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Zhao Y, Lin M, Zhai F, Chen J, Jin X. Exploring the Role of Ubiquitin-Proteasome System in the Pathogenesis of Parkinson's Disease. Pharmaceuticals (Basel) 2024; 17:782. [PMID: 38931449 PMCID: PMC11207014 DOI: 10.3390/ph17060782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/23/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
Parkinson's disease (PD) is a prevalent neurodegenerative disorder among the elderly population. The pathogenesis of PD encompasses genetic alterations, environmental factors, and age-related neurodegenerative processes. Numerous studies have demonstrated that aberrant functioning of the ubiquitin-proteasome system (UPS) plays a crucial role in the initiation and progression of PD. Notably, E3 ubiquitin ligases serve as pivotal components determining substrate specificity within UPS and are intimately associated with the regulation of various proteins implicated in PD pathology. This review comprehensively summarizes the mechanisms by which E3 ubiquitin ligases and deubiquitinating enzymes modulate PD-associated proteins and signaling pathways, while exploring the intricate relationship between UPS dysfunctions and PD etiology. Furthermore, this article discusses recent research advancements regarding inhibitors targeting PD-related E3 ubiquitin ligases.
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Affiliation(s)
- Yiting Zhao
- Department of Chemoradiotherapy, The Affiliated People’s Hospital of Ningbo University, Ningbo 315040, China; (Y.Z.); (M.L.)
- Department of Ultrasound Medicine, The Affiliated People’s Hospital of Ningbo University, Ningbo 315040, China
- Zhejiang Key Laboratory of Pathophysiology, Department of Biochemistry and Molecular Biology, Health Science Center of Ningbo University, Ningbo 315211, China;
| | - Man Lin
- Department of Chemoradiotherapy, The Affiliated People’s Hospital of Ningbo University, Ningbo 315040, China; (Y.Z.); (M.L.)
- Zhejiang Key Laboratory of Pathophysiology, Department of Biochemistry and Molecular Biology, Health Science Center of Ningbo University, Ningbo 315211, China;
| | - Fengguang Zhai
- Zhejiang Key Laboratory of Pathophysiology, Department of Biochemistry and Molecular Biology, Health Science Center of Ningbo University, Ningbo 315211, China;
| | - Jun Chen
- Department of Chemoradiotherapy, The Affiliated People’s Hospital of Ningbo University, Ningbo 315040, China; (Y.Z.); (M.L.)
- Zhejiang Key Laboratory of Pathophysiology, Department of Biochemistry and Molecular Biology, Health Science Center of Ningbo University, Ningbo 315211, China;
| | - Xiaofeng Jin
- Department of Chemoradiotherapy, The Affiliated People’s Hospital of Ningbo University, Ningbo 315040, China; (Y.Z.); (M.L.)
- Zhejiang Key Laboratory of Pathophysiology, Department of Biochemistry and Molecular Biology, Health Science Center of Ningbo University, Ningbo 315211, China;
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Majumder S, Srivastava M, Alam P, Saha S, Kumari R, Chand AK, Asthana S, Sen S, Maiti TK. Hotspot site microenvironment in the deubiquitinase OTUB1 drives its stability and aggregation. J Biol Chem 2024; 300:107315. [PMID: 38663827 PMCID: PMC11154711 DOI: 10.1016/j.jbc.2024.107315] [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: 01/27/2024] [Revised: 03/30/2024] [Accepted: 04/15/2024] [Indexed: 05/30/2024] Open
Abstract
Lewy bodies (LB) are aberrant protein accumulations observed in the brain cells of individuals affected by Parkinson's disease (PD). A comprehensive analysis of LB proteome identified over a hundred proteins, many co-enriched with α-synuclein, a major constituent of LB. Within this context, OTUB1, a deubiquitinase detected in LB, exhibits amyloidogenic properties, yet the mechanisms underlying its aggregation remain elusive. In this study, we identify two critical sites in OTUB1-namely, positions 133 and 173-that significantly impact its amyloid aggregation. Substituting alanine at position 133 and lysine at position 173 enhances both thermodynamic and kinetic stability, effectively preventing amyloid aggregation. Remarkably, lysine at position 173 demonstrates the highest stability without compromising enzymatic activity. The increased stability and inhibition of amyloid aggregation are attributed mainly to the changes in the specific microenvironment at the hotspot. In our exploration of the in-vivo co-occurrence of α-synuclein and OTUB1 in LB, we observed a synergistic modulation of each other's aggregation. Collectively, our study unveils the molecular determinants influencing OTUB1 aggregation, shedding light on the role of specific residues in modulating aggregation kinetics and structural transition. These findings contribute valuable insights into the complex interplay of amino acid properties and protein aggregation, with potential implications for understanding broader aspects of protein folding and aggregation phenomena.
