1
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Campos Alonso M, Knobeloch KP. In the moonlight: non-catalytic functions of ubiquitin and ubiquitin-like proteases. Front Mol Biosci 2024; 11:1349509. [PMID: 38455765 PMCID: PMC10919355 DOI: 10.3389/fmolb.2024.1349509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/05/2024] [Indexed: 03/09/2024] Open
Abstract
Proteases that cleave ubiquitin or ubiquitin-like proteins (UBLs) are critical players in maintaining the homeostasis of the organism. Concordantly, their dysregulation has been directly linked to various diseases, including cancer, neurodegeneration, developmental aberrations, cardiac disorders and inflammation. Given their potential as novel therapeutic targets, it is essential to fully understand their mechanisms of action. Traditionally, observed effects resulting from deficiencies in deubiquitinases (DUBs) and UBL proteases have often been attributed to the misregulation of substrate modification by ubiquitin or UBLs. Therefore, much research has focused on understanding the catalytic activities of these proteins. However, this view has overlooked the possibility that DUBs and UBL proteases might also have significant non-catalytic functions, which are more prevalent than previously believed and urgently require further investigation. Moreover, multiple examples have shown that either selective loss of only the protease activity or complete absence of these proteins can have different functional and physiological consequences. Furthermore, DUBs and UBL proteases have been shown to often contain domains or binding motifs that not only modulate their catalytic activity but can also mediate entirely different functions. This review aims to shed light on the non-catalytic, moonlighting functions of DUBs and UBL proteases, which extend beyond the hydrolysis of ubiquitin and UBL chains and are just beginning to emerge.
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Affiliation(s)
- Marta Campos Alonso
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Klaus-Peter Knobeloch
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- CIBSS—Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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2
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Luo VM, Shen C, Worme S, Bhagrath A, Simo-Cheyou E, Findlay S, Hébert S, Wai Lam Poon W, Aryanpour Z, Zhang T, Zahedi RP, Boulais J, Buchwald ZS, Borchers CH, Côté JF, Kleinman CL, Mandl JN, Orthwein A. The Deubiquitylase Otub1 Regulates the Chemotactic Response of Splenic B Cells by Modulating the Stability of the γ-Subunit Gng2. Mol Cell Biol 2024; 44:1-16. [PMID: 38270191 PMCID: PMC10829841 DOI: 10.1080/10985549.2023.2290434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 11/28/2023] [Indexed: 01/26/2024] Open
Abstract
The ubiquitin proteasome system performs the covalent attachment of lysine 48-linked polyubiquitin chains to substrate proteins, thereby targeting them for degradation, while deubiquitylating enzymes (DUBs) reverse this process. This posttranslational modification regulates key features both of innate and adaptative immunity, including antigen presentation, protein homeostasis and signal transduction. Here we show that loss of one of the most highly expressed DUBs, Otub1, results in changes in murine splenic B cell subsets, leading to a significant increase in marginal zone and transitional B cells and a concomitant decrease in follicular B cells. We demonstrate that Otub1 interacts with the γ-subunit of the heterotrimeric G protein, Gng2, and modulates its ubiquitylation status, thereby controlling Gng2 stability. Proximal mapping of Gng2 revealed an enrichment in partners associated with chemokine signaling, actin cytoskeleton and cell migration. In line with these findings, we show that Otub1-deficient B cells exhibit greater Ca2+ mobilization, F-actin polymerization and chemotactic responsiveness to Cxcl12, Cxcl13 and S1P in vitro, which manifests in vivo as altered localization of B cells within the spleen. Together, our data establishes Otub1 as a novel regulator of G-protein coupled receptor signaling in B cells, regulating their differentiation and positioning in the spleen.
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Affiliation(s)
- Vincent M. Luo
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
| | - Connie Shen
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
- McGill Research Centre for Complex Traits, McGill University, Montréal, Québec, Canada
| | - Samantha Worme
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Aanya Bhagrath
- McGill Research Centre for Complex Traits, McGill University, Montréal, Québec, Canada
- Department of Physiology, McGill University, Montréal, Québec, Canada
| | - Estelle Simo-Cheyou
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Steven Findlay
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Steven Hébert
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - William Wai Lam Poon
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Zahra Aryanpour
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
| | - Thomas Zhang
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
| | - René P. Zahedi
- Manitoba Centre for Proteomics & Systems Biology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- CancerCare Manitoba Research Institute, Winnipeg, Manitoba, Canada
| | - Jonathan Boulais
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Québec, Canada
| | - Zachary S. Buchwald
- Department of Radiation Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia, USA
| | - Christoph H. Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, McGill University, Montréal, Québec, Canada
- Gerald Bronfman Department of Oncology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Pathology, McGill University, Montreal, Québec, Canada
| | - Jean-Francois Côté
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Québec, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, Québec, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, Québec, Canada
- Département de Médecine (Programmes de Biologie Moléculaire), Université de Montréal, Montreal, Québec, Canada
| | - Claudia L. Kleinman
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Judith N. Mandl
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
- McGill Research Centre for Complex Traits, McGill University, Montréal, Québec, Canada
- Department of Physiology, McGill University, Montréal, Québec, Canada
| | - Alexandre Orthwein
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
- Department of Radiation Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia, USA
- Gerald Bronfman Department of Oncology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
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3
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Lemma B, Zhang D, Vamisetti GB, Wentz BG, Suga H, Brik A, Lubkowski J, Fushman D. Mechanism of selective recognition of Lys48-linked polyubiquitin by macrocyclic peptide inhibitors of proteasomal degradation. Nat Commun 2023; 14:7212. [PMID: 37938554 PMCID: PMC10632358 DOI: 10.1038/s41467-023-43025-4] [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: 03/11/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
Post-translational modification of proteins with polyubiquitin chains is a critical cellular signaling mechanism in eukaryotes with implications in various cellular states and processes. Unregulated ubiquitin-mediated protein degradation can be detrimental to cellular homeostasis, causing numerous diseases including cancers. Recently, macrocyclic peptides were developed that selectively target long Lysine-48-linked polyubiquitin chains (tetra-ubiquitin) to inhibit ubiquitin-proteasome system, leading to attenuation of tumor growth in vivo. However, structural determinants of the chain length and linkage selectivity by these cyclic peptides remained unclear. Here, we uncover the mechanism underlying cyclic peptide's affinity and binding selectivity by combining X-ray crystallography, solution NMR, and biochemical studies. We found that the peptide engages three consecutive ubiquitins that form a ring around the peptide and determined requirements for preferential selection of a specific trimer moiety in longer polyubiquitin chains. The structural insights gained from this work will guide the development of next-generation cyclic peptides with enhanced anti-cancer activity.
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Affiliation(s)
- Betsegaw Lemma
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Di Zhang
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Ganga B Vamisetti
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa, 3200008, Israel
| | - Bryan G Wentz
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa, 3200008, Israel.
| | - Jacek Lubkowski
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
| | - David Fushman
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA.
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4
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Deng H, Jia S, Tang J, Rong F, Xu C, Chen X, Wang Z, Zhu C, Sun X, Liao Q, Liu W, Li W, Xiao W, Liu X. SET7 methylates the deubiquitinase OTUB1 at Lys 122 to impair its binding to E2 enzyme UBC13 and relieve its suppressive role on ferroptosis. J Biol Chem 2023; 299:103054. [PMID: 36822329 PMCID: PMC10040876 DOI: 10.1016/j.jbc.2023.103054] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/23/2023] Open
Abstract
The deubiquitinating enzyme OTUB1 possesses canonical deubiquitinase (DUB) activity and noncanonical, catalytic-independent activity, which has been identified as an essential regulator of diverse physiological processes. Posttranslational modifications of OTUB1 affect both its DUB activity and its noncanonical activity of binding to the E2 ubiquitin-conjugation enzyme UBC13, but further investigation is needed to characterize the full inventory of modifications to OTUB1. Here, we demonstrate that SET7, a lysine monomethylase, directly interacts with OTUB1 to catalyze OTUB1 methylation at lysine 122. This modification does not affect DUB activity of OTUB1 but impairs its noncanonical activity, binding to UBC13. Moreover, we found using cell viability analysis and intracellular reactive oxygen species assay that SET7-mediated methylation of OTUB1 relieves its suppressive role on ferroptosis. Notably, the methylation-mimic mutant of OTUB1 not only loses the ability to bind to UBC13 but also relieves its suppressive role on Tert-Butyl hydroperoxide-induced cell death and Cystine starvation/Erastin-induced cellular reactive oxygen species. Collectively, our data identify a novel modification of OTUB1 that is critical for inhibiting its noncanonical activity.
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Affiliation(s)
- Hongyan Deng
- College of Life Science, Wuhan University, Wuhan, P. R. China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Shuke Jia
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China; University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Jinhua Tang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China; University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Fangjing Rong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China; University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Chenxi Xu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China; University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Xiaoyun Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China; University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Zixuan Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China; University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Chunchun Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China; University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Xueyi Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China; University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Qian Liao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China; University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Wen Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China; University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Wenhua Li
- College of Life Science, Wuhan University, Wuhan, P. R. China.
| | - Wuhan Xiao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China; University of Chinese Academy of Sciences, Beijing, P. R. China; Hubei Hongshan Laboratory, Wuhan, P. R. China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, P. R. China.
| | - Xing Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China; University of Chinese Academy of Sciences, Beijing, P. R. China; Hubei Hongshan Laboratory, Wuhan, P. R. China.
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5
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Fan G, Wang F, Chen Y, Zheng Q, Xiong J, Lv Q, Wu K, Xiong J, Wei L, Li D, Zhang J, Zhang W, Li F. The deubiquitinase OTUD1 noncanonically suppresses Akt activation through its N-terminal intrinsically disordered region. Cell Rep 2023; 42:111916. [PMID: 36640312 DOI: 10.1016/j.celrep.2022.111916] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 11/12/2022] [Accepted: 12/13/2022] [Indexed: 12/29/2022] Open
Abstract
Akt is commonly activated and serves as a valuable target in human cancer. In this study, OTUD1 is identified as an Akt-associated protein and is downregulated upon Akt activation. Ectopic OTUD1 inhibits Akt phosphorylation; however, its deubiquitinase activity contributes only slightly to this effect. A short peptide (OUN-36) located in the OTUD1 N-terminal intrinsically disordered region strongly binds to the Akt PH domain. The residues in the PH domain, which are required for PtdIns(3,4,5)P3 recognition, are also essential for OUN-36 binding. OUN-36 preferentially inhibits Akt-hyperactive tumor cells' proliferation and interferes with Akt cell membrane localization, presumably by disrupting PH domain-PIP3 interaction. Importantly, OUN-36-based therapy efficiently abrogates Akt feedback reactivation in response to MK-2206 treatment and sensitizes cancer cells to chemotherapy and immunotherapy. We therefore show a mechanism by which OTUD1 modulates Akt activity and suggest a potential peptide-based cancer therapeutic strategy implemented by targeting the Akt PH domain.
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Affiliation(s)
- Guanlan Fan
- Department of Gynecology and Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Fan Wang
- Department of Medical Genetics, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Yurou Chen
- Department of Gynecology and Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Qian Zheng
- Department of Medical Genetics, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Jie Xiong
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Qiongying Lv
- Department of Gynecology and Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Kejia Wu
- Department of Gynecology and Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Jiaqiang Xiong
- Department of Gynecology and Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Lei Wei
- Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Dongqing Li
- Department of Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Jiachen Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Wei Zhang
- Department of Gynecology and Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.
| | - Feng Li
- Department of Medical Genetics, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China; Hubei Provincial Key Laboratory of Allergy and Immunology, Wuhan 430071, China.
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6
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Seo SU, Woo SM, Kim MW, Lee EW, Min KJ, Kwon TK. Phosphorylation of OTUB1 at Tyr 26 stabilizes the mTORC1 component, Raptor. Cell Death Differ 2023; 30:82-93. [PMID: 35927303 PMCID: PMC9883261 DOI: 10.1038/s41418-022-01047-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 06/18/2022] [Accepted: 07/06/2022] [Indexed: 02/01/2023] Open
Abstract
Raptor plays a critical role in mTORC1 signaling. High expression of Raptor is associated with resistance of cancer cells to PI3K/mTOR inhibitors. Here, we found that OTUB1-stabilized Raptor in a non-canonical manner. Using biochemical assays, we found that the tyrosine 26 residue (Y26) of OTUB1 played a critical role in the interaction between OTUB1 and Raptor. Furthermore, non-receptor tyrosine kinases (Src and SRMS kinases) induced phosphorylation of OTUB1 at Y26, which stabilized Raptor. Interestingly, phosphorylation of OTUB1 at Y26 did not affect the stability of other OTUB1-targeted substrates. However, dephosphorylation of OTUB1 destabilized Raptor and sensitized cancer cells to anti-cancer drugs via mitochondrial reactive oxygen species-mediated mitochondrial dysfunction. Furthermore, we detected high levels of phospho-OTUB1 and Raptor in samples of patients with renal clear carcinoma. Our results suggested that regulation of OTUB1 phosphorylation may be an effective and selective therapeutic target for treating cancers via down-regulation of Raptor.
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Affiliation(s)
- Seung Un Seo
- Department of Immunology, School of Medicine, Keimyung University, Daegu, 42601, South Korea
| | - Seon Min Woo
- Department of Immunology, School of Medicine, Keimyung University, Daegu, 42601, South Korea
| | - Min Wook Kim
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, South Korea
| | - Eun-Woo Lee
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, South Korea.
