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Hu Q, Chen Y, Zhou Q, Deng S, Hou W, Yi Y, Li C, Tang J. ADAR promotes USP38 auto-deubiquitylation and stabilization in an RNA editing-independent manner in Esophageal Squamous Cell Carcinoma. J Biol Chem 2024:107789. [PMID: 39303916 DOI: 10.1016/j.jbc.2024.107789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 08/31/2024] [Accepted: 09/05/2024] [Indexed: 09/22/2024] Open
Abstract
Esophageal cancer is mainly divided into esophageal adenocarcinoma (EADC) and esophageal squamous cell carcinoma (ESCC). China is one of the high-incidence areas of esophageal cancer, of which about 90% are ESCC. The deubiquitinase USP38 has been reported to play significant roles in several biological processes, including inflammatory responses, antiviral infection, cell proliferation, migration, invasion, DNA damage repair, and chemotherapy resistance. However, the role and mechanisms of USP38 in ESCC development remain still unclear. Furthermore, although many substrates of USP38 have been identified, few upstream regulatory factors of USP38 have been identified. In this study, we found that USP38 was significantly upregulated in esophageal cancer tissues. Knockdown of USP38 inhibited ESCC growth. USP38 stabilized itself through auto-deubiquitylation. In addition, we demonstrate that ADAR could enhance the stability of USP38 protein and facilitate USP38 auto-deubiquitylation by interacting with USP38 in an RNA editing-independent manner. ADAR inhibition of ESCC cell proliferation depended on USP38. In summary, these results highlight that the potential of targeting the ADAR-USP38 axis for ESCC treatment.
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Affiliation(s)
- Qingyong Hu
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China; Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, China.
| | - Yahui Chen
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China; Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, China
| | - Qianru Zhou
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China; Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, China
| | - Shanshan Deng
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China; Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, China
| | - Wei Hou
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China; Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, China
| | - Yong Yi
- Center of Growth, Metabolism and Aging, Key Laboratory of Biological Resources and Ecological Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Chenghua Li
- Center of Growth, Metabolism and Aging, Key Laboratory of Biological Resources and Ecological Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jiancai Tang
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China; Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, China.
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Salomonsson J, Wallner B, Sjöstrand L, D'Arcy P, Sunnerhagen M, Ahlner A. Transient interdomain interactions in free USP14 shape its conformational ensemble. Protein Sci 2024; 33:e4975. [PMID: 38588275 PMCID: PMC11001199 DOI: 10.1002/pro.4975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/16/2024] [Accepted: 03/13/2024] [Indexed: 04/10/2024]
Abstract
The deubiquitinase (DUB) ubiquitin-specific protease 14 (USP14) is a dual domain protein that plays a regulatory role in proteasomal degradation and has been identified as a promising therapeutic target. USP14 comprises a conserved USP domain and a ubiquitin-like (Ubl) domain separated by a 25-residue linker. The enzyme activity of USP14 is autoinhibited in solution, but is enhanced when bound to the proteasome, where the Ubl and USP domains of USP14 bind to the Rpn1 and Rpt1/Rpt2 units, respectively. No structure of full-length USP14 in the absence of proteasome has yet been presented, however, earlier work has described how transient interactions between Ubl and USP domains in USP4 and USP7 regulate DUB activity. To better understand the roles of the Ubl and USP domains in USP14, we studied the Ubl domain alone and in full-length USP14 by nuclear magnetic resonance spectroscopy and used small angle x-ray scattering and molecular modeling to visualize the entire USP14 protein ensemble. Jointly, our results show how transient interdomain interactions between the Ubl and USP domains of USP14 predispose its conformational ensemble for proteasome binding, which may have functional implications for proteasome regulation and may be exploited in the design of future USP14 inhibitors.
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Affiliation(s)
| | - Björn Wallner
- Department of Physics, Chemistry and BiologyLinköping UniversityLinköpingSweden
| | - Linda Sjöstrand
- Department of Biomedical and Clinical SciencesLinköping UniversityLinköpingSweden
| | - Pádraig D'Arcy
- Department of Biomedical and Clinical SciencesLinköping UniversityLinköpingSweden
| | - Maria Sunnerhagen
- Department of Physics, Chemistry and BiologyLinköping UniversityLinköpingSweden
| | - Alexandra Ahlner
- Department of Physics, Chemistry and BiologyLinköping UniversityLinköpingSweden
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3
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Li X, Lai Y, Lane Z, Strollo H, Tanimura K, Sembrat JC, Zou C, Myerburg MM, Rojas M, Shapiro S, Jiang Y, Nyunoya T. Cigarette smoking is a secondary cause of folliculin loss. Thorax 2023; 78:402-408. [PMID: 35301243 PMCID: PMC9612398 DOI: 10.1136/thoraxjnl-2021-217197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 02/12/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND Birt-Hogg-Dubé syndrome (BHD) is a clinical syndrome manifesting with cystic lung disease and pneumothorax. Features of BHD result from the loss-of-function mutations of the folliculin (FLCN) gene. Chronic obstructive pulmonary disease (COPD), characterised by an irreversible airflow limitation, is primarily caused by cigarette smoking. OBJECTIVE Given that COPD often shares structural features with BHD, we investigated the link between COPD, cigarette smoke (CS) exposure and FLCN expression. METHODS We measured the expression of FLCN in human COPD lungs and CS-exposed mouse lungs, as well as in CS extract (CSE)-exposed immortalised human airway epithelial cells by immunoblotting. RESULTS We found that the lung FLCN protein levels in smokers with COPD and CS exposure mice exhibit a marked decrease compared with smokers without COPD and room air exposure mice, respectively. We confirmed CS induced degradation of FLCN in immortalised human bronchial epithelial Beas-2B cells via ubiquitin proteasome system. Further, siRNA targeting FLCN enhanced CSE-induced cytotoxicity. By contrast, FLCN overexpression protected cells from CSE-induced cytotoxicity. We found that FBXO23, the ubiquitin E3 ligase subunit, specifically binds to and targets FLCN for degradation. Inhibition of ATM (ataxia-telangiectasia mutated) attenuated CSE induced FLCN degradation, suggesting a role of ATM in FLCN proteolysis. We further confirmed that the mutant of major FLCN phosphorylation site serine 62A is resistant to CSE-induced degradation and cytotoxicity. CONCLUSIONS Our study demonstrates that CS exposure is a secondary cause of FLCN deficiency due to the enhanced proteolysis, which promoted airway epithelial cell death.
