraclonal evolution toward loss of quorum-sensing was associated with the gain-of-invasiveness to breach the airway epithelial barrier.

4.2. Cystic Fibrosis Most information about the evolution of intraclonal diversity of P. aeruginosa was obtained from retrospective cross-sectional and longitudinal analyses of isolates recovered from the atypical habitat of the CF lung. CF is a severe monogenic disorder of ion transport in exocrine glands that is caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. The basic defect predisposes to chronic bacterial airway infections, particularly with P. aeruginosa. The P. aeruginosa infections in CF are a paradigm of how environmental bacteria can conquer, adapt, and persist in an atypical habitat and successfully evade defense mechanisms and chemotherapy in a susceptible host. Airway infections with P. aeruginosa in individuals with CF are unique in that they chronically affect a host who is immunocompetent in terms of cellular and humoral responses but is immunocompromised by impaired airway clearance. Once P. aeruginosa has taken residence in the CF lungs, the organism is notoriously resistant to eradication by chemotherapy. The pseudomonads chronically colonize the bronchiolar lumen and virtually never breach the epithelial barrier (reviews: refs [26,89]). 4.2.1. Clonal Variations of Genotype in CF Lungs Most individuals with CF become chronically colonized with a single clone of P. aeruginosa that stays in the lungs for many years. Turnover of clones was seen in the author’s laboratory after 5–15 years in about half of the

Clonal Variations in Pseudomonas aeruginosa

investigated patients. Transient or permanent co-colonization with more than one clone was seen in 20–30% of patients. These conditions that CF lungs are chronically infected for years by one or a few P. aeruginosa clones are precisely those that theoretical studies predict for the evolution of mechanisms that augment the rate of variation. Determination of spontaneous mutation rates in 128 P. aeruginosa isolates from 30 CF patients revealed a high proportion (20%) with an increased mutation frequency (mutators).55,56 Seven out of 11 analyzed CF mutator strains were found to be defective in the mismatch repair system. The alterations in the mutS, mutL, and uvrD genes were found to be responsible for the mutator phenotype. In four cases (three mutS and one mutL), the genes contained frameshift mutations. The fourth mutS strain showed a 3.3 kb insertion after the 10th nucleotide of the mutS gene, and a 54 nucleotide deletion between two eight nucleotide direct repeats. This deletion, involving domain II of MutS, was found to be the main one responsible for mutS inactivation. The second mutL strain presented a K310M mutation, equivalent to K307 in E. coli MutL, a residue known to be essential for its ATPase activity. Finally, the uvrD strain had three amino acid substitutions within the conserved ATP binding site of the deduced UvrD polypeptide, showing defective mismatch repair activity. In summary, intraclonal evolution of P. aeruginosa in CF lungs can be driven by hypermutable clonal variants. Since the proportion of mutators in the population increases over time, point mutations preferentially accumulate during the late stages of the infection. Mutator strains were not found in 75 non-CF patients acutely infected with P. aeruginosa,56 but were also seen in 30 patients with non-CF underlying chronic respiratory diseases (22 with bronchiectasis and 8 with chronic obstructive pulmonary disease).46 Seventeen of the 30 patients were colonized with hypermutable strains. The mutS gene was inactivated in isolates from 11 patients. Multiple antimicrobial resistance was documented in 42% of the hypermutable strains in contrast to 0% of the non-hypermutable strains. This study demonstrates that ﬁrst, hypermutation is a key factor for the emergence of the multidrug resistance phenotype; and that second, in contrast to what has been described in acute processes, hypermutable P. aeruginosa strains are highly prevalent in chronic infections of the human respiratory tract.46,56 Besides the mismatch repair system and the targets that confer multiple antimicrobial resistance, further known hotspots for mutation in CF isolates are the mucA and lasR genes. Inactivation of lasR is often causative for the loss of production of N -acylhom*oserine lactones (AHL) which is not rare in CF, particularly if the lung is co-colonized with Burkholderia cepacia.19,24 The mucoid phenotype of P. aeruginosa has been linked to mutations in a gene cluster designated as the mucABCD genes that encode proteins that inhibit the activity of the alternative σ -factor AlgU.49 When alginate production is minimal, AlgU (also referred to as AlgT) is bound in a complex along with MucA and MucB, but under environmental stress conditions this complex is disrupted,

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leading to the release of AlgU into the cytosol. AlgU acts on the key alginate biosynthesis gene algD, which encodes a GDP mannose dehydrogenase, and on algR, a response regulator genes that increases alginate synthesis.74 Mutations in mucA, B, and D are held responsible for alginate overproduction and conversion to a stable mucoid phenotype in P. aeruginosa, while mutations in mucC do not cause any overt effects on alginate synthesis.9,49 Consistent with this hypothesis, mutations in mucA have been detected in mucoid P. aeruginosa strains isolated from chronically infected CF patients.2,9,10,75,84 Alginate production is also dependent on a second alternative σ -factor, RpoN, and likely on other mutations in genes which are not known at present. However, according to more recent studies mutations in the mucABD cluster are not exclusively correlated to overexpression of alginate in P. aeruginosa CF isolates.11,84 The combined analysis of quantitative alginate expression and mucA, mucB, mucD, and algU sequencing in 37 P. aeruginosa strains revealed that a distinct proportion of phenotypically non-mucoid P. aeruginosa strains carried mucA stop mutations which were also present in alginate-overexpressing, mucoid P. aeruginosa strains.11 Since sequence analysis of algU did not reveal any mutational genetic changes, other, unknown, mechanisms are presumably regulating alginate expression in these mucA mutated strains. P. aeruginosa in CF lungs is not only prone to point mutations, but also to gross changes of the chromosomal frame. When Ernst et al.20 analyzed 13 isolates from seven young CF children by hybridization on PAO1 whole genome DNA microarrays, they detected 2 strains with large deletions (strain CF250: 119 kb (PA1909–PA2010); strain CF5296: 189 kbp (PA2273–PA2409). The latter deletion eliminates the hypervariable pyoverdine locus. Reversible genome rearrangements were seen in CF isolates which were carrying the mobile genetic element pKLK106. pKLK106 reversibly recombined with sequential clone K chromosomes at one of the two tRNALys genes35 (Figure 9). In all investigated sequential clone K CF strains both episomal and chromosomal copies were detected. Physical mapping of 18 CF clone C isolates revealed inversions in eight strains, two of which were harboring two nested inversions.67 Besides one small scale inversion of 40 kb, the inversions ranged from 1 to 5 Mbp whereby their recombination endpoints scattered on the chromosome. In six cases the region of the terminus of replication was included in the recombinational exchange and was shifted by maximal 17% of genome size (Figure 4). A hotspot of recombination was mapped to the pKLC102 locus:40 All investigated clone C isolates from aquatic habitats and the hospital environment harbored chromosomal and episomal copies of pKLC102. However, many isolates from CF lungs contained either no (C5) or only chromosomally integrated pKLC102 (C2) (Figure 9). Of the four subgroups of clone C,67 subgroup C was exclusively represented by CF lung isolates and differed from the other three groups by the insertion of the class 1 composite transposon TNCP23 into chromosomally

Clonal Variations in Pseudomonas aeruginosa

Figure 9. Evolution of P. aeruginosa strains linked to plasmid DNA. (a) Reversible integration of plasmid DNA into two possible sites of clone K strains. (b) Different forms of plasmid DNA in clone C strains. In subgroup SG17M pKLC102 is found episomally and integrated into the genome at tRNALys (2). Strain C5 apparently lost the pKLC102 DNA, while strain C2 only harbors the integrated form. In subgroup C the integron TNCP23 inserted into chromosomally integrated pKLC102. Free plasmid is not detectable in subgroup C strains indicating that TNCP23 prevented mobilization. TNCP23 is ﬂanked by copies of IS6100. Intramolecular transposition of the left copy of IS6100-L is coupled with an inversion of the chromosomal region between the transposed copy and IS6100-L in some strains of subgroup C. For these strains C8, C9, C10, and C19, the tRNALys (1) area is not shown. Reproduced from the article by Klockgether et al.39 by permission of the authors and the American Society for Microbiology.

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integrated pKLC102, which may have been acquired because of the encoded aadB gene conferring gentamicin resistance (Figure 9). P. aeruginosa converges in CF lungs to a common phenotype characterized by the decreased production of membrane components, cellular appendages and secreted factors (see below). This phenotypic signature was partially gained in subgroup C strains by TNCP23-mediated chromosome remodeling. Intramolecular transposition of the active IS-6100 element of TNCP23 led to large chromosomal inversions which disrupted genes that are typically inactivated during the adaptation of P. aeruginosa to the atypical habitat of CF lungs (Figure 9). In parallel the integrity of pKLC102 was destroyed. The two attachment sites were separated so that the genetic contents of pKLC102 was irreversibly ﬁxed in the chromosome. In summary, Figure 9 visualizes the evolution of plasmid pKLC102 from a mobile genetic element to an irreversibly ﬁxed genome island that ﬁnally was disrupted and distributed to separate chromosomal regions. It should be noted that the increasing complexity of genome organization caused by insertion, transposition, and inversion was accompanied by mutation, deletion, and/or duplication of sequence close to the breakpoint. In summary, inversions, deletions, and point mutations are common for the intraclonal evolution of P. aeruginosa in CF lungs. 4.2.2. Clonal Variations of Phenotype in CF Lungs Apart from the evolution of genome organization, P. aeruginosa develops common phenotypic features irrespective of clonal descent. This phenotypic conversion is characteristic for the CF lung habitat and, on the whole, is genetically ﬁxed and irreversible. In other words, some aspects of intraclonal evolution are similar in all clones. Strains become LPS deﬁcient (non-typable or polyagglutinating rough strains) and sensitive to lysis by complement.27 On the other hand, CF isolates produce modiﬁed lipid A forms containing palmitate and aminoarabinose that are associated with resistance to cationic antimicrobial peptides and stronger induction of inﬂammatory responses such as interleukin 8 expression.21 P. aeruginosa strains vary in their differential repertoire of bacteriophage receptors and the production of pyocins, which lyse susceptible P. aeruginosa strains. These differential properties are gradually lost in most P. aeruginosa during chronic colonization of the CF lung. Susceptibility to phages and secretion of pyocins decrease within a few years time.65 The production of the major siderophore pyoverdine also changes over time. Pyoverdine-negative mutants emerge, but retain the capacity to take up pyoverdines.17 CF strains become immotile owing to the loss of their ﬂagella.47 CF isolates from early colonization were highly motile and expressed both ﬂagellin and pilin. However, about 40% of more than a 1000 examined isolates from chronically colonized CF patients lacked ﬂagellin expression and were nonmotile. Sequential isolates remained consistently nonmotile. Lack of motility was rare among environmental isolates (1.4%) and other clinical isolates (3.7%) of P. aeruginosa examined.47

Clonal Variations in Pseudomonas aeruginosa

Moreover, during chronic colonization of the CF lung most P. aeruginosa strains reduce or even abolish the production of type II and III secretion effector proteins and thus reduce cytotoxicity. While the killing of epithelial and phagocytic cells may be an important feature of acute infections, the same virulence mechanisms appear to be incompatible with chronic colonization of CF patients.26 P. aeruginosa isolates were examined that had been obtained from 7 patients soon after their initial colonization and then again more than a decade later, after the establishment of chronic lung infections.44 Early isolates were typically cytotoxic, the exception being the highly mucoid strains. Variants of the same clone, isolated years later from the same patients, were found to be nontoxic, suggesting that there has been a selection for loss of cytotoxicity. In many cases restoration of type III regulation, through the expression of the ExsA regulator, was able to reestablish ExoS secretion and cytotoxicity. However, this was not the only mechanism of attenuation since expression of ExsA was not able to restore ExoS secretion in all of the clinical isolates. Moreover, some strains accumulated more than one mutation in the type III secretion system so that ExoS secretion could be restored with ExsA expression; but cytotoxicity was still attenuated. What was also apparent from the pairwise comparisons of early and late isolates was that the phenomenon of delayed cytotoxicity associated with type II secretion effector proteins was also lost in later isolates. The respiratory tracts of CF patients therefore provide a strongly selective environment for the accumulation of pathoadaptive mutations, which favor a chronic existence that often necessitates the elimination of a potent cytotoxic mechanism. Another common feature of intraclonal evolution in the CF lung is the diversiﬁcation of morphotype, the hallmarks being the emergence of small colony variants28,29 and mucoid colonies.26,57 The alginate-overexpressing mucoid phenotype is typical for CF isolates and very uncommon in other habitats.26 A subgroup of hyperpiliated small colony variants is prone to bioﬁlm formation and induction of type II and type III secretion29,91 which leads to increased virulence in infection models in contrast to the notion that most P. aeruginosa isolates from chronically colonized CF lungs are typically attenuated in virulence (see above). Auxotrophy is common in CF, particularly in those with severe underlying pulmonary disease.87 At this late stage the auxotroph count exceeds more than 50% total CFU. The majority of auxotrophs required methionine as the sole factor.86 In summary, the common conversion of phenotype of P. aeruginosa in CF lungs starts with morphotype diversiﬁcation and loss of outer membrane constituents and cell appendages and ends with a progressive change from proto- to auxotrophy. At this ﬁnal stage of adaptation to the CF lung, the accumulation of pathoadaptive mutations will probably impair the ﬁtness of the bacteria to grow in other habitats. Besides this convergence in phenotype that progressively happens over time, numerous phenotypic features are ﬂuctuating in the P. aeruginosa CF

Burkhard Tummler ¨

lung communities. These periodic changes in phenotype probably result from the emergence and disappearance of clonal variants with differential ﬁtness. The repeated courses of regular antipseudomonal intravenous chemotherapy and the long-term administration of aerosolized aminoglycosides inadvertantly will select for resistant variants, and correspondingly ﬂuctuations in the susceptibility patterns to antipseudomonal agents are a common ﬁnding in CF sequential isolates. The adhesion phenotypes also vary strongly over time. P. aeruginosa mainly resides in the bronchiolar lumen of the CF airways embedded into a matrix of DNA, bacterial exopolysaccharides and human mucins.88 P. aeruginosa uses chieﬂy proteins of its ﬂagellar apparatus to initiate this binding and recognizes a variety of oligosaccharides that have been identiﬁed in mucins.6,62 Among these are both neutral oligosaccharides and several forms of acidic oligosaccharides derived from the Lewis antigens.72 Serial P. aeruginosa isolates from CF patients with advanced lung disease were characterized in their binding to CF human tracheobronchial mucins from three of these patients.88 The strains differed strongly in their speciﬁcity for and afﬁnity to mucin carbohydrate. Intra- and interclonal variation was equally pronounced indicating that the mucin-binding phenotype is not conserved within a particular clone. Binding capacity to the airway epithelium is another trait subject to intraclonal variation. P. aeruginosa binding capacity to respiratory epithelial cells was studied in a representative panel of 634 sequential P. aeruginosa strains isolated from 26 CF patients, from the onset of colonization for up to 15 years of infection.41 Adherence was strongly varying between clonal variants sampled at the same or different times, albeit three types divergent in the temporal evolution were noted: predominantly high binders, predominantly low binders at all times, or a shift from high binders at early colonization to low binders later on. Patients chronically harboring high binders had a worse prognosis than the others indicating that adhesion to the airway epithelium is a relevant pathogenic trait for P. aeruginosa to colonize and to persist in the CF lung. Intraclonal variation may also be caused by AHL-dependent signaling between B. cepacia and P. aeruginosa.24 When patients became transiently coinfected with an AHL-producing B. cepacia strain, AHL production by the co-residing P. aeruginosa isolates was switched off. However, months after the last B. cepacia-positive sputum the initial P. aeruginosa AHL proﬁle was regained suggesting that AHL-mediated cross-talk between the two pathogens may affect the virulence of the mixed consortium which, in turn, may have selected for P. aeruginosa mutants producing lowered amounts of AHLs. In summary, the CF lung habitat triggers a conversion of bacterial phenotype, but P. aeruginosa retains enough ﬂexibility to recognize its environment of host cells and polymers and to respond to selective pressures such as antimicrobial chemotherapy or co-colonization with other taxa.

Clonal Variations in Pseudomonas aeruginosa

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Clonal Variations in Pseudomonas aeruginosa

69. Salunkhe, P., G¨otz, F., Wiehlmann, L., Lauber, J., Buer, J., and T¨ummler B., 2002, GeneChip expression analysis of the response of Pseudomonas aeruginosa to paraquat-induced superoxide stress. Genome Lett., 1:165–174. 70. Salunkhe, P., T¨opfer, T., Buer, J., and T¨ummler, B., 2005, Genome-wide transcriptional proﬁling of the steady state response of Pseudomonas aeruginosa to hydrogen peroxide. J. Bacteriol., 187: 2565–2572. 71. Sato, H., Frank, D.W., Hillard, C.J., Feix, J.B., Pankhaniya, R.R., Moriyama, K., FinckBarbancon, V., Buchaklian, A., Lei, M., Long, R.M., Wiener-Kronish, J., and Sawa, T., 2003, The mechanism of action of the Pseudomonas aeruginosa-encoded type III cytotoxin, ExoU. EMBO J., 22:2959–2969. 72. Scharfman, A., Arora, S.K., Delmotte, P., Van Brussel, E., Mazurier, J., Ramphal, R., and Roussel, P., 2001, Recognition of Lewis x derivatives present on mucins by ﬂagellar components of Pseudomonas aeruginosa. Infect. Immun., 69:5243–5248. 73. Schmidt, K.D., T¨ummler, B., and R¨omling, U., 1996, Comparative genome mapping of Pseudomonas aeruginosa PAO with P. aeruginosa C, which belongs to a major clone in cystic ﬁbrosis patients and aquatic habitats. J. Bacteriol., 178:85–93. 74. Schurr, M.J., Martin, D.W., Mudd, M.H., and Deretic, V., 1994, Gene cluster controlling conversion to alginate-overproducing phenotype in Pseudomonas aeruginosa: functional analysis in a heterologous host and role in the instability of mucoidy. J. Bacteriol., 176:3375– 3382. 75. Schurr, M.J., Yu, H., Martinez-Salazar, J.M., Boucher, J.C., and Deretic, V., 1996, Control of AlgU, a member of the σ E -like family of stress sigma factors, by the negative regulators MucA and MucB and Pseudomonas aeruginosa conversion to mucoidy in cystic ﬁbrosis. J. Bacteriol., 178:4997–5004. 76. Scott, F.W., and Pitt, T.L., 2004, Identiﬁcation and characterization of transmissible Pseudomonas aeruginosa strains in cystic ﬁbrosis patients in England and Wales. J. Med. Microbiol., 53:609–615. 77. Selander, R.K., and Musser, J.M., 1990, Population genetics of bacterial pathogenesis, pp. 11– 36. In B.H. Iglewski, and V.L. Clark (eds.), Molecular Basis of Bacterial Pathogenesis, Vol. X. The Bacteria. Academic Press, San Diego, CA. 78. Simpson, A.J., Reinach, F.C., Arruda, P., Abreu, F.A., Acencio, M., Alvarenga, R., Alves, L.M., Araya, J.E., Baia, G.S., Baptista, C.S., Barros, M.H., Bonaccorsi, E.D., Bordin, S., Bove, J.M., Briones, M.R., Bueno, M.R., Camargo, A.A., Camargo, L.E., Carraro, D.M., Carrer, H., Colauto, N.B., Colombo, C, Costam F.F., Costa, M.C., Costa-Neto, C.M., Coutinho, L.L., Cristofani, M., Dias-Neto, E., Docena, C., El-Dorry, H., Facincani, A.P., Ferreira, A.J., Ferreira, V.C., Ferro, J.A., Fraga, J.S., Franca, S.C., Franco, M.C., Frohme, M., Furlan, L.R., Garnier, M., Goldman, G.H., Goldman, M.H., Gomes, S.L., Gruber, A., Ho, P.L., Hoheisel, J.D., Junqueira, M.L., Kemper, E.L., Kitajima, J.P., Krieger, J.E., Kuramae, E.E., Laigret, F., Lambais, M.R., Leite, L.C., Lemos, E.G., Lemos, M.V., Lopes, S.A., Lopes, C.R., Machado, J.A., Machado, M.A., Madeira, A.M., Madeira, H.M., Marino, C.L., Marques, M.V., Martins, E.A., Martins, E.M., Matsukuma, A.Y., Menck, C.F., Miracca, E.C., Miyaki, C.Y., Monteriro-Vitorello, C.B., Moon, D.H., Nagai, M.A., Nascimento, A.L., Netto, L.E., Nhani, A. Jr., Nobrega, F.G., Nunes, L.R., Oliveira, M.A., de Oliveira, M.C., de Oliveira, R.C., Palmieri, D.A., Paris, A., Peixoto, B.R., Pereira, G.A., Pereira, H.A. Jr., Pesquero, J.B., Quaggio, R.B., Roberto, P.G., Rodrigues, V., de M Rosa, A.J., de Rosa, V.E. Jr., de Sa, R.G., Santelli, R.V., Sawasaki, H.E., da Silva, A.C., da Silva, A.M., da Silva, F.R., da Silva, W.A. Jr., da Silveira, J.F., Silvestri, M.L., Siqueira, W.J., de Souza, A.A., de Souza, A.P., Terenzi, M.F., Trufﬁ, D., Tsai, S.M., Tsuhako, M.H., Vallada, H., Van Sluys, M.A., Verjovski-Almeida, S., Vettore, A.L., Zago, M.A., Zatz, M., Meidanis, J., and Setubal, J.C., 2000, The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa consortium of the organization for nucleotide sequencing and analysis. Nature, 406:151–157.

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79. Smith, E.E., Sims, E.H., Spencer, D.H., Kaul, R., and Olson, M.V., 2005, Evidence for diversifying selection at the pyoverdine locus of Pseudomonas aeruginosa. J. Bacteriol., 187:2138– 2147. 80. Smith, J.M., Smith, N.H., O’Rourke, M., and Spratt, B.G., 1993, How clonal are bacteria? Proc. Natl. Acad. Sci. USA, 90:4384–4388. 81. Spangenberg, C., Fislage, R., R¨omling, U., and T¨ummler B., 1997, Disrespectful type IV pilins. Mol. Microbiol., 25:203–204. 82. Spangenberg, C., Heuer, T., B¨urger, C., and T¨ummler, B., 1996, Genetic diversity of ﬂagellins of Pseudomonas aeruginosa. FEBS Lett., 396:213–217. 83. Spangenberg, C., Montie, T.C., and T¨ummler, B., 1998, Structural and functional implications of sequence diversity of Pseudomonas aeruginosa genes oriC, ampC and ﬂiC. Electrophoresis, 19:545–550. 84. Spencer, D.H., Kas, A., Smith, E.E., Raymond, C.K., Sims, E.H., Hastings, M., Burns, J.L., Kaul, R., and Olson M.V., 2003, Whole-genome sequence variation among multiple isolates of Pseudomonas aeruginosa. J. Bacteriol., 185:1316–1325. 85. Stover, C.K., Pham, X.Q., Erwin, A.L., Mizoguchi, S.D., Warrener, P., Hickey, M.J., Brinkman, F.S., Hufnagle, W.O., Kowalik, D.J., Lagrou, M., Garber, R.L., Goltry, L., Tolentino, E., Westbrock-Wadman, S., Yuan, Y., Brody, L.L., Coulter, S.N., Folger, K.R., Kas, A., Larbig, K., Lim, R., Smith, K., Spencer, D., Wong, GK., Wu, Z., Paulsen, I.T., Reizer, J., Saier, M.H., Hanco*ck, R.E., Lory, S., and Olson, M.V., 2000, Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature, 406:959–964. 86. Taylor, R.F., Hodson, M.E., and Pitt, T.L., 1992, Auxotrophy of Pseudomonas aeruginosa in cystic ﬁbrosis. FEMS Microbiol. Lett., 71:243–246. 87. Thomas, S.R., Ray, A., Hodson, M.E., and Pitt, T.L., 2000, Increased sputum amino acid concentrations and auxotrophy of Pseudomonas aeruginosa in severe cystic ﬁbrosis lung disease. Thorax, 55:795–797. 88. T¨ummler, B., Bosshammer, J., Breitenstein, S., Brockhausen, I., Gudowius, P., Herrmann, C., Herrmann, S., Heuer, T., Kubesch, P., Mekus, F., R¨omling, U., Schmidt, K.D., Spangenberg, C., and Walter, S., 1997, Infections with Pseudomonas aeruginosa in patients with cystic ﬁbrosis. Behring Inst. Mitt., 98:249–255. 89. T¨ummler, B., and Kiewitz C., 1999, Cystic ﬁbrosis: an inherited susceptibility to bacterial respiratory infections. Mol. Med. Today, 5:351–358. 90. Vallis, A.J., Finck-Barbancon, V., Yahr, T.L., and Frank, D.W., 1999, Biological effects of Pseudomonas aeruginosa type III-secreted proteins on CHO cells. Infect. Immun., 67:2040– 2044. 91. von G¨otz, F., H¨aussler, S., Jordan, D., Saravanamuthu, S.S., Wehmh¨oner, D., Str¨ussmann, A., Lauber, J., Attree, I., Buer, J., T¨ummler, B., and Steinmetz, I., 2004, Expression analysis of a highly adherent and cytotoxic small colony variant of Pseudomonas aeruginosa isolated from a lung of a patient with cystic ﬁbrosis. J. Bacteriol., 186:3837–3847. 92. Wehmh¨oner, D., H¨aussler, S., T¨ummler, B., Jansch, L., Bredenbruch, F., Wehland, J., and Steinmetz, I., 2003, Inter- and intraclonal diversity of the Pseudomonas aeruginosa proteome manifests within the secretome. J. Bacteriol., 185:5807–5814. 93. West, S.E., and Iglewski B.H., 1988, Codon usage in Pseudomonas aeruginosa. Nucleic Acids Res., 16:9323–9335. 94. Winstanley, C., Coulson, M.A., Wepner, B., Morgan, J.A., and Hart, C.A., 1996, Flagellin gene and protein variation amongst clinical isolates of Pseudomonas aeruginosa. Microbiology, 142:2145–2151. 95. Wolfgang, M.C., Kulasekara, B.R., Liang, X., Boyd, D., Wu, K., Yang, Q., Miyada, C.G., and Lory S., 2003, Conservation of genome content and virulence determinants among clinical and environmental isolates of Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. USA, 100:8484– 8489.

PSEUDOMONAS AERUGINOSA PHOSPHOLIPASES AND PHOSPHOLIPIDS Michael L. Vasil

University of Colorado at Denver and Health Sciences Center Aurora, CO 80045, USA

The diversity of roles that phospholipases play in biology and medicine is exceptional. In the past decade, this class of enzymes has proven to be considerably more complex than initially perceived and their impact on an assortment of basic cellular processes in eukaryotes, including oncogenesis and inﬂammation has become widely appreciated. Likewise, there are sundry functions for phospholipases in prokaryotic biology, including their noteworthy contributions to microbial virulence. For example, individual members of a hom*ologous class of phospholipases C (PLCs), usually produced by gram-positive bacteria (GPPLCs), serve vastly different functions in pathogenesis. One member of this class is an extremely potent extracellular toxin (e.g. Clostridium perfringens α toxin), while another contributes to the intricate mechanisms of the intracellular and intercellular trafﬁcking in a facultative intracellular pathogen (e.g. PlcA and PlcB of Listeria monocytogenes). There are several major distinct classes of phospholipases (Figure 1, Table 1). Even within a speciﬁc class (e.g. PLCs), there are subclassiﬁcations based on biochemical parameters (e.g. need for metal cofactors such as zinc) and differences in substrate preference (phosphatidylcholine vs. phosphatidylinositol). These differences can ultimately have a profound effect on whether a particular phospholipase will or will not have an impact in a particular environment, such as different locations in an infected host. In addition, it is important to note that the products created by phospholipases play a fundamental Pseudomonas, Volume 4, edited by Juan-Luis Ramos and Roger C. Levesque C 2006 Springer. Printed in the Netherlands.

Michael L. Vasil +

NH3

+ _

COO

C H2

PLD

CH2

PLC CH2

Serine

CH2

O C O

Ethanolamine

R OH

PLA2

PLA1

CH2

NH3

CH3

CH3 N

CH3

OH OH

CH2

CH2 Choline

Inositol

Figure 1. Structure of a typical glycerophospholipid (diacyl) with the cleavage sites for phospholipase C (PLC), phospholipase D (PLD), phospholipase A1 (PLA1), and phospholipase A2 (PLA2) designated by arrows. The structures of some of the possible head groups substituting for R are shown.

role in the biological effects ultimately attributed to phospholipases (Figure 2). Diacylglycerol (DAG) generated by a PLC can induce proliferative effects in eukaryotic cells, while ceramide generated by a sphingomyelinase (SMase) can cause cell death through apoptosis (Figure 2).20,21 In some cases, the same protein can have both PLC and SMase activity (see Section 4.1 below).41,76

1. PHOSPHOLIPASE C A PLC was the ﬁrst enzymatic activity to be associated with the mode of action of a bacterial toxin. In 1941, Macfarlane and Knight42 demonstrated that the highly cytotoxic α toxin of C. perfringens has PLC activity. Since then, PLC activity has been demonstrated in a variety of other pathogenic bacteria, including Staphylococcus aureus,44 Legionella pneumophila,3 Helicobacter pylori,6 Mycoplasma spp.,12 L. monocytogenes,7,45 Mycobacterium tuberculosis,30 Francisella tularensis,62 Burkholderia pseudomallei,35 and Pseudomonas aeruginosa.5,57,76 The biochemistry of some bacterial PLCs, particularly the α toxin of C. perfringens, was studied in detail early on because they were

plcN (PA3319) plcB (PA0026)

plcA (PA3464) exoU pldA (PA3487)

Phospholipase C Phospholipase C

Phospholipase C Phospholipase A Phospholipase D

46.6 74 116

73.5 34.5

78.4 78.4

MW mature protein (kDa)

Xcp Xcp

Sec ? Type III Unknown – periplasmic

TAT Sec

TAT TAT

Secretory pathway

? PpiP (PA0027) and PA0028 ? SpcU ?

PlcR PlcR

Chaperone

Known phospholipases of Pseudomonas aeruginosa.

PC, PS, PE LysoPC, PC (Others ?) PC (Others ?)

PC, SM erythro-ceramide and monoacyl or diacyl phosphatidyl choline PC, PS PC, PE, PS, SM

Substrate speciﬁcity

Annotation number given in parentheses (http//www.pseudomonas.com). exoU and spcU are not present in sequenced strain PAO1; CM, cytoplasmic membrane; OM, outer membrane.

plcH (PA0844) plcH (PA0844)

Phospholipase C Sphingomyel in synthase

Type

Gene designationa

Table 1.

Induces apoptosis

Activates caspase

Activates serine-threonine phosphatases

Essential for meiosis in yeast

Mediates anti-proliferative signals in B-cells

CH2

Inactivates PKC

O C O

Plays a role in agonistdependent cellular secretion.

CH 2

Regulates Retinoblastoma gene (Rb) product

CH2OH

Directly activates; PIP kinase, PKC, tyrosine phosphatase, Raf-1 kinase.

C O

Phosphatidic Acid

Arrest cells in G0-G1 phase

HO CH

Ceramide

Figure 2. Eukaryotic signaling effects from the products of phospholipases described in this chapter. Diacylglycerol is generated by PLC, Ceramide is generated by SMase, and Phosphatidic acid is generated by PLD.

Transformation, cell proliferation

Activates SMase

Activates platelet derived growth factor

Controls transcription factors

Activates Protein Kinase C (PKC)

C OC O

CH2 CH CH2OH

Diacylglycerol

Phospholipases and Phospholipids

useful tools for membranologists to probe the composition and organization of membrane phospholipids. In contrast, the role of PLCs in bacterial pathogenesis was largely ignored until a little over a decade ago there was a resurgence of interest in the potential role of PLC in prokaryotic pathogenesis. Camilli et al.,7 Geoffroy et al.17 , and Marquis et al.45 demonstrated that two PLCs, a phosphatidylinositol-speciﬁc PLC (PI-PLC) and a phosphatidylcholine-speciﬁc PLC (PC-PLC) of L. monocytogenes (PlcA and PlcB, respectively) contribute to the cell-to-cell spread of this opportunistic pathogen. Marquis et al.45 also provided evidence that activation of the PC-PLC precursor (proPC-PLC) is speciﬁc for certain compartments of eukaryotic cells and that this is controlled by a combination of bacterial and host factors. Wadsworth and Goldﬁne87 provided evidence that the DAG, generated by the L. monocytogenes PC-PLC, along with Listeriolysin O, resulted in increased intracellular Ca++ mediated by the translocation of protein kinase C (PKC) delta in murine macrophage. Contemporary studies of the C. perfringens α toxin provided a more detailed view of the molecular architecture of the GP-PLCs, as well as provided a better appreciation of their diverse functions.9 They also afforded a fresh perspective about the role of α toxin in the pathogenesis of clostridial myonecrosis (i.e. gas gangrene). More speciﬁcally the α toxin, in synergy with the pore-forming toxin, perfringolysin O (PFO), is required for necrosis of muscle tissue, inhibition of the inﬂux of polymorphonuclear leukocytes (PMN) into the tissue lesions, and thrombosis formation, all of which are pathognomonic of this severe condition.2 These data exemplify how a single class of zinc-dependent PLCs produced by distinct gram-positive pathogens can serve vastly dissimilar roles in pathogenic processes. Until the discovery of the PLCs of P. aeruginosa (see below), the GP-PLCs were the only bacterial PLCs that were well characterized, particularly with regard to their possible role in virulence. In the 1960s, Liu39 identiﬁed an extracellular PLC of P. aeruginosa and designated it the “Heat-labile Hemolysin” because heat inactivation of the PLC in extracellular fractions, simultaneously lead to inactivation of their hemolytic activity on human and sheep erythrocytes. It was not until nearly two decades later that a gene encoding a speciﬁc protein (hemolytic phospholipase C – PlcH) with both hemolytic and PLC activities was identiﬁed.60,84 Once the sequence of PlcH was determined, it became clear that it did not belong to any previously known class of PLCs, including the GP-PLCs.60 Although, it hydrolyses both phosphatidylcholine (PC) and sphingomyelin (SM), as do the PLCs from C. perfringens and L. monocytogenes basically, similarity ends there. The size of PlcH (78 kDa) is nearly twice as large as the largest previously known bacterial PLC (48 kDa) (i.e. C. perfringens α toxin). It has no requirement for zinc as a cofactor, as do GP-PLCs, nor is its sequence in any way even remotely similar to the GP-PLCs. PlcH consequently became the founding member of a novel class of prokaryotic PLCs.76 PlcH and another member (PlcN) of this new class of enzymes produced by P. aeruginosa

Michael L. Vasil

will be described in detail below. What is more, we have now identiﬁed two additional, previously unrecognized, PLCs of P. aeruginosa that belong to the GP-PLCs class of PLCs.5,77 These will also be discussed below.

2. PHOSPHOLIPASE D Phospholipases D (PLDs) are virtually ubiquitous in both plants and animals, but they are relatively scarce in prokaryotes.78 Most of the well-studied PLDs speciﬁcally hydrolyse PC to generate choline and phosphatidic acid (PA) (Figure 2), although phosphatidylinositol-speciﬁc PLDs have also been identiﬁed. PLDs, as well as their products (e.g. PA), have become the focus of intensive efforts to understand their wide-ranging functions in eukaryotic cell biology. Eukaryotic PLDs participate in such assorted processes as meiosis in yeast, phagocytosis, and intracellular killing of M. tuberculosis by macrophage and signal transduction in response to lipopolysaccharide (LPS).48 More recently, de Torres Zabela et al.13 reported that Arabidopsis PLDs are signiﬁcantly upregulated in response to Pseudomonas. syringae, leading to a hypersensitive response in this plant. When PLDs have been found in bacteria, including P. aeruginosa, they often play a role in virulence. The most notable of these is the PLD of Yersinia pestis. While it was initially called the “murine toxin” of plague and thought to be responsible for the death of certain mammalian hosts (e.g. rats), more recent studies directly implicated this PLD in, by far, more intricate pathogenic processes. First, contrary to its early designation as an extracellular toxin, in reality it is strictly a cytoplasmic protein of Y. pestis. Moreover, it does not participate in virulence in the mammalian host but is, in fact, required for the survival of Y. pestis in the midgut of the insect vector (i.e. ﬂea).25,26 With regard to other prokaryotic PLDs, Wilderman et al.89 recently identiﬁed and extensively characterized a PLD from P. aeruginosa that is hom*ologous to the mammalian subclass of the PLD Superfamily of enzymes. Its genetics, biochemistry, and role in virulence will be further discussed below.

3. PHOSPHOLIPASE A This class of phospholipases constitutes the most diverse group of phospholipid modifying enzymes and accordingly, display a remarkable range of biological functions. Phospholipases A (PLAs) have been mostly studied in terms of their roles in the generation of powerful lipid signaling molecules such as arachidonic acid (Figure 3).1,75 However, more recently they have been progressively better appreciated for their roles in intracellular membrane trafﬁcking events and their ability to directly affect the structure and function

phosphatase

Lipases

OH C O

LipI, EstA

C O C O LipA, LipC,

CH2 CH CH2OH O

CH2

CH3 CH3

OH OH

LPS

Fatty Acid (e.g. palmitate)

Pi uptake in Pi-starved P. aeruginosa

against high osmolarity

Carbon & energy source, polysaccharide biosynthesis (i.e. alginate)

glycerol-3-phosphate regulon glpF,glpK,glpD,glpM

PstC, PstA, PstB, PhoU.

C O

CH2

CH3

Glycine Betaine CH3 CH3 BetA N + choline Protection dehydrogenase

CH2 CH CH2

Glycerol

Inorganic Phosphate (Pi)

CH3

Choline

Figure 3. Potential products and their functions that can be generated by known enzymes of Pseudomonas aeruginosa from phosphatidylcholine starting with any of its four PLCs or ExoU (PLA2).

Inflammatory mediators

P OH

Diacylglycerol

Fatty Acid (e.g. arachidonate)

PLA2 (i.e. ExoU)

Eukaryotic Cyclooxygenase & Lipoxygenases LoxA of P.aeruginosa

C OC O

PlcH,PlcN PlcB,PlcA

CH2

CH3

CH2 PchP phosphorylcholine

CH3

Choline Phosphate

CH2

CH2 CH CH2

CH3

Phosphatidylcholine

Michael L. Vasil

of eukaryotic membranes.75 While there are two major subclasses of PLAs (i.e. PLA1 and PLA2; see Figure 1), PLA2s are by far the most widely and thoroughly characterized group. Belonging to the PLA2 class, there is also a newly classiﬁed group of proteins, now known as “patatins,” some of which are known to have PLA activity.27 They were initially identiﬁed in plants (i.e. potatoes), but proteins with hom*ologous regions (i.e. patatin domains) are also found in animals and bacteria. PLAs had been previously associated with virulence in H. pylori,36 L pneumophila,16 Yersinia enterocolitica,67 Rickettsia prowazekii,91 and Streptococcus pyogenes,51 but no protein with PLA activity had been formerly associated with P. aeruginosa. In the past few years, however, a domain of a well-established virulence factor of P. aeruginosa (ExoU) was found to align with patatin domains and with regions of human cytosolic and calcium independent PLA2s.61,66,79 Subsequently, two independent groups conﬁrmed that ExoU, which is secreted into the cytosol of eukaryotic cells via the Type III secretory system, has PLA activity.58,66 This novel toxin-enzyme and its potential role in the pathogenesis of P. aeruginosa infections will be examined below.

4. PLCS OF P. AERUGINOSA Until quite recently, there were only two known phospholipases of this opportunist, PlcH and PlcN.76 The sequences of both are notably similar and both belong to a growing number of hom*ologous proteins, some with known PLC activity, most frequently found in prokaryotes, which tend to have high G+C content (e.g. Pseudomonas spp. Mycobacterium spp. Streptomyces spp. Burkholderia spp. Bordetella spp., Xanthamonas spp. Caulobacter spp.).76 Some of these include PLCs that are known virulence determinants. Proteins belonging to this novel class of PLCs have been reported to exist in fungi (e.g. Aspergillus) and plants (e.g. Arabidopsis), as well.94 As stated earlier, these PLCs constitute a novel class of PLCs. They are not similar at the sequence or biochemical level to the GP-PLCs described above. Yet, a couple of years ago, we detected an unanticipated PLC activity in culture supernatants of a mutant with the inability to secrete either PlcH or PlcN (i.e. a twin arginine translocase mutant—TAT). Further analysis of this mutant (TatC) and a mutant with plcH and plcN deleted (PlcHPlcN) led to the discovery of a third PLC of P. aeruginosa that belongs to the GP-PLC class of PLCs described above.5 The nuances relating of the identiﬁcation of the gene encoding this third PLC of P. aeruginosa are described in greater detail elsewhere.5 This new PLC (PlcB) has sequence similarity, especially in the region of the active site, to the GP-PLC class and like the GP-PLCs its activity is zinc dependent. Subsequently, within the past year we discovered a fourth PLC that shares limited similarity in the active site region to PlcB and the GP-PLC class.77 We designated this PLC,

Phospholipases and Phospholipids

PlcA. The genetics, biochemistry, and biology of these four PLCs are reviewed below.

4.1. PlcH Early on, Liu39 reported that the hemolytic phospholipase (i.e. PlcH) is preferentially expressed under phosphate (Pi)-limiting conditions. This has led more than a few authors to surmise that the major purpose of PlcH, along with phosphatases, is to scavenge Pi by degrading host phospholipids (Figure 3). While this may indeed be of beneﬁt to P. aeruginosa in a Pi-limiting environment, it is a very limited perspective, vis-`a-vis the real potential of this virulence determinant. The Pi-starvation inducible expression of PlcH was veriﬁed at the transcriptional level and it was determined that PlcH is expressed from a threegene operon, which contains two overlapping genes encoding calcium-binding proteins (PlcR1 and PlcR2) that are chaperones for PlcH.10,60,76 However, further analyses revealed that Pi-starvation is not the sole condition under which the PlcHR operon is expressed. Shortridge et al.74 found that the PlcHR operon is still expressed even under Pi sufﬁcient conditions, provided choline is present in the environment (Table 2). Actually, there are two promoters for the PlcHR operon, one is a Pi-starvation inducible promoter and the other is induced by choline and independent of Pi-starvation. These and other data led to a new hypothesis that is parallel to the one in which Pi scavenging is the sole objective of PlcH. We put forward a scenario whereby this virulence determinant, through its ability to generate another moiety from phospholipids (choline phosphate), would provide much more than just a single ion (i.e. Pi) for the survival of P. aeruginosa. First, P. aeruginosa can utilize choline phosphate as a sole source of carbon, nitrogen and Pi (Figure 3).72 Consequently, it would be possible for this organism to survive solely on phospholipids for these needs if it is expressing PlcH or other PLCs. A further beneﬁt of choline phosphate is that it will enable P. aeruginosa to survive and grow in high osmolarity environments.74,85 Choline, once it is generated from choline phosphate by a phosphatase, in P. aeruginosa, as well as in other bacteria, can be readily taken up and converted to the osmolyte, glycine betaine (Figure 3). Under conditions of high osmolarity (e.g. lungs of CF patients) the ability of P. aeruginosa to generate choline, and convert it to glycine betaine, through the hydrolysis of phospholipids could allow it survive in this hostile environment.95 Other organisms that do not produce PLCs would be unable to survive in such a harsh milieu where phospholipids might be the only source of choline. It is worth mentioning that a signiﬁcant fraction of the phospholipids in mammalian membranes are choline phospholipids. Furthermore, only PlcH, but not any other P. aeruginosa PLCs, has a strict substrate requirement for choline containing phospholipids, principally PC and SM. Based on these data, it is more than likely that the function of PlcH

100

∼30 (associated with PAI-like element)

∼30 (associated with mobile element vgr)

PlcH

PlcB

ExoU

PldA

Unknown

Pi-starvation, Vfr, adenyl cyclase (CyaAB), quorum sensing Low calcium

Pi-starvation inducible, choline inducible

Genetic regulation

NT, not tested; Incidence, frequency gene is found in P. aeruginosa.

Incidence (%)

Name

Table 2.

Broad cytotoxicity to eukaryotic cells including yeast; requires eukaryotic cytosolic factor for cytotoxicity Unknown

Hemolytic; highly toxic to endothelial cells (pM), moderate toxicity to macrophage (nM), weakly cytotoxic (µM) to epithelial cells or ﬁbroblasts Unknown

Cytotoxic properties

Chemotaxis toward phospholipids

Chronic pulmonary – rats

Prokaryotic lipid signaling

Overt cytotoxicity; dissemination

Nutrient acquisition; osmoprotection; eukaryotic lipid signaling, cytotoxin, synthesis of sphingomyelin

Chronic pulmonary – rats; thermal injury – mice, acute; pulmonary – rabbits; endocarditis – rabbits

Acute pneumonia – mice

Putative function

Virulence in model infections

Genetics and role in virulence.

Phospholipases and Phospholipids

is not merely Pi scavenging; it also affords P. aeruginosa with other nutrients (C and N), as well as an osmoprotectant (choline). Although the above scenario presents a more expansive view of the function of PlcH, it is likewise probably too limited. P. aeruginosa also produces several extracellular lipases that can remove the fatty acids from DAG, but they cannot attack the fatty acid ester bonds when they are present in phospholipids (Figure 3). Consequently, once PlcH removes the choline phosphate head group from PC, free fatty acids can now be generated by the extracellular lipases of P. aeruginosa.63 Depending on the fatty acids that would be present on a particular kind of PC (e.g. arachidonyl, palmitoyl), there could be a vastly distinct biological outcomes from the action of PlcH and the extracellular DAG-lipases of P. aeruginosa. The fatty acids so generated by the action of these enzymes can be incorporated into its LPS (e.g. palmitoyl) or they (e.g. arachidonyl) may be further modiﬁed, into extremely potent inﬂammatory mediators, usually by eukaryotic enzymes (Figure 3).14,82 However, Vance et al.83 recently identiﬁed and characterized an extracellular lipoxygenase of P. aeruginosa that converts arachidonic acid into 15-hydroxyeicosatetraenoic acid (15-HETE), which has regulatory effects on immune and nonimmune cells. Finally, the glycerol moiety that would be left from the action of PlcH and DAG-lipases could be shunted into energy production or polysaccharide biosynthesis (e.g. alginate) (Figure 3)70,71 . Admittedly such scenarios are hypothetical, but they are supported by experimental data. Thus, it is exceedingly probable that the function of PlcH is, by far, more substantial than its ability to merely increase the availability Pi. Even though the above examples provide a compelling rationale that PlcH ultimately enables P. aeruginosa to utilize the entire phospholipid rather than just certain moieties (e.g. Pi), there are other properties of PlcH, which argue that its contribution to virulence is even more profound than nutrient acquisition. As noted above, PlcH is hemolytic for human erythrocytes, but not all mammalian red blood cells. Furthermore, some but not all, PLCs are hemolytic.85 For example, even the highly similar hom*olog of PlcH (i.e. PlcN) is not hemolytic for human erythrocytes, nor is the PlcB of P. aeruginosa despite the fact that all of these PLCs are able to hydrolyze, at least, some of the phospholipids in the membranes of these cells. More recently, we obtained data indicating that, not only is PlcH cytotoxic to live eukaryotic cells, it is selectively toxic (i.e. highly toxic to some kinds of cells and minimally toxic or nontoxic to others), not unlike the ADP-ribosyltransferase A-B type toxins of many bacteria (e.g. exotoxin A, diphtheria toxin, cholera toxin).76,77 We determined that highly puriﬁed preparations of PlcH induce programmed cell death (apoptosis) in an assortment of eukaryotic cell types (e.g. human monocytes, human endothelial cells). More exactly, even though it is highly cytotoxic to some cell types (e.g. endothelial) PlcH exhibits minimal cytotoxic effects to other cell types (e.g.

Michael L. Vasil

human epithelial, mouse ﬁbroblasts). These differences are vast. That is, human vascular endothelial cells (HUVEC) are highly susceptible to picomolar concentrations of PlcH, while micromolar concentrations of PlcH have little if any cytotoxic effect on A549 cells (human airway epithelial cells). Because both susceptible and resistant cell lines contain PC, as well as SM, in the outer leaﬂet of their cytoplasmic membranes, it is extremely unlikely that the cytotoxicity of PlcH is solely due to its ability to hydrolyze these phospholipids. We have also just obtained data indicating that PlcH interacts with a speciﬁc class of calcium-dependent eukaryotic cell receptors (i.e. integrins) through an RGD (Asp-Gly-Glu) motif on in PlcH.76,77 This highly speciﬁc cytotoxic nature of PlcH adds a novel dimension to its role in P. aeruginosa virulence. Although, the mechanism by which PlcH induces an apoptotic cell death in endothelial cells is not known at this time, this attribute may serve key functions during speciﬁc kinds of P. aeruginosa infections. The extreme toxicity of PlcH for endothelial cells is pertinent to the high mortality, blood-borne infections caused by P. aeruginosa in immunocompromised individuals with blood dyscrasias. In order for P. aeruginosa to enter tissues from blood vessels, they must adhere to and penetrate the endothelial lining of the vasculature. During septicemia, P. aeruginosa has the propensity to establish a nidus near the endothelial cell lining of blood vessels, thereby facilitating recurrent seeding of the bloodstream.80 These foci are often complicated by vasculitis and thrombosis. While endothelial cells may provide protection against P. aeruginosa through their increasingly recognized role in innate immune defenses (e.g. production of cytokines), it is also possible that the release of cytokine by PlcH stressed endothelial cells may be detrimental to the host.43 Only recently has it been recognized that repair of damage to the endothelial lining of the vasculature occurs not by localized proliferation of the undamaged endothelial cells, but that it takes place through circulating, bone marrow derived, progenitor endothelial cells.64 If PlcH is even moderately cytotoxic to these progenitor endothelial cells, then the healing of these lesions could also be in jeopardy. Moreover, PlcH has been shown to induce platelet aggregation and activation through a novel mechanism of action.11 Consequently it is not unrealistic to envision a scenario by which PlcH induces damage to the endothelial lining of blood vessels that cannot be repaired by progenitor endothelial cells, causing an inﬂux of platelets, that are then activated by PlcH, and contribute to blood clotting and the thrombotic lesions (i.e. ecthyma gangrenosum) pathognomonic of P. aeruginosa sepsis. Ultimately, it is probably unrealistic to entirely fathom the deﬁnitive contribution that a particular extracellular enzyme or virulence factor (i.e. PlcH) makes to the survival of a pathogen. Nevertheless, data about PlcH clearly indicate that it has a noteworthy repertoire of purposes. A corollary to this view is that the distinct biological role that PlcH may play, at a given time, may depend on a particular set of circ*mstances (e.g. a mammalian host or decaying plant

Phospholipases and Phospholipids

material) or a certain environment (e.g. low Pi or the presence of choline) in which P. aeruginosa ﬁnds itself. In this regard, there is yet another dimension of PlcH that supports these notions. It will be explained in Section 7.

4.2. PlcN The second extracellular PLC of P. aeruginosa was discovered once a PlcH deletion (PlcH) mutant was constructed in strain PAO1.57 A PlcH mutant still expressed an extracellular PLC activity that was detected when P. aeruginosa was grown under Pi-limiting conditions, but not when it was grown under Pi-sufﬁcient conditions (Table 2). However, such supernatants had no hemolytic activity on human or sheep erythrocytes. The cloning of the gene encoding this phospholipase (i.e. PlcN) revealed that it encodes a protein (73 kDa), with signiﬁcant similarity (55%) and size (73 kDa) to PlcH. Additional characterization of PlcN conﬁrmed that it is not hemolytic and that it has similar, but distinct, substrate preferences in comparison to PlcH.56 Although PlcN is active on PC, it has no detectable activity on SM. However, it is active on the non-choline containing phospholipid phosphatidylserine (PS). There are other features of PlcN, which further convincingly indicate that it is not simply redundant to PlcH in terms of its contribution to the biology to P. aeruginosa. Besides the differences already mentioned, the predicted isoelectric point of PlcN is basic (8.8), while the overall pI of PlcH is acidic (5.5). However, the deduced pI of each PLC is not uniform over their entire sequences. That is, while the pI of the N-terminal two-thirds of PlcH and PlcN are very similar (5.5 and 6.3, respectively), the pI of the remaining C-terminal portions of PlcH and PlcN (5.7 vs. 10.2) are very different.56,76 These and other data suggest that these extracellular PLCs are composed of distinct domains. Actually, the C-terminal portions (i.e. outside their conserved PLC domains) of PlcH and PlcN are now classiﬁed as separate domains of unknown functions (DUF756) under the Conserved Domain Search algorithm at the NCBI web site. Such a composite structure is quite common in eukaryotic PLCs where there is a core PLC domain, and separate domains that bestow additional functions (e.g. calcium binding, membrane binding) to the entire protein. These facets of PlcH and PlcN, along with others, plainly support the hypothesis that they provide distinct roles in the lifestyle of P. aeruginosa. Still, currently PlcN has not been nearly as well studied in terms of its participation in microbial virulence as PlcH. Thus, its role in pathogenesis is considerably less obvious than that of PlcH. In any event, it is salient to point out that eukaryotic cells undergoing apoptosis (e.g. PlcH induced) ﬂip the more PS rich cytoplasmic side of their membranes, to the extra cytoplasmic side.47 Perhaps, PlcN is able to hydrolyze this newly exposed PS, thereby accelerating eukaryotic cell death initiated by PlcH. Finally, as described below in Section 7, we propose that PlcN, along with PlcH, may under certain circ*mstances actually participate in phospholipid biosynthesis in P. aeruginosa.

Michael L. Vasil

4.3. PlcB and PlcA As recounted above, even hom*ologous phospholipases produced by the same organism may have distinct biochemical or biophysical properties that can determine whether they will or will not be active under a given set of circ*mstances. These and other factors undoubtedly contributed to the delayed discovery of the third and fourth extracellular PLCs of P. aeruginosa. PlcB was ﬁrst encountered in culture supernatants of a mutant that is deﬁcient in the secretion of PlcH and PlcN. The TAT secretory system is required for the secretion of these PLCs through the inner membrane of P. aeruginosa.53,86 However, the secretion of other extracellular proteins via the Sec-translocase is generally unaffected in a TatC mutant. We detected an unanticipated PLC activity in culture supernatants of a P. aeruginosa TatC mutant.5 Further characterization of this activity led to the identiﬁcation of the gene encoding PlcB. Prior to that, the plcB gene was annotated as PA0026, encoding a 36 kDa hypothetical protein with unknown, unclassiﬁed function (HUU). When the sequence of PlcB was further scrutinized using the Conserved Domain Search algorithm at the NCBI web site, we discovered that a limited region (∼60 amino acids) of PlcB shares some degree of similarity to the zinc-dependent GP-PLCs. Moreover, the conserved His residues in this hom*ologous region are required for coordination of three zinc ions in the active site of this class of PLCs.22,29 Mutagenesis of one of these His residues in PlcB resulted in abrogation of its PLC activity.5 The PlcB gene is part of a three-gene operon, which includes a gene (PA0027) encoding a peptidyl prolyl cis–trans isomerase (PpiP) and a gene (PA0028) encoding a protein predicted to be a proline rich lipoprotein.4 Although, the functions of these other proteins are not entirely clear at the present time, preliminary data suggest that one (PpiP) is required for the proper folding of PlcB, while the other (PA0028) is required for the secretion (e.g. chaperone) of PlcB through the membrane of P. aeruginosa.4 It is also of interest to point out that PpiP is secreted to the periplasm via the TAT secretory pathway. This feature exempliﬁes the cooperative nature of the Sec (PlcB) and the TAT translocation systems (PpiP) in terms of exporting proteins that may ultimately interact with each other. Such is the case with PlcH and PlcR1, which ultimately form an extracellular heterodimer. PlcH is exported to the periplasm via the TAT system, while PlcR is exported through Sec.76 The PlcHR1 heterodimer is then secreted through the outer membrane via the Xcp apparatus of P. aeruginosa. The substrate speciﬁcity of PlcB provided some hints with regard to its potential function in the biology of P. aeruginosa. PlcB is active on PC, SM, and PS; however in contrast to either PlcH or PlcN, it is also highly active on phosphatidylethanolamine (PE) (Figure 1, Table 1). Since, it had been previously reported that P. aeruginosa is able to exhibit twitching motility-mediated

Phospholipases and Phospholipids

chemotaxis up a gradient of this particular phospholipid, it was reasoned that PlcB might somehow play a role in this process.33 This supposition was conﬁrmed when it was demonstrated that PlcB is required for the chemotaxis of P. aeruginosa up a gradient of diolyl-PE or diolyl-PC, but it is not necessary for twitching-mediated chemotaxis toward the dilauryl forms of these phospholipids.5 It is probable that fatty acids (diolyl), released by the action of extracellular lipases on the DAG generated from the action of PlcB on PE or PC, ultimately contribute the speciﬁcity of this chemotactic response. From the perspective of the would-be role of PlcB in P. aeruginosa biology, it is germane that the major lipid constituent of mammalian lung surfactant is PC. In fact, both PC and PE, along with SM levels, are increased in the bronchoalveolar lavage ﬂuid (BAL) of young adults with cystic ﬁbrosis (CF) by comparison with BAL from age matched controls, without CF.49 It is possible that the increased levels of these phospholipids serve as a chemoattractants to P. aeruginosa, which initially colonizes the upper airways in a CF patient. The choline that would be generated by any of the P. aeruginosa PLCs from this PC rich resource could also protect it against the increased osmolarity it will encounter in the lower airways of the CF lung. The regulation of PlcB expression offers insights into the raison d’ˆetre for existence of yet another extracellular PLC in P. aeruginosa (Table 2). In spite of the fact that the expression of PlcH, PlcN, and PlcB is Pi-starvation inducible, there are several reports from independent investigators, based on microarray data, indicating that the expression of plcB (i.e PA0026), but not plcH or plcN, is dependent upon hom*oserine lactone-mediated quorum sensing.69,88 Additional microarray data support the view that other environmental factors differentially inﬂuence the expression of PlcH, PlcN, and PlcB, as well. Wolfgang et al.92 reported that the expression of PlcN and PlcB, but not PlcH, were increased when P. aeruginosa was exposed to muco-purulent airway liquids from chronically infected CF patients, as compared to when it was grown minimal media alone. In a separate study, these investigators provided experimental results indicating that expression of PlcB and PlcN are also affected by the P. aeruginosa cAMPbinding protein, Vfr, but regulation of PlcH expression was not.93 In contrast, an adenyl cyclase mutant (cyaAB) expressed signiﬁcantly reduced levels of PlcB transcript, but transcription of the PlcN and PlcH genes were unaffected or slightly increased in this mutant.93 The intricate differences in the regulation of plcB, plcH, and plcN further typify the distinct purpose for the proteins they encode, despite the fact that all are classiﬁed as PLCs. PlcA is the most recently identiﬁed PLC of P. aeruginosa, and therefore the least understood in terms of its utility to P. aeruginosa, much less its contribution to virulence. Once we had recognized that a portion of the PlcB sequence shares similarity with a region of the active site of the GP-PLCs, we were further analyzing its properties through an algorithm using Hidden Markov

Michael L. Vasil

Models that represent all proteins of known structure (http://supfam.mrclmb.cam.ac.uk/SUPERFAMILY/hmm.html).8 The results of this analysis revealed that the genome of P. aeruginosa actually encodes two separate proteins, containing the zinc-dependent PLC active site motif that is present in the PlcB of P. aeruginosa and the GP-PLCs. Of course one is PlcB (PA0026), but the other is encoded by a gene in the P. aeruginosa genome annotated as PA3464. PA3464, like PA0026 (i.e. PlcB), was annotated in P. aeruginosa Genome Project web site (http://www.pseudomonas.com) as encoding a hypothetical, unclassiﬁed, unknown protein. Paradoxically, the Superfamily site suggested that it is a PLC. We have now expressed the protein encoded by PA3464 and demonstrated that it has PLC activity on PC, PS, and PE, but it has no detectable activity on SM, as PlcB does.76 PlcA is predicted to be a 46.7 kDa acidic (pI 5.2) protein (Table 1). The P. aeruginosa Genome Project web site does indicate that, based on the PSORT algorithm, PlcA has a Sec-type signal peptide. Nevertheless, at the present its ultimate location in P. aeruginosa is unknown. Recently, we were able to detect the expression of PlcA in P. aeruginosa. Preliminary data indicate that its expression does not appear to be induced under Pi-limiting conditions and does appear to be inﬂuenced by choline. However, in contrast to the choline induced expression of PlcH, the expression of PlcA is inhibited by the presence of choline in the media. An even more concerted effort is going to be needed in order to tease out further information about the functionality of PlcA to P. aeruginosa.

5. PLDS OF P. AERUGINOSA As related above, this type of phospholipase is quite unusual in prokaryotes. However, it should be pointed out that PLDs belong to a rather large class of enzymes referred to as the “PLD Superfamily.”48,78 It includes mammalian and plant PLDs, a Vaccina virus protein, cardiolipin synthase and endonucleases, and phosphatidylserine synthetase. This classiﬁcation is based on the presence of conserved active site motif, HXKX4DX6G(G/S), which is usually present in two copies in most members (e.g. PLDs) and a single copy in others (e.g. endonucleases). Among the PLD members, there are two major subclassiﬁcations based on differences in hom*ology. Plant PLDs comprise one class, while the fungal (yeast) and animal (mammalian and nematode) comprise the other. Bacterial PLDs usually belong to the plant class. There is a wealth of information regarding critical roles of PLDs in notably various physiological and genetic processes in eukaryotic cells. In contrast, little is known about the role of PLDs in prokaryotes, which is largely due to their relative rare occurrence in bacteria. As mentioned above, the beststudied one is the so-called “murine toxin” of Y. pestis.25,26 However, there are members of the “PLD Superfamily” that are actually quite common in

Phospholipases and Phospholipids

prokaryotes. Cardiolipin, along with phosphatidylglycerol (PG) and PE, is a major phospholipid of prokaryotic membranes and it is formed in both grampositive and gram-negative bacteria by the transfer of a phosphatidyl group from one PG molecule to another via cardiolipin synthetase (CLS).81 In contrast, bona ﬁde PLDs, which remove the choline head group from PC are few and far between in these organisms. Moreover, CLSs are almost exclusively membrane bound while bacterial PLDs are more likely to be located in soluble fractions (e.g. cytoplasm, periplasm). Another signiﬁcant issue is that, while the substrate (e.g. PG) for CLSs is plentiful in bacteria, the preferred substrate for PLDs (i.e. PC) is usually very limited or absent in most bacteria.46 These differences illustrate the distinct functions that each of these subclasses of the PLD Superfamily plays in prokaryotic biology. Wilderman et al.89 initially identiﬁed a true PLD (i.e. not a CLS) activity in supernatants of late stationary grown P. aeruginosa strain PAO1. Examination of the annotated genomic database (http://www.pseudomonas.com) revealed that, in addition to genes encoding CLSs, there are two additional genes encoding proteins, each with two copies of the HXKX4DX6G(G/S) PLD motif. Further characterization of one of these putative PLDs (i.e. PldA) revealed that its primary location is actually periplasmic. The earlier detection of PLD activity in culture supernatants was likely due to release of PLD activity through lysis during stationary phase, not unlike that observed early on with the Y. pestis PLD. PldA has extended regions of hom*ology with animal PLDs, and very limited hom*ology to plant PLDs.89 There are also unique cassette-like regions with no hom*ology with any sequences in all the databases examined. These investigators proposed that the unique regions play a role in regulating PLD activity in P. aeruginosa and that they might roughly correspond to the domains in PLDs that interact with eukaryotic regulatory factors, such as ARF, Ras, and Rho. Since PldA uses PC as a preferred substrate, and it is located in the periplasm, it was difﬁcult to envisage how it might have access to this substrate because PC was not known to be present in either the inner or outer membranes of P. aeruginosa. This apparent paradox led Wilderman et al.90 to investigate whether P. aeruginosa is one of the relatively few bacteria capable of PC synthesis. Indeed, they reported that P. aeruginosa contains a small, but signiﬁcant amount of PC in both membranes, where it would be accessible to PldA. They also discovered that P. aeruginosa is able to synthesize PC, de novo, through the condensation of choline with CDP-DAG by a PC synthase (Pcs). Consequently, the presence of PC and the periplasmic location of PldA provided a new perspective into the possible role of PldA in P. aeruginosa. That is, in contrast to the extracellular nature of bacterial PLCs (e.g. PlcH and α toxin) and their propensity to affect host phospholipid metabolism, it is more likely that PldA plays a direct role in phospholipid-mediated signaling events in P. aeruginosa. This scenario, however, does not mitigate against PldA playing a role in P. aeruginosa pathogenesis. Wilderman et al.89 demonstrated that a PldA

Michael L. Vasil

deletion mutant (PldA) was deﬁcient in its ability to compete with the wildtype parental strain in a chronic pulmonary infection model in rats (Table 1). The PldA mutant had no apparent in vitro growth defect compared to the parental strain. Although these data do not shed any light on the speciﬁc role of PldA in virulence, they certainly are indicative of a more expansive role for bacterial phospholipases in pathogenesis. As a ﬁnal point about P. aeruginosa PLDs, Wilderman et al. reported that pldA is immediately adjacent to a highly variable genetic element (i.e. vgr). The vgr genes are components of multicopy rearrangement hot-spots (Rhs) ﬁrst described in Escherichia coli. Both E. coli and P. aeruginosa carry multiple copies of hom*ologs of vgr genes, but the actual number in any given strain in these bacteria is highly variable, ranging from 1 to 10 copies.24,89 The function of the proteins encoded by the vgr genes is unknown, but it is thought that they are located on the bacterial surface. In any case, Wilderman et al. found that approximately 30% of P. aeruginosa strains including those from patients with CF, as well as environmental strains, carry a gene encoding PldA. What is more, they noted that the pldA gene is invariably associated with a speciﬁc copy of a vgr gene and a gene encoding a hydrophobic lipoprotein of unknown function (Table 2). These three genes appear to comprise a pathogenicity island (PAI). They are either, entirely present, or wholly absent in all strains (57 isolates) of P. aeruginosa examined and, the regions ﬂanking this PAI are highly conserved whether the PAI is present or not. Perhaps this PAI provides a selective advantage to this P. aeruginosa in a niche, yet to be deﬁned. Although pldA encodes a protein most similar to eukaryotic PLDs, it may have been acquired from an unidentiﬁed prokaryotic intermediate along with a vgr.23,24,89 The possible involvement of the multiple copies of the highly variable vgr genes in the evolution of P. aeruginosa through recombination and horizontal gene transfer also has powerful implications in the ongoing evolution of this opportunistic pathogen. Notably, there is yet another gene in P. aeruginosa encoding a protein with signiﬁcant similarity to plant PLDs. This gene is likewise associated with a vgr gene and is present in a portion (∼90%) of P. aeruginosa strains examined.89

6. PLA2 (EXOU) OF P. AERUGINOSA Although this phospholipase (i.e. ExoU) has been recently competently reviewed elsewhere, there are a few additional comments apropos to the topics in this chapter.65 In contrast to the other phospholipases discussed herein that were initially identiﬁed by their enzymatic activities, ExoU was ﬁrst identiﬁed through its association with the Type III secretion system and by its association with certain strains of P. aeruginosa, which are highly cytotoxic to epithelial cells.15 It was eventually determined that the gene encoding ExoU is associated

Phospholipases and Phospholipids

with a PAI-like genome fragment and that it is present in approximately only 30% of P. aeruginosa strains thus far examined, including those from clinical and environmental sources.73 This frequency is reminiscent of that of the pldA gene, which is likewise associated with a PAI (see above). In contrast, the genes encoding PlcH, PlcN, PlcB, and PlcA appear to be associated with a more stable region of the P. aeruginosa core chromosome and we have not encountered any strain of P. aeruginosa that lacks any of these phospholipase genes.5,76,77,85 Perhaps, ExoU and PldA provide a selective advantage in only certain niches where P. aeruginosa resides. For example, ExoU does not appear to play a determinative role in the pathogenesis of P. aeruginosa to C. elegans or Arabidopsis, but data from several studies support the notion that ExoU contributes to speciﬁc kinds of human infections (e.g. hospital acquired pneumonias).58,68 The enzymatic activity of ExoU was only recently uncovered.65,66 Probably contributing to this delay is the fact that the PLA activity of this virulence factor requires an, as yet, unidentiﬁed eukaryotic cytosolic factor (Table 2). For this, and for the same reasons that PlcB was previously unrecognized as a PLC, it would not be too surprising if other proteins of P. aeruginosa, particularly those with the classiﬁcation HUU, are ultimately established to have phospholipase activity. The ﬁrst clue that ExoU might have phospholipase activity emerged from several independent observations that inhibitors of eukaryotic PLA2s also inhibited the cytotoxicity of ExoU.59 While data using enzymatic inhibitors can certainly be enticing, there are also pitfalls associated with their use. That is, they could be blocking cellular processes downstream of the primary effect of toxin (e.g. ExoU). The breakthrough that was perhaps more indicative of ExoU phospholipase activity came when it was discovered that a region of ExoU aligned to the patatin motif, and two human PLA2s. Mutagenesis of two amino acids of ExoU in its conserved PLA region reduced its toxicity.65,66 Similar to the other phospholipase described in this chapter, ExoU appears to have separate domains with distinct functions. Only the N-terminal half of ExoU contains the conserved patatin domain. The function of the other portion is unknown, but it is rational to suppose that it plays a role in interaction with the eukaryotic cytosolic factor required for its toxicity. The precise mechanism of the enzymatic activity of ExoU and its substrate preferences are still not well deﬁned. Furthermore, it is not at all certain how its phospholipase activity imparts cytotoxicity to ExoU. Based on its similarity to patatins and human PLA2 and some preliminary biochemical experiments with eukaryotic cell extracts, some investigators originally suggested that ExoU is a PLA2 (Figures 1 and 3). However, the latest experimental results suggest that ExoU should more speciﬁcally be classiﬁed as a lysophospholipase A.58,79 That is because ExoU is considerably more (10X) active on lysophospholipids (i.e. those that only have a single fatty acid chain in either the sn-1 or sn-2 position) than it is on phospholipids with two fatty acid moieties (e.g. dipalmitoyl-PC).

Michael L. Vasil

Part of the problem in identifying the speciﬁc nature of the enzymatic activity of ExoU emanates from its requirement for a eukaryotic cytosolic factor. In any case, at present, it is difﬁcult to envision how a lysophospholipase evokes such an extraordinary cytotoxic phenotype in a broad range of eukaryotic cells, including yeast. It does not seem likely that such an enzymatic activity could physically disrupt the integrity of eukaryotic cell membranes and lead to their rapid lysis. This is particularly true for live eukaryotic cells that are continually synthesizing new membrane phospholipids. Perhaps, downstream signaling events from the primary target of ExoU are responsible for the exuberant cytotoxicity attributed to this virulence determinant. A striking parallel to the conundrum of how the enzymatic activity of ExoU relates to its highly toxic (cytolytic) nature for eukaryotic cells, is also observed with PlcH. Although it is able to hydrolyze membrane phospholipids, it is rather difﬁcult to reconcile how the enzymatic activity of extremely small amounts of PlcH (see above) is connected to the induction of complex eukaryotic cell signaling process (i.e. apoptosis). It is possible that the biochemical information we currently have about all of the phospholipases discussed in this chapter is inadequate and that the enzymatic activities that actually are the cause of the observed biological phenotypes have yet to be clearly elucidated. The following section addresses some of these matters.

