Pseudomonas

PseudomonasEditedby Juan-Luis Ramos, CSIC, Granada, Spain

Volume I: Genomics, Life Style and Molecular ArchitectureVolume 2: Virulence and Gene RegulationVolume 3: Biosynthesis of Macromolecules and Molecular Metabolism

Pseudomonas

Volume 1 Genomics, Life Style and Molecular Architecture

Edited by

Juan-Luis Ramos CSIC Granada. Spain

Springer Science+Business Media, LLC

Library of Congress Cataloging-in-Publication Data

Pseudomonas / edited by Juan-Luis Ramos. p. cm.

Includes bibliographical references and index. ISBN 978-1-4613-4788-0 ISBN 978-1-4419-9086-0 (eBook) DOI 10.1007/978-1-4419-9086-0 1. Psesudomonas. 1. Ramos, Juan-Luis, 1956-

QR82.P78P772 2004 579.3'32-dc22

ISBN 978-1-4613-4788-0

2004043811

Aiso available as part of an indivisible set of ali 3 volumes 0-306-48378-5

© 2004 Springer Science+Business Media New York Originally published by Kluwer Academic/Plenum Publishers in 2004 Softcover reprint of the hardcover lst edition 2004

10 9 8 7 6 5 4 3 2 l

A C.1.P. record for this book is available from the Library of Congress.

Ali 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.

PREFACE

The time was ripe for a series of books on Pseudomonas to see the light.About 18 years have passed since Jack Sokatch first published his outstandingThe Biology ofPseudomonas back in 1986. This was followed by two bookspublished by the ASM that contained the presentations of the Pseudomonasmeetings held in Chicago in 1989 and Trieste in 1991. The earlier volume wasedited by Simon Silver, AI Chakrabarty, Barbara Iglewski and Sam Kaplan,and the later by Enrica Galli , Simon Silver and Bernard Witholt.

The present series of books was conceived at a meeting with Kluwerstaff members in August 2002 during the XI IUMS conference in Paris . In lessthan a year a group of outstanding scientists in the field, after devoting muchof their valuable time, managed to complete their manuscripts for the threevolumes of the series. It has been an honor for me to work with them .

The review proces s has also been of great importance to ensure the highstandard of each chapter. Renowned scientists have participated in the review,correction and editing of the chapters. Their assistance is immensely appreciated.I would like to express my most sincere appreciation to:

Daniel ArpConcepcion AzconGiovanni BertoniWilbert BitterRafael BlascoEmanuelle BouveretVolkmar BraunLori BurrowsAntonio Caba lleroMiguel CamaraJosep CasadesusAI ChakrabartyAlan CollmerJane Colmer-HamoodWilliam Costerton

John CronanDavid D' ArgenioFernando de la CruzVictor de LorenzoEduardo DiazManuel Espinosa, Sr.Manuel Espinosa-UrgelKensuke FurukawaBernardo GonzalezDieter HaasAbdul HamoodRobert E. HancockKlaus HantkeHermann HeipieperTimothy R. Hoover

Yoshifumi ItohJorge LalucatHiltrud LenkeBen LugtenbergSilvia MarquesVitor Martins do

SantosLazaro MolinaConrado Moreno

VivianJesus MurilloHideo NakanoPer NygaardAlejandro Pefialosa-

Vazquez

v

vi

Jose Perez-MartinDietrnar PieperKeith PooleCayo RamosM. Isabel Ramos­

GonzalezRafael RivillaPablo Rodriguez­

PalenzuelaFernando Rojo

Ramon RosselloRaquel RuizEduardo SanteroPedro SantosAna SeguraAurelio SerranoVictoria ShinglerKornelia SmallaAndreas StolzMasao Tsuda

Preface

David UsseryChristian van

DeldenVittorio VenturiChristian WeinelPaul WilliamsPeter WilliamsWalter Zumft

There has been growing interest in pseudomonads and a particular urgeto understand the biology underlying the complex metabolism of theseubiquitous microbes. These bacteria are capable of colonizing a wide rangeof niches, including the soil, the plant rhizosphere and phylosphere, andanimal tissues; more recently they have attracted attention because of theircapacity to form biofilms, a characteristic with potentially important medicaland environmental implications .

