Alvarez Biology of Rhodococcus

2010
ISBN: 978-3-642-12937-7
Verlag: Springer
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, Band 16, 368 Seiten

Reihe: Microbiology Monographs

Rhodococcus, a metabolically versatile actinobacteria which is frequently found in the environment, has gained increasing interest due to its potential biotechnological applications. This Microbiology Monographs volume provides a thorough review of the various aspects of the biochemistry, physiology and genetics of the Genus Rhodococcus. Following an overview of its taxonomy, chapters cover the structural aspects of rhodococcal cellular envelope, genomes and plasmids, metabolic and catabolic pathways, such as those of aromatic compounds, steroids and nitriles, and desulfurization pathways, as well as the adaption to organic solvents. Further reviews discuss applications of Rhodococcus in the bioremediation of contaminated environments, in triacylglycerol accumulation, and in phytopathogenic strategies, as well as the potential of biosurfactants. A final chapter describes the sole pathogenic Rhodococcus member, R. equi.

Autoren/Hrsg.

Alvarez, Héctor

Alvarez, Héctor M.

Inhaltsverzeichnis

1;Biology of Rhodococcus;3
1.1;Preface;5
1.2;Contents;7
1.3;Contributors;9
1.4;Systematics of Members of the Genus Rhodococcus (Zopf 1891) Emend Goodfellow et al. 1998;13
1.4.1;1 Introduction;14
1.4.2;2 The Past: A Brief History of the Genus Rhodococcus: A Red Coccus;15
1.4.3;3 Current Systematics;18
1.4.3.1;3.1 The Genus Rhodococcus;18
1.4.3.2;3.2 Current Species of Rhodococcus;20
1.4.4;4 Ecology of Rhodococcus spp.;22
1.4.5;5 Identifying New Rhodococcus Species;22
1.4.6;6 Tidying Up Rhodococcus Systematics;23
1.4.7;7 The Future of Rhodococcus Systematics;25
1.4.8;8 Note Added in Proof;30
1.4.9;References;32
1.5;The Rhodococcal Cell Envelope: Composition, Organisation and Biosynthesis;41
1.5.1;1 Introduction;42
1.5.2;2 Cell Envelope Composition in the Genus Rhodococcus: Covalently Associated Components;42
1.5.2.1;2.1 Mycolic Acids;42
1.5.2.2;2.2 The Peptidoglycan-Arabinogalactan Complex;44
1.5.3;3 Organisation of the Rhodococcal Cell Envelope;46
1.5.4;4 Non-Covalently Associated Cell Envelope Components;49
1.5.4.1;4.1 Channel Forming Porins;49
1.5.4.2;4.2 Lipoglycans;50
1.5.4.3;4.3 Cell Envelope Lipids;51
1.5.4.4;4.4 Capsules and Cell Envelope Polysaccharides;52
1.5.4.5;4.5 Lipoproteins;53
1.5.5;5 Biosynthesis of Key Cell Envelope Components;54
1.5.5.1;5.1 Mycolic Acid Biosynthesis;55
1.5.5.2;5.2 Arabinogalactan Biosynthesis;59
1.5.5.2.1;5.2.1 Linker Unit Synthesis;60
1.5.5.2.2;5.2.2 Galactan Synthesis;61
1.5.5.2.3;5.2.3 Arabinan Synthesis;62
1.5.5.2.4;5.2.4 Macromolecular Ligation;65
1.5.5.3;5.3 LAM Biosynthesis;68
1.5.6;6 Concluding Comments;71
1.5.7;References;72
1.6;Genomes and Plasmids in Rhodococcus;84
1.6.1;1 Introduction;85
1.6.2;2 Historical Context of Studies on Rhodococcus Genetics;85
1.6.3;3 Overview of Rhodococcus Genomes;87
1.6.3.1;3.1 Genome Size and Variability;88