- Department of Functional Genomics, University of Science and Technology (UST), Daejeon, 34141, South Korea.
| | - Kyoung-Jin Min
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu, 41061, South Korea.
| | - Taeg Kyu Kwon
- Department of Immunology, School of Medicine, Keimyung University, Daegu, 42601, South Korea.
- Center for Forensic Pharmaceutical Science, Keimyung University, Daegu, 42601, South Korea.
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7
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Gorka M, Magnussen HM, Kulathu Y. Chemical biology tools to study Deubiquitinases and Ubl proteases. Semin Cell Dev Biol 2022; 132:86-96. [PMID: 35216867 DOI: 10.1016/j.semcdb.2022.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 12/15/2022]
Abstract
The reversible attachment of ubiquitin (Ub) and ubiquitin like modifiers (Ubls) to proteins are crucial post-translational modifications (PTMs) for many cellular processes. Not only do cells possess hundreds of ligases to mediate substrate specific modification with Ub and Ubls, but they also have a repertoire of more than 100 dedicated enzymes for the specific removal of ubiquitin (Deubiquitinases or DUBs) and Ubl modifications (Ubl-specific proteases or ULPs). Over the past two decades, there has been significant progress in our understanding of how DUBs and ULPs function at a molecular level and many novel DUBs and ULPs, including several new DUB classes, have been identified. Here, the development of chemical tools that can bind and trap active DUBs has played a key role. Since the introduction of the first activity-based probe for DUBs in 1986, several innovations have led to the development of more sophisticated tools to study DUBs and ULPs. In this review we discuss how chemical biology has led to the development of activity-based probes and substrates that have been invaluable to the study of DUBs and ULPs. We summarise our currently available toolbox, highlight the main achievements and give an outlook of how these tools may be applied to gain a better understanding of the regulatory mechanisms of DUBs and ULPs.
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Affiliation(s)
- Magdalena Gorka
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Helge Magnus Magnussen
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Yogesh Kulathu
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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8
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Liu X, Deng H, Tang J, Wang Z, Zhu C, Cai X, Rong F, Chen X, Sun X, Jia S, Ouyang G, Li W, Xiao W. OTUB1 augments hypoxia signaling via its non-canonical ubiquitination inhibition of HIF-1α during hypoxia adaptation. Cell Death Dis 2022; 13:560. [PMID: 35732631 PMCID: PMC9217984 DOI: 10.1038/s41419-022-05008-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 05/27/2022] [Accepted: 06/08/2022] [Indexed: 01/21/2023]
Abstract
As a main regulator of cellular responses to hypoxia, the protein stability of hypoxia-inducible factor (HIF)-1α is strictly controlled by oxygen tension dependent of PHDs-catalyzed protein hydroxylation and pVHL complex-mediated proteasomal degradation. Whether HIF-1α protein stability as well as its activity can be further regulated under hypoxia is not well understood. In this study, we found that OTUB1 augments hypoxia signaling independent of PHDs/VHL and FIH. OTUB1 binds to HIF-1α and depletion of OTUB1 reduces endogenous HIF-1α protein under hypoxia. In addition, OTUB1 inhibits K48-linked polyubiquitination of HIF-1α via its non-canonical inhibition of ubiquitination activity. Furthermore, OTUB1 promotes hypoxia-induced glycolytic reprogramming for cellular metabolic adaptation. These findings define a novel regulation of HIF-1α under hypoxia and demonstrate that OTUB1-mediated HIF-1α stabilization positively regulates HIF-1α transcriptional activity and benefits cellular hypoxia adaptation.
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Affiliation(s)
- Xing Liu
- grid.429211.d0000 0004 1792 6029State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, PR China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 PR China ,grid.9227.e0000000119573309The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, 430072 PR China ,Hubei Hongshan Laboratory, Wuhan, 430070 PR China
| | - Hongyan Deng
- grid.49470.3e0000 0001 2331 6153College of Life Science, Wuhan University, Wuhan, 430072 PR China ,grid.49470.3e0000 0001 2331 6153Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072 PR China
| | - Jinhua Tang
- grid.429211.d0000 0004 1792 6029State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, PR China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 PR China
| | - Zixuan Wang
- grid.429211.d0000 0004 1792 6029State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, PR China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 PR China
| | - Chunchun Zhu
- grid.429211.d0000 0004 1792 6029State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, PR China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 PR China
| | - Xiaolian Cai
- grid.429211.d0000 0004 1792 6029State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, PR China ,grid.9227.e0000000119573309The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, 430072 PR China
| | - Fangjing Rong
- grid.429211.d0000 0004 1792 6029State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, PR China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 PR China
| | - Xiaoyun Chen
- grid.429211.d0000 0004 1792 6029State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, PR China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 PR China
| | - Xueyi Sun
- grid.429211.d0000 0004 1792 6029State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, PR China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 PR China
| | - Shuke Jia
- grid.429211.d0000 0004 1792 6029State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, PR China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 PR China
| | - Gang Ouyang
- grid.429211.d0000 0004 1792 6029State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, PR China ,grid.9227.e0000000119573309The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, 430072 PR China
| | - Wenhua Li
- grid.49470.3e0000 0001 2331 6153College of Life Science, Wuhan University, Wuhan, 430072 PR China ,grid.49470.3e0000 0001 2331 6153Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072 PR China
| | - Wuhan Xiao
- grid.429211.d0000 0004 1792 6029State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, PR China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 PR China ,grid.9227.e0000000119573309The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, 430072 PR China ,Hubei Hongshan Laboratory, Wuhan, 430070 PR China
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9
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Kumari R, Kumar R, Dey AK, Saha S, Maiti TK. S-Nitrosylation of OTUB1 Alters Its Stability and Ubc13 Binding. ACS Chem Neurosci 2022; 13:1517-1525. [PMID: 35500217 DOI: 10.1021/acschemneuro.1c00855] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
S-Nitrosylation is a reversible post-translational modification that regulates protein function involving the covalent attachment of the nitric oxide (NO) moiety to sulfhydryl residues of the protein. It is an important regulator in the cell signaling process under physiological conditions. However, the release of an excess amount of NO due to dysregulated NOS machinery causes aberrant S-nitrosylation of proteins, which affects protein folding, localization, and activity. Here, we have shown that OTUB1, a deubiquitinating enzyme, undergoes S-nitrosylation under redox stress conditions in vivo and in vitro. Previously, we have shown that OTUB1 forms an amyloid-like structure that promotes phosphorylation of α-synuclein and neuronal toxicity. However, the mechanistic insight into OTUB1 aggregation remains elusive. Here, we identified that OTUB1 undergoes S-nitrosylation in SH-SY5Y neuroblastoma cells under rotenone-induced stress, as well as excitotoxic conditions, and in rotenone-treated mouse brains. The in vitro S-nitrosylation of OTUB1 followed by mass-spectrometry analysis has identified cysteine-23 and cysteine-91 as S-nitrosylation sites. S-Nitrosylated OTUB1 (SNO-OTUB1) diminished its catalytic activity, impaired its native structure, promoted amyloid-like aggregation, and compromised its binding with Ubc13. Thus, our results demonstrated that nitrosylation of OTUB1 might play a crucial role in regulating the ubiquitin signaling and Parkinson's disease pathology.
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Affiliation(s)
- Raniki Kumari
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India
- Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, Odisha 751024, India
| | - Roshan Kumar
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India
| | - Amit Kumar Dey
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India
| | - Sandhini Saha
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India
| | - Tushar Kanti Maiti
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India
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10
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On the Study of Deubiquitinases: Using the Right Tools for the Job. Biomolecules 2022; 12:biom12050703. [PMID: 35625630 PMCID: PMC9139131 DOI: 10.3390/biom12050703] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 05/05/2022] [Accepted: 05/12/2022] [Indexed: 02/01/2023] Open
Abstract
Deubiquitinases (DUBs) have been the subject of intense scrutiny in recent years. Many of their diverse enzymatic mechanisms are well characterized in vitro; however, our understanding of these enzymes at the cellular level lags due to the lack of quality tool reagents. DUBs play a role in seemingly every biological process and are central to many human pathologies, thus rendering them very desirable and challenging therapeutic targets. This review aims to provide researchers entering the field of ubiquitination with knowledge of the pharmacological modulators and tool molecules available to study DUBs. A focus is placed on small molecule inhibitors, ubiquitin variants (UbVs), and activity-based probes (ABPs). Leveraging these tools to uncover DUB biology at the cellular level is of particular importance and may lead to significant breakthroughs. Despite significant drug discovery efforts, only approximately 15 chemical probe-quality small molecule inhibitors have been reported, hitting just 6 of about 100 DUB targets. UbV technology is a promising approach to rapidly expand the library of known DUB inhibitors and may be used as a combinatorial platform for structure-guided drug design.
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11
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Zhang JL, Du BB, Zhang DH, Li H, Kong LY, Fan GJ, Li YP, Li PC, Liang C, Wang Z, Yang LL, Hao ZY, Wu LM, Huang Z, Dong JZ, Zhang JY, Yao R, Wang SJ, Zhang YZ. OTUB1 alleviates NASH through inhibition of the TRAF6-ASK1 signaling pathways. Hepatology 2022; 75:1218-1234. [PMID: 34591986 DOI: 10.1002/hep.32179] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/09/2021] [Accepted: 09/22/2021] [Indexed: 12/26/2022]
Abstract
BACKGROUND AND AIMS NAFLD is considered as the hepatic manifestation of the metabolic syndrome, which includes insulin resistance, obesity and hyperlipidemia. NASH is a progressive stage of NAFLD with severe hepatic steatosis, hepatocyte death, inflammation, and fibrosis. Currently, no pharmacological interventions specifically tailored for NASH are approved. Ovarian tumor domain, ubiquitin aldehyde binding 1 (OTUB1), the founding member of deubiquitinases, regulates many metabolism-associated signaling pathways. However, the role of OTUB1 in NASH is unclarified. METHODS AND RESULTS We demonstrated that mice with Otub1 deficiency exhibited aggravated high-fat diet-induced and high-fat high-cholesterol (HFHC) diet-induced hyperinsulinemia and liver steatosis. Notably, hepatocyte-specific overexpression of Otub1 markedly alleviated HFHC diet-induced hepatic steatosis, inflammatory responses, and liver fibrosis. Mechanistically, we identified apoptosis signal-regulating kinase 1 (ASK1) as a key candidate target of OTUB1 through RNA-sequencing analysis and immunoblot analysis. Through immunoprecipitation-mass spectrometry analysis, we further found that OTUB1 directly bound to tumor necrosis factor receptor-associated factor 6 (TRAF6) and suppressed its lysine 63-linked polyubiquitination, thus inhibiting the activation of ASK1 and its downstream pathway. CONCLUSIONS OTUB1 is a key suppressor of NASH that inhibits polyubiquitinations of TRAF6 and attenuated TRAF6-mediated ASK1 activation. Targeting the OTUB1-TRAF6-ASK1 axis may be a promising therapeutic strategy for NASH.
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Affiliation(s)
- Jie-Lei Zhang
- Department of Endocrinologythe First Affiliated Hospital of Zhengzhou UniversityZhengzhou UniversityZhengzhouChina
| | - Bin-Bin Du
- Cardiovascular Hospitalthe First Affiliated Hospital of Zhengzhou UniversityZhengzhou UniversityZhengzhouChina
| | - Dian-Hong Zhang
- Cardiovascular Hospitalthe First Affiliated Hospital of Zhengzhou UniversityZhengzhou UniversityZhengzhouChina
| | - Huan Li
- Cardiovascular Hospitalthe First Affiliated Hospital of Zhengzhou UniversityZhengzhou UniversityZhengzhouChina
| | - Ling-Yao Kong
- Cardiovascular Hospitalthe First Affiliated Hospital of Zhengzhou UniversityZhengzhou UniversityZhengzhouChina
| | - Guang-Jian Fan
- Precision Research Center for Refractory Diseases, Institute for Clinical ResearchShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Ya-Peng Li
- Cardiovascular Hospitalthe First Affiliated Hospital of Zhengzhou UniversityZhengzhou UniversityZhengzhouChina
| | - Peng-Cheng Li
- Cardiovascular Hospitalthe First Affiliated Hospital of Zhengzhou UniversityZhengzhou UniversityZhengzhouChina
| | - Cui Liang
- Cardiovascular Hospitalthe First Affiliated Hospital of Zhengzhou UniversityZhengzhou UniversityZhengzhouChina
| | - Zheng Wang
- Cardiovascular Hospitalthe First Affiliated Hospital of Zhengzhou UniversityZhengzhou UniversityZhengzhouChina
| | - Lu-Lu Yang
- Cardiovascular Hospitalthe First Affiliated Hospital of Zhengzhou UniversityZhengzhou UniversityZhengzhouChina
| | - Zheng-Yang Hao
- Cardiovascular Hospitalthe First Affiliated Hospital of Zhengzhou UniversityZhengzhou UniversityZhengzhouChina
| | - Lei-Ming Wu
- Cardiovascular Hospitalthe First Affiliated Hospital of Zhengzhou UniversityZhengzhou UniversityZhengzhouChina
| | - Zhen Huang
- Cardiovascular Hospitalthe First Affiliated Hospital of Zhengzhou UniversityZhengzhou UniversityZhengzhouChina
| | - Jian-Zeng Dong
- Cardiovascular Hospitalthe First Affiliated Hospital of Zhengzhou UniversityZhengzhou UniversityZhengzhouChina
| | - Jin-Ying Zhang
- Cardiovascular Hospitalthe First Affiliated Hospital of Zhengzhou UniversityZhengzhou UniversityZhengzhouChina
| | - Rui Yao
- Cardiovascular Hospitalthe First Affiliated Hospital of Zhengzhou UniversityZhengzhou UniversityZhengzhouChina
| | - Shou-Jun Wang
- Department of Endocrinologythe First Affiliated Hospital of Zhengzhou UniversityZhengzhou UniversityZhengzhouChina
| | - Yan-Zhou Zhang
- Cardiovascular Hospitalthe First Affiliated Hospital of Zhengzhou UniversityZhengzhou UniversityZhengzhouChina
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12
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Toyobe M, Yakushiji F. Synthetic modifications of histones and their functional evaluation. Chem Asian J 2022; 17:e202200197. [PMID: 35489041 DOI: 10.1002/asia.202200197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/22/2022] [Indexed: 11/07/2022]
Abstract
Post-transrational modifications (PTMs) of histones play a key role in epigenetic regulation. Unraveling the roles of each epigenetic mark can provide new insights into their biological mechanisms. On the other hand, it is generally difficult to prepare homogeneously-modified histones/nucleosomes to investigate their specific functions. Therefore, synthetic approaches to acquire precisely mimicked histones/nucleosomes are in great demand, and further development of this research field is anticipated. In this review, synthetic strategies to modify histones/nucleosomes, including cysteine modifications, transformations of dehydroalanine residues and lysine acylation using a catalyst system, are cited. In addition, the functional evaluation of synthetically modified histones/nucleosomes is described.
