51
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Targeting the ubiquitin-proteasome pathway to overcome anti-cancer drug resistance. Drug Resist Updat 2020; 48:100663. [DOI: 10.1016/j.drup.2019.100663] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/01/2019] [Accepted: 11/03/2019] [Indexed: 02/07/2023]
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52
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The function and regulation of OTU deubiquitinases. Front Med 2019; 14:542-563. [PMID: 31884527 DOI: 10.1007/s11684-019-0734-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 10/31/2019] [Indexed: 12/19/2022]
Abstract
Post-translational modification of cellular proteins by ubiquitin regulates numerous cellular processes, including cell division, immune responses, and apoptosis. Ubiquitin-mediated control over these processes can be reversed by deubiquitinases (DUBs), which remove ubiquitin from target proteins and depolymerize polyubiquitin chains. Recently, much progress has been made in the DUBs. In humans, the ovarian tumor protease (OTU) subfamily of DUBs includes 16 members, most of which mediate cell signaling cascades. These OTUs show great variation in structure and function, which display a series of mechanistic features. In this review, we provide a comprehensive analysis of current progress in character, structure and function of OTUs, such as the substrate specificity and catalytic activity regulation. Then we discuss the relationship between some diseases and OTUs. Finally, we summarize the structure of viral OTUs and their function in immune escape and viral survival. Despite the challenges, OTUs might provide new therapeutic targets, due to their involvement in key regulatory processes.
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53
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Wu R, Zheng W, Tan J, Sammer R, Du L, Lu C. Protein partners of plant ubiquitin-specific proteases (UBPs). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 145:227-236. [PMID: 31630936 DOI: 10.1016/j.plaphy.2019.08.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/16/2019] [Accepted: 08/31/2019] [Indexed: 06/10/2023]
Abstract
As one type of deubiquitinases (DUBs), ubiquitin-specific proteases (UBPs) play an extensive and significant role in plant life involving the regulation of plant development and stress responses. However, comprehensive studies are still needed to determine the functional mechanisms, which are largely unclear. Here, we summarized recent progress of plant UBPs' functional partners, particularly the molecular mechanisms by which UBPs work with their partners. We believe that functional analyses of UBPs and their partners will provide new insights into protein deubiquitination and lead to a better understanding of the physiological roles of UBPs in plants.
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Affiliation(s)
- Ruihua Wu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Wenqing Zheng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jinyi Tan
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Rana Sammer
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Liang Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China; College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
| | - Cunfu Lu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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54
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Deng J, Hou G, Fang Z, Liu J, Lv XD. Distinct expression and prognostic value of OTU domain-containing proteins in non-small-cell lung cancer. Oncol Lett 2019; 18:5417-5427. [PMID: 31612050 PMCID: PMC6781715 DOI: 10.3892/ol.2019.10883] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 08/08/2019] [Indexed: 02/07/2023] Open
Abstract
The ubiquitin-proteasome pathway is an important protein degradation regulatory system in cells. This pathway is also a reversible process that is strictly regulated, and the regulation of deubiquitinating enzymes (DUBs) represents an important facet of the process. Ovarian tumor-associated proteases domain-containing proteins (OTUDs), as a subfamily within the DUB family, serve an important role in regulatory mechanisms of several biological processes, through the regulation of gene transcription, cell cycle, immune response, inflammation and tumor growth processes, and may be important in the diagnosis of various diseases and constitute novel drug targets. However, the role of OTUDs in non-small-cell lung cancer (NSCLC) has not been fully elucidated. In the present study, the Oncomine database was used to examine gene expression in NSCLC, and the prognostic value of each gene was analyzed by Kaplan-Meier analysis. The results indicated that high mRNA expression levels of OTUD1, OTUD3, OTUD4 and putative bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase ALG13 were associated with improved prognosis in all NSCLC and adenocarcinoma, but not in squamous cell carcinoma. By contrast, high expression levels of OTUD2 mRNA were associated with poorer overall survival in patients with NSCLC. These data suggested that these OTUD isozymes may be a potential drug target for NSCLC.
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Affiliation(s)
- Jingjing Deng
- Department of Respiration, Key Medical Discipline of Jiaxing, Jiaxing Lung Cancer Innovation Team, The First Hospital of Jiaxing, The First Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang 314000, P.R. China
| | - Gouxin Hou
- Department of Oncology, The First Hospital of Jiaxing, The First Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang 314000, P.R. China
| | - Zhixian Fang
- Department of Respiration, Key Medical Discipline of Jiaxing, Jiaxing Lung Cancer Innovation Team, The First Hospital of Jiaxing, The First Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang 314000, P.R. China
| | - Jialiang Liu
- Department of Respiration, Key Medical Discipline of Jiaxing, Jiaxing Lung Cancer Innovation Team, The First Hospital of Jiaxing, The First Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang 314000, P.R. China
| | - Xiao-Dong Lv
- Department of Respiration, Key Medical Discipline of Jiaxing, Jiaxing Lung Cancer Innovation Team, The First Hospital of Jiaxing, The First Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang 314000, P.R. China
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55
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Wu R, Shi Y, Zhang Q, Zheng W, Chen S, Du L, Lu C. Genome-Wide Identification and Characterization of the UBP Gene Family in Moso Bamboo ( Phyllostachys edulis). Int J Mol Sci 2019; 20:E4309. [PMID: 31484390 PMCID: PMC6747111 DOI: 10.3390/ijms20174309] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/25/2019] [Accepted: 08/29/2019] [Indexed: 02/02/2023] Open
Abstract
The largest group of deubiquitinases-ubiquitin-specific proteases (UBPs)-perform extensive and significant roles in plants, including the regulation of development and stress responses. A comprehensive analysis of UBP genes has been performed in Arabidopsis thaliana, but no systematic study has been conducted in moso bamboo (Phyllostachys edulis). In this study, the genome-wide identification, classification, gene, protein, promoter region characterization, divergence time, and expression pattern analyses of the UBPs in moso bamboo were conducted. In total, 48 putative UBP genes were identified in moso bamboo, which were divided into 14 distinct subfamilies in accordance with a comparative phylogenetic analysis using 132 full-length protein sequences, including 48, 27, 25, and 32 sequences from moso bamboo, A. thaliana, rice (Oryza sativa), and purple false brome (Brachypodium distachyon), respectively. Analyses of the evolutionary patterns and divergence levels revealed that the PeUBP genes experienced a duplication event approximately 15 million years ago and that the divergence between PeUBP and OsUBP occurred approximately 27 million years ago. Additionally, several PeUBP members were significantly upregulated under abscisic acid, methyl jasmonate, and salicylic acid treatments, indicating their potential roles in abiotic stress responses in plants.
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Affiliation(s)
- Ruihua Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yanrong Shi
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Qian Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Wenqing Zheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shaoliang Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Liang Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Cunfu Lu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
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56
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Bland T, Sahin GS, Zhu M, Dillon C, Impey S, Appleyard SM, Wayman GA. USP8 Deubiquitinates the Leptin Receptor and Is Necessary for Leptin-Mediated Synapse Formation. Endocrinology 2019; 160:1982-1998. [PMID: 31199479 PMCID: PMC6660906 DOI: 10.1210/en.2019-00107] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 06/08/2019] [Indexed: 11/19/2022]
Abstract
Leptin has neurotrophic actions in the hippocampus to increase synapse formation and stimulate neuronal plasticity. Leptin also enhances cognition and has antidepressive and anxiolytic-like effects, two hippocampal-dependent behaviors. In contrast, mice lacking leptin or the long form of the leptin receptor (LepRb) have lower cortical volume and decreased memory and exhibit depressive-like behaviors. A number of the signaling pathways regulated by LepRb are known, but how membrane LepRb levels are regulated in the central nervous system is not well understood. Here, we show that the lysosomal inhibitor chloroquine increases LepRb expression in hippocampal cultures, suggesting that LepRb is degraded in the lysosome. Furthermore, we show that leptin increases surface expression of its own receptor by decreasing the level of ubiquitinated LepRbs. This decrease is mediated by the deubiquitinase ubiquitin-specific protease 8 (USP8), which we show is in complex with LepRb. Acute leptin stimulation increases USP8 activity. Moreover, leptin stimulates USP8 gene expression through cAMP response element-binding protein (CREB)-dependent transcription, an effect blocked by expression of a dominant-negative CREB or with short hairpin RNA knockdown of CREB. Increased expression of USP8 causes increased surface localization of LepRb, which in turn enhances leptin-mediated activation of the MAPK kinase/extracellular signal-regulated kinase pathway and CREB activation. Lastly, increased USP8 expression increases glutamatergic synapse formation in hippocampal cultures, an effect dependent on expression of LepRbs. Leptin-stimulated synapse formation also requires USP8. In conclusion, we show that USP8 deubiquitinates LepRb, thus inhibiting lysosomal degradation and enhancing surface localization of LepRb, which are essential for leptin-stimulated synaptogenesis in the hippocampus.
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Affiliation(s)
- Tyler Bland
- Department of Integrated Physiology and Neuroscience, Washington State University, Pullman, Washington
| | - Gulcan Semra Sahin
- Department of Integrated Physiology and Neuroscience, Washington State University, Pullman, Washington
| | - Mingyan Zhu
- Department of Integrated Physiology and Neuroscience, Washington State University, Pullman, Washington
| | - Crystal Dillon
- Department of Integrated Physiology and Neuroscience, Washington State University, Pullman, Washington
| | - Soren Impey
- Oregon Stem Cell Center, Oregon Health and Sciences University, Portland, Oregon
| | - Suzanne M Appleyard
- Department of Integrated Physiology and Neuroscience, Washington State University, Pullman, Washington
| | - Gary A Wayman
- Department of Integrated Physiology and Neuroscience, Washington State University, Pullman, Washington
- Correspondence: Gary A. Wayman, PhD, Department of Integrative Physiology and Neuroscience, Program in Neuroscience, Washington State University, Pullman, Washington 99164. E-mail:
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57
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Uematsu A, Kido K, Takahashi H, Takahashi C, Yanagihara Y, Saeki N, Yoshida S, Maekawa M, Honda M, Kai T, Shimizu K, Higashiyama S, Imai Y, Tokunaga F, Sawasaki T. The E3 ubiquitin ligase MIB2 enhances inflammation by degrading the deubiquitinating enzyme CYLD. J Biol Chem 2019; 294:14135-14148. [PMID: 31366726 DOI: 10.1074/jbc.ra119.010119] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Indexed: 12/25/2022] Open
Abstract
The tumor suppressor CYLD is a deubiquitinating enzyme that suppresses polyubiquitin-dependent signaling pathways, including the proinflammatory and cell growth-promoting NF-κB pathway. Missense mutations in the CYLD gene are present in individuals with syndromes such as multiple familial trichoepithelioma (MFT), but the pathogenic roles of these mutations remain unclear. Recent studies have shown that CYLD interacts with a RING finger domain protein, mind bomb homologue 2 (MIB2), in the regulation of NOTCH signaling. However, whether MIB2 is an E3 ubiquitin ligase that acts on CYLD is unknown. Here, using the cell-free-based AlphaScreen and pulldown assays to detect protein-protein interactions, along with immunofluorescence assays and murine Mib2 knockout cells and animals, we demonstrate that MIB2 promotes proteasomal degradation of CYLD and enhances NF-κB signaling. Of note, arthritic inflammation was suppressed in Mib2-deficient mice. We further observed that the ankyrin repeat in MIB2 interacts with the third CAP domain in CYLD and that MIB2 catalyzes Lys-48-linked polyubiquitination of CYLD at Lys-338 and Lys-530. MIB2-dependent CYLD degradation activated NF-κB signaling via tumor necrosis factor alpha (TNFα) stimulation and the linear ubiquitination assembly complex (LUBAC). Mib2-knockout mice had reduced serum interleukin-6 (IL-6) and exhibited suppressed inflammatory responses in the K/BxN serum-transfer arthritis model. Interestingly, MIB2 significantly enhanced the degradation of a CYLDP904L variant identified in an individual with MFT, although the molecular pathogenesis of the disease was not clarified here. Together, these results suggest that MIB2 enhances NF-κB signaling in inflammation by promoting the ubiquitin-dependent degradation of CYLD.