1.6.3.2;3.2 Plasmids - Role of Linear and Circular Plasmids;90
1.6.3.3;3.3 Mobile Genetic Elements and Genetic Instability;91
1.6.4;4 The Genetic Basis of Catabolic Capabilities;93
1.6.5;5 Gene Regulation and Expression;94
1.6.6;6 Concluding Remarks;96
1.6.7;References;96
1.7;Central Metabolism of Species of the Genus Rhodococcus;102
1.7.1;1 Introduction;103
1.7.2;2 Glycolytic Pathways;104
1.7.3;3 Glycogen Synthesis and the Link with the Central Metabolism;111
1.7.4;4 Gluconeogenesis and the Phosphoenolpyruvate- Pyruvate-Oxalacetate Node;111
1.7.5;5 The Tricarboxylic Acid Cycle;114
1.7.6;6 The Glyoxylate Pathway;114
1.7.7;7 Litoautotrophic Processes in Rhodococcus;115
1.7.8;8 Concluding Remarks;116
1.7.9;References;117
1.8;Adaptation of Rhodococcus to Organic Solvents;120
1.8.1;1 Introduction;121
1.8.1.1;1.1 Predicting Solvent Toxicity;121
1.8.1.2;1.2 Effect of Solvents on Bacterial Cells;123
1.8.2;2 Intrinsic Resistance to Organic Solvents;124
1.8.3;3 Adaptation Mechanisms to Organic Solvents;127
1.8.3.1;3.1 Adaptation of the Cell Wall and of the Cellular Membrane;128
1.8.3.2;3.2 Biocatalysis and Biodegradation of the Toxic Compound;131
1.8.3.3;3.3 Other Mechanisms of Protection;135
1.8.4;4 Application;137
1.8.5;References;137
1.9;Catabolism of Aromatic Compounds and Steroids by Rhodococcus;143
1.9.1;1 Introduction;144
1.9.2;2 Mononuclear Aromatic Compounds;146
1.9.2.1;2.1 Underlying Strategies of Aromatic Compound Catabolism in Rhodococci;147
1.9.3;3 Peripheral Versus Central Aromatic Pathways;149
1.9.3.1;3.1 Central Pathways;149
1.9.3.1.1;3.1.1 beta-Ketoadipate Pathway;150
1.9.3.1.2;3.1.2 Modified beta-Ketoadipate Pathways;152
1.9.3.1.3;3.1.3 Phenylacetate (Paa) Pathway;153
1.9.3.2;3.2 Peripheral Pathways;155
1.9.3.2.1;3.2.1 Biphenyl and Alkylbenzene Pathways;156
1.9.3.2.2;3.2.2 Phthalate and Terephthalate Pathways;157
1.9.4;4 Polymeric and Halogenated Aromatic Compounds;158
1.9.4.1;4.1 Lignin Degradation;158
1.9.4.2;4.2 Polyaromatic Hydrocarbons;161
1.9.4.3;4.3 Halogenated Aromatic Compounds;162
1.9.4.3.1;4.3.1 PCBs and PBDEs;162
1.9.5;5 Steroids;163
1.9.5.1;5.1 Uptake of Sterols;165
1.9.5.2;5.2 Side-Chain Degradation;166
1.9.5.3;5.3 Nucleus Degradation;167
1.9.6;6 Conclusion and Prospects;169
1.9.7;References;170
1.10;Catabolism of Nitriles in Rhodococcus;180
1.10.1;1 Introduction;181
1.10.2;2 Occurrence of Nitrile-Converting Rhodococcus Strains;183
1.10.2.1;2.1 Strain Selection;183
1.10.2.2;2.2 Nitrilase-Producing Strains;184
1.10.2.3;2.3 Nitrile Hydratase-Producing Strains;184
1.10.3;3 Gene Organization and Regulation;188
1.10.3.1;3.1 Nitrilase Genes;188
1.10.3.2;3.2 Nitrile Hydratase Genes;189
1.10.3.2.1;3.2.1 Fe-Type Nitrile Hydratase;189
1.10.3.2.2;3.2.2 Co-Type Nitrile Hydratase;191
1.10.3.2.3;3.2.3 A Novel Type of Nitrile Hydratase;192
1.10.3.3;3.3 Amidase Genes;192
1.10.4;4 Enzyme Structural and Catalytic Properties;193
1.10.4.1;4.1 Nitrilase;193
1.10.4.1.1;4.1.1 Structural Variability;194
1.10.4.1.2;4.1.2 Chemoselectivity;195
