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Xu X, Wang Y, Huang W, Li D, Deng Z, Long F. Structural insights into the Clp protein degradation machinery. mBio 2024; 15:e0003124. [PMID: 38501868 PMCID: PMC11005422 DOI: 10.1128/mbio.00031-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/27/2024] [Indexed: 03/20/2024] Open
Abstract
The Clp protease system is important for maintaining proteostasis in bacteria. It consists of ClpP serine proteases and an AAA+ Clp-ATPase such as ClpC1. The hexameric ATPase ClpC1 utilizes the energy of ATP binding and hydrolysis to engage, unfold, and translocate substrates into the proteolytic chamber of homo- or hetero-tetradecameric ClpP for degradation. The assembly between the hetero-tetradecameric ClpP1P2 chamber and the Clp-ATPases containing tandem ATPase domains from the same species has not been studied in depth. Here, we present cryo-EM structures of the substrate-bound ClpC1:shClpP1P2 from Streptomyces hawaiiensis, and shClpP1P2 in complex with ADEP1, a natural compound produced by S. hawaiiensis and known to cause over-activation and dysregulation of the ClpP proteolytic core chamber. Our structures provide detailed information on the shClpP1-shClpP2, shClpP2-ClpC1, and ADEP1-shClpP1/P2 interactions, reveal conformational transition of ClpC1 during the substrate translocation, and capture a rotational ATP hydrolysis mechanism likely dominated by the D1 ATPase activity of chaperones.IMPORTANCEThe Clp-dependent proteolysis plays an important role in bacterial homeostasis and pathogenesis. The ClpP protease system is an effective drug target for antibacterial therapy. Streptomyces hawaiiensis can produce a class of potent acyldepsipeptide antibiotics such as ADEP1, which could affect the ClpP protease activity. Although S. hawaiiensis hosts one of the most intricate ClpP systems in nature, very little was known about its Clp protease mechanism and the impact of ADEP molecules on ClpP. The significance of our research is in dissecting the functional mechanism of the assembled Clp degradation machinery, as well as the interaction between ADEP1 and the ClpP proteolytic chamber, by solving high-resolution structures of the substrate-bound Clp system in S. hawaiiensis. The findings shed light on our understanding of the Clp-dependent proteolysis in bacteria, which will enhance the development of antimicrobial drugs targeting the Clp protease system, and help fighting against bacterial multidrug resistance.
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Affiliation(s)
- Xiaolong Xu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Yanhui Wang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Wei Huang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Danyang Li
- Cryo-EM Center and the Core Facility of Wuhan University, Wuhan, China
| | - Zixin Deng
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Feng Long
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
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2
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Jonsson E, Htet ZM, Bard JA, Dong KC, Martin A. Ubiquitin modulates 26 S proteasome conformational dynamics and promotes substrate degradation. SCIENCE ADVANCES 2022; 8:eadd9520. [PMID: 36563145 PMCID: PMC9788759 DOI: 10.1126/sciadv.add9520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
The 26S proteasome recognizes thousands of appropriate protein substrates in eukaryotic cells through attached ubiquitin chains and uses its adenosine triphosphatase (ATPase) motor for mechanical unfolding and translocation into a proteolytic chamber. Here, we used single-molecule Förster resonance energy transfer measurements to monitor the conformational dynamics of the proteasome, observe individual substrates during their progression toward degradation, and elucidate how these processes are regulated by ubiquitin chains. Rapid transitions between engagement- and processing-competent proteasome conformations control substrate access to the ATPase motor. Ubiquitin chain binding functions as an allosteric regulator to slow these transitions, stabilize the engagement-competent state, and aid substrate capture to accelerate degradation initiation. Upon substrate engagement, the proteasome remains in processing-competent states for translocation and unfolding, except for apparent motor slips when encountering stably folded domains. Our studies revealed how ubiquitin chains allosterically regulate degradation initiation, which ensures substrate selectivity in a crowded cellular environment.
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Affiliation(s)
- Erik Jonsson
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Zaw Min Htet
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA
| | | | - Ken C. Dong
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Andreas Martin
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA
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3
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Wang L, Sun X, He J, Liu Z. Functions and Molecular Mechanisms of Deltex Family Ubiquitin E3 Ligases in Development and Disease. Front Cell Dev Biol 2021; 9:706997. [PMID: 34513839 PMCID: PMC8424196 DOI: 10.3389/fcell.2021.706997] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 08/05/2021] [Indexed: 12/14/2022] Open
Abstract
Ubiquitination is a posttranslational modification of proteins that significantly affects protein stability and function. The specificity of substrate recognition is determined by ubiquitin E3 ligase during ubiquitination. Human Deltex (DTX) protein family, which functions as ubiquitin E3 ligases, comprises five members, namely, DTX1, DTX2, DTX3, DTX3L, and DTX4. The characteristics and functional diversity of the DTX family proteins have attracted significant attention over the last decade. DTX proteins have several physiological and pathological roles and are closely associated with cell signal transduction, growth, differentiation, and apoptosis, as well as the occurrence and development of various tumors. Although they have been extensively studied in various species, data on structural features, biological functions, and potential mechanisms of action of the DTX family proteins remain limited. In this review, recent research progress on each member of the DTX family is summarized, providing insights into future research directions and potential strategies in disease diagnosis and therapy.
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Affiliation(s)
- Lidong Wang
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiaodan Sun
- Postdoctoral Research Workstation, Jilin Cancer Hospital, Changchun, China
| | - Jingni He
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhen Liu
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
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4
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Determination of Proteasomal Unfolding Ability. Methods Mol Biol 2021. [PMID: 34432247 DOI: 10.1007/978-1-0716-1665-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
We use an in vitro degradation assay with a model substrate to assess proteasomal unfolding ability. Our substrate has an unstructured region that is the site of ubiquitination, followed by an easy-to-unfold domain and a difficult-to-unfold domain. Degradation proceeds through the unstructured and easy-to-unfold domains, but the difficult-to-unfold domain can be degraded completely or, if the proteasome stalls, can be released as a partially degraded fragment. The ratio between these two possible outcomes allows us to quantify the unfolding ability and determine how processively the proteasome degrades its substrates.
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5
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Xiang S, Shao X, Cao J, Yang B, He Q, Ying M. FAT10: Function and Relationship with Cancer. Curr Mol Pharmacol 2021; 13:182-191. [PMID: 31729307 DOI: 10.2174/1874467212666191113130312] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/20/2019] [Accepted: 10/22/2019] [Indexed: 11/22/2022]
Abstract
Posttranslational protein modifications are known to be extensively involved in cancer, and a growing number of studies have revealed that the ubiquitin-like modifier FAT10 is directly involved in cancer development. FAT10 was found to be highly upregulated in various cancer types, such as glioma, hepatocellular carcinoma, breast cancer and gastrointestinal cancer. Protein FAT10ylation and interactions with FAT10 lead to the functional change of proteins, including proteasomal degradation, subcellular delocalization and stabilization, eventually having significant effects on cancer cell proliferation, invasion, metastasis and even tumorigenesis. In this review, we summarized the current knowledge on FAT10 and discussed its biological functions in cancer, as well as potential therapeutic strategies based on the FAT10 pathway.