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Affiliation(s)
- Atsushi Uematsu
- Division of Cell-Free Sciences, Proteo-Science Center (PROS), 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Kohki Kido
- Division of Cell-Free Sciences, Proteo-Science Center (PROS), 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Hirotaka Takahashi
- Division of Cell-Free Sciences, Proteo-Science Center (PROS), 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Chikako Takahashi
- Division of Cell-Free Sciences, Proteo-Science Center (PROS), 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Yuta Yanagihara
- Division of Integrative Pathophysiology, PROS, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Noritaka Saeki
- Division of Integrative Pathophysiology, PROS, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Shuhei Yoshida
- Division of Integrative Pathophysiology, PROS, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Masashi Maekawa
- Division of Cell Growth and Tumor Regulation, PROS, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577.,Department of Biochemistry and Molecular Genetics, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Mamoru Honda
- Pharmaceuticals and Life Sciences Division, Shimadzu Techno-Research, Inc., Nishinokyo-Shimoaicho, Nakagyo-ku, Kyoto 604-8436, Japan
| | - Tsutomu Kai
- Pharmaceuticals and Life Sciences Division, Shimadzu Techno-Research, Inc., Nishinokyo-Shimoaicho, Nakagyo-ku, Kyoto 604-8436, Japan
| | - Kouhei Shimizu
- Division of Cell-Free Sciences, Proteo-Science Center (PROS), 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Shigeki Higashiyama
- Division of Cell Growth and Tumor Regulation, PROS, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577.,Department of Biochemistry and Molecular Genetics, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Yuuki Imai
- Division of Integrative Pathophysiology, PROS, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Fuminori Tokunaga
- Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, 1-4-3 Asahi-machi, Abeno-ku, Osaka 545-8585, Japan
| | - Tatsuya Sawasaki
- Division of Cell-Free Sciences, Proteo-Science Center (PROS), 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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58
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Lopes F, Torres F, Soares G, Barbosa M, Silva J, Duque F, Rocha M, Sá J, Oliveira G, Sá MJ, Temudo T, Sousa S, Marques C, Lopes S, Gomes C, Barros G, Jorge A, Rocha F, Martins C, Mesquita S, Loureiro S, Cardoso EM, Cálix MJ, Dias A, Martins C, Mota CR, Antunes D, Dupont J, Figueiredo S, Figueiroa S, Gama-de-Sousa S, Cruz S, Sampaio A, Eijk P, Weiss MM, Ylstra B, Rendeiro P, Tavares P, Reis-Lima M, Pinto-Basto J, Fortuna AM, Maciel P. Genomic imbalances defining novel intellectual disability associated loci. Orphanet J Rare Dis 2019; 14:164. [PMID: 31277718 PMCID: PMC6612161 DOI: 10.1186/s13023-019-1135-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 06/12/2019] [Indexed: 11/29/2022] Open
Abstract
Background High resolution genome-wide copy number analysis, routinely used in clinical diagnosis for several years, retrieves new and extremely rare copy number variations (CNVs) that provide novel candidate genes contributing to disease etiology. The aim of this work was to identify novel genetic causes of neurodevelopmental disease, inferred from CNVs detected by array comparative hybridization (aCGH), in a cohort of 325 Portuguese patients with intellectual disability (ID). Results We have detected CNVs in 30.1% of the patients, of which 5.2% corresponded to novel likely pathogenic CNVs. For these 11 rare CNVs (which encompass novel ID candidate genes), we identified those most likely to be relevant, and established genotype-phenotype correlations based on detailed clinical assessment. In the case of duplications, we performed expression analysis to assess the impact of the rearrangement. Interestingly, these novel candidate genes belong to known ID-related pathways. Within the 8% of patients with CNVs in known pathogenic loci, the majority had a clinical presentation fitting the phenotype(s) described in the literature, with a few interesting exceptions that are discussed. Conclusions Identification of such rare CNVs (some of which reported for the first time in ID patients/families) contributes to our understanding of the etiology of ID and for the ever-improving diagnosis of this group of patients. Electronic supplementary material The online version of this article (10.1186/s13023-019-1135-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fátima Lopes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Fátima Torres
- CGC Genetics, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Gabriela Soares
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal
| | - Mafalda Barbosa
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal.,Unit for Multidisciplinary Research in Biomedicine, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal.,The Mindich Child Health & Development Institute and the Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - João Silva
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal.,Centro de Genética Preditiva e Preventiva - CGPP, Instituto de Biologia Molecular e Celular - IBMC, Universidade do Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde - i3S, Universidade do Porto, Porto, Portugal
| | - Frederico Duque
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clínica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3041-80, Coimbra, Portugal.,University Clinic of Pediatrics and Institute for Biomedical Imaging and Life Science, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Miguel Rocha
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal.,Medical Genetics Unit, Hospital de Braga, Braga, Portugal
| | - Joaquim Sá
- CGC Genetics, Porto, Portugal.,Department of Medical Genetics, Hospital de Faro, Faro, Portugal
| | - Guiomar Oliveira
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clínica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3041-80, Coimbra, Portugal.,University Clinic of Pediatrics and Institute for Biomedical Imaging and Life Science, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Maria João Sá
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal.,Unit for Multidisciplinary Research in Biomedicine, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Teresa Temudo
- Pediatric Neurology Department, Centro Materno-Infantil Centro Hospitalar do Porto, Porto, Portugal
| | - Susana Sousa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.,Centro de Genética Preditiva e Preventiva - CGPP, Instituto de Biologia Molecular e Celular - IBMC, Universidade do Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde - i3S, Universidade do Porto, Porto, Portugal
| | - Carla Marques
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clínica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3041-80, Coimbra, Portugal
| | - Sofia Lopes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Catarina Gomes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Gisela Barros
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Arminda Jorge
- Development Unit, Pediatrics Service, Hospital Centre of Cova da Beira, Covilhã, Portugal.,CICS - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Felisbela Rocha
- Department of Pediatrics, Médio Ave Hospital Center, Vila Nova de Famalicão, Portugal
| | - Cecília Martins
- Department of Pediatrics, Médio Ave Hospital Center, Vila Nova de Famalicão, Portugal
| | - Sandra Mesquita
- Development Unit, Pediatrics Service, Hospital Centre of Cova da Beira, Covilhã, Portugal
| | - Susana Loureiro
- Department of Pediatrics, Hospital S. Teotónio, Tondela/Viseu Hospital Center, Viseu, Portugal
| | - Elisa Maria Cardoso
- Department of Pediatrics, Hospital S. Teotónio, Tondela/Viseu Hospital Center, Viseu, Portugal
| | - Maria José Cálix
- Department of Pediatrics, Hospital S. Teotónio, Tondela/Viseu Hospital Center, Viseu, Portugal
| | - Andreia Dias
- Department of Pediatrics, Hospital S. Teotónio, Tondela/Viseu Hospital Center, Viseu, Portugal
| | - Cristina Martins
- Neuropaediatric Unit - Garcia de Orta Hospital, Almada, Portugal
| | - Céu R Mota
- Pediatric and Neonatal Intensive Care, Department of Pediatrics, Porto Hospital Center, Porto, Portugal
| | - Diana Antunes
- Department of Genetics, Hospital D. Estefânia, Lisboa-Norte Hospital Center, Lisbon, Portugal
| | - Juliette Dupont
- Genetics Service, Paediatric Department, University Hospital Santa Maria, Lisbon, Portugal
| | - Sara Figueiredo
- Department of Pediatrics, Médio Ave Hospital Center, Santo Tirso, Portugal
| | - Sónia Figueiroa
- Division of Pediatric Neurology, Department of Child and Adolescent, Centro Hospitalar do Porto e Hospital de Santo António, Porto, Portugal
| | - Susana Gama-de-Sousa
- Department of Pediatrics, Médio Ave Hospital Center, Vila Nova de Famalicão, Portugal
| | - Sara Cruz
- Neuropsychophysiology Lab, CIPsi, School of Psychology, University of Minho, Braga, Portugal
| | - Adriana Sampaio
- Neuropsychophysiology Lab, CIPsi, School of Psychology, University of Minho, Braga, Portugal
| | - Paul Eijk
- Department of Pathology, VU University Medical Center, Amsterdam, 1007, MB, The Netherlands
| | - Marjan M Weiss
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, 1007, MB, The Netherlands
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, Amsterdam, 1007, MB, The Netherlands
| | | | | | - Margarida Reis-Lima
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal.,GDPN- SYNLAB, Porto, Portugal
| | | | - Ana Maria Fortuna
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal
| | - Patrícia Maciel
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal. .,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.
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59
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Peng H, Yang F, Hu Q, Sun J, Peng C, Zhao Y, Huang C. The ubiquitin-specific protease USP8 directly deubiquitinates SQSTM1/p62 to suppress its autophagic activity. Autophagy 2019; 16:698-708. [PMID: 31241013 DOI: 10.1080/15548627.2019.1635381] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
SQSTM1/p62 (sequestosome 1) is a critical macroautophagy/autophagy receptor that promotes the formation and degradation of ubiquitinated aggregates. SQSTM1 can be modified by ubiquitination, and this modification modulates its autophagic activity. However, the molecular mechanisms underpinning its reversible deubiquitination have never been described. Here we report that USP8 (ubiquitin specific peptidase 8) directly interacted with and deubiquitinated SQSTM1. USP8 preferentially removed the lysine 11 (K11)-linked ubiquitin chains from SQSTM1. Moreover, USP8 deubiquitinated SQSTM1 principally at K420 within its ubiquitin-association (UBA) domain. Finally, USP8 inhibited SQSTM1 degradation and autophagic influx in cells with wild-type SQSTM1, but not its mutant with substitution of K420 with an arginine. Taken together, USP8 acts as a negative regulator of autophagy by deubiquitinating SQSTM1 at K420.Abbreviations: BafA1: bafilomycin A1; BAP1: BRCA1 associated protein 1; DUB: deubiquitinating enzyme; ESCRT: endosomal sorting complex required for transport; HTT: huntingtin; K: lysine; KEAP1: kelch like ECH associated protein 1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MEF: mouse embryonic fibroblast; shRNA: short hairpin RNA; SQSTM1: sequestosome 1; Ub: ubiquitin; UBA: ubiquitin-association; UBE2D2: ubiquitin conjugating enzyme E2 D2; UBE2D3: ubiquitin conjugating enzyme E2 D3; USP: ubiquitin specific peptidase; WT: wild-type.
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Affiliation(s)
- Hong Peng
- Shanghai Institute of Immunology & Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Laboratory of Medical Virology, School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Fang Yang
- Shanghai Institute of Immunology & Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qianwen Hu
- Shanghai Institute of Immunology & Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Sun
- Department of Breast Surgery, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Cheng Peng
- Shanghai Institute of Immunology & Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yao Zhao
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chuanxin Huang
- Shanghai Institute of Immunology & Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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60
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Dharadhar S, Kim RQ, Uckelmann M, Sixma TK. Quantitative analysis of USP activity in vitro. Methods Enzymol 2019; 618:281-319. [PMID: 30850056 DOI: 10.1016/bs.mie.2018.12.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Ubiquitin-specific proteases (USPs) are an important class of deubiquitinating enzymes (DUBs) that carry out critical roles in cellular physiology and are regulated at multiple levels. Quantitative characterization of USP activity is crucial for mechanistic understanding of USP function and regulation. This requires kinetic analysis using in vitro activity assays on minimal and natural substrates with purified proteins. In this chapter we give advice for efficient design of USP constructs and their optimal expression, followed by a series of purification strategies. We then present protocols for studying USP activity quantitatively on minimal and more natural substrates, and we discuss how to include possible regulatory elements such as internal USP domains or external interacting proteins. Lastly, we examine different binding assays for studying USP interactions and discuss how these can be included in full kinetic analyses.
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Affiliation(s)
- Shreya Dharadhar
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Robbert Q Kim
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Michael Uckelmann
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Titia K Sixma
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.
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61
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Teyra J, Singer AU, Schmitges FW, Jaynes P, Kit Leng Lui S, Polyak MJ, Fodil N, Krieger JR, Tong J, Schwerdtfeger C, Brasher BB, Ceccarelli DFJ, Moffat J, Sicheri F, Moran MF, Gros P, Eichhorn PJA, Lenter M, Boehmelt G, Sidhu SS. Structural and Functional Characterization of Ubiquitin Variant Inhibitors of USP15. Structure 2019; 27:590-605.e5. [PMID: 30713027 DOI: 10.1016/j.str.2019.01.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/23/2018] [Accepted: 12/31/2018] [Indexed: 12/12/2022]
Abstract
The multi-domain deubiquitinase USP15 regulates diverse eukaryotic processes and has been implicated in numerous diseases. We developed ubiquitin variants (UbVs) that targeted either the catalytic domain or each of three adaptor domains in USP15, including the N-terminal DUSP domain. We also designed a linear dimer (diUbV), which targeted the DUSP and catalytic domains, and exhibited enhanced specificity and more potent inhibition of catalytic activity than either UbV alone. In cells, the UbVs inhibited the deubiquitination of two USP15 substrates, SMURF2 and TRIM25, and the diUbV inhibited the effects of USP15 on the transforming growth factor β pathway. Structural analyses revealed that three distinct UbVs bound to the catalytic domain and locked the active site in a closed, inactive conformation, and one UbV formed an unusual strand-swapped dimer and bound two DUSP domains simultaneously. These inhibitors will enable the study of USP15 function in oncology, neurology, immunology, and inflammation.
