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Fote GM, Eapen VV, Lim RG, Yu C, Salazar L, McClure NR, McKnight J, Nguyen TB, Heath MC, Lau AL, Villamil MA, Miramontes R, Kratter IH, Finkbeiner S, Reidling JC, Paulo JA, Kaiser P, Huang L, Housman DE, Thompson LM, Steffan JS. Huntingtin contains an ubiquitin-binding domain and regulates lysosomal targeting of mitochondrial and RNA-binding proteins. Proc Natl Acad Sci U S A 2024; 121:e2319091121. [PMID: 39074279 PMCID: PMC11317567 DOI: 10.1073/pnas.2319091121] [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: 11/20/2023] [Accepted: 06/20/2024] [Indexed: 07/31/2024] Open
Abstract
Understanding the normal function of the Huntingtin (HTT) protein is of significance in the design and implementation of therapeutic strategies for Huntington's disease (HD). Expansion of the CAG repeat in the HTT gene, encoding an expanded polyglutamine (polyQ) repeat within the HTT protein, causes HD and may compromise HTT's normal activity contributing to HD pathology. Here, we investigated the previously defined role of HTT in autophagy specifically through studying HTT's association with ubiquitin. We find that HTT interacts directly with ubiquitin in vitro. Tandem affinity purification was used to identify ubiquitinated and ubiquitin-associated proteins that copurify with a HTT N-terminal fragment under basal conditions. Copurification is enhanced by HTT polyQ expansion and reduced by mimicking HTT serine 421 phosphorylation. The identified HTT-interacting proteins include RNA-binding proteins (RBPs) involved in mRNA translation, proteins enriched in stress granules, the nuclear proteome, the defective ribosomal products (DRiPs) proteome and the brain-derived autophagosomal proteome. To determine whether the proteins interacting with HTT are autophagic targets, HTT knockout (KO) cells and immunoprecipitation of lysosomes were used to investigate autophagy in the absence of HTT. HTT KO was associated with reduced abundance of mitochondrial proteins in the lysosome, indicating a potential compromise in basal mitophagy, and increased lysosomal abundance of RBPs which may result from compensatory up-regulation of starvation-induced macroautophagy. We suggest HTT is critical for appropriate basal clearance of mitochondrial proteins and RBPs, hence reduced HTT proteostatic function with mutation may contribute to the neuropathology of HD.
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Affiliation(s)
- Gianna M. Fote
- Department of Biological Chemistry, UC Irvine School of Medicine, Irvine, CA92697
- Department of Neurological Surgery, UC Irvine School of Medicine, Orange, CA92868
| | - Vinay V. Eapen
- Department of Cell Biology, Harvard Medical School, Boston, MA02115
- Casma Therapeutics, Cambridge, MA02139
| | - Ryan G. Lim
- The University of California Irvine Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA92697
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California, Irvine, CA92697
| | - Lisa Salazar
- Department of Psychiatry and Human Behavior, UC Irvine School of Medicine, Orange, CA92868
| | - Nicolette R. McClure
- Department of Neurobiology and Behavior, University of California, Irvine, CA92697
| | - Jharrayne McKnight
- Department of Neurobiology and Behavior, University of California, Irvine, CA92697
| | - Thai B. Nguyen
- Department of Neurobiology and Behavior, University of California, Irvine, CA92697
| | - Marie C. Heath
- Department of Neurobiology and Behavior, University of California, Irvine, CA92697
| | - Alice L. Lau
- Department of Psychiatry and Human Behavior, UC Irvine School of Medicine, Orange, CA92868
| | - Mark A. Villamil
- Department of Biological Chemistry, UC Irvine School of Medicine, Irvine, CA92697
| | - Ricardo Miramontes
- Department of Psychiatry and Human Behavior, UC Irvine School of Medicine, Orange, CA92868
| | - Ian H. Kratter
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA94158
- Stanford Brain Stimulation Lab, Stanford, CA94304
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA94304
| | - Steven Finkbeiner
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA94158
- Department of Physiology, University of California, San Francisco, CA94158
- Department of Neurology, University of California, San Francisco, CA94158
| | - Jack C. Reidling
- The University of California Irvine Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA92697
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA02115
| | - Peter Kaiser
- Department of Biological Chemistry, UC Irvine School of Medicine, Irvine, CA92697
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, CA92697
| | - David E. Housman
- Koch Institute for Integrative Cancer Research, The Massachusetts Institute of Technology, Cambridge, MA02139
| | - Leslie M. Thompson
- Department of Biological Chemistry, UC Irvine School of Medicine, Irvine, CA92697
- The University of California Irvine Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA92697
- Department of Psychiatry and Human Behavior, UC Irvine School of Medicine, Orange, CA92868
- Department of Neurobiology and Behavior, University of California, Irvine, CA92697
- Center for Epigenetics and Metabolism, University of California, Irvine School of Medicine, University of California, Irvine, CA92697
| | - Joan S. Steffan
- The University of California Irvine Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA92697
- Department of Psychiatry and Human Behavior, UC Irvine School of Medicine, Orange, CA92868
- Center for Epigenetics and Metabolism, University of California, Irvine School of Medicine, University of California, Irvine, CA92697
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Li K, Xia Y, He J, Wang J, Li J, Ye M, Jin X. The SUMOylation and ubiquitination crosstalk in cancer. J Cancer Res Clin Oncol 2023; 149:16123-16146. [PMID: 37640846 DOI: 10.1007/s00432-023-05310-z] [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: 07/17/2023] [Accepted: 08/16/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND The cancer occurrence and progression are largely affected by the post-translational modifications (PTMs) of proteins. Currently, it has been shown that the relationship between ubiquitination and SUMOylation is highly complex and interactive. SUMOylation affects the process of ubiquitination and degradation of substrates. Contrarily, SUMOylation-related proteins are also regulated by the ubiquitination process thus altering their protein levels or activity. Emerging evidence suggests that the abnormal regulation between this crosstalk may lead to tumorigenesis. PURPOSE In this review, we have discussed the study of the relationship between ubiquitination and SUMOylation, as well as the possibility of a corresponding application in tumor therapy. METHODS The relevant literatures from PubMed have been reviewed for this article. CONCLUSION The interaction between ubiquitination and SUMOylation is crucial for the occurrence and development of cancer. A greater understanding of the crosstalk of SUMOylation and ubiquitination may be more conducive to the development of more selective and effective SUMOylation inhibitors, as well as a promotion of synergy with other tumor treatment strategies.
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Affiliation(s)
- Kailang Li
- Department of Oncology, The First Hospital of Ningbo University, Ningbo, 315020, China
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Yongming Xia
- Department of Oncology, Yuyao People's Hospital of Zhejiang, Yuyao, 315400, Zhejiang, China
| | - Jian He
- Department of Oncology, The First Hospital of Ningbo University, Ningbo, 315020, China
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Jie Wang
- Department of Oncology, The First Hospital of Ningbo University, Ningbo, 315020, China
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Jingyun Li
- Department of Oncology, The First Hospital of Ningbo University, Ningbo, 315020, China
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Meng Ye
- Department of Oncology, The First Hospital of Ningbo University, Ningbo, 315020, China.
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China.
| | - Xiaofeng Jin
- Department of Oncology, The First Hospital of Ningbo University, Ningbo, 315020, China.
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China.
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3
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Harumoto T. Self-stabilization mechanism encoded by a bacterial toxin facilitates reproductive parasitism. Curr Biol 2023; 33:4021-4029.e6. [PMID: 37673069 DOI: 10.1016/j.cub.2023.08.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/30/2023] [Accepted: 08/10/2023] [Indexed: 09/08/2023]
Abstract
A wide variety of maternally transmitted endosymbionts in insects are associated with reproductive parasitism, whereby they interfere with host reproduction to increase the ratio of infected females and spread within populations.1,2 Recent successes in identifying bacterial factors responsible for reproductive parasitism3,4,5,6,7 as well as further omics approaches8,9,10,11,12 have highlighted the common appearance of deubiquitinase domains, although their biological roles-in particular, how they link to distinct manipulative phenotypes-remain poorly defined. Spiroplasma poulsonii is a helical and motile bacterial endosymbiont of Drosophila,13,14 which selectively kills male progeny with a male-killing toxin Spaid (S. poulsonii androcidin), which encodes an ovarian tumor (OTU) deubiquitinase domain.6 Artificial expression of Spaid in flies reproduces male-killing-associated pathologies that include abnormal apoptosis and neural defects during embryogenesis6,15,16,17,18,19; moreover, it highly accumulates on the dosage-compensated male X chromosome,20 congruent with cellular defects such as the DNA damage/chromatin bridge breakage specifically induced upon that chromosome.6,21,22,23 Here, I show that without the function of OTU, Spaid is polyubiquitinated and degraded through the host ubiquitin-proteasome pathway, leading to the attenuation of male-killing activity as shown previously.6 Furthermore, I find that Spaid utilizes its OTU domain to deubiquitinate itself in an intermolecular manner. Collectively, the deubiquitinase domain of Spaid serves as a self-stabilization mechanism to facilitate male killing in flies, optimizing a molecular strategy of endosymbionts that enables the efficient manipulation of the host at a low energetic cost.
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Affiliation(s)
- Toshiyuki Harumoto
- Hakubi Center for Advanced Research, Kyoto University, Yoshida-honmachi, Sakyo-ku, Kyoto 606-8501, Japan; Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
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4
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Zhou L, Qin B, Yassine DM, Luo M, Liu X, Wang F, Wang Y. Structure and function of the highly homologous deubiquitinases ubiquitin specific peptidase 25 and 28: Insights into their pathophysiological and therapeutic roles. Biochem Pharmacol 2023; 213:115624. [PMID: 37245535 DOI: 10.1016/j.bcp.2023.115624] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 05/30/2023]
Abstract
Deubiquitination is the reverse process of ubiquitination, an important protein post-translational modification. Deubiquitination is assisted by deubiquitinating enzymes (DUBs), which catalyze the hydrolysis and removal of ubiquitin chains from targeted proteins and play an important role in regulating protein stability, cell signaling transduction, and programmed cell death. Ubiquitin-specific peptidases 25 and 28 (USP25 and USP28), important members of the USP subfamily of DUBs, are highly homologous, strictly regulated, and closely associated with various diseases, such as cancer and neurodegenerative diseases. Recently, the development of inhibitors targeting USP25 and USP28 for disease treatment has garnered extreme attention. Several non-selective and selective inhibitors have shown potential inhibitory effects. However, the specificity, potency, and action mechanism of these inhibitors remain to be further improved and clarified. Herein, we summarize the structure, regulation, emerging physiological roles, and target inhibition of USP25 and USP28 to provide a basis for the development of highly potent and specific inhibitors for the treatment of diseases, such as colorectal cancer, breast cancer and so on.
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Affiliation(s)
- Lihui Zhou
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Biying Qin
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Demna Mohamed Yassine
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Maoguo Luo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Xiaoling Liu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Feng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Yanfeng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
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Cai F, Song B, Yang Y, Liao H, Li R, Wang Z, Cao R, Chen H, Wang J, Wu Y, Zhang Y, Song W. USP25 contributes to defective neurogenesis and cognitive impairments. FASEB J 2023; 37:e22971. [PMID: 37171286 DOI: 10.1096/fj.202300057r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/25/2023] [Accepted: 05/01/2023] [Indexed: 05/13/2023]
Abstract
Both Down syndrome (DS) individuals and animal models exhibit hypo-cellularity in hippocampus and neocortex indicated by enhanced neuronal death and compromised neurogenesis. Ubiquitin-specific peptidase 25 (USP25), a human chromosome 21 (HSA21) gene, encodes for a deubiquitinating enzyme overexpressed in DS patients. Dysregulation of USP25 has been associated with Alzheimer's phenotypes in DS, but its role in defective neurogenesis in DS has not been defined. In this study, we found that USP25 upregulation impaired cell cycle regulation during embryonic neurogenesis and cortical development. Overexpression of USP25 in hippocampus promoted the neural stem cells to glial cell fates and suppressed neuronal cell fate by altering the balance between cyclin D1 and cyclin D2, thus reducing neurogenesis in the hippocampus. USP25-Tg mice showed increased anxiety/depression-like behaviors and learning and memory deficits. These results suggested that USP25 overexpression resulted in defective neurogenesis and cognitive impairments, which could contribute to the pathogenesis of DS. USP25 may be a potential pharmaceutical target for DS.
