Biology of Rhodococcus (eBook)

Héctor M. Alvarez (Herausgeber)

eBook Download: PDF

2010 | 2010
XII, 368 Seiten
Springer Berlin (Verlag)
978-3-642-12937-7 (ISBN)

Infos

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.

Inhalt

Biology of Rhodococcus 3
Preface 5
Contents 7
Contributors 9
Systematics of Members of the Genus Rhodococcus (Zopf 1891) Emend Goodfellow et al. 1998 13
1 Introduction 14
2 The Past: A Brief History of the Genus Rhodococcus: A Red Coccus 15
3 Current Systematics 18
3.1 The Genus Rhodococcus 18
3.2 Current Species of Rhodococcus 20
4 Ecology of Rhodococcus spp. 22
5 Identifying New Rhodococcus Species 22
6 Tidying Up Rhodococcus Systematics 23
7 The Future of Rhodococcus Systematics 25
8 Note Added in Proof 30
References 32
The Rhodococcal Cell Envelope: Composition, Organisation and Biosynthesis 41
1 Introduction 42
2 Cell Envelope Composition in the Genus Rhodococcus: Covalently Associated Components 42
2.1 Mycolic Acids 42
2.2 The Peptidoglycan-Arabinogalactan Complex 44
3 Organisation of the Rhodococcal Cell Envelope 46
4 Non-Covalently Associated Cell Envelope Components 49
4.1 Channel Forming Porins 49
4.2 Lipoglycans 50
4.3 Cell Envelope Lipids 51
4.4 Capsules and Cell Envelope Polysaccharides 52
4.5 Lipoproteins 53
5 Biosynthesis of Key Cell Envelope Components 54
5.1 Mycolic Acid Biosynthesis 55
5.2 Arabinogalactan Biosynthesis 59
5.2.1 Linker Unit Synthesis 60
5.2.2 Galactan Synthesis 61
5.2.3 Arabinan Synthesis 62
5.2.4 Macromolecular Ligation 65
5.3 LAM Biosynthesis 68
6 Concluding Comments 71
References 72
Genomes and Plasmids in Rhodococcus 84
1 Introduction 85
2 Historical Context of Studies on Rhodococcus Genetics 85
3 Overview of Rhodococcus Genomes 87
3.1 Genome Size and Variability 88
3.2 Plasmids - Role of Linear and Circular Plasmids 90
3.3 Mobile Genetic Elements and Genetic Instability 91
4 The Genetic Basis of Catabolic Capabilities 93
5 Gene Regulation and Expression 94
6 Concluding Remarks 96
References 96
Central Metabolism of Species of the Genus Rhodococcus 102
1 Introduction 103
2 Glycolytic Pathways 104
3 Glycogen Synthesis and the Link with the Central Metabolism 111
4 Gluconeogenesis and the Phosphoenolpyruvate- Pyruvate-Oxalacetate Node 111
5 The Tricarboxylic Acid Cycle 114
6 The Glyoxylate Pathway 114
7 Litoautotrophic Processes in Rhodococcus 115
8 Concluding Remarks 116
References 117
Adaptation of Rhodococcus to Organic Solvents 120
1 Introduction 121
1.1 Predicting Solvent Toxicity 121
1.2 Effect of Solvents on Bacterial Cells 123
2 Intrinsic Resistance to Organic Solvents 124
3 Adaptation Mechanisms to Organic Solvents 127
3.1 Adaptation of the Cell Wall and of the Cellular Membrane 128
3.2 Biocatalysis and Biodegradation of the Toxic Compound 131
3.3 Other Mechanisms of Protection 135
4 Application 137
References 137
Catabolism of Aromatic Compounds and Steroids by Rhodococcus 143
1 Introduction 144
2 Mononuclear Aromatic Compounds 146
2.1 Underlying Strategies of Aromatic Compound Catabolism in Rhodococci 147
3 Peripheral Versus Central Aromatic Pathways 149
3.1 Central Pathways 149
3.1.1 beta-Ketoadipate Pathway 150
3.1.2 Modified beta-Ketoadipate Pathways 152
3.1.3 Phenylacetate (Paa) Pathway 153
3.2 Peripheral Pathways 155
3.2.1 Biphenyl and Alkylbenzene Pathways 156
3.2.2 Phthalate and Terephthalate Pathways 157
