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Tao Y, Xu X, Shen R, Miao X, He S. Roles of ubiquitin‑specific protease 13 in normal physiology and tumors (Review). Oncol Lett 2024; 27:58. [PMID: 38192665 PMCID: PMC10773187 DOI: 10.3892/ol.2023.14191] [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] [Received: 09/18/2023] [Accepted: 11/24/2023] [Indexed: 01/10/2024] Open
Abstract
Ubiquitin-specific protease 13 (USP13) is one of the most important deubiquitinases involved in various diseases. As deubiquitinases are components of the deubiquitination process, a significant post-translational modification, they are potential treatment targets for different diseases. With recent technological developments, the structure of USP13 and its pathological and physiological functions have been investigated. However, USP13 expression and function differ in various diseases, especially in tumors, and the associated mechanisms are complex and remain to be fully investigated. The present review summarized the recent discoveries and the current understanding of the USP13 function in tumors.
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Affiliation(s)
- Yun Tao
- Department of Pathology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
- Department of Clinical Laboratory, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Xiaohong Xu
- Department of Hematological Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Rong Shen
- Department of Pathology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Xiaobing Miao
- Department of Pathology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Song He
- Department of Pathology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
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2
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Wang Q, Sun Z, Xia W, Sun L, Du Y, Zhang Y, Jia Z. Role of USP13 in physiology and diseases. Front Mol Biosci 2022; 9:977122. [PMID: 36188217 PMCID: PMC9515447 DOI: 10.3389/fmolb.2022.977122] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
Ubiquitin specific protease (USP)-13 is a deubiquitinase that removes ubiquitin from substrates to prevent protein degradation by the proteasome. Currently, the roles of USP13 in physiology and pathology have been reported. In physiology, USP13 is highly associated with cell cycle regulation, DNA damage repair, myoblast differentiation, quality control of the endoplasmic reticulum, and autophagy. In pathology, it has been reported that USP13 is important in the pathogenesis of infection, inflammation, idiopathic pulmonary fibrosis (IPF), neurodegenerative diseases, and cancers. This mini-review summarizes the most recent advances in USP13 studies involving its pathophysiological roles in different conditions and provides new insights into the prevention and treatment of relevant diseases, as well as further research on USP13.
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Affiliation(s)
- Qian Wang
- Nanjing Key Laboratory of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China
- Department of Nephrology, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Zhenzhen Sun
- Nanjing Key Laboratory of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China
- Department of Nephrology, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Weiwei Xia
- Nanjing Key Laboratory of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China
- Department of Nephrology, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Le Sun
- Nanjing Key Laboratory of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China
- Department of Nephrology, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Yang Du
- Nanjing Key Laboratory of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China
- Department of Nephrology, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Yue Zhang
- Nanjing Key Laboratory of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China
- Department of Nephrology, Children’s Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Yue Zhang, ; Zhanjun Jia,
| | - Zhanjun Jia
- Nanjing Key Laboratory of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China
- Department of Nephrology, Children’s Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Yue Zhang, ; Zhanjun Jia,
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Liu X, Balaraman K, Lynch CC, Hebron M, Shah PK, Hu S, Stevenson M, Wolf C, Moussa C. Inhibition of Ubiquitin-Specific Protease-13 Improves Behavioral Performance in Alpha-Synuclein Expressing Mice. Int J Mol Sci 2022; 23:ijms23158131. [PMID: 35897705 PMCID: PMC9330474 DOI: 10.3390/ijms23158131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 01/21/2023] Open
Abstract
Ubiquitin-Specific Protease-13 (USP13) promotes protein de-ubiquitination. USP13 levels are upregulated in post-mortem Parkinson's disease, whereas USP13 knockdown via shRNA reduces alpha-synuclein levels in animal models. We studied the role of USP13 in knockout mice expressing lentiviral human alpha-synuclein and investigated the impact of a small molecule inhibitor of USP13, BK50118-C, on alpha-synuclein pathology and animal behavior. Alpha-synuclein was expressed unilaterally in substantia nigra (SN) of USP13 deficient mice that were treated with a daily intraperitoneal injection of 100 mg/kg BK50118-C or DMSO for four consecutive weeks, and behavioral and functional assays were performed. Wild-type USP13+/+ mice expressing lentiviral human alpha-synuclein showed motor and behavioral defects that were not seen in partially (USP13+/-) or completely (USP13-/-) deficient USP13 mice. BK50118-C displayed a wide and favorable therapeutic dose range in vivo. Treatment with BK50118-C significantly reduced ubiquitinated alpha-synuclein, increased dopamine levels, and improved motor and behavioral symptoms in wild-type (USP13+/+), but not USP13 deficient, mice. These data suggest that USP13 is critical to the neuropathology of alpha-synuclein, whereas a novel small molecule inhibitor of USP13 is a potential therapeutic agent of alpha-synucleinopathies.
