Genomes and Genomics of Nitrogen-fixing Organisms
(Sprache: Englisch)
Genomes and Genomics of Nitrogen-fixing Organisms This is Volume 3 of a seven-volume series on all aspects of Nitrogen Fixation. The series aims to be the definitive authority in the field and to act as a benchmark for some years to come. Rather than...
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Klappentext zu „Genomes and Genomics of Nitrogen-fixing Organisms “
Genomes and Genomics of Nitrogen-fixing Organisms This is Volume 3 of a seven-volume series on all aspects of Nitrogen Fixation. The series aims to be the definitive authority in the field and to act as a benchmark for some years to come. Rather than attempting to cram the whole field into a single volume, the subject matter is divided among seven volumes to allow authors the luxury of writing in depth with a comprehensive reference base. All authors are recognized practicing scientists in the area of their contribution, which ensures the high quality, relevance, and readability of the chapters. In establishing the rationale for, and the organization of, this book, we realized the need to divide it into two sections. The first section should be organism based and should review our current knowledge of the genomes of nitrogen-fixing organisms and what these nucleotide sequences tell us. The second section should then be technology based. It should review what technologies are available to mine the data inherent in the nucleotide sequences and how they are now being used to produce gene-function data from differential gene expression.
Inhaltsverzeichnis zu „Genomes and Genomics of Nitrogen-fixing Organisms “
- Preface to the Seriesix Preface
xiii List of Contributors
xv Chapter 1 Origins of Genomics in Nitrogen-Fixation Research G. Dávila and R. Palacios 1
1. Introduction 1
2. Symbiotic Organisms 2
3. Free-Living Organism 3
4. Conclusion 5
- References 5
Chapter 2 Genomics of Diazotrophic Archaea J. A. Leigh 7
1. Introduction 7
2. The Core nif-gene Cluster 8
3. Other nif Genes 9
4. Other Nitrogen Assimilatory Genes 9
5. PII Proteins 10
- References 11
Chapter 3 Genomic Aspects of Nitrogen Fixation in the Clostridia J.-S. Chen 13
1. Introduction 13
2. The Nitrogen-Fixing Clostridia14
3. The Genome of the Clostridia15
4. Organization of the Nitrogen-Fixation Gene Cluster 17
5. Regulatory Genes for Nitrogen Metabolism 21
6. Altenative Nitrogen-Fixation (anf) Genes 23
7. Genes for Nitrogen Assimilation 23
8. Concluding Remarks 24
- References 24
Chapter 4 The Genome of the Filamentous Cyanobacterium Nostoc punctiforme J. C. Meeks 27
1. Introduction 27
2. Phenotypic Traits of N. punctiforme 29
3. Overview of the N. punctiforme Genome 37
4. N. punctiforme genes Involved in Heterocyst Formation, Nitrogenase Expression, and Ammonia and Nitrate Assimilation 46
5. Summary and Conclusions 63
- Acknowledgements 64
- References 64
Chapter 5 The nif Genes of Rhodobacter capsulatus, Rhodobacter sphaeroides and Rhodopseudomonas palustris R. Haselkorn and V. Kapatral 71
1. Introduction 71
2. Regulation of the Nitrogen-Fixation System 73
3. Operon Structure and Gene Organization 75
- Acknowledgement 80
- References 80
Chapter 6 Genomic Architecture of the Multiple Replicons of the Promiscuous Rhizobium Species NGR234 P. Mavingui, X. Perret and W. J. Broughton 83
1. Introduction 83
2. Promiscuity of NGR234 84
3. Structural Organization of the NGR234 Genome 85
4. Coding Capacity of eth NGR234 Genome 91
5. Conclusions and Perspectives 92
- References 93
Chapter 7 Facets of the Bradyrhizobium japonicum 110 Genome M. Göttfert, H. Hennecke and S.
