Genomes And Geomics of Nitrogen-fixing Organisms

by Palacios, Rafael; Newton, William E.

• ISBN13: 9781402030536
• ISBN10: 1402030533
• Format: Hardcover
• Copyright: 2005-02-28
• Publisher: Springer Verlag

Summary

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.

Table of Contents

Preface to the Series	ix
Preface	xiii
List of Contributors	xv
Origins of Genomics in Nitrogen-Fixation Research	1	(6)
G. Davila
R. Palacios
Introduction	1	(1)
Symbiotic Organisms	2	(1)
Free-Living Organism	3	(2)
Conclusion	5	(2)
References	5	(2)
Genomics of Diazotrophic Archaea	7	(6)
J. A. Leigh
Introduction	7	(1)
The Core nif-gene Cluster	8	(1)
Other nif Genes	9	(1)
Other Nitrogen Assimilatory Genes	9	(1)
PII Proteins	10	(3)
References	11	(2)
Genomic Aspects of Nitrogen Fixation in the Clostridia	13	(14)
J.-S. Chen
Introduction	13	(1)
The Nitrogen-Fixing Clostridia	14	(1)
The Genome of the Clostridia	15	(2)
Organization of the Nitrogen-Fixation Gene Cluster	17	(4)
Regulatory Genes for Nitrogen Metabolism	21	(2)
Altenative Nitrogen-Fixation (anf) Genes	23	(1)
Genes for Nitrogen Assimilation	23	(1)
Concluding Remarks	24	(3)
References	24	(3)
The Genome of the Filamentous Cyanobacterium Nostoc punctiforme	27	(44)
J. C. Meeks
Introduction	27	(2)
Phenotypic Traits of N. punctiforme	29	(8)
Overview of the N. punctiforme Genome	37	(9)
N. punctiforme genes Involved in Heterocyst Formation, Nitrogenase Expression, and Ammonia and Nitrate Assimilation	46	(17)
Summary and Conclusions	63	(8)
Acknowledgements	64	(1)
References	64	(7)
The nif Genes of Rhodobacter capsulatus, Rhodobacter sphaeroides and Rhodopseudomonas palustris	71	(12)
R. Haselkorn
V. Kapatral
Introduction	71	(2)
Regulation of the Nitrogen-Fixation System	73	(2)
Operon Structure and Gene Organization	75	(8)
Acknowledgement	80	(1)
References	80	(3)
Genomic Architecture of the Multiple Replicons of the Promiscuous Rhizobium Species NGR234	83	(16)
P. Mavingui
X. Perret
W. J. Broughton
Introduction	83	(1)
Promiscuity of NGR234	84	(1)
Structural Organization of the NGR234 Genome	85	(6)
Coding Capacity of eth NGR234 Genome	91	(1)
Conclusions and Perspectives	92	(7)
References	93	(6)
Facets of the Bradyrhizobium japonicum 110 Genome	99	(14)
M. Gottfert
H. Hennecke
S. Tabata
Introduction	99	(1)
Materials and Methods	100	(1)
Genome Characteristics	100	(8)
Perspectives	108	(5)
References	108	(5)
pSymA of Sinorhizobium meliloti: Nitrogen Fixation and More	113	(20)
M. J. Barnett
M. L. Kahn
Introduction	113	(1)
History	114	(1)
The pSymA Sequence Project	115	(1)
General Features of pSymA	115	(1)
Comparative Genomics	116	(1)
Plasmid Biology	117	(1)
Elements of External Origin	117	(2)
Transfer RNA Genes	119	(1)
Nodulation Genes	119	(1)
Nitrogen-Fixation Genes	120	(1)
Carbon and Nitrogen Metabolism	121	(2)
Chemotaxis and Pilus Formation	123	(1)
Transport	123	(1)
Regulation and Signal Transduction	124	(1)
Stress Responses	125	(1)
Sulfur Metabolism	126	(1)
Orphan Genes	126	(1)
Genome-Wide Analysis	127	(1)
A Strategy for Analyzing pSymA of S. meliloti	127	(6)
References	128	(5)
Rhizobium etli Genome Biology	133	(10)
G. Davila
V. Gonzalez
M. A. Ramirez-Romero
O. Rodriguez
Introduction	133	(1)