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Affiliation(s)
- Xiaoguang Liu
- Department of Neurology, Translational Neurotherapeutics Program, Laboratory for Dementia and Parkinsonism, Lewy Body Dementia Association, Research Center of Excellence, Georgetown University Medical Center, Washington, DC 20057, USA; (M.H.); (P.K.S.); (S.H.); (M.S.)
- Correspondence: (X.L.); (C.M.); Tel.: +1-202-687-7328 (C.M.); Fax: +1-202-687-7378 (C.M.)
| | - Kaluvu Balaraman
- Department of Chemistry, Georgetown University & Medicinal Chemistry Shared Resource, Georgetown University Medical Center, Washington, DC 20057, USA; (K.B.); (C.C.L.); (C.W.)
| | - Ciarán C. Lynch
- Department of Chemistry, Georgetown University & Medicinal Chemistry Shared Resource, Georgetown University Medical Center, Washington, DC 20057, USA; (K.B.); (C.C.L.); (C.W.)
| | - Michaeline Hebron
- Department of Neurology, Translational Neurotherapeutics Program, Laboratory for Dementia and Parkinsonism, Lewy Body Dementia Association, Research Center of Excellence, Georgetown University Medical Center, Washington, DC 20057, USA; (M.H.); (P.K.S.); (S.H.); (M.S.)
| | - Priya Ketankumar Shah
- Department of Neurology, Translational Neurotherapeutics Program, Laboratory for Dementia and Parkinsonism, Lewy Body Dementia Association, Research Center of Excellence, Georgetown University Medical Center, Washington, DC 20057, USA; (M.H.); (P.K.S.); (S.H.); (M.S.)
| | - Shicheng Hu
- Department of Neurology, Translational Neurotherapeutics Program, Laboratory for Dementia and Parkinsonism, Lewy Body Dementia Association, Research Center of Excellence, Georgetown University Medical Center, Washington, DC 20057, USA; (M.H.); (P.K.S.); (S.H.); (M.S.)
| | - Max Stevenson
- Department of Neurology, Translational Neurotherapeutics Program, Laboratory for Dementia and Parkinsonism, Lewy Body Dementia Association, Research Center of Excellence, Georgetown University Medical Center, Washington, DC 20057, USA; (M.H.); (P.K.S.); (S.H.); (M.S.)
| | - Christian Wolf
- Department of Chemistry, Georgetown University & Medicinal Chemistry Shared Resource, Georgetown University Medical Center, Washington, DC 20057, USA; (K.B.); (C.C.L.); (C.W.)
| | - Charbel Moussa
- Department of Neurology, Translational Neurotherapeutics Program, Laboratory for Dementia and Parkinsonism, Lewy Body Dementia Association, Research Center of Excellence, Georgetown University Medical Center, Washington, DC 20057, USA; (M.H.); (P.K.S.); (S.H.); (M.S.)
- Correspondence: (X.L.); (C.M.); Tel.: +1-202-687-7328 (C.M.); Fax: +1-202-687-7378 (C.M.)
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4
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Li X, Yang G, Zhang W, Qin B, Ye Z, Shi H, Zhao X, Chen Y, Song B, Mei Z, Zhao Q, Wang F. USP13: Multiple Functions and Target Inhibition. Front Cell Dev Biol 2022; 10:875124. [PMID: 35445009 PMCID: PMC9014248 DOI: 10.3389/fcell.2022.875124] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 03/08/2022] [Indexed: 12/13/2022] Open
Abstract
As a deubiquitination (DUB) enzyme, ubiquitin-specific protease 13 (USP13) is involved in a myriad of cellular processes, such as mitochondrial energy metabolism, autophagy, DNA damage response, and endoplasmic reticulum-associated degradation (ERAD), by regulating the deubiquitination of diverse key substrate proteins. Thus, dysregulation of USP13 can give rise to the occurrence and development of plenty of diseases, in particular malignant tumors. Given its implications in the stabilization of disease-related proteins and oncology targets, considerable efforts have been committed to the discovery of inhibitors targeting USP13. Here, we summarize an overview of the recent advances of the structure, function of USP13, and its relations to diseases, as well as discovery and development of inhibitors, aiming to provide the theoretical basis for investigation of the molecular mechanism of USP13 action and further development of more potent druggable inhibitors.