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Affiliation(s)
- Xiuying Li
- Medicine, VA Pittsburgh Healthcare System University Drive Division, Pittsburgh, Pennsylvania, USA
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yandong Lai
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Zachary Lane
- Medicine, VA Pittsburgh Healthcare System University Drive Division, Pittsburgh, Pennsylvania, USA
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Hilary Strollo
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kazuya Tanimura
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John C Sembrat
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Chunbin Zou
- Medicine, VA Pittsburgh Healthcare System University Drive Division, Pittsburgh, Pennsylvania, USA
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Michael M Myerburg
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mauricio Rojas
- The Ohio State University Medical Center, Columbus, Ohio, USA
| | - Steven Shapiro
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yu Jiang
- Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Toru Nyunoya
- Medicine, VA Pittsburgh Healthcare System University Drive Division, Pittsburgh, Pennsylvania, USA
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Luo ZJ, Li H, Yang L, Kang B, Cai T. Exome sequencing revealed USP9X and COL2A1 mutations in a large family with multiple epiphyseal dysplasia. Bone 2022; 163:116508. [PMID: 35907616 DOI: 10.1016/j.bone.2022.116508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/24/2022] [Accepted: 07/25/2022] [Indexed: 11/02/2022]
Abstract
Diagnosis of rare skeletal diseases is based primarily on clinical phenotype and radiographic analysis. Genetic etiology of these heterogeneous diseases remains largely unknown. Here, we report the identification of two genomic mutations using exome sequencing from patients with multiple epiphyseal dysplasia (MED) of an unusual family in autosomal dominant and X-linked inheritance. A dominant mutation (c.2224G > A; p.Gly687Ser) in the known causal COL2A1 gene was identified in three patients with MED, deformed femoral heads and vertebral dysplasia. Furthermore, a hemizygous mutation (c.2830G > A; p.Ala944Thr) in the USP9X gene was identified in the fourth patient with short stature, MED, deformed femoral head, thoracic and lumbar platyspondyly, right ankle condyle dysplasia, and subchondral sclerosis. This is the first identification of an X-linked candidate causative gene in a patient with MED, suggesting a new clinical entity. Our findings shed a new light on the role of USP9X in MED-associated disorders.
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Affiliation(s)
- Zhuo-Jing Luo
- Institute of Orthopaedics, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Hongzhuo Li
- Department of Orthopedics, Heping Hospital Attached to Changzhi Medical College, Changzhi, China
| | - Liu Yang
- Institute of Orthopaedics, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | | | - Tao Cai
- Experimental Medicine Section, National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, USA.
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5
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Liang RP, Zhang XX, Zhao J, Lu QW, Zhu RT, Wang WJ, Li J, Bo K, Zhang CX, Sun YL. RING finger and WD repeat domain 3 regulates proliferation and metastasis through the Wnt/β-catenin signalling pathways in hepatocellular carcinoma. World J Gastroenterol 2022; 28:3435-3454. [PMID: 36158256 PMCID: PMC9346462 DOI: 10.3748/wjg.v28.i27.3435] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/16/2022] [Accepted: 06/03/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) exhibits high invasiveness and mortality rates, and the molecular mechanisms of HCC have gained increasing research interest. The abnormal DNA damage response has long been recognized as one of the important factors for tumor occurrence and development. Recent studies have shown the potential of the protein RING finger and WD repeat domain 3 (RFWD3) that positively regulates p53 stability in response to DNA damage as a therapeutic target in cancers.
AIM To investigate the relationship between HCC and RFWD3 in vitro and in vivo and explored the underlying molecular signalling transduction pathways.
METHODS RFWD3 gene expression was analyzed in HCC tissues and adjacent normal tissues. Lentivirus was used to stably knockdown RFWD3 expression in HCC cell lines. After verifying the silencing efficiency, Celigo/cell cycle/apoptosis and MTT assays were used to evaluate cell proliferation and apoptosis. Subsequently, cell migration and invasion were assessed by wound healing and transwell assays. In addition, transduced cells were implanted subcutaneously and injected into the tail vein of nude mice to observe tumor growth and metastasis. Next, we used lentiviral-mediated rescue of RFWD3 shRNA to verify the phenotype. Finally, the microarray, ingenuity pathway analysis, and western blot analysis were used to analyze the regulatory network underlying HCC.
RESULTS Compared with adjacent tissues, RFWD3 expression levels were significantly higher in clinical HCC tissues and correlated with tumor size and TNM stage (P < 0.05), which indicated a poor prognosis state. RFWD3 silencing in BEL-7404 and HCC-LM3 cells increased apoptosis, decreased growth, and inhibited the migration in shRNAi cells compared with those in shCtrl cells (P < 0.05). Furthermore, the in vitro results were supported by the findings of the in vivo experiments with the reduction of tumor cell invasion and migration. Moreover, the rescue of RFWD3 shRNAi resulted in the resumption of invasion and metastasis in HCC cell lines. Finally, gene expression profiling and subsequent experimental verification revealed that RFWD3 might influence the proliferation and metastasis of HCC via the Wnt/β-catenin signalling pathway.