4 Polymeric and Halogenated Aromatic Compounds 158
4.1 Lignin Degradation 158
4.2 Polyaromatic Hydrocarbons 161
4.3 Halogenated Aromatic Compounds 162
4.3.1 PCBs and PBDEs 162
5 Steroids 163
5.1 Uptake of Sterols 165
5.2 Side-Chain Degradation 166
5.3 Nucleus Degradation 167
6 Conclusion and Prospects 169
References 170
Catabolism of Nitriles in Rhodococcus 180
1 Introduction 181
2 Occurrence of Nitrile-Converting Rhodococcus Strains 183
2.1 Strain Selection 183
2.2 Nitrilase-Producing Strains 184
2.3 Nitrile Hydratase-Producing Strains 184
3 Gene Organization and Regulation 188
3.1 Nitrilase Genes 188
3.2 Nitrile Hydratase Genes 189
3.2.1 Fe-Type Nitrile Hydratase 189
3.2.2 Co-Type Nitrile Hydratase 191
3.2.3 A Novel Type of Nitrile Hydratase 192
3.3 Amidase Genes 192
4 Enzyme Structural and Catalytic Properties 193
4.1 Nitrilase 193
4.1.1 Structural Variability 194
4.1.2 Chemoselectivity 195
4.1.3 Substrate Specificity Subgroups 195
4.2 Nitrile Hydratase 196
4.2.1 Structure and Photoreactivity of Fe-Type Nitrile Hydratase 196
4.2.2 Structure of Co-Type Nitrile Hydratase 197
4.2.3 Substrate Range 198
4.3 Amidase 198
4.3.1 Enantioselective Amidase 198
4.3.2 Short Chain Aliphatic Amidase 199
5 Applications of Nitrile-Converting Enzymes in Biocatalysis and Bioremediation 199
5.1 Biocatalyst Forms 200
5.2 Applications in Biocatalysis 201
5.3 Biodegradation of Aliphatic Nitrile Pollutants 201
5.3.1 Acrylonitrile 202
5.3.2 Saturated Nitriles 203
5.4 Biodegradation of Benzonitrile Herbicides 204
5.5 Biotransformation Monitoring 206
6 Conclusions and Outlook 207
References 208
The Desulfurization Pathway in Rhodococcus 216
1 Introduction 217
2 Biodesulfurization Pathways in Rhodococcus 218
2.1 DBT Biodesulfurization Pathway in Rhodococcus 219
2.2 BT Biodesulfurization Pathway in Rhodococcus 220
3 Enzymes Involved in Specific Desulfurization 221
3.1 Enzymes Involved in DBT Desulfurization of the 4S Pathway 221
3.1.1 DBT-MO 222
3.1.2 DBTO2-MO 222
3.1.3 HPBS Desulfinase 223
3.1.4 Flavin Reductase 225
3.2 Enzymes Involved in BT-Desulfurizing Pathway 225
4 Specific Desulfurizing Genes in Rhodococcus 226
5 Enhanced Biodesulfurization by Recombinant Bacteria 228
5.1 Coexpression of Flavin Reductases 228
5.2 Promoter Modification 229
5.3 Increasing the Expression of Key Enzymes 230
5.4 The Expression of Desulfurization Enzymes in Heterologous Hosts 231
5.5 Rearranging the dsz Gene Cluster 233
6 Future Perspectives 234
References 235
Application of Rhodococcus in Bioremediation of Contaminated Environments 240
1 Introduction 241
2 Why Are Rhodococci Considered as Most Suitable for Environment Bioremediation? 244
2.1 Pristine and Contaminated Environments Are Common Habitats for Rhodococcus Species 244
2.2 Rhodococci Can Be Successfully Enriched in Laboratory Hydrocarbon-Oxidizing Consortia 246
2.3 Outstanding Physiological, Biochemical, and Ecological Properties of Rhodococcus 248
2.3.1 Adaptation to Hydrocarbon Assimilation 248
2.3.2 Ecological Plasticity 250
2.3.3 Biosafety Aspects 253
3 Rhodococcus Applications in Bioremediation Technologies 254
3.1 In Situ Treatment 254
3.2 On Site Treatment 260
3.3 Bioreactor Treatment 262
4 Concluding Remarks 264
References 265
Physiology, Biochemistry, and Molecular Biology of Triacylglycerol Accumulation by Rhodococcus 272
1 Introduction 273
2 Triacylglycerol Accumulation by Rhodococcus 274
