Principles of Ubiquitin-Dependent Signaling

Oh, Eun Hae; Akopian, David; Rapé, Michael

doi:10.1146/annurev-cellbio-100617-062802

Cited by 246 publications

(219 citation statements)

References 212 publications

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“…The K48 and the K11 linkages are consistent with subsequent proteasomal degradation of TOP-DPCs. Whether the K63 ubiquitylation of TOP-DPCs serves as a platform for the engagement of DDR proteins remains to be determined (Oh et al, 2018).…”

Section: Sumo and Ub Linkages Of Top1-and Top2-dpcs In Human Cellsmentioning

confidence: 99%

A conserved SUMO-Ubiquitin pathway directed by RNF4/SLX5-SLX8 and PIAS4/SIZ1 drives proteasomal degradation of topoisomerase DNA-protein crosslinks

Sun

Jenkins

et al. 2019

Preprint

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HIGHLIGHTS• Abortive topoisomerase I (TOP1) and II (TOP2) cleavage complexes resulting in DNAprotein crosslinks (TOP-DPCs) are rapidly and sequentially modified by SUMO-2/3, SUMO-1 and ubiquitin before their proteasomal degradation. • PIAS4 SUMOylates TOP-DPCs via its DNA-binding SAP domain independently of DNA transactions and DNA damage responses. • RNF4 ubiquitylates SUMOylated TOP-DPCs and drives their proteasomal degradation.• TOP-DPC processing by the SUMO-Ub pathways is conserved in yeast and human cells. SUMMARYTopoisomerase cleavage complexes (TOPccs) can be stalled physiologically and by the anticancer drugs camptothecins (TOP1 inhibitors) and etoposide (TOP2 inhibitor), yielding irreversible TOP DNA-protein crosslinks (TOP-DPCs). Here we elucidate how TOP-DPCs are degraded via the SUMO-ubiquitin (Ub) pathway. We show that in human cells, TOP-DPCs are promptly and sequentially conjugated by SUMO-2/3, SUMO-1 and Ub. SUMOylation is catalyzed by the SUMO ligase PIAS4, which forms a complex with both TOP1 and TOP2a and b. RNF4 acts as the SUMO-targeted ubiquitin ligase (STUbL) for both TOP1-and TOP2-DPCs in a SUMOdependent but replication/transcription-independent manner. This SUMO-Ub pathway is conserved in yeast with Siz1 the ortholog of PIAS4 and Slx5-Slx8 the ortholog of RNF4. Our study reveals a conserved SUMO-dependent ubiquitylation pathway for proteasomal degradation of both TOP1-and TOP2-DPCs and potentially for other DPCs. phosphodiesterases (TDPs) that hydrolyze the covalent tyrosine-DNA bond, with TDP1 excising TOP1-DPCs (Pouliot et al., 1999) and TDP2 excising TOP2-DPCs in higher eukaryotes (Cortes Ledesma et al., 2009). In additions to TDPs, endonucleases such as Mre11 and XPF have been reported to play a key role in removing both TOP-DPCs presumably by incising the DNA adjacent to the TOP-DPC (Aparicio et al., 2016;Pommier et al., 2016;Sasanuma et al., 2018). Proteolytic degradation is required for TDP activities and earlier work showed that the ubiquitin (Ub)proteasome pathway (UPP) plays an important role in proteolyzing TOP-DPCs (Desai et al., 1997;Mao et al., 2001). Yet, the detailed molecular mechanisms by which the UPP targets TOP-DPCs are still poorly understood. In addition, small ubiquitin-like modifiers (SUMO) 1 and 2/3 have been implicated in TOP-DPC repair (Agostinho et al., 2008;Kanagasabai et al., 2009;Mao et al., 2000a;Mao et al., 2000b), but the functions of these modifications still remain elusive.SUMOylation has been linked to ubiquitylation, as polymeric SUMO chains can serve as mark for recognition by SUMO-targeted ubiquitin ligases (STUbLs) that attach Ub moieties on poly-SUMOylated substrates to promote their proteasomal degradation (Poulsen et al., 2013;Tatham et al., 2008;van Hagen et al., 2010). SUMO-Ub pathways orchestrate the proteolytic turnover of DNA damage response (DDR) and repair enzymes to facilitate DNA repair in mammalian cells (Jackson and Durocher, 2013;Ulrich, 2012). The Siz/PIAS RING family SUMO ligases PIAS1 and PIAS4 mediate SUMOylation as an early re...

