Genomes and Genomics of Nitrogen-fixing Organisms

1. Auflage. Softcover version of original hardcover Auflage 2005
ISBN: 978-90-481-6778-4
Verlag: Springer Netherlands

Buch, Englisch, Band 3, 242 Seiten, Paperback, Format (B × H): 160 mm x 240 mm, Gewicht: 428 g

Reihe: Nitrogen Fixation: Origins, Applications, and Research Progress

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.

Zielgruppe

Research

Autoren/Hrsg.

Newton, William E.

Palacios, Rafael

Fachgebiete

• Naturwissenschaften Biowissenschaften Tierkunde / Zoologie Tierphysiologie
• Naturwissenschaften Biowissenschaften Biowissenschaften
• Naturwissenschaften Biowissenschaften Biochemie (nichtmedizinisch)

Inhaltsverzeichnis

Preface to the Series. ix

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. GenomicAspects of Nitrogen Fixation in the Clostridia

J.-S. Chen. 13

1. Introduction. 13

2. The Nitrogen-Fixing Clostridia. 14

3. The Genome of the Clostridia. 15

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. 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 pSymA. 115

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 Research. 146

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. 162

Acknowledgements. 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 Microarrays. 172

4. S. meliloti Macroarrays. 175

5. Conclusions and Perspectives. 178

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