Genomes and genomics of nitrogen-fixing organisms /
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作 者：edited by Rafael Palacios and William E. Newton.
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ISBN：9781402030543
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简介
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.
目录
Preface to the Series
Preface
List of Contributors
Origins of Genomics in Nitrogen-Fixation Research
Introduction
Symbiotic Organisms
Free-Living Organism
Conclusion
References
Genomics of Diazotrophic Archaea
Introduction
The Core nif-gene Cluster
Other nif Genes
Other Nitrogen Assimilatory Genes
PII Proteins
References
Genomic Aspects of Nitrogen Fixation in the Clostridia
Introduction
The Nitrogen-Fixing Clostridia
The Genome of the Clostridia
Organization of the Nitrogen-Fixation Gene Cluster
Regulatory Genes for Nitrogen Metabolism
Altenative Nitrogen-Fixation (anf) Genes
Genes for Nitrogen Assimilation
Concluding Remarks
References
The Genome of the Filamentous Cyanobacterium Nostoc punctiforme
Introduction
Phenotypic Traits of N. punctiforme
Overview of the N. punctiforme Genome
N. punctiforme genes Involved in Heterocyst Formation, Nitrogenase Expression, and Ammonia and Nitrate Assimilation
Summary and Conclusions
Acknowledgements
References
The nif Genes of Rhodobacter capsulatus, Rhodobacter sphaeroides and Rhodopseudomonas palustris
Introduction
Regulation of the Nitrogen-Fixation System
Operon Structure and Gene Organization
Acknowledgement
References
Genomic Architecture of the Multiple Replicons of the Promiscuous Rhizobium Species NGR234
Introduction
Promiscuity of NGR234
Structural Organization of the NGR234 Genome
Coding Capacity of eth NGR234 Genome
Conclusions and Perspectives
References
Facets of the Bradyrhizobium japonicum 110 Genome
Introduction
Materials and Methods
Genome Characteristics
Perspectives
References
pSymA of Sinorhizobium meliloti: Nitrogen Fixation and More
Introduction
History
The pSymA Sequence Project
General Features of pSymA
Comparative Genomics
Plasmid Biology
Elements of External Origin
Transfer RNA Genes
Nodulation Genes
Nitrogen-Fixation Genes
Carbon and Nitrogen Metabolism
Chemotaxis and Pilus Formation
Transport
Regulation and Signal Transduction
Stress Responses
Sulfur Metabolism
Orphan Genes
Genome-Wide Analysis
A Strategy for Analyzing pSymA of S. meliloti
References
Rhizobium etli Genome Biology
Introduction
Rhizobium etli Genome Structure
Rhizobium Genome Plasticity
Rhizobium etli Taxomony and Evolution
Acknowledgements
References
The Dawn of Functional Genomics in Nitrogen-Fixation Research
Introduction
Functional Genomics - The Role of Gene-Expression Studies
The Transcriptome
Transcriptomics in Nitrogen-Fixation Research
Transcriptomics in Plants during Symbiotic Nitrogen Fixation
The Proteome
Proteomics and Nitrogen-Fixation Research
Proteomics in Plants during Symbiotic Nitrogen Fixation
Proteomics in Concert with Transcriptomics
Global Approaches to Study the R. etli-P. vulgaris Interaction
Protein-Protein Interactions: Applications of Molecular Maps
Transcriptomics, Proteomics and Bioinformatics
Conclusions
Acknowledgements
References
Transcriptomics in Sinorhizobium meliloti
Introduction to Transcriptomics
Introduction to the Biological System
Sinorhizobium meliloti Microarrays
S. meliloti Macroarrays
Conclusions and Perspectives
Acknowledgements
References
Genome Dynamics in Rhizobial Organisms
Introduction
Reiterated Sequences
Genomic Instability
Natural Gene Amplification
Artificial Gene Amplification
Dynamics of Genome Architecture
Prediction of Genome Rearrangements
Identification of Genome Rearrangements
Artificial Selection of Genomic Rearrangements
