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Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins.

Jordan IK, Kondrashov FA, Rogozin IB, Tatusov RL, Wolf YI, Koonin EV - Genome Biol. (2001)

Bottom Line: Amino-acid sequence evolution rates are significantly correlated on different branches of phylogenetic trees representing the great majority of analyzed orthologous protein sets from all three domains of life.Deviations from this rate constancy are probably due to changes in selective constraints associated with diversification between orthologs.However, the resolution afforded by the test designed specifically for genomic-scale datasets allowed us to identify numerous cases of possible functional diversification between orthologous proteins.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD20894, USA. Jordan@ncbi.nlm.nih.gov

ABSTRACT

Background: Detection of changes in a protein's evolutionary rate may reveal cases of change in that protein's function. We developed and implemented a simple relative rates test in an attempt to assess the rate constancy of protein evolution and to detect cases of functional diversification between orthologous proteins. The test was performed on clusters of orthologous protein sequences from complete bacterial genomes (Chlamydia trachomatis, C. muridarum and Chlamydophila pneumoniae), complete archaeal genomes (Pyrococcus horikoshii, P. abyssi and P. furiosus) and partially sequenced mammalian genomes (human, mouse and rat).

Results: Amino-acid sequence evolution rates are significantly correlated on different branches of phylogenetic trees representing the great majority of analyzed orthologous protein sets from all three domains of life. However, approximately 1% of the proteins from each group of species deviates from this pattern and instead shows variation that is consistent with an acceleration of the rate of amino-acid substitution, which may be due to functional diversification. Most of the putative functionally diversified proteins from all three species groups are predicted to function at the periphery of the cells and mediate their interaction with the environment.

Conclusions: Relative rates of protein evolution are remarkably constant for the three species groups analyzed here. Deviations from this rate constancy are probably due to changes in selective constraints associated with diversification between orthologs. Functional diversification between orthologs is thought to be a relatively rare event. However, the resolution afforded by the test designed specifically for genomic-scale datasets allowed us to identify numerous cases of possible functional diversification between orthologous proteins.

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Phylogenies of the three analyzed species groups. Branch lengths are the average of all branch lengths for a given species group. The different branches bA, bB and bC are indicated.
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Figure 2: Phylogenies of the three analyzed species groups. Branch lengths are the average of all branch lengths for a given species group. The different branches bA, bB and bC are indicated.

Mentions: These procedures resulted in a total of 703 Chlamydiaceae, 1,305 Pyrococcus and 2,112 mammalian orthologous protein sets. Each orthologous protein-sequence set was aligned and the evolutionary distances between sequences within the sets were computed. These distances were used in phylogenetic reconstructions for all orthologous protein sets. For each species group, branch lengths were averaged to produce the trees shown (Figure 2). Each of the trees contains two relatively short branches of virtually identical length and one long branch, forming two main phylogenetic partitions. The rate-constancy prediction holds that the evolutionary rates along these phylogenetic branches should be correlated. In other words, the length of branch A (bA) should be correlated with the length of branches B and C (bB + bC) (Figures 1,2) resulting, in an ideal case, in a constant bA/(bB+bC) ratio.


Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins.

Jordan IK, Kondrashov FA, Rogozin IB, Tatusov RL, Wolf YI, Koonin EV - Genome Biol. (2001)

Phylogenies of the three analyzed species groups. Branch lengths are the average of all branch lengths for a given species group. The different branches bA, bB and bC are indicated.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC64838&req=5

Figure 2: Phylogenies of the three analyzed species groups. Branch lengths are the average of all branch lengths for a given species group. The different branches bA, bB and bC are indicated.
Mentions: These procedures resulted in a total of 703 Chlamydiaceae, 1,305 Pyrococcus and 2,112 mammalian orthologous protein sets. Each orthologous protein-sequence set was aligned and the evolutionary distances between sequences within the sets were computed. These distances were used in phylogenetic reconstructions for all orthologous protein sets. For each species group, branch lengths were averaged to produce the trees shown (Figure 2). Each of the trees contains two relatively short branches of virtually identical length and one long branch, forming two main phylogenetic partitions. The rate-constancy prediction holds that the evolutionary rates along these phylogenetic branches should be correlated. In other words, the length of branch A (bA) should be correlated with the length of branches B and C (bB + bC) (Figures 1,2) resulting, in an ideal case, in a constant bA/(bB+bC) ratio.

Bottom Line: Amino-acid sequence evolution rates are significantly correlated on different branches of phylogenetic trees representing the great majority of analyzed orthologous protein sets from all three domains of life.Deviations from this rate constancy are probably due to changes in selective constraints associated with diversification between orthologs.However, the resolution afforded by the test designed specifically for genomic-scale datasets allowed us to identify numerous cases of possible functional diversification between orthologous proteins.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD20894, USA. Jordan@ncbi.nlm.nih.gov

ABSTRACT

Background: Detection of changes in a protein's evolutionary rate may reveal cases of change in that protein's function. We developed and implemented a simple relative rates test in an attempt to assess the rate constancy of protein evolution and to detect cases of functional diversification between orthologous proteins. The test was performed on clusters of orthologous protein sequences from complete bacterial genomes (Chlamydia trachomatis, C. muridarum and Chlamydophila pneumoniae), complete archaeal genomes (Pyrococcus horikoshii, P. abyssi and P. furiosus) and partially sequenced mammalian genomes (human, mouse and rat).

Results: Amino-acid sequence evolution rates are significantly correlated on different branches of phylogenetic trees representing the great majority of analyzed orthologous protein sets from all three domains of life. However, approximately 1% of the proteins from each group of species deviates from this pattern and instead shows variation that is consistent with an acceleration of the rate of amino-acid substitution, which may be due to functional diversification. Most of the putative functionally diversified proteins from all three species groups are predicted to function at the periphery of the cells and mediate their interaction with the environment.

Conclusions: Relative rates of protein evolution are remarkably constant for the three species groups analyzed here. Deviations from this rate constancy are probably due to changes in selective constraints associated with diversification between orthologs. Functional diversification between orthologs is thought to be a relatively rare event. However, the resolution afforded by the test designed specifically for genomic-scale datasets allowed us to identify numerous cases of possible functional diversification between orthologous proteins.

Show MeSH
Related in: MedlinePlus