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Section: Sumo and Ub Linkages Of Top1-and Top2-dpcs In Human Cellsmentioning

confidence: 99%

A conserved SUMO-Ubiquitin pathway directed by RNF4/SLX5-SLX8 and PIAS4/SIZ1 drives proteasomal degradation of topoisomerase DNA-protein crosslinks

Sun

Jenkins

et al. 2019

Preprint

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“…Ubiquitin (Ub) chains are a class of non-template-derived biopolymers with diverse structures that provide precise control over many biological pathways (Oh et al, 2018). The eight amino groups of Ub (M1, K6, K11, K27, K29, K33, K48, and K63), which decorate almost the entire surface, give rise to wide assortment of chain types (Swatek and Komander, 2016; Yau and Rape, 2016).…”

Section: Introductionmentioning

confidence: 99%

Proteasome-Bound UCH37 Debranches Ubiquitin Chains to Promote Degradation

et al. 2020

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1The linkage, length, and architecture of ubiquitin (Ub) chains are all important variables 2 in providing tight control over many biological paradigms. There are clear roles for 3 branched architectures in regulating proteasome-mediated degradation, however the 4 proteins that selectively recognize and process these atypical chains are unknown. Here, 5 using synthetic and enzyme-derived ubiquitin chains along with intact mass spectrometry, 6 we report that UCH37/UCHL5, a proteasome-associated deubiquitinase, exclusively 7 cleaves K48 branched chains. The activity and selectivity toward branched chains is 8 markedly enhanced by the proteasomal Ub receptor RPN13/ADRM1. Using proteasome 9 complexes reconstituted with either active or inactive UCH37 together with protein 10 substrates modified with branched chains, we find that chain debranching promotes 11 degradation under multi-turnover conditions. These results are further supported by 12 proteome-wide pulse-chase experiments, which show that the loss of UCH37 activity 13 impairs global protein turnover. Our work therefore defines UCH37 as a debranching 14 deubiquitinase important for promoting proteasomal degradation.

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“…Ub is not a singular modification, but is often itself modified by additional Ubs in the form of "chains", where Ubs are linked via one of eight different primary amino groups (lysine side-chains or the N-terminus) on another Ub. Precise ubiquitylation is catalyzed by specific combinations of E3 Ub ligases and E2 Ub conjugating enzymes, and the resultant Ub marks are recognized by Ub-binding domains that impart distinct fates to modified proteins (1)(2)(3)(4)(5)(6)(7)(8). As examples, K11-and K48-linked Ub chains -particularly in combination with each other -elicit proteasomal degradation, whereas K63-linked chains often modulate subcellular location or assembly and disassembly of macromolecular complexes.…”

Section: Introductionmentioning

confidence: 99%

A Protein Engineering Approach for Uncovering Cryptic Ubiquitin-binding Sites: from a Ubiquitin-Variant Inhibitor of APC/C to K48 Chain Binding

Watson

Grace

Zhang

et al. 2019

Preprint

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Ubiquitin-mediated proteolysis is a fundamental mechanism used by eukaryotic cells to maintain homeostasis and protein quality, and to control timing in biological processes. Two essential aspects of ubiquitin regulation are conjugation through E1-E2-E3 enzymatic cascades, and recognition by ubiquitin-binding domains. An emerging theme in the ubiquitin field is that these two properties are often amalgamated in conjugation enzymes. In addition to covalent thioester linkage to ubiquitin's C-terminus for ubiquitin transfer reactions, conjugation enzymes often bind non-covalently and weakly to ubiquitin at "exosites". However, identification of such sites is typically empirical and particularly challenging in large molecular machines. Here, studying the 1.2 MDa E3 ligase Anaphase-Promoting Complex/Cyclosome (APC/C), which controls cell division and many aspects of neurobiology, we discover a method for identifying unexpected ubiquitin-binding sites. Using a panel of ubiquitin variants (UbVs) we identify a protein-based inhibitor that blocks ubiquitin ligation to APC/C substrates in vitro and ex vivo. Biochemistry, NMR, and cryo EM structurally define the UbV interaction, explain its inhibitory activity through binding the surface on the APC2 subunit that recruits the E2 enzyme UBE2C, and ultimately reveal that this APC2 surface is also a ubiquitin-binding exosite with preference for K48-linked chains. The results provide a new tool for probing APC/C activity, have implications for the coordination of K48-linked Ub chain binding by APC/C with the multistep process of substrate polyubiquitylation, and demonstrate the power of UbV technology for identifying cryptic ubiquitin binding sites within large multiprotein complexes.

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Principles of Ubiquitin-Dependent Signaling

Cited by 246 publications

References 212 publications

A conserved SUMO-Ubiquitin pathway directed by RNF4/SLX5-SLX8 and PIAS4/SIZ1 drives proteasomal degradation of topoisomerase DNA-protein crosslinks

A conserved SUMO-Ubiquitin pathway directed by RNF4/SLX5-SLX8 and PIAS4/SIZ1 drives proteasomal degradation of topoisomerase DNA-protein crosslinks

Proteasome-Bound UCH37 Debranches Ubiquitin Chains to Promote Degradation

A Protein Engineering Approach for Uncovering Cryptic Ubiquitin-binding Sites: from a Ubiquitin-Variant Inhibitor of APC/C to K48 Chain Binding

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