There has been an explosion of vital new information about the genusPseudomonas. A rapid search for articles containing the word "Pseudomonas"in the title in the last 10 years produces more than 6,000 articles!Consequently, we cannot cover all possible topics relevant to this genus in justthree volumes, although our intention has been to be as thorough as possible.To organize the books, various topics have been grouped under a commonheading, although this has some limitations since certain chapters may seemequally appropriate under different headings.

In Volume I, the first chapter provides clues to the definition of the truePseudomonas genus and gives a historical perspective of research to date. Theinsights in this chapter will undoubtedly help us to ascribe potential new iso­lates to this genus. Several recent advances in genomics , plasmids and phagebiology, as well as a wealth of useful tools, are grouped under the heading"Genomics." These chapters reveal the basis for diversity within the genusPseudomonas at the molecular level, as well as key structural features. Thissection also describes a wide range of molecular tools to study gene expres­sion and cloning in Pseudomonas, which have also been of great use in theanalysis of other organisms. These chapters are therefore of potential interestto colleagues working in other genera in addition to Pseudomonas.

The section "Life styles" comprises a series of fascinating chapters thatexplain where pseudomonads can be found, their role in a particular niche,and how they interact with other members of the ecological community.Volume I concludes with a series of chapters on the architecture ofPseudomonas which explain the structure of the cell surfaces, their ability to

Preface vii

sense nutrients, and the use of the flagellar system of move toward chemoat­tractants or away from chemorepellent compounds. The molecular basis ofcell architecture is critical to understand life styles, such as adhesion andsecretion or extrusion of toxic substances including antibiotics and solvents.In all, I believe that the chapters included in this volume will by themselvesconstitute a book of general interest for microbiologists working on thebiology of Pseudomonas.

Volume 2 deals with two important issues : virulence and gene regula­tion. The chapters under the heading "Virulence" deal with well-establishedvirulence factors which make Pseudomonas aeruginosa, an opportunisticpathogen, and Pseudomonas syringae, a plant pathogen. Some issues on viru­lence were dealt with in Volume 1 under the heading "Life styles"; in Volume 2,the aim is to provide insights into the molecular mechanisms of virulence. Inphytopathogens , their life style overlaps with some beneficial properties ofnon-pathogenic soil bacteria, but what actually makes them different is criticalto our understanding of the biology of this group of Pseudomonas.

An astonishing finding from the analysis of the genomes sequenced todate is the wide battery of regulatory genes found in Pseudomonas. Also sur­prising is the wide range ofalternative sigma factors encoded by these bacteria.Many of these factors belong to the ECF family and are involved in iron acqui­sition. The regulators of Pseudomonas can be placed into two broad groups,namely those that belong to the two-component class, in which a sensor protein"senses" the signal and triggers the actual regulator(s), and those of a secondgroup in which sensing and regulatory functions are located in a singlepolypeptide. Volume 2 contains the most exhaustive and up-to-date compilationavailable of (T7o-dependent promoters in the genus Pseudomonas.

Volume 3 comprises the sections "Macromolecules," "Alternative respi­ratory substrates ," "Catabolism and biotransformations" and "Secondarymetabolism." The chapters in the section titled "Macromolecules" reviewsome of the most complex metabolic pathways in the bacterial kingdom, anddeal with the biosynthesis of LPS, fatty acids, alginate, rhamnolipids, cycliclipopeptides, heme groups and vitamin B12.

