Pseudomonas

BIOTECHNOLOGY HANDBOOKS Series Editors: Tony Atkinson and Roger F. Sherwood

Duramed Europe Ltd.

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Volume 10 PSEUDOMONAS Edited by Thomas C. Montie

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Pseudomonas

Edited by

Thomas C. Montie University of Tennessee Knoxville, Tennessee

Springer Science+ Business Media, LLC

Library of Congress Cataloging in Publication Data

Pseudomonas / edited by Thomas C. Montie. p. cm—(Biotechnology handbooks; v. 10).

Includes bibliographical references and index.

1. Pseudomonas. 2. Pseudomonas—Biotechnology. 3. Molecular microbiology. I. Montie, Thomas C. II. Series. QR82.P78P77 1998 98-41288 579.3'32—dc21 CIP

Cover: Electromicrograph of Pseudomonas aeruginosa showing polar pili and flagellum as surface structures. (Courtesy of Thomas C. Montie)

ISBN 978-1-4899-0122-4 ISBN 978-1-4899-0120-0 (eBook) DOI 10.1007/978-1-4899-0120-0

© Springer Science+Business Media New York 1998 Originally published by Plenum Press New York in 1998 Softcover reprint of the hardcover 1st edition 1998

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All rights reserved

No part of this book 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

Contributors

Robert E. W. Hancock • Department of Microbiology and Immunol­ogy, University of British Columbia, Vancouver V6T lZ4, British Columbia

Toshimitsu Hoshino • Mitsubishi Kasei Institute of Life Sciences, Machida-Shi, Tokyo 194, Japan

Sachiye Inouye • Department of Biochemistry, Yamaguchi U niver­sity School of Medicine, Ube, Yamaguchi 755-8505, Japan

Estelle J. McGroarty • Department of Biochemistry, Michigan State University, East Lansing, Michigan 48824

Jean-Marie Meyer • Laboratoire de Microbiologie et de Genetique, Unite de Recherche Associee au Centre National de la Recherche Scientifique No. 1481, Universite Louis-Pasteur, 67000 Strasbourg, France

Thomas C. Montie • Department of Microbiology, The University of Tennessee, Knoxville, Tennessee 37996-0845

Paul V. Phibbs, Jr. • Department of Microbiology and Immunology, East Carolina University School of Medicine, Greenville, North Car­olina 27858

Holly C. Pinkart • U.S. Environmental Protection Agency, Micro­bial Ecology Branch, Gulf Breeze, Florida 32514

Andrew E. Sage • World Wide Microbiology Group, Millipore Corp., Bedford, Massachusetts 01730

Herbert P. Schweizer • Department of Microbiology, Colorado State University College of Veterinary Medicine, Fort Collins, Colorado 80523

Alain Stintzi • Laboratoire de Microbiologie et de Genetique, Unite de Recherche Associee au Centre National de la Recherche Scien­tifique No. 1481, Universite Louis-Pasteur, 67000 Strasbourg, France

Louise M. Temple • Department of Biology, Drew University, Mad­ison, New Jersey 07940

v

vi CONTRIBUTORS

David C. White • Department of Microbiology and Center for Envi­ronmental Biotechnology, University of Tennessee, Knoxville, Ten­nessee 37932

Bernard WithoIt • Institute of Biotechnology, ETH Honggerberg, HPT, CH-8093 Zurich, Switzerland

Elizabeth A. Worobec • Department of Microbiology, University of Manitoba, Winnipeg R3T 2N2, Manitoba

Marcel G. WubboIts • DSM Research, 6160 MD Geleen, The Netherlands

Preface

The genus Pseudomonas represents a large group of medically and envi­ronmentally important bacteria. Interest in these bacteria is reflected in the extensive number of publications devoted to original research, re­views, and books on this subject. In this volume selected areas of Pseu­domonas research are presented in depth by persons who have been active in their fields over many years. The extensive reviews presented are an effort to provide a balanced perspective in a number of areas not readily available in the current literature. In the style of the previous Biotechnology Handbooks most of these topics have not been reviewed at all, and several are also presented from a new direction. For example, in addition to structural and compositional aspects, the chapter on lipids provides shifts in lipid parameters that result from environmental changes. This information will be invaluable to a cross section of Pseu­domonas researchers in pathogenesis and bioremediation.