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Affiliation(s)
- Fang Cai
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Alzheimer's Disease of Zhejiang Province, Zhejiang Provincial Clinical Research Center for Mental Disorders, Institute of Aging, School of Mental Health, Affiliated Kangning Hospital, The Second Affiliated Hospital, Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Townsend Family Laboratories, Department of Psychiatry, Graduate Program in Neuroscience, Djavad Mowafaghian Centre for Brain Health, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Beibei Song
- Townsend Family Laboratories, Department of Psychiatry, Graduate Program in Neuroscience, Djavad Mowafaghian Centre for Brain Health, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Yi Yang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Alzheimer's Disease of Zhejiang Province, Zhejiang Provincial Clinical Research Center for Mental Disorders, Institute of Aging, School of Mental Health, Affiliated Kangning Hospital, The Second Affiliated Hospital, Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Haikang Liao
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Alzheimer's Disease of Zhejiang Province, Zhejiang Provincial Clinical Research Center for Mental Disorders, Institute of Aging, School of Mental Health, Affiliated Kangning Hospital, The Second Affiliated Hospital, Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Ran Li
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Alzheimer's Disease of Zhejiang Province, Zhejiang Provincial Clinical Research Center for Mental Disorders, Institute of Aging, School of Mental Health, Affiliated Kangning Hospital, The Second Affiliated Hospital, Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhao Wang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Alzheimer's Disease of Zhejiang Province, Zhejiang Provincial Clinical Research Center for Mental Disorders, Institute of Aging, School of Mental Health, Affiliated Kangning Hospital, The Second Affiliated Hospital, Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Ruixue Cao
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Alzheimer's Disease of Zhejiang Province, Zhejiang Provincial Clinical Research Center for Mental Disorders, Institute of Aging, School of Mental Health, Affiliated Kangning Hospital, The Second Affiliated Hospital, Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Huaqiu Chen
- National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Juelu Wang
- Townsend Family Laboratories, Department of Psychiatry, Graduate Program in Neuroscience, Djavad Mowafaghian Centre for Brain Health, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Yili Wu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Alzheimer's Disease of Zhejiang Province, Zhejiang Provincial Clinical Research Center for Mental Disorders, Institute of Aging, School of Mental Health, Affiliated Kangning Hospital, The Second Affiliated Hospital, Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yun Zhang
- National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Weihong Song
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Alzheimer's Disease of Zhejiang Province, Zhejiang Provincial Clinical Research Center for Mental Disorders, Institute of Aging, School of Mental Health, Affiliated Kangning Hospital, The Second Affiliated Hospital, Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Townsend Family Laboratories, Department of Psychiatry, Graduate Program in Neuroscience, Djavad Mowafaghian Centre for Brain Health, The University of British Columbia, Vancouver, British Columbia, Canada
- National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing, China
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Abstract
Our understanding of the ubiquitin code has greatly evolved from conventional E1, E2 and E3 enzymes that modify Lys residues on specific substrates with a single type of ubiquitin chain to more complex processes that regulate and mediate ubiquitylation. In this Review, we discuss recently discovered endogenous mechanisms and unprecedented pathways by which pathogens rewrite the ubiquitin code to promote infection. These processes include unconventional ubiquitin modifications involving ester linkages with proteins, lipids and sugars, or ubiquitylation through a phosphoribosyl bridge involving Arg42 of ubiquitin. We also introduce the enzymatic pathways that write and reverse these modifications, such as the papain-like proteases of severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2. Furthermore, structural studies have revealed that the ultimate functions of ubiquitin are mediated not simply by straightforward recognition by ubiquitin-binding domains. Instead, elaborate multivalent interactions between ubiquitylated targets or ubiquitin chains and their readers (for example, the proteasome, the MLL1 complex or DOT1L) can elicit conformational changes that regulate protein degradation or transcription. The newly discovered mechanisms provide opportunities for innovative therapeutic interventions for diseases such as cancer and infectious diseases.
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Affiliation(s)
- Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany.
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7
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Li R, Song B, Xu L, Zheng J, Pan W, Cai F, Wang J, Wu Y, Song W. Regulation of USP25 by SP1 Associates with Amyloidogenesis. J Alzheimers Dis 2023; 92:1459-1472. [PMID: 36938736 DOI: 10.3233/jad-221184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
BACKGROUND Trisomy 21, an extra copy of human chromosome 21 (HSA21), causes most Down's syndrome (DS) cases. Individuals with DS inevitably develop Alzheimer's disease (AD) neuropathological phenotypes after middle age including amyloid plaques and tau neurofibrillary tangles. Ubiquitin Specific Peptidase 25 (USP25), encoding by USP25 gene located on HSA21, is a deubiquitinating enzyme, which plays an important role in both DS and AD pathogenesis. However, the regulation of USP25 remains unclear. OBJECTIVE We aimed to determine the regulation of USP25 by specificity protein 1 (SP1) in neuronal cells and its potential role in amyloidogenesis. METHODS The transcription start site and promoter activity was identified by SMART-RACE and Dual-luciferase assay. Functional SP1-responsive elements were examined by EMSA. USP25 expression was examined by RT-PCR and immunoblotting. Student's t-test or one-way ANOVA were applied or statistical analysis. RESULTS The transcription start site of human USP25 gene was identified. Three functional SP1 responsive elements in human USP25 gene were revealed. SP1 promotes USP25 transcription and subsequent USP25 protein expression, while SP1 inhibition significantly reduces USP25 expression in both non-neuronal and neuronal cells. Moreover, SP1 inhibition dramatically reduces amyloidogenesis. CONCLUSION We demonstrates that transcription factor SP1 regulates USP25 gene expression, which associates with amyloidogenesis. It suggests that SP1 signaling may play an important role in USP25 regulation and contribute to USP25-mediated DS and AD pathogenesis.
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Affiliation(s)
- Ran Li
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province,Zhejiang Provincial Clinical Research Center for Mental Disorders, School of Mental Health and Kangning Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Beibei Song
- Townsend Family Laboratories, Department of Psychiatry, Graduate Program in Neuroscience, The University of British Columbia, Vancouver, BC, Canada
| | - Lu Xu
- Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province,Zhejiang Provincial Clinical Research Center for Mental Disorders, School of Mental Health and Kangning Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jiali Zheng
- Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province,Zhejiang Provincial Clinical Research Center for Mental Disorders, School of Mental Health and Kangning Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Wenhao Pan
- Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province,Zhejiang Provincial Clinical Research Center for Mental Disorders, School of Mental Health and Kangning Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Fang Cai
- Townsend Family Laboratories, Department of Psychiatry, Graduate Program in Neuroscience, The University of British Columbia, Vancouver, BC, Canada
| | - Juelu Wang
- Townsend Family Laboratories, Department of Psychiatry, Graduate Program in Neuroscience, The University of British Columbia, Vancouver, BC, Canada
| | - Yili Wu
- Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province,Zhejiang Provincial Clinical Research Center for Mental Disorders, School of Mental Health and Kangning Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Oujiang Laboratory Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang, China
| | - Weihong Song
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province,Zhejiang Provincial Clinical Research Center for Mental Disorders, School of Mental Health and Kangning Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Oujiang Laboratory Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang, China
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8
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Feitosa WB, Morris PL. Post-ovulatory aging is associated with altered patterns for small ubiquitin-like modifier (SUMO) proteins and SUMO-specific proteases. FASEB J 2023; 37:e22816. [PMID: 36826436 DOI: 10.1096/fj.202200622r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/25/2023]
Abstract
Mammalian oocytes are ovulated arrested at metaphase of the second meiotic division. If they are not fertilized within a short period, the oocyte undergoes several progressive morphological, structural, and molecular changes during a process called oocyte aging. Herein, we focused on those functional events associated with proper cytoskeleton organization and those that correlate with spindle displacement and chromosome misalignment or scatter. Post-translational modifications by Small Ubiquitin-like Modifier (SUMO) proteins are involved in spindle organization and here we demonstrate that the SUMO pathway is involved in spindle morphology changes and chromosome movements during oocyte aging. SUMO-2/3 as well as the SUMO-specific proteases SENP-2 localization are affected by postovulatory aging in vitro. Consistent with these findings, UBC9 decreases during oocyte aging while differential ubiquitination patterns also correlate with in vitro oocyte aging. These results are consistent with postovulatory aging-related alterations in the posttranslational modifications of the spindle apparatus by SUMO and its SENP proteases. These findings are suggestive that such age-related changes in SUMOylation and the deSUMOylation of key target proteins in the spindle apparatus and kinetochore may be involved with spindle and chromosome alignment defects during mammalian oocyte postovulatory aging. Such findings may have implications for ART-related human oocyte aging in vitro regarding the activities of the SUMO pathway and fertilization success.
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Affiliation(s)
| | - Patricia L Morris
- Center for Biomedical Research, Population Council, New York, New York, USA.,The Rockefeller University, New York, New York, USA
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Ye B, Zhou H, Chen Y, Luo W, Lin W, Zhao Y, Han J, Han X, Huang W, Wu G, Wang X, Liang G. USP25 Ameliorates Pathological Cardiac Hypertrophy by Stabilizing SERCA2a in Cardiomyocytes. Circ Res 2023; 132:465-480. [PMID: 36722348 DOI: 10.1161/circresaha.122.321849] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND Pathological cardiac hypertrophy can lead to heart failure and is one of the leading causes of death globally. Understanding the molecular mechanism of pathological cardiac hypertrophy will contribute to the treatment of heart failure. DUBs (deubiquitinating enzymes) are essential to cardiac pathophysiology by precisely controlling protein function, localization, and degradation. This study set out to investigate the role and molecular mechanism of a DUB, USP25 (ubiquitin-specific peptidase 25), in pathological cardiac hypertrophy. METHODS The role of USP25 in myocardial hypertrophy was evaluated in murine cardiomyocytes in response to Ang II (angiotensin II) and transverse aortic constriction stimulation and in hypertrophic myocardium tissues of heart failure patients. Liquid chromotography with mass spectrometry/mass spectrometry analysis combined with Co-IP was used to identify SERCA2a (sarcoplasmic/endoplasmic reticulum Ca2+-ATPase 2A), an antihypertrophy protein, as an interacting protein of USP25. To clarify the molecular mechanism of USP25 in the regulation of SERCA2a, we constructed a series of mutant plasmids of USP25. In addition, we overexpressed USP25 and SERCA2a in the heart with adenoassociated virus serotype 9 vectors to validate the biological function of USP25 and SERCA2a interaction. RESULTS We revealed increased protein level of USP25 in murine cardiomyocytes subject to Ang II and transverse aortic constriction stimulation and in hypertrophic myocardium tissues of patients with heart failure. USP25 deficiency aggravated cardiac hypertrophy and cardiac dysfunction under Ang II and transverse aortic constriction treatment. Mechanistically, USP25 bound to SERCA2a directly via its USP (ubiquitin-specific protease) domain and cysteine at position 178 of USP25 exerts deubiquitination to maintain the stability of the SERCA2a protein by removing the K48 ubiquitin chain and preventing proteasomal pathway degradation, thereby maintaining calcium handling in cardiomyocytes. Moreover, restoration of USP25 expression via adenoassociated virus serotype 9 vectors in USP25-/- mice attenuated Ang II-induced cardiac hypertrophy and cardiac dysfunction, whereas myocardial overexpression of SERCA2a could mimic the effect of USP25. CONCLUSIONS We confirmed that USP25 inhibited cardiac hypertrophy by deubiquitinating and stabilizing SERCA2a.