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Affiliation(s)
- Senfeng Xiang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xuejing Shao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ji Cao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Bo Yang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qiaojun He
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Meidan Ying
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
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6
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Adelakun N, Obaseki I, Adeniyi A, Fapohunda O, Obaseki E, Omotuyi O. Discovery of new promising USP14 inhibitors: computational evaluation of the thumb-palm pocket. J Biomol Struct Dyn 2020; 40:3060-3070. [PMID: 33170088 DOI: 10.1080/07391102.2020.1844803] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ubiquitin-specific protease 14 (USP14) is a member of the deubiquitinating enzymes (DUBs) involved in disrupting the ubiquitin-proteasome regulation system, responsible for the degradation of impaired and misfolded proteins, which is an essential mechanism in eukaryotic cells. The involvement of USP14 in cancer progression and neurodegenerative disorders has been reported. Thereof USP14 is a prime therapeutic target; hence, designing efficacious inhibitors against USP14 is central in curbing these conditions. Herein, we relied on structural bioinformatics methods incorporating molecular docking, molecular mechanics generalized born surface area (MM-GBSA), molecular dynamics simulation (MD simulation), and ADME to identify potential allosteric USP14 inhibitors. A library of over 733 compounds from the PubChem repository with >90% match to the IU1 chemical structure was screened in a multi-step framework to attain prospective drug-like inhibitors. Two potential lead compounds (CID 43013232 and CID 112370349) were shown to record better binding affinity compared to IU1, but with subtle difference to IU1-47, a 10-fold potent compound when compared to IU1. The stability of the lead molecules complexed with USP14 was studied via MD simulation. The molecules were found to be stable within the binding site throughout the 50 ns simulation time. Moreover, the protein-ligand interactions across the simulation run time suggest Phe331, Tyr476, and Gln197 as crucial residues for USP14 inhibition. Furthermore, in-silico pharmacological evaluation revealed the lead compounds as pharmacological sound molecules. Overall, the methods deployed in this study revealed two novel candidates that may show selective inhibitory activity against USP14, which could be exploited to produce potent and harmless USP14 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Niyi Adelakun
- Chemogenomics Unit, Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Nigeria.,Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Ikponwmosa Obaseki
- Department of Biochemistry, Bells University of Technology, Ota, Nigeria
| | - Ayobami Adeniyi
- Chemogenomics Unit, Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Nigeria.,Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Oluwaseun Fapohunda
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Eseiwi Obaseki
- Department of Plant Science and Biotechnology, University of Benin, Benin City, Nigeria
| | - Olaposi Omotuyi
- Chemogenomics Unit, Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Nigeria.,Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Nigeria
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7
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Santoro AM, D’Urso A, Cunsolo A, Milardi D, Purrello R, Sbardella D, Tundo GR, Diana D, Fattorusso R, Dato AD, Paladino A, Persico M, Coletta M, Fattorusso C. Cooperative Binding of the Cationic Porphyrin Tris-T4 Enhances Catalytic Activity of 20S Proteasome Unveiling a Complex Distribution of Functional States. Int J Mol Sci 2020; 21:ijms21197190. [PMID: 33003385 PMCID: PMC7582714 DOI: 10.3390/ijms21197190] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/13/2020] [Accepted: 09/23/2020] [Indexed: 12/17/2022] Open
Abstract
The present study provides new evidence that cationic porphyrins may be considered as tunable platforms to interfere with the structural “key code” present on the 20S proteasome α-rings and, by consequence, with its catalytic activity. Here, we describe the functional and conformational effects on the 20S proteasome induced by the cooperative binding of the tri-cationic 5-(phenyl)-10,15,20-(tri N-methyl-4-pyridyl) porphyrin (Tris-T4). Our integrated kinetic, NMR, and in silico analysis allowed us to disclose a complex effect on the 20S catalytic activity depending on substrate/porphyrin concentration. The analysis of the kinetic data shows that Tris-T4 shifts the relative populations of the multiple interconverting 20S proteasome conformations leading to an increase in substrate hydrolysis by an allosteric pathway. Based on our Tris-T4/h20S interaction model, Tris-T4 is able to affect gating dynamics and substrate hydrolysis by binding to an array of negatively charged and hydrophobic residues present on the protein surface involved in the 20S molecular activation by the regulatory proteins (RPs). Accordingly, despite the fact that Tris-T4 also binds to the α3ΔN mutant, allosteric modulation is not observed since the molecular mechanism connecting gate dynamics with substrate hydrolysis is impaired. We envisage that the dynamic view of the 20S conformational equilibria, activated through cooperative Tris-T4 binding, may work as a simplified model for a better understanding of the intricate network of 20S conformational/functional states that may be mobilized by exogenous ligands, paving the way for the development of a new generation of proteasome allosteric modulators.
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Affiliation(s)
- Anna Maria Santoro
- Istituto di Cristallografia—CNR Sede Secondaria di Catania, Via P. Gaifami 9/18, 95126 Catania, Italy; (A.M.S.); (D.M.)
| | - Alessandro D’Urso
- Dipartimento di Scienze Chimiche, Università Degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy; (A.D.); (A.C.); (R.P.)
| | - Alessandra Cunsolo
- Dipartimento di Scienze Chimiche, Università Degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy; (A.D.); (A.C.); (R.P.)
- Department of Molecular Medicine, The University of Texas Health Science Center San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78245, USA
| | - Danilo Milardi
- Istituto di Cristallografia—CNR Sede Secondaria di Catania, Via P. Gaifami 9/18, 95126 Catania, Italy; (A.M.S.); (D.M.)
| | - Roberto Purrello
- Dipartimento di Scienze Chimiche, Università Degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy; (A.D.); (A.C.); (R.P.)
| | - Diego Sbardella
- IRCCS-Fondazione Bietti, 00198 Rome, Italy; (D.S.); (G.R.T.)
| | - Grazia R. Tundo
- IRCCS-Fondazione Bietti, 00198 Rome, Italy; (D.S.); (G.R.T.)
| | - Donatella Diana
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy;
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli” Via Vivaldi 43, 81100 Caserta, Italy;
| | - Antonio Di Dato
- Dipartimento di Farmacia, Università di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy; (A.D.D.); (M.P.)
| | - Antonella Paladino
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via M. Bianco 9, 20131 Milano, Italy;
| | - Marco Persico
- Dipartimento di Farmacia, Università di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy; (A.D.D.); (M.P.)
- Centro Interuniversitario di Ricerca sulla Malaria/Italian Malaria Network, 80131 Napoli, Italy
| | - Massimo Coletta
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, Via Montpellier 1, 00133 Roma, Italy
- Correspondence: (M.C.); (C.F.); Tel.: +39-06-72596365 (M.C.); +39-081-678544 (C.F.)
| | - Caterina Fattorusso
- Dipartimento di Farmacia, Università di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy; (A.D.D.); (M.P.)
- Centro Interuniversitario di Ricerca sulla Malaria/Italian Malaria Network, 80131 Napoli, Italy
- Correspondence: (M.C.); (C.F.); Tel.: +39-06-72596365 (M.C.); +39-081-678544 (C.F.)
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8
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Sewduth RN, Baietti MF, Sablina AA. Cracking the Monoubiquitin Code of Genetic Diseases. Int J Mol Sci 2020; 21:ijms21093036. [PMID: 32344852 PMCID: PMC7246618 DOI: 10.3390/ijms21093036] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/20/2020] [Accepted: 04/23/2020] [Indexed: 12/26/2022] Open
Abstract
Ubiquitination is a versatile and dynamic post-translational modification in which single ubiquitin molecules or polyubiquitin chains are attached to target proteins, giving rise to mono- or poly-ubiquitination, respectively. The majority of research in the ubiquitin field focused on degradative polyubiquitination, whereas more recent studies uncovered the role of single ubiquitin modification in important physiological processes. Monoubiquitination can modulate the stability, subcellular localization, binding properties, and activity of the target proteins. Understanding the function of monoubiquitination in normal physiology and pathology has important therapeutic implications, as alterations in the monoubiquitin pathway are found in a broad range of genetic diseases. This review highlights a link between monoubiquitin signaling and the pathogenesis of genetic disorders.
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Affiliation(s)
- Raj Nayan Sewduth
- VIB-KU Leuven Center for Cancer Biology, VIB, Herestraat 49, 3000 Leuven, Belgium; (R.N.S.); (M.F.B.)
- Department of Oncology, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Maria Francesca Baietti
- VIB-KU Leuven Center for Cancer Biology, VIB, Herestraat 49, 3000 Leuven, Belgium; (R.N.S.); (M.F.B.)
- Department of Oncology, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Anna A. Sablina
- VIB-KU Leuven Center for Cancer Biology, VIB, Herestraat 49, 3000 Leuven, Belgium; (R.N.S.); (M.F.B.)
- Department of Oncology, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
- Correspondence:
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9
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Santoro AM, Lanza V, Bellia F, Sbardella D, Tundo GR, Cannizzo A, Grasso G, Arizzi M, Nicoletti VG, Alcaro S, Costa G, Pietropaolo A, Malgieri G, D'Abrosca G, Fattorusso R, García‐Viñuales S, Ahmed IMM, Coletta M, Milardi D. Pyrazolones Activate the Proteasome by Gating Mechanisms and Protect Neuronal Cells from β‐Amyloid Toxicity. ChemMedChem 2019; 15:302-316. [DOI: 10.1002/cmdc.201900612] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/28/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Anna Maria Santoro
- Consiglio Nazionale delle Ricerche Istituto di Cristallografia Via P. Gaifami 18 95126 Catania Italy
| | - Valeria Lanza
- Consiglio Nazionale delle Ricerche Istituto di Cristallografia Via P. Gaifami 18 95126 Catania Italy
| | - Francesco Bellia
- Consiglio Nazionale delle Ricerche Istituto di Cristallografia Via P. Gaifami 18 95126 Catania Italy
| | - Diego Sbardella
- IRCCS – Fondazione G.B. Bietti Via Livenza 3 00189 Roma Italy
- Università di Roma Tor Vergata Dipartimento di Scienze Cliniche e Medicina Traslazionale Via Montpellier 1 00133 Roma Italy
| | - Grazia R. Tundo
- Università di Roma Tor Vergata Dipartimento di Scienze Cliniche e Medicina Traslazionale Via Montpellier 1 00133 Roma Italy
| | - Alessandra Cannizzo
- Università degli Studi di Catania Dipartimento di Scienze Chimiche V.le Andrea Doria 6 95125 Catania Italy
| | - Giuseppe Grasso
- Università degli Studi di Catania Dipartimento di Scienze Chimiche V.le Andrea Doria 6 95125 Catania Italy
| | - Mariaconcetta Arizzi
- Università degli Studi di Catania Dipartimento di Scienze Chimiche V.le Andrea Doria 6 95125 Catania Italy
| | - Vincenzo G. Nicoletti
- Università degli Studi di Catania Dipartimento di Scienze Biomediche e Biotecnologiche (BIOMETEC) Università di Catania Via Santa Sofia 97 95124 Catania
| | - Stefano Alcaro
- Università degli Studi Magna Graecia di Catanzaro Dipartimento di Scienze della Salute Viale Europa 88100 Catanzaro Italy
| | - Giosuè Costa
- Università degli Studi Magna Graecia di Catanzaro Dipartimento di Scienze della Salute Viale Europa 88100 Catanzaro Italy
| | - Adriana Pietropaolo
- Università degli Studi Magna Graecia di Catanzaro Dipartimento di Scienze della Salute Viale Europa 88100 Catanzaro Italy
| | - Gaetano Malgieri
- Università della Campania “Luigi Vanvitelli” Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche Via Vivaldi 43 81100 Caserta Italy
| | - Gianluca D'Abrosca
- Università della Campania “Luigi Vanvitelli” Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche Via Vivaldi 43 81100 Caserta Italy
| | - Roberto Fattorusso
- Università della Campania “Luigi Vanvitelli” Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche Via Vivaldi 43 81100 Caserta Italy
| | - Sara García‐Viñuales
- Consiglio Nazionale delle Ricerche Istituto di Cristallografia Via P. Gaifami 18 95126 Catania Italy
| | - Ikhlas M. M. Ahmed
- Consiglio Nazionale delle Ricerche Istituto di Cristallografia Via P. Gaifami 18 95126 Catania Italy
| | - Massimiliano Coletta
- Università di Roma Tor Vergata Dipartimento di Scienze Cliniche e Medicina Traslazionale Via Montpellier 1 00133 Roma Italy
| | - Danilo Milardi
- Consiglio Nazionale delle Ricerche Istituto di Cristallografia Via P. Gaifami 18 95126 Catania Italy
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10
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Duran EC, Lucius AL. Examination of the nucleotide-linked assembly mechanism of E. coli ClpA. Protein Sci 2019; 28:1312-1323. [PMID: 31054177 DOI: 10.1002/pro.3638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 04/23/2019] [Accepted: 04/24/2019] [Indexed: 11/08/2022]
Abstract
Escherichia coli ClpA is a AAA+ (ATPase Associated with diverse cellular Activities) chaperone that catalyzes the ATP-dependent unfolding and translocation of substrate proteins targeted for degradation by a protease, ClpP. ClpA hexamers associate with one or both ends of ClpP tetradecamers to form ClpAP complexes. Each ClpA protomer contains two nucleotide-binding sites, NBD1 and NBD2, and self-assembly into hexamers is thermodynamically linked to nucleotide binding. Despite a number of studies aimed at characterizing ClpA and ClpAP-catalyzed substrate unfolding and degradation, respectively, to date the field is unable to quantify the concentration of ClpA hexamers available to interact with ClpP for any given nucleotide and total ClpA concentration. In this work, sedimentation velocity studies are used to quantitatively examine the self-assembly of a ClpA Walker B variant in the presence of ATP. In addition to the hexamerization, we observe the formation of a previously unreported ClpA dodecamer in the presence of ATP. Further, we report apparent equilibrium constants for the formation of each ClpA oligomer obtained from direct boundary modeling of the sedimentation velocity data. The energetics of nucleotide binding to NBD1 and NBD2 are revealed by examining the dependence of the apparent association equilibrium constants on free nucleotide concentration.