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Affiliation(s)
- Xiaolong Li
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Ge Yang
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Wenyao Zhang
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Biying Qin
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Zifan Ye
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Huijing Shi
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Xinmeng Zhao
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Yihang Chen
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Bowei Song
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Ziqing Mei
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China
| | | | - Feng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
- *Correspondence: Feng Wang,
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Ning F, Xin H, Liu J, Lv C, Xu X, Wang M, Wang Y, Zhang W, Zhang X. Structure and function of USP5: Insight into physiological and pathophysiological roles. Pharmacol Res 2019; 157:104557. [PMID: 31756387 DOI: 10.1016/j.phrs.2019.104557] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 11/18/2019] [Accepted: 11/18/2019] [Indexed: 11/16/2022]
Abstract
Deubiquitinase (DUB)-mediated cleavage of ubiquitin chains from substrate proteins plays a crucial role in various cellular processes, such as DNA repair and protein stabilization and localization. DUBs can be classified into five families based on their sequence and structural homology, and the majority belong to the ubiquitin-specific proteinase (USP) family. As one of the USPs, ubiquitin-specific proteinase 5 (USP5) is unique in that it can specifically recognize unanchored (not conjugated to target proteins) polyubiquitin and is essential for maintaining homeostasis of the monoubiquitin pool. USP5 has also been implicated in a wide variety of cellular events. In the present review, we focus on USP5 and provide a comprehensive overview of the current knowledge regarding its structure, physiological roles in multiple cellular events, and pathophysiological roles in relevant diseases, especially cancer. Signaling pathways and emerging pharmacological profiles of USP5 are also introduced, which fully embody the therapeutic potential of USP5 for human diseases ranging from cancer to neurological diseases.
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Affiliation(s)
- Fengling Ning
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Hong Xin
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Junqiu Liu
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Chao Lv
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xin Xu
- Suzhou Institute of Systems Medicine, Center for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou 215123, China
| | - Mengling Wang
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yinhang Wang
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Weidong Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Xuemei Zhang
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China.
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Wang J, Liu Y, Tang L, Qi S, Mi Y, Liu D, Tian Q. Identification of candidate substrates of ubiquitin-specific protease 13 using 2D-DIGE. Int J Mol Med 2017; 40:47-56. [PMID: 28498477 PMCID: PMC5466393 DOI: 10.3892/ijmm.2017.2984] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 05/04/2017] [Indexed: 11/17/2022] Open
Abstract
The present study aimed to identify candidate substrates of ubiquitin-specific protease (USP)13 using two-dimensional fluorescence difference gel electrophoresis (2D-DIGE). USP13 is a well-characterized member of the USP family, which regulates diverse cellular functions by cleaving ubiquitin from ubiquitinated protein substrates. However, existing studies indicate that USP13 has no detectable hydrolytic activity in vitro. This finding implies that USP13 likely has different substrate specificity. In this study, a USP cleavage assay was performed using two different types of model substrates (glutathione S-transferase-Ub52 and ubiquitin-β-galactosidase) to detect the deubiquitinating enzyme (DUB) activity of USP13. In addition, a proteomic approach was taken by using 2D-DIGE to detect cellular proteins whose expressoin is significantly altered in 293T cell lines following the overexpression of USP13 or its C345S mutant (the catalytically inactive form). The data indicated that USP13 still has no detectable DUB activity in vitro nor does C345S. The results of 2D-DIGE demonstrated that the expression of several proteins increased or decreased significantly in 293T cells following the overexpression of USP13. Mass spec troscopy analysis of gel spots identified 7 proteins, including 4 proteins with an increased expression, namely vinculin, thimet oligopeptidase, cleavage and polyadenylation specific factor 3, and methylosome protein 50, and 3 proteins with a decreased expression, namely adenylosuccinate synthetase, annexin and phosphoglycerate mutase. In addition, in the samples of 293T cell lines after the overexpression of USP13 and USP13 C345S, vinculin exhibited an increased expression, suggesting that it may be a candidate substrate of USP13. However, sufficient follow-up validation studies are required in order to determine whether vinculin protein directly interacts with USP13.