CONCLUSION We provide evidence for the expression and function of RFWD3 in HCC. RFWD3 affects the prognosis, proliferation, invasion, and metastasis of HCC by regulating the Wnt/β-catenin signalling pathway.
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Affiliation(s)
- Ruo-Peng Liang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Xiao-Xue Zhang
- Department of Physical Examination, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Jie Zhao
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Qin-Wei Lu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Rong-Tao Zhu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Wei-Jie Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Jian Li
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Kai Bo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Chi-Xian Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Yu-Ling Sun
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
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6
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The emerging role of ubiquitin-specific protease 20 in tumorigenesis and cancer therapeutics. Cell Death Dis 2022; 13:434. [PMID: 35508480 PMCID: PMC9068925 DOI: 10.1038/s41419-022-04853-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 04/02/2022] [Accepted: 04/12/2022] [Indexed: 12/13/2022]
Abstract
As a critical member of the ubiquitin-specific proteolytic enzyme family, ubiquitin-specific peptidase 20 (USP20) regulates the stability of proteins via multiple signaling pathways. In addition, USP20 upregulation is associated with various cellular biological processes, such as cell cycle progression, proliferation, migration, and invasion. Emerging studies have revealed the pivotal role of USP20 in the tumorigenesis of various cancer types, such as breast cancer, colon cancer, lung cancer, gastric cancer and adult T cell leukemia. In our review, we highlight the different mechanisms of USP20 in various tumor types and demonstrate that USP20 regulates the stability of multiple proteins. Therefore, regulating the activity of USP20 is a novel tumor treatment. However, the clinical significance of USP20 in cancer treatment merits more evidence. Finally, different prospects exist for the continued research focus of USP20.
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7
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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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8
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Basar MA, Beck DB, Werner A. Deubiquitylases in developmental ubiquitin signaling and congenital diseases. Cell Death Differ 2021; 28:538-556. [PMID: 33335288 PMCID: PMC7862630 DOI: 10.1038/s41418-020-00697-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023] Open
Abstract
Metazoan development from a one-cell zygote to a fully formed organism requires complex cellular differentiation and communication pathways. To coordinate these processes, embryos frequently encode signaling information with the small protein modifier ubiquitin, which is typically attached to lysine residues within substrates. During ubiquitin signaling, a three-step enzymatic cascade modifies specific substrates with topologically unique ubiquitin modifications, which mediate changes in the substrate's stability, activity, localization, or interacting proteins. Ubiquitin signaling is critically regulated by deubiquitylases (DUBs), a class of ~100 human enzymes that oppose the conjugation of ubiquitin. DUBs control many essential cellular functions and various aspects of human physiology and development. Recent genetic studies have identified mutations in several DUBs that cause developmental disorders. Here we review principles controlling DUB activity and substrate recruitment that allow these enzymes to regulate ubiquitin signaling during development. We summarize key mechanisms of how DUBs control embryonic and postnatal differentiation processes, highlight developmental disorders that are caused by mutations in particular DUB members, and describe our current understanding of how these mutations disrupt development. Finally, we discuss how emerging tools from human disease genetics will enable the identification and study of novel congenital disease-causing DUBs.
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Affiliation(s)
- Mohammed A Basar
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David B Beck
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Achim Werner
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA.
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9
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Molecular Mechanisms of DUBs Regulation in Signaling and Disease. Int J Mol Sci 2021; 22:ijms22030986. [PMID: 33498168 PMCID: PMC7863924 DOI: 10.3390/ijms22030986] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 02/07/2023] Open
Abstract
The large family of deubiquitinating enzymes (DUBs) are involved in the regulation of a plethora of processes carried out inside the cell by protein ubiquitination. Ubiquitination is a basic pathway responsible for the correct protein homeostasis in the cell, which could regulate the fate of proteins through the ubiquitin–proteasome system (UPS). In this review we will focus on recent advances on the molecular mechanisms and specificities found for some types of DUBs enzymes, highlighting illustrative examples in which the regulatory mechanism for DUBs has been understood in depth at the molecular level by structural biology. DUB proteases are responsible for cleavage and regulation of the multiple types of ubiquitin linkages that can be synthesized inside the cell, known as the ubiquitin-code, which are tightly connected to specific substrate functions. We will display some strategies carried out by members of different DUB families to provide specificity on the cleavage of particular ubiquitin linkages. Finally, we will also discuss recent progress made for the development of drug compounds targeting DUB proteases, which are usually correlated to the progress of many pathologies such as cancer and neurodegenerative diseases.
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10
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USP24 stabilizes bromodomain containing proteins to promote lung cancer malignancy. Sci Rep 2020; 10:20870. [PMID: 33257797 PMCID: PMC7705756 DOI: 10.1038/s41598-020-78000-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/11/2020] [Indexed: 01/21/2023] Open
Abstract
Bromodomain (BRD)-containing proteins are important for chromatin remodeling to regulate gene expression. In this study, we found that the deubiquitinase USP24 interacted with BRD through its C-terminus increased the levels of most BRD-containing proteins through increasing their protein stability by the removal of ubiquitin from Lys391/Lys400 of the BRD. In addition, we found that USP24 and BRG1 could regulate each other through regulating the protein stability and the transcriptional activity, respectively, of the other, suggesting that the levels of USP24 and BRG1 are regulated to form a positive feedback loop in cancer progression. Loss of the interaction motif of USP24 eliminated the ability of USP24 to stabilize BRD-containing proteins and abolished the effect of USP24 on cancer progression, including its inhibition of cancer cell proliferation and promotion of cancer cell migration, suggesting that the interaction between USP24 and the BRD is important for USP24-mediated effects on cancer progression. The targeting of BRD-containing proteins has been developed as a strategy for cancer therapy. Based on our study, targeting USP24 to inhibit the levels of BRD-containing proteins may inhibit cancer progression.