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Affiliation(s)
- Sushanta Majumder
- Functional Proteomics Laboratory, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Mitul Srivastava
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Parvez Alam
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sandhini Saha
- Functional Proteomics Laboratory, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Raniki Kumari
- Functional Proteomics Laboratory, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Ajay Kumar Chand
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Shailendra Asthana
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Sobhan Sen
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Tushar Kanti Maiti
- Functional Proteomics Laboratory, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India.
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Kinger S, Jagtap YA, Kumar P, Choudhary A, Prasad A, Prajapati VK, Kumar A, Mehta G, Mishra A. Proteostasis in neurodegenerative diseases. Adv Clin Chem 2024; 121:270-333. [PMID: 38797543 DOI: 10.1016/bs.acc.2024.04.002] [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: 05/29/2024]
Abstract
Proteostasis is essential for normal function of proteins and vital for cellular health and survival. Proteostasis encompasses all stages in the "life" of a protein, that is, from translation to functional performance and, ultimately, to degradation. Proteins need native conformations for function and in the presence of multiple types of stress, their misfolding and aggregation can occur. A coordinated network of proteins is at the core of proteostasis in cells. Among these, chaperones are required for maintaining the integrity of protein conformations by preventing misfolding and aggregation and guide those with abnormal conformation to degradation. The ubiquitin-proteasome system (UPS) and autophagy are major cellular pathways for degrading proteins. Although failure or decreased functioning of components of this network can lead to proteotoxicity and disease, like neuron degenerative diseases, underlying factors are not completely understood. Accumulating misfolded and aggregated proteins are considered major pathomechanisms of neurodegeneration. In this chapter, we have described the components of three major branches required for proteostasis-chaperones, UPS and autophagy, the mechanistic basis of their function, and their potential for protection against various neurodegenerative conditions, like Alzheimer's, Parkinson's, and Huntington's disease. The modulation of various proteostasis network proteins, like chaperones, E3 ubiquitin ligases, proteasome, and autophagy-associated proteins as therapeutic targets by small molecules as well as new and unconventional approaches, shows promise.
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Affiliation(s)
- Sumit Kinger
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, India
| | - Yuvraj Anandrao Jagtap
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, India
| | - Prashant Kumar
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, India
| | - Akash Choudhary
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, India
| | - Amit Prasad
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, University of Delhi South Campus, Dhaula Kuan, New Delhi, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, Madhya Pradesh, India
| | - Gunjan Mehta
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, India.
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do Nascimento Amorim MDS, Silva França ÁR, Santos-Oliveira R, Rodrigues Sanches J, Marinho Melo T, Araújo Serra Pinto B, Barbosa LRS, Alencar LMR. Atomic Force Microscopy Applied to the Study of Tauopathies. ACS Chem Neurosci 2024; 15:699-715. [PMID: 38305187 DOI: 10.1021/acschemneuro.3c00819] [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: 02/03/2024] Open
Abstract
Atomic force microscopy (AFM) is a scanning probe microscopy technique which has a physical principle, the measurement of interatomic forces between a very thin tip and the surface of a sample, allowing the obtaining of quantitative data at the nanoscale, contributing to the surface study and mechanical characterization. Due to its great versatility, AFM has been used to investigate the structural and nanomechanical properties of several inorganic and biological materials, including neurons affected by tauopathies. Tauopathies are neurodegenerative diseases featured by aggregation of phosphorylated tau protein inside neurons, leading to functional loss and progressive neurotoxicity. In the broad universe of neurodegenerative diseases, tauopathies comprise the most prevalent, with Alzheimer's disease as its main representative. This review highlights the use of AFM as a suitable research technique for the study of cellular damages in tauopathies, even in early stages, allowing elucidation of pathogenic mechanisms of these diseases.
