1
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Vogel K, Isono E. Erasing marks: Functions of plant deubiquitylating enzymes in modulating the ubiquitin code. THE PLANT CELL 2024; 36:3057-3073. [PMID: 38656977 PMCID: PMC11371157 DOI: 10.1093/plcell/koae129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/18/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024]
Abstract
Plant cells need to respond to environmental stimuli and developmental signals accurately and promptly. Ubiquitylation is a reversible posttranslational modification that enables the adaptation of cellular proteostasis to internal or external factors. The different topologies of ubiquitin linkages serve as the structural basis for the ubiquitin code, which can be interpreted by ubiquitin-binding proteins or readers in specific processes. The ubiquitylation status of target proteins is regulated by ubiquitylating enzymes or writers, as well as deubiquitylating enzymes (DUBs) or erasers. DUBs can remove ubiquitin molecules from target proteins. Arabidopsis (A. thaliana) DUBs belong to 7 protein families and exhibit a wide range of functions and play an important role in regulating selective protein degradation processes, including proteasomal, endocytic, and autophagic protein degradation. DUBs also shape the epigenetic landscape and modulate DNA damage repair processes. In this review, we summarize the current knowledge on DUBs in plants, their cellular functions, and the molecular mechanisms involved in the regulation of plant DUBs.
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Affiliation(s)
- Karin Vogel
- Department of Biology, University of Konstanz, Konstanz 78464, Germany
| | - Erika Isono
- Department of Biology, University of Konstanz, Konstanz 78464, Germany
- Division of Molecular Cell Biology, National Institute for Basic Biology, Okazaki 444-8585 Aichi, Japan
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2
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Zheng LL, Wang LT, Pang YW, Sun LP, Shi L. Recent advances in the development of deubiquitinases inhibitors as antitumor agents. Eur J Med Chem 2024; 266:116161. [PMID: 38262120 DOI: 10.1016/j.ejmech.2024.116161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/25/2024]
Abstract
Ubiquitination is a type of post-translational modification that covalently links ubiquitin to a target protein, which plays a critical role in modulating protein activity, stability, and localization. In contrast, this process is reversed by deubiquitinases (DUBs), which remove ubiquitin from ubiquitinated substrates. Dysregulation of DUBs is associated with several human diseases, such as cancer, inflammation, neurodegenerative disorders, and autoimmune diseases. Thus, DUBs have become promising targets for drug development. Although the physiological and pathological effects of DUBs are increasingly well understood, the clinical drug discovery of selective DUB inhibitors has been challenging. Herein, we summarize the structures and functions of main classes of DUBs and discuss the recent progress in developing selective small-molecule DUB inhibitors as antitumor agents.
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Affiliation(s)
- Li-Li Zheng
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Li-Ting Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Ye-Wei Pang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Li-Ping Sun
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Lei Shi
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
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3
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Ren J, Yu P, Liu S, Li R, Niu X, Chen Y, Zhang Z, Zhou F, Zhang L. Deubiquitylating Enzymes in Cancer and Immunity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303807. [PMID: 37888853 PMCID: PMC10754134 DOI: 10.1002/advs.202303807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/30/2023] [Indexed: 10/28/2023]
Abstract
Deubiquitylating enzymes (DUBs) maintain relative homeostasis of the cellular ubiquitome by removing the post-translational modification ubiquitin moiety from substrates. Numerous DUBs have been demonstrated specificity for cleaving a certain type of ubiquitin linkage or positions within ubiquitin chains. Moreover, several DUBs perform functions through specific protein-protein interactions in a catalytically independent manner, which further expands the versatility and complexity of DUBs' functions. Dysregulation of DUBs disrupts the dynamic equilibrium of ubiquitome and causes various diseases, especially cancer and immune disorders. This review summarizes the Janus-faced roles of DUBs in cancer including proteasomal degradation, DNA repair, apoptosis, and tumor metastasis, as well as in immunity involving innate immune receptor signaling and inflammatory and autoimmune disorders. The prospects and challenges for the clinical development of DUB inhibitors are further discussed. The review provides a comprehensive understanding of the multi-faced roles of DUBs in cancer and immunity.
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Affiliation(s)
- Jiang Ren
- The Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033P. R. China
| | - Peng Yu
- Zhongshan Institute for Drug DiscoveryShanghai Institute of Materia MedicaChinese Academy of SciencesZhongshanGuangdongP. R. China
| | - Sijia Liu
- International Biomed‐X Research CenterSecond Affiliated Hospital of Zhejiang University School of MedicineZhejiang UniversityHangzhouP. R. China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang ProvinceHangzhou310058China
| | - Ran Li
- The Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033P. R. China
| | - Xin Niu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058P. R. China
| | - Yan Chen
- The Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033P. R. China
| | - Zhenyu Zhang
- Department of NeurosurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenan450003P. R. China
| | - Fangfang Zhou
- Institutes of Biology and Medical ScienceSoochow UniversitySuzhou215123P. R. China
| | - Long Zhang
- The Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033P. R. China
- International Biomed‐X Research CenterSecond Affiliated Hospital of Zhejiang University School of MedicineZhejiang UniversityHangzhouP. R. China
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058P. R. China
- Cancer CenterZhejiang UniversityHangzhouZhejiang310058P. R. China
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4
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Wang Y, Lan Q, Cheng X, Gao Y, Chang L, Xu P, Li Y. Quantitative Proteomics-Based Substrate Screening Revealed Cyclophilin Stabilization Regulated by Deubiquitinase Ubp7. J Proteome Res 2023; 22:2281-2292. [PMID: 37341107 DOI: 10.1021/acs.jproteome.2c00853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Quantitative proteomics has emerged as a crucial approach to identifying ubiquitinated substrates to investigate the functions of ubiquitination in cells. In this regard, although the substrate screening of certain enzymes in the ubiquitin system has been based on proteome or ubiquitinome level measurements, the direct comparison of these two approaches has not been determined to date. To quantitatively compare the efficiency and effectiveness of substrate screening from the entire proteomics to the ubiquitinomics filter, we used yeast deubiquitinating enzyme, Ubp7, as an example to evaluate it in this study. A total of 112 potential ubiquitinated substrates were identified from the ubiquitinomics level, whereas only 27 regulated substrates were identified from the entire proteomic screening, demonstrating the increased efficiency of ubiquitinomics quantitative analysis. Subsequently, we selected cyclophilin A (Cpr1) protein as an example, which was filtered out at the proteomics level but was a promising candidate according to the ubiquitinomics filter. Additional investigations revealed that Cpr1 possessed a K48-linked ubiquitin chain regulated by Ubp7, which may affect its homeostasis and, consequently, sensitivity to the therapeutic drug cyclosporine (CsA).
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Affiliation(s)
- Yonghong Wang
- Department of Biomedicine, School of Medicine, Guizhou University, Guiyang 550025, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, Changping District, Beijing 102206, China
| | - Qiuyan Lan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, Changping District, Beijing 102206, China
| | - Xinyu Cheng
- School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Yuan Gao
- Central Laboratory of College of Horticulture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, Changping District, Beijing 102206, China
| | - Ping Xu
- Department of Biomedicine, School of Medicine, Guizhou University, Guiyang 550025, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, Changping District, Beijing 102206, China
- School of Basic Medicine, Anhui Medical University, Hefei 230032, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, School of Life Sciences, Hebei University, Baoding 071002, China
| | - Yanchang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, Changping District, Beijing 102206, China
- School of Basic Medicine, Anhui Medical University, Hefei 230032, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, School of Life Sciences, Hebei University, Baoding 071002, China
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5
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Wang Y, Liu X, Huang W, Liang J, Chen Y. The intricate interplay between HIFs, ROS, and the ubiquitin system in the tumor hypoxic microenvironment. Pharmacol Ther 2022; 240:108303. [PMID: 36328089 DOI: 10.1016/j.pharmthera.2022.108303] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/16/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022]
Abstract
Alterations in protein ubiquitination and hypoxia-inducible factor (HIF) signaling both contribute to tumorigenesis and tumor progression. Ubiquitination is a dynamic process that is coordinately regulated by E3 ligases and deubiquitinases (DUBs), which have emerged as attractive therapeutic targets. HIF expression and transcriptional activity are usually increased in tumors, leading to poor clinical outcomes. Reactive oxygen species (ROS) are upregulated in tumors and have multiple effects on HIF signaling and the ubiquitin system. A growing body of evidence has shown that multiple E3 ligases and UBDs function synergistically to control the expression and activity of HIF, thereby allowing cancer cells to cope with the hypoxic microenvironment. Conversely, several E3 ligases and DUBs are regulated by hypoxia and/or HIF signaling. Hypoxia also induces ROS production, which in turn modulates the stability or activity of HIF, E3 ligases, and DUBs. Understanding the complex networks between E3 ligase, DUBs, ROS, and HIF will provide insights into the fundamental mechanism of the cellular response to hypoxia and help identify novel molecular targets for cancer treatment. We review the current knowledge on the comprehensive relationship between E3 ligase, DUBs, ROS, and HIF signaling, with a particular focus on the use of E3 ligase or DUB inhibitors in cancer.
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Affiliation(s)
- Yijie Wang
- Institute of Biomedical Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Center for Cell Structure and Function, College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, China
| | - Xiong Liu
- School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
| | - Weixiao Huang
- School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
| | - Junjie Liang
- The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510630, China.
| | - Yan Chen
- Institute of Biomedical Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Center for Cell Structure and Function, College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, China; School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China.
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6
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Di Carlo S, Häcker G, Gentle IE. GM‐CSF suppresses antioxidant signaling and drives IL‐1β secretion through NRF2 downregulation. EMBO Rep 2022; 23:e54226. [PMID: 35695080 PMCID: PMC9346485 DOI: 10.15252/embr.202154226] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 05/11/2022] [Accepted: 05/24/2022] [Indexed: 11/09/2022] Open
Abstract
GM‐CSF is a potent inflammatory cytokine regulating myeloid cell differentiation, hematopoiesis, and various other functions. It is functionally associated with a number of inflammatory pathologies including rheumatoid arthritis and inflammatory bowel disease. GM‐CSF has been found to promote NLRP3‐dependent IL‐1β secretion, which may have a significant role in driving inflammatory pathologies. However, the molecular mechanisms remain unknown. Here, we show that GM‐CSF induces IL‐1β secretion through a ROS‐dependent pathway. TNF is required for reactive oxygen species (ROS) generation that strikingly does not promote NLRP3 activation, but instead drives ubiquitylation of IL‐1β, promoting its cleavage through basal NRLP3 activity. GM‐CSF regulates this pathway through suppression of antioxidant responses via preventing upregulation of NRF2. Thus, the pro‐inflammatory effect of GM‐CSF on IL‐1β is through suppression of antioxidant responses, which leads to ubiquitylation of IL‐1β and enhanced processing. This study highlights the role of metabolic regulation of inflammatory signaling and reveals a novel mechanism for GM‐CSF to promote inflammation.