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Affiliation(s)
- Joan Teyra
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Alex U Singer
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Frank W Schmitges
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Patrick Jaynes
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Sarah Kit Leng Lui
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Maria J Polyak
- Department of Biochemistry, McGill University, Montreal, QC, Canada; Corbin Therapeutics, Montreal, QC, Canada
| | - Nassima Fodil
- Department of Biochemistry, McGill University, Montreal, QC, Canada; Corbin Therapeutics, Montreal, QC, Canada
| | - Jonathan R Krieger
- SPARC BioCentre, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jiefei Tong
- Cell Biology Program, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | | | - Bradley B Brasher
- Boston Biochem, a Bio-Techne Brand, 840 Memorial Drive, Cambridge, MA 02139, USA
| | - Derek F J Ceccarelli
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Jason Moffat
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Michael F Moran
- SPARC BioCentre, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Cell Biology Program, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Philippe Gros
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Pieter J A Eichhorn
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Martin Lenter
- Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany
| | | | - Sachdev S Sidhu
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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62
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Kim RQ, Geurink PP, Mulder MPC, Fish A, Ekkebus R, El Oualid F, van Dijk WJ, van Dalen D, Ovaa H, van Ingen H, Sixma TK. Kinetic analysis of multistep USP7 mechanism shows critical role for target protein in activity. Nat Commun 2019; 10:231. [PMID: 30651545 PMCID: PMC6335408 DOI: 10.1038/s41467-018-08231-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 12/21/2018] [Indexed: 12/31/2022] Open
Abstract
USP7 is a highly abundant deubiquitinating enzyme (DUB), involved in cellular processes including DNA damage response and apoptosis. USP7 has an unusual catalytic mechanism, where the low intrinsic activity of the catalytic domain (CD) increases when the C-terminal Ubl domains (Ubl45) fold onto the CD, allowing binding of the activating C-terminal tail near the catalytic site. Here we delineate how the target protein promotes the activation of USP7. Using NMR analysis and biochemistry we describe the order of activation steps, showing that ubiquitin binding is an instrumental step in USP7 activation. Using chemically synthesised p53-peptides we also demonstrate how the correct ubiquitinated substrate increases catalytic activity. We then used transient reaction kinetic modelling to define how the USP7 multistep mechanism is driven by target recognition. Our data show how this pleiotropic DUB can gain specificity for its cellular targets. Deubiquitinating enzymes (DUBs) are critical regulators of cellular processes by removing ubiquitin from specific targets. Here global kinetic modelling reveals the mechanism by which the low intrinsic activity of USP7 is substantially enhanced on a specific physiological target.
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Affiliation(s)
- Robbert Q Kim
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Paul P Geurink
- Division of Cell Biology II, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands.,Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Monique P C Mulder
- Division of Cell Biology II, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands.,Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Alexander Fish
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Reggy Ekkebus
- Division of Cell Biology II, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands.,Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Farid El Oualid
- UbiQ Bio BV, Science Park 408, 1098 XH, Amsterdam, the Netherlands
| | - Willem J van Dijk
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Duco van Dalen
- Division of Cell Biology II, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands.,Tumor Immunology department, Radboud Institute for Molecular Sciences, Nijmegen, the Netherlands
| | - Huib Ovaa
- Division of Cell Biology II, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands. .,Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Hugo van Ingen
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands. .,Bijvoet center, Utrecht University, Utrecht, the Netherlands.
| | - Titia K Sixma
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands.
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63
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Haq S, Das S, Kim DH, Chandrasekaran AP, Hong SH, Kim KS, Ramakrishna S. The stability and oncogenic function of LIN28A are regulated by USP28. Biochim Biophys Acta Mol Basis Dis 2018; 1865:599-610. [PMID: 30543854 DOI: 10.1016/j.bbadis.2018.12.006] [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: 04/26/2018] [Revised: 11/17/2018] [Accepted: 12/05/2018] [Indexed: 12/18/2022]
Abstract
RNA-binding protein LIN28A is often highly expressed in human malignant tumors and is involved in tumor metastasis and poor prognosis. Knowledge about post-translational regulatory mechanisms governing LIN28A protein stability and function is scarce. Here, we investigated the role of ubiquitination and deubiquitination on LIN28A protein stability and report that LIN28A protein undergoes ubiquitination. Ubiquitin-specific protease 28 (USP28), a deubiquitinating enzyme, interacts with and stabilizes LIN28A protein to extend its half-life. USP28, through its deubiquitinating activity, antagonizes LIN28A protein turnover by reversing its proteasomal degradation. Our study describes the consequential impacts of USP28-mediated stabilization of LIN28A protein on enhancing cancer cell viability, migration and ultimately augmenting LIN28A-mediated tumor progression. Overall, our data suggest that a synergistic, combinatorial approach of targeting LIN28A with USP28 would contribute to effective cancer therapeutics.
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Affiliation(s)
- Saba Haq
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, South Korea
| | - Soumyadip Das
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
| | - Dong-Ho Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
| | | | - Seok-Ho Hong
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon, South Korea
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea; College of Medicine, Hanyang University, Seoul 04763, South Korea
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea; College of Medicine, Hanyang University, Seoul 04763, South Korea.
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64
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Fu Y, Ma G, Liu G, Li B, Li H, Hao X, Liu L. USP14 as a novel prognostic marker promotes cisplatin resistance via Akt/ERK signaling pathways in gastric cancer. Cancer Med 2018; 7:5577-5588. [PMID: 30296012 PMCID: PMC6246950 DOI: 10.1002/cam4.1770] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 06/20/2018] [Accepted: 08/20/2018] [Indexed: 12/14/2022] Open
Abstract
Gastric cancer (GC) ranks the third leading cause of global cancer mortality. Despite recent progress in surgery combined with chemotherapy, the outcomes of GC patients have barely improved. Therefore, better understanding of the molecular mechanisms involved in chemoresistance of GC may help develop novel strategies to treat this deadly disease. Previous evidence has shown aberrant expressions of USP14 in multiple malignancies, suggesting an important role of USP14 in tumorigenesis. However, its role in modulating chemoresistance in GC still remains elusive. In this study, we observed that USP14 levels were significantly increased in GC tissues compared to the paired normal tissues. Multivariate analysis demonstrated that USP14 level was an independent prognostic factor for DFS in GC patients. Silencing of USP14 promoted proteasomal degradation of p‐ERK (T202/Y204) and p‐Akt (T308/S473), thus inactivating Akt and ERK signaling pathways. Interestingly, silencing of USP14 alone was not sufficient to cause overt effects on cell growth, proliferation, and apoptosis, while resulting in significant apoptosis in the presence of cisplatin in GC cells. Thus, knockdown of USP14 sensitized GC cells to cisplatin by triggering cisplatin‐induced apoptosis via impeding Akt and ERK signaling pathways. These results revealed a novel role of USP14 in modulating chemosensitivity of GC cells, suggesting USP14 may serve as not only a prognostic marker, but also a potential therapeutic target for GC patients.
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Affiliation(s)
- Ying Fu
- Department of Gastrointestinal Cancer Biology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Gang Ma
- Department of Gastrointestinal Cancer Biology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Guolong Liu
- Department of Gastrointestinal Cancer Biology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Bin Li
- Department of Gastrointestinal Surgery, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Hui Li
- Department of Gastrointestinal Cancer Biology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Xishan Hao
- Department of Gastrointestinal Surgery, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Liren Liu
- Department of Gastrointestinal Cancer Biology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
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65
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USP4 positively regulates RLR-induced NF-κB activation by targeting TRAF6 for K48-linked deubiquitination and inhibits enterovirus 71 replication. Sci Rep 2018; 8:13418. [PMID: 30194441 PMCID: PMC6128947 DOI: 10.1038/s41598-018-31734-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 08/24/2018] [Indexed: 12/25/2022] Open
Abstract
Retinoic acid-inducible gene I-like receptor (RLR) is one of the most important pattern recognition receptors of the innate immune system that detects positive and/or negative stranded RNA viruses. Subsequently, it stimulates downstream transcription of interferon regulatory factor 3 (IRF3) and nuclear factor κB (NF-κB) inducing the production of interferons (IFNs) and inflammatory cytokines. Tumour necrosis factor receptor associated factor 6 (TRAF6) is a key protein involved in the RLR-mediated antiviral signalling pathway, recruiting additional proteins to form a multiprotein complex capable of activating the NF-κB inflammatory pathway. Despite TRAF6 playing an important role in regulating host immunity and viral infection, the deubiquitination of TRAF6 induced by viral infection remains elusive. In this study, we found that enterovirus 71 (EV71) infection attenuated the expression of Ubiquitin-specific protease 4 (USP4) in vitro and in vivo, while overexpression of USP4 significantly suppressed EV71 replication. Furthermore, it was found that EV71 infection reduced the RLR signalling pathway and enhanced the degradation of TRAF6. USP4 was also found to interact with TRAF6 and positively regulate the RLR-induced NF-κB signalling pathway, inhibiting the replication of EV71. Therefore, as a novel positive regulator of TRAF6, USP4 plays an essential role in EV71 infection by deubiquitinating K48-linked ubiquitin chains.
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66
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Morrow ME, Morgan MT, Clerici M, Growkova K, Yan M, Komander D, Sixma TK, Simicek M, Wolberger C. Active site alanine mutations convert deubiquitinases into high-affinity ubiquitin-binding proteins. EMBO Rep 2018; 19:embr.201745680. [PMID: 30150323 PMCID: PMC6172466 DOI: 10.15252/embr.201745680] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 07/24/2018] [Accepted: 07/31/2018] [Indexed: 11/26/2022] Open
Abstract
A common strategy for exploring the biological roles of deubiquitinating enzymes (DUBs) in different pathways is to study the effects of replacing the wild‐type DUB with a catalytically inactive mutant in cells. We report here that a commonly studied DUB mutation, in which the catalytic cysteine is replaced with alanine, can dramatically increase the affinity of some DUBs for ubiquitin. Overexpression of these tight‐binding mutants thus has the potential to sequester cellular pools of monoubiquitin and ubiquitin chains. As a result, cells expressing these mutants may display unpredictable dominant negative physiological effects that are not related to loss of DUB activity. The structure of the SAGA DUB module bound to free ubiquitin reveals the structural basis for the 30‐fold higher affinity of Ubp8C146A for ubiquitin. We show that an alternative option, substituting the active site cysteine with arginine, can inactivate DUBs while also decreasing the affinity for ubiquitin.
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Affiliation(s)
- Marie E Morrow
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael T Morgan
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marcello Clerici
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Ming Yan
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David Komander
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Titia K Sixma
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Michal Simicek
- Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic.,Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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67
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Cross Talk Networks of Mammalian Target of Rapamycin Signaling With the Ubiquitin Proteasome System and Their Clinical Implications in Multiple Myeloma. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 343:219-297. [PMID: 30712673 DOI: 10.1016/bs.ircmb.2018.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Multiple myeloma (MM) is the second most common hematological malignancy and results from the clonal amplification of plasma cells. Despite recent advances in treatment, MM remains incurable with a median survival time of only 5-6years, thus necessitating further insights into MM biology and exploitation of novel therapeutic approaches. Both the ubiquitin proteasome system (UPS) and the PI3K/Akt/mTOR signaling pathways have been implicated in the pathogenesis, and treatment of MM and different lines of evidence suggest a close cross talk between these central cell-regulatory signaling networks. In this review, we outline the interplay between the UPS and mTOR pathways and discuss their implications for the pathophysiology and therapy of MM.
