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MBE Advance Access published online on March 1, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msj115
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted February 20, 2006

Research Article

Correlated Asymmetry of Sequence and Functional Divergence Between Duplicate Proteins of Saccharomyces cerevisiae

Seong-Ho Kim 1 and Soojin V. Yi 1 *

1 School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA

* To whom correspondence should be addressed.
Soojin V. Yi, E-mail: soojinyi{at}gatech.edu


  Abstract

The role of sequence divergence in functional divergence of duplicate genes is a topic of great interest. In this study, we compare the numbers of amino acid substitutions in each sequence since two yeast duplicates diverged, using a pre-duplication ancestral outgroup. Using this strategy, we explored the relationship between sequence divergence and functional divergence between duplicate partners. We show the degree of relative functional asymmetry between duplicate proteins is proportional to the relative sequence divergence between them. Furthermore, of the two duplicates, the copy closer to their ancestral sequence (fewer number of amino acid substitutions) interacts with more proteins and affects fitness more severely when deleted. Therefore, asymmetric sequence divergence between duplicates is correlated with asymmetric functional divergence, and may underlie the duplicate's role in genetic robustness against mutations. Among the functional traits considered, protein abundance appears to have the strongest correlation with the nonsynonymous divergence between duplicates. Taken together with the results from whole genome analyses, our results indicate that within species duplicates are subject to the same evolutionary force that acts on inter-specific sequence and functional divergence. In particular, we detect signs of purifying selection on the more slowly evolving duplicate.

Keywords: Saccharomyces cerevisiae; whole genome duplication; functional divergence; sequence divergence; gene duplication.
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