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Affiliation(s)
- Sara Di Carlo
- Institute of Medical Microbiology and Hygiene Faculty of Medicine Medical Center – University of Freiburg Freiburg Germany
| | - Georg Häcker
- Institute of Medical Microbiology and Hygiene Faculty of Medicine Medical Center – University of Freiburg Freiburg Germany
- BIOSS Centre for Biological Signalling Studies University of Freiburg Freiburg Germany
| | - Ian E Gentle
- Institute of Medical Microbiology and Hygiene Faculty of Medicine Medical Center – University of Freiburg Freiburg Germany
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7
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Wang Y, Chen J, Hua X, Meng X, Cai H, Wang R, Shi J, Deng H, Liu L, Li Y. Photocaging of Activity‐Based Ubiquitin Probes via a C‐Terminal Backbone Modification Strategy. Angew Chem Int Ed Engl 2022; 61:e202203792. [DOI: 10.1002/anie.202203792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Yu Wang
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Jingnan Chen
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
| | - Xiao Hua
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Xianbin Meng
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China
| | - Hongyi Cai
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Rongtian Wang
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
| | - Jing Shi
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Yi‐Ming Li
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
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8
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Wang Y, Chen J, Hua X, Meng X, Cai H, Wang R, Shi J, Deng H, Liu L, Li Y. Photocaging of Activity‐Based Ubiquitin Probes via a C‐Terminal Backbone Modification Strategy. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yu Wang
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Jingnan Chen
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
| | - Xiao Hua
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Xianbin Meng
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China
| | - Hongyi Cai
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Rongtian Wang
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
| | - Jing Shi
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Yi‐Ming Li
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
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9
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Puri S, Hsu STD. Oxidation of catalytic cysteine of human deubiquitinase BAP1 triggers misfolding and aggregation in addition to functional loss. Biochem Biophys Res Commun 2022; 599:57-62. [PMID: 35176625 DOI: 10.1016/j.bbrc.2022.02.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 02/09/2022] [Indexed: 11/02/2022]
Abstract
Deubiquitinating enzymes (DUBs) form a large protease family involved in a myriad of biological and pathological processes, including ROS sensors. ROS-mediated inhibition of their DUB activities is critical for fine-tuning the stress-activated signaling pathways. Here, we demonstrate that the ubiquitin C-terminal hydrolase (UCH) domain of BAP1 (BAP1-UCH) is highly sensitive to moderate oxidative stress. Oxidation of the catalytic C91 significantly destabilizes BAP1-UCH and increases the population of partially unfolded form, which is prone to aggregation. Unlike other DUBs, the oxidation-induced structural and functional loss of BAP1-UCH cannot be fully reversed by reducing agents. The oligomerization of oxidized BAP1-UCH is attributed to inter-molecular disulfide bond formation. Hydrogen-deuterium mass exchange spectrometry (HDX-MS) reveals increased fluctuations of the central β-sheet upon oxidation. Our findings suggest that oxidation-mediated functional loss and increased aggregation propensity may contribute to oncogenesis associated with BAP1.
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Affiliation(s)
- Sarita Puri
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan.
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10
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Larbret F, Biber P, Dubois N, Ivanov S, Lafanechere L, Tartare-Deckert S, Deckert M. Deubiquitinase Inhibitors Impair Leukemic Cell Migration Through Cofilin Oxidation and Alteration of Actin Reorganization. Front Pharmacol 2022; 12:778216. [PMID: 35069199 PMCID: PMC8782157 DOI: 10.3389/fphar.2021.778216] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/14/2021] [Indexed: 11/29/2022] Open
Abstract
Actin networks are dynamically regulated through constant depolymerization and polymerization cycles. Although the fundamental mechanisms that govern these processes have been identified, the nature and role of post-translational modifications (PTMs) of actin and actin regulatory proteins are not completely understood. Here, we employed Actin CytoFRET, a method that we developed for real time detection of fluorescence resonance energy transfer (FRET) signals generated by actin dynamics, to screen a small library of PTM-interfering compounds on a biosensor leukemic T cell line. This strategy led to the identification of small molecule inhibitors of deubiquitinating enzymes (DUBs) as potent inducers of actin polymerization and blockers of chemotactic cell migration. The examination of the underlying mechanism further revealed that the actin depolymerizing protein cofilin represents a major effector of DUB inhibitor (DUBi)-induced actin reorganization. We found that DUB blockade results in the accumulation of polyubiquitinated proteins and ROS production, associated with cofilin oxidation and dephosphorylation on serine 3, which provokes uncontrolled actin polymerization impairing cell migration. Together, our study highlights DUBs as novel regulators of actin dynamics through ROS-dependent cofilin modulation, and shows that DUBi represent attractive novel tools to impede leukemic cell migration.
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Affiliation(s)
- Frédéric Larbret
- Université Côte d'Azur, INSERM, C3M, Nice, France.,Team MicroCan, Equipe labellisée Ligue Contre le Cancer, Nice, France
| | - Pierric Biber
- Université Côte d'Azur, INSERM, C3M, Nice, France.,Team MicroCan, Equipe labellisée Ligue Contre le Cancer, Nice, France
| | | | | | - Laurence Lafanechere
- Université Grenoble Alpes, INSERM, Institut pour l'Avancée des Biosciences, La Tronche, France
| | - Sophie Tartare-Deckert
- Université Côte d'Azur, INSERM, C3M, Nice, France.,Team MicroCan, Equipe labellisée Ligue Contre le Cancer, Nice, France
| | - Marcel Deckert
- Université Côte d'Azur, INSERM, C3M, Nice, France.,Team MicroCan, Equipe labellisée Ligue Contre le Cancer, Nice, France
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11
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Hensley K, Danekas A, Farrell W, Garcia T, Mehboob W, White M. At the intersection of sulfur redox chemistry, cellular signal transduction and proteostasis: A useful perspective from which to understand and treat neurodegeneration. Free Radic Biol Med 2022; 178:161-173. [PMID: 34863876 DOI: 10.1016/j.freeradbiomed.2021.11.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 12/14/2022]
Abstract
Although we can thoroughly describe individual neurodegenerative diseases from the molecular level through cell biology to histology and clinical presentation, our understanding of them and hence treatment gains have been depressingly limited, partly due to difficulty conceptualizing different diseases as variations within the same overarching pathological rubric. This review endeavors to create such rubric by knitting together the seemingly disparate phenomena of oxidative stress, dysregulated proteostasis, and neuroinflammation into a cohesive triad that highlights mechanistic connectivities. We begin by considering that brain metabolic demands necessitate careful control of oxidative homeostasis, largely through sulfur redox chemistry and glutathione (GSH). GSH is essential for brain antioxidant defense, but also for redox signaling and thus neuroinflammation. Delicate regulation of neuroinflammatory pathways (NFκB, MAPK-p38, and NLRP3 particularly) occurs through S-glutathionylation of protein phosphatases but also through redox-sensing elements like ASK1; the 26S proteasome and cysteine deubiquitinases (DUBs). The relationship amongst triad elements is underscored by our discovery that LanCL1 (lanthionine synthetase-like protein-1) protects against oxidant toxicity; mediates GSH-dependent reactivation of oxidized DUBs; and antagonizes the pro-inflammatory cytokine, tumor necrosis factor-α (TNFα). We highlight currently promising pharmacological efforts to modulate key triad elements and suggest nexus points that might be exploited to further clinical advantage.
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Affiliation(s)
- Kenneth Hensley
- Department of Biochemistry, Cell and Molecular Biology, Arkansas College of Osteopathic Medicine, Fort Smith, AR, 72916, USA.
| | - Alexis Danekas
- Department of Biochemistry, Cell and Molecular Biology, Arkansas College of Osteopathic Medicine, Fort Smith, AR, 72916, USA
| | - William Farrell
- Department of Biochemistry, Cell and Molecular Biology, Arkansas College of Osteopathic Medicine, Fort Smith, AR, 72916, USA
| | - Tiera Garcia
- Department of Biochemistry, Cell and Molecular Biology, Arkansas College of Osteopathic Medicine, Fort Smith, AR, 72916, USA
| | - Wafa Mehboob
- Department of Biochemistry, Cell and Molecular Biology, Arkansas College of Osteopathic Medicine, Fort Smith, AR, 72916, USA
| | - Matthew White
- Department of Biochemistry, Cell and Molecular Biology, Arkansas College of Osteopathic Medicine, Fort Smith, AR, 72916, USA
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12
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Varca AC, Casalena D, Chan WC, Hu B, Magin RS, Roberts RM, Liu X, Zhu H, Seo HS, Dhe-Paganon S, Marto JA, Auld D, Buhrlage SJ. Identification and validation of selective deubiquitinase inhibitors. Cell Chem Biol 2021; 28:1758-1771.e13. [PMID: 34129829 PMCID: PMC9473745 DOI: 10.1016/j.chembiol.2021.05.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 03/11/2021] [Accepted: 05/19/2021] [Indexed: 12/17/2022]
Abstract
Deubiquitinating enzymes (DUBs) are a class of isopeptidases that regulate ubiquitin dynamics through catalytic cleavage of ubiquitin from protein substrates and ubiquitin precursors. Despite growing interest in DUB biological function and potential as therapeutic targets, few selective small-molecule inhibitors and no approved drugs currently exist. To identify chemical scaffolds targeting specific DUBs and establish a broader framework for future inhibitor development across the gene family, we performed high-throughput screening of a chemically diverse small-molecule library against eight different DUBs, spanning three well-characterized DUB families. Promising hit compounds were validated in a series of counter-screens and orthogonal assays, as well as further assessed for selectivity across expanded panels of DUBs. Through these efforts, we have identified multiple highly selective DUB inhibitors and developed a roadmap for rapidly identifying and validating selective inhibitors of related enzymes.
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Affiliation(s)
- Anthony C Varca
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Dominick Casalena
- FAST Lab, Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Wai Cheung Chan
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Bin Hu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert S Magin
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Rebekka M Roberts
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Xiaoxi Liu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - He Zhu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jarrod A Marto
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Douglas Auld
- FAST Lab, Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Sara J Buhrlage
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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13
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Tyagi A, Haq S, Ramakrishna S. Redox regulation of DUBs and its therapeutic implications in cancer. Redox Biol 2021; 48:102194. [PMID: 34814083 PMCID: PMC8608616 DOI: 10.1016/j.redox.2021.102194] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/19/2021] [Indexed: 02/06/2023] Open
Abstract
Reactive oxygen species (ROS) act as a double-edged sword in cancer, where low levels of ROS are beneficial but excessive accumulation leads to cancer progression. Elevated levels of ROS in cancer are counteracted by the antioxidant defense system. An imbalance between ROS generation and the antioxidant system alters gene expression and cellular signaling, leading to cancer progression or death. Post-translational modifications, such as ubiquitination, phosphorylation, and SUMOylation, play a critical role in the maintenance of ROS homeostasis by controlling ROS production and clearance. Recent evidence suggests that deubiquitinating enzymes (DUBs)-mediated ubiquitin removal from substrates is regulated by ROS. ROS-mediated oxidation of the catalytic cysteine (Cys) of DUBs, leading to their reversible inactivation, has emerged as a key mechanism regulating DUB-controlled cellular events. A better understanding of the mechanism by which DUBs are susceptible to ROS and exploring the ways to utilize ROS to pharmacologically modulate DUB-mediated signaling pathways might provide new insight for anticancer therapeutics. This review assesses the recent findings regarding ROS-mediated signaling in cancers, emphasizes DUB regulation by oxidation, highlights the relevant recent findings, and proposes directions of future research based on the ROS-induced modifications of DUB activity.
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Affiliation(s)
- Apoorvi Tyagi
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Saba Haq
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea; College of Medicine, Hanyang University, Seoul, 04763, South Korea.
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14
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Lange SM, Armstrong LA, Kulathu Y. Deubiquitinases: From mechanisms to their inhibition by small molecules. Mol Cell 2021; 82:15-29. [PMID: 34813758 DOI: 10.1016/j.molcel.2021.10.027] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/15/2021] [Accepted: 10/28/2021] [Indexed: 12/21/2022]
Abstract
Deubiquitinases (DUBs) are specialized proteases that remove ubiquitin from substrates or cleave within ubiquitin chains to regulate ubiquitylation and therefore play important roles in eukaryotic biology. Dysregulation of DUBs is implicated in several human diseases, highlighting the importance of DUB function. In addition, many pathogenic bacteria and viruses encode and deploy DUBs to manipulate host immune responses and establish infectious diseases in humans and animals. Hence, therapeutic targeting of DUBs is an increasingly explored area that requires an in-depth mechanistic understanding of human and pathogenic DUBs. In this review, we summarize the multiple layers of regulation that control autoinhibition, activation, and substrate specificity of DUBs. We discuss different strategies to inhibit DUBs and the progress in developing selective small-molecule DUB inhibitors. Finally, we propose a classification system of DUB inhibitors based on their mode of action.
