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

Abstract

BackgroundComparative 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.ResultsWe 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.ConclusionSyntenic 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.

Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance

“…In fact, genes in the same region were found to be often coexpressed in the Drosophila and human genomes [ 25 , 26 ]. Furthermore, synteny, gene regions keeping conserved across species, has been proposed to show expression correlation and functional association [ 27 ]. We believe the conservative head-to-head gene pairs contribute to the extensive distribution of synteny.…”

Secrets of Soil Survival Revealed by the Genome Sequence of Arthrobacter aurescens TC1

“…Plasmid pTC2 contains 111 ORFs with significant amino-acid identity to chromosomally-encoded proteins (Table S3). The sharing of nearly identical genes on plasmids and the chromosome in the same organism has previously been reported for soil [49,50] and other bacteria [51,52], and it is tempting to speculate that plasmid-encoded functions may allow for competitive success in the environment. While the origin of the redundant genes is unknown, they may have arisen from transposition events occurring between plasmids and the chromosome or via horizontal gene transfer, especially for redundant homologs (or paralogs) that have significant differences at the amino-acid level.…”

Genomic studies of nitrogen-fixing rhizobial strains from Phaseolus vulgaris seeds and nodules

“…For the study of paralog families, the inparalog files were used. Synteny was determined with an in-house Perl program using the ortholog files from OrthoMCL as described previously [ 19 ]. Function was assigned using the extended annotation of clusters of orthologous groups (COG) tool [ 20 ].…”