Overview

This book is the self-contained third volume of a comprehensive series on nitrogen fixation. It presents the state-of-the-art in regards to genomic sciences applied to nitrogen-fixation research. The advent of genomic sciences represents a new era for biology. The classic paradigm based on the gene has now changed to a paradigm that is based on the genome. The knowledge of the complete nucleotide sequence of a genome and its consequences with regard to both transcription and translation lead to an integral and comprehensive view of the biochemistry and physiology of an organism. Moreover, comparative genomic studies provide new insights for a better understanding of the evolutionary process. Nitrogen-fixation research has fully entered the genomics era since the first complete nucleotide sequences of a rhizobial symbiotic plasmid and a methanogenic archaeon were first reported in 1997. Now, the complete nucleotide sequences of many genomes of nitrogen-fixing organism from different taxonomic groups are available. This volume includes chapters devoted to the genomes of specific organisms as well as chapters that cross organismal lines and analyse general aspects centred on functional genomics, genome dynamics, taxonomy, and evolution. No other available work provides the up-to-date and in-depth coverage of this volume, which is intended to serve as an indispensable reference work for academic, governmental, and industrial scientists working in the areas of genomics, transcriptomics, and proteomics, including those studying evolution and taxonomy; to assist students to enter this challenging area of research; and to provide science administrators with ready access to vital relevant information.

Full Product Details

Author:   Rafael Palacios ,  William E. Newton
Publisher:   Springer
Imprint:   Springer
Edition:   Softcover reprint of hardcover 1st ed. 2005
Volume:   3
Dimensions:   Width: 16.00cm , Height: 1.40cm , Length: 24.00cm
Weight:   0.454kg
ISBN:  

9789048167784

ISBN 10:   9048167787
Pages:   242
Publication Date:   28 October 2010
Audience:   Professional and scholarly ,  Professional & Vocational
Format:   Paperback
Publisher's Status:   Active
Availability:   Out of stock  
The supplier is temporarily out of stock of this item. It will be ordered for you on backorder and shipped when it becomes available.

Table of Contents

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

Reviews

Author Information

Tab Content 6

Author Website:  

Customer Reviews

Recent Reviews

No review item found!

Add your own review!

Countries Available

All regions