7. PHOSPHOLIPASES: HYDROLASE OR SYNTHASE? Basically, the names of enzymes are deﬁned by their products, which are usually detected in an in vitro biochemical reaction. However, the detection of particular product in such experiments may not actually reﬂect biological reality. For example, the ADP ribosyltransferase toxins (e.g. exotoxin A, diphtheria toxin) will hydrolyze the ADP ribose moiety from NAD and transfer it to a water molecule (i.e. NAD glycohydrolase).19,40 Cholera toxin can also ADP-ribosylate small artiﬁcial substrates such as agmatine.55 However, the biologically relevant acceptor for the ADP ribose moiety is actually the eukaryotic protein, EF2, or a subunit of an adenyl cyclase regulator. Moreover, some proteins may have multiple enzymatic activities and preferred substrates (e.g. PC and SM for PlcH) further confounding the chance of identifying all the biologically signiﬁcant substrates and products. Such could be the case for any, or all, of phospholipases described herein. In terms of one of the phospholipases discussed in this chapter, Tamura et al.79 reported that glycerol, rather than, for instance water, might serve as an acceptor for the cleaved fatty acid in the ExoU-catalyzed lysophospholipase reaction. Provided this acyl transferase activity of ExoU occurs in the cytoplasm of eukaryotic cells then, this product (a monoacylglycerol) or its derivatives

Phospholipases and Phospholipids

(diacyl or triacyl glycerol), rather than fatty acids per se could ultimately be signiﬁcant to biological activity (e.g. cytotoxicity) of this protein. Also in relation to this issue, Luberto et al.41 veriﬁed that, although PlcH has PLC and SMase, they found that depending on whether ceramide (CM) is available or not, PlcH also has SM synthase activity (Figure 4) That is, it is able to transfer the choline phosphate head group from PC to CM resulting in the synthesis of SM and the production of DAG. The speciﬁcity of this activity is demonstrated by the fact that the choline phosphate must come from a phospholipid. PlcH will not use nonlipid substrates (e.g. nitrophenyl-phosphorylcholine) as a donor for the choline phosphate this reaction. However, if SM is present, without CM, PlcH will remove the choline phosphate head group from SM thereby generating CM. Transfer of a phosphorylcholine head group from SM to DAG is not observed. Hence, it is the relative concentrations of PC, SM, and CM, which determine whether PlcH has SMase, PLC (i.e hydrolase), or SM synthase activity. These three distinct enzymatic activities attributable to a single protein (i.e PlcH) beg the question; what are its actual biologically relevant substrates and products? More than likely, the answer depends upon the environment in which P. aeruginosa may be found at a given time. For example in lung surfactant, while there is plenty of PC and SM, there is little if any CM available. Consequently, one might imagine in such a situation PlcH would act as a PLC or as a SMase. On the other hand, in terms of the cytotoxicity of PlcH, because it induces apoptosis in endothelial cells, rather than a proliferative response, it is logical to suppose that the cytotoxicity of PlcH is primarily associated with its SMase activity rather than its PLC activity. The rationale for this hypothesis is that, as cited earlier, CM induces an apoptotic response in eukaryotic cells, while DAG, causes cell proliferation and transformation of eukaryotic cells (Figure 2).20 An alternative point of view that could change the perceived function of PlcH in P. aeruginosa is that, it is possible this organism could actually synthesize CM de novo and thereby provide a precursor for SM synthesis by PlcH, if it was otherwise not present (e.g. lung surfactant). However, this hypothesis would seem to challenge conventional wisdom because so far bacteria, with the possible but unproven exception of Mycoplasma, are not known to contain SM, much less synthesize it.52 Actually, there are some bacteria, not too distantly related to P. aeruginosa (i.e. Sphingomonas spp.), which contain glycosphingolids as part of their outer membranes, and Bacteriodes has been shown to contain CM in its membranes.38,52 In Sphingomonas spp., glycosphingolipids actually substitute for the ubiquitous LPS present in other gram-negative bacteria.32 While there are now ample data indicating that bacteria contain CM, nothing is known about the pathway for the synthesis of sphingolipids in these organisms. Even so, data are available indicating that the sphingosine precursor of CM, sphinganine, is also present in these bacteria (Figure 4).31 Concerning the possibility that P. aeruginosa is able to synthesize CM, it is interesting to point out that an

O C

CH 2

C O

COO

SCoA

CH2

NH3

CH 2OH

CH3

CH NH C O

CH CH CH

CH2

N +

CH3

reductase

NH 2

Sphingomyelin

PlcN (?)

Sphinganine

C O

Fatty Acid

CH2OH

PlcH SM Synthase

NH2

C OC O

CH2 CH CH2OH

Diacylglycerol

CH3

HO CH

Sphingosine

CH C O

CH2OH

O C O

CH 2 O

CH3

CH 2

CH2

CH 2

CH 3

N +

CH3

Phosphatidylcholine

pH 7.5

CDase (PA0845)

Ceramide HO CH

Figure 4. Proposed pathway for the synthesis of sphingomyelin (SM) and its precursors (e.g. ceramide and sphinganine) by extracellular enzymes (i.e. PlcH, PlcN, CDase) of P. aeruginosa.

Palmitoyl-CoA

CH 2

Phosphatidylserine

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extracellular ceramidase (CMase) of this organism has been isolated and well characterized.54 It is likewise notable that the gene encoding this enzyme is immediately adjacent (5 ) to the PlcH gene in P. aeruginosa. However, as shown in Figure 4, such an enzyme would actually be counterproductive in terms of SM synthesis because it would degrade CM, not synthesize it. At variance with this view is the fact that its designated enzymatic activity (i.e. CDase) is dependent upon certain speciﬁc conditions (see below). If different ones are present, this protein readily catalyzes the reverse reaction leading to CM synthesis.34 This P. aeruginosa protein was initially classiﬁed as an alkaline CMase because it is most active at an alkaline pH (pH optimum 8.5). Nevertheless, Kita et al.34 reported that the reverse reaction occurs very efﬁciently at near neutral pH (pH optimum 7.5). That is, this protein can catalyze the condensation of free fatty acids to sphingosine resulting in the synthesis of CM, rather than in its degradation (Figure 4). Consequently, it is now tenable to take the view that P. aeruginosa has the enzymes to actually synthesize SM when PC, sphingosine, and fatty acids are present in the environment. What is more, it is possible that PlcN also contributes to the de novo biosynthesis of SM in P. aeruginosa (Figure 4) through the production of a CM precursor.50 As mentioned earlier, PlcN, but not PlcH, is able to hydrolyze PS to phosphoryl serine and DAG. If PlcN like PlcH can transfer the head group of this phospholipid (i.e. serine) to something other than water, such as palmitoyl-CoA, then this reaction would actually yield sphinganine precursor (Figure 4).50 Sphinganine would then need to be reduced by an NADPH-dependent reductase (Figure 4). These are relatively minor modiﬁcations to convert sphinganine to sphingosine, but it is not improbable that either PlcN itself makes these minor alterations during the course of the reaction or that other P. aeruginosa enzymes can make these conversions (Figure 4). In any case, such a scenario would enable P. aeruginosa to completely synthesize SM de novo through PlcH, its so-called alkaline CDase (i.e a ceramide synthase), and PlcN. Perhaps one or two other as yet unidentiﬁed enzymes are also necessary. Even though P. aeruginosa may be able to synthesize SM the beneﬁt of such a phospholipid to its survival is not immediately obvious. P. aeruginosa can also synthesize the eukaryotic-like phospholipid PC and Wilderman et al.90 determined that PC deﬁcient mutants of P. aeruginosa are less ﬁt after being under certain environmental stresses (i.e. freezing). With regard to SM, this phospholipid contains long, largely saturated acyl chains thereby causing tighter packing in membranes and resulting in their concentration in lipid rafts in eukaryotic cells. SM also has a much higher melting temperature than glycerol containing phospholipids. Along with cholesterol and glycosphingolipids SM is the lipid that is most correlated with an increased viscosity of airway secretions. Of note, several independent studies reported increased levels of SM in the bronchiolar alveolar lavage ﬂuid of CF patients in comparison to non-CF patients, including those with other pulmonary diseases.18,49 A more

Michael L. Vasil

recent report also found that there is a signiﬁcant correlation between increased levels of PLC production by P. aeruginosa and poor pulmonary function in CF patients.37 While such data do not directly connect the synthesis of SM by P. aeruginosa with virulence, they offer novel perspectives into the potential capabilities of these enzymes in pathogenesis, whether they have hydrolase (i.e. PLC) or synthase activities. As a ﬁnal point, the paradigms regarding the role of all the phospholipases discussed in this chapter are admittedly biased toward their possible contributions to mammalian pathogenesis. It is just as likely that they also have utility in other aspects of the lifestyle of this organism, including its survival in riparian soil, in plants or even to its ability to compete with other microorganisms. PlcH was recently shown to be, in some way, involved in killing the opportunistic fungal pathogen, Candida albicans.28 Perhaps their multifunctional nature is merely a reﬂection of and contributes to the remarkable adaptability of P. aeruginosa.

ACKNOWLEDGMENTS The author gratefully acknowledges the thoughtful and friendly interactions with the remarkable colleagues: Howard Goldﬁne, Yusuf Hannun, Chiara Luberto who have taught him to better appreciate the more intricate, but critical, points of the biochemistry and enzymology of phospholipids and phospholipases. He very much appreciates the exceptionally hard work and highly valued intellectual input of the following postdoctoral fellows, technical personnel, and graduate students from his laboratory (alphabetically arranged) including: Adam Barker, Randy Berka, Adela Cota-G´omez, Gregory Gray, Kristine Johansen, Zaiga Johnson, Urs Ochsner, Rachel Ostroff, Sarah Parker, Arthur Pritchard, Andy Sage, Virginia Shortridge, Martin Stonehouse, Adriana Vasil, and P.J Wilderman. All made notable contributions to the information described in this chapter. Finally, he sincerely thanks all other exceedingly capable investigators, too numerous to mention herein, for their collaborative efforts that made key contributions as well.

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44. Marques, M.B., Weller, P.F., Parsonnet, J., Ransil, B.J., and Nicholson-Weller, A., 1989, Phosphatidylinositol-speciﬁc phospholipase C, a possible virulence factor of Staphylococcus aureus. J. Clin. Microbiol., 27:2451–2454. 45. Marquis, H., Goldﬁne, H., and Portnoy, D.A., 1997, Proteolytic pathways of activation and degradation of a bacterial phospholipase C during intracellular infection by Listeria monocytogenes. J. Cell. Biol., 137:1381–1392. 46. Mart´ınez-Morales, F., Schobert, M., Lopez-Lara, I.M., and Geiger, O., 2003, Pathways for phosphatidylcholine biosynthesis in bacteria. Microbiology, 149:3461–3471. 47. Maulik, N., Kagan, V.E., Tyurin, V.A., and Das, D.K., 1998, Redistribution of phosphatidylethanolamine and phosphatidylserine precedes reperfusion-induced apoptosis. Am. J. Physiol., 274:H242–H248. 48. McDermott, M., Wakelam, M.J., and Morris, A.J., 2004, Phospholipase D. Biochem. Cell. Biol., 82:225–253. 49. Meyer, K.C., Sharma, A., Brown, R., Weatherly, M., Moya, F.R., Lewandoski, J., and Zimmerman, J.J., 2000, Function and composition of pulmonary surfactant and surfactant-derived fatty acid proﬁles are altered in young adults with cystic ﬁbrosis. Chest, 118:164–174. 50. Meyer, S.G., and de Groot, H., 2003, [14C] serine from phosphatidylserine labels ceramide and sphingomyelin in L929 cells: evidence for a new metabolic relationship between glycerophospholipids and sphingolipids. Arch. Biochem. Biophys., 410:107–111. 51. Nagiec, M.J., Lei, B., Parker, S.K., Vasil, M.L., Matsumoto, M., Ireland, R.M., Beres, S.B., Hoe, N.P., and Musser, J.M., 2004, Analysis of a novel prophage-encoded group A Streptococcus extracellular phospholipase A(2). J. Biol. Chem., 279:45909–45918. 52. Naka, T., Fujiwara, N., Yabuuchi, E., Doe, M., Kobayashi, K., Kato, Y., and Yano, I., 2000, A novel sphingoglycolipid containing galacturonic acid and 2-hydroxy fatty acid in cellular lipids of Sphingomonas yanoikuyae. J. Bacteriol., 182:2660–2663. 53. Ochsner, U.A., Snyder, A., Vasil, A.I., and Vasil, M.L., 2002, Effects of the twin-arginine translocase on secretion of virulence factors, stress response, and pathogenesis. Proc. Natl. Acad. Sci. U.S.A., 99:8312–8317. 54. Okino, N., Ichinose, S., Omori, A., Imayama, S., Nakamura, T., and Ito, M., 1999, Molecular cloning, sequencing, and expression of the gene encoding alkaline ceramidase from Pseudomonas aeruginosa. Cloning of a ceramidase hom*ologue from Mycobacterium tuberculosis. J. Biol. Chem., 274:36616–36622. 55. Osborne, J.C., Jr., Stanley, S.J., and Moss, J., 1985, Kinetic mechanisms of two NAD:arginine ADP-ribosyltransferases: the soluble, salt-stimulated transferase from turkey erythrocytes and choleragen, a toxin from Vibrio cholerae. Biochemistry, 24:5235–5240. 56. Ostroff, R.M., Vasil, A.I., and Vasil, M.L., 1990, Molecular comparison of a nonhemolytic and a hemolytic phospholipase C from Pseudomonas aeruginosa. J. Bacteriol., 172:5915–5923. 57. Ostroff, R.M., and Vasil, M.L., 1987, Identiﬁcation of a new phospholipase C activity by analysis of an insertional mutation in the hemolytic phospholipase C structural gene of Pseudomonas aeruginosa. J. Bacteriol., 169:4597–601. 58. Pankhaniya, R.R., Tamura, M., Allmond, L.R., Moriyama, K., Ajayi, T., Wiener-Kronish, J.P., and Sawa, T., 2004, Pseudomonas aeruginosa causes acute lung injury via the catalytic activity of the patatin-like phospholipase domain of ExoU. Crit. Care Med., 32:2293–2299. 59. Phillips, R.M., Six, D.A., Dennis, E.A., and Ghosh, P., 2003, In vivo phospholipase activity of the Pseudomonas aeruginosa cytotoxin ExoU and protection of mammalian cells with phospholipase A2 inhibitors. J. Biol. Chem., 278:41326–41332. 60. Pritchard, A.E., and Vasil, M.L., 1986, Nucleotide sequence and expression of a phosphateregulated gene encoding a secreted hemolysin of Pseudomonas aeruginosa. J. Bacteriol., 167:291–298. 61. Rabin, S.D., and Hauser, A.R., 2005, Functional regions of the Pseudomonas aeruginosa cytotoxin ExoU. Infect. Immun., 73:573–582.

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62. Reilly, T.J., Baron, G.S., Nano, F.E., and Kuhlenschmidt, M.S., 1996, Characterization and sequencing of a respiratory burst-inhibiting acid phosphatase from Francisella tularensis. J. Biol. Chem., 271:10973–10983. 63. Rosenau, F., and Jaeger, K., 2000, Bacterial lipases from Pseudomonas: regulation of gene expression and mechanisms of secretion. Biochimie, 82:1023–1032. 64. Rosenzweig, A., 2003, Endothelial progenitor cells. N. Engl. J. Med., 348:581–582. 65. Sato, H., and Frank, D.W., 2004, ExoU is a potent intracellular phospholipase. Mol. Microbiol., 53:1279–1290. 66. Sato, H., Frank, D.W., Hillard, C.J., Feix, J.B., Pankhaniya, R.R., Moriyama, K., FinckBarbancon, V., Buchaklian, A., Lei, M., Long, R.M., Wiener-Kronish, J., and Sawa, T., 2003, The mechanism of action of the Pseudomonas aeruginosa-encoded type III cytotoxin, ExoU. EMBO. J., 22:2959–2969. 67. Schmiel, D.H., Wagar, E., Karamanou, L., Weeks, D., and Miller, V.L., 1998, Phospholipase A of Yersinia enterocolitica contributes to pathogenesis in a mouse model. Infect. Immun., 66:3941–3951. 68. Schulert, G.S., Feltman, H., Rabin, S.D., Martin, C.G., Battle, S.E., Rello, J., and Hauser, A.R., 2003, Secretion of the toxin ExoU is a marker for highly virulent Pseudomonas aeruginosa isolates obtained from patients with hospital-acquired pneumonia. J. Infect. Dis., 188:1695– 1706. 69. Schuster, M., Lostroh, C.P., Ogi, T., and Greenberg, E.P., 2003, Identiﬁcation, timing, and signal speciﬁcity of Pseudomonas aeruginosa quorum-controlled genes: a transcriptome analysis. J. Bacteriol., 185:2066–2079. 70. Schweizer, H.P., Jump, R., and Po, C., 1997, Structure and gene-polypeptide relationships of the region encoding glycerol diffusion facilitator (glpF) and glycerol kinase (glpK) of Pseudomonas aeruginosa. Microbiology, 143:1287–1297. 71. Schweizer, H.P., and Po, C., 1994, Cloning and nucleotide sequence of the glpD gene encoding sn-glycerol-3-phosphate dehydrogenase of Pseudomonas aeruginosa. J. Bacteriol., 176:2184– 2193. 72. Serra, A.L., Mariscotti, J.F., Barra, J.L., Lucchesi, G.I., Domenech, C.E., and Lisa, A.T., 2002, Glycine betaine transmethylase mutant of Pseudomonas aeruginosa. J. Bacteriol., 184:4301– 4303. 73. Shaver, C.M., and Hauser, A.R., 2004, Relative contributions of Pseudomonas aeruginosa ExoU, ExoS, and ExoT to virulence in the lung. Infect. Immun., 72:6969–6977. 74. Shortridge, V.D., Lazdunski, A., and Vasil, M.L., 1992, Osmoprotectants and phosphate regulate expression of phospholipase C in Pseudomonas aeruginosa. Mol. Microbiol., 6:863– 871. 75. Six, D.A., and Dennis, E.A., 2000, The expanding superfamily of phospholipase A(2) enzymes: classiﬁcation and characterization. Biochim. Biophys. Acta., 1488:1–19. 76. Stonehouse, M.J., Cota-Gomez, A., Parker, S.K., Martin, W.E., Hankin, J.A., Murphy, R.C., Chen, W., Lim, K.B., Hackett, M., Vasil, A.I., and Vasil, M.L., 2002, A novel class of microbial phosphocholine-speciﬁc phospholipases C. Mol. Microbiol., 46:661–676. 77. Stonehouse, M.J., and Vasil, M.L., 2005, unpublished observations. 78. Stuckey, J.A., and Dixon, J.E., 1999, Crystal structure of a phospholipase D family member. Nat. Struct. Biol., 6:278–284. 79. Tamura, M., Ajayi, T., Allmond, L.R., Moriyama, K., Wiener-Kronish, J.P., and Sawa, T., 2004, Lysophospholipase A activity of Pseudomonas aeruginosa type III secretory toxin ExoU. Biochem. Biophys. Res. Commun., 316:323–331. 80. Teplitz, C., 1965, Pathogenesis of Pseudomonas vasculitis and septic legions. Arch. Pathol., 80:297–307. 81. Tropp, B.E., 1997, Cardiolipin synthase from Escherichia coli. Biochim. Biophys. Acta., 1348:192–200.

Phospholipases and Phospholipids

82. Vance, D.E., and J.E., V., 2002, Biochemistry of Lipids, Lipoproteins and Membranes, 4th ed., Vol. 36. Elsevier, Boston. 83. Vance, R.E., Hong, S., Gronert, K., Serhan, C.N., and Mekalanos, J.J., 2004, The opportunistic pathogen Pseudomonas aeruginosa carries a secretable arachidonate 15-lipoxygenase. Proc. Natl. Acad. Sci. U.S.A., 101:2135–2139. 84. Vasil, M.L., Berka, R.M., Gray, G.L., and Nakai, H., 1982, Cloning of a phosphate-regulated hemolysin gene (phospholipase C) from Pseudomonas aeruginosa. J. Bacteriol., 152:431–440. 85. Vasil, M.L., Graham, L.M., Ostroff, R.M., Shortridge, V.D., and Vasil, A.I., 1991, Phospholipase C: molecular biology and contribution to the pathogenesis of Pseudomonas aeruginosa. Antibiot. Chemother., 44:34–47. 86. Voulhoux, R., Ball, G., Ize, B., Vasil, M.L., Lazdunski, A., Wu, L.F., and Filloux, A., 2001, Involvement of the twin-arginine translocation system in protein secretion via the type II pathway. EMBO J., 20:6735–6741. 87. Wadsworth, S.J., and Goldﬁne, H., 2002, Mobilization of protein kinase C in macrophages induced by Listeria monocytogenes affects its internalization and escape from the phagosome. Infect. Immun., 70:4650–4660. 88. Wagner, V.E., Bushnell, D., Passador, L., Brooks, A.I., and Iglewski, B.H., 2003, Microarray analysis of Pseudomonas aeruginosa quorum-sensing regulons: effects of growth phase and environment. J. Bacteriol., 185:2080–2095. 89. Wilderman, P.J., Vasil, A.I., Johnson, Z., and Vasil, M.L., 2001, Genetic and biochemical analyses of a eukaryotic-like phospholipase D of Pseudomonas aeruginosa suggest horizontal acquisition and a role for persistence in a chronic pulmonary infection model. Mol. Microbiol., 39:291–303. 90. Wilderman, P.J., Vasil, A.I., Martin, W.E., Murphy, R.C., and Vasil, M.L., 2002, Pseudomonas aeruginosa synthesizes phosphatidylcholine by use of the phosphatidylcholine synthase pathway. J. Bacteriol., 184:4792–4799. 91. Winkler, H.H., and Daugherty, R.M., 1989, Phospholipase A activity associated with the growth of Rickettsia prowazekii in L929 cells. Infect. Immun., 57:36–40. 92. Wolfgang, M.C., Jyot, J., Goodman, A.L., Ramphal, R., and Lory, S., 2004, Pseudomonas aeruginosa regulates ﬂagellin expression as part of a global response to airway ﬂuid from cystic ﬁbrosis patients. Proc. Natl. Acad. Sci. U.S.A., 101:6664–6668. 93. Wolfgang, M.C., Lee, V.T., Gilmore, M.E., and Lory, S., 2003, Coordinate regulation of bacterial virulence genes by a novel adenylate cyclase-dependent signaling pathway. Dev. Cell., 4:253–263. 94. Yuki, N., Awai, K., Matsuda, T., Yoshioka, Y., Takamiya, K., and Ohata, H., 2004, A novel phosphatidylcholine-hydrolyzing phospholipase C induced by phosphate starvation in Arabidopsis. J. Biol. Chem., 280:7469–7476. 95. Zabner, J., Smith, J.J., Karp, P.H., Widdicombe, J.H., and Welsh, M.J., 1998, Loss of CFTR chloride channels alters salt absorption by cystic ﬁbrosis airway epithelia in vitro. Mol. Cell., 2:397–403.

IN VIVO FUNCTIONAL GENOMICS OF PSEUDOMONAS: PCR-BASED SIGNATURE-TAGGED MUTAGENESIS Roger C. Levesque

Microbiologie Mol´eculaire et G´enie des Prot´eines D´epartement de Biologie M´edicale et Pavillon Charles-Eug`ene Marchand Facult´e de m´edecine Universit´e Laval Sainte-Foy, Qu´ebec G1K 7P4, Canada

1. INTRODUCTION The genus Pseudomonas encompasses closely related bacterial species that behave as pathogens in speciﬁc situations and can cross a large evolutionary gulf to naturally or experimentally infect organisms from other phyla or kingdoms. Hence, Pseudomonas can ﬁll practically any ecological niche including survival in inhospitable Mars-like environments, in livings hosts such as unicellular life-forms, in plants, in insects, in animals, and in humans.74,89 In humans, Pseudomonas aeruginosa has been considered an opportunistic pathogen; in most cases the opportunity being a conditional trauma such as immunosuppressed, cancer, and burn patients.25–27 Unusual situations in humans are also excellent opportunities for P. aeruginosa to initiate and establish a nosocomial infection such as in the hospital intensive care units where catheters, respiratory devices, and other medical implants are used in combination with an arsenal of immunomodulators and antibiotics.31,56 In addition, there is a speciﬁc and unusual human medical condition in Cystic Fibrosis where Pseudomonas species,

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mostly P. aeruginosa will cause a permanent chronic lung infection leading to irreversible tissue damage and death.71,93,95 Recent analysis of the 67% G + C 6.3 Mb genome content of P. aeruginosa strain PAO1 has revealed a repertoire of more than 468 open reading frames (ORFs) containing 543 regulatory motifs characteristic of transcriptional regulators, 55 sensors, 89 response regulators, and 14 sensor–response regulatory hybrids of two component systems and at least 12 potential RND efﬂux systems. These proteins represent approximately 8.4% of the genome coding capacity acting as sensors interacting with the environment or with the host permitting an adaptive response to aggression and to antibiotic resistance.36,83 Of the 5570 ORFs, P. aeruginosa strain PAO1 encodes 1780 (32%) genes having no hom*ology to any previously reported sequences, 1590 (28.5%) genes having a function proposed based on the presence of conserved amino acid motif, structural feature or limited hom*ology and 769 (13.8%) hom*ologues of previously reported genes of unknown function. In terms of genes characterized, 1059 (19%) have a function based upon a strongly hom*ologous gene experimentally demonstrated in another organism; whereas only 372 genes (6.7%) have a function experimentally demonstrated in P. aeruginosa. Hence, a massive amount of information implicated in virulence and for in vivo maintenance of P. aeruginosa is hiding in more than 1780 hypothetical and unknown proteins, in 1590 genes having conserved motifs and in 769 hom*ologues of previously reported genes of unknown function. This intractable problem can be addressed by signature-tagged mutagenesis (STM). A clear understanding how Pseudomonas has the capability to initiate, invade, maintain, and colonize a mammalian host to assure its survival is a prerequisite for understanding the virulence behavior of this organism in particular, and all opportunistic pathogens in general.3,11,21,28,34 Indeed, novel strategies are essential for identifying genes expressed solely in the host during the infection process and also genes which are absolutely essential for initiating and maintaining Pseudomonas in the host.19–21,42 Unfortunately, traditional screening in animal models of infection for mutants covering a complete genome and based upon a gene by gene mutational approach is not feasible in vivo, even with today’s capabilities in genomics and in proteomics. For example, a signiﬁcant analysis of virulence determinants for the P. aeruginosa 6.3 Mb genome encoding 5570 ORFs would require in a model of infection a minimum of 5570 animals; statistical validity would recommend groups of at least ﬁve individuals giving a total of 27,850 animals, an impossible and unjustiﬁable task. Identiﬁcation of function loss and hence of genes essential in the infection process can now be addressed by STM. This is an extremely powerful and elegant bacterial genetics approach for in vivo functional genomics, particularly when used in combination with bioinformatics, proteomics, and transcriptome analysis to identity genes and their products essential for in vivo maintenance.20,33,34,40,87,88

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The technology has become accessible to a larger number of small laboratories, especially as screening can now be done rapidly by using PCR instead of hybridization. The design of tags has been simpliﬁed, and several different mini-Tn5s, each with a unique phenotypic selection, can now be utilized.50,51 We will not discuss all the technical details here but will focus on the concept and results available to date with P. aeruginosa. The reader is referred to more technical publications for the PCR-based STM.50,51 These modiﬁcations of STM, developed in our laboratory, have been applied to the study of P. aeruginosa strain PAO1. In this chapter, we focus on the biological signiﬁcance of the data obtained in comparisons with other in vivo methods such as IVET, transcriptome, and proteome analysis.33,67 Application of IVET to Pseudomonas has been described in Volume I, Chapter 11. In studying in vivo maintenance and gene expression of P. aeruginosa, STM seemed more appropriate than IVET because the negative selection identiﬁes unique genes essential for in vivo survival. In contrast, IVET identiﬁes a large portion of housekeeping genes upregulated in these conditions. These genes certainly play signiﬁcant role for survival in vivo and IVET is a complementary approach and we, and others, have applied both approaches to Pseudomonas; in every case there seemed to be little overlaps in the results. Unfortunately, a highly versatile organism like Pseudomonas has alternative metabolic pathways to compensate IVET mutant deﬁciencies.

2. SIGNATURE-TAGGED MUTAGENESIS Transposable elements have been traditional tools in bacterial genetics for creating insertional mutations. Over the years, the limitations of transposons use in Pseudomonas such as bacterial host speciﬁcity and transfer and their caveats including problems of multiple insertions, chromosomal rearrangements, and in many cases, polar effects were eliminated by the development of mini-transposons, mobilizable suicide plasmid vectors, and optimized protocols in transfer using bacterial conjugation and electroporation.23,79,80,82 In addition to the development of mini-transposons, completely in vitro transposition methods are also available.23,32,77 STM, developed 10 years ago by David Holden and colleagues, represents a major application of an “en masse” transposon mutagenesis and high-throughput screening technique.38,81 STM is a mutation-based screening method that uses a population of bacterial mutants for the identiﬁcation of multiple virulence genes of microbial pathogens by negative selection. The technique depends upon in vivo selection of virulent organisms; while those mutants whose virulence genes are inactivated will not persist in vivo. This

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allows a relatively rapid, unbiased search for virulence genes, using experimental infection models as hosts to select against strains carrying mutations in genes affecting virulence and bacterial maintenance. The beauty of the technology is an in vivo selection process done by the host among a mixed population of mutants. Hence, to avoid the typical labor-intensive screening of individual mutants, each mutant is tagged with a different and unique DNA signature; the power of STM is that it allows large numbers of different mutants to be screened simultaneously in the same host. There is now enough data, experience, and knowledge from more than 10 years of work and from 40 distinct reports in different bacterial systems to indicate that STM has numerous applications.4 The power of the technique relies mostly on the rounds of selection done in an appropriate model being an animal, plant, insect, cell line, or environmental condition selected. In several cases, different host models can be tested with the same collection of mutants.49 In the classical STM, a comparative hybridization technique was used with a collection of transposons each modiﬁed by the incorporation of a distinct DNA tag sequence. The concept was that when the tagged transposon integrates into the bacterial chromosome, each individual mutant can be distinguished from every other by hybridization. The ﬁrst tag collections were designed as short DNA segments containing 40-bp variable regions giving probe speciﬁcity ﬂanked by invariant arms that facilitated the co-ampliﬁcation and radioactive labeling of the central portions by PCR, and which were subsequently used as hybridization probes.38 Colony or DNA dot blots were prepared from these mutants, and compared by hybridization to DNA prepared when the same pool of strains passaged in a model of infection. PCR was then used to prepare labeled probes, representing the tags present in a deﬁned inoculum (in vitro input) and recovered from the host (in vivo output). Hybridization of the tags from the input and the output pools were compared. This permitted the identiﬁcation of mutants that failed to grow in vivo, because these tags from mutants effective for in vivo maintenance will not be present in the output pools. These mutants can then be identiﬁed and recovered from the original bacterial arrays. The nucleotide sequence of genomic DNA ﬂanking the transposon insertion site can be determined and the inactivated gene identiﬁed. Because of inherent cross-hybridization signals between tags incorporated into mini-Tn5 transposons, their suitability was checked prior to use by hybridization of ampliﬁed labeled tags to DNA colony blots of mutants used to generate the probes. Mutants from the in vitro pool whose tags failed to yield clear signals were discarded; while those that gave good signals were assembled into new pools for screening into animals. This careful analysis was done prior to STM, so as to diminish the inherent problems of hybridization caused by problematic tags.64

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2.1. Description of the PCR-Based STM The PCR-based STM is an important variant of the hybridization method, easier to use and can be divided into two major steps. In contrast to the STM done by hybridization, the ﬁrst in vitro step involved the construction of deﬁned complementary oligonucleotides assembled to form double-stranded DNA tags which are speciﬁc for PCR ampliﬁcation, do not cross-amplify, and are optimized for PCR multiplex and polymerase priming.51 These tags are cloned as complementary oligonucleotides into a mini-transposable element; transposons are selected with different antibiotic markers as a reliable method to select for the recipients; and mutants are carefully assembled in an array of tagged mutants.50 The PCR-based STM method developed uses 24 pairs of complementary 21bp oligonucleotides. These pairs are annealed to generate 24 double-stranded DNA tags, which are then cloned into each of the four plasmid-located mini-Tn5 derivatives, mini-Tn5Km2, mini-Tn5Tc, mini-Tn5Cm, and mini-Tn5TcGFP.50 These Tn5-derived mini-transposons contain genes encoding kanamycin resistance (Km), tetracycline resistance (Tc), chloramphenicol (Cm) resistance, and green ﬂuorescent protein (GFP), respectively. All plasmids have unique cloning sites for tag insertion, and are ﬂanked by 19-bp terminal repeats encoding the I and the O ends for transposase action and are capable of only a single transposition event. The transposons are located on the pUT plasmid vector, an R6K-based suicide delivery plasmid where the Pi protein is furnished in trans by the donor bacteria. The PCR-based STM comprises a collection of 96 (24 tags × 4 mini-Tn5 plasmid vectors) tagged transposons (available upon request). The second step requires an experimental infection host system such as an animal or cell for in vivo screening of the library.70 We strongly believe that the model selected for screening the “output pool” of STM mutants for negative selection is the crux of STM. In this second phase, the experimental design needs to take into account: (1) the power and limitations of the model of infection used, (2) the number of rounds of STM screening to be done, and (3) the number of different hosts to be utilized. When performing analysis by STM, it is crucial to take into account crucial parameters including: (4) the inoculum size (from 1 to 106 bacteria/ml), (5) the number of STM mutants to be utilized in each experimental host (from 10 to 96), (6) the route for initiation of the infection, and (7) the duration of selection of STM mutant which may vary from a few hours to several weeks.6,8,35,60,65 Once this is determined and the selection process completed, crucial data must be obtained by PCR, negative clones selected by multiplex and single PCR analysis, determination of the DNA sequence around the site of the insertion mutation, which may be obtained by cloning the transposon marker or by RT-PCR. The ﬁnal phase, and the ultimate goal of STM, is to characterize genes shown to play a signiﬁcant role in virulence, and to deﬁne their function and

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role in pathogenicity. Hence, STM also involves a systematic characterization of single mutants selected in vivo by construction of gene knockouts giving a clear genetic background so as to eliminate polar effects. Additional analysis involves bacterial cell growth and maintenance in vitro for auxotrophy but more so in vivo by measuring the growth index and or the competitive index.8 To make fast progress in analysis of selected Pseudomonas STM mutants, several transposon mutant libraries of all PAO1 genes are now available upon requests as Pseudomonas or as BAC clones for analysis of speciﬁc genomic regions of interest.24,41,53 The general scheme for PCR-based STM is presented in Fig. 1. An alternative to the clone by clone analysis of STM mutants selected after screening, studies can now be combined with transcriptomics using the Affymetrix P. aeruginosa strains PAO1 DNA oligonucleotide chip; proteomics and IVET studies are also complementary prospects. Metabolomics can also be attempted with Pseudomonas STM mutants using the Phenotype MicroArrays system, a high-throughput technology for simultaneous testing of 700 cellular phenotypes by merely pipetting a cell suspension into microplate arrays.10,58,67,78

3. IN VIVO STM OF P. AERUGINOSA Our interest in P. aeruginosa STM has been prompted by several questions: what are the patterns of initiation, growth, establishment, and maintenance for progression of a chronic infection? What are the bacterial growth rates and population sizes at these different stages? What nutrients and substrates become available as infection progresses? How do bacteria metabolize them? What virulence determinants are produced at these different and speciﬁc periods during infection? How is the production of virulence determinants regulated? What are the effects of environmental parameters? Again one must remember that studies, including those done by STM must cover part of Koch’s postulates. This becomes a difﬁcult case when studying opportunistic pathogens including Pseudomonas because no adequate experimental models exist to represent infected host.59 To date, only two studies have been done by STM using P. aeruginosa strains PAO1 and TBFC10389. PAO1 was screened in the rat lung model of chronic infection and in Drosophila; while TBFC10389 was screened in tissue culture using polymorphonuclear (PMN) granulocytes.40,49,50,51,52,72,91

3.1. Global Analysis and Distribution of STM Mutants PCR-based STM was used for high-throughput screening of a collection of 7968 P. aeruginosa mutants in a rat model of chronic respiratory infection and is summarized in Figure 1 and in Figure 2.18,52 As depicted in Figure 2

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105

Master Plate

Culture

In vitro

In vivo Bacteria from the lung

PCR Tag 1-24 Km/Tc/GFP O

I 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 -

PCR 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 -

980 pbs s 820 pbs 220 pbs s

Figure 1. General scheme for the PCR-based STM using master plates assembled from a collection of 7968 P. aeruginosa clones carrying insertions of the mini-Tn5 Km, Tc or GFP markers.49,50,51,52,72

Figure 2. General scheme used for screening P. aeruginosa STM mutants using different models of infection.49,50,51,52,72,91

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and after three rounds of screening, a total of 214 mutants were shown to be attenuated in lung infection and were retained for further studies. Analysis of the genome distribution of 160 unique STM mutants represented transposition event into 148 distinct ORFs. Of signiﬁcance in virulence studies and indicating the power of STM for studying in vivo functional genomics was that many P. aeruginosa STM insertions were found into genes expressing hypothetical, unknown, unclassiﬁed proteins. Indeed, this ﬁrst group represented 67 of 148 insertion events (42.6%). The second interesting group included 26 proteins implicated in the transport of small molecules (9.5%), 7 proteins were secreted factors (4.8%), and 7 transcriptional regulators (4.8%). Few insertions were found in genes coding for classes of protein involved in adaptation and protection (2), amino acid biosynthesis and metabolism (4), carbon compound catabolism (2), cell division (1), cell wall and lipopolysaccharide biosynthesis (1), central intermediary metabolism (3), chaperone and heat shock (1). Bioinformatics analysis for protein localization indicated that 40% of P. aeruginosa STM mutants defective in vivo had defects in proteins localized at or near the surface of the bacterial cell such as the inner membrane, the periplasm, and the outer membrane; while 15% of STM mutants identiﬁed proteins whose localizations were unknown.53 Overall, the number of in vivo attenuated STM mutants identiﬁed represents ≈2% of the total 7968 P. aeruginosa STM mutant strains screened; this value is lower than the 4%–10% previously reported in different bacterial systems and may be due to the highly stringent conditions used when selecting STM clones by PCR screening.35,38,65 The complete list of STM mutants identiﬁed to date as essential for lung infection is available at: http://rclevesque.rsvs.ulaval.ca/ TablewebsiteTMlist.pdf

3.2. Detailed Analysis of P. aeruginosa STM mutants One of the gold standards of STM is to clearly demonstrate the capability of the method in identifying previously characterized virulence factors in a known bacterial system such as P. aeruginosa. Bacterial cellular processes essential for in vivo survival and known to be crucial for P. aeruginosa pathogenesis are intimately involved in motility and attachment such as pili and type IV ﬁmbriae.2,62 Bacterial ﬂagellins are mediators of pathogenicity and host immune responses in mucosa.76 The ﬂagellum is an exquisitely engineered chemi-osmotic nanomachine; nature’s most powerful rotary motor, harnessing a trans-membrane ion-motive force to drive a ﬁlamentous propeller.68 Flagella contribute to the virulence of pathogenic bacteria through chemotaxis, adhesion to and invasion of host surfaces. Flagellin is the structural protein that forms the major portion of ﬂagellar ﬁlaments. Thus, ﬂagellin consists of a

In Vivo Functional Genomics of Pseudomonas

Table 1.

107

P. aeruinosa genes essential for lung infection identiﬁed by STM and previously reported as essential for virulence72

Strain name

PA position

Gene namea

STM4528

PA4528

pilD

STM0410

PA0410

pilI

STM4554

PA4554

pilY1

STM0762

PA0762

algU

STM4446

PA4446

algW

STM0765

PA0765

mucC

STM1248

PA1248

aprf

STM3478

PA3478

rhlB

STM3831

PA3 831

pepA

STM5112

PA5112

estA

STM5449

PA5449

wbpX

Description

hom*ologueb

Motility and attachment Motility and attachment Motility and attachment Sigma factor

100% PilD P. aeruginosa 100% PilI P. aeruginosa 100% PilY1 P. aeruginosa 100% AlgU P. aeruginosa 100% AlgW P. aeruginosa 100% MucC P. aeruginosa 100% AprF P. aeruginosa 100% RhlB P. aeruginosa 100% PhpA P. aeruginosa 69% YtrP P. putida 100% WpbX P. aeruginosa

Secretion of alginate Transcription regulator Alkaline protease Rhamnosyl transferase Leucine amino peptidase Esterase Glycosyl transferase

Localizationc IM C IM C P U OM C C OM C

C, cytoplasmic; IM, inner membrane; P, periplasm; OM, outer membrane; U, unknown. The gene name assigned by the annotation and sequencing group at the http://www.pseudomonas.com internet site. b The name of the protein hom*ologue, when available with recent BLAST analysis and updating data from the http://www.pseudomonas.com site. There are four classes (1) Function experimentally demonstrated in P. aeruginosa; (2) Function of highly similar gene experimentally demonstrated in another organism, and gene context consistent of pathways it is involved in, if known; (3) Function proposed based on presence of conserved amino acid motif, structural feature, or limited sequence similarity to an experimentally studied gene; (4) hom*ologues of previously reported genes of unknown function, or no similarity to any previously reported sequences. c Protein localization was determined using PSORTB.

conserved domain that is widespread in bacterial species and is dedicated to ﬁlament polymerization. Conversely, mammalian hosts detect the conserved domain on ﬂagellin monomers through Toll-like receptor (TLR) 5, which triggers proinﬂammatory and adaptive immune responses.76 In agreement with these observations and as shown in Table 1, P. aeruginosa STM mutants screened in the rat lung had insertions in pilD (PA4528), pilI (PA0410), and pilY1 (PA4554), respectively. Signiﬁcant for in vivo maintenance and for the production of bioﬁlms, P. aeruginosa is notorious for the copious amounts of alginate and mucus it

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produces in the lungs of cystic ﬁbrosis patients.17 Alginate forms a physical/chemical barrier protecting the bacterium from its environment, behaves as a virulence factor by acting as an antiphagocytic agent, impairs the efﬁcacy of aminoglycoside antibiotics, and it suppresses neutrophil and lymphocyte function. Environmental stresses such as oxidative stress triggers dramatic increases in alginate biosynthesis and secretion, favors the appearance of the mucoid phenotype which has devastating effects on antibiotic treatment in CF individuals. Thus, the recovery of attenuated P. aeruginosa STM strains carrying mutations in algU (PA0762), algW (PA4446), and in mucC (PA0765), the functions of which are closely associated with alginate biosynthesis, its secretion and transcriptional regulation are highly relevant to validate STM.12,54,94 P. aeruginosa in a repertoire of extracytoplasmic factors implicated in virulence and in vivo maintenance. The need for iron in vivo is critical and mediated by siderophores or iron (III) chelators produced by P. aeruginosa in response to iron limitation, and their structure can be extremely diverse.85 The production of PVDs and their cognate receptors depends on two extracytoplasmic sigma factors (ECF-σ), PvdS, and FpvI. PvdS also controls the transcription of two P. aeruginosa extracellular virulence factors, the endoprotease PrpL and exotoxin.86 Recently, a microarray analysis of the P. aeruginosa genes transcribed under conditions of iron limitation in wild-type and in a pvdS mutant led to the discovery of new PvdS-regulated genes for the biosynthesis of PVDs.69 It has been suggested that extracellular virulence determinants might not be identiﬁed by STM because they can be complemented by other mutants in the pool.66 We have shown that P. aeruginosa STM mutants carried insertions in a plethora of secreted factors and toxins known to be critical in virulence including an alkaline protease (PA1248), a rhamnosyl surfactant (PA3478), an amino peptidase (PA3831), an esterase (PA5112), and a glycosyl transferase (PA5449) involved in LPS biosynthesis.7,39,55,61,72 After conﬁrming the attenuation of virulence with several rounds of screening in a selected host, one has to ﬁnd a strategy to evaluate the signiﬁcance of STM mutants isolated. One simple approach is to simply determine the expression of known virulence factors from STM mutants isolated. For P. aeruginosa STM mutants, this was done to determine whether the 148 STM strains had defects in the expression of known virulence factors such as proteases, lipases, phospholipases, exopolysaccharides, pyoverdine, pyocyanin, and motility.5,9,13–16,43 From the 148 STM strains tested, 36 were defective in the production of known virulence factors such as the proteases LasA and LasB (PA2895 and PA3498), pyocyanine (PA1157, PA2639, PA4887, PA5312), and pyoverdin (PA5441). Of those, the majority were defective in the swimming and swarming phenotype, and 14 STM mutants were found to have insertions in hypothetical or unknown proteins.44,45,63,72

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3.3. Screening in Drosophila and in PMN Cells Because of the repertoire of host models of infection available, P. aeruginosa STM mutants can be categorized further by in vivo screening in alternative hosts.1,37,42,47 Selected P. aeruginosa mutants obtained by various genetic methods have been screened in a repertoire of hosts including plants such as Arabidopsis thaliana and lettuce, the amoeba Dictyostelium discoideum, the nematode Caenorhabditis elegans, the wax moth Bombix mori, the ﬂy Drosophila melanogaster and mammalian hosts such as various strains of mouse and rat.22,47,57,75 Certain gene products may be directly or indirectly important for initiation or maintenance of the infection and would presumably be nichedependent or may be expressed speciﬁcally in certain host tissues only. In these various models, if the duration of the infection for STM screening in vivo is short presumably representing an acute infection, genes important for establishment of the infection will be found or, if the duration of infection is long or chronic, genes important for maintenance of infection could be identiﬁed. For example, the collection of 148 P. aeruginosa STM mutants defective for maintenance in the rat lung were screened in Drosophila and results are shown in Table 2; 8 mutants were found to be highly attenuated giving less than 15% lethality.72 In Drosophila, these P. aeruginosa STM mutants were found to have insertions mostly in genes encoding amino acid production, nucleotide biosynthesis, and in enzymes of central metabolism. Two STM mutants had insertions in pilI (PA0410) and one in a hypothetical gene (PA5441), but affecting pyoverdine overproduction. There is a precedent for particular interest of STM mutants defective in amino acid biosynthesis and a relationship to in vivo maintenance. An aroA deletion mutant of P. aeruginosa strain PAO1 showing auxotrophy for aromatic amino acids (as veriﬁed by the inability to grow on minimal media unless supplemented with aromatic amino acids) has been deﬁned as an excellent candidate for intranasal vaccine. When evaluated for safety and immunogenicity in mice, the PAO1aroA strain could be applied either intranasally or intraperitoneally at doses up to 5 × 109 CFU per mouse without adverse effects.73 Pyoverdine but more so pyocyanin is a blue redox-active secondary metabolite that is produced in large quantities in sputum from infected patients with CF.48 Pyocyanin is an evolutionary conserved virulence factor of P. aeruginosa hosts of multiple phyla and is crucial for lung infection in mice. Pyocyanin targets in yeasts have 60% mammalian orthologs which include the V-ATPase; their inhibition would presumably affect vesicular transport and protein trafﬁcking, ATP availability, cellular respiration via electron transport, and oxidative stress leading to injury and killing of lung epithelial cells.48 A distinct but complementary approach to PCR-based STM is a hybridization-based STM using a 40-mers tag adapted to the 67% G + C content

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Table 2. P. aeruginosa genes essential for lung infection and for killing of Drosophila72 STM clone PA position

Gene name

STMPA0410

pilI

Motility and attachment

STMPA3831 STMPA2876 STMPA5131 STMPA1927

PepA PyrF Pgm MetE

STMPA0552

Pgk

Leucine amino peptidase Orotidine decarboxylase Phosphoglycerate mutase hom*ocysteine methyl transferase Phosphoglycerate kinase

STMPA2639 STMPA2998 STMPA3286

NuoD NrqB C, hypothetical

STMPA4115

C, hypothetical

STMPA4488

C, hypothetical

STMPA4489

C, hypothetical

STMPA4491

C, hypothetical

STMPA5441

C, hypothetical

STMPA4564

C, hypothetical

STMPA2972

C, hypothetical

STMPA3756

C, hypothetical

STMPA4692

C, hypothetical

STMPA5078

C, hypothetical

STMPA3826

C, hypothetical

STMPA1009

Hypothetical

STMPA2895

Hypothetical

STMPA3173 STMPA3001

Description

NADH dehydrogenase Translocating oxido reductase Hypothetical, unclassiﬁed, unknown Hypothetical, unclassiﬁed, unknown Hypothetical, unclassiﬁed, unknown Hypothetical, unclassiﬁed, unknown Hypothetical, unclassiﬁed, unknown Hypothetical, unclassiﬁed, unknown Hypothetical, unclassiﬁed, unknown Hypothetical, unclassiﬁed, unknown Hypothetical, unclassiﬁed, unknown Hypothetical, unclassiﬁed, unknown Hypothetical, unclassiﬁed, unknown Hypothetical, unclassiﬁed, unknown Hypothetical, unclassiﬁed, unknown Hypothetical, unclassiﬁed, unknown Probable short-chain dehydrogenase Probable phosphate dehydrogenase

Relevant characteristics Twitching, swarming, Drosophila Swarming Drosophila Drosophila Swarming Lipase, pyocyanin, pyoverdine, Drosophila Pyocyanin, motility Swarming Swarming Swarming Swarming Drosophila Swarming Pyoverdine (++), Drosophila Swarming Swarming Swarming Swarming Swarming Swarming Swarming Protease Swarming Drosophila (Continued )

In Vivo Functional Genomics of Pseudomonas

Table 2. STM clone PA position

Gene name

STMPA3498 STMPA5312 STMPA5327 STMPA0041 STMPA0584 STMPA0090

cca

STMPA3876 STMPA4887 STMPA0073 STMPA0151

narK2

STMPA1863

ModA

STMPA1157

111

(Continued ) Description

Probable oxido reductase Probable aldehyde dehydrogenase Probable oxido reductase Probable hemagglutinin tRNA nucleotidyl transferase Probable ClpA/B-type chaperone Nitrite extrusion protein 2 Probable MFS transporter Probable ABC transporter Probable TonB-dependent receptor Molybdate-binding precursor Probable two-component regulator

Relevant characteristics Protease Pyocyanin Twitching Swarming Twitching, Drosophila Swarming Motility Pyocyanin (++) Swarming Bioﬁlm Swarming, twitching motility Pyocyanin (++)

C, conserved; ++ ,indicate higher levels of pyocyanin and of pyoverdine when compared to the wild-type.

of Pseudomonas and cloned into the plasmoson pTnModOGm.91 Even though the genomic sequence is unknown, the P. aeruginosa strain TBFC10389 was used instead of PAO1 because of its persistence in professional phagocytes.84 PMNs were infected with 480 P. aeruginosa STM mutants; 50 did not survive the negative selection in PMNs and were identiﬁed as defective in the expression of a gene or operon essential for the bacterium’s intracellular survival.91 As shown in Table 3, Several rounds of screening identiﬁed 6 clones defective in PMN maintenance with insertions in PA2613 (YcaJ, conserved hypothetical), PA3344 (RecQ, helicase), PA3953 (YrcD, conserved hypothetical), PA4621 (oxidoreductase), PA5252 (YheS, ABC transporter), and PA5349 (rubredoxin reductase); two mutants showed enhanced survival in granulocytes, namely mutants with insertions in PA1992 (two component sensor) and PA5040 (PilQ Type IV ﬁmbriae biogenesis) (Table 3). Oxidase stress response genes are essential for intracellular PMN survival; helicase is involved in the inactivation of peroxide or DNA repair; while rubredoxin reductase can substitute for superoxide dismutase and oxidates aliphatic hydrocarbons. The mutants that harbored transposons in the helicase or rubredoxin reductase genes did not grow in the presence of 0.8 mM hydrogen peroxide. Even with such minimal screening, a comparison between the 8 mutants (Table 3) obtained from the hybridization-based STM (480 mutants) screened in PMNs, the 148 STM mutants obtained from the PCR-based STM mutants (7968) screened in the chronic rat lung model of infection and comparisons

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Table 3. P. aeruginosa genes essential for maintenance in polymorphonuclear cells91 Strain name

PA position

Gene namea

STM2613

PA2613

YcaJ

STM3344 STM3953

PA3344 PA3953

RecQ YrdC

STM4621

PA4621

STM5252

PA5252

STM5349

PA5349

STM1992

PA1992

FlhS

STM5040

PA5040

PilQ

YheS

Description Conserved hypothetical ATP DNA helicase Conserved hypothetical Probable oxidoreductase ABC transporter Rubredoxin reductase Two-component sensor Type 4 ﬁmbrial precursor

hom*ologueb

Localizationc

74% Putative polynucleotide 66% RecQ E.coli 55% Hypothtical B. subtilis

U C U U

70% hypothetical E.coli 59% Rubredoxin A. calcoaceticus 56% FlhS P. denitriﬁcans 98% PilQ P. aeruginosa

U C C OM

with typical mutants defective in virulence, identiﬁed previously in various laboratories, revealed exciting features. For example, the P. aeruginosa 34 kDa H2 O2 -responsive transactivator OxyR encoded by PA5344 is required for full virulence in rodent and insect models of infection and for resistance to human neutrophils (Figure 3).46 P. aeruginosa lacking OxyR is exquisitely susceptible to H2 O2 , even with wild-type catalase activity. In addition, the OxyR mutant cannot grow on LB agar because the autoxidizable components in the medium generate H2 O2 at 1 µM which represents a concentration detected in peripheral blood from human donors and is sufﬁcient to kill these organisms.46 In STM screening by both methods, the hybridization-based STM has identiﬁed a mutant having a defect in PA5349 (rubredoxin reductase) essential for maintenance in PMNs; while the PCR-based STM has identiﬁed an insertion in PA5347 (hypothetical protein, unknown) essential for maintenance in the rat lung.72,91 It remains to be demonstrated if both genes are part of the same operon and are regulated by the PA5344 OxyR transactivator. Additional comparisons between the STM data obtained from both methods (Figure 3) identiﬁed a crucial operon in infection; an insertion in PA4621 (probable oxidoreductase) was found essential for PMN maintenance and an insertion into PA4620 having 52% identity with a 4-hydroxybenzoyl CoA reductase was crucial for maintenance in the rat lung.72,91 Similar comparative analysis of P. aeruginosa genes identiﬁed using STM, IVET and with mutants used for identiﬁcation of essential virulence genes has conﬁrmed decisively the impact of STM in virulence studies of Pseudomonas.

In Vivo Functional Genomics of Pseudomonas STM4620 PA4618

PA4619 PA4620

113 PMN4621 PA4621

A. 4-Hydroxybenzoyl CoA reductase Probable Oxidoreductase

STM5347

PA5343 PA5344

PA5345

OxyR Transactivator

PA5346

PMN5349

PA5349 PA5347 PA5350 PA5348 PA5351

Hypothetical

Rubredoxin reductase

Figure 3. Genomic organization of two regions in the chromosome of P. aeruginosa identiﬁed as essential for maintenance in the rat lung and in polymorphonuclear cells. (A) Structure of the PA4618–PA46221 operon; (B) Gene organization of the PA5343–PA5351 region encoding the OxyR (PA5344) transactivator essential for full virulence in rodent, in Drosophila, and in PMNs. Abbreviations: STM, signature-tagged mutagenesis; PMN, Polymorphonuclear cells. Details are given in the text.

4. STM AND CHIP ANALYSIS Since several genes found to be essential for lung infection have also been identiﬁed by other high-throughput screening methods such as microarrays and transcriptome analysis, it is crucial to compare the chip data with STM mutants found to date.30,78,87,90,92 However, such comparisons should be done with caution. The comparisons of chip data between different laboratories, where experiments have been done in different conditions had raised initially a certain amount of controversies which can now be resolved with the experience of using Pseudomonas chips and additional data available. Since the probes on the GeneChip from Affymetrix were designed in a sequence speciﬁc way, the small sequence differences between P. aeruginosa strains may result in several probes hybridizing poorly or not at all. When using the PA14 strain to hybridize the Affymetrix GeneChip, which was designed from the PAO1 sequence data, one should remember that the genomic sequence differences between PAO1 and PA14 are at least 5%. A BLAST result indicated that only about 75% of the probes on the Affymetrix chip are actually targeting a location in the PA14 genome, which means that 25% of probes will not hybridize properly and must be masked out before subsequent analysis. One additional caution is to link probes to the corresponding PA14 genes, which might be different in the PAO1 annotation. The hybridization of the Affymetrix GeneChip with a strain that was not designed for it represents difﬁcult work and there are even more difﬁculties in data analysis. If the P. aeruginosa strain used

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is not sequenced, it will be difﬁcult to ﬁnd out which probes are not working and which probes are targeting a different location in the genome that they were designed for. Hence, it will be difﬁcult to interpret whether what you have observed in the subsequent data analysis is real. Transcriptome analysis for identiﬁcation, timing, and signal speciﬁcity of P. aeruginosa quorum-controlled genes was compared to the PCR-based STM study.72,78 Even though the quorum sensing activity was not monitored in STM mutants essential for maintenance in the rat lung, the genes identiﬁed in both cases were PA158 (probable RND efﬂux transporter), PA3734 (hypothetical), PA4172 (probable nuclease), PA3284 (hypothetical), and PA4692 (conserved hypothetical). Comparisons between the data from the microarray analysis of ECF sigma factor AlgU (P. aeruginosa sigma E)-dependent gene expression in P. aeruginosa with the PCR-based STM data identiﬁed PA1592 (hypothetical, lptA).29,30 In addition to several of the typical known virulence factors, PCR-based STM identiﬁed a novel gene previously identiﬁed in the co-ordinate regulation of bacterial virulence genes by a novel calcium-dependent adenylate cyclase-dependent signaling pathway, PA4983, a two component response regulator.92 It was apparent that comparisons between the P. aeruginosa STM mutants and the transcriptome of cAMp- and Vfr-deﬁcient mutants indicated that numerous host-directed virulence determinants, including motility systems, attachment organelles, and the type II secretory pathway proteins of which many were identiﬁed by STM, are co-ordinately regulated under conditions that control expression of the type III secretion systems, which represents one of the more speciﬁc host-directed bacterial virulence determinants.72,92

5. CONCLUSION Obviously, functional genomics of Pseudomonas and particularly P. aeruginosa has beneﬁted immensely from the availability of the complete and annotated sequence of strain PAO1 and more recently of the completed sequence of PA14. Without this crucial information, it would be quite inconceivable to attempt functional genomics in vivo using STM, IVET or any other large-scale genomics method. Obviously, the ﬁeld of Pseudomonas will beneﬁt even more from the sequencing of additional species and strains of Pseudomonas. There is now clear evidence that P. aeruginosa strains can vary signiﬁcantly in their genome content from a few hundred base pairs to several megabases. What is available today as the annotated sequence of PAO1 may actually represent some core genomic sequences, and metagenomics analysis will be pertinent to understanding virulence in an opportunistic pathogen such as P. aeruginosa. Hence, what have we learned from STM? One of the ﬁrst signiﬁcance of STM in P. aeruginosa is the clean correlation between virulence factors identiﬁed

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with those previously known virulence factors reported by many laboratories around the world. In terms of functional genomics and signiﬁcance, STM has pinpointed and identiﬁed several hypothetical and unknown proteins whose function in vivo is crucial for maintenance of P. aeruginosa. An interesting future prospect will be to analyze STM mutants of the PAO1 strain and the PA14 strain in similar models of infection. Finally, re-analysis of the data from STM using various Pseudomonads in different models of infection coupled to transcriptomics and proteomics and its integration using a biological systems approach should give a better understanding of how an opportunistic pathogen competes and survives in any environment.

ACKNOWLEDGMENTS Work in R.C.L. laboratory is funded by the Canadian Institute for Health Research and a team grant from Le Fonds de la Recherche en Sant´e du Qu´ebec. R.C.L. is a scholar of exceptional merit from the FRSQ.

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26. Eberl, L. and Tummler, B., 2004, Pseudomonas aeruginosa and Burkholderia cepacia in cystic ﬁbrosis: genome evolution, interactions and adaptation. Int. J. Med. Microbiol., 294:123–131. 27. Ernst, R.K., D’Argenio, D.A., Ichikawa, J.K., Bangera, M.G., Selgrade, S., Burns, J.L., Hiatt, P., McCoy, K., Brittnacher, M., Kas, A., Spencer, D.H., Olson, M.V., Ramsey, B.W., Lory, S., and Miller, S.I., 2003, Genome mosaicism is conserved but not unique in Pseudomonas aeruginosa isolates from the airways of young children with cystic ﬁbrosis. Environ. Microbiol., 5:1341–1349. 28. Finnan, S., Morrissey, J.P., O’Gara, F., and Boyd, E.F., 2004, Genome diversity of Pseudomonas aeruginosa isolates from cystic ﬁbrosis patients and the hospital environment. J. Clin. Microbiol., 42:5783–5792. 29. Firoved, A.M., Boucher, J.C., and Deretic, V., 2002, Global genomic analysis of AlgU (sigma (E))-dependent promoters (sigmulon) in Pseudomonas aeruginosa and implications for inﬂammatory processes in cystic ﬁbrosis. J. Bacteriol., 184:1057–1064. 30. Firoved, A.M. and Deretic, V., 2003, Microarray analysis of global gene expression in mucoid Pseudomonas aeruginosa. J. Bacteriol., 185:1071–1081. 31. Gibson, R.L., Burns, J.L., and Ramsey, B.W., 2003, Pathophysiology and management of pulmonary infections in cystic ﬁbrosis. Am. J. Respir. Crit. Care Med., 168:918–951. 32. Goryshin, I.Y. and Reznikoff, W.S., 1998, Tn5 in vitro transposition. J. Biol. Chem., 273:7367– 7374. 33. Handﬁeld, M., Lehoux, D.E., Sanschagrin, F., Mahan, M.J., Woods, D.E., and Levesque, R.C., 2000, In vivo-induced genes in Pseudomonas aeruginosa. Infect. Immun., 68:2359–2362. 34. Handﬁeld, M. and Levesque, R.C., 1999, Strategies for isolation of in vivo expressed genes from bacteria. FEMS Microbiol Rev., 23:69–91. 35. Hava, D.L. and Camilli, A., 2002, Large-scale identiﬁcation of serotype 4 Streptococcus pneumoniae virulence factors. Mol. Microbiol., 45:1389–1406. 36. He, J., Baldini, R.L., Deziel, E., Saucier, M., Zhang, Q., Liberati, N.T., Lee, D., Urbach, J., Goodman, H.M., and Rahme, L.G., 2004, The broad host range pathogen Pseudomonas aeruginosa strain PA14 carries two pathogenicity islands harboring plant and animal virulence genes. Proc. Natl. Acad. Sci. U.S.A., 101:2530–2535. 37. Hendrickson, E.L., Plotnikova, J., Mahajan-Miklos, S., Rahme, L.G., and Ausubel, F.M., 2001, Differential roles of the Pseudomonas aeruginosa PA14 rpoN gene in pathogenicity in plants, nematodes, insects, and mice. J. Bacteriol., 183:7126–7134. 38. Hensel, M., Shea, J.E., Gleeson, C., Jones, M.D., Dalton, E., and Holden, D.W., 1995, Simultaneous identiﬁcation of bacterial virulence genes by negative selection. Science, 269:400–403. 39. Horvat, R.T. and Parmely, M.J., 1988, Pseudomonas aeruginosa alkaline protease degrades human gamma interferon and inhibits its bioactivity. Infect. Immun., 56:2925–2932. 40. Hunt, T.A., Kooi, C., Sokol, P.A., and Valvano, M.A., 2004, Identiﬁcation of Burkholderia cenocepacia genes required for bacterial survival in vivo. Infect. Immun., 72:4010–4022. 41. Jacobs, M.A., Alwood, A., Thaipisuttikul, I., Spencer, D., Haugen, E., Ernst, S., Will, O., Kaul, R., Raymond, C., Levy, R., Chun-Rong, L., Guenthner, D., Bovee, D., Olson, M.V., and Manoil, C., 2003, Comprehensive transposon mutant library of Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. U.S.A., 100:14339–14344. 42. Jander, G., Rahme, L.G., and Ausubel, F.M., 2000, Positive correlation between virulence of Pseudomonas aeruginosa mutants in mice and insects. J. Bacteriol., 182:3843–3845. 43. Kessler, E., Safrin, M., Gustin, J.K., and Ohman, D.E., 1998, Elastase and the LasA protease of Pseudomonas aeruginosa are secreted with their propeptides. J. Biol. Chem., 273:30225– 30231. 44. Kohler, T., Curty, L.K., Barja, F., van Delden, C., and Pechere, J.C., 2000, Swarming of Pseudomonas aeruginosa is dependent on cell-to-cell signaling and requires ﬂagella and pili. J. Bacteriol., 182:5990–5996.

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45. Konig, B., Jaeger, K.E., Sage, A.E., Vasil, M.L., and Konig, W., 1996, Role of Pseudomonas aeruginosa lipase in inﬂammatory mediator release from human inﬂammatory effector cells (platelets, granulocytes, and monocytes. Infect. Immun., 64:3252–3258. 46. Lau, G.W., Britigan, B.E., and Hassett, D.J., 2005, Pseudomonas aeruginosa OxyR is required for full virulence in rodent and insect models of infection and for resistance to human neutrophils. Infect. Immun., 73:2550–2553. 47. Lau, G.W., Goumnerov, B.C., Walendziewicz, C.L., Hewitson, J., Xiao, W., Mahajan-Miklos, S., Tompkins, R.G., Perkins, L.A., and Rahme, L.G., 2003, The Drosophila melanogaster toll pathway participates in resistance to infection by the gram-negative human pathogen Pseudomonas aeruginosa. Infect. Immun., 71:4059–4066. 48. Lau, G.W., Hassett, D.J., Ran, H., and Kong, F., 2004, The role of pyocyanin in Pseudomonas aeruginosa infection. Trends Mol. Med., 10:599–606. 49. Lehoux, D.E. and Levesque, R.C., 2000, Detection of genes essential in speciﬁc niches by signature-tagged mutagenesis. Curr. Opin. Biotechnol., 11:434–439. 50. Lehoux, D.E., Sanschagrin, F., Kukavica-Ibrulj, I., Potvin, E., and Levesque, R.C., 2004, Identiﬁcation of novel pathogenicity genes by PCR signature-tagged mutagenesis and related technologies. Methods Mol. Biol., 266:289–304. 51. Lehoux, D.E., Sanschagrin, F., and Levesque, R.C., 1999, Deﬁned oligonucleotide tag pools and PCR screening in signature-tagged mutagenesis of essential genes from bacteria. Biotechniques, 26:473–478, 480. 52. Lehoux, D.E., Sanschagrin, F., and Levesque, R.C., 2002, Identiﬁcation of in vivo essential genes from Pseudomonas aeruginosa by PCR-based signature-tagged mutagenesis. FEMS Microbiol. Lett., 210:73–80. 53. Lewenza, S., Gardy, J.L., Brinkman, F.S., and Hanco*ck, R.E., 2005, Genome-wide identiﬁcation of Pseudomonas aeruginosa exported proteins using a consensus computational strategy combined with a laboratory-based PhoA fusion screen. Genome. Res., 15:321–329. 54. Lizewski, S.E., Schurr, J.R., Jackson, D.W., Frisk, A., Carterson, A.J., and Schurr, M.J., 2004, Identiﬁcation of AlgR-regulated genes in Pseudomonas aeruginosa by use of microarray analysis. J. Bacteriol., 186:5672–5684. 55. Louis, D., Sorlier, P., and Wallach, J., 1998, Quantitation and enzymatic activity of the alkaline protease from Pseudomonas aeruginosa in culture supernatants from clinical strains. Clin. Chem. Lab. Med., 36:295–298. 56. Lyczak, J.B., Cannon, C.L., and Pier, G.B., 2002, Lung infections associated with cystic ﬁbrosis. Clin. Microbiol. Rev., 15:194–222. 57. Mahajan-Miklos, S., Rahme, L.G., and Ausubel, F.M., 2000, Elucidating the molecular mechanisms of bacterial virulence using non-mammalian hosts. Mol. Microbiol., 37:981–988. 58. Malhotra, S., Silo-Suh, L.A., Mathee, K., and Ohman, D.E., 2000, Proteome analysis of the effect of mucoid conversion on global protein expression in Pseudomonas aeruginosa strain PAO1 shows induction of the disulﬁde bond isomerase, dsbA. J. Bacteriol., 182:6999– 7006. 59. Manger, I.D. and Relman, D.A., 2000, How the host ‘sees’ pathogens: global gene expression responses to infection. Curr. Opin. Immunol., 12:215–218. 60. Maroncle, N., Balestrino, D., Rich, C., and Forestier, C., 2002, Identiﬁcation of Klebsiella pneumoniae genes involved in intestinal colonization and adhesion using signature-tagged mutagenesis. Infect. Immun., 70:4729–4734. 61. Marty, N., Pasquier, C., Dournes, J.L., Chemin, K., Chavagnat, F., Guinand, M., Chabanon, G., Pipy, B., and Montrozier, H., 1998, Effects of characterised Pseudomonas aeruginosa exopolysaccharides on adherence to human tracheal cells. J. Med. Microbiol., 47:129– 134. 62. Mattick, J.S., Whitchurch, C.B., and Alm, R.A., 1996, The molecular genetics of type-4 ﬁmbriae in Pseudomonas aeruginosa-a review. Gene, 179:147–155.

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63. Mavrodi, D.V., Bonsall, R.F., Delaney, S.M., Soule, M.J., Phillips, G., and Thomashow, L.S., 2001, Functional analysis of genes for biosynthesis of pyocyanin and phenazine-1-carboxamide from Pseudomonas aeruginosa PAO1. J. Bacteriol., 183:6454–6465. 64. Mecsas, J., 2002, Use of signature-tagged mutagenesis in pathogenesis studies. Curr. Opin. Microbiol., 5:33–37. 65. Merrell, D.S., Hava, D.L., and Camilli, A., 2002, Identiﬁcation of novel factors involved in colonization and acid tolerance of Vibrio cholerae. Mol. Microbiol., 43:1471–1491. 66. Miller, V.L., 1999, Signature-tagged mutagenesis and the hunt for virulence factors: response. Trends Microbiol., 7:388. 67. Nouwens, A.S., Walsh, B.J., and Cordwell, S.J., 2003, Application of proteomics to Pseudomonas aeruginosa. Adv. Biochem. Eng. Biotechnol., 83:117–140. 68. Pallen, M.J., Penn, C.W., and Chaudhuri, R.R., 2005, Bacterial ﬂagellar diversity in the postgenomic era. Trends Microbiol., 13:143–149. 69. Palma, M., Worgall, S., and Quadri, L.E., 2003, Transcriptome analysis of the Pseudomonas aeruginosa response to iron. Arch. Microbiol., 180:374–379. 70. Pedersen, S.S., Shand, G.H., Hansen, B.L., and Hansen, G.N., 1990, Induction of experimental chronic Pseudomonas aeruginosa lung infection with P. aeruginosa entrapped in alginate microspheres. Apmis, 98:203–211. 71. Pier, G.B., 2002, CFTR mutations and host susceptibility to Pseudomonas aeruginosa lung infection. Curr. Opin. Microbiol., 5:81–86. 72. Potvin, E., Lehoux, D.E., Kukavica-Ibrulj, I., Richard, K.L., Sanschagrin, F., Lau, G.W., and Levesque, R.C., 2003, In vivo functional genomics of Pseudomonas aeruginosa for highthroughput screening of new virulence factors and antibacterial targets. Environ. Microbiol., 5:1294–1308. 73. Priebe, G.P., Brinig, M.M., Hatano, K., Grout, M., Coleman, F.T., Pier, G.B., and Goldberg, J.B., 2002, Construction and characterization of a live, attenuated aroA deletion mutant of Pseudomonas aeruginosa as a candidate intranasal vaccine. Infect. Immun., 70:1507–1517. 74. Rahme, L.G., Ausubel, F.M., Cao, H., Drenkard, E., Goumnerov, B.C., Lau, G.W., MahajanMiklos, S., Plotnikova, J., Tan, M.W., Tsongalis, J., Walendziewicz, C.L., and Tompkins, R.G., 2000, Plants and animals share functionally common bacterial virulence factors. Proc. Natl. Acad. Sci. U.S.A., 97:8815–8821. 75. Rahme, L.G., Tan, M.W., Le, L., Wong, S.M., Tompkins, R.G., Calderwood, S.B., and Ausubel, F.M., 1997, Use of model plant hosts to identify Pseudomonas aeruginosa virulence factors. Proc. Natl. Acad. Sci. U.S.A., 94:13245–13250. 76. Ramos, H.C., Rumbo, M., and Sirard, J.C., 2004, Bacterial ﬂagellins: mediators of pathogenicity and host immune responses in mucosa. Trends Microbiol., 12:509–517. 77. Reznikoff, W.S., Goryshin, I.Y., and Jendrisak, J.J., 2004, Tn5 as a molecular genetics tool: in vitro transposition and the coupling of in vitro technologies with in vivo transposition. Methods Mol. Biol., 260:83–96. 78. Schuster, M., Lostroh, C.P., Ogi, T., and Greenberg, E.P., 2003, Identiﬁcation, timing, and signal speciﬁcity of Pseudomonas aeruginosa quorum-controlled genes: a transcriptome analysis. J. Bacteriol., 185:2066–2079. 79. Schweizer, H.P., 1991, Escherichia-Pseudomonas shuttle vectors derived from pUC18/19. Gene, 97:109–121. 80. Schweizer, H.P., Klassen, T., and Hoang, T., 1996, In K.F. Teruko Nakazawa, Dieter Haas, Simon Silvert (ed.), Molecular Biology of Pseudomonads. pp. 229–237, ASM Press, Washington, DC. 81. Shea, J.E., Santangelo, J.D., and Feldman, R.G., 2000, Signature-tagged mutagenesis in the identiﬁcation of virulence genes in pathogens. Curr. Opin. Microbiol., 3:451–458. 82. Simon, R., Priefer, U., and P¨uhler, A., 1983, A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in Gram negative bacteria. BioTechnology, 1:784– 791.

