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Genetics, Vol. 167, 1507-1512, July 2004, Copyright © 2004
doi:10.1534/genetics.104.026344
Genome-Wide Patterns of Nucleotide Substitution Reveal Stringent Functional Constraints on the Protein Sequences of Thermophiles
Robert Friedman*,
John W. Drake
and
Austin L. Hughes*,1
* Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208
Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709-2233
1 Corresponding author: Department of Biological Sciences, University of South Carolina, 700 Sumter St., Columbia, SC 29208.
E-mail: austin{at}biol.sc.edu
To test the hypothesis that the proteins of thermophilic prokaryotes are subject to unusually stringent functional constraints, we estimated the numbers of synonymous and nonsynonymous nucleotide substitutions per site between 17,957 pairs of orthologous genes from 22 pairs of closely related species of Archaea and Bacteria. The average ratio of nonsynonymous to synonymous substitutions was significantly lower in thermophiles than in nonthermophiles, and this effect was observed in both Archaea and Bacteria. There was no evidence that this difference could be explained by factors such as nucleotide content bias. Rather, the results support the hypothesis that proteins of thermophiles are subject to unusually strong purifying selection, leading to a reduced overall level of amino acid evolution per mutational event. The results show that genome-wide patterns of sequence evolution can be influenced by natural selection exerted by a species' environment and shed light on a previous observation that relatively few of the mutations arising in a thermophilic archaeon were nucleotide substitutions in contrast to indels.
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