1
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Wu CJ, Li X, Sommers CL, Kurima K, Huh S, Bugos G, Dong L, Li W, Griffith AJ, Samelson LE. Expression of a TMC6-TMC8-CIB1 heterotrimeric complex in lymphocytes is regulated by each of the components. J Biol Chem 2020; 295:16086-16099. [PMID: 32917726 DOI: 10.1074/jbc.ra120.013045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 09/09/2020] [Indexed: 11/06/2022] Open
Abstract
The TMC genes encode a set of homologous transmembrane proteins whose functions are not well understood. Biallelic mutations in either TMC6 or TMC8 are detected in more than half of cases of the pre-malignant skin disease epidermodysplasia verruciformis (EV). It is controversial whether EV induced by mutations in TMC6 or TMC8 originates from keratinocyte or lymphocyte defects. Quantification of TMC6 and TMC8 RNA levels in various organs revealed that lymphoid tissues have the highest levels of expression of both genes, and custom antibodies confirmed protein expression in mouse lymphocytes. To study the function of these proteins we generated mice with targeted deletion mutant alleles of Tmc6 or Tmc8 Either TMC6 or TMC8 deficiency induced a reduction in apparent molecular weight and/or amount of the other TMC molecule. Co-immunoprecipitation experiments indicated that TMC6 and TMC8 formed a protein complex in mouse and human T cells. MS and biochemical analysis demonstrated that TMC6 and TMC8 additionally interacted with the CIB1 protein to form TMC6-TMC8-CIB1 trimers. We demonstrated that TMC6 and TMC8 regulated CIB1 levels by protecting CIB1 from ubiquitination and proteasomal degradation. Reciprocally, CIB1 was needed for stabilizing TMC6 and TMC8 levels. These results suggest why inactivating mutations in any of the three human genes leads to similar clinical presentations. We also demonstrated that TMC6 and TMC8 levels are drastically lower and the proteins are less active in regulating CIB1 in keratinocytes than in T cells. Our study suggests that defects in lymphocytes may contribute to the etiology and pathogenesis of EV.
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Affiliation(s)
- Chuan-Jin Wu
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Xing Li
- Molecular Biology and Genetics Section, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Rockville, Maryland, USA
| | - Connie L Sommers
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Kiyoto Kurima
- Molecular Biology and Genetics Section, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Rockville, Maryland, USA
| | - Sunmee Huh
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Grace Bugos
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Lijin Dong
- Genetic Engineering Core, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Wenmei Li
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Andrew J Griffith
- Molecular Biology and Genetics Section, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Rockville, Maryland, USA
| | - Lawrence E Samelson
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.
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2
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Sivakumar D, Kumar V, Naumann M, Stein M. Activation and selectivity of OTUB-1 and OTUB-2 deubiquitinylases. J Biol Chem 2020; 295:6972-6982. [PMID: 32265297 DOI: 10.1074/jbc.ra120.013073] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/06/2020] [Indexed: 12/16/2022] Open
Abstract
The ovarian tumor domain (OTU) deubiquitinylating cysteine proteases OTUB1 and OTUB2 (OTU ubiquitin aldehyde binding 1 and 2) are representative members of the OTU subfamily of deubiquitinylases. Deubiquitinylation critically regulates a multitude of important cellular processes, such as apoptosis, cell signaling, and growth. Moreover, elevated OTUB expression has been observed in various cancers, including glioma, endometrial cancer, ovarian cancer, and breast cancer. Here, using molecular dynamics simulation approaches, we found that both OTUB1 and OTUB2 display a catalytic triad characteristic of proteases but differ in their configuration and protonation states. The OTUB1 protein had a prearranged catalytic site, with strong electrostatic interactions between the active-site residues His265 and Asp267 In OTUB2, however, the arrangement of the catalytic triad was different. In the absence of ubiquitin, the neutral states of the catalytic-site residues in OTUB2 were more stable, resulting in larger distances between these residues. Only upon ubiquitin binding did the catalytic triad in OTUB2 rearrange and bring the active site into a catalytically feasible state. An analysis of water access channels revealed only a few diffusion trajectories for the catalytically active form of OTUB1, whereas in OTUB2 the catalytic site was solvent-accessible, and a larger number of water molecules reached and left the binding pocket. Interestingly, in OTUB2, the catalytic residues His224 and Asn226 formed a stable hydrogen bond. We propose that the observed differences in activation kinetics, protonation states, water channels, and active-site accessibility between OTUB1 and OTUB2 may be relevant for the selective design of OTU inhibitors.