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11
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Wang D, Ma H, Zhao Y, Zhao J. Ubiquitin-specific protease 14 is a new therapeutic target for the treatment of diseases. J Cell Physiol 2020; 236:3396-3405. [PMID: 33135160 DOI: 10.1002/jcp.30124] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/08/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022]
Abstract
Ubiquitin-specific protease 14 (USP14) is a ubiquitin-specific protease that is associated with the proteasome and plays important roles in cellular functions, viral infection, inflammatory responses, neurodegenerative diseases, and tumorigenesis. USP14 appears to have a dual function in regulating intracellular proteolytic degradation. USP14 impedes degradation of ubiquitinated proteins by removing ubiquitin chains from its substrates, while it could promote protein degradation via increasing proteasome activation. Increasing evidence has shown that USP14 is also involved in the regulation of autophagy. Thus, USP14 might act as a key regulator in two major intracellular proteolytic pathways: the ubiquitin-proteasome system (UPS) and autophagy. The important roles of USP14 in multiple diseases have encouraged the development of clinically viable USP14 antagonists. This review summarizes the current state of knowledge about the regulation of USP14 expression, activity, and its functions in physiological and pathological processes.
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Affiliation(s)
- Dan Wang
- Department of Anesthesia, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Haichun Ma
- Department of Anesthesia, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Yutong Zhao
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, Ohio, USA
| | - Jing Zhao
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, Ohio, USA
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12
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Wu R, Zheng W, Tan J, Sammer R, Du L, Lu C. Protein partners of plant ubiquitin-specific proteases (UBPs). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 145:227-236. [PMID: 31630936 DOI: 10.1016/j.plaphy.2019.08.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/16/2019] [Accepted: 08/31/2019] [Indexed: 06/10/2023]
Abstract
As one type of deubiquitinases (DUBs), ubiquitin-specific proteases (UBPs) play an extensive and significant role in plant life involving the regulation of plant development and stress responses. However, comprehensive studies are still needed to determine the functional mechanisms, which are largely unclear. Here, we summarized recent progress of plant UBPs' functional partners, particularly the molecular mechanisms by which UBPs work with their partners. We believe that functional analyses of UBPs and their partners will provide new insights into protein deubiquitination and lead to a better understanding of the physiological roles of UBPs in plants.
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Affiliation(s)
- Ruihua Wu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Wenqing Zheng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jinyi Tan
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Rana Sammer
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Liang Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China; College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
| | - Cunfu Lu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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13
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Wang D, Zhao J, Li S, Wei J, Nan L, Mallampalli RK, Weathington NM, Ma H, Zhao Y. Phosphorylated E2F1 is stabilized by nuclear USP11 to drive Peg10 gene expression and activate lung epithelial cells. J Mol Cell Biol 2019; 10:60-73. [PMID: 28992046 DOI: 10.1093/jmcb/mjx034] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 08/15/2017] [Indexed: 12/21/2022] Open
Abstract
Phosphorylation affects ubiquitination, stability, and activity of transcriptional factors, thus regulating various cellular functions. E2F transcriptional factor 1 (E2F1) regulates paternally expressed imprinted gene 10 (Peg10) expression, thereby promoting cell proliferation. However, the effect of E2F1 stability on Peg10 expression and the molecular regulation of E2F1 stability by its phosphorylation have not been well demonstrated. Here, we describe a new pathway in which phosphorylation of E2F1 by GSK3β increases E2F1 association with the deubiquitinating enzyme, ubiquitin-specific protease 11 (USP11), which removes K63-linked ubiquitin chains thereby preventing E2F1 degradation in the nuclei. Downregulation of USP11 increases E2F1 ubiquitination and reduces E2F1 stability and protein levels, thereby decreasing Peg10 mRNA levels. Physiologically, USP11 depletion suppresses cell proliferation and wound healing in lung epithelial cells, and these effects are reversed by E2F1 and PEG10 overexpression. Thus, our study reveals a new molecular model that phosphorylation promotes substrate stability through increasing its association with a deubiquitinating enzyme. The data suggest that GSK3β and USP11 act in concert to modulate E2F1 abundance and PEG10 expression in lung epithelial cells to affect cell wound healing. This study provides new therapeutic targets to lessen lung injury by improving lung epithelial cell repair and remodeling after injury.
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Affiliation(s)
- Dan Wang
- Department of Anesthesia, the First Affiliated Hospital of Jilin University, Changchun, China
| | - Jing Zhao
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Shuang Li
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, USA.,Department of General Surgery, the First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jianxin Wei
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Ling Nan
- Department of Anesthesia, the First Affiliated Hospital of Jilin University, Changchun, China
| | - Rama K Mallampalli
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, USA.,Acute Lung Injury Center of Excellence and Vascular Medical Institute, University of Pittsburgh, Pittsburgh, USA
| | - Nathaniel M Weathington
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, USA.,Acute Lung Injury Center of Excellence and Vascular Medical Institute, University of Pittsburgh, Pittsburgh, USA
| | - Haichun Ma
- Department of Anesthesia, the First Affiliated Hospital of Jilin University, Changchun, China
| | - Yutong Zhao
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, USA.,Acute Lung Injury Center of Excellence and Vascular Medical Institute, University of Pittsburgh, Pittsburgh, USA
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14
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Pickel C, Günter J, Ruiz-Serrano A, Spielmann P, Fabrizio JA, Wolski W, Peet DJ, Wenger RH, Scholz CC. Oxygen-dependent bond formation with FIH regulates the activity of the client protein OTUB1. Redox Biol 2019; 26:101265. [PMID: 31299612 PMCID: PMC6624438 DOI: 10.1016/j.redox.2019.101265] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/28/2019] [Accepted: 06/30/2019] [Indexed: 12/30/2022] Open
Abstract
Protein:protein interactions are the basis of molecular communication and are usually of transient non-covalent nature, while covalent interactions other than ubiquitination are rare. For cellular adaptations, the cellular oxygen and peroxide sensor factor inhibiting HIF (FIH) confers oxygen and oxidant stress sensitivity to the hypoxia inducible factor (HIF) by asparagine hydroxylation. We investigated whether FIH contributes to hypoxia adaptation also through other mechanisms and identified a hypoxia sensitive, likely covalent, bond formation by FIH with several client proteins, including the deubiquitinase ovarian tumor domain containing ubiquitin aldehyde binding protein 1 (OTUB1). Biochemical analyses were consistent with a co-translational amide bond formation between FIH and OTUB1, occurring within mammalian and bacterial cells but not between separately purified proteins. Bond formation is catalysed by FIH and highly dependent on oxygen availability in the cellular microenvironment. Within cells, a heterotrimeric complex is formed, consisting of two FIH and one covalently linked OTUB1. Complexation of OTUB1 by FIH regulates OTUB1 deubiquitinase activity. Our findings reveal an alternative mechanism for hypoxia adaptation with remarkably high oxygen sensitivity, mediated through covalent protein-protein interactions catalysed by an asparagine modifying dioxygenase. FIH forms a (likely amide) bond with client proteins. Bond formation is highly hypoxia sensitive and occurs co-translationally. FIH forms a heterotrimer with the client protein OTUB1 (FIH2OTUB11). Complex formation between OTUB1 and FIH regulates OTUB1 deubiquitinase activity. Bond formation by hydroxylases is an alternative mechanism for hypoxia adaptation.
