Genomes and Genomics of Nitrogen-fixing Organisms by Rafael PalaciosGenomes and Genomics of Nitrogen-fixing Organisms by Rafael Palacios

Genomes and Genomics of Nitrogen-fixing Organisms

EditorRafael Palacios, William E. Newton

Paperback | October 28, 2010

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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.
Title:Genomes and Genomics of Nitrogen-fixing OrganismsFormat:PaperbackDimensions:260 pages, 9.45 × 6.3 × 0 inPublished:October 28, 2010Publisher:Springer NetherlandsLanguage:English

The following ISBNs are associated with this title:

ISBN - 10:9048167787

ISBN - 13:9789048167784

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Table of Contents

Preface to the Series. Preface. List of Contributors.1: Origins of Genomics in Nitrogen-Fixation Research; G. Dávila and R. Palacios1. Introduction2. Symbiotic Organisms3. Free-Living Organism4. ConclusionReferences2: Genomics of Diazotrophic Archaea; J.A. Leigh1. Introduction2. The Core nif-gene Cluster3. Other nif Genes4. Other Nitrogen Assimilatory Genes5. PII ProteinsReferences3: Genomic Aspects of Nitrogen Fixation in the Clostridia; J.-S. Chen1. Introduction2. The Nitrogen-Fixing Clostridia3. The Genome of the Clostridia4. Organization of the Nitrogen-Fixation Gene Cluster5. Regulatory Genes for Nitrogen Metabolism6. Altenative Nitrogen-Fixation (anf) Genes7. Genes for Nitrogen Assimilation8. Concluding RemarksReferences4: The Genome of the Filamentous Cyanobacterium Nostoc punctiforme; J.C. Meeks1. Introduction2. Phenotypic Traits of N. punctiforme3. Overview of the N. punctiforme Genome4. N. punctiforme genes Involved in Heterocyst Formation, Nitrogenase Expression, and Ammonia and Nitrate Assimilation5. Summary and ConclusionsAcknowledgementsReferences5: The nif Genes of Rhodobacter capsulatus, Rhodobacter sphaeroides and Rhodopseudomonas palustris; R. Haselkorn and V. Kapatral1. Introduction2. Regulation of the Nitrogen-Fixation System3. Operon Structure and Gene OrganizationAcknowledgementReferences6: Genomic Architecture of the Multiple Replicons of the Promiscuous Rhizobium Species NGR234; P. Mavingui, X. Perret and W. J. Broughton1. Introduction2. Promiscuity of NGR2343. Structural Organization of the NGR234 Genome4. Coding Capacity of eth NGR234 Genome5. Conclusions and PerspectivesReferences7: Facets of the Bradyrhizobium japonicum 110 Genome; M. Göttfert, H. Henneckeand S. Tabata1. Introduction2. Materials and Methods3. Genome Characteristics4. PerspectivesReferences8: pSymA of Sinorhizobium meliloti: Nitrogen Fixation and More; M.J. Barnett and M.L. Kahn1. Introduction2. History3. The pSymA Sequence Project4. General Features of pSymA5. Comparative Genomics6. Plasmid Biology7. Elements of External Origin8. Transfer RNA Genes9. Nodulation Genes10. Nitrogen-Fixation Genes11. Carbon and Nitrogen Metabolism12. Chemotaxis and Pilus Formation13. Transport14. Regulation and Signal Transduction15. Stress Responses16. Sulfur Metabolism17. Orphan Genes18. Genome-Wide Analysis19. A Strategy for Analyzing pSymA of S. meliloti References9: Rhizobium etli Genome Biology; G. Dávila, V. González, M.A. Ramírez-Romero and O. Rodríguez1. Introduction 2. Rhizobium etli Genome Structure 3. Rhizobium Genome Plasticity 4. Rhizobium etli Taxomony and Evolution Acknowledgements References10: The Dawn of Functional Genomics in Nitrogen-Fixation Research; S. Encarnación 1. Introduction2. Functional Genomics - The Role of Gene-Expression Studies3. The Transcriptome4. Transcriptomics in Nitrogen-Fixation Research5. Transcriptomics in Plants during Symbiotic Nitrogen Fixation6. The Proteome7. Proteomics and Nitrogen-Fixation Research8. Proteomics in Plants during Symbiotic Nitrogen Fixation9. Proteomics in Concert with Transcriptomics10. Global Approaches to Study the R. etli-P. vulgaris Interaction11. Protein-Protein Interactions: Applications of Molecular Maps12. Transcriptomics, Proteomics and Bioinformatics13. ConclusionsAcknowledgementsReferences11: Transcriptomics in Sinorhizobium meliloti; A. Becker and F. J. De Bruijn1. Introduction to Transcriptomics2. Introduction to the Biological System3. Sinorhizobium meliloti Microarray4. S. meliloti Macroarrays5. Conclusions and PerspectiveAcknowledgementsReferences12: Genome Dynamics in Rhizobial Organisms; R. Palacios and M. Flores1. Introduction2. Reiterated Sequences3. Genomic Instability4. Natural Gene Amplification5. Artificial Gene Amplification6. Dynamics of Genome Architecture7. Prediction of Genome Rearrangements8. Identification of Genome Rearrangements9. Artificial Selection of Genomic Rearrangements10. Natural Genomic Design11. Concluding RemarksAcknowledgementsReferences 13: Impact of Genomics on the Reconstruction of Evolutionary Relationships of Nitrogen-Fixing Bacteria and Implications for Taxonomy; P. Van Berkum and B. D. Eardly1. Systematics2. Current Reflections for Evolution of Diazotrophy3. Reconstruction of Evolutionary Relationships among Members of the Kingdom Monera4. The Rapid Spread of Antibiotic Resistance: Implications of Reticulate Microbial Evolution5. Mechanisms of Horizontal Gene Transfer in Microbes6. Significance of Horizontal Gene transfer in Nature7. Evidence for Lateral Gene Transfers and Recombination in Microbial Genomes8. Genomic Islands9. Microbial Evolution and Genetic Recombination10. Established Species Concepts Applied to Bacteria11. A Proposed Unified Species for Bacteria12. Relevant Insights from Recent Genomic Comparisons13. Implications and Future StrategiesAcknowledgementsReferences 14: The Phylogeny and Evolution of Nitrogenases; J.P.W. Young1. Introduction2. The Genetic Organization of Nitrogenase Genes3. Nitrogenase Genes from Genome Sequencing Projects4. Organization of the Nitrogenase Genes5. Evolutionary Relationships of the Nitrogenase Genes6. Nitrogenase Phylogeny versus Organism Phylogeny7. Nitrogenase Genes in their Genomic Context8. Conclusions and ProspectsReferencesSubject Index