Differential evolutionary rates of duplicated genes in protein interaction network

Takashi Makino, Yoshiyuki Suzuki, Takashi Gojobori*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

20 Scopus citations


In the network of protein-protein interactions (PPIs), a loss and gain of the partnering proteins can cause drastic changes of network formation during evolution. With the aim of examining the evolutionary effects of the loss and gain of the partnering proteins on PPIs, we examined a relationship between evolutionary rates and losses and/or gains of PPIs for duplicated gene pairs encoding proteins involved in the PPI network. For duplicated pairs, which provided us with a unique opportunity of making fair comparisons of the genes with the same initial condition, we found that the evolutionary rate of the protein with more PPI partners is much slower than that of the other with fewer PPI partners. Moreover, when the ratio of evolutionary rates (faster rate/slower rate) was computed for each of the duplicated pairs, the ratio for the duplicated pair sharing any PPI partners was significantly lower than that for the pair sharing no PPI partners. These results indicate that the duplicated gene pairs differentiate through the losses and/or gains of the PPI partners, resulting in a change in their evolutionary rates. In particular, we point out that the PPI losses for the duplicated gene products that are involved in the functional classes of 'transcription' and 'protein fate' have an impact on their evolutionary rates more than the PPI losses for others.

Original languageEnglish (US)
Pages (from-to)57-63
Number of pages7
StatePublished - Dec 30 2006

Bibliographical note

Funding Information:
We are grateful to Yoshio Tateno, Kazuho Ikeo, Matthew Webster, two anonymous reviewers and all the members of the DNA Analysis Laboratory for valuable comments and discussion. This research was supported by Grants-in-Aid for Creative Basic Research from the Ministry of Education, Culture, Sports, Science and Technology, Japan (to T.G.).


  • Functional divergence
  • Gene duplication
  • Protein-protein interaction
  • Saccharomyces cerevisiae

ASJC Scopus subject areas

  • Genetics


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