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68
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Rao G, Houson H, Nkepang G, Yari H, Teng C, Awasthi V. Induction of gut proteasome activity in hemorrhagic shock and its recovery by treatment with diphenyldihaloketones CLEFMA and EF24. Am J Physiol Gastrointest Liver Physiol 2018; 315:G318-G327. [PMID: 29746173 PMCID: PMC6139642 DOI: 10.1152/ajpgi.00066.2018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/02/2018] [Accepted: 05/02/2018] [Indexed: 01/31/2023]
Abstract
Multiorgan failure in hemorrhagic shock is triggered by gut barrier dysfunction and consequent systemic infiltration of proinflammatory factors. Our previous study has shown that diphenyldihaloketone drugs 4-[3,5-bis[(2-chlorophenyl)methylene]-4-oxo-1-piperidinyl]-4-oxo-2-butenoic acid (CLEFMA) and 3,5-bis[(2-fluorophenyl)methylene]-4-piperidinone (EF24) restore gut barrier dysfunction and reduce systemic inflammatory response in hemorrhagic shock. We investigated the effect of hemorrhagic shock on proteasome activity of intestinal epithelium and how CLEFMA and EF24 treatments modulate proteasome function in hemorrhagic shock. CLEFMA or EF24 (0.4 mg/kg) were given 1 h after withdrawing 50% of blood from Sprague-Dawley rats; no other resuscitation was provided. After another 5 h of compensation, small gut was collected to process tissue for proteasome activity, immunoblotting, and mRNA levels of genes responsible for unfolded-protein response (XBP1, ATF4, glucose-regulated protein of 78/95 kDa, and growth arrest and DNA damage inducible genes 153/34), polyubiquitin B and C, and immunoproteasome subunits β type-8 and -10 and proteasome activator subunit 1. We found that hemorrhagic shock induced proteasome activity in gut tissue and reduced the amounts of ubiquitinated proteins displayed on antiubiquitin immunoblots. However, simultaneous induction of unfolded-protein response or immunoproteasome genes was not observed. CLEFMA and EF24 treatments abolished the hemorrhagic shock-induced increase in proteasome activity. Further investigations revealed that the induction of proteasome in hemorrhagic shock is associated with disassembly of 26S proteasome; CLEFMA and EF24 prevented this disassembly. Consistent with these data, CLEFMA and EF24 reduced hemorrhagic shock-induced degradation of 20S substrate ornithine decarboxylase in gut tissue. These results suggest that activated proteasome plays an important role in ischemic gut pathophysiology, and it can be a druggable target in shock-induced gut dysfunction. NEW & NOTEWORTHY Ischemic injury to the gut is a trigger for the systemic inflammatory response and multiple organ failure in trauma and hemorrhagic shock. We show for the first time that hemorrhagic shock induces the gut proteasome activity by engendering 26S proteasome disassembly. Diphenyldihaloketones 4-[3,5-bis[(2-chlorophenyl)methylene]-4-oxo-1-piperidinyl]-4-oxo-2-butenoic acid and 3,5-bis[(2-fluorophenyl)methylene]-4-piperidinone treatment prevented the 26S disassembly. Understanding the role of proteasome in shock-associated gut injury will assist in the development of therapeutic means to address it.
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Affiliation(s)
- Geeta Rao
- Department of Pharmaceutical Sciences, University of Oklahoma Health Science Center , Oklahoma City, Oklahoma
| | - Hailey Houson
- Department of Pharmaceutical Sciences, University of Oklahoma Health Science Center , Oklahoma City, Oklahoma
| | - Gregory Nkepang
- Department of Pharmaceutical Sciences, University of Oklahoma Health Science Center , Oklahoma City, Oklahoma
| | - Hooman Yari
- Department of Pharmaceutical Sciences, University of Oklahoma Health Science Center , Oklahoma City, Oklahoma
| | - Chengwen Teng
- Department of Pharmaceutical Sciences, University of Oklahoma Health Science Center , Oklahoma City, Oklahoma
| | - Vibhudutta Awasthi
- Department of Pharmaceutical Sciences, University of Oklahoma Health Science Center , Oklahoma City, Oklahoma
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69
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Jama N, Farquhar N, Butt Z, Coupland SE, Sacco JJ, Scase T, Fielding AB, Coulson JM, Kalirai H, Killick DR. Altered Nuclear Expression of the Deubiquitylase BAP1 Cannot be Used as a Prognostic Marker for Canine Melanoma. J Comp Pathol 2018; 162:50-58. [PMID: 30060843 PMCID: PMC6078709 DOI: 10.1016/j.jcpa.2018.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 05/29/2018] [Accepted: 06/13/2018] [Indexed: 12/02/2022]
Abstract
BRCA1-associated protein-1 (BAP1) is a nuclear localized deubiquitylating enzyme that belongs to the ubiquitin c-terminal hydrolase subfamily. The encoded protein is highly homologous between man and dogs, suggesting a functional significance preserved by evolution. BAP1 has multiple properties, including tumour suppressor activity. Loss of BAP1 function is implicated in the oncogenesis of several types of cancers including uveal, mucosal and some cutaneous melanomas in humans, as well as in mesothelioma. In this study we investigate the significance of BAP1 in canine melanoma. Nuclear BAP1 protein was detected in five canine oral melanoma cell lines using an antibody commonly used for analysis of human tissues. BAP1 loss of function mutations often lead to loss of nuclear BAP1 (nBAP1) expression in humans; this is associated with a poorer prognosis in uveal and mucosal melanoma. Therefore, as a prelude to a study evaluating the prognostic significance of nBAP1 expression in dogs, immunohistochemistry (IHC) was used to assess cases of canine melanoma for nBAP1 expression. In 89 cases where tumour cells were identified by melan-A labelling, 100% of tumour cells were positive for nBAP1 expression, including eight uveal tract and 29 oral mucosal melanomas. This finding indicates that BAP1 IHC cannot be used as a prognostic marker in canine uveal and mucosal melanoma. Moreover, this observation suggests that either BAP1 has a different functional significance in canine melanoma or that loss of BAP1 function is achieved by a different route. This is a novel finding that warrants further investigation to determine the comparative biological relevance.
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Affiliation(s)
- N Jama
- Department of Small Animal Clinical Sciences, Institute of Veterinary Science, University of Liverpool, Liverpool, UK; Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK; Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - N Farquhar
- Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Z Butt
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - S E Coupland
- Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - J J Sacco
- Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - T Scase
- Bridge Pathology Ltd., 637 Gloucester Road, Bristol, UK
| | - A B Fielding
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - J M Coulson
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - H Kalirai
- Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - D R Killick
- Department of Small Animal Clinical Sciences, Institute of Veterinary Science, University of Liverpool, Liverpool, UK.
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70
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Blount JR, Libohova K, Marsh GB, Sutton JR, Todi SV. Expression and Regulation of Deubiquitinase-Resistant, Unanchored Ubiquitin Chains in Drosophila. Sci Rep 2018; 8:8513. [PMID: 29855490 PMCID: PMC5981470 DOI: 10.1038/s41598-018-26364-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/10/2018] [Indexed: 01/03/2023] Open
Abstract
The modifier protein, ubiquitin (Ub) regulates various cellular pathways by controlling the fate of substrates to which it is conjugated. Ub moieties are also conjugated to each other, forming chains of various topologies. In cells, poly-Ub is attached to proteins and also exists in unanchored form. Accumulation of unanchored poly-Ub is thought to be harmful and quickly dispersed through dismantling by deubiquitinases (DUBs). We wondered whether disassembly by DUBs is necessary to control unanchored Ub chains in vivo. We generated Drosophila melanogaster lines that express Ub chains non-cleavable into mono-Ub by DUBs. These chains are rapidly modified with different linkages and represent various types of unanchored species. We found that unanchored poly-Ub is not devastating in Drosophila, under normal conditions or during stress. The DUB-resistant, free Ub chains are degraded by the proteasome, at least in part through the assistance of VCP and its cofactor, p47. Also, unanchored poly-Ub that cannot be cleaved by DUBs can be conjugated en bloc, in vivo. Our results indicate that unanchored poly-Ub species need not be intrinsically toxic; they can be controlled independently of DUB-based disassembly by being degraded, or through conjugation onto other proteins.
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Affiliation(s)
- Jessica R Blount
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Kozeta Libohova
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Gregory B Marsh
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Joanna R Sutton
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sokol V Todi
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA. .,Department of Neurology, Wayne State University School of Medicine, Detroit, MI, USA.
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71
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Ubiquitin Proteasome pathway proteins as potential drug targets in parasite Trypanosoma cruzi. Sci Rep 2018; 8:8399. [PMID: 29849031 PMCID: PMC5976635 DOI: 10.1038/s41598-018-26532-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/15/2018] [Indexed: 12/11/2022] Open
Abstract
Trypanosomiasis infects more than 21 million people and claims approximately 2 million lives annually. Due to the development of resistance against currently available anti-trypanosomal drugs, there is a growing need for specific inhibitors and novel drug targets. Of late, the proteins from the Ubiquitin Proteasome Pathway (UPP): ubiquitin ligases and deubiquitinase have received attention as potential drug targets in other parasites from the apicomplexan family. The completion of Trypanosoma cruzi (Tc) genome sequencing in 2005 and subsequent availability of database resources like TriTrypDB has provided a platform for the systematic study of the proteome of this parasite. Here, we present the first comprehensive survey of the UPP enzymes, their homologs and other associated proteins in trypanosomes and the UPPs from T. cruzi were explored in detail. After extensive computational analyses using various bioinformatics tools, we have identified 269 putative UPP proteins in the T. cruzi proteome along with their homologs in other Trypanosoma species. Characterization of T. cruzi proteome was done based on their predicted subcellular localization, domain architecture and overall expression profiles. Specifically, unique domain architectures of the enzymes and the UPP players expressed exclusively in the amastigote stage provide a rationale for designing inhibitors against parasite UPP proteins.
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72
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The deubiquitylase USP15 regulates topoisomerase II alpha to maintain genome integrity. Oncogene 2018; 37:2326-2342. [PMID: 29429988 PMCID: PMC5916918 DOI: 10.1038/s41388-017-0092-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/25/2017] [Accepted: 11/24/2017] [Indexed: 02/04/2023]
Abstract
Ubiquitin-specific protease 15 (USP15) is a widely expressed deubiquitylase that has been implicated in diverse cellular processes in cancer. Here we identify topoisomerase II (TOP2A) as a novel protein that is regulated by USP15. TOP2A accumulates during G2 and functions to decatenate intertwined sister chromatids at prophase, ensuring the replicated genome can be accurately divided into daughter cells at anaphase. We show that USP15 is required for TOP2A accumulation, and that USP15 depletion leads to the formation of anaphase chromosome bridges. These bridges fail to decatenate, and at mitotic exit form micronuclei that are indicative of genome instability. We also describe the cell cycle-dependent behaviour for two major isoforms of USP15, which differ by a short serine-rich insertion that is retained in isoform-1 but not in isoform-2. Although USP15 is predominantly cytoplasmic in interphase, we show that both isoforms move into the nucleus at prophase, but that isoform-1 is phosphorylated on its unique S229 residue at mitotic entry. The micronuclei phenotype we observe on USP15 depletion can be rescued by either USP15 isoform and requires USP15 catalytic activity. Importantly, however, an S229D phospho-mimetic mutant of USP15 isoform-1 cannot rescue either the micronuclei phenotype, or accumulation of TOP2A. Thus, S229 phosphorylation selectively abrogates this role of USP15 in maintaining genome integrity in an isoform-specific manner. Finally, we show that USP15 isoform-1 is preferentially upregulated in a panel of non-small cell lung cancer cell lines, and propose that isoform imbalance may contribute to genome instability in cancer. Our data provide the first example of isoform-specific deubiquitylase phospho-regulation and reveal a novel role for USP15 in guarding genome integrity.
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73
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Romero-Barrios N, Vert G. Proteasome-independent functions of lysine-63 polyubiquitination in plants. THE NEW PHYTOLOGIST 2018; 217:995-1011. [PMID: 29194634 DOI: 10.1111/nph.14915] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 10/12/2017] [Indexed: 05/21/2023]
Abstract
Contents Summary 995 I. Introduction 995 II. The plant Ub machinery 996 III. From Ub to Ub linkage types in plants 997 IV. Increasing analytical resolution for K63 polyUb in plants 998 V. How to build K63 polyUb chains? 998 VI. Cellular roles of K63 polyUb in plants 999 VII. Physiological roles of K63 polyUb in plants 1004 VIII. Future perspectives: towards the next level of the Ub code 1006 Acknowledgements 1006 References 1007 SUMMARY: Ubiquitination is a post-translational modification essential for the regulation of eukaryotic proteins, having an impact on protein fate, function, localization or activity. What originally appeared to be a simple system to regulate protein turnover by the 26S proteasome is now known to be the most intricate regulatory process cells have evolved. Ubiquitin can be arranged in countless chain assemblies, triggering various cellular outcomes. Polyubiquitin chains using lysine-63 from ubiquitin represent the second most abundant type of ubiquitin modification. Recent studies have exposed their common function in proteasome-independent functions in non-plant model organisms. The existence of lysine-63 polyubiquitination in plants is, however, only just emerging. In this review, we discuss the recent advances on the characterization of ubiquitin chains and the molecular mechanisms driving the formation of lysine-63-linked ubiquitin modifications. We provide an overview of the roles associated with lysine-63 polyubiquitination in plant cells in the light of what is known in non-plant models. Finally, we review the crucial roles of lysine-63 polyubiquitin-dependent processes in plant growth, development and responses to environmental conditions.
