Differential evolutionary rates of duplicated genes in protein interaction network

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.