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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 function and sign of values of ortholog products obtained with polarity. From left to right, proportions of functional classes 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 Hypothetical functions (14). Bar colors: green, negative; red, positive. Asterisks denote significant differences with p < 0.05, Fisher's exact test.
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Figure 5: Relationship between function and sign of values of ortholog products obtained with polarity. From left to right, proportions of functional classes 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 Hypothetical functions (14). Bar colors: green, negative; red, positive. Asterisks denote significant differences with p < 0.05, Fisher's exact test.

Mentions: Given the observed functional tendencies described above, we divided the products having the same sign in the five species and obtained functional distributions. We found an interesting relationship between the functional role of the protein and its sign from the physico-chemical property evaluation, which could be related to specific biochemical requirements for functional performance. For polarity, functions of metabolism and processes were related to negative signs, while informational functions were strongly related to positive signs (significant differences with p < 0.05, calculated with Fisher's exact test) (Figure 5). Several other remarkable features were found: for secondary structure, the negative sign (related to abundant alpha-helical structures) was associated with informational functions, and the positive sign (abundant coils) was related with synthesis of the cellular envelope and hypothetical proteins (Additional file 5). Hypothetical proteins showed significant abundance of low level amino acid composition (i. e., atypical composition); translation was abundant in protein sequences with positive charge; and energy and translation functional classes showed residues with high molecular volume (Additional file 5).


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 function and sign of values of ortholog products obtained with polarity. From left to right, proportions of functional classes 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 Hypothetical functions (14). Bar colors: green, negative; red, positive. 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 5: Relationship between function and sign of values of ortholog products obtained with polarity. From left to right, proportions of functional classes 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 Hypothetical functions (14). Bar colors: green, negative; red, positive. Asterisks denote significant differences with p < 0.05, Fisher's exact test.
Mentions: Given the observed functional tendencies described above, we divided the products having the same sign in the five species and obtained functional distributions. We found an interesting relationship between the functional role of the protein and its sign from the physico-chemical property evaluation, which could be related to specific biochemical requirements for functional performance. For polarity, functions of metabolism and processes were related to negative signs, while informational functions were strongly related to positive signs (significant differences with p < 0.05, calculated with Fisher's exact test) (Figure 5). Several other remarkable features were found: for secondary structure, the negative sign (related to abundant alpha-helical structures) was associated with informational functions, and the positive sign (abundant coils) was related with synthesis of the cellular envelope and hypothetical proteins (Additional file 5). Hypothetical proteins showed significant abundance of low level amino acid composition (i. e., atypical composition); translation was abundant in protein sequences with positive charge; and energy and translation functional classes showed residues with high molecular volume (Additional file 5).

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