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Affiliation(s)
- Dakshinamurthy Sivakumar
- Max Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, 39106 Magdeburg, Germany
| | - Vikash Kumar
- Max Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, 39106 Magdeburg, Germany.,Institute of Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Michael Naumann
- Institute of Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Matthias Stein
- Max Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, 39106 Magdeburg, Germany
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3
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Vengayil V, Rashida Z, Laxman S. The E3 ubiquitin ligase Pib1 regulates effective gluconeogenic shutdown upon glucose availability. J Biol Chem 2019; 294:17209-17223. [PMID: 31604822 PMCID: PMC6873170 DOI: 10.1074/jbc.ra119.009822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/27/2019] [Indexed: 12/31/2022] Open
Abstract
Cells use multiple mechanisms to regulate their metabolic states in response to changes in their nutrient environment. One example is the response of cells to glucose. In Saccharomyces cerevisiae growing in glucose-depleted medium, the re-availability of glucose leads to the down-regulation of gluconeogenesis and the activation of glycolysis, leading to "glucose repression." However, our knowledge of the mechanisms mediating the glucose-dependent down-regulation of the gluconeogenic transcription factors is limited. Using the major gluconeogenic transcription factor Rds2 as a candidate, we identify here a novel role for the E3 ubiquitin ligase Pib1 in regulating the stability and degradation of Rds2. Glucose addition to cells growing under glucose limitation results in a rapid ubiquitination of Rds2, followed by its proteasomal degradation. Through in vivo and in vitro experiments, we establish Pib1 as the ubiquitin E3 ligase that regulates Rds2 ubiquitination and stability. Notably, this Pib1-mediated Rds2 ubiquitination, followed by proteasomal degradation, is specific to the presence of glucose. This Pib1-mediated ubiquitination of Rds2 depends on the phosphorylation state of Rds2, suggesting a cross-talk between ubiquitination and phosphorylation to achieve a metabolic state change. Using stable isotope-based metabolic flux experiments, we find that the loss of Pib1 results in an imbalanced gluconeogenic state, regardless of glucose availability. Pib1 is required for complete glucose repression and enables cells to optimally grow in competitive environments when glucose again becomes available. Our results reveal the existence of a Pib1-mediated regulatory program that mediates glucose repression when glucose availability is restored.
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Affiliation(s)
- Vineeth Vengayil
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Post, Bellary Road, Bangalore 560065, India
- Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Zeenat Rashida
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Post, Bellary Road, Bangalore 560065, India
- Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Post, Bellary Road, Bangalore 560065, India
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4
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Wu Y, Qin J, Li F, Yang C, Li Z, Zhou Z, Zhang H, Li Y, Wang X, Liu R, Tao Q, Chen W, Chen C. USP3 promotes breast cancer cell proliferation by deubiquitinating KLF5. J Biol Chem 2019; 294:17837-17847. [PMID: 31624151 DOI: 10.1074/jbc.ra119.009102] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 10/03/2019] [Indexed: 12/12/2022] Open
Abstract
The Krüppel-like factor 5 (KLF5) transcription factor is highly expressed in basal type breast cancer and promotes breast cancer cell proliferation, survival, migration, and tumorigenesis. KLF5 protein stability is regulated by ubiquitination. In this study, ubiquitin-specific protease 3 (USP3) was identified as a new KLF5 deubiquitinase by genome-wide siRNA library screening. We demonstrated that USP3 interacts with KLF5 and stabilizes KLF5 via deubiquitination. USP3 knockdown inhibits breast cancer cell proliferation in vitro and tumorigenesis in vivo, which can be partially rescued by ectopic expression of KLF5. Furthermore, we observed a positive correlation between USP3 and KLF5 protein expression levels in human breast cancer samples. These findings suggest that USP3 is a new KLF5 deubiquitinase and that USP3 may represent a potential therapeutic target for breast cancer.
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Affiliation(s)
- Yingying Wu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,University of the Chinese Academy of Sciences, Beijing 101407, China.,First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, China
| | - Junying Qin
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Fubing Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Chuanyu Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Zhen Li
- Department of Breast Surgery, Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, China
| | - Zhongmei Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Hailin Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Yunxi Li
- Department of Breast Surgery, Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, China
| | - Xinye Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Rong Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Qian Tao
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, Sir Y. K. Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, Chinese University of Hong Kong, Hong Kong 518172, China
| | - Wenlin Chen
- Department of Breast Surgery, Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, China
| | - Ceshi Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China .,Kunming Institute of Zoology-Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Institute of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Beijing, 100101, China
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5
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Spiliotopoulos A, Blokpoel Ferreras L, Densham RM, Caulton SG, Maddison BC, Morris JR, Dixon JE, Gough KC, Dreveny I. Discovery of peptide ligands targeting a specific ubiquitin-like domain-binding site in the deubiquitinase USP11. J Biol Chem 2019; 294:424-436. [PMID: 30373771 PMCID: PMC6333900 DOI: 10.1074/jbc.ra118.004469] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/11/2018] [Indexed: 11/25/2022] Open
Abstract
Ubiquitin-specific proteases (USPs) reverse ubiquitination and regulate virtually all cellular processes. Defined noncatalytic domains in USP4 and USP15 are known to interact with E3 ligases and substrate recruitment factors. No such interactions have been reported for these domains in the paralog USP11, a key regulator of DNA double-strand break repair by homologous recombination. We hypothesized that USP11 domains adjacent to its protease domain harbor unique peptide-binding sites. Here, using a next-generation phage display (NGPD) strategy, combining phage display library screening with next-generation sequencing, we discovered unique USP11-interacting peptide motifs. Isothermal titration calorimetry disclosed that the highest affinity peptides (KD of ∼10 μm) exhibit exclusive selectivity for USP11 over USP4 and USP15 in vitro Furthermore, a crystal structure of a USP11-peptide complex revealed a previously unknown binding site in USP11's noncatalytic ubiquitin-like (UBL) region. This site interacted with a helical motif and is absent in USP4 and USP15. Reporter assays using USP11-WT versus a binding pocket-deficient double mutant disclosed that this binding site modulates USP11's function in homologous recombination-mediated DNA repair. The highest affinity USP11 peptide binder fused to a cellular delivery sequence induced significant nuclear localization and cell cycle arrest in S phase, affecting the viability of different mammalian cell lines. The USP11 peptide ligands and the paralog-specific functional site in USP11 identified here provide a framework for the development of new biochemical tools and therapeutic agents. We propose that an NGPD-based strategy for identifying interacting peptides may be applied also to other cellular targets.