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Affiliation(s)
- Moe Toyobe
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Fumika Yakushiji
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
- Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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13
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Ye D, Wang S, Wang X, Lin Y, Huang Y, Chi P. Overexpression of OTU domain-containing ubiquitin aldehyde-binding protein 1 exacerbates colorectal cancer malignancy by inhibiting protein degradation of β-Catenin via Ubiquitin-proteasome pathway. Bioengineered 2022; 13:9106-9116. [PMID: 35354355 PMCID: PMC9161894 DOI: 10.1080/21655979.2022.2057897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Although major advances were achieved in colorectal cancer (CRC) therapy, major concerns still remain on proper control of cancer metastasis and chemo-resistance in order to achieve satisfactory general treatment response. Previous studies suggested that OTUB1 (OTU domain-containing ubiquitin aldehyde-binding protein 1) serves as regulator of gene ubiquitination and participates in the pathogenesis of multiple malignancies. Therefore, to discover its molecular mechanism in CRC tumor growth and metastasis will contribute in CRC treatment strategy development. Clinical tissues and CRC cancer cell lines were utilized to evaluate OTUB1 expression pattern. Functional tests including cellular proliferation, migration and invasion, as well as chemo-resistance, etc., were evaluated to investigate the role of OTUB1/β-catenin regulatory pathway on CRC malignant biological behaviors. Both CRC tumor tissues and CRC cell lines exhibited promoted OTUB1 expression level. Subsequent experiments further suggested that OTUB1 promoted CRC malignancy by enhancing protein stability of β-catenin, via inhibition of its protein degradation by UPP pathway, which indicated its crucial role in enhancement of CRC tumor cellular proliferative and chemo-resistant capabilities. This study reported that OTUB1 exhibited novel pro-survival and pro-metastatic function by interaction of β-Catenin via Ubiquitin-proteasome pathway. Our research indicated that OTUB1/β-Catenin regulatory axis might be potential druggable target for CRC cancer patients’ treatment.
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Affiliation(s)
- Daoxiong Ye
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, China
| | - Sisi Wang
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, China
| | - Xiaojie Wang
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, China
| | - Yu Lin
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, China
| | - Ying Huang
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, China
| | - Pan Chi
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, China
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14
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Liu Q, Yan T, Tan X, Wei Z, Li Y, Sun Z, Zhang H, Chen J. Genome-Wide Identification and Gene Expression Analysis of the OTU DUB Family in Oryza sativa. Viruses 2022; 14:v14020392. [PMID: 35215984 PMCID: PMC8878984 DOI: 10.3390/v14020392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/03/2022] [Accepted: 02/11/2022] [Indexed: 12/10/2022] Open
Abstract
Ovarian tumor domain (OTU)-containing deubiquitinating enzymes (DUBs) are an essential DUB to maintain protein stability in plants and play important roles in plant growth development and stress response. However, there is little genome-wide identification and analysis of the OTU gene family in rice. In this study, we identified 20 genes of the OTU family in rice genome, which were classified into four groups based on the phylogenetic analysis. Their gene structures, conserved motifs and domains, chromosomal distribution, and cis elements in promoters were further studied. In addition, OTU gene expression patterns in response to plant hormone treatments, including SA, MeJA, NAA, BL, and ABA, were investigated by RT-qPCR analysis. The results showed that the expression profile of OsOTU genes exhibited plant hormone-specific expression. Expression levels of most of the rice OTU genes were significantly changed in response to rice stripe virus (RSV), rice black-streaked dwarf virus (RBSDV), Southern rice black-streaked dwarf virus (SRBSDV), and Rice stripe mosaic virus (RSMV). These results suggest that the rice OTU genes are involved in diverse hormone signaling pathways and in varied responses to virus infection, providing new insights for further functional study of OsOTU genes.
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Affiliation(s)
- Qiannan Liu
- College of Plant Protection, Northwest Agriculture and Forestry University, Yangling, Xianyang 712100, China; (Q.L.); (T.Y.); (X.T.)
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (Z.W.); (Y.L.); (Z.S.)
| | - Tingyun Yan
- College of Plant Protection, Northwest Agriculture and Forestry University, Yangling, Xianyang 712100, China; (Q.L.); (T.Y.); (X.T.)
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (Z.W.); (Y.L.); (Z.S.)
| | - Xiaoxiang Tan
- College of Plant Protection, Northwest Agriculture and Forestry University, Yangling, Xianyang 712100, China; (Q.L.); (T.Y.); (X.T.)
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (Z.W.); (Y.L.); (Z.S.)
| | - Zhongyan Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (Z.W.); (Y.L.); (Z.S.)
| | - Yanjun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (Z.W.); (Y.L.); (Z.S.)
| | - Zongtao Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (Z.W.); (Y.L.); (Z.S.)
| | - Hehong Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (Z.W.); (Y.L.); (Z.S.)
- Correspondence: (H.Z.); (J.C.)
| | - Jianping Chen
- College of Plant Protection, Northwest Agriculture and Forestry University, Yangling, Xianyang 712100, China; (Q.L.); (T.Y.); (X.T.)
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (Z.W.); (Y.L.); (Z.S.)
- Correspondence: (H.Z.); (J.C.)
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15
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Liao Y, Yang M, Wang K, Wang Y, Zhong B, Jiang N. Deubiquitinating enzyme OTUB1 in immunity and cancer: Good player or bad actor? Cancer Lett 2022; 526:248-258. [PMID: 34875341 DOI: 10.1016/j.canlet.2021.12.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 12/21/2022]
Abstract
OTU domain-containing ubiquitin aldehyde-binding proteins 1 (OTUB1) is the most important element of the deubiquitinase OTU superfamily, which has been identified as an essential regulator of diverse physiological processes, such as DNA damage repair and cytokines secretion. Recently, we found that the pro-carcinogenesis role of OTUB1 and the relationship between OTUB1 and immune response have gradually become the research hot-spot. OTUB1 regulates NK/CD8 T cell activation, autoimmune diseases, PD-L1 mediated immune evasion, viral or bacterial infection related immune response and the occurrence and progression of various cancers via deubiquitinating and stabilizing related proteins. This review provides a comprehensive description about the role and regulatory axis of OTUB1. We can explore the balance between immune response and defense via regulating the level of OTUB1, and targeting OTUB1 might restrain the progression of cancers. This review highlights the experimental evidence that OTUB1 is a feasible and potential therapeutic target against various cancers progression and immune diseases or disorder.
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Affiliation(s)
- Yihao Liao
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, 300211, China
| | - Mengyue Yang
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, 150000, China
| | - Keke Wang
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, 300211, China
| | - Youzhi Wang
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, 300211, China
| | - Boqiang Zhong
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, 300211, China
| | - Ning Jiang
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, 300211, China.
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16
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The Deubiquitinase OTUB1 Is a Key Regulator of Energy Metabolism. Int J Mol Sci 2022; 23:ijms23031536. [PMID: 35163456 PMCID: PMC8836018 DOI: 10.3390/ijms23031536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 11/17/2022] Open
Abstract
Dysregulated energy metabolism is a major contributor to a multitude of pathologies, including obesity and diabetes. Understanding the regulation of metabolic homeostasis is of utmost importance for the identification of therapeutic targets for the treatment of metabolically driven diseases. We previously identified the deubiquitinase OTUB1 as substrate for the cellular oxygen sensor factor-inhibiting HIF (FIH) with regulatory effects on cellular energy metabolism, but the physiological relevance of OTUB1 is unclear. Here, we report that the induced global deletion of OTUB1 in adult mice (Otub1 iKO) elevated energy expenditure, reduced age-dependent body weight gain, facilitated blood glucose clearance and lowered basal plasma insulin levels. The respiratory exchange ratio was maintained, indicating an unaltered nutrient oxidation. In addition, Otub1 deletion in cells enhanced AKT activity, leading to a larger cell size, higher ATP levels and reduced AMPK phosphorylation. AKT is an integral part of insulin-mediated signaling and Otub1 iKO mice presented with increased AKT phosphorylation following acute insulin administration combined with insulin hypersensitivity. We conclude that OTUB1 is an important regulator of metabolic homeostasis.
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17
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Zhu L, Zhang Q, Cordeiro CD, Banjade S, Sardana R, Mao Y, Emr SD. Adaptor linked K63 di-ubiquitin activates Nedd4/Rsp5 E3 ligase. eLife 2022; 11:77424. [PMID: 35770973 PMCID: PMC9282857 DOI: 10.7554/elife.77424] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Nedd4/Rsp5 family E3 ligases mediate numerous cellular processes, many of which require the E3 ligase to interact with PY motif containing adaptor proteins. Several arrestin-related trafficking adaptors (ARTs) of Rsp5 were self-ubiquitinated for activation, but the regulation mechanism remains elusive. Remarkably, we demonstrate that Art1, Art4, and Art5 undergo K63-linked di-ubiquitination by Rsp5. This modification enhances the plasma membrane recruitment of Rsp5 by Art1 or Art5 upon substrate induction, required for cargo protein ubiquitination. In agreement with these observations, we find that di-ubiquitin strengthens the interaction between the pombe orthologs of Rsp5 and Art1, Pub1, and Any1. Furthermore, we discover that the homologous to E6AP C-terminus (HECT) domain exosite protects the K63-linked di-ubiquitin on the adaptors from cleavage by the deubiquitination enzyme Ubp2. Together, our study uncovers a novel ubiquitination modification implemented by Rsp5 adaptor proteins, underscoring the regulatory mechanism of how adaptor proteins control the recruitment, and activity of Rsp5 for the turnover of membrane proteins.
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Affiliation(s)
- Lu Zhu
- Weill Institute of Cell and Molecular Biology, Cornell UniversityIthacaUnited States,Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Qing Zhang
- Weill Institute of Cell and Molecular Biology, Cornell UniversityIthacaUnited States,Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Ciro D Cordeiro
- Weill Institute of Cell and Molecular Biology, Cornell UniversityIthacaUnited States,Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Sudeep Banjade
- Weill Institute of Cell and Molecular Biology, Cornell UniversityIthacaUnited States,Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Richa Sardana
- Weill Institute of Cell and Molecular Biology, Cornell UniversityIthacaUnited States,Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Yuxin Mao
- Weill Institute of Cell and Molecular Biology, Cornell UniversityIthacaUnited States,Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Scott D Emr
- Weill Institute of Cell and Molecular Biology, Cornell UniversityIthacaUnited States,Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
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18
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Ruiz-Serrano A, Monné Rodríguez JM, Günter J, Sherman SPM, Jucht AE, Fluechter P, Volkova YL, Pfundstein S, Pellegrini G, Wagner CA, Schneider C, Wenger RH, Scholz CC. OTUB1 regulates lung development, adult lung tissue homeostasis, and respiratory control. FASEB J 2021; 35:e22039. [PMID: 34793600 DOI: 10.1096/fj.202100346r] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 09/17/2021] [Accepted: 10/28/2021] [Indexed: 12/30/2022]
Abstract
OTUB1 is one of the most highly expressed deubiquitinases, counter-regulating the two most abundant ubiquitin chain types. OTUB1 expression is linked to the development and progression of lung cancer and idiopathic pulmonary fibrosis in humans. However, the physiological function of OTUB1 is unknown. Here, we show that constitutive whole-body Otub1 deletion in mice leads to perinatal lethality by asphyxiation. Analysis of (single-cell) RNA sequencing and proteome data demonstrated that OTUB1 is expressed in all lung cell types with a particularly high expression during late-stage lung development (E16.5, E18.5). At E18.5, the lungs of animals with Otub1 deletion presented with increased cell proliferation that decreased saccular air space and prevented inhalation. Flow cytometry-based analysis of E18.5 lung tissue revealed that Otub1 deletion increased proliferation of major lung parenchymal and mesenchymal/other non-hematopoietic cell types. Adult mice with conditional whole-body Otub1 deletion (wbOtub1del/del ) also displayed increased lung cell proliferation in addition to hyperventilation and failure to adapt the respiratory pattern to hypoxia. On the molecular level, Otub1 deletion enhanced mTOR signaling in embryonic and adult lung tissues. Based on these results, we propose that OTUB1 is a negative regulator of mTOR signaling with essential functions for lung cell proliferation, lung development, adult lung tissue homeostasis, and respiratory regulation.