Pseudomonads are well known for their extreme nutritional versatilityand their ability to produce added-value products from simple, cheap carbonand nitrogen sources. The chapters in Volume 3 deal with the metabolism ofcertain amino acids and other natural compounds such as alkanes, as well assome xenobiotics and recalcitrant compounds such as aromatics. Some of theenzymatic properties of pseudomonads have been exploited to produce added­value products , which makes non-pathogenic Pseudomonas strains of greatinterest for certain industrial processes . This, in addition to the ability ofcertain strains to biosynthesize secondary products and influence the life styleof certain strains, also makes them of interest for the industry.

viii Preface

In recent years, it has become clearer that pseudomonads are able tocolonize anaerobic niches. In these niches, many strains are able to respirealternative electron acceptors , and the process of denitrification is indeed wellunderstood in some strains of the genus Pseudomonas. More recently, a strainable to respire nitroorganic compounds has been reported, and recent studieshave revealed that this property may be more widespread than was initiallythought.

There remains no doubt in my mind that in the next 10 years we willsee myriad articles dealing with Pseudomonas and shedding further light onour current understanding of the broad group of bacteria in the genusPseudomonas as it is now defined. However, I am confident that this series ofbooks has assembled a significant part of the current knowledge ofPseudomonas in the best possible manner. More importantly, I hope it willopen new lines ofresearch that will lead to a better understanding ofthis groupof saprophytic microorganisms.

Last but not least, I would like to acknowledge the enthusiasm andassistance ofCarmen Lorente in the compilation of the three volumes that con­stitute the Pseudomonas series.

CONTENTS

List of Contributors Xlll

Taxonomy

I. Taxonomy of Pseudomonads: Experimental Approaches 3Norberto 1. Palleroni and Edward R.B. Moore

Genomics

2. The Genome of Pseudomonas aeruginosa .47Bridget R. Kulasekara and Stephen Lory

3. Genomic Features of Pseudomonas putida Strain KT2440 77Vitor A.P. Martins dos Santos, Kenneth N. Timmis ,Burkhard Tummler and Christian Weinel

4. The Genome of Pseudomonas syringae Tomato DC3000and Functional Genomic Studies to better UnderstandPlant Pathogenesis 113Yashitola Jamir, Xiaoyan Tang and James R. Alfano

5. Comparative Genomics of Four Pseudomonas Species 139Lars Juhl Jensen, Marie Skovgaard, Thomas Sicheritz-Ponten,Niclas Tue Hansen, Helle Johansson, Merete Kjer Jorgensen,Kristoffer Kiil, Peter F. Hallin and David Ussery

