Exploring a Local Genetic Interaction Network Using Evolutionary Replay Experiments

Understanding how genes interact is a central challenge in biology. Experimental evolution provides a useful, but underutilized, tool for identifying genetic interactions, particularly those that involve non-loss-of-function mutations or mutations in essential genes. We previously identified a strong positive genetic interaction between specific mutations in KEL1 (P344T) and HSL7 (A695fs) that arose in an experimentally evolved Saccharomyces cerevisiae population. Because this genetic interaction is not phenocopied by gene deletion, it was previously unknown. Using evolutionary replay experiments, we identified additional mutations that have positive genetic interactions with the kel1-P344T mutation. We replayed the evolution of this population 672 times from six timepoints. We identified 30 populations where the kel1-P3441 mutation reached high frequency. We performed whole-genome sequencing on these populations to identify genes in which mutations arose specifically in the kel1-P344T background. We reconstructed mutations in the ancestral and kel1-P344T backgrounds to validate positive genetic interactions. We identify several genetic interactors with KEL1, we validate these interactions by reconstruction experiments, and we show these interactions are not recapitulated by loss-of-function mutations. Our results demonstrate the power of experimental evolution to identify genetic interactions that are positive, allele specific, and not readily detected by other methods, shedding light on an underexplored region of the yeast genetic interaction network.

Automated summary

Experimental evolution is a powerful tool for identifying genetic interactions, especially those involving non-loss-of-function mutations or mutations in essential genes. Researchers identified a strong positive genetic interaction between specific mutations in KEL1 and HSL7 in an experimentally evolved Saccharomyces cerevisiae population. By replaying the evolution of the population and performing whole-genome sequencing, they identified additional mutations with positive genetic interactions and validated these interactions through reconstruction experiments. This study highlights the ability of experimental evolution to uncover positive, allele-specific genetic interactions that are not easily detected by other methods, providing insights into unexplored areas of the yeast genetic interaction network.