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Affiliation(s)
- Sven M Lange
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Lee A Armstrong
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Yogesh Kulathu
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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15
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The cell envelope of Staphylococcus aureus selectively controls the sorting of virulence factors. Nat Commun 2021; 12:6193. [PMID: 34702812 PMCID: PMC8548510 DOI: 10.1038/s41467-021-26517-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 10/05/2021] [Indexed: 11/08/2022] Open
Abstract
Staphylococcus aureus bi-component pore-forming leukocidins are secreted toxins that directly target and lyse immune cells. Intriguingly, one of the leukocidins, Leukocidin AB (LukAB), is found associated with the bacterial cell envelope in addition to secreted into the extracellular milieu. Here, we report that retention of LukAB on the bacterial cells provides S. aureus with a pre-synthesized active toxin that kills immune cells. On the bacteria, LukAB is distributed as discrete foci in two distinct compartments: membrane-proximal and surface-exposed. Through genetic screens, we show that a membrane lipid, lysyl-phosphatidylglycerol (LPG), and lipoteichoic acid (LTA) contribute to LukAB deposition and release. Furthermore, by studying non-covalently surface-bound proteins we discovered that the sorting of additional exoproteins, such as IsaB, Hel, ScaH, and Geh, are also controlled by LPG and LTA. Collectively, our study reveals a multistep secretion system that controls exoprotein storage and protein translocation across the S. aureus cell wall.
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16
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Snyder NA, Silva GM. Deubiquitinating enzymes (DUBs): Regulation, homeostasis, and oxidative stress response. J Biol Chem 2021; 297:101077. [PMID: 34391779 PMCID: PMC8424594 DOI: 10.1016/j.jbc.2021.101077] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/17/2022] Open
Abstract
Ubiquitin signaling is a conserved, widespread, and dynamic process in which protein substrates are rapidly modified by ubiquitin to impact protein activity, localization, or stability. To regulate this process, deubiquitinating enzymes (DUBs) counter the signal induced by ubiquitin conjugases and ligases by removing ubiquitin from these substrates. Many DUBs selectively regulate physiological pathways employing conserved mechanisms of ubiquitin bond cleavage. DUB activity is highly regulated in dynamic environments through protein-protein interaction, posttranslational modification, and relocalization. The largest family of DUBs, cysteine proteases, are also sensitive to regulation by oxidative stress, as reactive oxygen species (ROS) directly modify the catalytic cysteine required for their enzymatic activity. Current research has implicated DUB activity in human diseases, including various cancers and neurodegenerative disorders. Due to their selectivity and functional roles, DUBs have become important targets for therapeutic development to treat these conditions. This review will discuss the main classes of DUBs and their regulatory mechanisms with a particular focus on DUB redox regulation and its physiological impact during oxidative stress.
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Affiliation(s)
- Nathan A Snyder
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Gustavo M Silva
- Department of Biology, Duke University, Durham, North Carolina, USA.
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17
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Cruz L, Soares P, Correia M. Ubiquitin-Specific Proteases: Players in Cancer Cellular Processes. Pharmaceuticals (Basel) 2021; 14:ph14090848. [PMID: 34577547 PMCID: PMC8469789 DOI: 10.3390/ph14090848] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/20/2021] [Accepted: 08/21/2021] [Indexed: 12/14/2022] Open
Abstract
Ubiquitination represents a post-translational modification (PTM) essential for the maintenance of cellular homeostasis. Ubiquitination is involved in the regulation of protein function, localization and turnover through the attachment of a ubiquitin molecule(s) to a target protein. Ubiquitination can be reversed through the action of deubiquitinating enzymes (DUBs). The DUB enzymes have the ability to remove the mono- or poly-ubiquitination signals and are involved in the maturation, recycling, editing and rearrangement of ubiquitin(s). Ubiquitin-specific proteases (USPs) are the biggest family of DUBs, responsible for numerous cellular functions through interactions with different cellular targets. Over the past few years, several studies have focused on the role of USPs in carcinogenesis, which has led to an increasing development of therapies based on USP inhibitors. In this review, we intend to describe different cellular functions, such as the cell cycle, DNA damage repair, chromatin remodeling and several signaling pathways, in which USPs are involved in the development or progression of cancer. In addition, we describe existing therapies that target the inhibition of USPs.
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Affiliation(s)
- Lucas Cruz
- i3S—Instituto de Investigação e Inovação Em Saúde, Universidade Do Porto, 4200-135 Porto, Portugal; (L.C.); (P.S.)
- Ipatimup—Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4250-475 Porto, Portugal
- FCUP—Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Paula Soares
- i3S—Instituto de Investigação e Inovação Em Saúde, Universidade Do Porto, 4200-135 Porto, Portugal; (L.C.); (P.S.)
- Ipatimup—Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4250-475 Porto, Portugal
- FCUP—Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
- Departamento de Patologia, Faculdade de Medicina da Universidade Do Porto, 4200-139 Porto, Portugal
| | - Marcelo Correia
- i3S—Instituto de Investigação e Inovação Em Saúde, Universidade Do Porto, 4200-135 Porto, Portugal; (L.C.); (P.S.)
- Ipatimup—Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4250-475 Porto, Portugal
- Correspondence:
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18
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Wang Y, Wang F. Post-Translational Modifications of Deubiquitinating Enzymes: Expanding the Ubiquitin Code. Front Pharmacol 2021; 12:685011. [PMID: 34177595 PMCID: PMC8224227 DOI: 10.3389/fphar.2021.685011] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022] Open
Abstract
Post-translational modifications such as ubiquitination play important regulatory roles in several biological processes in eukaryotes. This process could be reversed by deubiquitinating enzymes (DUBs), which remove conjugated ubiquitin molecules from target substrates. Owing to their role as essential enzymes in regulating all ubiquitin-related processes, the abundance, localization, and catalytic activity of DUBs are tightly regulated. Dysregulation of DUBs can cause dramatic physiological consequences and a variety of disorders such as cancer, and neurodegenerative and inflammatory diseases. Multiple factors, such as transcription and translation of associated genes, and the presence of accessory domains, binding proteins, and inhibitors have been implicated in several aspects of DUB regulation. Beyond this level of regulation, emerging studies show that the function of DUBs can be regulated by a variety of post-translational modifications, which significantly affect the abundance, localization, and catalytic activity of DUBs. The most extensively studied post-translational modification of DUBs is phosphorylation. Besides phosphorylation, ubiquitination, SUMOylation, acetylation, oxidation, and hydroxylation are also reported in DUBs. In this review, we summarize the current knowledge on the regulatory effects of post-translational modifications of DUBs.
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Affiliation(s)
- Yanfeng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Feng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
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19
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Hwang I, Tang D, Paik J. Oxidative stress sensing and response in neural stem cell fate. Free Radic Biol Med 2021; 169:74-83. [PMID: 33862161 PMCID: PMC9594080 DOI: 10.1016/j.freeradbiomed.2021.03.043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/13/2021] [Accepted: 03/25/2021] [Indexed: 12/22/2022]
Abstract
Neural stem/progenitor cells (NSPCs) contribute to the physiological cellular turnover of the adult brain and make up its regenerative potential. It is thus essential to understand how different factors influence their proliferation and differentiation to gain better insight into potential therapeutic targets in neurodegenerative diseases and traumatic brain injuries. Recent evidences indicate the roles of redox stress sensing and coping mechanisms in mediating the balance between NSPC self-renewal and differentiation. Such mechanisms involve direct cysteine modification, signaling and metabolic reprogramming, epigenetic alterations and transcription changes leading to adaptive responses like autophagy. Here, we discuss emerging findings on the involvement of redox sensors and effectors and their mechanisms in influencing changes in cellular redox potential and NSPC fate.
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Affiliation(s)
- Inah Hwang
- R&D Center, OneCureGEN Co., Ltd, Daejeon, 34141, Republic of Korea; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Deanna Tang
- University of Chicago, Chicago, IL, 60637, USA
| | - Jihye Paik
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10021, USA.
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20
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Harshuk-Shabso D, Castel N, Israeli R, Harari S, Pick E. Saccharomyces cerevisiae as a Toolkit for COP9 Signalosome Research. Biomolecules 2021; 11:biom11040497. [PMID: 33806190 PMCID: PMC8065851 DOI: 10.3390/biom11040497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/14/2021] [Accepted: 03/20/2021] [Indexed: 11/16/2022] Open
Abstract
The COP9 signalosome (CSN) is a highly conserved eukaryotic multi-subunit enzyme, regulating cullin RING ligase activities and accordingly, substrate ubiquitination and degradation. We showed that the CSN complex of Saccharomyces cerevisiae that is deviated in subunit composition and in sequence homology harbors a highly conserved cullin deneddylase enzymatic core complex. We took advantage of the non-essentiality of the S. cerevisiae CSN-NEDD8/Rub1 axis, together with the enzyme-substrate cross-species activity, to develop a sensitive fluorescence readout assay, suitable for biochemical assessment of cullin deneddylation by CSNs from various origins. We also demonstrated that the yeast catalytic subunit, CSN5/Jab1, is targeted by an inhibitor that was selected for the human orthologue. Treatment of yeast by the inhibitor led to the accumulation of neddylated cullins and the formation of reactive oxygen species. Overall, our data revealed S. cerevisiae as a general platform that can be used for studies of CSN deneddylation and for testing the efficacy of selected CSN inhibitors.
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Affiliation(s)
- Dana Harshuk-Shabso
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa 31905, Israel;
| | - Noam Castel
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa 31905, Israel;
| | - Ran Israeli
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 36006, Israel; (R.I.); (S.H.)
| | - Sheri Harari
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 36006, Israel; (R.I.); (S.H.)
| | - Elah Pick
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa 31905, Israel;
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa 31905, Israel;
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 36006, Israel; (R.I.); (S.H.)
- Correspondence:
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21
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Kahles T, Poon C, Qian L, Palfini V, Srinivasan SP, Swaminathan S, Blanco I, Rodney-Sandy R, Iadecola C, Zhou P, Hochrainer K. Elevated post-ischemic ubiquitination results from suppression of deubiquitinase activity and not proteasome inhibition. Cell Mol Life Sci 2021; 78:2169-2183. [PMID: 32889561 PMCID: PMC7933347 DOI: 10.1007/s00018-020-03625-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/28/2020] [Accepted: 08/18/2020] [Indexed: 12/24/2022]
Abstract
Cerebral ischemia-reperfusion increases intraneuronal levels of ubiquitinated proteins, but the factors driving ubiquitination and whether it results from altered proteostasis remain unclear. To address these questions, we used in vivo and in vitro models of cerebral ischemia-reperfusion, in which hippocampal slices were transiently deprived of oxygen and glucose to simulate ischemia followed by reperfusion, or the middle cerebral artery was temporarily occluded in mice. We found that post-ischemic ubiquitination results from two key steps: restoration of ATP at reperfusion, which allows initiation of protein ubiquitination, and free radical production, which, in the presence of sufficient ATP, increases ubiquitination above pre-ischemic levels. Surprisingly, free radicals did not augment ubiquitination through inhibition of the proteasome as previously believed. Although reduced proteasomal activity was detected after ischemia, this was neither caused by free radicals nor sufficient in magnitude to induce appreciable accumulation of proteasomal target proteins or ubiquitin-proteasome reporters. Instead, we found that ischemia-derived free radicals inhibit deubiquitinases, a class of proteases that cleaves ubiquitin chains from proteins, which was sufficient to elevate ubiquitination after ischemia. Our data provide evidence that free radical-dependent deubiquitinase inactivation rather than proteasomal inhibition drives ubiquitination following ischemia-reperfusion, and as such call for a reevaluation of the mechanisms of post-ischemic ubiquitination, previously attributed to altered proteostasis. Since deubiquitinase inhibition is considered an endogenous neuroprotective mechanism to shield proteins from oxidative damage, modulation of deubiquitinase activity may be of therapeutic value to maintain protein integrity after an ischemic insult.