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Affiliation(s)
- Bozhi Ye
- Chemical Biology Research Center, School of Pharmaceutical Sciences (B.Y., Y.C.,W. Luo, W. Lin, Y. Z, J.H., G.L.), Wenzhou Medical University, Zhejiang, China.,Department of Cardiology and the Key Laboratory of Cardiovascular Disease of Wenzhou, the First Affiliated Hospital (B.Y., H.Z., Y.C., W. Luo, W. Lin, W.H., G.W., G.L.), Wenzhou Medical University, Zhejiang, China
| | - Hao Zhou
- Department of Cardiology and the Key Laboratory of Cardiovascular Disease of Wenzhou, the First Affiliated Hospital (B.Y., H.Z., Y.C., W. Luo, W. Lin, W.H., G.W., G.L.), Wenzhou Medical University, Zhejiang, China
| | - Yanghao Chen
- Chemical Biology Research Center, School of Pharmaceutical Sciences (B.Y., Y.C.,W. Luo, W. Lin, Y. Z, J.H., G.L.), Wenzhou Medical University, Zhejiang, China.,Department of Cardiology and the Key Laboratory of Cardiovascular Disease of Wenzhou, the First Affiliated Hospital (B.Y., H.Z., Y.C., W. Luo, W. Lin, W.H., G.W., G.L.), Wenzhou Medical University, Zhejiang, China
| | - Wu Luo
- Chemical Biology Research Center, School of Pharmaceutical Sciences (B.Y., Y.C.,W. Luo, W. Lin, Y. Z, J.H., G.L.), Wenzhou Medical University, Zhejiang, China.,Department of Cardiology and the Key Laboratory of Cardiovascular Disease of Wenzhou, the First Affiliated Hospital (B.Y., H.Z., Y.C., W. Luo, W. Lin, W.H., G.W., G.L.), Wenzhou Medical University, Zhejiang, China
| | - Wante Lin
- Chemical Biology Research Center, School of Pharmaceutical Sciences (B.Y., Y.C.,W. Luo, W. Lin, Y. Z, J.H., G.L.), Wenzhou Medical University, Zhejiang, China.,Department of Cardiology and the Key Laboratory of Cardiovascular Disease of Wenzhou, the First Affiliated Hospital (B.Y., H.Z., Y.C., W. Luo, W. Lin, W.H., G.W., G.L.), Wenzhou Medical University, Zhejiang, China
| | - Ying Zhao
- Chemical Biology Research Center, School of Pharmaceutical Sciences (B.Y., Y.C.,W. Luo, W. Lin, Y. Z, J.H., G.L.), Wenzhou Medical University, Zhejiang, China
| | - Jibo Han
- Chemical Biology Research Center, School of Pharmaceutical Sciences (B.Y., Y.C.,W. Luo, W. Lin, Y. Z, J.H., G.L.), Wenzhou Medical University, Zhejiang, China
| | - Xue Han
- School of Pharmaceutical Sciences, Hangzhou Medical College, Zhejiang, China (X.H., G.L.)
| | - Weijian Huang
- Department of Cardiology and the Key Laboratory of Cardiovascular Disease of Wenzhou, the First Affiliated Hospital (B.Y., H.Z., Y.C., W. Luo, W. Lin, W.H., G.W., G.L.), Wenzhou Medical University, Zhejiang, China
| | - Gaojun Wu
- Department of Cardiology and the Key Laboratory of Cardiovascular Disease of Wenzhou, the First Affiliated Hospital (B.Y., H.Z., Y.C., W. Luo, W. Lin, W.H., G.W., G.L.), Wenzhou Medical University, Zhejiang, China
| | - Xu Wang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Sciences (X.W.), Wenzhou Medical University, Zhejiang, China
| | - Guang Liang
- Chemical Biology Research Center, School of Pharmaceutical Sciences (B.Y., Y.C.,W. Luo, W. Lin, Y. Z, J.H., G.L.), Wenzhou Medical University, Zhejiang, China.,Department of Cardiology and the Key Laboratory of Cardiovascular Disease of Wenzhou, the First Affiliated Hospital (B.Y., H.Z., Y.C., W. Luo, W. Lin, W.H., G.W., G.L.), Wenzhou Medical University, Zhejiang, China.,School of Pharmaceutical Sciences, Hangzhou Medical College, Zhejiang, China (X.H., G.L.)
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10
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Jiang Q, Foglizzo M, Morozov YI, Yang X, Datta A, Tian L, Thada V, Li W, Zeqiraj E, Greenberg RA. Autologous K63 deubiquitylation within the BRCA1-A complex licenses DNA damage recognition. J Cell Biol 2022; 221:e202111050. [PMID: 35938958 PMCID: PMC9386975 DOI: 10.1083/jcb.202111050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 05/15/2022] [Accepted: 07/15/2022] [Indexed: 02/03/2023] Open
Abstract
The BRCA1-A complex contains matching lysine-63 ubiquitin (K63-Ub) binding and deubiquitylating activities. How these functionalities are coordinated to effectively respond to DNA damage remains unknown. We generated Brcc36 deubiquitylating enzyme (DUB) inactive mice to address this gap in knowledge in a physiologic system. DUB inactivation impaired BRCA1-A complex damage localization and repair activities while causing early lethality when combined with Brca2 mutation. Damage response dysfunction in DUB-inactive cells corresponded to increased K63-Ub on RAP80 and BRCC36. Chemical cross-linking coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS) and cryogenic-electron microscopy (cryo-EM) analyses of isolated BRCA1-A complexes demonstrated the RAP80 ubiquitin interaction motifs are occupied by ubiquitin exclusively in the DUB-inactive complex, linking auto-inhibition by internal K63-Ub chains to loss of damage site ubiquitin recognition. These findings identify RAP80 and BRCC36 as autologous DUB substrates in the BRCA1-A complex, thus explaining the evolution of matching ubiquitin-binding and hydrolysis activities within a single macromolecular assembly.
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Affiliation(s)
- Qinqin Jiang
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Martina Foglizzo
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Yaroslav I. Morozov
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Xuejiao Yang
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Arindam Datta
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Lei Tian
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Vaughn Thada
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Weihua Li
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Elton Zeqiraj
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Roger A. Greenberg
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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11
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Ubiquitin Specific Protease USP48 Destabilizes NF-κB/p65 in Retinal Pigment Epithelium Cells. Int J Mol Sci 2022; 23:ijms23179682. [PMID: 36077078 PMCID: PMC9456453 DOI: 10.3390/ijms23179682] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 12/14/2022] Open
Abstract
Activation of NF-κB transcription factor is strictly regulated to accurately direct cellular processes including inflammation, immunity, and cell survival. In the retina, the modulation of the NF-κB pathway is essential to prevent excessive inflammatory responses, which plays a pivotal role in many retinal neurodegenerative diseases, such as age-related macular degeneration (AMD), diabetic retinopathy (DR), and inherited retinal dystrophies (IRDs). A critical cytokine mediating inflammatory responses in retinal cells is tumor necrosis factor-alpha (TNFα), leading to the activation of several transductional pathways, including NF-κB. However, the multiple factors orchestrating the appropriate regulation of NF-κB in retinal cells still remain unclear. The present study explores how the ubiquitin-specific protease 48 (USP48) downregulation impacts the stability and transcriptional activity of NF-κB/p65 in retinal pigment epithelium (RPE), at both basal conditions and following TNFα stimulation. We described that USP48 downregulation stabilizes p65. Notably, the accumulation of p65 is mainly detectable in the nuclear compartment and it is accompanied by an increased NF-κB transcriptional activity. These results delineate a novel role of USP48 in negatively regulating NF-κB in retinal cells, providing new opportunities for therapeutic intervention in retinal pathologies.
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12
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Estavoyer B, Messmer C, Echbicheb M, Rudd CE, Milot E, Affar EB. Mechanisms orchestrating the enzymatic activity and cellular functions of deubiquitinases. J Biol Chem 2022; 298:102198. [PMID: 35764170 PMCID: PMC9356280 DOI: 10.1016/j.jbc.2022.102198] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 06/13/2022] [Accepted: 06/22/2022] [Indexed: 11/30/2022] Open
Abstract
Deubiquitinases (DUBs) are required for the reverse reaction of ubiquitination and act as major regulators of ubiquitin signaling processes. Emerging evidence suggests that these enzymes are regulated at multiple levels in order to ensure proper and timely substrate targeting and to prevent the adverse consequences of promiscuous deubiquitination. The importance of DUB regulation is highlighted by disease-associated mutations that inhibit or activate DUBs, deregulating their ability to coordinate cellular processes. Here, we describe the diverse mechanisms governing protein stability, enzymatic activity, and function of DUBs. In particular, we outline how DUBs are regulated by their protein domains and interacting partners. Intramolecular interactions can promote protein stability of DUBs, influence their subcellular localization, and/or modulate their enzymatic activity. Remarkably, these intramolecular interactions can induce self-deubiquitination to counteract DUB ubiquitination by cognate E3 ubiquitin ligases. In addition to intramolecular interactions, DUBs can also oligomerize and interact with a wide variety of cellular proteins, thereby forming obligate or facultative complexes that regulate their enzymatic activity and function. The importance of signaling and post-translational modifications in the integrated control of DUB function will also be discussed. While several DUBs are described with respect to the multiple layers of their regulation, the tumor suppressor BAP1 will be outlined as a model enzyme whose localization, stability, enzymatic activity, and substrate recognition are highly orchestrated by interacting partners and post-translational modifications.
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Affiliation(s)
- Benjamin Estavoyer
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada
| | - Clémence Messmer
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada
| | - Mohamed Echbicheb
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada
| | - Christopher E Rudd
- Laboratory for Cell Signaling in Immunotherapy, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada; Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada
| | - Eric Milot
- Laboratory for Malignant Hematopoiesis and Epigenetic Regulation of Gene Expression, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada; Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada
| | - El Bachir Affar
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada; Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada.
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13
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Veggiani G, Yates BP, Martyn GD, Manczyk N, Singer AU, Kurinov I, Sicheri F, Sidhu SS. Panel of Engineered Ubiquitin Variants Targeting the Family of Human Ubiquitin Interacting Motifs. ACS Chem Biol 2022; 17:941-956. [PMID: 35385646 PMCID: PMC9305627 DOI: 10.1021/acschembio.2c00089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ubiquitin (Ub)-binding domains embedded in intracellular proteins act as readers of the complex Ub code and contribute to regulation of numerous eukaryotic processes. Ub-interacting motifs (UIMs) are short α-helical modular recognition elements whose role in controlling proteostasis and signal transduction has been poorly investigated. Moreover, impaired or aberrant activity of UIM-containing proteins has been implicated in numerous diseases, but targeting modular recognition elements in proteins remains a major challenge. To overcome this limitation, we developed Ub variants (UbVs) that bind to 42 UIMs in the human proteome with high affinity and specificity. Structural analysis of a UbV:UIM complex revealed the molecular determinants of enhanced affinity and specificity. Furthermore, we showed that a UbV targeting a UIM in the cancer-associated Ub-specific protease 28 potently inhibited catalytic activity. Our work demonstrates the versatility of UbVs to target short α-helical Ub receptors with high affinity and specificity. Moreover, the UbVs provide a toolkit to investigate the role of UIMs in regulating and transducing Ub signals and establish a general strategy for the systematic development of probes for Ub-binding domains.
