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Pseudomonas: model organism, pathogen, cell factory

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Format:	Buch
Sprache:	English
Veröffentlicht:	Weinheim Wiley-VCH 2008
Schlagworte:	Pseudomonas Aufsatzsammlung
Online-Zugang:	Inhaltstext Inhaltsverzeichnis Klappentext
Beschreibung:	Literaturangaben
Beschreibung:	XXI, 402 S. Ill., graph. Darst. 25 cm
ISBN:	9783527319145 352731914X

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Datensatz im Suchindex

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adam_text	Contents Preface XV List of Contributors XVII 1 Comparative Cenomics of Pseudomonas 1 Kristoffer KHI, Tim T. B'mnewies, Harmi Willenbrock, Susse Kirkelund Hansen, Lei Yang, Larsjelsbak, David W. Ussery, and Carsten Friis 1.1 Introduction 1 1.1.1 Other Species of Pseudomonas 2 1.1.2 Obtaining Sequence Data on Pseudomonas 4 1.2 Pan/Core Genome of Pseudomonas 4 1.3 Phylogeny of Pseudomonas 6 1.4 Blast Atlas of Pseudomonas Genomes б 1.4.1 Region 5 243 000-5 361 000 12 1.4.2 Region 713 000-785 000 14 1.5 Functional Categories 14 1.6 Codon Usage and Expression 17 1.7 Future Outlook 20 References 21 2 Clinical Relevance of Pseudomonas aeruginosa: A Master of Adaptation and Survival Strategies 25 Niels H0Íby, Helle Krogh Johansen, Claus Moser, and Oana Ciofu 2.1 Introduction 25 2.2 CF 26 2.3 Survival of P. aeruginosa by Adaptation to the Inflammatory Defense System 27 2.4 Conductive and the Respiratory Zones of the Lungs 31 2.5 Survival of P. aeruginosa by Adaptation to the Respiratory Zone of the Lungs 32 VI Contents 2.6 Survival of P. aeruginosa by Adaptation to the Conductive Zone of the Lungs 33 2.7 Survival of P. aeruginosa by Adaptation to the Antibiotic Therapy 35 2.8 Evolutionary Implications of the Adaptability of P. aeruginosa 37 References 37 3 Adherence of Pseudomonas aeruginosa 45 Randall T. Irvin 3.1 Introduction 45 3.2 What is Adherence? 46 3.3 Role of Adherence in Infection 46 3.4 How is Bacterial Adherence Associated with Virulence? 47 3.5 P. aeruginosa Adhesins 50 3.6 Surface Receptor Requirements of the Pilus Adhesin 52 3.7 How Does PilA Mediate Attachment to Human Mucosal Surfaces? 53 3.8 X-ray Crystallograpbic Structural Studies of the Pilin Structural Protein 56 3.9 Structure of the Pilus Fiber 60 3.10 Structure of the Receptor-Binding Domain and Location on the Pilus 63 3.11 Structural Nature of the Receptor-Binding Domain 66 3.12 Twitching Motility 68 3.13 How Does the Pilus Attach to a Solid Surface? 69 3.14 The Monkey-Bar Swing Paradox 72 3.15 Molecular Basis for Receptor-binding Domain Interaction with Steel Surfaces 73 3.16 Pili as Nanowires for Redox Reactions 76 3.17 What is the Most Important Role of Adherence to P. aeruginosa 76 References 77 4 Flagella and Pili of Pseudomonas aeruginosa 85 Jeevanjyot and Reuben Ramphal 4.1 Introduction 85 4.2 Flagellum of P. aeruginosa 85 4.2.1 Structure of the P. aeruginosa Flagellum 86 4.2.2 Chromosomal Organization of the Flagellar Genes of P. aeruginosa 86 4.2.3 Transcriptional Hierarchy of the Flagellar Genes 90 4.2.4 Model Proposed for Flagellar Assembly in P. aeruginosa 91 4.2.5 Environmental/Nonflagellar Regulators of Flagellar Expression 92 4.2.6 Posttranslational Modification of Flagellin 93 4.2.6.1 Flagellar Glycosylation Islands (GIs) in P. aeruginosa 93 4.2.6.2 Polymorphism of the P. aeruginosa a-type GI 94 4.2.7 Role of Flagella in Inflammation 95 4.2.8 Role of Flagellum in Pathogenesis 95 4.3 Pili of P. aeruginosa 96 Contents VII 4.3.1 Structure of P. «eruginoso Pilus 97 4.3.2 Pilus/Fimbrial