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Affiliation(s)
- Timo Kahles
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Neurology, Cantonal Hospital Aarau, 5001, Aarau, Switzerland
| | - Carrie Poon
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Liping Qian
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Victoria Palfini
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10065, USA
| | | | - Shilpa Swaminathan
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Ismary Blanco
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Reunet Rodney-Sandy
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Costantino Iadecola
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Ping Zhou
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Karin Hochrainer
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10065, USA.
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22
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Cross-over Loop Cysteine C152 Acts as an Antioxidant to Maintain the Folding Stability and Deubiquitinase Activity of UCH-L1 Under Oxidative Stress. J Mol Biol 2021; 433:166879. [PMID: 33617897 DOI: 10.1016/j.jmb.2021.166879] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/07/2021] [Accepted: 02/12/2021] [Indexed: 11/20/2022]
Abstract
Redox-dependent inactivation of deubiquitinases (DUBs) is a critical factor for attenuating their DUB activity in response to cellular oxidative stress. Ubiquitin C-terminal hydrolase isoform (UCH-L1) is an important DUB that is highly expressed in human neuronal cells and is implicated in a myriad of human diseases such as neurodegenerative diseases and cancer. Increasing evidence suggests an important role of UCH-L1 in redox regulation and the protection of neuronal cells from oxidative stress. In this study, we examined the molecular basis of how UCH-L1 responds to oxidation in a reversible manner. Using H2O2 as a model oxidant, we showed by mass spectrometry that a subset of methionine and cysteine residues, namely (M1, M6, M12, C90, and C152) were more susceptible to oxidation. Spectroscopic analysis showed that oxidation of C90 can lead to profound structural changes in addition to the loss of function. Importantly, we further demonstrated that C152, which is located at the substrate recognition cross-over loop, serves as a reactive oxygen species (ROS) scavenger to protect catalytic C90 from oxidation under moderate oxidative conditions. Hydrogen-deuterium exchange mass spectrometry analysis provided detailed structural mapping of the destabilizing effect of H2O2-mediated oxidation, which resulted in global destabilization far beyond the oxidation sites. These perturbations may be responsible for irreversible aggregation when subject to prolonged oxidative stress.
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23
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Zong Z, Zhang Z, Wu L, Zhang L, Zhou F. The Functional Deubiquitinating Enzymes in Control of Innate Antiviral Immunity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2002484. [PMID: 33511009 PMCID: PMC7816709 DOI: 10.1002/advs.202002484] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/09/2020] [Indexed: 05/11/2023]
Abstract
Innate antiviral immunity is the first line of host defense against invading viral pathogens. Immunity activation primarily relies on the recognition of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRRs). Viral proteins or nucleic acids mainly engage three classes of PRRs: Toll-like receptors (TLRs), retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs), and DNA sensor cyclic GMP-AMP (cGAMP) synthase (cGAS). These receptors initiate a series of signaling cascades that lead to the production of proinflammatory cytokines and type I interferon (IFN-I) in response to viral infection. This system requires precise regulation to avoid aberrant activation. Emerging evidence has unveiled the crucial roles that the ubiquitin system, especially deubiquitinating enzymes (DUBs), play in controlling immune responses. In this review, an overview of the most current findings on the function of DUBs in the innate antiviral immune pathways is provided. Insights into the role of viral DUBs in counteracting host immune responses are also provided. Furthermore, the prospects and challenges of utilizing DUBs as therapeutic targets for infectious diseases are discussed.
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Affiliation(s)
- Zhi Zong
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003P. R. China
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058P. R. China
| | - Zhengkui Zhang
- Institute of Biology and Medical ScienceSoochow UniversitySuzhou215123P. R. China
| | - Liming Wu
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003P. R. China
| | - Long Zhang
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003P. R. China
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058P. R. China
| | - Fangfang Zhou
- Institute of Biology and Medical ScienceSoochow UniversitySuzhou215123P. R. China
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24
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Downey A, Olcott M, Spector D, Bird K, Ter Doest A, Pierce Z, Quach E, Sparks S, Super C, Naifeh J, Powers A, White M, Hensley K. Stable knockout of lanthionine synthase C-like protein-1 (LanCL1) from HeLa cells indicates a role for LanCL1 in redox regulation of deubiquitinating enzymes. Free Radic Biol Med 2020; 161:115-124. [PMID: 33049334 DOI: 10.1016/j.freeradbiomed.2020.10.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/28/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022]
Abstract
Lanthionine synthase C-like protein-1 (LanCL1) is a glutathione (GSH)-binding protein of uncertain function, widely expressed in mammalian cells. Recent data suggests that LanCL1 has glutathione S-transferase (GST)-like activity, while other reports claim that LanCL1 suppresses mitogen-activated kinase (MAPK) phosphorylation. In the present study, recombinant human LanCL1 had less than 10% the specific activity of GST. When CRISPR-Cas9 was used to stably ablate LanCL1 from HeLa cells, the resulting line was sensitized to H2O2 toxicity. [GSH], [GSSG], [GSH]/[GSSG] and GST activity were unaltered by LanCL1 knockout but glutathione reductase and glutathione peroxidase activities were significantly elevated. LanCL1-KO cells did not differ in basal or H2O2-induced p38-MAPK, ERK p42/p44 or JNK phosphorylation; however, MAPK-targeted transcription factor regulators c-Jun and IκBα were significantly decreased. Because c-Jun and IκBα levels are ubiquitin regulated, experiments addressed the hypothesis that LanCL1 affects ubiquitination dynamics. In the presence of the 26S proteasome inhibitor bortezomib, ubiquitinated proteins accumulated faster in LanCL1-KO cells, suggesting that LanCL1 positively regulates deubiquitination. The activity of ubiquitin C-terminal hydrolase (UCH), a major deubiquitinase (DUB) subclass, was significantly decreased in LanCL1-KO cells while protein levels of A20/TNFAIP3, USP9X and USP10 DUBs were significantly reduced. UCH activity in HeLa cell lysates was lost upon treatment with H2O2 and significantly recovered by addition of recombinant LanCL1 plus GSH. Taken together these data suggest that LanCL1 likely does not act as a GST-like enzyme in vivo, but rather modulates ubiquitin-dependent cell signaling pathways through positive regulation of redox-sensitive DUBs.
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Affiliation(s)
- Aaron Downey
- Arkansas College of Osteopathic Medicine, Fort Smith, AR, USA
| | - Melissa Olcott
- Arkansas College of Osteopathic Medicine, Fort Smith, AR, USA
| | - Daniel Spector
- Arkansas College of Osteopathic Medicine, Fort Smith, AR, USA
| | - Kayla Bird
- Arkansas College of Osteopathic Medicine, Fort Smith, AR, USA
| | | | - Zachary Pierce
- Arkansas College of Osteopathic Medicine, Fort Smith, AR, USA
| | - Evan Quach
- Arkansas College of Osteopathic Medicine, Fort Smith, AR, USA
| | - Sawyer Sparks
- Arkansas College of Osteopathic Medicine, Fort Smith, AR, USA
| | - Christa Super
- Arkansas College of Osteopathic Medicine, Fort Smith, AR, USA
| | - Jefferey Naifeh
- Arkansas College of Osteopathic Medicine, Fort Smith, AR, USA
| | - Andrea Powers
- Arkansas College of Osteopathic Medicine, Fort Smith, AR, USA
| | - Matthew White
- Arkansas College of Osteopathic Medicine, Fort Smith, AR, USA
| | - Kenneth Hensley
- Arkansas College of Osteopathic Medicine, Fort Smith, AR, USA.
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25
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Reeg S, Castro JP, Hugo M, Grune T. Accumulation of polyubiquitinated proteins: A consequence of early inactivation of the 26S proteasome. Free Radic Biol Med 2020; 160:293-302. [PMID: 32822745 DOI: 10.1016/j.freeradbiomed.2020.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 11/18/2022]
Abstract
The proteasomal degradation system is one of the most important protein degradation systems in the cytosol and nucleus. This system is present in two major forms: the ATP-stimulated 26S/30 S proteasome or the ATP-independent 20S core proteasome. While the first recognize ubiquitin-tagged target proteins and degrade them, the 20S proteasome works also independent from ATP, but requires partially unfolded substrates. While the role of the proteasome in the selective removal of oxidized proteins is undoubted, the debate about a selective ubiquitination of oxidized proteins is still ongoing. Here we demonstrate, that under some conditions of oxidative stress an accumulation of oxidized and of K48-ubiquitinated proteins occurs. However, the removal of oxidized proteins seems not to be linked to ubiquitination. In further experiments, we could show that the accumulation of ubiquitinated proteins under certain oxidative stress conditions is rather a result of a different sensitivity of the 26S proteasome and the ubiquitination machinery towards oxidants.
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Affiliation(s)
- Sandra Reeg
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbrücke, 14558, Nuthetal, Germany
| | - José P Castro
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbrücke, 14558, Nuthetal, Germany; German Center for Diabetes Research (DZD), 85764, München-Neuherberg, Germany
| | - Martin Hugo
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbrücke, 14558, Nuthetal, Germany
| | - Tilman Grune
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbrücke, 14558, Nuthetal, Germany; German Center for Diabetes Research (DZD), 85764, München-Neuherberg, Germany; German Center for Cardiovascular Research (DZHK), 10117, Berlin, Germany; University of Potsdam, Institute of Nutritional Science, 14558, Nuthetal, Germany.
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26
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Gong Q, Hu J, Wang P, Li X, Zhang X. A comprehensive review on β-lapachone: Mechanisms, structural modifications, and therapeutic potentials. Eur J Med Chem 2020; 210:112962. [PMID: 33158575 DOI: 10.1016/j.ejmech.2020.112962] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/03/2020] [Accepted: 10/19/2020] [Indexed: 12/24/2022]
Abstract
β-Lapachone (β-lap, 1), an ortho-naphthoquinone natural product isolated from the lapacho tree (Tabebuia avellanedae) in many regions of South America, has received extensive attention due to various pharmacological activities, such as antitumor, anti-Trypanosoma cruzi, anti-Mycobacterium tuberculosis, antibacterial, and antimalarial activities. Related mechanisms of β-lap have been widely investigated for a full understanding of its therapeutic potentials. Numerous derivatives of β-lap have been reported with aims to generate new chemical entities, improve the corresponding biological potency, and overcome disadvantages of its physical and chemical properties and safety profiles. This review will give insight into the pharmacological mechanisms of β-lap and provide a comprehensive understanding of its structural modifications with regard to different therapeutic potentials. The available clinical trials related to β-lap and its derivatives are also summarized.
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Affiliation(s)
- Qijie Gong
- Jiangsu Key Laboratory of Drug Design and Optimization, And Department of Chemistry, China Pharmaceutical University, Nanjing, 211198, China
| | - Jiabao Hu
- Jiangsu Key Laboratory of Drug Design and Optimization, And Department of Chemistry, China Pharmaceutical University, Nanjing, 211198, China
| | - Pengfei Wang
- Department of Pharmaceutical Engineering, China Pharmaceutical University, Nanjing, 211198, China
| | - Xiang Li
- Department of Pharmaceutical Engineering, China Pharmaceutical University, Nanjing, 211198, China.
| | - Xiaojin Zhang
- Jiangsu Key Laboratory of Drug Design and Optimization, And Department of Chemistry, China Pharmaceutical University, Nanjing, 211198, China.
