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 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.


CONCLUSIONS
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.
Guerrero
Gabriela
G
Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, PO Box 565-A, Cuernavaca, Morelos, 62210, Mexico. gabriela@ccg.unam.mx
Peralta
Humberto
H
Aguilar
Alejandro
A
Díaz
Rafael
R
Villalobos
Miguel Angel
MA
Medrano-Soto
Arturo
A
Mora
Jaime
J
D016960:Agrobacterium tumefaciens / Q000235:genetics; D001483:Base Sequence; D017347:Brucella melitensis; D002874:Chromosome Mapping; D002876:Chromosomes, Bacterial; D003062:Codon; D017124:Conserved Sequence; D019143:Evolution, Molecular; D023061:Gene Order; D022761:Gene Transfer, Horizontal; D005798:Genes, Bacterial; D008040:Genetic Linkage; D014644:Genetic Variation; D016678:Genome; D016680:Genome, Bacterial; D007526:Isoelectric Point; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D010957:Plasmids / Q000378:metabolism; D011487:Protein Conformation; D040901:Proteomics / Q000379:methods; D011995:Recombination, Genetic; D016962:Sinorhizobium meliloti / Q000235:genetics; D013045:Species Specificity; D026801:Synteny
D003062:Codon