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Affiliation(s)
- Natali Romero-Barrios
- Institute for Integrative Biology of the Cell (I2BC), CNRS/CEA/Univ. Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, 91198, France
| | - Grégory Vert
- Institute for Integrative Biology of the Cell (I2BC), CNRS/CEA/Univ. Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, 91198, France
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74
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Molecular Mechanisms and Cellular Pathways Implicated in Machado-Joseph Disease Pathogenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1049:349-367. [PMID: 29427113 DOI: 10.1007/978-3-319-71779-1_18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Machado-Joseph disease (MJD) is a dominantly inherited disorder originally described in people of Portuguese descent, and associated with the expansion of a CAG tract in the coding region of the causative gene MJD1/ATX3. The CAG repeats range from 10 to 51 in the normal population and from 55 to 87 in SCA3/MJD patients. MJD1 encodes ataxin-3, a protein whose physiological function has been linked to ubiquitin-mediated proteolysis. Despite the identification of the causative mutation, the pathogenic process leading to the neurodegeneration observed in the disease is not yet completely understood. In the past years, several studies identified different molecular mechanisms and cellular pathways as being impaired or deregulated in MJD. Autophagy, proteolysis or post-translational modifications, among other processes, were implicated in MJD pathogenesis. From these studies it was possible to identify new targets for therapeutic intervention, which in some cases proved successful in models of disease.
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75
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Wang DH, Song W, Wei SW, Zheng YF, Chen ZS, Han JD, Zhang HT, Luo JC, Qin YM, Xu ZH, Bai SN. Characterization of the Ubiquitin C-Terminal Hydrolase and Ubiquitin-Specific Protease Families in Rice ( Oryza sativa). FRONTIERS IN PLANT SCIENCE 2018; 9:1636. [PMID: 30498503 PMCID: PMC6249995 DOI: 10.3389/fpls.2018.01636] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/22/2018] [Indexed: 05/11/2023]
Abstract
The ubiquitin C-terminal hydrolase (UCH) and ubiquitin-specific processing protease (UBP) protein families both function in protein deubiquitination, playing important roles in a wide range of biological processes in animals, fungi, and plants. Little is known about the functions of these proteins in rice (Oryza sativa), and the numbers of genes reported for these families have not been consistent between different rice database resources. To further explore their functions, it is necessary to first clarify the basic molecular and biochemical nature of these two gene families. Using a database similarity search, we clarified the numbers of genes in these two families in the rice genome, examined the enzyme activities of their corresponding proteins, and characterized the expression patterns of all OsUCH and representative OsUBP genes. Five OsUCH and 44 OsUBP genes were identified in the rice genome, with four OsUCH proteins and 10 of 16 tested representative OsUBP proteins showing enzymatic activities. Two OsUCHs and five OsUBPs were found to be preferentially expressed in the early development of rice stamens. This work thus lays down a reliable bioinformatic foundation for future investigations of genes in these two families, particularly for exploring their potential roles in rice stamen development.
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Affiliation(s)
- Dong-Hui Wang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- National Center of Plant Gene Research, Beijing, China
| | - Wei Song
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- National Center of Plant Gene Research, Beijing, China
| | - Shao-Wei Wei
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- National Center of Plant Gene Research, Beijing, China
| | - Ya-Feng Zheng
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- National Center of Plant Gene Research, Beijing, China
| | - Zhi-Shan Chen
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- National Center of Plant Gene Research, Beijing, China
| | - Jing-Dan Han
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hong-Tao Zhang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- National Center of Plant Gene Research, Beijing, China
| | - Jing-Chu Luo
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- National Center of Plant Gene Research, Beijing, China
| | - Yong-Mei Qin
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- National Center of Plant Gene Research, Beijing, China
| | - Zhi-Hong Xu
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- National Center of Plant Gene Research, Beijing, China
| | - Shu-Nong Bai
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing, China
- National Center of Plant Gene Research, Beijing, China
- *Correspondence: Shu-Nong Bai,
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76
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Jupin I, Ayach M, Jomat L, Fieulaine S, Bressanelli S. A mobile loop near the active site acts as a switch between the dual activities of a viral protease/deubiquitinase. PLoS Pathog 2017; 13:e1006714. [PMID: 29117247 PMCID: PMC5695851 DOI: 10.1371/journal.ppat.1006714] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 11/20/2017] [Accepted: 10/25/2017] [Indexed: 12/21/2022] Open
Abstract
The positive-strand RNA virus Turnip yellow mosaic virus (TYMV) encodes an ovarian tumor (OTU)-like protease/deubiquitinase (PRO/DUB) protein domain involved both in proteolytic processing of the viral polyprotein through its PRO activity, and in removal of ubiquitin chains from ubiquitylated substrates through its DUB activity. Here, the crystal structures of TYMV PRO/DUB mutants and molecular dynamics simulations reveal that an idiosyncratic mobile loop participates in reversibly constricting its unusual catalytic site by adopting "open", "intermediate" or "closed" conformations. The two cis-prolines of the loop form a rigid flap that in the most closed conformation zips up against the other side of the catalytic cleft. The intermediate and closed conformations also correlate with a reordering of the TYMV PRO/DUB catalytic dyad, that then assumes a classical, yet still unusually mobile, OTU DUB alignment. Further structure-based mutants designed to interfere with the loop's mobility were assessed for enzymatic activity in vitro and in vivo, and were shown to display reduced DUB activity while retaining PRO activity. This indicates that control of the switching between the dual PRO/DUB activities resides prominently within this loop next to the active site. Introduction of mutations into the viral genome revealed that the DUB activity contributes to the extent of viral RNA accumulation both in single cells and in whole plants. In addition, the conformation of the mobile flap was also found to influence symptoms severity in planta. Such mutants now provide powerful tools with which to study the specific roles of reversible ubiquitylation in viral infection. Viruses have much smaller genomes than their hosts. Consequently, they often encode proteins which are multifunctional. For instance, some viral proteases have a dual function, being also deubiquitinases, i.e. enzymes capable of removing ubiquitin tags grafted onto proteins and that often target them for destruction. The protease and deubiquitinase activities share a single active site that is used alternately for one function or the other, but how this switch between activities may be regulated is presently unknown. To answer this question, we studied a simple plant virus that is a useful model system for these complex molecular biology phenomena, and that encodes a simplified protease/deubiquitinase. Here, thanks to a combination of structural and functional analyses, we managed to decouple the two activities, killing the deubiquitinase activity while preserving the protease one. This successful decoupling relies on our discovery that a loop inserted next to the active site is mobile, and can thus act as a switch between the two activities. This result allowed us to demonstrate the importance of the specific deubiquinase activity in viral multiplication. In addition, viral symptoms were also severely affected by mutations affecting the loop mobility. Our data provide powerful tools for further studies, that may also be relevant for more complex or medically relevant viruses.
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Affiliation(s)
- Isabelle Jupin
- Institut Jacques Monod, CNRS—Univ Paris-Diderot, Paris, France
- * E-mail: (IJ); (SB)
| | - Maya Ayach
- Institute for Integrative Biology of the Cell, CEA—CNRS—Univ Paris-Saclay, Gif sur Yvette, France
| | - Lucile Jomat
- Institut Jacques Monod, CNRS—Univ Paris-Diderot, Paris, France
| | - Sonia Fieulaine
- Institute for Integrative Biology of the Cell, CEA—CNRS—Univ Paris-Saclay, Gif sur Yvette, France
| | - Stéphane Bressanelli
- Institute for Integrative Biology of the Cell, CEA—CNRS—Univ Paris-Saclay, Gif sur Yvette, France
- * E-mail: (IJ); (SB)
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77
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Darling S, Fielding AB, Sabat-Pośpiech D, Prior IA, Coulson JM. Regulation of the cell cycle and centrosome biology by deubiquitylases. Biochem Soc Trans 2017; 45:1125-1136. [PMID: 28900014 PMCID: PMC5652225 DOI: 10.1042/bst20170087] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 08/04/2017] [Accepted: 08/07/2017] [Indexed: 12/12/2022]
Abstract
Post-translational modification of proteins by ubiquitylation is increasingly recognised as a highly complex code that contributes to the regulation of diverse cellular processes. In humans, a family of almost 100 deubiquitylase enzymes (DUBs) are assigned to six subfamilies and many of these DUBs can remove ubiquitin from proteins to reverse signals. Roles for individual DUBs have been delineated within specific cellular processes, including many that are dysregulated in diseases, particularly cancer. As potentially druggable enzymes, disease-associated DUBs are of increasing interest as pharmaceutical targets. The biology, structure and regulation of DUBs have been extensively reviewed elsewhere, so here we focus specifically on roles of DUBs in regulating cell cycle processes in mammalian cells. Over a quarter of all DUBs, representing four different families, have been shown to play roles either in the unidirectional progression of the cell cycle through specific checkpoints, or in the DNA damage response and repair pathways. We catalogue these roles and discuss specific examples. Centrosomes are the major microtubule nucleating centres within a cell and play a key role in forming the bipolar mitotic spindle required to accurately divide genetic material between daughter cells during cell division. To enable this mitotic role, centrosomes undergo a complex replication cycle that is intimately linked to the cell division cycle. Here, we also catalogue and discuss DUBs that have been linked to centrosome replication or function, including centrosome clustering, a mitotic survival strategy unique to cancer cells with supernumerary centrosomes.
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Affiliation(s)
- Sarah Darling
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, U.K
| | - Andrew B Fielding
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, U.K
| | - Dorota Sabat-Pośpiech
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, U.K
| | - Ian A Prior
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, U.K
| | - Judy M Coulson
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, U.K.
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78
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Inhibition of USP10 induces degradation of oncogenic FLT3. Nat Chem Biol 2017; 13:1207-1215. [PMID: 28967922 DOI: 10.1038/nchembio.2486] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 08/25/2017] [Indexed: 01/07/2023]
Abstract
Oncogenic forms of the kinase FLT3 are important therapeutic targets in acute myeloid leukemia (AML); however, clinical responses to small-molecule kinase inhibitors are short-lived as a result of the rapid emergence of resistance due to point mutations or compensatory increases in FLT3 expression. We sought to develop a complementary pharmacological approach whereby proteasome-mediated FLT3 degradation could be promoted by inhibitors of the deubiquitinating enzymes (DUBs) responsible for cleaving ubiquitin from FLT3. Because the relevant DUBs for FLT3 are not known, we assembled a focused library of most reported small-molecule DUB inhibitors and carried out a cellular phenotypic screen to identify compounds that could induce the degradation of oncogenic FLT3. Subsequent target deconvolution efforts allowed us to identify USP10 as the critical DUB required to stabilize FLT3. Targeting of USP10 showed efficacy in preclinical models of mutant-FLT3 AML, including cell lines, primary patient specimens and mouse models of oncogenic-FLT3-driven leukemia.
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79
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Setz C, Friedrich M, Rauch P, Fraedrich K, Matthaei A, Traxdorf M, Schubert U. Inhibitors of Deubiquitinating Enzymes Block HIV-1 Replication and Augment the Presentation of Gag-Derived MHC-I Epitopes. Viruses 2017; 9:v9080222. [PMID: 28805676 PMCID: PMC5580479 DOI: 10.3390/v9080222] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/04/2017] [Accepted: 08/08/2017] [Indexed: 12/18/2022] Open
Abstract
In recent years it has been well established that two major constituent parts of the ubiquitin proteasome system (UPS)—the proteasome holoenzymes and a number of ubiquitin ligases—play a crucial role, not only in virus replication but also in the regulation of the immunogenicity of human immunodeficiency virus type 1 (HIV-1). However, the role in HIV-1 replication of the third major component, the deubiquitinating enzymes (DUBs), has remained largely unknown. In this study, we show that the DUB-inhibitors (DIs) P22077 and PR-619, specific for the DUBs USP7 and USP47, impair Gag processing and thereby reduce the infectivity of released virions without affecting viral protease activity. Furthermore, the replication capacity of X4- and R5-tropic HIV-1NL4-3 in human lymphatic tissue is decreased upon treatment with these inhibitors without affecting cell viability. Most strikingly, combinatory treatment with DIs and proteasome inhibitors synergistically blocks virus replication at concentrations where mono-treatment was ineffective, indicating that DIs can boost the therapeutic effect of proteasome inhibitors. In addition, P22077 and PR-619 increase the polyubiquitination of Gag and thus its entry into the UPS and the major histocompatibility complex (MHC)-I pathway. In summary, our data point towards a model in which specific inhibitors of DUBs not only interfere with virus spread but also increase the immune recognition of HIV-1 expressing cells.