Rhizobium etli Genome Structure	134	(2)
Rhizobium Genome Plasticity	136	(2)
Rhizobium etli Taxomony and Evolution	138	(5)
Acknowledgements	140	(1)
References	141	(2)
The Dawn of Functional Genomics in Nitrogen-Fixation Research	143	(26)
S. Encarnacion
Introduction	143	(1)
Functional Genomics -- The Role of Gene-Expression Studies	144	(1)
The Transcriptome	145	(1)
Transcriptomics in Nitrogen-Fixation Research	146	(2)
Transcriptomics in Plants during Symbiotic Nitrogen Fixation	148	(2)
The Proteome	150	(2)
Proteomics and Nitrogen-Fixation Research	152	(4)
Proteomics in Plants during Symbiotic Nitrogen Fixation	156	(1)
Proteomics in Concert with Transcriptomics	157	(1)
Global Approaches to Study the R. etli-P. vulgaris Interaction	158	(2)
Protein-Protein Interactions: Applications of Molecular Maps	160	(1)
Transcriptomics, Proteomics and Bioinformatics	160	(2)
Conclusions	162	(7)
Acknowledgements	163	(1)
References	163	(6)
Transcriptomics in Sinorhizobium meliloti	169	(14)
A. Becker
F. J. De Bruijn
Introduction to Transcriptomics	169	(2)
Introduction to the Biological System	171	(1)
Sinorhizobium meliloti Microarrays	172	(3)
S. meliloti Macroarrays	175	(3)
Conclusions and Perspectives	178	(5)
Acknowledgements	179	(1)
References	180	(3)
Genome Dynamics in Rhizobial Organisms	183	(18)
R. Palacios
M. Flores
Introduction	183	(1)
Reiterated Sequences	184	(2)
Genomic Instability	186	(2)
Natural Gene Amplication	188	(1)
Artificial Gene Amplification	189	(2)
Dynamics of Genome Architecture	191	(2)
Prediction of Genome Rearrangements	193	(1)
Identification of Genome Rearrangements	194	(1)
Artificial Selection of Genomic Rearrangements	195	(2)
Natural Genomic Design	197	(1)
Concluding Remarks	197	(4)
Acknowledgements	197	(1)
References	198	(3)
Impact of Genomics on the Reconstruction of Evolutionary Relationships of Nitrogen-Fixing Bacteria and Implications for Taxomony	201	(20)
P. Van Berkum
B. D. Eardly
Systematics	201	(2)
Current Reflections for Evolution of Diazotrophy	203	(1)
Reconstruction of Evolutionary Relationships among Members of the Kingdom Monera	203	(2)
The Rapid Spread of Antibiotic Resistance: Implications of Reticulate Microbial Evolution	205	(1)
Mechanisms of Horizontal Gene Transfer in Microbes	205	(1)
Significance of Horizontal Gene transfer in Nature	206	(2)
Evidence for Lateral Gene Transfers and Recombination in Microbial Genomes	208	(1)
Genomic Islands	209	(1)
Microbial Evolution and Genetic Recombination	210	(1)
Established Species Concepts Applied to Bacteria	210	(2)
A Proposed Unified Species fro Bacteria	212	(1)
Relevant Insights from Recent Genomic Comparisons	212	(1)
Implications and Future Strategies	213	(8)
Acknowledgements	214	(1)
References	214	(7)
The Phylogeny and Evolution of Nitrogenases	221	(22)
J. P. W. Young
Introduction	221	(1)
The Genetic Organization of Nitrogenase Genes	222	(2)
Nitrogenase Genes from Genome Sequencing Projects	224	(1)
Organization of the Nitrogenase Genes	225	(1)
Evolutionary Relationships of the Nitrogenase Genes	225	(6)
Nitrogenase Phylogeny versus Organism Phylogeny	231	(7)
Nitrogenase Genes in their Genomic Context	238	(1)
Conclusions and Prospects	238	(5)
References	239	(4)
Subject Index	243