... mehr
Tabata 99
1. Introduction 99
2. Materials and Methods 100
3. Genome Characteristics 100
4. Perspectives 108
- References 108
Chapter 8 pSymA of Sinorhizobium meliloti: Nitrogen Fixation and More M. J. Barnett and M. L. Kahn 113
1. Introduction 113
2. History 114
3. The pSymA Sequence Project 115
4. General Features of pSymA115
5. Comparative Genomics 116
6. Plasmid Biology 117
7. Elements of External Origin 117
8. Transfer RNA Genes 119
9. Nodulation Genes 119
10. Nitrogen-Fixation Genes 120
11. Carbon and Nitrogen Metabolism 121
12. Chemotaxis and Pilus Formation 123
13. Transport 123
14. Regulation and Signal Transduction 124
15. Stress Responses 125
16. Sulfur Metabolism 126
17. Orphan Genes 126
18. Genome-Wide Analysis 127
19. A Strategy for Analyzing pSymA of S. meliloti 127
- References 128
Chapter 9 Rhizobium etli Genome Biology 133
1. Introduction 133
2. Rhizobium etli Genome Structure 134
3. Rhizobium Genome Plasticity 136
4. Rhizobium etli Taxomony and Evolution 138
- Acknowledgements 140
- References 141
Chapter 10 The Dawn of Functional Genomics in Nitrogen-Fixation Research S. Encarnación 143
1. Introduction 143
2. Functional Genomics - The Role of Gene-Expression Studies 144
3. The Transcriptome 145
4. Transcriptomics in Nitrogen-Fixation Research146
5. Transcriptomics in Plants during Symbiotic Nitrogen Fixation 148
6. The Proteome 150
7. Proteomics and Nitrogen-Fixation Research 152
8. Proteomics in Plants during Symbiotic Nitrogen Fixation 156
9. Proteomics in Concert with Transcriptomics 157
10. Global Approaches to Study the R. etli-P. vulgaris Interaction 158
11. Protein-Protein Interactions: Applications of Molecular Maps 160
12. Transcriptomics, Proteomics and Bioinformatics 160
13. Conclusions 162Acknowledgements 163
- References 163
Chapter 11 Transcriptomics in Sinorhizobium meliloti A. Becker and F. J. De Bruijn 169
1. Introduction to Transcriptomics 169
2. Introduction to the Biological System 171
3. Sinorhizobium meliloti Microarrays172
4. S. meliloti Macroarrays 175
5. Conclusions and Perspectives178
- Acknowledgements 179
- References 180
Chapter 12 Genome Dynamics in Rhizobial Organisms R. Palacios and M. Flores 183
1. Introduction 183
2. Reiterated Sequences 184
3. Genomic Instability 186
4. Natural Gene Amplication 188
5. Artificial Gene Amplification 189
6. Dynamics of Genome Architecture 191
7. Prediction of Genome Rearrangements 193
8. Identification of Genome Rearrangements 194
9. Artificial Selection of Genomic Rearrangements 195
10. Natural Genomic Design 197
11. Concluding Remarks 197
- Acknowledgements 197
- References 198
Chapter 13 Impact of Genomics on the Reconstruction of Evolutionary Relationships of Nitrogen-Fixing Bacteria and Implications for Taxomony P. Van Berkum and B. D. Eardly 201
1. Systematics 201
2. Current Reflections for Evolution of Diazotrophy 203
3. Reconstruction of Evolutionary Relationships among Members of the Kingdom Monera 203
4. The Rapid Spread of Antibiotic Resistance: Implications of Reticulate Microbial Evolution 205
5. Mechanisms of Horizontal Gene Transfer in Microbes 205
6. Significance of Horizontal Gene transfer in Nature 206
7. Evidence for Lateral Gene Transfers and Recombination in Microbial Genomes 208
8. Genomic Islands 209
9. Microbial Evolution and Genetic Recombination 210
10. Established Species Concepts Applied to Bacteria 210
11. A Proposed Unified Species fro Bacteria 212
12. Relevant Insights from Recent Genomic Comparisons 212
13. Implications and Future Strategies 213
- Acknowledgements 214
- References 214
Chapter 14 The Phylogeny and Evolution of Nitrogenases J. P. W. Young 221
1. Introduction 221
2. The Genetic Organization of Nitrogenase Genes 222
3. Nitrogenase Genes from Genome Sequencing Projects 224
4. Organization of the Nitrogenase Genes 225
5. Evolutionary Relationships of the Nitrogenase Genes 225
6. Nitrogenase Phylogeny versus Organism Phylogeny 231
7. Nitrogenase Genes in their Genomic Context 238
8. Conclusions and Prospects 238
- References 239
- Subject Index 243
1. Introduction 99
2. Materials and Methods 100
3. Genome Characteristics 100
4. Perspectives 108
- References 108