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Affiliation(s)
- Christian Setz
- Institute of Virology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen 91054, Germany.
| | - Melanie Friedrich
- Institute of Virology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen 91054, Germany.
| | - Pia Rauch
- Institute of Virology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen 91054, Germany.
| | - Kirsten Fraedrich
- Institute of Virology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen 91054, Germany.
| | - Alina Matthaei
- Institute of Virology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen 91054, Germany.
| | - Maximilian Traxdorf
- Department of Otorhinolaryngology, Head and Neck Surgery, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen 91054, Germany.
| | - Ulrich Schubert
- Institute of Virology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen 91054, Germany.
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80
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Lai KP, Cheung AHY, Tse WKF. DeubiquitinaseUsp18prevents cellular apoptosis from oxidative stress in liver cells. Cell Biol Int 2017; 41:914-921. [DOI: 10.1002/cbin.10799] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 05/25/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Keng Po Lai
- Department of Biology and Chemistry; City University of Hong Kong; Hong Kong SAR China
| | - Angela Hoi Yan Cheung
- Department of Biology and Chemistry; City University of Hong Kong; Hong Kong SAR China
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81
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Deubiquitylating enzymes in receptor endocytosis and trafficking. Biochem J 2017; 473:4507-4525. [PMID: 27941029 DOI: 10.1042/bcj20160826] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 09/15/2016] [Accepted: 09/16/2016] [Indexed: 12/25/2022]
Abstract
In recent times, our knowledge of the roles ubiquitin plays in multiple cellular processes has expanded exponentially, with one example being the role of ubiquitin in receptor endocytosis and trafficking. This has prompted a multitude of studies examining how the different machinery involved in the addition and removal of ubiquitin can influence this process. Multiple deubiquitylating enzymes (DUBs) have been implicated either in facilitating receptor endocytosis and lysosomal degradation or in rescuing receptor levels by preventing endocytosis and/or promoting recycling to the plasma membrane. In this review, we will discuss in detail what is currently known about the role of DUBs in regulating the endocytosis of various transmembrane receptors and ion channels. We will also expand upon the role DUBs play in receptor sorting at the multivesicular body to determine whether a receptor is recycled or trafficked to the lysosome for degradation. Finally, we will briefly discuss how the DUBs implicated in these processes may contribute to the pathogenesis of a range of diseases, and thus the potential these have as therapeutic targets.
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82
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Bednash JS, Weathington N, Londino J, Rojas M, Gulick DL, Fort R, Han S, McKelvey AC, Chen BB, Mallampalli RK. Targeting the deubiquitinase STAMBP inhibits NALP7 inflammasome activity. Nat Commun 2017; 8:15203. [PMID: 28492230 PMCID: PMC5437278 DOI: 10.1038/ncomms15203] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 03/08/2017] [Indexed: 01/06/2023] Open
Abstract
Inflammasomes regulate innate immune responses by facilitating maturation of inflammatory cytokines, interleukin (IL)-1β and IL-18. NACHT, LRR and PYD domains-containing protein 7 (NALP7) is one inflammasome constituent, but little is known about its cellular handling. Here we show a mechanism for NALP7 protein stabilization and activation of the inflammasome by Toll-like receptor (TLR) agonism with bacterial lipopolysaccharide (LPS) and the synthetic acylated lipopeptide Pam3CSK4. NALP7 is constitutively ubiquitinated and recruited to the endolysosome for degradation. With TLR ligation, the deubiquitinase enzyme, STAM-binding protein (STAMBP) impedes NALP7 trafficking to lysosomes to increase NALP7 abundance. STAMBP deubiquitinates NALP7 and STAMBP knockdown abrogates LPS or Pam3CSK4-induced increases in NALP7 protein. A small-molecule inhibitor of STAMBP deubiquitinase activity, BC-1471, decreases NALP7 protein levels and suppresses IL-1β release after TLR agonism. These findings describe a unique pathway of inflammasome regulation with the identification of STAMBP as a potential therapeutic target to reduce pro-inflammatory stress.
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Affiliation(s)
- Joseph S. Bednash
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, UPMC Montefiore, NW 628, Pittsburgh, Pennsylvania 15213, USA
| | - Nathaniel Weathington
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, UPMC Montefiore, NW 628, Pittsburgh, Pennsylvania 15213, USA
| | - James Londino
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, UPMC Montefiore, NW 628, Pittsburgh, Pennsylvania 15213, USA
| | - Mauricio Rojas
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, UPMC Montefiore, NW 628, Pittsburgh, Pennsylvania 15213, USA
| | - Dexter L. Gulick
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, UPMC Montefiore, NW 628, Pittsburgh, Pennsylvania 15213, USA
| | - Robert Fort
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, UPMC Montefiore, NW 628, Pittsburgh, Pennsylvania 15213, USA
| | - SeungHye Han
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, UPMC Montefiore, NW 628, Pittsburgh, Pennsylvania 15213, USA
| | - Alison C. McKelvey
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, UPMC Montefiore, NW 628, Pittsburgh, Pennsylvania 15213, USA
| | - Bill B. Chen
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, UPMC Montefiore, NW 628, Pittsburgh, Pennsylvania 15213, USA
| | - Rama K. Mallampalli
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, UPMC Montefiore, NW 628, Pittsburgh, Pennsylvania 15213, USA
- Departments of Cell Biology and Physiology and Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
- Medical Specialty Service Line, Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania 15240, USA
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83
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USP7 deubiquitinase controls HIV-1 production by stabilizing Tat protein. Biochem J 2017; 474:1653-1668. [PMID: 28280111 DOI: 10.1042/bcj20160304] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 03/08/2017] [Accepted: 03/09/2017] [Indexed: 12/24/2022]
Abstract
Deubiquitinases (DUBs) are key regulators of complex cellular processes. HIV-1 Tat is synthesized early after infection and is mainly responsible for enhancing viral production. Here, we report that one of the DUBs, USP7, stabilized the HIV-1 Tat protein through its deubiquitination. Treatment with either a general DUB inhibitor (PR-619) or USP7-specific inhibitor (P5091) resulted in Tat protein degradation. The USP7-specific inhibitor reduced virus production in a latently infected T-lymphocytic cell line J1.1, which produces large amounts of HIV-1 upon stimulation. A potent increase in Tat-mediated HIV-1 production was observed with USP7 in a dose-dependent manner. As expected, deletion of the USP7 gene using the CRISPR-Cas9 method reduced the Tat protein and supported less virus production. Interestingly, the levels of endogenous USP7 increased after HIV-1 infection in human T-cells (MOLT-3) and in mammalian cells transfected with HIV-1 proviral DNA. Thus, HIV-1 Tat is stabilized by the host cell deubiquitinase USP7, leading to enhanced viral production, and HIV-1 in turn up-regulates the USP7 protein level.
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84
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Ho HC, MacGurn JA, Emr SD. Deubiquitinating enzymes Ubp2 and Ubp15 regulate endocytosis by limiting ubiquitination and degradation of ARTs. Mol Biol Cell 2017; 28:1271-1283. [PMID: 28298493 PMCID: PMC5415021 DOI: 10.1091/mbc.e17-01-0008] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 02/27/2017] [Accepted: 02/28/2017] [Indexed: 12/18/2022] Open
Abstract
Endocytic down-regulation of cell-surface proteins is a fundamental cellular process for cell survival and adaptation to environmental stimuli. Ubiquitination of cargo proteins serves as the sorting signal for downstream trafficking and relies on the arrestin-related trafficking adaptor (ART)-Rsp5 ubiquitin ligase adaptor network in yeast. Hence proper regulation of the abundance and activity of these ligase-adaptor complexes is critical for main-tenance of optimal plasma membrane protein composition. Here we report that the stability of ARTs is regulated by the deubiquitinating enzymes (DUBs) Ubp2 and Ubp15. By counteracting the E3 ubiquitin ligase Rsp5, Ubp2 and Ubp15 prevent hyperubiquitination and proteasomal degradation of ARTs. Specifically, we show that loss of both Ubp2 and Ubp15 results in a defect in Hxt6 endocytosis associated with Art4 instability. Our results uncover a novel function for DUBs in the endocytic pathway by which Ubp2 and Ubp15 positively regulate the ART-Rsp5 network.
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Affiliation(s)
- Hsuan-Chung Ho
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Jason A MacGurn
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240
| | - Scott D Emr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
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85
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Potu H, Peterson LF, Kandarpa M, Pal A, Sun H, Durham A, Harms PW, Hollenhorst PC, Eskiocak U, Talpaz M, Donato NJ. Usp9x regulates Ets-1 ubiquitination and stability to control NRAS expression and tumorigenicity in melanoma. Nat Commun 2017; 8:14449. [PMID: 28198367 PMCID: PMC5316860 DOI: 10.1038/ncomms14449] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 12/30/2016] [Indexed: 01/20/2023] Open
Abstract
ETS transcription factors are commonly deregulated in cancer by chromosomal translocation, overexpression or post-translational modification to induce gene expression programs essential in tumorigenicity. Targeted destruction of these proteins may have therapeutic impact. Here we report that Ets-1 destruction is regulated by the deubiquitinating enzyme, Usp9x, and has major impact on the tumorigenic program of metastatic melanoma. Ets-1 deubiquitination blocks its proteasomal destruction and enhances tumorigenicity, which could be reversed by Usp9x knockdown or inhibition. Usp9x and Ets-1 levels are coincidently elevated in melanoma with highest levels detected in metastatic tumours versus normal skin or benign skin lesions. Notably, Ets-1 is induced by BRAF or MEK kinase inhibition, resulting in increased NRAS expression, which could be blocked by inactivation of Usp9x and therapeutic combination of Usp9x and MEK inhibitor fully suppressed melanoma growth. Thus, Usp9x modulates the Ets-1/NRAS regulatory network and may have biologic and therapeutic implications.
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Affiliation(s)
- Harish Potu
- Department of Internal Medicine/Division of Hematology/Oncology, University of Michigan School of Medicine and Comprehensive Cancer Center, Ann Arbor, Michigan 48109, USA
| | - Luke F. Peterson
- Department of Internal Medicine/Division of Hematology/Oncology, University of Michigan School of Medicine and Comprehensive Cancer Center, Ann Arbor, Michigan 48109, USA
| | - Malathi Kandarpa
- Department of Internal Medicine/Division of Hematology/Oncology, University of Michigan School of Medicine and Comprehensive Cancer Center, Ann Arbor, Michigan 48109, USA
| | - Anupama Pal
- Department of Internal Medicine/Division of Hematology/Oncology, University of Michigan School of Medicine and Comprehensive Cancer Center, Ann Arbor, Michigan 48109, USA
| | - Hanshi Sun
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, Michigan 48109, USA
| | - Alison Durham
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan 48109, USA
| | - Paul W. Harms
- Departments of Pathology and Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan 48109, USA
| | - Peter C. Hollenhorst
- Department of Biochemistry and Molecular Biology, Medical Sciences Program, Indiana University Bloomington, 1001 Third St, Bloomington, Indiana 47405, USA
| | - Ugur Eskiocak
- Children's Research Institute and Department of Pediatrics, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Moshe Talpaz
- Department of Internal Medicine/Division of Hematology/Oncology, University of Michigan School of Medicine and Comprehensive Cancer Center, Ann Arbor, Michigan 48109, USA
| | - Nicholas J. Donato
- Department of Pharmacology, University of Michigan School of Medicine, Ann Arbor, Michigan 48109, USA
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86
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Ubiquitin C-terminal hydrolase37 regulates Tcf7 DNA binding for the activation of Wnt signalling. Sci Rep 2017; 7:42590. [PMID: 28198400 PMCID: PMC5309806 DOI: 10.1038/srep42590] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 01/11/2017] [Indexed: 12/18/2022] Open
Abstract
The Tcf/Lef family of transcription factors mediates the Wnt/β-catenin pathway that is involved in a wide range of biological processes, including vertebrate embryogenesis and diverse pathogenesis. Post-translational modifications, including phosphorylation, sumoylation and acetylation, are known to be important for the regulation of Tcf/Lef proteins. However, the importance of ubiquitination and ubiquitin-mediated regulatory mechanisms for Tcf/Lef activity are still unclear. Here, we newly show that ubiquitin C-terminal hydrolase 37 (Uch37), a deubiquitinase, interacts with Tcf7 (formerly named Tcf1) to activate Wnt signalling. Biochemical analyses demonstrated that deubiquitinating activity of Uch37 is not involved in Tcf7 protein stability but is required for the association of Tcf7 to target gene promoter in both Xenopus embryo and human liver cancer cells. In vivo analyses further revealed that Uch37 functions as a positive regulator of the Wnt/β-catenin pathway downstream of β-catenin stabilization that is required for the expression of ventrolateral mesoderm genes during Xenopus gastrulation. Our study provides a new mechanism for chromatin occupancy of Tcf7 and uncovers the physiological significance of Uch37 during early vertebrate development by regulating the Wnt/β-catenin pathway.