6. Genomics of Catabolic Plasmids 165Peter A. Williams, Rheinallt M. Jones and Gerben Zylstra

7. Plasmids of the Genus Pseudomonas 197Christopher M. Thomas and Anthony S. Haines

8. Phages of Pseudomonas 233Tetsuya Hayashi and Keisuke Nakayama

ix

x Contents

9. Transposition and Other Mutational Processesin Pseudomonas 261Maia Kivisaar

10. Molecular Tools for Genetic Analysis of Pseudomonads 317Herbert P. Schweizer and Victor de Lorenzo

11. In Vivo Gene Expression: The IVET System 351Manuel Espinosa-Urgel and Maria Isabel Ramos-Gonzalez

Life Styles

12. Pseudomonas in the Soil Environment 369Jan Serensen and Ole Nybroe

13. Life in the Rhizosphere .403Ben J.1. Lugtenberg and Guido V. Bloemberg

14. Life in the Phyllosphere .431Mark 1. Bailey

15. Life as a Biocontrol Pseudomonad .457Yvan Moenne-Loccoz and Genevieve Defago

16. The Pathogenic Lifestyle of Pseudomonas aeruginosain Model Systems of Virulence .477David A. D' Argenio

17. Pseudomonas aeruginosa Interactions with Host Cells 505Gerald B. Pier and Joanna B. Goldberg

18. The Biofilm Lifestyle of Pseudomonads .547Tim Tolker-Nielsen and Seren Molin

CellArchitecture

19. The Outer Membranes of Pseudomonads 575Sandeep Tamber and Robert E.W. Hancock

20. The Tol-OprL System of Pseudomonas 603Jose 1. Rodriguez-Herva and Maria A. Llamas

21. Efflux Pumps 635Keith Poole

22. The Flagellar System of Pseudomonas aeruginosa 675Nandini Dasgupta, Shiwani K. Arora and Reuben Ramphal

Contents xi

23. Mechanisms of Adhesion by Pseudomonads 699Shannon M. Hinsaand George A. O'Toole

24. Fimbrial Genes in Pseudomonas aeruginosaand Pseudomonas putida 721Alain Filloux, Sophie de Bentzmann, Marianne Aurouze,Andree Lazdunski and Isabelle Vallet

25. Protein Secretion Mechanisms in Pseudomonas 749Alain Filloux, Sophie Bleves, Petervan Ulsen and Jan Tommassen

26. Chemotaxis in Pseudomonads 793Rebecca E. Parales, Abel Ferrandez and Caroline S. Harwood

Index 817

LIST OF CONTRIBUTORS

James R. AlfanoPlant Science Initiative and Department of Plant Pathology, University ofNebraska, Lincoln, NE 68588-0660, USA

Shiwani K. AroraUniversity of Florida, Gainesville, Florida, USA

Marianne AurouzeCentre National de la Recherche Scientifique, Institut de Biologie Structuraleet Microbiologie, Laboratoire d'Ingenierie des Systemes Macrornoleculaires,Marseille, France

Mark J. BaileyNatural Environment Research Council, Molecular Microbial Ecology Group ,CEH-Oxford, Virology and Environmental Microbiology, Mansfield Road,Oxford OXI 3SR, UK

Sophie BlevesCentre National de la Recherche Scientifique, Institut de Biologie Structuraleet Microbiologie, Laboratoire d'Ingenierie des Systemes Macromoleculaires,Marseille , France

Guido V. BloembergLeiden University, Institute of Biology, Clusius Laboratory, Wassenaarseweg64, 2333 AL Leiden, The Netherlands

David A. D' ArgenioDepartment of Microbiology, University of Washington , HSB K140, Box357710,1959 Pacific St. N.E., Seattle , WA 981950-7710, USA

Sophie de BentzmannCentre National de la Recherche Scientifique, Institut de Biologie Structuraleet Microbiologie, Laboratoire d'Ingenierie des Systemes Macromoleculaires,Marseille , France

xiii

xiv List of Contributors

Nandini DasguptaUniversity of Florida, Gainesville, Florida, USA

Genevieve DefagoPhytopathology Group, Institute of Plant Sciences, Swiss Federal Institute ofTechnology (ETH), CH-80n Zurich, Switzerland

Victor de LorenzoDepartamento de Microbiologia, Centro Nacional de Biotecnologia,Universidad Aut6noma de Madrid, Cantoblanco 28049 Madrid, Spain

Vitor A. P. Martins dos SantosDivision Microbiology, Gesellschaft fiir Biotechnologische Forschung,Braunschweig, Germany

Manuel Espinosa-UrgelDepartment of Biochemistry and Molecular and Cell Biology of Plants,Estaci6n Experimental del Zaidin, CSIC, Granada 18008, Spain

Abel FerrandezDSM Nutritional Products, Basel, Switzerland

Alain FillouxCentre National de la Recherche Scientifique, Institut de Biologie Structuraleet Microbiologie, Laboratoire d'Ingenierie des Systernes Macromoleculaires,Marseille, France

Joanna B. GoldbergDepartment of Microbiology, University of Virginia Health Sciences Center,Charlottesville, VA 22908, USA

Anthony S. HainesSchool of Biosciences , University of Birmingham, Edgbaston, BirminghamBl5 2TT, UK