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Affiliation(s)
- Anastasios Spiliotopoulos
- From the Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD
- the School of Veterinary Medicine and Science, Sutton Bonington Campus, College Road, Sutton Bonington, Leicestershire LE12 5RD
| | - Lia Blokpoel Ferreras
- From the Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD
| | - Ruth M Densham
- the Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, Medical and Dental Schools, University of Birmingham, Birmingham B15 2TT, and
| | - Simon G Caulton
- From the Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD
| | - Ben C Maddison
- ADAS, School of Veterinary Medicine and Science, Bonington Campus, College Road, Sutton Bonington, Leicestershire LE12 5RD, United Kingdom
| | - Joanna R Morris
- the Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, Medical and Dental Schools, University of Birmingham, Birmingham B15 2TT, and
| | - James E Dixon
- From the Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD
| | - Kevin C Gough
- the School of Veterinary Medicine and Science, Sutton Bonington Campus, College Road, Sutton Bonington, Leicestershire LE12 5RD,
| | - Ingrid Dreveny
- From the Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD,
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6
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Zhang C, Hoang N, Leng F, Saxena L, Lee L, Alejo S, Qi D, Khal A, Sun H, Lu F, Zhang H. LSD1 demethylase and the methyl-binding protein PHF20L1 prevent SET7 methyltransferase-dependent proteolysis of the stem-cell protein SOX2. J Biol Chem 2018; 293:3663-3674. [PMID: 29358331 DOI: 10.1074/jbc.ra117.000342] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 01/12/2018] [Indexed: 11/06/2022] Open
Abstract
The pluripotency-controlling stem-cell protein SRY-box 2 (SOX2) plays a pivotal role in maintaining the self-renewal and pluripotency of embryonic stem cells and also of teratocarcinoma or embryonic carcinoma cells. SOX2 is monomethylated at lysine 119 (Lys-119) in mouse embryonic stem cells by the SET7 methyltransferase, and this methylation triggers ubiquitin-dependent SOX2 proteolysis. However, the molecular regulators and mechanisms controlling SET7-induced SOX2 proteolysis are unknown. Here, we report that in human ovarian teratocarcinoma PA-1 cells, methylation-dependent SOX2 proteolysis is dynamically regulated by the LSD1 lysine demethylase and a methyl-binding protein, PHD finger protein 20-like 1 (PHF20L1). We found that LSD1 not only removes the methyl group from monomethylated Lys-117 (equivalent to Lys-119 in mouse SOX2), but it also demethylates monomethylated Lys-42 in SOX2, a reaction that SET7 also regulated and that also triggered SOX2 proteolysis. Our studies further revealed that PHF20L1 binds both monomethylated Lys-42 and Lys-117 in SOX2 and thereby prevents SOX2 proteolysis. Down-regulation of either LSD1 or PHF20L1 promoted SOX2 proteolysis, which was prevented by SET7 inactivation in both PA-1 and mouse embryonic stem cells. Our studies also disclosed that LSD1 and PHF20L1 normally regulate the growth of pluripotent mouse embryonic stem cells and PA-1 cells by preventing methylation-dependent SOX2 proteolysis. In conclusion, our findings reveal an important mechanism by which the stability of the pluripotency-controlling stem-cell protein SOX2 is dynamically regulated by the activities of SET7, LSD1, and PHF20L1 in pluripotent stem cells.