The chapters presented include basic aspects of plasmid biology and carbohydrate metabolism and regulation. A major emphasis is placed on the Pseudomonas aeruginosa cell surface. Chapters cover lipo­polysaccharide, capsular polysaccharide and alginate, the outer mem­brane, transport systems, and the flagellum. Uptake of iron is also neces­sarily an important portion of the chapter on iron metabolism. Although the emphasis in this text is on Pseudomonas aeruginosa, many chapters include detailed and comparative discussions of other important species, such as Burkholderia cepacia (formerly Pseudomonas cepacia) and Pseudo­monas putida. A final chapter on selected industrial biotransformations reveals the tremendous catalytic properties and potential of this group of organisms.

This volume should be of great interest to researchers in molecular biology and biotechnology in industry, academia and various research institutes, and as a resource for graduate students and advanced under­graduates.

vii

Contents

Chapter 1

Plasmids ................................................. 1

Sachiye Inouye

1. Introduction ........................................... 1 2. General Properties of Plasmid DNA from Pseudomonas ..... 1

2.1. Replication and Conjugation .............. , . . . . . .. . . 1 2.2. Isolation of Plasmid DNA .......................... 2

3. Antibiotic-Resistant Plasmids (R-Plasmids) ................. 2 3.1. RPl, RP4, RK2 .................................... 3 3.2. pMGl ............................................ 4 3.3. RSFIOIO and Rlb679 .............................. 4 3.4. pMS350 .......................................... 4 3.5. pSa............................................... 6

4. Resistance to Metal Ions, Pesticides, and UV Light ......... 6 4.1. pMRl, pMERPH .................................. 6 4.2. pPT23D, pPSRI ................................... 7 4.3. pCMSI ........................................... 8 4.4 pMG2............................................. 8

5. Plasmids for Biosynthesis ................................ 9 5.1. Indole-3-Acetic Acid (IAA) Production .............. 9 5.2. Ethylene-Forming Enzyme. . . . . . . . . . . . . . . . . . . . . . . . . . 9 5.3. Coronatine Production. .. . . .. . . . . . . . . . . .. . . .. . . . . .. 9 5.4. Syringolide Production............................. 10 5.5. Malonate Assimilation.. . . .. . ... . . .. . . .. . . .. . . . . .. . . 10

6. Degradative Plasmids ................................... 10 6.1. CAM............................................. 11 6.2. OCT............................................. 11 6.3. TOL(pWWO)...................................... 13 6.4. NAH(NAH7) and SAL(SALl) ...................... 16 6.5. pHMT112 ........................................ 17

7. Cloning Vectors ........................................ 17

ix

x CONTENTS

7.1. Incompatibility Group P4/Q ........................ 18 7.2. Incompatibility Group PI .......................... 19 7.3. Incompatibility Group W ........................... 19

8. Conclusions and Perspectives ............................ 20 References ............................................. 21

Chapter 2

Carbohydrate Catabolism in Pseudomonas aeruginosa

Louise M. Temple, Andrew E. Sage, Herbert P. Schweizer, and Paul V. Phibbs, Jr.

35

1. Introduction .......................................... 35 2. Glucose Utilization via Phosphorylation. . . .. . . ... . .. .. . . . 41

2.1. Transport........................................ 41 2.2. Phosphorylation .................................. 44

3. Oxidative Pathway of Glucose Utilization ................ 45 4. Fructose Utilization. . . . .. . . .. . . .. . . .. . . .. . . . . .. . . .. . . . . 46 5. Mannitol Utilization ................................... 47 6. Glycerol and Glycerol 3-Phosphate Utilization.. . . .. . . . . .. 48

6.1. Glycerol and Glycerol-P Uptake. . .. . . .... . . .. . . . . .. 49 6.2. Glycerol Transport.. . . . .. . . . . . .. . . .. . . . . .. . . . . .. .. 49 6.3. Uptake of Glycerol-P . . . . . . . . . . . . . . . . • . . . . . . . . . . . . . 52 6.4. Glycerol-P Dehydrogenase.. . . .. . . .. . . .. .. . . . ... . . . 52 6.5. The GlpM Protein ................................ 53 6.6. Glycerol Kinase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54 6.7. Regulatory Loci .................................. 55 6.8. Chromosomal Mapping of Glycerol Metabolism Genes . . . 56

7. Central Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 7.1. Fructose 1,6-Bisphosphate Aldolase ................ 57 7.2. Fructose 1,6-Bisphosphatase ....................... 57 7.3. Phosphoglucoisomerase ........................... 58 7.4. Glucose 6-Phosphate Dehydrogenase ............... 58 7.5. Entner-Doudoroff Dehydratase.................... 58 7.6. Entner-Doudoroff Aldolase....................... 59