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Affiliation(s)
- Maria do Socorro do Nascimento Amorim
- Laboratory of Biophysics and Nanosystems, Department of Physics, Federal University of Maranhão, Campus Bacanga, São Luís 65080-805, Maranhão, Brazil
| | - Álefe Roger Silva França
- Laboratory of Biophysics and Nanosystems, Department of Physics, Federal University of Maranhão, Campus Bacanga, São Luís 65080-805, Maranhão, Brazil
| | - Ralph Santos-Oliveira
- Nuclear Engineering Institute, Brazilian Nuclear Energy Commission, Rio de Janeiro 21941906, Brazil
- Laboratory of Nanoradiopharmacy, Rio de Janeiro State University, Rio de Janeiro 23070200, Brazil
| | - Jonas Rodrigues Sanches
- Laboratory of Experimental Physiology, Department of Physiological Sciences, Federal University of Maranhão, Campus Bacanga, São Luís, 65080-805, Maranhão, Brazil
| | - Thamys Marinho Melo
- Laboratory of Experimental Physiology, Department of Physiological Sciences, Federal University of Maranhão, Campus Bacanga, São Luís, 65080-805, Maranhão, Brazil
| | - Bruno Araújo Serra Pinto
- Laboratory of Experimental Physiology, Department of Physiological Sciences, Federal University of Maranhão, Campus Bacanga, São Luís, 65080-805, Maranhão, Brazil
| | - Leandro R S Barbosa
- Department of General Physics, Institute of Physics, University of São Paulo, São Paulo 05508-000, SP, Brazil
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-100, SP, Brazil
| | - Luciana Magalhães Rebelo Alencar
- Laboratory of Biophysics and Nanosystems, Department of Physics, Federal University of Maranhão, Campus Bacanga, São Luís 65080-805, Maranhão, Brazil
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Liang Y, Zhong G, Ren M, Sun T, Li Y, Ye M, Ma C, Guo Y, Liu C. The Role of Ubiquitin-Proteasome System and Mitophagy in the Pathogenesis of Parkinson's Disease. Neuromolecular Med 2023; 25:471-488. [PMID: 37698835 DOI: 10.1007/s12017-023-08755-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 08/24/2023] [Indexed: 09/13/2023]
Abstract
Parkinson's disease (PD) is a common neurodegenerative disease that is mainly in middle-aged people and elderly people, and the pathogenesis of PD is complex and diverse. The ubiquitin-proteasome system (UPS) is a master regulator of neural development and the maintenance of brain structure and function. Dysfunction of components and substrates of this UPS has been linked to neurodegenerative diseases such as Parkinson's disease and Alzheimer's disease. Moreover, UPS can regulate α-synuclein misfolding and aggregation, mitophagy, neuroinflammation and oxidative stress to affect the development of PD. In the present study, we review the role of several related E3 ubiquitin ligases and deubiquitinating enzymes (DUBs) on the pathogenesis of PD such as Parkin, CHIP, USP8, etc. On this basis, we summarize the connections and differences of different E3 ubiquitin ligases in the pathogenesis, and elaborate on the regulatory progress of different DUBs on the pathogenesis of PD. Therefore, we can better understand their relationships and provide feasible and valuable therapeutic clues for UPS-related PD treatment research.