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A GENOME-WIDE MUTANT LIBRARY OF PSEUDOMONAS AERUGINOSA Michael A. Jacobs1 and Colin Manoil2 1

Genome Center, Department of Medicine University of Washington Seattle, WA 98105 2 Department of Genome Sciences University of Washington Seattle, WA 98195, USA

Key Words: transposon, mutant library, gene fusion, essential gene

1. INTRODUCTION Although transcription microarray and proteomic technologies can identify large numbers of genes expressed under a particular condition, the biological meaning of such correlations is generally unclear without further analysis. Mutant studies can help clarify such a gene’s function in the process being studied, but the generation large numbers of mutations inactivating candidate genes is time-consuming and commonly limits the number of genes examined. This chapter summarizes the construction and attributes of a large transposon mutant library of Pseudomonas aeruginosa designed to help overcome this limitation. The library includes multiple insertions in most nonessential genes of the bacterium, and can be used systematically to examine the phenotypes of mutations in candidate genes that have been associated with a biological process of interest using other approaches. In addition, the library can be screened directly to provide virtually complete identiﬁcation of genes required for any Pseudomonas, Volume 4, edited by Juan-Luis Ramos and Roger C. Levesque C 2006 Springer. Printed in the Netherlands.

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process for which a suitable screen can be devised. In addition to the generation of loss-of-function insertion mutations, the transposons used to generate the strain library have attributes which facilitate additional downstream genetic studies.

2. CONSTRUCTION OF THE TRANSPOSON MUTANT COLLECTION Two transposon Tn5 derivatives, ISphoA/hah and ISlacZ/hah, were used to generate the mutant library (Figure 1).1,6 The transposons generate alkaline phosphatase or β-galactosidase translational gene fusions if inserted in target genes in the appropriate orientation and reading frame (Figure 2). Such inframe insertions may be converted into 63 codon insertions (“i63”) by loxP X loxP recombination catalyzed by Cre recombinase (Figures 1 and 2). The resulting sequence encodes an internal tag which includes an inﬂuenza hemagglutinin epitope and a hexahistidine metal afﬁnity puriﬁcation motif, which may facilitate further studies of individual gene products.1 The recombination event also eliminates the tetracycline resistant determinant of the transposon, making it possible to reutilize the marker in constructing multiple mutants.4 As summarized in the process schematic (Figure 3), transposon insertions were generated in P. aeruginosa PAO1 (from L. Passador and B. Iglewski, University of Rochester) by mating the strain with either of two Escherichia coli donors carrying conjugation-proﬁcient transposon delivery suicide plasmids derived from pUT.5 The mutagenized cultures were plated on large bioassayscale L agar plates containing tetracycline (to select for transposon insertions), chloramphenicol (to select against donor cells), and chromogenic indicator (5-bromo-4-chloro-3-indolyl galactoside [Xgal] or 5-bromo-4-chloro-3-indolyl phosphate [XP]) to detect hybrid proteins.6 Colonies were arrayed into 384well plates using a Qpix robot (Genetix Ltd.). The robot arrays a 384-well plate in about 15 min, and can array colonies into several 384-well plates from a single bioassay plate while running unattended. In our experience, an expert technician requires at least an hour to array a single 384-well plate, and the risk of cross-contamination and other errors is considerably greater than with robotic arraying. In the arraying step, we generally used colony selection criteria that were as conservative as possible to help ensure that unique colonies were picked and that “fake” colonies were avoided. For plates on which colonies were scarce, it was necessary to relax the criteria in order to pick as many colonies as possible, a practice which typically resulted in a greater number of duplicate picks (due to overlapping images guiding the picking) and to a larger number of blank wells due to recognition errors. Even given these complications, automated picking is

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ISphoA/hah (4829 bp) P

‘phoA

tet

loxP

ISlacZ/hah (6163 bp) P

‘lacZ loxP

tet loxP

i63 insert (180 bp)

loxP Figure 1. Transposon derivatives. The structures of transposons ISphoA/hah and ISlacZ/hah are diagrammed, as is the structure of the i63 insertion element generated by loxP X loxP recombination from either transposon. Sequences derived from IS50 are represented as ﬁlled rectangles. The sequences corresponding to different parts of ISphoA/hah are (in bp): IS50 outside end 1–51; loxP, 66–99; ‘phoA, 116–1448; tet, 2123–3310; loxP, 4714–4747; IS50 inside end, 4810–4829. The sequences in bp corresponding to different parts of ISlacZ/hah are: IS50 outside end,1–51; loxP, 66–99; “lacZ, 126–3170; tet, 3778–4965; loxP, 6049–6082; IS50 inside end, 6144–6163. The i63 insert carries a single loxP sequence at bp 66–99. Insertions of all three elements have nine bp duplications of target DNA at the insertion sites. When inserted in-frame, the i63 insertion encodes the following sequence: (SPTA)DSYTQVASWTEPFPFSIQGDLITSYNVCYTKLLIKHHHHHHYPYDVPDYARDPRSDQET(VADEG)XX, where the residues in parentheses are alternative possibilities encoded in part by target gene sequences, “X” refers to residues encoded entirely by tare gene sequences duplicated at the insertion site, and the hemagglutinin epitope is underlined. The DNA sequences of the three elements are available at: http://www.gs.washington.edu/labs/manoil/ index.htm.

essential in constructing a collection such as this consisting of tens of thousands of strains. During picking, we attempted to select only white colonies for some plates, and only blue colonies for other plates, although the robot occasionally made “incorrect” color assignments. When picking blue colonies, we grew

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Figure 2. Generation of gene fusions and internal tags by transposon insertion. The diagram represents the generation of a β-galactosidase and alkaline phosphatase translational gene fusions by ISphoA/hah and ISlacZ/hah insertion and the conversion of such insertions into i63 insertions by Cre recombination. Transposon mutagenesis of P. aeruginosa was carried out through conjugal transfer of a suicide plasmid (pCM639 or pIT2) using an E. coli donor.6 LoxP X loxP recombination may be induced through the conjugal introduction of a nonreplicating plasmid carrying cre.1

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‘phoA or ‘lacZ

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tet

PA01 Genome

Selection: Plating on agar containing antibiotics and chromogenic indicator to select cells with transposon insertions and identify those expressing active gene fusions (~1000 colonies / plate) Mutagenesis: Conjugation of PAO1 with donor strain carrying transposon on suicide plasmid (~50 matings)

Mapping: 384 well PCR and sequencing Automated analysis: quality and crossmatch to position insertions in genome Arraying: Robot-assisted colony selection and arraying into 384-well microtiter plates (42,240 colonies arrayed)

Database Construction: Well-by-well correlation of mapping and phenotype results (Filtering to remove siblings and sequencing failures, sequencing and mapping quality assessments, phenotype characteristics, plate and well address)

Phenotyping: Assessment of phenotypes after spotting mutant on appropriate media Interactive viewer: Positions of insertions in genome

Figure 3. Generation, analysis, and maintenance of the P. aeruginosa PAO1 mutant library. The steps used to generate transposon insertions, amplify insertion junction fragments, sequence the fragments, and assign insertion sites to the P. aeruginosa genome are summarized.

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plates to near-conﬂuence, in order that blue colonies stood out against a white colony background and were easier for the robot to recognize. Although this tactic probably increased the frequency at which arrayed mutants were contaminated by adjacent cells, streak tests of representative samples on indicator indicated this contamination was not a major problem. High throughput methods were essential for sequence-mapping and storing the mutant collection.6 The methods utilized were originally developed for sequencing genomes, in which low quality reads were efﬁciently screened out, and individual strains stored in glycerol plates were rarely re-used. By utilizing a 384-well format, the volumes of reagents and associated costs of PCR and sequencing were minimized. In addition, the 384-well format allows for efﬁcient storage of all of the strains. However, the spatial constriction of this format also presents difﬁculties for P. aeruginosa, since the cells often stick to each other, forming ﬁlms at the surfaces of some wells. When using a 384-pin replicator to distribute cells from such a culture, large clumps of cells may stick to a pin, forming a globule that is large enough to contaminate adjacent wells upon inoculation. This property also added to the difﬁculty of carrying out PCR.6 We found that the problem was reduced if partially thawed glycerol stocks were used as a source of template in PCR reactions and for inoculating replica plates. The mutant collection consists of 111 plates (384 strains/plate) and may be stored comfortably on one shelf of a standard −80◦ freezer. Optimizing conditions for long-term storage of the strains and replication if the library is continuing. It is our experience that Pseudomonas strains stored in glycerol at 80◦ C for long periods lose viability, and it has been suggested that DMSO cultures survive better (R. Hanco*ck, personal communication). We maintain several copies of the collection in separate locations. The original strains are kept as pristine as possible and a rotating stock of replica plates is produced for purposes of distributing strains, which requires repeated free-thaw cycles. Mapping of the strains was made possible by using the reference genome sequence for P. aeruginosa PAO1.8 DNA fragments which included transposon insertion junctions were ampliﬁed and sequenced using a semi-degenerate PCR scheme,6 as described in detail at http://www.genome.washington.edu/UWGC/ pseudomonas/pdf/Supplementary Methods.pdf A PERL script, illustrated as a ﬂow chart in Figure 4, was used to crossmatch the junction sequences against the transposon sequence and the P. aeruginosa genome, and then to determine the orientation and position of the insertions relative to annotated open reading frames. Data from the collection were stored in a Microsoft Access database. Visual Basic code was written to determine the number of unique hits (and to screen out duplicate hits), and to determine the number of cases of discrepancies (for strains that had been re-sequenced). A subset of these data was incorporated into an Oracle database for access by outside investigators (see below).

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Sequencer output: chromatogram traces

Phred analysis

Output: file with junction fragment Sequence with quality scores Input: reference transposon sequence Crossmatch compares junction and transposon sequences

Output: file with transposon sequence removed Input: Reference genome sequence

Output: position of transposonAdjacent sequence In genome Input: Reference Annotation Table

Final output: file with assignment of Insertion to annotated ORF Figure 4. Assignment of transposon insertions to the P. aeruginosa genome sequence. The ﬂow chart summarizes the computational steps used to position transposon insertions in the P. aeruginosa genome. In many cases, the quality of the junction fragment sequence was insufﬁcient to allow the transposon end to be recognized, and other parts of the sequence were used to make an (approximate) assignment. The Phred and Crossmatch algorithms have been described.2,3

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Table 1.

Makeup of the P. aeruginosa mutant library.

Mutants Arrayed Insertions Mapped Mapping Success Rate Identical insertion locations Unique insertion locations Insertions within ORFs Insertions between ORFs ORFs hit internally ORFs never hit internally Average hits per ORF In-frame insertion locations Reporter-active (blue colony) in-frame insertions ORFs with in-frame insertions Mutants scored for colony phenotype Twitching (swarming) – defective mutants ORFs with twitching (swarming) – defective mutations Auxotrophic mutants ORFs with auxotrophic mutations

42,240 36,154 80% 4423 30,100 27,263 2837 4892 678 5.05X 4823 2546 2582 42,240 709 360 813 546

3. COMPOSITION OF THE MUTANT COLLECTION The collection is made up of 42,240 strains. Of these, 34,837 have insertions mapped to a location in the P. aeruginosa genome, a success rate of 82%. Once duplicate records and siblings were eliminated, 30,100 unique insertion locations were identiﬁed (Table 1). Approximately 90% of insertions were within ORFs, corresponding well to the fraction of the genome predicted to be coding.8 Reporter gene activities of the strains based on colony color on chromogenic indicator media are summarized in Table 2, and indicate that Table 2. Results of reporter active–inactive (blue–white) scoring.

Unique Insertions Reporter active (blue colony) Reporter inactive (white colony) Total ORFs with ≥1 insertion ORFs with ≥1 active insertion ORFs with ≥1 inactive insertion ORFs with both active and inactive insertions Unique in-frame insertions Active in-frame insertions Inactive in-frame insertions ORFS with in-frame insertions ORFS with active in-frame insertions ORFs with inactive in-frame insertions ORFS with both active and inactive in-frame insertions

ISphoA/hah insertions

ISlacZ/hah insertions

15,063 1973 13,090 4313 954 4206 847 2821 1387 1434 1761 738 1167 144

15,037 2416 12,621 4430 1436 4221 1227 2002 1159 843 1432 768 729 65

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Figure 5. Searching the P. aeruginosa mutant collection. The window shown (at http://www. genome.washington.edu/UWGC/index.cfm) is used to search the mutant library for strains of interest. The example shows the input for a search for mutants in mex family genes. Clicking the “Find mutant library” button leads to the window shown in Figure 6.

roughly half of the in-frame insertions generated are expressed under the isolation conditions. 678 ORFs were never hit by a transposon insertion, and are called “candidate essential genes.”6

4. MUTANT DISTRIBUTION A primary motivation for assembling the P. aeruginosa library was to create a resource of mutants for researchers worldwide. Researchers may use reverse genetic techniques, such as bioinformatic searches, microarray data, or proteomics data to identify genes of interest in P. aeruginosa. Once a list of interesting genes is generated, the corresponding mutant strains may be obtained, saving time and resources that would otherwise be required for constructing the mutants. To facilitate the distribution of mutant strains, we created a publicly accessible website at http://www.genome.washington.edu/UWGC/index.cfm. Researchers may search for strains by ORF number, gene name or gene abbreviation. (The transposon insertion positions are also accessible though the Pseudomonas.com website in the Gbrowse viewer.) An example of a search for

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mutants affecting the mex (Multidrug efﬂux) family of genes7 is illustrated in Figures 2 and 6 and summarized in Table 6. The requestor can search for mutants affecting a family of genes by selecting the appropriate gene abbreviation (“mex”) and the “like” function instead of the “exactly matches” function. (In searching for insertions in speciﬁc genes, the most accurate way to search is by PA ORF number, since gene names may change between updates.) Requestors can register their information, and then activate a search in which mutants of interest may be saved for an order to be placed (Figure 6). We prepare mutants for distribution by streaking the appropriate strain onto an L agar plate, and after growth making a stab using cells from a heavy part of the streak (rather than from a single colony). Immediately after receipt, we recommend that each strain be streaked out on tetracycline selective, and that a representative sample from the thickest part of the streak be stored frozen. This is to preserve all strains in a streak in the event of multiple strains are pretent. We also strongly recommend that the identity of all strains be conﬁrmed prior to use (see below). In order to distribute mutant strains without restriction, we require shipping expenses be paid by individuals making requests. All other costs are carried by the University of Washington Genome Center. We ask that requestors provide an account number for Federal Express (the only authorized shipper for transporting biological hazards in the US) when submitting their requests. For international shipments, we also require that requestors determine the necessary import permits required by their countries for dangerous goods. Up to 50 strains may be placed in a single shipping container, and shipping costs at present (October, 2004) are approximately $40 per order for domestic orders and $150 for international orders.

5. CONFIRMATION OF MUTANT IDENTITY Some wells of the mutant library plates contain more than one strain, a consequence of the high throughput methodology used to assemble and replicate the collection. Accordingly, it is essential that the strains obtained from the collection be conﬁrmed prior to experimental use. After receiving a strain we recommend that cells from the stab be streaked to L agar, followed by assay of several individual colonies using PCR. Two tests are necessary, one to show that the intact gene corresponding to the insertion is absent, and a second to show that the transposon insertion location is approximately correct. For each gene of interest, primers ﬂanking the gene are designed (“f ” and “r” in Figure 7), and used to test ampliﬁcation of the wild-type fragment using the mutant strains and the wild-type parent. Depending on PCR conditions, no fragment or a fragment corresponding to a very large product will result from a correctly assigned mutant strain. Assigning the position of a transposon insertion requires a transposonspeciﬁc primer (either “Hah minus 138” (5 -cgggtgcagtaatatcgccct-3 ) for

Figure 6. Requesting strains. The ﬁrst four entries from the list of mutants returned in response to the query illustrated in Figure 5 are shown. A summary of the total list (97 hits in 10 genes) is presented in Table 6. To request a particular strain, the corresponding box is checked (strain 3235 in the example shown). As indicated, strain 3235 is an in-frame (+2) insertion of ISlacZ/hah at bp 364 out of 444 in mexR. The mutant forms LacZ+ (blue) colonies on L agar containing X-Gal indicator. After strains of interest from the list have been selected, the “Submit mutant strains” button is clicked, and the next screen will show “Your mutant request has been saved”. Additional searches and requests may then be carried out, and when the process has been completed, the “Submit my mutant request” button is clicked and the compete request is submitted.

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Michael A. Jacobs and Colin Manoil Transposon primer

Transposon, oriented parallel to gene Flanking Primer f Gene X, oriented 5’ to 3’ Flanking Primer r Transposon primer

Transposon, oriented anti-parallel to gene Flanking Primer f Gene X, oriented 5’ to 3’ Flanking Primer r

900 bp 800 bp 700 bp 600 bp 500 bp 400 bp 300 bp 200 bp 100 bp

Figure 7. Verifying mutant identity. A summary of the procedure used to verify the identify of mutants obtained from the P. aeruginosa mutant collection is presented. The top of the ﬁgure represents the two possible orientations of an ISlacZ/hah transposon in a gene and the primers (two gene-speciﬁc and one transposon-speciﬁc) used for the analysis. The gel represented at the bottom corresponds to a (hypothetical) PCR analysis of two single colonies derived from a streak from a stab of strain 3235 which has a lacZ transposon insertion orientel parallel to ORF PA 0424 (Figure 6). Primers amplifying the entire mexR gene (444 bp) plus 40 bp (20 bp for each primer) would generate a PCR product of 464 bp (lane 2). If the colony carried the expected insertion, ampliﬁcation using primes f and r would not yield a wild-type sized product (lane 3) nor would a reaction using ﬂanking primer r and the transposon primer. However, ampliﬁcation with the f primer and lacZ 148 would generate a 552 bp fragment (364 bp between the start of the gene, 148 bp between lacZ 148 and the junction, and 2 primers of 20 bp each). Lanes 6 and 7 represent a pattern sometimes observed in which both wild-type and insertion fragments are observed, perhaps due to insertion of the transposon in one copy of a genomic tandem duplication.

ISphoA/hah insertions or “lacZ 148” (5 -gggtaacgccagggttttcc-3 ) for ISlacZ/ hah insertions). The appropriate transposon primer is used in conjunction with one of the ﬂanking primers used in the ﬁrst PCR test, depending on the orientation of the transposon relative to the gene (Figure 7).

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Table 3. Mutants requested (by functional category). ORF function Chemotaxis Motility and attachment Secreted factors Protein secretion/export apparatus DNA replication, recombination, modiﬁcation, and repair Cell wall/LPS/capsule Antibiotic resistance and susceptibility Adaptation, protection Transcriptional regulators Two-component regulatory systems Related to phage, transposon, or plasmid Chaperones and heat shock proteins Membrane proteins Fatty acid and phospholipid metabolism Transport of small molecules Translation, post-translational modiﬁcation, degradation Hypothetical, unclassiﬁed, unknown Energy metabolism Carbon compound catabolism Central intermediary metabolism Amino acid biosynthesis and metabolism Putative enzymes Cell division Biosynthesis of cofactors, prosthetic groups, and carriers Transcription, RNA processing, and degradation Nucleotide biosynthesis and metabolism

Strains available 411 615 493 372 418 340 165 430 1949 1030 443 275 259 369 4851 503 12,547 1061 735 458 1280 2905 62 412 226 236

Strains requested 186 264 167 117 121 95 45 107 482 213 78 41 36 46 541 55 1297 107 68 37 96 215 4 16 3 1

Proportion (%) 45 43 34 31 29 28 27 25 25 21 18 15 14 12 11 11 10 10 9 8 8 7 6 4 1 <1

6. MUTANTS DISTRIBUTED FROM SEATTLE As of October 15th, 2004, 4575 strains have been shipped to 127 researchers corresponding to 79 cities in 15 countries. When the strains are sorted by functional category, independent of ORFs, it is clear that some categories are far more popular than others. Chemotaxis, motility and attachment, and secreted factors are the most frequently requested (Table 3), likely due to their known involvement in virulence and recognition by host immune responses. When the collection is viewed in the context of individual genes, the number of genes with insertions is roughly proportional to their representation by functional category in the genome (Table 4). In the most popular categories, mutations in all of the genes with insertions (“available” genes). The ten “most popular” genes include three regulators and one gene needed for the synthesis of an extracellular regulatory molecule (Table 5).

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Table 4.

Michael A. Jacobs and Colin Manoil

Mutants requested (by fraction of genes in different functional categories).

Gene function Antibiotic resistance and susceptibility Chemotaxis Motility and attachment Related to phage, transposon, or plasmid Cell wall/LPS/capsule DNA replication, recombination, modiﬁcation, and repair Two-component regulatory systems Protein secretion/export apparatus Secreted factors Adaptation, protection Transport of small molecules Membrane proteins Chaperones and heat shock proteins Fatty acid and phospholipid metabolism Transcriptional regulators Central intermediary metabolism Energy metabolism Hypothetical, unclassiﬁed, unknown Translation, post-translational modiﬁcation, degradation Putative enzymes Carbon compound catabolism Amino acid biosynthesis and metabolism Cell division Biosynthesis of cofactors, prosthetic groups, and carriers Transcription, RNA processing, and degradation Nucleotide biosynthesis and metabolism Totals

Number of genes

% of genes

Genes with insertions

Genes with insertions requested

% genes with insertions requested

0.3

100

45 67 62

0.8 1.2 1.1

45 65 54

45 55 41

100 85 76

86 81

1.5 1.5

56 66

39 45

70 68

116

2.1

113

1.5

60 66 559 43 52

1.1 1.2 10.0 0.8 0.9

55 57 533 39 44

33 30 263 18 20

60 53 49 46 46

1.0

403 65

7.2 1.2

376 58

161 19

43 33

170 2381

3.1 42.7

135 2120

42 592

31 28

149

2.7

457 134 151

8.2 2.4 2.7

432 123 138

104 28 31

24 23 23

26 132

0.5 2.4

15 88

3 11

20 13

0.8

1.1

4892

1751

5570

Genome-Wide Mutant Library of P. aeruginosa

Table 5.

135

The most popular genes in P. aeruginosa.

PA ORF number

Times requested

Gene name

PA4525 PA1092 PA1003 PA3477 PA3790 PA3622 PA0652 PA3841 PA3930 PA3724 PA0996

30 30 26 25 23 23 23 21 18 17 17

pilA ﬂiC pqsR (mvfR) rhlR oprC rpoS vfr exoS cioA lasB pqsA

Table 6.

Function Motility and attachment Motility and attachment Transcriptional regulators; Quinolone signal response Transcriptional regulators; Quorum sensing Transport of small molecules Transcriptional regulators Transcriptional regulators Secreted factors (toxins, enzymes, alginate) Energy metabolism Secreted factors (toxins, enzymes, alginate) Quinolone signal response

Mex mutants in the P. aeruginosa mutant library.

Gene

PA ORF

Hits

mexR mexA mexB mexH, mexY, amrB mexG, mexX, amrA mexZ amrR mexE mexF mexD mexC

PA0424 PA0425 PA0426 PA2018 PA2019 PA2020 PA2493 PA2494 PA4598 PA4599

3 9 19 10 1 2 5 15 24 9

7. WHOLE LIBRARY PHENOTYPIC SCREENS We found that it is feasible to carry out phenotypic screens of the entire mutant library. On the basis of comparisons with earlier studies of two well-deﬁned processes (twitching or swarming motility and growth on minimal medium), the approach appears to provide virtually complete lists of genes in which loss-of-function mutations confer the phenotypes of interest.6 The collection has more recently also been screened for mutants showing reduced growth under anaerobic conditions and altered sensitivity to the antibiotic tobramycin (I. Thaipittsukul; S. Lee, unpublished results). In each case, the protocol followed was to spot small aliquots of each mutant onto appropriate medium using a 384-pin pronging device, followed by incubation, digital imaging, and one or more rounds of scoring by visual inspection.

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No tobramycin

+ sublethal tobramycin

Figure 8. Screen for increased tobramycin sensitivity. The growth of mutants from one of the 384well mutant library plates is shown on L agar devoid of tobramycin (top) or containing a sublethal concentration of tobramycin (1 µg/ml) (bottom). The position of one mutant appearing to be highly tobramycin sensitive is indicated. Note that several other mutant spots also show reduced growth in the presence of tobramycin.

An example of the results from the tobramycin resistance screen are shown in Figure 8. Although cells in all 384 positions grew on the no tobramycin plate, one failed to grow and several show reduced growth on agar containing a sublethal concentration of the antibiotic, indicating hypersensitivity. Additional studies are required to determine which of the gene-phenotype associations indicated by results such as these are valid, including examination of the other insertion alleles of the gene.

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Our experience with whole library screening has led to several general conclusions: r The existence of multiple alleles for most genes largely compensates for the low-level contamination of some wells since alleles of the same genes from uncontaminated wells can be phenotypically identiﬁed even if the contaminated mutants cannot. r The fraction of mutations in a particular gene which are identiﬁed in a given screen is a function of the strength of the phenotype and the extent to which contaminating cells interfere with recognition. For example, mutations leading to tobramycin resistance were very efﬁciently identiﬁed, presumably because the existence of sensitive contaminants did not interfere with resistant cell growth. In contrast, twitching (swarming)-deﬁcient mutants were less efﬁciently detected, presumably because the presence of small numbers of motile bacteria obscured the sharp colony edge of nonmotile mutants. r Setting a low threshold for including potential mutants showing to a phenotype helps associate the largest number of genes with the property of interest. The corresponding increased number of false identiﬁcations tends to be compensated for by the redundancy of mutants in the collection, since only the genes for which a signiﬁcant fraction of alleles are detected are typically considered promising for further analysis. r Saving permanent images of phenotyping plates makes it possible to re-examine results after an initial screen has been completed. Our general experience has been that as a ﬁrst screen has progressed, the ability to recognize more subtle phenotypic variants has increased, so that re-screening has identiﬁed mutants missed in the ﬁrst screen. r For some screens, it is helpful to spot duplicate plates to provide two independent tests of behavior under a particular condition. This practice allows an immediate check on the reproducibility of the phenotype observed for a given mutant, and is particularly valuable for phenotypes for which variability in the number of cells transferred in the original spotting step signiﬁcantly affects scoring.

8. CONCLUSIONS The P. aeruginosa mutant library appears to be a useful resource both as a source of mutants to analyze gene associations revealed using other techniques and directly for comprehensive screens for particular phenotypes. Increased automation in such phenotyping should substantially increase the utility of such screens in the future.

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ACKNOWLEDGMENTS We gratefully acknowledge Sam Lee for providing the data shown in Figure 8, Elizabeth Sims for shipping and maintaining the strain collection, Gregory Alexander for construction and management of the web site, Stephen Ernst for database utility design, and Iyarit Thaipisuttikul, Sam Lee, Rajinder Kaul, and Maynard Olson for helpful discussions. This work was supported by grants from the Cystic Fibrosis Foundation.

REFERENCES 1. Bailey, J. and Manoil, C., 2002, Genome-wide internal tagging of bacterial exported proteins. Nature Biotechnol., 20:839–841. 2. Ewing, B., Hillier, L. et al., 1998, Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res., 8:175–185. 3. Ewing, B. and Green, P., 1998, Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res., 8:186–194. 4. Gallagher, L., McKnight, S., Kuznetsova, M., Pesci, E., and Manoil, C., 2002, Functions required for extracellular quinolone signaling by Pseudomonas aeruginosa. J. Bacteriol., 184:6472–6480. 5. Herrero, M., de Lorenzo, V., and Timmis, K.N., 1990, Transposon vectors containing nonantibiotic resistance selection markers for cloning and stable chromosomal insertion of foreign genes in gram-negative bacteria. J. Bacteriol., 172:6557–6567. 6. Jacobs, M.A., Alwood, A., Thaipisuttikul, I., Spencer, D., Haugen, E., Ernst, S., Will, O., Kaul, R., Raymond, C., Levy, R., Chun-Rong, L., Guenthner, D., Bovee, D., Olson, M.V., Manoil, C., 2003, Comprehensive transposon mutant library of Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. USA, 100:14339–14344. 7. Poole, K., 2004, Efﬂux pumps, pp. 635–674. In J.-L. Ramos (ed.), Pseudomonas vol. 1, Chapter 21. Plenum Publishers, New York. 8. Stover, C.K. et al., 2000, Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature, 406:959–964.

BIOGENESIS AND FUNCTION OF TYPE IV PILI IN PSEUDOMONAS SPECIES Cynthia B. Whitchurch

Department of Microbiology Monash University, Clayton Victoria 3800, Australia

Key Words: ﬁmbriae, twitching motility, natural transformation, infection, adhesion, bioﬁlm

1. INTRODUCTION Type IV pili or ﬁmbriae are non-ﬂagellar, ﬁlamentous surface appendages that are associated with a number of biological activities in bacteria. These processes include a form of surface translocation termed twitching motility; bacteriophage sensitivity; attachment to biotic (bacteria, plant, animal) and abiotic surfaces; bioﬁlm development; and the uptake of naked DNA by natural transformation. Many of these biological functions are reliant on the ability of these structures to extend and retract. Type IV pili/ﬁmbriae are found throughout the eubacteria. They are produced by many species of Gram-negative bacteria and have been most extensively studied in Pseudomonas aeruginosa, Neisseria gonorrhoeae, N. meningitidis, Dichelobacter nodosus, Moraxella bovis, Myxococcus xanthus, and Synechocystis species PCC 6803, enteropathogenic Eschericia coli (EPEC) and Vibrio cholerae.98,99,143 Type IV pili/ﬁmbriae are also produced by some Gram-positive bacteria including Ruminococcus albus163,168 and probably Pseudomonas, Volume 4, edited by Juan-Luis Ramos and Roger C. Levesque C 2006 Springer. Printed in the Netherlands.

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Cynthia B. Whitchurch

Streptococcus sanguis100 though evidence for the latter awaits conﬁrmation via molecular analyses. The nomenclature “type IV” is derived from the classiﬁcation scheme outlined by Ottow in 1975 in which he grouped non-ﬂagellar ﬁlamentous structures into six types based largely on morphological characteristics.156 Interestingly, throughout this nomenclature system Ottow reserved the use of the term “pili” to speciﬁcally refer to conjugative sex pili and used the term “ﬁmbriae” for all other non-ﬂagellar ﬁlamentous surface organelles. The term “ﬁmbriae” was also favored by other investigators72,82 however, historically, the terms “pili” and “ﬁmbriae” have been used interchangeably. In reference to the non-ﬂagellar ﬁlamentous structures that were classiﬁed by Ottow as “Group IV,” the terminology “type IV pili” and its abbreviation “tfp” have become very much the vogue in recent years and will be adopted in this review. As deﬁned by Ottow (1975) type IV pili are “. . . ﬂexible, rod-like, polarly inserted ﬁmbriae.” The tfp of P. aeruginosa were amongst the ﬁrst of this class described in bacteria.20,21,25,82,104,226 P. aeruginosa tfp have a diameter of 5–6 nm25,50,77,226 and a hollow core of 1.2 nm.77 Due to their retractile nature, the length of these structures varies signiﬁcantly, but on average are about 1–4 µm in length22,24,27 although they can range in length up to 10 µm.25,226 A number of studies have examined tfp production by P. aeruginosa under different culture conditions and have shown that P. aeruginosa tfp are produced throughout plate culture;22,119,209,226 in logarithmic broth culture with gentle agitation;22,25,226 and by stationary phase bacteria when cultured without aeration or with only gentle agitation22,119,209,226 whereas vigorously shaken stationary phase P. aeruginosa cultures do not produce detectable tfp.22,119,209,226 Type IV pili have also been identiﬁed in other Pseudomonas species including P. syringae,180–183 P. stutzeri84,98 and P. ﬂuorescens138 (see Section 2.6). Historically, however, P. aeruginosa has served as one of the primary model organisms for the investigation of tfp and its associated functions in bacteria. It is for this reason that this chapter will largely focus on the tfp of P. aeruginosa. This chapter will review the current state of knowledge relating to the structure, biogenesis, and function of the tfp of the genus Pseudomonas and will also highlight advances made in the study of these structures in other type IV piliated bacteria.

2. STRUCTURE AND BIOGENESIS OF TYPE IV PILI By deﬁnition, type IV pili are long, ﬂexible ﬁlaments attached at the poles of the bacterial cell.156 In stark contrast to the relative simplicity of the external pilus ﬁber which is composed of several thousand copies of a single protein subunit,81,159 the type IV pilus structure located within the bacterial cell wall

Biogenesis and Function of Type IV Pili in Pseudomonas Species

141

is a sophisticated multimeric protein machinery that mediates assembly and retraction of the extracellular tfp ﬁlaments and which shares many similarities to the type II protein secretion systems and archeal ﬂagella.162 The regulation of tfp biogenesis and function is also extremely complex involving the integration of numerous regulatory systems. To date, nearly 40 proteins have been identiﬁed that are involved in the biogenesis, function, and regulation of tfp in P. aeruginosa.

2.1. The Major Subunit PilA The extracellular type IV pilus ﬁber is comprised of several thousand copies of a single subunit protein termed pilin or PilA in P. aeruginosa. P. aeruginosa PilA and related pilins are synthesized as a precursor with a short, basic, highly conserved N-terminal leader sequence that is removed by endoproteolytic cleavage between an invariant glycine residue and a phenylalanine that is then N-methylated in the mature protein80,152,157,161,192,213 (Figure 1). Type IV pilin proteins from diverse species are highly conserved across the leader peptide and approximately the ﬁrst 30 residues of the mature protein (Figure 1). This domain is highly hydrophobic and is thought to be involved in subunit– subunit interactions in the assembled ﬁlament.50 This hydrophobic domain may also be involved in directing the pilin subunits to the inner membrane for processing by the endopeptidase PilD, and for accumulation of a subunit pool for ﬁlament assembly and pilin recycling during disassembly (see Sections 2.3 and 2.4). The remainder of the pilin molecule contains moderately conserved and hypervariable regions (Figure 1). Type IV pilin proteins can be grouped into two subfamilies, the classic type IVa pilins include those from P. aeruginosa, N. gonorrhoeae, D. nodosus, and M. bovis whereas the pilins from second subgroup include those of the toxin-coregulated pili (TCP) of V. cholerae and the bundle-forming pili (BFP) of enteropathogenic E. coli are classiﬁed as type IVb pilins (Figure 1a). The Type IVb pilin precursors are closely related to the type IVa pilins but are synthesized with longer leader peptides, have either methionine, valine or leucine rather than phenylalanine as the ﬁrst amino acid of the mature protein and are generally larger than the type IVa pilins. As shown in Figure 1b, the pilins of P. syringae, P. ﬂuorescens, P. stutzeri, and P. putida are closely related to that of P. aeruginosa and would be classiﬁed as type IVa. A conserved feature of the Pseudomonas pilin proteins is the presence of an intrachain disulphide bond loop (DSL) located at the far C-terminus of the molecule (Figure 1b). In P. aeruginosa the DSL has been shown to contain the epithelial cell-receptor-binding domain which, despite a high degree of primary sequence divergence between P. aeruginosa strains, is antigenically conserved and demonstrates conservation of receptor speciﬁcity (see Section 4.1).

L I I A

A D K T

Pa PAK PilA Ng MS11 pilin K Ec BfpA G Vc TcpA

G S T A A N D -

G G G G G G G G

G G N -

Pa PAK PilA Pa K122-4 PilA Pa PAO1 PilA Pa PA14 PilA Psy pv tomato PilA Pf PfO-1 PilA Pp KT2440 PilA Pst PilAI

A S S A F A A N

S E A L V T K T

M M M M M M M A

G V Y G

K K T M

S L E S

G G S G K P P A

G A A D D P

K K K T N K K Q

P K G D

K G N N

V A V L

P S P A G A A G

A D P V S

A A A A A K G M

K W V F

E K P I

N E M N

K A K P I P N K

I S C S A L

Q Q Q Q Q Q Q Q

N F N E

V Y F F

P G S S

N I N T L V A F

V V S A D I D T

K K K K K Q R K

K C I N

P V G S

L Q A I

K K A Q T L L D

K S K R T T V S

G G G G G G G G

G G S S

L K G F

K K T Q

G G T L T G G G

S S I V A N A T

F F F F F F I F

K Q S A

G E E P

T S S V

K A K G D Q K K

G A K W A V A D

T T T T T T T T

I P E A

V V L R

T A A A

I V V A T T A T

T T I N K N L E

L L L L L L L L

I V N A

A E N N

V V I L

I I I S C V L I

G P G A V A G G

I I I I I I I I

T T N A

A V V A

E T N T

M V

T T T Y S T T T

T K T Q G G G Y

E E E E E E E E

L R I E

D K G A

E E G Q

V K

L V L A L L L L

E D T A V T Q I

L L L L L L L L

T T T T

P -

A Y L T

S E

T S N S T T T N

D T A G T T P G

M M M M M L M M

R D S G

A -

L Y Y Y

K E

R R R G P R R R

N L -

I I I I I I I I

T D F V

N -

S L I R

I H

T K T V A T T

P -

V V V V V V V V

A D G G

A N N A

R N G G

M D

A T I -

A Q S A S A A I

V V V V V V V V

A N A G A A S A

T Y T G G T T T

A A A A A A A A

A T N V

N G N N

G H Q L

M N K

I I I I I I I I

D D D S A A T D

K D A A A Q A D

D V S I

K V T K

G T G

M N K K

G G G I A A S G

K I T T T N H S

I I I I V I I I

G A A K

L V A A

K S N

K T K T

L V V D G G G E

E G E S T C C T

G G G G G G G G

L D D S

G T F F

W W Y Y

A L Y G

W W W W S W W W

V F T K G T A S

I I I I I I I I

W A Q I

T A G A

S P S P

Q Q E Q

K N A G P S A S

P T Y Y A L I Y

L L L L L L L L

K K A A

I T Y I

E G A

K K K E

C C C C V C C C

L E V V V A T C

A A A A A A A A

C D A P

A M Y S

L -

G G G G

T K K A T K T A

G S G T N A A D

A A A A A T T A

T G K A

L L L V

D -

F F L M

S I S S W F T S

V T V S K S S V

I I I V V I I I

S K S S

K S T D

S -

T T S T

D T T D S S D T

A L E V M G G D

A A A A A A A A

D E T K

P S L G

T -

L L L L

Q K Q S Y G I L

A L P Q E K K L

I I I L I L L L

A N

G T -

I -

I I I L

D T D N T S E D

D D D I I V A D

P P P P P P P P

V R -

L -

E E E E

P A G -

A G A A T A A T

Q Q Q A S Q M A

Q I I L

N L L

V N L T

L L S V

T V -

N S N E A D D A

Y Y Y Y Y Y Y Y

D D T D

D N D T

K N N A

M M A I

A S -

K G K A T G G A

Q Q Q Q Q S T Q

E T P L

P E K Q

S T T D

I I M I

W S -

L K L T S T S D

N D N D N K N D

Q K A T

A I A A

G S S A

V V V V

G -

G S G G A G G G

Y Y Y Y Y Y H Y

D K A Q

T A A T

V I L L

T -

T Q V E A T S H

V T V T A Q Q T

G G C C

G G I A

A A A G

D -

I I I I I I I I

A A A I K A A V

T K V K

T V P A

I I L I

R -

A Q A T T T V E

R R R R K R R R

F H E H

A K S T

E A D S

I V A M

N -

L V V V A C C C

S T S A A A S S

I L A V

D L L L

D S N K

G G A G

P -

P D I F P L L A

G V G V Y V A A

K S T K

T L T T

P K T

L L V V

A -

D N E N N L V K

A T A T T T A A

DSL

M -

K T A T T T T T

E Q E R A K K N

P P A E

I S A I

P Y L

I I T V

L -

P A -

S R S E E A A A

G T A L

S D S

A A T S

T -

A K D A -

A A A G V G G A

C C C C

T G

A A A A

A -

D D S N -

L V L V L I L L

S R K K

T L

I V G G

G -

G G G V -

A S A G A A L A

R D N G

N V

A A V V

T -

G -

S E T L A E E E

N T T

I L M V

L -

N -

V V I A M A I I

D -

P P F T

K P -

I -

N S N A A S S T

F S A

Q A Y L

E P P A A K D A

P -

P A P S S A A P

D T P

L W L Y

Y Y Y A

Q N M R C D D K

A -

L L L A V L L G

A N F

T A N I

Q Q Q Q

T T A S -

I A T A T S A K

F Y F F V Y L Y

T T T T T V T I

V V

T R G I

Y Y A A

N -

K K K K K K K K

K K G

F R L A

N D S R

P P P P N T P P

A V G T -

T A T L A N A G

T A

M E T K

V T S I

K A K S G T K G

D E D L -

V A V I V F M F

Y F

G N S A

A A D D

G N G E Y S G K

I L I V G

G G -

C C C C V C C C

T V T F G

E E E D V E D E

M N

A S K G

G G A G

F G

S A N Q

R R S S

S P D R K P K S

L A F T -

E S E S C D L Q

K S

G A

E Q K N

N G G

R K N

T T T P -

A A S S A V R A

G V S M

V A

F L F Y -

L I L A A I L I

A S Q T

T G Q V -

S L S T Q N N N

S E N K

M K T Q -

R E R A Q A D E

Figure 1. Alignment of type IV pilin sequences. (A). Alignment of type IVa pilins of P. aeruginosa (Pa) and N. gonorrhoeae (Ng), and type IVb pilins of enteropathogenic E. coli (Ec) and V. cholerae (Vc). Similar residues are shaded. Arrow indicates the site of endoproteolytic cleavage of the prepilin sequence. (B) Alignment of pilins from P. aeruginosa (Pa), P. ﬂuorescens (Pf), P. syringae (Psy), P. putida (Pp) and P. stutzeri (Pst). Arrow indicates the site of endoproteolytic cleavage of the prepilin sequence. Similar residues are shaded. The C-terminal DSL is indicated. Alignments were performed R Accelrys (Software Inc.). using the CLUSTALW alignment tool in MacVector

W K I E T S K

Pa PAK PilA Pa K122-4 PilA Pa PAO1 PilA Pa PA14 PilA Psy pv tomato PilA Pf PfO-1 PilA Pp KT2440 PilA Pst PilAI

T I I N

A L S Q

Pa PAK PilA PaK 122-4 PilA Pa PAO1 PilA Pa PA14 PilA Psy pv tomato PilA Pf PfO-1 PilA PpK T2440 PilA Pst PilAI

Pa PAK PilA Ng MS11 pilin Ec BfpA Vc TcpA

Pa PAK PilA Ng MS11 pilin Ec Bf pA Vc Tc pA

A A A A

Pa PAK PilA Ng MS11 pilin Ec BfpA Vc TcpA M

Biogenesis and Function of Type IV Pili in Pseudomonas Species

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The full-length crystal structures of P. aeruginosa strain PAK and N. gonorroheae strain MS11 pilin as well as structures of N-terminal (1–28) truncations of the pilins from P. aeruginosa strains PAK and K122-4 and V. cholerae have been solved.5,51,78,93,160 These structures indicate that overall, both type IVa and IVb pilins share a similar ladle-like architecture with an extended N-terminal α helical spine and a C-terminal globular head domain which exposes the hypervariable regions of the pilin subunits to the solvent. The ﬁrst 28 residues of the N-terminal α helix are highly hydrophobic and are thought to be involved in packing of the pilin subunits into the ﬁber.160 The remainder of the α helix pack onto the globular head domain which confers many of the biological functions of the tfp including adhesion to epithelial cells, phage attachment, and antigenic variability.50 A recent survey of pilins from more than 290 environmental, rectal, clinical, and cystic ﬁbrosis (CF) isolates of P. aeruginosa has found that there are 5 distinct phylogenetic groups of P. aeruginosa pilin and that 4 of these are associated with a distinct accessory gene or set of genes that are located immediately downstream of pilA.127 About 30% of pilins identiﬁed in this survey are not post-translationally modiﬁed and include the PilA proteins of strains PAK, PAO1, and K122-4.127 The most common class of pilin alleles are associated with the previously identiﬁed accessory gene pilO,37 the product of which is responsible for glycosylation of the C-terminal serine residue of the pilin of P. aeruginosa strain 1244.37,38,46 To avoid confusion with the tfp biogenesis gene required for tfp assembly and which is also termed pilO (see Section 2.4), and to bring the nomenclature in line with that used for the other pilin accessory genes, Kus et al. have proposed that the 1244 pilA-associated accessory gene pilO should be renamed tfpO.127 It is presumed that the accessory genes associated with other pilA alleles are also responsible for post-translational modiﬁcation of the pilin subunit, though the nature of these modiﬁcations have yet to be determined.127

2.2. Structure of the Extracellular Tfp Filament In 1981, Folkhard et al.77 used X-ray diffraction to examine the structure of puriﬁed tfp of P. aeruginosa strains PAO1 and PAK.77 They determined that the X-ray diffraction patterns were best satisﬁed if the tfp were comprised of pilin subunits arranged in a helical symmetry of 4 subunits per turn with each turn having a pitch of 4.1 nm. At the time of these analyses, the pilin subunits of PAK and PAO1 were estimated to be 18–19 kDa based on mobility in SDS polyacrylamide gels and amino acid composition81,159 and Folkhard et al.77 determined that at high-subunit-packing density, 4 subunits per turn could be accommodated in the PAK and PAO1 tfp ﬁlaments.77 When more accurate estimations of pilin subunit size (∼15 kDa) were obtained from amino acid sequence analysis of PAK pilin193 , the helical symmetry of the PAK and PAO1

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tfp ﬁbers was reinterpreted to be 5 subunits per turn.224 Recently, however, computational modeling of the PAK pilus ﬁlament combining both the X-ray diffraction data of Folkhard et al.77 and the X-ray crystal structure of fulllength PAK pilin51 predicts that there is insufﬁcient space in the tfp ﬁlament to accommodate 5 subunits per turn without unacceptable steric clashes.50 This computational modeling approach does, however, predict that the P. aeruginosa PAK pilin subunits can be satisfactorily arranged in a right-handed one-start helix with 4 subunits per turn and a pitch of 4.1 nm.50 Also consistent with the structural and diffraction data is a model for the PAK tfp ﬁber in which pilin is arranged in a left-handed 3 start helix with 4 subunits per turn with a pitch of 12.2 nm per single-turn of a helix and strands separated by 4.1 nm.50 In either case it appears that at least in the tfp ﬁlaments of P. aeruginosa PAK, pilin subunits are arranged in a helical ﬁber at 4 subunits per turn. Thus it appears that the original model by Folkhard et al.77 may well have been accurate. There also remains some controversy regarding the polarity of the modeled tfp ﬁlament relative to the bacterial cell as it is unclear which end of the assembled ﬁlament models represents the distal tip and which is the base. The original N. gonorrhoeae tfp ﬁlament model upon which the subsequent P. aeruginosa ﬁlament models have been based, proposed that the long hydrophobic N-terminal domains might be inserted into the bacterial membrane.160 Recently, however, other investigators have proposed an alternate polarity to the ﬁlament model arguing greater accessibility to the DSL domain at the ﬁlament tip.93 To add to the confusion, the recently revized 4 subunit per turn P. aeruginosa ﬁlament model predicts greater solvent accessibility of the DSL domain in the original ﬁlament orientation.50 It is unclear at this time which polarity accurately reﬂects the biological arrangement of the tfp ﬁlament relative to the bacterial cell.

2.3. Retraction of Type IV Pili Type IV pili are associated with an astounding number of biological functions including bacteriophage sensitivity, natural transformation, translocation across solid surfaces via twitching motility, bioﬁlm development, and attachment to host cell surfaces. Many if not all of these functions are dependent upon the ability of tfp to retract. The retractile nature of type IV pili was ﬁrst proposed by David Bradley during his studies on the infection mechanisms of bacteriophage that specifically bind to the tfp of P. aeruginosa. In these studies, Bradley observed that tfp-speciﬁc bacteriophage were located at the bacterial cell surface at the junction of the pilus and the bacterial cell pole of wildtype P. aeruginosa cells.21–29 He also noted that for many phage types, adsorption resulted in an increase in both the average number of pili/pole and the average length of the

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tfp.22,23,25,26,30 Similar results were obtained with labeling experiments using pili-speciﬁc antisera.22 Bradley interpreted these observations as evidence that tfp are retractile and that tfp retraction was inhibited by either phage or antibody adsorption. Bradley also investigated the effects of phage or antibody adsorption to the tfp of a class of P. aeruginosa mutants that were resistant to tfp-speciﬁc phage and that appeared hyperpiliated by electron microscopy. With this class of mutants, tfp-speciﬁc bacteriophages were found to be distributed randomly along the pili, and phage or antibody adsorption did not result in signiﬁcant alterations in piliation levels. Bradley concluded from these observations that the tfp present on these mutants were non-retractile.22,23,28,30 During their studies with hyperpiliated bacteriophage φ6-resistant derivatives of P. syringae, Romantschuk and Bamford also concluded that the pili to which this bacteriophage binds are retractile.183 These φ6-speciﬁc pili were later conﬁrmed to be tfp by molecular analyses.180 Twitching motility is a mode of surface translocation demonstrated by many bacteria that possess type IV pili.98,99 In 1980, David Bradley proposed that the motive force for twitching motility was attributable to the retraction of tfp.29 This hypothesis was based upon his observations that P. aeruginosa mutants which either lacked tfp or possessed non-retractile tfp did not demonstrate twitching motility and that prevention of tfp retraction by adsorption of pili-speciﬁc phage or antisera was inhibitory to twitching motility.29 Bradley’s hypotheses that tfp are retractile and that tfp retraction is the motive force powering twitching motility were considered somewhat controversial at the time.99 However, both tfp retraction and its role in twitching motility have been conﬁrmed in recent years. Molecular analysis of the hyperpiliated, non-twitching, phage resistant P. aeruginosa mutants used by Bradley has demonstrated that these mutants contained small deletions in the gene pilT227,232 and it is now evident that PilT is a powerful molecular motor which provides the driving force for tfp retraction.145 In a beautiful study by Skerker and Berg, direct observation of extension and retraction of tfp in vivo was achieved for the ﬁrst time.206 In this study, P. aeruginosa cells were labeled with an amino speciﬁc ﬂuorescent dye and pilus function directly visualized via internal reﬂection microscopy. Using this technique tfp ﬁlaments were generally seen to emerge from only one pole of the cell and to extend and retract independently of one another. This study also conﬁrmed that cellular translocation during twitching motility is achieved through retraction and not extension of the type IV pilus as tfp that were attached to the quartz surface via their distal end were observed to retract and pull the P. aeruginosa cells forward toward the tethered end whereas pili extension was never observed to cause cellular translocation.206 Tfp-dependent social gliding motility in M. xanthus is equivalent to twitching motility seen in other type IV piliated bacteria.143,199 During

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examination of this motility on methylcellulose covered surfaces, Sun et al.215 noted that occasionally wildtype M. xanthus cells could be seen standing perpendicular to the surface tethered by the polar tfp. These cells were able to move vertically up and down until they were retracted to the surface.215 In contrast, vertically tethered cells of M. xanthus pilT mutants which possess non-retractile tfp, were never observed to move215 conﬁrming that tfp retraction is responsible for cellular motility and that PilT is essential for this process. Independent conﬁrmation that tfp retract and that tfp retraction provides the force that powers twitching motility has been obtained in series of elegant studies in which laser tweezers were used to measure the forces generated by retracting tfp of N. gonorrhoeae.140,145 N. gonorrhoeae pilT mutants were found to be incapable of generating retractile forces indicating that PilT is the molecular motor that powers tfp retraction. In wildtype N. gonorrhoeae, single pilus ﬁlaments were able to retract with forces measured at greater than 100 pN making PilT the strongest molecular motor described to date.140 The mechanism of tfp retraction is thought to occur via disassembly of the tfp ﬁlament into pilin subunit components. The rate of ﬁlament disassembly has been estimated to occur at about 1000 subunits/sec.145 It has been recently estimated that in the absence of pilin recycling, tfp biogenesis would require most of the protein synthesis capacity of the bacterial cell,144 thus it seems highly likely that pilin subunits are recycled into the tfp ﬁlament during successive rounds of tfp ﬁlament extension and retraction. Supportive evidence for this model comes from the studies of Skerker and Berg who observed that there was no apparent loss of ﬂuorescence intensity of the ﬂuorescently labeled P. aeruginosa tfp during cycles of extension and retraction.206 This observation suggests that the labeled pilin subunits are being recycled into newly assembled tfp. A recent study using electron microscopy and de-biotinylation protection assays in N. gonorrhoeae has demonstrated that tfp ﬁlament retraction involves translocation of the extracellular pilin subunits to pools in the cytoplasmic membrane.147 Thus it appears that during tfp retraction, pilin subunits are rapidly disassembled and reside in cytoplasmic membrane pools to be recycled into new ﬁlaments, thereby providing enormous energy conservation for the cell.

2.4. Components of the P. aeruginosa Tfp Structure and Biogenesis Machinery In addition to the major pilin subunit PilA, over 40 other proteins have been identiﬁed that are involved in the biogenesis, function, and regulation of tfp and twitching motility in P. aeruginosa (Table 1; Figures 2 and 3). In this section, proteins that are involved in the structure, assembly or mechanical function of P. aeruginosa tfp will be described. Section 2.5 will discuss genes involved in the regulation of tfp biogenesis and function.

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147

Table 1. Pseudomonas proteins involved in the biogenesis, function, and regulation of tfp a

P. aeruginosa protein

Proposed function

P. syringae pv. tomato str. DC3000

P. ﬂuorescens PfO-1

P. putida KT2440

Biogenesis and function PilA Major pilin subunit PilB ATPase – assembly motor PilC Pilus assembly PilD (XcpA) Prepilin peptidase FimT Pseudopilin FimU Pseudopilin PilV Pseudopilin PilW Pseudopilin PilX Pseudopilin PilY1 Retraction regulator PilY2 Unknown PilE Pseudopilin PilM Pilus assembly

39/50 79/80

36/49 78/89

39/52 Absent

73/87 79/87 28/44 31/47 35/71 33/55 38/66 24/39 Absent 62/81 85/93

74/86 68/82 27/42 29/47 36/70 40/59 32/66 25/39 Absent 35/51 82/90

PilN PilO

Pilus assembly Pilus assembly

73/86 74/85

68/83 74/82

PilP

Lipoprotein, PilQ assembly pilotin Secretin

72/87

61/78

72/83

72/82

ATPase – retraction motor ATPase – PilB/PilT modulator? Assembly Assembly Peptidoglycan remodeling? PMF energy transducer, component of TonB import pump ExbD hom*olog, component of TonB import pump

87/96

87/94

43/69 64/78 24/44 Absent Absent Absent 33/57 Absent Absent 32/48 31/53 (N-terminus only) 27/51 24/40 (fusion with PilP) 37/57 (fusion with PilO) 59/75 (C-terminus only) 50/74

Absent

62/81 88/94 45/58

64/80 88/95 47/60

55/71 Absent 43/54

69/83

72/84

68/84

60/77

62/79

62/74

62/77

60/76

Absent

77/86

79/87

Absent

PilQ PilT PilU PilF PilZ FimV TonB3

PA2982

Regulation PilS PilR

Sensor kinase; controls pilA transcription Response regulator; controls pilA transcription

(Continued )

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Cynthia B. Whitchurch

Table 1.

(Continued ) a

P. aeruginosa protein RpoN FimS (AlgZ)

AlgR

PilG PilH PilI PilJ PilK ChpA ChpB ChpC FimL Vfr

FimX Crc

RpoS Ppk a

Proposed function Sigma factor; controls pilA transcription Atypical sensor kinase; controls ﬁmT-pilE gene cluster transcription Response regulator; controls ﬁmT-pilE gene cluster transcription Chemosensory, CheY hom*olog Chemosensory, CheY hom*olog Chemosensory, CheW hom*olog Chemosensory, ligand binding MCP Chemosensory, CheR hom*olog Chemosensory, CheA/CheY hybrid Chemosensory, CheB hom*olog Chemosensory, CheW hom*olog Controls vfr transcription cAMP Binding transcriptional regulator; multiple targets Multidomain signal transduction protein Catabolite repression control; inﬂuences pilA, pilB transcription Stationary phase sigma factor Polyphosphate kinase

P. syringae pv. tomato str. DC3000

P. ﬂuorescens PfO-1

P. putida KT2440

84/93

85/93

86 /93

71/81

Absent

82/93

81/91

78/88

87/90

89/92

79/91

91/96

90/95

77/89

58/74

63/73

058/72

77/86

78/88

76/88

Absent

51/65

49/62

48/64

Absent

59/70

57/74

55/66

Absent

78/87

82/89

81/85

Absent

86/93

88/94

86/93

88/93

88/92

87/93

81/90

81/91

82/91

percent identity/percent similarity to P. aeruginosa PAO1 protein. Determined by BLAST analyses of genome sequences at NCBI (http://www.ncbi.nlm.nih.gov/sutils/genom table.cgi).

pilZ PA2982

pilU

pilA

pilF

pilQ

pilB

fimV

pilP pilO pilN

fimT fimU pilV pilW pilX

pilT

pilM

pilY1

pilC

pilY2 pilE

pilD (xcpA)

1 Kb

tonB3

Figure 2. Genes involved in the structure, assembly and mechanical function of type IV pili in P. aeruginosa are dispersed around the 6.3 Mb chromosome of PAO1.212 Genes are depicted by shaded boxes. Genes that confer resistance to tfp-speciﬁc bacteriophage when disrupted are depicted in dark shading. The direction of transcription is indicated by position of the box relative to the line (above is plus strand and below is minus strand).

vfr

rpoS

pilG pilH pilI

ppk

rpoN

pilJ

crc

fimX

chpA

pilK

1 Kb

pilR

algR fimS (algZ)

pilS

fimL

chpB chpC

Figure 3. Genes involved in regulation of type IV pili biogenesis and function in P. aeruginosa are dispersed around the 6.3 Mb chromosome of PAO1.212 Genes are depicted by shaded boxes. Genes that confer resistance to tfp-speciﬁc bacteriophage when disrupted are depicted in dark shading. The direction of transcription is indicated by position of the box relative to the line (above is plus strand and below is minus strand).

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The majority of the structural and biogenesis tfp genes are found in four main gene clusters on the P. aeruginosa PAO1 genome (Figure 2). Many of the tfp structural and biogenesis proteins are multiply hom*ologous to components of bacterial type II secretion systems. In recent years, it has become increasingly apparent that tfp, type II secretion systems and archeal ﬂagella are related machineries which are thought to be comprised of “pseudopilus-like” structures in the cell wall.162,195,220 Situated immediately upstream of pilA and in the opposite transcriptional orientation are pilB, pilC, and pilD each of which are absolutely required for tfp assembly.151 Mutants of pilB, pilC, and pilD do not produce surface assembled tfp, are non-twitching and resistant to tfp-speciﬁc bacteriophage. PilC is a polytopic inner membrane protein that is essential for tfp assembly though the exact role for this protein is unknown. PilD is a bifunctional enzyme that is required for both cleavage of the prepilin leader sequence and N-methylation of the N-terminal phenylalanine of PilA.213 PilD is also referred to as XcpA and is responsible for processing of the prepilin-like components of the type II secretion system of P. aeruginosa.7 PilB is predicted to be an NTPase that provides energy for pilus assembly and is hom*ologous to the molecular motor PilT that powers tfp retraction as well as to PilU which also appears to play a role in tfp retraction. Both pilT and pilU are situated together in a region of the genome separate from other tfp biogenesis genes (Figure 2). As noted above, loss of pilT renders the tfp of the mutant non-retractile and as a consequence these strains are hyperpiliated, non-twitching, and resistant to tfp-speciﬁc bacteriophage.227,232 In contrast, pilU mutants are hyperpiliated and non-twitching yet remain sensitive to these bacteriophage.232 This latter phenotype suggests that despite the hyperpiliated phenotype, the tfp of pilU mutants are sufﬁciently retractile to enable phage infection. The role of PilU in tfp biogenesis and function is unclear but this protein may serve to modulate the antagonistic activities of either PilB and/or PilT. PilT has recently been shown to be the molecular motor that powers tfp retraction and twitching motility in N. gonorrhoeae and is capable of producing forces exceeding 100 pN140,145 (see Section 2.3). PilT proteins from Aquifex aeolicus and Synechocystis species PCC6803 and the PilB protein from the plasmid R64 thin pili tfp systems have been experimentally demonstrated to have ATPase activity.101,155,190 Indeed PilB, PilT, and PilU belong to a large family of bacterial ATPases involved in tfp assembly and retraction, type II secretion, type IV secretion and DNA uptake.34,42,76,162,164,191 Members of this family are cytoplasmic proteins that are associated with the inner face of the inner membrane via protein–protein interactions with integral membrane components of the multimeric protein assembly.53,76,191 PilT and related proteins from type II and type IV secretion systems have been shown to oligomerise into large hexameric ring structures that are thought to change conformation upon ATP binding.79,177,196,242 It is not yet clear how these molecular

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machines harness the energy from ATP binding and hydrolysis to power the various biological functions associated with these systems. The third cluster of tfp structural and biogenesis genes encodes the pilinlike proteins FimT, FimU, PilV, PilW, PilX, and PilE (Figure 2). Each of these proteins possesses a prepilin-like N-terminal leader peptide which is presumably cleaved by PilD, though this has not been formally demonstrated. They also contain the signature hydrophobic N-terminal α-helical domain that is thought to be involved in protein–protein interactions and in directing the proteins to the inner membrane (see Section 2.1). It is possible that these pilin-like proteins assemble into a pseudopilus structure that spans the periplasm forming the base of the tfp structure. Alternatively they may be involved in initiating, modulating, or capping PilA assembly into the tfp ﬁlament. PilV, PilW, PilX, and PilE are each essential for tfp assembly, sensitivity to tfp-speciﬁc bacteriophage and twitching motility suggesting a crucial role in tfp assembly.2–4,188 Interestingly, ﬁmU mutants are non-twitching, do not produce detectable surface assembled tfp but retain sensitivity to the tfp-speciﬁc bacteriophage PO4, though the plaques produced are smaller and more turbid than wildtype,4 suggesting the presence of some tfp structures at the cell-surface sufﬁcient for phage infection. In contrast, FimT does not appear to be required for tfp assembly, PO4 phage sensitivity or twitching motility though it can functionally substitute for FimU to restore twitching motility to ﬁmU mutants.4 The exact roles for each of these pilin-like proteins in tfp assembly and function, and their intermolecular interactions have yet to be determined. Also located within this gene cluster are the genes pilY1 and pilY2 (Figure 2). Mutants of pilY1 are non-twitching, show no surface assembled tfp but have wildtype sensitivity to tfp-speciﬁc bacteriophage2 which suggests that these mutants produce some surface tfp sufﬁcient for phage binding and infection. PilY2 is a small protein that may play a subtle role in tfp biogenesis and is found exclusively in preparations of sheared surface pili suggesting association with the tfp ﬁlament.2 PilY1 is also found associated with sheared tfp but unlike PilY2, is mainly found in the membrane fraction. BLAST search analyses show that the C-terminal region of PilY1 is hom*ologous to the Cterminal regions of the PilC proteins of N. gonorrheae and N. meningitidis. The Neisserial PilC proteins have been recently found to regulate retraction of the tfp ﬁlament possibly by acting as a clip on the pilus ﬁlament.147 Given the hom*ology between the C-terminal domains of P. aeruginosa PilY1 and the Neisserial PilC proteins, it would be very interesting to determine if PilY1 functions in a similar manner to control tfp retraction. The fourth cluster of P. aeruginosa tfp assembly/structural genes encodes the proteins PilM, PilN, PilO, PilP, and PilQ (Figure 2). Mutations in these genes block surface assembly of tfp and confer a non-twitching, phage resistant phenotype.141,142 PilQ is a member of a family of bacterial integral outer membrane proteins termed secretins. Secretin family members are components of

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153

complex multicomponent protein machineries including the type II and type III secretion pathways, the machinery responsible for ﬁlamentous phage biogenesis, and tfp.13 Secretins form large, stable multimeric ring-shaped gated pores in the outer membrane through which macromolecules are transported. Transmission electron microscopy analyses of P. aeruginosa and N. meningitidis PilQ complexes have shown that PilQ monomers assemble into doughnut shaped complexes comprised of 12 subunits with an internal diameter of about 50– 60 nm which closely resembles the diameter of the tfp ﬁlament.14,43–45 Recent structural analysis of the N. meningitidis PilQ complex indicates that the PilQ hom*ododecamer is probably comprised of a tetramer of trimers.45 Elegant genetic evidence obtained in N. gonorrhoeae has conﬁrmed that PilQ proteins form the transport channel in the outer membrane through which the tfp ﬁber is extruded.235 N. gonorrhoeae mutants lacking both PilQ and the tfp retraction motor PilT were observed to produce tfp structures that were unable to extrude through the outer membrane due to the absence of the PilQ secretin and thus were trapped in the periplasm forming long, pili-like membrane-bound extensions.235 Stable oligomerisation of N. gonorrhoeae PilQ has been shown to require the lipoprotein PilP.70 Presumably the P. aeruginosa ortholog (PilP) also serves a similar function. The functions of PilM, PilN, and PilO in tfp biogenesis are currently unknown. PilN and PilO both have long N-terminal stretches of hydrophobic residues that may serve to anchor the proteins to the cytoplasmic membrane. PilM shows hom*ology to the actin-like prokaryotic proteins MreB (rod-shape determining) and FtsA (cell-division) and by primary sequence is predicted to belong to the actin-like ATPase superfamily of proteins.73,136,142 Given these hom*ologies, it is possible that PilM may undergo ATP-dependent oligomerisation. The observation that deletion mutants of PilM are dominant negative when introduced into wildtype P. aeruginosa does suggest that PilM may be part of a multimeric complex.142 Type IV pili assembly also requires the genes pilF and pilZ which are each located at distinct loci on the P. aeruginosa genome (Figure 2). Mutants of these genes do not assemble tfp, are non-twitching and resistant to PO4 phage indicating that these proteins have essential roles in tfp assembly.1,223 The function of PilZ is unknown though interestingly, pilZ may be transcriptionally coupled to holB which encodes the δ subunit of DNA polymerase III.1 PilF possesses a signal sequence and 5 tandemly arranged 34 amino acid tetratricopeptide repeat (TPR) domains that mediate protein–protein interactions and the assembly of multiprotein complexes.15,54 The interacting target protein(s) of PilF and the role of PilF in P. aeruginosa tfp biogenesis are unknown. Interestingly the outer membrane located Tgl protein of M. xanthus is similar in size to PilF and possesses a signal sequence as well as 6 TPR domains. Mutants of M. xanthus that are tgl- and pilA+, or tgl+ and pilA- do not produce surface tfp and are non-motile. However when mixed

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together the tgl+/pilA- cells can stimulate the tgl-/pilA+ cells to assemble tfp on their surface and restore motility.178,179,203,221,222 It remains to be determined if P. aeruginosa PilF plays a similar role in contact stimulation of tfp assembly. Tfp biogenesis and twitching motility in P. aeruginosa also requires the activities of the gene products of ﬁmV, tonB3, and PA2982.105,198 Mutants of ﬁmV and tonB3 have been shown to produce little to no surface assembled ﬁmbriae and are sensitive to tfp-speciﬁc bacteriophage.105,198 These mutants are capable of some twitching motility though this is very aberrant compared to the highly co-ordinated process observed with wildtype P. aeruginosa (see Section 5.2). Interestingly, P. aeruginosa ﬁmV, tonB3, and PA2982 mutants exhibit reduced virulence in the fruit ﬂy Drosophila melanogaster whereas mutants that are completely impaired in tfp biogenesis retain wildtype virulence in the fruit ﬂy model.55 These observations suggest that tfp and twitching motility are not required for fruit ﬂy killing and that FimV, TonB3, and PA2982 have additional roles to those involved in tfp biogenesis. FimV is a highly acidic protein that contains a putative peptidoglycanbinding domain and is probably located in the cytoplasmic membrane.198 Overexpression of FimV causes extreme elongation of the cells and it has been proposed that FimV might be involved in remodeling of the peptidoglycan layer to enable assembly of the tfp structure and associated machinery.198 The TonB systems of Gram-negative bacteria function to transduce the protonmotive energy of the cytoplasmic membrane for the active uptake of receptor-bound ligands at the outer-membrane.166 These systems also appear to provide energy to efﬂux pumps for the export of antibiotics and toxic solvents from the cell.169 The TonB systems are a complex of three membrane-spanning proteins, TonB, ExbB, and ExbD.166 The P. aeruginosa genome encodes 3 tonB genes, only one of which (tonB3) is required for normal twitching motility and assembly of surface tfp.105 Interestingly PA2982 is an ExbD hom*olog and like TonB3 is required for both twitching motility and Drosophila killing.55 It is not yet known if this ExbD hom*olog complexes with TonB3 nor what role the TonB3 system of P. aeruginosa plays in tfp biogenesis and twitching motility. Since the Gram-negative TonB systems are involved in transducing protonmotive energy to the outer-membrane, it is possible that the P. aeruginosa TonB3/PA2982 system is involved in providing energy to an outer-membrane protein or outer-membrane-associated protein that is involved in tfp biogenesis, function, or response to environmental cues. Interestingly the outer-membrane tfp secretin PilQ possesses a short highly conserved domain (STN) which has been identiﬁed by the Pfam protein families database to be present in many members the bacterial secretin family as well as in many TonB-dependent receptor proteins (http://www.sanger. ac.uk/Software/Pfam).9 Thus it is possible that the TonB3/PA2982 system may interact with PilQ to provide energy for PilQ function in the outer-membrane.

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2.5. Regulation of Tfp Biogenesis and Function Whilst much is known about the molecular genetics of tfp biogenesis in P. aeruginosa, very little is known about the environmental cues and signal transduction events that govern tfp biogenesis and function. In recent years, it has become evident that the control of tfp biogenesis and twitching motility in P. aeruginosa is a complex process involving the integration of a large number of regulatory proteins (Table 1; Figure 3). This section will address the various regulatory systems and proteins that have thus far been shown to inﬂuence tfp gene expression and to control tfp function in P. aeruginosa. The two component sensor-regulator pair PilS and PilR along with the alternate sigma factor RpoN (σ54 ) are essential for transcription of the pilin subunit gene pilA.18,102,109,110 Based on current knowledge of PilS structure and function PilS can be divided into three regions, an N-terminal transmembrane region (residues 1–174), a cytosolic linker region (175–296) and a cytosolic C-terminal transmitter domain (297–530).74 The N-terminal domain is highly hydrophobic, forms six transmembrane helices and is required for membrane insertion and probably detection of the activating stimulus which has not yet been identiﬁed. The linker domain is required for localization of PilS to both poles of the cell, placing PilS in the same subcellular region as the tfp structures and pilin subunit pools. The signiﬁcance of this co-localization is unclear and may be co-incidental. Interestingly PilS is not polarly localized in E. coli suggesting interaction of the PilS linker domain with a speciﬁc polarly located molecule in P. aeruginosa.17 Tfp and the polar ﬂagellum have been ruled out as the polar anchor.17 The C-terminal domain of PilS contains all of the conserved residues that are characteristic of sensor kinases including the invariant histidine residue (H319), which is probably the site of autophosphorylation. PilS is believed to transfer this high-energy phosphate to the conserved aspartate residue in the N-terminal response regulator domain of PilR.17,19,74 The response regulator PilR is a typical RpoN-dependent transcriptional activator and as such possesses a N-terminal response regulator domain, a central ATPase domain and a C-terminal DNA-binding domain which mediates binding of activated PilR to 4 cis-acting sequences upstream of the pilA promoter. PilR interacts with the σ54 -RNA polymerase holoenzyme to initiate pilA transcription.102,110,113 PilS also appears to act as a phosphatase of PilR and thus may serve dual functions in the control of pilA transcription.19 PilS and PilR and the alternate sigma factor σ54 are essential for pilA transcription in P. aeruginosa and consequently mutants of pilS, pilR, or rpoN do not produce surface assembled tfp, are resistant to tfp-speciﬁc bacteriophage and are non-twitching.18,102,110 Interestingly, expression of pilA from a heterologous promoter in a P. aeruginosa rpoN mutant is able to restore tfp production and phage sensitivity to this mutant.123 This observation suggests that there are no other RpoN-dependent genes that are required for tfp biogenesis in P.