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27
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Ma X, Tang TS, Guo C. Regulation of translesion DNA synthesis in mammalian cells. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:680-692. [PMID: 31983077 DOI: 10.1002/em.22359] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/29/2019] [Accepted: 01/21/2020] [Indexed: 06/10/2023]
Abstract
The genomes of all living cells are under endogenous and exogenous attacks every day, causing diverse genomic lesions. Most of the lesions can be timely repaired by multiple DNA repair pathways. However, some may persist during S-phase, block DNA replication, and challenge genome integrity. Eukaryotic cells have evolved DNA damage tolerance (DDT) to mitigate the lethal effects of arrested DNA replication without prior removal of the offending DNA damage. As one important mode of DDT, translesion DNA synthesis (TLS) utilizes multiple low-fidelity DNA polymerases to incorporate nucleotides opposite DNA lesions to maintain genome integrity. Three different mechanisms have been proposed to regulate the polymerase switching between high-fidelity DNA polymerases in the replicative machinery and one or more specialized enzymes. Additionally, it is known that proliferating cell nuclear antigen (PCNA) mono-ubiquitination is essential for optimal TLS. Given its error-prone property, TLS is closely associated with spontaneous and drug-induced mutations in cells, which can potentially lead to tumorigenesis and chemotherapy resistance. Therefore, TLS process must be tightly modulated to avoid unwanted mutagenesis. In this review, we will focus on polymerase switching and PCNA mono-ubiquitination, the two key events in TLS pathway in mammalian cells, and summarize current understandings of regulation of TLS process at the levels of protein-protein interactions, post-translational modifications as well as transcription and noncoding RNAs. Environ. Mol. Mutagen. 61:680-692, 2020. © 2020 Wiley Periodicals, Inc.
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Affiliation(s)
- Xiaolu Ma
- College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, China
| | - Tie-Shan Tang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Caixia Guo
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
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28
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Do DT, Le TQT, Le NQK. Using deep neural networks and biological subwords to detect protein S-sulfenylation sites. Brief Bioinform 2020; 22:5866114. [PMID: 32613242 DOI: 10.1093/bib/bbaa128] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/11/2020] [Accepted: 05/26/2020] [Indexed: 12/11/2022] Open
Abstract
Protein S-sulfenylation is one kind of crucial post-translational modifications (PTMs) in which the hydroxyl group covalently binds to the thiol of cysteine. Some recent studies have shown that this modification plays an important role in signaling transduction, transcriptional regulation and apoptosis. To date, the dynamic of sulfenic acids in proteins remains unclear because of its fleeting nature. Identifying S-sulfenylation sites, therefore, could be the key to decipher its mysterious structures and functions, which are important in cell biology and diseases. However, due to the lack of effective methods, scientists in this field tend to be limited in merely a handful of some wet lab techniques that are time-consuming and not cost-effective. Thus, this motivated us to develop an in silico model for detecting S-sulfenylation sites only from protein sequence information. In this study, protein sequences served as natural language sentences comprising biological subwords. The deep neural network was consequentially employed to perform classification. The performance statistics within the independent dataset including sensitivity, specificity, accuracy, Matthews correlation coefficient and area under the curve rates achieved 85.71%, 69.47%, 77.09%, 0.5554 and 0.833, respectively. Our results suggested that the proposed method (fastSulf-DNN) achieved excellent performance in predicting S-sulfenylation sites compared to other well-known tools on a benchmark dataset.
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Affiliation(s)
- Duyen Thi Do
- Faculty of Applied Sciences, Ton Duc Thang University
| | | | - Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, Taipei Medical University
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29
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Regulation of Deubiquitinating Enzymes by Post-Translational Modifications. Int J Mol Sci 2020; 21:ijms21114028. [PMID: 32512887 PMCID: PMC7312083 DOI: 10.3390/ijms21114028] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/01/2020] [Accepted: 06/01/2020] [Indexed: 01/04/2023] Open
Abstract
Ubiquitination and deubiquitination play a critical role in all aspects of cellular processes, and the enzymes involved are tightly regulated by multiple factors including posttranslational modifications like most other proteins. Dysfunction or misregulation of these enzymes could have dramatic physiological consequences, sometimes leading to diseases. Therefore, it is important to have a clear understanding of these regulatory processes. Here, we have reviewed the posttranslational modifications of deubiquitinating enzymes and their consequences on the catalytic activity, stability, abundance, localization, and interaction with the partner proteins.
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30
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Petushkova AI, Zamyatnin AA. Redox-Mediated Post-Translational Modifications of Proteolytic Enzymes and Their Role in Protease Functioning. Biomolecules 2020; 10:biom10040650. [PMID: 32340246 PMCID: PMC7226053 DOI: 10.3390/biom10040650] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 12/13/2022] Open
Abstract
Proteolytic enzymes play a crucial role in metabolic processes, providing the cell with amino acids through the hydrolysis of multiple endogenous and exogenous proteins. In addition to this function, proteases are involved in numerous protein cascades to maintain cellular and extracellular homeostasis. The redox regulation of proteolysis provides a flexible dose-dependent mechanism for proteolytic activity control. The excessive reactive oxygen species (ROS) and reactive nitrogen species (RNS) in living organisms indicate pathological conditions, so redox-sensitive proteases can swiftly induce pro-survival responses or regulated cell death (RCD). At the same time, severe protein oxidation can lead to the dysregulation of proteolysis, which induces either protein aggregation or superfluous protein hydrolysis. Therefore, oxidative stress contributes to the onset of age-related dysfunction. In the present review, we consider the post-translational modifications (PTMs) of proteolytic enzymes and their impact on homeostasis.
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Affiliation(s)
- Anastasiia I. Petushkova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | - Andrey A. Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Correspondence:
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31
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Preclinical Study Using ABT263 to Increase Enzalutamide Sensitivity to Suppress Prostate Cancer Progression Via Targeting BCL2/ROS/USP26 Axis Through Altering ARv7 Protein Degradation. Cancers (Basel) 2020; 12:cancers12040831. [PMID: 32235588 PMCID: PMC7226306 DOI: 10.3390/cancers12040831] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/15/2020] [Accepted: 03/23/2020] [Indexed: 12/22/2022] Open
Abstract
Background: The recently developed antiandrogen, Enzalutamide (Enz), has reformed the standard of care for castration resistant prostate cancer (CRPC) patients. However, Enz-resistance inevitably emerges despite success of Enz in prolonging CRPC patients’ survival. Here we found that Enz-resistant prostate cancer (PCa) cells had higher BCL2 expression. We aimed to test whether targeting BCL2 would influence Enz sensitivity of prostate cancer (PCa) and identify the potential mechanism. Methods: The study was designed to target Enz-induced BCL2 with inhibitor ABT263 and test Enz sensitivity in Enz-resistant PCa cells by MTT assay. Cellular reactive oxygen species (ROS) levels were detected with dihydroethidium staining, and in vitro deubiquitinating enzyme activity assay was used to evaluate ubiquitin specific protease 26 (USP26) activity. Results: ABT263 could increase Enz sensitivity in both Enz-sensitive and Enz-resistant PCa cells via inducing ROS generation. Elevated cellular ROS levels might then inhibit USP26 activity to increase the ubiquitination of androgen receptor (AR) and AR splice variant 7 (ARv7) and their ubiquitin/proteasome-dependent degradation, which contributed to the increase of Enz sensitivity. In vivo mouse model also demonstrates that ABT263 will suppress the PCa progression. Conclusion: This study demonstrated that targeting Enz-induced BCL2 with inhibitor ABT263 could increase Enz sensitivity in both Enz-sensitive and Enz-resistant PCa cells through induction of cellular ROS levels and suppression of USP26 activity with a consequent increase of ubiquitin/proteasome-dependent degradation of AR and ARv7 protein expression.
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32
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Dougherty SE, Maduka AO, Inada T, Silva GM. Expanding Role of Ubiquitin in Translational Control. Int J Mol Sci 2020; 21:E1151. [PMID: 32050486 PMCID: PMC7037965 DOI: 10.3390/ijms21031151] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 12/22/2022] Open
Abstract
The eukaryotic proteome has to be precisely regulated at multiple levels of gene expression, from transcription, translation, and degradation of RNA and protein to adjust to several cellular conditions. Particularly at the translational level, regulation is controlled by a variety of RNA binding proteins, translation and associated factors, numerous enzymes, and by post-translational modifications (PTM). Ubiquitination, a prominent PTM discovered as the signal for protein degradation, has newly emerged as a modulator of protein synthesis by controlling several processes in translation. Advances in proteomics and cryo-electron microscopy have identified ubiquitin modifications of several ribosomal proteins and provided numerous insights on how this modification affects ribosome structure and function. The variety of pathways and functions of translation controlled by ubiquitin are determined by the various enzymes involved in ubiquitin conjugation and removal, by the ubiquitin chain type used, by the target sites of ubiquitination, and by the physiologic signals triggering its accumulation. Current research is now elucidating multiple ubiquitin-mediated mechanisms of translational control, including ribosome biogenesis, ribosome degradation, ribosome-associated protein quality control (RQC), and redox control of translation by ubiquitin (RTU). This review discusses the central role of ubiquitin in modulating the dynamism of the cellular proteome and explores the molecular aspects responsible for the expanding puzzle of ubiquitin signals and functions in translation.
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Affiliation(s)
- Shannon E. Dougherty
- Department of Biology, Duke University, Durham, NC 27708-0338, USA; (S.E.D.); (A.O.M.)
| | - Austin O. Maduka
- Department of Biology, Duke University, Durham, NC 27708-0338, USA; (S.E.D.); (A.O.M.)
| | - Toshifumi Inada
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan;
| | - Gustavo M. Silva
- Department of Biology, Duke University, Durham, NC 27708-0338, USA; (S.E.D.); (A.O.M.)
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33
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Li P, Liu HM. Recent advances in the development of ubiquitin-specific-processing protease 7 (USP7) inhibitors. Eur J Med Chem 2020; 191:112107. [PMID: 32092586 DOI: 10.1016/j.ejmech.2020.112107] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/14/2020] [Accepted: 01/28/2020] [Indexed: 12/16/2022]
Abstract
Ubiquitin-specific-processing protease 7 (USP7) is one among the several deubiquitinating enzymes gaining central attention in the current cancer research. Most recent studies have focused on illustrating how USP7 is involved in the cancer process, while few articles reported the development of small molecule USP7 inhibitors. Although some review articles dealt with USP7, they mainly focused on its physiological role and not on the development of USP7 inhibitors. In this review, we systematically summarise the structures, activities and structure-activity relationship (SAR) of small molecule USP7 inhibitors, recently disclosed in scientific articles and patents from 2000 to 2019. The binding modes of typical compounds and their interactions with USP7 are also presented, while other deubiquitinase inhibitors are described in detail. Meanwhile, we briefly introduce the biochemical and physiological functions of USP7. Finally, challenges and potential strategies in developing small molecule USP7 inhibitors are also discussed.
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Affiliation(s)
- Peng Li
- Key Laboratory of Advanced Technology of Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, And School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan, 450001, China
| | - Hong-Min Liu
- Key Laboratory of Advanced Technology of Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, And School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan, 450001, China.