1.10.4.1.3;4.1.3 Substrate Specificity Subgroups;195
1.10.4.2;4.2 Nitrile Hydratase;196
1.10.4.2.1;4.2.1 Structure and Photoreactivity of Fe-Type Nitrile Hydratase;196
1.10.4.2.2;4.2.2 Structure of Co-Type Nitrile Hydratase;197
1.10.4.2.3;4.2.3 Substrate Range;198
1.10.4.3;4.3 Amidase;198
1.10.4.3.1;4.3.1 Enantioselective Amidase;198
1.10.4.3.2;4.3.2 Short Chain Aliphatic Amidase;199
1.10.5;5 Applications of Nitrile-Converting Enzymes in Biocatalysis and Bioremediation;199
1.10.5.1;5.1 Biocatalyst Forms;200
1.10.5.2;5.2 Applications in Biocatalysis;201
1.10.5.3;5.3 Biodegradation of Aliphatic Nitrile Pollutants;201
1.10.5.3.1;5.3.1 Acrylonitrile;202
1.10.5.3.2;5.3.2 Saturated Nitriles;203
1.10.5.4;5.4 Biodegradation of Benzonitrile Herbicides;204
1.10.5.5;5.5 Biotransformation Monitoring;206
1.10.6;6 Conclusions and Outlook;207
1.10.7;References;208
1.11;The Desulfurization Pathway in Rhodococcus;216
1.11.1;1 Introduction;217
1.11.2;2 Biodesulfurization Pathways in Rhodococcus;218
1.11.2.1;2.1 DBT Biodesulfurization Pathway in Rhodococcus;219
1.11.2.2;2.2 BT Biodesulfurization Pathway in Rhodococcus;220
1.11.3;3 Enzymes Involved in Specific Desulfurization;221
1.11.3.1;3.1 Enzymes Involved in DBT Desulfurization of the 4S Pathway;221
1.11.3.1.1;3.1.1 DBT-MO;222
1.11.3.1.2;3.1.2 DBTO2-MO;222
1.11.3.1.3;3.1.3 HPBS Desulfinase;223
1.11.3.1.4;3.1.4 Flavin Reductase;225
1.11.3.2;3.2 Enzymes Involved in BT-Desulfurizing Pathway;225
1.11.4;4 Specific Desulfurizing Genes in Rhodococcus;226
1.11.5;5 Enhanced Biodesulfurization by Recombinant Bacteria;228
1.11.5.1;5.1 Coexpression of Flavin Reductases;228
1.11.5.2;5.2 Promoter Modification;229
1.11.5.3;5.3 Increasing the Expression of Key Enzymes;230
1.11.5.4;5.4 The Expression of Desulfurization Enzymes in Heterologous Hosts;231
1.11.5.5;5.5 Rearranging the dsz Gene Cluster;233
1.11.6;6 Future Perspectives;234
1.11.7;References;235
1.12;Application of Rhodococcus in Bioremediation of Contaminated Environments;240
1.12.1;1 Introduction;241
1.12.2;2 Why Are Rhodococci Considered as Most Suitable for Environment Bioremediation?;244
1.12.2.1;2.1 Pristine and Contaminated Environments Are Common Habitats for Rhodococcus Species;244
1.12.2.2;2.2 Rhodococci Can Be Successfully Enriched in Laboratory Hydrocarbon-Oxidizing Consortia;246
1.12.2.3;2.3 Outstanding Physiological, Biochemical, and Ecological Properties of Rhodococcus;248
1.12.2.3.1;2.3.1 Adaptation to Hydrocarbon Assimilation;248
1.12.2.3.2;2.3.2 Ecological Plasticity;250
1.12.2.3.3;2.3.3 Biosafety Aspects;253
1.12.3;3 Rhodococcus Applications in Bioremediation Technologies;254
1.12.3.1;3.1 In Situ Treatment;254
1.12.3.2;3.2 On Site Treatment;260
1.12.3.3;3.3 Bioreactor Treatment;262
1.12.4;4 Concluding Remarks;264
1.12.5;References;265
1.13;Physiology, Biochemistry, and Molecular Biology of Triacylglycerol Accumulation by Rhodococcus;272
1.13.1;1 Introduction;273
1.13.2;2 Triacylglycerol Accumulation by Rhodococcus;274
1.13.3;3 Composition and Structure of Rhodococcal Triacylglycerols;276
