Abstract
Cells rapidly alter gene expression in response to environmental stimuli such as nutrients, hormones, and drugs. During the imposed “remodeling” of gene expression, changes in the levels of particular mRNAs do not necessarily correlate with those of the encoded proteins, which could in part rely on the differential recruitment of mRNAs to translating ribosomes. To systematically address this issue, we have established an approach to rapidly access the translational status of each mRNA in the yeast Saccharomyces cerevisiae by affinity purification of endogenously formed ribosomes and the analysis of associated mRNAs with DNA microarrays. Using this method, we compared changes in total mRNA levels (transcriptome) with ribosome associations (translatome) after the application of different conditions of cellular stress. Severe stresses, induced by amino acid depletion or osmotic shock, stimulated highly correlated responses affecting about 15% of both total RNA levels and translatome. Many of the regulated messages code for functionally related proteins, thus reflecting logical responses to the particular stress. In contrast, mild stress provoked by addition of Calcofluor-white and menadione altered the translatome of approximately 1% of messages with only marginal effects on total mRNA, suggesting largely uncorrelated responses of transcriptome and translatome. Among these putative translationally regulated messages were most components of the mitochondrial ATPase. Increased polysome associations of corresponding messages and higher mitochondrial ATPase activities upon treatment confirmed the relevance for regulation of this macromolecular complex. Our results suggest the presence of highly sensitive translational regulatory networks that coordinate functionally related messages. These networks are preferentially activated for rapid adaptation of cells to minor environmental perturbations.
Highlights
Gene expression is regulated at diverse levels to achieve coordinate synthesis of the cell’s macromolecular components
We systematically compared global transcript levels with global alterations in the levels of ribosome association of transcripts when yeast cells are exposed to different stresses to determine how significant the discrepancy between transcript and protein levels can be
In this case, remodeling of gene expression is mainly executed at the translational level by modulating mRNA association with ribosomes
Summary
Gene expression is regulated at diverse levels to achieve coordinate synthesis of the cell’s macromolecular components. It has become increasingly evident that gene expression is controlled by a network of highly interconnected posttranscriptional regulatory factors, such as RNA-binding proteins and noncoding RNAs [1,2,3,4]. Modification of initiation factors, such as phosphorylation of eIF2a, prevents formation of the initiation complex and globally represses translation initiation of most messages. The availability of initiation factors, such as eIF4e, is controlled by 4E-binding proteins that inhibit association of the 40S subunit with the mRNA [8]. Many regulatory RBPs interact with functionally related groups of mRNAs, referred to as ‘‘posttranscriptional operons,’’ suggesting highly coordinated control at all steps of posttranscriptional gene regulation [2,12,13,14]
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