Genes of P. aeruginosa 97 4.3.3 Regulation of Pilus Assembly and Twitching Motility 99 4.3.4 Assembly of Type IV Pili 100 4.3.5 Pilin Classification 100 4.3.5.1 Type IV a and b Pilins 100 4.3.5.2 Group I-V Pilins 101 4.3.6 Pseudopilins 101 4.3.7 Chaperone-Usher Pathways 101 4.3.8 flp-tad-rcp Gene Cluster 202 4.3.9 Posttranslational Modifications of Pilin 103 4.3.10 Role of Pili in Pathogenesis 103 4-А Conclusions 104 References 304 5 Pseudomonas Motility and Chemotaxis 109 Junichi Kato 5.1 Introduction 209 5.2 Chemotaxis Assay Methods 209 5.3 Ecological Aspects of Chemotaxis 222 5.3.1 Host-Microbe Interactions 222 5.3.2 Nitrogen Cycle 113 5.3.3 Bioremediation and Chemotaxis Toward Environmental Pollutants 113 5.4 Molecular Biology of Chemotaxis in Pseudomonas 114 5.4.1 Molecular Mechanism of Bacterial Chemotaxis 224 5.4.2 MCPs in Pseudomonas 115 5.4.3 Che Proteins in Pseudomonas 123 5.4.4 Polar Localization of MCPs and Che Proteins 224 5.5 Pseudomonas as Model Microorganisms for Chemotaxis Research 225 References 226 6 Iron Transport and Signaling in Pseudomonads 229 Francesco Imperi, Karla A. Mettrkk, Matt Shirley, Federica Tiburzi, Richard С Draper, Paolo Visca and lain L Lamont 6.1 Introduction 129 6.2 Siderophores Used by Pseudomonads 131 6.2.1 Chemical Diversity of Siderophores 131 6.2.2 Endogenous Siderophores of Pseudomonads 133 6.2.2.1 Pyoverdines 133 6.2.2.2 Pyochelin 134 6.2.2.3 Other Endogenous Siderophores 134 6.2.3 Exogenous Siderophores Utilized by Pseudomonads 235 6.2.3.1 Enterobactin 135 6.2.3.2 Desferrioxamines 236 6.2.3.3 Ferrichromes 236 VIII Contents 6.2.3.4 Aerobactin 136 6.2.3.5 Citrate 136 6.3 Siderophore Synthesis 136 6.3.1 Nonribosomal Peptide Synthesis 136 6.3.2 Pyoverdine Biosynthetic Pathways 137 6.3.3 Synthesis of other Pseudomonas Siderophores 141 6.4 Ferri- Siderophore Transport 142 6.4.1 Overview 142 6.4.2 Outer Membrane Ferri- Siderophore Receptors 142 6.4.3 TonB Complex 144 6.4.4 Transport of Ferri- Siderophores into the Periplasm 145 6.4.5 Iron Transport Across the Cytoplasmic Membrane 146 6.5 Regulation of Siderophore Synthesis and Transport 146 6.5.1 Fur Protein as Master Repressor 146 6.5.2 ECF σ Factors 148 6.5.3 QS and Expression of Iron Transport Genes 149 6.6 Introduction to Signaling 150 6.6.1 Pyoverdine-Mediated Signaling 150 6.6.1.1 FpvA and Pyoverdine 150 6.6.1.2 Transfer of Signal: Role of FpvR 151 6.6.2 Pyochelin: An Alternative Signaling Mechanism 152 6.6.3 Enterobactm 153 6.6.4 Multiplicity of Heterologous Siderophore Signaling Systems in Pseudomonads 154 6.7 Concluding Remarks and Future Perspectives 154 References 156 7 Quorum Sensing in Pseudomonads 167 S.P. Diggle, S. HeebJ.F. Dubern, M.P. Fletcher, S.A. Crusz, P. Williams, and M. Cámara 7.1 Introduction to Quorum Sensing 167 7.2 AHL QS in Pseudomonas aeruginosa 168 7.3 AHL-Dependent QS in Other Pseudomonads 172 7.4 AHQ-Dependent QS in Pseudomonads 174 7.4.1 Regulation and Biosynthesis of AHQs 175 1'.4.2 Function of AHQs in P. aeruginosa 176 7.4.3 AHQs in Other Pseudomonads 178 7.5 Gac/Rsm System in Pseudomonads 178 7.5.1 Gac/Rsm as the Principal QS System 179 7.5.2 Gac/Rsm as a QS Fine-tuning System 180 7.6 QS and Infection 182 7.6.1 Role of QS in the Pathogenesis of P. aeruginosa Infections 182 7.6.2 Evidence for QS In vivo 182 7.6.3 QS and Biofilms in P. aeruginosa 183 7.6.4 QS Molecules and the Host 185 Contents 7.6.5 Disruption of QS Represents a Novel Approach for Managing P. aeruginosa Infections 186 7.7 Conclusions 187 References 188 8 Regulatory Networks in Pseudomonas aeruginosa: Role of Cyclic-diß'.S'J-Guanylic Acid 195 Ute