Saccharomyces cerevisiae DNA Polymerase δ: High fidelity for base substitutions but lower fidelity for single-and multi-base deletions

Eukaryotic DNA polymerase δ (Pol δ) plays an essential role in replicating large nuclear genomes, a process that must be accurate to maintain stability over many generations. Based on kinetic studies of insertion of individual dNTPs opposite a template guanine, Pol δ is believed to have high selectivity for inserting correct nucleotides. This high selectivity, in conjunction with an intrinsic 3′-exonuclease activity, implies that Pol δ should have high base substitution fidelity. Here we demonstrate that the wild type Saccharomyces cerevisiae three-subunit Pol δ does indeed have high base substitution fidelity for the 12 possible base-base mismatches, producing on average less than 1.3 stable misincorporations/100,000 nucleotides polymerized. Measurements with exonuclease-deficient Pol δ confirm the high nucleotide selectivity of the polymerase and further indicate that proofreading enhances the base substitution fidelity of the wild type enzyme by at least 60-fold. However, Pol δ inefficiently proofreads single nucleotide deletion mismatches in homopolymeric runs, such that the error rate is 30 single nucleotide deletions/ 100,000 nucleotides polymerized. Moreover, wild type Pol δ frequently deletes larger numbers of nucleotides between distantly spaced direct repeats of three or more base pairs. Although wild type Pol δ and Pol ε both have high base substitution fidelity, Pol δ is much less accurate than Pol ε for deletions involving repetitive sequences. Thus, strand slippage during replication by wild type Pol δ may be a primary source of insertion and deletion mutagenesis in eukaryotic genomes.