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aeruginosa. This observation also suggests that there are no other targets of PilS and PilR that are essential for tfp biogenesis and function. The atypical sensor-regulator pair comprised of FimS and AlgR is also required for tfp biogenesis and twitching motility in P. aeruginosa.228 FimS is also sometimes referred to as AlgZ,244 but since there exists another unrelated P. aeruginosa protein which is also termed AlgZ,10 for the sake of simplicity the product of the gene located upstream of algR will be referred to as FimS here. Mutants of ﬁmS or algR show very-defective twitching motility and are sensitive to tfp-speciﬁc bacteriophage. ﬁmS and algR mutants produce normal levels of cell-associated pilin though only a small amount of assembled tfp can be detected at the cell surface suggesting a defect at the level of tfp assembly.228,230 Recent whole genome transcriptional analyses have shown that AlgR is a global positive and negative regulator of numerous P. aeruginosa genes, many of which are involved in P. aeruginosa pathogenesis.36,134 Microarray analyses indicated that the genes ﬁmU, pilV, pilW, pilX, pilY1, and pilY2 were potentially activated by AlgR. Expression of the whole gene cluster encompassing ﬁmT, ﬁmU, pilV, pilW, pilX, pilY1, pilY2, and pilE from an exogenous promoter was shown to complement twitching motility to the algR mutant, conﬁrming that these genes are the tfp-related transcriptional targets of AlgR. This study also concluded that the pilM, pilN, pilO, pilP, pilQ operon could be indirectly activated by AlgR.134 The authors of the latter study also reported a personal communication from M. Wolfgang stating that the genes ﬁmU, pilV, pilW, pilX, pilY1, pilY2, and pilE have also been identiﬁed through microarray analyses as amongst the most FimS-dependent genes.134 Thus it appears that FimS and AlgR control tfp biogenesis and function through control of expression of the genes ﬁmU, pilV, pilW, pilX, pilY1, pilY2, and pilE. Interestingly mutants of these target genes produce no detectable surface pili and are resistant to tfp-speciﬁc bacteriophage (see Section 2.4) whereas ﬁmS and algR mutants produce small amounts of surface assembled pili and are phage sensitive.228,230 These observations suggest that there is a low level of target tfp gene expression in ﬁmS and algR mutants that allows assembly of tfp structures sufﬁcient for phage infection. AlgR possesses a conserved response regulator domain at its N-terminus and a novel LytTR-type DNA-binding domain located at the C-terminus.150 Site-directed mutagenesis of the highly conserved phosphate-accepting aspartate (D54) in the N-terminal response regulator domain of AlgR has shown that this residue is essential for tfp biogenesis and twitching motility in P. aeruginosa.230 AlgR has also been shown to be phosphorylated in vitro at this residue via the E. coli histidine kinase CheA.230 Taken together these observations suggest that phosphorylation of AlgR at D54 is required for expression of the ﬁmT–pilE locus. Transcriptional activators such as AlgR are generally phosphorylated at the conserved aspartate in their response regulator module by their cognate histidine kinase.210 The putative cognate partner of AlgR, FimS, possesses

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many of the hallmarks of a 2-component histidine kinase including the presence of a conserved histidine that would be the predicted site of autophosphorylation. However, FimS lacks several of the conserved residues that are essential for nucleotide binding and thus would appear to be incapable of autophosphorylation.228 Interestingly loss of ﬁmS results in similar phenotypes with respect to tfp biogenesis and function as mutants expressing the D54N allele of AlgR,228,230 which suggests that FimS may have some role in phosphorylation of AlgR, possibly by acting as an intermediate in a phosphorelay cascade originating with another histidine kinase. The manner in which AlgR is phosphorylated in vivo and interacts with FimS to control tfp gene expression, and the environmental signals to which these proteins respond remain to be determined. Type IV pili biogenesis and twitching motility in P. aeruginosa is controlled by a complex signal transduction pathway which has many modules in common with chemosensory systems that control ﬂagella rotation in bacteria. This chemotaxis-like system is referred to as the Chp system and is comprised of the P. aeruginosa proteins PilG, PilH, PilI, PilJ, PilK, ChpA, ChpB, and ChpC.57–59,231 The most extensively studied bacterial chemosensory systems are those that control swimming chemotaxis in enteric species.225,234 The enteric chemotaxis systems are comprised of membrane bound chemoreceptors referred to as methyl-accepting chemotaxis proteins (MCPs). MCPs interact directly with both the adaptor protein CheW and the multidomain histidine protein kinase CheA. The MCPs function to modulate the kinase activity of CheA in response to chemical stimuli. CheA possesses in its C-terminus conserved motifs required for nucleotide binding. Autophosphorylation occurs at a conserved histidine in the N-terminus of the protein in a conserved HPt domain. The high-energy phosphoryl group is then transferred from the histidine of CheA to a conserved aspartate in the response regulator CheY, which then interacts directly with the ﬂagellar motor to switch the direction of ﬂagellar rotation. The rate of autocatalytic dephosphorylation of CheY-P is enhanced through interaction with CheZ. Sensory adaptation which allows temporal control of swimming motility occurs through methylation of speciﬁc glutamate residues on the MCP to reset it into a non-signaling state. The methylation status of the MCP is adjusted via competing activities of the methyltransferase CheR and the methylesterase CheB. CheB also possesses a response regulator module and is competitively phosphorylated by CheA.225,234 The P. aeruginosa Chp chemosensory system controls twitching motility and tfp biogenesis at two levels: through control of pili assembly and/or retraction as well as expression of the pilin subunit gene pilA.231 The Chp system consists of a putative methyl-accepting chemoreceptor (PilJ), a methyltransferase CheR-like protein (PilK), 2 CheW hom*ologs (PilI and ChpC) and a methylesterase CheB hom*olog (ChpB). In addition to the response regulator domain of ChpB, the Chp system has a further 3 CheY response regulators modules (PilG, PilH and a domain located at the C-terminus of the CheA-like

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histidine kinase of this pathway, ChpA). ChpA is quite possibly the most complex signaling protein yet described in nature with nine putative sites of phosphorylation: 6 histidine-containing phosphotransfer (HPt) domains, 2 novel serine- and threonine-containing phosphotransfer domains (SPt, TPt) and the CheY-like receiver domain at its C-terminus. It is likely that ChpA is responsible for phosphotransfer reactions with PilG, PilH, and ChpB as well as an intramolecular phosphotransfer to its CheY domain and may well feed into other as yet unidentiﬁed response regulator modules. By analogy with the enteric swimming chemotaxis system in which CheY interacts with the ﬂagella motor to regulate swimming motility, either or both of the CheY hom*ologs PilG and PilH may interact with the putative tfp motor to control tfp extension/retraction. The Chp system, like many other bacterial chemotaxis systems, lacks a hom*olog of the enteric CheZ which serves to accelerate dephosphorylation of phosphorylated CheY. Other bacterial chemotaxis systems such as that of Sinorhizobium meliloti utilize a second CheY protein to act as a phosphate sink to add a similar layer of regulation to the system.208 It is possible that either of PilG, PilH and /or the C-terminal CheY domain of ChpA serve a similar function in this system. Interestingly the P. aeruginosa genome encodes at least 26 putative MCPs52,212 and the Chp system possesses 2 CheW hom*ologs (PilI and ChpC). This raises the possibility that PilI and ChpC may serve to complex a number of MCPs to the histidine kinase ChpA for the input of multiple environmental signals which are integrated by the Chp system to control (at least) tfp biogenesis and twitching motility. Another P. aeruginosa transcriptional regulator that inﬂuences tfp biogenesis and function in P. aeruginosa is the cyclic AMP receptor protein Vfr.11 Mutants of vfr remain sensitive to tfp-speciﬁc bacteriophage, demonstrate reduced levels of surface-assembled tfp and show severely compromised twitching motility.11 Recent whole genome transcriptional proﬁling has implicated Vfr in the regulation of over 200 genes of P. aeruginosa.236 Included in this list of Vfr responsive genes are the majority of the genes required for the biogenesis, function and regulation of tfp (pilDEGHIJKNOPQSUVWXY2Z, ﬁmUVSX, chpABC) which places Vfr as a global regulator of tfp biogenesis and function in P. aeruginosa. It appears that P. aeruginosa possesses another layer of gene regulation situated above Vfr. Mutants of the recently identiﬁed gene ﬁmL are phenotypically very similar to isogenic vfr mutants with respect to twitching motility, phage sensitivity, tfp assembly, and presentation of an autolytic phenotype.229 Expression of cloned vfr is able to complement these phenotypes to ﬁmL mutants.229 Interestingly, P. aeruginosa ﬁmL mutants show reduced vfr transcription and expression when assayed from plate culture or in the presence of epithelial cells in vitro, but not from agitated broth culture229 which suggests that FimL’s inﬂuence over Vfr expression may be speciﬁc to conditions in which functional tfp are required. P. aeruginosa ﬁmL mutants also frequently revert to

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wildtype phenotypes suggesting that an extragenic suppressor mutation is able to overcome the loss of ﬁmL. These revertants show elevated levels of vfr transcription and expression which suggests that the site of spontaneous mutation is in a gene which lies upstream of vfr.229 The mechanism via which FimL inﬂuences vfr transcription has not yet been elucidated. FimL is hom*ologous to the N-terminal 570 amino acids of ChpA, except that the putative histidine and threonine phosphotransfer sites have been replaced with glutamines and thus would be incapable of phosphate acceptance. The signiﬁcance of this hom*ology with the N-proximal domain of ChpA is not known but may suggest some interaction with the Chp chemosensory system. Recently, there has been some controversy surrounding the involvement of the P. aeruginosa quorum sensing systems in twitching motility. It was initially reported that twitching motility in P. aeruginosa is dependent on the las and rhl quorum sensing systems83 whereas other investigators found that lasI, lasR, rhlI, and rhlR null mutants all exhibit normal twitching motility.12 The discrepancy between these studies is probably accounted for by the observation that P. aeruginosa quorum-sensing mutants are susceptible to the acquisition of second-site mutations in genes which encode regulators that are required for twitching motility such algR in the case of rhlI mutants and vfr in the case of lasI mutants.12 The non-twitching rhlI mutants were found to have acquired a GGGGT→GGGGG transversion in algR causing a V241G substitution in the DNA-binding domain of this regulator.12 The lasI mutants that demonstrated reduced twitching zones were found to have acquired a 15 nucleotide deletion in the second half of a imperfect tandem repeat situated within the cAMP-binding pocket of Vfr.12 Interestingly, expression of this allele (VfrEQERS) is able to complement elastase production but not twitching motility to vfr null mutants, suggesting that Vfr may be able to differentially regulate discrete regulons.11 Thus it seems that in the absence of the las quorum sensing system, P. aeruginosa strains acquire a mutation in Vfr that is speciﬁc for a subset of Vfr target genes that includes those required for twitching motility. These observations indicate that mutations in one regulatory system (such as lasI, rhlI, or ﬁmL), may create distortions that select during subsequent culturing for compensatory mutations in other regulatory genes within the network. This highlights the need for vigilance to the possibility of secondary mutation when working with these regulatory systems and emphasizes the importance of complementation studies when attributing phenotype to genetic mutation. Twitching motility in P. aeruginosa is also inﬂuenced by the multidomain protein FimX that possesses several modules that are often found in bacterial signal transduction proteins.106 Mutants of ﬁmX exhibit low levels of surfaceassembled tfp and reduced twitching motility. FimX is polarly localized and this appears to be dependent upon Vfr but not other tfp-related genes which suggests that Vfr or a target of Vfr is responsible for targeting FimX to the cell pole.106 FimX is necessary for the stimulation of twitching motility in

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response to tryptone and mucin (see Section 5.3) though it is not known how FimX controls twitching motility in response to these environmental cues.106 The N-terminus of FimX shows some similarity to response regulator modules though it lacks several conserved features including the critical phosphate accepting aspartate residue normally found in these domains. FimX also possesses a PAS–PAC domain which is present in a range of proteins involved in light, oxygen and redox sensing165,248 as well as putative GGDEF and EAL domains which are thought to be involved in cyclic di-GMP (c-di-GMP) production and degradation respectively.56,111,202 In recent years a number of studies have shown that bacterial proteins containing GGDEF and/or EAL domains are involved in the modiﬁcation of cell surface adhesiveness and motility and that c-di-GMP is likely to be a global second messenger involved in the control of these processes.56,111,202 Interestingly, Simm et al. observed that overexpression of a GGDEF domain protein in Salmonella enterica serovar Typhimurium increased c-di-GMP levels in plate-grown bacteria and signiﬁcantly repressed twitching motility when the cloned gene was introduced into P. aeruginosa.202 Conversely, overexpression of an EAL domain protein was found to reduce c-di-GMP levels in S. enterica serovar Typhimurium and enhanced twitching motility in P. aeruginosa.202 Whilst c-di-GMP synthesis and degradation activities have not yet been demonstrated for FimX, it seems reasonable to expect that FimX modulates tfp biogenesis and twitching motility in P. aeruginosa via c-di-GMP metabolism. The biogenesis and function of P. aeruginosa tfp also appears to be linked to the metabolic status of the cell via a number of global regulatory systems. For instance, both the alternate sigma factor RpoS and polyphosphate kinase (Ppk) are required for survival in the stationary phase of growth and in adapting to nutritional stringencies and environmental stresses124,219 and mutants of either rpoS or ppk show reduced twitching motility.176,214 As noted above, the alternate sigma factor RpoN is required for expression of the pilin subunit gene pilA and RpoN is also required for the expression of genes required for nitrogen assimilation in P. aeruginosa.218 The P. aeruginosa catabolite repression control protein Crc which is involved in the regulation of carbon metabolism has also been found to inﬂuence expression of pilA and pilB, and crc mutants show reduced twitching motility and numbers of surface assembled tfp.153 Thus it appears that control of tfp biogenesis and function in P. aeruginosa is a complex process with many layers of regulation, the details of which are only beginning to be deciphered.

2.6. Tfp in Other Pseudomonas Species Molecular studies of the tfp of P. stutzeri and P. syringae have demonstrated that many of the structural and biogenesis components of the tfp of these

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species are functionally interchangeable with the corresponding components of P. aeruginosa tfp.63,84,87,180,181 Indeed BLAST analyses of the publicly available completed genome sequences of P syringae pv. tomato32 and the unﬁnished genome sequences of P. ﬂuorescens PfO-1 (Genbank Accession NC007492) show that both P. syringae and P. ﬂuorescens have tfp biogenesis and regulatory systems that are very closely related to that of P. aeruginosa (Table 1). It seems reasonable to expect, therefore, that much of what is known about the biogenesis and function of tfp of P. aeruginosa will be applicable to other type IV piliated Pseudomonas species. Interestingly, similar in silico analyses of the P. putida KT2440 genome149 on the other hand suggests that this species may either have a more distantly related tfp system or is no longer capable of producing functional tfp as many of the structural and biogenesis components found in the other Pseudomonas species are missing or truncated in the P. putida KT2440 genome sequences (Table 1). This is consistent with observations made by deGroot et al.63 who observed that the pilB gene was missing from the pilA–pilD gene cluster of P. putida WCS358. These investigators were also unable to observe surface assembled tfp on P. putida WCS358.63 However, they did ﬁnd that heterologous expression of the P. putida pilA gene in P. aeruginosa resulted in the production of surface assembled tfp containing P. putida PilA subunits63 which indicates conservation of the tfp machinery of P. putida and P. aeruginosa. Given the high degree of conservation between the tfp machineries of other Pseudomonas species it seems most likely that the P. putida strains KT2440 and WCS358 have acquired mutations in key tfp genes and as a consequence are no longer able to produce tfp.

3. TYPE IV PILI AND NATURAL TRANSFORMATION IN PSEUDOMONAS SPECIES Natural transformation involves the acquisition of naked DNA from the environment and the subsequent heritable incorporation of its genetic information. Many bacterial species from diverse taxonomic groups including archaebacteria have the capacity to transport DNA from the extracellular milieu into the cytoplasm.135 DNA uptake is a complex process which (in most cases) involves the assembly of a competence pseudopilus that is related to tfp and type II secretion systems.39 In naturally transformable species that also possess tfp, there is an apparent correlation between the presence of tfp and DNA uptake, though it is not clear if in these bacteria the tfp per se have a direct role in the transport of DNA across the bacterial cell wall or if a subset of tfp components contribute to the assembly of a competence pseudopilus that is speciﬁcally responsible for DNA uptake.39

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The molecular genetics of natural transformation in Pseudomonas species strains has as yet only been studied in P. stutzeri.84–87 Consistent with observations made with other naturally transformable tfp producing bacteria such as N. gonorrhoeae39 and Synechocystis species PCC6803,155,243 natural transformation in P. stutzeri is dependent upon a number of tfp components including PilC and PilT, and the tfp subunit PilA1.84,87 P. stutzeri also possesses other tfp-related components that appear to have speciﬁc roles in natural transformation. For instance, co-transcribed with pilA1 is the gene pilAII which encodes a closely related PilA1 hom*olog. PilAII is not required for tfp biogenesis or twitching motility but appears to be a negative regulator of natural transformation.86 In a similar arrangement to that found in P. aeruginosa, the P. stutzeri gene pilU is located immediately downstream of pilT. However, unlike P. aeruginosa pilU mutants which are hyperpiliated and non-twitching232 , P. stutzeri pilU mutants are unaffected in piliation and twitching motility but have transformation efﬁciency reduced to about 10% of wildtype levels.87 Interestingly, heterologous expression of P. aeruginosa pilU genes restores natural transformation to P. stutzeri pilU mutants87 which is consistent with the high degree of similarity observed between the PilU proteins of these 2 species. In addition to tfp-related genes, natural transformation in P. stutzeri also requires the non-tfp-related competence genes comA and exbB which are thought to be involved in late stages of translocation of DNA across the inner membrane.85 BLAST search analysis of the completed genome sequences of P. aeruginosa, P. putida, P syringae, and P. ﬂuorescens indicates that these species each possesses hom*ologs of P. stutzeri ComA (69–76% similarity) and ExbB (89–92% similarity) in a similar genetic arrangement which suggests that these species may also have the genetic capability for natural transformation. In the early 1980s, a survey of natural transformation in Pseudomonas species demonstrated this capacity in some strains of P. stutzeri, P. pseudoalcaligenes, P. alcaligenes, and P. mendocina but not in P. aeruginosa, P. ﬂuorescens, P. syringae, and P. putida.35 However, it is feasible that P. aeruginosa and other Pseudomonas species are also capable of natural transformation under speciﬁc competence conditions. Indeed, natural transformation has been recently demonstrated in P. ﬂuorescens when cultured in soil microcosms but not in a range of in vitro conditions tested.64 These observations suggest that speciﬁc conditions found in soil culture are required to induce competence for natural transformation in P. ﬂuorescens. P. aeruginosa has also been found to be capable of uptake and maintenance of plasmid DNA via natural transformation in a tfp dependent manner, albeit at very-low frequency under the in vitro conditions used (C.B. Whitchurch, unpublished observations). Thus the capacity for natural transformation may in fact be widespread in Pseudomonas species, but the speciﬁc conditions for inducing the competence state have yet to be identiﬁed.

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4. ROLES OF TYPE IV PILI IN COLONIZATION AND INFECTION BY PSEUDOMONAS SPECIES Many members of the Pseudomonas genus are important phytopathogens (P. syringae), phytostimulators (P. ﬂuorescens), or opportunistic pathogens of animals, plants, insects, and fungi (P. aeruginosa). Type IV pili-related functions that contribute to the colonization and infection process include mediating initial adhesion to host tissues, colony expansion via twitching motility, and the development of intractable bioﬁlms that are recalcitrant to host immune attack and antibiotic therapy. Type IV pili have been shown to mediate attachment of various P. syringae pathovars to the leaves of both susceptible and non-susceptible plants. P. syringae tfp mutants show signiﬁcantly reduced adhesion to plant tissues and the ability to generate symptoms in host plants when spray inoculated also correlates with the presence of tfp.181,184–185 Taken together these results indicate that tfp-mediated adhesion of P. syringae phytopathogens to plant tissues is an important factor in the disease process. Tfp may also play a role in colonization of tomato roots by the plant growth promoting P. ﬂuorescens WCS365.138 The identity of speciﬁc plant receptors, if any, for tfp-mediated adhesion to plant tissues has not been established. P. aeruginosa is an important opportunistic pathogen of humans but is also a pathogen of plants, animals, and yeast. Various plant (Arabidopsis, lettuce, basil, and alfalfa), animal (mouse, rat, hamster, nematode, fruit ﬂy, and moth) and yeast (Candida albicans) models of infection have been developed to identify and characterize virulence genes of P. aeruginosa. To date, the involvement of P. aeruginosa tfp in infection of plants or nematodes has not been investigated. As mentioned above, it has been shown that P. aeruginosa tfp are not required for virulence of Drosophila melanogaster (fruit ﬂy).55 It has also been demonstrated that rpoN mutants of P. aeruginosa (which do not produce tfp), are not impaired in virulence of Galleria mellonella (greater wax moth).96 Thus it seems that tfp are not essential for virulence in these insect pathogenicity models. P. aeruginosa tfp are, however, involved in initial attachment to ﬁlamentous C. albicans103 and are essential for virulence in various mouse models of infection.40,47,75,88,217,249

4.1. P. aeruginosa Tfp and Adhesion to Mammalian Tissues It is generally accepted that a crucial component of successful colonization and infection of host tissues by bacteria is irreversible adherence to host cell surfaces.89,182 Adhesion to human mucosal tissues is an essential step in P. aeruginosa pathogenesis.114–116,239 Over the past 20 years a wealth of studies utilizing tfp mutants, competitive inhibition with puriﬁed tfp, and/or polyclonal

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and monoclonal antisera have conﬁrmed that tfp contribute signiﬁcantly to the adherence of P. aeruginosa to mammalian cells. P. aeruginosa tfp have been shown to mediate adhesion to primary human buccal and tracheal cells,68,69,240 injured dog and mouse tracheal epithelia,174,250 injured mouse and rabbit corneal epithelia,95,249 primary bovine tracheal epithelial monolayers,189 and primary mouse epidermal cells.194 P. aeruginosa tfp have also been established as the major adhesins that are responsible for about 90% of the attachment of the pathogen to various cultured epithelial cell lines.40,47,75,90 Injury or disease of epithelial tissues appears to be a prerequisite for P. aeruginosa adherence in vivo62,172,174,175,250 presumably due to the exposure and/or upregulation of tfp receptors on the epithelial cell surface. Much attention has focused on the asialylated glycosphingolids (asialo-GSL) asiolo-GM1 and asiolo-GM2 as the putative epithelial tfpreceptors.6,31,48,61,88,89,125,126,132,133,201,245 The minimum carbohydrate moiety present on asialo-GSLs that is thought to be recognized by P. aeruginosa tfp is GalNAcβ(1-4)Gal.126,201 However, the role of asialo-GSLs as the major epithelial cell receptor for P. aeruginosa remains controversial.60,90,107,197,204,247 To date, a candidate epithelial cell surface component that is speciﬁcally recognized by P. aeruginosa tfp and which contributes to the majority of tfp-mediated adhesion of P. aeruginosa cells has not as yet been isolated. It is also possible that P. aeruginosa tfp binding to epithelial cells may be either multivalent or nonspeciﬁc. Various other molecules which have been identiﬁed as potential epithelial cell receptors for P. aeruginosa tfp include sialylated glycosphingolipids, sialic acid, N -acetylmannoseamine, glycoproteins, and other non-glycosylated polypeptides.6,67,89,94,108,173 How do P. aeruginosa tfp mediate attachment to epithelial cell receptors? Unlike some other ﬁmbrial types P. aeruginosa tfp do not contain a speciﬁc tip associated adhesin that mediates attachment to epithelial cells. Instead, it appears that the C-terminal DSL of the pilin protein (PilA) contains the receptorbinding domain. This has been established through a series of studies which demonstrated (a) that monoclonal antibodies speciﬁc for the DSL, or proteolytic and synthetic peptides corresponding to the DSL were able to inhibit P. aeruginosa attachment to epithelial cells and asialo-GM1 ; (b) that biotinylated DSL peptides bound to asialo-GM1 ; and (c) that mutagenesis of the DSL domain of the tfp pilin subunit did not affect assembly of the ﬁlament but dramatically inhibited binding to epithelial cells to the levels of isogenic mutants that lacked tfp.68,69,75,108,130–133,201,237,238,245,246 Immuno-electron microscopy has demonstrated that the PilA DSL is exposed only at the tip of the tfp-ﬁlament.132 The DSL domain of P. aeruginosa pilin has substantial sequence variability amongst different strains yet they are able to compete for and bind to the same receptors on epithelial cells and cross-reactive antibodies speciﬁc for the DSL have been identiﬁed.68,174,239 The solved crystal structures of the pilin subunits of P. aeruginosa strains PAK and K122-4 predict that the tfp pilin receptor-binding

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site is formed by structurally constrained main-chain atoms which accounts for the apparent conservation in receptor speciﬁcity between divergent DSL sequences.5,93 Taken together the above observations indicate that up to 90% of the binding of P. aeruginosa to damaged epithelia is mediated via type IV pili through the structurally conserved DSL domain exposed at the tip of the ﬁlament and that this process is essential to the establishment of infection. However, P. aeruginosa binding to epithelial surfaces may not be relevant in the airways of CF patients. Instead, P. aeruginosa appears to preferentially bind to mucus present in the CF airways rather than epithelial cell surfaces and indeed mucin binding is believed to be important in the initial colonization of the airways of CF patients by P. aeruginosa.170,241 Furthermore, established P. aeruginosa macrocolonies are found within the airway luminal mucus of CF patients at some distance from the airway epithelial surface.241 These observations suggest that adhesion of P. aeruginosa to mucin rather than epithelia is important in the colonization of CF airways. The tendency for P. aeruginosa to bind to mucin may assist with the clearance of this opportunistic pathogen from healthy lungs via the mucus elevator, but this potential may also be a contributing factor to infection of CF airways due to the presence of thickened dehydrated mucus that is not cleared effectively and which allows P. aeruginosa to successfully colonize the mucus layer of CF airways.241 Whilst it seems that P. aeruginosa does not access the CF epithelia, and tfp are not essential for mucin binding,171 P. aeruginosa tfp may still play an important role in the colonization of CF airways as twitching motility is extremely enhanced in the presence of airway secretions including mucin (see Section 5.3).

4.2. Other Roles of P. aeruginosa Tfp in Mammalian Infections Type IV pili are also important in host immune system defences against P. aeruginosa. P. aeruginosa tfp have been shown to induce T-cell responses in mice,207 humoral responses toward tfp are protective33,187,200 and tfp-mediated attachment to human and mouse macrophages and polymorphonuclear leukocytes is thought to contribute to non-opsonic phagocytosis of P. aeruginosa through interaction with macrophages, though tfp per se are not sufﬁcient to trigger phagocytosis.119,139,209 Tfp have also been implicated in the efﬁcient secretion of virulence factors via the related type II secretion pathway. This effect is believed to be mediated via direct interaction of the pilin subunit with components of the secretion apparatus.137 P. aeruginosa tfp are also required for type III secretion systemdependent cytotoxicity and apoptosis, presumably due to a requirement for tfp to

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mediate attachment of the bacterium to host epithelial cells before translocation of effector proteins can occur.47,48,112,117,216 As we have seen, the tfp of P. aeruginosa participate in numerous aspects of P. aeruginosa pathogenesis. Interestingly, P. aeruginosa pilT or pilU mutants, which are hyperpiliated and at least in the case of pilT mutants produce non-retractile tfp, show signiﬁcantly reduced adhesion to and cytotoxicity of epithelial cell monolayers in vitro, are deﬁcient in the ability to promote corneal disease, and are not fully virulent in a mouse model of acute pneumonia.47,95,249 These observations suggest that many of the virulence-associated roles of tfp require fully functional tfp. It is possible that tfp retraction might be required to enable intimate adherence to the epithelial cells, possibly by engaging secondary receptors at the bacterial cell surface. These observations also suggest that twitching motility is required for successful colonization and spread of infection.

5. TWITCHING MOTILITY Twitching motility is a form of ﬂagella independent surface motility and as such is distinct from swimming or swarming motilities, which are both powered by ﬂagella. As noted above, the locomotive force facilitating cellular translocation via twitching motility is a function of tfp retraction. Twitching motility was ﬁrst described by Lautrop in 1961 when describing this motility in Acinetobacter calcoaceticus.128 Lautrop coined the term “twitching” in 1965 to describe this motility.129 The term is derived from the observation that individual cells appear to move in a jerky or “twitchy” fashion when viewed in suspension. Twitching motility has since been shown to occur in a wide range of Gram-negative bacteria including the Pseudomonas species P. aeruginosa and P. stutzeri98,99,143 as well as in the Gram-positive bacterium S. sanguis.100 Interestingly, twitching motility has not as yet been reported in either P. syringae or P. ﬂuorescens despite the fact that both appear genetically capable of this motility (see Section 2.6; Table 1).

5.1. Twitching Motility in P. aeruginosa When cultured in humid conditions on air-dried agar, P. aeruginosa colonies grow as ﬂat, rough spreading colonies with a characteristic “ground glass” edge. In contrast, mutants which are no longer capable of twitching motility produce smooth, domed colonies.199 This obvious distinction in colony morphology has been exploited in various genetic screens to identify twitching motility mutants for molecular genetic analysis of this phenomenon and tfp biogenesis in P. aeruginosa.

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Over recent years it has become evident that P. aeruginosa exhibits extremely active twitching motility at the interstitial surface between agar and the plastic petri dish.199 When a small inoculum of wildtype P. aeruginosa is “stabbed” through to the plastic at the bottom of a petri dish, a large halo of colony expansion is produced at the agar/plastic interface after overnight incubation, whereas non-twitching mutants produce no such zone. To aid visualization the zone of colony expansion is often post-stained with Coomassie Brilliant Blue or a vital dye such as tetrazolium red is incorporated into the growth medium.199 This “stab assay” is now frequently used as a de facto measurement of twitching motility activity in the presence of different environmental stimuli and in P. aeruginosa mutants that display only subtle defects in twitching motility. The development of rapid twitching motility at the interstitial surface between the agar and the plastic may be attributed, at least in part, to the smoothness of the surface of the agar set against the plastic. Indeed, Semmler et al.199 found that colony expansion due to twitching motility can also occur very rapidly on air-exposed agar if the agar is inverted such that the surface that was set against the plastic is now exposed to the air. When this surface is inoculated and incubated overnight, the resultant zone of colony expansion approaches the size of that obtained via the stab assay technique.199 This implies that the irregularities on the surface of agar that is exposed to air whilst solidifying are inhibitory to twitching motility. There does, however, appear to be some contribution of the abiotic surface to twitching motility at the agar/plastic interface. Twitching motility is greatly enhanced on the air-exposed surface of nutrient media set with either agar or gellan gum when the inoculum is covered with glass coverslips, a phenomenon that has been exploited for microscopic examination of twitching motility in recent years.199 We now know that translocation of individual P. aeruginosa cells during twitching motility on quartz is mediated by retraction of tfp after adhesion of the distal tfp tip to the quartz surface.206 Furthermore, colony expansion at the agar–plastic interface is also greatly enhanced if plastic petri dishes that have been specially treated for use in mammalian tissue culture are used229 presumably because tfp interactions with the treated plastic surface are enhanced.

5.2. Microscopic Examination of Colony Expansion Due to Twitching Motility Early microscopy studies of twitching motility examined cellular movements at the outer edges of colonies grown on air-dried agar surfaces in humid conditions. Under these conditions twitching motility was observed to be a relatively slow, disorganized mode of translocation in which cells moved predominantly singly in an intermittent and jerky fashion.97 Microscopic examination

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of twitching-mediated colony expansion has been greatly facilitated in recent years by exploiting the observation that rapid colony expansion occurs at the interstitial surface between a glass coverslip and a thin layer of nutrient media solidiﬁed with gellan gum which provides greater optical clarity than agar.199 The most striking feature of the twitching-dependent colony expansion that occurs in this system is the intricate lattice network of cells that forms behind the outgoing leading edge rafts.199 It is clear under these conditions that twitching motility manifests as a rapid, highly organized multicellular mechanism of colony expansion presumably to enable rapid colonization of large areas. Time-lapse video microscopy has been used to examine cellular movements during colony expansion at the gellan gum/glass interface.199 Using this technique, Semmler et al.199 observed that at the outermost edge of the expanding colony, large aggregates or rafts of cells assemble and move radially outward from the colony into unoccupied territory. The cells within these leading edge rafts are densely packed and aligned along the longitudinal axis of the cell. Occasionally individual cells are seen to reverse direction and head back toward the colony remaining conﬁned to the area previously traversed by the outgoing raft. It is possible that the pioneering rafts lay down “trails” of an unknown substance that serves to lubricate or in some other way facilitate individual cellular movements in the ensuing network. Cells within these trails move rapidly either as individuals or as small groups, often reversing direction and sliding past each other but always following the long axis of the cell. Occasionally aggregates of cells move off in new directions to make connections with other trails of cells, a process that ultimately leads to the formation of a ﬁne network of cells behind the leading edge rafts. P. aeruginosa cells seem to prefer to be aligned along the long axis of the cell and are often seen to rapidly snap into alignment after contacting a new cell or group of cells.199 It is now clear that individual P. aeruginosa cells are capable of translocation across glass surface via twitching motility.205,206 However, during colony expansion on nutrient media it appears that virgin areas are only ever traversed by aggregates of cells, never by individual cells.199 The signiﬁcance of this observation is unclear but does suggest that the combined effort of a number of cells is required to traverse new areas. The mechanism that enables large aggregates of cells to move en masse is unknown but presumably involves tfp retraction. Furthermore, Semmler et al. also reported that whilst cells within the network behind the leading edge rafts are capable of moving individually, this only occurs when they are within the vicinity of other cells and that when cells become isolated they are unable to move until other cells approach to within a couple of µm199 – a distance consistent with the length of a tfp ﬁlament. It was recently shown that individual N. gonorrhoeae cells are pulled into a microcolony of cells via tfp retraction.145 It is conceivable therefore, that retraction of the tfp after adhesion to a neighboring cell (rather than the substrate) is the motive force behind cellular translocation of individual P. aeruginosa cells in the

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network trails. This “chain gang” arrangement of cells might also account for the apparent conﬁnement of cells to “trails” in the expanding colony network. In the past few years, signiﬁcant advances have been made in our understanding of how tfp facilitate translocation of individual cells across abiotic surfaces. However, we do not yet fully understand how this phenomenon is translated into the variety of multicellular behaviors that occur during twitching motility dependent colony expansion in P. aeruginosa. It is evident however, that twitching motility, as it occurs in the context of colony expansion, is a highly complex social phenomenon that is dependent on tfp and requires cell–cell contact.

5.3. Environmental Signals That Inﬂuence Twitching Motility In recent years, studies that have identiﬁed environmental cues that inﬂuence twitching motility have generally utilized the subsurface stab assay as a quasi-quantitative measure of the rate of expeditionary twitching motility in P. aeruginosa. It should be appreciated however, that this assay is in reality a measure of the rate of colony expansion, which is a complex process with many contributing factors, including the rate of cellular movements via twitching motility, but is probably also inﬂuenced by the rate of cell division. It is also not clear if alterations in the rate of expeditionary twitching motility as assessed by colony expansion at the agar/petri dish interface is a function of signal transduction-mediated events such as chemotaxis (motility up or down a chemical gradient) toward unoccupied regions of the agar, or chemokinesis (increased rate of motility stimulated by a chemical), or if the effect is more passive and a consequence of physical changes to the substrate, or increased growth rate. It has long been established that conditions of high humidity are conducive to rapid colony expansion on the agar surface.99 The concentration of agar used in the subsurface stab assay also has as a signiﬁcant inﬂuence on the resultant size of the colony expansion zone with optimal motility occurring at an agar concentration of 1% (w/vol) (C.B. Whitchurch, A.B.T Semmler, and J.S. Mattick, unpublished observations). Presumably at this concentration the relative humidity at the interstitial surface is optimal for twitching motility. We have also found that the brand of agar used can have a dramatic inﬂuence on the size of the colony expansion zone (C.B. Whitchurch and J.S Mattick, unpublished observations). We have recently identiﬁed a number of environmental cues that stimulate or inhibit colony expansion via twitching motility in P. aeruginosa (C.B. Whitchurch, A.B.T Semmler, and J.S Mattick, unpublished observations).106 In this survey, different chemicals were added to a common base media [0.05% (w/vol) yeast extract, 100 mM potassium phosphate buffer pH 7.0, 1% w/vol (agar)] and colony expansion at the interstitial surface between the agar and the standard plastic petri dish was assessed by the subsurface stab assay. Compounds

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that were found to repress twitching motility were generally those that increase the osmolarity of the medium such as NaCl (300 mM), KCl (300 mM), sucrose (5% w/vol), glucose (10% w/vol), glycerol (5% vol/vol), and polyvynilpyrrolidone (2% w/vol). On the other hand, we found that increasing the tryptone and yeast extract components of Luria Bertani medium either together or individually to 3–5 times standard concentrations was stimulatory to colony expansion (C.B. Whitchurch, A.B.T Semmler, and J.S Mattick, unpublished observations). A similar result was obtained when tryptone (3–5% w/vol) was added to the base media. Interestingly, addition of equivalent amounts of Casamino acids to the base media had the opposite effect on colony expansion and was inhibitory (C. B. Whitchurch and J. S. Mattick, unpublished observations). Both tryptone and Casamino acids are derived from casein, the former being a tryptic digest of the protein and thus comprised of peptides, and the latter an acid digest and is comprised of amino acids. Thus it seems that peptides and not amino acids are stimulatory to twitching motility in P. aeruginosa. Interestingly, certain oligopeptides have been shown to be chemoattractive for swimming motility in P. aeruginosa120 and thus it seems possible that peptides may also stimulate twitching motility via related chemosensory phenomena such as chemotaxis and/or chemokinesis. We also found that bovine serum albumin (BSA) is extremely stimulatory to twitching motility at very low concentrations in this system.106 It is not known if the effect of BSA on twitching motility is via transduction of a speciﬁc signal or through passive facilitation of twitching motility. Tfp have been shown to bind to several large polypeptides89,158 thus twitching motility in the presence of BSA may be enhanced through increased binding of tfp to the protein in the agar substrate. It is also possible that secreted proteases of P. aeruginosa may play a role in digesting these proteins into stimulatory peptides that are then sensed by speciﬁc signal transducing proteins to stimulate twitching motility. The glycoprotein mucin was also found to be extremely stimulatory to twitching motility at low concentration.106 Mucins are high-molecular-weight glycoproteins with hundreds of branched oligosaccharide side chains linked to a protein core.186 P. aeruginosa has been shown to display swimming chemotaxis toward sources of mucin and mucin-associated sugars and amino acids148 thus it is possible that a similar chemosensory mechanism may be involved in controlling twitching motility in response to mucin. However, extensive dialysis of mucin prior to the addition to the agar base media does not reduce the stimulatory effect of mucin106 which suggests that the glycoprotein per se is enhancing colony expansion either by lubricating cellular movements and/or through a speciﬁc signaling cascade for mucin or mucin derivatives that may be elicited through the action of secreted enzymes. The observation that the putative P. aeruginosa signal transduction protein FimX is required for stimulation of twitching motility by mucin and tryptone but not BSA106 suggests that the response to mucin occurs via a transduced mucin-speciﬁc signal.

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Another common protein component of airway secretions, lactoferrin has also been found to be stimulatory to twitching motility in P. aeruginosa.205 This inﬂuence on twitching motility appears to be mediated by the ability of lactoferrin to sequester iron.205 Addition of the iron chelator deforaxamine to agar plates was also found to stimulate twitching motility as assessed by the subsurface stab assay, and this effect could be reversed with the addition of free-iron.205 Interestingly, mucin is an iron-binding glycoprotein,49,167 thus it is possible that at least some of the stimulation of twitching motility observed in the presence of mucin is due to iron sequestration. Given the role of FimX in stimulating twitching motility in response to mucin,106 it would be interesting to determine if FimX is involved in controlling twitching motility in response to iron availability. It has recently been reported that twitching motility in P. aeruginosa is responsive to phosphatidylethanolamine (PE) isolated from late log phase P. aeruginosa culture.118 These investigators demonstrated that P. aeruginosa colonies expand via directed twitching motility up gradients on non-nutrient agar of P. aeruginosa-derived PE or certain synthesized PE species. They also demonstrated that addition of certain synthetic PE species uniformly to the agar plate enhanced overall colony expansion.118 Since these responses showed a degree of speciﬁcity for the fatty acid moiety of the PE these investigators favored the notion that at least part of the response to PE by P. aeruginosa involves chemokinesis elicited via signal transduction rather than merely passive facilitation of cellular movements by the surfactant properties of PE. Recently Barker et al. have shown that the extracellular phospholipase C PlcB is required for directed twitching motility up gradients of certain synthetic species of PE and phosphatidylcholine (PC).8 This observation indicates that either or both of the PlcB hydrolytic products of PE or PC are required to elicit the directed twitching motility response. It is also possible that further degradation of these products might be required to produce the actual chemical signal that triggers the observed response to PE or PC. The fact that P. aeruginosa displays directed twitching motility in response to P. aeruginosa-derived phospholipids suggests the twitching motility and colony expansion might be controlled via chemotaxis and/or chemokinesis in response to these endogenous signals. Whatever the mechanisms via which phospholipids, lactoferrin, mucin, and albumin stimulate twitching motility, it is possible that these responses may be important in P. aeruginosa pathogenesis. Human lung surfactant is comprised of 80–90% lipid by weight, more than 80% of which is phospholipid and of this 60–70% is PC and 5–10% PE.66 The PE and PC content appears to be further elevated in surfactant isolated from the lungs of young adult CF patients.146 Albumin, lacotoferrin, and mucin are also prominent components of respiratory secretions.16 The fact that several components of airway secretions enhance expeditionary twitching motility by P. aeruginosa implies that twitching motility

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may also be an important component of colonization of airway mucosa. On one hand, stimulation of twitching motility by these compounds might facilitate extensive colonization of airways and other mucosal tissues by this pathogen. On the other hand, however, as postulated by Singh et al.205 stimulation of twitching motility may prevent bioﬁlm development (see Section 5.3) thus making P. aeruginosa more susceptible to host defence mechanisms. Therefore, it seems that up-regulation of twitching motility in response to human airway secretions may be a double-edged sword for this opportunistic pathogen and suggests that successful colonization of mucosal tissues is a complex process.

6. TFP AND BIOFILM DEVELOPMENT Bacterial bioﬁlms are matrix-encased communities of sessile bacteria that are attached to a surface.211 It is now clear that the development of P. aeruginosa bioﬁlms is a complex social phenomenon that is dependent upon tfp and twitching motility. The ﬁrst evidence for a role of tfp in bioﬁlm development was obtained through mutant screens to identify P. aeruginosa mutants which were defective in the early stages of the development of bioﬁlms grown in static media.154 Phase contrast time-lapse microscopy showed that, in this system, wildtype P. aeruginosa ﬁrst formed a monolayer of cells on the abiotic surface after which microcolonies appeared which were dispersed throughout the monolayer. Flagella were identiﬁed as being responsible for mediating the initial attachment of cells to the abiotic surface and tfp were found to be required for cells to move across the abiotic surface and to aggregate into microcolonies.154 Microscopic examination of the development of P. aeruginosa bioﬁlms grown in laminar ﬂow cells have shown that the structure of the mature bioﬁlm is largely dependent upon the carbon source. For instance, when deﬁned media containing citrate as the carbon source is used, P. aeruginosa forms ﬂat dynamic bioﬁlms whereas when glucose is the available carbon source the resultant bioﬁlm is comprised of mushroom-shaped multicellular structures separated by water-ﬁlled channels.121 Confocal laser scanning microscopy was used to characterize the development steps involved in the formation of these different bioﬁlms and it was found that twitching motility was the most important factor prescribing the structure of the bioﬁlm.121 In citrate-grown bioﬁlms, P. aeruginosa cells continue to exhibit extensive twitching motility across the abiotic surface beyond the initial phases of bioﬁlm development and that this continued motility results in the development of ﬂat undifferentiated bioﬁlms that lacked microcolonies. In contrast, the larger heterogenous bioﬁlms that are formed when glucose is provided as the carbon source are due to the activities of two subpopulations of cells that form the “stalks” or the “caps” of the mushroomlike structures. The “stalks” are formed by the proliferation of non-twitching cells whereas the mushroom “caps” are comprised of a subpopulation of cells

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that use twitching motility to clamber up the sides of the stalk to aggregate on the top, presumably to gain access to the ﬂow of nutrient media.121,122 Twitching motility also appears to play a role in the maintenance of bioﬁlm morphology in mature bioﬁlms. Chiang and Burrows41 reported recently that the hyperpiliated pilT mutants of P. aeruginosa strain PAK formed denser cell mats in the early stages of bioﬁlm development and larger, more tightly packed mushroom-like structures in the mature bioﬁlm than was observed with isogenic wildtype P. aeruginosa in ﬂow cell bioﬁlms using minimal media in which glucose was the provided carbon source.41 Under the experimental conditions used by Chiang and Burrows, an isogenic PAK pilA mutant was non-adherent to the glass surface and did not form bioﬁlms.41 These observations indicated that under these experimental conditions, tfp were the major adhesin mediating attachment to the glass surface, an obvious prerequisite for bioﬁlm formation. In contrast, Klausen et al.121 observed that in their experimental conditions and with their strain background (PAO1), even in glucose minimal media their isogenic pilA mutant was capable of some adhesion to the glass surface and formed large, irregularly shaped mushrooms.121 Presumably, in both cases, the three-dimensional structures formed by the non-twitching pilT and pilA mutants are due to clonal growth. Both colony expansion and bioﬁlm formation by P. aeruginosa are multicellular social phenomena that involve tfp and twitching motility. An interesting correlation between the two has recently emerged. Singh et al.205 have found that iron sequestering compounds such as lactoferrin and deferoxamine inhibit the formation of P. aeruginosa bioﬁlms in ﬂow cells. Interestingly, it was also found that iron chelation causes enhanced colony expansion at the interstitial surface between agar and plastic in the twitching stab assay described above.205 Thus from these observations it seems that conditions that promote rapid colony expansion are inhibitory to bioﬁlm development suggesting an inverse relationship between the two colonial behaviors. Time-lapse microscopy of cellular movements during the early stages of bioﬁlm development in the presence of lactoferrin showed that individual cells did not settle down to form the microcolonies that are required to initiate bioﬁlm development but rather continued to move across the ﬂow cell surface by twitching motility,205 similar to what was observed during bioﬁlm development using citrate as the carbon source.121 Presumably the developmental switch that produces a subpopulation of non-motile cells upon which the mushroom structures develop is not initiated in low iron conditions or in the presence of citrate. Thus it appears that both rapid colony expansion on nutrient media and inhibition of bioﬁlm development are due to stimulation of twitching motility. It will be interesting to determine if other environmental signals that have been found to promote rapid colony expansion on solid nutrient media (see Section 5.2) also prevent bioﬁlm development on abiotic surfaces in ﬂow cells, and conversely if colony expansion is enhanced in the presence of citrate.

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It is now evident that P. aeruginosa tfp and twitching motility are required for normal bioﬁlm development. P. aeruginosa bioﬁlms are complex communities of cells that are held together by an extracellular matrix comprised of exopolysaccharides, DNA and proteins.211,229 Given the adhesive and aggregative properties of tfp it seems plausible that tfp may also provide a structural role in the bioﬁlm either by binding bacterial cells to the components of the matrix or by intertwining and meshing cells together. Interestingly, small colony variants (SCVs) of P. aeruginosa isolated from bioﬁlm grown cultures either in vitro or from the lungs of chronically infected CF patients are hyperpiliated, autoaggregative, highly adherent and demonstrate increased bioﬁlm formation capabilities.65,71,92 It has been suggested that the SCVs represent a speciﬁc bioﬁlm phenotype that is either switched on via phase variation or is the outcome of adaptive mutation.65,71,91 Small colony variants are often observed in vitro to revert to wildtype phenotypes either through phase variation switching or through further adaptive mutation.65,71,91 The rate of SCV reversion is controlled by a putative 2-component response regulator PvrR which is thought to act upstream of the phenotypic switch.71 The genetic mechanism via which the phenotypic switching is occurring has yet to be determined.

7. FUTURE DIRECTIONS The study of type IV pili began over 50 years ago and continues to be an area of active investigation. It is now evident that type IV pili are highly complex multimeric structures that facilitate a variety of biological functions in bacteria including phage sensitivity, attachment to and colonization of biotic and abiotic surfaces, natural transformation, twitching motility, colony expansion, and bioﬁlm development. Whilst over 40 genes have now been identiﬁed which are involved in the biogenesis and regulation of tfp in P. aeruginosa, we still have much to learn about how the structural proteins are assembled and interact with one another to form dynamic, powerful motors that mediate assembly and retraction of tfp to promote twitching motility. We also have much to learn about how twitching motility is co-ordinated into complex multicellular behaviors such as colony expansion and bioﬁlm development and how these processes are regulated in response to environmental stimuli. Thus it appears that this fascinating area of biology will continue to be of interest to scientists for some time to come.

ACKNOWLEDGMENTS During preparation of this manuscript CBW was supported by an NHMRC R. Douglas Wright Career Development Award.

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242. Yeo, H.J., Savvides, S.N., Herr, A.B., Lanka, E., and Waksman, G., 2000, Crystal structure of the hexameric trafﬁc ATPase of the Helicobacter pylori type IV secretion system. Mol. Cell, 6:1461–1472. 243. Yoshihara, S., Geng, X., Okamoto, S., Yura, K., Murata, T., Go, M., Ohmori, M., and Ikeuchi, M., 2001, Mutational analysis of genes involved in pilus structure, motility and transformation competency in the unicellular motile cyanobacterium Synechocystis sp. PCC 6803. Plant Cell Physiol., 42:63–73. 244. Yu, H., Mudd, M., Boucher, J.C., Schurr, M.J., and Deretic, V., 1997, Identiﬁcation of the algZ gene upstream of the response regulator algR and its participation in control of alginate production in Pseudomonas aeruginosa. J. Bacteriol., 179:187–193. 245. Yu, L., Lee, K.K., Hodges, R.S., Paranchych, W., and Irvin, R.T., 1994, Adherence of Pseudomonas aeruginosa and Candida albicans to glycosphingolipid (Asialo-GM1) receptors is achieved by a conserved receptor-binding domain present on their adhesins. Infect. Immun., 62:5213–5219. 246. Yu, L., Lee, K.K., Paranchych, W., Hodges, R.S., and Irvin, R.T., 1996, Use of synthetic peptides to conﬁrm that the Pseudomonas aeruginosa PAK pilus adhesin and the Candida albicans ﬁmbrial adhesin possess a hom*ologous receptor-binding domain. Mol. Microbiol., 19:1107–1116. 247. Zhao, Z., and Panjwani, N., 1995, Pseudomonas aeruginosa infection of the cornea and asialo GM1. Infect. Immun., 63:353–355. 248. Zhulin, I.B., Taylor, B.L., and Dixon, R., 1997, PAS domain S-boxes in Archaea, Bacteria and sensors for oxygen and redox. Trends Biochem. Sci., 22:331–333. 249. Zolfa*ghar, I., Evans, D.J., and Fleiszig, S.M., 2003, Twitching motility contributes to the role of pili in corneal infection caused by Pseudomonas aeruginosa. Infect. Immun., 71:5389– 5393. 250. Zoutman, D.E., Hulbert, W.C., Pasloske, B.L., Joffe, A.M., Volpel, K., Trebilco*ck, M.K., and Paranchych, W., 1991, The role of polar pili in the adherence of Pseudomonas aeruginosa to injured canine tracheal cells: a semiquantitative morphologic study. Scan. Microsc., 5:109– 126.

EVOLUTION OF CATABOLIC PATHWAYS IN PSEUDOMONAS THROUGH GENE TRANSFER Jan Roelof van der Meer

Department of Fundamental Microbiology Bˆatiment de Biologie University of Lausanne 1015 Lausanne, Switzerland

1. INTRODUCTION Pseudomonads are recognized for their extraordinary capacity to catabolize a large number of different carbon compounds.39,40 This property is evident from a relatively large number of uptake systems, a more than median genome size, and a large proportion of genetic material devoted to carbon compound catabolism.120 The catabolic capacity of pseudomonads is shared with a number of other bacteria, mainly from the groups of Gamma-, Beta-, and Alphaproteobacteria, such as Acinetobacter, Ralstonia spp., Burkholderia spp., and sphingomonads, and probably many more to become analyzed in the future (e.g. Alcanivorax, Rhodococcus). Notwithstanding the catabolic capacities of individual Pseudomonas isolates, there has been a certain overinterpretation of the catabolic and ecological importance of the genus Pseudomonas as a whole, perhaps because, ﬁrst of all, many original “Pseudomonas” isolates were later renamed to other genera. Secondly, because many pseudomonads were isolated by enrichment techniques which selected for the fastest growing microorganisms but not necessarily for the most environmentally abundant. Thirdly, because the true catabolic activity of microbes in the natural environment is very difﬁcult to measure and can only now be beginning to be studied Pseudomonas, Volume 4, edited by Juan-Luis Ramos and Roger C. Levesque C 2006 Springer. Printed in the Netherlands.

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with the use of isotopic labeling techniques or direct in situ mRNA analyses. Finally, because a substantial part of the catabolic properties is part of what might be called the “mobile gene pool,” to which different genera have “access,” but which gives a certain volatile status, being subject to both functional gain and loss. On the other hand, whatever the status on the “true” role of pseudomonads in carbon compound catabolism in the environment may become, they have served as paradigms in many aspects. The speciﬁc purpose of this overview is not to list and categorize all possible carbon compound catabolic pathways in pseudomonads and related “catabolic specialists,” but to describe the mechanisms by which these groups of organisms (with a majority of examples from true Pseudomonas spp.) may have evolved a multitude of pathways and continue to expand catabolic capacities to new substrates, many of which are of synthetic nature. Many different evolutive genetic mechanisms have been clariﬁed on a molecular level, presenting a detailed picture on the possibilities for adaptation by catabolic expansion. Pseudomonads have also here served as unique model systems for our understanding of catabolic pathway evolution. However, also in our thinking on catabolic pathway evolution we may have been biased by a choice of target organisms and catabolic pathways, and it should not be forgotten that the same sort of adaptive mechanisms are a very general feature for all bacteria.

2. CATABOLIC PATHWAYS It is thought that the catabolic expertise of pseudomonads and other organisms is a reﬂection of their (natural) ecological niches as degraders of plant material,39,63,91,93 plants being able to synthesize the most differentiated carbon structures among living beings.187 It is not surprising then to ﬁnd many potential catabolic pathways for phenolic, carboxylic, and methoxylated aromatic compounds in pseudomonads (Table 1), which must have evolved during millions of years of bacteria being exposed to (decaying) plant material. A relatively good idea of these “core” catabolic processes in Pseudomonas (in contrast to the “mobile and expandable parts”) can nowadays be obtained from full genome sequences such as those recently ﬁnished of P. putida KT2440,91 P. syringae or P. aeruginosa.199 It is perhaps good to spend a few words on the terminology of catabolic pathways. In a more general sense catabolic pathways describe all those metabolic processes which lead to a breakdown of carbon compounds to a level at which they can be used as intermediates for building new cellular macromolecules or are used in redox processes for energy generation. For pseudomonads, catabolic pathways usually “end” at the point of pyruvate, acetylCoA, or as direct intermediates of the citric acid or tricarboxylic acid – TCA cycle (e.g. succinyl-CoA or fumarate). Pyruvate and acetate are transformed to

Evolution of Catabolic Pathways in Pseudomonas

Table 1.

Main substrate(s)

Non-exhaustive overview of peripheral catabolic pathways in pseudomonads. Key intermediates or intermediate pathway

13,133

paa2, pad, pha, chromosome

2,91

phh, tyr, hpd, hmgABC, fah, chromosome

5,91

P. putida sp. strain 86, P. putida KT2440 P. putida KT2440, P. putida PRS2000, Pseudomonas sp. strain HR199

oxo, qorMSL, chromosome

31,91

Phenylacetyl-CoA

P. putida KT2440

fad, pha, chromosome

Catechol, 3-oxoadipate Benzoate plus phenol, catechol, 3-oxoadipate Catechol, 3-oxoadipate

P. putida KT2440

ben, catBCA, chromosome

(Methyl-)catechol, meta cleavage Methylcatechol, meta cleavage

Phenylacetate

Phenylacetyl-CoA

L-Phenylalanine,

hom*ogentisate

L-tyrosine,

Phenoxyacetic acid, phenol

Toluene, benzene, ethylbenzene Toluene, o-xylene

Reference(s)

sty, paa1, paa2, chromosome

Phenylacetate, phenylacetylCoA

Ferulate, caffeate, vanillate, vanillin, eugenol, coniferyl alcohol, p-coumate, p-hydroxybenzoate Phenylhexanoate, phenylheptanoate phenyloctanoate Benzylamine, benzoate Phenylbenzoate

Strain(s)

Genetic nomenclature and gene location

Pseudomonas sp. Y2, P. putida CA-3, P. ﬂuorescens ST, Pseudomonas sp. VLB120 Pseudomonas sp. Y2, P. putida KT2440 P. putida U, P. putida KT2440

Styrene

3-OHphenylacetate Quinoline, quinate

191

Protocatechuate, 3-oxoadipate Protocatechuate, 3-oxoadipate

cal, fcs, ech, vdh, van, pob, pca, chromosome

159

Pseudomonas sp. strain TR3

Pseudomonas sp. strain B13

79,91,136

P. putida F1

tfdA-S from pJP4 introduced on plasmid pKJS32 tod, chromosome

248

P. stutzeri OX1

Chromosome

(Continued )

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Table 1. Main substrate(s) Toluene, m- and p-xylene, benzylalcohols, benzylaldehyde, pseudocumene Toluene

Benzene Toluene, ethylbenzene, isopropylbenzene Isopropylbenzene Naphthalene

1-Methyl, 2-methylnaphthalene, benzylalcohol (not toluene or xylene) Naphthalene

Benzene, toluene, m-, p-xylene, ethylbenzene, biphenyl p-Cymene, cumene, npropylbenzene, n-butylbenzene, biphenyl Naphthalene, phenanthrene, anthracene Carbazole

Key intermediates or intermediate pathway

(Continued )

Strain(s)

Genetic nomenclature and gene location

Reference(s) 60,236

Benzoate, catechol, meta cleavage

P. putida mt-2

xyl, pWW0

p-Cresol, protocatechuate, 3-oxoadipate Catechol, 3-oxoadipate (Alkyl)catechol, meta cleavage

P. mendocina KR1

tmo, chromosome

244

P. putida ML2

203

P. putida o1G3

bed, plasmid pHMT2 ebd, chromosome

(Alkyl)catechol, meta cleavage Salicylate, catechol, meta cleavage

P. putida RE204

ipb, Plasmid pRE4

P. putida NCIB 9816-4, P. putida PpG7, Pseudomonas sp. strain ND6 P. putida CSV86

nah, pDTG1, NAH7, pND6-1

47,111,245

Plasmid likely

P. stutzeri AN10

nah, chromosome

Benzoate, catechol, ortho cleavage, naphthoic acids (and no further)

Salicylate, catechol, meta cleavage Meta cleavage

P. putida BP18

p-Cumate, meta cleavage

P. putida F1 mutants

Mutation in cymR, cmtE, chromosome

Salicylate

P. aeruginosa 57

pah/nah/dox-like, No plasmid

Anthranilate, catechol, meta cleavage

P. stutzeri OM1, P. resinovorans CA10

ant, car, pCAR1 plasmid

113,135

Evolution of Catabolic Pathways in Pseudomonas

Table 1. Main substrate(s)

Key intermediates or intermediate pathway

2-Hydroxybiphenyl, 2,2 -dihydroxybiphenyl Biphenyl, 3-, 4methylbiphenyl Biphenyl

Benzoate (salicylate), catechol, meta cleavage (Methyl)benzoate

Biphenyl, salicylate

Benzoate, echol, cleavage Salicylate

catmeta

Salicylate, chol

cate-

Dibenzothiophene, naphthalene Dibenzofuran, dibenzo- pdioxin Naphthalene, phenanthrene, anthracene Phenol (transformation only of 2,4- and 2,5-dimethylphenol) 3-Alkyl, 4-alkylphenol Phenol, 4-methylphenol 3,4-, 2,4dimethylphenol 3,4-, 2,4dimethylphenol Nitrobenzene o-Nitrophenol 4-Nitrotoluene, 4-nitrobenzoate Nitrobenzene

Aromatic amines, m-toluate, aniline

Benzoate

Salicylate

Catechol, meta cleavage

Catechol, meta cleavage Catechol, meta cleavage Catechol, meta cleavage Protocatechuate, ortho 2-Aminophenol, meta cleavage Catechol, nitrite Benzoate, catechol, meta cleavage 2-Aminophenol, meta cleavage Catechols, meta cleavage

193

(Continued )

Strain(s)

Genetic nomenclature and gene location

Reference(s)

P. azelaica HBP1

hbp, no plasmid

101

Pseudomonas strain IC P. pseudoalcaligenes KF707 P. putida KF715

bph, chromosome

bph

201

80,126

Pseudomonas sp. strain C18

bph, chromosome, Bph-Sal element dox, plasmidlocalized

P. veronii PH-03

Unknown

Pseudomonas sp. strains 5R, DFC49, DFC50 P. stutzeri OX1

pKA plasmids

170

tou, chromosome

Pseudomonas sp. strain KL28 Pseudomonas sp. CF600 P. mendocina PC1

lap, no plasmid

P. ﬂuorescens PC18, PC24 P. putida HS12 P. putida B2 Pseudomonas sp. strain TW3 P. pseudoalcaligenes JS45 P. putida UCC22

dmp, pVI150 plasmid

127,151 231 231

nbz, pNB1, pNB2

138 246

ntn, pnb, chromosome Chromosome

pTDN1 plasmid

44,188

168

(Continued )

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Table 1. Main substrate(s) 4-Chlorobenzoate 2-Chlorobenzoate, 2,4-dichlorobenzoate Toluene, chlorobenzene Toluene, chlorobenzene Monochloro, 1,2-, 1,4-dichloro, 1,2,4-trichlorobenzene 4-Chlorophenol, 3chlorobenzoate 1,2,3,4Tetrachlorobenzene p-Cymene, p-cumate Abietane diterpenoids Dodecylbenzene sulfonate, citronellol C5–C12 alkanes, toluene, naphthalene

Key intermediates or intermediate pathway

Strain(s)

Genetic nomenclature and gene location

Reference(s) 172

Protocatechuate, 3-oxoadipate Chlorocatechol, 3-oxoadipate

Pseudomonas sp. strain CBS3 P. aeruginosa 142

Chromosome ohb, clc, chromosome

41,212

3-methyl, 3chlorocatechol, meta cleavage Methyl-, chlorocatechol Chlorocatechol, 3-oxoadipate

P. putida GJ31

cbz, plasmid

116,117

Chlorocatechol, 3-oxoadipate Tetrachlorocatechol, chlorooxoadipate p-Cumate

Pseudomonas sp. strain JS6 Pseudomonas sp. strain P51

227

Pseudomonas sp. strain B13

clc, mobile genomic island

52,154

P. chlororaphis RW71

tet, IS1071

149,150

P. putida F1

cym, cmt, chromosome dit

Pseudomonas sp.

C6–C12 n-alkanes 1,3-Dichloropropene, 1,2dibromoethane Sole N-source, to cyanuric acid

143

tcb, plasmid pP51

P. abietaniphila BKME-9 P. aeruginosa W51D

C12–C16 alkanes

Atrazine

(Continued )

P. ﬂuorescens CHA0 P. putida Gpo1 P. pavonaceae 170, Pseudomonas sp. GJ1 Pseudomonas sp. strain ADP

54 118 29

Psychrophilic, OCT-like and NAH-like plasmid coexisting

234

186

alk, OCT deh

atz, pADP1

57,220 147

119

Evolution of Catabolic Pathways in Pseudomonas

195

acetyl-CoA to feed the TCA cycle and lead to production of reduced coenzymes (NADH2 , NADPH2 , FADH2 ), anabolic building blocks, and ATP. Often, however, the terminology “catabolic pathways” is used for a more limited capacity, such as producing catechol from benzoate, in which case also the term “peripheral metabolism” is used.91,120 Catechol is considered in this case as a key intermediate, feeding into an “intermediate” pathway, because it occurs as the “end point” of a number of different peripheral pathways (e.g. benzoate, benzene, toluene, salicylate, or naphthalene). Several such key intermediates have been deﬁned, which on their turn can be seen as “nodes” of pathway convergence, “funneling” into the TCA cycle (scientiﬁc literature offers various metaphores for this concept). Pseudomonads like P. putida KT2440 carry four of these intermediate pathways: protocatechuate and catechol ortho cleavage (both converge via 3-oxoadipate to succinyl- and acetyl-CoA), the hom*ogentisate (to fumarate and acetoacetate), and the phenylacetyl-CoA pathway.91,120 This last pathway does not seem to be present in P. aeruginosa PAO1 and P. syringae. Similar intermediate pathways are present among other Proteobacteria (e.g. Ralstonia, P. aeruginosa, Acinetobacter), but also in other taxonomic groups (e.g. Rhodococcus).91,120 Despite analogy of function, the gene orders for the intermediate pathways in different microorganisms are not very conserved and resemble mosaics, suggesting that there is no evolutionary constraint on gene order.91 Various other intermediate pathways exist as well, such as catechol via meta cleavage, chlorocatechol to 3-oxoadipate, hydroquinone or gentisate, which do not form part of the “core” in e.g. P. putida KT2440 but are present in other pseudomonads or are part of the “mobile” genome (Table 1). Therefore, we must conclude that although the concept of “funneling” is useful to comprehend catabolic processes, there is not one speciﬁc intermediate pathway which can be considered to be an absolute requirement for the core cellular catabolism. We will see later how intermediate pathways are or can become part of the mobile gene pool. In terms of metabolic strategies for microorganisms, the analogy of a “tree” is often used, with the stem being TCA cycle or the like, large limbs being the intermediate pathways, and several smaller twigs being peripheral pathways feeding into larger limbs. However, like any analogy this has a certain danger of not exposing the overall variability and redundancy of the system. Consider, for example, enzymes with the capacity to convert more than one substrate and feeding into different “pathways,” or incomplete pathways, consider enzyme paralogs in the same cell (e.g. two catechol 1,2-dioxygenases in P. putida KT2440,120 or the many other uncharacterized potential catabolic functions (e.g. 15 predicted monooxygenases in P. putida KT2440 with unknown speciﬁcity). Rather than “trees” or “funnels,” one might consider operonic organizations or regulons as being the structural “entities.” This has some advantage in understanding hierarchical regulatory and control processes in the cell, but

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again lacks the ﬂexibility and redundancy of genetic systems for adaptation and evolutionary development. For example, although some organisms have formed “superoperonic” organization of catabolic gene functions (e.g. Acinetobacter sp. ADP1 qui, cat, ben, pca operons185 ), others do very well without (e.g. Sphingomonas paucimobilis lin genes50 ), which suggests that there is no obligatory evolutionary tendency to form large operons in order to become an “effective” catabolic microorganism. In most genomes, redundant and uncharacterized gene functions exist, which may have a silent role under most growth conditions but become more pronounced under speciﬁc niche adaptations.

3. MICROORGANISMS AND CATABOLIC ADAPTATION Although we can speculate about the natural niche of microbes and the reasons for the evolutionary processes which have led to present day’s genomes, it has become apparent that the natural ecological niche of many microbes probably no longer is the same in the age of large-scale agricultural, industrial, livestock, and waste management activities. Pollutants (e.g. industrial solvents or agricultural pesticides and herbicides) are unlike plant material; their carbon structures or substituents may be unlike anything found under natural conditions. Hence, we might expect that human activities have selected for bacteria with new characteristics, including new catabolic properties. A ﬁrst glance at Table 1 shows that in essence this expectation has been correct (as we will see below); many pseudomonads catabolize compounds which are hard to be considered “natural” (Table 1). Although it will always remain disputable whether a compound is a naturally occurring or fully synthetic one,93,174,209,222 there are many different aspects to the selective pressure achieved by environmental pollutants, waste, and industrial activities. Consider, for example, modern wastewater treatment installations, which are large-scale reactors cultivating huge quantities of bacterial biomass on a variety of carbon substrates present in industrial or household wastewater. These bacteria certainly were not exposed to such enormous substrate quantities before or to the general process regime of the wastewater treatment plant. Due to the huge biomass densities and presence of taxonomically very different microbial groups lateral genetic interactions may have become favored which otherwise occurred perhaps only infrequently. Hence, many new niches and processes must have favored adaptation and differentiation of microorganisms, an aspect in wastewater treatment plants which still remains relatively unexplored. In other areas, such as agricultural soils or industrial dumpsites, the release of

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toxic compounds (e.g. heavy metals, antimicrobial compounds, toxic solvents, or agricultural pesticides) must have eliminated sensitive microbial populations and favored resistances, thus leading to community shifts. Finally, on the level of carbon substrates the selective force of waste products and pollutants is a very strong one, since any cell metabolizing a speciﬁc carbon substrate will immediately be able to grow and divide (if not otherwise limited in nutrients) and increase its population size proportional to those who cannot gain carbon or energy from the compound. Hence, it becomes easy to envision that when chemicals are released into the environment, which naturally only occurred in trace quantities or in restricted locations (e.g. oil), they will rapidly select for faster growing microbial populations capable of using the compounds for carbon and energy metabolism. Likewise, it can be foreseen that release of carbon compounds for which no known metabolic pathways are existing, may lead to selection of any mutants with the right catabolic properties on the basis of enhanced growth rate. Bacteria with speciﬁc catabolic properties isolated from such selective environments have undergone a natural selection, and have been exposed to the full genetic potential of all the organisms present in that environment. They can be examined in order to learn how adaptation processes and catabolic pathway evolution have “worked.”93,196,208,221

4. GENETIC ADAPTATION MECHANISMS In order to understand genetic adaptation mechanisms we can combine information gathered from numerous different experiments. In the ﬁrst place, there is what I would call “comparative historic” evidence. By comparing genetic structures (individual genes, operons, clusters, or genomes) from bacterial isolates it is easy to establish sequence relationships, ﬁnd analogies in genetic organization and with the help of statistical tools, trace nucleotide abberations in genome sequences, which may point to recombined or laterally acquired DNAs. This work is like doing molecular archeology and it can help to ﬁnd traces of mechanisms that must have been taking place for millions of years. More recent evolutionary events can be traced when gene sequences from bacteria thought to have been selected for a completely new catabolic property are examined and compared. In some of those cases (see below) we can get a clear idea of the genealogy, the different steps in the formation of the present day’s gene and pathway structure, and even to ﬁnd DNA-donating partners in the same microbial community. Secondly, there is laboratory evidence for evolutive mechanisms on single pure cultures or simple combinations of two or more bacterial strains. Pure strains can be grown under different conditions, and due to the relatively short generation time of bacteria, mutants will develop which can be examined for genetic changes. Mutants can also be generated in speciﬁc recombinatory

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pathways, which can be subsequently studied to determine the possible role of such recombinations for genetic adaptation. Insertions elements, integrons, or transposons can be examined for their activity and the mechanisms of regulation. Two or more bacterial strains can be grown together under speciﬁc conditions to observe whether offspring develops which has exchanged parts of their genetic material, or to determine when plasmids conjugate and by which mechanisms. What can we conclude from the different lines of evidence? In a nutshell, we must assume that all microorganisms have in some way or another an evolutionary toolbox,3 which is responsible for generating a certain genetic ﬂexibility inside a single cell, creating mutations that can subsequently be passed on to daughter cells. In addition, all microorganisms in a microbial community have to some extent access to the genetic information of each other through the action of lateral gene transfer mechanisms that seem to operate in a selﬁsh independent way.24,129 How does the content of the toolbox look like? The genomes of probably all bacteria can be subject to small-scale changes (single to a few nucleotides), which are the consequences of DNA replication errors,53 or are caused by mismatch repair or nucleotide excision systems,56 perhaps even by DNA topoisomerase242 or DNA gyrase activity.157 Despite being small, the effects of such changes can be very signiﬁcant and comprise things like complete loss of gene function (e.g. frameshift mutations), alteration of enzyme or protein speciﬁcity, or altered gene expression level.222 Many of these genetic processes and their effects have been carefully documented for several bacterial species, including pseudomonads. They are not speciﬁc for catabolic adaptation, although some nice examples exist in which catabolic enzymes acquired a change in substrate speciﬁcity by small “spontaneous” mutations and subsequently allowed the host bacterium to catabolize a new carbon compound.37,65,152 It further has become clear that even point mutation generating processes are not completely random, but may exhibit preferences for certain DNA sequences, or DNA structures, and the mutation rates themselves may be prone to strong variations.242 A well documented example of this are the hypermutator strains, in which the proofreading capacity of DNA polymerase or the mismatch repair system itself are mutated, leading to strongly elevated mutation rates.58,108 Interestingly, such strains are not per se less viable than strains with a normal proofreading activity.108 In addition, it has been established that starving cells in stationary phase may exhibit elevated mutation rates.171 Other genetic mechanisms operate at a larger scale, resulting in DNA duplications, deletions, inversions, recombinations, insertions, and the like. These effects are generally thought to be caused by RecA-dependent recombinatory mechanisms184 or site-speciﬁc recombinases, but can also occur through illegitimate recombination (i.e. between regions without noticeable identity), which might involve the activity of DNA topoisomerases or gyrase.157,121,200

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From fascinating research on the highly recombinatory strains P. stutzeri and Acinetobacter sp. strain ADP1 it has become clear that DNA recombination can even take place with only four identical base pairs between two targets (albeit at low frequencies) and can also give rise to large intrachromosomal duplications.65,121,157 In addition to general recombination activities, many different site-speciﬁc recombinatory systems may operate in the bacterial cell, such as encoded by insertion (IS) elements and transposons,114,115 integrons or integrases. The cut-and-paste mechanisms of insertion elements may lead to deleting, recombining, and inserting intervening or ﬂanking DNA. Although this again is not something speciﬁc for catabolic pathways, a number of good examples exist in which insertion elements are ﬂanking catabolic genes,202,222,243 transposing parts of or complete catabolic pathway gene clusters (e.g. the xyl genes on the TOL plasmid pWW0) or have been assumed to be responsible for the acquisition of parts of the catabolic genes (see below and Figure 1). Quite astonishingly, a number of extremely promiscuous IS elements exist with absolute sequence conservation (Table 2). Most notably at this moment are IS6100 and IS1071, two IS elements associated to a number of catabolic gene clusters, which are very widespread among completely different bacterial taxa, while remaining 100% sequence identity. This in itself already demonstrates that IS elements are being transferred between different bacterial genera and are extremely resistant against mutational drift. Furthermore, IS elements may carry promoter sequences,96 provide regulatory signals, and thus determine activation or deactivation of silent genes.22,47,64,96,110 A very peculiar example in this case is found in P. stutzeri OX1.22 This bacterium can use toluene and o-xylene as sole carbon and energy source, but in addition has a silent catabolic pathway for m- and p-xylene, which is blocked by the insertion of the IS element ISPs1. Spontaneous m- and p-xylene-degrading mutants develop which at the same time have lost the ability to utilize o-xylene. In these mutants the IS element has excised from its position upstream of the xylC gene and integrated into the genes for toluene/o-xylene monooxygenase (ToMO).12,22 Increasingly, also integrases from prophages and from genomic islands are implicated in the gain and loss of function through excision or integration of large genomic regions. Most bacterial genomes contain a dozen or so of predicted integrase genes24,28,49 and very often detectable traces of large-scale inversions or insertions of “foreign” material in their genomes (see below).68 Integrases from integrons can catalyze an interesting inverse process of capturing speciﬁc circular DNA molecules at speciﬁc target sites located downstream of the integrase,71 forming under certain cases cassette-like structures known as superintegrons.167 Apart from mechanisms operating within one cell, spectacular actions are performed by lateral or horizontal gene transfer processes, in which more than one partner contribute to the outcome. Several microorganisms take up DNA molecules spontaneously from the extracellular environment during parts

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Figure 1. Schematic structures of completely sequenced “catabolic” plasmids and other mobile genetic elements. Plasmids are drawn in linear fashion as a thin black line. Regions of interest for catabolic gene functions, plasmid maintenance, conjugative transfer, and for mobile elements are schematically indicated as boxes, drawn approximately to scale. Insertion sequences are shaded gray, genes for integrases are black. The incompatibility group and hom*ologies of conjugative systems (as % amino acid identity) are indicated on the right, if known. Transposable structures are depicted below as dotted lines. References and gene assignments: pDTG1 (Genbank accession number AF491307), P. putida NCIB 9816-4,47 par/res, plasmid partitioning and resolution; nah, naphthalene degradation upper pathway; sal, salicylate degradation; tra, transfer and nicking;

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of their normal growth cycle137 and can efﬁciently incorporate (parts of) this DNA in their own genome. Among pseudomonads, P. stutzeri is the only known member to have this potential.112 On the other hand, “inducible” transformation by electrical current from lightning has been implicated in DNA uptake by non-spontaneously transformable bacteria.112 Phage transduction is a further mechanism of potential DNA transfer to new recipients, and most genomes contain prophages or parts of prophages which potentially can be transduced, cotransduced, or at some point in their history were transducable. There is a current revival of phage genomics and its contribution to shaping genome structure.30 However, the role of phages in catabolic evolution per se is not well described. Particularly pronounced in catabolic pathway evolution are conjugative systems, which lead to the duplication and mobilization of genes from one cell to another. In the ﬁrst place, conjugation may be mediated by plasmids. Indeed, a large number of conjugative plasmids carrying catabolic genes have been described173,237 (Table 1 and Figure 1). Conjugative plasmids are ideal vehicles for acquiring and collecting DNA from a microbial community, and they do not only carry catabolic genes, but equally frequently antibiotic resistance genes, heavy metal resistances and often additional unknown functions.95 Plasmids probably play such an important evolutive role, ﬁrst of all because they are extrachromosomal self-replicating DNA molecules and therefore possess a high level of ﬂexibility compared to chromosomes by allowing extensive DNA rearrangements without disturbing cell integrity. Secondly, plasmids are intrinsically prone to DNA recombinations due to frequent carriage of IS elements or transposons (Figure 1). Thirdly and most importantly, large plasmids are self-transmissible and can often mobilize co-resident plasmid replicons ← mpf, mating pair formation. Plasmid pWW0 (AJ344068) from P. putida mt-2,67 xyl, genes for xylene degradation. Plasmid pADP-1 (U66917) from Pseudomonas sp. strain ADP1,119 atz, atrazine catabolism; mer, mercury resistance; trb, type IV secretion system. P. resinovorans CA10113 plasmid pCAR1 (AB088420), ant, genes for anthranilate degradation; car, genes for carbazole to anthranilate conversion; trh, conjugative transfer system. Sphingomonas aromaticivorans165 plasmid pNL1 (NC 002033), bph, genes involved in biphenyl degradation. Pseudomonas sp. strain ND6111 plasmid pND6-1 (AY208917), cat, genes hom*ologous to those encoding catechol degradation via ortho cleavage. Cupriavidus necator (Ralstonia eutropha) JMP134211 plasmid pJP4 (AY365053), tfd, genes involved in degradation of 2,4-dichlorophenoxyacetic acid. A. xylosoxidans230 plasmid pEST4011 (AY540995). Delftia acidovorans strain B189 plasmid pUO1 (AB063332), deh, genes for dehaloacetate dehalogenase. IncP-1beta plasmids R751,205 pB382 and pB10175 (AJ564903), Ab-R, genes for antibiotic resistances. Achromobacter xylosoxidans (Jencova et al., unpublished results) plasmid pA81 (AJ515144), mocp, chlorocatechol degradation; hyb, salicylate hydroxylase gene; ohb, ortho-halobenzoate 1,2-dioxygenase. Ralstonia oxalatica A5210 biphenyl transposon Tn4371 (AJ536756). Pseudomonas sp. strain B13 (Gaillard et al., unpublished results) clc element (AJ617740), clc, genes for chlorocatechol degradation, amn, genes for 2-aminophenol degradation, “virB4,” gene with hom*ology to virB4, hel, putative DNA helicase, ssb, putative single-stranded DNA binding protein.