3 Composition and Structure of Rhodococcal Triacylglycerols 276
4 Conditions for Triacylglycerol Accumulation and Mobilization 278
5 Triacylglycerol Biosynthesis by Rhodococcus 279
5.1 Production of Key Metabolic Precursors for Fatty Acid Biosynthesis 279
5.2 Biosynthesis of Fatty Acids 281
5.3 Biosynthesis of Triacylglycerols 283
6 Biogenesis of TAG Inclusion Bodies 287
7 Physiological Functions of TAGs in Rhodococcus 288
7.1 TAGs as Endogenous Carbon and Energy Sources 289
7.2 TAGs as Source of Precursors for Membranes and Cell Envelope 291
7.3 TAGs as a Form to Detoxify Free Fatty Acids 291
7.4 TAGs as a Form to Balance Central Metabolism 292
7.5 TAGs as Source of Intermediates for Secondary Metabolism 292
8 Biotechnological Significance of Rhodococcal TAGs 293
9 Concluding Remarks 294
References 295
Rhodococcus Biosurfactants: Biosynthesis, Properties, and Potential Applications 300
1 Introduction 301
2 Surfactant Production by Rhodococcus Species and Related Actinobacteria 302
3 Structures and Physicochemical Properties 304
4 Biosynthesis and Recovery 306
5 Physiological Roles and Biological Activity 311
6 Industrial Potential 312
6.1 Environmental Applications 313
6.2 Other Potential Applications 316
7 Conclusion 317
References 318
Phytopathogenic Strategies of Rhodococcus fascians 323
1 History of the Rhodococcus fascians Research 324
2 Rhodococcus fascians Infections Are a Threat for the Ornamentals Industry 326
3 A Linear Plasmid Carries Essential Virulence Functions 327
4 Unique Region U1 of pFiD188 Is the Pathogenicity Region 329
5 The fas Locus of Region U1 Encodes the Production of Cytokinins, the Main Virulence Factors of R. fascians 329
6 Virulence Gene Expression Is Subjected to a Complex Regulation 331
7 The Chromosome Plays a Role in the Interaction 332
8 Rhodococcus fascians Infection Has a Strong Molecular Impact on the Host Plant 333
9 Concluding Remarks 334
References 335
Rhodococcus equi and Its Pathogenic Mechanisms 338
1 Introduction 339
2 R. equi: A Multihost Animal Pathogen 340
2.1 Taxonomic Position and Population Genetics 340
2.2 R. equi Infection in Horses 342
2.3 Other R. equi Hosts 343
3 Pathogenesis and Epidemiology 344
3.1 Ecology and Transmission 344
3.2 Pathobiology of R. equi Infection 344
3.3 Molecular Epidemiology 346
4 Molecular Determinants of Virulence 348
4.1 Plasmid Virulence Genes: The vap Pathogenicity Island 348
4.2 Environmental Control of vap PAI Gene Expression 352
4.3 The vap Multigene Family: A Role in Host Tropism? 353
4.4 Chromosomal Determinants 354
5 The R. equi Genome Project 357
6 Concluding Remarks and Perspectives 358
References 359
Index 367

Produkt-Details

• Erscheint lt. Verlag: 7.9.2010
• Reihe/Serie: Microbiology Monographs
• Reihe/Serie: Microbiology Monographs
• Zusatzinfo: XII, 368 p. 49 illus., 14 illus. in color.
• Verlagsort: Berlin
• Sprache: englisch
• Themenwelt: Studium ► 1. Studienabschnitt (Vorklinik) ► Biochemie / Molekularbiologie
• Themenwelt: Naturwissenschaften ► Biologie ► Mikrobiologie / Immunologie
• Themenwelt: Technik
• Schlagworte: Bacterial catabolism • Bacterial metabolism • biochemistry • bioremediation • Biosurfactants • Biotransformation • Cell envelope • Chemistry • Metabolism • Microbiology • pathogen • Physiology • Triacylglycerol accumulation
• ISBN-10: 3-642-12937-4 / 3642129374
• ISBN-13: 978-3-642-12937-7 / 9783642129377