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

Abstract

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 Illuminabased 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.

Yeast Tolerance to Various Stresses Relies on the Trehalose-6P Synthase (Tps1) Protein, Not on Trehalose

“…However, doubts about this stress-protecting function have been recently raised from contradictory results, notably in thermotolerance and desiccation (51)(52)(53). A main reason for this ambiguity was the inability to directly assess the physiological function of trehalose in yeast cells without interfering with its metabolism, as well as with stress applied.…”

Considerations for the use of transcriptomics in identifying the ‘genes that matter’ for environmental adaptation

“…Pretreatment of the same collection of yeast deletion strains to 37°C prior to increasing temperature to 50°C, identified only 10 genes (0.2% of genes assayed) that were able to modify acquired thermotolerance. These 10 strains were largely a subset of the 55 genes shown to influence tolerance toward acute heat stress, suggesting that only a small number of genes underlie both innate and acquired thermotolerance in yeast (Gibney et al, 2013). Additional genome-wide analyses in S. cerevisiae support this conclusion.…”

“…However, results suggest that in these species, the probability of any one gene significantly influencing fitness, even under shifting environmental conditions, is low. In the yeast S. cerevisiae, exposure of 4783 single gene deletion strains to acute heat stress (increasing temperature from 30 to 50°C) yielded only 55 deletions (1.2% of genes assayed) that differed significantly in heat sensitivity relative to control populations (Gibney et al, 2013). Similar trends also seem to underlie acquired thermotolerance in yeast, where exposure to an initial mild stress confers resistance toward a subsequent more severe stress.…”

“…Of the 29 heat shock proteins induced or repressed in response to heat stress in yeast, only two, jjj2 (a member of the DnaJ family of chaperones) and hsp104, significantly affected survival ( Fig. 2C; Gibney et al, 2013). Lack of concordance between gene expression and functional significance is actually a well-established outcome in studies of environmental tolerance in yeast.…”

“…Hub genes interact with far more than the average number of protein partners, and therefore are much more likely to display phenotypes when knocked-out compared with genes whose proteins have no or few interacting partners (Jeong et al, 2001;Han et al, 2004;Feder and Walser, 2005). Gene functional annotation shows that the subset of genes capable of modifying thermotolerance in yeast, almost all of which do not respond transcriptionally to heat stress, contain a significantly higher proportion of genes involved in cell signaling and chromatin regulation (Gibney et al, 2013;Jarolim et al, 2013), and therefore may act as hub genes by influencing the expression and/or activity of a large number of downstream genes. For example, several genes identified as necessary for heat shock survival in S. cerevisiae are either kinases that covalently attach phosphate groups to proteins (e.g.…”