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Affiliation(s)
- Chunxiao Zhang
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and.,the Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Nam Hoang
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Feng Leng
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and.,the Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Lovely Saxena
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Logan Lee
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Salvador Alejo
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Dandan Qi
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and.,the Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Anthony Khal
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Hong Sun
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Fei Lu
- the Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Hui Zhang
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
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7
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Yonezawa T, Takahashi H, Shikata S, Liu X, Tamura M, Asada S, Fukushima T, Fukuyama T, Tanaka Y, Sawasaki T, Kitamura T, Goyama S. The ubiquitin ligase STUB1 regulates stability and activity of RUNX1 and RUNX1-RUNX1T1. J Biol Chem 2017; 292:12528-12541. [PMID: 28536267 DOI: 10.1074/jbc.m117.785675] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/19/2017] [Indexed: 12/18/2022] Open
Abstract
RUNX1 is a member of RUNX transcription factors and plays important roles in hematopoiesis. Disruption of RUNX1 activity has been implicated in the development of hematopoietic neoplasms. Chromosomal translocations involving the RUNX1 gene are associated with several types of leukemia, including acute myeloid leukemia driven by a leukemogenic fusion protein RUNX1-RUNX1T1. Previous studies have shown that RUNX1 is an unstable protein and is subjected to proteolytic degradation mediated by the ubiquitin-proteasome pathway. However, the precise mechanisms of RUNX1 ubiquitination have not been fully understood. Furthermore, much less is known about the mechanisms to regulate the stability of RUNX1-RUNX1T1. In this study, we identified several RUNX1-interacting E3 ubiquitin ligases using a novel high-throughput binding assay. Among them, we found that STUB1 bound to RUNX1 and induced its ubiquitination and degradation mainly in the nucleus. Immunofluorescence analyses revealed that the STUB1-induced ubiquitination also promoted nuclear export of RUNX1, which probably contributes to the reduced transcriptional activity of RUNX1 in STUB1-overexpressing cells. STUB1 also induced ubiquitination of RUNX1-RUNX1T1 and down-regulated its expression. Importantly, STUB1 overexpression showed a substantial growth-inhibitory effect in myeloid leukemia cells that harbor RUNX1-RUNX1T1, whereas it showed only a marginal effect in other non-RUNX1-RUNX1T1 leukemia cells and normal human cord blood cells. Taken together, these data suggest that the E3 ubiquitin ligase STUB1 is a negative regulator of both RUNX1 and RUNX1-RUNX1T1. Activation of STUB1 could be a promising therapeutic strategy for RUNX1-RUNX1T1 leukemia.
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Affiliation(s)
- Taishi Yonezawa
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639
| | - Hirotaka Takahashi
- Proteo-Science Center (PROS), Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Shiori Shikata
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639
| | - Xiaoxiao Liu
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639
| | - Moe Tamura
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639
| | - Shuhei Asada
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639
| | - Tsuyoshi Fukushima
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639
| | - Tomofusa Fukuyama
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639
| | - Yosuke Tanaka
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639
| | - Tatsuya Sawasaki
- Proteo-Science Center (PROS), Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Toshio Kitamura
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639
| | - Susumu Goyama
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639.
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8
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Mergner J, Kuster B, Schwechheimer C. DENEDDYLASE1 Protein Counters Automodification of Neddylating Enzymes to Maintain NEDD8 Protein Homeostasis in Arabidopsis. J Biol Chem 2017; 292:3854-3865. [PMID: 28096463 DOI: 10.1074/jbc.m116.767103] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/10/2017] [Indexed: 11/06/2022] Open
Abstract
In eukaryotes, the conjugation of the ubiquitin-like protein NEDD8 onto protein targets is an important post-translational modification. The best understood neddylation targets are the cullins, scaffold subunits of E3 ubiquitin ligases, where neddylation as well as deneddylation, facilitated by the protease activity of the CSN (COP9 signalosome), are required to control ubiquitin ligase assembly, function, and ultimately substrate degradation. Little is known about the role of other deneddylating enzymes besides CSN and the role of neddylation and deneddylation of their substrates. We previously characterized Arabidopsis thaliana mutants with defects in the conserved NEDD8-specific protease DEN1 (DENEDDYLASE1). These mutants display only subtle growth phenotypes despite the strong accumulation of a broad range of neddylated proteins. Specifically, we identified AXR1 (AUXIN-RESISTANT1), a subunit of the heterodimeric NAE (E1 NEDD8-ACTIVATING ENZYME), as highly neddylated in den1 mutants. Here, we examined the mechanism and consequences of AXR1 neddylation in more detail. We find that AXR1 as well as other neddylation enzymes are autoneddylated at multiple lysines. NAE autoneddylation can be linked to reduced NCE (E2 NEDD8-CONJUGATING ENZYME) NEDD8 thioester levels, either by critically reducing the pool of free NEDD8 or by reducing NAE activity. In planta, increasing NEDD8 gene dosage is sufficient to suppress den1 mutant phenotypes. We therefore suggest that DEN1 serves to recover diverted NEDD8 moieties from autoneddylated NAE subunits, and possibly also other neddylated proteins, to maintain NEDD8 pathway activity toward other NEDD8-dependent processes such as cullin E3 ligase regulation.