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Affiliation(s)
- Yu Liang
- School of Clinical Medicine, Bengbu Medical College, Bengbu, 233000, China
| | - Guangshang Zhong
- School of Life Sciences, Bengbu Medical College, Bengbu, 233000, China
| | - Mingxin Ren
- School of Clinical Medicine, Bengbu Medical College, Bengbu, 233000, China
| | - Tingting Sun
- School of Life Sciences, Bengbu Medical College, Bengbu, 233000, China
| | - Yangyang Li
- School of Life Sciences, Bengbu Medical College, Bengbu, 233000, China
| | - Ming Ye
- Department of Neurology, The First Affiliated Hospital of Bengbu Medical College, Bengbu Medical College, Bengbu, 233000, China
| | - Caiyun Ma
- School of Life Sciences, Bengbu Medical College, Bengbu, 233000, China
| | - Yu Guo
- School of Life Sciences, Bengbu Medical College, Bengbu, 233000, China.
| | - Changqing Liu
- School of Clinical Medicine, Bengbu Medical College, Bengbu, 233000, China.
- School of Life Sciences, Bengbu Medical College, Bengbu, 233000, China.
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Wu S, Lin T, Xu Y. Polymorphic USP8 allele promotes Parkinson's disease by inducing the accumulation of α-synuclein through deubiquitination. Cell Mol Life Sci 2023; 80:363. [PMID: 37981592 PMCID: PMC11072815 DOI: 10.1007/s00018-023-05006-0] [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: 07/07/2023] [Revised: 10/14/2023] [Accepted: 10/16/2023] [Indexed: 11/21/2023]
Abstract
Parkinson's disease (PD) is one of the most common neuro-degenerative diseases characterized by α-synuclein accumulation and degeneration of dopaminergic neurons. Employing genome-wide sequencing, we identified a polymorphic USP8 allele (USP8D442G) significantly enriched in Chinese PD patients. To test the involvement of this polymorphism in PD pathogenesis, we derived dopaminergic neurons (DAn) from human-induced pluripotent stem cells (hiPSCs) reprogrammed from fibroblasts of PD patients harboring USP8D442G allele and their healthy siblings. In addition, we knock-in D442G polymorphic site into the endogenous USP8 gene of human embryonic stem cells (hESCs) and derived DAn from these knock-in hESCs to explore their cellular phenotypes and molecular mechanism. We found that expression of USP8D442G in DAn induces the accumulation and abnormal subcellular localization of α-Synuclein (α-Syn). Mechanistically, we demonstrate that D442G polymorphism enhances the interaction between α-Syn and USP8 and thus increases the K63-specific deubiquitination and stability of α-Syn . We discover a pathogenic polymorphism for PD that represent a promising therapeutic and diagnostic target for PD.
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Affiliation(s)
- Shouhai Wu
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Center for Regenerative and Translational Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Tongxiang Lin
- Center for Regenerative and Translational Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- College of Animal Sciences, Fujian Agriculture and Forestory University, 15 ShangXiaDian Road, CangShan District, Fuzhou City, Fujian Province, China
| | - Yang Xu
- Department of Cardiology, Cardiovascular Key Lab of Zhejiang Province, State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, Zhejiang, China.
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Park SS, Do HA, Park HB, Choi HS, Baek KH. Deubiquitinating enzyme YOD1 deubiquitinates and destabilizes α-synuclein. Biochem Biophys Res Commun 2023; 645:124-131. [PMID: 36682332 DOI: 10.1016/j.bbrc.2023.01.030] [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: 12/14/2022] [Revised: 01/02/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023]
Abstract
α-synuclein is one of the proteins involved in degenerative neuronal diseases such as Parkinson's disease (PD) or Lewy body dementia (LBD). The pathogenesis is imparted by the abnormal accumulation of α-synuclein resulting in the formation of a Lewy body (LB) and exerting neurotoxicity via an unknown mechanism. Regulation of α-synuclein is achieved by the ubiquitin-proteasome system (UPS), which influences protein homeostasis via inducing proteasome-dependent degradation by attaching a small molecule (ubiquitin) to the substrate. Deubiquitinating enzymes (DUBs) control the UPS by cleaving the peptide or isopeptide bond between ubiquitin and its substrate proteins. In a previous study, we found that YOD1 deubiquitinates and regulates the cellular function of neural precursor cell expressed developmentally down-regulated protein 4 (NEDD4), an E3 ligase that induces α-synuclein degradation. We hypothesized that YOD1 acts as a DUB involved in a modulated pathway of α-synuclein. In the current study, we found that YOD1 directly interacts with α-synuclein and deubiquitinates K6-, K11-, K29-, K33-, and K63-linked polyubiquitin chains on α-synuclein. Furthermore, YOD1 destabilizes α-synuclein protein stability by upregulating NEDD4. Collectively, this suggests the possibility that YOD1 is potentially a new regulator in the NEDD4-α-synuclein pathway.
