Abstract
We have analyzed the heat stress response in the yeast Saccharomyces cerevisiae by determining mRNA levels and transcription rates for the whole transcriptome after a shift from 25°C to 37°C. Using an established mathematical algorithm, theoretical mRNA decay rates have also been calculated from the experimental data. We have verified the mathematical predictions for selected genes by determining their mRNA decay rates at different times during heat stress response using the regulatable tetO promoter. This study indicates that the yeast response to heat shock is not only due to changes in transcription rates, but also to changes in the mRNA stabilities. mRNA stability is affected in 62% of the yeast genes and it is particularly important in shaping the mRNA profile of the genes belonging to the environmental stress response. In most cases, changes in transcription rates and mRNA stabilities are homodirectional for both parameters, although some interesting cases of antagonist behavior are found. The statistical analysis of gene targets and sequence motifs within the clusters of genes with similar behaviors shows that both transcriptional and post-transcriptional regulons apparently contribute to the general heat stress response by means of transcriptional factors and RNA binding proteins.
Highlights
Cells respond to a variety of environmental stresses by reprogramming the expression of specific sets of genes which depend on the particular stress
The heat shock response in yeast is mediated by the transcription factors (TF) Hsf1 and Msn2/Msn4, and involves the upregulation of a number of genes for heat-shock proteins (Hsps) that participate in protein folding, trafficking and maturation, and the genes for the protein degradation machinery
To minimize undesirable side effects on the cell cycle, which could disturb the direct effects of heat shock on general transcription and mRNA stability, we employed mild stress conditions that minimally affected exponential growth, but still induced the expression of the genes taking part in the heat shock response
Summary
Cells respond to a variety of environmental stresses by reprogramming the expression of specific sets of genes which depend on the particular stress. The heat shock response in yeast is mediated by the transcription factors (TF) Hsf and Msn2/Msn, and involves the upregulation of a number of genes for heat-shock proteins (Hsps) that participate in protein folding, trafficking and maturation, and the genes for the protein degradation machinery. This is paralleled by a downregulation of the genes for ribosome biogenesis [8]. Partial overlapping has been described between the heat shock response and the unfolded protein response, which is induced by misfolded proteins at the endoplasmic reticulum and mediated by the Hac TF [13] Both types of stress share a number of transcription targets
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