Chapter 8 pSymA of Sinorhizobium meliloti: Nitrogen Fixation and More M. J. Barnett and M. L. Kahn 113
1. Introduction 113
2. History 114
3. The pSymA Sequence Project 115
4. General Features of pSymA115
5. Comparative Genomics 116
6. Plasmid Biology 117
7. Elements of External Origin 117
8. Transfer RNA Genes 119
9. Nodulation Genes 119
10. Nitrogen-Fixation Genes 120
11. Carbon and Nitrogen Metabolism 121
12. Chemotaxis and Pilus Formation 123
13. Transport 123
14. Regulation and Signal Transduction 124
15. Stress Responses 125
16. Sulfur Metabolism 126
17. Orphan Genes 126
18. Genome-Wide Analysis 127
19. A Strategy for Analyzing pSymA of S. meliloti 127
- References 128
Chapter 9 Rhizobium etli Genome Biology 133
1. Introduction 133
2. Rhizobium etli Genome Structure 134
3. Rhizobium Genome Plasticity 136
4. Rhizobium etli Taxomony and Evolution 138
- Acknowledgements 140
- References 141
Chapter 10 The Dawn of Functional Genomics in Nitrogen-Fixation Research S. Encarnación 143
1. Introduction 143
2. Functional Genomics - The Role of Gene-Expression Studies 144
3. The Transcriptome 145
4. Transcriptomics in Nitrogen-Fixation Research146
5. Transcriptomics in Plants during Symbiotic Nitrogen Fixation 148
6. The Proteome 150
7. Proteomics and Nitrogen-Fixation Research 152
8. Proteomics in Plants during Symbiotic Nitrogen Fixation 156
9. Proteomics in Concert with Transcriptomics 157
10. Global Approaches to Study the R. etli-P. vulgaris Interaction 158
11. Protein-Protein Interactions: Applications of Molecular Maps 160
12. Transcriptomics, Proteomics and Bioinformatics 160
13. Conclusions 162Acknowledgements 163
- References 163
Chapter 11 Transcriptomics in Sinorhizobium meliloti A. Becker and F. J. De Bruijn 169
1. Introduction to Transcriptomics 169
2. Introduction to the Biological System 171
3. Sinorhizobium meliloti Microarrays172
4. S. meliloti Macroarrays 175
5. Conclusions and Perspectives178
- Acknowledgements 179
- References 180
Chapter 12 Genome Dynamics in Rhizobial Organisms R. Palacios and M. Flores 183
1. Introduction 183
2. Reiterated Sequences 184
3. Genomic Instability 186
4. Natural Gene Amplication 188
5. Artificial Gene Amplification 189
6. Dynamics of Genome Architecture 191
7. Prediction of Genome Rearrangements 193
8. Identification of Genome Rearrangements 194
9. Artificial Selection of Genomic Rearrangements 195
10. Natural Genomic Design 197
11. Concluding Remarks 197
- Acknowledgements 197
- References 198
Chapter 13 Impact of Genomics on the Reconstruction of Evolutionary Relationships of Nitrogen-Fixing Bacteria and Implications for Taxomony P. Van Berkum and B. D. Eardly 201
1. Systematics 201
2. Current Reflections for Evolution of Diazotrophy 203
3. Reconstruction of Evolutionary Relationships among Members of the Kingdom Monera 203
4. The Rapid Spread of Antibiotic Resistance: Implications of Reticulate Microbial Evolution 205
5. Mechanisms of Horizontal Gene Transfer in Microbes 205
6. Significance of Horizontal Gene transfer in Nature 206
7. Evidence for Lateral Gene Transfers and Recombination in Microbial Genomes 208
8. Genomic Islands 209
9. Microbial Evolution and Genetic Recombination 210
10. Established Species Concepts Applied to Bacteria 210
11. A Proposed Unified Species fro Bacteria 212
12. Relevant Insights from Recent Genomic Comparisons 212
13. Implications and Future Strategies 213
- Acknowledgements 214
- References 214
Chapter 14 The Phylogeny and Evolution of Nitrogenases J. P. W. Young 221
1. Introduction 221
2. The Genetic Organization of Nitrogenase Genes 222
3. Nitrogenase Genes from Genome Sequencing Projects 224
4. Organization of the Nitrogenase Genes 225
5. Evolutionary Relationships of the Nitrogenase Genes 225
6. Nitrogenase Phylogeny versus Organism Phylogeny 231
7. Nitrogenase Genes in their Genomic Context 238
8. Conclusions and Prospects 238
- References 239
- Subject Index 243
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Bibliographische Angaben
- 2005, 242 Seiten, Maße: 23,2 cm, Gebunden, Englisch
- Herausgegeben:Palacios, Rafael; Newton, William E.
- Verlag: Springer Netherlands
- ISBN-10: 1402030533
- ISBN-13: 9781402030536
Sprache:
Englisch
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