Römling and Susanne Haussier 8.1 Introduction - The History of Cydic-diß'.S'J-Guanylic Acid Detection 195 8.2 Principles of c-di-GMP Signaling 196 8.2.1 Transition between Motility and Sessility 196 8.2.2 Di-guanylate Cyclases 298 8.2.3 Phosphodiesterases 198 8.2.4 Principle Concepts of c-di-GMP Signaling 199 8.3 GGDEF and EAL Domain Proteins in P. aeruginosa 199 8.4 c-di-GMP Signaling in Biofilm Formation 199 8.5 c-di-GMP Signaling in Fimbrial Biogenesis 202 8.6 c-di-GMP Signaling in Exopolysaccharide Production 203 8.7 c-di-GMP Signaling and Motility 203 8.8 c-di-GMP Signaling in the Formation of Small Colony Variants 204 8.9 c-di-GMP Signaling in Virulence 205 8.10 c-di-GMP-Binding Proteins in P. aeruginosa 206 8.11 Perspectives 207 References 208 9 Pseudomonas aeruginosa: A Model for Biofilm Formation 215 Diane McDougald, Janosch Klebensberger, Tim Tolker-Nielsen, Jeremy 5. Webb, Tim Conibear, Scott A. Rice, Sylvia M. Kirov, Carsten Matz, and Staffan Kjelleberg 9.1 Introduction 215 9.2 Biofilm Development 216 9.2.1 Early Attachment and Colonization Events 217 9.2.1.1 Translocation and Attachment to Surfaces 217 9.2.1.2 Role of Flagella and Fimbriae in Reversible and Irreversible Attachment 218 9.2.2 Extracellular Matrix 219 9.2.2.1 Polysaccharide 219 9.2.2.2 Protein 220 9.2.2.3 DNA 221 9.2.3 Phenotypic and Genotypie Diversification in Pseudomonas Biofilms 223 9.2.3.1 Ecological and Genetic Causes of Diversity in Pseudomonas Biofilms 223 9.2.3.2 Colony Morphology Variation in P. Aeruginosa Biofilms 224 X Contents 9.2.3.3 GacS Sensor Kinase 224 9.2.3.4 Bacteriophage and SCVs 225 9.2.4 Biofilm Dispersal 226 9.2.4.1 Role ofc-di-GMP in Dispersal 226 9.2.4.2 Denitrifkation, Nitric Oxide and Dispersal in P. aeruginosa 226 9.2.4.3 Microcolony-based Biofilm Dispersal 228 9.3 Regulatory Mechanisms of P. ae.rugi.nosa Biofilms 229 9.3.1 c-di-GMP 229 9.3.1.1 c-di-GMP Regulation of SCVs 230 9.3.1.2 Autoaggregation and c-di-GMP 231 9.3.1.3 Motility 231 9.3.1.4 Environmental Stimuli and Targets ofc-di-GMP Signaling 232 9.3.2 QS and P. aeruginosa Biofilms 233 9.3.2.1 Effect of Nutrient on QS Regulation of Biofilm Formation 233 9.3.2.2 QS, Central Metabolism and Biofilm Gradients 235 9.3.2.3 QS and Chronic Infection 236 9.4 Biofilm/ Eukaryote Interactions 237 9.4.1 Clinical P. aeruginosa Biofilm Infections 237 9.4.1.1 Chronic Lung Infections in C F 237 9.4.1.2 Conversion to Mucoidy and Anaerobic Growth 238 9.4.1.3 Phenotypic and Genotypie Analyses of P. aeruginosa in CF Infection 239 9.4.2 Similarities Across P. aeruginosa Biofilm-Host Interactions 241 9.4.2.1 Interactions with Host Immune Cells 241 9.4.2.2 Interactions with Free-living Protozoa 242 9.4.2.3 Interactions with Fungi 243 9.5 Future Perspectives 244 References 246 10 Bacteriophages of Pseudomonas 255 Kirsten Hertveldt and Rob Lavigne 10.1 Introduction 255 10.1.1 Bacteriophage Propagation Cycle 255 10.1.1.1 Temperate versus Lytic Phages 255 10.1.1.2 Lytic Infection Cycle 256 10.1.2 Phage Classification 259 10.1.3 Phages of Pseudomonas Spp. 259 10.1.4 Applications of Pseudomonas Bacteriophages 263 10.2 Pseudomonas Phage Representatives 263 10.2.1 Introduction 263 10.2.1.1 Tailed Phages 264 10.2.1.2 Tailless Phages 264 10.2.2 Pseiidomonas-Infecting Myoviridae 264 10.2.2.1 Phage фСТХ 264 10.2.2.2 Giant Virulent Pseudomonas Phages 265 Contents XI 10.2.3 Pseudomonas-lníecúng Siphoviridae 268 10.2.3.1 ОЗШ/ВЗ-ііке Pseudomonas Phages 268 10.2.3.2 Bacteriophage D3 272 10.2.4 Pseudomonas-lnfecting Podoviridae 275 10.2.4.1 gh-1: A 17- like Member of the Podoviridae 275 10.2.4.2 φΚΜν -Like Viruses 