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Table 2. Occurrence of IS1071 (A) and IS6100 (B) in different bacteria. (A) Organisma Delftia acidovorans Pseudomonas sp. Arthrobacter aurescens Cupriavidus necator (Ralstonia eutropha) JMP134 Comamonas testosteroni C. testosteroni BR60 Delftia acidovorans Delftia acidovorans Ralstonia metallidurens CH34 Achromobacter xylooxidans Uncultured organism Pseudomonas putida Burkholderia cepacia Pseudomonas pavonaceae (B) Distribution of IS6100b Mycobacterium fortuitum Pseudomonas aeruginosa Xanthom*onas campestris Acinetobacter baumanni Klebsiella pneumoniae Sphingomonas paucimobilis Corynebacterium diphteria Shigella ﬂexneri Agrobacterium tumefaciens Serratia marcescens Sphingomonas herbicidovorans Arthrobacter sp. Klebsiella oxytoca Corynebacterium glutamicum Salmonella enteritica Pseudaminobacter Ochrobactrum sp. strain mp-3 Escherichia coli Arcanobacter pyogenes Aeromonas salmonicida a b

As per Genbank screening d.d. January 2005. As per Genbank screening d.d. July 2004.

Plasmid or gene cluster

Number of copies

pUO1 pADP1 pJP4

2 copies 3 copies 2 copies 1 copy

pTSA pBR60 pdeA gene cluster tfd genes pMOL28 pEST4011 pB10 pTDN1 mdc cluster deh genes

2 copies 2 copies 1 copy 1 copy (partial) 1 copy (partial) 2 copies 1 copy, 1 partial 1 copy, 1 partial 1 copy 1 copy

Tn610 Plasmid R1033 Integron Integron ≈10 copies 2 copies

R478 plasmid pOAD2 plasmid, pACM1 plasmid pTET3 plasmid,

pHSH pAP2 pRAS1

5 copies

3 copies 2 copies

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and even plasmid replicons in a contacted cell (retrotransfer).206 By doing so they transfer, pickup, and distribute any newly formed catabolic operons (or any other captured DNA) throughout microbial communities. The promiscuous and selﬁsh nature of plasmids is demonstrated by their ability to inﬂuence their host to cope and survive in hostile environments95 and to maintain their own life style. In this respect plasmid-located operons for catabolism of alternative carbon sources (e.g. xenobiotic compounds) give a similar advantage to their bacterial host. The “selﬁshness” of plasmids is clear from such functions as copy number control, a system for multimer resolution, partitioning, post-segregational killing, conjugative transfer, and mobilization to guarantee their own maintenance and distribution. The genes for those functions are organized in the form of inter-regulated and often juxtaposed operons collectively termed the plasmid backbone.204 There is now growing evidence that speciﬁc chromosomal regions may also be mobilizable or self-transferable, or iterate between a plasmid replicative and a chromosomally integrated state (a class of elements known as integrative and conjugative elements, ICE), which means that some of the exclusivity and ﬂexibility which previously had been reserved for conjugative plasmids is also available to chromosomal regions.28,49,226 For a number of catabolic pathways, the complete sequence of the “vehicle” carrying the pathway genes has been determined (Figure 1). Among those we now ﬁnd conjugative and non-conjugative plasmids and two ICE, but this list will surely expand in the next few years. Some details of these mobile catabolic entities will be presented further below, but an overall picture emerges of more or less independent vehicles which can acquire accessory genes in regions of the “backbone” which are ﬂexible enough to withstand insertions. Quite a number of them belong to the IncP1-beta subgroup (e.g. pJP4, pUO1, R751, pA81, pB10, pADP1), which has allowed detailed hypotheses on how the current plasmid structures evolved by insertions into an ancestor core IncP1-beta plasmid (e.g. R751 or pB10). We can also conclude that there is no big difference for vehicles carrying catabolic genes, antibiotic resistance genes, or virulence functions. This became again obvious from the IncP1-beta group,175 which has members of both kinds (catabolic and resistance), and from ICE such as the clc element, which have large regions of high hom*ology to pathogenicity islands (see further below).49,226

5. EXPANSION OF CATABOLIC PATHWAYS BY LATERAL GENE TRANSFER Many ideas on catabolic gene evolution started with the dissection of (now) typical degradation pathways such as those for octane, xylene, toluene, naphthalene, or biphenyl. It became obvious very early on that the properties to

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degrade octane, xylene, toluene, or naphthalene were often located on plasmid DNA, which could be transferred from the organisms degrading the compound (donor cell) to other recipient bacteria.9 Numerous other plasmids have been described in the literature carrying genes for catabolic pathways, both fragments or individual complementary genes to a pathway, or clusters for complete “peripheral plus intermediate” pathways (e.g. toluene or naphthalene). Many of these plasmids were shown to be self-transmissible in the laboratory, or could be mobilized by other conjugative systems. Transfer to a new recipient can result in an active degradation pathway in the recipient cell, but this must not be necessarily so. In ﬁrst instance, selection for transconjugants in laboratory conjugation experiments had always been for the property to use the carbon compound for which the catabolic enzymes were encoded on the plasmid. But in other approaches in which other selectable (i.e. antibiotic resistances) or non-selectable markers (i.e. GFP) were introduced on the catabolic plasmids,38 it became apparent that transfer is also taking place to hosts without pathway selection.43 There is now ample evidence to prove that plasmid transfer is not a laboratory artifact, but is actually taking place in natural environments. On several occasions, plasmids migrated from deliberately introduced donating strains to recipient cells in the same microbial community. This had been clearly shown in experiments in which researchers attempted to accelerate the degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) in soils by inoculating the bacterium Ralstonia eutropha JMP134 (pJP4), and the pJP4 plasmid turned up among the native microbial cells.45,125 In other experimental systems, it could be demonstrated that the same plasmid with the genes for naphthalene degradation (pDTG1) showed up in several different host bacteria when the environment was contaminated with polycyclic aromatic hydrocarbons.81,241 A very peculiar situation occurred in which a plasmid from a deliberately released phenol-degrading P. putida could be reisolated after a number of years from bacteria in the same environment, although the original donor strain could not be retrieved.142

6. TOLUENE DEGRADATION AND THE TOL PLASMIDS Although we cannot argue that toluene is a novel synthetic compound, exposure to toluene (and benzene, xylenes, and ethylbenzene; collectively called the BTEX compounds) is one of the most frequent human-caused pollution disasters.197,198 Therefore, we have to assume that BTEX spills nevertheless disturbed many microbial communities and perhaps selected for bacteria with more efﬁcient BTEX metabolic properties. Toluene degradation is very common among pseudomonads and at least ﬁve different pathways are known for aerobic degradation. The classical TOL plasmid (pWW0) harbors a fully functional

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set of genes for the degradation of m-, p-xylene, and toluene via (meta-) toluate and (methyl-) catechol to pyruvate and acetaldehyde, including a sophisticated regulatory system for pathway expression.9,237 In our deﬁnition from above, this means that pWW0 provides not just “peripheral” catabolism, but a complete catabolic pathway, since the end products directly enter at the level of pyruvate and acetyl-CoA, thus feeding into the TCA cycle. The intermediate catabolic pathway is known as the meta cleavage pathway,76 because of the action of a catechol 2,3-dioxygenase that cleaves (methyl-) catechol at the meta position with respect to the two hydroxyl groups. At closer look, even the meta cleavage pathway for catechol degradation itself is a redundant intermediate pathway, since two branches (e.g. (i) 2-hydroxymuconic-semialdehyde dehydrogenase, 4-oxalocrotonate isomerase, and 4-oxalocrotonate decarboxylase and (ii) 2hydroxymuconic-semialdehyde hydrolase) produce the same downstream intermediate (2-oxopentenoate).76 The genetic organization for and regulation of the toluene and xylene catabolic pathway of TOL plasmid pWW0236 has been studied in great detail. The genes for toluene and xylene degradation (the xyl genes) on pWW0 are clustered in two operons, named the upper and meta pathway operon according to their encoded functions73–76,238 (Figure 2). Both operons are separated by some 14-kbp DNA.60 Expression of the structural xyl genes on pWW0 is controlled by two positively acting regulatory proteins encoded by the genes xylR and xylS,59,87 located adjacent to the 3 end of the meta pathway operon and transcribed divergently.192 All the other known TOL plasmids also carry the two operon types mentioned above with remarkably conserved gene order and with xylS and xylR regulatory genes, although the number of operons and regulatory genes may vary (see below). The pWW0 plasmid with the xyl gene clusters contains various (potential) transposable and insertion elements. First of all, the xyl operons are ﬂanked by two identical insertion sequences in direct orientation and 39 kb apart, named IS1246.158 Although their activity has not been demonstrated experimentally, the two copies of IS1246 have been associated with duplications181 and deletions of the intervening 39-kb DNA segment.15,89,181,239 The 39-kb region is enclosed within a 56-kb large transposon Tn4651. Tn4651 itself is part of an even larger (70-kb) sized transposon Tn4653. Both Tn4651 and Tn4653 are functional class II transposons of the Tn3 family.214–216 On the related TOL plasmid pWW53 a 39-kb transposon (Tn4656) is found.213 Its transposase TnpA and TnpR resolvase are 95% and 87%, respectively, identical and functionally interchangeable with those of Tn4653.213 Both Tn4651 and Tn4653 were shown to transpose into various plasmid replicons34,89,107 and to the bacterial chromosome.89,181 P. putida strain MW1000 even carries a Tn4651-like TOL transposon in its chromosome.182 Transposition functions are assumed to be present on pWW15 and the related TOL plasmids pWW14 and pWW74 as well.35 Two other IS elements are present on pWW0, one of which is 100% identical to the IL-IS 2 element

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Figure 2. Mosaical variation of TOL plasmids. (a) Organization of the xyl genes on pWW0, with indication of transcription from mapped promoters. (b) Comparison between xyl clusters of pWW0 and other TOL plasmids pWW53, pDK1,7–8,134,180 pWW15,98,130,235 and pSVSs.177 For further explanation, see main text. Figure courtesy of Vladimir Sentchilo.

of the deep-sea Gammaproteobacterium Idiomarina loihiensis. The sequence of pWW0 and its comparison to others suggest that the current structure can be derived from a single original insertion of the Tn4563 transposon into an IncP-9 ancestor plasmid.67 All the further insertions took subsequently place in Tn4563. The self-transfer process of pWW0 is mediated by a conjugative system encoded by the tra and mpf genes. The incompatibility determinants of pWW0 belong to the IncP-9 group. Best matches of the counterparts of tra and mpf of pWW0 with around 70–80% predicted amino acid sequence identity are

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currently two other conjugative plasmids in Pseudomonas: pBI709 (which encodes no further catabolic properties) and pDTG1, a 83.0-kb plasmid carrying gene clusters for naphthalene degradation (Figure 1).67 Survey of many more environmental Pseudomonas isolates with TOLlike plasmids have shown that they are widely distributed, and almost exclusively related to a phenotype of toluene, m-xylene and meta-toluate degradation via meta cleavage. Interestingly, these surveys revealed that in essence the “natural” variation of xyl genes is limited to (currently) three distinguishable groups (Figure 2). Plasmid pWW0 carries the xyl genes in single copy only (upper and meta pathway operon, one copy each of xylS and xylR). Many TOL plasmids, however, carry duplications of the xyl genes. For example, two highly hom*ologous yet distinguishable copies of the meta pathway operon (meta I and II) are present on pWW53,134 on the related TOL plasmids pWW5, pWW74, and pWW88,35 and on various pSVS plasmids from Pseudomonas isolates from Belarus177 (Figure 2). Nucleotide alignments showed that the meta, meta I, and meta II operons constitute three distinguishable groups.177,183 Plasmids pWW15, pWW14, pWW20, and pWW7435,98,240 carry duplications of both xyl operons, with one of the meta pathway operons being incomplete.130,235 Two non-identical copies of the regulatory xylS gene are found on pDK16,180 and three on pWW53.6 Three groups of upper pathway clusters were also postulated on the basis of a comparative survey of two dozen Pseudomonas mxylene degraders from Belarus and the classical pWW0, pWW53, and pWW15 plasmids.177 Variations among the pSVS-type TOL plasmids included single or double copies of the operons for meta cleavage of catechol, and small insertions and nucleotide polymorphisms in individual xyl genes. Whether the xyl gene cluster duplications occurred via recombination with other replicons or resulted from one ancient duplication event and kept afterward remains an open question. Duplications are potentially unstable and prone to deletions of intervening DNA via hom*ologous recombination, which has often been observed in toluene-degrading organisms maintained in the lab during cultivation on benzoate.15,102,144,180 However, double copies of xyl operons persist in many natural isolates pointing at some selective advantage. An important ﬁnding was that the plasmid backbones (the “vector”) into which the xyl genes had been inserted, were very variable, suggesting that the xyl operons themselves move as stable entities which can only be proﬁtably transferred as a whole. Whereas pWW0 belongs to the IncP-9 plasmid incompatibility group,10 most other studied TOL plasmids were shown to belong to different and even unknown incompatibility groups.177 Only pRA1000 from Alcaligenes eutrophus strain 345, which exhibited a virtual identical restriction enzyme proﬁles as pWW0,86 and pSVS15 from P. graminis,177 were shown to belong to the IncP-9 group. Other TOL plasmids also differed considerably in size and restriction enzyme proﬁles from each other and from pWW0. Furthermore, not all TOL plasmids are transmissible, indicating that xyl genes

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are carried on different plasmid backbones. Whether distribution of the whole xyl pathway to different plasmids is associated with the transposons Tn4651, Tn4653, and Tn4656 cannot be ﬁrmly concluded due to lack of detailed knowledge about the plasmid backbones and the DNA regions ﬂanking the xyl genes on the different TOL plasmids. Our knowledge about the evolution of the xyl genes itself is mainly based on pWW0. Several studies concluded that (i) the meta pathway operon originated as a fusion product of two independently evolved gene blocks, xylXYZL and xylTEGFJQKIH77 ; (ii) the upper and meta pathway operons evolved separately72 ; and (iii) the meta pathway operon, in the strict sense (i.e. xylT through xylH), probably resulted from a recombination event itself.20,77 This assumption was based on the ﬁnding that the xylK gene of TOL plasmid pWW102 was more hom*ologous to nahO of the naphthalene catabolism plasmid pWW6022145 than to corresponding sequences of pWW0 and pDK11 Also the xylE gene of pWW0 was proposed to have originated via recombination between xylE of pDK1 and nahH of naphthalene plasmid NAH7.20 It should be noted that the possibility to catabolize toluene is not solely given by the xyl-encoded pathways. At least four other aerobic pathways for toluene degradation have been characterized (Table 1), none of which, however, are located on a mobile genetic element. Nevertheless, although no evidence exist for spontaneous transfer of the tod genes, parts of it apparently have become captured in the formation of chlorobenzene degradation pathways (see below). Also the gene clusters for the other toluene pathways show evidence for mosaic-like combinations of individual genes or gene blocks, a point that has been observed previously and discussed extensively.221 However, based on DNA sequence relationships most of these presumed combinations must have taken place a long time ago and direct evidence for the combinatory mechanisms can no longer be retrieved.

7. POLYAROMATIC PATHWAYS The xyl-encoded pathways for toluene and xylene degradation are closely related to the nah-encoded ones for naphthalene degradation, but strangely, the two are almost never found together in one Pseudomonas, although there seems to be no apparent enzymatic reason for this to be so (e.g. enzyme incompatibilities). The few existing examples in which toluene and naphthalene degradation are both present in the same cell do seem to involve a plasmid with nah genes, but no TOL-like plasmid (Table 1). By the pioneering work of Harayama et al. it was demonstrated that the nah and xyl pathways are probably ancient hybrids.78 In fact, naphthalene degradation also proceeds via a meta cleavage intermediate pathway which is very similar to that operative in m-xylene degradation. A comparison between the two was one of the ﬁrst occasions to

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postulate “cassette”-like recombination mechanisms, by which bacteria could evolve new catabolic pathways not by slow single base pair polymorphisms but rather by recombining larger gene blocks in new proﬁtable combinations, like natural recombinatorial chemistry. The blocks or cassettes which could be recognized by comparing xyl and nah genes were (i) a meta cleavage pathway (common to both), (ii) the upper pathway for xylene oxidation to meta-toluate (xylUWCMABN), (iii) a meta-toluate oxidation cluster (xylXYZL), both speciﬁc for the xylene pathway, (iv) a naphthalene upper pathway cluster and (v) salicylate hydroxylase (nahG), and ﬁnally regulatory genes (xylR, xylS, nahR).76,77,78,233 As said above, the exact mechanisms of formation for these (evolutionary old) hybrids can no longer be derived with certainty. The fact that nah gene clusters occur on the same replicon types as xyl genes may be one reason as to why they have become mutually “exclusive.” However, nah genes are also found in chromosomal locations, such as in P. stutzeri AN10 or in P. aeruginosa 57 (Table 1). We have already mentioned the relatedness of the tra and mpf systems of pWW0 and pDTG1; the only other completely sequenced NAH plasmid, the 101-kb plasmid pND6-1, has a par system which is around 98% identical to that of the pL6.5 plasmid of P. ﬂuorescens.111 Available sequence information points to the existence of a few distinguishable operons for naphthalene degradation, but an overall very high degree of sequence conservation. On the classical NAH7 plasmid two clusters of nah genes occur, both of which are transcribed in the same direction with less than 5 kb of intervening DNA.245 Only the nahR gene, located upstream of the second cluster is oriented divergently. Both nah clusters on the recently completely sequenced plasmids pDTG1 from P. putida strain NCIB 9816-447 and pND6-1 from Pseudomonas sp. strain ND6111 are oriented face to face, although the gene order within the clusters is the same as for the NAH7 plasmid. In addition, the nahR gene on pND6-1 is much further away from the nahG gene as on NAH7 and pDTG1, which was attributed to the insertion of mobile elements. Both nah clusters on pND6-1 and pDTG1 have a larger intervening DNA sequence, with a few insertion elements (Figure 1). Interestingly, the nah-encoded meta cleavage pathway on pDTG1 is non-functional due to the insertion of an IS element between nahG and nahT, which probably prevents expression of the downstream located nah genes.47 The strain can still grow on naphthalene by the use of a chromosomally encoded ortho cleavage pathway for catechol degradation. The 83-kb pDTG1 plasmid has a typical IncP-9 backbone of about 33 kb, based on partitioning, replication, and transfer functions. The gene organizations of those are very similar to those of pWW0.47 In addition, also other regions, but with unknown function, are conserved between pDTG1 and pWW0. Dennis and Zylstra proposed that an ancestor of pDTG1 (perhaps of the same sort as the pWW0 ancestor) underwent several DNA integration steps before the ﬁnal formation of the present-day’s naphthalene pathway genes. An initial

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insertion of 6-kb of DNA from the plasmid pCAR1 took place into the ancestor ruvB gene.47 Subsequently, a single insertion of nah pathway genes might have taken place in the intA gene of the pCAR1 fragment, and ﬁnally, several other ISs (such as ISPre1) entered into this region. pND6-1, on the contrary, does not carry the ISPre1 sequences, but it does show an additional duplication of the nahG and nahF genes.111 This it has in common with the chromosomally located nah region of P. stutzeri AN10.23 Biphenyl degradation is also very widespread among bacteria both from gram-positive as well as gram-negative groups.195,221 Typically, biphenyl degradation (and in some cases simultaneously monochlorobiphenyl) is mediated by the bph gene products, leading to hydroxylation and cleavage of one ring, and formation of benzoate and 2-hydroxypenta-2,4-dienoic acid. All known bph genes share common ancestry, although the individual genes in the bph operons have been subject to reshufﬂing, deletion or new insertions.195,221 In contrast to the genes for naphthalene and toluene metabolism, those for biphenyl degradation are mostly not present on plasmids.195 Although there is no particular reason why bph genes would not be on plasmids, only few reports clearly demonstrate the involvement of plasmids in biphenyl degradation.85 On the contrary, despite being chromosomally located, genes for biphenyl degradation are reported to be transferable.126,193 One of the best characterized elements is Tn4371, the biphenyl catabolic transposon from a strain now classiﬁed as Ralstonia oxalatica A5.210 Although Tn4371 itself was not capable of independent transfer, it carries genes similar to tra and trb of IncP1-beta plasmids (Figure 1), of which apparently traI and traK are missing.210 The transposon can be mobilized on other plasmids, such as pSS50 or RP4.195 No evidence was found for the Tn4371 transposon in biphenyl-degrading pseudomonads,195 despite hom*ology of the bph genes. However, also the bph genes in P. putida KF715 seem to occur on a mobile region of the chromosome.126 This 90-kb DNA region was named the “bph-sal” element and contained in addition to the bph genes three genes for salicylate degradation. The element could be transferred from strain KF715 to other P. putida and from those to again others, suggesting independent self-transfer by the element. At least one other degradation pathway exists, which nicely illustrates the concepts seen above: reshufﬂing of a few operons with genes for catabolic pathways, either on conjugative plasmids or with help of transposable elements. This example consists of the degradation of carbazole, a heteroaromatic dibenzofuran-like molecule, which is degraded to anthranilate and 2hydroxypenta-2,4-dienoic acid via angular dioxygenation.113 Anthranilate is converted to catechol and 2-hydroxypenta-2,4-dienoic acid to acetyl-CoA.217 The genes for these enzymatic activities are located on plasmids in several Pseudomonas strains. For example, in one of these, P. resinovorans strain CA 10, a 199-kb plasmid pCAR1 was found, which was recently completely sequenced.113 The genes for carbazole degradation are organized in two clusters,

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ant and car, which are both contained within the 73-kb transposon Tn4676 (Figure 1). Several other IS elements ﬂank the ant and car gene clusters, suggesting that they were transposed onto an ancestor pCAR1 plasmid. Like for the xyl and nah clusters, also the ant and car genes have been found on other plasmids related to pCAR1, and in the chromosome.113 In short, these data on toluene, naphthalene, carbazole, and biphenyl degradation demonstrate that more or less coherent gene clusters have evolved, which have common ancestry (like between nah and bph, or nah and xyl), but now remain intact and are distributed via transposons and plasmids onto different replicons and in different bacteria. By detailed analysis it was possible to derive cluster analogies and postulate some of the past events that led to formation of the current structure of pathway genes. Small polymorphisms still found between genes for related degradation pathways argue for a continuing “evolution.” However, it seems that no further pathway expansion has been taking place in these classical pathways, which is in contrast to what is observed for catabolic pathways of more synthetic compounds.

8. CATABOLIC EXPANSION BY LATERAL GENE TRANSFER The best examples in my eyes for forward catabolic expansion come from those cases in which selection substrates were used which had no natural counterparts. Although it has been argued that we can never know which compounds truly are natural or synthetic,174 both the chemical nature and the large quantity of some applied synthetic compounds have almost certainly resulted in forward catabolic expansion of single bacterial strains by genetic mechanisms. The examples treated here consist of degradation of chlorobenzenes, atrazine, 2,4-D, and nitrobenzenes. In these cases the evidence has become very convincing that new catabolic pathways have evolved since the introduction of the synthetic compounds by acquisition of genetic material from different sources, which was successfully combined within a single organism.93,196,208,221 From analysis of different chlorobenzene degraders, we can even assume that the same events occur reproducibly in different organisms.

9. HERBICIDE DEGRADATION Microbial degradation of herbicides has served as outstanding example for the adaptive capabilities of microbial communities with respect to catabolic pathways. Most notably, bacterial strains have been isolated that had developed new pathways for degradation of 2,4-D, atrazine and to a lesser extent,

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Figure 3. Mosaical patterns in gene clusters for 2,4-dichlorophenoxyacetic acid and chlorocatechol degradation. Boxes indicate open reading frames, with their gene name assignment inside, and orientation (upper, lower strand 5 –3 ). Shadings compare highest percentages of identity among functionally related genes: black = ≈100%, gray (Delftia vs. pJP4) ≈ 82% amino acid identity, light gray (Delftia vs. pJP4) ≈ 55%. For further explanations, see main text. References, see Figure 1, or Delftia acidovorans,83 pP51,224 Variovorax paradoxus,218 Burkholderia cepacia.148

chloroaniline or other phenoxyalkanoic acids. To illustrate the potential of herbicides to act as selective carbon sources, it is worth to mention the worldwide production. Around 50,000 tons 2,4-D have been produced yearly,164 of which it was estimated that 100% entered the open environment. Depending on the application, target ﬁelds are treated with between 0.3 and 4.5 kg of active compound per hectare. Apparently, this has been sufﬁcient to select for a wide range of different bacteria capable of degrading 2,4-D, most of which occur in the Proteobacteria.61,62,94,97,219 The most thoroughly studied bacterium degrading 2,4-D is certainly Ralstonia eutropha (now Cupriavidus necator) JMP134 (pJP4),51 which culminated recently in the complete genome of the plasmid pJP4 (Figure 1)211 and a draft genome for the complete organism. For unknown reasons, true Pseudomonas spp. form a minority among 2,4-D degrading microorganisms. Rather, Beta- and Alphaproteobacteria dominate among 2,4-D degraders, but still the story is illustrative from the perspective of catabolic gene evolution. 2,4-D degradation capacities can be broadly divided in two groups: those of Beta- and Gammaproteobacteria, and those of Alphaproteobacteria, such as Sphingomonas or Bradyrhizobium61,219 . The beta and gamma groups have genes and gene organizations for 2,4-D degradation quite similar to those found on the pJP4 plasmid of R. eutropha JMP134, and are very often located on plasmids as well61,207,219 (Figure 3). Genes for 2,4-D degradation from the alpha group are quite different from those of pJP4. 2,4-D degrading organisms

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are most abundant in 2,4-D exposed areas, but occur even in sites with no prior history of 2,4-D application.94,97 Ralstonia eutropha JMP134 (pJP4) was ﬁrst described by Pemberton and colleagues.51 It was initially identiﬁed as Alcaligenes eutrophus and has now seen its name changed to Cupriavidus necator. The ability of R. eutropha to degrade 2,4-D lies encoded on the pJP4 plasmid, which further confers resistance to mercuric chloride, phenylmercury acetate, and merbromin. The 87.7-kb plasmid pJP4 belongs to the IncP1-beta incompatibility group.183 From the complete sequence it has become apparent that the plasmid backbone of pJP4 is highly related to that of other IncP1-beta plasmids (Figure 1), which has been the basis to postulate that an ancestor plasmid (perhaps like R751, pB10, or pB3) captured different catabolic and antibiotic resistance modules. The pJP4 plasmid is self-transmissible to various bacterial strains including E. coli, Agrobacterium tumefaciens, Rhizobium sp., P. putida, P. ﬂuorescens, and Acinetobacter calcoaceticus.51 The tfd genes are clustered on a 22-kb DNA fragment (Figure 3) and essentially comprise three gene cassettes from different origins103 : tfdA, encoding the ﬁrst enzyme needed to attack 2,4-D (α-ketoglutarate-dependent dioxygenase), tfdTCDEFB, and tfdRD I I C I I E I I FI I B I I K . The latter two clusters principally encode a pathway to convert chlorinated phenols via chlorocatechols and ortho cleavage to 3-oxoadipate.104,105,139,140,146 The ortho cleavage pathway for chlorocatechols is different from the chromosomally encoded ortho cleavage pathway for catechol (cat), but does not offer the organism a complete intermediate catabolic pathway, since it ends at 3-oxoadipate which cannot directly feed into the TCA cycle. Therefore, chromosomally located enzymes which convert 3-oxoadipate to succinyl- and acetyl-CoA are necessary to confer growth on 2,4-D. It has been argued that pathways for chlorocatechol degradation such as those encoded by tfdCDEF are considerably older than the 50 years or so that 2,4-D or other chlorinated substrates have been applied.174 Its original function probably was the same as it is today, i.e. the catabolism of chlorocatechols, which are commonly found in nature as are other chloroaromatics, such as chlorophenols.124 Interestingly, also 2,4-dichlorophenol exists as a natural compound, produced as a metabolite by a Penicillium sp.164 This may explain the existence, in a pre-2,4-D era, of a gene like tfdB and of the chlorocatechol pathway. However, the combination of a gene cluster for chlorophenol– chlorocatechol degradation with the gene for α-ketoglutarate-dependent 2,4-D dioxygenase (tfdA) must have been a recent event, given the truly remarkable mosaical variety of different genes for 2,4-D utilization61,219 (Figure 3). Already the pJP4 plasmid itself harbors two essentially complete and similar sets of genes for chlorophenol degradation with nevertheless different origins. Gene orders for the chlorophenol cluster are not conserved. Other more recently sequenced plasmids and gene clusters for 2,4-D and chlorophenol degradation conﬁrm this. On the pEST4011 plasmid from Achromobacter

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denitriﬁcans,230 the gene order of the tfd genes is: tfdD (ORF), iaaH, tfdRCEBKAF (Figure 3). The tfd genes of pEST4011 are up to 99% identical to those of plasmid pIJB1 of Burkholderia cepacia148 and of Variovorax paradoxus218 with a conservation of gene order, except for a small duplication in the region of tfdD and iaaH. However, they are only between 74% and 90% identical in predicted amino acid sequence to the gene products of the tfdII cluster of pJP4. Evolutionary events have taken another course in plasmid pMAB1 of B. cepacia.21 This plasmid displays an identical set of tfdCDEFB genes as pJP4, however, the second tfd cluster of pJP4 is lacking, possibly by a recombination between tfdT and tfdR. Finally, in Delftia acidovorans yet another combination of tfd clusters can be found,83 partially related to the tfd of pJP4, to that of pEST4011, and to the tcb genes for chlorocatechol degradation of Pseudomonas sp. strain P51.224 The activity of insertion elements in the formation of the tfd pathways has been postulated. A potentially transposable element comprising the IS element ISJP4 and a partial copy including one of its recognition ends is encompassing the complete tfdRD I I C I I E I I FI I B I I K cluster.110 The same bordering elements with an antibiotic resistance gene in between were shown to be functionally transposing in R. eutropha JMP289, a plasmid-free derivative of JMP134. Transposition of ISJP4 to the chromosome of JMP134 could also be detected. In addition, pJP4 carries a copy of the widely distributed IS element IS1071 (Table 2), which was shown to be responsible for large-scale plasmid rearrangements of pJP4 in growing cultures of R. eutropha and might have been inserting the ﬁrst tfd gene module in a pJP4 ancestor plasmid.211 Finally, a Tn3-related transposon with 86% amino acid sequence identity to a tnpA of the NAH plasmid pND6-1 is encoded on pJP4.211 The tfd genes on plasmids pEST4011 and pIJB1 are part of a 48-kb transposable element (Tn5530) ﬂanked by two copies of a hybrid insertion element IS1071::IS1471.148,230 Furthermore, an insertion element related to ISBPH is present downstream of the tfdF gene on pEST4011. The tfd genes of D. acidovorans are not plasmid, but chromosomally located. They are ﬂanked by two copies of IS1071 and IS1380, which form part of a larger duplicated region involving tfdR and tfdC as well.83 The components of the predicted conjugative system of pJP4 (trb and tra) are up to 99% identical in amino acid sequence with those of the IncP1beta plasmids R751 of Enterobacter aerogenes and pB3, an environmentally captured plasmid.211 Although pIJB1 belongs to the IncP1-beta group, the backbone of pEST4011 is different from pJP4 as well and Tra and Trb systems point to about 80% sequence conservation with those of pB3 pseudomonads.230 Another fascinating example for catabolic gene evolution is that of the pathway for atrazine degradation. We have to assume that atrazine, like 2,4-D, is a fully synthetic compound, which was speciﬁcally developed as herbicide and of which large quantities were released into the environment. A wide variety of bacteria capable of degrading atrazine have now been reported, which were isolated from agricultural soils exposed to this herbicide. They include members

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of the genera Pseudomonas, Rhizobium, Acinetobacter, Arthrobacter, Nocardiodes, and Agrobacterium.119,166,169,209 For Pseudomonas sp. strain ADP1, the genes for atrazine degradation are localized on the 100-kb pADP1 plasmid, but form four distinct clusters: atzA, atzB, atzC, and atzDEF (Figure 1).119 The atzA, atzB, and atzC genes have also been detected in other organisms with up to 100% sequence conservation, are almost exclusively present on plasmids (of different nature) and are frequently unstable and lost by recombination via insertion elements.209 In some strains, the function encoded by atzA is performed by the trzN gene product, which in itself is very widespread and conserved as well.169,209 Recent sequencing of a plasmid fragment from Arthrobacter aurescens conﬁrmed the identity of atzB, atzC, and trzN in this strain and demonstrated that large fragments apparently have been exchanged and newly recombined between pADP1 plasmids and other Arthrobacter plasmids.169 Further indication for the recent (independent) integration of the atzA, atzB, and atzC genes on pADP1 and similar vehicles is the complete absence of regulation for gene expression.119 The wide distribution of atz and trz genes on different vehicles and in different bacterial genera shows that probably transposition and conjugative events together were responsible. Furthermore, it seems to suggest that evolution of the atrazine degradation pathway occurred independently and reproducible, and cannot be attributed to a singular arisal and further distribution.

10. CHLORO- AND NITROAROMATIC DEGRADATION Degradation of chlorobenzenes has been taken as a good test case for demonstrating the capacity of microbial communities to expand their catabolic properties. Chlorobenzenes are only known as synthetic compounds, although other natural chlorinated aromatic compounds do exist (e.g. chlorophenols, see above). Microorganisms do not generally appreciate chlorobenzenes, probably because of their immediate toxicity to the membrane or the formation of toxic intermediates. It had been recognized very early on160,161,163 that toluenedegrading bacteria such as P. putida F1 were capable of at least partially transforming chlorobenzenes to chlorocatechols by the activity of their toluene dioxygenase systems. However, toluene-degrading organisms tend to induce a catechol 2,3-dioxygenase activity when growing on toluene and this enzyme mostly cannot deal effectively with chlorocatechols as substrates.99 Recently, some exceptions to this were described.116,117 It was therefore attempted to combine by “natural genetic engineering” (conjugative transfer) a toluene degradation pathway and one for chlorocatechol degradation within one organism. Indeed, this could be accomplished, for example, by matings between P. putida F1 and Pseudomonas sp. strain B13, a 3-chlorobenzoate-degrading organism, in which case the genes for 3-chlorocatechol degradation are transferred from B13 to F1.154,156,161,162 Interestingly, however, microorganisms could also be isolated

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from chlorobenzene contaminated environments or from artiﬁcially contaminated natural environments in the laboratory, which were capable of growing on chlorobenzenes as sole carbon and energy source.18,19,70,123,191,225,228 Although initially classiﬁed as Pseudomonas, most of these strains were afterward shown to belong to the Betaproteobacteria, but this does not change the interest in the accomplishment. Genetic analysis showed that almost exclusively and reproducibly a natural recombination between a toluene degradation pathway (of the tod-type) and a chlorocatechol degradation pathway had occurred. In three cases the genes for the toluene dioxygenase and cis-dihydrodiol dehydrogenase had been transferred to the new recipient, in one case without a complete todF gene (normally upstream of the toluene dioxygenase genes), but in all cases without a functional todE gene (normally downstream of the toluene dioxygenase genes). In all three cases, insertion elements were nearby the newly inserted genes, forming still active transposable structures (e.g. Tn5280, the tcb chlorobenzene transposon of Pseudomonas sp. strain P51229 ) or non-active structures (the mcb genes of Ralstonia sp. strain JS705123 ). In Pseudomonas sp. strain P51 the tcb genes had recombined on a transferable plasmid (pP51) already encoding a chlorocatechol degradation pathway (tcbRCDEF genes).227 The tcbRCDEF genes on their turn also show up in the pathway for 2,4-D degradation in D. acidovorans (Figure 3), on the pA81 plasmid from A. xylosooxidans (Figure 1) (Jencova, V., unpublished results) and in a pathway for 4-chlorobenzoate degradation in R. eutropha NH9.132 In Ralstonia sp. strain JS705 the mcb genes had recombined within the clc genes for chlorocatechol degradation on a self-transmissable genomic island.123 On the basis of PCR ampliﬁcation and sequencing it became apparent that the same IS elements seemed to have captured a tod-like region twice, but in a slightly different form and in a slightly different organism19 (Figure 4). Most interestingly, for Ralstonia sp. strain JS705 it was possible to trace back the ancestor donor of the mcb genes, which was isolated from groundwater in the same area. This “donor” strain was a toluene-degrading organism with a 100% identical nucleotide sequence of the mcb genes.123 The border of the excised and transferred fragment could be exactly determined. As more and more sequences will become available, it will probably be clear for other cases of catabolic expansion as to where the donating genes may have come from, but until then the case of Ralstonia sp. strain JS705 stands as one of the few where ongoing pathway evolution by “natural recombination” has been observed. It is now known that a second possibility to form a monochlorobenzene degradation pathway is existing in bacteria in the environment. In these organisms, like P. putida GJ31 or P. ﬂuorescens SK-1, the catechol 2,3dioxygenase (cbzE), in contrast to for example todE, is capable of converting 3-chlorocatechol and eliminating the chlorine atom during formation of muconic semialdehyde, which can then subsequently be degraded in a classical meta cleavage pathway.66,117 However, it is not known whether speciﬁc adaptive

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HOOC

COOH

HOOC OH

OH CI

Toluene

H OH

O COOH

OH pyruvate OH

OH CH3 H

CH3

OH H

CH3

OH OH CI

Figure 4. Reproducible gene capturing of a cluster for toluene dioxygenase in the formation of the degradation pathway for chlorobenzene. (a) Clc-mcb gene region of Ralstonia sp. strain JS705,123,228 tcb gene regions of plasmid pP51 in Pseudomonas sp. strain P51,226,233 and tec regions in Burkholderia sp. strain PS12.19 (b) Conceptual idea of pathway formation by gene capture and natural recombination. For further explanation, see main text.

mechanisms were necessary to “evolve” this pathway or if it had not been detected because of slower growth of the organisms compared to those degrading chlorobenzene via a modiﬁed ortho cleavage pathway. Similar evidence for pathway expansion has been retrieved from detailed studies on degradation of nitroaromatic compounds, in particular for nitrobenzene and 2,4-dinitrotoluene190 (Table 1). Nitrobenzene degradation involves the linkage of a conserved aminophenol degradation pathway with ﬁrst a reduction

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of the nitro group to hydroxylaminobenzene and secondly a rearrangement to 2-aminophenol. 2-Aminophenol degradation proceeds analogously to catechol degradation via meta cleavage, except that the individual enzymes accommodate amino substituents. The pathways were characterized from P. pseudoalcaligenes JS4593 and P. putida HS12.138 Until now it is rather mysterious as from where the genes for nitrobenzene nitroreductase originated, as they only show limited hom*ology to other ﬂavoprotein reductases and even to 4-nitrobenzoate nitroreductases.93 The mutase enzyme needed for the second step, on the contrary, is widely present in pathways such as for nitrophenol and 2-nitrobenzoate. The two hydroxylaminobenzene mutase genes from strains JS45 and HS12 are highly hom*ologous, but strain JS45 carries a second paralogous enzyme with only 44% amino acid identity.44 The mutase gene in strain HS12 is carried on a separate plasmid than the rest of the genes for 2-aminophenol degradation (pNB1, pNB2, Table 1). The pathway for 2,4-dinitrotoluene seems composed from three modules.92 First a multicomponent dioxygenase closely related to naphthalene dioxygenase, but with inclusion of two genes for a terminal oxygenase for salicylate hydroxylase, which, however are not needed for the dinitrotoluene pathway. Secondly, a ﬂavoprotein monooxygenase encoded by the gene dntB, which is responsible for attacking the 4-methyl-5-nitrocatechol that results from the ﬁrst module’s activity. There is no closely related ortholog known for this enzyme at present. The ﬁnal module consists of a pathway for trihydroxytoluene degradation which begins with a ring-ﬁssion oxygenase dissimilar to other known oxygenases and continues with a pathway analogous to amino acids degradation. In one organism degrading 2,4-dinitrotoluene, Burkholderia cepacia R34 the genes for these modules were clustered in a 20-kb region on a plasmid. In another Burkholderia sp. strain DNT the genes were present on a plasmid as well, but did not cluster in one region.93

11. THE CLC ELEMENT We have seen the large involvement of conjugative plasmids as vehicles for acquisition and distribution of genes for catabolic pathways. One last paragraph will be devoted to describing the curious clc element, a conjugative element that integrates into and excises from the chromosome. This ﬁnal example will show that the possibilities for acquisition of mobilization of genes is not limited to plasmids, but can in essence comprise all chromosomal genes as well. Furthermore, it serves to demonstrate that formation of catabolic pathway clusters employs the same mechanisms as generation and distribution of pathogenic functions. In the bacterium Pseudomonas sp. strain B13, the ﬁrst bacterium described to degrade 3-chlorobenzoate,52 self-transfer of the capacity for

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chlorocatechol degradation was well known but ﬁnally could not be attributed to plasmid mobilization.232 Instead, this transferable element turned out to be an excisable genomic region and is now known as the clc element because of its ability to provide chlorocatechol degradation to the host.154 In addition, the clc element carries a complete cluster of genes for 2-aminophenol degradation (Figure 1). The clc element is known as a genomic island (GEI), among which pathogenicity islands are found as well, although most genomic islands are (no longer) mobile. Fully functional GEI are also part of what was previously designated as ICE; integrative and conjugative elements.26 The clc element has a size of 105 kb and we know of one natural variant which is very closely related. This clc-like element was present in Ralstonia sp. strain JS705 (see above), an organism degrading chlorobenzenes and was isolated from contaminated groundwater in the United States.123,228 The clc element is not only self-transferable in laboratory “matings,” but also transfers in more complex communities and technical systems from strain B13 to other Beta- and Gammaproteobacteria, such as Ralstonia, Pseudomonas putida, Burkholderia sp. and P. aeruginosa.156,162,194,247 This demonstrated that the clc element is not a laboratory curiosity, but a type of mobile DNA element present in natural microbial communities which previously had not been recognized. With the current explosion of bacterial genome data and detailed bioinformatic approaches for comparative genome analyses, it has become apparent that GEI are very widespread and must have been important for shaping the bacteria genome structure.24,129 The evidence for the existence of genomic islands had been obtained long before the large-scale genome sequencing projects.69 Mostly known as pathogenicity islands (PAI), they were known to be involved in the instability or spontaneous loss of virulence functions in pathogenic bacteria. Now, by combining information from various approaches, such as genometry and experimental genetics, genomic islands appear as a widely diverse class of DNA elements in different stages of functionality with relationships to bacteriophages, conjugative transposons, and plasmids.26,49 Genomic islands are therefore, like plasmids, evolutionary and adaptively very interesting elements, because (i) they are plentiful in most bacterial chromosomes and seem to be responsible for shaping a large part of the bacterial genome,28 (ii) they occur in different “stages” of functionality or evolutionary development, (iii) they seem to be hot spots for acquisition of auxiliary functions and contribute to horizontal gene transfer, and (iv) they seem to have a life style of their own, but may inﬂuence central processes of the core bacterial genome.26,49,128,226 A GEI has features different from conjugative plasmids. It carries one or more of the following features: a more or less speciﬁc chromosomal insertion site, a mechanism for inserting and excising from that site, functions for self-transfer (either via phage particles, conjugation, or unknown), regulatory

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functions which control integration, excision or transfer, and a variable region. The core regions on genomic islands (insertion sites, integration and excision functions, and transfer and mobilization) are not free from deletions or acquisitions either (as expected).100 In many cases, genomic data only show traces for a genomic island: a gene for an integrase nearby a gene for tRNA, but no further evidence for transfer and mobilization functions, or perhaps not even for the target site duplication.141 In some cases, even the integrase gene is unfunctional or absent and the region of the genomic island can only be detected by aberrant nucleotide sequence composition compared to the rest of the chromosome of the host cell. Transfer and mobilization functions may exist,26 although several genomic islands (as explained below) seem to have transfer systems unsimilar to those of conjugative transposons or conjugative plasmids. Variable regions have attracted much interest, because their characterization showed that genomic islands can acquire different functions whilst keeping a certain “core” necessary for integration, excision, transfer, and regulation.16,106,131 Variable regions can contain pathogenicity determinants such as virulence factors, adhesins, small molecule metabolism, multidrug resistance genes, hence the term pathogenicity islands.49 However, the pathogenicity character may be less pronounced and instead the variable region may encode functions such as degradation of aromatic compounds or even symbiosis factors. As their deﬁnition says, genomic islands (GEI) reside on the chromosome. However, their position is not random and they are often located nearby tRNA genes.26 From the few examples of which mechanistic information exist, it is known that GEI, like bacteriophages and conjugative transposons have at some point integrated at those positions, using site-speciﬁc recombination mechanisms.25,36,155 In all hosts examined, the clc element resides sitespeciﬁcally in the chromosome at the most 3 18-bp sequence of a tRNAGly gene.154,155,194 Depending on the host, the clc element can be present in one, two, or more copies. Also in strain B13 two copies are present. At the other end of the element, a copy of this 18-bp sequence is found. A critical feature of the clc element’s life style is formed by the integrase, the gene of which (intB13) is found close to the tRNAGly insertion site and oriented away from it. The integration process into the chromosome is mediated by the IntB13 integrase enzyme.155 One of the important features of GEI is that they do not remain stably integrated in the chromosome, but can excise by recombination between both “ends.”27,109,155,176 Small amounts of the excised clc element can be detected in cultures of strain B13 itself by Southern hybridization and PCR.155 Sequencing of this excised form showed that it consists of a closed DNA molecule in which both 18-bp repeats have recombined again to one.155 The current hypothesis therefore is that the integrated clc element can excise from its chromosomal location and form a closed “circular” intermediate. The closed intermediate can either reintegrate or be transferred to a new recipient cell, in which it can again integrate. The existence of a closed circular excised GEI form was also

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demonstrated for the SXT element, for HPI and several others by cloning the junction regions by inverse PCR and subsequent DNA sequencing.27,109,155,176 In some cases, like for HPI and the clc element, recombination of the right and left ends positions a strong promoter at the left end in front of the integrase gene.153,179 The idea is that this conﬁguration results in temporary overexpression of the integrase and efﬁcient reintegration into the chromosomal target. On the other hand, expression of the integrase in the integrated form is mostly silent.179 Self-transfer of the clc element is not a well-described and generalized process, in contrast to conjugative transposons or plasmid conjugation. It must contain all the factors essential for self-transfer, since it can transfer from the strain B13 to an intermediate recipient and from there to another species.178 However, details on the transfer process are not known and no clear hom*ologies exist to classical type IV conjugative systems. Other GEI and ICE have partly conjugative functions recognizable from existing type IV conjugative systems. For example, the 100-kb SXT element of V. cholerae is self-transmissable between gram-negative species by a conjugative process. The sequence of SXT shows a number of regions with strong similarities to the tra genes of plasmid R27 and the Agrobacterium Ti plasmid16,17 and, to a lesser extent, to those of the pCAR1 plasmid (Figure 1). An example in which transfer functions are recognizable but partially dysfunctional is the Tn4371 in Ralstonia oxalatica A5 which carries the genes for biphenyl degradation (Figure 1).122,210 The transfer functions on Tn4371 are similar to those of IncP and Ti plasmids, however, the element is unable to transfer by itself, because of missing TraI and TraK functions. Interestingly, the clc element is a very close relative to a series of GEI in P. aeruginosa, Xylella fastidiosa, Burkholderia xenovorans, and Ralstonia metallidurens, which are not known for self-transfer but contribute to pathogenicity and catabolic functions in Beta- and Gammaproteobacteria.100,106,128,226 Most notably, two 100-kb GEI in P. aeruginosa isolates, designated PAGI-2 and PAGI3, have large regions in common to the clc element. Some elements nicely seem to point to a continuum between episomal and integrated forms.100 One of these, pKLC102 of P. aeruginosa, shows a mosaic of fragments with different origins. Parts of PAGI-2 and PAGI-3 are recognizable, but also a clear pil system and an oriV related to Pseudomonas syringae and Azotobacter vinelandii. A XerCtype integrase seems responsible for integration of pKLC102 into tRNA-Lys. Strangely enough, in P. aeruginosa isolates from cystic ﬁbrosis patients, a 23-kb integron sequence has integrated near the pil region on pKLC102. This integron carries resistance genes for gentamycin and tobramycin, and further bears tra-like and par genes. A further chromosomal recombination can occur between IS6100 of the integron and a IS6100 copy elsewhere on the chromosome, which removes the integrase from pKLC102 and renders the element incapable of excision.100

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12. CONCLUDING REMARKS Investigating the molecular archeology of catabolic pathways in pseudomonads and related bacteria and dissecting the different adaptation bacterial mechanisms has given an extremely detailed picture on the ways how environmentally successful mutants developed new genetic structures for pollutant metabolism. Principally, the picture is reinforced of extremely effective mechanisms to capture gene fragments from different sources, recombine them de novo and distribute on whatever mobile conjugative element is at hand.

ACKNOWLEDGMENTS I am much indebted to Vladimir Sentchilo and Johan Leveau for their help in preparing part of this material.

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and tfdB genes according to PCR-RFLP analysis. FEMS Microbiol. Ecol., 20:163– 172. van Beilen, J.B., Eggink, G., Enequist, H., Bos, R., and Witholt, B., 1992, DNA sequence determination and functional characterization of the OCT-plasmid-encoded alkJKL genes of Pseudomonas oleovorans. Mol. Microbiol., 6:3121–3136. van der Meer, J.R., 1997, Evolution of novel metabolic pathways for the degradation of aromatic compounds. Antonie van Leeuwenhoek Int. J. Microbiol., 71:159–178. van der Meer, J.R., 2002, Evolution of metabolic pathways for degradation of environmental pollutants., pp. 1194–1207. In G. Bitton (ed.), Encyclopedia of Environmental Microbiology. John Wiley & Sons, New York. van der Meer, J.R., de Vos, W.M., Harayama, S., and Zehnder, A.J.B., 1992, Molecular mechanisms of genetic adaptation to xenobiotic compounds. Microbiol. Rev., 56:677–694. van der Meer, J.R., Eggen, R.I.L., Zehnder, A.J.B., and de Vos, W.M. 1991, Sequence analysis of the Pseudomonas sp. strain P51 tcb gene cluster, which encodes metabolism of chlorinated catechols: evidence for specialization of catechol 1,2-dioxygenases for chlorinated substrates. J. Bacteriol., 173:2425–2434. van der Meer, J.R., Roelofsen, W., Schraa, G., and Zehnder, A.J.B., 1987, Degradation of low concentrations of dichlorobenzenes and 1,2,4-trichlorobenzene by Pseudomonas sp. strain P51 in nonsterile soil columns. FEMS Microbiol. Ecol., 45:333–341. van der Meer, J.R., and Sentchilo, V.S., 2003, Genomic islands and evolution of catabolic pathways in bacteria. Curr. Opin. Biotechnol., 14:248–254. van der Meer, J.R., van Neerven, A.R.W., de Vries, E.J., de Vos, W.M., and Zehnder, A.J.B., 1991, Cloning and characterization of plasmid-encoded genes for the degradation of 1,2dichloro-, 1,4-dichloro-, and 1,2,4-trichlorobenzene of Pseudomonas sp. strain P51. J. Bacteriol., 173:6–15. van der Meer, J.R., Werlen, C., Nishino, S., and Spain, J.C., 1998, Evolution of a pathway for chlorobenzene metabolism leads to natural attenuation in a contaminated groundwater. Appl. Environ. Microbiol., 64:4185–4193. van der Meer, J.R., Zehnder, A.J.B., and de Vos, W.M., 1991, Identiﬁcation of a novel composite transposable element, Tn5280, carrying chlorobenzene dioxygenase genes of Pseudomonas sp. strain P51. J. Bacteriol., 173:7077–7083. Vedler, E., Vahter, M., and Heinaru, A., 2004, The completely sequenced plasmid pEST4011 contains a novel IncP1 backbone and a catabolic transposon harboring tfd genes for 2,4dichlorophenoxyacetic acid degradation. J. Bacteriol., 186:7161–7174. Viggor, S., Heinaru, E., Loponen, J., Merimaa, M., Tenno, T., and Heinaru, A., 2002, Biodegradation of dimethylphenols by bacteria with different ring-cleavage pathways of phenolic compounds. Environ. Sci. Pollut. Res. Int., 1:19–26. Weisshaar, M.-P., Franklin, F.C.H., and Reineke, W., 1987, Molecular cloning and expression of the 3-chlorobenzoate-degrading genes from Pseudomonas sp. strain B13. J. Bacteriol., 169:394–402. Werlen, C., Kohler, H.-P.E., and van der Meer, J.R., 1996, The broad substrate chlorobenzene dioxygenase and cis-chlorobenzene dihydrodiol dehydrogenase of Pseudomonas sp. strain P51 are linked evolutionarily to the enzymes for benzene and toluene degradation. J. Biol. Chem., 271:4009–4016. Whyte, L.G., Bourbonni`ere, L., and Greer, C.W., 1997, Biodegradation of petroleum hydrocarbons by psychrotrophic Pseudomonas strains possessing both alkane (alk) and naphthalene (nah) catabolic pathways. Appl. Environ. Microbiol., 63:3719–3723. Williams, P.A., Assinder, S.J., De Marco, P., O’Donnell, K.J., Poh, C.L., Shaw, L.E., and Winson, M.K., 1992, Catabolic gene duplications in TOL plasmids, pp. 341–353. In E. Galli, S. Silver, and B. Witholt (eds.), Pseudomonas: Molecular Biology and Biotechnology. American Society for Microbiology, Washington, DC.

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236. Williams, P.A., and Murray, K., 1974, Metabolism of benzoate and the methylbenzoates by Pseudomonas putida (arvilla) mt-2: evidence for the existence of a TOL plasmid. J. Bacteriol., 120:416–423. 237. Williams, P.A., and Sayers, J.R., 1994, The evolution of pathways for aromatic hydrocarbon oxidation in Pseudomonas. Biodegradation, 5:195–218. 238. Williams, P.A., Shaw, L.M., Pitt, C.W., and Vrecl, M., 1997, XylUW, two genes at the start of the upper pathway operon of TOL plasmid pWW0, appear to play no essential part in determining its catabolic phenotype. Microbiology, 143:101–107. 239. Williams, P.A., Taylor, S.D., and Gibb, L.E., 1988, Loss of the toluene–xylene catabolic genes of TOL plasmid pWW0 during growth of Pseudomonas putida on benzoate is due to a selective growth advantage of ‘cured’ segregants. J. Gen. Microbiol., 134:2039–2048. 240. Williams, P.A., and Worsey, M.J., 1976, Ubiquity of plasmids in coding for toluene and xylene metabolism in soil bacteria: evidence for the existence of new TOL plasmids. J. Bacteriol., 125:818–828. 241. Wilson, M.S., Herrick, J.B., Jeon, C.O., Hinman, D.E., and Madsen, E.L., 2003, Horizontal transfer of phnAc dioxygenase genes within one of two phenotypically and genotypically distinctive naphthalene-degrading guilds from adjacent soil environments. Appl. Environ. Microbiol., 69:2172–2181. 242. Wright, B.E., 2000, A biochemical mechanism for nonrandom mutations and evolution. J. Bacteriol., 182:2993–3001. 243. Wyndham, R.C., Cashore, A.E., Nakatsu, C.H., and Peel, M.C., 1994, Catabolic transposons. Biodegradation, 5:323–342. 244. Yen, K.-M., Karl, M.R., Blatt, L.M., Simon, M.J., Winter, R.B., Fausset, P.R., Lu, H.S., Harcourt, A.A., and Chen, K.K., 1991, Cloning and characterization of a Pseudomonas mendocina KR1 gene cluster encoding toluene-4-monooxygenase. J. Bacteriol., 173:5315–5327. 245. Yen, K.-M., and Serdar, C.M., 1988, Genetics of naphthalene catabolism in Pseudomonads. CRC Crit. Rev. Microbiol., 15:247–268. 246. Zeyer, J., Kocher, H.P., and Timmis, K.N., 1986, Inﬂuence of para-substituents on the oxidative metabolism of o-nitrophenols by Pseudomonas putida B2. Appl. Environ. Microbiol., 52:334– 339. 247. Zhou, J.Z., and Tiedje, J.M., 1995, Gene transfer from a bacterium injected into an aquifer to indigenous bacteria. Mol. Ecol., 4:613–618. 248. Zylstra, G.J., and Gibson, D.T., 1989, Toluene degradation by Pseudomonas putida F1. J. Biol. Chem., 264:14940–14946.

CONTROLLING REGIOSPECIFIC OXIDATION OF AROMATICS AND THE DEGRADATION OF CHLORINATED ALIPHATICS VIA ACTIVE SITE ENGINEERING OF TOLUENE MONOOXYGENASES Ayelet Fishman, Ying Tao, G¨on¨ul Vardar, Lingyun Rui, and Thomas K. Wood

Departments of Chemical Engineering and Biology University of Texas AdM College Station, TX 77843-3122, USA

1. SUMMARY Toluene monooxygenases from pseudomonads are powerful enzymes whose activities have not been fully appreciated. Recently the literature was corrected to show there was no true, predominantly meta-hydroxylating enzyme, and it was discovered that these enzymes perform two and three successive hydroxylations of benzene. The physiological relevance of these successive hydroxylations by toluene p-monooxygenase (TpMO) was discerned for the toluene degradation pathway of Ralstonia pickettii PKO1. More importantly, these successive hydroxylations create the possibility of producing substituted aromatics for industrially important syntheses. To take advantage of this potential and to probe the hydroxylation reaction itself, DNA shufﬂing has been used to determine the residues that control the regiospeciﬁc catalytic activity. This regiospeciﬁc activity was ﬁne tuned using saturation mutagenesis to create Pseudomonas, Volume 4, edited by Juan-Luis Ramos and Roger C. Levesque C 2006 Springer. Printed in the Netherlands.

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monooxygenases that, along with the wild-type enzymes, are able to form various doubly hydroxylated, substituted aromatics including 3-nitrocatechol, 4-nitrocatechol, nitrohydroquinone, methylhydroquinone, 4-methylresorcinol, methoxyresorcinol, 3-methoxycatechol, 2-naphthol, and 1-hydroxyﬂuorene. The regiospeciﬁc control of hydroxylation has reached the point where toluene may be hydroxylated at the ortho-, meta-, and para-positions by altering just two amino acids near the diiron active site, and these residues may be altered to create the ﬁrst predominantly meta-hydroxylating enzyme. Also, regiospeciﬁc oxidation of naphthalene may be controlled to form both 1- and 2-naphthol (ﬁrst report of microbial formation of this compound), and the regiospeciﬁc oxidation of indole may be controlled so that a single enzyme [toluene o-monooxygenase (TOM) of Burkholderia cepacia G4] may be used to form a variety of indigoids including predominantly indigo, isoindigo, indirubin, and isatin. To control the successive hydroxylations, two-phase reactors have also been designed to produce phenol from benzene and 2-naphthol from naphthalene using toluene 4-monooxygenase (T4MO) from Pseudomonas mendocina KR1. To show the utility of these enzymes for pathway engineering, they have been combined with both glutathione S-transferases as well as epoxide hydrolases to create engineered bacteria that have accelerated degradation rates for chlorinated ethenes as well as to take advantage of the fact that only one oxygenase has been shown to oxidize tetrachloroethylene (toluene o-xylene monooxygenase of Pseudomonas stutzeri OX1). Similar monooxygenation reactions for substituted aromatics have been discovered using dinitrotoluene dioxygenases.

2. INTRODUCTION Enzymes are attractive catalysts for chemical synthesis due to their exceptional enantio and regioselectivities; hence, enzymes can be used in both simple and complex syntheses without the need for the blocking and deblocking steps often found in their organic counterparts105,106 . The number of biocatalytic processes that are being performed on a large scale is rapidly increasing, and it is projected that this growth will continue48,114 to become 30% of the chemical business by 2050122 . Although the majority of the currently used industrial enzymes are hydrolases48 , there is growing interest in the application of oxygenases122 . Oxidative biotransformations use oxygen as an inexpensive, environmentally friendly oxidant in contrast to toxic chemical oxidants, and they exceed their chemical equivalent regiospeciﬁcity and enantioselectivity10,58 . Among bacterial oxygenases, toluene monooxygenases have much potential for bioremediation and chemical synthesis as we have used mutagenesis to make, among other things, variants that remediate one of the world’s worst pollutants (chlorinated ethenes)15,97,99 , that form a rainbow of colors from indole

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with a single enzyme, that make the anticancer compound indirubin100 , and that make useful compounds like 1-naphthol (15,000 ton/year market15 ), nitrohydroquinone (precursor for therapeutics for Alzheimer’s and Parkinson’s disease)127 , and 4-nitrocatechol (inhibitor of nitric oxide synthase)27 . For these industrial applications, control of regiospeciﬁc oxidation of aromatics is of vital importance. Further, regiospeciﬁc oxidation of toluene, substituted benzenes, and naphthalene by these monooxygenases presents an important challenge both in terms of the three distinct regiospeciﬁc oxidations possible for the initial hydroxylation of toluene as well as the usefulness of both the mono- and di-hydroxylated products. TpMO, formerly known as T3MO30 of Ralstonia pickettii PKO1 is a soluble, non-heme, diiron monooxygenase52 and is composed of six proteins encoded by tbuA1UBVA2C12 . TbuA1, TbuA2, and TbuU are the α, β, and γ subunits, respectively, of the hydroxylase component (209 kDa with α2 β2 γ2 quaternary structure) which controls regiospeciﬁcity73,90 . TbuB is a Rieske-type [2Fe-2S] ferredoxin (12.3 kDa), and TbuV is an effector protein (11.7 kDa). TbuC is a NADH oxidoreductase (36.1 kDa) which is responsible for the transfer of electrons from reduced nucleotides via the redox center to the terminal oxygenase12 . R. pickettii PKO1 cells expressing the TpMO pathway were shown to degrade trichloroethylene (TCE) when induced by toluene or TCE53,86 . T4MO115 of Pseudomonas mendocina KR1, TOM77 of Burkholderia cepacia G4, and toluene/o-xylene monooxygenase (ToMO)3 of Pseudomonas stutzeri OX1 are similar enzymes52,79 except TOM contains a relatively unknown subunit (from tomA0) rather than a Rieske-type [2Fe-2S] ferredoxin. The TpMO tbu locus is most similar to T4MO tmo genes in the DNA sequence (>60%)54 , but both T4MO and TpMO are only distantly related to TOM and are substantially different enzymes (as evidenced by their different hydroxylation of toluene) since the hydroxylase alpha fragments of TpMO and T4MO share only 48% DNA identity and only 23% protein identity with TOM. To probe the catalytic potential of these four enzymes it is necessary to clone them into a background devoid of competing monooxygenase and dioxygenase reactions. Whole Escherichia coli TG1 cells are an excellent host for studying these enzymes due to the lack of background oxygenases (when grown in LB medium), to the relatively strong expression of the multiple components of these enzymes (three-component hydroxylase, reductase, mediating protein, and ferredoxin), and to the ample production of the necessary cofactor NADH (which likely limits industrial production to whole cells). We have constructed plasmids like that shown in Figure 1 to express TOM, ToMO, TpMO, and T4MO in E. coli. Using these constructs, we have found the catalytic potential of monooxygenases is best harnessed using the random mutagenesis tool of DNA shufﬂing followed by saturation mutagenesis rather than site-directed mutagenesis.

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Not I (1) touF (reductase)

F(-) origin Amp

touE (beta)

KanR

pBS(Kan)ToMO 8983 bp

touD (mediator)

∆Amp touC (ferredoxin) touB (gamma) ColE1 origin

Sal I (5444)

lac promoter touA (alpha) Bst EII (4739)

Kpn I (4059) Mlu I (4130)

Figure 1. Vector pBS(Kan)ToMO for constitutive expression of wild-type ToMO and its mutants. KanR is the kanamycin resistance gene. The six genes for ToMO are touABE (encoding the three-component hydroxylase, A2 B2 E2 ), touC (encoding ferredoxin), touD (encoding the mediating protein) and touF (encoding the NADH-ferredoxin oxidoreductase). Similar constructs pBS(Kan)TOM, pBS(Kan)T3MO, and pBS(Kan)T4MO were made.

Using this approach, we have discovered that the ToMO-equivalent alpha subunit residues I100 (gate residue)15 , A101127 , A107100 , A110127 , M180124,128 , and E214 (gate residue)124,127 inﬂuence catalysis in this family of monooxygenases. Furthermore, puriﬁcation of these complex proteins is not necessary to gauge changes in regiospeciﬁc activity. The novel enzymes produced are all active; often their activity on the wild-type substrate toluene exceeds that of the wild-type enzyme27,98,118 . We have also found relationships between oxidation rate and regiospeciﬁcity27,98,118 , as well as between electrophilic resonance/inductive effects and regiospeciﬁcity28 . With these enzymes and their variants, we can now synthesize nitrohydroquinone, 4-methylresorcinol, 1-hydroxyﬂuorene, 3-hydroxyﬂuorene, 4-hydroxyﬂuorene, 2-naphthol, 2,6dihydroxynaphthalene, and 3,6-dihydroxyﬂuorene whereas there were no previous reports of the synthesis of these compounds with speciﬁc enzymes117,127,128 .

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3. SUCCESSIVE HYDROXYLATIONS OF TOLUENE MONOXYGENASES It was reported previously that no catechol derivatives were detected using T4MO with toluene and benzene as substrates91 , and that there was no further hydroxylation of p-cresol by the T4MO G103L mutant created by sitedirected mutagenesis73 . Also, all previous publications indicate that T4MO only hydroxylates unactivated benzene nuclei but not phenolic compounds52,73,91 . However, it was discovered recently in our laboratory that T4MO produces catechol at physiological rates using both benzene and phenol as substrates119 as well as produces trihydroxybenzene (THB), so toluene monooxygenases (TOM, ToMO, TpMO, and T4MO) are capable of not one but three successive hydroxylations of benzene119 . Catechols are important intermediates for synthesis of pharmaceuticals, agrochemicals, ﬂavors, polymerization inhibitors, and antioxidants20,21 . Currently, catechol is produced primarily by the oxidation of phenol, mdiisopropylbenzene, or by coal-tar distillation41 . However, the industrial routes to catechols are environmentally unsafe, e.g. the use of elevated metal, temperature, pressure, and solvent conditions1,41 . These chemical routes are often lengthy, energy-intensive, multi-step reactions that require expensive starting materials and are plagued with isomerization and rearrangement problems 1,93 ; hence, microbial production of catechols is attractive. Previously, catechol has been produced by transforming D-glucose with a genetically modiﬁed E. coli AB2834/pKD136/pKD9.069A expressing 3-dehydroshikimic acid dehydratase and protocatechuic acid decarboxylase20,21 and by benzene oxidation with Pseudomonas putida 6–12 expressing toluene/benzene dioxygenase while lacking catechol 1, 2-oxygenase and catechol 2, 3-oxygenase93 . It was discovered that T4MO of P. mendocina KR1, TpMO of R. pickettii PKO1, ToMO of P. stutzeri OX1, and TOM of B. cepacia G4 convert benzene to phenol, catechol, and 1,2,3-THB by successive hydroxylations118,128 (Figure 2). At a concentration of 165 µM, under control of a constitutive lac promoter, E. coli TG1/pBS(Kan)T4MO expressing T4MO formed phenol from benzene at 19 ± 1.6 nmol/min/mg protein, catechol from phenol at 13.6 ± 0.3 nmol/min/mg protein, and 1,2,3-THB from catechol at 2.5 ± 0.5 nmol/min/mg protein (Table 1). The catechol and 1,2,3-THB products were identiﬁed by both high performance liquid chromatography (HPLC) and mass spectrometry. Using analogous plasmid constructs, E. coli TG1/pBS(Kan)T3MO expressing TpMO (plasmid constructed before realization that monooxygenase was a para-hydroxylating enzyme) formed phenol, catechol, 1,2,3-THB at a rate of 3 ± 1, 3.1 ± 0.3, and 0.26 ± 0.09 nmol/min/mg protein, respectively, and E. coli TG1/pBS(Kan)TOM expressing TOM formed 1,2,3-THB at a rate of 1.7 ± 0.3 nmol/min/mg protein (phenol and catechol formation rates were

Figure 2. Successive hydroxylations of benzene by TG1(T4MO), TG1(TpMO), TG1(TOM), and TG1(ToMO).

