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

Biology Direct

Humberto Peralta¹  Gabriela Guerrero¹  Alejandro Aguilar¹  Jaime Mora¹ 

[1] Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México. Apdo. postal 565-A, Cuernavaca, Morelos, México

关键词: adaptation;    nonsynonymous substitution;    evolutionary rates;    comparative genomics;    rhizobia;   

Others  :  797092
DOI  :  10.1186/1745-6150-6-48

 received in 2011-04-11, accepted in 2011-10-04,  发布年份 2011

【 摘 要 】

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.

This article was reviewed by Dr. Purificación López-García, Prof. Jeffrey Townsend (nominated by Dr. J. Peter Gogarten), and Ms. Olga Kamneva.

【 授权许可】

   
2011 Peralta et al; licensee BioMed Central Ltd.

【 图 表 】

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