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Affiliation(s)
- Elizabeth C Duran
- Chemistry Department, University of Alabama at Birmingham, Birmingham, Alabama, 35205
| | - Aaron L Lucius
- Chemistry Department, University of Alabama at Birmingham, Birmingham, Alabama, 35205
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11
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Moreno-Cinos C, Goossens K, Salado IG, Van Der Veken P, De Winter H, Augustyns K. ClpP Protease, a Promising Antimicrobial Target. Int J Mol Sci 2019; 20:ijms20092232. [PMID: 31067645 PMCID: PMC6540193 DOI: 10.3390/ijms20092232] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/18/2019] [Accepted: 04/29/2019] [Indexed: 01/25/2023] Open
Abstract
The caseinolytic protease proteolytic subunit (ClpP) is a serine protease playing an important role in proteostasis of eukaryotic organelles and prokaryotic cells. Alteration of ClpP function has been proved to affect the virulence and infectivity of a number of pathogens. Increased bacterial resistance to antibiotics has become a global problem and new classes of antibiotics with novel mechanisms of action are needed. In this regard, ClpP has emerged as an attractive and potentially viable option to tackle pathogen fitness without suffering cross-resistance to established antibiotic classes and, when not an essential target, without causing an evolutionary selection pressure. This opens a greater window of opportunity for the host immune system to clear the infection by itself or by co-administration with commonly prescribed antibiotics. A comprehensive overview of the function, regulation and structure of ClpP across the different organisms is given. Discussion about mechanism of action of this protease in bacterial pathogenesis and human diseases are outlined, focusing on the compounds developed in order to target the activation or inhibition of ClpP.
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Affiliation(s)
- Carlos Moreno-Cinos
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Kenneth Goossens
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Irene G Salado
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Pieter Van Der Veken
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Hans De Winter
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
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12
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Wang Y, Jiang Y, Ding S, Li J, Song N, Ren Y, Hong D, Wu C, Li B, Wang F, He W, Wang J, Mei Z. Small molecule inhibitors reveal allosteric regulation of USP14 via steric blockade. Cell Res 2018; 28:1186-1194. [PMID: 30254335 PMCID: PMC6274642 DOI: 10.1038/s41422-018-0091-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/13/2018] [Accepted: 08/30/2018] [Indexed: 01/13/2023] Open
Abstract
The ubiquitin system is important for drug discovery, and the discovery of selective small-molecule inhibitors of deubiquitinating enzymes (DUBs) remains an active yet extremely challenging task. With a few exceptions, previously developed inhibitors have been found to bind the evolutionarily conserved catalytic centers of DUBs, resulting in poor selectivity. The small molecule IU1 was the first-ever specific inhibitor identified and exhibited surprisingly excellent selectivity for USP14 over other DUBs. However, the molecular mechanism for this selectivity was elusive. Herein, we report the high-resolution co-crystal structures of the catalytic domain of USP14 bound to IU1 and three IU1 derivatives. All the structures of these complexes indicate that IU1 and its analogs bind to a previously unknown steric binding site in USP14, thus blocking the access of the C-terminus of ubiquitin to the active site of USP14 and abrogating USP14 activity. Importantly, this steric site in USP14 is very unique, as suggested by structural alignments of USP14 with several known DUB X-ray structures. These results, in conjunction with biochemical characterization, indicate a coherent steric blockade mechanism for USP14 inhibition by compounds of the IU series. In light of the recent report of steric blockade of USP7 by FT671, this work suggests a potential generally applicable allosteric mechanism for the regulation of DUBs via steric blockade, as showcased by our discovery of IU1-248 which is 10-fold more potent than IU1.
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Affiliation(s)
- Yiwei Wang
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuxuan Jiang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Shan Ding
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiawang Li
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Ningjing Song
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, 230026, China
| | - Yujing Ren
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Danning Hong
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Cai Wu
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Bin Li
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Feng Wang
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
| | - Wei He
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China.
| | - Jiawei Wang
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Ziqing Mei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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13
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Duran EC, Lucius AL. ATP hydrolysis inactivating Walker B mutation perturbs E. coli ClpA self-assembly energetics in the absence of nucleotide. Biophys Chem 2018; 242:6-14. [PMID: 30173103 DOI: 10.1016/j.bpc.2018.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 08/22/2018] [Accepted: 08/23/2018] [Indexed: 02/03/2023]
Abstract
E. coli ClpA is an AAA+ (ATPase Associated with diverse cellular Activities) chaperone that catalyzes the ATP-dependent unfolding and translocation of substrate proteins for the purposes of proper proteome maintenance. Biologically active ClpA hexamers contain two nucleotide binding domains (NBD) per protomer, D1 and D2. Despite extensive study, complete understanding of how the twelve NBDs within a ClpA hexamer coordinate ATP binding and hydrolysis to polypeptide translocation is currently lacking. To examine nucleotide binding and coordination at D1 and D2, ClpA Walker B variants deficient in ATP hydrolysis at one or both NBDs have been employed in various studies. In the presence of ATP, it is widely assumed that ClpA Walker B variants are entirely hexameric. However, a thermodynamically rigorous examination of the self-assembly mechanism has not been obtained. Differences in the assembly due to the mutation can be misattributed to the active NBD, leading to potential misinterpretations of kinetic studies. Here we use sedimentation velocity studies to quantitatively examine the self-assembly mechanism of ClpA Walker B variants deficient in ATP hydrolysis at D1, D2, and both NBDs. We found that the Walker B mutations had clear, if modest, effects on the assembly. Most notably, the Walker B mutation stabilizes the population of a larger oligomer in the absence of nucleotide, that is not present for analogous concentrations of wild type ClpA. Our results indicate that Walker B mutants, widely used in studies of AAA+ family proteins, require additional characterization as the mutation affects not only ATP hydrolysis, but also the ligand linked assembly of these complexes. This linkage must be considered in investigations of unfolding or other ATP dependent functions.
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Affiliation(s)
- Elizabeth C Duran
- University of Alabama at Birmingham, Chemistry Department, Birmingham, AL, United States
| | - Aaron L Lucius
- University of Alabama at Birmingham, Chemistry Department, Birmingham, AL, United States.
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14
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Wang CH, Lu SX, Liu LL, Li Y, Yang X, He YF, Chen SL, Cai SH, Wang H, Yun JP. POH1 Knockdown Induces Cancer Cell Apoptosis via p53 and Bim. Neoplasia 2018; 20:411-424. [PMID: 29573636 PMCID: PMC5915990 DOI: 10.1016/j.neo.2018.02.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 02/13/2018] [Accepted: 02/19/2018] [Indexed: 12/02/2022] Open
Abstract
The ubiquitin-proteasome system is implicated in cell apoptosis that is frequently dysregulated in human cancers. POH1/rpn11/PSMD14, as a part of the 19S proteasomal subunit, contributes to the progression of malignancy, but its role in apoptosis remains unclear. Here, we showed that POH1 expression was increased and associated with poor outcomes in three independent cohorts of patients with hepatocellular carcinoma (HCC), esophageal cancer (EC), and colorectal cancer (CRC). The knockdown of POH1 significantly inhibited tumor cell proliferation and induced apoptosis mediated by the mitochondrial pathway in vitro. Intratumoral injection of POH1 small interfering RNA (siRNA) significantly reduced the progression of tumor growth and induced apoptosis in vivo. Furthermore, p53 or Bim siRNA markedly attenuated the apoptosis induced by POH1 depletion. POH1 depletion resulted in cell apoptosis by increasing the stability of p53 and Bim and inhibiting their ubiquitination. Overall, POH1 knockdown induced cell apoptosis through increased expression of p53 and Bim via enhanced protein stability and attenuated degradation. Thus, POH1 may serve as a potential prognostic marker and therapeutic target in human cancers.
