Yeast metabolic and signaling genes are required for heat-shock survival and have little overlap with the heat-induced genes

Significance We used the model eukaryote Saccharomyces cerevisiae to investigate which genes are important for survival of heat stress. Previously, this question was addressed by examining which genes are turned on by mild heat stress; in this study, we examined gene-deletion mutants for increased sensitivity to lethal heat stress. This approach reveals that these two sets of genes are largely nonoverlapping, demonstrating that mutant analysis is a powerful complementary approach to gene-expression analysis. In addition, many of the genes identified as important for heat survival are involved in metabolism or signaling, or their function is completely uncharacterized, suggesting that our understanding of the systems-level response to heat stress is incomplete. Genome-wide gene-expression studies have shown that hundreds of yeast genes are induced or repressed transiently by changes in temperature; many are annotated to stress response on this basis. To obtain a genome-scale assessment of which genes are functionally important for innate and/or acquired thermotolerance, we combined the use of a barcoded pool of ∼4,800 nonessential, prototrophic Saccharomyces cerevisiae deletion strains with Illumina-based deep-sequencing technology. As reported in other recent studies that have used deletion mutants to study stress responses, we observed that gene deletions resulting in the highest thermosensitivity generally are not the same as those transcriptionally induced in response to heat stress. Functional analysis of identified genes revealed that metabolism, cellular signaling, and chromatin regulation play roles in regulating thermotolerance and in acquired thermotolerance. However, for most of the genes identified, the molecular mechanism behind this action remains unclear. In fact, a large fraction of identified genes are annotated as having unknown functions, further underscoring our incomplete understanding of the response to heat shock. We suggest that survival after heat shock depends on a small number of genes that function in assessing the metabolic health of the cell and/or regulate its growth in a changing environment.