Sequence variability of Rhizobiales orthologs and relationship with physico-chemical characteristics of proteins

Biol Direct. 2011 Oct 4;6:48. doi: 10.1186/1745-6150-6-48.


Background: Chromosomal orthologs can reveal the shared ancestral gene set and their evolutionary trends. Additionally, physico-chemical properties of encoded proteins could provide information about functional adaptation and ecological niche requirements.

Results: We analyzed 7080 genes (five groups of 1416 orthologs each) from Rhizobiales species (S. meliloti, R. etli, and M. loti, plant symbionts; A. tumefaciens, a plant pathogen; and B. melitensis, an animal pathogen). We evaluated their phylogenetic relationships and observed three main topologies. The first, with closer association of R. etli to A. tumefaciens; the second with R. etli closer to S. meliloti; and the third with A. tumefaciens and S. meliloti as the closest pair. This was not unusual, given the close relatedness of these three species. We calculated the synonymous (dS) and nonsynonymous (dN) substitution rates of these orthologs, and found that informational and metabolic functions showed relatively low dN rates; in contrast, genes from hypothetical functions and cellular processes showed high dN rates. An alternative measure of sequence variability, percentage of changes by species, was used to evaluate the most specific proportion of amino acid residues from alignments. When dN was compared with that measure a high correlation was obtained, revealing that much of evolutive information was extracted with the percentage of changes by species at the amino acid level. By analyzing the sequence variability of orthologs with a set of five properties (polarity, electrostatic charge, formation of secondary structures, molecular volume, and amino acid composition), we found that physico-chemical characteristics of proteins correlated with specific functional roles, and association of species did not follow their typical phylogeny, probably reflecting more adaptation to their life styles and niche preferences. In addition, orthologs with low dN rates had residues with more positive values of polarity, volume and electrostatic charge.

Conclusions: These findings revealed that even when orthologs perform the same function in each genomic background, their sequences reveal important evolutionary tendencies and differences related to adaptation.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Substitution*
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Chemical Phenomena
  • Chromosomes, Bacterial / chemistry
  • Chromosomes, Bacterial / genetics
  • Evolution, Molecular
  • Genes, Bacterial*
  • Isoelectric Point
  • Membrane Proteins / chemistry
  • Membrane Proteins / genetics
  • Phylogeny
  • Protein Structure, Secondary*
  • Rhizobiaceae / chemistry
  • Rhizobiaceae / classification
  • Rhizobiaceae / genetics*
  • Sequence Alignment
  • Sequence Analysis, Protein
  • Sequence Homology, Amino Acid
  • Species Specificity
  • Synteny


  • Bacterial Proteins
  • Membrane Proteins