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Affiliation(s)
- Chun-Hua Wang
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, 651# Dong Feng Road East, Guangzhou 510060, China; Department of Pathology, Sun Yat-sen University Cancer Center, 651# Dong Feng Road East, Guangzhou 510060, China.
| | - Shi-Xun Lu
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, 651# Dong Feng Road East, Guangzhou 510060, China; Department of Pathology, Sun Yat-sen University Cancer Center, 651# Dong Feng Road East, Guangzhou 510060, China.
| | - Li-Li Liu
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, 651# Dong Feng Road East, Guangzhou 510060, China; Department of Pathology, Sun Yat-sen University Cancer Center, 651# Dong Feng Road East, Guangzhou 510060, China.
| | - Yong Li
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, 651# Dong Feng Road East, Guangzhou 510060, China; Department of Pathology, Sun Yat-sen University Cancer Center, 651# Dong Feng Road East, Guangzhou 510060, China.
| | - Xia Yang
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, 651# Dong Feng Road East, Guangzhou 510060, China; Department of Pathology, Sun Yat-sen University Cancer Center, 651# Dong Feng Road East, Guangzhou 510060, China.
| | - Yang-Fan He
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, 651# Dong Feng Road East, Guangzhou 510060, China; Department of Pathology, Sun Yat-sen University Cancer Center, 651# Dong Feng Road East, Guangzhou 510060, China.
| | - Shi-Lu Chen
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, 651# Dong Feng Road East, Guangzhou 510060, China; Department of Pathology, Sun Yat-sen University Cancer Center, 651# Dong Feng Road East, Guangzhou 510060, China.
| | - Shao-Hang Cai
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, 651# Dong Feng Road East, Guangzhou 510060, China; Department of Pathology, Sun Yat-sen University Cancer Center, 651# Dong Feng Road East, Guangzhou 510060, China.
| | - Hong Wang
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, 651# Dong Feng Road East, Guangzhou 510060, China; Department of Pathology, Sun Yat-sen University Cancer Center, 651# Dong Feng Road East, Guangzhou 510060, China.
| | - Jing-Ping Yun
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, 651# Dong Feng Road East, Guangzhou 510060, China; Department of Pathology, Sun Yat-sen University Cancer Center, 651# Dong Feng Road East, Guangzhou 510060, China.
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15
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Miller JM, Chaudhary H, Marsee JD. Phylogenetic analysis predicts structural divergence for proteobacterial ClpC proteins. J Struct Biol 2017; 201:52-62. [PMID: 29129755 DOI: 10.1016/j.jsb.2017.11.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 11/06/2017] [Accepted: 11/08/2017] [Indexed: 12/29/2022]
Abstract
Regulated proteolysis is required in all organisms for the removal of misfolded or degradation-tagged protein substrates in cellular quality control pathways. The molecular machines that catalyze this process are known as ATP-dependent proteases with examples that include ClpAP and ClpCP. Clp/Hsp100 subunits form ring-structures that couple the energy of ATP binding and hydrolysis to protein unfolding and subsequent translocation of denatured protein into the compartmentalized ClpP protease for degradation. Copies of the clpA, clpC, clpE, clpK, and clpL genes are present in all characterized bacteria and their gene products are highly conserved in structure and function. However, the evolutionary relationship between these proteins remains unclear. Here we report a comprehensive phylogenetic analysis that suggests divergent evolution yielded ClpA from an ancestral ClpC protein and that ClpE/ClpL represent intermediates between ClpA/ClpC. This analysis also identifies a group of proteobacterial ClpC proteins that are likely not functional in regulated proteolysis. Our results strongly suggest that bacterial ClpC proteins should not be assumed to all function identically due to the structural differences identified here.
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Affiliation(s)
- Justin M Miller
- Middle Tennessee State University, Department of Chemistry, 1301 East Main Street, Murfreesboro, TN 37132, United States.
| | - Hamza Chaudhary
- Middle Tennessee State University, Department of Chemistry, 1301 East Main Street, Murfreesboro, TN 37132, United States
| | - Justin D Marsee
- Middle Tennessee State University, Department of Chemistry, 1301 East Main Street, Murfreesboro, TN 37132, United States
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16
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Boselli M, Lee BH, Robert J, Prado MA, Min SW, Cheng C, Silva MC, Seong C, Elsasser S, Hatle KM, Gahman TC, Gygi SP, Haggarty SJ, Gan L, King RW, Finley D. An inhibitor of the proteasomal deubiquitinating enzyme USP14 induces tau elimination in cultured neurons. J Biol Chem 2017; 292:19209-19225. [PMID: 28972160 DOI: 10.1074/jbc.m117.815126] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Indexed: 11/06/2022] Open
Abstract
The ubiquitin-proteasome system (UPS) is responsible for most selective protein degradation in eukaryotes and regulates numerous cellular processes, including cell cycle control and protein quality control. A component of this system, the deubiquitinating enzyme USP14, associates with the proteasome where it can rescue substrates from degradation by removal of the ubiquitin tag. We previously found that a small-molecule inhibitor of USP14, known as IU1, can increase the rate of degradation of a subset of proteasome substrates. We report here the synthesis and characterization of 87 variants of IU1, which resulted in the identification of a 10-fold more potent USP14 inhibitor that retains specificity for USP14. The capacity of this compound, IU1-47, to enhance protein degradation in cells was tested using as a reporter the microtubule-associated protein tau, which has been implicated in many neurodegenerative diseases. Using primary neuronal cultures, IU1-47 was found to accelerate the rate of degradation of wild-type tau, the pathological tau mutants P301L and P301S, and the A152T tau variant. We also report that a specific residue in tau, lysine 174, is critical for the IU1-47-mediated tau degradation by the proteasome. Finally, we show that IU1-47 stimulates autophagic flux in primary neurons. In summary, these findings provide a powerful research tool for investigating the complex biology of USP14.
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Affiliation(s)
- Monica Boselli
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Byung-Hoon Lee
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115.,the Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, 42988 Daegu, Korea
| | - Jessica Robert
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Miguel A Prado
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Sang-Won Min
- the Department of Neurology, Gladstone Institute of Neurological Diseases, University of California, San Francisco, California 94158
| | - Chialin Cheng
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
| | - M Catarina Silva
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
| | - Changhyun Seong
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115.,Regeneron Pharmaceuticals, Tarrytown, New York 10591, and
| | - Suzanne Elsasser
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Ketki M Hatle
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Timothy C Gahman
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, La Jolla, California 92093
| | - Steven P Gygi
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Stephen J Haggarty
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
| | - Li Gan
- the Department of Neurology, Gladstone Institute of Neurological Diseases, University of California, San Francisco, California 94158
| | - Randall W King
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115,
| | - Daniel Finley
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115,
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17
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Regulating protein breakdown through proteasome phosphorylation. Biochem J 2017; 474:3355-3371. [PMID: 28947610 DOI: 10.1042/bcj20160809] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/28/2017] [Accepted: 08/30/2017] [Indexed: 12/31/2022]
Abstract
The ubiquitin proteasome system degrades the great majority of proteins in mammalian cells. Countless studies have described how ubiquitination promotes the selective degradation of different cell proteins. However, there is a small but the growing literature that protein half-lives can also be regulated by post-translational modifications of the 26S proteasome. The present study reviews the ability of several kinases to alter proteasome function through subunit phosphorylation. For example, PKA (protein kinase A) and DYRK2 (dual-specificity tyrosine-regulated kinase 2) stimulate the proteasome's ability to degrade ubiquitinated proteins, peptides, and adenosine triphosphate, while one kinase, ASK1 (apoptosis signal-regulating kinase 1), inhibits proteasome function during apoptosis. Proteasome phosphorylation is likely to be important in regulating protein degradation because it occurs downstream from many hormones and neurotransmitters, in conditions that raise cyclic adenosine monophosphate or cyclic guanosine monophosphate levels, after calcium influx following synaptic depolarization, and during phases of the cell cycle. Beyond its physiological importance, pharmacological manipulation of proteasome phosphorylation has the potential to combat various diseases. Inhibitors of phosphodiesterases by activating PKA or PKG (protein kinase G) can stimulate proteasomal degradation of misfolded proteins that cause neurodegenerative or myocardial diseases and even reduce the associated pathology in mouse models. These observations are promising since in many proteotoxic diseases, aggregation-prone proteins impair proteasome function, and disrupt protein homeostasis. Conversely, preventing subunit phosphorylation by DYRK2 slows cell cycle progression and tumor growth. However, further research is essential to determine how phosphorylation of different subunits by these (or other) kinases alters the properties of this complex molecular machine and thus influence protein degradation rates.