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Affiliation(s)
- Christina Pickel
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland
| | - Julia Günter
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland; National Centre of Competence in Research 'Kidney.CH', Switzerland
| | | | - Patrick Spielmann
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland
| | | | - Witold Wolski
- Functional Genomics Center Zurich, University of Zurich, 8057, Zurich, Switzerland
| | - Daniel J Peet
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Roland H Wenger
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland; National Centre of Competence in Research 'Kidney.CH', Switzerland.
| | - Carsten C Scholz
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland; National Centre of Competence in Research 'Kidney.CH', Switzerland.
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15
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USP4 deficiency exacerbates hepatic ischaemia/reperfusion injury via TAK1 signalling. Clin Sci (Lond) 2019; 133:335-349. [PMID: 30622220 DOI: 10.1042/cs20180959] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 01/06/2019] [Accepted: 01/07/2019] [Indexed: 02/06/2023]
Abstract
Ubiquitin-specific peptidase 4 (USP4) protein is a type of deubiquitination enzyme that is correlated with many important biological processes. However, the function of USP4 in hepatic ischaemia/reperfusion (I/R) injury remains unknown. The aim of the present study was to explore the role of USP4 in hepatic I/R injury. USP4 gene knockout mice and primary hepatocytes were used to construct hepatic I/R models. The effect of USP4 on hepatic I/R injury was examined via pathological and molecular analyses. Our results indicated that USP4 was significantly up-regulated in liver of mice subjected to hepatic I/R injury. USP4 knockout mice exhibited exacerbated hepatic I/R injury, as evidenced by enhanced liver inflammation via the nuclear factor κB (NF-κB) signalling pathway and increased hepatocyte apoptosis. Additionally, USP4 overexpression inhibited hepatocyte inflammation and apoptosis on hepatic I/R stimulation. Mechanistically, our study demonstrates that USP4 deficiency exerts its detrimental effects on hepatic I/R injury by inducing activation of the transforming growth factor β-activated kinase 1 (TAK1)/JNK signalling pathways. TAK1 was required for USP4 function in hepatic I/R injury as TAK1 inhibition abolished USP4 function in vitro In conclusion, our study demonstrates that USP4 deficiency plays a detrimental role in hepatic I/R injury by promoting activation of the TAK1/JNK signalling pathways. Modulation of this axis may be a novel strategy to alleviate the pathological process of hepatic I/R injury.
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16
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Zhao Y, Mudge MC, Soll JM, Rodrigues RB, Byrum AK, Schwarzkopf EA, Bradstreet TR, Gygi SP, Edelson BT, Mosammaparast N. OTUD4 Is a Phospho-Activated K63 Deubiquitinase that Regulates MyD88-Dependent Signaling. Mol Cell 2019; 69:505-516.e5. [PMID: 29395066 DOI: 10.1016/j.molcel.2018.01.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 11/02/2017] [Accepted: 01/04/2018] [Indexed: 10/18/2022]
Abstract
Ubiquitination is a major mechanism that regulates numerous cellular processes, including autophagy, DNA damage signaling, and inflammation. While hundreds of ubiquitin ligases exist to conjugate ubiquitin onto substrates, approximately 100 deubiquitinases are encoded by the human genome. Thus, deubiquitinases are likely regulated by unidentified mechanisms to target distinct substrates and cellular functions. Here, we demonstrate that the deubiquitinase OTUD4, which nominally encodes a K48-specific deubiquitinase, is phosphorylated near its catalytic domain, activating a latent K63-specific deubiquitinase. Besides phosphorylation, this latter activity requires an adjacent ubiquitin-interacting motif, which increases the affinity of OTUD4 for K63-linked chains. We reveal the Toll-like receptor (TLR)-associated factor MyD88 as a target of this K63 deubiquitinase activity. Consequently, TLR-mediated activation of NF-κB is negatively regulated by OTUD4, and macrophages from Otud4-/- mice exhibit increased inflammatory signaling upon TLR stimulation. Our results reveal insights into how a deubiquitinase may modulate diverse processes through post-translational modification.
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Affiliation(s)
- Yu Zhao
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis MO, 63110, USA
| | - Miranda C Mudge
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis MO, 63110, USA
| | - Jennifer M Soll
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis MO, 63110, USA
| | | | - Andrea K Byrum
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis MO, 63110, USA
| | - Elizabeth A Schwarzkopf
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis MO, 63110, USA
| | - Tara R Bradstreet
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis MO, 63110, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston MA, 02115
| | - Brian T Edelson
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis MO, 63110, USA
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis MO, 63110, USA.
