Characterizing the SUMO-targeted ubiquitin ligase pathway in the proteotoxic stress response

  • Throughout their life cells of eukaryotic organisms can be confronted with a variety of proteotoxic stresses and in order to survive, corresponding resistance mechanisms had to evolve. Proteotoxic stresses can cause misfolding of proteins and accumulation of toxic protein aggregates. Failure to remove aggregates of misfolded proteins compromises cellular function and can ultimately cause cell death and disease. To deal with this challenge, cells utilize a complex network of protein quality control pathways, including chaperones, the ubiquitin-proteasome system and the autophagy system. Another mechanism to cope with proteotoxic stresses is the stalling of translation initiation in order to save valuable resources and prevent faulty translation. Upon stress, intrinsically disordered RNA-binding proteins such as TIA-1 or G3BP1/2 are recruited to stalled preinitiation complexes and a network of multivalent interactions between RNAs and proteins is formed. These mRNP networks can merge with each other and phase separate into membraneless liquid-like structures called stress granules (SGs). Once stress is released, SGs are quickly resolved and translation continues. Yet, chronic stress or mutations of SG-associated proteins can cause persistent SGs, which can sequester misfolded proteins and have been linked to neurodegenerative diseases such as amyotrophic lateral sclerosis or frontotemporal dementia. In mammalian cells, three isoforms of the small ubiquitin-related modifier (SUMO), SUMO1, SUMO2 and SUMO3 are covalently attached to lysine residues of target proteins. SUMO conjugation is catalyzed via an enzymatic cascade of an heteromeric E1 activating enzyme, the E2 conjugating enzyme Ubc9 and in some cases one of a limited number of E3 SUMO ligases. SUMOylation is a dynamic modification and can be reversed by SUMO isopeptidases, the best characterized of which belong to the SENP family. Cellular stresses such as heat or oxidative stress strongly induce SUMOylation resulting in increased numbers of poly-SUMOylation (formation of SUMO2/3 chains) on nuclear proteins. The SUMO-targeted ubiquitin ligase (STUbL) RNF4 harbors four SUMO interaction motifs in its N-terminal domain. This feature allows RNF4 to specifically bind poly-SUMOylated proteins and catalyze their proteolytic or non-proteolytic ubiquitylation. A variety of substrate proteins have been shown to undergo SUMO-primed ubiquitylation by RNF4 in response to stress or DNA damage. RNF4-mediated ubiquitylation is often a signal for proteolytic degradation of these substrates. In this work we aimed by identify novel RNF4 targets, in heat-stressed cells in order to gain a wider understanding of the nuclear proteotoxic stress response. Analysis by mass spectrometry revealed that a large fraction of RNF4-interacting proteins in heatstressed cells are nuclear RNA-binding proteins, many of which shuttle outside the nucleus and associate with SGs upon stress. We validated, that nuclear RNA-binding proteins, such as TDP-43 and hnRNP M are indeed heat-induced targets of SUMOprimed ubiquitylation by RNF4. These initial results led us to further investigate the links between the SUMO/RNF4-mediated, nuclear protein quality control and the dynamics of cytosolic heat- or arsenite-induced SGs. SUMO2/3 and RNF4 are mainly nuclear proteins and we confirmed that they do not associate with SGs. Yet, we could demonstrate that depletion of SUMO2/3, the E3 SUMO ligase PML or RNF4 as well as chemical inhibition of SUMOylation strongly delayed SG clearance upon stress release, indicating that a functional STUbL pathway is essential for the timely clearance of SGs. Next, we investigated how stress-induced poly-SUMOylation is regulated. Our data shows that SENP levels and activities are reduced in response to heat and arsenite stress, which allows the buildup of poly-SUMO chains on nuclear proteins. Limitation of poly-SUMOylation by overexpression of the SUMO chain-specific isopeptidases SENP6 and SENP7 induced SG formation. In contrast, poly-SUMO-priming by chemical depletion of SENP6 with the drug hinokiflavone drastically limited SG formation upon stress treatment. These results indicate a clear role of chain-specific SENPs in the regulation of stress-induced poly-SUMOylation and SG dynamics. Last, we investigated whether the STUbL pathway could affect the phase separation of FUSP525 (an ALS-linked mutant of the SG-associated protein FUS) and observed that perturbations of the STUbL pathway lead to an increased phase separation of FUSP525L. Thus, our work connects the SUMO/RNF4 protein quality control mechanism to the dynamics of SGs supporting the hypothesis that release of proteotoxic stress in the nucleus facilitates the clearance of cytosolic SGs. Thereby, we discovered a previously unknown link between the nuclear and cytosolic axis of proteotoxic stress response.

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Author:Jan Keiten-Schmitz
Place of publication:Frankfurt am Main
Referee:Volker DötschORCiDGND, Stefan Müller
Advisor:Stefan Müller
Document Type:Doctoral Thesis
Date of Publication (online):2021/03/08
Year of first Publication:2020
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Granting Institution:Johann Wolfgang Goethe-Universität
Date of final exam:2020/12/12
Release Date:2021/03/08
Page Number:156
Institutes:Biochemie, Chemie und Pharmazie
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
Licence (German):License LogoDeutsches Urheberrecht