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Chen R, Zhang H, Li L, Li J, Xie J, Weng J, Tan H, Liu Y, Guo T, Wang M. Roles of ubiquitin-specific proteases in inflammatory diseases. Front Immunol 2024; 15:1258740. [PMID: 38322269 PMCID: PMC10844489 DOI: 10.3389/fimmu.2024.1258740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 01/02/2024] [Indexed: 02/08/2024] Open
Abstract
Ubiquitin-specific proteases (USPs), as one of the deubiquitinating enzymes (DUBs) families, regulate the fate of proteins and signaling pathway transduction by removing ubiquitin chains from the target proteins. USPs are essential for the modulation of a variety of physiological processes, such as DNA repair, cell metabolism and differentiation, epigenetic modulations as well as protein stability. Recently, extensive research has demonstrated that USPs exert a significant impact on innate and adaptive immune reactions, metabolic syndromes, inflammatory disorders, and infection via post-translational modification processes. This review summarizes the important roles of the USPs in the onset and progression of inflammatory diseases, including periodontitis, pneumonia, atherosclerosis, inflammatory bowel disease, sepsis, hepatitis, diabetes, and obesity. Moreover, we highlight a comprehensive overview of the pathogenesis of USPs in these inflammatory diseases as well as post-translational modifications in the inflammatory responses and pave the way for future prospect of targeted therapies in these inflammatory diseases.
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Affiliation(s)
- Rui Chen
- Center of Obesity and Metabolic Diseases, Department of General Surgery, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- Department of Stomatology, The Third People's Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, Chengdu, Sichuan, China
- College of Medicine, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Hui Zhang
- College of Medicine, Southwest Jiaotong University, Chengdu, Sichuan, China
- College of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Linke Li
- Center of Obesity and Metabolic Diseases, Department of General Surgery, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- Department of Stomatology, The Third People's Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Jinsheng Li
- College of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Jiang Xie
- Department of Pediatrics, Chengdu Third People's Hospital, Chengdu, Sichuan, China
| | - Jie Weng
- College of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Huan Tan
- Center of Obesity and Metabolic Diseases, Department of General Surgery, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- College of Medicine, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Yanjun Liu
- Center of Obesity and Metabolic Diseases, Department of General Surgery, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- College of Medicine, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Tailin Guo
- Center of Obesity and Metabolic Diseases, Department of General Surgery, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- College of Medicine, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Mengyuan Wang
- Center of Obesity and Metabolic Diseases, Department of General Surgery, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- Department of Stomatology, The Third People's Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, Chengdu, Sichuan, China
- College of Medicine, Southwest Jiaotong University, Chengdu, Sichuan, China
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Lethier M, Huard K, Hons M, Favier A, Brutscher B, Boeri Erba E, Abbott DW, Cusack S, Pellegrini E. Structure shows that the BIR2 domain of E3 ligase XIAP binds across the RIPK2 kinase dimer interface. Life Sci Alliance 2023; 6:e202201784. [PMID: 37673444 PMCID: PMC10485824 DOI: 10.26508/lsa.202201784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 08/09/2023] [Accepted: 08/09/2023] [Indexed: 09/08/2023] Open
Abstract
RIPK2 is an essential adaptor for NOD signalling and its kinase domain is a drug target for NOD-related diseases, such as inflammatory bowel disease. However, recent work indicates that the phosphorylation activity of RIPK2 is dispensable for signalling and that inhibitors of both RIPK2 activity and RIPK2 ubiquitination prevent the essential interaction between RIPK2 and the BIR2 domain of XIAP, the key RIPK2 ubiquitin E3 ligase. Moreover, XIAP BIR2 antagonists also block this interaction. To reveal the molecular mechanisms involved, we combined native mass spectrometry, NMR, and cryo-electron microscopy to determine the structure of the RIPK2 kinase BIR2 domain complex and validated the interface with in cellulo assays. The structure shows that BIR2 binds across the RIPK2 kinase antiparallel dimer and provides an explanation for both inhibitory mechanisms. It also highlights why phosphorylation of the kinase activation loop is dispensable for signalling while revealing the structural role of RIPK2-K209 residue in the RIPK2-XIAP BIR2 interaction. Our results clarify the features of the RIPK2 conformation essential for its role as a scaffold protein for ubiquitination.