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Affiliation(s)
| | - Josep M Monné Rodríguez
- Laboratory for Animal Model Pathology (LAMP), Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - Julia Günter
- Institute of Physiology, University of Zurich, Zurich, Switzerland.,National Centre of Competence in Research 'Kidney.CH', Zurich, Switzerland
| | | | | | - Pascal Fluechter
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Yulia L Volkova
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | | | - Giovanni Pellegrini
- Laboratory for Animal Model Pathology (LAMP), Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - Carsten A Wagner
- Institute of Physiology, University of Zurich, Zurich, Switzerland.,National Centre of Competence in Research 'Kidney.CH', Zurich, Switzerland
| | | | - Roland H Wenger
- Institute of Physiology, University of Zurich, Zurich, Switzerland.,National Centre of Competence in Research 'Kidney.CH', Zurich, Switzerland
| | - Carsten C Scholz
- Institute of Physiology, University of Zurich, Zurich, Switzerland.,National Centre of Competence in Research 'Kidney.CH', Zurich, Switzerland
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19
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Koschel J, Nishanth G, Just S, Harit K, Kröger A, Deckert M, Naumann M, Schlüter D. OTUB1 prevents lethal hepatocyte necroptosis through stabilization of c-IAP1 during murine liver inflammation. Cell Death Differ 2021; 28:2257-2275. [PMID: 33712742 PMCID: PMC8257688 DOI: 10.1038/s41418-021-00752-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 01/25/2021] [Accepted: 02/04/2021] [Indexed: 01/31/2023] Open
Abstract
In bacterial and sterile inflammation of the liver, hepatocyte apoptosis is, in contrast to necroptosis, a common feature. The molecular mechanisms preventing hepatocyte necroptosis and the potential consequences of hepatocyte necroptosis are largely unknown. Apoptosis and necroptosis are critically regulated by the ubiquitination of signaling molecules but especially the regulatory function of deubiquitinating enzymes (DUBs) is imperfectly defined. Here, we addressed the role of the DUB OTU domain aldehyde binding-1 (OTUB1) in hepatocyte cell death upon both infection with the hepatocyte-infecting bacterium Listeria monocytogenes (Lm) and D-Galactosamine (DGal)/Tumor necrosis factor (TNF)-induced sterile inflammation. Combined in vivo and in vitro experiments comprising mice lacking OTUB1 specifically in liver parenchymal cells (OTUB1LPC-KO) and human OTUB1-deficient HepG2 cells revealed that OTUB1 prevented hepatocyte necroptosis but not apoptosis upon infection with Lm and DGal/TNF challenge. Lm-induced necroptosis in OTUB1LPC-KO mice resulted in increased alanine aminotransferase (ALT) and lactate dehydrogenase (LDH) release and rapid lethality. Treatment with the receptor-interacting serine/threonine-protein kinase (RIPK) 1 inhibitor necrostatin-1s and deletion of the pseudokinase mixed lineage kinase domain-like protein (MLKL) prevented liver damage and death of infected OTUB1LPC-KO mice. Mechanistically, OTUB1 reduced K48-linked polyubiquitination of the cellular inhibitor of apoptosis 1 (c-IAP1), thereby diminishing its degradation. In the absence of OTUB1, c-IAP1 degradation resulted in reduced K63-linked polyubiquitination and increased phosphorylation of RIPK1, RIPK1/RIPK3 necrosome formation, MLKL-phosphorylation and hepatocyte death. Additionally, OTUB1-deficiency induced RIPK1-dependent extracellular-signal-regulated kinase (ERK) activation and TNF production in Lm-infected hepatocytes. Collectively, these findings identify OTUB1 as a novel regulator of hepatocyte-intrinsic necroptosis and a critical factor for survival of bacterial hepatitis and TNF challenge.
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Affiliation(s)
- Josephin Koschel
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
- Institute of Experimental Internal Medicine, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Gopala Nishanth
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany.
- Institute of Medical Microbiology and Hospital Hygiene, Otto von Guericke University Magdeburg, Magdeburg, Germany.
| | - Sissy Just
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Kunjan Harit
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Andrea Kröger
- Institute of Medical Microbiology and Hospital Hygiene, Otto von Guericke University Magdeburg, Magdeburg, Germany
- Innate Immunity and Infection Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Martina Deckert
- Department of Neuropathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Michael Naumann
- Institute of Experimental Internal Medicine, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Dirk Schlüter
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany.
- Institute of Medical Microbiology and Hospital Hygiene, Otto von Guericke University Magdeburg, Magdeburg, Germany.
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.
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20
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Rossio V, Paulo JA, Chick J, Brasher B, Gygi SP, King RW. Proteomics of broad deubiquitylase inhibition unmasks redundant enzyme function to reveal substrates and assess enzyme specificity. Cell Chem Biol 2021; 28:487-502.e5. [PMID: 33417828 PMCID: PMC8052291 DOI: 10.1016/j.chembiol.2020.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/30/2020] [Accepted: 12/16/2020] [Indexed: 01/30/2023]
Abstract
Deubiquitylating enzymes (DUBs) counteract ubiquitylation to control stability or activity of substrates. Identification of DUB substrates is challenging because multiple DUBs can act on the same substrate, thwarting genetic approaches. Here, we circumvent redundancy by chemically inhibiting multiple DUBs simultaneously in Xenopus egg extract. We used quantitative mass spectrometry to identify proteins whose ubiquitylation or stability is altered by broad DUB inhibition, and confirmed their DUB-dependent regulation with human orthologs, demonstrating evolutionary conservation. We next extended this method to profile DUB specificity. By adding recombinant DUBs to extract where DUB activity was broadly inhibited, but ubiquitylation and degradation were active at physiological rates, we profiled the ability of DUBs to rescue degradation of these substrates. We found that USP7 has a unique ability to broadly antagonize degradation. Together, we present an approach to identify DUB substrates and characterize DUB specificity that overcomes challenges posed by DUB redundancy.
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Affiliation(s)
- Valentina Rossio
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Joel Chick
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Bradley Brasher
- Boston Biochem, a Bio-Techne Brand, Cambridge, MA 02139, USA
| | - Steven P Gygi
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Randall W King
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA.
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21
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Shin D, Bhattacharya A, Cheng YL, Alonso MC, Mehdipour AR, van der Heden van Noort GJ, Ovaa H, Hummer G, Dikic I. Bacterial OTU deubiquitinases regulate substrate ubiquitination upon Legionella infection. eLife 2020; 9:58277. [PMID: 33185526 PMCID: PMC7690952 DOI: 10.7554/elife.58277] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 11/12/2020] [Indexed: 12/16/2022] Open
Abstract
Legionella pneumophila causes a severe pneumonia known as Legionnaires' disease. During the infection, Legionella injects more than 300 effector proteins into host cells. Among them are enzymes involved in altering the host-ubiquitination system. Here, we identified two LegionellaOTU (ovarian tumor)-like deubiquitinases (LOT-DUBs; LotB [Lpg1621/Ceg23] and LotC [Lpg2529]). The crystal structure of the LotC catalytic core (LotC14-310) was determined at 2.4 Å. Unlike the classical OTU-family, the LOT-family shows an extended helical lobe between the Cys-loop and the variable loop, which defines them as a unique class of OTU-DUBs. LotB has an additional ubiquitin-binding site (S1'), which enables the specific cleavage of Lys63-linked polyubiquitin chains. By contrast, LotC only contains the S1 site and cleaves different species of ubiquitin chains. MS analysis of LotB and LotC identified different categories of host-interacting proteins and substrates. Together, our results provide new structural insights into bacterial OTU-DUBs and indicate distinct roles in host-pathogen interactions.
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Affiliation(s)
- Donghyuk Shin
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany.,Max Planck Institute of Biophysics, Frankfurt, Germany.,Department of Nano-Bioengineering, Incheon National University, Incheon, Republic of Korea
| | - Anshu Bhattacharya
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Yi-Lin Cheng
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Marta Campos Alonso
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | | | | | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, Netherlands
| | - Gerhard Hummer
- Max Planck Institute of Biophysics, Frankfurt, Germany.,Institute of Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany.,Max Planck Institute of Biophysics, Frankfurt, Germany
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22
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Zhang W, Qiu W. OTUB1 Recruits Tumor Infiltrating Lymphocytes and Is a Prognostic Marker in Digestive Cancers. Front Mol Biosci 2020; 7:212. [PMID: 33240928 PMCID: PMC7677501 DOI: 10.3389/fmolb.2020.00212] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 08/03/2020] [Indexed: 12/22/2022] Open
Abstract
Background The deubiquitinating enzyme (DUB) OTUB1 can regulate the process of ubiquitination, but the influence of OTUB1 on immunity, apoptosis, autophagy, and the prognosis of digestive cancers requires further exploration. Methods OTUB1 expression was analyzed with the Oncomine and TIMER database. Kaplan-Meier plotter was used to calculate the association between OTUB1 and clinical prognosis. The regulation of OTUB1 on cancer immunocyte infiltration was determined by the TIMER database. The interaction between OTUB1 and immune genes, gene expression profiling (GEP), key genes of apoptosis and autophagy were analyzed via GEPIA. Protein-protein interaction (PPI), gene expression profiling (GEP), and functional pathway enrichment were also performed with the STRING and Pathway Common databases, respectively. Results High OTUB1 expression was found in CHOL, LIHC, READ, ESCA, and COAD, which was significantly associated with the poorer OS of LIHC (HR = 2.07, 95% CI = 1.30-3.30, P = 0.002), with modifications by sex, stage, grade, and mutant burden. OTUB1 can promote the recruitment of B cells, CD8 + T cells, macrophages in ESCA, B cells, and neutrophils in LIHC. We determined a significant interaction between OTUB1 and USP8, RNF128, LRIG1, UBB, UBC, STAM2, RNF41, EGFR, RPS27A, and HGS by PPI. This functional pathway indicates the regulatory role of OTUB1on immune, apoptosis, and autophagy through its interaction with TP53 and ATG. Conclusions OTUB1 performed as a molecular indicator of poor prognosis in digestive cancers, regulated the infiltration of tumor immunocytes, and exerted a significant influence on apoptosis and autophagy. OTUB1 is a potential antitumor target for digestive tumors.
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Affiliation(s)
- Wenhao Zhang
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Wenlong Qiu
- Qilu Hospital, Shandong University, Jinan, China
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23
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Suresh HG, Pascoe N, Andrews B. The structure and function of deubiquitinases: lessons from budding yeast. Open Biol 2020; 10:200279. [PMID: 33081638 PMCID: PMC7653365 DOI: 10.1098/rsob.200279] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Protein ubiquitination is a key post-translational modification that regulates diverse cellular processes in eukaryotic cells. The specificity of ubiquitin (Ub) signalling for different bioprocesses and pathways is dictated by the large variety of mono-ubiquitination and polyubiquitination events, including many possible chain architectures. Deubiquitinases (DUBs) reverse or edit Ub signals with high sophistication and specificity, forming an integral arm of the Ub signalling machinery, thus impinging on fundamental cellular processes including DNA damage repair, gene expression, protein quality control and organellar integrity. In this review, we discuss the many layers of DUB function and regulation, with a focus on insights gained from budding yeast. Our review provides a framework to understand key aspects of DUB biology.
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Affiliation(s)
- Harsha Garadi Suresh
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Natasha Pascoe
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Brenda Andrews
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 3E1
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24
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Chatrin C, Gabrielsen M, Buetow L, Nakasone MA, Ahmed SF, Sumpton D, Sibbet GJ, Smith BO, Huang DT. Structural insights into ADP-ribosylation of ubiquitin by Deltex family E3 ubiquitin ligases. SCIENCE ADVANCES 2020; 6:eabc0418. [PMID: 32948590 PMCID: PMC7500938 DOI: 10.1126/sciadv.abc0418] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/28/2020] [Indexed: 05/07/2023]
Abstract
Cellular cross-talk between ubiquitination and other posttranslational modifications contributes to the regulation of numerous processes. One example is ADP-ribosylation of the carboxyl terminus of ubiquitin by the E3 DTX3L/ADP-ribosyltransferase PARP9 heterodimer, but the mechanism remains elusive. Here, we show that independently of PARP9, the conserved carboxyl-terminal RING and DTC (Deltex carboxyl-terminal) domains of DTX3L and other human Deltex proteins (DTX1 to DTX4) catalyze ADP-ribosylation of ubiquitin's Gly76 Structural studies reveal a hitherto unknown function of the DTC domain in binding NAD+ Deltex RING domain recruits E2 thioesterified with ubiquitin and juxtaposes it with NAD+ bound to the DTC domain to facilitate ADP-ribosylation of ubiquitin. This ubiquitin modification prevents its activation but is reversed by the linkage nonspecific deubiquitinases. Our study provides mechanistic insights into ADP-ribosylation of ubiquitin by Deltex E3s and will enable future studies directed at understanding the increasingly complex network of ubiquitin cross-talk.
