Genome-wide identification of genes involved in tolerance to various environmental stresses inSaccharomyces cerevisiae

Abstract

During fermentation, yeast cells are exposed to a number of stresses -- such as high alcohol concentration, high osmotic pressure, and temperature fluctuation - so some overlap of mechanisms involved in the response to these stresses has been suggested. To identify the genes required for tolerance to alcohol (ethanol, methanol, and 1-propanol), heat, osmotic stress, and oxidative stress, we performed genome-wide screening by using 4828 yeast deletion mutants. Our screens identified 95, 54, 125, 178, 42, and 30 deletion mutants sensitive to ethanol, methanol, 1-propanol, heat, NaCl, and H2O2, respectively. These deleted genes were then classified based on their cellular functions, and cross-sensitivities between stresses were determined. A large number of genes involved in vacuolar H(+)-ATPase (V-ATPase) function, cytoskeleton biogenesis, and cell wall integrity, were required for tolerance to alcohol, suggesting their protective role against alcohol stress. Our results revealed a partial overlap between genes required for alcohol tolerance and those required for thermotolerance. Genes involved in cell wall integrity and the actin cytoskeleton are required for both alcohol tolerance and thermotolerance, whereas the RNA polymerase II mediator complex seems to be specific to heat tolerance. However, no significant overlap of genes required for osmotic stress and oxidative stress with those required for other stresses was observed. Interestingly, although mitochondrial function is likely involved in tolerance to several stresses, it was found to be less important for thermotolerance. The genes identified in this study should be helpful for future research into the molecular mechanisms of stress response.

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

“…In a clear illustration of this premise, 23 of the 55 genes shown to influence heat sensitivity in S. cerevisiae annotate as having unknown functions (Gibney et al, 2013). Similarly, 17%, 10% and 6% of the genes significantly affecting tolerance toward ethanol, H 2 O 2 and NaCl in S. cerevisiae were also classified as unknown genes, respectively (Auesukaree et al, 2009). Among the genes that modify the capacity for protein folding in C. elegans, 19% are of unknown function.…”

“…Studies in yeast also suggest relatively small numbers of genes are capable of modifying sensitivity toward other abiotic factors. A screen of 4828 yeast deletion strains identified only 95 genes (2% of genes assayed) that alter sensitivity toward ethanol, 42 genes (0.9% of genes assayed) capable of modifying osmotic stress tolerance, and 30 genes (0.6% of genes assayed) that change tolerance toward oxidative stress (Auesukaree et al, 2009). At least in yeast, only a small subset of protein-coding genes appear capable of modifying tolerance toward abiotic factors.…”

Auxotrophic Mutations Reduce Tolerance of Saccharomyces cerevisiae to Very High Levels of Ethanol Stress

“…Ethanol tolerance is a complex property that is determined by numerous genetic and environmental factors (1,7,14,(17)(18)(19)(20)(21)(22)(23)(24). Several genome-wide analyses have been performed to decipher the genetic basis of ethanol tolerance in S. cerevisiae, as comprehensively reviewed by Stanley et al (25).…”

“…Several genome-wide analyses have been performed to decipher the genetic basis of ethanol tolerance in S. cerevisiae, as comprehensively reviewed by Stanley et al (25). Virtually all of these studies focused on the tolerance of laboratory strains to moderate concentrations of ethanol (i.e., 6 to 12%) and were performed by determining the sensitivity of the yeast deletion strain collection to such ethanol concentrations under different conditions (17,18,20,22,23). Another study used genome-wide transcriptomics to study differences between the responses of natural S. cerevisiae strains to 5% ethanol (14).…”

“…Another study used genome-wide transcriptomics to study differences between the responses of natural S. cerevisiae strains to 5% ethanol (14). Although the above-mentioned studies identified hundreds of genes that are required for ethanol tolerance in S. cerevisiae, they showed little overlap between the genes identified under the different conditions used (14,17,18,20,22,23). This discrepancy suggests that the mechanisms of ethanol sensitivity depend on the genetic background, the growth conditions, and the ethanol concentration used.…”