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Affiliation(s)
- Sang-Soo Park
- Department of Biomedical Science, CHA University, Gyeonggi-Do, 13488, Republic of Korea
| | - Hyeon-Ah Do
- Department of Biomedical Science, CHA University, Gyeonggi-Do, 13488, Republic of Korea
| | - Hong-Beom Park
- Department of Biomedical Science, CHA University, Gyeonggi-Do, 13488, Republic of Korea
| | - Hae-Seul Choi
- Department of Biomedical Science, CHA University, Gyeonggi-Do, 13488, Republic of Korea
| | - Kwang-Hyun Baek
- Department of Biomedical Science, CHA University, Gyeonggi-Do, 13488, Republic of Korea.
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Nielsen PYØ, Okarmus J, Meyer M. Role of Deubiquitinases in Parkinson's Disease-Therapeutic Perspectives. Cells 2023; 12:651. [PMID: 36831318 PMCID: PMC9954239 DOI: 10.3390/cells12040651] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder that has been associated with mitochondrial dysfunction, oxidative stress, and defects in mitophagy as well as α-synuclein-positive inclusions, termed Lewy bodies (LBs), which are a common pathological hallmark in PD. Mitophagy is a process that maintains cellular health by eliminating dysfunctional mitochondria, and it is triggered by ubiquitination of mitochondrial-associated proteins-e.g., through the PINK1/Parkin pathway-which results in engulfment by the autophagosome and degradation in lysosomes. Deubiquitinating enzymes (DUBs) can regulate this process at several levels by deubiquitinating mitochondrial substrates and other targets in the mitophagic pathway, such as Parkin. Moreover, DUBs can affect α-synuclein aggregation through regulation of degradative pathways, deubiquitination of α-synuclein itself, and/or via co-localization with α-synuclein in inclusions. DUBs with a known association to PD are described in this paper, along with their function. Of interest, DUBs could be useful as novel therapeutic targets against PD through regulation of PD-associated defects.
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Affiliation(s)
- Pernille Y. Ø. Nielsen
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | - Justyna Okarmus
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | - Morten Meyer
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
- Department of Neurology, Odense University Hospital, 5000 Odense, Denmark
- BRIDGE—Brain Research Inter-Disciplinary Guided Excellence, Department of Clinical Research, University of Southern Denmark, 5000 Odense, Denmark
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Xing X, Xu F, Wang Y, Liu H. Role of the OTUB1/IRF7/NOX4 axis in oxidative stress injury and inflammatory responses in mice with Parkinson's disease. Psychogeriatrics 2023; 23:32-44. [PMID: 36332656 DOI: 10.1111/psyg.12900] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/21/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Parkinson's disease (PD) is one of the most devastating neurodegenerative disorders and is associated with oxidative stress injury (OSI) and inflammatory responses. This study sought to investigate the mechanism of ovarian tumour domain-containing ubiquitin aldehyde binding 1 (OTUB1) in OSI and inflammatory responses in PD, providing a theoretical foundation for PD treatment. METHODS The PD mouse model was established by an intraperitoneal injection of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine, followed by behavioural tests, observation of brain pathological changes, and quantification of inflammatory (TNF-α, IL-1β, and IL-10) and OS (ROS, SOD, and MDA) factors. Next, the expression levels of OTUB1, interferon regulatory factor 7 (IRF7), and NADPH oxidase 4 (NOX4) levels were determined by real-time quantitative polymerase chain reaction and western blot assay, the binding of OTUB1 to IRF7 was analysed by co-immunoprecipitation, and the ubiquitination level of IRF7 and the enrichment and binding of IRF7 and the NOX4 promoter were measured by chromatin immunoprecipitation and dual-luciferase assays. Afterwards, rescue experiments were performed with IRF7 or NOX4 overexpression in OTUB1 knockout PD mice. RESULTS OTUB1 was upregulated in brain tissues of PD mice. Inhibition of OTUB1 alleviated PD progression, OSI, and inflammatory responses. OTUB1 stabilized IRF7 through deubiquitination, and IRF7 bound to the NOX4 promoter to promote NOX4 expression. IRF7 or NOX4 overexpression reversed the effects of silencing OTUB1 on OSI and inflammatory responses in PD mice. CONCLUSION OTUB1-mediated deubiquitination stabilized IRF7 and upregulated NOX4 expression, thereby promoting OSI and inflammatory responses in PD mice.
