Starvation-induced proteasome assemblies in the nucleus link amino acid supply to apoptosis

Maxime Uriarte,Frédérick A Mallette,Anaïs Darracq,Bruno Larrivée,Clémence Messmer,Daryl A Ronato ,Hugo Würtele ,Salima Daou,Mohammadjavad Paydar,Przemyslaw Sapieha,Karine Boulay,Mikhail Sergeev,Claire Viallard,Benjamin H Kwok,Nicolas Desjardins‐Lecavalier ,Oumaima Ahmed,Jean‐Yves Masson ,Abdelhadi Djaïleb ,Louis Masclef,Roch Tremblay,Nazar Mashtalir,Haithem Barbour,Éric Milot ,Laura Hulea,Nadine Sen Nkwe,Marion Voide,El Bachir Affar

doi:10.1038/s41467-021-27306-4

Abstract

Eukaryotic cells have evolved highly orchestrated protein catabolic machineries responsible for the timely and selective disposal of proteins and organelles, thereby ensuring amino acid recycling. However, how protein degradation is coordinated with amino acid supply and protein synthesis has remained largely elusive. Here we show that the mammalian proteasome undergoes liquid-liquid phase separation in the nucleus upon amino acid deprivation. We termed these proteasome condensates SIPAN (Starvation-Induced Proteasome Assemblies in the Nucleus) and show that these are a common response of mammalian cells to amino acid deprivation. SIPAN undergo fusion events, rapidly exchange proteasome particles with the surrounding milieu and quickly dissolve following amino acid replenishment. We further show that: (i) SIPAN contain K48-conjugated ubiquitin, (ii) proteasome inhibition accelerates SIPAN formation, (iii) deubiquitinase inhibition prevents SIPAN resolution and (iv) RAD23B proteasome shuttling factor is required for SIPAN formation. Finally, SIPAN formation is associated with decreased cell survival and p53-mediated apoptosis, which might contribute to tissue fitness in diverse pathophysiological conditions.

Highlights

Eukaryotic cells have evolved highly orchestrated protein catabolic machineries responsible for the timely and selective disposal of proteins and organelles, thereby ensuring amino acid recycling
The 26S proteasome particle translocate to the cytoplasm and form proteasome storage granules (PSG), in response to carbon starvation or quiescence entry[16,18], but whether the mammalian proteasome is subjected to a similar regulation has remained unknown
Nutrient-deprived IMR90 cells showed a rapid loss of 4EBP1 phosphorylation[21], which is indicative of cell starvation, no major changes were observed on the abundance of proteasome subunits or accessory factors (Fig. 1a, b)

Summary

Introduction

Eukaryotic cells have evolved highly orchestrated protein catabolic machineries responsible for the timely and selective disposal of proteins and organelles, thereby ensuring amino acid recycling. We show that the mammalian proteasome undergoes liquid-liquid phase separation in the nucleus upon amino acid deprivation. The CP contains the proteases with CASPASE-like, trypsin-like and chymotrypsin-like activities that are responsible for substrate degradation into small peptides[7,8] This particle is the target of the widely used proteasome inhibitors (e.g., MG132 and Bortezomib)[7,8]. It was originally found that, following amino acid deprivation in mammalian cells, proteasome activity is required to replenish the cellular amino acid pool, ensuring protein synthesis[10]. Ostensibly conflicting results exist on the link between the mechanistic target of rapamycin (mTOR) kinase, which promotes anabolism and protein synthesis, and the signaling pathways that coordinate proteasome function. While the reasons behind these discrepancies remain unclear, these studies provided evidence for the intricate relationships between cell growth signaling and protein degradation

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Results

Conclusion