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Affiliation(s)
- Jianmin Wang
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China
| | - Yingli Liu
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China
| | - Lijuan Tang
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China
| | - Sufen Qi
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China
| | - Yingjun Mi
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China
| | - Dianwu Liu
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China
| | - Qingbao Tian
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China
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Tsihlis ND, Kapadia MR, Vavra AK, Flannery WD, Oustwani CS, Jiang Q, Kibbe MR. Nitric oxide may inhibit neointimal hyperplasia by decreasing isopeptidase T levels and activity in the vasculature. J Vasc Surg 2013; 58:179-86. [PMID: 23375434 DOI: 10.1016/j.jvs.2012.10.066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 09/27/2012] [Accepted: 10/01/2012] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Isopeptidase T is a cysteine protease deubiquitinating enzyme that hydrolyzes unanchored polyubiquitin chains to free monoubiquitin. Nitric oxide (NO) decreases 26S proteasome activity in vascular smooth muscle cells (VSMCs) and inhibits neointimal hyperplasia in animal models. As NO can cause S-nitrosylation of active-site cysteines, we hypothesize that NO inhibits isopeptidase T activity through S-nitrosylation. Because accumulation of polyubiquitin chains inhibits the 26S proteasome, this may be one mechanism through which NO prevents neointimal hyperplasia. METHODS To investigate our hypothesis, we examined the effect of NO on isopeptidase T activity, levels, and localization in VSMCs in vitro and in a rat carotid balloon injury model in vivo. RESULTS NO inhibited recombinant isopeptidase T activity by 82.8% (t = 60 minutes, P < .001 vs control). Dithiothreitol and glutathione (5 mmol/L) both significantly reversed NO-mediated inhibition of isopeptidase T activity (P < .001). NO caused a time-dependent increase in S-nitrosylated isopeptidase T levels in VSMCs, which was reversible with dithiothreitol, indicating that isopeptidase T undergoes reversible S-nitrosylation on exposure to NO in vitro. Although NO did not affect isopeptidase T levels or subcellular localization in VSMCs in vitro, it decreased isopeptidase T levels and increased ubiquitinated proteins after balloon injury in vivo. CONCLUSIONS Local administration of NO may prevent neointimal hyperplasia by inhibiting isopeptidase T levels and activity in the vasculature, thereby inhibiting the 26S proteasome in VSMCs. These data provide additional mechanistic insights into the ability of NO to prevent neointimal hyperplasia after vascular interventions.
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Affiliation(s)
- Nick D Tsihlis
- Division of Vascular Surgery, Northwestern University, Chicago, IL 60611, USA
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Zhang YH, Zhou CJ, Zhou ZR, Song AX, Hu HY. Domain analysis reveals that a deubiquitinating enzyme USP13 performs non-activating catalysis for Lys63-linked polyubiquitin. PLoS One 2011; 6:e29362. [PMID: 22216260 PMCID: PMC3247260 DOI: 10.1371/journal.pone.0029362] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 11/27/2011] [Indexed: 11/18/2022] Open
Abstract
Deubiquitination is a reverse process of cellular ubiquitination important for many biological events. Ubiquitin (Ub)-specific protease 13 (USP13) is an ortholog of USP5 implicated in catalyzing hydrolysis of various Ub chains, but its enzymatic properties and catalytic regulation remain to be explored. Here we report studies of the roles of the Ub-binding domains of USP13 in regulatory catalysis by biochemical and NMR structural approaches. Our data demonstrate that USP13, distinct from USP5, exhibits a weak deubiquitinating activity preferring to Lys63-linked polyubiquitin (K63-polyUb) in a non-activation manner. The zinc finger (ZnF) domain of USP13 shares a similar fold with that of USP5, but it cannot bind with Ub, so that USP13 has lost its ability to be activated by free Ub. Substitution of the ZnF domain with that of USP5 confers USP13 the property of catalytic activation. The tandem Ub-associated (UBA) domains of USP13 can bind with different types of diUb but preferentially with K63-linked, providing a possible explanation for the weak activity preferring to K63-polyUb. USP13 can also regulate the protein level of CD3δ in cells, probably depending on its weak deubiquitinating activity and the Ub-binding properties of the UBA domains. Thus, the non-activating catalysis of USP13 for K63-polyUb chains implies that it may function differently from USP5 in cellular deubiquitination processes.