8. Lower Embden-Meyerhoff-Parnas (EMP) Pathway ...... 60 8.1. Glyceraldehyde 3-Phosphate Dehydrogenase........ 60 8.2. Phosphoglycerate Kinase .......................... 61 8.3. Phosphoglycerate Mutase (Pgm), Enolase (Eno),

and Pyruvate Kinase(Pyc) .. .... .... .... ...... ...... 61 8.4. Pyruvate Carboxylase ............................. 61

CONTENTS xi

9. Recycling of Glyceraldehyde 3-Phosphate ................ 61 10. Regulation of Central and Lower EMP Pathways.......... 62 11. Catabolite Repression Control (CRC) .................... 64 12. Clustering of Genes for Glycoltyic Enzymes .............. 65

References ............................................ 66

Chapter 3

Polysaccharides: Lipopolysaccharide and Capsular Polysaccharide ........................................... 73

Estelle J. McGroarty

1. Introduction ........................................... 73 2. Lipopolysaccharide ..................................... 74

2.1. Structure ........................................ 74 2.2. Lipopolysaccharide Heterogeneity. .. . . .. . . .. . . .. . . . 78 2.3. Biosynthesis and Genetic Regulation of LPS ... . . .. . . 80 2.4. Lipopolysaccharide Physical Properties. .. . . .. . . .. . . . 83 2.5. Biological Activity of Lipopolysaccharide. . . . . . . . . . . . 84 2.6. Immunology of LPS .............................. 84

3. Capsular Polysaccharides and Slime ...................... 85 3.1. Introduction ..................................... 85 3.2. O-Capsular Polysaccharide-Structure.. . . . .. . . .. . . . 86 3.3. O-Capsule Function .............................. 87 3.4. O-Capsule as an Antigen .......................... 87 3.5. Alginate-Introduction ........................... 88 3.6. Alginate-Structure and Physical Properties ........ 88 3.7. Alginate-Biosynthesis............................ 90 3.8. Regulation of Alginate Synthesis ................... 92 3.9. Immunology of Alginate .......................... 95

3.10. Alginate Function ................................ 96 References ............................................. 97

Chapter 4

Lipids of Pseudomonas III

Holly C. Pinkart and David C. White

1. Introduction ........................................... III

xii CONTENTS

2. Lipids of the Genus Pseudomonas .. . . . . . . . . . . . . . . . . . . . . . . III 2.1. Membrane Lipids.................................. 111 2.2. Fatty Acids ........................................ 115 2.3. Storage Lipids ................... " ...... " . . .. .. . . 126 2.4. Exolipids.......................................... 128

3. Alteration of Lipids in Response to Environmental Conditions. . . .... . . . . .. . . . . .. . . .. . . .. . . .. . . . . . . .. . . .... 130 3.1. Growth Temperature .............................. 130 3.2. Oxygen Tension................................... 131 3.3. Desiccation........................................ 131 3.4. Nutrient Deprivation ......... '" ... . . . .... . . .. . . . . . 132 3.5. Solvent Tolerance ..... " .. . . .. . .. . .... . . . . .. . . .. .. . 133 3.6. Antibiotic Resistance ............................... 133

4. Summary .............................................. 134 References ............................................. 134

Chapter 5

<>uterMembr.aneProteins ................................. 139

Robert E. W. Hancock and Elizabeth A. Worobec

1. Introduction .......................................... 139 2. Role in Antibiotic Susceptibility ......................... 139 3. IROMPs: FpvA, FptA, pfeA ............................ 140 4.0prC ................................................. 145 5.0prJ ................................................. 146 6. AlgE ................................................. 146 7. OprN ................................................. 146 8. OprK ................................................. 147 9.0prM ................................................ 147

10.0prP ................................................. 148 11. OprO ................................................ 149 12. OprB .... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153 13. OprD ................................................. 154 14.0prE ................................................. 155 15. E2 ................................................... 156 16. OprF ................................................. 156 17. OprG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159 18. OprH ................................................ 159 19.0prL ................................................. 160

CONTENTS xiii

20.0prI ................................................. 160 References ............................................ 161

Chapter 6

Transport Systems in Pseudomonas 169

Toshimitsu Hoshino

1. Introduction ........................................... 169 2. Sugars. . . . . . .. . . . .. . . . . . . . .. . . .. . . . . ... . ... . . .. . . . .. . . . 171