277 10.2.4.3 Pseudomonas Phage РаРЗ 278 10.2.4.4 Pseudomonas Phage F116 279 10.2.5 Pseudomonas-lníecting Levivirídae 279 10.2.6 Pseudomonas-lníecting Cystoviridae 282 10.2.6.1 Bacteriophage ф6 282 10.2.6.2 Bacteriophages ф8, ф12 and фіЗ 283 10.2.7 Pseudomonas-Infecting Inoviridae 284 10.2.7.1 Introduction 284 10.2.7.2 Phages Pfl and Pf3 285 10.2.8 Prophage Sequences in Pseudomonas Bacterial Chromosomes 286 References 286 11 Pseudomonas Plasmids 293 Christopher M. Thomas, Anthony S. Haines, Irina A. Kosheieva, and Alexander Boronin 11.1 Introduction 293 11.2 Plasmid Groups in Pseudomonas 294 11.3 Defining Characteristics of Pseudomonas Plasmids 303 11.4 Isolation of Plasmids 304 11.5 Use of PCR Primers and Associated Probes for Pseudomonas Plasmids 306 11.6 Plasmid Replication 306 11.7 Plasmid Maintenance 309 11.8 Determinants of Incompatibility 312 11.9 Determinants of Host Range ЗІЗ 11.10 Plasmid Transfer 326 11.11 Phenotypic Cargo of Pseudomonas Plasmids 318 11.12 Conclusions 319 References 320 12 Biosynthesis and Regulation of Phenazine Compounds in Pseudomonas spp. 331 Dmitri V. Mavrodi, Linda S. Thomashow, and Wulf Blankenfeldt 12.1 Introduction 331 12.2 Diversity of Phenazine Compounds Produced by Pseudomonas spp 331 12.3 Biosynthesis of Phenazines and Evolution of Pathways 333 12.3.1 Core Biosynthetic Pathway and Assembly of the Phenazine Scaffold 333 XII Contents 12.3.2 Phenazine-Modifying Genes 337 12.3.3 Evolution of Phenazine Pathways 338 12.4 Regulation of Phenazine Production in Pseudomonas Spp. 339 12.4.1 Phenazine Biosynthesis and N-Acyl-Homoserine Lactone (Acyl-HSLj-Based Quorum Sensing (QS) 339 12.4.2 Global Regulation 340 12.5 Biological Activity and Role of Phenazine Compounds from Pseudomonas Spp. 340 12.5.1 Spectrum of Biological Activity of Phenazines 340 12.5.2 Mode of Action and Mechanisms of Self-Defense 341 12.5.3 Redox Homeostasis and Other Physiological Roles 343 12.6 Conclusions 344 References 344 13 Pseudomonas-Plant Interactions 353 S.H. Miller, C.L Mark, A. Franks, and F. O'Cara 13.1 Introduction 353 13.2 Beneficial Pseudomonas-Plant Interactions 354 13.2.1 Biocontrol 358 13.2.2 ISR 359 13.2.3 Biofertilization 359 13.2.4 Phytostimulation 360 13.2.5 Rhizoremediation 361 13.3 Pseudomonas-Plant Signaling 362 13.3.1 Plant Root Exudates 362 13.3.2 Plant-Derived Signals and Bacterial Gene Expression 364 13.3.3 N-Acyl-Homoserine Lactone (AHL) Signaling 364 13.3.4 Pathogen-Associated Molecular Patterns (PAMPs) 366 13.4 Current and Future Prospects for the Study of Pseudomonas-Plant Interactions 367 13.4.1 Transcriptomics 367 13.4.2 Proteomics 367 13.4.3 Metabolomics 368 13.4.4 In Situ Analysis of Pseudomonas-Plant Interactions 368 13.4.5 Plant-Beneficial Microbial Consortia 369 13.5 Conclusions 370 References 370 14 Biotechnological Relevance of Pseudomonads 377 Bernd H.A. Rehm 14.1 Introduction 377 14.2 Biodegradation 377 14.2.1 Microbial Degradation of PAHs 378 14.2.2 Metabolic Engineering of Strains for Biodegradation 379 14.3 Biotransformation/Bioconversion 381 Contents XIII 14.4 Low-molecular-weight Compounds: Microbial Production of Biosurfactants 383 14 A.I Rhamnolipids as Biosurfactants 384 14.4.1.1 Rhamnolipid Biosynthesis 385 14.5 Biopolymer Production 386 14.5.1 Alginate Biosynthesis 386 14.5.1.1 Applications 388 14.5.2 Elastomeric Bioplastics: Medium-chain-length PHAs 388 14.5.2.1 Biosynthesis of Medium-chain-length PHAs 388 14.5.2.2 Potential Applications of Medium-chain-length PHAs 389 14.6 Recombinant Protein Production 389 14.7 Biocontrol Agents: Plant Growth Promotion 390 14.8 Outlook 391 References 