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Affiliation(s)
- Gianluca Veggiani
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Bradley P. Yates
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Gregory D. Martyn
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Noah Manczyk
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
| | - Alex U. Singer
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, NE-CAT, Cornell University, Argonne, Illinois 60439, United States
| | - Frank Sicheri
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
| | - Sachdev S. Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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14
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Zhu W, Zheng D, Wang D, Yang L, Zhao C, Huang X. Emerging Roles of Ubiquitin-Specific Protease 25 in Diseases. Front Cell Dev Biol 2021; 9:698751. [PMID: 34249948 PMCID: PMC8262611 DOI: 10.3389/fcell.2021.698751] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/01/2021] [Indexed: 12/20/2022] Open
Abstract
The balance of ubiquitination and deubiquitination plays diverse roles in regulating protein stability and cellular homeostasis. Deubiquitinating enzymes catalyze the hydrolysis and removal of ubiquitin chains from target proteins and play critical roles in various disease processes, including cancer, immune responses to viral infections and neurodegeneration. This article aims to summarize roles of the deubiquitinating enzyme ubiquitin-specific protease 25 (USP25) in disease onset and progression. Previous studies have focused on the role of USP25 in antiviral immunity and neurodegenerative diseases. Recently, however, as the structural similarities and differences between USP25 and its homolog USP28 have become clear, mechanisms of action of USP25 in cancer and other diseases have been gradually revealed.
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Affiliation(s)
- Wenjing Zhu
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Dandan Zheng
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Dandan Wang
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Lehe Yang
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Chengguang Zhao
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xiaoying Huang
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
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15
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Wang Y, Wang F. Post-Translational Modifications of Deubiquitinating Enzymes: Expanding the Ubiquitin Code. Front Pharmacol 2021; 12:685011. [PMID: 34177595 PMCID: PMC8224227 DOI: 10.3389/fphar.2021.685011] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022] Open
Abstract
Post-translational modifications such as ubiquitination play important regulatory roles in several biological processes in eukaryotes. This process could be reversed by deubiquitinating enzymes (DUBs), which remove conjugated ubiquitin molecules from target substrates. Owing to their role as essential enzymes in regulating all ubiquitin-related processes, the abundance, localization, and catalytic activity of DUBs are tightly regulated. Dysregulation of DUBs can cause dramatic physiological consequences and a variety of disorders such as cancer, and neurodegenerative and inflammatory diseases. Multiple factors, such as transcription and translation of associated genes, and the presence of accessory domains, binding proteins, and inhibitors have been implicated in several aspects of DUB regulation. Beyond this level of regulation, emerging studies show that the function of DUBs can be regulated by a variety of post-translational modifications, which significantly affect the abundance, localization, and catalytic activity of DUBs. The most extensively studied post-translational modification of DUBs is phosphorylation. Besides phosphorylation, ubiquitination, SUMOylation, acetylation, oxidation, and hydroxylation are also reported in DUBs. In this review, we summarize the current knowledge on the regulatory effects of post-translational modifications of DUBs.
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Affiliation(s)
- Yanfeng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Feng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
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16
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Hou Z, Shi W, Feng J, Wang W, Zheng E, Lin H, Yu C, Li L. Self-stabilizing regulation of deubiquitinating enzymes in an enzymatic activity-dependent manner. Int J Biol Macromol 2021; 181:1081-1091. [PMID: 33864866 DOI: 10.1016/j.ijbiomac.2021.04.073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 03/30/2021] [Accepted: 04/12/2021] [Indexed: 11/18/2022]
Abstract
Deubiquitinating enzymes (DUBs) play important roles in many physiological and pathological processes by modulating the ubiquitination of their substrates. DUBs undergo post-translational modifications including ubiquitination. However, whether DUBs can reverse their own ubiquitination and regulate their own protein stability requires further investigation. To answer this question, we screened an expression library of DUBs and their enzymatic activity mutants and found that some DUBs regulated their own protein stability in an enzymatic activity- and homomeric interaction-dependent manner. Taking Ubiquitin-specific-processing protease 29 (USP29) as an example, we found that USP29 deubiquitinates itself and protects itself from proteasomal degradation. We also revealed that the N-terminal region of USP29 is critical for its protein stability. Taken together, our work demonstrates that at least some DUBs regulate their own ubiquitination and protein stability. Our findings provide novel molecular insight into the diverse regulation of DUBs.
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Affiliation(s)
- Zhenzhu Hou
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Wanyan Shi
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Jinan Feng
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Wei Wang
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Enrun Zheng
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Hanbin Lin
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Cheng Yu
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Lisheng Li
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China; Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, 1 Xueyuan Road, Minhou, Fuzhou, China.
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17
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Regulation of Deubiquitinating Enzymes by Post-Translational Modifications. Int J Mol Sci 2020; 21:ijms21114028. [PMID: 32512887 PMCID: PMC7312083 DOI: 10.3390/ijms21114028] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/01/2020] [Accepted: 06/01/2020] [Indexed: 01/04/2023] Open
Abstract
Ubiquitination and deubiquitination play a critical role in all aspects of cellular processes, and the enzymes involved are tightly regulated by multiple factors including posttranslational modifications like most other proteins. Dysfunction or misregulation of these enzymes could have dramatic physiological consequences, sometimes leading to diseases. Therefore, it is important to have a clear understanding of these regulatory processes. Here, we have reviewed the posttranslational modifications of deubiquitinating enzymes and their consequences on the catalytic activity, stability, abundance, localization, and interaction with the partner proteins.
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18
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Shibata N, Ohoka N, Tsuji G, Demizu Y, Miyawaza K, Ui-Tei K, Akiyama T, Naito M. Deubiquitylase USP25 prevents degradation of BCR-ABL protein and ensures proliferation of Ph-positive leukemia cells. Oncogene 2020; 39:3867-3878. [PMID: 32203161 DOI: 10.1038/s41388-020-1253-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 02/27/2020] [Accepted: 02/27/2020] [Indexed: 02/07/2023]
Abstract
Fusion genes resulting from chromosomal rearrangements are frequently found in a variety of cancer cells. Some of these are known to be driver oncogenes, such as BCR-ABL in chronic myelogenous leukemia (CML). The products of such fusion genes are abnormal proteins that are ordinarily degraded in cells by a mechanism known as protein quality control. This suggests that the degradation of BCR-ABL protein is suppressed in CML cells to ensure their proliferative activity. Here, we show that ubiquitin-specific protease 25 (USP25) suppresses the degradation of BCR-ABL protein in cells harboring Philadelphia chromosome (Ph). USP25 was found proximal to BCR-ABL protein in cells. Depletion of USP25 using shRNA-mediated gene silencing increased the ubiquitylated BCR-ABL, and reduced the level of BCR-ABL protein. Accordingly, BCR-ABL-mediated signaling and cell proliferation were suppressed in BCR-ABL-positive leukemia cells by the depletion of USP25. We further found that pharmacological inhibition of USP25 induced rapid degradation of BCR-ABL protein in Ph-positive leukemia cells, regardless of their sensitivity to tyrosine kinase inhibitors. These results indicate that USP25 is a novel target for inducing the degradation of oncogenic BCR-ABL protein in Ph-positive leukemia cells. This could be an effective approach to overcome resistance to kinase inhibitors.
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MESH Headings
- Cell Proliferation/drug effects
- Deubiquitinating Enzymes/genetics
- Drug Resistance, Neoplasm/genetics
- Gene Silencing/drug effects
- Genes, abl/genetics
- Humans
- Jurkat Cells
- K562 Cells
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Philadelphia Chromosome
- Protein Kinase Inhibitors/pharmacology
- Proteolysis/drug effects
- RNA, Small Interfering/genetics
- Ubiquitin Thiolesterase/genetics
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Affiliation(s)
- Norihito Shibata
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kanagawa, 210-9501, Japan
| | - Nobumichi Ohoka
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kanagawa, 210-9501, Japan
| | - Genichiro Tsuji
- Division of Organic Chemistry, National Institute of Health Sciences, Kanagawa, 210-9501, Japan
| | - Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences, Kanagawa, 210-9501, Japan
| | - Keiji Miyawaza
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Yamanashi, 409-3898, Japan
| | - Kumiko Ui-Tei
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan
| | - Tetsu Akiyama
- Laboratory of Molecular and Genetic Information, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Mikihiko Naito
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kanagawa, 210-9501, Japan.
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19
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Differential Oligomerization of the Deubiquitinases USP25 and USP28 Regulates Their Activities. Mol Cell 2019; 74:421-435.e10. [PMID: 30926243 DOI: 10.1016/j.molcel.2019.02.029] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 12/13/2018] [Accepted: 02/20/2019] [Indexed: 12/12/2022]
Abstract
Deubiquitinases have emerged as promising drug targets for cancer therapy. The two DUBs USP25 and USP28 share high similarity but vary in their cellular functions. USP28 is known for its tumor-promoting role, whereas USP25 is a regulator of the innate immune system and, recently, a role in tumorigenesis was proposed. We solved the structures of the catalytic domains of both proteins and established substantial differences in their activities. While USP28 is a constitutively active dimer, USP25 presents an auto-inhibited tetramer. Our data indicate that the activation of USP25 is not achieved through substrate or ubiquitin binding. USP25 cancer-associated mutations lead to activation in vitro and in vivo, thereby providing a functional link between auto-inhibition and the cancer-promoting role of the enzyme. Our work led to the identification of significant differences between USP25 and USP28 and provided the molecular basis for the development of new and highly specific anti-cancer drugs.
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20
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The ubiquitin interacting motifs of USP37 act on the proximal Ub of a di-Ub chain to enhance catalytic efficiency. Sci Rep 2019; 9:4119. [PMID: 30858488 PMCID: PMC6412040 DOI: 10.1038/s41598-019-40815-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 01/14/2019] [Indexed: 02/08/2023] Open
Abstract
USP37 is a deubiquitinase (DUB) with roles in the regulation of DNA damage repair and the cohesion of sister chromatids during mitosis. USP37 contains a unique insert of three ubiquitin interacting motifs (UIMs) within its catalytic DUB domain. We investigated the role of the three UIMs in the ability of USP37 to cleave di-ubiquitin chains. We found that the third UIM of USP37 recognizes the proximal ubiquitin moiety of K48 di-Ub to potentiate cleavage activity and posit that this mechanism of action may be generalizable to other chain types. In the case of K48-linked ubiquitin chains this potentiation stemmed largely from a dramatic increase in catalytic rate (kcat). We also developed and characterized three ubiquitin variant (UbV) inhibitors that selectively engage distinct binding sites in USP37. In addition to validating the deduced functional roles of the three UIMs in catalysis, the UbVs highlight a novel and effective means to selectively inhibit members of the difficult to drug DUB family.
