Abstract
SummaryCellular responses to environmental stress are frequently mediated by RNA-binding proteins (RBPs). Here, we examined global RBP dynamics in Saccharomyces cerevisiae in response to glucose starvation and heat shock. Each stress induced rapid remodeling of the RNA-protein interactome without corresponding changes in RBP abundance. Consistent with general translation shutdown, ribosomal proteins contacting the mRNA showed decreased RNA association. Among translation components, RNA association was most reduced for initiation factors involved in 40S scanning (eukaryotic initiation factor 4A [eIF4A], eIF4B, and Ded1), indicating a common mechanism of translational repression. In unstressed cells, eIF4A, eIF4B, and Ded1 primarily targeted the 5′ ends of mRNAs. Following glucose withdrawal, 5′ binding was abolished within 30 s, explaining the rapid translation shutdown, but mRNAs remained stable. Heat shock induced progressive loss of 5′ RNA binding by initiation factors over ∼16 min and provoked mRNA degradation, particularly for translation-related factors, mediated by Xrn1. Taken together, these results reveal mechanisms underlying translational control of gene expression during stress.
Highlights
All organisms are subject to a continuously changing environment, to which they must adapt in order to survive
Budding yeast respond to stress by inducing global changes in gene expression. This involves the activation of the environmental stress response, in which hundreds of stress-response genes are upregulated and genes encoding ribosome maturation and protein synthesis factors are suppressed
Global RNA-binding proteins (RBPs) Dynamics in Response to Cell Stress We previously developed TRAPP as a method to characterize the global RNA-binding proteome (Shchepachev et al, 2019)
Summary
All organisms are subject to a continuously changing environment, to which they must adapt in order to survive. Cytoplasmic translation is dramatically attenuated in response to a variety of environmental stresses, including various types of nutrient deprivation, and physical stresses involving changes in temperature, osmotic balance, or oxidation state. In terms of both speed and scale, glucose starvation triggers the most drastic translational shutdown of any stress (Ashe et al, 2000; Kuhn et al, 2001). Glucose is the preferred energy and carbon source for yeast, and its absence quickly reduces cellular biosynthetic capacity Physical stresses, such as heat shock, can limit biosynthesis while damaging the existing proteome. Cells halt bulk protein synthesis until protective measures are in place
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