1.13.4;4 Conditions for Triacylglycerol Accumulation and Mobilization;278
1.13.5;5 Triacylglycerol Biosynthesis by Rhodococcus;279
1.13.5.1;5.1 Production of Key Metabolic Precursors for Fatty Acid Biosynthesis;279
1.13.5.2;5.2 Biosynthesis of Fatty Acids;281
1.13.5.3;5.3 Biosynthesis of Triacylglycerols;283
1.13.6;6 Biogenesis of TAG Inclusion Bodies;287
1.13.7;7 Physiological Functions of TAGs in Rhodococcus;288
1.13.7.1;7.1 TAGs as Endogenous Carbon and Energy Sources;289
1.13.7.2;7.2 TAGs as Source of Precursors for Membranes and Cell Envelope;291
1.13.7.3;7.3 TAGs as a Form to Detoxify Free Fatty Acids;291
1.13.7.4;7.4 TAGs as a Form to Balance Central Metabolism;292
1.13.7.5;7.5 TAGs as Source of Intermediates for Secondary Metabolism;292
1.13.8;8 Biotechnological Significance of Rhodococcal TAGs;293
1.13.9;9 Concluding Remarks;294
1.13.10;References;295
1.14;Rhodococcus Biosurfactants: Biosynthesis, Properties, and Potential Applications;300
1.14.1;1 Introduction;301
1.14.2;2 Surfactant Production by Rhodococcus Species and Related Actinobacteria;302
1.14.3;3 Structures and Physicochemical Properties;304
1.14.4;4 Biosynthesis and Recovery;306
1.14.5;5 Physiological Roles and Biological Activity;311
1.14.6;6 Industrial Potential;312
1.14.6.1;6.1 Environmental Applications;313
1.14.6.2;6.2 Other Potential Applications;316
1.14.7;7 Conclusion;317
1.14.8;References;318
1.15;Phytopathogenic Strategies of Rhodococcus fascians;323
1.15.1;1 History of the Rhodococcus fascians Research;324
1.15.2;2 Rhodococcus fascians Infections Are a Threat for the Ornamentals Industry;326
1.15.3;3 A Linear Plasmid Carries Essential Virulence Functions;327
1.15.4;4 Unique Region U1 of pFiD188 Is the Pathogenicity Region;329
1.15.5;5 The fas Locus of Region U1 Encodes the Production of Cytokinins, the Main Virulence Factors of R. fascians;329
1.15.6;6 Virulence Gene Expression Is Subjected to a Complex Regulation;331
1.15.7;7 The Chromosome Plays a Role in the Interaction;332
1.15.8;8 Rhodococcus fascians Infection Has a Strong Molecular Impact on the Host Plant;333
1.15.9;9 Concluding Remarks;334
1.15.10;References;335
1.16;Rhodococcus equi and Its Pathogenic Mechanisms;338
1.16.1;1 Introduction;339
1.16.2;2 R. equi: A Multihost Animal Pathogen;340
1.16.2.1;2.1 Taxonomic Position and Population Genetics;340
1.16.2.2;2.2 R. equi Infection in Horses;342
1.16.2.3;2.3 Other R. equi Hosts;343
1.16.3;3 Pathogenesis and Epidemiology;344
1.16.3.1;3.1 Ecology and Transmission;344
1.16.3.2;3.2 Pathobiology of R. equi Infection;344
1.16.3.3;3.3 Molecular Epidemiology;346
1.16.4;4 Molecular Determinants of Virulence;348
1.16.4.1;4.1 Plasmid Virulence Genes: The vap Pathogenicity Island;348
1.16.4.2;4.2 Environmental Control of vap PAI Gene Expression;352
1.16.4.3;4.3 The vap Multigene Family: A Role in Host Tropism?;353
1.16.4.4;4.4 Chromosomal Determinants;354
1.16.5;5 The R. equi Genome Project;357
1.16.6;6 Concluding Remarks and Perspectives;358
1.16.7;References;359
1.17;Index;367