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Affiliation(s)
- Julia Mergner
- From the Chair of Plant Systems Biology, Technische Universität München, Emil-Ramann-Strasse 8 and.,the Chair of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
| | - Bernhard Kuster
- the Chair of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
| | - Claus Schwechheimer
- From the Chair of Plant Systems Biology, Technische Universität München, Emil-Ramann-Strasse 8 and
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9
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Davis MI, Pragani R, Fox JT, Shen M, Parmar K, Gaudiano EF, Liu L, Tanega C, McGee L, Hall MD, McKnight C, Shinn P, Nelson H, Chattopadhyay D, D'Andrea AD, Auld DS, DeLucas LJ, Li Z, Boxer MB, Simeonov A. Small Molecule Inhibition of the Ubiquitin-specific Protease USP2 Accelerates cyclin D1 Degradation and Leads to Cell Cycle Arrest in Colorectal Cancer and Mantle Cell Lymphoma Models. J Biol Chem 2016; 291:24628-24640. [PMID: 27681596 DOI: 10.1074/jbc.m116.738567] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 09/04/2016] [Indexed: 12/11/2022] Open
Abstract
Deubiquitinases are important components of the protein degradation regulatory network. We report the discovery of ML364, a small molecule inhibitor of the deubiquitinase USP2 and its use to interrogate the biology of USP2 and its putative substrate cyclin D1. ML364 has an IC50 of 1.1 μm in a biochemical assay using an internally quenched fluorescent di-ubiquitin substrate. Direct binding of ML364 to USP2 was demonstrated using microscale thermophoresis. ML364 induced an increase in cellular cyclin D1 degradation and caused cell cycle arrest as shown in Western blottings and flow cytometry assays utilizing both Mino and HCT116 cancer cell lines. ML364, and not the inactive analog 2, was antiproliferative in cancer cell lines. Consistent with the role of cyclin D1 in DNA damage response, ML364 also caused a decrease in homologous recombination-mediated DNA repair. These effects by a small molecule inhibitor support a key role for USP2 as a regulator of cell cycle, DNA repair, and tumor cell growth.
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Affiliation(s)
- Mindy I Davis
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Rajan Pragani
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Jennifer T Fox
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Min Shen
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Kalindi Parmar
- the Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, and
| | - Emily F Gaudiano
- the Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, and
| | - Li Liu
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Cordelle Tanega
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Lauren McGee
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Matthew D Hall
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Crystal McKnight
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Paul Shinn
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Henrike Nelson
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Debasish Chattopadhyay
- the Center for Structural Biology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Alan D D'Andrea
- the Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, and
| | - Douglas S Auld
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Larry J DeLucas
- the Center for Structural Biology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Zhuyin Li
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892
| | - Matthew B Boxer
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892,.
| | - Anton Simeonov
- From the NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892,.
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10
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Zhang Q, Harding R, Hou F, Dong A, Walker JR, Bteich J, Tong Y. Structural Basis of the Recruitment of Ubiquitin-specific Protease USP15 by Spliceosome Recycling Factor SART3. J Biol Chem 2016; 291:17283-92. [PMID: 27255711 DOI: 10.1074/jbc.m116.740787] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Indexed: 12/21/2022] Open
Abstract
Ubiquitin-specific proteases (USPs) USP15 and USP4 belong to a subset of USPs featuring an N-terminal tandem domain in USP (DUSP) and ubiquitin-like (UBL) domain. Squamous cell carcinoma antigen recognized by T-cell 3 (SART3), a spliceosome recycling factor, binds to the DUSP-UBL domain of USP15 and USP4, recruiting them to the nucleus from the cytosol to control deubiquitination of histone H2B and spliceosomal proteins, respectively. To provide structural insight, we solved crystal structures of SART3 in the apo-form and in complex with the DUSP-UBL domain of USP15 at 2.0 and 3.0 Å, respectively. Structural analysis reveals SART3 contains 12 half-a-tetratricopeptide (HAT) repeats, organized into two subdomains, HAT-N and HAT-C. SART3 dimerizes through the concave surface of HAT-C, whereas the HAT-C convex surface binds USP15 in a novel bipartite mode. Isothermal titration calorimetry measurements and mutagenesis analysis confirmed key residues of USP15 involved in the interaction and indicated USP15 binds 20-fold stronger than USP4.
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Affiliation(s)
- Qi Zhang
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Rachel Harding
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Feng Hou
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Aiping Dong
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - John R Walker
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Joseph Bteich
- the Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, and
| | - Yufeng Tong
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, the Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5G 1L7, Canada
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11
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Abstract
Ubiquitin modification at double strand breaks (DSB) sites is an essential regulator of signaling and repair. γH2AX extends from DSB sites and provides a platform for subsequent recruitment and amplification of DNA repair proteins and signaling factors. Here, we found that RNF8/RNF168 ubiquitylates γH2AX. We identified that USP11 is a unique deubiquitylation enzyme for γH2AX. USP11 deubiquitylates γH2AX both in vivo and in vitro but not the canonical (ub)-K119-H2A and (ub)-K120-H2B in vitro, and USP11 ablation enhances the levels of γH2AX ubiquitylation. We also found that USP11 interacts with γH2AX both in vivo and in vitro. We found that 53BP1 and ubiquitin-conjugated proteins are misregulated to be retained longer and stronger at DSB sites after knockdown of USP11. We further found that cells are hypersensitive to γ-irradiation after ablation of USP11. Together, our findings elucidate deeply and extensively the mechanism of RNF8/RNF168 and USP11 to maintain the proper status of ubiquitylation γH2AX to repair DSB.