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87
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Canzonetta C, Leo M, Guarino SR, Montanari A, Francisci S, Filetici P. SAGA complex and Gcn5 are necessary for respiration in budding yeast. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:3160-3168. [DOI: 10.1016/j.bbamcr.2016.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/13/2016] [Accepted: 10/07/2016] [Indexed: 10/25/2022]
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88
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Deubiquitinase activity is required for the proteasomal degradation of misfolded cytosolic proteins upon heat-stress. Nat Commun 2016; 7:12907. [PMID: 27698423 PMCID: PMC5059457 DOI: 10.1038/ncomms12907] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 08/12/2016] [Indexed: 12/25/2022] Open
Abstract
Elimination of misfolded proteins is crucial for proteostasis and to prevent proteinopathies. Nedd4/Rsp5 emerged as a major E3-ligase involved in multiple quality control pathways that target misfolded plasma membrane proteins, aggregated polypeptides and cytosolic heat-induced misfolded proteins for degradation. It remained unclear how in one case cytosolic heat-induced Rsp5 substrates are destined for proteasomal degradation, whereas other Rsp5 quality control substrates are otherwise directed to lysosomal degradation. Here we find that Ubp2 and Ubp3 deubiquitinases are required for the proteasomal degradation of cytosolic misfolded proteins targeted by Rsp5 after heat-shock (HS). The two deubiquitinases associate more with Rsp5 upon heat-stress to prevent the assembly of K63-linked ubiquitin on Rsp5 heat-induced substrates. This activity was required to promote the K48-mediated proteasomal degradation of Rsp5 HS-induced substrates. Our results indicate that ubiquitin chain editing is key to the cytosolic protein quality control under stress conditions. Ubiquitination of misfolded proteins usually results in protein degradation. Here, the authors show that two deubiquitinases—enzymes that remove ubiquitin—are required for the proteasomal degradation of misfolded proteins in response to heat-shock in yeast.
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89
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Heride C, Rigden DJ, Bertsoulaki E, Cucchi D, De Smaele E, Clague MJ, Urbé S. The centrosomal deubiquitylase USP21 regulates Gli1 transcriptional activity and stability. J Cell Sci 2016; 129:4001-4013. [PMID: 27621083 PMCID: PMC5117204 DOI: 10.1242/jcs.188516] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 09/05/2016] [Indexed: 12/23/2022] Open
Abstract
USP21 is a centrosome-associated deubiquitylase (DUB) that has been implicated in the formation of primary cilia – crucial organelles for the regulation of the Hedgehog (Hh) signaling pathway in vertebrates. Here, we identify KCTD6 – a cullin-3 E3-ligase substrate adapter that has been previously linked to Hh signaling – as well as Gli1, the key transcription factor responsible for Hh signal amplification, as new interacting partners of USP21. We identify a cryptic structured protein interaction domain in KCTD6, which is predicted to have a similar fold to Smr domains. Importantly, we show that both depletion and overexpression of catalytically active USP21 suppress Gli1-dependent transcription. Gli proteins are negatively regulated through protein kinase A (PKA)-dependent phosphorylation. We provide evidence that USP21 recruits and stabilises Gli1 at the centrosome where it promotes its phosphorylation by PKA. By revealing an intriguing functional pairing between a spatially restricted deubiquitylase and a kinase, our study highlights the centrosome as an important hub for signal coordination. Summary: We identify a Hedgehog-pathway-associated ubiquitin ligase adapter as a direct interaction partner of the deubiquitylase USP21 and discover a close interplay between USP21 and protein kinase A in regulating Gli1.
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Affiliation(s)
- Claire Heride
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool L69 3BX, UK
| | - Daniel J Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Erithelgi Bertsoulaki
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool L69 3BX, UK
| | - Danilo Cucchi
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Enrico De Smaele
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Michael J Clague
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool L69 3BX, UK
| | - Sylvie Urbé
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool L69 3BX, UK
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90
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Crowe SO, Pham GH, Ziegler JC, Deol KK, Guenette RG, Ge Y, Strieter ER. Subunit-Specific Labeling of Ubiquitin Chains by Using Sortase: Insights into the Selectivity of Deubiquitinases. Chembiochem 2016; 17:1525-31. [PMID: 27256865 PMCID: PMC5459594 DOI: 10.1002/cbic.201600276] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Indexed: 12/12/2022]
Abstract
Information embedded in different ubiquitin chains is transduced by proteins with ubiquitin-binding domains (UBDs) and erased by a set of hydrolytic enzymes referred to as deubiquitinases (DUBs). Understanding the selectivity of UBDs and DUBs is necessary for decoding the functions of different ubiquitin chains. Critical to these efforts is the access to chemically defined ubiquitin chains bearing site-specific fluorescent labels. One approach toward constructing such molecules involves peptide ligation by sortase (SrtA), a bacterial transpeptidase responsible for covalently attaching cell surface proteins to the cell wall. Here, we demonstrate the utility of SrtA in modifying individual subunits of ubiquitin chains. Using ubiquitin derivatives in which an N-terminal glycine is unveiled after protease-mediated digestion, we synthesized ubiquitin dimers, trimers, and tetramers with different isopeptide linkages. SrtA was then used in combination with fluorescent depsipeptide substrates to effect the modification of each subunit in a chain. By constructing branched ubiquitin chains with individual subunits tagged with a fluorophore, we provide evidence that the ubiquitin-specific protease USP15 prefers ubiquitin trimers but has little preference for a particular isopeptide linkage. Our results emphasize the importance of subunit-specific labeling of ubiquitin chains when studying how DUBs process these chains.
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Affiliation(s)
- Sean O Crowe
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Grace H Pham
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jacob C Ziegler
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Kirandeep K Deol
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Robert G Guenette
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, 53706, USA
| | - Eric R Strieter
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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91
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Anta B, Martín-Rodríguez C, Gomis-Perez C, Calvo L, López-Benito S, Calderón-García AA, Vicente-García C, Villarroel Á, Arévalo JC. Ubiquitin-specific Protease 36 (USP36) Controls Neuronal Precursor Cell-expressed Developmentally Down-regulated 4-2 (Nedd4-2) Actions over the Neurotrophin Receptor TrkA and Potassium Voltage-gated Channels 7.2/3 (Kv7.2/3). J Biol Chem 2016; 291:19132-45. [PMID: 27445338 DOI: 10.1074/jbc.m116.722637] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Indexed: 11/06/2022] Open
Abstract
Ubiquitination of the TrkA neurotrophin receptor in response to NGF is critical in the regulation of TrkA activation and functions. TrkA is ubiquitinated, among other E3 ubiquitin ligases, by Nedd4-2. To understand mechanistically how TrkA ubiquitination is regulated, we performed a siRNA screening to identify deubiquitinating enzymes and found that USP36 acts as an important regulator of TrkA activation kinetics and ubiquitination. However, USP36 action on TrkA was indirect because it does not deubiquitinate TrkA. Instead, USP36 binds to Nedd4-2 and regulates the association of TrkA and Nedd4-2. In addition, depletion of USP36 increases TrkA·Nedd4-2 complex formation, whereas USP36 expression disrupts the complex, resulting in an enhancement or impairment of Nedd4-2-dependent TrkA ubiquitination, respectively. Moreover, USP36 depletion leads to enhanced total and surface TrkA expression that results in increased NGF-mediated TrkA activation and signaling that augments PC12 cell differentiation. USP36 actions extend beyond TrkA because the presence of USP36 interferes with Nedd4-2-dependent Kv7.2/3 channel regulation. Our results demonstrate that USP36 binds to and regulates the actions of Nedd4-2 over different substrates affecting their expression and functions.
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Affiliation(s)
- Begoña Anta
- From the Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain, the Institute of Biomedical Research of Salamanca, 47195 Salamanca, Spain, and
| | - Carlos Martín-Rodríguez
- From the Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain, the Institute of Biomedical Research of Salamanca, 47195 Salamanca, Spain, and
| | - Carolina Gomis-Perez
- the Unidad de Biofísica, Consejo Superior de Investigaciones Científicas, CSIC, UPV/EHU, Universidad del País Vasco, barrio Sarriena s/n, 48940 Leoia, Spain
| | - Laura Calvo
- From the Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain, the Institute of Biomedical Research of Salamanca, 47195 Salamanca, Spain, and
| | - Saray López-Benito
- From the Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain, the Institute of Biomedical Research of Salamanca, 47195 Salamanca, Spain, and
| | - Andrés A Calderón-García
- From the Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain
| | - Cristina Vicente-García
- From the Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain, the Institute of Biomedical Research of Salamanca, 47195 Salamanca, Spain, and
| | - Álvaro Villarroel
- the Unidad de Biofísica, Consejo Superior de Investigaciones Científicas, CSIC, UPV/EHU, Universidad del País Vasco, barrio Sarriena s/n, 48940 Leoia, Spain
| | - Juan C Arévalo
- From the Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain, the Institute of Biomedical Research of Salamanca, 47195 Salamanca, Spain, and
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92
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Publisher’s Note. DNA Repair (Amst) 2016. [DOI: 10.1016/j.dnarep.2016.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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93
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Yeates EFA, Tesco G. The Endosome-associated Deubiquitinating Enzyme USP8 Regulates BACE1 Enzyme Ubiquitination and Degradation. J Biol Chem 2016; 291:15753-66. [PMID: 27302062 DOI: 10.1074/jbc.m116.718023] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Indexed: 01/04/2023] Open
Abstract
The β-site amyloid precursor protein-cleaving enzyme (BACE1) is the rate-limiting enzyme in the production of amyloid-β, the toxic peptide that accumulates in the brain of subjects affected by Alzheimer disease. Our previous studies have shown that BACE1 is degraded via the lysosomal pathway and that that depletion of the trafficking molecule Golgi-localized γ-ear-containing ARF-binding protein 3 (GGA3) results in increased BACE1 levels and activity because of impaired lysosomal degradation. We also determined that GGA3 regulation of BACE1 levels requires its ability to bind ubiquitin. Accordingly, we reported that BACE1 is ubiquitinated at lysine 501 and that lack of ubiquitination at lysine 501 produces BACE1 stabilization. Ubiquitin conjugation is a reversible process mediated by deubiquitinating enzymes. The ubiquitin-specific peptidase 8 (USP8), an endosome-associated deubiquitinating enzyme, regulates the ubiquitination, trafficking, and lysosomal degradation of several plasma membrane proteins. Here, we report that RNAi-mediated depletion of USP8 reduced levels of both ectopically expressed and endogenous BACE1 in H4 human neuroglioma cells. Moreover, USP8 depletion increased BACE1 ubiquitination, promoted BACE1 accumulation in the early endosomes and late endosomes/lysosomes, and decreased levels of BACE1 in the recycling endosomes. We also found that decreased BACE1 protein levels were accompanied by a decrease in BACE1-mediated amyloid precursor protein cleavage and amyloid-β levels. Our findings demonstrate that USP8 plays a key role in the trafficking and degradation of BACE1 by deubiquitinating lysine 501. These studies suggest that therapies able to accelerate BACE1 degradation (e.g. by increasing BACE1 ubiquitination) may represent a potential treatment for Alzheimer disease.
