Selection to maintain paralogous amino acid differences under the pressure of gene conversion in the heat-shock protein genes in yeast.

A genome scan for the signatures of selection for paralogous functional amino acid differences was performed with yeast genomes. This recently developed method makes it possible to localize the target sites of selection under the pressure of gene conversion. We found that two gene pairs have strong signatures of selection. The two pairs of duplicated genes happened to be heat shock genes (Ssa1/ Ssa2 and Ssb1/Ssb2), which have similar protein structures to each other, although the amino acid sequence identity between Ssa and Ssb is not high ( approximately 60%). Interestingly, the two gene pairs exhibit signature of selection at almost identical positions within the substrate-binding domain beta. Because this domain specifies the substrate polypeptides, it is presumed that functional divergence may be advantageous in this domain. Evolutionary analysis demonstrated that the observed divergence in the two gene pairs has been maintained in many yeast species independently, suggesting long-term operation of strong selection.