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Affiliation(s)
- Xiaolian Xing
- Department of Neurology, Taiyuan Central Hospital, Shanxi Medical University, Taiyuan, China
| | - Fei Xu
- Department of Neurology, Taiyuan Central Hospital, Shanxi Medical University, Taiyuan, China
| | - Yu Wang
- Departments of Emergency Internal Medicine, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tong ji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Hongwei Liu
- Department of Neurology, Taiyuan Central Hospital, Shanxi Medical University, Taiyuan, China
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Liu N, Lin MM, Wang Y. The Emerging Roles of E3 Ligases and DUBs in Neurodegenerative Diseases. Mol Neurobiol 2022; 60:247-263. [PMID: 36260224 DOI: 10.1007/s12035-022-03063-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 09/27/2022] [Indexed: 10/24/2022]
Abstract
Despite annual increases in the incidence and prevalence of neurodegenerative diseases, there is a lack of effective treatment strategies. An increasing number of E3 ubiquitin ligases (E3s) and deubiquitinating enzymes (DUBs) have been observed to participate in the pathogenesis mechanisms of neurodegenerative diseases, on the basis of which we conducted a systematic literature review of the studies. This review will help to explore promising therapeutic targets from highly dynamic ubiquitination modification processes.
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Affiliation(s)
- Na Liu
- Department of Pharmacology College of Pharmaceutical Sciences, Suzhou Key Laboratory of Aging and Nervous Diseases, and Jiangsu Key Laboratory of Neuropsychiatric Diseases, Soochow University, Suzhou, Jiangsu, China
| | - Miao-Miao Lin
- Department of Pharmacology College of Pharmaceutical Sciences, Suzhou Key Laboratory of Aging and Nervous Diseases, and Jiangsu Key Laboratory of Neuropsychiatric Diseases, Soochow University, Suzhou, Jiangsu, China
| | - Yan Wang
- Department of Pharmacology College of Pharmaceutical Sciences, Suzhou Key Laboratory of Aging and Nervous Diseases, and Jiangsu Key Laboratory of Neuropsychiatric Diseases, Soochow University, Suzhou, Jiangsu, China.
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Bouron A, Fauvarque MO. Genome-wide analysis of genes encoding core components of the ubiquitin system during cerebral cortex development. Mol Brain 2022; 15:72. [PMID: 35974412 PMCID: PMC9380329 DOI: 10.1186/s13041-022-00958-z] [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: 06/03/2022] [Accepted: 08/02/2022] [Indexed: 11/21/2022] Open
Abstract
Ubiquitination involves three types of enzymes (E1, E2, and E3) that sequentially attach ubiquitin (Ub) to target proteins. This posttranslational modification controls key cellular processes, such as the degradation, endocytosis, subcellular localization and activity of proteins. Ubiquitination, which can be reversed by deubiquitinating enzymes (DUBs), plays important roles during brain development. Furthermore, deregulation of the Ub system is linked to the pathogenesis of various diseases, including neurodegenerative disorders. We used a publicly available RNA-seq database to perform an extensive genome-wide gene expression analysis of the core components of the ubiquitination machinery, covering Ub genes as well as E1, E2, E3 and DUB genes. The ubiquitination network was governed by only Uba1 and Ube2m, the predominant E1 and E2 genes, respectively; their expression was positively regulated during cortical formation. The principal genes encoding HECT (homologous to the E6-AP carboxyl terminus), RBR (RING-in-between-RING), and RING (really interesting new gene) E3 Ub ligases were also highly regulated. Pja1, Dtx3 (RING ligases) and Stub1 (U-box RING) were the most highly expressed E3 Ub ligase genes and displayed distinct developmental expression patterns. Moreover, more than 80 DUB genes were expressed during corticogenesis, with two prominent genes, Uch-l1 and Usp22, showing highly upregulated expression. Several components of the Ub system overexpressed in cancers were also highly expressed in the cerebral cortex under conditions not related to tumour formation or progression. Altogether, this work provides an in-depth overview of transcriptomic changes during embryonic formation of the cerebral cortex. The data also offer new insight into the characterization of the Ub system and may contribute to a better understanding of its involvement in the pathogenesis of neurodevelopmental disorders.