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21
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Liu B, Sureda-Gómez M, Zhen Y, Amador V, Reverter D. A quaternary tetramer assembly inhibits the deubiquitinating activity of USP25. Nat Commun 2018; 9:4973. [PMID: 30478318 PMCID: PMC6255862 DOI: 10.1038/s41467-018-07510-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 11/01/2018] [Indexed: 01/13/2023] Open
Abstract
USP25 deubiquitinating enzyme is a key member of the ubiquitin system, which acts as a positive regulator of the Wnt/β-catenin signaling by promoting the deubiquitination and stabilization of tankyrases. USP25 is characterized by the presence of a long insertion in the middle of the conserved catalytic domain. The crystal structure of USP25 displays an unexpected homotetrameric quaternary assembly that is directly involved in the inhibition of its enzymatic activity. The tetramer is assembled by the association of two dimers and includes contacts between the coiled-coil insertion domain and the ubiquitin-binding pocket at the catalytic domain, revealing a distinctive autoinhibitory mechanism. Biochemical and kinetic assays with dimer, tetramer and truncation constructs of USP25 support this mechanism, displaying higher catalytic activity in the dimer assembly. Moreover, the high stabilization of tankyrases in cultured cells by ectopic expression of a constitutive dimer of USP25 supports a biological relevance of this tetramerization/inhibition mechanism. USP25 is a deubiquitinating enzyme and a positive regulator of Wnt/β-catenin signaling. Here the authors present the crystal structure of USP25 in a tetrameric inactive state and their biochemical and kinetic assays support an USP25 autoinhibitory mechanism that is mediated through a dimer to tetramerization transition.
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Affiliation(s)
- Bing Liu
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.,Dept. de Bioquímica i Biologia Molecular, Serra Hunter Fellow, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - Marta Sureda-Gómez
- Institut de Investigacions Biomèdiques Agustí Pi i Sunyer (IDIBABS), Barcelona, 08036, Spain
| | - Yang Zhen
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.,Dept. de Bioquímica i Biologia Molecular, Serra Hunter Fellow, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - Virginia Amador
- Institut de Investigacions Biomèdiques Agustí Pi i Sunyer (IDIBABS), Barcelona, 08036, Spain
| | - David Reverter
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain. .,Dept. de Bioquímica i Biologia Molecular, Serra Hunter Fellow, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.
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22
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Habtemichael EN, Li DT, Alcázar-Román A, Westergaard XO, Li M, Petersen MC, Li H, DeVries SG, Li E, Julca-Zevallos O, Wolenski JS, Bogan JS. Usp25m protease regulates ubiquitin-like processing of TUG proteins to control GLUT4 glucose transporter translocation in adipocytes. J Biol Chem 2018; 293:10466-10486. [PMID: 29773651 DOI: 10.1074/jbc.ra118.003021] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/09/2018] [Indexed: 12/14/2022] Open
Abstract
Insulin stimulates the exocytic translocation of specialized vesicles in adipocytes, which inserts GLUT4 glucose transporters into the plasma membrane to enhance glucose uptake. Previous results support a model in which TUG (Tether containing a UBX domain for GLUT4) proteins trap these GLUT4 storage vesicles at the Golgi matrix and in which insulin triggers endoproteolytic cleavage of TUG to translocate GLUT4. Here, we identify the muscle splice form of Usp25 (Usp25m) as a protease required for insulin-stimulated TUG cleavage and GLUT4 translocation in adipocytes. Usp25m is expressed in adipocytes, binds TUG and GLUT4, dissociates from TUG-bound vesicles after insulin addition, and colocalizes with TUG and insulin-responsive cargoes in unstimulated cells. Previous results show that TUG proteolysis generates the ubiquitin-like protein, TUGUL (for TUGubiquitin-like). We now show that TUGUL modifies the kinesin motor protein, KIF5B, and that TUG proteolysis is required to load GLUT4 onto these motors. Insulin stimulates TUG proteolytic processing independently of phosphatidylinositol 3-kinase. In nonadipocytes, TUG cleavage can be reconstituted by transfection of Usp25m, but not the related Usp25a isoform, together with other proteins present on GLUT4 vesicles. In rodents with diet-induced insulin resistance, TUG proteolysis and Usp25m protein abundance are reduced in adipose tissue. These effects occur soon after dietary manipulation, prior to the attenuation of insulin signaling to Akt. Together with previous data, these results support a model whereby insulin acts through Usp25m to mediate TUG cleavage, which liberates GLUT4 storage vesicles from the Golgi matrix and activates their microtubule-based movement to the plasma membrane. This TUG proteolytic pathway for insulin action is independent of Akt and is impaired by nutritional excess.
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Affiliation(s)
| | - Don T Li
- From the Section of Endocrinology and Metabolism, Department of Internal Medicine and.,the Departments of Cell Biology and
| | - Abel Alcázar-Román
- From the Section of Endocrinology and Metabolism, Department of Internal Medicine and
| | - Xavier O Westergaard
- From the Section of Endocrinology and Metabolism, Department of Internal Medicine and
| | - Muyi Li
- From the Section of Endocrinology and Metabolism, Department of Internal Medicine and
| | - Max C Petersen
- From the Section of Endocrinology and Metabolism, Department of Internal Medicine and.,Cellular and Molecular Physiology, Yale University School of Medicine
| | - Hanbing Li
- From the Section of Endocrinology and Metabolism, Department of Internal Medicine and.,the Institute of Pharmacology, Department of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
| | - Stephen G DeVries
- From the Section of Endocrinology and Metabolism, Department of Internal Medicine and
| | - Eric Li
- From the Section of Endocrinology and Metabolism, Department of Internal Medicine and
| | - Omar Julca-Zevallos
- From the Section of Endocrinology and Metabolism, Department of Internal Medicine and.,the Departments of Cell Biology and
| | - Joseph S Wolenski
- the Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, and
| | - Jonathan S Bogan
- From the Section of Endocrinology and Metabolism, Department of Internal Medicine and .,the Departments of Cell Biology and
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23
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Kessler BM, Bursomanno S, McGouran JF, Hickson ID, Liu Y. Biochemical and Mass Spectrometry-Based Approaches to Profile SUMOylation in Human Cells. Methods Mol Biol 2018; 1491:131-144. [PMID: 27778286 DOI: 10.1007/978-1-4939-6439-0_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Posttranslational modification of proteins with the small ubiquitin-like modifier (SUMO) regulates protein function in the context of cell cycle and DNA repair. The occurrence of SUMOylation is less frequent as compared to protein modification with ubiquitin, and appears to be controlled by a smaller pool of conjugating and deconjugating enzymes. Mass spectrometry has been instrumental in defining specific as well as proteome-wide views of SUMO-dependent biological processes, and several methodological approaches have been developed in the recent past. Here, we provide an overview of the latest experimental approaches to the study of SUMOylation, and also describe hands-on protocols using a combination of biochemistry and mass spectrometry-based technologies to profile proteins that are SUMOylated in human cells.
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Affiliation(s)
- Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
| | - Sara Bursomanno
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Astra Zeneca, Godsmottagningen MA1, Pepparedsleden, 43183, Mölndal, Sweden
| | - Joanna F McGouran
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.,School of Chemistry, Trinity College Dublin, University of Dublin, College Green, Dublin 2, Ireland
| | - Ian D Hickson
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Astra Zeneca, Godsmottagningen MA1, Pepparedsleden, 43183, Mölndal, Sweden
| | - Ying Liu
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Astra Zeneca, Godsmottagningen MA1, Pepparedsleden, 43183, Mölndal, Sweden
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24
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Abstract
Although growing numbers of oncoproteins and pro-metastatic proteins have been extensively characterized, many of these tumor-promoting proteins are not good drug targets, which represent a major barrier to curing breast cancer and other cancers. There is a need, therefore, for alternative therapeutic approaches to destroying cancer-promoting proteins. The human genome encodes approximately 100 deubiquitinating enzymes (DUBs, also called deubiquitinases), which are amenable to pharmacologic inhibition by small molecules. By removing monoubiquitin or polyubiquitin chains from the target protein, DUBs can modulate the degradation, localization, activity, trafficking, and recycling of the substrate, thereby contributing substantially to the regulation of cancer proteins and pathways. Targeting certain DUBs may lead to destabilization or functional inactivation of some key oncoproteins or pro-metastatic proteins, including non-druggable ones, which will provide therapeutic benefits to cancer patients. In breast cancer, growing numbers of DUBs are found to be aberrantly expressed. Depending on their substrates, specific DUBs can either promote or suppress mammary tumors. In this article, we review the role and mechanisms of action of DUBs in breast cancer and discuss the potential of targeting DUBs for cancer treatment.
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25
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Site-specific identification and quantitation of endogenous SUMO modifications under native conditions. Nat Commun 2017; 8:1171. [PMID: 29079793 PMCID: PMC5660086 DOI: 10.1038/s41467-017-01271-3] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 09/01/2017] [Indexed: 11/25/2022] Open
Abstract
Small ubiquitin-like modifier (SUMO) modification regulates numerous cellular processes. Unlike ubiquitin, detection of endogenous SUMOylated proteins is limited by the lack of naturally occurring protease sites in the C-terminal tail of SUMO proteins. Proteome-wide detection of SUMOylation sites on target proteins typically requires ectopic expression of mutant SUMOs with introduced tryptic sites. Here, we report a method for proteome-wide, site-level detection of endogenous SUMOylation that uses α-lytic protease, WaLP. WaLP digestion of SUMOylated proteins generates peptides containing SUMO-remnant diglycyl-lysine (KGG) at the site of SUMO modification. Using previously developed immuno-affinity isolation of KGG-containing peptides followed by mass spectrometry, we identified 1209 unique endogenous SUMO modification sites. We also demonstrate the impact of proteasome inhibition on ubiquitin and SUMO-modified proteomes using parallel quantitation of ubiquitylated and SUMOylated peptides. This methodological advancement enables determination of endogenous SUMOylated proteins under completely native conditions. SUMOylation is post-translational modification implicated in several biological pathways. Here the authors describe an approach for the global profiling of SUMO attachment sites under native conditions that also allows the parallel determination of SUMO and Ub attachments.
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26
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Yang Y, Shi L, Ding Y, Shi Y, Hu HY, Wen Y, Zhang N. Structural and Functional Investigations of the N-Terminal Ubiquitin Binding Region of Usp25. Biophys J 2017; 112:2099-2108. [PMID: 28538147 DOI: 10.1016/j.bpj.2017.04.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 04/11/2017] [Accepted: 04/18/2017] [Indexed: 10/19/2022] Open
Abstract
Ubiquitin-specific protease 25 (Usp25) is a deubiquitinase that is involved in multiple biological processes. The N-terminal ubiquitin-binding region (UBR) of Usp25 contains one ubiquitin-associated domain, one small ubiquitin-like modifier (SUMO)-interacting motif and two ubiquitin-interacting motifs. Previous studies suggest that the covalent sumoylation in the UBR of Usp25 impairs its enzymatic activity. Here, we raise the hypothesis that non-covalent binding of SUMO, a prerequisite for efficient sumoylation, will impair Usp25's catalytic activity as well. To test our hypothesis and elucidate the underlying molecular mechanism, we investigated the structure and function of the Usp25 N-terminal UBR. The solution structure of Usp251-146 is obtained, and the key residues responsible for recognition of ubiquitin and SUMO2 are identified. Our data suggest inhibition of Usp25's catalytic activity upon the non-covalent binding of SUMO2 to the Usp25 SUMO-interacting motif. We also find that SUMO2 can competitively block the interaction between the Usp25 UBR and its ubiquitin substrates. Based on our findings, we have proposed a working model to depict the regulatory role of the Usp25 UBR in the functional display of the enzyme.
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Affiliation(s)
- Yuanyuan Yang
- CAS Key Laboratory of Receptor Research, Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Li Shi
- CAS Key Laboratory of Receptor Research, Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yiluan Ding
- CAS Key Laboratory of Receptor Research, Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yanhong Shi
- CAS Key Laboratory of Receptor Research, Department of Analytical Chemistry, Shanghai Institute of Materia Medica, 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
| | - Yi Wen
- CAS Key Laboratory of Receptor Research, Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
| | - Naixia Zhang
- CAS Key Laboratory of Receptor Research, Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China.
