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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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The percentage of changes by species (%chSp) of 1416 chromosomal orthologs from five Rhizobiales. The panels show 1416 orthologs for each of the species (7080 ortholog products in total). A, the %chSp arranged progressively according to the % of common identity of each ortholog from the five organisms (black line). Color dots: orange, R. etli; red, A. tumefaciens; blue, S. meliloti; green, Brucella melitensis; and yellow (or brown) M. loti. B, frequency distribution curves for the %chSp of the five organisms. Values above 50% were omitted for clarity. Color lines as in A, with exception of brown for M. loti. C, functional distribution of orthologs by species signature. Data from R. etli products. Functions were classified into Metabolism (red line, including amino acid, nucleotide, fatty acid, and cofactor biosynthesis, central intermediary metabolism, and energy generation), Information (green line, DNA metabolism, transcription, translation, and transcriptional regulators), Processes (blue line, transport; cellular envelope synthesis, and other cellular processes), and Hypothetical functions or poorly characterized proteins (orange line).
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Figure 1: The percentage of changes by species (%chSp) of 1416 chromosomal orthologs from five Rhizobiales. The panels show 1416 orthologs for each of the species (7080 ortholog products in total). A, the %chSp arranged progressively according to the % of common identity of each ortholog from the five organisms (black line). Color dots: orange, R. etli; red, A. tumefaciens; blue, S. meliloti; green, Brucella melitensis; and yellow (or brown) M. loti. B, frequency distribution curves for the %chSp of the five organisms. Values above 50% were omitted for clarity. Color lines as in A, with exception of brown for M. loti. C, functional distribution of orthologs by species signature. Data from R. etli products. Functions were classified into Metabolism (red line, including amino acid, nucleotide, fatty acid, and cofactor biosynthesis, central intermediary metabolism, and energy generation), Information (green line, DNA metabolism, transcription, translation, and transcriptional regulators), Processes (blue line, transport; cellular envelope synthesis, and other cellular processes), and Hypothetical functions or poorly characterized proteins (orange line).

Mentions: With the %chSp we wanted to find the specific differences in protein sequences of the orthologs for each of the species studied. The %chSp was calculated by normalizing the number of residues in the ortholog sequence that occur only once in individual alignment columns [4]. This measure denotes the amount of most specific residues in the orthologs, and is expressed as a percentage of the total number of amino acids in the proteins. In Figure 1A, the %chSp of the orthologs studied is shown. Two groups can be clearly distinguished, with S. meliloti grouped with A. tumefaciens and R. etli, and M. loti and B. melitensis in another group. That grouping reflects the phylogenetic relationship of these species. Frequency distribution curves of the %chSp values were plotted to illustrate in detail the separation of these groups (Figure 1B).


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

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

The percentage of changes by species (%chSp) of 1416 chromosomal orthologs from five Rhizobiales. The panels show 1416 orthologs for each of the species (7080 ortholog products in total). A, the %chSp arranged progressively according to the % of common identity of each ortholog from the five organisms (black line). Color dots: orange, R. etli; red, A. tumefaciens; blue, S. meliloti; green, Brucella melitensis; and yellow (or brown) M. loti. B, frequency distribution curves for the %chSp of the five organisms. Values above 50% were omitted for clarity. Color lines as in A, with exception of brown for M. loti. C, functional distribution of orthologs by species signature. Data from R. etli products. Functions were classified into Metabolism (red line, including amino acid, nucleotide, fatty acid, and cofactor biosynthesis, central intermediary metabolism, and energy generation), Information (green line, DNA metabolism, transcription, translation, and transcriptional regulators), Processes (blue line, transport; cellular envelope synthesis, and other cellular processes), and Hypothetical functions or poorly characterized proteins (orange line).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: The percentage of changes by species (%chSp) of 1416 chromosomal orthologs from five Rhizobiales. The panels show 1416 orthologs for each of the species (7080 ortholog products in total). A, the %chSp arranged progressively according to the % of common identity of each ortholog from the five organisms (black line). Color dots: orange, R. etli; red, A. tumefaciens; blue, S. meliloti; green, Brucella melitensis; and yellow (or brown) M. loti. B, frequency distribution curves for the %chSp of the five organisms. Values above 50% were omitted for clarity. Color lines as in A, with exception of brown for M. loti. C, functional distribution of orthologs by species signature. Data from R. etli products. Functions were classified into Metabolism (red line, including amino acid, nucleotide, fatty acid, and cofactor biosynthesis, central intermediary metabolism, and energy generation), Information (green line, DNA metabolism, transcription, translation, and transcriptional regulators), Processes (blue line, transport; cellular envelope synthesis, and other cellular processes), and Hypothetical functions or poorly characterized proteins (orange line).
Mentions: With the %chSp we wanted to find the specific differences in protein sequences of the orthologs for each of the species studied. The %chSp was calculated by normalizing the number of residues in the ortholog sequence that occur only once in individual alignment columns [4]. This measure denotes the amount of most specific residues in the orthologs, and is expressed as a percentage of the total number of amino acids in the proteins. In Figure 1A, the %chSp of the orthologs studied is shown. Two groups can be clearly distinguished, with S. meliloti grouped with A. tumefaciens and R. etli, and M. loti and B. melitensis in another group. That grouping reflects the phylogenetic relationship of these species. Frequency distribution curves of the %chSp values were plotted to illustrate in detail the separation of these groups (Figure 1B).

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