Stress-Dependent Coordination of Transcriptome and Translatome in Yeast

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.

Genome-wide ribosome profiling reveals complex translational regulation in response to oxidative stress

“…Translatome and transcriptome in yeast are regulated conjointly in response to various stresses, such as amino acid depletion, osmotic shock, and sorbitol treatment (7). Thus the genes up-regulated at the level of transcription also yield more protein product as well, a process that is termed "potentiation."…”

“…However, they are designed for the quantification of individual proteins rather than for addressing the details of translation. Indirect approaches, such as comparative microarray profiling of mRNAs within monosomes and polysomes, are popular as well (5)(6)(7)(8). These methods enable estimation of the mRNA transcripts that are being translated.…”

Mechanism and Regulation of Protein Synthesis in Saccharomyces cerevisiae

“…Stresses found to deplete bulk polysomes include the sudden withdrawal of glucose (Ashe et al 2000;Arribere et al 2011;Vaidyanathan et al 2014) or amino acids (Smirnova et al 2005); nutrient limitation that induces sporulation (Brar et al 2012); temperature shift (Preiss et al 2003); and the addition of cellular stress agents: hyperosmotic salt (Melamed et al 2008), hydrogen peroxide (Shenton et al 2006), fusel alcohols (Smirnova et al 2005), or drugs: rapamycin (Preiss et al 2003), calcofluor-white (Halbeisen and Gerber 2009), and chlorpromazine (Deloche et al 2004). These studies have shown that there is widespread reprogramming of translation following stress with diminished ribosome association of some mRNAs hypersensitive to stress, while the translation of other mRNAs is relatively resistant to the stress.…”

Cellular stress induces cytoplasmic RNA granules in fission yeast

“…The cell enters a program where resources are directed from rapid growth to stress protection. Components of ribosomes and gene products required for ribosomal biogenesis are strictly down-regulated on the levels of transcriptional initiation, translation, and mRNA turnover (Tang et al 2001;Grigull et al 2004;Halbeisen and Gerber 2009). On the other hand, mRNAs encoding proteins required for survival in stress conditions are stabilized and preferentially translated (Lü et al 2006;Halbeisen and Gerber 2009;Molin et al 2009;Powley et al 2009).…”