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

Peralta H, Guerrero G, Aguilar A, Mora J - Biol. Direct (2011)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

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

ABSTRACT

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.

Show MeSH
Relationship of the percentage of changes by species (%chSp) of orthologs with synonymous (dS) and nonsynonymous (dN) substitution rates. A, relationship of dN with the %chSp. B, relationship of dS with the %chSp. dN and dS values were obtained with PAML [22]. Dot colors: orange, R. etli; red, A. tumefaciens; blue, S. meliloti; green, B. melitensis; and yellow, M. loti.
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Figure 2: Relationship of the percentage of changes by species (%chSp) of orthologs with synonymous (dS) and nonsynonymous (dN) substitution rates. A, relationship of dN with the %chSp. B, relationship of dS with the %chSp. dN and dS values were obtained with PAML [22]. Dot colors: orange, R. etli; red, A. tumefaciens; blue, S. meliloti; green, B. melitensis; and yellow, M. loti.

Mentions: To determine the usefulness of the %chSp, we compared this parameter with the codon evolution of the orthologs. To do this, we calculated the synonymous (dS) and nonsynonymous (dN) substitution rates by the maximum likelihood method with PAML [22]. Some genes showed dS saturation and were eliminated from the analysis; 985 genes remained with dS values lower than 5. We obtained very high correlations between the %chSp and dN (Figure 2A) and dS (Figure 2B), with Pearson coefficients of r = 0.932 to 0.953 (with p < 0.05) for relation with dN, and r = 0.517 to 0.587 (p < 0.05) for dS. These data revealed that the %chSp was well correlated with codon evolution and is a useful tool to extract directly the evolutive change at the protein level. In comparison, other measures of sequence conservation, such as protein identity or similarity, gave lower Pearson coefficients with dN or dS (for example, in S. meliloti, dN-common identity r = -0.798, dN-common similarity r = -0.650; dS-common identity r = -0.511, dS-common similarity r = -0.400) (not shown). dN and the %chSp are related measures, but they are not derived from the same sequence information: dN is calculated from nonsynonymous codons in nucleotide sequences, while the %chSp is calculated directly from protein sequences by extracting the most specific residue for each homologous position after sequence alignment.


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

Peralta H, Guerrero G, Aguilar A, Mora J - Biol. Direct (2011)

Relationship of the percentage of changes by species (%chSp) of orthologs with synonymous (dS) and nonsynonymous (dN) substitution rates. A, relationship of dN with the %chSp. B, relationship of dS with the %chSp. dN and dS values were obtained with PAML [22]. Dot colors: orange, R. etli; red, A. tumefaciens; blue, S. meliloti; green, B. melitensis; and yellow, M. loti.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3198989&req=5

Figure 2: Relationship of the percentage of changes by species (%chSp) of orthologs with synonymous (dS) and nonsynonymous (dN) substitution rates. A, relationship of dN with the %chSp. B, relationship of dS with the %chSp. dN and dS values were obtained with PAML [22]. Dot colors: orange, R. etli; red, A. tumefaciens; blue, S. meliloti; green, B. melitensis; and yellow, M. loti.
Mentions: To determine the usefulness of the %chSp, we compared this parameter with the codon evolution of the orthologs. To do this, we calculated the synonymous (dS) and nonsynonymous (dN) substitution rates by the maximum likelihood method with PAML [22]. Some genes showed dS saturation and were eliminated from the analysis; 985 genes remained with dS values lower than 5. We obtained very high correlations between the %chSp and dN (Figure 2A) and dS (Figure 2B), with Pearson coefficients of r = 0.932 to 0.953 (with p < 0.05) for relation with dN, and r = 0.517 to 0.587 (p < 0.05) for dS. These data revealed that the %chSp was well correlated with codon evolution and is a useful tool to extract directly the evolutive change at the protein level. In comparison, other measures of sequence conservation, such as protein identity or similarity, gave lower Pearson coefficients with dN or dS (for example, in S. meliloti, dN-common identity r = -0.798, dN-common similarity r = -0.650; dS-common identity r = -0.511, dS-common similarity r = -0.400) (not shown). dN and the %chSp are related measures, but they are not derived from the same sequence information: dN is calculated from nonsynonymous codons in nucleotide sequences, while the %chSp is calculated directly from protein sequences by extracting the most specific residue for each homologous position after sequence alignment.

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

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

ABSTRACT

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.

Show MeSH