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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
Functional distribution of orthologs divided by low or high nonsynonymous substitution rate (dN). The graph was generated using 985 orthologs with dS < 5; they were divided as described in the Methods section. Functions were grouped into Metabolism (1, amino acid biosynthesis; 2, nucleotide biosynthesis; 3, fatty acid biosynthesis; 4, cofactor biosynthesis; 5, central intermediary metabolism; and 6, energy generation), Information (7, DNA metabolism; 8, transcription; 9, translation; and 10, transcriptional regulators), Processes (11, transport; 12, cellular envelope synthesis; and 13, other cellular processes), and 14, Hypothetical functions. Bar colors: red, orthologs with low dN; blue, orthologs with high dN. Asterisks denote significant differences with p < 0.05, Fisher's exact test.
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Figure 3: Functional distribution of orthologs divided by low or high nonsynonymous substitution rate (dN). The graph was generated using 985 orthologs with dS < 5; they were divided as described in the Methods section. Functions were grouped into Metabolism (1, amino acid biosynthesis; 2, nucleotide biosynthesis; 3, fatty acid biosynthesis; 4, cofactor biosynthesis; 5, central intermediary metabolism; and 6, energy generation), Information (7, DNA metabolism; 8, transcription; 9, translation; and 10, transcriptional regulators), Processes (11, transport; 12, cellular envelope synthesis; and 13, other cellular processes), and 14, Hypothetical functions. Bar colors: red, orthologs with low dN; blue, orthologs with high dN. Asterisks denote significant differences with p < 0.05, Fisher's exact test.

Mentions: Based on values obtained from each of the five species (see Methods section), the orthologs were classified into groups either with low or high dN: 426 were classified as having a low dN value, and 559 as having a high dN value. A functional distribution was generated and, significantly, metabolism (amino acid and nucleotide biosynthesis and energy generation), and informational (transcription and translation) functions tended to be encoded by genes with low dN values (Figure 3, significant difference by Fisher's exact test, with p < 0.05). In contrast, genes belonging to the high dN group had significant abundance of hypothetical functions, and also contributed particularly to cellular processes (transport and cellular envelope). The significance of these differences is explained in the Discussion section.


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

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

Functional distribution of orthologs divided by low or high nonsynonymous substitution rate (dN). The graph was generated using 985 orthologs with dS < 5; they were divided as described in the Methods section. Functions were grouped into Metabolism (1, amino acid biosynthesis; 2, nucleotide biosynthesis; 3, fatty acid biosynthesis; 4, cofactor biosynthesis; 5, central intermediary metabolism; and 6, energy generation), Information (7, DNA metabolism; 8, transcription; 9, translation; and 10, transcriptional regulators), Processes (11, transport; 12, cellular envelope synthesis; and 13, other cellular processes), and 14, Hypothetical functions. Bar colors: red, orthologs with low dN; blue, orthologs with high dN. Asterisks denote significant differences with p < 0.05, Fisher's exact test.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Functional distribution of orthologs divided by low or high nonsynonymous substitution rate (dN). The graph was generated using 985 orthologs with dS < 5; they were divided as described in the Methods section. Functions were grouped into Metabolism (1, amino acid biosynthesis; 2, nucleotide biosynthesis; 3, fatty acid biosynthesis; 4, cofactor biosynthesis; 5, central intermediary metabolism; and 6, energy generation), Information (7, DNA metabolism; 8, transcription; 9, translation; and 10, transcriptional regulators), Processes (11, transport; 12, cellular envelope synthesis; and 13, other cellular processes), and 14, Hypothetical functions. Bar colors: red, orthologs with low dN; blue, orthologs with high dN. Asterisks denote significant differences with p < 0.05, Fisher's exact test.
Mentions: Based on values obtained from each of the five species (see Methods section), the orthologs were classified into groups either with low or high dN: 426 were classified as having a low dN value, and 559 as having a high dN value. A functional distribution was generated and, significantly, metabolism (amino acid and nucleotide biosynthesis and energy generation), and informational (transcription and translation) functions tended to be encoded by genes with low dN values (Figure 3, significant difference by Fisher's exact test, with p < 0.05). In contrast, genes belonging to the high dN group had significant abundance of hypothetical functions, and also contributed particularly to cellular processes (transport and cellular envelope). The significance of these differences is explained in the Discussion section.

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