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Affiliation(s)
- Alexandre Bouron
- Université Grenoble Alpes, Inserm, CEA, UMR 1292, 38000, Grenoble, France. .,Genetics and Chemogenomics Lab, Building C3, CEA, 17 rue des Martyrs, 38054, Grenoble Cedex 9, France.
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Sahoo S, Padhy AA, Kumari V, Mishra P. Role of Ubiquitin-Proteasome and Autophagy-Lysosome Pathways in α-Synuclein Aggregate Clearance. Mol Neurobiol 2022; 59:5379-5407. [PMID: 35699874 DOI: 10.1007/s12035-022-02897-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/21/2022] [Indexed: 11/26/2022]
Abstract
Synuclein aggregation in neuronal cells is the primary underlying cause of synucleinopathies. Changes in gene expression patterns, structural modifications, and altered interactions with other cellular proteins often trigger aggregation of α-synuclein, which accumulates as oligomers or fibrils in Lewy bodies. Although fibrillar forms of α-synuclein are primarily considered pathological, recent studies have revealed that even the intermediate states of aggregates are neurotoxic, complicating the development of therapeutic interventions. Autophagy and ubiquitin-proteasome pathways play a significant role in maintaining the soluble levels of α-synuclein inside cells; however, the heterogeneous nature of the aggregates presents a significant bottleneck to its degradation by these cellular pathways. With studies focused on identifying the proteins that modulate synuclein aggregation and clearance, detailed mechanistic insights are emerging about the individual and synergistic effects of these degradation pathways in regulating soluble α-synuclein levels. In this article, we discuss the impact of α-synuclein aggregation on autophagy-lysosome and ubiquitin-proteasome pathways and the therapeutic strategies that target various aspects of synuclein aggregation or degradation via these pathways. Additionally, we also highlight the natural and synthetic compounds that have shown promise in alleviating the cellular damage caused due to synuclein aggregation.
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Affiliation(s)
- Subhashree Sahoo
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Amrita Arpita Padhy
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Varsha Kumari
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Parul Mishra
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India.
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Kumari R, Kumar R, Dey AK, Saha S, Maiti TK. S-Nitrosylation of OTUB1 Alters Its Stability and Ubc13 Binding. ACS Chem Neurosci 2022; 13:1517-1525. [PMID: 35500217 DOI: 10.1021/acschemneuro.1c00855] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
S-Nitrosylation is a reversible post-translational modification that regulates protein function involving the covalent attachment of the nitric oxide (NO) moiety to sulfhydryl residues of the protein. It is an important regulator in the cell signaling process under physiological conditions. However, the release of an excess amount of NO due to dysregulated NOS machinery causes aberrant S-nitrosylation of proteins, which affects protein folding, localization, and activity. Here, we have shown that OTUB1, a deubiquitinating enzyme, undergoes S-nitrosylation under redox stress conditions in vivo and in vitro. Previously, we have shown that OTUB1 forms an amyloid-like structure that promotes phosphorylation of α-synuclein and neuronal toxicity. However, the mechanistic insight into OTUB1 aggregation remains elusive. Here, we identified that OTUB1 undergoes S-nitrosylation in SH-SY5Y neuroblastoma cells under rotenone-induced stress, as well as excitotoxic conditions, and in rotenone-treated mouse brains. The in vitro S-nitrosylation of OTUB1 followed by mass-spectrometry analysis has identified cysteine-23 and cysteine-91 as S-nitrosylation sites. S-Nitrosylated OTUB1 (SNO-OTUB1) diminished its catalytic activity, impaired its native structure, promoted amyloid-like aggregation, and compromised its binding with Ubc13. Thus, our results demonstrated that nitrosylation of OTUB1 might play a crucial role in regulating the ubiquitin signaling and Parkinson's disease pathology.