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27
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Affiliation(s)
- Tycho E.T. Mevissen
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - David Komander
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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28
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Abstract
Deubiquitylating enzymes (DUBs) reverse the ubiquitylation of target proteins, thereby regulating diverse cellular functions. In contrast to the plethora of research being conducted on the ability of DUBs to counter the degradation of cellular proteins or auto-ubiquitylated E3 ligases, very little is known about the mechanisms of DUB regulation. In this review paper, we summarize a novel possible mechanism of DUB deubiquitylation by other DUBs. The available data suggest the need for further experiments to validate and characterize this notion of 'Dubbing DUBs'. The current studies indicate that the idea of deubiquitylation of DUBs by other DUBs is still in its infancy. Nevertheless, future research holds the promise of validation of this concept.
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Affiliation(s)
- Saba Haq
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, South Korea
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
- College of Medicine, Hanyang University, Seoul, South Korea
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29
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Audagnotto M, Dal Peraro M. Protein post-translational modifications: In silico prediction tools and molecular modeling. Comput Struct Biotechnol J 2017; 15:307-319. [PMID: 28458782 PMCID: PMC5397102 DOI: 10.1016/j.csbj.2017.03.004] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 03/17/2017] [Accepted: 03/21/2017] [Indexed: 02/09/2023] Open
Abstract
Post-translational modifications (PTMs) occur in almost all proteins and play an important role in numerous biological processes by significantly affecting proteins' structure and dynamics. Several computational approaches have been developed to study PTMs (e.g., phosphorylation, sumoylation or palmitoylation) showing the importance of these techniques in predicting modified sites that can be further investigated with experimental approaches. In this review, we summarize some of the available online platforms and their contribution in the study of PTMs. Moreover, we discuss the emerging capabilities of molecular modeling and simulation that are able to complement these bioinformatics methods, providing deeper molecular insights into the biological function of post-translational modified proteins.
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Affiliation(s)
- Martina Audagnotto
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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30
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Kawaguchi K, Uo K, Tanaka T, Komada M. Tandem UIMs confer Lys48 ubiquitin chain substrate preference to deubiquitinase USP25. Sci Rep 2017; 7:45037. [PMID: 28327663 PMCID: PMC5361193 DOI: 10.1038/srep45037] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/20/2017] [Indexed: 11/21/2022] Open
Abstract
Ubiquitin-specific protease (USP) 25, belonging to the USP family of deubiquitinases, harbors two tandem ubiquitin-interacting motifs (UIMs), a ~20-amino-acid α-helical stretch that binds to ubiquitin. However, the role of the UIMs in USP25 remains unclear. Here we show that the tandem UIM region binds to Lys48-, but not Lys63-, linked ubiquitin chains, where the two UIMs played a critical and cooperative role. Purified USP25 exhibited higher ubiquitin isopeptidase activity to Lys48-, than to Lys63-, linked ubiquitin chains. Mutations that disrupted the ubiquitin-binding ability of the tandem UIMs resulted in a reduced ubiquitin isopeptidase activity of USP25, suggesting a role for the UIMs in exerting the full catalytic activity of USP25. Moreover, when mutations that convert the binding preference from Lys48- to Lys63-linked ubiquitin chains were introduced into the tandem UIM region, the USP25 mutants acquired elevated and reduced isopeptidase activity toward Lys63- and Lys48-linked ubiquitin chains, respectively. These results suggested that the binding preference of the tandem UIMs toward Lys48-linked ubiquitin chains contributes not only to the full catalytic activity but also to the ubiquitin chain substrate preference of USP25, possibly by selectively holding the Lys48-linked ubiquitin chain substrates in the proximity of the catalytic core.
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Affiliation(s)
- Kohei Kawaguchi
- Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Kazune Uo
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Toshiaki Tanaka
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Masayuki Komada
- Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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31
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Masoumi KC, Marfany G, Wu Y, Massoumi R. Putative role of SUMOylation in controlling the activity of deubiquitinating enzymes in cancer. Future Oncol 2016; 12:565-74. [PMID: 26777062 DOI: 10.2217/fon.15.320] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Deubiquitinating enzymes (DUBs) are specialized proteins that can recognize ubiquitinated proteins, and after direct interaction, deconjugate monomeric or polymeric ubiquitin chains, thus changing the fate of the substrates. This process is instrumental in mediating or changing downstream signaling pathways. Beside mutations and alterations in their expression levels, the activity and stability of deubiquitinating enzymes is vital for their function. SUMOylations consist of the conjugation of the small peptide SUMO to protein substrates which is very similar to ubiquitination in the mechanistic and machinery required. In this review, we will focus on how SUMOylation can regulate DUB enzymatic activity, stability or DUB interaction with partners and substrates, in cancer. Furthermore, we will discuss the impact of these recent findings in the identification of new potential tools for efficient anticancer treatment strategies.
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Affiliation(s)
- Katarzyna C Masoumi
- Department of Laboratory Medicine, Medicon Village, Lund University, 22381 Lund, Sweden
| | - Gemma Marfany
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain.,Institut de Biomedicina (IBUB), Universitat de Barcelona, 08007 Barcelona, Spain.,CIBERER, Instituto de Salud Carlos III, Barcelona, Spain
| | - Yingli Wu
- Department of Pathophysiology, Chemical Biology Division of Shanghai Universities E-Institutes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ramin Massoumi
- Department of Laboratory Medicine, Medicon Village, Lund University, 22381 Lund, Sweden
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32
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The N-terminal ubiquitin-binding region of ubiquitin-specific protease 28 modulates its deubiquitination function: NMR structural and mechanistic insights. Biochem J 2015; 471:155-65. [DOI: 10.1042/bj20150088] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 08/12/2015] [Indexed: 11/17/2022]
Abstract
We have characterized the structure and function of the N-terminal UBR of Usp28 in this study. Our findings are helpful for a better understanding of the underlying molecular mechanism in the control of catalytic activity of DUBs.
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33
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Zhang H, Wang D, Zhong H, Luo R, Shang M, Liu D, Chen H, Fang L, Xiao S. Ubiquitin-specific Protease 15 Negatively Regulates Virus-induced Type I Interferon Signaling via Catalytically-dependent and -independent Mechanisms. Sci Rep 2015; 5:11220. [PMID: 26061460 PMCID: PMC4650652 DOI: 10.1038/srep11220] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 05/18/2015] [Indexed: 01/07/2023] Open
Abstract
Viral infection triggers a series of signaling cascades, which converge to activate the transcription factors nuclear factor-κB (NF-κB) and interferon regulatory factor 3 (IRF3), thereby inducing the transcription of type I interferons (IFNs). Although not fully characterized, these innate antiviral responses are fine-tuned by dynamic ubiquitination and deubiquitination processes. In this study, we report ubiquitin-specific protease (USP) 15 is involved in regulation of the retinoic acid-inducible gene I (RIG-I)-dependent type I IFN induction pathway. Knockdown of endogenous USP15 augmented cellular antiviral responses. Overexpression of USP15 inhibited the transcription of IFN-β. Further analyses identified histidine 862 as a critical residue for USP15's catalytic activity. Interestingly, USP15 specifically removed lysine 63-linked polyubiquitin chains from RIG-I among the essential components in RIG-I-like receptor-dependent pathway. In addition, we demonstrated that in contrast to USP15 de-ubiquitinating (DUB) activity, USP15-mediated inhibition of IFN signaling was not abolished by mutations eliminating the catalytic activity, indicating that a fraction of USP15-mediated IFN antagonism was independent of the DUB activity. Catalytically inactive USP15 mutants, as did the wild-type protein, disrupted virus-induced interaction of RIG-I and IFN-β promoter stimulator 1. Taken together, our data demonstrate that USP15 acts as a negative regulator of RIG-I signaling via DUB-dependent and independent mechanisms.
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Affiliation(s)
- Huan Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Dang Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Huijuan Zhong
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Rui Luo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Min Shang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Dezhi Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Liurong Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
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34
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Vaccinia-Related Kinase 2 Controls the Stability of the Eukaryotic Chaperonin TRiC/CCT by Inhibiting the Deubiquitinating Enzyme USP25. Mol Cell Biol 2015; 35:1754-62. [PMID: 25755282 DOI: 10.1128/mcb.01325-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/25/2015] [Indexed: 11/20/2022] Open
Abstract
Molecular chaperones monitor the proper folding of misfolded proteins and function as the first line of defense against mutant protein aggregation in neurodegenerative diseases. The eukaryotic chaperonin TRiC is a potent suppressor of mutant protein aggregation and toxicity in early stages of disease progression. Elucidation of TRiC functional regulation will enable us to better understand the pathological mechanisms of neurodegeneration. We have previously shown that vaccinia-related kinase 2 (VRK2) downregulates TRiC protein levels through the ubiquitin-proteasome system by recruiting the E3 ligase COP1. However, although VRK2 activity was necessary in TRiC downregulation, the phosphorylated substrate was not determined. Here, we report that USP25 is a novel TRiC interacting protein that is also phosphorylated by VRK2. USP25 catalyzed deubiquitination of the TRiC protein and stabilized the chaperonin, thereby reducing accumulation of misfolded polyglutamine protein aggregates. Notably, USP25 deubiquitinating activity was suppressed when VRK2 phosphorylated the Thr(680), Thr(727), and Ser(745) residues. Impaired USP25 deubiquitinating activity after VRK2-mediated phosphorylation may be a critical pathway in TRiC protein destabilization.
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35
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Zhen Y, Knobel PA, Stracker TH, Reverter D. Regulation of USP28 deubiquitinating activity by SUMO conjugation. J Biol Chem 2014; 289:34838-50. [PMID: 25359778 DOI: 10.1074/jbc.m114.601849] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
USP28 (ubiquitin-specific protease 28) is a deubiquitinating enzyme that has been implicated in the DNA damage response, the regulation of Myc signaling, and cancer progression. The half-life stability of major regulators of critical cellular pathways depends on the activities of specific ubiquitin E3 ligases that target them for proteosomal degradation and deubiquitinating enzymes that promote their stabilization. One function of the post-translational small ubiquitin modifier (SUMO) is the regulation of enzymatic activity of protein targets. In this work, we demonstrate that the SUMO modification of the N-terminal domain of USP28 negatively regulates its deubiquitinating activity, revealing a role for the N-terminal region as a regulatory module in the control of USP28 activity. Despite the presence of ubiquitin-binding domains in the N-terminal domain, its truncation does not impair deubiquitinating activity on diubiquitin or polyubiquitin chain substrates. In contrast to other characterized USP deubiquitinases, our results indicate that USP28 has a chain preference activity for Lys(11), Lys(48), and Lys(63) diubiquitin linkages.
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Affiliation(s)
- Yang Zhen
- From the Institut de Biotecnologia i de Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain and
| | - Philip A Knobel
- the Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | | | - David Reverter
- From the Institut de Biotecnologia i de Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain and
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36
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Shi L, Wen Y, Zhang N. ¹H, ¹³C and ¹⁵N backbone and side-chain resonance assignments of the N-terminal ubiquitin-binding domains of USP25. BIOMOLECULAR NMR ASSIGNMENTS 2014; 8:255-258. [PMID: 23754700 DOI: 10.1007/s12104-013-9495-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 06/03/2013] [Indexed: 06/02/2023]
Abstract
Ubiquitin Specific Protease 25 (USP25), a member of the deubiquitinase family, is involved in several disease-related signal pathways including myogenesis, immunity and protein degradation. It specially catalyzes the hydrolysis of the K48-linked and K63-linked polyubiquitin chains. USP25 contains one ubiquitin-associated domain and two ubiquitin-interacting motifs (UIMs) in its N-terminal region, which interact with ubiquitin and play a role in substrate recognition. Besides, it has been shown that the catalysis activity of USP25 is either impaired by sumoylation or enhanced by ubiquitination within its UIM. To elucidate the structural basis of the cross-regulation of USP25 function by non-covalent binding and covalent modifications of ubiquitin and SUMO2/3, a systematic structural biology study of USP25 is required. Here, we report the (1)H, (13)C and (15)N backbone and side-chain resonance assignments of the N-terminal ubiquitin binding domains (UBDs) of USP25 with BMRB accession number of 19111, which is the first step of the systematic structural biology study of the enzyme.