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18
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Elsholz AKW, Birk MS, Charpentier E, Turgay K. Functional Diversity of AAA+ Protease Complexes in Bacillus subtilis. Front Mol Biosci 2017; 4:44. [PMID: 28748186 PMCID: PMC5506225 DOI: 10.3389/fmolb.2017.00044] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 06/15/2017] [Indexed: 12/20/2022] Open
Abstract
Here, we review the diverse roles and functions of AAA+ protease complexes in protein homeostasis, control of stress response and cellular development pathways by regulatory and general proteolysis in the Gram-positive model organism Bacillus subtilis. We discuss in detail the intricate involvement of AAA+ protein complexes in controlling sporulation, the heat shock response and the role of adaptor proteins in these processes. The investigation of these protein complexes and their adaptor proteins has revealed their relevance for Gram-positive pathogens and their potential as targets for new antibiotics.
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Affiliation(s)
- Alexander K W Elsholz
- Department of Regulation in Infection Biology, Max Planck Institute for Infection BiologyBerlin, Germany
| | - Marlene S Birk
- Department of Regulation in Infection Biology, Max Planck Institute for Infection BiologyBerlin, Germany
| | - Emmanuelle Charpentier
- Department of Regulation in Infection Biology, Max Planck Institute for Infection BiologyBerlin, Germany.,The Laboratory for Molecular Infection Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå UniversityUmeå, Sweden.,Humboldt UniversityBerlin, Germany
| | - Kürşad Turgay
- Faculty of Natural Sciences, Institute of Microbiology, Leibniz UniversitätHannover, Germany
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19
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Yedidi RS, Wendler P, Enenkel C. AAA-ATPases in Protein Degradation. Front Mol Biosci 2017; 4:42. [PMID: 28676851 PMCID: PMC5476697 DOI: 10.3389/fmolb.2017.00042] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 06/06/2017] [Indexed: 11/13/2022] Open
Abstract
Proteolytic machineries containing multisubunit protease complexes and AAA-ATPases play a key role in protein quality control and the regulation of protein homeostasis. In these protein degradation machineries, the proteolytically active sites are formed by either threonines or serines which are buried inside interior cavities of cylinder-shaped complexes. In eukaryotic cells, the proteasome is the most prominent protease complex harboring AAA-ATPases. To degrade protein substrates, the gates of the axial entry ports of the protease need to be open. Gate opening is accomplished by AAA-ATPases, which form a hexameric ring flanking the entry ports of the protease. Protein substrates with unstructured domains can loop into the entry ports without the assistance of AAA-ATPases. However, folded proteins require the action of AAA-ATPases to unveil an unstructured terminus or domain. Cycles of ATP binding/hydrolysis fuel the unfolding of protein substrates which are gripped by loops lining up the central pore of the AAA-ATPase ring. The AAA-ATPases pull on the unfolded polypeptide chain for translocation into the proteolytic cavity of the protease. Conformational changes within the AAA-ATPase ring and the adjacent protease chamber create a peristaltic movement for substrate degradation. The review focuses on new technologies toward the understanding of the function and structure of AAA-ATPases to achieve substrate recognition, unfolding and translocation into proteasomes in yeast and mammalian cells and into proteasome-equivalent proteases in bacteria and archaea.
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Affiliation(s)
| | - Petra Wendler
- Department of Biochemistry, Institute of Biochemistry and Biology, University of PotsdamPotsdam, Germany
| | - Cordula Enenkel
- Department of Biochemistry, University of TorontoToronto, ON, Canada
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20
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Guerra-Moreno A, Hanna J. Induction of proteotoxic stress by the mycotoxin patulin. Toxicol Lett 2017; 276:85-91. [PMID: 28529145 DOI: 10.1016/j.toxlet.2017.05.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/24/2017] [Accepted: 05/14/2017] [Indexed: 01/04/2023]
Abstract
Patulin is a naturally occurring mycotoxin produced by a number of molds and may contaminate a wide variety of food products. In practice, patulin's main societal relevance concerns apple juice and its products. Multiple advisory bodies, including the U.S. Food and Drug Administration and the World Health Organization, recommend that producers monitor and limit patulin levels in apple juice products. The mechanism of patulin toxicity remains largely unknown. Here we show that patulin induces proteotoxic stress in the yeast S. cerevisiae. The transcription factor Rpn4 controls the abundance of the proteasome, the complex multisubunit protease that destroys proteins, including misfolded proteins. Rpn4 protein is strongly induced by patulin, and Rpn4 levels normalize over time, consistent with homeostatic regulation. A rpn4Δ mutant is highly sensitive to patulin, confirming the physiologic relevance of this response. Rpn4 is known to be regulated both transcriptionally and post-translationally. Patulin induces both pathways of regulation, but the post-transcriptional pathway predominates in controlling Rpn4 protein levels. These results indicate that proteotoxicity represents a major aspect of patulin toxicity. They not only have implications for patulin detoxification but in addition suggest the possibility of some potentially useful patulin applications.
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Affiliation(s)
- Angel Guerra-Moreno
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - John Hanna
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States.
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21
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Ling X, Huang Q, Xu Y, Jin Y, Feng Y, Shi W, Ye X, Lin Y, Hou L, Lin X. The deubiquitinating enzyme Usp5 regulates Notch and RTK signaling duringDrosophilaeye development. FEBS Lett 2017; 591:875-888. [PMID: 28140449 DOI: 10.1002/1873-3468.12580] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 01/24/2017] [Accepted: 01/25/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Xuemei Ling
- School of Optometry and Ophthalmology and Eye Hospital; Wenzhou Medical University; Zhejiang China
| | - Qinzhu Huang
- Taizhou Hospital of Zhejiang Province; Wenzhou Medical University; Linhai Zhejiang China
| | - Yanqin Xu
- School of Optometry and Ophthalmology and Eye Hospital; Wenzhou Medical University; Zhejiang China
| | - Yuxiao Jin
- School of Optometry and Ophthalmology and Eye Hospital; Wenzhou Medical University; Zhejiang China
| | - Ying Feng
- School of Optometry and Ophthalmology and Eye Hospital; Wenzhou Medical University; Zhejiang China
| | - Weijie Shi
- School of Optometry and Ophthalmology and Eye Hospital; Wenzhou Medical University; Zhejiang China
| | - Xiaolei Ye
- School of Optometry and Ophthalmology and Eye Hospital; Wenzhou Medical University; Zhejiang China
| | - Yi Lin
- School of Optometry and Ophthalmology and Eye Hospital; Wenzhou Medical University; Zhejiang China
| | - Ling Hou
- School of Optometry and Ophthalmology and Eye Hospital; Wenzhou Medical University; Zhejiang China
| | - Xinhua Lin
- School of Optometry and Ophthalmology and Eye Hospital; Wenzhou Medical University; Zhejiang China
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22
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Ligand-induced and small-molecule control of substrate loading in a hexameric helicase. Proc Natl Acad Sci U S A 2016; 113:13714-13719. [PMID: 27821776 DOI: 10.1073/pnas.1616749113] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Processive, ring-shaped protein and nucleic acid protein translocases control essential biochemical processes throughout biology and are considered high-prospect therapeutic targets. The Escherichia coli Rho factor is an exemplar hexameric RNA translocase that terminates transcription in bacteria. As with many ring-shaped motor proteins, Rho activity is modulated by a variety of poorly understood mechanisms, including small-molecule therapeutics, protein-protein interactions, and the sequence of its translocation substrate. Here, we establish the mechanism of action of two Rho effectors, the antibiotic bicyclomycin and nucleic acids that bind to Rho's primary RNA recruitment site. Using small-angle X-ray scattering and a fluorescence-based assay to monitor the ability of Rho to switch between open-ring (RNA-loading) and closed-ring (RNA-translocation) states, we found bicyclomycin to be a direct antagonist of ring closure. Reciprocally, the binding of nucleic acids to its N-terminal RNA recruitment domains is shown to promote the formation of a closed-ring Rho state, with increasing primary-site occupancy providing additive stimulatory effects. This study establishes bicyclomycin as a conformational inhibitor of Rho ring dynamics, highlighting the utility of developing assays that read out protein conformation as a prospective screening tool for ring-ATPase inhibitors. Our findings further show that the RNA sequence specificity used for guiding Rho-dependent termination derives in part from an intrinsic ability of the motor to couple the recognition of pyrimidine patterns in nascent transcripts to RNA loading and activity.
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23
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Fundamental Characteristics of AAA+ Protein Family Structure and Function. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2016; 2016:9294307. [PMID: 27703410 PMCID: PMC5039278 DOI: 10.1155/2016/9294307] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 07/21/2016] [Indexed: 12/22/2022]
Abstract
Many complex cellular events depend on multiprotein complexes known as molecular machines to efficiently couple the energy derived from adenosine triphosphate hydrolysis to the generation of mechanical force. Members of the AAA+ ATPase superfamily (ATPases Associated with various cellular Activities) are critical components of many molecular machines. AAA+ proteins are defined by conserved modules that precisely position the active site elements of two adjacent subunits to catalyze ATP hydrolysis. In many cases, AAA+ proteins form a ring structure that translocates a polymeric substrate through the central channel using specialized loops that project into the central channel. We discuss the major features of AAA+ protein structure and function with an emphasis on pivotal aspects elucidated with archaeal proteins.
