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In silico evidence for functional specialization after genome duplication in yeast

  1. Ossi Turunen1,
  2. Ralph Seelke2,
  3. Jed Macosko3

Article first published online: 3 NOV 2008

DOI: 10.1111/j.1567-1364.2008.00451.x

Issue

FEMS Yeast Research

FEMS Yeast Research

Volume 9, Issue 1, pages 16–31, February 2009

Additional Information

How to Cite

Turunen, O., Seelke, R. and Macosko, J. (2009), In silico evidence for functional specialization after genome duplication in yeast. FEMS Yeast Research, 9: 16–31. doi: 10.1111/j.1567-1364.2008.00451.x

Author Information

  1. 1

    Department of Biotechnology and Chemical Technology, Helsinki University of Technology, Espoo, Finland

  2. 2

    Department of Biology and Earth Sciences, University of Wisconsin-Superior, Superior, WI, USA

  3. 3

    Department of Physics, Wake Forest University, Winston-Salem, NC, USA

*Correspondence: Ossi Turunen, Department of Biotechnology and Chemical Technology, Helsinki University of Technology, PO Box 6100, 02015 TKK, Finland. Tel.: +358 9 4512551; fax: +358 9 462373; e-mail: ossi.turunen@tkk.fi

  1. Editor: André Goffeau

Publication History

  1. Issue published online: 8 JAN 2009
  2. Article first published online: 3 NOV 2008
  3. Received 26 March 2008; revised 2 September 2008; accepted 2 September 2008.First published online 3 November 2008.

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Keywords:

  • gene duplication;
  • yeast genome;
  • protein evolution;
  • sequence analysis;
  • structural analysis

Abstract

A fairly recent whole-genome duplication (WGD) event in yeast enables the effects of gene duplication and subsequent functional divergence to be characterized. We examined 15 ohnolog pairs (i.e. paralogs from a WGD) out of c. 500 Saccharomyces cerevisiae ohnolog pairs that have persisted over an estimated 100 million years of evolution. These 15 pairs were chosen for their high levels of asymmetry, i.e. within the pair, one ohnolog had evolved much faster than the other. Sequence comparisons of the 15 pairs revealed that the faster evolving duplicated genes typically appear to have experienced partially – but not fully – relaxed negative selection as evidenced by an average nonsynonymous/synonymous substitution ratio (dN/dSavg=0.44) that is higher than the slow-evolving genes' ratio (dN/dSavg=0.14) but still <1. Increased number of insertions and deletions in the fast-evolving genes also indicated loosened structural constraints. Sequence and structural comparisons indicated that a subset of these pairs had significant differences in their catalytically important residues and active or cofactor-binding sites. A literature survey revealed that several of the fast-evolving genes have gained a specialized function. Our results indicate that subfunctionalization and even neofunctionalization has occurred along with degenerative evolution, in which unneeded functions were destroyed by mutations.

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