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Affiliation(s)
- Li Shi
- Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
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37
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Li Y, Sun XX, Elferich J, Shinde U, David LL, Dai MS. Monoubiquitination is critical for ovarian tumor domain-containing ubiquitin aldehyde binding protein 1 (Otub1) to suppress UbcH5 enzyme and stabilize p53 protein. J Biol Chem 2014; 289:5097-108. [PMID: 24403071 PMCID: PMC3931068 DOI: 10.1074/jbc.m113.533109] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 01/07/2014] [Indexed: 01/09/2023] Open
Abstract
Ovarian tumor domain-containing ubiquitin (Ub) aldehyde binding protein 1 (Otub1) regulates p53 stability and activity via non-canonical inhibition of the MDM2 cognate Ub-conjugating enzyme (E2) UbcH5. However, it is not clear how this activity of Otub1 is regulated in cells. Here we report that Otub1 is monoubiquitinated by UbcH5 in cells and in vitro, primarily at the lysine 59 and 109 residues. This monoubiquitination, in turn, contributes to the activity of Otub1 to suppress UbcH5. The lysine-free Otub1 mutant (Otub1(K0)) fails to be monoubiquitinated and is unable to suppress the Ub-conjugating activity of UbcH5 in vitro and the MDM2-mediated p53 ubiquitination in cells. Consistently, this mutant is unable to stabilize p53, induce apoptosis, and suppress cell proliferation. Overexpression of Otub1(K0) inhibits DNA-damage induced apoptosis. Adding either Lys-59 or Lys-109 back to the Otub1(K0) mutant restores the monoubiquitination of Otub1 and its function to stabilize and activate p53. We further show that UbcH5 preferentially binds to the monoubiquitinated Otub1 via Ub interaction with its backside donor Ub-interacting surface, suggesting that this binding interferes with the self-assembly of Ub-charged UbcH5 (UbcH5∼Ub) conjugates, which is critical for Ub transfer. Thus, our data reveal novel insights into the Otub1 inhibition of E2 wherein monoubiquitination promotes the interaction of Otub1 with UbcH5 and the function to suppress it.
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Affiliation(s)
- Yuhuang Li
- From the Departments of Molecular and Medical Genetics and
- the Oregon Health and Science University Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239
| | - Xiao-Xin Sun
- From the Departments of Molecular and Medical Genetics and
- the Oregon Health and Science University Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239
| | | | - Ujwal Shinde
- Biochemistry and Molecular Biology, School of Medicine, and
| | - Larry L. David
- Biochemistry and Molecular Biology, School of Medicine, and
- the Oregon Health and Science University Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239
| | - Mu-Shui Dai
- From the Departments of Molecular and Medical Genetics and
- the Oregon Health and Science University Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239
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38
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Tanno H, Shigematsu T, Nishikawa S, Hayakawa A, Denda K, Tanaka T, Komada M. Ubiquitin-interacting motifs confer full catalytic activity, but not ubiquitin chain substrate specificity, to deubiquitinating enzyme USP37. J Biol Chem 2013; 289:2415-23. [PMID: 24324262 DOI: 10.1074/jbc.m113.528372] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ubiquitin-specific proteases (USPs) consist of a family of deubiquitinating enzymes with more than 50 members in humans. Three of them, including USP37, contain ubiquitin-interacting motifs (UIMs), an ∼20-amino acid α-helical stretch that binds to ubiquitin. However, the roles of the UIMs in these USP enzymes remain unknown. USP37 has three UIMs, designated here as UIMs 1, 2, and 3 from the N-terminal side, between the Cys and His boxes comprising the catalytic core. Here, we examined the role of the UIMs in USP37 using its mutants that harbor mutations in the UIMs. The nuclear localization of USP37 was not affected by the UIM mutations. However, mutations in UIM2 or UIM3, but not UIM1, resulted in a significant decrease in USP37 binding to ubiquitinated proteins in the cell. In vitro, a region of USP37 harboring the three UIMs also bound to both Lys(48)-linked and Lys(63)-linked ubiquitin chains in a UIM2- and UIM3-dependent manner. The level of USP37 ubiquitination was also reduced by mutations in UIM2 or UIM3, suggesting their role in ubiquitination of USP37 itself. Finally, mutants lacking functional UIM2 or UIM3 exhibited a reduced isopeptidase activity toward ubiquitinated proteins in the cell and both Lys(48)-linked and Lys(63)-linked ubiquitin chains. These results suggested that the UIMs in USP37 contribute to the full enzymatic activity, but not ubiquitin chain substrate specificity, of USP37 possibly by holding the ubiquitin chain substrate in the proximity of the catalytic core.
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Affiliation(s)
- Hidetaka Tanno
- From the Department of Biological Sciences, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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39
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Zhong H, Wang D, Fang L, Zhang H, Luo R, Shang M, Ouyang C, Ouyang H, Chen H, Xiao S. Ubiquitin-specific proteases 25 negatively regulates virus-induced type I interferon signaling. PLoS One 2013; 8:e80976. [PMID: 24260525 PMCID: PMC3832446 DOI: 10.1371/journal.pone.0080976] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 10/08/2013] [Indexed: 12/28/2022] Open
Abstract
Ubiquitination and deubiquitination have emerged as critical regulatory processes in the virus-triggered type I interferon (IFN) induction pathway. In this study, we carried out a targeted siRNA screen of 54 ubiquitin-specific proteases (USPs) and identified USP25 as a negative regulator of the virus-triggered type I IFN signaling pathway. Overexpression of USP25 inhibited virus-induced activation of IFN-β, interferon regulation factor 3 (IRF3) and nuclear factor-kappa B (NF-κB), as well as the phosphorylation of IRF3 and NF-κB subunit p65. Furthermore, Knockdown of USP25 potentiated virus-induced induction of the IFN-β. In addition, detailed analysis demonstrated that USP25 cleaved lysine 48- and lysine 63-linked polyubiquitin chains in vitro and in vivo, and its deubiquitinating enzyme (DUB) activity, were dependent on a cysteine residue (Cys178) and a histidine residue (His607). USP25 mutants lacking DUB activity lost the ability to block virus-induced type I IFN to some degree. Mechanistically, USP25 deubiquitinated retinoic acid-inducible gene I (RIG-I), tumornecrosis factor (TNF) receptor-associated factor 2 (TRAF2), and TRAF6 to inhibit RIG-I-like receptor-mediated IFN signaling. Our findings suggest that USP25 is a novel DUB negatively regulating virus-induced type I IFN production.
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Affiliation(s)
- Huijuan Zhong
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Dang Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Liurong Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- * E-mail:
| | - Huan Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Rui Luo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Min Shang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Chao Ouyang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Haiping Ouyang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
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40
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Tsou WL, Burr AA, Ouyang M, Blount JR, Scaglione KM, Todi SV. Ubiquitination regulates the neuroprotective function of the deubiquitinase ataxin-3 in vivo. J Biol Chem 2013; 288:34460-9. [PMID: 24106274 DOI: 10.1074/jbc.m113.513903] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Deubiquitinases (DUBs) are proteases that regulate various cellular processes by controlling protein ubiquitination. Cell-based studies indicate that the regulation of the activity of DUBs is important for homeostasis and is achieved by multiple mechanisms, including through their own ubiquitination. However, the physiological significance of the ubiquitination of DUBs to their functions in vivo is unclear. Here, we report that ubiquitination of the DUB ataxin-3 at lysine residue 117, which markedly enhances its protease activity in vitro, is critical for its ability to suppress toxic protein-dependent degeneration in Drosophila melanogaster. Compared with ataxin-3 with only Lys-117 present, ataxin-3 that does not become ubiquitinated performs significantly less efficiently in suppressing or delaying the onset of toxic protein-dependent degeneration in flies. According to further studies, the C terminus of Hsc70-interacting protein (CHIP), an E3 ubiquitin ligase that ubiquitinates ataxin-3 in vitro, is dispensable for its ubiquitination in vivo and is not required for the neuroprotective function of this DUB in Drosophila. Our work also suggests that ataxin-3 suppresses degeneration by regulating toxic protein aggregation rather than stability.
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Affiliation(s)
- Wei-Ling Tsou
- From the Departments of Pharmacology and Neurology and
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41
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Zhong B, Liu X, Wang X, Liu X, Li H, Darnay BG, Lin X, Sun SC, Dong C. Ubiquitin-specific protease 25 regulates TLR4-dependent innate immune responses through deubiquitination of the adaptor protein TRAF3. Sci Signal 2013; 6:ra35. [PMID: 23674823 DOI: 10.1126/scisignal.2003708] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Protein ubiquitination plays a critical role in Toll-like receptor (TLR) signaling and innate immunity. Although several E3 ubiquitin ligases have been identified downstream of TLRs, the regulation of protein deubiquitination in TLR-triggered innate immune responses is poorly understood. We identified ubiquitin-specific protease 25 (USP25) as a regulator of TLR signaling. USP25 was recruited to the TLR4 signaling complex, and it associated with the adaptor proteins tumor necrosis factor receptor-associated factor 3 (TRAF3) and TRAF6 after stimulation of TLR4 with its ligand lipopolysaccharide (LPS). USP25 specifically reversed the Lys(48)-linked ubiquitination of TRAF3 that was mediated by the E3 ubiquitin ligase cIAP2 (cellular inhibitor of apoptosis 2). Deficiency in USP25 enhanced the extent of ubiquitination of TRAF3 and accelerated its degradation after TLR4 activation, which potentiated TLR4-induced activation of NF-κB (nuclear factor κB) and MAPK (mitogen-activated protein kinase) signaling, but inhibited activation of the transcription factor IRF3 (interferon regulatory factor 3). USP25-deficient mice exhibited increased susceptibility to LPS-induced septic shock compared to their wild-type counterparts, which was associated with enhanced production of proinflammatory cytokines and decreased production of interferon-α. Thus, by inhibiting the degradation of TRAF3 during TLR4 activation, USP25 enables a balanced innate immune response.
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Affiliation(s)
- Bo Zhong
- Department of Immunology, Center for Inflammation and Cancer, MD Anderson Cancer Center, Houston, TX 77054, USA
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42
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Seki T, Gong L, Williams AJ, Sakai N, Todi SV, Paulson HL. JosD1, a membrane-targeted deubiquitinating enzyme, is activated by ubiquitination and regulates membrane dynamics, cell motility, and endocytosis. J Biol Chem 2013; 288:17145-55. [PMID: 23625928 DOI: 10.1074/jbc.m113.463406] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The functional diversity of deubiquitinating enzymes (DUBs) is not well understood. The MJD family of DUBs consists of four cysteine proteases that share a catalytic "Josephin" domain. The family is named after the DUB ATXN3, which causes the neurodegenerative disease Machado-Joseph disease. The two closely related Josephin domain-containing (JosD) proteins 1 and 2 consist of little more than the Josephin domain. To gain insight into the properties of Josephin domains, we investigated JosD1 and JosD2. JosD1 and JosD2 were found to differ fundamentally in many respects. In vitro, only JosD2 can cleave ubiquitin chains. In contrast, JosD1 cleaves ubiquitin chains only after it is monoubiquitinated, a form of posttranslational-dependent regulation shared with ATXN3. A significant fraction of JosD1 is monoubiquitinated in diverse mouse tissues. In cell-based studies, JosD2 localizes to the cytoplasm whereas JosD1 preferentially localizes to the plasma membrane, particularly when ubiquitinated. The membrane occupancy by JosD1 suggests that it could participate in membrane-dependent events such as cell motility and endocytosis. Indeed, time-lapse imaging revealed that JosD1 enhances membrane dynamics and cell motility. JosD1 also influences endocytosis in cultured cells by increasing the uptake of endocytic markers of macropinocytosis while decreasing those for clathrin- and caveolae-mediated endocytosis. Our results establish that two closely related DUBs differ markedly in activity and function and that JosD1, a membrane-associated DUB whose activity is regulated by ubiquitination, helps regulate membrane dynamics, cell motility, and endocytosis.
