Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes

TLDR

The study examined genome‑wide expression changes in *Saccharomyces cerevisiae* across diverse environmental perturbations. Transcript levels were profiled over time using DNA microarrays for nearly all yeast genes under temperature, oxidative, osmotic, nutrient, and stationary‑phase stresses. Approximately 900 genes exhibited a common, drastic response to most stresses, while distinct transcription factors (Yap1p, Msn2p, Msn4p) and novel regulatory elements mediated condition‑specific responses, revealing physiological themes of stress impact.

Abstract

We explored genomic expression patterns in the yeastSaccharomyces cerevisiae responding to diverse environmental transitions. DNA microarrays were used to measure changes in transcript levels over time for almost every yeast gene, as cells responded to temperature shocks, hydrogen peroxide, the superoxide-generating drug menadione, the sulfhydryl-oxidizing agent diamide, the disulfide-reducing agent dithiothreitol, hyper- and hypo-osmotic shock, amino acid starvation, nitrogen source depletion, and progression into stationary phase. A large set of genes (∼ 900) showed a similar drastic response to almost all of these environmental changes. Additional features of the genomic responses were specialized for specific conditions. Promoter analysis and subsequent characterization of the responses of mutant strains implicated the transcription factors Yap1p, as well as Msn2p and Msn4p, in mediating specific features of the transcriptional response, while the identification of novel sequence elements provided clues to novel regulators. Physiological themes in the genomic responses to specific environmental stresses provided insights into the effects of those stresses on the cell.