Genomic expression programs in the response of yeast cells to environmental changes

Abstract

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.

Figure 1

Genomic expression programs in response to environmental changes. The entire set of yeast genes identified at the time of our analysis (∼6,200) was clustered based on their expression patterns in 142 array experiments that followed wild-type yeast responding to environmental changes. Here, data from 94 arrays are shown, omitting duplicate experiments that were considered in the clustering analysis (see web supplemental MATERIALS AND METHODS for details). Experiments are labeled according to the color key depicted: time course experiments are indicated with colored triangles, while steady-state experiments are labeled with colored squares. Individual clusters of coregulated genes that are discussed in the text and web supplements are labeled as follows: A. WSC2 cluster, B. CIS3 cluster, C. LHS1 cluster, D. Glycolysis cluster, E. SSA2 cluster, F. Repressed ESR cluster, G. Amino acid transporters, H. Amino acid and purine genes, I. Chaperone cluster, J. KAR2 cluster, K. Proteasome and Endocytosis cluster L. TRR1 and TRR2 clusters, M. DAL cluster, N. Oxidative phosphorylation cluster, O. Glyoxylate and TCA cycle cluster, P. Induced ESR cluster, Q. TRX2 cluster.

Figure 2

Transient changes in genomic expression following environmental change. (A-B) The expression of ∼ 1000 genes that changed by a factor of at least twofold in response to heat shock is shown as the cells responded to (A) 25°C to 37°C heat shock and (B) 29°C to 33°C heat shock. (C-D) The average expression changes of genes displayed in (A) and (B), respectively, are shown. The average expression of genes induced in each response is depicted by a red curve, while the average expression of genes repressed in each response is depicted by a green curve.

Figure 3

Overview of the Environmental Stress Response (ESR). Genes that participate in the ESR were chosen based strictly on the genomic cluster analysis shown in Figure 1. Two extended clusters of genes, one corresponding to repressed genes and one corresponding to induced genes, displayed nearly identical but opposite patterns of gene expression in response to environmental stress. Color scale and array identification are indicated.

Figure 4

Characterized genes induced in the ESR. Characterized genes that are induced in the ESR are displayed according to their involvement in (A) carbohydrate metabolism, (B) cellular redox reactions and defense against reactive oxygen species, (C) protein folding, (D) protein degradation and vacuolar functions, (E) DNA damage repair, and (F) intracellular signaling. Additional functional categories can be viewed on the web supplement.

Figure 5

Differentially regulated isozymes in the ESR. The expression of genes encoding differentially regulated isozymes is shown. Isozymes regulated in the ESR are labeled in purple. Color scale and array identification are shown.

Figure 6

Reciprocal expression of the ESR following reciprocal environmental changes. (A-B) The expression of ESR genes is shown for (A) cells transferred from 25°C to 37°C (▴) and cells transferred from 37°C to 25°C (▵), and (B) cells exposed to hyper-osmotic shock (▴) and reverse osmotic shock (▵) over the course of 1 h. Steady-state expression at each condition is also shown and is indicated by a closed or open square. The genes represented are the same as those shown in Figure 3. (C-D) The average expression changes of genes displayed in (A) and (B), respectively, over time are graphed. Genes normally induced in the ESR are represented by a red curve, and genes normally repressed in the ESR are represented by a green curve on each plot.

Figure 7

Genes dependent on Msn2/Msn4p. Wild-type, msn2 msn4, and yap1 strains were exposed to H₂O₂ and heat shock, and genes whose expression was affected in the msn2 msn4 mutant strain are shown. The display represents data averaged from duplicate experiments. The effects on these genes of overexpression of MSN2, MSN4 (this study), and YAP1 (DeRisi et al., 1997) are also shown. Genes fell into three classes based on their expression patterns, marked by bars to the right of the cluster diagram: (A) genes partially dependent on Msn2/Msn4p in response to both stresses; (B) genes largely dependent on Msn2/Msn4p in response to both stresses; and (C) genes dependent on Msn2/4p only in response to heat shock.

Figure 8

ESR genes dependent on Msn2/Msn4p and Yap1p. (A) Gene expression in the wild-type, msn2 msn4, and yap1 strains was monitored following heat shock and H₂O₂ treatment as described. The expression ratios for each gene in this diagram represent the average from duplicate array experiments. Transcripts of the GRE2 and YOL150C genes (*) are highly homologous and are likely to cross-hybridize on the microarrays. (B) The bar graphs depict the average change in expression for the genes shown in (A) in each of the strains tested.