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24
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Abstract
The endoplasmic reticulum is the port of entry for proteins into the secretory pathway and the site of synthesis for several important lipids, including cholesterol, triacylglycerol, and phospholipids. Protein production within the endoplasmic reticulum is tightly regulated by a cohort of resident machinery that coordinates the folding, modification, and deployment of secreted and integral membrane proteins. Proteins failing to attain their native conformation are degraded through the endoplasmic reticulum-associated degradation (ERAD) pathway via a series of tightly coupled steps: substrate recognition, dislocation, and ubiquitin-dependent proteasomal destruction. The same ERAD machinery also controls the flux through various metabolic pathways by coupling the turnover of metabolic enzymes to the levels of key metabolites. We review the current understanding and biological significance of ERAD-mediated regulation of lipid metabolism in mammalian cells.
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Affiliation(s)
- Julian Stevenson
- Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720;
| | - Edmond Y Huang
- Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720;
| | - James A Olzmann
- Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720;
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25
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Guerra-Moreno A, Hanna J. Tmc1 Is a Dynamically Regulated Effector of the Rpn4 Proteotoxic Stress Response. J Biol Chem 2016; 291:14788-95. [PMID: 27226598 DOI: 10.1074/jbc.m116.726398] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Indexed: 11/06/2022] Open
Abstract
The ubiquitin-proteasome system represents the major pathway of selective intracellular protein degradation in eukaryotes. Misfolded proteins represent an important class of substrates for this pathway, and the failure to destroy misfolded proteins is associated with a number of human diseases. The transcription factor Rpn4 mediates a key proteotoxic stress response whose best known function is to control proteasome abundance by a homeostatic feedback mechanism. Here we identify the uncharacterized zinc finger protein Tmc1 as a dynamically regulated stress-responsive protein. Rpn4 induces TMC1 transcription in response to misfolded proteins. However, this response is counteracted by rapid proteasome-dependent degradation of Tmc1, which serves to normalize Tmc1 protein levels after induction. Precise control of Tmc1 levels is needed in vivo to survive multiple stressors related to proteostasis. Thus, Tmc1 represents a novel effector and substrate of the Rpn4 proteotoxic stress response.
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Affiliation(s)
- Angel Guerra-Moreno
- From the Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - John Hanna
- From the Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
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26
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Open-gate mutants of the mammalian proteasome show enhanced ubiquitin-conjugate degradation. Nat Commun 2016; 7:10963. [PMID: 26957043 PMCID: PMC4786872 DOI: 10.1038/ncomms10963] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 02/04/2016] [Indexed: 12/20/2022] Open
Abstract
When in the closed form, the substrate translocation channel of the proteasome core
particle (CP) is blocked by the convergent N termini of α-subunits. To
probe the role of channel gating in mammalian proteasomes, we deleted the N-terminal
tail of α3; the resulting α3ΔN proteasomes are intact
but hyperactive in the hydrolysis of fluorogenic peptide substrates and the
degradation of polyubiquitinated proteins. Cells expressing the hyperactive
proteasomes show markedly elevated degradation of many established proteasome
substrates and resistance to oxidative stress. Multiplexed quantitative proteomics
revealed ∼200 proteins with reduced levels in the mutant cells. Potentially
toxic proteins such as tau exhibit reduced accumulation and aggregate formation.
These data demonstrate that the CP gate is a key negative regulator of proteasome
function in mammals, and that opening the CP gate may be an effective strategy to
increase proteasome activity and reduce levels of toxic proteins in cells. The proteasome plays a key role in proteostasis by mediating the
degradation of ubiquitinated substrates. Here the authors show that an open-gate mutant
of the proteasome is hyperactive towards a subset of substrates and can effectively
delay the accumulation of toxic protein aggregates.
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27
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Śledź P, Baumeister W. Structure-Driven Developments of 26S Proteasome Inhibitors. Annu Rev Pharmacol Toxicol 2016; 56:191-209. [DOI: 10.1146/annurev-pharmtox-010814-124727] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Paweł Śledź
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
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28
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Olivares AO, Baker TA, Sauer RT. Mechanistic insights into bacterial AAA+ proteases and protein-remodelling machines. Nat Rev Microbiol 2015; 14:33-44. [PMID: 26639779 DOI: 10.1038/nrmicro.2015.4] [Citation(s) in RCA: 207] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
To maintain protein homeostasis, AAA+ proteolytic machines degrade damaged and unneeded proteins in bacteria, archaea and eukaryotes. This process involves the ATP-dependent unfolding of a target protein and its subsequent translocation into a self-compartmentalized proteolytic chamber. Related AAA+ enzymes also disaggregate and remodel proteins. Recent structural and biochemical studies, in combination with direct visualization of unfolding and translocation in single-molecule experiments, have illuminated the molecular mechanisms behind these processes and suggest how remodelling of macromolecular complexes by AAA+ enzymes could occur without global denaturation. In this Review, we discuss the structural and mechanistic features of AAA+ proteases and remodelling machines, focusing on the bacterial ClpXP and ClpX as paradigms. We also consider the potential of these enzymes as antibacterial targets and outline future challenges for the field.
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Affiliation(s)
- Adrian O Olivares
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Tania A Baker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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29
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Li X, Li Y, Arendt CS, Hochstrasser M. Distinct Elements in the Proteasomal β5 Subunit Propeptide Required for Autocatalytic Processing and Proteasome Assembly. J Biol Chem 2015; 291:1991-2003. [PMID: 26627836 DOI: 10.1074/jbc.m115.677047] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Indexed: 01/02/2023] Open
Abstract
Eukaryotic 20S proteasome assembly remains poorly understood. The subunits stack into four heteroheptameric rings; three inner-ring subunits (β1, β2, and β5) bear the protease catalytic residues and are synthesized with N-terminal propeptides. These propeptides are removed autocatalytically late in assembly. In Saccharomyces cerevisiae, β5 (Doa3/Pre2) has a 75-residue propeptide, β5pro, that is essential for proteasome assembly and can work in trans. We show that deletion of the poorly conserved N-terminal half of the β5 propeptide nonetheless causes substantial defects in proteasome maturation. Sequences closer to the cleavage site have critical but redundant roles in both assembly and self-cleavage. A conserved histidine two residues upstream of the autocleavage site strongly promotes processing. Surprisingly, although β5pro is functionally linked to the Ump1 assembly factor, trans-expressed β5pro associates only weakly with Ump1-containing precursors. Several genes were identified as dosage suppressors of trans-expressed β5pro mutants; the strongest encoded the β7 proteasome subunit. Previous data suggested that β7 and β5pro have overlapping roles in bringing together two half-proteasomes, but the timing of β7 addition relative to half-mer joining was unclear. Here we report conditions where dimerization lags behind β7 incorporation into the half-mer. Our results suggest that β7 insertion precedes half-mer dimerization, and the β7 tail and β5 propeptide have unequal roles in half-mer joining.
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Affiliation(s)
- Xia Li
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 and
| | - Yanjie Li
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 and
| | - Cassandra S Arendt
- the Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Mark Hochstrasser
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 and.
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30
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Middleton AJ, Day CL. The molecular basis of lysine 48 ubiquitin chain synthesis by Ube2K. Sci Rep 2015; 5:16793. [PMID: 26592444 PMCID: PMC4655369 DOI: 10.1038/srep16793] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 10/20/2015] [Indexed: 12/14/2022] Open
Abstract
The post-translational modification of proteins by ubiquitin is central to the regulation of eukaryotic cells. Substrate-bound ubiquitin chains linked by lysine 11 and 48 target proteins to the proteasome for degradation and determine protein abundance in cells, while other ubiquitin chain linkages regulate protein interactions. The specificity of chain-linkage type is usually determined by ubiquitin-conjugating enzymes (E2s). The degradative E2, Ube2K, preferentially catalyses formation of Lys48-linked chains, but like most E2s, the molecular basis for chain formation is not well understood. Here we report the crystal structure of a Ube2K~ubiquitin conjugate and demonstrate that even though it is monomeric, Ube2K can synthesize Lys48-linked ubiquitin chains. Using site-directed mutagenesis and modelling, our studies reveal a molecular understanding of the catalytic complex and identify key features required for synthesis of degradative Lys48-linked chains. The position of the acceptor ubiquitin described here is likely conserved in other E2s that catalyse Lys48-linked ubiquitin chain synthesis.
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Affiliation(s)
- Adam J Middleton
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Catherine L Day
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand
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31
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Monroe N, Hill CP. Meiotic Clade AAA ATPases: Protein Polymer Disassembly Machines. J Mol Biol 2015; 428:1897-911. [PMID: 26555750 DOI: 10.1016/j.jmb.2015.11.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/03/2015] [Accepted: 11/04/2015] [Indexed: 12/20/2022]
Abstract
Meiotic clade AAA ATPases (ATPases associated with diverse cellular activities), which were initially grouped on the basis of phylogenetic classification of their AAA ATPase cassette, include four relatively well characterized family members, Vps4, spastin, katanin and fidgetin. These enzymes all function to disassemble specific polymeric protein structures, with Vps4 disassembling the ESCRT-III polymers that are central to the many membrane-remodeling activities of the ESCRT (endosomal sorting complexes required for transport) pathway and spastin, katanin p60 and fidgetin affecting multiple aspects of cellular dynamics by severing microtubules. They share a common domain architecture that features an N-terminal MIT (microtubule interacting and trafficking) domain followed by a single AAA ATPase cassette. Meiotic clade AAA ATPases function as hexamers that can cycle between the active assembly and inactive monomers/dimers in a regulated process, and they appear to disassemble their polymeric substrates by translocating subunits through the central pore of their hexameric ring. Recent studies with Vps4 have shown that nucleotide-induced asymmetry is a requirement for substrate binding to the pore loops and that recruitment to the protein lattice via MIT domains also relieves autoinhibition and primes the AAA ATPase cassettes for substrate binding. The most striking, unifying feature of meiotic clade AAA ATPases may be their MIT domain, which is a module that is found in a wide variety of proteins that localize to ESCRT-III polymers. Spastin also displays an adjacent microtubule binding sequence, and the presence of both ESCRT-III and microtubule binding elements may underlie the recent findings that the ESCRT-III disassembly function of Vps4 and the microtubule-severing function of spastin, as well as potentially katanin and fidgetin, are highly coordinated.