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34
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Chen X, Bao G, Liu F. Inhibition of USP15 Prevent Glutamate-Induced Oxidative Damage by Activating Nrf2/HO-1 Signaling Pathway in HT22 Cells. Cell Mol Neurobiol 2020; 40:999-1010. [PMID: 31933062 DOI: 10.1007/s10571-020-00789-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/07/2020] [Indexed: 02/07/2023]
Abstract
Oxidative stress has been identified as the significant mediator in epilepsy, which is a chronic disorder in central nervous system. About 30% of epilepsy patients are refractory to antiepileptic drug treatment. However, the underlying mechanism of oxidative damage in epilepsy needs further investigation. In our study, we first find that ubiquitin-specific peptidase 15 (USP15) expression was upregulated in a pentylenetetrazole (PTZ) kindled rat model of epilepsy. Silencing USP15 protected against glutamate-mediated neuronal cell death, and inhibited the high expression levels of cleaved caspase-3. Knockout of USP15 significantly reduced intracellular reactive oxygen species (ROS) levels and enhanced superoxide dismutase (SOD) activity in HT22 cells under the exposure to glutamate treatment. Furthermore, USP15 inhibition induced nuclear factor erythroid-derived 2-related factor2 (Nrf2) nuclear translocation and promoted protein expression level of heme oxygenase (HO-1). Taken together, our findings first reveal a role of USP15 in the pathogenesis of epilepsy, and silencing USP15 in vitro protects against glutamate-mediated cytotoxicity in HT22 cells. Pharmacological inhibition of USP15 may alleviate epileptic seizures via fighting against oxidative damage, providing a novel antiepileptic target.
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Affiliation(s)
- Xiaojie Chen
- Department of Neurology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 201999, China
| | - Guanshui Bao
- Department of Neurology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 201999, China.
| | - Fangfang Liu
- Department of Neurology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 201999, China
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35
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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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36
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Functional analysis of deubiquitylating enzymes in tumorigenesis and development. Biochim Biophys Acta Rev Cancer 2019; 1872:188312. [DOI: 10.1016/j.bbcan.2019.188312] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/16/2019] [Accepted: 08/16/2019] [Indexed: 02/06/2023]
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37
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Bangham CRM, Miura M, Kulkarni A, Matsuoka M. Regulation of Latency in the Human T Cell Leukemia Virus, HTLV-1. Annu Rev Virol 2019; 6:365-385. [PMID: 31283437 DOI: 10.1146/annurev-virology-092818-015501] [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] [Indexed: 11/09/2022]
Abstract
The human T cell leukemia virus persists in vivo in 103 to 106 clones of T lymphocytes that appear to survive for the lifetime of the host. The plus strand of the provirus is typically transcriptionally silent in freshly isolated lymphocytes, but the strong, persistently activated cytotoxic T lymphocyte (CTL) response to the viral antigens indicates that the virus is not constantly latent in vivo. There is now evidence that the plus strand is transcribed in intense intermittent bursts that are triggered by cellular stress, modulated by hypoxia and glycolysis, and inhibited by polycomb repressive complex 1 (PRC1). The minus-strand gene hbz is transcribed at a lower, more constant level but is silent in a proportion of infected cells at a given time. Viral genes in the sense and antisense strands of the provirus play different respective roles in latency and de novo infection: Expression of the plus-strand gene tax is essential for de novo infection, whereas hbz appears to facilitate survival of the infected T cell clone in vivo.
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Affiliation(s)
- Charles R M Bangham
- Division of Infectious Diseases, Department of Medicine, Imperial College London, London W2 1PG, United Kingdom;
| | - Michi Miura
- Division of Infectious Diseases, Department of Medicine, Imperial College London, London W2 1PG, United Kingdom;
| | - Anurag Kulkarni
- Division of Infectious Diseases, Department of Medicine, Imperial College London, London W2 1PG, United Kingdom;
| | - Masao Matsuoka
- Laboratory of Virus Control, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan.,Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University School of Medicine, Kumamoto 860-8556, Japan;
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38
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Wiezel GA, Rustiguel JK, Morgenstern D, Zoccal KF, Faccioli LH, Nonato MC, Ueberheide B, Arantes EC. Insights into the structure, function and stability of bordonein-L, the first L-amino acid oxidase from Crotalus durissus terrificus snake venom. Biochimie 2019; 163:33-49. [DOI: 10.1016/j.biochi.2019.05.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/06/2019] [Indexed: 01/18/2023]
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39
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Neves JLB, Imperial JS, Morgenstern D, Ueberheide B, Gajewiak J, Antunes A, Robinson SD, Espino S, Watkins M, Vasconcelos V, Olivera BM. Characterization of the First Conotoxin from Conus ateralbus, a Vermivorous Cone Snail from the Cabo Verde Archipelago. Mar Drugs 2019; 17:md17080432. [PMID: 31344776 PMCID: PMC6723684 DOI: 10.3390/md17080432] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/15/2019] [Accepted: 07/19/2019] [Indexed: 02/02/2023] Open
Abstract
Conus ateralbus is a cone snail endemic to the west side of the island of Sal, in the Cabo Verde Archipelago off West Africa. We describe the isolation and characterization of the first bioactive peptide from the venom of this species. This 30AA venom peptide is named conotoxin AtVIA (δ-conotoxin-like). An excitatory activity was manifested by the peptide on a majority of mouse lumbar dorsal root ganglion neurons. An analog of AtVIA with conservative changes on three amino acid residues at the C-terminal region was synthesized and this analog produced an identical effect on the mouse neurons. AtVIA has homology with δ-conotoxins from other worm-hunters, which include conserved sequence elements that are shared with δ-conotoxins from fish-hunting Conus. In contrast, there is no comparable sequence similarity with δ-conotoxins from the venoms of molluscivorous Conus species. A rationale for the potential presence of δ-conotoxins, that are potent in vertebrate systems in two different lineages of worm-hunting cone snails, is discussed.
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Affiliation(s)
- Jorge L B Neves
- Department of Biology, University of Utah, 257 S 1400 E, Salt Lake City, UT 84112, USA.
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros, do Porto de Leixões, 4450-208 Porto, Portugal.
- FECM-Faculty of Engineering and Marine Science, University of Cabo Verde, Mindelo CP 163, Cabo Verde.
| | - Julita S Imperial
- Department of Biology, University of Utah, 257 S 1400 E, Salt Lake City, UT 84112, USA
| | - David Morgenstern
- Langone Medical Center, Department of Biochemistry and Molecular Pharmacology, New York University, New York, NY 10016, USA
| | - Beatrix Ueberheide
- Langone Medical Center, Department of Biochemistry and Molecular Pharmacology, New York University, New York, NY 10016, USA
| | - Joanna Gajewiak
- Department of Biology, University of Utah, 257 S 1400 E, Salt Lake City, UT 84112, USA
| | - Agostinho Antunes
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros, do Porto de Leixões, 4450-208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Samuel D Robinson
- Department of Biology, University of Utah, 257 S 1400 E, Salt Lake City, UT 84112, USA
| | - Samuel Espino
- Department of Biology, University of Utah, 257 S 1400 E, Salt Lake City, UT 84112, USA
| | - Maren Watkins
- Department of Biology, University of Utah, 257 S 1400 E, Salt Lake City, UT 84112, USA
| | - Vitor Vasconcelos
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros, do Porto de Leixões, 4450-208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Baldomero M Olivera
- Department of Biology, University of Utah, 257 S 1400 E, Salt Lake City, UT 84112, USA
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40
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Yin Z, Yang L, Wu F, Fan J, Xu J, Jin Y, Yang G. Reactive Oxygen Species-Mediated Cezanne Inactivation by Oxidation of its Catalytic Cysteine Residue in Hepatocellular Carcinoma. Oncol Res 2019; 27:1069-1077. [PMID: 31072419 PMCID: PMC7848393 DOI: 10.3727/096504019x15566157027506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Cysteine oxidation occurs at the active site of deubiquitinases (DUBs) during many biologic signaling cascades. Here we report that hepatocellular carcinoma cells (HCCs) generated higher levels of endogenous reactive oxygen species (ROS). This elevated ROS production was inhibited by NADPH oxidase inhibitor diphenylene iodonium (DPI) and mitochondria electron chain inhibitor rotenone in HCC cells. Moreover, we found that H2O2 could activate NF-κB-dependent inflammatory effect through increased induction of matrix metalloproteinase 2 (MMP2), MMP9, and intercellular adhesion molecule 1 (ICAM1) expression levels. In addition, we found that H2O2 could prolong NF-κB activation by suppressing the negative regulatory functions of Cezanne in HCC cells. Ubiquitin-derived thiol-reactive probe (HA-UbVME) assay and biotin-tagged 1,3-cyclohexadione derivative (DCP-Bio1) assay showed that H2O2 has the capacity to inhibit the catalytic activity of Cezanne, and the reducing agent, DTT, could reactivate the Cezanne deubiquitinating enzyme activity. Taken all together, these findings demonstrated an important role for oxidation of Cezanne by ROS in regulation of the inflammatory effect of hepatocellular carcinoma.
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Affiliation(s)
- Zhongyuan Yin
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Lin Yang
- Oncology Department, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Feng Wu
- Department of Respiratory Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Jinshuo Fan
- Department of Respiratory Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Juanjuan Xu
- Department of Respiratory Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Yang Jin
- Department of Respiratory Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Guanghai Yang
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
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41
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Harris IS, Endress JE, Coloff JL, Selfors LM, McBrayer SK, Rosenbluth JM, Takahashi N, Dhakal S, Koduri V, Oser MG, Schauer NJ, Doherty LM, Hong AL, Kang YP, Younger ST, Doench JG, Hahn WC, Buhrlage SJ, DeNicola GM, Kaelin WG, Brugge JS. Deubiquitinases Maintain Protein Homeostasis and Survival of Cancer Cells upon Glutathione Depletion. Cell Metab 2019; 29:1166-1181.e6. [PMID: 30799286 PMCID: PMC6506399 DOI: 10.1016/j.cmet.2019.01.020] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 11/30/2018] [Accepted: 01/23/2019] [Indexed: 12/22/2022]
Abstract
Cells are subjected to oxidative stress during the initiation and progression of tumors, and this imposes selective pressure for cancer cells to adapt mechanisms to tolerate these conditions. Here, we examined the dependency of cancer cells on glutathione (GSH), the most abundant cellular antioxidant. While cancer cell lines displayed a broad range of sensitivities to inhibition of GSH synthesis, the majority were resistant to GSH depletion. To identify cellular pathways required for this resistance, we carried out genetic and pharmacologic screens. Both approaches revealed that inhibition of deubiquitinating enzymes (DUBs) sensitizes cancer cells to GSH depletion. Inhibition of GSH synthesis, in combination with DUB inhibition, led to an accumulation of polyubiquitinated proteins, induction of proteotoxic stress, and cell death. These results indicate that depletion of GSH renders cancer cells dependent on DUB activity to maintain protein homeostasis and cell viability and reveal a potentially exploitable vulnerability for cancer therapy.
