Genomic expression programs in the response of yeast cells to environmental changes.
We explored genomic expression patterns in the yeast Saccharomyces 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 (approximately 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.
Gasch
A P
AP
Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5428, USA.
Spellman
P T
PT
Kao
C M
CM
Carmel-Harel
O
O
Eisen
M B
MB
Storz
G
G
Botstein
D
D
Brown
P O
PO
D002244:Carbon / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000502:physiology; D003958:Diamide / Q000494:pharmacology; D004229:Dithiothreitol / Q000494:pharmacology; D004777:Environment; D005656:Fungal Proteins / Q000235:genetics / Q000502:physiology; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D006361:Heating; D006861:Hydrogen Peroxide / Q000494:pharmacology; D009584:Nitrogen / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D009997:Osmotic Pressure; D012441:Saccharomyces cerevisiae / Q000187:drug effects / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins; D013439:Sulfhydryl Reagents / Q000494:pharmacology; D014157:Transcription Factors / Q000235:genetics / Q000502:physiology; D014812:Vitamin K / Q000494:pharmacology
D004268:DNA-Binding Proteins; D005656:Fungal Proteins; C081935:MSN2 protein, S cerevisiae; C081937:MSN4 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D013439:Sulfhydryl Reagents; D014157:Transcription Factors; C086677:YAP1 protein, S cerevisiae; D003958:Diamide; D014812:Vitamin K; D002244:Carbon; D006861:Hydrogen Peroxide; D009584:Nitrogen; D004229:Dithiothreitol