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Affiliation(s)
- Yu-Hang Zhang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chen-Jie Zhou
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zi-Ren Zhou
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ai-Xin Song
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hong-Yu Hu
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail:
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9
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Zhao X, Fiske B, Kawakami A, Li J, Fisher DE. Regulation of MITF stability by the USP13 deubiquitinase. Nat Commun 2011; 2:414. [PMID: 21811243 DOI: 10.1038/ncomms1421] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Accepted: 07/05/2011] [Indexed: 11/09/2022] Open
Abstract
The microphthalmia-associated transcription factor (MITF) is essential for melanocyte development. Mutation-induced MAPK pathway activation is common in melanoma and induces MITF phosphorylation, ubiquitination, and proteolysis. Little is known about the enzymes involved in MITF ubiquitination/deubiquitination. Here we report the identification of a deubiquitinating enzyme, named ubiquitin-specific protease 13 (USP13) that appears to be responsible for MITF deubiquitination, utilizing a short hairpin RNA library against known deubiquitinating enzymes. Through deubiquitination, USP13 stabilizes and upregulates MITF protein levels. Conversely, suppression of USP13 (through knockdown) leads to dramatic loss of MITF protein, but not messenger RNA. Through its effects on MITF deubiquitination, USP13 was observed to modulate expression of MITF downstream target genes and, thereby, to be essential for melanoma growth in soft agar and in nude mice. These observations suggest that as a potentially drugable protease, USP13 might be a viable therapeutic target for melanoma.
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Affiliation(s)
- Xiansi Zhao
- Cutaneous Biology Research Center & Melanoma Program, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
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10
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Scortegagna M, Subtil T, Qi J, Kim H, Zhao W, Gu W, Kluger H, Ronai ZA. USP13 enzyme regulates Siah2 ligase stability and activity via noncatalytic ubiquitin-binding domains. J Biol Chem 2011; 286:27333-41. [PMID: 21659512 DOI: 10.1074/jbc.m111.218214] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The RING finger E3 ubiquitin ligase Siah2 is implicated in control of diverse cellular biological events, including MAPK signaling and hypoxia. Here we demonstrate that Siah2 is subject to regulation by the deubiquitinating enzyme USP13. Overexpression of USP13 increases Siah2 stability by attenuating its autodegradation. Consequently, the ability of Siah2 to target its substrates prolyl hydroxylase 3 and Spry2 (Sprouty2) for ubiquitin-mediated proteasomal degradation is attenuated. Conversely, inhibition of USP13 expression with corresponding shRNA decreases the stability of both Siah2 and its substrate Spry2. Thus, USP13 limits Siah2 autodegradation and its ubiquitin ligase activity against its target substrates. Strikingly, the effect of USP13 on Siah2 is not mediated by its isopeptidase activity: mutations in its ubiquitin-binding sequences positioned within the ubiquitin-specific processing protease and ubiquitin-binding domains, but not within putative catalytic sites, abolish USP13 binding to and effect on Siah2 autodegradation and targeted ubiquitination. Notably, USP13 expression is attenuated in melanoma cells maintained under hypoxia, thereby relieving Siah2 inhibition and increasing its activity under low oxygen levels. Significantly, on melanoma tissue microarray, high nuclear expression of USP13 coincided with high nuclear expression of Siah2. Overall, this study identifies a new layer of Siah2 regulation mediated by USP13 binding to ubiquitinated Siah2 protein with a concomitant inhibitory effect on its activity under normoxia.
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Affiliation(s)
- Marzia Scortegagna
- Signal Transduction Program, Sanford-Burnham Medical Research Institute, La Jolla, California 92130, USA
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11
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Scanlon TC, Gottlieb B, Durcan TM, Fon EA, Beitel LK, Trifiro MA. Isolation of human proteasomes and putative proteasome-interacting proteins using a novel affinity chromatography method. Exp Cell Res 2008; 315:176-89. [PMID: 19013454 DOI: 10.1016/j.yexcr.2008.10.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Revised: 10/24/2008] [Accepted: 10/24/2008] [Indexed: 02/02/2023]
Abstract
The proteasome is the primary subcellular organelle responsible for protein degradation. It is a dynamic assemblage of 34 core subunits and many differentially expressed, transiently interacting, modulatory proteins. This paper describes a novel affinity chromatography method for the purification of functional human holoproteasome complexes using mild conditions. Human proteasomes purified by this simple procedure maintained the ability to proteolytically process synthetic peptide substrates and degrade ubiquitinated parkin. Furthermore, the entire purification fraction was analyzed by mass spectrometry in order to identify proteasomal proteins and putative proteasome-interacting proteins. The mild purification conditions maintained transient physical interactions between holoproteasomes and a number of known modulatory proteins. In addition, several classes of putative interacting proteins co-purified with the proteasomes, including proteins with a role in the ubiquitin proteasome system for protein degradation or DNA repair. These results demonstrate the efficacy of using this affinity purification strategy for isolating functional human proteasomes and identifying proteins that may physically interact with human proteasomes.