Peter F. HallinCenter for Biological Sequence Analysis, BioCentrum-DTU, Building 208,The Technical University of Denmark, DK-2800 Lyngby, Denmark

Robert E.W. HancockDepartment of Microbiology and Immunology, University of BritishColumbia , #300, 6174 University Boulevard, Vancouver, British Columbia,V6S lZl, Canada

Niclas The HansenCenter for Biological Sequence Analysis, BioCentrum-DTU, Building 208,The Technical University of Denmark, DK-2800 Lyngby, Denmark

List of Contributors xv

Caroline S. HarwoodDepartment of Microbiology and Center for Biocatalysis and Bioprocessing,The University of Iowa, Iowa City, lA, USA

Tetsuya HayashiDepartment of Microbiology, Miyazaki Medical College, 5200 Kiyotake,Miyazaki 889-1692, Japan

Shannon M. HinsaDepartment of Microbiology and Immunology, Dartmouth Medical School,Hanover, NH 03755, USA

Yashitola JamirPlant Science Initiative and Department of Plant Pathology, University ofNebraska, Lincoln, NE 68588-0660, USA

Lars Juhl JensenCenter for Biological Sequence Analysis, BioCentrum-DTU, Building 208,The Technical University of Denmark, DK-2800 Lyngby, DenmarkStructural and Computational Biology Unit, European Molecular Biologylaboratory, Meyerhofstrasse 1, D-691l7 Heidelberg, GermanyMax-Delbriick-Centre fiir Molecular Medicine, Robert-Rossle-Strasse 10,D-13092 Berlin, Germany

Helle JohanssonCenter for Biological Sequence Analysis, BioCentrum-DTU, Building 208,The Technical University of Denmark, DK-2800 Lyngby, Denmark

Rheinallt M. JonesSchool of Biological Sciences, University of Wales, Bangor, UK

Merete Kjrer JorgensenCenter for Biological Sequence Analysis, BioCentrum-DTU, Building 208,The Technical University of Denmark, DK-2800 Lyngby, Denmark

Kristoffer KiilCenter for Biological Sequence Analysis, BioCentrum-DTU, Building 208,The Technical University of Denmark, DK-2800 Lyngby, Denmark

Maia KivisaarInstitute of Molecular and Cell Biology, Tartu University and EstonianBiocentre, 23 Riia Street, 51010 Tartu, Estonia

Bridget R. KulasekaraDepartment of Microbiology and Molecular Genetics, Harvard MedicalSchool, Boston, MA 02115, USA

xvi List of Contributors

Andree LazdunskiCentre National de la Recherche Scientifique, Institut de Biologie Structuraleet Microbiologie, Laboratoire d'Ingenierie des Systemes Macromoleculaires,Marseille, France

Maria A. LlamasDepartment of Medical Microbiology and Infection Prevention, VU MedicalCenter, Van der Boechorststraat 7, 1081 BT, Amsterdam , The Netherlands

Stephen LoryDepartment of Microbiology and Molecular Genetics , Harvard MedicalSchool, Boston, MA 02115, USA

Ben J.J. LugtenbergLeiden University, Institute of Biology, Clusius Laboratory, Wassenaarseweg64, 2333 AL Leiden, The Netherlands

Yvan Moenne-LoccozUMR CNRS 5557 Ecologie Microbienne, Universite Claude Bernard (Lyon I),F-69622 Villeurbanne Cedex, France

Seren MolinMolecular Microbial Ecology Group, BioCentrum, Technical University ofDenmark, Denmark

Edward R.B. MooreEnvironmental Sciences Group, Macaulay Institute , Craigiebuckler, AberdeenAB 158QH, Scotland, UK

Keisuke NakayamaDepartment of Microbiology, Miyazaki Medical College, 5200 Kiyotake,Miyazaki 889-1692, Japan

