A DNA polymerase epsilon mutant that specifically causes +1 frameshift mutations within homonucleotide runs in yeast

The DNA polymerases delta and epsilon are the major replicative polymerases in the yeast Saccharomyces cerevisiae that possess 3' --> 5' exonuclease p roofreading activity. Many errors arising during replication are corrected by these exonuclease activities. We have investigated the contributions of regions of Pol epsilon other than thr proofreading motifs to replication ac curacy. An allele, pol2-C1089Y, was identified in a screen of Pol epsilon m utants that in combination with an exonuclease I (exo1) mutation could caus e a synergistic increase in mutations within homonucleotide runs. In contra st to other polymerase mutators, this allele specifically results in insert ion frameshifts. When pol2-C1089Y was combined with deletions of EXO1 or RA D27 (homologue of human FEN1), mutation rates were increased for +1 framesh ifts while there was almost no effect on -1 frame shifts. On the basis of g enetic analysis, the pol2-C1089Y mutation did not cause a defect in proofre ading. In combination with a deletion of the mismatch repair gene MSH2, the +1 frameshift mutation rate for a short homonucleotide run was increased n early 100-fold whereas the -1 frameshift rate was unchanged. This suggests that the Pol2-C1089Y protein makes +1 frameshift errors during replication of homonucleotide mns and that these errors can be corrected by either mism atch repair (MMR) or proofreading (in short runs). This is the first report of a + 1-specific mutator for homonucleotide runs in vivo. The pol2-C1089Y mutation defines a functionally important residue in Pol epsilon.