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Affiliation(s)
- Thomas C Scanlon
- Lady Davis Institute for Medical Research, SMBD-Jewish General Hospital, Montreal, Canada
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Reyes-Turcu FE, Shanks JR, Komander D, Wilkinson KD. Recognition of polyubiquitin isoforms by the multiple ubiquitin binding modules of isopeptidase T. J Biol Chem 2008; 283:19581-92. [PMID: 18482987 DOI: 10.1074/jbc.m800947200] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The conjugation of polyubiquitin to target proteins acts as a signal that regulates target stability, localization, and function. Several ubiquitin binding domains have been described, and while much is known about ubiquitin binding to the isolated domains, little is known with regard to how the domains interact with polyubiquitin in the context of full-length proteins. Isopeptidase T (IsoT/USP5) is a deubiquitinating enzyme that is largely responsible for the disassembly of unanchored polyubiquitin in the cell. IsoT has four ubiquitin binding domains: a zinc finger domain (ZnF UBP), which binds the proximal ubiquitin, a UBP domain that forms the active site, and two ubiquitin-associated (UBA) domains whose roles are unknown. Here, we show that the UBA domains are involved in binding two different polyubiquitin isoforms, linear and K48-linked. Using isothermal titration calorimetry, we show that IsoT has at least four ubiquitin binding sites for both polyubiquitin isoforms. The thermodynamics of the interactions reveal that the binding is enthalpy-driven. Mutation of the UBA domains suggests that UBA1 and UBA2 domains of IsoT interact with the third and fourth ubiquitins in both polyubiquitin isoforms, respectively. These data suggest that recognition of the polyubiquitin isoforms by IsoT involves considerable conformational mobility in the polyubiquitin ligand, in the enzyme, or in both.
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Affiliation(s)
- Francisca E Reyes-Turcu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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13
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Borodovsky A, Ovaa H, Meester WJN, Venanzi ES, Bogyo MS, Hekking BG, Ploegh HL, Kessler BM, Overkleeft HS. Small-molecule inhibitors and probes for ubiquitin- and ubiquitin-like-specific proteases. Chembiochem 2005; 6:287-91. [PMID: 15651044 DOI: 10.1002/cbic.200400236] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Anna Borodovsky
- BiogenIdec Inc. 12 Cambridge Center, Cambridge, MA 02142, USA
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14
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Borodovsky A, Ovaa H, Kolli N, Gan-Erdene T, Wilkinson KD, Ploegh HL, Kessler BM. Chemistry-based functional proteomics reveals novel members of the deubiquitinating enzyme family. CHEMISTRY & BIOLOGY 2002; 9:1149-59. [PMID: 12401499 DOI: 10.1016/s1074-5521(02)00248-x] [Citation(s) in RCA: 452] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ubiquitin (Ub)-proteasome system includes a large family of deubiquitinating enzymes (DUBs). Many members are assigned to this enzyme class by sequence similarity but without evidence for biological activity. A panel of novel DUB-specific probes was generated by a chemical ligation method. These probes allowed identification of DUBs and associated components by tandem mass spectrometry, as well as rapid demonstration of enzymatic activity for gene products whose functions were inferred from primary structure. We identified 23 active DUBs in EL4 cells, including the tumor suppressor CYLD1. At least two DUBs tightly interact with the proteasome 19S regulatory complex. An OTU domain-containing protein, with no sequence homology to any known DUBs, was isolated. We show that this polypeptide reacts with the C terminus of Ub, thus demonstrating DUB-like enzymatic activity for this novel superfamily of proteases.