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Affiliation(s)
- Miao Yu
- From the Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function and
| | - Kun Liu
- From the Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function and
| | - Zebin Mao
- From the Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function and
| | - Jianyuan Luo
- the Department of Genetics, Peking University Health Science Center, Beijing, 100191, China and
| | - Wei Gu
- the Institute for Cancer Genetics, and Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, New York 10032
| | - Wenhui Zhao
- From the Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function and
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12
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Textoris-Taube K, Keller C, Liepe J, Henklein P, Sidney J, Sette A, Kloetzel PM, Mishto M. The T210M Substitution in the HLA-a*02:01 gp100 Epitope Strongly Affects Overall Proteasomal Cleavage Site Usage and Antigen Processing. J Biol Chem 2015; 290:30417-28. [PMID: 26507656 DOI: 10.1074/jbc.m115.695189] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Indexed: 01/01/2023] Open
Abstract
MHC class I-restricted epitopes, which carry a tumor-specific mutation resulting in improved MHC binding affinity, are preferred T cell receptor targets in innovative adoptive T cell therapies. However, T cell therapy requires efficient generation of the selected epitope. How such mutations may affect proteasome-mediated antigen processing has so far not been studied. Therefore, we analyzed by in vitro experiments the effect on antigen processing and recognition of a T210M exchange, which previously had been introduced into the melanoma gp100209-217 tumor epitope to improve the HLA-A*02:01 binding and its immunogenicity. A quantitative analysis of the main steps of antigen processing shows that the T210M exchange affects proteasomal cleavage site usage within the mutgp100201-230 polypeptide, leading to the generation of an unique set of cleavage products. The T210M substitution qualitatively affects the proteasome-catalyzed generation of spliced and non-spliced peptides predicted to bind HLA-A or -B complexes. The T210M substitution also induces an enhanced production of the mutgp100209-217 epitope and its N-terminally extended peptides. The T210M exchange revealed no effect on ERAP1-mediated N-terminal trimming of the precursor peptides. However, mutant N-terminally extended peptides exhibited significantly increased HLA-A*02:01 binding affinity and elicited CD8(+) T cell stimulation in vitro similar to the wtgp100209-217 epitope. Thus, our experiments demonstrate that amino acid exchanges within an epitope can result in the generation of an altered peptide pool with new antigenic peptides and in a wider CD8(+) T cell response also towards N-terminally extended versions of the minimal epitope.
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Affiliation(s)
- Kathrin Textoris-Taube
- From the Institut für Biochemie, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Christin Keller
- From the Institut für Biochemie, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Juliane Liepe
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, SW7 2AZ, United Kingdom, and
| | - Petra Henklein
- From the Institut für Biochemie, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037
| | - Peter M Kloetzel
- From the Institut für Biochemie, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany,
| | - Michele Mishto
- From the Institut für Biochemie, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany,
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13
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Chen ST, Okada M, Nakato R, Izumi K, Bando M, Shirahige K. The Deubiquitinating Enzyme USP7 Regulates Androgen Receptor Activity by Modulating Its Binding to Chromatin. J Biol Chem 2015; 290:21713-23. [PMID: 26175158 DOI: 10.1074/jbc.m114.628255] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Indexed: 01/21/2023] Open
Abstract
The androgen receptor (AR), a nuclear receptor superfamily transcription factor, plays a key role in prostate cancer. AR signaling is the principal target for prostate cancer treatment, but current androgen-deprivation therapies cannot completely abolish AR signaling because of the heterogeneity of prostate cancers. Therefore, unraveling the mechanism of AR reactivation in androgen-depleted conditions can identify effective prostate cancer therapeutic targets. Increasing evidence indicates that AR activity is mediated by the interplay of modifying/demodifying enzymatic co-regulators. To better understand the mechanism of AR transcriptional activity regulation, we used antibodies against AR for affinity purification and identified the deubiquitinating enzyme ubiquitin-specific protease 7, USP7 as a novel AR co-regulator in prostate cancer cells. We showed that USP7 associates with AR in an androgen-dependent manner and mediates AR deubiquitination. Sequential ChIP assays indicated that USP7 forms a complex with AR on androgen-responsive elements of target genes upon stimulation with the androgen 5α-dihydrotestosterone. Further investigation indicated that USP7 is necessary to facilitate androgen-activated AR binding to chromatin. Transcriptome profile analysis of USP7-knockdown LNCaP cells also revealed the essential role of USP7 in the expression of a subset of androgen-responsive genes. Hence, inhibition of USP7 represents a compelling therapeutic strategy for the treatment of prostate cancer.