144 ± 47

122 ± 43

27 ± 12

19 ± 1.6

3±1

0.89 ± 0.07

Enzyme

T4MOc

TpMOc

TOMd

1.8 ± 0.5

3.1 ± 0.3

13.6 ± 0.3 140 ± 7

119 ± 13

103 ± 10

Maximum production, µM

Catechol formation from phenol Initial formation rate, nmol/ min/mg protein 2.5 ± 0.5 1.7 ± 0.3

0.26 ± 0.09

103 ± 22

73 ± 4

132 ± 22

Maximum production, µM

1,2,3-THB formation from catechol Initial formation rate, nmol/ min/mg protein

2.4 ± 0.3

4 ± 0.6

10 ± 0.8

Toluene oxidation rate, nmol/min/mg protein

Based on HPLC analysis, the mean ± standard deviation of at least two independent results are shown. Initial benzene liquid concentrations of 165 µM based on a Henry’s law constant of 0.2219 (400 µM added if all the benzene in the liquid phase), and the initial toluene concentration was 165 µM based on a Henry’s law constant of 0.2719 (455 µM added if all the toluene in the liquid phase). c Protein concentration 0.24 mg protein/(mL × OD). d Protein concentration 0.22 mg protein/(mL × OD).

Maximum production, µM

Phenol formation from benzene

Synthesisa of phenol from benzene, catechol from phenol, and 1,2,3-THB from catechol by E. coli TG1 cells expressing wild-type T4MO, TpMO, and TOM. Initial concentration of substrates was 165 µMb .

Initial formation rate, nmol/ min/mg protein

Table 1.

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0.89 ± 0.07 and 1.5 ± 0.3 nmol/min/mg protein, respectively). Hence, the rates of synthesis of catechol by both TpMO and T4MO and the 1,2,3-THB formation rate by TOM were found to be comparable to the rates of oxidation of the natural substrate toluene for these enzymes (10.0 ± 0.8, 4.0 ± 0.6, and 2.4 ± 0.3 nmol/min/mg protein for T4MO, TpMO, and TOM, respectively, at 165 µM toluene). Previously, it was reported that P. mendocina KR1 utilizes toluene as a sole carbon and energy source converting it to p-cresol via T4MO131 . This single hydroxylation is followed by oxidation of the methyl group by p-cresol methylhydroxylase and p-hydroxybenzaldehyde dehydrogenase, resulting in phydroxybenzoate, which is oxidized to protocatechuate131 . Protocatechuate is metabolized through an ortho-cleavage pathway131 . R. pickettii PKO1 metabolizes benzene and toluene to phenol and m-cresol, respectively, via TpMO13 . Phenol and m-cresol are then further oxidized by phenol hydroxylase to catechol and 3-methylcatechol, respectively, which are then cleaved by a meta-ﬁssion dioxygenase13 . Therefore, it was surprising to ﬁnd here that T4MO and TpMO further oxidize phenol and catechol as they do not appear to be physiologically relevant reactions. At least four monooxygenases capable of successive hydroxylations of aromatics have been found. TOM77 and toluene/benzene 2-monooxygenase of Burkholderia sp. strain JS15045 transform toluene to o-cresol and then ocresol to 3-methylcatechol. p-Nitrophenol monooxygenase from Burkholderia sphaericus JS905 converts p-nitrophenol to 4-nitrocatechol, and then removes the nitro group and forms the 1,2,4-THB46 . ToMO also catalyzes toluene or oxylene oxidation into methylcatechols by two subsequent monooxygenations3 but was reported to only transform benzene to phenol3 . Before this report, based on their ability to perform successive hydroxylations, TOM and toluene/benzene 2-monooxygenase were thought to be most similar to phenol hydroxylases rather than to other toluene monooxygenases52,73 ; however, the accumulation of catechol from benzene by TG1(T4MO) and TG1(TpMO) encoding T4MO and TpMO, respectively, indicates that these two monooxygenases possess a sequential hydroxylation pathway similar to that of TOM of B. cepacia G477 , ToMO of P. stutzeri OX13 , and toluene/benzene 2-monooxygenase of Burkholderia sp. strain JS15045 .

4. PHYSIOLOGICAL RELEVANCE OF SUCCESSIVE HYDROXYLATIONS OF TpMO Xylene monooxygenase of Pseudomonas putida mt-2 hydroxylates toluene at the methyl side chain resulting in benzyl alcohol7 , and TOM of B. cepacia G4 hydroxylates the benzene ring at the ortho position to form

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o-cresol which is further oxidized to 3-methylcatechol77,109 . T4MO of P. mendocina KR1 is speciﬁc for para hydroxylations producing primarily pcresol134 , and TpMO of R. pickettii PKO1 was reported to hydroxylate toluene at the meta position83 resulting in m-cresol. However, using gas chromatography (GC) and 1 H-nuclear magnetic resonance spectroscopy, we discovered that TpMO hydroxylates monosubstituted benzenes predominantly at the para position30 . E. coli TG1/pBS(Kan)T3MO cells expressing TpMO oxidized toluene at a maximal rate of 11.5 ± 0.33 nmol/min/mg protein with an apparent K m value of 250 µM, and produced 90% p-cresol and 10% mcresol. This product mixture was successively transformed to 4-methylcatechol by TpMO. T4MO, in comparison, produces 97% p-cresol and 3% m-cresol. P. aeruginosa POA1 harboring pRO1966 (the original TpMO-bearing plasmid) also exhibited the same product distribution as TG1/pBS(Kan)T3MO. TG1/pBS(Kan)T3MO produced 66% p-nitrophenol and 34% m-nitrophenol from nitrobenzene, 100% p-methoxyphenol from methoxybenzene, as well as 62% 1-naphthol and 38% 2-naphthol from naphthalene; similar results were found with TG1/pBS(Kan)T4MO. Sequencing of the tbu locus from pBS(Kan)T3MO and pRO1966 revealed complete identity between the two thus eliminating any possible cloning errors. Hence, there is no true metahydroxylating enzyme. We propose a modiﬁcation (Figure 3) of the degradation pathway originally described by Olsen et al.83 that now relies primarily on TpMO for conversion of toluene directly to 4-methylcatechol in two successive hydroxylations. Toluene is converted primarily to p-cresol instead of m-cresol and then both m-cresol and p-cresol are oxidized to 4-methylcatechol since both m-cresol and p-cresol were found to be good substrates for E. coli expressing TpMO (Vmax /K m =0.046, 0.036, and 0.055 mM/min/mg protein for the oxidation of toluene, m-cresol, and p-cresol, respectively)29 . In light of the broader activity of TpMO, phenol hydroxylase (encoded by tbuD), a ﬂavin monooxygenase50 , appears to facilitate conversion of any mcresol or p-cresol formed from toluene oxidation by TpMO to 4-methylcatechol; hence, the cell has a redundant method for making this important intermediate 4-methylcatechol (note that phenol hydroxylase cannot initiate the degradation of toluene) as this reaction was shown to be performed effectively by TpMO with comparable Vmax /K m values as toluene oxidation. The existence of multiple monooxygenases in one strain may provide the cell with a competitive advantage and with the ability to utilize a large range of chemically different substrates effectively. Note the phenol hydroxylase is also redundant with respect to hydroxylation of phenol as this reaction was also shown to be performed efﬁciently by TpMO119 . Similarly, a recent study by Cafaro et al. shows that both ToMO and phenol hydroxylase of P. stutzeri OX1 oxidize benzene to phenol and phenol to catechol, albeit at different efﬁciencies; the phenol hydroxylase

CH3

toluene

O2 + NADH + H+ TpMO

m-cresol induces PH and meta cleavage pathway

m-cresol 10%

H2O + NAD+

CH3

p-cresol 90%

+ OH OH

O2 + NADH + H+ TpMO + PH

H2O + NAD+ CH3

4-methyl catechol

OH OH

O2 TbuE

2-hydroxy-5-methyl-2,4-hexadienedioic acid

CH3

O C H

COOCOO-

2-hydroxy-5-methyl-cis,cis muconic semialdehyde

COO-

TbuG

OH OH

TbuH

TbuF HCOOH CH3

CH3

COOCOO

TbuI

2-hydroxy-2-hexenoic acid

COO-

CO2 OH

cis-2-methyl-5-oxo-3-hexenedioic acid

TbuJ

CH3 HO

4-hydroxy-2-oxo-hexanoic acid COO-

TbuK

COO-

O H3C

C H

+ O

propionic aldehyde

pyruvate

Figure 3. Proposed modiﬁcation of the pathway for degradation of toluene by R. pickettii PKO1 based on the ability of TpMO to perform successive hydroxylations. Abbreviations are: TpMO, toluene para-monooxygenase; PH, phenol hydroxylase; TbuE, catechol-2,3-dioxygenase; TbuF, 2-hydroxymuconate semialdehyde hydrolase; TbuG, 2-hydroxymuconate semialdehyde dehydrogenase; TbuH, 4-oxalocrotonate isomerase; TbuI, 4-oxalocrotonate decarboxylase; TbuJ, 2hydroxypent-2,4-dienoate hydratase; and TbuK, 4-hydroxy-2-oxovalerate aldolase.

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appears to mainly drain the mono-hydroxylated compounds and prevent them for accumulating within the cell14 . Further, we suggest that the physiological relevance of the 10% m-cresol formed from toluene oxidation by TpMO is for induction of the meta-cleavage operon tbuWEFGKIHJ to enable full metabolism of toluene since p-cresol (and o-cresol) do not induce the meta-cleavage pathway. Additionally, the 10% mcresol serves to induce the redundant phenol hydroxylase. Therefore, the double hydroxylation of toluene by TpMO and its somewhat relaxed regiospeciﬁcity are of physiological relevance to R. pickettii PKO1. Purely para-hydroxylating enzymes are possible as we have constructed one with reasonable activity from T4MO (TmoA variant G103S/A107T)118 ; hence, the cell must choose to make some m-cresol as a result of a regulation artifact possibly related to recent acquisition of the lower meta-cleavage pathway.

5. DISCOVERY OF RESIDUES THAT CONTROL CATALYTIC ACTIVITY IN TOLUENE MONOOXYGENASES The soluble methane monooxygenase (sMMO) active site residues have been identiﬁed by X-ray crystallography24,94,95 , and by comparison to sMMO, the active site residues for T4MO, TpMO, and toluene 2-monooxygenase from Pseudomonas sp. strain JS150 were predicted by Pikus et al.91 . Based on this crystal structure, Fox and co-workers previously found mutations in T4MO of P. mendocina KR1 that inﬂuence its regiospeciﬁcity73,90,91 . For the oxidation of m-xylene by T4MO mutant Q141C of tmoA, 3-methylbenzyl alcohol formation increased six-fold from 2.2% to 11.7%, and for p-xylene oxidation, the product distribution completely switched to 2,5-dimethylphenol (78%) from 4methylbenzyl alcohol (22%)91 . From toluene, the alpha subunit variant TmoA T201F yielded nearly equal amounts of o- and p-cresol (49.1 and 46.6% respectively) and a substantial amount of benzyl alcohol (11.5%) compared with the wild-type enzyme which makes 97% p-cresol and 3% m-cresol90 . Another beneﬁcial T4MO TmoA mutant, F205I, produced 81% p-cresol, 14.5% m-cresol and insigniﬁcant amounts of o-cresol and benzyl alcohol91 . The most notable change was found with mutant TmoA G103L that inﬂuenced the selectivity for ortho-hydroxylation of toluene yielding 55.4% o-cresol73 . Using DNA shufﬂing, toluene monooxygenase alpha subunit positions I100, A107, M180, and E214 of the ToMO hydroxylase have been discovered to control activity15,124,127,128 . Leucine 110 of MmoX in sMMO of Methylococcus capsulatus (Bath), the analogous position to ToMO TouA I100 (residue for the similar protein TpMO is shown in Figure 4a), was shown to divide the active site pocket into two cavities and was hypothesized to function in

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A) wild-type Ile100

Gly103

His137 Glu104 FeA

Phe176 Glu231 Fe B

Ala107 Phe180

Glu197

His234

B) A107G Ile100

Gly103 His137

Glu104 Fe A Phe176

Glu231 Fe B

Phe180

Gly107

Glu197

His234

Figure 4. Docking of cresols in the active site of the TpMO TbuA1 α-subunit to indicate how o-, m-, and p-cresol are formed. Mutated residues in red at positions I100, G103, and A107. Residues in purple (E104, H137, E197, E231, and H234) (E134 not shown for clarity) are the coordinating residues anchoring the diiron-binding sites (silver spheres). Residues in light blue are

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C) I100S/G103S Ser100

Ser103

His137

Glu104

Fe A Phe176 Glu231 Fe B Ala107 Phe180

Glu197

His234

D) A107T Ile100 His137

Gly103

Glu104

Fe A Phe176

Glu231 Fe B Thr107 His234 Phe180

Glu197

Figure 4. (Continued) part of the hydrophobic shell (F176 and F180). Cresol (dark blue with oxygen in red) is docked inside the active site taking into consideration both energy minimization and steric hindrance. Panel (a) Wild-type TpMO forming p-cresol, (b) Variant A107G forming o-cresol, (c) Variant I100S/G103S forming m-cresol, and (d) Variant A107T forming p-cresol.

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controlling the access of substrates to the diiron center94 . Support of this role was provided by Canada et al.15 in the ﬁrst DNA shufﬂing of a non-heme monooxygenase in which the function of the analogous position in TmoA3 of TOM of B. cepacia G4, V106, was discerned; the V106A variant was able to hydroxylate bulky three-ring polyaromatics such as phenanthrene at higher rates, indicating that a decrease in the size of the side chain allows larger substrates to enter the active site. This variant and two other mutants, V106E and V106F, had decreased regiospeciﬁcity for toluene oxidation, altering the strict ortho-hydroxylation capability of wild-type TOM to create relaxed catalysts that produce all three cresols98 . With T4MO of P. mendocina KR1, TmoA mutants I100S and I100A exhibited higher oxidation rates (evidenced by higher apparent Vmax /K m values) for toluene, nitrobenzene, and nitrophenol oxidation in comparison with the wild-type enzyme27 . The regiospeciﬁcity of toluene and nitrobenzene oxidation also changed resulting in higher percentages of the meta isomers. A different TmoA mutant, I100C, had altered enantioselectivity for butadiene epoxidation, forming 60% (R)-butadiene epoxide and 40% (S)butadiene epoxide compared with 33% (R)- and 67% (S)-epoxide produced by wild-type T4MO albeit at the expense of a lower toluene oxidation rate113 . Position I100 in TouA of ToMO of P. stutzeri OX1, the most non-speciﬁc of the toluene-oxidizing enzymes, was shown to inﬂuence the regiospeciﬁc oxidation of cresols and phenol to double hydroxylated products128 . For example, variant I100Q, which was found through saturation mutagenesis, produced 80% hydroquinone and 20% catechol from phenol compared with 100% catechol formed by wild-type ToMO. In addition, this mutant produced substantial amounts of nitrohydroquinone from m-nitrophenol whereas wild-type ToMO produced only 4-nitrocathechol127 . Alpha subunit position A107 (Figure 4a) is conserved in all monooxygenases studied suggesting it offers some evolutionary advantage52 . DNA shufﬂing of TOM of B. cepacia G4 showed that this position (TomA3 A113) is involved in color formation of indigoid compounds by inﬂuencing whether the two positions of the pyrrole ring or benzene ring are hydroxylated100 . More speciﬁcally, variant A113G (analogous to TpMO TbuA1 A107G which was discovered to be an ortho-hydroxylating enzyme) was found to hydroxylate the indole benzene ring rather than the pyrrole ring oxidized by wild-type TOM. Other variants at this position (A113F, A113S, and A113I) were found to produce high amounts of indirubin from indole oxidation (C-2 and C-3 pyrrole hydroxylation) while wild-type TOM produced primarily isoindigo (C-2 pyrrole hydroxylation). A T4MO site-directed mutant TmoA A107S was shown to improve the enantioselectivity of butadiene epoxidation113 (84% S-butadiene epoxide formed vs. 67% for the wild-type T4MO) further demonstrating that a hydrophilic residue is tolerable at this conserved position. DNA shufﬂing of ToMO from P. stutzeri OX1 for altered methyl- and nitro-aromatic activities (rates or regiospeciﬁc changes) led to the discoveries

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Figure 5. Catalytic residues M180 and E214 of the hydroxylase alpha subunit (TouA) of ToMO. The C-terminal loop of helix E (yellow) and the N-terminal loop of helix H (yellow) form a channel opening at the surface of TouA. Side chains shown in green are the metal-binding residues forming the diiron center (TouA-E104, E134, H137, E197, E231, H234). TouA M180 is pink and TouA E214 is black. The wild-type ToMO hydroxylase (Protein Data Bank accession code 1t0q103 ) was visualized using Swiss-Pdb Viewer program (DeepView)35,87,107 . TouA E214 forms the entrance ◦ of the channel and is ∼23 A away from the active site, whereas TouA M180 is much closer to the ◦ active site (∼8 A). Mutations at E214 that show this residue controls the channel are indicated (E214A, E214G, E214V, and E214W). Also variants E214F, E214Q, and E214P were created but are not shown for clarity.

that residues A101, A110, M180 (Figure 5) and E214 (Figure 5) inﬂuence catalysis124,126−128 . Regiospeciﬁc hydroxylation of o-cresol, m-cresol, p-cresol, phenol, catechol, and resorcinol were altered by most of the TouA M180 variants as conﬁrmed by HPLC124 . For example, from o-cresol, TouA variant M180H formed 3-methylcatechol (50%), methylhydroquinone (43%), and 4-methylresorcinol (7%), whereas wild-type ToMO formed only 3methylcatechol (100%)124 . Also, a shift in regiospeciﬁc toluene hydroxylation was observed for variants M180S, M180Q, M180Y, and M180N with o-cresol (52%, 59%, 52%, and 19%), m-cresol (19%, 15%, 20%, and 19%), and p-cresol (29%, 26%, 28%, and 62%) formed, respectively (wild-type ToMO forms 32% o-cresol, 21% m-cresol, and 47% p-cresol).

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ToMO TouA E214 is located in the TouA◦ E-helix (closer to the FeA site of the diiron center than FeB ), and is ∼23 A away from the active site, whereas TouA M180 is closer to FeB diiron site and is much closer to the active ◦ site (∼8 A) (Figure 5). Hence, all of known beneﬁcial residues that inﬂuence regiospeciﬁcity are nearby the active site, whereas position TouA E214, which inﬂuences the rate of oxidation, is not. It appears that TouA E214 is the last residue of helix E and forms an opening of a substrate channel at the northern end of the molecule124 . Introduction of glycine at this position enhances the rate of oxidation of nitro aromatics including nitrobenzene, o-nitrophenol, mnitrophenol, and p-nitrophenol. However, the substitutions phenylalanine and glutamine (which are about the same size as glutamic acid) do not enhance the oxidation rate. In contrast, p-nitrophenol oxidation by ToMO is enhanced by substituting alanine (four-fold) or valine (1.3-fold) at E214 which are less than that of glycine (15-fold) which is expected if size of the residue at this position is critical. Furthermore, the introduction of the large residue tryptophan reduces the rate six-fold. Therefore, it appears that having a smaller amino acid at TouA position 214 may facilitate substrate entrance/product efﬂux by increasing the size of the channel opening (Figure 5). This is the second rate enhancing (but not regiospeciﬁc mutation) found from DNA shufﬂing as the TomA3 V106A mutation in TOM (analogous residue I100 in ToMO) allowed greater access to the catalytic center with large substrates such as phenanthrene15 . Hence, residues M180 and E214 are newly discovered alpha subunit residues of ToMO that inﬂuence regiospeciﬁc hydroxylation and reaction rates, respectively. Table 2 summarizes the effect of mutations at these key toluene monooxygenase subunit positions. Note positions 100, 103, and 107 of the alpha subunit of the hydroxylase protein are located in the active site pocket of the B-helix close to the diiron center (Figure 4). As the residues are four amino acids apart from one another they are spatially located one above the other on the α helix6 . All three amino acids are part of the hydrophobic region surrounding the active site similar to corresponding residues in other diiron monooxygenases52,90 . Hydrogen bond formation in the active site is important for catalysis with toluene monooxygenases. For example, structure hom*ology modeling suggests that hydrogen bonding interactions of the hydroxyl groups of T4MO and TpMO altered alpha subunit residues S103, S107, and T107 inﬂuence the regiospeciﬁcity of the oxygenase reaction with methoxyaromatics and toluene28,118 . The importance of hydrogen bonding for protein function has been shown in many cases. For example, in phenol 2-monooxygenase from Trichosporon cutaneum, Y289 was reported to play an important role in leading to ortho attack of the substrate by forming a hydrogen bond with phenol substrate71,133 , and the thermophilic xylose isomerase from Clostridium thermosulfurogenes increased kcat for glucose by 38% with an additional hydrogen bond to the C6 –OH group of the substrate upon the mutation V186T70 . In addition, disruption of hydrogen bonds may cause the important amino acids in the catalytic site to lose their

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Table 2. Summary of important residues in the alpha subunits of toluene monooxygenases. Corresponding ToMO residue

Enzyme

Effect on catalysis

I100

ToMO I100Q

Gate residue; Changes the regiospeciﬁc oxidation of methyl and nitro aromatics and enhances TCE degradation126−128 Enhances 3-methoxycatechol formation from guaiacol118 Enhances 4-nitrocatechol formation from nitrobenzene27 Changes the regiospeciﬁc oxidation of butadiene113 Enhances TCE and naphthalene oxidation15 Enhances chloroform oxidation and p-cresol formation from toluene98 Converts para speciﬁc TpMO into a meta enzyme28 Changes the regiospeciﬁc oxidation of toluene127 Enhances o-cresol formation from toluene73 Changes the regiospeciﬁc oxidation of methoxy aromatics118 Changes the regiospeciﬁc oxidation of methyl and methoxy aromatics118 Converts para speciﬁc T4MO into an ortho enzyme72 Converts nonspeciﬁc ToMO into a para enzyme127 Converts para speciﬁc TpMO into an ortho enzyme28 Converts TpMO into a better para enzyme28 Alters indole oxidation to produce primarily indigo (wild-type produces isoindigo)100 Alters indole oxidation to produce primarily indirubin100 Alters indole oxidation to produce primarily isatin100 Changes the regiospeciﬁc oxidation of toluene127 Enhances 3-methylbenzyl alcohol formation from m-xylene91 Enhances and changes the regiospeciﬁc oxidation of methyl and nitro aromatics124,127,128 Enhances 2,5-dimethylphenol formation from p-xylene90 Enhances benzyl alcohol formation from toluene90 Enhances m-cresol formation from toluene91 Changes the regiospeciﬁc oxidation of methyl and nitro aromatics127,128 Gate residue; Enhances nitro aromatic oxidation and cis-DCE degradation124,126,127

T4MO I100L T4MO I100A T4MO I100C TOM V106A TOM V106F I100/E103 A101T E103 E103/A107

TpMO I100S/G103S ToMO A101T/M114T T4MO G103L T4MO G103A/A107S T4MO G103S/A107T T4MO G103L/A107G

A107/E214 A107

ToMO A107T/E214A TpMO A107G TpMO A107T TOM A113V TOM A113I TOM A113H

A110 Q141

ToMO A110T T4MO Q141C

M180

ToMO M180T

T201

T4MO T201G

F205

T4MO T201F T4MO F205I ToMO F205G

E214

ToMO E214G

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Ayelet Fishman et al.

catalytic activity2,60 . For the toluene monooxygenases, the formation of additional hydrogen bonds with the backbone carbonyl, Fe-coordinating carbonyl, and with the substrates may cause the substrate to be oriented in a different position, and this may possibly explain the altered regiospeciﬁcity of oxidation for o-cresol and o-methoxyphenol by these mutants118 . Through mutagenesis, we have also found that whole cells expressing the variant enzymes (e.g. V106A, V106E, and V106F alpha subunit variants of wild-type TOM98 ) often have higher activity toward toluene, the physiological substrate. However, there is usually a tradeoff in that the wild-type enzyme usually has higher regiospeciﬁcity for toluene oxidation; hence, there appears to be an evolutionary balance between activity and regiospeciﬁcity. One may increase the rate of oxidation of the physiological substrate toluene at the expense of regiospeciﬁcity27,98,118,127 or increase the regiospeciﬁcity at the expense of rate28,118 .

6. SATURATION MUTAGENESIS Saturation mutagenesis is extremely powerful in creating new catalysts as it can be used to introduce all possible mutations at key sites or adjacent sites to explore a larger fraction of the protein sequence space that can be achieved with site-directed mutagenesis102 . It can provide much more comprehensive information than can be achieved by single amino acid substitutions as well as overcome the drawbacks of random mutagenesis in that a single mutation randomly placed in codons generates on average only 5.6 out of 19 possible substitutions11 . To use saturation mutagenesis effectively, it is necessary to determine the number colonies that must be screened. To determine the number of independent clones from saturation mutagenesis that need to be screened to ensure each possible codon has been tested, a multi nomial distribution equation was used98 . For saturation mutagenesis at one position, it is assumed that each of the 64 possible outcomes has the same probability based on the random synthesis of the primers and the fact that electroporation and plating should have no bias. A program in C language was developed to solve the following equation96 which was used to describe the number of colonies N that should be tested to make sure the probability that each of the 64 outcomes has been sampled at least once is around 1.098 : N! p n 1 p n 2 · · · prnr P{X 1 = n 1 , X 2 = n 2 , . . . , X r = n r } = n 1 !n 2 ! · · · n r ! 1 2 where p1 , p2 , . . . , pr are the respective probabilities of any one of r possible outcomes (e.g. r = 64 possible codons) resulting from independent and identical experiments, A1 , A2 , . . . , Ar (e.g. A1 could be the codon “CAC”);

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pi = 1; P{X 1 = n 1 , X 1 = n 1 , . . . , X r = n r } is the probability that A1 happens n 1 times, A2 happensn 2 times, . . . , Ar happens n r times in N experiments (e.g. N = 300 colonies); n i = N ; and X i is the number of n experiments that result in outcome number i (e.g. X 5 = 10 means codon 5 was seen 10 times in the population). In saturation mutagenesis of one site, there are 64 possible outcomes and the program calculates the number of colonies so that each X i ≥ 1 which means every possible codon has been sampled at least once. With two sites subjected to simultaneous saturation mutagenesis, two independent multinomial distributions apply. The probability that all possible mutants are sampled is found from multiplying the two independent probabilities, and the determination of the number of colonies needed to be sampled is based on that P1 {X 1 = n 1 , X 1 = n 1 , . . . , X r = n r } × P2 {X 1 = n 1 , X 1 = n 1 , . . . , X r = n r } = 1.0. Our program indicates that 922 independent clones are needed to ensure the probability that all 64 possible outcomes from the single site random mutagenesis has been sampled is 1.098 . If the probability is decreased to 0.99, only 292 colonies need to be screened98 . If two residues are subject to simultaneous saturation mutagenesis, 342 independent clones need to be sampled to ensure the 0.99 probability that all the possible outcomes have been checked98 .

7. CONTROL OF THE REGIOSPECIFIC HYDROXYLATION OF TOLUENE A primary goal of protein engineering is to control catalytic activity. As there is no known enzyme which hydroxylates primarily at the meta position for toluene30 , we were interested in performing mutagenesis on TpMO to enable it to make substantial amounts of meta-hydroxylated compounds from substituted benzenes. Furthermore, we also desired to ﬁne-tune the regiospeciﬁcity of TpMO via saturation or site-directed mutagenesis, to render it an orthohydroxylating enzyme similar to TOM or a more complete para-hydroxylating enzyme than even wild-type T4MO. This was the ﬁrst report of the mutagenesis of TpMO of R. pickettii PKO128 . We have shown28 that through mutagenesis of three active site residues, the catalytic activity of a multi-component monooxygenase is altered so that it hydroxylates all three positions of toluene (Figure 6) as well as both positions of naphthalene (Table 3). Hence, for the ﬁrst time, an enzyme has been engineered so that the complete regiospeciﬁc oxidation of a substrate can be controlled. Through the A107G mutation in the alpha subunit of TpMO, a variant was formed that hydroxylates toluene primarily at the ortho position while converting naphthalene to 1-naphthol. Conversely, the A107T variant produces >98% p-cresol and p-nitrophenol from toluene and nitrobenzene,

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Ayelet Fishman et al. CH3 OH

o-cresol (80%)

07 A1

G CH3

CH3

I100S/G103S m-cresol (75%)

Toluene

07 T

CH3

p-cresol (98%)

Figure 6. Control of the regiospeciﬁcity of toluene oxidation by the TpMO TbuA1 mutants A107G (o-cresol), I100S/G103S (m-cresol), and A107T ( p-cresol). Note that wild-type TpMO produces 88% p-cresol, 10% m-cresol, and 2% o-cresol.

respectively, as well as produces 2-naphthol from naphthalene. The mutation I100S/G103S produced a TpMO variant that forms 75% m-cresol from toluene and 100% m-nitrophenol from nitrobenzene; thus; a true meta-hydroxylating toluene monooxygenase was created. This is the ﬁrst report of the transformation of a single enzyme into a regiospeciﬁc catalyst that hydroxylates the aromatic ring at all possible positions producing ortho-, meta-, and para-cresols from toluene and producing 1- and 2-naphthol from naphthalene (there are no previous reports for making 2-naphthol with microorganisms, and the Western world demand for 2-naphthol is three-fold greater than that of 1-naphthol 41 ). Evidence of these regiospeciﬁc shifts were also shown with nitrobenzene and methoxybenzene (Table 3). Recently, the crystal structure of ToMO of P. stutzeri OX1 was published illustrating the importance of various active site residues on the catalytic

100 1 2 0 8 0 80 0

0 2 10 33 29 75 6 2

0 97 88 67 63 25 14 98

0 0 0 0 0 0 0 0

0 10 34 65 96 100 85 0

0 90 66 35 4 0 15 100

100 0 0 0 28 0 88 0

0 0 0 0 4 18 0 0

0 100 100 100 68 82 12 100

100 52 63 17 80 43 97 27

0 48 37 83 20 57 3 73

Each experiment with an enzyme and substrate was conducted twice with independent cultures and the results represent an average of these data (determined with two to three time points). b Initial rate of toluene oxidation from a linear plot of substrate degradation with time (liquid phase concentration 90 µ M based on Henry’s law constant of 0.2719 ; 250 µ M added if all the toluene in the liquid phase). c Benzyl alcohol was formed in negligible amounts by WT T4MO and TpMO with <1.5%. d Based on HPLC analysis over a 45 min time period (initial NB concentration was 200 µ M). e Based on HPLC analysis over a 60 min time period (initial MB concentration was 500 µ M). f Based on HPLC analysis over a 2 h time period (initial naphthalene concentration was 5 mM). Naphthalene solubility in water is 0.23 mM 89 .

1.30 ± 0.06 4.40 ± 0.3 2.20 ± 0.2 3.70 ± 0.7 0.74 ± 0.06 1.43 ± 0.08 0.84 ± 0.06 0.62 ± 0.1

2-naphthol

Naphthalene oxidation f

p-MP 1-naphthol

MB oxidatione

p-NP o-MP m-MP

NB oxidationd

p-cresol o-NP m-NP

Toluene oxidationb,c

nmol/min/mg protein o-cresol m-cresol

Toluene rateb

Regiospeciﬁc oxidation of toluene (with rate), nitrobenzene (NB), methoxybenzene (MB), and naphthalene by TG1 cells expressing wild-type (WT) TOM, WT T4MO, WT TpMO, and TpMO TbuA1 mutantsa .

WT TOM WT T4MO WT TpMO TbuA1 I100S TbuA1 G103S TbuA1 I100S/G103S TbuA1 A107G TbuA1 A107T

Enzyme

Table 3.

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Ayelet Fishman et al.

activity of this enzyme103 . Using this structure, we docked the cresol products from toluene into the TpMO active site to reveal the mechanism of the altered regiospeciﬁc reactions (Figure 4). Docking calculations showed signiﬁcant binding preferences for the favored isoform of each mutant, which agreed well with the experimental data concerning toluene oxidation regiospeciﬁcity. For variant A107G, the major change in the active site is the reduction of size of the side chain of residue 107 which allows the benzene ring of toluene to shift toward G107 and replace the methyl group of A107, thereby promoting o-cresol formation by oxidation of the C-2 carbon (Figure 4b). The same considerations apply for 1-naphthol formation from naphthalene. The I100S/G103S double mutant that produces 75% m-cresol from toluene and 100% m-nitrophenol from nitrobenzene may be explained by the increased size of the TpMO channel leading to the Fe A site (side of the active site pocket); this larger space accommodates the methyl group of toluene such that the C-3 carbon is directed toward the diiron center (Figure 4c). Additionally, the presence of serine at position 103 bears a resemblance to glutamic acid at this position in TouA of ToMO. ToMO produces 21% m-cresol from toluene, as well as 47% p-cresol and 32% o-cresol128 and this lack of speciﬁcity is attributed partially to E103103 . Similar considerations may apply to the meta-hydroxylation capability of TbuA1 I100S/G103S. The A107T mutation appears to restrict the substrates into more rigid positions relative to the diiron center by shrinking the active site (Figure 4d) and may be responsible for the most speciﬁc product proﬁle obtained (98% p-cresol/2% m-cresol and 100% p-nitrophenol). The hydroxyl group of T107 may form a hydrogen bond with the backbone carbonyl of G103 supporting the orientation of this residue in a way that directs the C-4 carbon in toluene towards the diiron center (forming only p-cresol) or the C-2 carbon in naphthalene, resulting in 2-naphthol formation. The fact that the same enzyme can react differently with several substrates of similar structure (Table 3) underlines the importance of electrophilic resonance and inductive effects. For example, none of the enzymes formed o-nitrophenol from nitrobenzene including the newly constructed orthohydroxylating TpMO variant TbuA1 A107G and the ortho-hydroxylating wildtype TOM. Nitrobenzene is 10 million times less reactive than benzene68 and this may explain the lack of reactivity of TOM towards this substrate. In addition, the nitro group has a strong electron withdrawing ability through inductive and resonance effects, thereby directing the electrophilic substitution to the meta position68 . The product distribution of nitrobenzene oxidation by wild-type T4MO, wild-type TpMO, and its TbuA1 variants, in which a higher percentage of m-nitrophenol is formed from nitrobenzene relative to m-cresol formed from toluene, implies again that both active site orientation of the substrate and electronic effects inﬂuence the regiospeciﬁcity of the reaction. In contrast to

Regiospeciﬁc Oxidation of Aromatics via Monooxygenases

259

O H N

dimerization O2

N H

2H2O

O indigo

2H2O 3/2O2 NAD+ NADH

H O NA2 D+

C3o xid ati on

O NA 2 DH

oxidation

N H 3-hydroxyindole (indoxyl)

O dimerization O O2

N H

2H2O

H N

O OH

N H 2-hydroxyindole

O indirubin

3/2O2 2H2O NADH NAD+

io at id ox

O + H2 D NA

2 C-

oxidation

N H isatin

O2 H D NA

N H indole

dimerization O O2

2H2O

isoindigo

N H

C-3

indole

C-2 N H

N H

Figure 7. Proposed pathways for converting indole to indigoid compounds via TOM of B. cepacia G4 (a) and resonance structure of indole (b).

nitrobenzene, the methyl substituent of toluene and the methoxy substituent of methoxybenzene are ortho- and para-directing activators, with the methoxy group having more pronounced activation due to the resonance effect 68 . Consequently, para-hydroxylation is more complete in methoxybenzene oxidation compared with toluene oxidation (e.g. wild-type T4MO, TpMO, TbuA1 I100S, and TbuA1 A107T in Table 3).

8. CONTROL OF THE REGIOSPECIFIC HYDROXYLATION OF INDOLE Indigo (Figure 7a) is one of the oldest dyes26 and is still used worldwide for textiles with 22,000 tons produced annually worth $200 million64,132 . Production of indigo is primarily by chemical syntheses such as the Adolf

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von Baeyer 1890 chemical synthesis33 which resulted in the ﬁfth Noble Prize in chemistry. More recently, bacterial systems for commercial indigo production have been developed74 , which were inspired by the discovery that recombinant E. coli expressing naphthalene dioxygenase from P. putida PpG7 in rich medium resulted in the formation of indigo26 . Indigo is formed as the result of the cloned enzyme oxygenating C-3 of the indole pyrrole ring (Figure 7a), and indole is produced from tryptophan via tryptophanase in E. coli 26 . Though limited to the production of a single hue, various monooxygenases and dioxygenases that allow growth on aromatic hydrocarbons have been identiﬁed that are capable of indole oxidation to form indigo4,26,33,80,81 , and these biological processes are inherently safer than the chemical processes since they do not produce such toxins as aromatic amines (bladder carcinogens) and cyanide32,132 . Indirubin (Figure 7a), a pink pigment, has important therapeutic applications40 . It is the active ingredient of a traditional Chinese medicine used to treat diseases such as chronic myelocytic leukaemia (CML) and was found to be a potent inhibitor of cyclin-dependent kinases and therefore belongs to a group of promising anticancer compounds9,40 . B. cepacia G4 was isolated as the ﬁrst pure strain that degrades TCE76 , and TOM has been shown to oxidize mixtures of chlorinated compounds, including TCE111 . TOM originally was not considered as an indigo-forming enzyme75,110 , but our laboratory found it was responsible for color development and indole hydroxylation61 . During growth in complex medium, recombinant E. coli expressing TOM forms brown colonies on rich agar plates and brown color in broth, whereas typical indole-oxygenating enzymes in whole cells form blue colonies on agar plates and blue, water-insoluble pigments in liquid medium. One TOM variant with a single amino acid change V106A of the hydroxylase alpha-subunit (TomA3) was created by us15 and was identiﬁed as a potential indigo-forming enzyme based on the green color of its colonies on agar plates and in culture. In this variant, a single mutation was responsible for the cell color change, presumably due to the alteration in the hydroxylation of indole. Consequently, further DNA shufﬂing was used to isolate a random TOM mutant that turned blue due to mutation TomA3 A113V100 . To better understand the TOM reaction mechanism, the speciﬁcity of indole hydroxylation was studied using a spectrum of colored TOM mutants expressed in E. coli TG1 and formed as a result of saturation mutagenesis at TomA3 positions A113 and V106. Colonies expressing these altered enzymes range in color from blue through green and purple to orange, and enzyme products were identiﬁed using thin-layer chromatography, HPLC, and LC-mass spectroscopy. Derived from the single TOM template, enzymes were identiﬁed that produce primarily isoindigo (wild-type TOM), indigo (A113V), indirubin (A113I), and isatin (A113H and V106A/A113G) (Figure 8). The discovery that wild-type TOM

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Figure 8. Colored chloroform LB culture extracts (no indole) of wild-type TOM and alpha subunit variants with mutations at position TomA3 A113 along with standards indigo, indirubin, isatin, and isoindigo (a). Cell color extracts of TomA3 A113G mutants (b).

forms isoindigo via C-2 hydroxylation of the indole pyrrole ring makes this the ﬁrst oxygenase shown to form this compound. Variant TOM A113G is unable to form indigo, indirubin, or isoindigo (so it does not hydroxylate the indole pyrrole ring), but produces 4-hydroxyindole and unknown yellow compounds from C-4 hydroxylation of the indole benzene ring. Mutations at V106 in addition to A113G restored C-3 indole oxidation so along with C-2 indole oxidation, isatin, indigo, and indirubin were formed. Other TomA3 V106/A113 mutants with hydrophobic, polar, or charged amino acids in place of the Val and/or Ala residues hydroxylated indole at the C-3 and C-2 positions forming isatin, indigo, and indirubin in a variety of distributions. Hence, a single enzyme may be genetically modiﬁed to produce a wide range of colors from indole; a single or double amino acid change can create catalytically distinct enzyme variants that hydroxylate indole in different regiospeciﬁc positions on the pyrrole and the benzene ring.

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9. CONTROL OF THE REGIOSPECIFIC HYDROXYLATION OF METHYL AND METHOXY AROMATICS BY T4MO Another goal of our work was to seek further improvements in T4MO activity for the regiospeciﬁc hydroxylation of methoxyaromatics (Table 4)118 ; there were no previous reports for making functionalized di-hydroxylated aromatics with T4MO as these were previously undiscovered reactions119 . Saturation mutagenesis was used to change the regiospeciﬁcity and to expand the product spectrum for three novel, industrially signiﬁcant products (3-methoxycatechol, methoxyhydroquinone, and methylhydroquinone) and to convert T4MO into an ortho-hydroxylating enzyme as well as a better parahydroxylating enzyme. Six dihydroxylated products (82% 3-methoxycatechol, 87% 4-methoxyresorcinol, 80% methoxyhydroquinone, 98% 3-methylcatechol, 100% 4-methylcatechol, and 92% methylhydroquinone) may be synthesized with high purity by a single T4MO enzyme and its variants via a one-step reaction. On the basis of the observed catalytic activity and product distribution for toluene, o-cresol, and o-methoxyphenol, we conclude that G103 and A107 are part of the substrate-binding pocket and that T4MO TmoA positions G103S and A107S have a signiﬁcant role in orienting the substrate for attack at regioselective positions of these phenol substrates. Substituted catechols, especially 3-substituted catechols, are useful precursors for making pharmaceuticals38 ; one of these, 3-methoxycatechol, is an important intermediate for the antivascular agents combretastatin A-1 and combretastatin B-18 . Methoxyhydroquinone is used in the synthesis of triptycene quinones that have been shown to have antileukemia cell activity42 and methylhydroquinone has been recently reported to be used in the synthesis of (±)helibisabonol A and puraquinonic acid which are precursors to agrochemical herbicides and antileukemia drugs, respectively39,62 . Manufacture of these substituted dihydroxylated compounds by chemical routes is difﬁcult due to the employment of aggressive reagents, expensive and complicated starting materials, multiple reaction steps, and low yields38 . Therefore, alternatives to chemical synthesis of those important industrial intermediates have been investigated. First, T4MO was discovered to oxidize o-cresol to 3-methylcatechol (91%) and methylhydroquinone (9%), to oxidize m-cresol and p-cresol to 4-methylcatechol (100%), as well as to oxidize o-methoxyphenol to 4-methoxyresorcinol (87%), 3-methoxycatechol (11%), and methoxyhydroquinone (2%). Apparent Vmax values of 6.6 ± 0.9 to 10.7 ± 0.1 nmol/min/mg protein were obtained for o-, m-, and p-cresol oxidation by wild-type T4MO that are comparable to the toluene oxidation rates (15.1 ± 0.8 nmol/min/mg protein). After discovering these new reactions, saturation mutagenesis was performed near the diiron catalytic center at positions I100, G103, and A107 of

11 20 52 82 <1 30

2 7 7 5 80 35

MxH, %

MxH formation rated (nmol/ min/mg protein) 0.07 ± 0.03 ∼0 ∼0 ∼0 0.36 ± 0.01 0.08

Via HPLC Relative Activityb Via colorimetric assay 0.21 ± 0.01 0.8 ± 0.2 1.2 ± 0.2 1.5 ± 0.2 ∼0 NDc 1 4 6 7 0 0

0.2 0.9–1.3 0.7–2.7 1.9 0 0

3MxC formation rate (nmol/min/mg protein)

Activity determined at the saturation substrate concentration of 1 mM. Relative values based on HPLC analysis whereas the colorimetric assay corroborated this data. c ND, not determined. d The o-methoxyphenol substrate was oxidized to as many as 3 different products but only the MxH formation rate is shown.

87 73 41 13 19 35

4MxR, % 3MxC, %

Regiospeciﬁcity of o-methoxyphenol oxidation

4.1 ± 1.1 2.4 ± 0.8 2.1 ± 0.5 1.9 0.4 NDc

o-methoxyphenol oxidation (nmol/min/mg protein)

3-Methoxycatechol (3MxC), methoxyhydroquinone (MxH), and 4-methoxyresorcinol (4MxR) synthesis from o-methoxyphenol by E. coli TG1 expressing wild-type T4MO and saturation mutagenesis TmoA variantsa .

Wild-type I100L G103A G103A/A107S G103S G103S/A107T

Enzyme

Table 4.

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the alpha subunit of the hydroxylase (TmoA) based on directed evolution of the related TOM of B. cepacia G415,100 (positions I100 & A107) and a previously reported T4MO G103L regiospeciﬁc mutation73 . Using o-cresol and o-methoxyphenol as model substrates, regiospeciﬁc mutants of T4MO were created; for example, TmoA variant G103A/A107S produced 3-methylcatechol (98%) from o-cresol two-fold faster and produced 3-methoxycatechol (82%) from 1 mM o-methoxyphenol seven times faster than wild-type T4MO (1.5 ± 0.2 vs. 0.21 ± 0.01 nmol/min/mg protein). Variant I100L produced 3-methoxycatechol from o-methoxyphenol four times faster than wild-type T4MO, and G103S/A107T produced methylhydroquinone (92%) from o-cresol four-fold faster than wild-type T4MO and 10 times more as in terms of percentage product. Variant G103S produced methoxyhydroquinone from o-methoxyphenol 40-fold higher than the wild-type enzyme (80% vs. 2%) and produced methylhydroquinone (80%) from o-cresol. Hence the regiospeciﬁc oxidation of o-methoxyphenol and o-cresol was changed for signiﬁcant synthesis of 3-methoxycatechol, methoxyhydroquinone, 3-methylcatechol, and methylhydroquinone (Table 4). The enzyme variants also demonstrated altered mono-hydroxylation regiospeciﬁcity for toluene; for example, G103S/A107G formed 82% o-cresol, so saturation mutagenesis converted T4MO into an ortho-hydroxylating enzyme. Furthermore, G103S/A107T formed 100% p-cresol from toluene; hence, a better p-hydroxylating enzyme than wild-type T4MO was formed. Structure hom*ology modeling suggests that hydrogen bonding interactions of the hydroxyl groups of altered residues S103, S107, and T107 inﬂuence the regiospeciﬁcity of the oxygenase reaction. These ﬁndings not only correct the misunderstanding that wild-type T4MO can only hydroxylate benzenes to mono-hydroxylated products and cannot subsequently hydroxylate phenols52,73,90,131 , but also show that wild-type T4MO is a good biocatalyst for making some industrially signiﬁcant, substituted, catecholic compounds.

10. CONTROL OF THE REGIOSPECIFIC HYDROXYLATION OF METHYL AROMATICS BY ToMO Di- and tri-hydroxy aromatics (Figures 9–11) are important industrial chemicals with many applications as evidenced by worldwide production of catechol, resorcinol, and hydroquinone at 110,000 tons/year84 . Catechol is used as an intermediate in the food, pharmaceutical, and agrochemical industries84 , and hydroquinone is used in photography, in cosmetics, and in both medical and industrial X-ray ﬁlms34,84 . Resorcinol and its derivatives are used to inhibit rust in

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265

CH3 R1

Toluene

o-cresol: m-cresol: p-cresol: 3-methylcatechol: 4-methylcatechol: methylhydroquinone: 4-methylresorcinol:

R1=OH R2=OH R3=OH R1,R2=OH R2,R3=OH R1,R4=OH R1,R3=OH

o-nitrophenol: m-nitrophenol: p-nitrophenol: 3-nitrocatechol: 4-nitrocatechol: nitrohydroquinone: 4-nitroresorcinol:

R5=OH R6=OH R7=OH R5,R6=OH R6,R7=OH R5,R8=OH R5,R7=OH

o-methoxyphenol: m-methoxyphenol: p-methoxyphenol: 3-methoxycatechol: 4-methoxycatechol: methoxyhydroquinone: 4-methoxyresorcinol:

R9=OH R10=OH R11=OH R9,R10=OH R10,R11=OH R9,R12=OH R9,R11=OH

NO2

NO2 R5

Nitrobenzene (NB)

R6 R7

OCH3

OCH3 R9

R12

Methoxybenzene (MB)

R10 R11

R13 R14

1-naphthol: 2-naphthol:

R13=OH R14=OH

Naphthalene

Figure 9. Structures of substituted aromatics discussed in this chapter.

paints, to regulate plant growth, and to act as capacitor electrolytes22,49,135 . Production of 4-methylresorcinol is uncommon and prices can exceed $200,000/kg (Apin Chemicals, http://www.apinchemicals.com). 1,2,3-THB (pyrogallol), the ﬁrst synthetic dye for hair, is primarily used as a modiﬁer in oxidation dyes120 , as a pharmaceutical intermediate, and has been used as a topical antipsoriatic84 .

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benzene ToMO I100Q F205G M180T/E284G OH

phenol F205G, 11% (0.070) F205G, 13% (0.090)

ToMO, 100% (1.5)

I100Q, 80% (1.2)

I100Q, 20% (0.28)

M180T/E284G, 2% (0.040)

F205G, 76% (0.52) M180T/E284G, 98% (2.0) OH

OH catechol

hydroquinone

resorcinol F205G, 100% ToMO, 100% I100Q, 100%

M180T/E284G, 14% (0.16)

M180T/E284G, 23% ToMO, 100% (0.71)

ToMO, 100%

I100Q, 100%

I100Q, 100% F205G, 100%

M180T/E284G, 86% (1.0)

M180T/E284G, 77%

M180T/E284G, 100% OH

OH OH

OH 1,2,4-trihydroxybenzene

1,2,3-trihydroxybenzene

1,2,4-trihydroxybenzene

Figure 10. Pathways for the oxidation of benzene (0.8 mM) to phenol, phenol (0.8 mM) to dihydroxy-benzenes, and dihydroxy-benzenes (0.8 mM) to THBs by E. coli TG1/pBS(Kan)ToMO expressing wild-type ToMO and TouA variants I100Q, F205G, and M180T/E284G. Molar product percentages are shown followed by bold numbers in parenthesis, ( ), which indicate the product formation rates in nmol/min/mg protein.

Hydroxyhydroquinone (1,2,4-THB) has been used in dyes and as a corrosion inhibitor41 . Since some of these compounds cannot be easily synthesized chemically, direct microbial synthesis of such compounds from inexpensive substrates might provide a more cost effective and more environmentally benign approach. ToMO from P. stutzeri OX1 oxidizes toluene to 3- and 4-methylcatechol (Figure 11) as well as oxidizes benzene to form phenol (Figure 10); ToMO was found by us to also form catechol and 1,2,3-THB from phenol128 . To synthesize novel dihydroxy and trihydroxy derivatives of benzene and toluene, DNA shufﬂing of the alpha hydroxylase fragment of ToMO (TouA) and saturation mutagenesis of the TouA active site residues I100, Q141, T201, and F205 were used to

3-methylcatechol

CH3

M180T/E284G, 85% (1.5)

M180T/E284G, 15% (0.19)

I100Q, 50% (0.49)

F205G, 22% (0.25)

I100Q, 50% (0.50)

ToMO, 100% (1.1)

F205G, 8% (0.088)

I100Q, 50% (0.44)

methylhydroquinone

CH3

M180T/E284G, 4% (0.012)

CH3

3-methylcatechol

CH3

M180T/E284G, 4% (0.039)

F205G, 22% (0.080)

ToMO, 4% (0.034)

m-cresol

M180T/E284G, 28%

4-methylcatechol

CH3

M180T/E284G, 92% (1.7)

I100Q, 50% (0.45)

F205G, 78% (0.28)

ToMO, 96% (1.0) p-cresol

CH3

M180T/E284G, 88% (1.8)

I100Q, 100% (1.1)

F205G, 78% (0.46)

ToMO, 100% (1.3)

M180T/E284G, 42%

F205G, 43%

I100Q, 34%

ToMO, 47%

OH 4-methylresorcinol

CH3 OH

M180T/E284G, 12% (0.25) F205G, 22% (0.13)

Figure 11. Pathways for the oxidation of toluene (0.8 mM) to o-cresol, m-cresol, and p-cresol, and oxidation of o-cresol (0.8 mM), m-cresol (0.8 mM), and p-cresol (0.8 mM) to methylcatechols, methyl-resorcinols, and methylhydroquinone by E. coli TG1/pBS(Kan)ToMO expressing wild-type ToMO and TouA variants I100Q, F205G, and M180T/E284G. Bold numbers in parenthesis, ( ), indicate the product formation rates in nmol/min/mg protein. Molar product percentages are shown before the rate values.

4-methylresorcinol

CH3

F205G, 70% (0.78)

o-cresol

CH3

I100Q, 44%

M180T/E284G, 30% F205G, 33%

ToMO, 21%

toluene

F205G, 24%

I100Q, 22%

ToMO, 32%

CH3

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generate random mutants. The mutants were initially identiﬁed by screening via a rapid agar plate assay and then were further examined by HPLC and GC. Overall, ﬁve new reactions were found for wild-type ToMO (catechol formation from phenol, 1,2,3-THB from catechol, 1,2,4-THB from resorcinol, 1,2,4-THB from hydroquinone, and 3-methylcatechol from m-cresol), and protein engineering was used to make mutants that synthesize eight novel, industrially signiﬁcant products (resorcinol, hydroquinone, 4-methylresorcinol, methylhydroquinone, 1,2,3-THB, 1,2,4-THB, 3-methylcatechol, and 4-methylcatechol)128 . Several regiospeciﬁc mutants with high rates of activity were identiﬁed128 ; for example, E. coli TG1/pBS(Kan)ToMO expressing TouA saturation mutagenesis variant F205G formed 4-methylresorcinol (0.78 nmol/min/mg protein), 3-methylcatechol (0.25 nmol/min/mg protein), and methylhydroquinone (0.088 nmol/min/mg protein) from o-cresol whereas wild-type ToMO formed only 3-methylcatechol (1.1 nmol/min/mg protein) (Figure 11). From o-cresol, saturation mutagenesis mutant I100Q and DNA shufﬂing mutant M180T/E284G formed methylhydroquinone (0.50 and 0.19 nmol/min/mg protein, respectively) and 3-methylcatechol (0.49 and 1.5 nmol/min/mg protein, respectively). F205G formed catechol (0.52 nmol/min/mg protein), resorcinol (0.090 nmol/min/mg protein), and hydroquinone (0.070 nmol/min/mg protein) from phenol whereas wild-type ToMO formed only catechol (1.5 nmol/min/mg protein). Both I100Q and M180T/E284G formed hydroquinone (1.2 and 0.040 nmol/min/mg protein, respectively) and catechol (0.28 and 2.0 nmol/min/mg protein, respectively) from phenol. Dihydroxybenzenes were further oxidized to THBs with different regiospeciﬁcities; for example, I100Q formed 1,2,4-THB from catechol whereas wild-type ToMO formed 1,2,3-THB (pyrogallol). Regiospeciﬁc oxidation of the natural substrate toluene was also checked, for example, I100Q forms 22%, 44%, and 34% of o-, m-, and p-cresol, respectively, whereas wild-type ToMO forms 32%, 21%, and 47% of o-, m-, and p-cresol, respectively.

11. CONTROL OF THE REGIOSPECIFIC HYDROXYLATION OF NITRO AROMATICS Nitrocatechols have been found to be useful intermediates for the synthesis of pharmaceuticals such as Flexinoxan, an antihypertensive drug37,104 . Recently, nitrocatechol compounds were discovered as potent inhibitors of catechol-o-methyltransferase and are under clinical evaluation for the treatment of Parkinson’s disease and other nervous system disorders55,56 . In another study, 4-nitrocatechol and 3-nitrocatechol were found to be competitive inhibitors of nitric oxide synthase with potential antinociceptive (pain relieving) activity85 ; however, there is only one worldwide source of 3-nitrocatechol and its

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269

price is $20,000/g (Vitas-M Laboratory, Ltd.). Furthermore, nitrohydroquinone has been used to synthesize dephostatin, an inhibitor of the protein tyrosine phosphatase36 which is a candidate therapeutic agent for diabetes mellitus and neural diseases such as Alzheimer’s disease and Parkinson’s disease121 . As chemical synthesis of these compounds is problematic in terms of yield and selectivity85 , the utilization of oxygenases is advantageous. The high redox potential of oxygenases enables them to perform reactions with chemically stable substrates as well as provide a high degree of regio- and enantio-selectivity10,58 . Transforming selectively an inexpensive and abundant chemical as nitrobenzene into a valuable feedstock for drug production (e.g. 4-nitrocatechol) is therefore of great signiﬁcance. Here we summarize our work on the mutagenesis of both T4MO and ToMO for nitroaromatics. After discovering that T4MO of P. mendocina KR1 oxidizes nitrobenzene to 4-nitrocatechol, albeit at a very low rate, this reaction was improved using directed evolution and saturation mutagenesis. Screening 550 colonies from a random mutagenesis library generated by error-prone PCR of tmoAB using E. coli TG1/pBS(Kan)T4MO on agar plates containing nitrobenzene led to the discovery of nitrocatechol-producing mutants. One mutant, NB1, contained six amino acid substitutions (TmoA Y22N, I84Y, S95T, I100S, S400C; TmoB D79N). It was believed that position I100 of the alpha subunit of the hydroxylase (TmoA) is the most signiﬁcant for the change in substrate reactivity due to previous results in our lab with a similar enzyme, TOM of B. cepacia G415 . Saturation mutagenesis at this position resulted in the generation of two more nitrocatechol mutants, I100A and I100S; the rate of 4-nitrocatechol formation by I100A was more than 16 times higher than that of wild-type T4MO at 200 µM nitrobenzene (0.13 ± 0.01 vs. 0.008 ± 0.001 nmol/min/mg protein). HPLC and mass spectrometry analysis revealed that variants NB1, I100A, and I100S produce 4-nitrocatechol via m-nitrophenol, while the wild-type produces primarily p-nitrophenol and negligible amounts of nitrocatechol. Relative to wild-type T4MO, whole cells expressing variant I100A convert nitrobenzene into m-nitrophenol with a Vmax of 0.61 ± 0.037 vs. 0.16 ± 0.071 nmol/min/mg protein and convert m-nitrophenol into nitrocatechol with a Vmax of 3.93 ± 0.26 vs. 0.58 ± 0.033 nmol/min/mg protein. Hence the regiospeciﬁcity of nitrobenzene oxidation was changed by the random mutagenesis, and this led to a signiﬁcant increase in 4-nitrocatechol production. The regiospeciﬁcity of toluene oxidation was also altered, and all of the mutants produced 20% m-cresol and 80% p-cresol, whereas the wildtype produces 96% p-cresol. Interestingly, the rate of toluene oxidation (the natural substrate of the enzyme) by I100A was also higher by 65% (7.2 ± 1.2 vs. 4.4 ± 0.3 nmol/min/mg protein). hom*ology-based modeling of TmoA suggests reducing the size of the side chain of I100 leads to an increase in the width of the active site channel which facilitates access of substrates and promotes more ﬂexible orientations.

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ToMO from P. stutzeri OX1 was found to oxidize nitrobenzene to form m-nitrophenol (72%) and p-nitrophenol (28%)127 . It was also discovered that wild-type ToMO forms 4-nitrocatechol from m-nitrophenol and p-nitrophenol and 3-nitrocatechol (18%) and nitrohydroquinone (82%) from o-nitrophenol. To increase the oxidation rate and alter the oxidation regiospeciﬁcity of nitro aromatics as well as to study the role of the active site residues, DNA shufﬂing and saturation mutagenesis were performed on the alpha hydroxylase fragment of ToMO (TouA). Several mutants with higher rates of activities and with different regiospeciﬁcities were identiﬁed; for example, Escherichia coli TG1 cells expressing either TouA mutant M180T/E284G or E214G/D312N/M399V produce 4-NC 4.5-fold and 20-fold faster than wildtype ToMO from p-nitrophenol, respectively. TouA mutant A107T/E214A had the regiospeciﬁcity of nitrobenzene changed signiﬁcantly from 28% to 79% p-nitrophenol. From 200 µM nitrobenzene, TouA variants A101T/M114T, A110T/E392D, M180T/E284G, and E214G/D312N/M399V produce 4-NC whereas wild-type ToMO does not. From m-nitrophenol, TouA mutant I100Q produces 4-nitrocatechol (37%) and nitrohydroquinone (63%), whereas wildtype ToMO produces only 4- nitrocatechol (100%). Variant A107T/E214A acts like a para enzyme and forms p-cresol as the major product (93%) from toluene with enhanced activity (2.3 fold), whereas wild-type ToMO forms 32%, 21%, and 47% of o-, m-, and p-cresol, respectively. Hence, the nonspeciﬁc ToMO was converted into a regiospeciﬁc enzyme, which rivals T4MO of Pseudomonas mendocina KR1 and TOMO of Burkholderia cepacia G4 in its speciﬁcity.

12. REGIOSPECIFIC HYDROXYLATION OF NAPHTHALENE AND FLUORENE Naphthalene and ﬂuorene (Figure 12) serve as model bi- and tri-cyclic aromatic hydrocarbons for understanding the properties of a large class of PAHs17 , and there is no report of producing 2-naphthol with enzymes. Hence, we explored the regiospeciﬁc oxidation of naphthalene and ﬂuorene with E. coli strains expressing wild-type T4MO, TpMO, TOM, ToMO, and T4MO variants (Table 5 and Figure 12)117 . T4MO oxidized toluene, naphthalene, and ﬂuorene faster than the other wild-type enzymes (2- to 22-fold) and produced a mixture of 1-naphthol (52%) and 2-naphthol (48%) from naphthalene which was successively transformed to a mixture of 2,3-, 2,7-, 1,7-, and 2,6-dihydroxynaphthalenes (7%, 10%, 20%, and 63%, respectively). TOM and ToMO made 1,7-dihydroxynaphthalene from 1-naphthol, and ToMO made a mixture of 2,3-, 2,6-, 2,7-, and 1,7-dihydroxynaphthalene (26%, 22%, 1%, and 44%, respectively) from

Figure 12. Pathway of naphthalene and ﬂuorene oxidation by wild-type toluene monooxygenases, TOM variant TomA3 V106A, and T4MO TmoA variants.

Naphthalene oxidationb

Fluorene oxidationc

0 0 0 7 82 12 9

19.1 ± 0.8 22.7 ± 1.6 15.1 ± 2.3 17.7 ± 0.2 1.5 ± 0.3 20.1 ± 0.4 18.1 ± 1.7

TmoA I100A TmoA I100S TmoA I100G TmoA I100L TmoA G103S/A107G TmoA G103A TmoA G103S

20 20 13 3 7 13 15

0 33 21 10 3 80 80 87 90 11 75 76

0 17 47 90 96 7.0 ± 1.5 5.5 ± 1.6 7.6 ± 0.5 3.2 ± 1.5 0.5 ± 0.1 5.6 ± 1.5 5.9 ± 0.1

0.9 ± 0.2 3.4 ± 0.5 4.2 ± 2.3 0.9 ± 0.2 7.7 ± 1.5 8 5 12 83 99 81 83

99 99 90 63 52 92 95 88 17 <1 19 17

<1 <1 10 37 48 0.57 ± 0.03 0.49 ± 0.13 0.57 ± 0.11 0.38 ± 0.18 0.15 ± 0.04 0.38 ± 0.04 0.23 ± 0.02

0.10 ± 0.01 0.17 ± 0.02 0.03 ± 0.01 0.21 ± 0.01 0.68 ± 0.04

0 0 0 0 28 0 0

12 33 4 0 0

16d 17d 17d 13d 18 22d 14d

26 7 29d 14d 14d

84d 83d 83d 87d 53 78d 86d

21 8 67d 86d 86d

Toluene oxidation rate and regiospeciﬁcity determined via GC with 109 µM toluenecalculated based on Henry’s law. Total naphthol formation rate and regiospeciﬁcity determined via HPLC with 5 mM (naphthalene solubility is 0.23 mM in water). c Fluorene oxidation rate determined via HPLC and regiospeciﬁcity determined via GC except for TOM and TOM TomA3 V106A where regiospeciﬁcity was determined via GC-MS. Activity determined at the saturation concentration of 0.2 mM so the initial rate values represent Vmax . Hf, hydroxy ﬂuovene. d Regiospeciﬁcity conﬁrmed by HPLC with a supelcosil-ABZ alky-amide column.

>98 50 32 0 <1

2.5 ± 0.1 4.8 ± 1.1 6.1 ± 0.1 4.1 ± 0.2 12.1 ± 0.8

0 0 0 0 0 0 0

41 51 0 0 0

Regiospeciﬁcity (%) Regiospeciﬁcity (%) Regiospeciﬁcity (%) Rate, nmol/min/ Rate, nmol/min/ Rate, nmol/min/ mg protein o-cresol m-cresol p-cresol mg protein 1-naphthol 2-naphthol mg protein 1-HF 2-HF 3-HF 4-HF

Toluene oxidationa

Aromatic oxidation rate and regiospeciﬁcity by TG1 cells expressing wild-type T4MO, ToMO, TOM, TOM TomA3 V106A, and T4MO TmoA variants.

Wild-type TOM TOM TmoA3 V106A Wild-type ToMO Wild-type TpMO Wild-type T4MO

Enzyme

Table 5.

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2-naphthol. TOM had no activity on 2-naphthol, and T4MO had no activity on 1-naphthol. To take advantage of the high activity of wild-type T4MO but to increase its regiospeciﬁcity on naphthalene, 7 engineered enzymes containing mutations in T4MO alpha hydroxylase TmoA were examined; the selectivity for 2-naphthol by T4MO I100A, I100S, and I100G was enhanced to 88%–95%, and the selectivity for 1-naphthol was enhanced to 87% and 99% by T4MO I100L and G103S/A107G, respectively, while high oxidation rates were maintained except for G103S/A107G (Table 5). Therefore, the regiospeciﬁcity for naphthalene oxidation was altered to practically pure 1-naphthol or 2-naphthol. All four wild-type monooxygenases were able to oxidize ﬂuorene to different mono-hydroxylated products; T4MO oxidized ﬂuorene successively to 3-hydroxyﬂuorene and 3,6-dihydroxyﬂuorene, which were conﬁrmed by GCmass spectrometry and 1 H nuclear magnetic resonance analysis. TOM and its variant TomA3 V106A oxidize ﬂuorene to a mixture of 1-, 2-, 3-, and 4hydroxyﬂuorene. This is the ﬁrst report of using enzymes to synthesize 1-, 3-, and 4-hydroxyﬂuorene, and 3,6-dihydroxyﬂuorene from ﬂuorene as well as 2-naphthol and 2,6-dihydroxynaphthalene from naphthalene.

13. TWO-PHASE REACTORS FOR SYNTHESIZING PHENOL AND 2-NAPHTHOL Phenol and naphthol compounds are important precursors for the manufacture of many dyes, drugs, perfumes, insecticides, and surfactants (e.g. pigment intermediate Tobias acid from 2-naphthol)41 . World production for phenol is huge (6,600,000 ton/year) and that of 1-naphthol and 2-naphthol is around 15,000 and 50,000 ton/year, respectively41,78 . Industrially, 90% of the world phenol production is manufactured by a three-step, cumene process59 that relies on the co-production of acetone and has low yields78 . Hence, attempts to direct conversion of benzene to phenol by one-step reactions have been investigated51,59,63,69,88 . However, the remaining signiﬁcant challenge in the chemical synthesis of phenol is the low conversion of benzene per pass of these processes (<10%). Current commercial methods of manufacturing 2-naphthol include oxidation and aromatization of tetralin, caustic fusion of sodium 1naphthalenesulfonate with sodium hydroxide in a ﬁve-step reaction, and hydroxylation of 2-isopropylnaphthalene41 . The selectivity for 2-naphthol based on naphthol isomer distribution using those chemical methods is 90% or better. However, chemical synthesis is hampered by toxic reagents such as naphthalene1-sulfonic acid, high concentration of acids and bases such as hydrogen ﬂuoride, complicated, multiple-step reactions, extreme temperature conditions, and coproduction of acetone41 . For example, in order to obtain high selectivity (98%),

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a ﬂuorosulfuric acid–sulfuryl chloride ﬂuoride solution at -60˚C to −78˚C was used for 2-naphthol production from naphthalene 82 . To our knowledge, there is no domestic producer of 2-naphthol in the United States since 1982 when the hydroperoxidation process ceased production41 due to environmental problems, and China became the major supplier. It is predicted that production of 2-naphthol will be reduced if China intensiﬁes its environmental protection policies, and the impact of a supply shortage may spread to the global market18 . Since recombinant E. coli TG1 expressing wild-type T4MO performs successive hydroxylations of benzene to phenol, catechol, and 1,2,3-THB119 (Figure 2), and E. coli TG1 expressing an evolved T4MO with alpha subunit mutation I100A may be used to hydroxylate naphthalene to 92% 2-naphthol (ﬁrst production in a microbial system) and 8% 1-naphthol which are subsequently oxidized to dihydroxynaphthalenes117 (Figure 12), we explored using a twophase system for maximizing production of these important intermediates116 . In the single-phase reaction, phenol production from benzene by T4MO was greatly reduced by the further conversion of phenol to catechol, and the production of 2-naphthol was limited by the toxicity of naphthalene and 2-naphthol to the biocatalyst and the low solubility of naphthalene in water. In contrast, the two-phase system allowed for the transformation of benzene to phenol and naphthalene to 2-naphthol using whole cells expressing wild-type T4MO and T4MO TmoA I100A. The solubility of naphthalene was enhanced and the toxicity of the naphthols was prevented by the use of a water (80 vol%)dioctyl phthalate (20 vol%) system which yielded 21-fold more 2-naphthol using TG1/pBS(Kan)T4MOI100A (10.6 ± 1.3 mM in the two-phase system vs. 0.5 ± 0.05 mM in the single phase). More than 99% 2-naphthol was extracted to the dioctyl phthalate phase, further conversion of 2-naphthol was prevented, 92% 2-naphthol was formed, and 12% naphthalene was converted. In addition, using 50% vol dioctyl phthalate and an initial concentration of 39 mM, a 51 ± 9% conversion of benzene was obtained by TG1/pBS(Kan)T4MO, and phenol was produced at a purity of 97% (in the organic phase) with an average volumetric productivity of 0.4 ± 0.04 g phenol/Laqueous /h. Relative to the one-phase system, there was a 12-fold reduction in byproduct catechol formation (96% phenol vs. 8% phenol after 3 h). This is the ﬁrst report of using toluene monooxygenases in two-liquid phase systems for synthesizing industrially signiﬁcant, phenolic compounds.