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Affiliation(s)
- Nicole Monroe
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112-5650, USA
| | - Christopher P Hill
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112-5650, USA.
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32
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Han H, Monroe N, Votteler J, Shakya B, Sundquist WI, Hill CP. Binding of Substrates to the Central Pore of the Vps4 ATPase Is Autoinhibited by the Microtubule Interacting and Trafficking (MIT) Domain and Activated by MIT Interacting Motifs (MIMs). J Biol Chem 2015; 290:13490-9. [PMID: 25833946 DOI: 10.1074/jbc.m115.642355] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Indexed: 12/21/2022] Open
Abstract
The endosomal sorting complexes required for transport (ESCRT) pathway drives reverse topology membrane fission events within multiple cellular pathways, including cytokinesis, multivesicular body biogenesis, repair of the plasma membrane, nuclear membrane vesicle formation, and HIV budding. The AAA ATPase Vps4 is recruited to membrane necks shortly before fission, where it catalyzes disassembly of the ESCRT-III lattice. The N-terminal Vps4 microtubule-interacting and trafficking (MIT) domains initially bind the C-terminal MIT-interacting motifs (MIMs) of ESCRT-III subunits, but it is unclear how the enzyme then remodels these substrates in response to ATP hydrolysis. Here, we report quantitative binding studies that demonstrate that residues from helix 5 of the Vps2p subunit of ESCRT-III bind to the central pore of an asymmetric Vps4p hexamer in a manner that is dependent upon the presence of flexible nucleotide analogs that can mimic multiple states in the ATP hydrolysis cycle. We also find that substrate engagement is autoinhibited by the Vps4p MIT domain and that this inhibition is relieved by binding of either Type 1 or Type 2 MIM elements, which bind the Vps4p MIT domain through different interfaces. These observations support the model that Vps4 substrates are initially recruited by an MIM-MIT interaction that activates the Vps4 central pore to engage substrates and generate force, thereby triggering ESCRT-III disassembly.
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Affiliation(s)
- Han Han
- From the Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650
| | - Nicole Monroe
- From the Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650
| | - Jörg Votteler
- From the Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650
| | - Binita Shakya
- From the Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650
| | - Wesley I Sundquist
- From the Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650
| | - Christopher P Hill
- From the Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650
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33
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Mitsiades CS. Therapeutic landscape of carfilzomib and other modulators of the ubiquitin-proteasome pathway. J Clin Oncol 2015; 33:782-5. [PMID: 25605842 PMCID: PMC4517049 DOI: 10.1200/jco.2014.55.5748] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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34
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Bacterial proteasome activator bpa (rv3780) is a novel ring-shaped interactor of the mycobacterial proteasome. PLoS One 2014; 9:e114348. [PMID: 25469515 PMCID: PMC4254994 DOI: 10.1371/journal.pone.0114348] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 11/06/2014] [Indexed: 12/14/2022] Open
Abstract
The occurrence of the proteasome in bacteria is limited to the phylum of actinobacteria, where it is maintained in parallel to the usual bacterial compartmentalizing proteases. The role it plays in these organisms is still not fully understood, but in the human pathogen Mycobacterium tuberculosis (Mtb) the proteasome supports persistence in the host. In complex with the ring-shaped ATPase Mpa (called ARC in other actinobacteria), the proteasome can degrade proteins that have been post-translationally modified with the prokaryotic ubiquitin-like protein Pup. Unlike for the eukaryotic proteasome core particle, no other bacterial proteasome interactors have been identified to date. Here we describe and characterize a novel bacterial proteasome activator of Mycobacterium tuberculosis we termed Bpa (Rv3780), using a combination of biochemical and biophysical methods. Bpa features a canonical C-terminal proteasome interaction motif referred to as the HbYX motif, and its orthologs are only found in those actinobacteria encoding the proteasomal subunits. Bpa can inhibit degradation of Pup-tagged substrates in vitro by competing with Mpa for association with the proteasome. Using negative-stain electron microscopy, we show that Bpa forms a ring-shaped homooligomer that can bind coaxially to the face of the proteasome cylinder. Interestingly, Bpa can stimulate the proteasomal degradation of the model substrate β-casein, which suggests it could play a role in the removal of non-native or damaged proteins.
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35
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Besche HC, Sha Z, Kukushkin NV, Peth A, Hock EM, Kim W, Gygi S, Gutierrez JA, Liao H, Dick L, Goldberg AL. Autoubiquitination of the 26S proteasome on Rpn13 regulates breakdown of ubiquitin conjugates. EMBO J 2014; 33:1159-76. [PMID: 24811749 PMCID: PMC4193922 DOI: 10.1002/embj.201386906] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 03/12/2014] [Accepted: 04/01/2014] [Indexed: 11/09/2022] Open
Abstract
Degradation rates of most proteins in eukaryotic cells are determined by their rates of ubiquitination. However, possible regulation of the proteasome's capacity to degrade ubiquitinated proteins has received little attention, although proteasome inhibitors are widely used in research and cancer treatment. We show here that mammalian 26S proteasomes have five associated ubiquitin ligases and that multiple proteasome subunits are ubiquitinated in cells, especially the ubiquitin receptor subunit, Rpn13. When proteolysis is even partially inhibited in cells or purified 26S proteasomes with various inhibitors, Rpn13 becomes extensively and selectively poly-ubiquitinated by the proteasome-associated ubiquitin ligase, Ube3c/Hul5. This modification also occurs in cells during heat-shock or arsenite treatment, when poly-ubiquitinated proteins accumulate. Rpn13 ubiquitination strongly decreases the proteasome's ability to bind and degrade ubiquitin-conjugated proteins, but not its activity against peptide substrates. This autoinhibitory mechanism presumably evolved to prevent binding of ubiquitin conjugates to defective or stalled proteasomes, but this modification may also be useful as a biomarker indicating the presence of proteotoxic stress and reduced proteasomal capacity in cells or patients.
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Affiliation(s)
| | - Zhe Sha
- Harvard Medical School, Boston, MA, USA
| | | | | | | | - Woong Kim
- Harvard Medical School, Boston, MA, USA
| | | | | | - Hua Liao
- Millennium Pharmaceuticals Inc., Cambridge, MA, USA
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36
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Abstract
The ubiquitin proteasome system (UPS) is the main ATP-dependent protein degradation pathway in the cytosol and nucleus of eukaryotic cells. At its centre is the 26S proteasome, which degrades regulatory proteins and misfolded or damaged proteins. In a major breakthrough, several groups have determined high-resolution structures of the entire 26S proteasome particle in different nucleotide conditions and with and without substrate using cryo-electron microscopy combined with other techniques. These structures provide some surprising insights into the functional mechanism of the proteasome and will give invaluable guidance for genetic and biochemical studies of this key regulatory system.
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37
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Huang H, Ceccarelli DF, Orlicky S, St-Cyr DJ, Ziemba A, Garg P, Plamondon S, Auer M, Sidhu S, Marinier A, Kleiger G, Tyers M, Sicheri F. E2 enzyme inhibition by stabilization of a low-affinity interface with ubiquitin. Nat Chem Biol 2014; 10:156-163. [PMID: 24316736 PMCID: PMC3905752 DOI: 10.1038/nchembio.1412] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 10/31/2013] [Indexed: 11/09/2022]
Abstract
Weak protein interactions between ubiquitin and the ubiquitin-proteasome system (UPS) enzymes that mediate its covalent attachment to substrates serve to position ubiquitin for optimal catalytic transfer. We show that a small-molecule inhibitor of the E2 ubiquitin-conjugating enzyme Cdc34A, called CC0651, acts by trapping a weak interaction between ubiquitin and the E2 donor ubiquitin-binding site. A structure of the ternary CC0651-Cdc34A-ubiquitin complex reveals that the inhibitor engages a composite binding pocket formed from Cdc34A and ubiquitin. CC0651 also suppresses the spontaneous hydrolysis rate of the Cdc34A-ubiquitin thioester without decreasing the interaction between Cdc34A and the RING domain subunit of the E3 enzyme. Stabilization of the numerous other weak interactions between ubiquitin and UPS enzymes by small molecules may be a feasible strategy to selectively inhibit different UPS activities.
