TRIP12 promotes small-molecule-induced degradation through K29/K48-branched ubiquitin chains

Kaiho-Soma, Ai; Akizuki, Yoshino; Igarashi, Katsuhide; Endo, Akinori; Shoda, Takuji; Kawase, Yasuko; Demizu, Yosuke; Naito, Mikihiko; Saeki, Yasushi; Tanaka, Keiji; Ohtake, Fumiaki

doi:10.1016/j.molcel.2021.01.023

Cited by 63 publications

(53 citation statements)

References 58 publications

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“…Recently, it was reported that 10-20% of polyUb chains in cells may contain branches 26 . With a few exceptions 28,29,45,46 , very little is known about the distributions of Ub-Ub linkages in branched polyUb chains, or the identities of the proteins modified by branched forms of polyUb. Upon osmotic or oxidative stresses, we observed cellular inclusions that contain proteasomes and are stained by a K11/K48 bi-specific antibody, suggesting that at least a subset of proteins in those inclusions are modified with branched polyUb chains.…”

Section: Discussionmentioning

confidence: 99%

“…(B) UCH37 exclusively cleaves the K48 linkage in a branched chain. Ub 3 substrates were incubated with the indicated DUB (i.e., UCH37-RPN13 C complex or OTUB1) and the reaction products were detected using either the K6 linkage-specific anti-Ub affimer 45 or K48 linkage-specific anti-Ub antibody. In Lane 5, OTUB1 was added after UCH37-RPN13 C had completely hydrolyzed the K6/K48 branched Ub 3 , thereby producing K6-linked Ub 2 that was refractory to OTUB1.…”

Section: Nmr Experiments and Chemical Shift Perturbation Mappingmentioning

confidence: 99%

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Branched ubiquitin chain binding and deubiquitination by UCH37 facilitate proteasome clearance of stress-induced inclusions

Song

Hazlett

Abeykoon

et al. 2021

eLife

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UCH37, also known as UCHL5, is a highly conserved deubiquitinating enzyme (DUB) that associates with the 26S proteasome. Recently, it was reported that UCH37 activity is stimulated by branched ubiquitin (Ub) chain architectures. To understand how UCH37 achieves its unique debranching specificity, we performed biochemical and Nuclear Magnetic Resonance (NMR) structural analyses and found that UCH37 is activated by contacts with the hydrophobic patches of both distal Ubs that emanate from a branched Ub. In addition, RPN13, which recruits UCH37 to the proteasome, further enhances branched-chain specificity by restricting linear Ub chains from having access to the UCH37 active site. In cultured human cells under conditions of proteolytic stress, we show that substrate clearance by the proteasome is promoted by both binding and deubiquitination of branched polyubiquitin by UCH37. Proteasomes containing UCH37(C88A), which is catalytically inactive, aberrantly retain polyubiquitinated species as well as the RAD23B substrate shuttle factor, suggesting a defect in recycling of the proteasome for the next round of substrate processing. These findings provide a foundation to understand how proteasome degradation of substrates modified by a unique Ub chain architecture is aided by a DUB.

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Section: Discussionmentioning

confidence: 99%

Section: Nmr Experiments and Chemical Shift Perturbation Mappingmentioning

confidence: 99%

Branched ubiquitin chain binding and deubiquitination by UCH37 facilitate proteasome clearance of stress-induced inclusions

Song

Hazlett

Abeykoon

et al. 2021

eLife

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“…As the understanding of proteostasis machinery accumulates across cellular environments, we will have a better appreciation for the intricacies of Ub code, 74 , 96 redundancies of 600 Ub ligases, 97 or lack thereof, regulation of CRL4 network dynamics, 98 and protein turnover rates. 99 Going forward, the identification of underlying mechanisms that amplify POI destruction upon degrader recruitment, such as potentiating proteasomal flux 100 or enhancing Ub-chain elaboration, 101 can unlock unique synergies to complement degrader approaches. Equally exciting, the degradation of disease-relevant protein aggregates 102 and polymerized Bcl6 59 have already shifted naïve perceptions on processing and unfolding activities by the proteasome.…”

Section: Cellular Context Is Critical To Finding Efficient Degradersmentioning

confidence: 99%

Unifying Catalysis Framework to Dissect Proteasomal Degradation Paradigms

Rodriguez‐Rivera

Levi

2021

ACS Cent. Sci.

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Diverging from traditional target inhibition, proteasomal protein degradation approaches have emerged as novel therapeutic modalities that embody distinct pharmacological profiles and can access previously undrugged targets. Small molecule degraders have the potential to catalytically destroy target proteins at substoichiometric concentrations, thus lowering administered doses and extending pharmacological effects. With this mechanistic premise, research efforts have advanced the development of small molecule degraders that benefit from stable and increased affinity ternary complexes. However, a holistic framework that evaluates different degradation modes from a catalytic perspective, including focusing on kinetically favored degradation mechanisms, is lacking. In this Outlook, we introduce the concept of an induced cooperativity spectrum as a unifying framework to mechanistically understand catalytic degradation profiles. This framework is bolstered by key examples of published molecular degraders extending from molecular glues to bivalent degraders. Critically, we discuss remaining challenges and future opportunities in drug discovery to rationally design and phenotypically screen for efficient degraders.

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“…Moreover, the precise mechanism of action of the degradation machinery in several techniques, including AUTAC, remains unclear [106,107]. A recent report demonstrated that PROTAC-based polyubiquitination could be facilitated by the thyroid hormone receptor-interacting protein 12 (TRIP12), rather than the hijacking of the enzyme by an E3 ligase binder, thus highlighting a role for TRIP12 as an accelerator of PROTAC-directed degradation [108]. Further research on proteolytic pathways may allow the selection of a proteolytic system according to the characteristics of the target protein.…”

Section: Discussionmentioning

confidence: 99%

Strategies for Post-Translational Control of Protein Expression and Their Applications

Utsugi

Miyamae

2021

Applied Sciences

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Proteins are fundamental biomolecules of living cells, and their expression levels depend on the balance between the synthesis and degradation. Researchers often aim to control protein expression levels for the investigation of protein function and its relationship with physiological phenomena. The genetic manipulation of the target protein using CRISPR/Cas9, Cre/loxP, tetracyclin system, and RNA interference, are widely used for the regulation of proteins at the DNA, transcriptional, or mRNA level. However, the significant time delay in controlling protein levels is a limitation of these techniques; the knockout or knockdown effects cannot be observed until the previously transcribed and synthesized protein is degraded. Recently, researchers have developed various types of molecular tools for the regulation of protein expression at the post-translational level, which rely on harnessing cellular proteolytic machinery including ubiquitin–proteasome pathway, autophagy-lysosome pathway, and endocytosis. The post-translational control of protein expression using small molecules, antibodies, and light can offer significant advantages regarding speed, tunability, and reversibility. These technologies are expected to be applied to pharmacotherapy and cell therapy, as well as research tools for fundamental biological studies. Here, we review the established and recently developed technologies, provide an update on their applications, and anticipate potential future directions.

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TRIP12 promotes small-molecule-induced degradation through K29/K48-branched ubiquitin chains

Cited by 63 publications

References 58 publications

Branched ubiquitin chain binding and deubiquitination by UCH37 facilitate proteasome clearance of stress-induced inclusions

Branched ubiquitin chain binding and deubiquitination by UCH37 facilitate proteasome clearance of stress-induced inclusions

Unifying Catalysis Framework to Dissect Proteasomal Degradation Paradigms

Strategies for Post-Translational Control of Protein Expression and Their Applications

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