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Affiliation(s)
- Chatrin Chatrin
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Mads Gabrielsen
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Lori Buetow
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Mark A Nakasone
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Syed F Ahmed
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - David Sumpton
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Gary J Sibbet
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Brian O Smith
- Institute of Molecular Cell and System Biology, University of Glasgow, Glasgow G12 8QQ, UK
| | - Danny T Huang
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK
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25
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Kitao T, Nagai H, Kubori T. Divergence of Legionella Effectors Reversing Conventional and Unconventional Ubiquitination. Front Cell Infect Microbiol 2020; 10:448. [PMID: 32974222 PMCID: PMC7472693 DOI: 10.3389/fcimb.2020.00448] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/21/2020] [Indexed: 02/05/2023] Open
Abstract
The intracellular bacterial pathogen Legionella pneumophila employs bacteria-derived effector proteins in a variety of functions to exploit host cellular systems. The ubiquitination machinery constitutes a crucial eukaryotic system for the regulation of numerous cellular processes, and is a representative target for effector-mediated bacterial manipulation. L. pneumophila transports over 300 effector proteins into host cells through its Dot/Icm type IV secretion system. Among these, several effector proteins have been found to function as ubiquitin ligases, including unprecedented enzymes that catalyze ubiquitination through unconventional mechanisms. Recent studies have identified many L. pneumophila effector proteins that can interfere with ubiquitination. These effectors include proteins that are distantly related to the ovarian tumor protein superfamily described as deubiquitinases (DUBs), which regulate important signaling cascades in human cells. Intriguingly, L. pneumophila DUBs are not limited to enzymes that exhibit canonical DUB activity. Some L. pneumophila DUBs can catalyze the cleavage of the unconventional linkage between ubiquitin and substrates. Furthermore, novel mechanisms have been found that adversely affect the function of specific ubiquitin ligases; for instance, effector-mediated posttranslational modifications of ubiquitin ligases result in the inhibition of their activity. In the context of L. pneumophila infection, the existence of enzymes that reverse ubiquitination primarily relates to a fine tuning of biogenesis and remodeling of the Legionella-containing vacuole as a replicative niche. The complexity of the effector arrays reflects sophisticated strategies that bacteria have adopted to adapt their host environment and enable their survival in host cells. This review summarizes the current state of knowledge on the divergent mechanisms of the L. pneumophila effectors that can reverse ubiquitination, which is mediated by other effectors as well as the host ubiquitin machinery.
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Affiliation(s)
- Tomoe Kitao
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Hiroki Nagai
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Japan
- G-CHAIN, Gifu University, Gifu, Japan
| | - Tomoko Kubori
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Japan
- G-CHAIN, Gifu University, Gifu, Japan
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26
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Cho J, Park J, Kim EE, Song EJ. Assay Systems for Profiling Deubiquitinating Activity. Int J Mol Sci 2020; 21:E5638. [PMID: 32781716 PMCID: PMC7460613 DOI: 10.3390/ijms21165638] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 01/22/2023] Open
Abstract
Deubiquitinating enzymes regulate various cellular processes, particularly protein degradation, localization, and protein-protein interactions. The dysregulation of deubiquitinating enzyme (DUB) activity has been linked to several diseases; however, the function of many DUBs has not been identified. Therefore, the development of methods to assess DUB activity is important to identify novel DUBs, characterize DUB selectivity, and profile dynamic DUB substrates. Here, we review various methods of evaluating DUB activity using cell lysates or purified DUBs, as well as the types of probes used in these methods. In addition, we introduce some techniques that can deliver DUB probes into the cells and cell-permeable activity-based probes to directly visualize and quantify DUB activity in live cells. This review could contribute to the development of DUB inhibitors by providing important information on the characteristics and applications of various probes used to evaluate and detect DUB activity in vitro and in vivo.
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Affiliation(s)
- Jinhong Cho
- Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (J.C.); (E.E.K.)
| | - Jinyoung Park
- Molecular Recognition Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea;
| | - Eunice EunKyeong Kim
- Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (J.C.); (E.E.K.)
| | - Eun Joo Song
- Graduate School of Pharmaceutical Sciences and College of Pharmacy, Ewha Womans University, Seoul 03760, Korea
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27
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Li T, Zou C. The Role of Deubiquitinating Enzymes in Acute Lung Injury and Acute Respiratory Distress Syndrome. Int J Mol Sci 2020; 21:E4842. [PMID: 32650621 PMCID: PMC7402294 DOI: 10.3390/ijms21144842] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/02/2020] [Accepted: 07/05/2020] [Indexed: 12/11/2022] Open
Abstract
Acute lung injury and acute respiratory distress syndrome (ALI/ARDS) are characterized by an inflammatory response, alveolar edema, and hypoxemia. ARDS occurs most often in the settings of pneumonia, sepsis, aspiration of gastric contents, or severe trauma. The prevalence of ARDS is approximately 10% in patients of intensive care. There is no effective remedy with mortality high at 30-40%. Most functional proteins are dynamic and stringently governed by ubiquitin proteasomal degradation. Protein ubiquitination is reversible, the covalently attached monoubiquitin or polyubiquitin moieties within the targeted protein can be removed by a group of enzymes called deubiquitinating enzymes (DUBs). Deubiquitination plays an important role in the pathobiology of ALI/ARDS as it regulates proteins critical in engagement of the alveolo-capillary barrier and in the inflammatory response. In this review, we provide an overview of how DUBs emerge in pathogen-induced pulmonary inflammation and related aspects in ALI/ARDS. Better understanding of deubiquitination-relatedsignaling may lead to novel therapeutic approaches by targeting specific elements of the deubiquitination pathways.
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Affiliation(s)
| | - Chunbin Zou
- Division of Pulmonary, Allergy, Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA;
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28
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Sivakumar D, Kumar V, Naumann M, Stein M. Activation and selectivity of OTUB-1 and OTUB-2 deubiquitinylases. J Biol Chem 2020; 295:6972-6982. [PMID: 32265297 DOI: 10.1074/jbc.ra120.013073] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/06/2020] [Indexed: 12/16/2022] Open
Abstract
The ovarian tumor domain (OTU) deubiquitinylating cysteine proteases OTUB1 and OTUB2 (OTU ubiquitin aldehyde binding 1 and 2) are representative members of the OTU subfamily of deubiquitinylases. Deubiquitinylation critically regulates a multitude of important cellular processes, such as apoptosis, cell signaling, and growth. Moreover, elevated OTUB expression has been observed in various cancers, including glioma, endometrial cancer, ovarian cancer, and breast cancer. Here, using molecular dynamics simulation approaches, we found that both OTUB1 and OTUB2 display a catalytic triad characteristic of proteases but differ in their configuration and protonation states. The OTUB1 protein had a prearranged catalytic site, with strong electrostatic interactions between the active-site residues His265 and Asp267 In OTUB2, however, the arrangement of the catalytic triad was different. In the absence of ubiquitin, the neutral states of the catalytic-site residues in OTUB2 were more stable, resulting in larger distances between these residues. Only upon ubiquitin binding did the catalytic triad in OTUB2 rearrange and bring the active site into a catalytically feasible state. An analysis of water access channels revealed only a few diffusion trajectories for the catalytically active form of OTUB1, whereas in OTUB2 the catalytic site was solvent-accessible, and a larger number of water molecules reached and left the binding pocket. Interestingly, in OTUB2, the catalytic residues His224 and Asn226 formed a stable hydrogen bond. We propose that the observed differences in activation kinetics, protonation states, water channels, and active-site accessibility between OTUB1 and OTUB2 may be relevant for the selective design of OTU inhibitors.
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Affiliation(s)
- Dakshinamurthy Sivakumar
- Max Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, 39106 Magdeburg, Germany
| | - Vikash Kumar
- Max Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, 39106 Magdeburg, Germany.,Institute of Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Michael Naumann
- Institute of Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Matthias Stein
- Max Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, 39106 Magdeburg, Germany
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29
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Abstract
OTUB1 is a highly expressed cysteine protease that specifically cleaves K48-linked polyubiquitin chains. This unique deubiquitinating enzyme (DUB) can bind to a subset of E2 ubiquitin conjugating enzymes, forming complexes in which the two enzymes can regulate one another's activity. OTUB1 can noncatalytically suppress the ubiquitin conjugating activity of its E2 partners by sequestering the charged E2∼Ub thioester and preventing ubiquitin transfer. The same E2 enzymes, when uncharged, can stimulate the DUB activity of OTUB1 in vitro, although the importance of OTUB1 stimulation in vivo remains unclear. To assess the potential balance between these activities that might occur in cells, we characterized the kinetics and thermodynamics governing the formation and activity of OTUB1:E2 complexes. We show that both stimulation of OTUB1 by E2 enzymes and noncatalytic inhibition of E2 enzymes by OTUB1 occur at physiologically relevant concentrations of both partners. Whereas E2 partners differ in their ability to stimulate OTUB1 activity, we find that this variability is not correlated with the affinity of each E2 for OTUB1. In addition to UBE2N and the UBE2D isoforms, we find that OTUB1 inhibits the polyubiquitination activity of all three UBE2E enzymes, UBE2E1, UBE2E2, and UBE2E3. Interestingly, although OTUB1 also inhibits the auto-monoubiquitination and autopolyubiquitination activity of UBE2E1 and UBE2E2, it is unable to suppress autoubiquitination by UBE2E3. Our quantitative analysis provides a basis for further exploring the biological roles of OTUB1:E2 complexes in cells.
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Affiliation(s)
- Lauren T. Que
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21210-2185 USA
| | - Marie E. Morrow
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21210-2185 USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21210-2185 USA
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30
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Jahan AS, Biquand E, Muñoz-Moreno R, Le Quang A, Mok CKP, Wong HH, Teo QW, Valkenburg SA, Chin AWH, Man Poon LL, Te Velthuis A, García-Sastre A, Demeret C, Sanyal S. OTUB1 Is a Key Regulator of RIG-I-Dependent Immune Signaling and Is Targeted for Proteasomal Degradation by Influenza A NS1. Cell Rep 2020; 30:1570-1584.e6. [PMID: 32023470 DOI: 10.1016/j.celrep.2020.01.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 10/21/2019] [Accepted: 01/02/2020] [Indexed: 12/16/2022] Open
Abstract
Deubiquitylases (DUBs) regulate critical signaling pathways at the intersection of host immunity and viral pathogenesis. Although RIG-I activation is heavily dependent on ubiquitylation, systematic analyses of DUBs that regulate this pathway have not been performed. Using a ubiquitin C-terminal electrophile, we profile DUBs that function during influenza A virus (IAV) infection and isolate OTUB1 as a key regulator of RIG-I-dependent antiviral responses. Upon infection, OTUB1 relocalizes from the nucleus to mitochondrial membranes together with RIG-I, viral PB2, and NS1. Its expression depends on competing effects of interferon stimulation and IAV-triggered degradation. OTUB1 activates RIG-I via a dual mechanism of K48 polyubiquitin hydrolysis and formation of an E2-repressive complex with UBCH5c. We reconstitute this mechanism in a cell-free system comprising [35S]IRF3, purified RIG-I, mitochondrial membranes, and cytosol expressing OTUB1 variants. A range of IAV NS1 proteins trigger proteasomal degradation of OTUB1, antagonizing the RIG-I signaling cascade and antiviral responses.
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Affiliation(s)
- Akhee Sabiha Jahan
- HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong; School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Elise Biquand
- Molecular Genetics of RNA Viruses, CNRS UMR 3569, Université de Paris, Institut Pasteur, Paris, France
| | - Raquel Muñoz-Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Agathe Le Quang
- HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong; School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Chris Ka-Pun Mok
- HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong; School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Ho Him Wong
- HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong; School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Qi Wen Teo
- HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong; School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Sophie A Valkenburg
- HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong; School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Alex W H Chin
- School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Leo Lit Man Poon
- School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Artejan Te Velthuis
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA; Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Caroline Demeret
- Molecular Genetics of RNA Viruses, CNRS UMR 3569, Université de Paris, Institut Pasteur, Paris, France
| | - Sumana Sanyal
- HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong; School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong; School of Biomedical Sciences, LKS Faculty of Medicine, University of Hong Kong, Hong Kong.
