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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.

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Relationship between the physico-chemical properties and the percentage of changes by species (%chSp). A, dot plot graph of the average %chSp and polarity (range). Tendency lines for the five clusters are shown. B, molecular weight (average) of syntenic ortholog products, following the order of the slope of clusters (up to down). C, isoelectric point (average) of syntenic ortholog products, following the order of the slope of clusters.
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Figure 6: Relationship between the physico-chemical properties and the percentage of changes by species (%chSp). A, dot plot graph of the average %chSp and polarity (range). Tendency lines for the five clusters are shown. B, molecular weight (average) of syntenic ortholog products, following the order of the slope of clusters (up to down). C, isoelectric point (average) of syntenic ortholog products, following the order of the slope of clusters.

Mentions: To determine the relationship of the %chSp with physico-chemical properties, we generated a dispersion graph, considering the average of the %chSp and the range of polarity, as shown for example in Figure 6A. A positive relationship was obtained, revealing that sequence variability corresponded with diversity in the character evaluated (a similar tendency was observed in the rest of the properties, not shown). The dispersion was analyzed by obtaining clusters with high correlation values (see Methods). Strikingly, clear tendencies in molecular weight and isoelectric point were obtained. The molecular weight was progressively reduced according with a negative slope (Figure 6B), while the opposite was observed for isoelectric point (Figure 6C). Similar tendencies were observed in the three other properties, with the exception of electrostatic charge (not shown). The first cluster had significant abundance of proteins from the functional classes of amino acid biosynthesis, transcription and energy generation (Fisher exact test, p < 0.05), and the last one was abundant with proteins of hypothetical functions and some cellular processes (not shown).


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 between the physico-chemical properties and the percentage of changes by species (%chSp). A, dot plot graph of the average %chSp and polarity (range). Tendency lines for the five clusters are shown. B, molecular weight (average) of syntenic ortholog products, following the order of the slope of clusters (up to down). C, isoelectric point (average) of syntenic ortholog products, following the order of the slope of clusters.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Relationship between the physico-chemical properties and the percentage of changes by species (%chSp). A, dot plot graph of the average %chSp and polarity (range). Tendency lines for the five clusters are shown. B, molecular weight (average) of syntenic ortholog products, following the order of the slope of clusters (up to down). C, isoelectric point (average) of syntenic ortholog products, following the order of the slope of clusters.
Mentions: To determine the relationship of the %chSp with physico-chemical properties, we generated a dispersion graph, considering the average of the %chSp and the range of polarity, as shown for example in Figure 6A. A positive relationship was obtained, revealing that sequence variability corresponded with diversity in the character evaluated (a similar tendency was observed in the rest of the properties, not shown). The dispersion was analyzed by obtaining clusters with high correlation values (see Methods). Strikingly, clear tendencies in molecular weight and isoelectric point were obtained. The molecular weight was progressively reduced according with a negative slope (Figure 6B), while the opposite was observed for isoelectric point (Figure 6C). Similar tendencies were observed in the three other properties, with the exception of electrostatic charge (not shown). The first cluster had significant abundance of proteins from the functional classes of amino acid biosynthesis, transcription and energy generation (Fisher exact test, p < 0.05), and the last one was abundant with proteins of hypothetical functions and some cellular processes (not shown).

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