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Affiliation(s)
- Anna Borodovsky
- Department of Pathology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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15
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Sloper-Mould KE, Eyre HJ, Wang XW, Sutherland GR, Baker RT. Characterization and chromosomal localization of USP3, a novel human ubiquitin-specific protease. J Biol Chem 1999; 274:26878-84. [PMID: 10480896 DOI: 10.1074/jbc.274.38.26878] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Conjugation to the small eukaryotic protein ubiquitin can functionally modify or target proteins for degradation by the proteasome. Removal of the ubiquitin modification, or deubiquitination, is performed by ubiquitin-specific proteases and is an important mechanism regulating this pathway. Here we describe a novel human ubiquitin-specific protease, USP3, initially identified as a partial cDNA clone similar to one of two highly conserved sequence regions common to all ubiquitin-specific proteases. We have isolated a complete USP3 cDNA clone containing both of these conserved sequence regions. The USP3 gene appears to be single copy and maps to human chromosome 15q22.3. A USP3 probe detects two mRNA transcripts, one of which corresponds in length to the cDNA. Both are expressed at low levels in all tissues examined, with highest expression in pancreas. The USP3 protein is a functional ubiquitin-specific protease in vitro, and is able to inhibit ubiquitin-dependent degradation of both an N-end Rule substrate and abnormal endogenous proteins in yeast. USP3 is also only the second known ubiquitin-specific protease capable of efficiently cleaving a ubiquitin-proline bond.
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Affiliation(s)
- K E Sloper-Mould
- Molecular Genetics Group, John Curtin School of Medical Research, Australian National University, G. P. O. Box 334, Canberra, Australian Capital Territory 2601, Australia
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16
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Baker RT, Wang XW, Woollatt E, White JA, Sutherland GR. Identification, functional characterization, and chromosomal localization of USP15, a novel human ubiquitin-specific protease related to the UNP oncoprotein, and a systematic nomenclature for human ubiquitin-specific proteases. Genomics 1999; 59:264-74. [PMID: 10444327 DOI: 10.1006/geno.1999.5879] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have identified a novel gene, USP15, encoding a human ubiquitin-specific protease (USP). The USP15 protein consists of 952 amino acids with a predicted molecular mass of 109.2 kDa and contains the highly conserved Cys and His boxes present in all members of the UBP family of deubiquitinating enzymes. USP15 shares 60.5% sequence identity and 76% sequence similarity with the human homolog (UNP/Unph/USP4) of the mouse Unp proto-oncogene. Recombinant USP15 demonstrated ubiquitin-specific protease activity against engineered linear fusions of ubiquitin to beta-galactosidase and glutathione S-transferase. USP15 can also cleave the ubiquitin-proline bond, a property previously unique to Unp/UNP. Chromosomal mapping by fluorescence in situ hybridization and radiation hybrid analyses localized the USP15 gene to chromosome band 12q14, a different location than that of UNP (3p21.3). Analysis of expressed sequence tag databases reveals evidence of alternate polyadenylation sites in the USP15 gene and also indicates that the gene may possess an exon/intron structure similar to that of the Unp gene, suggesting they have descended from a common ancestor. A systematic nomenclature for the human USPs is proposed.
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Affiliation(s)
- R T Baker
- Division of Molecular Medicine, Australian National University, Canberra, ACT, 2601, Australia.
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17
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Abstract
Ubiquitin is a ubiquitous and highly conserved protein of 76 amino acid residues, that can be covalently attached to cellular acceptor proteins. The attachment of ubiquitin to target proteins is achieved through a multi-step enzymatic pathway, which involves activities of ubiquitin-activating E1 enzymes, ubiquitin-conjugating E2 enzymes, and ligating E3 enzymes. Mono- or poly-ubiquitination of proteins can lead to protein degradation or modification of protein activity. Many components of the complex ubiquitin system show remarkable evolutionary conservation, from yeast to mammalian species. The ubiquitin system is essential to all eukaryotic cells. Among others, several signal transduction cascades show involvement of the ubiquitin system, but there are currently little data supporting a specific role of the ubiquitin system in hormonal control of reproduction. Interestingly, during gametogenesis, many specialized and important aspects of the ubiquitin system become apparent. Components of the ubiquitin system appear to be involved in different steps and processes during gametogenesis, including control of meiosis, and reorganization of chromatin structure.
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Affiliation(s)
- W M Baarends
- Department of Endocrinology and Reproduction, Faculty of Medicine and Health Sciences, Erasmus University Rotterdam, The Netherlands.
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