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Affiliation(s)
- Isaac S Harris
- Ludwig Cancer Center, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Jennifer E Endress
- Ludwig Cancer Center, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan L Coloff
- Ludwig Cancer Center, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | | | | | - Jennifer M Rosenbluth
- Ludwig Cancer Center, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Nobuaki Takahashi
- Ludwig Cancer Center, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | | | | | - Andrew L Hong
- Dana-Farber Cancer Institute, Boston, MA 02115, USA; Boston Children's Hospital, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Yun Pyo Kang
- Department of Cancer Physiology, Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Scott T Younger
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - John G Doench
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - William C Hahn
- Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Sara J Buhrlage
- Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Gina M DeNicola
- Department of Cancer Physiology, Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | | | - Joan S Brugge
- Ludwig Cancer Center, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
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42
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Wiezel GA, Bordon KC, Silva RR, Gomes MS, Cabral H, Rodrigues VM, Ueberheide B, Arantes EC. Subproteome of Lachesis muta rhombeata venom and preliminary studies on LmrSP-4, a novel snake venom serine proteinase. J Venom Anim Toxins Incl Trop Dis 2019; 25:e147018. [PMID: 31131000 PMCID: PMC6521711 DOI: 10.1590/1678-9199-jvatitd-1470-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/02/2018] [Indexed: 11/22/2022] Open
Abstract
Background: Lachesis muta rhombeata is one of the venomous snakes of
medical importance in Brazil whose envenoming is characterized by local and
systemic effects which may produce even shock and death. Its venom is mainly
comprised of serine and metalloproteinases, phospholipases A2 and
bradykinin-potentiating peptides. Based on a previously reported
fractionation of L. m. rhombeata venom (LmrV), we decided
to perform a subproteome analysis of its major fraction and investigated a
novel component present in this venom. Methods: LmrV was fractionated through molecular exclusion chromatography and the main
fraction (S5) was submitted to fibrinogenolytic activity assay and
fractionated by reversed-phase chromatography. The N-terminal sequences of
the subfractions eluted from reversed-phase chromatography were determined
by automated Edman degradation. Enzyme activity of LmrSP-4 was evaluated
upon chromogenic substrates for thrombin (S-2238), plasma kallikrein
(S-2302), plasmin and streptokinase-activated plasminogen (S-2251) and
Factor Xa (S-2222) and upon fibrinogen. All assays were carried out in the
presence or absence of possible inhibitors. The fluorescence resonance
energy transfer substrate Abz-KLRSSKQ-EDDnp was used to determine the
optimal conditions for LmrSP-4 activity. Molecular mass of LmrSP-4 was
determined by MALDI-TOF and digested peptides after trypsin and Glu-C
treatments were analyzed by high resolution MS/MS using different
fragmentation modes. Results: Fraction S5 showed strong proteolytic activity upon fibrinogen. Its
fractionation by reversed-phase chromatography gave rise to 6 main fractions
(S5C1-S5C6). S5C1-S5C5 fractions correspond to serine proteinases whereas
S5C6 represents a C-type lectin. S5C4 (named LmrSP-4) had its N-terminal
determined by Edman degradation up to the 53rd amino acid residue
and was chosen for characterization studies. LmrSP-4 is a fibrinogenolytic
serine proteinase with high activity against S-2302, being inhibited by PMSF
and benzamidine, but not by 1,10-phenantroline. In addition, this enzyme
exhibited maximum activity within the pH range from neutral to basic and
between 40 and 50 °C. About 68% of the LmrSP-4 primary structure was
covered, and its molecular mass is 28,190 Da. Conclusions: Novel serine proteinase isoforms and a lectin were identified in LmrV.
Additionally, a kallikrein-like serine proteinase that might be useful as
molecular tool for investigating bradykinin-involving process was isolated
and partially characterized.
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Affiliation(s)
- Gisele A Wiezel
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n, 14040-903, Ribeirão Preto, SP, Brazil
| | - Karla Cf Bordon
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n, 14040-903, Ribeirão Preto, SP, Brazil
| | - Ronivaldo R Silva
- Institute of Biosciences, Letters and Exact Sciences, Universidade Estadual Paulista, Rua Cristóvão Colombo, 2265, 15054-000, São José do Rio Preto, SP, Brazil
| | - Mário Sr Gomes
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Av. Pará, 1720, 38400-902, Uberlândia, MG, Brazil.,Department of Chemical and Physical, State University of Southwest Bahia, Rua José Moreira Sobrinho, até 873 874, 45506-210, Jequié, BA, Brazil
| | - Hamilton Cabral
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n, 14040-903, Ribeirão Preto, SP, Brazil
| | - Veridiana M Rodrigues
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Av. Pará, 1720, 38400-902, Uberlândia, MG, Brazil
| | - Beatrix Ueberheide
- Proteomics Resource Center, New York University Langone Medical Center, 430 East 29th St., 10016, New York City, USA
| | - Eliane C Arantes
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n, 14040-903, Ribeirão Preto, SP, Brazil
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43
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Leser M, Chapman JR, Khine M, Pegan J, Law M, Makkaoui ME, Ueberheide BM, Brenowitz M. Chemical Generation of Hydroxyl Radical for Oxidative 'Footprinting'. Protein Pept Lett 2019; 26:61-69. [PMID: 30543161 DOI: 10.2174/0929866526666181212164812] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/21/2018] [Accepted: 10/30/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND For almost four decades, hydroxyl radical chemically generated by Fenton chemistry has been a mainstay for the oxidative 'footprinting' of macromolecules. OBJECTIVE In this article, we start by reviewing the application of chemical generation of hydroxyl radical to the development of oxidative footprinting of DNA and RNA and the subsequent application of the method to oxidative footprinting of proteins. We next discuss a novel strategy for generating hydroxyl radicals by Fenton chemistry that immobilizes catalytic iron on a solid surface (Pyrite Shrink Wrap laminate) for the application of nucleic acid and protein footprinting. METHOD Pyrite Shrink-Wrap Laminate is fabricated by depositing pyrite (Fe-S2, aka 'fool's gold') nanocrystals onto thermolabile plastic (Shrinky Dink). The laminate can be thermoformed into a microtiter plate format into which samples are deposited for oxidation. RESULTS We demonstrate the utility of the Pyrite Shrink-Wrap Laminate for the chemical generation of hydroxyl radicals by mapping the surface of the T-cell co-stimulatory protein Programmed Death - 1 (PD-1) and the interface of the complex with its ligand PD-L1. CONCLUSION We have developed and validated an affordable and reliable benchtop method of hydroxyl radical generation that will broaden the application of protein oxidative footprinting. Due to the minimal equipment required to implement this method, it should be easily adaptable by many laboratories with access to mass spectrometry.
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Affiliation(s)
- Micheal Leser
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Jessica R Chapman
- Proteomics Laboratory, Department of Biochemistry, New York University School of Medicine, New York, NY, United States
| | - Michelle Khine
- Department of Biomedical Engineering, University of California, Irvine, CA, United States.,Department of Chemical Engineering & Materials Science, University of California, Irvine, CA, United States
| | - Jonathan Pegan
- Department of Biomedical Engineering, University of California, Irvine, CA, United States
| | - Matt Law
- Department of Chemical Engineering & Materials Science, University of California, Irvine, CA, United States.,Department of Chemistry, University of California, Irvine, CA, United States
| | - Mohammed El Makkaoui
- Department of Chemical Engineering & Materials Science, University of California, Irvine, CA, United States.,Department of Chemistry, University of California, Irvine, CA, United States
| | - Beatrix M Ueberheide
- Proteomics Laboratory, Department of Biochemistry, New York University School of Medicine, New York, NY, United States.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States
| | - Michael Brenowitz
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, United States
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44
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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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45
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Jin Q, Martinez CA, Arcipowski KM, Zhu Y, Gutierrez-Diaz BT, Wang KK, Johnson MR, Volk AG, Wang F, Wu J, Grove C, Wang H, Sokirniy I, Thomas PM, Goo YA, Abshiru NA, Hijiya N, Peirs S, Vandamme N, Berx G, Goosens S, Marshall SA, Rendleman EJ, Takahashi YH, Wang L, Rawat R, Bartom ET, Collings CK, Van Vlierberghe P, Strikoudis A, Kelly S, Ueberheide B, Mantis C, Kandela I, Bourquin JP, Bornhauser B, Serafin V, Bresolin S, Paganin M, Accordi B, Basso G, Kelleher NL, Weinstock J, Kumar S, Crispino JD, Shilatifard A, Ntziachristos P. USP7 Cooperates with NOTCH1 to Drive the Oncogenic Transcriptional Program in T-Cell Leukemia. Clin Cancer Res 2019; 25:222-239. [PMID: 30224337 PMCID: PMC6320313 DOI: 10.1158/1078-0432.ccr-18-1740] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/18/2018] [Accepted: 09/11/2018] [Indexed: 12/12/2022]
Abstract
PURPOSE T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive disease, affecting children and adults. Chemotherapy treatments show high response rates but have debilitating effects and carry risk of relapse. Previous work implicated NOTCH1 and other oncogenes. However, direct inhibition of these pathways affects healthy tissues and cancer alike. Our goal in this work has been to identify enzymes active in T-ALL whose activity could be targeted for therapeutic purposes. EXPERIMENTAL DESIGN To identify and characterize new NOTCH1 druggable partners in T-ALL, we coupled studies of the NOTCH1 interactome to expression analysis and a series of functional analyses in cell lines, patient samples, and xenograft models. RESULTS We demonstrate that ubiquitin-specific protease 7 (USP7) interacts with NOTCH1 and controls leukemia growth by stabilizing the levels of NOTCH1 and JMJD3 histone demethylase. USP7 is highly expressed in T-ALL and is transcriptionally regulated by NOTCH1. In turn, USP7 controls NOTCH1 levels through deubiquitination. USP7 binds oncogenic targets and controls gene expression through stabilization of NOTCH1 and JMJD3 and ultimately H3K27me3 changes. We also show that USP7 and NOTCH1 bind T-ALL superenhancers, and inhibition of USP7 leads to a decrease of the transcriptional levels of NOTCH1 targets and significantly blocks T-ALL cell growth in vitro and in vivo. CONCLUSIONS These results provide a new model for USP7 deubiquitinase activity through recruitment to oncogenic chromatin loci and regulation of both oncogenic transcription factors and chromatin marks to promote leukemia. Our studies also show that targeting USP7 inhibition could be a therapeutic strategy in aggressive leukemia.
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Affiliation(s)
- Qi Jin
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois
| | - Carlos A Martinez
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois
| | - Kelly M Arcipowski
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois
| | - Yixing Zhu
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois
| | - Blanca T Gutierrez-Diaz
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois
| | - Kenneth K Wang
- Master of Science in Biotechnology Graduate Program, Northwestern University, Evanston, Illinois
| | - Megan R Johnson
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois
| | - Andrew G Volk
- Division of Hematology/Oncology, Department of Medicine, Northwestern University, Chicago, Illinois
| | - Feng Wang
- Progenra Inc., Malvern, Pennsylvania
| | - Jian Wu
- Progenra Inc., Malvern, Pennsylvania
| | | | - Hui Wang
- Progenra Inc., Malvern, Pennsylvania
| | | | - Paul M Thomas
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois
| | - Young Ah Goo
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois
| | - Nebiyu A Abshiru
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois
| | - Nobuko Hijiya
- Ann & Robert H. Lurie Children's Hospital, Northwestern University, Chicago, Illinois
| | - Sofie Peirs
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Niels Vandamme
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Molecular Cellular Oncology Lab, Department for Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Geert Berx
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Molecular Cellular Oncology Lab, Department for Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Steven Goosens
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Molecular Cellular Oncology Lab, Department for Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Stacy A Marshall
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois
| | - Emily J Rendleman
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois
| | - Yoh-Hei Takahashi
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois
| | - Lu Wang
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois
| | - Radhika Rawat
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois
| | - Clayton K Collings
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois
| | - Pieter Van Vlierberghe
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | | | - Stephen Kelly
- Department of Pathology, New York University, New York, New York
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, New York University, New York, New York
| | - Christine Mantis
- Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois
| | - Irawati Kandela
- Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois
| | - Jean-Pierre Bourquin
- University Children's Hospital, Division of Pediatric Oncology, University of Zurich, Switzerland
| | - Beat Bornhauser
- University Children's Hospital, Division of Pediatric Oncology, University of Zurich, Switzerland
| | - Valentina Serafin
- Oncohematology Laboratory, Department of Woman's and Child's Health, University of Padova, Padova, Italy
| | - Silvia Bresolin
- Oncohematology Laboratory, Department of Woman's and Child's Health, University of Padova, Padova, Italy
| | - Maddalena Paganin
- Oncohematology Laboratory, Department of Woman's and Child's Health, University of Padova, Padova, Italy
| | - Benedetta Accordi
- Oncohematology Laboratory, Department of Woman's and Child's Health, University of Padova, Padova, Italy
| | - Giuseppe Basso
- Oncohematology Laboratory, Department of Woman's and Child's Health, University of Padova, Padova, Italy
| | - Neil L Kelleher
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois
- Department of Chemistry, Northwestern University, Chicago, Illinois
| | | | | | - John D Crispino
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois
- Division of Hematology/Oncology, Department of Medicine, Northwestern University, Chicago, Illinois
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois
| | - Panagiotis Ntziachristos
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois.
