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Evolutionary, structural and functional relationships revealed by comparative analysis of syntenic genes in Rhizobiales

BACKGROUND: Comparative genomics has provided valuable insights into the nature of gene sequence variation and chromosomal organization of closely related bacterial species. However, questions about the biological significance of gene order conservation, or synteny, remain open. Moreover, few compre...

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Autores principales: Guerrero, Gabriela, Peralta, Humberto, Aguilar, Alejandro, Díaz, Rafael, Villalobos, Miguel Angel, Medrano-Soto, Arturo, Mora, Jaime
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2005
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1276791/
https://www.ncbi.nlm.nih.gov/pubmed/16229745
http://dx.doi.org/10.1186/1471-2148-5-55
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author Guerrero, Gabriela
Peralta, Humberto
Aguilar, Alejandro
Díaz, Rafael
Villalobos, Miguel Angel
Medrano-Soto, Arturo
Mora, Jaime
author_facet Guerrero, Gabriela
Peralta, Humberto
Aguilar, Alejandro
Díaz, Rafael
Villalobos, Miguel Angel
Medrano-Soto, Arturo
Mora, Jaime
author_sort Guerrero, Gabriela
collection PubMed
description BACKGROUND: Comparative genomics has provided valuable insights into the nature of gene sequence variation and chromosomal organization of closely related bacterial species. However, questions about the biological significance of gene order conservation, or synteny, remain open. Moreover, few comprehensive studies have been reported for rhizobial genomes. RESULTS: We analyzed the genomic sequences of four fast growing Rhizobiales (Sinorhizobium meliloti, Agrobacterium tumefaciens, Mesorhizobium loti and Brucella melitensis). We made a comprehensive gene classification to define chromosomal orthologs, genes with homologs in other replicons such as plasmids, and those which were species-specific. About two thousand genes were predicted to be orthologs in each chromosome and about 80% of these were syntenic. A striking gene colinearity was found in pairs of organisms and a large fraction of the microsyntenic regions and operons were similar. Syntenic products showed higher identity levels than non-syntenic ones, suggesting a resistance to sequence variation due to functional constraints; also, an unusually high fraction of syntenic products contained membranal segments. Syntenic genes encode a high proportion of essential cell functions, presented a high level of functional relationships and a very low horizontal gene transfer rate. The sequence variability of the proteins can be considered the species signature in response to specific niche adaptation. Comparatively, an analysis with genomes of Enterobacteriales showed a different gene organization but gave similar results in the synteny conservation, essential role of syntenic genes and higher functional linkage among the genes of the microsyntenic regions. CONCLUSION: Syntenic bacterial genes represent a commonly evolved group. They not only reveal the core chromosomal segments present in the last common ancestor and determine the metabolic characteristics shared by these microorganisms, but also show resistance to sequence variation and rearrangement, possibly due to their essential character. In Rhizobiales and Enterobacteriales, syntenic genes encode a high proportion of essential cell functions and presented a high level of functional relationships.
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spelling pubmed-12767912005-11-03 Evolutionary, structural and functional relationships revealed by comparative analysis of syntenic genes in Rhizobiales Guerrero, Gabriela Peralta, Humberto Aguilar, Alejandro Díaz, Rafael Villalobos, Miguel Angel Medrano-Soto, Arturo Mora, Jaime BMC Evol Biol Research Article BACKGROUND: Comparative genomics has provided valuable insights into the nature of gene sequence variation and chromosomal organization of closely related bacterial species. However, questions about the biological significance of gene order conservation, or synteny, remain open. Moreover, few comprehensive studies have been reported for rhizobial genomes. RESULTS: We analyzed the genomic sequences of four fast growing Rhizobiales (Sinorhizobium meliloti, Agrobacterium tumefaciens, Mesorhizobium loti and Brucella melitensis). We made a comprehensive gene classification to define chromosomal orthologs, genes with homologs in other replicons such as plasmids, and those which were species-specific. About two thousand genes were predicted to be orthologs in each chromosome and about 80% of these were syntenic. A striking gene colinearity was found in pairs of organisms and a large fraction of the microsyntenic regions and operons were similar. Syntenic products showed higher identity levels than non-syntenic ones, suggesting a resistance to sequence variation due to functional constraints; also, an unusually high fraction of syntenic products contained membranal segments. Syntenic genes encode a high proportion of essential cell functions, presented a high level of functional relationships and a very low horizontal gene transfer rate. The sequence variability of the proteins can be considered the species signature in response to specific niche adaptation. Comparatively, an analysis with genomes of Enterobacteriales showed a different gene organization but gave similar results in the synteny conservation, essential role of syntenic genes and higher functional linkage among the genes of the microsyntenic regions. CONCLUSION: Syntenic bacterial genes represent a commonly evolved group. They not only reveal the core chromosomal segments present in the last common ancestor and determine the metabolic characteristics shared by these microorganisms, but also show resistance to sequence variation and rearrangement, possibly due to their essential character. In Rhizobiales and Enterobacteriales, syntenic genes encode a high proportion of essential cell functions and presented a high level of functional relationships. BioMed Central 2005-10-17 /pmc/articles/PMC1276791/ /pubmed/16229745 http://dx.doi.org/10.1186/1471-2148-5-55 Text en Copyright © 2005 Guerrero et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Guerrero, Gabriela
Peralta, Humberto
Aguilar, Alejandro
Díaz, Rafael
Villalobos, Miguel Angel
Medrano-Soto, Arturo
Mora, Jaime
Evolutionary, structural and functional relationships revealed by comparative analysis of syntenic genes in Rhizobiales
title Evolutionary, structural and functional relationships revealed by comparative analysis of syntenic genes in Rhizobiales
title_full Evolutionary, structural and functional relationships revealed by comparative analysis of syntenic genes in Rhizobiales
title_fullStr Evolutionary, structural and functional relationships revealed by comparative analysis of syntenic genes in Rhizobiales
title_full_unstemmed Evolutionary, structural and functional relationships revealed by comparative analysis of syntenic genes in Rhizobiales
title_short Evolutionary, structural and functional relationships revealed by comparative analysis of syntenic genes in Rhizobiales
title_sort evolutionary, structural and functional relationships revealed by comparative analysis of syntenic genes in rhizobiales
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1276791/
https://www.ncbi.nlm.nih.gov/pubmed/16229745
http://dx.doi.org/10.1186/1471-2148-5-55
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