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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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Association among species by physico-chemical characteristics of ortholog products. A, polarity is shown as example. The panel shows 705 syntenic ortholog products per species. Letters at the top: At, A. tumefaciens; Re, R. etli; Sm, S. meliloti; Bm, B. melitensis; and Ml, M. loti. Lines at left denote clusters of orthologs with similar profile in the five species (ten were selected and analyzed in the text). B, comparison of two R. etli strains with polarity. The panel shows 705 syntenic ortholog products per strain. Letters at the top: Re, R. etli strain CFN42; CIAT, R. etli strain CIAT652. Clustering was performed with MeV TM4 [23]. Scales for normalized values (green for negative values, white for zero, and red for positive).
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Figure 4: Association among species by physico-chemical characteristics of ortholog products. A, polarity is shown as example. The panel shows 705 syntenic ortholog products per species. Letters at the top: At, A. tumefaciens; Re, R. etli; Sm, S. meliloti; Bm, B. melitensis; and Ml, M. loti. Lines at left denote clusters of orthologs with similar profile in the five species (ten were selected and analyzed in the text). B, comparison of two R. etli strains with polarity. The panel shows 705 syntenic ortholog products per strain. Letters at the top: Re, R. etli strain CFN42; CIAT, R. etli strain CIAT652. Clustering was performed with MeV TM4 [23]. Scales for normalized values (green for negative values, white for zero, and red for positive).

Mentions: With a clustering method [23], we tried to find relationships among species derived from the physico-chemical nature of the residues encoded by the orthologs. We generated clustering profiles for each property (shown for polarity, Figure 4A, and the rest in the Additional file 2) with the most conserved gene set (705 syntenic orthologs with dS < 5). A high level of variation among each ortholog can be observed, reflecting specific changes in each of the species. For polarity, a closer association of R. etli with S. meliloti, followed by A. tumefaciens in another branch, was observed (an RS-A-BM association, Table 1); this relationship was similar to the second most abundant phylogeny described above. For the rest of the properties, other associations were observed: RA-S-BM for secondary structure, electrostatic charge, and volume (Additional file 2 and Table 1), and again RS-A-BM for amino acid composition (Table 1). These associations revealed which physico-chemical character links most closely with the species, reflecting the phylogenetic relationship and also the lifestyle of the organisms. When the complete 1416-ortholog set was analyzed, B. melitensis departed clearly from the rest of species in polarity, charge and amino acid composition (Table 1, denoted as M-B in independent branches). In the group of Rhizobiales analyzed, Brucella is the only non free-living organism.


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

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

Association among species by physico-chemical characteristics of ortholog products. A, polarity is shown as example. The panel shows 705 syntenic ortholog products per species. Letters at the top: At, A. tumefaciens; Re, R. etli; Sm, S. meliloti; Bm, B. melitensis; and Ml, M. loti. Lines at left denote clusters of orthologs with similar profile in the five species (ten were selected and analyzed in the text). B, comparison of two R. etli strains with polarity. The panel shows 705 syntenic ortholog products per strain. Letters at the top: Re, R. etli strain CFN42; CIAT, R. etli strain CIAT652. Clustering was performed with MeV TM4 [23]. Scales for normalized values (green for negative values, white for zero, and red for positive).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Association among species by physico-chemical characteristics of ortholog products. A, polarity is shown as example. The panel shows 705 syntenic ortholog products per species. Letters at the top: At, A. tumefaciens; Re, R. etli; Sm, S. meliloti; Bm, B. melitensis; and Ml, M. loti. Lines at left denote clusters of orthologs with similar profile in the five species (ten were selected and analyzed in the text). B, comparison of two R. etli strains with polarity. The panel shows 705 syntenic ortholog products per strain. Letters at the top: Re, R. etli strain CFN42; CIAT, R. etli strain CIAT652. Clustering was performed with MeV TM4 [23]. Scales for normalized values (green for negative values, white for zero, and red for positive).
Mentions: With a clustering method [23], we tried to find relationships among species derived from the physico-chemical nature of the residues encoded by the orthologs. We generated clustering profiles for each property (shown for polarity, Figure 4A, and the rest in the Additional file 2) with the most conserved gene set (705 syntenic orthologs with dS < 5). A high level of variation among each ortholog can be observed, reflecting specific changes in each of the species. For polarity, a closer association of R. etli with S. meliloti, followed by A. tumefaciens in another branch, was observed (an RS-A-BM association, Table 1); this relationship was similar to the second most abundant phylogeny described above. For the rest of the properties, other associations were observed: RA-S-BM for secondary structure, electrostatic charge, and volume (Additional file 2 and Table 1), and again RS-A-BM for amino acid composition (Table 1). These associations revealed which physico-chemical character links most closely with the species, reflecting the phylogenetic relationship and also the lifestyle of the organisms. When the complete 1416-ortholog set was analyzed, B. melitensis departed clearly from the rest of species in polarity, charge and amino acid composition (Table 1, denoted as M-B in independent branches). In the group of Rhizobiales analyzed, Brucella is the only non free-living organism.

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
Related in: MedlinePlus