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Affiliation(s)
- Hao Huang
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada M5G 1X5
| | - Derek F Ceccarelli
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada M5G 1X5
| | - Stephen Orlicky
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada M5G 1X5
| | - Daniel J. St-Cyr
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3C 3J7, Canada
| | - Amy Ziemba
- Department of Chemistry, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, NV, 89154
| | - Pankaj Garg
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Serge Plamondon
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3C 3J7, Canada
| | - Manfred Auer
- School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR United Kingdom
| | - Sachdev Sidhu
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Anne Marinier
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3C 3J7, Canada
- Department of Chemistry, University of Montreal, Montreal, Québec H3C 3J7, Canada
| | - Gary Kleiger
- Department of Chemistry, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, NV, 89154
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3C 3J7, Canada
- Department of Medicine, University of Montreal, Montreal, Québec H3C 3J7, Canada
| | - Frank Sicheri
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada M5G 1X5
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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38
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Worden EJ, Padovani C, Martin A. Structure of the Rpn11-Rpn8 dimer reveals mechanisms of substrate deubiquitination during proteasomal degradation. Nat Struct Mol Biol 2014; 21:220-7. [PMID: 24463465 DOI: 10.1038/nsmb.2771] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 01/15/2014] [Indexed: 12/21/2022]
Abstract
Polyubiquitin chains target protein substrates to the 26S proteasome, where they are removed by the deubiquitinase Rpn11 to allow efficient substrate degradation. Despite Rpn11's essential function during substrate processing, its detailed structural and biochemical characterization has been hindered by difficulties in purifying the isolated enzyme. Here we report the 2.0-Å crystal structures of Zn(2+)-free and Zn(2+)-bound Saccharomyces cerevisiae Rpn11 in an MPN-domain heterodimer with Rpn8. The Rpn11-Rpn8 interaction occurs via two distinct interfaces that may be conserved in related MPN-domain complexes. Our structural and mutational studies reveal that Rpn11 lacks a conserved surface to bind the ubiquitin Ile44 patch, does not interact with the moiety on the proximal side of the scissile isopeptide bond and exhibits no linkage specificity for ubiquitin cleavage. These findings explain how Rpn11 functions as a promiscuous deubiquitinase for cotranslocational substrate deubiquitination during proteasomal degradation.
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Affiliation(s)
- Evan J Worden
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Chris Padovani
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Andreas Martin
- 1] Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA. [2] California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, USA
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39
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Nyquist K, Martin A. Marching to the beat of the ring: polypeptide translocation by AAA+ proteases. Trends Biochem Sci 2013; 39:53-60. [PMID: 24316303 DOI: 10.1016/j.tibs.2013.11.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 11/07/2013] [Accepted: 11/12/2013] [Indexed: 11/28/2022]
Abstract
ATP-dependent proteases exist in all cells and are crucial regulators of the proteome. These machines consist of a hexameric, ring-shaped motor responsible for engaging, unfolding, and translocating protein substrates into an associated peptidase for degradation. Here, we discuss recent work that has established how the six motor subunits coordinate their ATP-hydrolysis and translocation activities. The closed topology of the ring and the rigidity of subunit/subunit interfaces cause conformational changes within a single subunit to drive motions in other subunits of the hexamer. This structural effect generates allostery between the ATP-binding sites, leading to a preferred order of binding and hydrolysis events among the motor subunits as well as a unique biphasic mechanism of translocation.
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Affiliation(s)
- Kristofor Nyquist
- QB3 Institute, University of California, Berkeley, CA 94720, USA; Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
| | - Andreas Martin
- QB3 Institute, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
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40
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Hanna J, Waterman D, Isasa M, Elsasser S, Shi Y, Gygi S, Finley D. Cuz1/Ynl155w, a zinc-dependent ubiquitin-binding protein, protects cells from metalloid-induced proteotoxicity. J Biol Chem 2013; 289:1876-85. [PMID: 24297164 DOI: 10.1074/jbc.m113.534032] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein misfolding is a universal threat to cells. The ubiquitin-proteasome system mediates a cellular stress response capable of eliminating misfolded proteins. Here we identify Cuz1/Ynl155w as a component of the ubiquitin system, capable of interacting with both the proteasome and Cdc48. Cuz1/Ynl155w is regulated by the transcription factor Rpn4, and is required for cells to survive exposure to the trivalent metalloids arsenic and antimony. A related protein, Yor052c, shows similar phenotypes, suggesting a multicomponent stress response pathway. Cuz1/Ynl155w functions as a zinc-dependent ubiquitin-binding protein. Thus, Cuz1/Ynl155w is proposed to protect cells from metalloid-induced proteotoxicity by delivering ubiquitinated substrates to Cdc48 and the proteasome for destruction.
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Affiliation(s)
- John Hanna
- From the Department of Pathology, Brigham and Women's Hospital, and
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41
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Activation of Bothrops jararaca snake venom gland and venom production: A proteomic approach. J Proteomics 2013; 94:460-72. [DOI: 10.1016/j.jprot.2013.10.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 09/28/2013] [Accepted: 10/18/2013] [Indexed: 02/08/2023]
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42
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Min M, Mayor U, Lindon C. Ubiquitination site preferences in anaphase promoting complex/cyclosome (APC/C) substrates. Open Biol 2013; 3:130097. [PMID: 24004664 PMCID: PMC3787748 DOI: 10.1098/rsob.130097] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 08/06/2013] [Indexed: 01/13/2023] Open
Abstract
Ordered progression of mitosis requires precise control in abundance of mitotic regulators. The anaphase promoting complex/cyclosome (APC/C) ubiquitin ligase plays a key role by directing ubiquitin-mediated destruction of targets in a temporally and spatially defined manner. Specificity in APC/C targeting is conferred through recognition of substrate D-box and KEN degrons, while the specificity of ubiquitination sites, as another possible regulated dimension, has not yet been explored. Here, we present the first analysis of ubiquitination sites in the APC/C substrate ubiquitome. We show that KEN is a preferred ubiquitin acceptor in APC/C substrates and that acceptor sites are enriched in predicted disordered regions and flanked by serine residues. Our experimental data confirm a role for the KEN lysine as an ubiquitin acceptor contributing to substrate destruction during mitotic progression. Using Aurora A and Nek2 kinases as examples, we show that phosphorylation on the flanking serine residue could directly regulate ubiquitination and subsequent degradation of substrates. We propose a novel layer of regulation in substrate ubiquitination, via phosphorylation adjacent to the KEN motif, in APC/C-mediated targeting.
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Affiliation(s)
- Mingwei Min
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Ugo Mayor
- CIC bioGUNE, Bizkaia Technology Park, Building 801-A, Derio 48160, Spain
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| | - Catherine Lindon
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
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43
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Morrow ME, Kim MI, Ronau JA, Sheedlo MJ, White RR, Chaney J, Paul LN, Lill MA, Artavanis-Tsakonas K, Das C. Stabilization of an unusual salt bridge in ubiquitin by the extra C-terminal domain of the proteasome-associated deubiquitinase UCH37 as a mechanism of its exo specificity. Biochemistry 2013; 52:3564-78. [PMID: 23617878 PMCID: PMC3898853 DOI: 10.1021/bi4003106] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Ubiquitination is countered by a group of enzymes collectively called deubiquitinases (DUBs); ∼100 of them can be found in the human genome. One of the most interesting aspects of these enzymes is the ability of some members to selectively recognize specific linkage types between ubiquitin in polyubiquitin chains and their endo and exo specificity. The structural basis of exo-specific deubiquitination catalyzed by a DUB is poorly understood. UCH37, a cysteine DUB conserved from fungi to humans, is a proteasome-associated factor that regulates the proteasome by sequentially cleaving polyubiquitin chains from their distal ends, i.e., by exo-specific deubiquitination. In addition to the catalytic domain, the DUB features a functionally uncharacterized UCH37-like domain (ULD), presumed to keep the enzyme in an inhibited state in its proteasome-free form. Herein we report the crystal structure of two constructs of UCH37 from Trichinella spiralis in complex with a ubiquitin-based suicide inhibitor, ubiquitin vinyl methyl ester (UbVME). These structures show that the ULD makes direct contact with ubiquitin stabilizing a highly unusual intramolecular salt bridge between Lys48 and Glu51 of ubiquitin, an interaction that would be favored only with the distal ubiquitin but not with the internal ones in a Lys48-linked polyubiquitin chain. An inspection of 39 DUB-ubiquitin structures in the Protein Data Bank reveals the uniqueness of the salt bridge in ubiquitin bound to UCH37, an interaction that disappears when the ULD is deleted, as revealed in the structure of the catalytic domain alone bound to UbVME. The structural data are consistent with previously reported mutational data on the mammalian enzyme, which, together with the fact that the ULD residues that bind to ubiquitin are conserved, points to a similar mechanism behind the exo specificity of the human enzyme. To the best of our knowledge, these data provide the only structural example so far of how the exo specificity of a DUB can be determined by its noncatalytic domain. Thus, our data show that, contrary to its proposed inhibitory role, the ULD actually contributes to substrate recognition and could be a major determinant of the proteasome-associated function of UCH37. Moreover, our structures show that the unproductively oriented catalytic cysteine in the free enzyme is aligned correctly when ubiquitin binds, suggesting a mechanism for ubiquitin selectivity.
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Affiliation(s)
- Marie E. Morrow
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Myung-Il Kim
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Judith A. Ronau
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Michael J. Sheedlo
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Rhiannon R. White
- Division of Cell and Molecular Biology, Imperial College London, Sir Alexander Fleming Bldg, Imperial College Road, London, SW7 2AZ, UK
| | - Joseph Chaney
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Lake N. Paul
- Bindley Biosciences Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Markus A. Lill
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN, 47907, USA
| | - Katerina Artavanis-Tsakonas
- Division of Cell and Molecular Biology, Imperial College London, Sir Alexander Fleming Bldg, Imperial College Road, London, SW7 2AZ, UK
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA,To whom correspondence should be addressed: Chittaranjan Das, Brown Laboratory of Chemistry, 560 Oval Drive, West Lafayette, IN, 47907, (765)-494-5478, Fax: (765)-494-0239,
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