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Genomes and Genomics of Nitrogen-fixing Organisms de Rafael Palacios

Genomes and Genomics of Nitrogen-fixing Organisms: Nitrogen Fixation: Origins, Applications, and Research Progress, cartea 3

Editat de Rafael Palacios, William E. Newton
en Limba Engleză Hardback – 15 feb 2005
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.
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Specificații

ISBN-13: 9781402030536
ISBN-10: 1402030533
Pagini: 264
Ilustrații: XVIII, 242 p.
Dimensiuni: 156 x 232 x 22 mm
Greutate: 0.55 kg
Ediția:2005
Editura: SPRINGER NETHERLANDS
Colecția Springer
Seria Nitrogen Fixation: Origins, Applications, and Research Progress

Locul publicării:Dordrecht, Netherlands

Public țintă

Research

Cuprins

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