14. DEGRADATION OF PCE, TCE, AND CHLOROFORM Highly chlorinated compounds are recalcitrant and threaten the environment. For example, tetrachloroethylene [perchloroethylene (PCE)] is one of the ﬁve most-frequently detected volatile organic compounds found in municipal

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groundwater supplies130 since it has been used extensively as an industrial degreasing solvent and fumigant16 . PCE is also one of 14 volatile organic compounds on the United States EPA’s Priority Pollutant List16 . Because this solvent is toxic and is a suspected human carcinogen57 , PCE is regulated under the Safe Drinking Water Act to a maximum contaminant level of 5 parts per billion. Bacterial degradation of PCE had never been achieved in the presence of oxygen25,65,66 until work with TOMO101 . However, degradation through oxygen attack of fully halogenated chlorotriﬂuoroethylene has been achieved by puriﬁed sMMO of Methylosinus trichosporium OB3b; the lack of PCE degradation by this enzyme was suggested to be due to steric hindrance31 . Since ﬂuorine is more electronegative and more tightly bound than chlorine, chlorotriﬂuoroethylene should be more difﬁcult to oxidize than PCE. Therefore it is reasonable that a monooxygenase can degrade PCE. It is very well established that PCE is degraded anaerobically via reductive dehalogenation to the less-chlorinated ethenes TCE, trans-1,2-dichloroethylene (trans-DCE), cis-1,2-dichloroethylene (cis-DCE), 1,1-dichloroethylene (1,1DCE), vinyl chloride (VC), and ethene as well as to ethane108 . The dechlorination of PCE is often incomplete when it does occur, with VC and cis-DCE formed primarily66 ; however, dehalorespiration of PCE to ethene is possible65 . VC generated is a known human carcinogen66 and both VC and cis-DCE are US EPA priority pollutants5 . Surprisingly, the wastewater bacterium P. stutzeri OX1 was found to degrade aerobically 0.56 µmol of 2.0 µmol PCE in 21 h (Vmax ∼ = 2.5 nmol/min/mg protein and K M ∼ = 34 µM)101 . These results were corroborated by the generation of 0.48 µmol of the degradation product, chloride ions. This degradation was conﬁrmed to be a result of expression of ToMO since cloning and expressing this enzyme in E. coli led to the aerobic degradation of 0.19 µmol of 2.0 µmol PCE and the generation of stoichiometric amounts of chloride. PCE also induces formation of ToMO which leads to its degradation in P. stutzeri OX1101 . Since this strain is also chemotactic toward PCE125 , that means a single bacterium will move toward this pollutant, the pollutant will induce the genes for the degradation enzyme, and will subsequently be degraded. TCE is the most-frequently detected groundwater contaminant; hence, directed evolution was used to increase the activity of TOM of B. cepacia G4 for chlorinated ethenes. When expressed in E. coli, the alpha subunit variant V106A (TOM-Green) degrades more rapidly TCE (2.5 ± 0.3 vs. 1.39 ± 0.05 nmoles/min/mg protein), 1,1-DCE, and trans-DCE. These results show clearly that random, in vitro protein engineering can be used to improve a large multisubunit protein for multiple functions including environmental restoration. Mutagenesis of the alpha subunit of ToMO also led to enhanced TCE degradation126 . ToMO TouA saturation mutagenesis variant I100Q was

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identiﬁed that degrades TCE 2.8 times better than the wild-type enzyme. Another variant, E214G/D312N/M399V, degrades cis-DCE 2.5 faster, and variant M180T/E284G also has enhanced cis-DCE activity. Like TCE, chloroform is a widely used chlorinated solvent and a common groundwater contaminant due to improper disposal and accumulation from anaerobic dehalogenation of carbon tetrachloride at contaminated sites23 . Chloroform is also a suspected carcinogen67 . Whole cells expressing TOM are also able to degrade mixtures of chlorinated aliphatics including TCE and chloroform111 . To enhance chloroform degradation, saturation mutagenesis was performed on TOM at alpha subunit position V106 since this position had been identiﬁed by DNA shufﬂing to be important for the degradation of chlorinated ethenes15 . Variant A106F was identiﬁed that has 2.8 times better chloroform degradation activity based on GC (Vmax of 2.61 vs. 0.95 nmol/min/mg protein and unchanged K m ) and chloride release (0.034 ± 0.002 vs. 0.012 ± 0.001 nmol/min/mg protein)98 . Variant A106F also has similar protein expression as A106 and 62% better toluene oxidation activity than wild-type TOM (2.11 ± 0.3 vs. 1.30 ± 0.06 nmol/min/mg protein)98 .

15. METABOLIC ENGINEERING FOR DEGRADING CHLORINATED ETHENES Based on the Gibbs free energy calculation of aerobic degradation of chlorinated ethenes to water, carbon dioxide and HCl, growth on nearly all chlorinated aliphatics is thermodynamically possible (e.g. the Gibbs free energy change for the aerobic mineralization of cis-DCE is -1143 kJ/mol)123 . If the reactive intermediates may be effectively detoxiﬁed, the main biochemical factor that hampers chlorinated ethenes from supporting cell growth is the lack of appropriate enzymes to harvest their energy. Hence it is feasible to construct bacteria which grow on these chlorinated ethenes and create a niche for their aerobic degradation. Currently, the aerobic degradation of chlorinated ethenes is fortuitous and provides no beneﬁt to the cell; in fact, it leads to cell death and thus is selected against (Figure 13). The toxic epoxides generated during the aerobic biodegradation of chlorinated ethenes limit their transformation. Hydrolysis of the toxic epoxide by epoxide hydrolases represents one of the major biological detoxiﬁcation strategy; however, chlorinated epoxyethanes are not accepted by known bacterial epoxide hydrolase. The epoxide hydrolase from Agrobacterium radiobacter AD1 (EchA), which enables growth on epichlorohydrin, was tuned by us to accept cis-1,2-dichloroepoxyethane as a substrate by accumulating beneﬁcial mutations from three rounds of saturation mutagenesis at three selected active site residues: F108, I219, and C24897 . The EchA F108L/I219L/C248I variant

Figure 13. Metabolic engineering to enhance cis-DCE mineralization by cloning an evolved epoxide hydrolase (EchA) or glutathione S-transferase (IsoILR1) along with an evolved TOM (TOM-Green) (adapted from van Hylckama Vlieg and Janssen123 ). Steps 1 and 2 are the two possible spontaneous transformation pathways for cis-DCE epoxide, while step 3 and step 4 represent two major detoxiﬁcation strategies in with cis-DCE epoxide may be biologically converted by either an epoxide hydrolase or glutathione S-transferase (IsoILR1).

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co-expressed with DNA shufﬂed TOM (TOM-Green, alpha subunit V106A mutation), which initiates attack on the chlorinated ethene, allowed for the degradation of cis-dichloroethylene (cis-DCE) at low concentrations (6.8 µM) (wild-type EchA has no activity at this concentration) and enhanced degradation 10 fold at high concentrations (540 µM). EchA variants with single mutations (F108L, I219F, or C248I) enhanced cis-DCE mineralization 2.5 fold (540 µM), and EchA variants with double mutations, I219L/C248I and F108L/C248I, increased cis-DCE mineralization four-fold and seven-fold, respectively (540 µM). For complete degradation of cis-DCE to chloride ions, the apparent Vmax /K m for the recombinant Escherichia coli strain expressing the EchA F108L/I219L/C248I variant was increased over ﬁve-fold as a result of the evolution of EchA. The EchA F108L/I219L/C248I variant also had enhanced activity for 1,2-epoxyhexane (two-fold) and the natural substrate epichlorohydrin (six-fold)97 . A similar approach using glutathione S-transferases instead of the engineered epoxide hydrolase has also been implemented by us (Figure 13)99 .

16. ENGINEERING DIOXYGENASES FOR SINGLE HYDROXYLATIONS OF AROMATICS Like toluene monooxygenases, dioxygenases may be evolved for monohydroxylation of aromatics. Saturation mutagenesis of the 2,4-dinitrotoluene dioxygenase of Burkholderia cepacia R34 (DDO) at position valine 350 of the DntAc α-subunit generated mutant V350F with signiﬁcantly increased activity toward o-nitrophenol (47 times), m-nitrophenol (34 times), and omethoxyphenol (174 times) as well as an expanded substrate range that now includes m-methoxyphenol, o-cresol, and m-cresol (wild-type DDO had no detectable activity for these substrates)47 . V350F produced both nitrohydroquinone at a rate of 0.75 ± 0.15 nmol/min/mg protein and 3-nitrocatechol at a rate of 0.069 ± 0.001 nmol/min/mg protein from o-nitrophenol, 4-nitrocatechol from m-nitrophenol at 0.29 ± 0.02 nmol/min/mg protein, methoxyhydroquinone from o-methoxyphenol at 2.5 ± 0.6 nmol/min/mg protein, methoxyhydroquinone from m-methoxyphenol 0.55 ± 0.02 nmol/min/mg protein, both methylhydroquinone at 1.52 ± 0.02 nmol/min/mg protein and 2-hydroxybenzyl alcohol at 0.74 ± 0.053 nmol/min/mg protein from o-cresol, and methylhydroquinone at 0.43 ± 0.12 nmol/min/mg protein from m-cresol. The DDO variant V350F also exhibited 10-fold enhanced activity towards naphthalene (8.2 ± 2.6 nmol/min/mg protein), forming (1R, 2S)-cis-1,2-dihydro-1,2dihydroxynaphthalene. Hence, mutagenesis of the wild-type DDO through active site engineering generated variants with relatively high rates toward a previously uncharacterized class of substituted phenols for the nitroarene

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dioxygenases; seven previously uncharacterized substrates were evaluated for the wild-type DDO, and four novel monooxygenase-like products were found for the DDO variant V350F (methoxyhydroquinone, methylhydroquinone, 2hydroxybenzyl alcohol, and 3-nitrocatechol)47 . Single hydroxylations have been reported previously for dioxygenases; for example, formation of phenol from methoxybenzene using naphthalene dioxygenase (NDO) of Pseudomonas sp. strain NCIB 9816-4 has been previously reported by Resnick et al.92 , and NDO is also capable of other monooxygenase-like reactions such as the oxidation of indene to (+)-(1S)indenol92 . However, NDO has been reported to be unable to catalyze the oxidation of the aromatic nucleus92 . Toluene dioxygenase (TOD) from P. putida F1 has also been reported to produce 4-methylcatechol from p-cresol and 3nitrocatechol from m-nitrophenol112 ; however, o- and m-cresol or o- and pnitrophenol have not been reported to be substrates for TOD112 . Because of these limitations in TOD and NDO, DDO was studied here.

17. CONCLUSIONS AND FUTURE DIRECTIONS Protein engineering of toluene monooxygenases is beginning to reach the point that the regiospeciﬁcity of hydroxylation may be controlled so that a myriad of industrially relevant chemicals may be synthesized, many of which had not been synthesized previously with bacteria (e.g. 2-naphthol), and bacteria may be engineered to help remediate contaminated sites. Furthermore, the structure/function lessons learned from mutagenesis of these non-heme enzymes should be directly applicable to intractable non-heme enzymes such as sMMO of Methylosinus trichosporium OB3b. Active sMMO has only been expressed in Agrobacterium tumefaciens, Rhizobium meliloti, and pseudomonads by our group but never in E. coli43,44 ; hence, there are no reports of beneﬁcial mutations of the hydroxylase for this enzyme, the best enzyme for oxidizing methane to methanol. By understanding toluene monooxygenases, we may begin to understand how the C–H bond of methane is activated by sMMO. The random mutagenesis approaches described here may also be used now to study the other, non-hydroxylase components of these multi-component enzymes to gain an even deeper understanding of the catalytic mechanism.

ACKNOWLEDGMENTS This research was supported by the National Science Foundation (BES9911469, BES-0331416, and BES-0124401), the US Environmental Protection Agency, and the US Army Research Ofﬁce (DAAD19-00-1-0568).

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AROMATIC RING HYDROXYLATING DIOXYGENASES Rebecca E. Parales1 and Sol M. Resnick2 1

Section of Microbiology University of California Davis, CA 95616, USA and 2 Biotechnology R&D The Dow Chemical Company San Diego, CA 92121, USA

Abbreviations: NDO, Naphthalene dioxygenase; TDO, toluene dioxygenase; NBDO, nitrobenzene dioxygenase; BPDO, biphenyl dioxygenase; PCB, polychlorinated biphenyl; TCE, trichloroethylene; PAH, polycyclic aromatic hydrocarbon

1. INTRODUCTION The initial oxidation of the aromatic ring is the most difﬁcult catalytic step in the aerobic degradation of aromatic compounds. Bacterial aromatic ring hydroxylating dioxygenases (also known as Rieske non-heme iron dioxygenases) catalyze the addition of hydroxyl groups to the highly stable aromatic ring, setting the stage for further oxidation, and eventual ring cleavage. Aromatic ring hydroxylating dioxygenases are known to catalyze the initial reaction in the bacterial biodegradation of a diverse array of aromatic and polycyclic aromatic hydrocarbons (PAHs), chlorinated aromatic, nitroaromatic, aminoaromatic, and heterocyclic aromatic compounds, and aromatic acids. Aromatic ring hydroxylating dioxygenases use molecular oxygen as a substrate, adding both atoms Pseudomonas, Volume 4, edited by Juan-Luis Ramos and Roger C. Levesque C 2006 Springer. Printed in the Netherlands.

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of O2 to the aromatic ring of the substrate. To date, over 100 aromatic ring hydroxylating dioxygenases have been identiﬁed based on biological activity or nucleotide sequence identity. These enzymes are distributed among a variety of Gram-negative and Gram-positive bacteria and are important for the catabolism of a wide range of environmental pollutants. Aromatic ring hydroxylating dioxygenases are multicomponent enzyme systems (E.C. 1.14.12.-) that catalyze reductive dihydroxylation of their substrates, and are distinct from aromatic ring cleavage (or ring ﬁssion) dioxygenases (E.C. 1.13.11.-), which act on the downstream catechol intermediates in many of the same catabolic pathways. Many of these enzymes are typically quite promiscuous, catalyzing the oxidation of a wide range of compounds in addition to their native substrates. At the same time, however, many of these enzyme systems are highly enantioselective, producing chiral cis-dihydrodiols or other chiral products in high enantiomeric purity. These properties have made aromatic ring hydroxylating dioxygenases attractive as biocatalysts. This chapter will focus primarily on the aromatic ring hydroxylating dioxygenases present in pseudomonads and related proteobacteria, but it is important to keep in mind that closely related enzyme systems have been identiﬁed in a variety of other bacterial genera, including Rhodococcus, Nocardia, Mycobacterium, etc. Aspects described in this chapter include dioxygenase classiﬁcation, enzymology, structure and mechanism, and applications in biotechnology. Much of our understanding of the structure and function of aromatic hydrocarbon dioxygenases comes from studies of naphthalene dioxygenase (NDO), and characteristics of this enzyme system will be described in detail and used as a basis for comparisons with other dioxygenases.

2. DISTRIBUTION OF RING HYDROXYLATING DIOXYGENASES IN CATABOLIC PATHWAYS Bacterial pathways for the degradation of numerous aromatic hydrocarbons, PAHs, chlorinated aromatic compounds, nitroaromatic compounds, aminoaromatic compounds, aromatic acids, and heterocyclic aromatic compounds are initiated by aromatic ring hydroxylating dioxygenases (Figure 1). Many of these compounds are toxic environmental pollutants. Some, including various chlorinated and nitroarene compounds, are man-made, while many others are naturally occurring biological products or components of petroleum. Regardless of the source, bacterial pathways for the degradation of this group of chemicals are important both in the recycling of carbon on earth and in the removal of toxic pollutants at contaminated sites.

Aromatic Ring Hydroxylating Dioxygenases CH3

CH2CH3

HC = CH2

289 CH3

CH3CH2CH3

CH3

Benzene

Toluene

Ethylbenzene

Anthracene

COOH

Styrene

Biphenyl

COOH

Phenanthrene

COOH

NH2

o-Xylene

Isopropylbenzene (cumene)

Chrysene

COOH

Tetralin

Naphthalene

Pyrene

COOH

OH Cl

CH3 COOH

Benzoate

Anthranilate

Salicylate

Chlorobenzoates

Phthalate

COOH

Isophthalate

Toluates (o, m)

Terephthalate

COOH

CH3

HC = CH

CH2CH2COOH

OCH3 OCH3 3-Phenylpropionic acid

CH3

H3C

Isopropylbenzoate (p-cumate)

4-Methoxybenzoate

Cinnamic acid

CH3

COOH

7-Oxodehydroabietic acid

Vanillate

NH2 NO2

CH3

CH3 NO2 O2N

Nitrobenzene

CH3 NO2

2,6-Dinitrotoluene

2-Nitrotoluene

NO2

Aniline

NO2

NH2

2-Oxo-1, 2-dihydroquinoline

2,4-Dinitrotoluene

Pyrazon

COOH O O N

Carbazole

COOH

Dibenzofuran

Fluorenone

CH3

Carboxydiphenylethers

Dibenzodioxin

HOOC

SO3

COOH

NH2

Chlorobenzene

SO3 p-Sulfobenzoate

SO3

2-Aminobenzene sulfonate

p-Toluene sulfonate

H3CO

OH OH

OCH3

5,5’-Dihydrodivanillic acid

Figure 1. Aromatic compounds degraded by bacterial pathways that are initiated by aromatic ring hydroxylating dioxygenases.

2.1. Types of Reactions Catalyzed The initial reaction catalyzed by aromatic ring hydroxylating dioxygenases on aromatic hydrocarbons and certain other substrates is a cisdihydroxylation of the carbon–carbon double bond of adjacent unsubstituted carbon atoms. This reaction typically generates a chiral cis-dihydrodiol as seen with the reaction on naphthalene (Reaction A, Table 1). Oxidation of aromatic

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Table 1. Representative types of cis-dihydroxylation reactions catalyzed by aromatic ring hydroxylating dioxygenases. Reaction Type

Substrate

Enzyme

Product OH

Naphthalene dioxygenase

A. cis-dihydroxylation

O2 Naphthalene

Naphthalene cis 1,2-dihydrodiol

COOH B. cis-dihydroxylation

Benzoate dioxygenase

HOOC

OH OH H

Benzoate

C. cis-dihydroxylation and dehalogenation

Benzoate cis 1,2-dihydrodiol

Chlorobenzene dioxygenase

OH OH H

Cl-

O2 Chlorobenzene

D. cis-dihydroxylation, dehalogenation and decarboxylation

COOH Cl

Catechol

Chlorobenzoate dioxygenase

HOOC

OH OH Cl

CO2+HCl

2-Chlorobenzoate

Catechol

NO2

O2N

Nitrobenzene dioxygenase

E. cis-dihydroxylation and nitrite elimination

OH H

NO2-

Nitrobenzene

NH2

Catechol

Aniline dioxygenase

F. cis-dihydroxylation and deamination

H2 N

OH OH H

NH3

Aniline

G. cis-dihydroxylation, deamination and decarboxylation

Catechol

COOH NH2

Anthranilate dioxygenase

HOOC

OH OH NH2

CO2 + NH3

Anthranilate

Catechol

COOH p-Sulfobenzoate dioxygenase

H. cis-dihydroxylation, and desufonation

HSO3-

SO3

O3 S OH

p-Sulfobenzoate

COOH

H OH

OH OH Protocatechuate

I. Angular dihydroxylation

Dibenzofuran dioxygenase

O Dibenzofuran

O HO

2, 2’, 3-trihydroxy biphenyl

Aromatic Ring Hydroxylating Dioxygenases

291

acids such as benzoate occurs at a carboxylated carbon and an adjacent unsubstituted carbon, and results in the formation of chiral cis-dihydroxylated cyclohexadiene carboxylic acids (Reaction B, Table 1). Dioxygenase-catalyzed dechlorination has also been demonstrated for chlorinated benzoates, benzenes, and biphenyls (Reactions C and D, Table 1). Dioxygenation at a chlorinesubstituted carbon results in concomitant elimination of chloride.88,113,193 Similar reactions have been shown with nitroaromatic, aminoaromatic, and sulfoaromatic substrates (Reactions E–H, Table 1), resulting in nitrite, ammonia, or sulﬁte elimination.4,47,94,177,199,259 In these cases, the displacement reactions result in the formation of dihydroxylated (catecholic) products that are activated for further metabolism. A specialized group of ring hydroxylating dioxygenases catalyzes angular dioxygenation, as seen with dibenzofuran48,81 (Reaction I, Table 1). Other substrates that are oxidized by angular dioxygenation include carbazole, diphenylethers, and dibenzo- p-dioxin.80,239,297 Two recent reviews provide excellent summaries of angular dioxygenases and the pathways in which they operate.200,202 Finally, certain members of this large family of multicomponent enzymes function as monooxygenases, as exempliﬁed by methoxybenzoate monooxygenase26 and salicylate 5-hydroxylase (Reactions N and P, Table 2).305 Very recently, multicomponent salicylate 1-hydroxylases have been identiﬁed in three different sphingomonads.55,68,220

2.2. Classiﬁcation of Ring Hydroxylating Dioxygenases Historically, Rieske non-heme iron oxygenases were classiﬁed using the Batie system, which was based on the electron transfer components present in the 10 Rieske non-heme iron oxygenase systems known at that time.20 Twocomponent (reductase and oxygenase; Class I) and three-component (reductase, ferredoxin, and oxygenase; Class II, III) enzyme systems were represented, and the classes were further subdivided based on the type of ﬂavin cofactor (FAD or FMN) in the reductase, the presence or absence of an iron–sulfur center in the reductase, the number of proteins in the oxygenase, and if a ferredoxin was involved, the type of iron–sulfur center (plant or Rieske) in the ferredoxin. This classiﬁcation system worked well with a small number of known enzymes, but as more enzyme systems with diverse properties were identiﬁed, not all of the new enzymes ﬁt into this classiﬁcation system. A second classiﬁcation system based on amino acid sequence alignments of the available oxygenase α subunits was proposed by Werlen et al., and it identiﬁed four dioxygenase families (naphthalene, toluene/benzene, biphenyl, and benzoate/toluate).293 This classiﬁcation system was based on the catalytic activity of the enzymes because the α subunit of the oxygenase plays a major role in determining substrate speciﬁcity.17,24,186,209,212,275,307 The results of the Werlen et al. study demonstrated that, in general, related dioxygenases coded for enzymes with similar substrates. Nakatsu et al.192 subsequently built upon this classiﬁcation system,

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Table 2.

Other types of oxidation reactions catalyzed by aromatic ring hydroxylating dioxygenases.

Reaction Type

Substrate

Enzyme

Product OH

Naphthalene dioxygenase

J. Benzylic hydroxylation

Indenol

Indene

CH3 K. Methyl group hydroxylation

NO2

CH2OH

Naphthalene dioxygenase

NO2

2-Nitrobenzyl alcohol

2-Nitrotoluene

L. Oxygen-dependent desaturation

Naphthalene dioxygenase O2 Indan

Indene

CH3 M. Sulfoxidation

CH3 Naphthalene dioxygenase

Methyl phenyl sulfoxide

Methyl phenyl sulfide

COOH

N. O-Dealkylation

COOH Naphthalene dioxygenase O2

OCH3

4-Hydroxybenzoate 4-Methoxybenzoate

NHCH3 O. N-Dealkylation

O2 Aniline

N-Methylaniline

P. Net aromatic ring hydroxylation

NH2

Naphthalene dioxygenase

COOH OH

COOH Salicylate 5- hydroxylase

Salicylate

OH HO Gentisate

Aromatic Ring Hydroxylating Dioxygenases

293

adding the αn dioxygenases (those in the Batie system Class IA) to the Werlen system and demonstrating that these αn oxygenases formed a separate lineage. Two modiﬁed classiﬁcation systems, also based on the phylogeny of the oxygenase α subunits have been proposed, each of which divided the known enzymes into four families or groups (Groups I–IV, or phthalate, benzoate, naphthalene, and toluene/biphenyl families respectively106,196 ). From current phylogenetic analyses, additional families or groups are apparent, as well as several enzymes that do not cluster tightly with any of the distinct families (Figure 2). In some of the families, enzymes with similar native substrates cluster together. The benzoate family (Figure 2) includes enzymes with activities toward various aromatic acids and aminoaromatic compounds. Monocyclic aromatic hydrocarbon dioxygenases, biphenyl dioxygenases (BPDOs), and chlorinated aromatic hydrocarbon dioxygenases from both Gram-negative and Gram-positive bacteria are tightly clustered in the toluene/biphenyl family. Enzymes for naphthalene and PAH degradation from Gram-negative and Grampositive bacteria form separate clusters (naphthalene and Gram-positive PAH families, respectively), and nitroarene dioxygenases cluster tightly with NDO from Gram-negative bacteria. The phthalate family (Figure 2), which consists of all of the Rieske non-heme iron oxygenases that contain only α subunits, is a very diverse group of enzymes that catalyze the oxidation of a variety of structurally unrelated aromatic compounds. Substrates for the phthalate family include aromatic acids such as phthalate, p-toluene sulfonate, and phenoxybenzoate, as well as carbazole and 2-oxo-1,2-dihydroquinoline. Two phthalate dioxygenases from Gram-positive bacteria were recently identiﬁed.76,260 These enzymes do not cluster with the phthalate family but with the Gram-positive PAH dioxygenases (Figure 2), and in addition, are comprised of both α and β subunits. A new family has recently emerged, and is designated here as the salicylate family (Figure 2). This family consists of enzymes that catalyze oxidation at either the 1- or 5-position of salicylate,55,68,220,305 as well as other substrates. There are now a number of enzymes that are quite distantly related to those found in the core of these groups or families (Figure 2), and thus, none of the classiﬁcation systems can completely describe the diversity of enzymes that have been identiﬁed to date.

2.3. Diversity of NDO and Related Nitroarene Dioxygenases Based on sequence alignments of NDO α subunit genes, the genes from Gram-negative bacteria were found to fall into three distinct groups that have been designated nah-like, dnt/ntd-like (sometimes called nag-like), and phnlike.165,176 An additional distantly related naphthalene/phenanthrene dioxygenase (A5 PhnA1, Figure 2) was identiﬁed from a marine Cycloclasticus isolate (strain A5) that grows on several PAHs.144 Tetralin dioxygenase (TFA ThnA1,

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TOLUENE/BIPHENYL (Group IV)

IPO1 CumA1 B4 BphA1 CA-4 EdoA1 KF707 BphA1 JR1 IpbA1 LB400 BphA RE204 IpbAa M5 BpdC1 Cam-1 BphA B-356 BphA P6 BphA1 ML2 BedC1 JB1 BphA1 RHA1 BphA1 BE81 BnzA KKS102 BphA1 BD2 IpbA1 F1 TodC1 RB1 XylC1 DOT-T1E TodC1 JS705 McbAa PS12 TecA1 P51 TcbAa

TA421 BphA1

CB3 CarAa RW1 DxnA1 DBF63 DbfA1

K12 HcaA DK17 AkbA1a RHA1 EtbA1

NAPHTHALENE (Group III)

PYR-1 PhtAa 12B PhtAa

Gram+ PAH/ PHTHALATE

TFA ThnA1 PYR-1 NidA 6PY1 PdoA1

A5 PhnA1

KP7 PhdA 6PY1 PdoA2

RP007 PhnAc

NCIMB12038 NarAa I24 NidAa

U2 NagAc JS42 NtdAc JS765 NbzAc DNT DntAc 9816-4 NahAc BS202 NahA3 ATCC17484 NdoC2 G7 NahAc OUS82 PahAc 294 NdoB AN10 NahAc PaK1 PahA3

BKME-9 DitA1

ANA-18 TdnA1 UCC22 TdnA1 7N ORF7NC YAA AtdA1

AC1100 TftA

pWWO XylX ADP1 BenA 19070 BopX 2CBS CbdA TH2 CbdA NK8 CbeA

M2 MsmA O-1 AbsA

ADP1 AntA CA10 AntA R. pal 7 PsbAb F1 CmtAb

BENZOATE (Group II)

86 OxoO JB2 OhbB 142 OhbB U2 NagG CHY-1 PhnA1b P2 AdhA1c P2 AdhA1e DBO1 AndAc T7 TerZa YZW-D TphA2 P2 AdhA1d

OM1 CarAa CA10 CarAa ADP1 VanA WCS358 VanA HR199 VanA T-2 TsaM

PHTHALATE ( αn) (Group I)

YZW-D IphA2 BR60 CbaA

POB310 PobA DBO1 OphA2 SYK-2 LigX NMH102-2 Pht3

SALICYLATE

Figure 2. Phylogenetic tree of α subunits of aromatic ring hydroxylating dioxygenases. Sequences were aligned and the tree was generated using the Clustal W package. [277]. α subunit sequences are from the following organisms/dioxygenase systems. PaK1 PahA3, NDO: P. aeruginosa PaK1 (D84146); AN10 NahAc, NDO: P. stutzeri AN10 (AF039533); 294 NdoB, NDO: P. ﬂuorescens 294 (AF004283); OUS82 PahAc, NDO: P. putida OUS82 (D16629); G7 NahAc, NDO: P. putida G7 (M86949); ATCC17484 NdoC2, NDO: P. putida ATCC17484 (AF004284); BS202 NahA3, NDO: P. putida BS202 (AF010471); 9816-4 NahAc, NDO: Pseudomonas sp. NCIB 9816-4 (U49496); U2 NagAc, NDO: Ralstonia sp. U2 (AF036940); JS42 NtdAc, 2-nitrotoluene dioxygenase: Acidovorax sp. JS42 (U49504); JS765 NbzAc, NBDO: Comamonas sp. JS765 (AF379638); DNT DntAc, 2,4-dinitrotoluene dioxygenase: Burkholderia sp. DNT (U62430); RP007 PhnAc, PAH dioxygenase: Burkholderia sp. RP007 (AF061751); A5 PhnA1, PAH dioxygenase: Cycloclasticus sp. A5 (AB102786); TFA ThnA1, tetralin dioxygenase: Sphingopyxis macrogoltabida TFA (AF157565); RHA1 EtbA1, ethylbenzene dioxygenase: Rhocococcus sp. RHA1 (AB120955); DK17 AkbA1a, alkylbenzene dioxygenase: Rhodococcus sp. DK17 (AY502075); K-12 HcaA, 3-phenylpropionate dioxygenase: E. coli K-12 (NC000913); TA421 BphA1, BPDO: R. erythopolis TA421 (D88020); P51 TcbAa, chlorobenzene dioxygenase: Pseudomonas sp. P51 (U15298); PS12 TecA1, chlorobenzene dioxygenase: Burkholderia sp. PS12 (U78099); JS705 McbAa, chlorobenzene dioxygenase: Ralstonia sp. JS705 (AJ006307); F1 TodC1, TDO: P. putida F1 (J04996); DOT-T1E TodC1, TDO: P. putida DOT-T1E (Y18245); BE81 BnzA, benzene dioxygenase P. putida BE81 (M17904); ML2 BedC1, benzene dioxygenase: P. putida ML2 (AF148496); M5 BpdC1, BPDO: Rhodococcus sp. M5 (U27591); P6 BphA1, BPDO: Rhodococcus globerulus P6 (X80041); RHA1 BphA1, BPDO: Rhodococcus sp. RHA1 (D32142); BD2 IpbA1, isopropylbenzene dioxygenase: R. erythropolis BD2 (U24277);

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Figure 2 (continued ). B4 BphA1, BPDO: Pseudomonas sp. B4 (AJ251217); 28, KF707 BphA1, BPDO: P. pseudoalcaligenes KF707 (AF049345); LB400 BphA, BPDO: B. xenovorans LB400 (M86348); Cam-1 BphA, BPDO: Pseudomonas sp. Cam-1 (AY027651); IPO1 CumA1, isopropylbenzene dioxygenase: P. ﬂuorescens IPO1 (D37828); CA-4 EdoA1, ethylbenzene dioxygenase: P. ﬂuorescens CA-4 (AF049851); JR1 IpbA1, isopropylbenzene dioxygenase: Pseudomonas sp. JR1 (U53507); RE204 IpbAa, isopropylbenzene dioxygenase: P. putida RE204 (AF006691); B356 BphA, BPDO: C. testosteroni B-356 (U47637); JB1 BphA1, BPDO: Burkholderia sp. JB1 (AJ010057); KKS102 BphA1, BPDO: Pseudomonas sp. KKS102 (D17319); RB1 XylC1, aromatic hydrocarbon dioxygenase: Cycloclasticus oligotrophicus RB1 (U51165); CB3 CarAa, carbazole dioxygenase: Sphingomonas sp. CB3 (AF060489); RW1 DxnA1, dioxin dioxygenase: Sphingomonas sp. RW1 (X72850); DBF63 DbfA1, dibenzofuran dioxygenase: Terrabacter sp. DBF63 (AB054975); PYR-1 PhtAa, phthalate dioxygenase: Mycobacterium vanbaalenii PYR-1 (AY365117); 12B PhtAa, phthalate dioxygenase: Arthrobacter keyseri 12B (AF331043); PYR-1 NidA, naphthalene-inducible dioxygenase: M. vanbaalenii PYR-1 (AF249301); 6PY1 PdoA1, PAH dioxygenase: Mycobacterium sp. 6PY1 (AJ494745); KP7 PhdA, phenanthrene dioxygenase: Nocardioides sp. KP7 (AB017794); 6PY1 PdoA2, PAH dioxygenase: Mycobacterium sp. 6PY1 (AJ494743); NCIMB12038 NarAa, NDO: Rhodococcus sp. NCIMB12038 (AF082663); I24 NidAa, naphthalene-inducible dioxygenase: Rhodococcus sp. I24 (AF121905); BKME-9 DitA1, diterpenoid dioxygenase: P. abietaniphila BKME-9 (AF119621); ANA-18 TdnA1, aniline dioxygenase: Fraturia sp. ANA-18 (AB089795); UCC22 TdnA1, aniline dioxygenase: P. putida UCC22 (D85415); 7N ORF7NC, aniline dioxygenase: Delftia acidovorans 7N (AB177545); YAA AtdA1, aniline dioxygenase: Acinetobacter sp. YAA (D86080); AC1100 TftA, 2,4,5trichlorophenoxyacetic acid oxygenase: B. cepacia AC1100 (U11420); pWWO XylX, toluate dioxygenase: P. putida pWWO (AJ344068); ADP1 BenA, benzoate dioxygenase: Acinetobacter sp. ADP1 (AF009224); 19070 BopX, benzoate dioxygenase: Rhodococcus sp. 19070 (AF279141); 2CBS CbdC, 2-halobenzoate dioxyegnase: B. cepacia 2CBS (X79076); TH2 CbdA, 2-halobenzoate dioxyegnase: Burkholderia sp. TH2 (AB035324); NK8 CbeA, chlorobenzoate dioxygenase: Burkholderia sp. NK8 (AB024746); ADP1 AntA, anthranilate dioxygenase: Acinetobacter sp. ADP1 (AF071556); AntA, CA10, anthranilate dioxygenase: P. resinovorans CA10 (NC 004444); R. pal 7 PsbAb, cumate dioxygenase: R. palustris 7 (AB022919); F1 CmtAb, cumate dioxygenase: P. putida F1 (AB042508); JB2 OhbB, o-halobenzoate dioxygenase: P. aeruginosa JB2 (AF422937); 142 OhbB, o-halobenzoate dioxygenase: P. aeruginosa 142 (AF121970); U2 NagG, salicylate 5-hydroxylase: Ralstonia sp. U2 (AF036940); CHY-1 PhnA1b, salicylate 1-hydroxylase: Sphingomonas sp. CHY-1 (AJ633552); P2 AdhA1c, salicylate 1-hydroxylase: Sphingobium sp. P2 (AB091693); DBO1 AndAc, anthranilate dioxygenase: B. cepacia DBO1 (AY223539); P2 AdhA1d, salicylate 1-hydroxylase: Sphingobium sp. P2 (AB091692); T7 TerZa, terephthalate dioxygenase: Delftia sp. T7 (AB081091); YZW-D TphA2, terephthalate dioxygenase: C. testosteroni YZWD (AY923836); AdhA1e, salicylate 1-hydroxylase: Sphingobium sp. P2 (AB091692); POB310 PobA, phenoxybenzoate dioxygenase: P. pseudoalcaligenes POB310 (X78823); SYK-2 LigX, 5,5 dehydrodivanillic acid O-demethylase: S. paucimobilis SYK-2 (AB021319); NMH102-2 Pht3, phthalate dioxygenase: P. putida NMH102-2 (D13229); DBO1 OphA2, phthalate dioxygenase: B. cepacia DBO1 (AF095748); BR60 CbaA, 3-chlorobenzoate dioxygenase: C. testosteroni BR60 (U18133.2); YZW-D IphA2, iosphthalate dioxygenase: C. testosteroni YZW-D (AY923836); T-2 TsaM, p-toluenesulfonate monooxygenase: C. testosteroni T-2 (AF311437); HR199 VanA, vanillate O-demethylase: Pseudomonas sp. HR199 (Y11521); WCS358 VanA, vanillate O-demethylase: P. putida WCS358 (Y14759); ADP1 VanA, vanillate O-demethylase: Acinetobacter sp. ADP1 (AF009672); OM1 CarAa, carbazole dioxygenase: P. stutzeri OM1 (AB088757); CA10 CarAa, carbazole dioxygenase: P. resinovorans CA10 (AB088420); 86 OxoO, 1-oxo-1,2-dihydroquinoline 8-monooxygenase: P. putida 86 (Y12655); O-1 AbsA, 2-aminobenzene sulfonate dioxygenase: Alcaligenes sp. O-1 (AF109074); M2 MsmA, methanesulfonic acid monooxygenase: Methylsulfomonas methylovora M2 (AF091716).

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Figure 2) from Sphingopyxis macrogoltabida TFA is also distantly related to members of this family.187 The nah-like group contains enzymes (Figure 2) from various Pseudomonas species (P. putida, P. ﬂuorescens, P. aeruginosa, P. stutzeri34,69,274 ) and includes the well-studied NDO from Pseudomonas sp. NCIB 9816-4 and P. putida G7.256 Sequence and gene order in this group appears to be conserved. Based on further sequence analysis, the nah-like group has been divided into two subgroups, and a few strains were shown to contain copies of both types of NDO genes.87 The dnt/ntd group (Figure 2) is represented by dioxygenases for naphthalene and nitroarene compounds (nitrobenzene and nitrotoluenes) and these enzymes are from members of the β-proteobacteria, such as Ralstonia, Burkholderia, Comamonas, and Acidovorax, rather than the γ-proteobacteria. Recent studies have suggested that NDO in the dnt/ntd group may be more common in nature than previously thought.73,295 Comamonas sp. strain JS765, Acidovorax sp. strain JS42, and Burkholderia sp. strain DNT contain nitroarene dioxygenases that are capable of attack at the nitro-substituted carbons of nitrobenzene, 2-nitrotoluene, or 2,4-dinitrotoluene, respectively, resulting in the removal of the nitro group as nitrite and rearomatization of the aromatic ring to form a catechol.173,208,265 These enzyme systems are very closely related to NDO, in particular that from Ralstonia sp. strain U2 (nagA; 94% DNA sequence identity92 ), and are believed to have evolved from an ancestral NDO.92,210 The phn-like group is represented by the naphthalene/phenanthrene dioxygenase from Burkholderia sp. RP007 (Figure 2).165 Additional phn-like dioxygenases have recently been identiﬁed from several other Burkholderia species.296 The gene order of the cluster from RP007 is very different from that of the nah-like or dnt/ntd group of NDO. Genes encoding electron transport components were not found within the 11-kb sequenced region.165 In addition, the presence of genes encoding a LysR-type regulator that is very distantly related to NahR from P. putida G7 (21% similarity) and a regulator of the NtrC family suggests that the genes may be controlled differently from those of the other two groups of NDO genes, possibly in a manner reminiscent of the regulation of the TOL plasmid genes.165,226 A series of naphthalene and/or phenanthrene and pyrene dioxygenases (Gram-positive PAH family, Figure 2) have been identiﬁed in Grampositive organisms, including Rhodococcus,5,157,164,281 Nocardioides,238 and Mycobacterium.149,156 The sequences of the α subunit genes from Grampositive bacteria cluster together, and it is of note that they are quite distantly related to those from Gram-negative bacteria (Figure 2). The order of the naphthalene pathway genes differs from those of the γ- and β-proteobacteria, and the ferredoxin and reductase genes have only been identiﬁed in Nocardioides sp. strain KP7. In this strain, the ferredoxin and reductase genes are located approximately 3-kb downstream of the dioxygenase α and β subunit genes,238

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but the ferredoxin and reductase genes do not appear to be co-localized with the dioxygenase genes in Rhodococcus or Mycobacterium.149,157,281 The ferredoxin from strain KP7 has features of a [3Fe–4S] or a [4Fe–4S] type ferredoxin rather than a [2Fe–2S] type ferredoxin.238 Another example of a [3Fe–4S] or a [4Fe–4S] type ferredoxin participating in electron transfer to a Rieske non-heme iron oxygenase is in the diterpenoid dioxygenases from Pseudomonas abietaniphila BKME-9 (Figure 2).182 These two enzyme systems represent examples of oxygenases that do not ﬁt the Batie classiﬁcation system.

2.4. Diversity of Toluene/Biphenyl Family Dioxygenases In contrast to enzymes for naphthalene and PAH degradation, the toluene/biphenyl family of dioxygenases is a cohesive group with enzymes from both Gram-positive and Gram-negative organisms represented. This family is comprised of three-component enzymes from pathways for the degradation of benzene, alkylbenzenes, chlorobenzenes, and biphenyl. Dioxygenases that initiate pathways for the degradation of benzene in P. putida ML2 and BE81,131,276 and benzene, toluene, and ethylbenzene degradation in P. putida F1308,309 and P. putida DOT-T1E,189 are members of this family (Figure 2). However, P. putida ML2 uses an ortho-cleavage pathway,13 P. putida BE-81 can use either an ortho or a meta pathway,254 and P. putida F1 and DOT-T1E use a meta pathway for completing the conversion of these substrates to TCA cycle intermediates. Chlorobenzene dioxygenases23,190,293 also fall into this family, and those that have been sequenced thus far cluster with benzene and toluene dioxygenases. These enzymes catalyze cis-dihydroxylation and dechlorination of their substrates (Reaction C, Table 1). The chlorobenzene dioxygenases from Pseudomonas sp. P51293 and Ralstonia (formerly Pseudomonas) sp. PS1223 allow these strains to grow with multiply chlorinated benzenes. Both enzymes have broad substrate speciﬁcities.221,227 The ethylbenzene-degrading isolate P. ﬂuorescens CA-459,60 apparently uses one pathway for the degradation of toluene, ethylbenzene, propylbenzene, and sec-butylbenzene, and the dioxygenase that initiates degradation of these compounds is most closely related to the isopropylbenzene dioxygenase from Pseudomonas sp. JR1 (see below). Numerous biphenyl degradation pathways in both Gram-negative and Gram-positive bacteria are initiated by BPDOs. BPDOs from Pseudomonas pseudoalcaligenes KF707,96 Burkholderia xenovorans LB400,85 BPDO Comamonas testosteroni B-356,271 and Rhodococcus sp. RHA1184 have been studied in some detail. Closely related enzyme systems can be found in Rhodococcus globerulus P6,12 and P. putida KF715,119 and many of these enzymes have the ability to attack various polychlorinated biphenyls (PCB) congeners (see Section 4.5). One BPDO, from Rhodococcus erythropolis TA421,7 does not cluster tightly with this family (Figure 2).

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Isopropylbenzene (cumene) dioxygenases (Figure 2) have been identiﬁed from several bacteria. P. putida RE204 and P. ﬂuorescens IP01 were isolated by selective enrichment for growth with isopropylbenzene as sole carbon and energy source.6,77 P. putida RE204 also grew with toluene, ethylbenzene and n-butylbenzene, but not benzene. P. ﬂuorescens IP01 also grew with toluene, ethylbenzene, sec-butylbenzene, and tert-butylbenzene, but not biphenyl or benzene.6 Pseudomonas sp. JR1 was isolated from an isopropylbenzene enrichment and was able to grow with toluene. Several Gram-positive isopropylbenzene degraders have been characterized. Rhodococcus erythropolis BD2 was isolated from a toluene- and TCE-contaminated soil sample with isopropylbenzene as sole carbon source.63 BD2 utilizes a linear conjugative plasmid-encoded isopropylbenzene degradation pathway identical to that described for P. putida RE204.62 The isopropylbenzene dioxygenase proteins in R. erythropolis BD2 are most closely related to the corresponding proteins from the biphenyl pathway in Rhodococcus sp. RHA1, ranging from 87 to 99% amino acid sequence identity.148 Compared to other alkylbenzenes, there have been few reports of bacterial isolates capable of growth with o-xylene, and most characterized strains utilize a monooxygenase-mediated pathway.14,29,31 Recently, however, Rhodococcus sp. strain DK17 was isolated for its ability to grow with o-xylene.152 DK17 also grows with benzene, toluene, ethylbenzene, and isopropylbenzene, and a single mutation eliminated the ability to grow with all of these substrates as well as the ability to convert indole to indigo. These results suggested that a single oxygenase carries out the initial oxidation of all substrates, but two different pathways are used to complete the degradation of benzene and alkylbenzenes. Results of catechol dioxygenase assays demonstrated that the alkybenzenes were degraded through a meta pathway, but growth with benzene induced an ortho-cleavage dioxygenase.152 Surprisingly, the genes encoding the oxygenase subunits, ferredoxin and reductase components (akbA1A2A3A4) were identical in sequence to the ethylbenzene dioxygenase components from Rhodococcus sp. RHA1 and the α subunits do not cluster with the toluene/biphenyl family (RHA1 EtbA1; DK17 AkbA1a, Figure 2).151

2.5. Diversity of Benzoate Family Dioxygenases The benzoate family is thus far represented by two-component enzymes (reductase and dioxygenase) where the dioxygenase is composed of both α and β subunits. Substrates for these enzymes include various aromatic acids and aniline. Enzymes that have been characterized include benzoate dioxygenases from Acinetobacter sp. ADP1,197 P. putida mt-2,132 and Rhodococcus sp. strain 19070,112 and toluate dioxygenase from P. putida pWWO116 (Reaction B, Table 1). Closely related enzymes for anthranilate degradation have been identiﬁed in several organisms, including Pseudomonas resinovorans CA10203 and

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Acinetobacter sp. ADP1.47,79 Interestingly, the anthranilate dioxygenase from Burkholderia cepacia DBO152 is a three-component enzyme whose α subunit sequence clusters with the salicylate family (DBO1 AndAc, Figure 2). In each case, however, these enzymes catalyze cis-dihydroxylation, deamination, and decarboxylation to form catechol (Reaction G, Table 1). In addition, cumate (isopropylbenzoate) dioxygenase and 2,4,5-trichlorophenoxyacetate oxygenase have been characterized from P. putida F175 and B. cepacia AC1100,64 respectively. The 2-halobenzoate-1,2-dioxygenases from Burkholderia (formerly Pseudomonas) cepacia 2CBS and Burkholderia sp. TH2 and chlorobenzoate dioxygenase from Burkholderia sp. NK8 also fall into this family.90,109,270 These enzymes catalyze cis-dihydroxylation, decarboxylation, and dehalogenation of o-halogenated aromatic acids (Reaction D, Table 1), although they differ in structure and sequence from enzymes catalyzing similar reactions (see Section 2.6). Finally, aniline dioxygenases from P. putida UCC22 (pTDN1),94 Acinetobacter sp. YAA aniline dioxygenase,93 Delftia acidovorans 7N,284 and Fraturia sp. ANA-18191 also group with this family. These enzymes catalyze cis-dihydroxylation and deamination of aniline to form catechol (Reaction F, Table 1).

2.6. Diversity of Salicylate Family Dioxygenases Salicylate 5-hydroxylase (Figure 2) from Ralstonia sp. strain U2305 catalyzes the conversion of salicylate to gentisate (Reaction P, Table 2), and is a key enzyme in the naphthalene degradation pathway in this strain (Figure 3).92,137 Interestingly, the ferredoxin and reductase components of salicylate 5-hydroxylase are shared with NDO.305 Five multicomponent salicylate 1-hydroxylases were recently identiﬁed in three different sphingomonads.55,68,220 These enzymes catalyze the conversion of salicylate to catechol, but are unrelated to the wellcharacterized single polypeptide ﬂavoprotein monooxygenases that are known to catalyze the same reaction in other organisms. The salicylate 1-hydroxylase from Sphingomonas yanoikuyae B1 was shown to share its ferredoxin and reductase components with a NDO/BPDO and toluate dioxygenase,55 and this also appears to be the case in the other two sphingomonads.68,220 It is not clear at this time, however, whether these multicomponent salicylate 1hydroxylases catalyze an initial dioxygenation of the aromatic ring of salicylate with the formation of an unstable compound that rearranges, releasing water and CO2 (analogous to Reaction G, Table 1), or if they actually function as monooxygenases that attack directly at the carboxyl-substituted carbon. P. aeruginosa strains 142 and JB2 utilize halobenzoates using an interesting three-component dioxygenase that is related to the salicylate hydroxylases (Figure 2). The enzyme catalyzes the oxygenolytic ortho-dehalogenation

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Naphthalene

Naphthalene 1,2-dioxygenase nahAaAbAcAd nagAaAbAcAd

OH OH

Naphthalene cis-1,2-dihydrodiol

Pseudomonas putida G7 Pseudomonas sp. NCIB 9816-4

OH COOH

Catechol 2,3dioxygenase nahH

Ralstonia sp. U2

Salicylate

COOH

OH hydroxylase nahG

CH O

Salicylate 5hydroxylase

COOH

nagI

HO Catechol

Salicylate

Gentisate 1,2-

OH Dioxygenase

OH nagAaAbGH

O C COOH COOH

HO Gentisate

TCA cycle

Figure 3. Pathways for the aerobic degradation of naphthalene in pseudomonads and Ralstonia sp. U2.

of 2-chlorobenzoate to form catechol (Reaction D, Table 1).283 The electron transport protein-encoding genes are not co-localized with the oxygenase α and β subunit genes in either strain.120,283 Terephthalate dioxygenase is also related to these enzymes252,291 and is different from phthalate dioxygenases in structure and sequence (see Section 2.7). Like other members of the salicylate family, terephthalate dioxygenase has two components, reductase and oxygenase, and the oxygenase is composed of α and β subunits.241,252,291 As mentioned in Section 2.5, the unusual anthranilate dioxygenase from B. cepacia DBO1 clusters with this family.52

2.7. Diversity of Phthalate Family Dioxygenases Most current members of the phthalate family of Rieske non-heme iron oxygenases are two-component enzymes, each consisting of an αn oxygenase component (lacking β subunits) and a reductase component. Phthalate dioxygenase, the namesake of this family, has been identiﬁed in a number of different Gram-positive and Gram-negative bacteria.76,111,204,260 The well-studied phthalate dioxygenase from Burkholderia cepacia DBO119,20,61 is encoded by

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the ophA1 and ophA2 genes, which are separated by the genes encoding the next two steps in phthalate degradation [dihydrodiol dehydrogenase (ophB) and decarboxylase (ophC)].53 Genes encoding the oxidation of isophthalate have recently been identiﬁed from C. testosteroni YZW-D.291 Like phthalate dioxygenase, isophthalate dioxygenase is a two-component enzyme with a hom*omultimeric oxygenase. A related enzyme is the chlorobenzoate 3,4-dioxygenase (CbaAB) from Alcaligenes sp. (BR60), which catalyzes the cis-dihydroxylation and dechlorination of 3-chlorobenzoate (Reaction C, Table 1).193 The phenoxybenzoate dioxygenase from P. pseudoalcaligenes POB310 catalyzes the angular dioxygenation (Reaction I, Table 1) of 3- and 4carboxydiphenyl ether.66 The unstable product of the reaction spontaneously rearranges to release phenol and protocatechuate. Like other members of this family, the enzyme has two components, PobA and PobB and the oxygenase (PobA) lacks a β subunit. Some enzymes in this family do not appear to function as dioxygenases with their native substrates, but as monooxygenases. 2-Oxo-1,2dihydroquinoline-8-monooxygenase from P. putida 86236 is involved in the degradation of quinoline. This two-component enzyme is encoded by oxoO (oxygenase component) and oxoR (reductase component), which are separated by 15 kb of DNA.237 The reaction results in net monooxygenation (Reaction P, Table 2) of the aromatic ring of 2-oxo-1,2-dihydroquinoline. Toluene sulfonate methyl-monooxygenase from C. testosteroni T-2 oxidizes the methyl group of toluene sulfonate, converting it to 4-sulfobenzyl alcohol (Reaction K, Table 2). The tsaMB genes encode the two components (oxygenase and reductase) of the enzyme.139 The same strain, C. testosteroni T-2, also has a sulfobenzoate 3,4-dioxygenase that catalyzes the dioxygenation and desulfonation of sulfobenzoate (Reaction H, Table 1) to form protocatechuate and sulﬁte.177 Vanillate demethylase, encoded by the vanAB genes, has been identiﬁed in P. putida WCS358,286 Acinetobacter sp. ADP1,245 Pseudomonas sp. ATCC 19151,46 P. ﬂuorescens BF13,56 and Pseudomonas sp. HR199.223 This enzyme catalyzes the oxygenative demethylation (Reaction N, Table 2) of vanillate to protocatechuate, and plays an important role in the degradation of the common plant metabolite ferulate. The product of the ligX gene from Sphingomonas paucimobilis SYK-6 encodes a 5,5 -dehydrodivanillic acid O-demethylase that participates in the complex pathway of lignin metabolism in this strain.258 Unlike other members of this family, carbazole dioxygenases from P. resinovorans CA10 and P. stutzeri OM1 are three-component enzymes, consisting of oxygenase (α3 ), ferredoxin (Rieske [2Fe–2S]), and reductase (plant-type [2Fe–2S] and FAD).207,239 Interestingly, both strains carry adjacent duplicate dioxygenase genes (CarAa). Carbazole dioxygenase catalyzes an angular dioxygenation (Reaction I, Table 1) to form 2 -aminobiphenyl2,3-diol.

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2.8. Other Ring Hydroxylating Dioxygenases Several additional multicomponent Rieske non-heme iron oxygenases do not fall into any of the major families. The diterpenoid dioxygenase from P. abietaniphila BKME-9 catalyzes the dioxygenation of 7-oxo-dehydroabietic acid (Figure 1). A large gene cluster encoding several steps in the abietane diterpenoid degradation pathway has been characterized.183,182,257 The ditA1A2 genes encode the dioxygenase, which is not closely related to other dioxygenases (Figure 2); and the ditA3 gene encodes an atypical [4Fe–4S] or [3Fe–4S] ferredoxin.182 Apparently, the gene encoding the reductase has not yet been identiﬁed. The 3-phenylpropionate dioxygenase from Escherichia coli K-12 catalyzes the initial dioxygenation of 3-phenylpropionate and cinnamate to the corresponding cis-2,3-dihydrodiols.71 This three-component enzyme is most closely related to members of the toluene/biphenyl family of enzymes, but does not cluster with the family (Figure 2). Several enzymes that catalyze angular dioxygenation (Reaction I, Table 1) on their respective substrates do not cluster tightly with the deﬁned dioxygenase families (Figure 2). Terrabacter sp. strain DBF63 has an interesting angular dioxygenase that catalyzes the initial oxidation of dibenzofuran. The dbfA1A2 genes encode dibenzofuran 4,4a-dioxygenase, and these proteins do not cluster with their counterparts in any of the dioxygenase families.145 The ferredoxin component is encoded by the dbfA3 gene, which is located 2.5 kb downstream of the dbfA1A2 genes.111 The ferredoxin contains a [3Fe–4S] center rather than a typical [2Fe–2S] center,145,272 and the reductase component has not yet been identiﬁed. In contrast, a tightly clustered set of four genes encoding dibenzofuran dioxygenase was cloned from Terrabacter sp. YK3.129 Several differences were noted between the Terrabacter sp. YK3 and Terrabacter sp. strain DBF63 dibenzofuran dioxygenases. The dioxygenase α and β subunits from YK3 were quite distantly related to those from DBF63, the YK3 ferredoxin carried a [2Fe–2S] cluster rather than a [3Fe–4S] center as in DBF63, and the gene encoding the YK3 FAD-containing reductase was located just downstream of the ferredoxin gene. The dibenzofuran/dibenzo- p-dioxin dioxygenase from Sphingomonas wittichii RW1300 also catalyzes angular dioxygenation on these substrates.48 The α and β subunits of the RW1 dioxygenase are only distantly related to those from DBF63 and YK.39,129,145 Two isofunctional putidaredoxintype (rather than the more common Rieske type) ferredoxins and two isofunctional ﬂavin-containing reductases were shown to have the ability to transfer electrons to the oxygenase, and the genes encoding these components are apparently dispersed on the chromosome.8,10,11 The carbazole dioxygenase from Sphingomonas sp. CB3 also does not group with any of the main families.251 This three-component carbazole dioxygenase is very different from that from P. resinovorans CA10. The oxygenase has both α and β subunits unlike that

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from CA10, and the α subunits from these two proteins only share 13% amino acid sequence identity. At the time it was identiﬁed, the CB3 carbazole dioxygenase was actually most closely related to isopropylbenzene dioxygenases and BPDOs from Gram-positive bacteria, but it does not cluster with the toluene/biphenyl family. More recently, it was found to be more closely related to the dioxin dioxygenase from Sphingomonas wittichii RW1.200 Nojiri et al.200 have argued that the enzyme from Sphingomonas sp. CB3 may not actually be a carbazole dioxygenase, because the only evidence for its role in carbazole degradation is the fact that the genes are induced during growth with carbazole. However, it is unlikely to be a BPDO, because biphenyl is not a growth substrate for CB3 and carbazole-grown CB3 cells do not oxidize biphenyl.251 2-Aminobenzene sulfonate dioxygenase is a two-component enzyme system comprised of an oxygenase with both α and β subunits, and a reductase. The oxygenase has been puriﬁed and characterized.181 The enzyme (O-1 AbsA, Figure 2) from Alcaligenes sp. O-1 initiates the pathway for 2-aminobenzoate degradation by catalyzing cis-dihydroxylation and deamination to form 3sulfocatechol (Reaction F, Table 1). The most closely related enzyme to AbsA, surprisingly, is methanesulfonic acid monooxygenase (M2 MsmA, Figure 2) from Methylosulfonomonas methylovora M2, an enzyme that oxidizes a nonaromatic substrate.65 The enzyme has three components. The oxygenase is composed of α and β subunits and has an unusual iron–sulfur center-binding motif: while most α subunits of Rieske centers have 15–17 residues between the two Cys-His pairs, this enzyme has 26. The ferredoxin and reductase components are more like those from diiron center-containing monooxygenases such as toluene 4-monooxygenase from P. mendocina KR1, than from aromatic ring hydroxylating dioxygenase systems, making this quite an unusual enzyme.65

3. RING HYDROXYLATING DIOXYGENASE STRUCTURE AND FUNCTION To date, protein components from several dioxygenase systems have been puriﬁed and studied in detail. In this chapter, we will focus on NDO as a model system and as a basis for comparison to other related enzyme systems.

3.1. Enzymology of NDO from Pseudomonas sp. NCIB 9816-4 Two pathways for the aerobic degradation of naphthalene have been described (Figure 3). Both pathways utilize naphthalene 1,2-dioxygenase (E.C. 1.14.12.12) to convert naphthalene to (+)-naphthalene cis-(1R,2S)dihydrodiol (naphthalene cis-dihydrodiol). Naphthalene cis-dihydrodiol

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2H+

2H+ NADH + H+

NAD+

Prosthetic group

Reduced

Reductase

Ferredoxin

Oxygenase

Oxidized

FAD [2Fe-2S]

[2Fe-2S]

[2Fe-2S] Fe2+

Naphthalene

OH OH

Naphthalene cis-1,2-dihydrodiol

Figure 4. Reaction catalyzed by the three-component naphthalene dioxygenase (NDO) system. Electrons from NADH are transferred by the iron–sulfur ﬂavoprotein reductase to the Rieske [2Fe– 2S] ferredoxin. An electron is then transferred from the ferredoxin to one of the Rieske centers in the oxygenase. Reduced oxygenase catalyzes the addition of both atoms of O2 to naphthalene, forming enantiomerically pure (+)-naphthalene cis-(1R, 2S)-dihydrodiol.

dehydrogenase (E.C. 1.3.1.29) then oxidizes naphthalene cis-dihydrodiol to 1,2-dihydroxynaphthalene. The oxidized ring is then cleaved and further degraded to form salicylate (Figure 3). Pseudomonads and some Gram-positive organisms convert salicylate to catechol, which is degraded by a standard meta cleavage pathway,34,50,158,301 although variants that use the ortho pathway have been reported.50,89 In contrast, Ralstonia sp. strain U2 and some strains of Rhodococcus convert salicylate to gentisate and utilize a gentisate dioxygenase pathway to complete naphthalene degradation (Figure 3).3,70,305,306 NDO is a three-component enzyme system that catalyzes the addition of both atoms of oxygen to the aromatic ring of naphthalene (Figure 4). All three protein components of NDO have been puriﬁed from Pseudomonas sp. NCIB 9816-4.82,114,115 The reductase is a 35 kDa monomer that contains one molecule of FAD and a plant-type iron–sulfur center. It can accept electrons from either NADH or NADPH.115,256 The ferredoxin is a Rieske [2Fe–2S] center-containing monomer of approximately 11.4 kDa.114,256 The catalytic oxygenase component is an α3 β3 hexamer consisting of large (α. ) and small (β) subunits.147 Each α subunit contains two redox centers, a Rieske [2Fe–2S] center and mononuclear Fe2+ at the active site. Individually puriﬁed α and β subunits of the oxygenase were reconstituted,263,264 demonstrating that both subunits are essential for activity, a result consistent with those obtained with BPDO127 and toluene dioxygenase.135 As puriﬁed, the Rieske center of the oxygenase is oxidized, and the iron at the active site is reduced. Electrons are transferred sequentially from NAD(P)H to the reductase, to the ferredoxin, to the Rieske center of the oxygenase, and ﬁnally to the iron at the active site of the oxygenase. The reduced oxygenase catalyzes the addition of both atoms of O2 to the aromatic ring. Two electrons are necessary to complete the reaction cycle. Among the aromatic ring hydroxylating dioxygenases that have been identiﬁed to date, two types of oxygenase structures are known: those with both α and β subunits, such as NDO, and those consisting of only α subunits,

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such as phthalate dioxygenase. Based on studies of hybrid dioxygenases, in which the individual α and β subunits from different enzymes were substituted, it appears that the α subunits of NDO and the closely related enzymes 2-nitrotoluene dioxygenase and 2,4-dinitrotoluene dioxygenase control substrate speciﬁcity.209,212 Similar results were reported with BPDO hybrids, toluene dioxygenase-tetrachlorobenzene dioxygenase hybrids, and benzeneBPDO hybrids.17,24,186,275,307 These results are consistent with the crystal structures of NDO and related dioxygenases (see Section 3.2), which showed that no β subunit residues are near the active site.91,98,147 Other studies have suggested, however, that β subunits may play a role determining substrate speciﬁcity in toluene, toluate, and other BPDOs.54,117,121,128 Therefore, it seems as though the β subunit has a structural function in most dioxygenases, but in some cases, the β subunit may be capable of modulating substrate speciﬁcity.

3.2. Dioxygenase Structure and Mechanism Crystal structures of the oxygenase component of NDO have been determined in the presence and absence of various substrates.51,143,147 NDO is an α3 β3 hexamer. The β subunits contain no redox centers and based on the currently available crystal structures of NDO, nitrobenzene dioxygenase (NBDO) from Comamonas sp. strain JS765, cumene dioxygenase from P. ﬂuorescens IP01, and BPDO from Rhodococcus sp. strain RHA1, the β subunit residues are distant from the active sites in each enzyme.91,98,147 The α3 β3 hexamer of NDO contains three active sites, which are located at the junctions of adjacent α subunits. Each α subunit contains a Rieske [2Fe–2S] center, which is coordinated by two histidines (His83; His104) and two cysteines (Cys81; Cys101), and mononuclear non-heme iron. This iron at the active site is in a distorted octahedral conformation coordinated by His208, His213, Asp362 and a water molecule (Figure 5).147 These two redox center-binding motifs (C-XH-X15−26 -C-X2 -H and H-X4−5 -H-Xn -D) are conserved in all sequenced Rieske non-heme iron oxygenases. The 2-His-1-carboxylate mode of mononuclear iron coordination has also been identiﬁed in a variety of non-heme iron-containing enzymes that catalyze a wide range of reactions, including not only Rieske non-heme iron oxygenases, but meta-cleavage dioxygenases, pterin-dependent hydroxylases such as tyrosine hydroxyase, and a family of β-lactam biosynthesis enzymes.163,224 The recently published crystal structures of the Comamonas sp. strain JS765 NBDO, Rhodococcus sp. RHA1 BPDO, and P. ﬂuorescens IP01 cumene dioxygenase showed very similar overall structures compared to NDO, including similar relative positions of the redox centers.74,98 One difference was apparent between NDO and the two members of the toluene/biphenyl family of Rieske non-heme iron oxygenases. The conserved Asp residue that coordinates the active site iron in NDO (Asp 362) does so in a bidentate fashion with both coordinating carboxyl oxygen atoms approximately equidistant from the

Rieske [2Fe-2S] Cluster

Fe Fe

His 104

His 83

α subunit B

Asp 205

His 208

His 213

Catalytic Fe Site

H2O

O C

Asp 362

Figure 5. The junction between two α subunits in NDO based on the crystal structure of the enzyme. Shown are the Rieske [2Fe–2S] center and mononuclear iron at the active site. Amino acids Cys81, His83, Cys101, and His104 coordinate the Rieske center; His208, His213, and Asp362 coordinate mononuclear iron at the active site. See text for additional details.

Cys 101

Cys 81

α subunit A

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iron.147 In contrast, the corresponding aspartate residues in BPDO and cumene dioxygenase (Asp 378 and 388, respectively), are coordinated to the iron via a single carboxyl oxygen; in both cases, the other carboxyl oxygen is apparently too far away to coordinate the iron. Therefore, the coordination geometry of the mononuclear iron in both BPDO and cumene dioxygenase is distorted tetrahedral.74,98 Substitution of Asp362 with an alanine inactivated NDO, demonstrating that this iron-coordinating residue is essential.214 In an earlier study, site directed mutagenesis of toluene dioxygenase (TDO) demonstrated that the conserved residues Glu214, Asp219, His222, and His228 (corresponding to Glu200, Asp205, His208, and His213 in NDO) were essential for enzyme activity, and were suggested to be mononuclear iron ligands.136 Substitution of the corresponding histidines in benzene dioxygenase also resulted in loss of enzyme activity.49 Of the four potential iron ligands, only the histidines were found to coordinate iron based on the NDO structure.147 The loss of activity in the other two TDO mutants can be explained using the NDO structure. The structure revealed that Glu200 provides an important contact between adjacent α subunits by forming a salt link with Arg84.146 Asp205 in NDO is hydrogen bonded to the Rieske center ligand His104 and mononuclear iron ligand His208. Based on this structural conformation, Asp205 appeared to participate in the electron transfer pathway between the NDO Rieske center and active site iron in adjacent α subunits in (Figure 5).147 This hypothesis was supported by the analysis of mutant forms of NDO in which Asp205 was replaced by Ala, Glu, Gln, or Asn.215 The modiﬁed proteins had little or no dioxygenase activity, although they appeared to have no major structural defects. Additional support for this role for Asp205 was provided when benzene, an efﬁcient uncoupling agent for wild-type NDO,168 was unable to stimulate oxygen uptake by the puriﬁed Gln205-containing enzyme. This result suggests that electrons cannot be passed from the Rieske center to the active site iron in the mutant form of the enzyme.215 An alternative role for this conserved aspartate was proposed in studies of anthranilate dioxygenase, an enzyme that catalyzes the ﬁrst step in anthranilate catabolism in Acinetobacter sp. strain ADP. In anthranilate dioxygenase, substitution of the aspartate corresponding to Asp205 in NDO with Ala, Glu, or Asn resulted in completely inactive enzymes. Analysis of wild-type and mutant forms of anthranilate dioxygenase at various pH values suggested that this aspartate may play a role in maintaining the reduction potential and the protonation state of the Rieske center of the oxygenase.22 As puriﬁed, NDO contains an oxidized Rieske center and ferrous iron at the active site. Spectroscopic studies with the Burkholderia cepacia DBO1 phthalate dioxygenase, which catalyzes the cis-dihydroxylation of phthalate, demonstrated that the iron is in a six-coordinate octahedral conﬁguration in the absence of substrate, but a ﬁve-coordinate conﬁguration results when substrate

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is bound.101,217,282 This result is in contrast to crystal structure data for NDO, which indicates that the coordination of iron does not change upon substrate binding, and in fact no signiﬁcant conformational changes occur anywhere in the active site when substrate binds.51,143 The crystal structure of the Rhodococcus sp. RHA1 BPDO revealed that when biphenyl was bound, signiﬁcant conformational changes occurred at the active site.98 These conformational changes in BPDO resulted in the formation of an entryway and an expansion of the substrate-binding pocket to allow biphenyl to enter and bind the active site pocket. The active site pockets of the Rhodococcus sp. RHA1 BPDO and the P. ﬂuorescens IP01 cumene dioxygenase are strikingly similar,74 which is consistent with their overall level of primary amino acid sequence identity (67%). The nature of the iron-oxygen species involved in catalysis is not known. Studies of 4-methoxybenzoate monooxygenase suggested an attack by a ferric-peroxo intermediate in the monooxygenation and cis-dihydroxylation reactions,27 and recent work with NDO supports this possibility.51,143,168 The participation of a high valent iron-oxo species, as in the methane monooxygenase175 and cytochrome P450242 cam reaction cycles, has also been proposed.225,298,299 Single turnover studies with NDO demonstrated that 0.85 units of product were formed per electron added, and both the Rieske center and mononuclear iron were oxidized during the reaction,299 and peroxidemediated turnover with NDO was recently reported.298 The observation that the reaction stopped after one turnover is consistent with the idea that the release of product requires the input of a second electron. NDO is known to catalyze other reaction types in addition to cis-dihydroxylation (dioxygenation), including benzylic monohydroxylation (monooxygenation234,288 ), O- and N dealkylation,229 sulfoxidation,169 and desaturation107,280 reactions (Table 2). However, the cis-dihydroxylation reaction is unique to bacterial aromatic ringhydroxylating dioxygenases, and it has implications for the mechanism of the enzyme. Recent crystal structure data demonstrated that oxygen binds side-on to the iron at the active site of NDO, and the substrates naphthalene or indole ◦ bind in a long cleft in the active site approximately 4 A from the iron atom.51,143 ◦ Alone, dioxygen binds side-on approximately 2.2 A from the iron, but measurably closer to the iron when substrate is present.143 This series of NDO crystal structures with substrate, oxygen, both substrate and oxygen, or product (naphthalene cis-dihydrodiol) bound suggest a concerted reaction mechanism in which both atoms of molecular oxygen react with the carbon atoms of the substrate double bond in a way that would explain the cis-speciﬁc dioxygenation catalyzed by this class of enzymes. Based on the structures of NDO alone and in complex with substrate, oxygen, and product, the reaction cycle shown in Figure 6 was proposed.143 Three ferredoxin reductase structures from three different dioxygenase systems are currently available. The phthalate dioxygenase reductase

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O N

Ferredoxin Fe2+ OH2

[2Fe2S]OX

Fe2+

OH2

Air oxidation

[2Fe2S]RED

(1) (2) Substrate O

Ferredoxin

O2 O

Fe2+

O O N

[2Fe2S]RED Fe3+

(3)

Fe2+ OH2

HO [2Fe2S]RED

[2Fe2S]OX (6)

(4)

Substrate

2H+

O O N

Fe3+

O [2Fe2S]OX (5)

Figure 6. Proposed mechanism of NDO based on crystal structures of the enzyme alone, with bound substrate (naphthalene or indole), with bound O2 , with bound substrate and O2 , or with bound product (naphthalene cis-dihydrodiol). (1) As puriﬁed, the enzyme has an oxidized Rieske site. (2) One electron is transferred from the ferredoxin. Either oxygen (3) or substrate (naphthalene) (4) can bind at the active site. (5) Ternary complex with naphthalene and oxygen bound at the active site. (6) Product formation; release of product requires input of an additional electron from the ferredoxin. Reproduced wth permission from Karlsson et al. [143].

(PDR) from Burkholderia (formerly Pseudomonas) cepacia DB0161 and the benzoate dioxygenase reductase (BenC) from Acinetobacter sp. strain ADP1142 are members of the NADP+ -ferredoxin reductase superfamily. PDR is the most well-studied of the electron transfer partners from this family of dioxygenases.19,61,99,100,102 Benzoate and phthalate dioxygenases are twocomponent systems consisting of an oxygenase and a ferredoxin reductase.20 The ferredoxin reductases are both composed of three distinct domains, for binding a plant-type [2Fe–2S] center, NAD, and ﬂavin (FMN in PDR; FAD in BenC), but the arrangement of the domains differs in the two proteins.61 The BPDO reductase (BphA4) from the three-component enzyme in Pseudomonas sp. strain KKS102 has very low sequence identity with other aromatic ring-hydroxylating dioxygenase reductase components.150 It contains NADand FAD-binding domains, but no iron–sulfur cluster; electrons are transferred from BphA4 to the [2Fe–2S] center in an intermediary ferredoxin protein. The

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protein fold of BphA4 is actually similar to that of glutathione reductases248 and putidaredoxin reductase from P. putida cytochrome P450cam .250 Although these reductases belong to two distinct families, the overall structures of the NAD- and FAD-binding domains are quite similar.142. On the basis of modeling studies, the NDO reductase structure is predicted to be similar to that of benzoate dioxygenase reductase.142 The structure of the BPDO ferredoxin component (BphF) from ◦ Burkholderia sp. strain LB400 was determined at 1.6 A resolution.57 The structure of the carbazole dioxygenase ferredoxin component (CarAc) from P. resinovorans CA10 was solved by molecular replacement with the BphF structure.194 Although the sequences of the two proteins are only 34% identical, their structures were very similar, and the location of the Rieske center at the surface of the proteins may have implications for docking with the reductase and oxygenase components to allow electron transfer. One notable difference was in the surface charges of the two proteins, which probably determine the ability to interact productively (and speciﬁcally) with the respective oxygenases of each enzyme system.194 To our knowledge, no reports have yet been published demonstrating co-crystallization of non-covalent complexes of ferredoxins with their corresponding oxygenases or ferredoxin reductases for any of the three-component aromatic ring hydroxylating dioxygenase systems, and information regarding speciﬁc protein–protein interactions is limited. However, cross-linking studies with the three toluene dioxygenase components suggested the involvement of electrostatic interactions between the proteins, and argued against the formation of a ternary complex.167 These results imply that the ferredoxin in three-component enzyme systems alternately binds to the reductase and oxygenase components using the same surface near the exposed Rieske center in order to carry out electron transfer.