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Affiliation(s)
- Shu-Ting Chen
- From the Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032 and
| | - Maiko Okada
- the Department of Translational Oncology, St. Marianna University Graduate School of Medicine, Kawasaki 216-8511, Japan
| | - Ryuichiro Nakato
- From the Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032 and
| | - Kosuke Izumi
- From the Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032 and
| | - Masashige Bando
- From the Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032 and
| | - Katsuhiko Shirahige
- From the Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032 and
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14
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Reed BJ, Locke MN, Gardner RG. A Conserved Deubiquitinating Enzyme Uses Intrinsically Disordered Regions to Scaffold Multiple Protein Interaction Sites. J Biol Chem 2015; 290:20601-12. [PMID: 26149687 DOI: 10.1074/jbc.m115.650952] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Indexed: 12/24/2022] Open
Abstract
In the canonical view of protein function, it is generally accepted that the three-dimensional structure of a protein determines its function. However, the past decade has seen a dramatic growth in the identification of proteins with extensive intrinsically disordered regions (IDRs), which are conformationally plastic and do not appear to adopt single three-dimensional structures. One current paradigm for IDR function is that disorder enables IDRs to adopt multiple conformations, expanding the ability of a protein to interact with a wide variety of disparate proteins. The capacity for many interactions is an important feature of proteins that occupy the hubs of protein networks, in particular protein-modifying enzymes that usually have a broad spectrum of substrates. One such protein modification is ubiquitination, where ubiquitin is attached to proteins through ubiquitin ligases (E3s) and removed through deubiquitinating enzymes. Numerous proteomic studies have found that thousands of proteins are dynamically regulated by cycles of ubiquitination and deubiquitination. Thus, how these enzymes target their wide array of substrates is of considerable importance for understanding the function of the cell's diverse ubiquitination networks. Here, we characterize a yeast deubiquitinating enzyme, Ubp10, that possesses IDRs flanking its catalytic protease domain. We show that Ubp10 possesses multiple, distinct binding modules within its IDRs that are necessary and sufficient for directing protein interactions important for Ubp10's known roles in gene silencing and ribosome biogenesis. The human homolog of Ubp10, USP36, also has IDRs flanking its catalytic domain, and these IDRs similarly contain binding modules important for protein interactions. This work highlights the significant protein interaction scaffolding abilities of IDRs in the regulation of dynamic protein ubiquitination.
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Affiliation(s)
- Benjamin J Reed
- From the Department of Pharmacology, University of Washington, Seattle, Washington 98195
| | - Melissa N Locke
- From the Department of Pharmacology, University of Washington, Seattle, Washington 98195
| | - Richard G Gardner
- From the Department of Pharmacology, University of Washington, Seattle, Washington 98195
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15
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Hendriks IA, Schimmel J, Eifler K, Olsen JV, Vertegaal ACO. Ubiquitin-specific Protease 11 (USP11) Deubiquitinates Hybrid Small Ubiquitin-like Modifier (SUMO)-Ubiquitin Chains to Counteract RING Finger Protein 4 (RNF4). J Biol Chem 2015; 290:15526-15537. [PMID: 25969536 DOI: 10.1074/jbc.m114.618132] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Indexed: 11/06/2022] Open
Abstract
Ring finger protein 4 (RNF4) is a SUMO-targeted ubiquitin E3 ligase with a pivotal function in the DNA damage response (DDR). SUMO interaction motifs (SIMs) in the N-terminal part of RNF4 tightly bind to SUMO polymers, and RNF4 can ubiquitinate these polymers in vitro. Using a proteomic approach, we identified the deubiquitinating enzyme ubiquitin-specific protease 11 (USP11), a known DDR-component, as a functional interactor of RNF4. USP11 can deubiquitinate hybrid SUMO-ubiquitin chains to counteract RNF4. SUMO-enriched nuclear bodies are stabilized by USP11, which functions downstream of RNF4 as a counterbalancing factor. In response to DNA damage induced by methyl methanesulfonate, USP11 could counteract RNF4 to inhibit the dissolution of nuclear bodies. Thus, we provide novel insight into cross-talk between ubiquitin and SUMO and uncover USP11 and RNF4 as a balanced SUMO-targeted ubiquitin ligase/protease pair with a role in the DDR.
