Abstract
Maintenance of protein quality control has implications in various processes such as neurodegeneration and ageing. To investigate how environmental insults affect this process, we analysed the proteome of yeast continuously exposed to mild heat stress. In agreement with previous transcriptomics studies, amongst the most marked changes, we found up-regulation of cytoprotective factors; a shift from oxidative phosphorylation to fermentation; and down-regulation of translation. Importantly, we also identified a novel, post-translationally controlled, component of the heat shock response. The abundance of Ncs2p and Ncs6p, two members of the URM1 pathway responsible for the thiolation of wobble uridines in cytoplasmic tRNAs tKUUU, tQUUG and tEUUC, is down-regulated in a proteasomal dependent fashion. Using random forests we show that this results in differential translation of transcripts with a biased content for the corresponding codons. We propose that the role of this pathway in promoting catabolic and inhibiting anabolic processes, affords cells with additional time and resources needed to attain proper protein folding under periods of stress.
Highlights
Robust and rapid response to ever changing extracellular environmental conditions is a prerequisite for the survival of all life forms
To study the differential proteome composition of yeast cells grown at 30◦C versus 37◦C, we used SILAC-based quantitative proteomics
Each sample was fractionated into 12 fractions using isoelectric focussing with OffGel electrophoresis to help increase proteome coverage (Figure 1A). This led to the identification of 4663 proteins at a ProteinProphet [26] calculated 1% false discovery rate (FDR)
Summary
Robust and rapid response to ever changing extracellular environmental conditions is a prerequisite for the survival of all life forms. The mechanism, timing and intensity of ESR gene expression is tied to the kind and severity of the stress [3]. Complementing this common expression program, several genes are distinctly controlled by specific stress conditions. Under stress conditions cells regulate the abundance of ribosomes and tRNAs to slow down translation [1,2,7]. Proteins such as the translation initiation factors and ribosomal structural proteins are post-translationally modified to modulate their activity [8,9,10]
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