Pif1 family helicases promote mutation avoidance during DNA replication

Pif1 family 5 ' -> 3 ' DNA helicases are important for replication fork progression and genome stability. The budding yeast Saccharomyces cerevisiae encodes two Pif1 family helicases, Rrm3 and Pif1, both of which are multi-functional. Here we describe novel functions for Rrm3 in promoting mutation avoidance during DNA replication. We show that loss of RRM3 results in elevated spontaneous mutations made by DNA polymerases Pols epsilon and delta, which are subject to DNA mismatch repair. The absence of RRM3 also causes higher mutagenesis by the fourth B-family DNA polymerase Pol zeta. By genome-wide analysis, we show that the mutational consequences due to loss of RRM3 vary depending on the genomic locus. Rrm3 promotes the accuracy of DNA replication by Pols epsilon and delta across the genome, and it is particularly important for preventing Pol zeta-dependent mutagenesis at tRNA genes. In addition, mutation avoidance by Rrm3 depends on its helicase activity, and Pif1 serves as a backup for Rrm3 in suppressing mutagenesis. We present evidence that the sole human Pif1 family helicase in human cells likely also promotes replication fidelity, suggesting that a role for Pif1 family helicases in mutation avoidance may be evolutionarily conserved, a possible underlying mechanism for its potential tumor-suppressor function.

Automated summary

This study identifies a novel function for the Pif1 family 5'->3' DNA helicase Rrm3 in promoting mutation avoidance during DNA replication. The loss of Rrm3 leads to increased spontaneous mutations made by DNA polymerases Pols epsilon and delta, as well as higher mutagenesis by Pol zeta. The genomic loci affected by the loss of Rrm3 vary, and Rrm3 is particularly important for preventing Pol zeta-dependent mutagenesis at tRNA genes. The helicase activity of Rrm3 is essential for its role in mutation avoidance, and Pif1 serves as a backup for Rrm3 in suppressing mutagenesis. Additionally, the findings suggest that the sole human Pif1 family helicase may also play a role in replication fidelity, potentially contributing to its tumor-suppressor function.