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Kumari R, Kumar R, Kumar S, Singh AK, Hanpude P, Jangir D, Maiti TK. Amyloid aggregates of the deubiquitinase OTUB1 are neurotoxic, suggesting that they contribute to the development of Parkinson's disease. J Biol Chem 2020; 295:3466-3484. [PMID: 32005664 DOI: 10.1074/jbc.ra119.009546] [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] [Received: 05/29/2019] [Revised: 01/18/2020] [Indexed: 01/10/2023] Open
Abstract
Parkinson's disease (PD) is a multifactorial malady and the second most common neurodegenerative disorder, characterized by loss of dopaminergic neurons in the midbrain. A hallmark of PD pathology is the formation of intracellular protein inclusions, termed Lewy bodies (LBs). Recent MS studies have shown that OTU deubiquitinase ubiquitin aldehyde-binding 1 (OTUB1), a deubiquitinating enzyme of the OTU family, is enriched together with α-synuclein in LBs from individuals with PD and is also present in amyloid plaques associated with Alzheimer's disease. In the present study, using mammalian cell cultures and a PD mouse model, along with CD spectroscopy, atomic force microscopy, immunofluorescence-based imaging, and various biochemical assays, we demonstrate that after heat-induced protein aggregation, OTUB1 reacts strongly with both anti-A11 and anti-osteocalcin antibodies, detecting oligomeric, prefibrillar structures or fibrillar species of amyloidogenic proteins, respectively. Further, recombinant OTUB1 exhibited high thioflavin-T and Congo red binding and increased β-sheet formation upon heat induction. The oligomeric OTUB1 aggregates were highly cytotoxic, characteristic of many amyloid proteins. OTUB1 formed inclusions in neuronal cells and co-localized with thioflavin S and with α-synuclein during rotenone-induced stress. It also co-localized with the disease-associated variant pS129-α-synuclein in rotenone-exposed mouse brains. Interestingly, OTUB1 aggregates were also associated with severe cytoskeleton damage, rapid internalization inside the neuronal cells, and mitochondrial damage, all of which contribute to neurotoxicity. In conclusion, the results of our study indicate that OTUB1 may contribute to LB pathology through its amyloidogenic properties.
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Affiliation(s)
- Raniki Kumari
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, Faridabad 121001, India; Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, Odisha 751024, India
| | - Roshan Kumar
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, Faridabad 121001, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Sanjay Kumar
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, Faridabad 121001, India; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Abhishek Kumar Singh
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, Faridabad 121001, India
| | - Pranita Hanpude
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, Faridabad 121001, India
| | - Deepak Jangir
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, Faridabad 121001, India
| | - Tushar Kanti Maiti
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, Faridabad 121001, India.
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32
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The function and regulation of OTU deubiquitinases. Front Med 2019; 14:542-563. [PMID: 31884527 DOI: 10.1007/s11684-019-0734-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 10/31/2019] [Indexed: 12/19/2022]
Abstract
Post-translational modification of cellular proteins by ubiquitin regulates numerous cellular processes, including cell division, immune responses, and apoptosis. Ubiquitin-mediated control over these processes can be reversed by deubiquitinases (DUBs), which remove ubiquitin from target proteins and depolymerize polyubiquitin chains. Recently, much progress has been made in the DUBs. In humans, the ovarian tumor protease (OTU) subfamily of DUBs includes 16 members, most of which mediate cell signaling cascades. These OTUs show great variation in structure and function, which display a series of mechanistic features. In this review, we provide a comprehensive analysis of current progress in character, structure and function of OTUs, such as the substrate specificity and catalytic activity regulation. Then we discuss the relationship between some diseases and OTUs. Finally, we summarize the structure of viral OTUs and their function in immune escape and viral survival. Despite the challenges, OTUs might provide new therapeutic targets, due to their involvement in key regulatory processes.
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33
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High-affinity free ubiquitin sensors for quantifying ubiquitin homeostasis and deubiquitination. Nat Methods 2019; 16:771-777. [PMID: 31308549 PMCID: PMC6669086 DOI: 10.1038/s41592-019-0469-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 05/21/2019] [Indexed: 02/07/2023]
Abstract
Ubiquitin (Ub) conjugation is an essential post-translational modification that affects nearly all proteins in eukaryotes. The functions and mechanisms of ubiquitination are areas of extensive study, and yet the dynamics and regulation of even free (i.e., unconjugated) Ub are poorly understood. A major impediment has been the lack of simple and robust techniques to quantify Ub levels in cells and to monitor Ub release from conjugates. Here we describe avidity-based fluorescent sensors that address this need. The sensors bind specifically to free Ub, have Kd values down to 60 pM, and, in concert with a newly developed workflow, allow us to distinguish and quantify the pools of free, protein-conjugated, and thioesterified forms of Ub from cell lysates. Alternatively, free Ub in fixed cells can be visualized microscopically by staining with a sensor. Real-time assays using the sensors afford unprecedented flexibility and precision to measure deubiquitination of virtually any (poly)Ub conjugate.
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Pickel C, Günter J, Ruiz-Serrano A, Spielmann P, Fabrizio JA, Wolski W, Peet DJ, Wenger RH, Scholz CC. Oxygen-dependent bond formation with FIH regulates the activity of the client protein OTUB1. Redox Biol 2019; 26:101265. [PMID: 31299612 PMCID: PMC6624438 DOI: 10.1016/j.redox.2019.101265] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/28/2019] [Accepted: 06/30/2019] [Indexed: 12/30/2022] Open
Abstract
Protein:protein interactions are the basis of molecular communication and are usually of transient non-covalent nature, while covalent interactions other than ubiquitination are rare. For cellular adaptations, the cellular oxygen and peroxide sensor factor inhibiting HIF (FIH) confers oxygen and oxidant stress sensitivity to the hypoxia inducible factor (HIF) by asparagine hydroxylation. We investigated whether FIH contributes to hypoxia adaptation also through other mechanisms and identified a hypoxia sensitive, likely covalent, bond formation by FIH with several client proteins, including the deubiquitinase ovarian tumor domain containing ubiquitin aldehyde binding protein 1 (OTUB1). Biochemical analyses were consistent with a co-translational amide bond formation between FIH and OTUB1, occurring within mammalian and bacterial cells but not between separately purified proteins. Bond formation is catalysed by FIH and highly dependent on oxygen availability in the cellular microenvironment. Within cells, a heterotrimeric complex is formed, consisting of two FIH and one covalently linked OTUB1. Complexation of OTUB1 by FIH regulates OTUB1 deubiquitinase activity. Our findings reveal an alternative mechanism for hypoxia adaptation with remarkably high oxygen sensitivity, mediated through covalent protein-protein interactions catalysed by an asparagine modifying dioxygenase. FIH forms a (likely amide) bond with client proteins. Bond formation is highly hypoxia sensitive and occurs co-translationally. FIH forms a heterotrimer with the client protein OTUB1 (FIH2OTUB11). Complex formation between OTUB1 and FIH regulates OTUB1 deubiquitinase activity. Bond formation by hydroxylases is an alternative mechanism for hypoxia adaptation.
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Affiliation(s)
- Christina Pickel
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland
| | - Julia Günter
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland; National Centre of Competence in Research 'Kidney.CH', Switzerland
| | | | - Patrick Spielmann
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland
| | | | - Witold Wolski
- Functional Genomics Center Zurich, University of Zurich, 8057, Zurich, Switzerland
| | - Daniel J Peet
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Roland H Wenger
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland; National Centre of Competence in Research 'Kidney.CH', Switzerland.
| | - Carsten C Scholz
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland; National Centre of Competence in Research 'Kidney.CH', Switzerland.
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The deubiquitinase Otub1 controls the activation of CD8 + T cells and NK cells by regulating IL-15-mediated priming. Nat Immunol 2019; 20:879-889. [PMID: 31182807 PMCID: PMC6588407 DOI: 10.1038/s41590-019-0405-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 04/18/2019] [Indexed: 01/01/2023]
Abstract
CD8 T cells and natural killer (NK) cells, central cellular components of immune responses against pathogens and cancer, rely on IL-15 for homeostasis. Here we show that IL-15 also mediates homeostatic priming of CD8 T cells for antigen-stimulated activation, which is controlled by a deubiquitinase, Otub1. IL-15 mediates membrane recruitment of Otub1, which inhibits ubiquitin-dependent activation of AKT, a pivotal kinase for T cell activation and metabolism. Otub1 deficiency in mice causes aberrant responses of CD8 T cells to IL-15, rendering naive CD8 T cells hyper-sensitive to antigen stimulation characterized by enhanced metabolic reprograming and effector functions. Otub1 also controls the maturation and activation of NK cells. Consistently, Otub1 deletion profoundly enhances anticancer immunity through unleashing the activity of CD8 T cells and NK cells. These findings suggest that Otub1 controls the activation of CD8 T cells and NK cells by functioning as a checkpoint of IL-15-mediated priming.
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Wang X, Mulas F, Yi W, Brunn A, Nishanth G, Just S, Waisman A, Brück W, Deckert M, Schlüter D. OTUB1 inhibits CNS autoimmunity by preventing IFN-γ-induced hyperactivation of astrocytes. EMBO J 2019; 38:embj.2018100947. [PMID: 30944096 DOI: 10.15252/embj.2018100947] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 02/20/2019] [Accepted: 02/28/2019] [Indexed: 01/31/2023] Open
Abstract
Astrocytes are critical regulators of neuroinflammation in multiple sclerosis (MS) and its animal model experimental autoimmune encephalomyelitis (EAE). Growing evidence indicates that ubiquitination of signaling molecules is an important cell-intrinsic mechanism governing astrocyte function during MS and EAE Here, we identified an upregulation of the deubiquitinase OTU domain, ubiquitin aldehyde binding 1 (OTUB1) in astrocytes during MS and EAE Mice with astrocyte-specific OTUB1 ablation developed more severe EAE due to increased leukocyte accumulation, proinflammatory gene transcription, and demyelination in the spinal cord as compared to control mice. OTUB1-deficient astrocytes were hyperactivated in response to IFN-γ, a fingerprint cytokine of encephalitogenic T cells, and produced more proinflammatory cytokines and chemokines than control astrocytes. Mechanistically, OTUB1 inhibited IFN-γ-induced Janus kinase (JAK)/signal transducer and activator of transcription (STAT) signaling by K48 deubiquitination and stabilization of the JAK2 inhibitor suppressor of cytokine signaling 1 (SOCS1). Thus, astrocyte-specific OTUB1 is a critical inhibitor of neuroinflammation in CNS autoimmunity.
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Affiliation(s)
- Xu Wang
- Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University Magdeburg, Magdeburg, Germany .,Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Floriana Mulas
- Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.,Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Wenjing Yi
- Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.,Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Anna Brunn
- Department of Neuropathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Gopala Nishanth
- Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.,Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Sissy Just
- Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.,Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Ari Waisman
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Wolfgang Brück
- Institute of Neuropathology, University Medical Center Göttingen, Göttingen, Germany
| | - Martina Deckert
- Department of Neuropathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Dirk Schlüter
- Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University Magdeburg, Magdeburg, Germany .,Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany.,Organ-specific Immune Regulation, Helmholtz-Center for Infection Research, Braunschweig, Germany
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USP15 Participates in Hepatitis C Virus Propagation through Regulation of Viral RNA Translation and Lipid Droplet Formation. J Virol 2019; 93:JVI.01708-18. [PMID: 30626683 DOI: 10.1128/jvi.01708-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 12/23/2018] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) utilizes cellular factors for efficient propagation. Ubiquitin is covalently conjugated to the substrate to alter its stability or to modulate signal transduction. In this study, we examined the importance of ubiquitination for HCV propagation. We found that inhibition of deubiquitinating enzymes (DUBs) or overexpression of nonspecific DUBs impaired HCV replication, suggesting that ubiquitination regulates HCV replication. To identify specific DUBs involved in HCV propagation, we set up RNA interference (RNAi) screening against DUBs and successfully identified ubiquitin-specific protease 15 (USP15) as a novel host factor for HCV propagation. Our studies showed that USP15 is involved in translation of HCV RNA and production of infectious HCV particles. In addition, deficiency of USP15 in human hepatic cell lines (Huh7 and Hep3B/miR-122 cells) but not in a nonhepatic cell line (293T cells) impaired HCV propagation, suggesting that USP15 participates in HCV propagation through the regulation of hepatocyte-specific functions. Moreover, we showed that loss of USP15 had no effect on innate immune responses in vitro and in vivo We also found that USP15-deficient Huh7 cells showed reductions in the amounts of lipid droplets (LDs), and the addition of palmitic acids restored the production of infectious HCV particles. Taken together, these data suggest that USP15 participates in HCV propagation by regulating the translation of HCV RNA and the formation of LDs.IMPORTANCE Although ubiquitination has been shown to play important roles in the HCV life cycle, the roles of deubiquitinating enzymes (DUBs), which cleave ubiquitin chains from their substrates, in HCV propagation have not been investigated. Here, we identified USP15 as a DUB regulating HCV propagation. USP15 showed no interaction with viral proteins and no participation in innate immune responses. Deficiency of USP15 in Huh7 cells resulted in suppression of the translation of HCV RNA and reduction in the amounts of lipid droplets, and the addition of fatty acids partially restored the production of infectious HCV particles. These data suggest that USP15 participates in HCV propagation in hepatic cells through the regulation of viral RNA translation and lipid metabolism.
