Comprehensive Mutational Landscape of Yeast Mutator Strains Reveals the Genetic Basis of Mutational Signatures in Cancer

Spontaneous mutation rates and spectra are influenced by an intricate interplay of processes including DNA replication, proofreading, and diverse DNA damage repair pathways. Although significant progress has been made in characterizing the functions of individual genes involved in these processes, their direct effects on mutation rates and spectra remain unclear. In this study, we employed a systematic gene knockout approach coupled with mutation accumulation (MA) experiments and whole-genome sequencing (WGS) to investigate the mutational landscape of Saccharomyces cerevisiae. We targeted 136 gene-deletion strains encompassing nearly all known genes associated with DNA replication and repair. Analysis of 1,081 MA lines revealed that 114 of the 136 genes significantly influenced at least one type of mutation rate. Furthermore, deletions of specific genes led to marked shifts in mutational biases and spectra, with some deletions amplifying existing biases and others reversing them entirely. In contrast, mitochondrial mutation rates were notably less affected, with no significant impact detected. Importantly, comparative analysis revealed striking similarities between yeast mutational spectrum and those observed in human cancers with the same pathway deficiencies, suggesting conserved functional roles across species. In conclusion, our findings provided critical insights into the genetic underpinnings of these signatures and underscoring the utility of yeast as a model for studying the molecular basis of cancer-associated mutational processes.