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Affiliation(s)
- Ivo A Hendriks
- Department of Molecular Cell Biology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Joost Schimmel
- Department of Molecular Cell Biology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Karolin Eifler
- Department of Molecular Cell Biology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Alfred C O Vertegaal
- Department of Molecular Cell Biology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
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16
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Wang W, Huang X, Xin HB, Fu M, Xue A, Wu ZH. TRAF Family Member-associated NF-κB Activator (TANK) Inhibits Genotoxic Nuclear Factor κB Activation by Facilitating Deubiquitinase USP10-dependent Deubiquitination of TRAF6 Ligase. J Biol Chem 2015; 290:13372-85. [PMID: 25861989 DOI: 10.1074/jbc.m115.643767] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Indexed: 01/26/2023] Open
Abstract
DNA damage-induced NF-κB activation plays a critical role in regulating cellular response to genotoxic stress. However, the molecular mechanisms controlling the magnitude and duration of this genotoxic NF-κB signaling cascade are poorly understood. We recently demonstrated that genotoxic NF-κB activation is regulated by reversible ubiquitination of several essential mediators involved in this signaling pathway. Here we show that TRAF family member-associated NF-κB activator (TANK) negatively regulates NF-κB activation by DNA damage via inhibiting ubiquitination of TRAF6. Despite the lack of a deubiquitination enzyme domain, TANK has been shown to negatively regulate the ubiquitination of TRAF proteins. We found TANK formed a complex with MCPIP1 (also known as ZC3H12A) and a deubiquitinase, USP10, which was essential for the USP10-dependent deubiquitination of TRAF6 and the resolution of genotoxic NF-κB activation upon DNA damage. Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-mediated deletion of TANK in human cells significantly enhanced NF-κB activation by genotoxic treatment, resulting in enhanced cell survival and increased inflammatory cytokine production. Furthermore, we found that the TANK-MCPIP1-USP10 complex also decreased TRAF6 ubiquitination in cells treated with IL-1β or LPS. In accordance, depletion of USP10 enhanced NF-κB activation induced by IL-1β or LPS. Collectively, our data demonstrate that TANK serves as an important negative regulator of NF-κB signaling cascades induced by genotoxic stress and IL-1R/Toll-like receptor stimulation in a manner dependent on MCPIP1/USP10-mediated TRAF6 deubiquitination.
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Affiliation(s)
- Wei Wang
- From the Department of Pathology and Laboratory Medicine and Center for Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee 38163
| | - Xuan Huang
- the Institute of Translational Medicine, Nanchang University, Nanchang 330031, China
| | - Hong-Bo Xin
- the Institute of Translational Medicine, Nanchang University, Nanchang 330031, China
| | - Mingui Fu
- the Department of Basic Medical Science, University of Missouri Kansas City, Kansas City, Missouri 64108, and
| | - Aimin Xue
- the Department of Forensic Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Zhao-Hui Wu
- From the Department of Pathology and Laboratory Medicine and Center for Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee 38163,
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17
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Abstract
Upon virus infection, the innate immune response provides the first line of protection and rapidly induces type I interferons (IFNα/β), which mediate potent antiviral effects. To maintain homeostasis and prevent autoimmunity, IFN production is tightly regulated; however, the mechanisms of negative regulation are poorly understood. Herein, we demonstrate that the A20 binding inhibitor of NF-κB 1 (ABIN1) is a novel negative regulator of antiviral signaling. Overexpression of ABIN1 inhibited IFN-β promoter activation in response to virus infection or poly(I:C) transfection, whereas siRNA-mediated knockdown of ABIN1 enhanced IFN-β production upon virus infection. ABIN1 interacted with the A20 regulatory molecule TAX1BP1 and was essential for the recruitment of TAX1BP1 and A20 to the noncanonical IκB kinases TBK1 and IKKi in response to poly(I:C) transfection. ABIN1 and TAX1BP1 together disrupted the interactions between the E3 ubiquitin ligase TRAF3 and TBK1/IKKi to attenuate lysine 63-linked polyubiquitination of TBK1/IKKi. Finally, an intact ubiquitin binding domain of ABIN1 was essential for ABIN1 to interact with TBK1/IKKi and inhibit IFN-β production upon poly(I:C) transfection or virus infection. Together, these results suggest that ABIN1 requires its ubiquitin binding domain and cooperates with TAX1BP1 and A20 to restrict antiviral signaling.
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Affiliation(s)
- Linlin Gao
- From the Department of Microbiology and Immunology, Graduate Program in Cancer Biology, Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, Florida 33136
| | - Helen Coope
- the Division of Immune Cell Biology, National Institute for Medical Research, Mill Hill, London, NW7 1AA, United Kingdom, and
| | - Susan Grant
- the Division of Immune Cell Biology, National Institute for Medical Research, Mill Hill, London, NW7 1AA, United Kingdom, and
| | - Averil Ma
- the Department of Medicine, University of California at San Francisco, San Francisco, California 94143
| | - Steven C. Ley
- the Division of Immune Cell Biology, National Institute for Medical Research, Mill Hill, London, NW7 1AA, United Kingdom, and
| | - Edward W. Harhaj
- From the Department of Microbiology and Immunology, Graduate Program in Cancer Biology, Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, Florida 33136, , To whom correspondence should be addressed: Dept. of Microbiology and Immunology, Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, 1550 NW 10 Ave., Miami, FL 33136. Tel.: 305-243-7893; Fax: 305-243-6410; E-mail:
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