A ribosome assembly stress response regulates transcription to maintain proteome homeostasis.

Benjamin Albert,Anthony K Henras,Xu Zhang,Martin Kos,Maria Paula Rueda,David Shore,Christophe Dez,Isabelle C Kos-Braun,Olivier Gadal

doi:10.7554/elife.45002

Benjamin Albert, Anthony K Henras + Show 7 more

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https://doi.org/10.7554/elife.45002

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Abstract

Ribosome biogenesis is a complex and energy-demanding process requiring tight coordination of ribosomal RNA (rRNA) and ribosomal protein (RP) production. Given the extremely high level of RP synthesis in rapidly growing cells, alteration of any step in the ribosome assembly process may impact growth by leading to proteotoxic stress. Although the transcription factor Hsf1 has emerged as a central regulator of proteostasis, how its activity is coordinated with ribosome biogenesis is unknown. Here, we show that arrest of ribosome biogenesis in the budding yeast Saccharomyces cerevisiae triggers rapid activation of a highly specific stress pathway that coordinately upregulates Hsf1 target genes and downregulates RP genes. Activation of Hsf1 target genes requires neo-synthesis of RPs, which accumulate in an insoluble fraction and presumably titrate a negative regulator of Hsf1, the Hsp70 chaperone. RP aggregation is also coincident with that of the RP gene activator Ifh1, a transcription factor that is rapidly released from RP gene promoters. Our data support a model in which the levels of newly synthetized RPs, imported into the nucleus but not yet assembled into ribosomes, work to continuously balance Hsf1 and Ifh1 activity, thus guarding against proteotoxic stress during ribosome assembly.

Highlights

Ribosome assembly is the most energy demanding process linked to cell growth and requires coordinated production of processed ribosomal RNAs, ribosomal proteins (RPs) and ribosome biogenesis (RiBi) factors
Topoisomerase depletion triggers a rapid repression of RP genes and activation of proteostasis genes In an effort to understand the role of the two major eukaryotic DNA topoisomerases in proteincoding gene transcription, we generated yeast strains in which Top1, Top2, or both of these enzymes are rapidly degraded by the auxin-induced degron (AID) method ((Nishimura et al, 2009) and confirmed by Western blotting that significant depletion of either protein was obtained between 10 and 20 minutes following auxin addition to the medium, and that Top2 depletion, as expected, prevents cell growth (Figure S1A, B; Table S1)
In this study we demonstrate the existence of a regulatory mechanism, which we refer to as Ribosomal Assembly Stress Response (RAStR), that allows yeast cells to coordinate the activity of two transcription factor (TF), Heat shock factor 1 (Hsf1) and Ifh1, with the functional state of ribosome assembly

Summary

Introduction

Ribosome assembly is the most energy demanding process linked to cell growth and requires coordinated production of processed ribosomal RNAs (rRNAs), ribosomal proteins (RPs) and ribosome biogenesis (RiBi) factors. This massive biosynthetic program permits rapidly growing yeast cells to produce about 2,000 ribosomes per minutes (Warner, 1999). Given the absence of p53 in yeasts, S. cerevisiae promises to be a good model system in which to uncover ancestral processes that regulate growth and protein homeostasis in eukaryotes

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