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17
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Gupta I, Varshney NK, Khan S. Emergence of Members of TRAF and DUB of Ubiquitin Proteasome System in the Regulation of Hypertrophic Cardiomyopathy. Front Genet 2018; 9:336. [PMID: 30186311 PMCID: PMC6110912 DOI: 10.3389/fgene.2018.00336] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/03/2018] [Indexed: 01/10/2023] Open
Abstract
The ubiquitin proteasome system (UPS) plays an imperative role in many critical cellular processes, frequently by mediating the selective degradation of misfolded and damaged proteins and also by playing a non-degradative role especially important as in many signaling pathways. Over the last three decades, accumulated evidence indicated that UPS proteins are primal modulators of cell cycle progression, DNA replication, and repair, transcription, immune responses, and apoptosis. Comparatively, latest studies have demonstrated a substantial complexity by the UPS regulation in the heart. In addition, various UPS proteins especially ubiquitin ligases and proteasome have been identified to play a significant role in the cardiac development and dynamic physiology of cardiac pathologies such as ischemia/reperfusion injury, hypertrophy, and heart failure. However, our understanding of the contribution of UPS dysfunction in the plausible development of cardiac pathophysiology and the complete list of UPS proteins regulating these afflictions is still in infancy. The recent emergence of the roles of TNF receptor-associated factor (TRAFs) and deubiquitinating enzymes (DUBs) superfamily in hypertrophic cardiomyopathy has enhanced our knowledge. In this review, we have mainly compiled the TRAF superfamily of E3 ligases and few DUBs proteins with other well-documented E3 ligases such as MDM2, MuRF-1, Atrogin-I, and TRIM 32 that are specific to myocardial hypertrophy. In this review, we also aim to highlight their expression profile following physiological and pathological stimulation leading to the onset of hypertrophic phenotype in the heart that can serve as biomarkers and the opportunity for the development of novel therapies.
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Affiliation(s)
- Ishita Gupta
- Structural Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.,Drug Discovery Research Center, Translational Health Science and Technology Institute, Faridabad, India
| | - Nishant K Varshney
- Drug Discovery Research Center, Translational Health Science and Technology Institute, Faridabad, India
| | - Sameena Khan
- Drug Discovery Research Center, Translational Health Science and Technology Institute, Faridabad, India
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18
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Zukowski A, Al-Afaleq NO, Duncan ED, Yao T, Johnson AM. Recruitment and allosteric stimulation of a histone-deubiquitinating enzyme during heterochromatin assembly. J Biol Chem 2017; 293:2498-2509. [PMID: 29288197 DOI: 10.1074/jbc.ra117.000498] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/22/2017] [Indexed: 02/02/2023] Open
Abstract
Heterochromatin formation in budding yeast is regulated by the silent information regulator (SIR) complex. The SIR complex comprises the NAD-dependent deacetylase Sir2, the scaffolding protein Sir4, and the nucleosome-binding protein Sir3. Transcriptionally active regions present a challenge to SIR complex-mediated de novo heterochromatic silencing due to the presence of antagonistic histone post-translational modifications, including acetylation and methylation. Methylation of histone H3K4 and H3K79 is dependent on monoubiquitination of histone H2B (H2B-Ub). The SIR complex cannot erase H2B-Ub or histone methylation on its own. The deubiquitinase (DUB) Ubp10 is thought to promote heterochromatic silencing by maintaining low H2B-Ub at sub-telomeres. Here, we biochemically characterized the interactions between Ubp10 and the SIR complex machinery. We demonstrate that a direct interaction between Ubp10 and the Sir2/4 sub-complex facilitates Ubp10 recruitment to chromatin via a co-assembly mechanism. Using hydrolyzable H2B-Ub analogs, we show that Ubp10 activity is lower on nucleosomes compared with H2B-Ub in solution. We find that Sir2/4 stimulates Ubp10 DUB activity on nucleosomes, likely through a combination of targeting and allosteric regulation. This coupling mechanism between the silencing machinery and its DUB partner allows erasure of active PTMs and the de novo transition of a transcriptionally active DNA region to a silent chromatin state.
