Evidence that DNA polymerase δ proofreads errors made by DNA polymerase α across the Saccharomyces cerevisiae nuclear genome

DNA Repair (Amst). 2024 Nov:143:103768. doi: 10.1016/j.dnarep.2024.103768. Epub 2024 Sep 21.

Abstract

We show that the rates of single base substitutions, additions, and deletions across the nuclear genome are strongly increased in a strain harboring a mutator variant of DNA polymerase α combined with a mutation that inactivates the 3´-5´ exonuclease activity of DNA polymerase δ. Moreover, tetrad dissections attempting to produce a haploid triple mutant lacking Msh6, which is essential for DNA mismatch repair (MMR) of base•base mismatches made during replication, result in tiny colonies that grow very slowly and appear to be aneuploid and/or defective in oxidative metabolism. These observations are consistent with the hypothesis that during initiation of nuclear DNA replication, single-base mismatches made by naturally exonuclease-deficient DNA polymerase α are extrinsically proofread by DNA polymerase δ, such that in the absence of this proofreading, the mutation rate is strongly elevated. Several implications of these data are discussed, including that the mutational signature of defective extrinsic proofreading in yeast could appear in human tumors.

Keywords: Extrinsic proofreading; Replication fidelity.

MeSH terms

  • Base Pair Mismatch
  • DNA Mismatch Repair
  • DNA Polymerase I* / genetics
  • DNA Polymerase I* / metabolism
  • DNA Polymerase III* / genetics
  • DNA Polymerase III* / metabolism
  • DNA Replication
  • DNA, Fungal / metabolism
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Genome, Fungal
  • Mutation
  • Mutation Rate
  • Saccharomyces cerevisiae Proteins* / genetics
  • Saccharomyces cerevisiae Proteins* / metabolism
  • Saccharomyces cerevisiae* / enzymology
  • Saccharomyces cerevisiae* / genetics
  • Saccharomyces cerevisiae* / metabolism

Substances

  • DNA Polymerase III
  • Saccharomyces cerevisiae Proteins
  • DNA Polymerase I
  • MSH6 protein, S cerevisiae
  • DNA-Binding Proteins
  • DNA, Fungal