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Bialas J, Boehm AN, Catone N, Aichem A, Groettrup M. The ubiquitin-like modifier FAT10 stimulates the activity of deubiquitylating enzyme OTUB1. J Biol Chem 2019; 294:4315-4330. [PMID: 30718280 DOI: 10.1074/jbc.ra118.005406] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 01/16/2019] [Indexed: 11/06/2022] Open
Abstract
The deubiquitylation of target proteins is mediated by deubiquitylating enzymes (DUB) such as OTUB1, which plays an important role in immune response, cell cycle progression, and DNA repair. Within these processes, OTUB1 reduces the ubiquitylation of target proteins in two distinct ways, either by using its catalytic DUB activity or in a noncatalytic manner by inhibiting the E2-conjugating enzyme. Here, we show that the ubiquitin-like modifier FAT10 regulates OTUB1 stability and functionality in different ways. Covalent FAT10ylation of OTUB1 resulted in its proteasomal degradation, whereas a noncovalent interaction stabilized OTUB1. We provide evidence that OTUB1 interacts directly with FAT10 and the E2-conjugating enzyme USE1. This interaction strongly stimulated OTUB1 DUB activity toward Lys-48-linked diubiquitin. Furthermore, the noncovalent interaction between FAT10 and OTUB1 not only enhanced its isopeptidase activity toward Lys-48-linked ubiquitin moieties but also strengthened its noncatalytic activity in reducing Lys-63 polyubiquitylation of its target protein TRAF3 (TNF receptor-associated factor 3). Additionally, the cellular clearance of overall polyubiquitylation by OTUB1 was strongly stimulated through the presence of FAT10. The addition of FAT10 also led to an increased interaction between OTUB1 and its cognate E2 UbcH5B, implying a function of FAT10 in the inhibition of polyubiquitylation. Overall, these data indicate that FAT10 not only plays a role in covalent modification, leading its substrates to proteasomal degradation, but also regulates the stability and functionality of target proteins by interacting in a noncovalent manner. FAT10 is thereby able to exert a major influence on ubiquitylation processes.
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Affiliation(s)
- Johanna Bialas
- From the Division of Immunology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany and.,the Biotechnology Institute Thurgau at the University of Konstanz, 8280 Kreuzlingen, Switzerland
| | - Annika N Boehm
- From the Division of Immunology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany and.,the Biotechnology Institute Thurgau at the University of Konstanz, 8280 Kreuzlingen, Switzerland
| | - Nicola Catone
- the Biotechnology Institute Thurgau at the University of Konstanz, 8280 Kreuzlingen, Switzerland
| | - Annette Aichem
- From the Division of Immunology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany and .,the Biotechnology Institute Thurgau at the University of Konstanz, 8280 Kreuzlingen, Switzerland
| | - Marcus Groettrup
- From the Division of Immunology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany and.,the Biotechnology Institute Thurgau at the University of Konstanz, 8280 Kreuzlingen, Switzerland
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Dzimianski JV, Beldon BS, Daczkowski CM, Goodwin OY, Scholte FEM, Bergeron É, Pegan SD. Probing the impact of nairovirus genomic diversity on viral ovarian tumor domain protease (vOTU) structure and deubiquitinase activity. PLoS Pathog 2019; 15:e1007515. [PMID: 30629698 PMCID: PMC6343935 DOI: 10.1371/journal.ppat.1007515] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/23/2019] [Accepted: 12/09/2018] [Indexed: 01/27/2023] Open
Abstract
Post-translational modification of host and viral proteins by ubiquitin (Ub) and Ub-like proteins, such as interferon stimulated gene product 15 (ISG15), plays a key role in response to infection. Viruses have been increasingly identified that contain proteases possessing deubiquitinase (DUB) and/or deISGylase functions. This includes viruses in the Nairoviridae family that encode a viral homologue of the ovarian tumor protease (vOTU). vOTU activity was recently demonstrated to be critical for replication of the often-fatal Crimean-Congo hemorrhagic fever virus, with DUB activity suppressing the type I interferon responses and deISGylase activity broadly removing ISG15 conjugated proteins. There are currently about 40 known nairoviruses classified into fourteen species. Recent genomic characterization has revealed a high degree of diversity, with vOTUs showing less than 25% amino acids identities within the family. Previous investigations have been limited to only a few closely related nairoviruses, leaving it unclear what impact this diversity has on vOTU function. To probe the effects of vOTU diversity on enzyme activity and specificity, we assessed representative vOTUs spanning the Nairoviridae family towards Ub and ISG15 fluorogenic substrates. This revealed great variation in enzymatic activity and specific substrate preferences. A subset of the vOTUs were further assayed against eight biologically relevant di-Ub substrates, uncovering both common trends and distinct preferences of poly-Ub linkages by vOTUs. Four novel X-ray crystal structures were obtained that provide a biochemical rationale for vOTU substrate preferences and elucidate structural features that distinguish the vOTUs, including a motif in the Hughes orthonairovirus species that has not been previously observed in OTU domains. Additionally, structure-informed mutagenesis provided the first direct evidence of a second site involved in di-Ub binding for vOTUs. These results provide new insight into nairovirus evolution and pathogenesis, and further enhances the development of tools for therapeutic purposes. Viruses utilize a variety of mechanisms to manipulate and suppress host responses to infection. One specific mechanism used by nairoviruses is the production of a deubiquitinating enzyme, termed the vOTU, that disrupts the innate immune response. This enzyme has been shown to play a key role in efficient replication of Crimean-Congo hemorrhagic fever virus (CCHFV), a severe human pathogen causing outbreaks with high case fatality rates. Recent genomic studies have revealed a high degree of sequence variation for the vOTU among nairoviruses, but knowledge relating to the functional impact of this diversity is lacking. Here we investigated the effects of this diversity on the structure and function of vOTUs from a wide range of nairoviruses. This revealed that vOTUs from different nairoviruses possess distinct preferences for certain host proteins. In addition, we found that different vOTUs possess distinguishing structural features, including a unique motif present in one that was previously undescribed. Utilizing this information, we were able to provide a rational basis for the observed differences in the vOTUs. This work provides a foundation to understand nairovirus evolution by providing insight into a mechanism that influences virus host adaptation and pathogenesis.
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Affiliation(s)
- John V. Dzimianski
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Brianna S. Beldon
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Courtney M. Daczkowski
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Octavia Y. Goodwin
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Florine E. M. Scholte
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Éric Bergeron
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Scott D. Pegan
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
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Abstract
Ubiquitin signaling requires tight control of all aspects of protein ubiquitination, including the timing, locale, extent, and type of modification. Dysregulation of any of these signaling features can lead to severe human disease. One key mode of regulation is through the controlled removal of the ubiquitin signal by dedicated families of proteases, termed deubiquitinases. In light of their key roles in signal regulation, deubiquitinases have become a recent focus for therapeutic intervention as a means to regulate protein abundance. This work and recent discoveries of novel deubiquitinases in humans, viruses, and bacteria, provide the impetus for this chapter on methods for evaluating the activities and structures of deubiquitinases. An array of available deubiquitinase substrates for biochemical characterization are presented and their limitations as standalone tools are discussed. Methods for the determination and analysis of deubiquitinase structure are also presented, with a focus on visualizing recognition of the ubiquitin substrate.
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Affiliation(s)
- Jonathan N. Pruneda
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, United States
| | - David Komander
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia,Corresponding author:
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41
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TUBE and UbiCRest assays for elucidating polyubiquitin modifications in protein complexes. Methods Enzymol 2019; 625:339-350. [DOI: 10.1016/bs.mie.2019.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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42
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Pasupala N, Morrow ME, Que LT, Malynn BA, Ma A, Wolberger C. OTUB1 non-catalytically stabilizes the E2 ubiquitin-conjugating enzyme UBE2E1 by preventing its autoubiquitination. J Biol Chem 2018; 293:18285-18295. [PMID: 30282802 PMCID: PMC6254341 DOI: 10.1074/jbc.ra118.004677] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/04/2018] [Indexed: 01/08/2023] Open
Abstract
OTUB1 is a deubiquitinating enzyme that cleaves Lys-48–linked polyubiquitin chains and also regulates ubiquitin signaling through a unique, noncatalytic mechanism. OTUB1 binds to a subset of E2 ubiquitin-conjugating enzymes and inhibits their activity by trapping the E2∼ubiquitin thioester and preventing ubiquitin transfer. The same set of E2s stimulate the deubiquitinating activity of OTUB1 when the E2 is not charged with ubiquitin. Previous studies have shown that, in cells, OTUB1 binds to E2-conjugating enzymes of the UBE2D (UBCH5) and UBE2E families, as well as to UBE2N (UBC13). Cellular roles have been identified for the interaction of OTUB1 with UBE2N and members of the UBE2D family, but not for interactions with UBE2E E2 enzymes. We report here a novel role for OTUB1–E2 interactions in modulating E2 protein ubiquitination. We observe that Otub1−/− knockout mice exhibit late-stage embryonic lethality. We find that OTUB1 depletion dramatically destabilizes the E2-conjugating enzyme UBE2E1 (UBCH6) in both mouse and human OTUB1 knockout cell lines. Of note, this effect is independent of the catalytic activity of OTUB1, but depends on its ability to bind to UBE2E1. We show that OTUB1 suppresses UBE2E1 autoubiquitination in vitro and in cells, thereby preventing UBE2E1 from being targeted to the proteasome for degradation. Taken together, we provide evidence that OTUB1 rescues UBE2E1 from degradation in vivo.
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Affiliation(s)
- Nagesh Pasupala
- From the Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185 and
| | - Marie E Morrow
- From the Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185 and
| | - Lauren T Que
- From the Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185 and
| | - Barbara A Malynn
- the Department of Medicine, University of California San Francisco, San Francisco, California 94117
| | - Averil Ma
- the Department of Medicine, University of California San Francisco, San Francisco, California 94117
| | - Cynthia Wolberger
- From the Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185 and.
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43
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Bhat S, Hwang Y, Gibson MD, Morgan MT, Taverna SD, Zhao Y, Wolberger C, Poirier MG, Cole PA. Hydrazide Mimics for Protein Lysine Acylation To Assess Nucleosome Dynamics and Deubiquitinase Action. J Am Chem Soc 2018; 140:9478-9485. [PMID: 29991262 PMCID: PMC6070418 DOI: 10.1021/jacs.8b03572] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A range of acyl-lysine (acyl-Lys) modifications on histones and other proteins have been mapped over the past decade but for most, their functional and structural significance remains poorly characterized. One limitation in the study of acyl-Lys containing proteins is the challenge of producing them or their mimics in site-specifically modified forms. We describe a cysteine alkylation-based method to install hydrazide mimics of acyl-Lys post-translational modifications (PTMs) on proteins. We have applied this method to install mimics of acetyl-Lys, 2-hydroxyisobutyryl-Lys, and ubiquityl-Lys that could be recognized selectively by relevant acyl-Lys modification antibodies. The acyl-Lys modified histone H3 proteins were reconstituted into nucleosomes to study nucleosome dynamics and stability as a function of modification type and site. We also installed a ubiquityl-Lys mimic in histone H2B and generated a diubiquitin analog, both of which could be cleaved by deubiquitinating enzymes. Nucleosomes containing the H2B ubiquityl-Lys mimic were used to study the SAGA deubiquitinating module's molecular recognition. These results suggest that acyl-Lys mimics offer a relatively simple and promising strategy to study the role of acyl-Lys modifications in the function, structure, and regulation of proteins and protein complexes.
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Affiliation(s)
- Shridhar Bhat
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Yousang Hwang
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Matthew D. Gibson
- Department of Physics, Ohio State University, Columbus, Ohio 43210, USA
| | - Michael T. Morgan
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Sean D. Taverna
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | | | - Philip A. Cole
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Division of Genetics, Brigham and Women’s Hospital; Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 77 Ave Louis Pasteur, HMS New Research Building, Boston, Massachusetts 02115, USA
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44
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Hewings DS, Heideker J, Ma TP, AhYoung AP, El Oualid F, Amore A, Costakes GT, Kirchhofer D, Brasher B, Pillow T, Popovych N, Maurer T, Schwerdtfeger C, Forrest WF, Yu K, Flygare J, Bogyo M, Wertz IE. Reactive-site-centric chemoproteomics identifies a distinct class of deubiquitinase enzymes. Nat Commun 2018; 9:1162. [PMID: 29563501 PMCID: PMC5862848 DOI: 10.1038/s41467-018-03511-6] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/20/2018] [Indexed: 11/25/2022] Open
Abstract
Activity-based probes (ABPs) are widely used to monitor the activity of enzyme families in biological systems. Inferring enzyme activity from probe reactivity requires that the probe reacts with the enzyme at its active site; however, probe-labeling sites are rarely verified. Here we present an enhanced chemoproteomic approach to evaluate the activity and probe reactivity of deubiquitinase enzymes, using bioorthogonally tagged ABPs and a sequential on-bead digestion protocol to enhance the identification of probe-labeling sites. We confirm probe labeling of deubiquitinase catalytic Cys residues and reveal unexpected labeling of deubiquitinases on non-catalytic Cys residues and of non-deubiquitinase proteins. In doing so, we identify ZUFSP (ZUP1) as a previously unannotated deubiquitinase with high selectivity toward cleaving K63-linked chains. ZUFSP interacts with and modulates ubiquitination of the replication protein A (RPA) complex. Our reactive-site-centric chemoproteomics method is broadly applicable for identifying the reaction sites of covalent molecules, which may expand our understanding of enzymatic mechanisms. Deubiquitinases are proteases that cleave after the C-terminus of ubiquitin to hydrolyze ubiquitin chains and cleave ubiquitin from substrates. Here the authors describe a reactive-site-centric chemoproteomics approach to studying deubiquitinase activity, and expand the repertoire of known deubiquitinases.