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Affiliation(s)
- Alexis Zukowski
- From the Department of Biochemistry and Molecular Genetics and.,Molecular Biology Program, University of Colorado, Denver-Anschutz Medical Campus, Aurora, Colorado 80045 and
| | - Nouf Omar Al-Afaleq
- the Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
| | - Emily D Duncan
- From the Department of Biochemistry and Molecular Genetics and.,Molecular Biology Program, University of Colorado, Denver-Anschutz Medical Campus, Aurora, Colorado 80045 and
| | - Tingting Yao
- the Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
| | - Aaron M Johnson
- From the Department of Biochemistry and Molecular Genetics and .,Molecular Biology Program, University of Colorado, Denver-Anschutz Medical Campus, Aurora, Colorado 80045 and
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19
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Jupin I, Ayach M, Jomat L, Fieulaine S, Bressanelli S. A mobile loop near the active site acts as a switch between the dual activities of a viral protease/deubiquitinase. PLoS Pathog 2017; 13:e1006714. [PMID: 29117247 PMCID: PMC5695851 DOI: 10.1371/journal.ppat.1006714] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 11/20/2017] [Accepted: 10/25/2017] [Indexed: 12/21/2022] Open
Abstract
The positive-strand RNA virus Turnip yellow mosaic virus (TYMV) encodes an ovarian tumor (OTU)-like protease/deubiquitinase (PRO/DUB) protein domain involved both in proteolytic processing of the viral polyprotein through its PRO activity, and in removal of ubiquitin chains from ubiquitylated substrates through its DUB activity. Here, the crystal structures of TYMV PRO/DUB mutants and molecular dynamics simulations reveal that an idiosyncratic mobile loop participates in reversibly constricting its unusual catalytic site by adopting "open", "intermediate" or "closed" conformations. The two cis-prolines of the loop form a rigid flap that in the most closed conformation zips up against the other side of the catalytic cleft. The intermediate and closed conformations also correlate with a reordering of the TYMV PRO/DUB catalytic dyad, that then assumes a classical, yet still unusually mobile, OTU DUB alignment. Further structure-based mutants designed to interfere with the loop's mobility were assessed for enzymatic activity in vitro and in vivo, and were shown to display reduced DUB activity while retaining PRO activity. This indicates that control of the switching between the dual PRO/DUB activities resides prominently within this loop next to the active site. Introduction of mutations into the viral genome revealed that the DUB activity contributes to the extent of viral RNA accumulation both in single cells and in whole plants. In addition, the conformation of the mobile flap was also found to influence symptoms severity in planta. Such mutants now provide powerful tools with which to study the specific roles of reversible ubiquitylation in viral infection. Viruses have much smaller genomes than their hosts. Consequently, they often encode proteins which are multifunctional. For instance, some viral proteases have a dual function, being also deubiquitinases, i.e. enzymes capable of removing ubiquitin tags grafted onto proteins and that often target them for destruction. The protease and deubiquitinase activities share a single active site that is used alternately for one function or the other, but how this switch between activities may be regulated is presently unknown. To answer this question, we studied a simple plant virus that is a useful model system for these complex molecular biology phenomena, and that encodes a simplified protease/deubiquitinase. Here, thanks to a combination of structural and functional analyses, we managed to decouple the two activities, killing the deubiquitinase activity while preserving the protease one. This successful decoupling relies on our discovery that a loop inserted next to the active site is mobile, and can thus act as a switch between the two activities. This result allowed us to demonstrate the importance of the specific deubiquinase activity in viral multiplication. In addition, viral symptoms were also severely affected by mutations affecting the loop mobility. Our data provide powerful tools for further studies, that may also be relevant for more complex or medically relevant viruses.
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Affiliation(s)
- Isabelle Jupin
- Institut Jacques Monod, CNRS—Univ Paris-Diderot, Paris, France
- * E-mail: (IJ); (SB)
| | - Maya Ayach
- Institute for Integrative Biology of the Cell, CEA—CNRS—Univ Paris-Saclay, Gif sur Yvette, France
| | - Lucile Jomat
- Institut Jacques Monod, CNRS—Univ Paris-Diderot, Paris, France
| | - Sonia Fieulaine
- Institute for Integrative Biology of the Cell, CEA—CNRS—Univ Paris-Saclay, Gif sur Yvette, France
| | - Stéphane Bressanelli
- Institute for Integrative Biology of the Cell, CEA—CNRS—Univ Paris-Saclay, Gif sur Yvette, France
- * E-mail: (IJ); (SB)
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20
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Korovila I, Hugo M, Castro JP, Weber D, Höhn A, Grune T, Jung T. Proteostasis, oxidative stress and aging. Redox Biol 2017; 13:550-567. [PMID: 28763764 PMCID: PMC5536880 DOI: 10.1016/j.redox.2017.07.008] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 07/04/2017] [Accepted: 07/09/2017] [Indexed: 12/21/2022] Open
Abstract
The production of reactive species is an inevitable by-product of metabolism and thus, life itself. Since reactive species are able to damage cellular structures, especially proteins, as the most abundant macromolecule of mammalian cells, systems are necessary which regulate and preserve a functional cellular protein pool, in a process termed “proteostasis”. Not only the mammalian protein pool is subject of a constant turnover, organelles are also degraded and rebuild. The most important systems for these removal processes are the “ubiquitin-proteasomal system” (UPS), the central proteolytic machinery of mammalian cells, mainly responsible for proteostasis, as well as the “autophagy-lysosomal system”, which mediates the turnover of organelles and large aggregates. Many age-related pathologies and the aging process itself are accompanied by a dysregulation of UPS, autophagy and the cross-talk between both systems. This review will describe the sources and effects of oxidative stress, preservation of cellular protein- and organelle-homeostasis and the effects of aging on proteostasis in mammalian cells.
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Affiliation(s)
- Ioanna Korovila
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany
| | - Martín Hugo
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany
| | - José Pedro Castro
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany; German Center for Diabetes Research (DZD), 85764 Muenchen-Neuherberg, Germany; Faculty of Medicine, Department of Biomedicine, University of Porto, 4200-319, Portugal; Institute for Innovation and Health Research (I3S), Aging and Stress Group, R. Alfredo Allen, 4200-135 Porto, Portugal
| | - Daniela Weber
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany; NutriAct - Competence Cluster Nutrition Research Berlin-Potsdam, 14558 Nuthetal, Germany
| | - Annika Höhn
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany; German Center for Diabetes Research (DZD), 85764 Muenchen-Neuherberg, Germany
| | - Tilman Grune
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany; German Center for Diabetes Research (DZD), 85764 Muenchen-Neuherberg, Germany; German Center for Cardiovascular Research (DZHK), 10117 Berlin, Germany; NutriAct - Competence Cluster Nutrition Research Berlin-Potsdam, 14558 Nuthetal, Germany
| | - Tobias Jung
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany; German Center for Cardiovascular Research (DZHK), 10117 Berlin, Germany.