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Affiliation(s)
- Mathilde Lethier
- https://ror.org/01zjc6908 European Molecular Biology Laboratory, Grenoble, France
| | - Karine Huard
- https://ror.org/01zjc6908 European Molecular Biology Laboratory, Grenoble, France
| | - Michael Hons
- https://ror.org/01zjc6908 European Molecular Biology Laboratory, Grenoble, France
| | - Adrien Favier
- University Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Bernhard Brutscher
- University Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Elisabetta Boeri Erba
- University Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Derek W Abbott
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Stephen Cusack
- https://ror.org/01zjc6908 European Molecular Biology Laboratory, Grenoble, France
| | - Erika Pellegrini
- https://ror.org/01zjc6908 European Molecular Biology Laboratory, Grenoble, France
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Gupta R, Kumari S, Tripathi R, Ambasta RK, Kumar P. Unwinding the modalities of necrosome activation and necroptosis machinery in neurological diseases. Ageing Res Rev 2023; 86:101855. [PMID: 36681250 DOI: 10.1016/j.arr.2023.101855] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/09/2022] [Accepted: 01/15/2023] [Indexed: 01/20/2023]
Abstract
Necroptosis, a regulated form of cell death, is involved in the genesis and development of various life-threatening diseases, including cancer, neurological disorders, cardiac myopathy, and diabetes. Necroptosis initiates with the formation and activation of a necrosome complex, which consists of RIPK1, RIPK2, RIPK3, and MLKL. Emerging studies has demonstrated the regulation of the necroptosis cell death pathway through the implication of numerous post-translational modifications, namely ubiquitination, acetylation, methylation, SUMOylation, hydroxylation, and others. In addition, the negative regulation of the necroptosis pathway has been shown to interfere with brain homeostasis through the regulation of axonal degeneration, mitochondrial dynamics, lysosomal defects, and inflammatory response. Necroptosis is controlled by the activity and expression of signaling molecules, namely VEGF/VEGFR, PI3K/Akt/GSK-3β, c-Jun N-terminal kinases (JNK), ERK/MAPK, and Wnt/β-catenin. Herein, we briefly discussed the implication and potential of necrosome activation in the pathogenesis and progression of neurological manifestations, such as Alzheimer's disease, Parkinson's disease, multiple sclerosis, traumatic brain injury, and others. Further, we present a detailed picture of natural compounds, micro-RNAs, and chemical compounds as therapeutic agents for treating neurological manifestations.
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Affiliation(s)
- Rohan Gupta
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), India
| | - Smita Kumari
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), India
| | - Rahul Tripathi
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), India
| | - Rashmi K Ambasta
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), India.
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Bhat SA, Vasi Z, Adhikari R, Gudur A, Ali A, Jiang L, Ferguson R, Liang D, Kuchay S. Ubiquitin proteasome system in immune regulation and therapeutics. Curr Opin Pharmacol 2022; 67:102310. [PMID: 36288660 PMCID: PMC10163937 DOI: 10.1016/j.coph.2022.102310] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/03/2022] [Accepted: 09/20/2022] [Indexed: 01/25/2023]
Abstract
The ubiquitin proteasome system (UPS) is a proteolytic machinery for the degradation of protein substrates that are post-translationally conjugated with ubiquitin polymers through the enzymatic action of ubiquitin ligases, in a process termed ubiquitylation. Ubiquitylation of substrates precedes their proteolysis via proteasomes, a hierarchical feature of UPS. E3-ubiquitin ligases recruit protein substrates providing specificity for ubiquitylation. Innate and adaptive immune system networks are regulated by ubiquitylation and substrate degradation via E3-ligases/UPS. Deregulation of E3-ligases/UPS components in immune cells is involved in the development of lymphomas, neurodevelopmental abnormalities, and cancers. Targeting E3-ligases for therapeutic intervention provides opportunities to mitigate the unintended broad effects of 26S proteasome inhibition. Recently, bifunctional moieties such as PROTACs and molecular glues have been developed to re-purpose E3-ligases for targeted degradation of unwanted aberrant proteins, with a potential for clinical use. Here, we summarize the involvement of E3-ligases/UPS components in immune-related diseases with perspectives.
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Affiliation(s)
- Sameer Ahmed Bhat
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago (UIC), Chicago, IL, 60607, USA
| | - Zahra Vasi
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago (UIC), Chicago, IL, 60607, USA
| | - Ritika Adhikari
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago (UIC), Chicago, IL, 60607, USA
| | - Anish Gudur
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago (UIC), Chicago, IL, 60607, USA
| | - Asceal Ali
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago (UIC), Chicago, IL, 60607, USA
| | - Liping Jiang
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago (UIC), Chicago, IL, 60607, USA
| | - Rachel Ferguson
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago (UIC), Chicago, IL, 60607, USA
| | - David Liang
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago (UIC), Chicago, IL, 60607, USA
| | - Shafi Kuchay
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago (UIC), Chicago, IL, 60607, USA.
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Zhang H, Situ C, Guo X. Recent progress of proteomic analysis on spermatogenesis. Biol Reprod 2022; 107:109-117. [DOI: 10.1093/biolre/ioac065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Testis, the only organ responsible for generating sperm, is by far the organ with the largest variety of proteins and tissue-specific proteins in humans. In testis, spermatogenesis is a multi-step complex process well-accepted that protein and mRNA are decoupled in certain stages of spermatogenesis. With the fast development of mass spectrometry-based proteomics, it is possible to systemically study protein abundances and modifications in testis and sperm to help us understand the molecular mechanisms of spermatogenesis. This review provides an overview of the recent progress of proteomics analysis on spermatogenesis, including protein expression and multiple PTMs, such as phosphorylation, glycosylation, ubiquitylation, and acetylation.
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Affiliation(s)
- Haotian Zhang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Chenghao Situ
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
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