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Affiliation(s)
- David S Hewings
- Discovery Oncology, Genentech, South San Francisco, California, 94080, USA.,Early Discovery Biochemistry, Genentech, South San Francisco, California, 94080, USA.,Discovery Chemistry, Genentech, South San Francisco, California, 94080, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Johanna Heideker
- Discovery Oncology, Genentech, South San Francisco, California, 94080, USA.,Early Discovery Biochemistry, Genentech, South San Francisco, California, 94080, USA
| | - Taylur P Ma
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, 94080, USA
| | - Andrew P AhYoung
- Early Discovery Biochemistry, Genentech, South San Francisco, California, 94080, USA
| | - Farid El Oualid
- UbiQ Bio BV, Science Park 408, 1098 XH, Amsterdam, The Netherlands
| | - Alessia Amore
- UbiQ Bio BV, Science Park 408, 1098 XH, Amsterdam, The Netherlands
| | - Gregory T Costakes
- Boston Biochem Inc., 840 Memorial Drive, Cambridge, Massachussetts, 02139, USA
| | - Daniel Kirchhofer
- Early Discovery Biochemistry, Genentech, South San Francisco, California, 94080, USA
| | - Bradley Brasher
- Boston Biochem Inc., 840 Memorial Drive, Cambridge, Massachussetts, 02139, USA
| | - Thomas Pillow
- Discovery Chemistry, Genentech, South San Francisco, California, 94080, USA
| | - Nataliya Popovych
- Early Discovery Biochemistry, Genentech, South San Francisco, California, 94080, USA
| | - Till Maurer
- Structural Biology, Genentech, South San Francisco, California, 94080, USA
| | | | - William F Forrest
- Bioinformatics, Genentech, South San Francisco, California, 94080, USA
| | - Kebing Yu
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, 94080, USA
| | - John Flygare
- Discovery Chemistry, Genentech, South San Francisco, California, 94080, USA.,Merck, 630 Gateway Boulevard, South San Francisco, California, 94080, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Ingrid E Wertz
- Discovery Oncology, Genentech, South San Francisco, California, 94080, USA. .,Early Discovery Biochemistry, Genentech, South San Francisco, California, 94080, USA.
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45
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Si Y, Liang L, Tang S, Qi Y, Huang Y, Liu L. Semi-synthesis of disulfide-linked branched tri-ubiquitin mimics. Sci China Chem 2018. [DOI: 10.1007/s11426-017-9189-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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46
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Impact of different ionization states of phosphorylated Serine-65 on ubiquitin structure and interactions. Sci Rep 2018; 8:2651. [PMID: 29422536 PMCID: PMC5805711 DOI: 10.1038/s41598-018-20860-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 01/23/2018] [Indexed: 01/13/2023] Open
Abstract
The covalent attachment of ubiquitin (Ub) or Ub chains to cellular proteins is a versatile post-translational modification involved in a variety of eukaryotic cellular events. Recently, the post-translational modification of Ub itself by phosphorylation has emerged as an important component of the Ub-signaling system. Specifically, Ub phosphorylation at serine-65 was shown to activate parkin-mediated mitochondrial quality control. However, the impact of phosphorylation on Ub structure and interactions is poorly understood. Here we investigate the recently reported structural changes in Ub upon serine-65 phosphorylation, namely, the equilibrium between a native-like and a novel, alternate conformer of phosphorylated Ub (pUb). We show that this equilibrium is pH-dependent, and the two pUb conformers are linked to the different charge states of the phosphate group. We examined pUb binding to a known Ub-receptor and found that the alternate conformer is binding incompetent. Furthermore, serine-65 phosphorylation affects the conformational equilibrium of K48-linked Ub dimers. Lastly, our crystal structure of S65D Ub and NMR data indicate that phosphomimetic mutations do not adequately reproduce the salient features of pUb. Our results suggest that the pH-dependence of the conformations and binding properties of phosphorylated Ub and polyUb could provide an additional level of modulation in Ub-mediated signaling.
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47
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Zhao L, Wang X, Yu Y, Deng L, Chen L, Peng X, Jiao C, Gao G, Tan X, Pan W, Ge X, Wang P. OTUB1 protein suppresses mTOR complex 1 (mTORC1) activity by deubiquitinating the mTORC1 inhibitor DEPTOR. J Biol Chem 2018; 293:4883-4892. [PMID: 29382726 DOI: 10.1074/jbc.m117.809533] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 01/22/2018] [Indexed: 01/05/2023] Open
Abstract
Mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) integrates various environmental signals to regulate cell growth and metabolism. DEPTOR, also termed DEPDC6, is an endogenous inhibitor of mTORC1 and mTORC2 activities. The abundance of DEPTOR centrally orchestrates the mTOR signaling network. However, the mechanisms by which DEPTOR stability is regulated are still elusive. Here, we report that OTU domain-containing ubiquitin aldehyde-binding protein 1 (OTUB1) specifically deubiquitinates DEPTOR in a deubiquitination assay. We found that OTUB1 directly interacted with DEPTOR via its N-terminal domain, deubiquitinated DEPTOR, and thereby stabilized DEPTOR in a Cys-91-independent but Asp-88-dependent manner, suggesting that OTUB1 targets DEPTOR for deubiquitination via a deubiquitinase activity-independent non-canonical mechanism. The interaction between OTUB1 and DEPTOR was enhanced when the cells were treated with amino acids. Moreover, OTUB1 suppressed amino acid-induced activation of mTORC1 in a DEPTOR-dependent manner and thereby ultimately controlled cellular autophagy, cell proliferation, and size. Our findings reveal a mechanism that stabilizes the mTORC1 inhibitor DEPTOR via OTUB1's deubiquitinase activity. Our insights may inform research into various mTOR activity-related diseases, such as cancer, and may contribute to the identification of new diagnostic markers and therapeutic strategies for cancer treatments.
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Affiliation(s)
- Linlin Zhao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xinbo Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yue Yu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lu Deng
- Department of Central Laboratory, Shanghai Tenth People's Hospital of Tongji University, School of Medicine, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Lei Chen
- Department of Central Laboratory, Shanghai Tenth People's Hospital of Tongji University, School of Medicine, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiaoping Peng
- Department of Central Laboratory, Shanghai Tenth People's Hospital of Tongji University, School of Medicine, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Chenchen Jiao
- Department of Central Laboratory, Shanghai Tenth People's Hospital of Tongji University, School of Medicine, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Guoli Gao
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiao Tan
- Department of Central Laboratory, Shanghai Tenth People's Hospital of Tongji University, School of Medicine, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Weijuan Pan
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xin Ge
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.
| | - Ping Wang
- Department of Central Laboratory, Shanghai Tenth People's Hospital of Tongji University, School of Medicine, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
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48
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Wang Y, Zhou X, Xu M, Weng W, Zhang Q, Yang Y, Wei P, Du X. OTUB1-catalyzed deubiquitination of FOXM1 facilitates tumor progression and predicts a poor prognosis in ovarian cancer. Oncotarget 2017; 7:36681-36697. [PMID: 27167337 PMCID: PMC5095031 DOI: 10.18632/oncotarget.9160] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 04/22/2016] [Indexed: 12/17/2022] Open
Abstract
Ubiquitination is essential for regulation of cell physiology, protein stability, and signal transduction [1]. Its dysregulation is an important factor in many diseases, including cancer. We explored the potential OTUB1-catalyzed deubiquitination of FOXM1, a transcription factor linked to carcinogenesis, and the biological consequence of that interaction in ovarian cancer. We found that FOXM1 is ubiquitinated by multiple polyUb chains and targeted for proteosomal degradation in a reaction dependent on its ubiquitination-required KEN box. Additionally, the OTUB1 N-terminus and catalytic triad bind to FOXM1, specifically catalyzing cleavage of the K48-specific ubiquitin linkage from FOXM1. Moreover, OTUB1-FOXM1 interaction drives tumor progression and OTUB1 expression predicts a poor prognosis in ovarian cancer. Our study suggests that inhibiting OTUB1-FOXM1 interaction is a potential new avenue for ovarian cancer therapy.
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Affiliation(s)
- Yiqin Wang
- Department of Pathology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200044, China
| | - Xianrong Zhou
- Department of Pathology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200044, China
| | - Midie Xu
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Pathology, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Institute of Pathology, Fudan University, Shanghai 200032, China.,Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Weiwei Weng
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Pathology, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Institute of Pathology, Fudan University, Shanghai 200032, China.,Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Qiongyan Zhang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Pathology, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Institute of Pathology, Fudan University, Shanghai 200032, China.,Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yusi Yang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Pathology, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Institute of Pathology, Fudan University, Shanghai 200032, China.,Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Ping Wei
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Institute of Pathology, Fudan University, Shanghai 200032, China.,Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Xiang Du
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Pathology, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Institute of Pathology, Fudan University, Shanghai 200032, China.,Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
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49
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Nakasone MA, Lewis TA, Walker O, Thakur A, Mansour W, Castañeda CA, Goeckeler-Fried JL, Parlati F, Chou TF, Hayat O, Zhang D, Camara CM, Bonn SM, Nowicka UK, Krueger S, Glickman MH, Brodsky JL, Deshaies RJ, Fushman D. Structural Basis for the Inhibitory Effects of Ubistatins in the Ubiquitin-Proteasome Pathway. Structure 2017; 25:1839-1855.e11. [PMID: 29153505 PMCID: PMC5731780 DOI: 10.1016/j.str.2017.10.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/09/2017] [Accepted: 10/24/2017] [Indexed: 02/02/2023]
Abstract
The discovery of ubistatins, small molecules that impair proteasomal degradation of proteins by directly binding to polyubiquitin, makes ubiquitin itself a potential therapeutic target. Although ubistatins have the potential for drug development and clinical applications, the lack of structural details of ubiquitin-ubistatin interactions has impeded their development. Here, we characterized a panel of new ubistatin derivatives using functional and binding assays. The structures of ubiquitin complexes with ubistatin B and hemi-ubistatin revealed direct interactions with ubiquitin's hydrophobic surface patch and the basic/polar residues surrounding it. Ubistatin B binds ubiquitin and diubiquitin tighter than a high-affinity ubiquitin receptor and shows strong preference for K48 linkages over K11 and K63. Furthermore, ubistatin B shields ubiquitin conjugates from disassembly by a range of deubiquitinases and by the 26S proteasome. Finally, ubistatin B penetrates cancer cells and alters the cellular ubiquitin landscape. These findings highlight versatile properties of ubistatins and have implications for their future development and use in targeting ubiquitin-signaling pathways.
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Affiliation(s)
- Mark A Nakasone
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA; Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Timothy A Lewis
- Center for the Science of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Olivier Walker
- Institut des Sciences Analytiques, UMR 5280, CNRS, Université de Lyon, Université Lyon 1, ENS Lyon, 69100 Villeurbanne, France
| | - Anita Thakur
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Wissam Mansour
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Carlos A Castañeda
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | | | - Frank Parlati
- Howard Hughes Medical Institute, Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Tsui-Fen Chou
- Howard Hughes Medical Institute, Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Ortal Hayat
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Daoning Zhang
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Christina M Camara
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Steven M Bonn
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Urszula K Nowicka
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Susan Krueger
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Michael H Glickman
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Raymond J Deshaies
- Howard Hughes Medical Institute, Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA.
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50
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Tan XL, Pan M, Zheng Y, Gao S, Liang LJ, Li YM. Sortase-mediated chemical protein synthesis reveals the bidentate binding of bisphosphorylated p62 with K63 diubiquitin. Chem Sci 2017; 8:6881-6887. [PMID: 29147513 PMCID: PMC5636944 DOI: 10.1039/c7sc02937c] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 08/03/2017] [Indexed: 12/21/2022] Open
Abstract
Phosphorylation of S403 or S407 of the autophagic receptor protein p62 has recently been discovered to enhance the binding of p62 with ubiquitinated protein substrates to upregulate selective autophagy. To elucidate the molecular mechanism of how phosphorylation regulates the recruitment of ubiquitinated proteins, we report the first chemical synthesis of homogeneously phosphorylated p62, which enables the setting up of accurate in vitro systems for biochemical studies. Our synthesis employs the technology of sortase A-mediated protein hydrazide ligation, which successfully affords three types of phosphorylated p62 at the multi-milligram scale. Quantitative biochemical measurements show that the binding affinity of S403/S407-bisphosphorylated p62 to K63 diubiquitin is significantly higher than that of mono-phosphorylated p62. This finding suggests that phosphorylated S403 and S407 sites should bind to different epitopes on the ubiquitin chain. Furthermore, glutamate mutation is found to give a significantly impaired binding affinity, implying the necessity of using chemically synthesized phosphorylated p62 for the biochemical study of selective autophagy.
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Affiliation(s)
- Xiang-Long Tan
- Tsinghua-Peking Center for Life Sciences , Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology , Department of Chemistry , Tsinghua University , Beijing 100084 , China.,School of Biological and Medical Engineering , Hefei University of Technology , Hefei , Anhui 230009 , China .
| | - Man Pan
- Tsinghua-Peking Center for Life Sciences , Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology , Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | - Yong Zheng
- School of Biological and Medical Engineering , Hefei University of Technology , Hefei , Anhui 230009 , China . .,High Magnetic Field Laboratory , Chinese Academy of Sciences , Hefei 230031 , China
| | - Shuai Gao
- Tsinghua-Peking Center for Life Sciences , Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology , Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | - Lu-Jun Liang
- Tsinghua-Peking Center for Life Sciences , Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology , Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | - Yi-Ming Li
- School of Biological and Medical Engineering , Hefei University of Technology , Hefei , Anhui 230009 , China .
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