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21
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Abstract
For over a century, the abnormal movement or number of centrosomes has been linked with errors of chromosomes distribution in mitosis. While not essential for the formation of the mitotic spindle, the presence and location of centrosomes has a major influence on the manner in which microtubules interact with the kinetochores of replicated sister chromatids and the accuracy with which they migrate to resulting daughter cells. A complex network has evolved to ensure that cells contain the proper number of centrosomes and that their location is optimal for effective attachment of emanating spindle fibers with the kinetochores. The components of this network are regulated through a series of post-translational modifications, including ubiquitin and ubiquitin-like modifiers, which coordinate the timing and strength of signaling events key to the centrosome cycle. In this review, we examine the role of the ubiquitin system in the events relating to centriole duplication and centrosome separation, and discuss how the disruption of these functions impacts chromosome segregation.
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22
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The ubiquitin-like modifier FAT10 in cancer development. Int J Biochem Cell Biol 2016; 79:451-461. [PMID: 27393295 DOI: 10.1016/j.biocel.2016.07.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 06/30/2016] [Accepted: 07/01/2016] [Indexed: 12/13/2022]
Abstract
During the last years it has emerged that the ubiquitin-like modifier FAT10 is directly involved in cancer development. FAT10 expression is highly up-regulated by pro-inflammatory cytokines IFN-γ and TNF-α in all cell types and tissues and it was also found to be up-regulated in many cancer types such as glioma, colorectal, liver or gastric cancer. While pro-inflammatory cytokines within the tumor microenvironment probably contribute to FAT10 overexpression, an increasing body of evidence argues that pro-malignant capacities of FAT10 itself largely underlie its broad and intense overexpression in tumor tissues. FAT10 thereby regulates pathways involved in cancer development such as the NF-κB- or Wnt-signaling. Moreover, FAT10 directly interacts with and influences downstream targets such as MAD2, p53 or β-catenin, leading to enhanced survival, proliferation, invasion and metastasis formation of cancer cells but also of non-malignant cells. In this review we will provide an overview of the regulation of FAT10 expression as well as its function in carcinogenesis.
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23
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Abstract
Conjugation and deconjugation of ubiquitin and ubiquitin-like proteins (Ubls) to cellular proteins are highly regulated processes integral to cellular homeostasis. Most often, the C-termini of these small polypeptides are attached to lysine side chains of target proteins by an amide (isopeptide) linkage. Deubiquitinating enzymes (DUBs) and Ubl-specific proteases (ULPs) comprise a diverse group of proteases that recognize and remove ubiquitin and Ubls from their substrates. How DUBs and ULPs distinguish among different modifiers, or different polymeric forms of these modifiers, remains poorly understood. The specificity of ubiquitin/Ubl-deconjugating enzymes for particular substrates depends on multiple factors, ranging from the topography of specific substrate features, as in different polyubiquitin chain types, to structural elements unique to each enzyme. Here we summarize recent structural and biochemical studies that provide insights into mechanisms of substrate specificity among various DUBs and ULPs. We also discuss the unexpected specificities of non-eukaryotic proteases in these families.
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Affiliation(s)
- Judith A Ronau
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - John F Beckmann
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
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24
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Abstract
A majority of proteins in the cell can be modified by ubiquitination, thereby altering their function or stability. This ubiquitination is controlled by both ubiquitinating and deubiquitinating enzymes (DUBs). The number of ubiquitin ligases exceeds that of DUBs by about eightfold, indicating that DUBs may have much broader substrate specificity. Despite this, DUBs have been shown to have quite specific physiological functions. This functional specificity is likely due to very precise regulation of activity arising from the sophisticated use of all mechanisms of enzyme regulation. In this commentary, we briefly review key features of DUBs with more emphasis on regulation. In particular, we focus on localization of the enzymes as a critical regulatory mechanism which when integrated with control of expression, substrate activation, allosteric regulation, and post-translational modifications results in precise spatial and temporal deubiquitination of proteins and therefore specific physiological functions. Identification of compounds that target the structural elements in DUBs that dictate localization may be a more promising approach to development of drugs with specificity of action than targeting the enzymatic activity, which for most DUBs is dependent on a thiol group that can react non-specifically with many compounds in large-scale screening.
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Affiliation(s)
- Erin S Coyne
- Polypeptide Laboratory, Departments of Medicine and Biochemistry, McGill University, McGill University Health Centre Research Institute, Montreal, QC, Canada
| | - Simon S Wing
- Polypeptide Laboratory, Departments of Medicine and Biochemistry, McGill University, McGill University Health Centre Research Institute, Montreal, QC, Canada
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25
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Nguyen LK. Dynamics of ubiquitin-mediated signalling: insights from mathematical modelling and experimental studies. Brief Bioinform 2015. [DOI: 10.1093/bib/bbv052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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26
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Yan M, Wolberger C. Uncovering the role of Sgf73 in maintaining SAGA deubiquitinating module structure and activity. J Mol Biol 2014; 427:1765-78. [PMID: 25526805 DOI: 10.1016/j.jmb.2014.12.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 10/24/2022]
Abstract
The SAGA (Spt-Ada-Gcn5 acetyltransferase) complex performs multiple functions in transcription activation including deubiquitinating histone H2B, which is mediated by a subcomplex called the deubiquitinating module (DUBm). The yeast DUBm comprises a catalytic subunit, Ubp8, and three additional subunits, Sgf11, Sus1 and Sgf73, all of which are required for DUBm activity. A portion of the non-globular Sgf73 subunit lies between the Ubp8 catalytic domain and the ZnF-UBP domain and has been proposed to contribute to deubiquitinating activity by maintaining the catalytic domain in an active conformation. We report structural and solution studies of the DUBm containing two different Sgf73 point mutations that disrupt deubiquitinating activity. We find that the Sgf73 mutations abrogate deubiquitinating activity by impacting the Ubp8 ubiquitin-binding fingers region and they have an unexpected effect on the overall folding and stability of the DUBm complex. Taken together, our data suggest a role for Sgf73 in maintaining both the organization and the ubiquitin-binding conformation of Ubp8, thereby contributing to overall DUBm activity.
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Affiliation(s)
- Ming Yan
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA.
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