Natural Genomic Design
Concluding Remarks
Acknowledgements
References
Impact of Genomics on the Reconstruction of Evo
Preface
List of Contributors
Origins of Genomics in Nitrogen-Fixation Research
Introduction
Symbiotic Organisms
Free-Living Organism
Conclusion
References
Genomics of Diazotrophic Archaea
Introduction
The Core nif-gene Cluster
Other nif Genes
Other Nitrogen Assimilatory Genes
PII Proteins
References
Genomic Aspects of Nitrogen Fixation in the Clostridia
Introduction
The Nitrogen-Fixing Clostridia
The Genome of the Clostridia
Organization of the Nitrogen-Fixation Gene Cluster
Regulatory Genes for Nitrogen Metabolism
Altenative Nitrogen-Fixation (anf) Genes
Genes for Nitrogen Assimilation
Concluding Remarks
References
The Genome of the Filamentous Cyanobacterium Nostoc punctiforme
Introduction
Phenotypic Traits of N. punctiforme
Overview of the N. punctiforme Genome
N. punctiforme genes Involved in Heterocyst Formation, Nitrogenase Expression, and Ammonia and Nitrate Assimilation
Summary and Conclusions
Acknowledgements
References
The nif Genes of Rhodobacter capsulatus, Rhodobacter sphaeroides and Rhodopseudomonas palustris
Introduction
Regulation of the Nitrogen-Fixation System
Operon Structure and Gene Organization
Acknowledgement
References
Genomic Architecture of the Multiple Replicons of the Promiscuous Rhizobium Species NGR234
Introduction
Promiscuity of NGR234
Structural Organization of the NGR234 Genome
Coding Capacity of eth NGR234 Genome
Conclusions and Perspectives
References
Facets of the Bradyrhizobium japonicum 110 Genome
Introduction
Materials and Methods
Genome Characteristics
Perspectives
References
pSymA of Sinorhizobium meliloti: Nitrogen Fixation and More
Introduction
History
The pSymA Sequence Project
General Features of pSymA
Comparative Genomics
Plasmid Biology
Elements of External Origin
Transfer RNA Genes
Nodulation Genes
Nitrogen-Fixation Genes
Carbon and Nitrogen Metabolism
Chemotaxis and Pilus Formation
Transport
Regulation and Signal Transduction
Stress Responses
Sulfur Metabolism
Orphan Genes
Genome-Wide Analysis
A Strategy for Analyzing pSymA of S. meliloti
References
Rhizobium etli Genome Biology
Introduction
Rhizobium etli Genome Structure
Rhizobium Genome Plasticity
Rhizobium etli Taxomony and Evolution
Acknowledgements
References
The Dawn of Functional Genomics in Nitrogen-Fixation Research
Introduction
Functional Genomics - The Role of Gene-Expression Studies
The Transcriptome
Transcriptomics in Nitrogen-Fixation Research
Transcriptomics in Plants during Symbiotic Nitrogen Fixation
The Proteome
Proteomics and Nitrogen-Fixation Research
Proteomics in Plants during Symbiotic Nitrogen Fixation
Proteomics in Concert with Transcriptomics
Global Approaches to Study the R. etli-P. vulgaris Interaction
Protein-Protein Interactions: Applications of Molecular Maps
Transcriptomics, Proteomics and Bioinformatics
Conclusions
Acknowledgements
References
Transcriptomics in Sinorhizobium meliloti
Introduction to Transcriptomics
Introduction to the Biological System
Sinorhizobium meliloti Microarrays
S. meliloti Macroarrays
Conclusions and Perspectives
Acknowledgements
References
Genome Dynamics in Rhizobial Organisms
Introduction
Reiterated Sequences
Genomic Instability
Natural Gene Amplification
Artificial Gene Amplification
Dynamics of Genome Architecture
Prediction of Genome Rearrangements
Identification of Genome Rearrangements
Artificial Selection of Genomic Rearrangements
Natural Genomic Design
Concluding Remarks
Acknowledgements
References
Impact of Genomics on the Reconstruction of Evo
Genomes and genomics of nitrogen-fixing organisms /
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