Comprehensive analysis of genes involved in the oxidative stress tolerance using yeast heterozygous deletion collection

Abstract

In Saccharomyces cerevisiae, oxidative stress plays an inhibitory role during industrial fermentation. Although previous reports have identified genes required for oxidative stress tolerance, employing the yeast genome-wide screening, these screenings used a homozygous mutant collection which did not include the essential genes whose deletions result in lethality. Here, we report a truly genome-wide screening for the genes required for oxidative stress tolerance, using a heterozygous mutant collection which includes both essential and nonessential genes. Approximately 6300 heterozygous deletion mutants were grown in the presence or absence of H2 O2 . The screening identified a total of 331 genes whose heterozygotes conferred hypersensitivity to H2 O2 , indicating that these genes are required for oxidative stress tolerance. Notably, among these genes, 71 were essential genes. We classified these 71 essential genes based on localization, indicating that the localization of gene products from these essential genes was enriched in the nucleus and nucleolus. Classification of these essential genes based on functional categorizations showed that rRNA synthesis and tRNA synthesis were over-represented, suggesting that nuclear function, such as RNA synthesis, is important in the response to oxidative stress. These results provide a helpful resource for the understanding of the molecular basis of oxidative stress-tolerant mechanisms.

Integrating Rio1 activities discloses its nutrient-activated network in Saccharomyces cerevisiae

“…Hence we used Fisher’s exact test to compare Rio1’s transcriptome dataset with those of other regulatory networks in yeast. We found that the Rio1 gene regulon significantly overlapped with those of the heat ( P -value = 1.4E-07), osmotic ( P -value = 3.7E-56), nutritional ( P -value = 7.2E-22) and oxidative ( P -value = 7.3E-04) stress-response systems (107–111) (the transcriptomes are size-weighted in Figure 7A, individual genes are listed in Supplementary Table S10). This observation suggested that Rio1 and its network are physically and functionally integrated with these response networks.…”

Adaptive differentiation coincides with local bioclimatic conditions along an elevational cline in populations of a lichen-forming fungus

“…Taurine is a solute required in osmoregulation, and has been linked to the survival of the fungus Ochroconis mirabilis in different habitats [69]. In the same functional category, we found candidate SNPs in genes such as a flavin-binding monooxygenase, and in the putative essential subunit of U3-containing 90S preribosome ( NOP9 ), which has been reported among the 71 essential genes required for oxidative stress tolerance in Saccharomyces cerevisiae [70]. Additionally we found the calcium channel subunit Cch1 , which has been reported to be involved in the Ca 2+ release in response to exogenous oxidative stress in yeast [71], and a putative flap endonuclease, which is part of the base-excision repair pathway that removes lesions resulting from exposure to reactive oxygen species in yeast [72, 73].…”

Coevolution with bacteria drives the evolution of aerobic fermentation in Lachancea kluyveri

“…cerevisiae (S3B Table). The relevant variants were in DNA replication stress and DNA damage response ( RAS1 , RAS2 , RSR1 ) [26, 27] and cell wall integrity pathway ( PTS1 , ECM33 ) [28, 29], ER maintenance and oxidative stress ( SRP102 ) [30]. Some of these pathways were similar between MAC and RYT strains, suggesting these pathways are the primary response when fermentative ability of yeast is increased.…”