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.
Preface to the Series. Preface. List of Contributors.
1: Origins of Genomics in Nitrogen-Fixation Research; G. Dávila and R. Palacios
1. Introduction
2. Symbiotic Organisms
3. Free-Living Organism
4. Conclusion
References
2: Genomics of Diazotrophic Archaea; J.A. Leigh
1. Introduction
2. The Core nif-gene Cluster
3. Other nif Genes
4. Other Nitrogen Assimilatory Genes
5. PII Proteins
References
3: Genomic Aspects of Nitrogen Fixation in the Clostridia; J.-S. Chen
1. Introduction
2. The Nitrogen-Fixing Clostridia
3. The Genome of the Clostridia
4. Organization of the Nitrogen-Fixation Gene Cluster
5. Regulatory Genes for Nitrogen Metabolism
6. Altenative Nitrogen-Fixation (anf) Genes
7. Genes for Nitrogen Assimilation
8. Concluding Remarks
References
4: The Genome of the Filamentous Cyanobacterium Nostoc punctiforme; J.C. Meeks
1. Introduction
2. Phenotypic Traits of N. punctiforme
3. Overview of the N. punctiforme Genome
4. N. punctiforme genes Involved in Heterocyst Formation, Nitrogenase Expression, and Ammonia and Nitrate Assimilation
5. Summary and Conclusions
Acknowledgements
References
5: The nif Genes of Rhodobacter capsulatus, Rhodobacter sphaeroides and Rhodopseudomonas palustris; R. Haselkorn and V. Kapatral
1. Introduction
2. Regulation of the Nitrogen-Fixation System
3. Operon Structure and Gene Organization
Acknowledgement
References
6: Genomic Architecture of the Multiple Replicons of the Promiscuous Rhizobium Species NGR234; P. Mavingui, X. Perret and W. J. Broughton
1. Introduction
2. Promiscuity of NGR234
3. Structural Organization of the NGR234 Genome
4. Coding Capacity of eth NGR234 Genome
5. Conclusions and Perspectives
References
7: Facets of the Bradyrhizobium japonicum 110 Genome; M. Göttfert, H. Hennecke
and S. Tabata
1. Introduction
2. Materials and Methods
3. Genome Characteristics
4. Perspectives
References
8: pSymA of Sinorhizobium meliloti: Nitrogen Fixation and More; M.J. Barnett and M.L. Kahn
1. Introduction
2. History
3. The pSymA Sequence Project
4. General Features of pSymA
5. Comparative Genomics
6. Plasmid Biology
7. Elements of External Origin
8. Transfer RNA Genes
9. Nodulation Genes
10. Nitrogen-Fixation Genes
11. Carbon and Nitrogen Metabolism
12. Chemotaxis and Pilus Formation
13. Transport
14. Regulation and Signal Transduction
15. Stress Responses
16. Sulfur Metabolism
17. Orphan Genes
18. Genome-Wide Analysis
19. A Strategy for Analyzing pSymA of S. meliloti
References
9: Rhizobium etli Genome Biology; G. Dávila, V. González, M.A. Ramírez-Romero and O. Rodríguez
1. Introduction
2. Rhizobium etli Genome Structure
3. Rhizobium Genome Plasticity
4. Rhizobium etli Taxomony and Evolution
Acknowledgements
References
10: The Dawn of Functional Genomics in Nitrogen-Fixation Research; S. Encarnación
1. Introduction
2. Functional Genomics – The Role of Gene-Expression Studies
3. The Transcriptome
4. Transcriptomics in Nitrogen-Fixation Research
5. Transcriptomics in Plants during Symbiotic Nitrogen Fixation
6. The Proteome
7. Proteomics and Nitrogen-Fixation Research
8. Proteomics in Plants during Symbiotic Nitrogen Fixation
9. Proteomics in Concert with Transcriptomics
10. Global Approaches to Study the R. etli-P. vulgaris Interaction
11. Protein-Protein Interactions: Applications of Molecular Maps
12. Transcriptomics, Proteomics and Bioinformatics
13. Conclusions
Acknowledgements
References
11: Transcriptomics in Sinorhizobium meliloti; A. Becker and F. J. De Bruijn
1. Introduction to Transcriptomics
2. Introduction to the Biological System
3. Sinorhizobium meliloti Microarray
4. S. meliloti Macroarrays
5. Conclusions and Perspective
Acknowledgements
References
12: Genome Dynamics in Rhizobial Organisms; R. Palacios and M. Flores
1. Introduction
2. Reiterated Sequences
3. Genomic Instability
4. Natural Gene Amplification
5. Artificial Gene Amplification
6. Dynamics of Genome Architecture
7. Prediction of Genome Rearrangements
8. Identification of Genome Rearrangements
9. Artificial Selection of Genomic Rearrangements
10. Natural Genomic Design
11. Concluding Remarks
Acknowledgements
References
13: Impact of Genomics on the Reconstruction of Evolutionary Relationships of Nitrogen-Fixing Bacteria and Implications for Taxonomy; P. Van Berkum and B. D. Eardly
1. Systematics
2. Current Reflections for Evolution of Diazotrophy
3. Reconstruction of Evolutionary Relationships among Members of the Kingdom Monera
4. The Rapid Spread of Antibiotic Resistance: Implications of Reticulate Microbial Evolution
5. Mechanisms of Horizontal Gene Transfer in Microbes
6. Significance of Horizontal Gene transfer in Nature
7. Evidence for Lateral Gene Transfers and Recombination in Microbial Genomes
8. Genomic Islands
9. Microbial Evolution and Genetic Recombination
10. Established Species Concepts Applied to Bacteria
11. A Proposed Unified Species for Bacteria
12. Relevant Insights from Recent Genomic Comparisons
13. Implications and Future Strategies
AcknowledgementsReferences
14: The Phylogeny and Evolution of Nitrogenases; J.P.W. Young
1. Introduction
2. The Genetic Organization of Nitrogenase Genes
3. Nitrogenase Genes from Genome Sequencing Projects
4. Organization of the Nitrogenase Genes
5. Evolutionary Relationships of the Nitrogenase Genes
6. Nitrogenase Phylogeny versus Organism Phylogeny
7. Nitrogenase Genes in their Genomic Context
8. Conclusions and Prospects
References
Subject Index