3.3. Substrate Speciﬁcity of NDO and Other Dioxygenases In general, aromatic ring hydroxylating dioxygenases are capable of initiating oxidative attack on a very wide range of substrates.41,232 Many of these enzymes display remarkable diversity in the number of substrates oxidized and the types of reactions catalyzed. Our understanding of the mechanism of substrate oxidation has been based on studies with blocked mutant strains that accumulate the products of dioxygenase-catalyzed reactions, recombinant strains expressing dioxygenase genes, and in some cases with puriﬁed enzymes. NDO from Pseudomonas sp. NCIB 9816-4 is known to catalyze the oxidation of more than 75 different substrates by reactions including cis-dihydroxylation, monooxygenation,234,288 desaturation,107,280 O- and N dealkylation,229 and sulfoxidation169 (Tables 2 and 3). The complete list of substrates oxidized and products formed by NDO is summarized in a useful

Aromatic hydrocarbons Naphthalene Benzene Toluene Ethylbenzene Styrene Isopropylbenzene o-Xylene Biphenyl Anthracene Phenanthrene 9,10-Dihydrophenanthrene Chrysene Pyrene Fluoranthene Acenaphthene Fluorene Substituted aromatic compounds Aniline Anthranilate Benzoate Salicylate o-Halobenzoates Chlorobenzoates

Substrate

X/T

X X X X X/T X X X X/T X/T T T X X

X X

Dihydroxylations

T T

Type of oxidation reactiona,b

Monohydroxylations O

(Continued)

90,192,193

90,109,270,283

55,68,220,305

112,132,197

47,52,191

93,94,284

108,231,247

246

201,261

149,156,290

35,39,104

40,230

134,165,238

1,134,201

7,12,85,96,119,184,271

152,171

6,63,77

141,140,170,292

59,171

171,189,262,309

103,130,276

33,69,83,133,164,256,274

References

Table 3. Representative reactions catalyzed by Rieske non-heme iron oxygenases for speciﬁc pathway substrates.

X X X T T X

Isopropylbenzoate 3-Phenylpropionate Cinnamate Chlorobenzenes (poly)Chlorobiphenyls Phthalate (o-) Isophthalate Terephthalate Toluates (o-, m-) 4-Methoxybenzoate Vanillate p-Toluene sulfonate Aminobenzene sulfonate p-Sulfobenzoate Nitrobenzene 2-Nitrotoluene 3-Nitrotoluene 4-Nitrotoluene 2,4-Dinitrotoluene 2,6-Dinitrotoluene 2,2 -Dinitrobiphenyl 1,2,4-Trimethylbenzene 1- and 2-substituted naphthalenes Dimethylnaphthalenes 7-Oxodehydroabietic acid 5,5 -Dihydrodivanillic acid Heterocyclic aromatic compounds Carbazole Dibenzofuran Dibenzodioxin

T T T

Substrate

X X X

X T

X X T T X X T

Dihydroxylations

(Continued )

X X X

Type of oxidation reactiona,b

Table 3.

T T T T

X X

Monohydroxylations O

8–11,244

48,129,145,231,244,272

110,201,207,233,239,251

258

182

30,246

30,44,67,154,294

246

244

198

173,266

173,235

4,208,212,235

173

177

181

139,178

46,223,245

116

241,252,291

291

53,76,111,195,207

15,21,105,206,249

23,126,285

References

T T T

Type of oxidation reactiona,b

(Continued )

T T T T T

T T

Monohydroxylations

T T T

166

232

229

169

2,169

187,255

78,280

58,107,281

43,107,288

246

240

236,237

38,41

246,247

155,201,231

References

The types of reactions are shown in Tables 1 and 2: A, cis-dihydroxylation (C=C); B, cis-dihydroxylation (at and adjacent to a carboxyl bearing carbon); C, cis-dihydroxylation and dehalogenation; D, cis-dihydroxylation, decarboxylation, and dehalogenation; E, cis-dihydroxylation and nitrite elimination; F, cis-dihydroxylation and deamination; G, cisdihydroxylation, deamination, and decarboxylation; H, dihydroxylation and desulfonation; I, angular dihydroxylation; J, benzylic hydroxylation; K, methyl group hydroxylation; L, oxygen-dependent desaturation; M, sulfoxidation; N, O-dealkylation; O, N -dealkylation; P, net aromatic ring monohydroxylation. b “X ” denotes reactions catalyzed for growth substrates; “T ” indicates a transformation reaction catalyzed for a non-growth substrate. This list is not exhaustive and additional information, particularly on transformation substrates, can be found in recent reviews.36,42,125,232

Dibenzothiophene X/T Indole T Fluorenone T Quinolines T 2-Oxo-1,2-dihydroquinoline Pyrazon X 3-Methyl benzothiophene 2-Methylbenzo-1,3-thiole Carbocyclic, alkyl-aryl ether, thioether or N-alkyl substrates Indan Indene T 1,2-Dihydronaphthalene T Tetralin X Methyl phenyl sulﬁde Ethyl phenyl sulﬁde Methyl p-tolyl sulﬁde p-Methoxyphenyl methyl sulﬁde Methyl p-nitrophenyl sulﬁde Anisole T Phenetole T Carboxydiphenylethers N -Methylindole N -Methylaniline N ,N -Dimethylaniline

Substrate

Dihydroxylations

Table 3.

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review.232 TDO from P. putida F1 is even more impressive in its substrate range, with the ability to catalyze over 100 oxidation reactions on monocyclic aromatic compounds, fused and linked aromatic compounds, heterocyclic aromatic compounds, and a variety of halogenated and non-halogenated aliphatic oleﬁns.42,125,161 TDO has overlapping but frequently distinct speciﬁcity from NDO, and as with NDO, multiple reaction types are catalyzed by TDO [dioxygenation, monooxygenation,288 desaturation,280 and sulfoxidation2,169 (Tables 2 and 3)]. For example, TDO oxidizes indan to (1R)-indanol and converts indene to cis-(1S, 2R)-indandiol and (1R)-indenol288 while NDO oxidizes indan to (1S)-indanol and oxidizes indene to cis-(1R, 2S)-indandiol and (1S)indenol.107 Similar trends in enantioselectivity are typically observed for the cis-dihydroxylation, benzylic monohydroxylation, and sulfoxidation reactions catalyzed by NDO.232 The range of multi-ring substrates oxidized by the angular dioxygenase carbazole 1,9a-dioxygenase from P. resinovorans CA10 has been reported and these results were compared with the products formed by the Terrabacter sp. dibenzofuran dioxygenase.201,273 Both enzymes are capable of standard cis-dihydroxylation, angular dioxygenation, and monooxygenation depending on the substrate, suggesting that the speciﬁcity is determined by the position of the substrate in the active site relative to the active site iron atom.

3.4. Critical Amino Acids at the Active Site of NDO and Other Dioxygenases The active site iron of NDO is located in a hydrophobic pocket that accommodates the predominantly hydrophobic substrates for the enzyme. The amino acids located near the active site were identiﬁed from the crystal structure of NDO.51,143 Site-directed mutagenesis of residues near the active site iron has identiﬁed those that are important in determining the substrate speciﬁcity and enantioselectivity of NDO. These studies demonstrated that NDO was able to tolerate a wide range of single amino acid substitutions near the active site.214,216 Enzymes with substitutions at position 352 of the oxygenase α subunit (phenylalanine in the wild-type enzyme) had the most striking changes in substrate speciﬁcity. These enzymes had altered enantioselectivity with naphthalene, biphenyl, phenanthrene, and anthracene, and changes in the regioselectivity were seen when biphenyl and phenanthrene were provided as substrates.214,216 Replacement of Phe352 with smaller amino acids (Gly, Ala, Val, Ile, Leu, Thr) resulted in enzymes that produced increased amounts of biphenyl cis-3,4-dihydrodiol relative to biphenyl cis-2,3-dihydrodiol, and the stereochemistry of the biphenyl cis-3,4-dihydrodiol was altered. The NDOF352V and NDO-F352T enzymes formed signiﬁcant amounts of (−)-biphenyl cis-(3S,4R)-dihydrodiol, a compound not produced by wild-type NDO. A major shift in the regioselectivity was also seen with enzymes carrying substitutions

Aromatic Ring Hydroxylating Dioxygenases

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at Phe352 with phenanthrene as a substrate. In addition, enzymes with substitutions at position 206 (NDO-A206I and NDO-A206I/L253T) formed signiﬁcantly more phenanthrene cis-1,2-dihydrodiol than wild type.302 Several of the enzymes formed phenanthrene cis-9,10-dihydrodiol, a new product not formed by the wild type. An attempt to engineer NDO into an enzyme with the substrate speciﬁcity of 2-nitrotoluene dioxygenase by making the corresponding amino acid substitutions in the active site was only partially successful. The α subunits of the two enzymes are 84% identical in primary amino acid sequence, with only ﬁve amino acid differences at the active site. The substrate speciﬁcities of the two enzymes are signiﬁcantly different.209 Only two amino acid substitutions at the active site of NDO (F352I, A206I) were necessary to change the enantioselectivity with naphthalene to that of 2-nitrotoluene dioxygenase, which forms 70% (+)(1R,2S)-cis-naphthalene dihydrodiol.302 Wild-type NDO makes >99% (+)(1R,2S)-cis-naphthalene dihydrodiol. None of the mutant forms of NDO was capable of oxidizing the aromatic ring of 2-nitrotoluene with release of nitrite. In fact, enzymes with four or more amino acid substitutions were inactive,302 and all of the mutant enzymes had lower overall product formation rates with all tested substrates.214,216,302 The nitrobenzene and 2-nitrotoluene dioxygenase components have been puriﬁed213 and the crystal structure of the oxygenase component of NBDO has been solved.91 The overall structure of the α3 β3 hexamer of NBDO looks strikingly similar to that of NDO,147 and an overlay of the αβ heterodimers from the two enzymes highlights the similarity (Figure 7a). However, several amino acid differences at the active site can account for the observed differences in substrate speciﬁcity. In particular, an asparagine at position 258 in the α subunit of NBDO (corresponding to Val260 in NDO) was shown to form a hydrogen bond with the nitro groups of nitro-substituted aromatic compounds (Figure 7b). This hydrogen bond positions the nitroarene substrates for oxidation at the nitro-substituted carbon.91 Replacement of this asparagine with a valine in NBDO resulted in an enzyme with a signiﬁcantly reduced ability to oxidize the aromatic ring of nitro-substituted aromatics.138 A similar result was obtained with the same substitution in 2-nitrotoluene dioxygenase.172 It therefore appears that the orientation of the nitroarene substrate in the active site governs the regioselectivity of the enzyme. Recent studies have used the crystal structure of the NDO active site to predict active site residues in related dioxygenases. Based on such a model, the active site of the tetrachlorobenzene dioxygenase from Ralstonia sp. PC12 (TecA) was modiﬁed to identify speciﬁc amino acids involved in controlling both regioselectivity and product formation rate.222 Substitution of Phe366 in the α subunit of TecA (corresponds to Phe352 in NDO) with tyrosine or tryptophan resulted in inactive enzymes,222 a result similar to that obtained with the corresponding NDO mutants.216 Substitution of smaller residues at this position

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Rebecca E. Parales and Sol M. Resnick

Ala206 Phe352

Gly204

Ile 350

Phe251 Leu253

Phe293

His295

Asn258

Val260

Figure 7. Comparison of the NDO and NBDO structures. (a) Overlay of αβ heterodimers (NDO in blue; NBDO in red). The α subunits are toward the top and β subunits toward the bottom of the ﬁgure. The active site iron and coordinating histidine side chains are visible in the α subunit. (b) Overlay of active site structures of NDO and NBDO (NDO in blue; NBDO in red). Histidine and aspartate residues coordinating iron at the active site are in light blue and pink for NDO and NBDO, respectively. Five residues at the active that differ between the two enzymes are shown. Bound naphthalene in NDO is aqua; bound nitrobenzene in NBDO is yellow.

in TecA resulted in a shift from dioxygenation of the aromatic ring to monooxygenation of the methyl group of mono- and dichlorotoluenes. Replacement of Leu272 with tryptophan or phenylalanine resulted in enzymes with improved rates of dichlorotoluene transformation but little or no change in regioselectivity. This residue corresponds to Val260 in NDO, and Asn258 in NBDO and 2-nitrotoluene dioxygenase. Therefore, based on substrates tested to date, the residue at this position plays a role in controlling regioselectivity in NBDO and 2-nitrotoluene dioxygenase, but not NDO or TecA.91,210,214,222 In a similar study, the α subunit of BPDO from P. pseudoalcaligenes KF707 was subjected to site-directed mutagenesis based on modeling with the NDO coordinates. This study demonstrated that Phe227, Ile335, Thr376, and Phe377 were important for determining the position of oxidation with various PCB congeners.269 Thr376 had been previously identiﬁed as playing an important role in determining substrate speciﬁcity based on sequence comparisons of BPDOs with different speciﬁcities.153,186 In contrast, changing the corresponding residue in NDO (Thr351) did not seem to affect substrate speciﬁcity.214 Similarly, substitutions in NDO at Phe202 (corresponds to Phe227 in BPDOKF707 ) had little or no effect on substrate speciﬁcity. Phe377 corresponds to Phe352 in NDO, however, so the amino acid at this position has now been shown to be critical in TecA, NDO, and BPDOKF707 . From these studies, it appears that certain residues, such as Phe352 in NDO, may be important in determining the speciﬁcity in many

Aromatic Ring Hydroxylating Dioxygenases

317

(or all) dioxygenase active sites, while others may play a speciﬁc role in just a small subset of enzymes. With more crystal structures becoming available, other key residues effecting substrate catalysis and dioxygenase selectivity may be identiﬁed.

4. BIOTECHNOLOGY APPLICATIONS A number of biotechnology applications have been enabled by the high regioselectivity and enantioselectivity of aromatic hydrocarbon dioxygenases. Several examples include: (1) dioxygenase catalyzed synthesis of a wide range of chiral intermediates, some which have been subsequently used in the preparation of natural products, polyfuntionalized metabolites, or pharmaceutical intermediates, (2) recombinant expression of NDO in a multi-step pathway engineered for the fermentation based production of indigo from glucose, and (3) target-speciﬁc agents for biodegradation of environmental pollutants.

4.1. Production of Chiral Synthons As noted in Section 3.3, several well-characterized aromatic hydrocarbon dioxygenases have been shown to catalyze diverse types of oxidation reactions for a wide range of substrates.36,125,232 TDOs from P. putida F1 and UV4 have extremely broad speciﬁcity with respect to the monocyclic, substituted aromatic substrates, which are typically oxidized to arene-cis-dihydrodiols of high enantiopurity. Similarly, NDO,232 BPDO,36 and carbazole dioxygenase201 catalyze cis-dihydroxyation, as well as other oxidations on a range of polycyclic, heterocyclic, and substituted aromatic compounds. Interested readers are referred to recent reviews detailing the chiral cis-dihydrodiols obtained to date, rational approaches for expanding asymmetric (synthetic) methodology, and their versatile application in synthesis of natural products.34,36,125 The range of available metabolites resulting mainly from cis-dihydroxylation have been utilized in numerous syntheses for the preparation of ﬁne chemicals, natural products, pharmaceutical intermediates, and compounds with biological activity (Table 4). It should be noted that many, but not all, metabolites described are amenable to large-scale production using whole cell biocatalysis. This wholecell or resting-cell biotransformation approach has facilitated the production of multi-kilogram quantities of chiral metabolites and relies on the integrity of multicomponent dioxygenases activity, typically expressed in recombinant hosts with reduced cofactors supplied through the metabolism of exogenous carbon substrates (e.g. glucose). Alternatively, the use of puriﬁed oxygenases can be facilitated by the inclusion systems for enzymatic243 or electrochemical122,123 regeneration of reduced NAD(P)H cofactor.

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Table 4. Examples of synthetic reactions and compounds accessible from cis-dihydrodiols. Compounds that can be synthesized from chiral cis-dihydrodiolsa Azasugars, aminosugars, ﬂuorodeoxysugars, perdeuterosugars Conduritols, conduramines Deoxysugar analogs Erythroses Inositols, inositol oligimers Kifunensine Lycoricidine Narcliclasine Nojirimycin analogs Pancreastatin, (+) and (−)-7-deoxypancreastatin Prostaglandin intermediates (PGE2α) Pinitols Pyrrolizidine alkaloids Shikimic acid, methyl shikimate Specionin Zeylena Synthetic reactions conducted utilizing chiral cis-dihydrodiolsa Cycloadditions of dienediols and their acetonides Diels–Alder reactions Oxidative cleavage-reductive cyclization Cyclopropanation a

See Hudlicky et al. [125] for a detailed review of chiral synthons, product structures, and primary literature.

4.2. Indigo Production The oxidation of indole to indigo was initially shown in E. coli strains expressing NDO from Pseudomonas sp. NCIB 9816-4.84 NDO was shown to oxidize indole to an unstable cis-dihydroindolediol, which dehydrates to indoxyl, and undergoes spontanteous oxidation to indigo. Since the reaction is catalyzed by many related dioxygenases, this discovery has been widely utilized for detection and isolation of strains expressing mono- and dioxygenases. Commercial interest in the reaction led Genencor International to genetically engineer recombinant E. coli for the cost-competitive, multi-step production of indigo from glucose.28 The fermentation process was based on a single strain expressing a modiﬁed tryptophan pathway (allowing high level indole production) and NDO from P. putida.28 Several strategies were employed (e.g. gene dosage, gene ampliﬁcation, gene inactivation) to improve metabolite ﬂux, enzymatically eliminate the formation of isatin byproduct, and ultimately increase production of indigo to levels exceeding 18 g/l. Despite technical successes, the process for indigo production has not been implemented at an industrial scale.

Aromatic Ring Hydroxylating Dioxygenases

319

4.3. Indinavir Production Interest in enantiopure (−)-cis-(1S, 2R)-indandiol is based on its direct conversion to cis-(1S)-amino-(2R)-indanol, a key intermediate in the chemical R 58 synthesis of Merck’s HIV-1 protease inhibitor Indinivir Sulfate (Crixivan). Biotransformations conducted with P. putida F39/D (a mutant strain lacking cis-dihydrodiol dehydrogenase activity) or a recombinant TDO expressed in E. coli indicated that wild-type TDO oxidized indene to (−)-cis-(1S, 2R)indandiol (∼30% e.e.) and (1R)-indenol as main products, with traces of 1indenone.228,288 The (−)-cis-(1S, 2R)-indandiol could be obtained in >98% e.e. in late stages of indene conversion with wild-type P. putida F158 or by coexpression of cis-dihydrodiol dehydrogenase (todD) with recombinant TDO in E. coli.228 The upgraded cis-(1S, 2R)-indandiol enantiopurity occurs at the expense of total indandiol yield as a result of kinetic resolution catalyzed by the cis-dihydrodiol dehydrogenase, which is selective for the unwanted (+)cis-(1R, 2S)-indandiol.228 Directed evolution of TDO was conducted to select for reduced levels of the indene by-products, 1-indenol and 1-indenone, while maintaining the highest (−)-cis-(1S, 2R)-indandiol enantiopurity.303 After three rounds of mutagenesis, variants were obtained that produced significantly more cis-indandiol relative to the undesired by-product indenol. However, the stereoselectivity was changed to favor the production of the undesired (+)-cis-indandiol enantiomer.303 These strategies, as well as the application of Rhodococcus-derived oxygenases,205 were unable to alleviate formation of indene by-products and limited the maximum yields to <60% (−)-cis-(1S, 2R)-indandiol. The TDO-catalyzed enantioselective monohydroxylation of 2indanol to (−)-cis-(1S, 2R)-indandiol in high e.e. represents an alternative route to the vicinal aminoindanol and served as the basis for a process to prepare chiral 1-hydroxy-2-substituted indan intermediates.32 TDO expressed in P. putida strain UV-437 and strain P. putida F39/D oxidized 2-indenol to (−)-cis-(1S, 2R)-indandiol in >98% e.e. and in >85% yield, while minor products included trans-1,2-indandiol (<15%) and 2-hydroxy-1-indanone (<2%).160

4.4. Bioremediation of TCE Contamination Trichloroethylene (TCE) is widely used as a solvent and is classiﬁed as an Environmental Protection Agency priority pollutant. It is difﬁcult to degrade and no bacteria are known to utilize it as a carbon and energy source. TDO and other dioxygenases are capable of oxidizing TCE.148,180,287 TDO converts TCE into non-toxic products: formic acid and glyoxylic acid,174 but the host strain does not obtain energy from the reaction. TCE is actually capable of inducing the genes encoding TDO,253 but P. putida F1 cells in resting cultures exposed to TCE rapidly lost TCE oxidation ability.287 A recent study demonstrated that the addition of benzene or toluene restored TCE-degrading activity to P. putida

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Rebecca E. Parales and Sol M. Resnick

F1,188 suggesting TCE degradation by this strain could be optimized using this strategy. In another study, a hybrid TDO–BPDO was found to have an enhanced ability to degrade TCE.97 Characterization of the puriﬁed hybrid protein showed that it had higher catalytic efﬁciency and a lower Km for TCE than wild-type TDO.180 A cooxidation strategy for bioremediation of TCE in the ﬁeld has been reported.124 In this study, toluene or phenol and oxygen or hydrogen peroxide were added as co-substrates to stimulate in situ TCE degradation.

4.5. Improved Biodegradation of PCBs Genetic engineering has been used to improve a variety of bacterial enzymes and pathways for more efﬁcient degradation of environmental pollutants.185,211,218,219,278,279 Engineered forms of various dioxygenases have been generated with a variety of methods, and have led to the development of enzymes with novel or enhanced activities, and have provided insights into the control of substrate speciﬁcity. Various BPDOs have very different abilities to oxidize PCBs.105 Using sequence alignments of BPDOs from B. xenovorans LB400 and P. pseudoalcaligenes KF707 as a guide, Mondello and coworkers generated hybrid and site-directed mutant forms of BPDO. This work resulted in the identiﬁcation of regions of the protein and speciﬁc amino acid residues in the α subunit that controlled substrate speciﬁcity.86,186 These and other studies153 produced engineered enzymes with the ability to oxidize a wider range of PCB congeners. In particular, this work identiﬁed the important role of the residue at position 377 in the B. xenovorans LB400 enzyme in the oxidation of 2,5,2 ,5 -tetrachlorobiphenyl. Using DNA shufﬂing,304 variant forms of BPDO with enhanced abilities to degrade single-ring aromatic hydrocarbons, PCBs, and heterocyclic aromatic compounds have been generated.16,95,159,267,268 Recently, Barriault et al.18 used random mutagenesis of the B. xenovorans LB400 BPDO bphA gene to improve enzymatic activity with PCB congeners. Their results showed that amino acid substitutions at Thr335 and Phe336 in BphA caused changes in regiospeciﬁcity toward 2,2 -dichlorobiphenyl.

4.6. Construction of New Biodegradation Pathways Ring hydroxylating dioxygenases have been used to construct new pathways for the degradation of particularly recalcitrant compounds. An attempt was made to assemble a pathway for 2-chlorotoluene degradation by expressing the todC1C2BA genes encoding TDO from P. putida F1 (to convert 2-chlorotoluene to 2-chlorobenzylalcohol) with the upper TOL pathway genes from pWWO of P. putida strain mt-2 encoding benzylalcohol dehydrogenase and benzaldehyde dehydrogenase (to convert 2-chlorobenzylalcohol to 2-chlorobenzoate).118 These genes were expressed in two different host strains carrying either the ortho

Aromatic Ring Hydroxylating Dioxygenases

321

or modiﬁed ortho pathways. Unfortunately, due to the production of dead-end products and unfavorable metabolic ﬂux, the pathway was not functional – even though each individual part of the pathway was functional.118 In a more successful pathway construction strategy, expression of genes encoding TDO from P. putida F1 and cytochrome P450cam monooxygenase resulted in an engineered Pseudomonas strain capable of metabolizing polyhalogenated compounds through sequential reductive and oxidative reactions. In this constructed pathway, cytochrome P450cam catalyzed the conversion of polyhalogenated ethanes, such as pentachloroethane, to TCE under low oxygen tension, and TDO oxidized TCE to glyoxalate and formate.289 Many bacterial strains degrade only a limited number of toxic aromatic compounds, and genetic engineering has been used to increase the substrate range of speciﬁc organisms. A constructed cassette carrying genes for the conversion of styrene to phenylacetate was introduced into phenylacetate-degrading bacteria to generate strains capable of using styrene as the sole source of carbon and energy.179 When the plasmid-borne styrene cassette was introduced into P. putida F1 carrying the TOL plasmid, the new strain was capable of growth on an increased number of aromatic hydrocarbons, including benzene, toluene, ethylbenzene, m-xylene, p-xylene, and styrene. To reduce the possibility of horizontal transfer of genetically engineered DNA among bacteria, the cassette was inserted into a minitransposon carrying an engineered gene containment system.72 The tod genes encoding TDO have also been cloned into the chromosome of Deinococcus radiodurans, a bacterium that is highly resistant to radiation. This new strain was capable of degrading toluene and related aromatic hydrocarbons in the presence of high levels of radiation.162 Expression of the mercury resistance gene (merA) together with the toluene dioxygenase genes in D. radiodurans resulted the integration of multiple remediation functions in a single engineered strain, which could be used for amelioration of mixed radioactive waste containing aromatic hydrocarbon pollutants and the heavy metal mercury.45

5. CONCLUSIONS Aromatic ring hydroxylating dioxygenases play a key role in the biodegradation of numerous environmental pollutants, both in the natural environment (via natural attenuation) and in the engineered bioremediation systems. Recent structural and mechanistic information, together with enzyme engineering and strain construction strategies should allow the development of engineered microorganisms with new and/or optimized degradation abilities. The continued application of these approaches should also facilitate the development of Rieske non-heme iron dioxygenases with requisite selectivities for speciﬁc opportunities in target direct biocatalysis or metabolic engineering.

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Rebecca E. Parales and Sol M. Resnick

ACKNOWLEDGMENTS Research in the author’s laboratory is supported by the Army Research Ofﬁce, the Strategic Environmental Research and Development Program, and the University of California Toxic Substances Research and Teaching Program (REP). We thank Rosmarie Friemann and Juan Parales for providing ﬁgures.

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THE PSEUDOMONAS GENOME DATABASE Fiona S. L. Brinkman

Department of Molecular Biology and Biochemistry Simon Fraser University Burnaby, B.C., Canada

1. PREAMBLE – THE PSEUDOMONAS GENOME DATABASE PHILOSOPHY AND SCOPE The Pseudomonas Genome Database (www.pseudomonas.com) was initially developed with the goal of providing genome sequence and annotation data for Pseudomonas aeruginosa strain PAO1 in r A user-friendly web-based format r A format that facilitates continually updated, community-based annotation The database continues to maintain these priorities, but a new version (version 2) has since developed further to address the following needs r Comparative analysis of multiple Pseudomonas genomes r Further enabling alternate annotations to be viewed, or development of alternative views of the same annotations r Providing new computational analyses that facilitate the identiﬁcation of genome components of medical importance In the future, this resource aims to continue to meet these goals while also further expanding its collection of information directly relevant to P. aeruginosa Pseudomonas, Volume 4, edited by Juan-Luis Ramos and Roger C. Levesque C 2006 Springer. Printed in the Netherlands.

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infectious disease pathogenesis, vaccine development, and treatment. This collection of information will continue to be derived from new computational and laboratory analyses being performed by groups directly involved in this database development, and other research groups worldwide. One key to this approach will be continued focus on community involvement and providing more access to multiple different views of a given research problem or research data. It is hoped that the resulting diverse data collection, customized to help facilitate the development of new approaches for P. aeruginosa control, will become a signiﬁcant research aid that may serve as a model for how a community can come together to reach a common goal. I and the other project coordinators of course encourage suggestions for improvement to the database structure, possible analyses, and content. A review of this database is therefore provided below, with these goals in mind. This review provides further explanation of the history, goals, and philosophy of this project, along with what types of analyses are possible, or may be possible in the future. This will hopefully help more researchers realize how they may use this database to aid their research and spur them to participate in helping to maintain this database as a critical resource for Pseudomonas research in general.

2. INITIAL DATABASE DEVELOPMENT AND COMMUNITY ANNOTATION APPROACH – THE PSEUDOMONAS COMMUNITY COMES TOGETHER When the Pseudomonas aeruginosa PAO1 Genome Project was ﬁrst initiated in 1997, the major participants in this project wrestled with how to best annotate gene descriptions and other information for this genome, as have many ﬁrst-time genome project organizers. At the time, genome annotation approaches were very much centralized, and concepts like open annotation, annotation jamborees, and web-based annotation submission had not yet been developed. Pseudomonas aeruginosa, an important pathogen and major cause of morbidity and mortality for Cystic Fibrosis patients, was the largest bacterial genome sequenced to date, with an estimated 6000 genes, and the third most cited bacterium in Medline. Robert Hanco*ck and I decided to initiate a community-aided approach to capitalize on the large number of researchers studying this bacterium. Furthermore, we decided that the project should be conducted entirely through the Internet, in an effort to keep project costs down. Our approach therefore involved enlisting the expertise of volunteer researchers from the Pseudomonas research community to annotate genes or gene families with which they were familiar. One moderator coordinated this

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project, termed the Pseudomonas Community Annotation Project or PseudoCAP, and provided supportive documentation, including computer-generated annotation, and example curated annotations of selected genes, through the project’s dedicated web site. On September 15, 1998, a formal request for participants was sent by email to members of the Pseudomonas research community. In all, 47 members of the research community initially expressed interest. Annotations provided by the participants were subjected to peer-review by a Pseudomonas aeruginosa genome analysis committee (PAGAC), before overlaying these annotations on a genome viewer console containing layers of other automatically generated analyses and literature reference information. This resource, coupled with a critical, conservative annotation approach, was used to generate the ﬁnal genome annotations which were made available at www.pseudomonas.com31 . One of the most surprising results from our investigation of this internetbased community annotation approach was the higher than anticipated participation rate in PseudoCAP. Of the 47 participants who initially expressed interest in the project, over 90% submitted annotations and, as word spread of the project, a total of 61 participants from 11 countries ended up making 1741 submissions. This is an exceptional participation rate, considering that participants provided their expertise on a volunteer basis only. Notably, most of the later participants were researchers not involved in Pseudomonas research, but rather researchers studying certain classes of genes who wished to help annotate the hom*ologous genes in this particular genome. The high participation rate observed may reﬂect the research community’s signiﬁcant interest in increasing the quality of genome annotation3 . We also observed that, even on a volunteer basis, some participants submitted very high-quality annotations. Regardless, if such high-quality annotations had been used exclusively, the ﬁnal annotations would have contained numerous signiﬁcant inconsistencies. Therefore, we found that one important step in the project involved using a small set of curators to provide a ﬁltering step for consistency, and ensure conservative, critical annotation. This meant the ﬁnal annotations were based almost exclusively on functional studies of the gene in question, or hom*ology only to functionally studied proteins. This process essentially allowed us to incorporate expert knowledge from researchers who had been studying a particular set of genes for years – while formatting this knowledge into a consistent, relatively conservative, format that could potentially aid future genome-wide analyses. We have therefore proposed3 that this PseudoCAP method, complemented with a more decentralized approach using a distributed annotation system6 such as GBrowse30 (mentioned below), is an approach that best suits many genome projects, as it permits both the development of centralized annotation for all to use as a reference (i.e. gene names) combined with a system to facilitate easy access to alternate annotations. A number of other community annotation

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Figure 1. Schematic overview of the Pseudomonas Genome Database and PseudoCAP annotation update process. Squares with thick lines/borders denote database and application components. Circles reﬂect processes in the annotation update approach. Elements with thin lines/borders reﬂect human intervention. Shaded boxes denote new features added in version 2 of the database.

approaches have been developed with components of this philosophy in mind, including WormBase29 , the PeerGAD system5 , and ASAP12 . Our currently expanded annotation approach, as outlined in Figure 1, has now been utilized by other genome projects, reﬂecting the interest in combining both peer-reviewed centralized, and unreviewed decentralized, data resources that utilize a combination of previously reported approaches, including the “open annotation” approach15 and community annotation project (CAP) input3 .

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3. PSEUDOCAP TODAY – FACILITATING CONTINUALLY UPDATED ANNOTATION While PseudoCAP was invaluable during initial annotation efforts, this CAP approach continues to be used today in a more ﬂexible, expanded fashion to enable annotations to be continually updated. Annotation updates now occur through a combination of researcher submissions, reviews of the literature, and computational analyses35 . A log ﬁle is maintained of the updates that is searchable, and indicates what update type was made, who was involved, when the update occurred, and what rationale was used for the update (literature reference, computational analysis, or other). The ability of the database to perform concise Boolean searches and sorting of results is an important feature, since such functionality will become increasingly important as log ﬁles for updates become larger and more complex.

3.1. Annotation Updates by PseudoCAP Participants Submission by a researcher can be made either by simply ﬁlling in a web-based form, sending an email to the project coordinator, or by creating a user ID and logging into the system (the latter is useful when making many submissions). All submissions are subject to initial review by the PseudoCAP coordinator. The coordinator examines the submission and then responds with any requests for additional information/clariﬁcation, if required. At this point a protein name conﬁdence level is assigned or changed, using our previously developed classiﬁcation system31 (see Box 1). In addition, a conﬁdence level is assigned/changed for protein subcellular localization, as part of our expanded conﬁdence system. Any suitable Gene Ontology2 (GO) annotation is also now evaluated and associated with the annotation change. The submission is then reviewed by at least one additional reviewer from the research community and a collection of all annotations made over a 2year period are subject to additional review at the biennial International Pseudomonas conference. We feel this latter review step is important to provide the community with an efﬁcient mechanism to review annotation updates collectively and examine and discuss any systematic annotation issues. Management of the review stages by a coordinator is also important to ensure consistency in annotation updates and to ensure that additional reviewers chosen from the research community are appropriate for a given annotation update case. Note that both sequence information and annotations can be updated. Sequence changes, if they involve an insertion or deletion of a nucleotide, can affect the nucleotide coordinates of all annotations downstream of the change, however our unique ID system for numbering genes ensures that researchers

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Box 1. Conﬁdence level classiﬁcation One of the most frequent questions we receive is “what is the conﬁdence level classiﬁcation?”. This system was designed to aid researchers who wish to identify only those proteins annotated with a certain level of conﬁdence, such as identifying all those proteins with an experimentally determined subcellular localization, versus identifying all those who subcellular localization was computationally predicted using a particular method. For subcellular localization annotations, this classiﬁcation system is relatively straightforward. For the protein description this classiﬁcation is a little more subjective, however, in general a protein description is given a class 1 rating (meaning “function experimentally determined in Pseudomonas aeruginosa”) if the protein name primarily reﬂects the function that has been experimentally studied. It is this class 1 rating that has apparently been the most useful, as it reﬂects a dataset of genes/proteins that have been experimentally studied. Of course this constantly needs to be updated, and so researchers are encouraged to send the project coordinator a quick note about any annotation that should be designated as a class 1. For more information about the classiﬁcation system, see the “Frequently asked questions” (FAQ) list on the Pseudomonas Genome Database website.

can refer to a given gene using a coordinate (the unique ID) that will not change (see Box 2).

3.2. Annotation Updates Based on Literature Review In addition to PseudoCAP participant submissions, the Pseudomonas research literature is also reviewed weekly using PubCrawler14 and papers are noted that report new gene names, gene functions, or other information that may impact on the genome annotation. The corresponding author of the paper is contacted with a proposal for an annotation submission that is based on the paper’s work. If agreed to, the submission is directly accepted (because it has been already subject to peer-review during publication) and the log ﬁle notes both that this was a submission based on literature review and provides information on the accepting author and journal citations.

3.3. Annotation Updates Based on Computational Analyses In addition to annotation updates based on experimental data, the integration of computationally based predictions are also encouraged – as long as they

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Box 2. The beneﬁt of function-independent unique identiﬁers (or “why you should cite the PA number”) For the P. aeruginosa strain PAO1 genome annotation, records in both the original and updated annotations are uniquely identiﬁed by a locus ID consisting of “PA” (for P. aeruginosa) followed by a four-digit number representing the order of ORFs around the chromosome starting at the origin of replication. In consultation with the Pseudomonas research community, we have adapted the convention of using a decimal system to account for newly described ORFs (i.e. PA1000.1 would be between PA1000 and PA1001; PA1001.01 would be between PA1000 and PA1000.1)35 . These identiﬁers can link to external databases such as TIGR’s comprehensive microbial resource (CMR24 ), which represents an alternate annotation view, and the NCBI RefSeq25 that we submit updates to. In the future we would also like to implement a similar unique ID number system for other genomic features, such as promoters and other regulatory elements. But why have such a numbering system, rather than using a unique gene name (or other annotation name) for each annotation, which could be easier to remember? A unique ID that is function-independent is useful because it will not need to be changed if a change in function is identiﬁed for a given gene. For example, based on an initial analysis, a (ﬁctional) protein could be found to be involved in arginine uptake, and named ArgQ, but then later it is discovered that in fact the protein has a more general function involving uptake of basic amino acids. Meanwhile, another protein is found also to be involved more speciﬁcally in arginine uptake – prompting a proposed gene name change. Therefore, we strictly maintain the PA number as a unique identiﬁer of a gene/protein that will never change, while allowing the use of multiple gene/protein names (a primary name and “alt”, or alternative, names). This best reﬂects the continual evolution of protein descriptions, and in some cases gene names, as functions are better elucidated. This also handles the inevitable updates involving corrections to the sequence, which may change sequence coordinates for a given gene). Therefore, in short, a researcher should always refer to the PA number (or other annotation unique identiﬁer) to best clarify what gene/protein is being referred to in a given analysis/experiment. We encourage the use of similar identiﬁers for other future Pseudomonas genome projects. We also discourage the development of gene IDs in related genomes on the basis of orthology (since, like function a proposed orthology may change as further information is obtained about the true relatedness of genes between given strains). One of the simplest conventions is therefore to number the genes around the genome as we, and many other genome projects, have done, and so I encourage this simple numbering system for other future genome projects.

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Box 3. Literature-based annotation updates – constraints that should perhaps change? Note that currently we only automatically review literature that involves a study of P. aeruginosa strain PAO1 speciﬁcally (i.e. we do not annotate the PAO1 strain genome-based on a published study in another P. aeruginosa strain). This means that it is important that a researcher clearly indicate in their publication what strain was used for a given experiment. However, in the interests of gathering more data, we are now considering in the future incorporating information from other strains, as long as we clearly differentiate such data from PAO1-based data. Of course, as illustrated in the ﬁrst P. aeruginosa genome publication31 , there are multiple versions of the PAO1 strain in existence in research laboratories – some with notable inversions versus the sequenced strain. Therefore, even studies based on the PAO1 strain are not clear cut. Also, some annotations previously developed may have been based on data involving other strains that we were not aware of. Therefore, we are interested in incorporating more data from other strains, however, we feel it is important to emphasize the need to maintain strain speciﬁc information as much as possible, to maintain a database of the highest quality.

are clearly classiﬁed as such by our classiﬁcation system, and the computational approach used is clearly noted. Since the accuracy of computational methods may change dramatically depending on the method used, indicating the speciﬁc method used and version number is critical. We also plan to incorporate more information about the accuracy of each method as small help ﬁles that would be associated with each computational analysis. For example, a signal peptide prediction method may have only about 80% precision, while the PSORTb method for protein subcellular localization prediction has over 95% precision. If a researcher knows of a particular computational analyses that they have found very useful, we encourage them to contact the project manager, Geoff Winsor, about it, as usually we can easily incorporate the analysis into the database (see the description of GBrowse, below). In general, I encourage as much community participation in this project, as is possible, recognizing that the project must review the literature regularly to identify suitable annotation updates that may not be reported to us. Through the combination of community participation, literature review, and the addition of additional high-throughput analyses, such as computational analyses, this resource will hopefully continue to be current and maintain its usefulness in facilitating Pseudomonas research.

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Figure 2. Screenshot of a comparison between annotations from different Pseudomonas species in the Pseudomonas Genome Database. To obtain this comparison, ﬁrst a search was performed against all Pseudomonas species genomes available, and then the genes of interest selected and added to a “clipboard”. Then a “compare” button is clicked, resulting in the illustrated display (a section of which is shown). Note how one can easily view difference in annotation (such as product name) and differences in gene order in the chosen sequence region. In addition, selecting the “Align” button for DNA or protein sequences generates a multiple sequence alignment using Clustal33 of the selected genes/proteins being compared. The resulting alignment may be viewed directly or downloaded for further analysis.

4. DATABASE STRUCTURE OVERVIEW An overview of the database structure for versions 1 and 2 of the database is shown schematically in Figure 2 (new features available in version 2 are shaded). The Pseudomonas Genome Database currently comprises (1) the original P. aeruginosa PAO1 genome annotation published in the year 2000 (an important reference dataset31 ), (2) the continually updated P. aeruginosa PAO1 annotation and log ﬁle of updates35 and (3) annotations of other Pseudomonas species/strain genomes that may be examined for comparative purposes. Visitors entering the site can examine any of these genomes and choose to browse, search or compare speciﬁc annotations as well as download tab-delimited ﬁles of information from

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a search/comparison. Alternatively, one can submit an annotation update, either as a guest or as a registered PseudoCAP participant (the latter is required for more complex submissions). Eventually, we will develop this database further, to facilitate continual updating of the annotations of other Pseudomonas strains, in particular the P. aeruginosa strain data that we will be hosting as part of genome projects we are involved with. We are happy to assist researchers who either wish to host their Pseudomonas strain data on our system, or wish to host their strain data themselves on their own system – but using our database structure. The database structure and source code is freely available under an open source license (GNU GPL). As mentioned in Box 2, a unique identiﬁer (“PA number”) is assigned to each gene. Records for each ORF contain information on the primary name associated with the ORF and its product as well as any alternate names that have been used. Furthermore, multiple functional classiﬁcations, genomic context, structure, predicted localization of the product as well as reactions and predicted pathways the product is involved in, PubMed references and DNA and protein sequences are stored. Fields are searchable using a Boolean search interface with the ability to ﬂexibly sort the data and then either view the data directly or download the search results in tab-delimited format. ORFs can also be browsed by their order around the genome or by functional classiﬁcation of their product. With regard to nucleotide and protein sequences, a BLAST search can be performed against genomic DNA and protein sequences using BLASTALL from NCBI (16). In addition, subsequences of the PAO1 genome (DNA or translated sequences) can be downloaded by specifying the base-pair coordinates of the DNA sequence. Finally, the amino acid sequence of proteins can be obtained by specifying the PA number of the gene encoding it.

5. COMPARATIVE GENOMICS CAPABILITY In addition to the P. aeruginosa PAO1 genome annotations (original and updated), a new version (version 2) of this database now also contains annotations and sequence information for other Pseudomonas species/strains4,21 . While the focus of the database is still centered around the P. aeruginosa PAO1 sequence and annotation, there has been a growing appreciation of the need to facilitate research discoveries through comparative genomics. Therefore, the database is moving further towards the development of more comparative views/analyses of multiple Pseudomonas genomes at once. Ironically the “Pseudomonas Genome Database” may ﬁnally now live up to its name. One can now perform a search involving multiple Pseudomonas genomes at once, and perform a “compare” of multiple annotations – either across multiple different genomes, or within one genome, or a combination of the two. An example of a comparison is illustrated in Figure 2. From such comparisons, one can then

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perform additional comparative analyses, such as multiple sequence alignment of the selected gene/protein sequences. This comparative feature is useful for comparing gene order between species or between genes that are a member of a particular gene family (for example, efﬂux proteins). It is also useful for comparing what is known about gene function for particular genes across species (or within gene families) or even for detecting anomalies or errors in gene annotation between species. Sequence alignments may also be easily obtained for the set of genes being compared, and links are available to more detailed annotations. In the future, comparative analyses will be expanded to facilitate additional types of comparisons, such as comparative identiﬁcation of insertions/ genomic islands. The comparisons will also be made more ﬂexible, for example allowing one to select which annotations they wish to view in the comparison and, for gene order graphics, invert a particular gene order in one organism, versus another organism, to facilitate making gene order comparisons between species whose genomes have large inversions in some regions.

6. GBROWSE – A DISTRIBUTED ANNOTATION SYSTEM THAT ALLOWS RESEARCHERS TO VIEW ALTERNATE ANNOTATIONS AND ADDITIONAL ANALYSES Comparisons can also be made through GBrowse – an application that allows one to view multiple different annotations for a given sequence region/gene at once. With the increase in annotations available to microbiologists via the internet, it is becoming increasingly necessary to visualize genomic annotation information from multiple sources in a single viewer. We also feel that it is important to encourage alternate scientiﬁc views by allowing researchers to view any alternate annotations relative to our database’s primary, peer-reviewed, annotation information. To facilitate this, we have incorporated a platformindependent web application called GBrowse developed by Stein et al.30 . Using checkboxes, one can select diverse annotation information to view, including alternate gene annotations, motifs/structures, metabolic pathway data, gene knockout data, and ortholog data (the latter reﬂects comparisons with other genomes). One can perform a search based on criteria speciﬁed (for example, particular base-pair coordinates or a gene name) or just link to GBrowse from a particular gene entry in the main database. GBrowse then fetches the region of the genome speciﬁed by the search criteria and presents a view containing one or more horizontal tracks representing different sequence features for that area. The user is free to zoom in and out according to level of magniﬁcation/resolution desired. “Landmarks” (icons or glyphs) on each track usually

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contain a link to detailed information contained on additional websites. One can select, and even reorder, what tracks are shown, and can also upload their own data (for example functional genomics data), for viewing alongside the other tracks. Uploaded data can be privately viewed by implementing the Distributed Annotation System6 . Through this system, researchers can upload annotation data to a server where others can also view this data within a GBrowse track by entering the URL of the reference server. In essence, Pseudomonas GBrowse

Figure 3. Screenshot showing selected tracks in a GBrowse display, illustrating the variety of different annotations that may be shown. Genomic coordinates for the selected region are shown at top, followed by a series of tracks containing “landmarks” (glyphs, or colored icons) that link to additional information. For example, the ﬁrst track links to P. aeruginosa PAO1 gene annotations at Pseudomonas.com, while the second links to NCBI data and the third links to operon prediction information for these genes. Information about each track can be set to either be verbose or compact. For example, for the operon prediction track, the color of the landmarks between genes reﬂects the probability that the two genes are cotranscribed without a promoter between them34 . However under “track options” this track can be changed to show also the speciﬁc p-value for the prediction. Conversely, the track of “all proteins with NCBI links” can be changed to the compact form, which doesn’t list the long protein names, permitting the track to be displayed as one line. Track order can also be changed and one can zoom in or out of the sequence at any level desired. For a full list of all currently available tracks, see Table 1.

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and DAS allow researchers to easily view alternate annotations while promoting open discussion leading to better annotations for the Pseudomonas research community. An example of a GBrowse view of a genomic region is illustrated in Figure 3 and a list of all currently available tracks of annotations is described in Table 1.

7. INTEGRATION WITH OTHER DATA VIEWS, SUCH AS PATHWAY-BASED VISUALIZATIONS In addition to the gene/genome-centric views of the main Pseudomonas Genome Database, a metabolic pathway-based view of the data called PseudoCyc is also maintained. It is based on a database schema developed by Karp et al.17 using their Pathway Tools software. PseudoCyc, created by Romero and Karp in 200327 (curation taken over by PseudoCAP in 200435 ), contains information on Pseudomonas aeruginosa PAO1 genes and proteins along with 821 enzymatic reactions and 141 biochemical pathways involving 738 enzymes and 651 compounds. Updates to gene and protein names that have changed since the original annotation in 2000 have also been updated in PseudoCyc, though annotation updates that were made during the initial curation of the PseudoCyc pathways27 have been maintained. PseudoCyc is fully integrated with the Pseudomonas Genome Database and contains additional interactive functionalities including the ability to upload and view gene expression data in the context of the pathways. Eventually it would be suitable to expand this database to include signaling pathways, as is now occurring for other selected Pathway Tools-based databases.

8. EXAMPLES OF ANALYSIS TOOLS ASSOCIATED WITH THIS DATABASE: UTILITY FOR RESEARCH AND DRUG/VACCINE DISCOVERY There are many tools and analyses that we are interested in incorporating into this database, including functional genomics data, other computational predictions (particularly medically relevant ones, such as improved epitope prediction), and other inter-genome comparison tools. Below is a short highlight of some tools/analyses currently available, illustrating how diverse types of analyses/tool are being made available, some of which provide insight into Pseudomonas biology and some of which may also be useful for development of Pseudomonas infection controls.

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Table 1. GBrowse tracks of annotation data that is currently available.

GBrowse track All genes with links to www.Pseudomonas.com All Proteins with NCBI links Operon Finding Software V1.234 Predictions (probability that adjacent genes on the same strand are cotranscribed)b Putative Pseudomonas putida KT2440 orthologs (“reciprocal BLAST analysis” only) Putative Pseudomonas syringae DC3000 orthologs (“reciprocal BLAST analysis” only) Putative Pseudomonas syringae B728a orthologs (“reciprocal BLAST analysis” only) Putative Pseudomonas aeruginosa PAO1 orthologs (“reciprocal BLAST analysis” only) All COGs32 with links to NCBI COG database PFAM predictions (with links to PFAM database)28 Predicted TIGRFAMs (with links to TIGRFAMs)24 Predicted TIGR Roles and Sub Roles24 Subcellular localization (with conﬁdence level)10,11,18 Non-Coding RNA Genes KEGG Metabolic Pathways23 PRODORIC Regulons20 Protein Data Bank (Hits to known 3D structures by PEDANT)9 Intergenic Sequences (for ease of retrieval) Rho-independent Terminators (from CMR)7 Rho-independent Terminators (additional terminators identiﬁed by the Brinkman group)35 phoA/lacZ transposon mutants (University of Washington Genome Centre)16 TN5 lux transposon mutants (UBC)19 DNA sequence (at high resolution <= 130 bp)/% GC Content (at low resolution > 130 bp)30 3-frame translation (forward)30 3-frame translation (reverse)30 a

Database version that track was ﬁrst available for P. aeruginosa PAO1

Track available for other Pseudomonas genomes

1 1 1

Yes Yes Noa

Yesc

N/A

Yes

2 2 2 2 2 1 1 1 1

Yes Yes Yes Yes Yesd No Yes No Noa

1 1 1

No Noa No

1 1

No Yes

1 1

Yes Yes

These tracks will likely be implemented by the end of 2006. More accurately, this track containing operon predictions could be referred to as the probability that two adjacent genes encoded on the same strand do not contain a promoter between them. Note that it is possible to have two genes be cotranscribed but also have an additional promoter located between the two genes to further modulate expression of the downstream gene. c Not applicable for the GBrowse database for the same Pseudomonas strain as is listed here for this track d Only annotations computationally predicted by PSORTb are provided for other Pseudomonas genomes, while the P. aeruginosa PAO1 genome annotation additionally contains information about localizations experimentally conﬁrmed in laboratory experiments18,35 . b

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8.1. Motif Search We have created a user-friendly search tool that can be used to ﬁnd speciﬁed DNA motifs within the strain PAO1 genomic DNA sequence35 . This search tool accepts IUPAC-formatted variable length DNA sequence motifs as a query, and then, upon search completion, an online report or downloadable tab-delimited ﬁle is produced containing information on all regions the motif is found in. We used this tool to discover a previously undescribed rho-independent terminator subset containing a common sequence string (Sequence: AAAGC{3,4}SN{5,30}SGGGCTTT; occurrences not previously reported in the CMR terminator GBrowse track are viewable under the Brinkman terminator track under GBrowse)35 . The P. aeruginosa PAO1 genome had the highest total number of occurrences of this terminator subset compared to all complete genomes available, with related Pseudomonas species genomes containing slightly higher than average occurrences as a proportion of their genome, perhaps reﬂecting an evolutionary relationship in the evolution of this terminator sequence. The discovery of this surprisingly terminator-speciﬁc and species-speciﬁc sequence motif is just one example of how integration of such elementary tools has led to new insights through Pseudomonas genome analysis.

8.2. Subcellular Localization Predictions The protein subcellular localization information that we have recently made available is of particular note since subcellular localization information can be an important component of vaccine/drug target identiﬁcation, and is critical for many downstream protein studies. We previously developed the most precise predictor of subcellular localization, termed PSORTb11 which the project has used to make predictions of localization, in addition to laboratoryderived data that we have obtained from the literature26 and experiments18 . This PSORTb method was updated in 2005, permitting more predictions to be made while retaining the same high level of precision (greater than 95%)10 . We have found that the level of accuracy is now exceeding that of most high-throughput laboratory studies of subcellular localization. This resource is an example of an analysis that can aid many researchers in identifying proteins of interest (such as cell-surface proteins) that are not well studied, since frequently predictions of subcellular localization can be made for proteins of unknown function. For example, using the database search, one can easily identify all proteins predicted to be secreted which are annotated as “hypothetical protein”. We hope to incorporate more such analyses into the database, focusing primarily on those that have high precision, to ensure that a quality database is maintained. In addition, this database project will move further toward using more advanced data mining techniques to perform more sophisticated analyses of the genomic data, along with incorporating more analyses speciﬁcally

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Box 4. Database “Helpful Hints” – Click on the “blue question mark” symbol near anything in the database, if you want to learn more about it. – If you can’t ﬁnd something during a search, try a “wildcard” search (which allows text before and after your query text). For example, you may search for “urease” under product name for the strain PAO1 annotation, but not ﬁnd anything because the name is actually “urease alpha subunit”. If you search for “urease” with a wildcard speciﬁcation though, you will ﬁnd it. – When searching by gene name, try to search under both gene name and alt gene name. – Remember, you can combine searches under the advanced search option. For example, identifying all those proteins predicted to be outer membrane proteins which are not class 1 (i.e. have not been experimentally studied). – Additional GBrowse annotations are best reached by ﬁrst going to a relevant gene entry in the main database (usually through a search), and then clicking on the GBrowse link. – In GBrowse, you can turn on and off what annotation tracks you wish to view, and sort them in a different order. If you zoom into the sequence enough, some tracks change to show additional information, such as more descriptive names, or nucleotide sequence (for the G+C track). – In GBrowse, here are tracks of information about orthologs between different Pseudomonas strains, and you can click on these to view data on the orthologous gene (gene that is most likely the “same” in the other species) and therefore move between genomes easily through these orthologs. – For some genome sequences, there may be little gene name information, and annotation quality/degree of detail will vary markedly. Therefore, just because you don’t see a ureC gene in one genome for example, that doesn’t mean its not there. You should always ensure that you use complementary sequence search capabilities, in addition to annotation text searches. – If you have a very large search you want to perform (i.e. that would result in greater than 1000 “hits” in your search) you should consider either contacting us to perform a custom search for you, or download a copy of the annotations so you may perform the query on your own machine. Very large searches = very slow on a website that gets many queries in a day as this database does. Note that we do not allow excessively large searchers, regardless (an automated message will appear that will indicate that the search is too big and you should contact us for help).

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relevant to uncovering new approaches for P. aeruginosa infection control (immune modulators, epitope identiﬁcation, small molecule interactions, etc).

9. CONCLUSIONS The initial sequencing and annotation of the P. aeruginosa PAO1 genome sequence was a landmark event for Pseudomonas research. It revealed that this microbe contained a complex metabolic capacity with surprisingly large gene families identiﬁed that explain in part the versatility of this organism. Subsequent laboratory and computational studies of the encoded genes, proteins, and regulatory regions are revealing a further level of complexity. Such analyses are also identifying notable new targets for new therapeutics, vaccines, diagnostics, as well as providing insights into P. aeruginosa function, antimicrobial resistance, and pathogenicity. There is much promise in P. aeruginosa research today1,8,13,22,36,37 . This database of genome annotation information was initiated with the simple goals of providing a user-friendly resource that capitalized on input from the Pseudomonas research community. This community input has continued, with the number of PseudoCAP participants increasing from 61 in the year 2000 to 107 as of the end of 2004. These individuals, from over 11 countries worldwide, have contributed over 1000 annotation updates, not including the submissions made prior to the genome sequence publication, or particular highthroughput analyses. However, additional annotation updates made through review of recent peer-reviewed publications were also useful and are increasingly forming a larger proportion of annotation updates being made. To make such literature review as effective as possible, it is critical that researchers clearly indicate which strain is being used in a given study, so that through text searches, strain-speciﬁc studies can be identiﬁed and any associated annotation updated. Of course it only beneﬁts the community if individuals notify the genome database coordinator or manager of any suitable changes/corrections as they notice them. Updates such as nucleotide sequence corrections reinforce the need for having a clear unique identiﬁer for all genes in a genome, since the nucleotide coordinates can easily change for all genes downstream of corrections that involve an insertion or deletion. We have utilized the PA number, with its additional decimal system as described above, as a primary key, and discourage the use of the gene name as a primary identiﬁer, due to its potential to change in some cases, as knowledge of a gene’s function increases. We therefore encourage researchers to always reference the PA number (or similar number in another strain) for a particular study, while often continuing to also use the gene name as a useful term because of its functional meaning. This database is centered around the philosophy that both centralized annotation, as well as access to decentralized annotations, is critical. Continually

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updated annotation approaches that do not have a reference annotation that is subject to review are susceptible to increased confusion, as researchers sort through which annotation information to trust or report in the context of their laboratory or computational analysis. Continually updated annotation approaches that only provide a single primary reference annotation run the risk of stiﬂing alternate biological views. Of course, static annotations that are not subject to updating risk becoming obsolete and the workload involved in highquality, re-curation of whole genomes can render occasional re-annotation of a whole genome unfeasible, in contrast to the incremental approach we perform as we keep abreast of the research literature and PseudoCAP submissions. In addition, we propose strong links between different Pseudomonas databases, and have started to implement this as part of the comparative genomics component of the database. Each Pseudomonas database has unique expertise to offer, and through the power of internet links, these expertises can be integrated at each site, potentially focusing on slightly different viewpoints suitable for the needs of particular Pseudomonas communities. As signiﬁcantly more genomes are sequenced, comparative genomics tools will become increasingly necessary if we are to manage the continuing ﬂood of genomic data. PseudoCAP and the Pseudomonas Genome Database has hopefully facilitated the collaboration of Pseudomonas researchers, capitalized on their experience, and stimulated interaction and collaboration while furthering our understanding of Pseudomonas biology. Through the centralized peer-review process, we have been able to attain a high-quality genome annotation for a model P. aeruginosa strain that takes into account levels of conﬁdence for each annotation. This has been achieved with minimal cost by taking advantage of the internet as an effective means of collecting, distributing, and analyzing information. Through its availability as an open source package, with additional utilization of other open source packages such as GBrowse that are already available, this database, and the associated continually updated annotation approach will potentially act as base for additional Pseudomonas genome projects in the future. The P. aeruginosa PAO1 genome sequence and database is clearly only the beginning of many Pseudomonas genome projects. Many interesting strains still need to be sequenced from this facilitating genus, and there is optimism that we will make great strides in understanding P. aeruginosa and other Pseudomonas through a combination of sequence analysis, other biological study, and integration of the resulting data.

ACKNOWLEDGMENTS The author is indebted to Robert E. W. Hanco*ck, Geoff Winsor, and Raymond Lo for their critical coordination, guidance, and database development efforts. All members of the Pseudomonas research community who provided

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important input on this project, annotation information, and corrections are thankfully acknowledged – in particular those involved in galvanizing the initial CAP. Matthew Laird and other members of the Brinkman Laboratory are thanked for their critical input regarding database development, and Peter Karp and Randy Gobbel are acknowledged for their assistance with implementing the necessary changes to PseudoCyc for its integration. Primary funding for this project was provided by the Cystic Fibrosis Foundation. Ancillary funding was provided by Genome Prairie, Genome BC, Inimex Pharmaceuticals and the Canadian Cystic Fibrosis Foundation. The author is a Michael Smith Foundation for Health Research Scholar and a Canadian Institutes of Health Research New Investigator.

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INDEX

A A549 cells, 80 ABC transporter, 3 Acinetobacter calcoaceticus, 166 adenyl cyclase mutant (cyaAB), 83 ADP ribosyltransferase toxins, 88 Aeromonas hydrophila, 14 aerosolized aminoglycosides, 62 Affymetrix GeneChip technology, 24 Agrobacterium radiobacter, 276 AlgR, 156 apoptosis, see programmed cell death Arg residues, role of, 10 aromatic ring hydroxylating dioxygenases, 287 α subunits of, 294–295 biodegradation pathways, construction of, 320–321 biotechnology application of, 317 classiﬁcation of, 291–293 catalyzed reactions, types of, 289–292, 311–314 structure and mechanism of, 305–310 ASAP, 344 aspartate β-semialdehyde, 5 B bacterial ﬂagellins, 106 β-barrel, 10, 16 B-band gene island, 41 bidentate chelating groups, 3 biphenyl degradation, 210 β-lactams, 55 BLAST results, 113, 152 bovine serum albumin (BSA), 170 5-bromo-4-chloro-3-indolyl galactoside [Xgal], 122

5-bromo-4-chloro-3-indolyl phosphate [XP], 122 bronchoalveolar lavage ﬂuid (BAL), 83 BTEX compounds, 204 Burkholderia cepacia complex, 3–4 Burkholderia cepacia DBO1, 307 Burkholderia cepacia, 57 Burkholderia sp. strain JS15045, 244 C Candida albicans, 92 carbazole dioxygenase ferredoxin component (CarAc), 310 carcinogen, 276 cardiolipin, 85 catabolic pathways in P. aeruginosa, 191–194 expansion of, 203–204, 211 catechols, 241, 264 CF isolates, 41 CF mutator strains, 57 CF transmembrane conductance regulator (CFTR) gene, 56 chiral synthons, 317 synthetic reactions of, 318 chlorinated ethenes, degradation of, 276–278 chlorobenzenes, degradation of, 215–218 chloroform, degradation of, 274–276 chronic myelocytic leukaemia (CML), 260 clc element, 218–222 clinical isolates, ﬁrst report of, 56 clonal salmonella, 35 Clostridium perfringens α toxin, 69, 73 Cycloclasticus isolate, 293 cystic ﬁbrosis, clonal variations of genotypes, 56–60 phenotypes, 60–62

363

364 D diacylglycerol (DAG), 70 dioxygenases for aromatic hydroxylases, 278–279 diversity of benzoate family, 298–299 other members, 302–303 phthalate family, 300–301 salicylate family, 299–300 toluene/biphenyl family of, 297–298 dipyridyl, 21 disulphide bond loop (DSL), 141 Drosophila melanogaster, 154 drug resistant clones, 55 DUF756, 81 E E. coli TG1/pBS(Kan)T3MO expressing TpMO, 241 E. coli vitamin B12 OMT, 15 epidemic clones, 50 Escherichia coli TG1 cells, 239 extracytoplasmic function (ECF) sigma factor, 22 F FepA structure, effect of, 9 FepBCDG hom*ologs, 21 ferredoxin reductases, 308 ferredoxin, 291, 297 ferric-enterobactin receptor in E.coli, 11, 14 in P. aeruginosa, 22 ferritin, 1 FhuA-ferrichrome structure, effect of, 9 ﬁmbriae, see type IV pili FimS, 156 FimX, 160, 170–171 ﬂagellins, 39 biosynthesis genes, 39 ﬂuorescent Pseudomonas, 4–5 ﬂuorine, regiospeciﬁc hydroxylation of, 270–273 FpvAI-III, 4 FpvA-Pvd complex, 10, 16 FpvA-Pvd-Ga complexes, 12, 17 Fur protein, 21 G gallium, 3

Index GBrowse, 351–354 DNA motifs search, 355 subcellular localization predictions, 355–357 GC content, 37 genetic adaptation mechanisms, of bacterial species, 198–203 genome diversity of accessory genome, 43–49 of core genome, 36–42 of P. aeruginosa, 49–52 of phenotype, 52–55 genomic islands (GEI), 219–220 global mRNA expression proﬁles, 53 glycerophospholipid, structure of, 70 glycine, 252 glycoprotein mucin, 170 glycosylation island, 39 gram negative bacteria ferric-siderophore uptake in, 17 formation mechanism of, 14 H haptoglobin, 3 HasB machinery, 19 heat-labile hemolysin, 73 heme acquisitions, 18–19 hemolytic phospholipase (PlcH) effect on endothelial lining, 80 objective of, 77 Pi-starvation inducible expression of, 77–78 SM synthase activity of, 89 hemopexin, 3 Hemophilus inﬂuenzae, 21 hemophore, 18 herbicide degradation, 211–215 hidden Markov models, 84 histidine residue (H319), 155 human airway epithelial cells, see A549 cells human vascular endothelial cells HUVEC, see human vascular endothelial cells 15-hydroxyeicosatetraenoic acid (15-HETE), 79 I Idiomarina loihiensis, 206 IncP1-beta group, 203 indigo, 259, 318 indinavir, 319

Index indirubin, 260 individual environmental stress, effect of, 108 indole, regiospeciﬁc activity of, 259–261 infections, hospital acquired, 55–56 iron uptake mechanisms via ferric siderophore transport by OMT, 12–16 via siderophores ornibactins, 6 outer membrane transporters, 7–12 pyochelin, 6 pyoverdine, 4–5 Pvd-Fe uptake mechanism, 16–18 iron, 1, 3 chelation of, 5 extracellular, 1 free, in body, 2 intracellular, 1 transport regulation, 21–23 uptake, in Gram-negative bacteria, 2, 21 iron-free dicitrate, 10 ISlacZ/hah, 122–123 ISphoA/hah, 122–123 K Krebs cycle, 4 L L-2,4-diaminobutyrate, 5 lactoferrins, see transferrin Listeria monocytogenes, 69 M M. xanthus pilT mutants, 146 methoxyaromatics, regiospeciﬁc hydroxylation of, 262 methoxyhydroquinone, 262 methyl aromatics, regiospeciﬁc hydroxylation of, 264–268 methyl-accepting chemotaxis proteins (MCPs), 157 MexAB-OprM expression, 55 mobile gene pool, 190 mobile genetic elements, 43 muco-purulent airway liquids, 83 murine toxin, 74 mutants, by functional category, 133–134 N N -acylhom*oserine lactones (AHL), 57

365 nah gene clusters, 209 naphthalene, regiospeciﬁc hydroxylation of, 270–273 2-naphthol, synthesis, 273–274 NDO amino acids, at sites of, 314–317 enzymology of, 304–305 substrate speciﬁcity of, 310, 314 Neisseria gonorrhoeae, 35 Neisserial PilC proteins, 152 nitroaromatics degradation of, 215–218 regiospeciﬁc hydroxylation of, 268–270 nitrobenzene, 258 nitrohydroquinone, 239 N -methylated phenylalanine, 40 nonribosomal peptide synthetases (NRPSs), 5 O OMT-siderophore-iron complex, formation of, 14–15 open reading frames (ORFs), 45, 100 ornibactins, 6 outer membrane transporter (OMT), 3 ligand transport by, 15–16 P PA4525, 40 PAO1 microarrays, 36 PAO1 sequence coordinates, for high sequence diversity, 38 patatins, 76 pathogenic bacteria Pseudomonas, 2 Pseudomonas aeruginosa, 2, 4–7, 35 pathogenicity islands (PAI), 219 PCB congeners, 316 pchDEFG genes, 6 PCR ampliﬁcation, 103 PeerGAD system, 344 perchloroethylene (PCE), degradation of, 274–276 perfringolysin O (PFO), 73 phage transduction, 201 Phe352 replacement, effect of, 314 phenol synthesis, 273–274 phospholipase C (PLC), 70–74 activity of, 70 in prokaryotic pathogenesis, role of, 73 phospholipases A (PLAs), 74

366 phospholipases D (PLDs), 74 Arabidopsis, 74 eukaryotic, role of, 74 phospholipases, classes of, 69, 71 phospholipid phosphatidylserine (PS), 81 phuSTUVW, 18 pilin genes, 40 PirR–PirS system, 22 pKLK106, 47–48, 58 PlcHR1 heterodimer, 82 plug, 7, 9 polyaromatic pathways, 208–211 polymerase priming, 103 polymorphic proteins, 39 programmed cell death, 79 protein tyrosine phosphatase, 269 protocatechuate, 244 Pseudobactin B10-Fe(III), 5 PseudoCAP method, 343 Pseudomonas, 2 ﬂuorescent, 4–5 iron uptake in, 3 Pseudomonas aeruginosa, 35 binding capacity of, 62 bioﬁlms of, 172–174 catabolic pathways in, 191–194 Chp chemosensory system, role, 157 effector proteins of, 40 evolution of, linked to DNA plasmid, 59 genes for lung infection, 107, 110–111 for polymorphonuclear cells, 112 genome analysis committee, 343 genome content of, effect of, 100 genome database, 341, 349–350 genome island of, 45 genome project web site, 84, 342 hemolytic phospholipase (PlcH) of, 77 lipopolysaccharide (LPS), 41 mutant collection, composition of, 128 mutant distribution in, 128–129 mutant identity of, 130–132 O-antigens of, 41 PLA2 (EXOU) of, 86 PlcA, 82 PlcB, 82 PlcN, 81 PLCs of, 76 PLDs of, 84–86 popular genes in, 135 transformation of tfp in, 161–162

Index in septicemia, 80 STM technique, 100 toluene monooxygenases from, 237 transposon mutant, construction of, 122–127 transposon insertion in, 122 twitching motility in, 159, 166–167 Pseudomonas Community Annotation Project, 24, 345–349 Pseudomonas putida, 47 Pvd G4R-Ga(III), 5 pvdA gene, 6 Pvd-Fe, binding of, 16 Pvd-Ga(III), 5 PvdH, 5 pyochelin, 4, 6 pyoverdine, 37, 39, 60 Q quinolobactin, 4 R Ralstonia eutropha JMP134 (pJP4), 204 Ralstonia metallidurans CH34 chromosome, 45–46 rapid cell death, 40 replacement island phenomenon, 41 hotspots for, 45 RGD (Asp-Gly-Glu) motif, 80 Rhodococcus erythropolis BD2, 298 Rieske non-heme iron dioxygenases, 287 Rieske-type [2Fe-2S] ferredoxin, 239 RpoN-dependent genes, 155 Ruminococcus albus, 139 S Safe Drinking Water Act, 275 salicylic acid, 4 Salmonella enterica, 36 saturation mutagenesis, 254–255, 269 Serratia marcescens, 9, 18 siderophore outer membrane transporters, 7–12 binding properties of, 9–12 structure of, 7–9 siderophore pyoverdine (Pvd), 3 siderophores, 2 siderotyping, 5 signature-tagged mutagenesis (STM), 100 and chip analysis, 113–114 description of, 103

Index Drosphilia screening, 109 in vivo, of P. aeruginosa, 104 mutants analysis and distribution of, 104–106 for lung infection, 107, 110–111 for polymorphonuclear cells, 112 Sinorhizobium meliloti, 158 SMase activity, 70 SNP genotype, 50 SpeI macrorestriction fragment, 43 stab assay, 167 Streptococcus sanguis, 140 superintegrons, 199 T T4MO G103L regiospeciﬁc mutation, 264 TAT secretory system, 82 terephthalate dioxygenase, 300 tetrachloroethylene, degradation of, 274–276 tfp, see type IV pili thawed glycerol stocks, 126 time-lapse video microscopy, 168 TmoA G103L, 247 toll-like receptor (TLR) 5, 107 toluene degradation, 204–208 toluene monooxygenases, 237, 239 active site residues of, 247, 253 activity control of, 255–259 hydroxylations, 241–244, 251 regiospeciﬁc oxidation of, 257 ToMO-equivalent alpha subunit residues, 240 TonB box, 15 TonB machinery, 12, 16–17, 19 TonB protein, 15 TonB–ExbB–ExbD complex, 3 structure and stoichiometry of, 12–13

367 TpMO, 239 transferring, 1, 3–4 trichloroethylene contamination, bioremediation of, 319–320 type IV pili, 139 colonization, in Pseudomonas species, 163–166 deﬁnition of, 140 extracellular, structure of, 143–144 infection, in Pseudomonas species, 163–166 in other Pseudomonas species, 160–161 major subunit of, 141–143 Neisseria gonorrhoeae, 144 Pseudomonas proteins, in biogenesis and function of, 147–148 PilU, role of, 151 retraction of, 144–146 transformation of, in Pseudomonas aeruginosa, 161–162 Vfr, effect of, 158 V vaccina virus protein, 84 Vfr, 158 vgr genes, 86 virulence determinants, 76 Vogel-Bonner medium, 54 W WormBase, 344 Y YAC hybridizations, 43 Yersinia pestis, 74

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