391 Index 397 I he pseudomonads comprise bacterial species which emerged as model organisms to study important microbial processes such as biofilm formation, plant-growth promotion and biodégradation. The use of Pseudomonas bacteria in biotechnological production has exponen¬ tially increased over the past few years. Pseudomonas-relateå products and services are found across a wide range of industrial areas, including the manufacture of chemicals, biopharmaceuticals and biocatalysts. Concise and up-to-date, this handy guide fills a gap in the literature by providing the essential knowledge for everyone with an interest in the topic. The result is a comprehensive overview of the most important model organism in applied and medical microbiology that covers basic biology, pathology and biotechnological applications. Bernd Rehm is Professor and Chair of Microbiology at Massey University in New Zealand. Having obtained his academic degrees at the Universities of Bochum and Münster (Germa¬ ny), he spent two years at the University of British Columbia (Canada), before establishing his own research program at ifie University of Münster. In 2003, he took up his present appointment at Massey University. Bernd Rehm authored and co-authored over ninety scientific publications. He is sole editor of three books, co-organizer of the international symposium on biological polyester and member of the editorial board for several scientificjournals.
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genre_facet	Aufsatzsammlung
id	DE-604.BV035721631
illustrated	Illustrated
indexdate	2024-07-20T10:19:02Z
institution	BVB
isbn	9783527319145 352731914X
language	English
oai_aleph_id	oai:aleph.bib-bvb.de:BVB01-017998401
oclc_num	180478869
open_access_boolean
owner	DE-355 DE-BY-UBR DE-11
owner_facet	DE-355 DE-BY-UBR DE-11
physical	XXI, 402 S. Ill., graph. Darst. 25 cm
publishDate	2008
publishDateSearch	2008
publishDateSort	2008
publisher	Wiley-VCH
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spelling	Pseudomonas model organism, pathogen, cell factory ed. by Bernd H. A. Rehm Weinheim Wiley-VCH 2008 XXI, 402 S. Ill., graph. Darst. 25 cm txt rdacontent n rdamedia nc rdacarrier Literaturangaben Pseudomonas Pseudomonas (DE-588)4210233-9 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Pseudomonas (DE-588)4210233-9 s DE-604 Rehm, Bernd H. A. Sonstige oth text/html http://deposit.dnb.de/cgi-bin/dokserv?id=3008955&prov=M&dok_var=1&dok_ext=htm Inhaltstext Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017998401&sequence=000005&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017998401&sequence=000006&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA Klappentext
spellingShingle	Pseudomonas model organism, pathogen, cell factory Pseudomonas Pseudomonas (DE-588)4210233-9 gnd
subject_GND	(DE-588)4210233-9 (DE-588)4143413-4
title	Pseudomonas model organism, pathogen, cell factory
title_auth	Pseudomonas model organism, pathogen, cell factory
title_exact_search	Pseudomonas model organism, pathogen, cell factory
title_full	Pseudomonas model organism, pathogen, cell factory ed. by Bernd H. A. Rehm
title_fullStr	Pseudomonas model organism, pathogen, cell factory ed. by Bernd H. A. Rehm
title_full_unstemmed	Pseudomonas model organism, pathogen, cell factory ed. by Bernd H. A. Rehm
title_short	Pseudomonas
title_sort	pseudomonas model organism pathogen cell factory
title_sub	model organism, pathogen, cell factory
topic	Pseudomonas Pseudomonas (DE-588)4210233-9 gnd
topic_facet	Pseudomonas Aufsatzsammlung
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