- Division of Hematology/Oncology, Department of Medicine, Northwestern University, Chicago, Illinois
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois
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Wiezel GA, Shibao PYT, Cologna CT, Morandi Filho R, Ueira-Vieira C, De Pauw E, Quinton L, Arantes EC. In-Depth Venome of the Brazilian Rattlesnake Crotalus durissus terrificus: An Integrative Approach Combining Its Venom Gland Transcriptome and Venom Proteome. J Proteome Res 2018; 17:3941-3958. [PMID: 30270628 DOI: 10.1021/acs.jproteome.8b00610] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Snake venoms are complex mixtures mainly composed of proteins and small peptides. Crotoxin is one of the most studied components from Crotalus venoms, but many other components are less known due to their low abundance. The venome of Crotalus durissus terrificus, the most lethal Brazilian snake, was investigated by combining its venom gland transcriptome and proteome to create a holistic database of venom compounds unraveling novel toxins. We constructed a cDNA library from C. d. terrificus venom gland using the Illumina platform and investigated its venom proteome through high resolution liquid chromotography-tandem mass spectrometry. After integrating data from both data sets, more than 30 venom components classes were identified by the transcriptomic analysis and 15 of them were detected in the venom proteome. However, few of them (PLA2, SVMP, SVSP, and VEGF) were relatively abundant. Furthermore, only seven expressed transcripts contributed to ∼82% and ∼73% of the abundance in the transcriptome and proteome, respectively. Additionally, novel venom proteins are reported, and we highlight the importance of using different databases to perform the data integration and discuss the structure of the venom components-related transcripts identified. Concluding, this research paves the way for novel investigations and discovery of future pharmacological agents or targets in the antivenom therapy.
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Affiliation(s)
- Gisele A Wiezel
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto , University of São Paulo , Av. do Café, s/n , 14040-903 Ribeirão Preto , Brazil
| | - Priscila Y T Shibao
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto , University of São Paulo , Av. do Café, s/n , 14040-903 Ribeirão Preto , Brazil
| | - Camila T Cologna
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto , University of São Paulo , Av. do Café, s/n , 14040-903 Ribeirão Preto , Brazil
| | - Romualdo Morandi Filho
- Laboratory of Genetics, Biotechnology Institute , Federal University of Uberlândia , Rua Acre, s/n , 38400-902 Uberlândia , Brazil
| | - Carlos Ueira-Vieira
- Laboratory of Genetics, Biotechnology Institute , Federal University of Uberlândia , Rua Acre, s/n , 38400-902 Uberlândia , Brazil
| | - Edwin De Pauw
- Laboratory of Mass Spectrometry, MolSys Research Unit, Department of Chemistry , University of Liège , Bat. B6c , 4000 Liège , Belgium
| | - Loïc Quinton
- Laboratory of Mass Spectrometry, MolSys Research Unit, Department of Chemistry , University of Liège , Bat. B6c , 4000 Liège , Belgium
| | - Eliane C Arantes
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto , University of São Paulo , Av. do Café, s/n , 14040-903 Ribeirão Preto , Brazil
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47
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Palazón-Riquelme P, Worboys JD, Green J, Valera A, Martín-Sánchez F, Pellegrini C, Brough D, López-Castejón G. USP7 and USP47 deubiquitinases regulate NLRP3 inflammasome activation. EMBO Rep 2018; 19:embr.201744766. [PMID: 30206189 PMCID: PMC6172458 DOI: 10.15252/embr.201744766] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/02/2018] [Accepted: 08/07/2018] [Indexed: 01/28/2023] Open
Abstract
The assembly and activation of the inflammasomes are tightly regulated by post‐translational modifications, including ubiquitin. Deubiquitinases (DUBs) counteract the addition of ubiquitin and are essential regulators of immune signalling pathways, including those acting on the inflammasome. How DUBs control the assembly and activation of inflammasomes is unclear. Here, we show that the DUBs USP7 and USP47 regulate inflammasome activation in macrophages. Chemical inhibition of USP7 and USP47 blocks inflammasome formation, independently of transcription, by preventing ASC oligomerisation and speck formation. We also provide evidence that the ubiquitination status of NLRP3 itself is altered by inhibition of USP7 and USP47. Interestingly, we found that the activity of USP7 and USP47 increased in response to inflammasome activators. Using CRISPR/Cas9 in the macrophage cell line THP‐1, we show that inflammasome activation is reduced when both USP7 and USP47 are knocked down. Altogether, these data reveal a new post‐transcriptional role for USP47 and USP7 in inflammation by regulating inflammasome activation and the release of the pro‐inflammatory cytokines IL‐1β and IL‐18, and implicate dual USP7 and USP47 inhibitors as potential therapeutic agents for inflammatory disease.
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Affiliation(s)
- Pablo Palazón-Riquelme
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, Manchester Collaborative Centre of Inflammation Research, Manchester Academic Health Science Centre, Core Technology Facility, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Jonathan D Worboys
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, Manchester Collaborative Centre of Inflammation Research, Manchester Academic Health Science Centre, Core Technology Facility, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Jack Green
- Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre School of Biological Sciences University of Manchester, Manchester, UK
| | - Ana Valera
- Departamento de Biología Celular e Histología, Facultad de Biología, Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Universidad de Murcia, Murcia, Spain
| | - Fatima Martín-Sánchez
- Grupo de Inflamación Molecular, Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas, Hospital Clínico Universitario Virgen de la Arrixaca (IMIB-Arrixaca), Murcia, Spain
| | - Carolina Pellegrini
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - David Brough
- Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre School of Biological Sciences University of Manchester, Manchester, UK
| | - Gloria López-Castejón
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, Manchester Collaborative Centre of Inflammation Research, Manchester Academic Health Science Centre, Core Technology Facility, School of Biological Sciences, University of Manchester, Manchester, UK
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48
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Stankovic-Valentin N, Melchior F. Control of SUMO and Ubiquitin by ROS: Signaling and disease implications. Mol Aspects Med 2018; 63:3-17. [PMID: 30059710 DOI: 10.1016/j.mam.2018.07.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/23/2018] [Accepted: 07/27/2018] [Indexed: 01/06/2023]
Abstract
Reversible post-translational modifications (PTMs) ensure rapid signal transmission from sensors to effectors. Reversible modification of proteins by the small proteins Ubiquitin and SUMO are involved in virtually all cellular processes and can modify thousands of proteins. Ubiquitination or SUMOylation is the reversible attachment of these modifiers to lysine residues of a target via isopeptide bond formation. These modifications require ATP and an enzymatic cascade composed of three classes of proteins: E1 activating enzymes, E2 conjugating enzymes and E3 ligases. The reversibility of the modification is ensured by specific isopeptidases. E1 and E2 enzymes, some E3 ligases and most isopeptidases have catalytic cysteine residues, which make them potentially susceptible for oxidation. Indeed, an increasing number of examples reveal regulation of ubiquitination and SUMOylation by reactive oxygen species, both in the context of redox signaling and in severe oxidative stress. Importantly, ubiquitination and SUMOylation play essential roles in the regulation of ROS homeostasis, participating in the control of ROS production and clearance. In this review, we will discuss the interplay between ROS homeostasis, Ubiquitin and SUMO pathways and the implications for the oxidative stress response and cell signaling.
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Affiliation(s)
- Nicolas Stankovic-Valentin
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ - ZMBH Alliance, Heidelberg, Germany.
| | - Frauke Melchior
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ - ZMBH Alliance, Heidelberg, Germany.
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de la Parra C, Ernlund A, Alard A, Ruggles K, Ueberheide B, Schneider RJ. A widespread alternate form of cap-dependent mRNA translation initiation. Nat Commun 2018; 9:3068. [PMID: 30076308 PMCID: PMC6076257 DOI: 10.1038/s41467-018-05539-0] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/06/2018] [Indexed: 11/30/2022] Open
Abstract
Translation initiation of most mammalian mRNAs is mediated by a 5′ cap structure that binds eukaryotic initiation factor 4E (eIF4E). However, inactivation of eIF4E does not impair translation of many capped mRNAs, suggesting an unknown alternate mechanism may exist for cap-dependent but eIF4E-independent translation. We show that DAP5, an eIF4GI homolog that lacks eIF4E binding, utilizes eIF3d to facilitate cap-dependent translation of approximately 20% of mRNAs. Genome-wide transcriptomic and translatomic analyses indicate that DAP5 is required for translation of many transcription factors and receptor capped mRNAs and their mRNA targets involved in cell survival, motility, DNA repair and translation initiation, among other mRNAs. Mass spectrometry and crosslinking studies demonstrate that eIF3d is a direct binding partner of DAP5. In vitro translation and ribosome complex studies demonstrate that DAP5 and eIF3d are both essential for eIF4E-independent capped-mRNA translation. These studies disclose a widespread and previously unknown mechanism for cap-dependent mRNA translation by DAP5-eIF3d complexes. Binding of eIF4E to the 5′ cap of mRNAs is a key early step in canonical translation initiation, but the requirement for eIF4E is not universal. Here the authors show that the eIF4G homolog DAP5 interacts with eIF3 to promote cap-dependent translation of a significant number of mRNA in an eIF4E-independent manner.
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Affiliation(s)
- Columba de la Parra
- Department of Microbiology, NYU School of Medicine, New York, NY, 10016, USA.,Perlmutter Cancer Center, NYU School of Medicine, New York, NY, 10016, USA
| | - Amanda Ernlund
- Department of Microbiology, NYU School of Medicine, New York, NY, 10016, USA
| | - Amandine Alard
- Department of Microbiology, NYU School of Medicine, New York, NY, 10016, USA
| | - Kelly Ruggles
- Department of Medicine, NYU School of Medicine, New York, NY, 10016, USA
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY, 10016, USA
| | - Robert J Schneider
- Department of Microbiology, NYU School of Medicine, New York, NY, 10016, USA. .,Perlmutter Cancer Center, NYU School of Medicine, New York, NY, 10016, USA.
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Lee J, Homma T, Kobayashi S, Ishii N, Fujii J. Unveiling systemic organ disorders associated with impaired lipid catabolism in fasted SOD1-deficient mice. Arch Biochem Biophys 2018; 654:163-171. [PMID: 30056077 DOI: 10.1016/j.abb.2018.07.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/08/2018] [Accepted: 07/25/2018] [Indexed: 12/12/2022]
Abstract
Oxidative stress triggers the formation of lipid droplets in the liver by stimulating lipogenesis and simultaneously suppresses lipoprotein secretion under hypernutritional conditions. Herein we report on the observation of systemic organ failure that is associated with lipid droplet accumulation in fasting, SOD1-knockout (KO) mice. Upon a three-day fasting period, the KO mice were observed to be vulnerable, could not be rescued by refeeding and had largely died, while wild-type mice were totally recovered. Visceral fat was rapidly consumed during fasting, which resulted in energy shortage and increased fatality in the KO mice. Lipid droplets had accumulated and continued to remain in KO mouse organs that routinely catalyze fatty acids via β-oxidation, even though the levels of free fatty acids and β-hydroxybutyrate, a ketone body, in blood plasma were less in KO mice compared to WT mice during the fasting period. The fasting-triggered organ failure in the KO mice was effectively mitigated by feeding a high calorie-diet for 2 weeks prior to fasting, even though the mice had an excessive accumulation of lipid droplets in the liver. These collective data suggest that the lipid-catabolizing system is the sensitive target of oxidative stress triggered by fasting conditions in the KO mice.
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Affiliation(s)
- Jaeyong Lee
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, Japan
| | - Takujiro Homma
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, Japan
| | - Sho Kobayashi
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, Japan
| | - Naoki Ishii
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, Japan
| | - Junichi Fujii
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, Japan.
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