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Affiliation(s)
| | - Giuseppina Tesco
- From the Department of Neuroscience, Tufts University School of Medicine, Boston, Massachusetts 02111
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94
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Abdul Rehman SA, Kristariyanto YA, Choi SY, Nkosi PJ, Weidlich S, Labib K, Hofmann K, Kulathu Y. MINDY-1 Is a Member of an Evolutionarily Conserved and Structurally Distinct New Family of Deubiquitinating Enzymes. Mol Cell 2016; 63:146-55. [PMID: 27292798 PMCID: PMC4942677 DOI: 10.1016/j.molcel.2016.05.009] [Citation(s) in RCA: 254] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/15/2016] [Accepted: 05/05/2016] [Indexed: 12/22/2022]
Abstract
Deubiquitinating enzymes (DUBs) remove ubiquitin (Ub) from Ub-conjugated substrates to regulate the functional outcome of ubiquitylation. Here we report the discovery of a new family of DUBs, which we have named MINDY (motif interacting with Ub-containing novel DUB family). Found in all eukaryotes, MINDY-family DUBs are highly selective at cleaving K48-linked polyUb, a signal that targets proteins for degradation. We identify the catalytic activity to be encoded within a previously unannotated domain, the crystal structure of which reveals a distinct protein fold with no homology to any of the known DUBs. The crystal structure of MINDY-1 (also known as FAM63A) in complex with propargylated Ub reveals conformational changes that realign the active site for catalysis. MINDY-1 prefers cleaving long polyUb chains and works by trimming chains from the distal end. Collectively, our results reveal a new family of DUBs that may have specialized roles in regulating proteostasis.
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Affiliation(s)
- Syed Arif Abdul Rehman
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Yosua Adi Kristariyanto
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Soo-Youn Choi
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Pedro Junior Nkosi
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Simone Weidlich
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Karim Labib
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674 Cologne, Germany
| | - Yogesh Kulathu
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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95
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Abstract
Nucleotide excision repair (NER) protects genome stability by eliminating DNA helix distorting lesions, such as those induced by UV radiation. The addition and removal of ubiquitin, namely, ubiquitination and deubiquitination, have recently been demonstrated as general mechanisms to regulate protein functions. Accumulating evidence shows that several NER factors are subjected to extensive regulation by ubiquitination and deubiquitination. Thus, the balance between E3 ligases and deubiquitinating enzyme activities can dynamically alter the ubiquitin landscape at DNA damage sites, thereby regulating NER efficiency. Current knowledge about XPC ubiquitination by different ubiquitin E3 ligases highlights the importance of ubiquitin linkage types in regulating XPC binding and release from damaged DNA. Here, we discuss the emerging roles of deubiquitinating enzymes and their ubiquitin linkage specificities in NER.
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96
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Kim RQ, van Dijk WJ, Sixma TK. Structure of USP7 catalytic domain and three Ubl-domains reveals a connector α-helix with regulatory role. J Struct Biol 2016; 195:11-8. [PMID: 27183903 DOI: 10.1016/j.jsb.2016.05.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 05/12/2016] [Accepted: 05/13/2016] [Indexed: 12/11/2022]
Abstract
Ubiquitin conjugation is an important signal in cellular pathways, changing the fate of a target protein, by degradation, relocalisation or complex formation. These signals are balanced by deubiquitinating enzymes (DUBs), which antagonize ubiquitination of specific protein substrates. Because ubiquitination pathways are critically important, DUB activity is often carefully controlled. USP7 is a highly abundant DUB with numerous targets that plays complex roles in diverse pathways, including DNA regulation, p53 stress response and endosomal protein recycling. Full-length USP7 switches between an inactive and an active state, tuned by the positioning of 5 Ubl folds in the C-terminal HUBL domain. The active state requires interaction between the last two Ubls (USP7(45)) and the catalytic domain (USP7(CD)), and this can be promoted by allosteric interaction from the first 3 Ubl domains of USP7 (USP7(123)) interacting with GMPS. Here we study the transition between USP7 states. We provide a crystal structure of USP7(CD123) and show that CD and Ubl123 are connected via an extended charged alpha helix. Mutational analysis is used to determine whether the charge and rigidity of this 'connector helix' are important for full USP7 activity.
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Affiliation(s)
- Robbert Q Kim
- Division of Biochemistry and Cancer Genomics Center, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Willem J van Dijk
- Division of Biochemistry and Cancer Genomics Center, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Titia K Sixma
- Division of Biochemistry and Cancer Genomics Center, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
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97
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Esquerdo M, Grau-Bové X, Garanto A, Toulis V, Garcia-Monclús S, Millo E, López-Iniesta MJ, Abad-Morales V, Ruiz-Trillo I, Marfany G. Expression Atlas of the Deubiquitinating Enzymes in the Adult Mouse Retina, Their Evolutionary Diversification and Phenotypic Roles. PLoS One 2016; 11:e0150364. [PMID: 26934049 PMCID: PMC4774998 DOI: 10.1371/journal.pone.0150364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/12/2016] [Indexed: 12/31/2022] Open
Abstract
Ubiquitination is a relevant cell regulatory mechanism to determine protein fate and function. Most data has focused on the role of ubiquitin as a tag molecule to target substrates to proteasome degradation, and on its impact in the control of cell cycle, protein homeostasis and cancer. Only recently, systematic assays have pointed to the relevance of the ubiquitin pathway in the development and differentiation of tissues and organs, and its implication in hereditary diseases. Moreover, although the activity and composition of ubiquitin ligases has been largely addressed, the role of the deubiquitinating enzymes (DUBs) in specific tissues, such as the retina, remains mainly unknown. In this work, we undertook a systematic analysis of the transcriptional levels of DUB genes in the adult mouse retina by RT-qPCR and analyzed the expression pattern by in situ hybridization and fluorescent immunohistochemistry, thus providing a unique spatial reference map of retinal DUB expression. We also performed a systematic phylogenetic analysis to understand the origin and the presence/absence of DUB genes in the genomes of diverse animal taxa that represent most of the known animal diversity. The expression landscape obtained supports the potential subfunctionalization of paralogs in those families that expanded in vertebrates. Overall, our results constitute a reference framework for further characterization of the DUB roles in the retina and suggest new candidates for inherited retinal disorders.
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Affiliation(s)
- Mariona Esquerdo
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Xavier Grau-Bové
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Biologia Evolutiva (CSIC- Universitat Pompeu Fabra), Barcelona, Spain
| | - Alejandro Garanto
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Vasileios Toulis
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Sílvia Garcia-Monclús
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Erica Millo
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Ma José López-Iniesta
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Víctor Abad-Morales
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Iñaki Ruiz-Trillo
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Biologia Evolutiva (CSIC- Universitat Pompeu Fabra), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Gemma Marfany
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
- * E-mail:
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98
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Ristic G, Tsou WL, Guzi E, Kanack AJ, Scaglione KM, Todi SV. USP5 Is Dispensable for Monoubiquitin Maintenance in Drosophila. J Biol Chem 2016; 291:9161-72. [PMID: 26917723 DOI: 10.1074/jbc.m115.703504] [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] [Received: 11/11/2015] [Indexed: 11/06/2022] Open
Abstract
Ubiquitination is a post-translational modification that regulates most cellular pathways and processes, including degradation of proteins by the proteasome. Substrate ubiquitination is controlled at various stages, including through its reversal by deubiquitinases (DUBs). A critical outcome of this process is the recycling of monoubiquitin. One DUB whose function has been proposed to include monoubiquitin recycling is USP5. Here, we investigated whether Drosophila USP5 is important for maintaining monoubiquitin in vivo We found that the fruit fly orthologue of USP5 has catalytic preferences similar to its human counterpart and that this DUB is necessary during fly development. Our biochemical and genetic experiments indicate that reduction of USP5 does not lead to monoubiquitin depletion in developing flies. Also, introduction of exogenous ubiquitin does not suppress developmental lethality caused by loss of endogenous USP5. Our work indicates that a primary physiological role of USP5 is not to recycle monoubiquitin for reutilization, but that it may involve disassembly of conjugated ubiquitin to maintain proteasome function.
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Affiliation(s)
| | | | - Ermal Guzi
- From the Departments of Pharmacology and
| | - Adam J Kanack
- the Department of Biochemistry and the Neuroscience Research Center, Medical College of Wisconsin, Milwaukee Wisconsin 53226
| | - Kenneth Matthew Scaglione
- the Department of Biochemistry and the Neuroscience Research Center, Medical College of Wisconsin, Milwaukee Wisconsin 53226
| | - Sokol V Todi
- From the Departments of Pharmacology and Neurology, Wayne State University School of Medicine, Detroit, Michigan 48201 and
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99
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Jean-Charles PY, Zhang L, Wu JH, Han SO, Brian L, Freedman NJ, Shenoy SK. Ubiquitin-specific Protease 20 Regulates the Reciprocal Functions of β-Arrestin2 in Toll-like Receptor 4-promoted Nuclear Factor κB (NFκB) Activation. J Biol Chem 2016; 291:7450-64. [PMID: 26839314 DOI: 10.1074/jbc.m115.687129] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Indexed: 12/19/2022] Open
Abstract
Toll-like receptor 4 (TLR4) promotes vascular inflammatory disorders such as neointimal hyperplasia and atherosclerosis. TLR4 triggers NFκB signaling through the ubiquitin ligase TRAF6 (tumor necrosis factor receptor-associated factor 6). TRAF6 activity can be impeded by deubiquitinating enzymes like ubiquitin-specific protease 20 (USP20), which can reverse TRAF6 autoubiquitination, and by association with the multifunctional adaptor protein β-arrestin2. Although β-arrestin2 effects on TRAF6 suggest an anti-inflammatory role, physiologic β-arrestin2 promotes inflammation in atherosclerosis and neointimal hyperplasia. We hypothesized that anti- and proinflammatory dimensions of β-arrestin2 activity could be dictated by β-arrestin2's ubiquitination status, which has been linked with its ability to scaffold and localize activated ERK1/2 to signalosomes. With purified proteins and in intact cells, our protein interaction studies showed that TRAF6/USP20 association and subsequent USP20-mediated TRAF6 deubiquitination were β-arrestin2-dependent. Generation of transgenic mice with smooth muscle cell-specific expression of either USP20 or its catalytically inactive mutant revealed anti-inflammatory effects of USP20in vivoandin vitro Carotid endothelial denudation showed that antagonizing smooth muscle cell USP20 activity increased NFκB activation and neointimal hyperplasia. We found that β-arrestin2 ubiquitination was promoted by TLR4 and reversed by USP20. The association of USP20 with β-arrestin2 was augmented when β-arrestin2 ubiquitination was prevented and reduced when β-arrestin2 ubiquitination was rendered constitutive. Constitutive β-arrestin2 ubiquitination also augmented NFκB activation. We infer that pro- and anti-inflammatory activities of β-arrestin2 are determined by β-arrestin2 ubiquitination and that changes in USP20 expression and/or activity can therefore regulate inflammatory responses, at least in part, by defining the ubiquitination status of β-arrestin2.
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Affiliation(s)
| | | | - Jiao-Hui Wu
- From the Departments of Medicine (Cardiology) and
| | - Sang-Oh Han
- From the Departments of Medicine (Cardiology) and
| | - Leigh Brian
- From the Departments of Medicine (Cardiology) and
| | - Neil J Freedman
- From the Departments of Medicine (Cardiology) and Cell Biology, Duke University Medical Center, Durham, North Carolina 27710
| | - Sudha K Shenoy
- From the Departments of Medicine (Cardiology) and Cell Biology, Duke University Medical Center, Durham, North Carolina 27710
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100
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Abstract
Ubiquitylation is a reversible posttranslational modification that is critical for most, if not all, cellular processes and essential for viability. Ubiquitin conjugates to substrate proteins either as a single moiety (monoubiquitylation) or as polymers composed of ubiquitin molecules linked to each other with various topologies and structures (polyubiquitylation). This contributes to an elaborate ubiquitin code that is decrypted by specific ubiquitin-binding proteins. Indeed, these different types of ubiquitylation have different functional outcomes, notably affecting the stability of the substrate, its interactions, its activity, or its subcellular localization. In this chapter, we describe protocols to determine whether a protein is ubiquitylated, to identify the site that is ubiquitylated, and provide direction to study the topology of the ubiquitin modification, in the yeast Saccharomyces cerevisiae.
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Affiliation(s)
- Junie Hovsepian
- Institut Jacques Monod, UMR 7592 CNRS/Univ. Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Michel Becuwe
- Institut Jacques Monod, UMR 7592 CNRS/Univ. Paris Diderot, Sorbonne Paris Cité, Paris, France
- Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA, 02115, USA
| | - Oded Kleifeld
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Michael H Glickman
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Sébastien Léon
- Institut Jacques Monod, UMR 7592 CNRS/Univ. Paris Diderot, Sorbonne Paris Cité, Paris, France.
- Membrane Trafficking, Ubiquitin and Signaling Lab, Institut Jacques Monod, UMR7592 CNRS/Université Paris-Diderot, 15 Rue Hélène Brion, Bât. Buffon, 75205, Paris Cedex 13, France.
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