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Affiliation(s)
- Takahiro Seki
- Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109, USA
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43
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Zhong B, Liu X, Wang X, Chang SH, Liu X, Wang A, Reynolds JM, Dong C. Negative regulation of IL-17-mediated signaling and inflammation by the ubiquitin-specific protease USP25. Nat Immunol 2012; 13:1110-7. [PMID: 23042150 PMCID: PMC3477275 DOI: 10.1038/ni.2427] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 08/21/2012] [Indexed: 01/12/2023]
Abstract
Interleukin 17 (IL-17) plays an important role in infection and autoimmunity; how it signals remains poorly understood. In this study, we identified ubiquitin-specific protease 25 (USP25) as a negative regulator of IL-17-mediated signaling and inflammation. Overexpression of USP25 inhibited IL-17-triggered signaling, while USP25 deficiency resulted in increased phosphorylation of IκBα and Jnk, increased expression of chemokines and cytokines as well as prolonged half-life of Cxcl1 mRNA following IL-17 treatment. Consistently, Usp25-/- mice exhibited increased sensitivity to IL-17-dependent inflammation and autoimmunity in vivo. Mechanistically, IL-17 stimulation induced the association of USP25 with TRAF5 and TRAF6 and USP25 induced removal of Act1-mediated K63-linked ubiquitination in TRAF5 and TRAF6. Thus, our results demonstrate that USP25 is a deubiquitinating enzyme (DUB) that negatively regulates IL-17-triggered signaling.
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Affiliation(s)
- Bo Zhong
- Department of Immunology and Center for Inflammation and Cancer, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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44
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Blount JR, Burr AA, Denuc A, Marfany G, Todi SV. Ubiquitin-specific protease 25 functions in Endoplasmic Reticulum-associated degradation. PLoS One 2012; 7:e36542. [PMID: 22590560 PMCID: PMC3348923 DOI: 10.1371/journal.pone.0036542] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 04/06/2012] [Indexed: 11/29/2022] Open
Abstract
Endoplasmic Reticulum (ER)-associated degradation (ERAD) discards abnormal proteins synthesized in the ER. Through coordinated actions of ERAD components, misfolded/anomalous proteins are recognized, ubiquitinated, extracted from the ER and ultimately delivered to the proteasome for degradation. It is not well understood how ubiquitination of ERAD substrates is regulated. Here, we present evidence that the deubiquitinating enzyme Ubiquitin-Specific Protease 25 (USP25) is involved in ERAD. Our data support a model where USP25 counteracts ubiquitination of ERAD substrates by the ubiquitin ligase HRD1, rescuing them from degradation by the proteasome.
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Affiliation(s)
- Jessica R. Blount
- Department of Pharmacology and Department of Neurology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Aaron A. Burr
- Department of Pharmacology and Department of Neurology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Graduate Program in Cancer Biology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Amanda Denuc
- Department of Genetics, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Gemma Marfany
- Department of Genetics, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Sokol V. Todi
- Department of Pharmacology and Department of Neurology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Graduate Program in Cancer Biology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- * E-mail: .
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45
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Husnjak K, Dikic I. Ubiquitin-binding proteins: decoders of ubiquitin-mediated cellular functions. Annu Rev Biochem 2012; 81:291-322. [PMID: 22482907 DOI: 10.1146/annurev-biochem-051810-094654] [Citation(s) in RCA: 580] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ubiquitin acts as a versatile cellular signal that controls a wide range of biological processes including protein degradation, DNA repair, endocytosis, autophagy, transcription, immunity, and inflammation. The specificity of ubiquitin signaling is achieved by alternative conjugation signals (monoubiquitin and ubiquitin chains) and interactions with ubiquitin-binding proteins (known as ubiquitin receptors) that decode ubiquitinated target signals into biochemical cascades in the cell. Herein, we review the current knowledge pertaining to the structural and functional features of ubiquitin-binding proteins and the mechanisms by which they recognize various types of ubiquitin topologies. The combinatorial use of diverse ubiquitin-binding domains (UBDs) in full-length proteins, selective recognition of chains with distinct linkages and length, and posttranslational modifications of ubiquitin receptors or multivalent interactions within protein complexes illustrate a few mechanisms by which a circuitry of signaling networks can be rewired by ubiquitin-binding proteins to control cellular functions in vivo.
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Affiliation(s)
- Koraljka Husnjak
- Institute of Biochemistry II, School of Medicine, Goethe University, 60590 Frankfurt am Main, Germany.
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46
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Praefcke GJK, Hofmann K, Dohmen RJ. SUMO playing tag with ubiquitin. Trends Biochem Sci 2011; 37:23-31. [PMID: 22018829 DOI: 10.1016/j.tibs.2011.09.002] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 09/13/2011] [Accepted: 09/15/2011] [Indexed: 10/16/2022]
Abstract
In addition to being structurally related, the protein modifiers ubiquitin and SUMO (small ubiquitin-related modifier), share a multitude of functional interrelations. These include the targeting of the same attachment sites in certain substrates, and SUMO-dependent ubiquitylation in others. Notably, several cellular processes, including the targeting of repair machinery to DNA damage sites, require the sequential sumoylation and ubiquitylation of distinct substrates. Some proteins promote both modifications. By contrast, the activity of some enzymes that control either sumoylation or ubiquitylation is regulated by the respective other modification. In this review, we summarize recent findings regarding intersections between SUMO and ubiquitin that influence genome stability and cell growth and which are relevant in pathogen resistance and cancer treatment.
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Affiliation(s)
- Gerrit J K Praefcke
- Center for Molecular Medicine Cologne, Institute for Genetics, University of Cologne, Cologne Biocenter, Zülpicher Straße 47a, D-50674 Cologne, Germany
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47
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Yang K, Moldovan GL, Vinciguerra P, Murai J, Takeda S, D'Andrea AD. Regulation of the Fanconi anemia pathway by a SUMO-like delivery network. Genes Dev 2011; 25:1847-58. [PMID: 21896657 DOI: 10.1101/gad.17020911] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The USP1/UAF1 complex deubiquitinates the Fanconi anemia protein FANCD2, thereby promoting homologous recombination and DNA cross-link repair. How USP1/UAF1 is targeted to the FANCD2/FANCI heterodimer has remained unknown. Here we show that UAF1 contains a tandem repeat of SUMO-like domains in its C terminus (SLD1 and SLD2). SLD2 binds directly to a SUMO-like domain-interacting motif (SIM) on FANCI. Deletion of the SLD2 sequence of UAF1 or mutation of the SIM on FANCI disrupts UAF1/FANCI binding and inhibits FANCD2 deubiquitination and DNA repair. The USP1/UAF1 complex also deubiquitinates PCNA-Ub, and deubiquitination requires the PCNA-binding protein hELG1. The SLD2 sequence of UAF1 binds to a SIM on hELG1, thus targeting the USP1/UAF1 complex to its PCNA-Ub substrate. We propose that the regulated targeting of USP1/UAF1 to its DNA repair substrates, FANCD2-Ub and PCNA-Ub, by SLD-SIM interactions coordinates homologous recombination and translesion DNA synthesis.
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Affiliation(s)
- Kailin Yang
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
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48
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Kessler BM, Edelmann MJ. PTMs in conversation: activity and function of deubiquitinating enzymes regulated via post-translational modifications. Cell Biochem Biophys 2011; 60:21-38. [PMID: 21480003 PMCID: PMC3094536 DOI: 10.1007/s12013-011-9176-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Deubiquitinating enzymes (DUBs) constitute a diverse protein family and their impact on numerous biological and pathological processes has now been widely appreciated. Many DUB functions have to be tightly controlled within the cell, and this can be achieved in several ways, such as substrate-induced conformational changes, binding to adaptor proteins, proteolytic cleavage, and post-translational modifications (PTMs). This review is focused on the role of PTMs including monoubiquitination, sumoylation, acetylation, and phosphorylation as characterized and putative regulative factors of DUB function. Although this aspect of DUB functionality has not been yet thoroughly studied, PTMs represent a versatile and reversible method of controlling the role of DUBs in biological processes. In several cases PTMs might constitute a feedback mechanism insuring proper functioning of the ubiquitin proteasome system and other DUB-related pathways.
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Affiliation(s)
- Benedikt M Kessler
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
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49
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Weissman AM, Shabek N, Ciechanover A. The predator becomes the prey: regulating the ubiquitin system by ubiquitylation and degradation. Nat Rev Mol Cell Biol 2011; 12:605-20. [PMID: 21860393 PMCID: PMC3545438 DOI: 10.1038/nrm3173] [Citation(s) in RCA: 240] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ubiquitylation (also known as ubiquitination) regulates essentially all of the intracellular processes in eukaryotes through highly specific modification of numerous cellular proteins, which is often tightly regulated in a spatial and temporal manner. Although most often associated with proteasomal degradation, ubiquitylation frequently serves non-proteolytic functions. In light of its central roles in cellular regulation, it has not been surprising to find that many of the components of the ubiquitin system itself are regulated by ubiquitylation. This observation has broad implications for pathophysiology.
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Affiliation(s)
- Allan M. Weissman
- Laboratory of Protein Dynamics and Signaling, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Nitzan Shabek
- Cancer and Vascular Biology Research Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Aaron Ciechanover
- Cancer and Vascular Biology Research Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 31096, Israel
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Bozza WP, Zhuang Z. Biochemical characterization of a multidomain deubiquitinating enzyme Ubp15 and the regulatory role of its terminal domains. Biochemistry 2011; 50:6423-32. [PMID: 21710968 DOI: 10.1021/bi200529z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Deubiquitinating enzymes (DUBs) have emerged as essential players in a myriad of cellular processes, yet the regulation of DUB function remains largely unknown. While some DUBs rely on the formation of complex for regulation of enzymatic activity, many DUBs utilize interdomain interactions to regulate catalysis. Here we report the biochemical characterization of a multidomain deubiquitinating enzyme, Ubp15, from Saccharomyces cerevisiae. Steady-state kinetic investigation showed that Ubp15 is a highly active DUB. We identified active-site residues that are required for catalysis. We have also identified key residues on Ubp15 required for ubiquitin binding and catalysis. We further demonstrated that Ubp15's enzymatic activity is regulated by the N- and C-terminal domains that flank the catalytic core domain. Moreover, we demonstrated that Ubp15 physically interacts with a WD40 repeat-containing protein, Cdh1, by copurification experiments. Interestingly, unlike other DUBs that specifically interact with WD40 repeat-containing proteins, Cdh1 does not function in stimulating Ubp15's activity. The possible cellular function of Ubp15 in cell cycle regulation is discussed in view of the specific interaction between Ubp15 and Cdh1, an activator of the anaphase-promoting complex/cyclosome (APC/C).
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Affiliation(s)
- William P Bozza
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, Delaware 19716, USA
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