2.1. Glucose and Gluconate ............................. 171 2.2. Fructose and Mannitol ............................. 173

3. Amino Acids........................................... 174 3.1. Branched-Chain Amino Acids ...................... 174 3.2. Basic Amino Acids (Arginine, Lysine, Histidine) ...... 182 3.3. Proline ........................................... 183 3.4. Aromatic Amino Acids............................. 184 3.5. Methionine........................................ 184

4. Inorganic Ions ......................................... 185 4.1. Cations........................................... 185 4.2. Anions............................................ 185

5. Other Compounds...................................... 187 5.1. Compounds Catabolized by the J3-Ketoadipate

Pathway. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187 5.2. Myo-inositol ....................................... 190 5.3. Steroids........................................... 191 References ............................................. 192

Chapter 7

Iron Metabolism and Siderophores in Pseudomonas and Related Species . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201

Jean-Marie Meyer and Alain Stintzi

1. Introduction ........................................... 201 2. Siderophores at the Bench. . . .. . . .. . ... . ... . . .. . . .. . . . . .. 202

2.1. Optimization of Siderophore Production ............ 202

xiv CONTENTS

2.2. Detection of Siderophores .......................... 203 2.3. Purification of Siderophores ........................ 204

3. Siderophore-Mediated Iron Uptake Systems in Fluorescent Pseudomonas .............................. 209 3.1. Fluorescent Pseudomonas Siderophores ............... 209 3.2. Internalization of Iron ............................. 214 3.3. Iron Uptake from Other Iron Sources............... 215 3.4. Biosynthesis, Genetic Organization,

and Regulation of Siderophores . . . . . . . . . . . . . . . . . . . . . 217 4. Siderophore-Mediated Iron Uptake Systems in

Nonfluorescent Pseudomonas and Related Strains ........... 223 4.1. Pseudomonas stutzeri .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223 4.2. Burkholderia (Formerly Pseudomonas) cepacia and Related

Strains ............................................ 224 4.3. Other Strains . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 226

5. Iron, Siderophores, and Biotechnology ................... 227 5.1. Iron, Siderophores, and Plant-Related Biocontrol ..... 227 5.2. Iron, Siderophores, and Human Pathogenicity ....... 227 5.3. Siderotyping and Searching for New Siderophones:

Back to the Bench ................................. 229 References ............................................. 230

Chapter 8

The Flagellum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245

Thomas C. Montie

1. Introduction ........................................... 245 2. Biochemistry ........................................... 245

2.1. General Morphology ............................... 245 2.2. Purification ....................................... 246 2.3. Molecular Weights of Flagellins ..................... 246 2.4. Amino Acid Composition........................... 248

3. Posttranslational Modifications of Flagellins ............... 250 3.1. Phosphorylation ................................... 250 3.2. Glycosylation ...................................... 252

4. Comparative Analysis of [liC Genes ...................... 254 4.1. Flagellin b-Type Genes. ... . .... ... . ... . .... . . .... . . 254 4.2. Flagellin a-Type Genes ............................. 257

CONTENTS xv

5. Flagella and Chemotaxis Genes and Regulation . . . . . . . . . . . . 260 5.1. Regulation of Flagella Biosynthesis and Assembly . . . . . 260 5.2. Chemotaxis Genes ................................. 262

6. Antigenicity and Immunogenicity ........................ 262 6.1. Antigenicity ....................................... 262 6.2. Immunogenicity and Passive Protection. . . . . . . .. . . . . . 263

7. Virulence .............................................. 264 8. Other Pseudomonads ................................... 265

References ............................................. 266

Chapter 9

Selected Industrial Biotransformations 271

Marcel G. Wubbolts and Bernard Witholt

1. Introduction ........................................... 271 1.1. Metabolites of Pseudomonas in Biotechnology ......... 272 1.2. Biocatalysis versus Chemical Catalysis. . . . . . . . . . . . . . . . 273

2. Biocatalysts and Their Practical Application. . . . . . . . . . . . . . . 279 2.1. Oxidoreductases................................... 279 2.2. Transferases ...................................... 291 2.3. Hydrolases........................................ 294 2.4. Lyases ............................................ 304 2.5. Isomerases and Racemases . . .. . . . . . . .. . . .. . . . . . . . . . . 308 2.6. Ligases ........................................... 311

3. The Impact of Molecular Biology on Biocatalyst Development ........................................... 311 3.1. Constructing "Tailor-Made" Biocatalysts ............. 311 References ............................................. 313

Index.................................................... 331