Ole NybroeSection of Genetics and Microbiology, Department of Ecology, RoyalVeterinary and Agricultural University, Thorvaldsensvej 40, DK-1871Frederiksberg C, Denmark

George A. O'TooleDepartment of Microbiology and Immunology, Dartmouth Medical School,Hanover, NH 03755, USA

Norberto J. PalleroniDepartment of Biochemistry and Microbiology, Rutgers University, NewBrunswick 08901-8525 , NJ, USA

List of Contributors xvii

Rebecca E. ParalesSection of Microbiology, University of Californ ia, Davis, CA, USA

Gerald B. PierChanning Laboratory, Department of Medicine , Brigham and Women'sHospital, Harvard Medical School, Boston, MA 02115, USA

Keith PooleDepartment of Microbiology and Immunology, Queen's University, Kingston,ON, Canada K7L 3N6

Maria Isabel Ramos-GonzalezDepartment of Biochemistry and Molecular and Cell Biology of Plants,Estacion Experimental del Zaidin, CSIC, Granada 18008, Spain

Reuben RamphalUniversity of Florida, Gainesville , Florida, USA

Jose J. Rodriguez-HervaDepartment of Molecular Microbiology, Utrecht University, Padualaan 8,3584 CH Utrecht, The Netherlands

Herbert P. SchweizerDepartment of Microbiology, Immunology and Pathology, Colorado StateUniversity, Fort Collins, CO 80523-1682, USA

Thomas Sicheritz-PontenCenter for Biological Sequence Analysis, BioCentrum-DTU, Building 208,The Technical University of Denmark, DK-2800 Lyngby, DenmarkDepartment of Medicinal Chemistry, Division of Pharmacognosy BMC,Husargatan 3, Uppsala, Sweden

Marie SkovgaardCenter for Biological Sequence Analysis, BioCentrum-DTU, Building 208,The Technical University of Denmark, DK-2800 Lyngby, Denmark

Jan SorensenSection of Genetics and Microbiology, Department of Ecology, RoyalVeterinary and Agricultural University, Thorvaldsensvej 40, DK-1871Frederiksberg C, Denmark

Sandeep TamberDepartment of Microbiology and Immunology, University of BritishColumbia, #300, 6174 University Boulevard, Vancouver, British Columbia,V6S IZI, Canada

xviii List of Contributors

Xiaoyan TangDepartment of Plant Pathology, Kansas State University, Manhattan, KS66506-5502, USA

Christopher M. ThomasSchool of Biosciences, University of Birmingham, Edgbaston, BirminghamB15 2TT, UK

Kenneth N. TimmisDivision Microbiology, Gesellschaft fur Biotechnologische Forschung,Braunschweig, Germany, and Department of Biological Sciences, Universityof Essex, Colchester, UK

Tim Tolker-NielsenMolecular Microbial Ecology Group, BioCentrum, Technical University ofDenmark, Denmark

Jan TommassenDepartment of Molecular Microbiology and Institute of Biomembranes,Utrecht University, Utrecht, The Netherlands

Burkhard TummlerKlinische Forschergruppe, Medizinische Hochschule Hannover, Germany

Peter van VlsenDepartment of Molecular Microbiology and Institute of Biomembranes,Utrecht University, Utrecht, The Netherlands

David UsseryCenter for Biological Sequence Analysis, BioCentrum-DTU, Building 208,The Technical University of Denmark, DK-2800 Lyngby, Denmark

Isabelle ValletCentre National de la Recherche Scientifique, Institut de Biologie Structuraleet Microbiologie, Laboratoire d'Ingenierie des Systemes Macromoleculaires,Marseille, France

Christian WeinelKlinische Forschergruppe, Medizinische Hochschule Hannover, Germany

Peter A. WilliamsSchool of Biological Sciences, University of Wales, Bangor, UK

Gerben ZylstraBiotechnology Center for Agriculture and the Environment, RutgersUniversity, New Brunswick, New Jersey