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Affiliation(s)
- Raniki Kumari
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India
- Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, Odisha 751024, India
| | - Roshan Kumar
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India
| | - Amit Kumar Dey
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India
| | - Sandhini Saha
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India
| | - Tushar Kanti Maiti
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India
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14
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Deubiquitinating enzymes (DUBs): decipher underlying basis of neurodegenerative diseases. Mol Psychiatry 2022; 27:259-268. [PMID: 34285347 DOI: 10.1038/s41380-021-01233-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/25/2021] [Accepted: 07/06/2021] [Indexed: 02/07/2023]
Abstract
Neurodegenerative diseases (NDs) are characterized by the aggregation of neurotoxic proteins in the central nervous system. Aberrant protein accumulation in NDs is largely caused by the dysfunction of the two principal protein catabolism pathways, the ubiquitin-proteasome system (UPS), and the autophagy-lysosomal pathway (ALP). The two protein quality control pathways are bridged by ubiquitination, a post-translational modification that can induce protein degradation via both the UPS and the ALP. Perturbed ubiquitination leads to the formation of toxic aggregates and inclusion bodies that are deleterious to neurons. Ubiquitination is promoted by a cascade of ubiquitinating enzymes and counter-regulated by deubiquitinating enzymes (DUBs). As fine-tuning regulators of ubiquitination and protein degradation, DUBs modulate the stability of ND-associated pathogenic proteins including amyloid β protein, Tau, and α-synuclein. Besides, DUBs also influence ND-associated mitophagy, protein secretion, and neuroinflammation. Given the various and critical functions of DUBs in NDs, DUBs may become potential therapeutic targets for NDs.
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15
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Do HA, Baek KH. Cellular functions regulated by deubiquitinating enzymes in neurodegenerative diseases. Ageing Res Rev 2021; 69:101367. [PMID: 34023421 DOI: 10.1016/j.arr.2021.101367] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/07/2021] [Accepted: 05/17/2021] [Indexed: 12/24/2022]
Abstract
Neurodegenerative diseases are one of the most common diseases in mankind. Although there are reports of several candidates that cause neurodegenerative diseases, the exact mechanism of pathogenesis is poorly understood. The ubiquitin-proteasome system (UPS) is an important posttranslational modification for protein degradation and control of homeostasis. Enzymes such as E1, E2, E3 ligases, and deubiquitinating enzymes (DUBs) participating in UPS, regulate disease-inducing proteins by controlling the degree of ubiquitination. Therefore, the development of treatments targeting enzymes for degenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS), is emerging as an attractive perspective. In particular, as DUBs are able to regulate one or more degenerative disease-related proteins, the potential as a therapeutic target is even more evident. DUBs influence the regulation of toxic proteins that cause neurodegenerative diseases by not only their removal, but also by regulating signals associated with mitophagy, autophagy, and endoplasmic reticulum-associated degradation (ERAD). In this review, we analyze not only the cellular processes of DUBs, which control neurodegenerative disease-inducing proteins, but also their potentials as a therapeutic agent for neurodegenerative diseases.
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16
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Zhu Q, Fu Y, Li L, Liu CH, Zhang L. The functions and regulation of Otubains in protein homeostasis and diseases. Ageing Res Rev 2021; 67:101303. [PMID: 33609777 DOI: 10.1016/j.arr.2021.101303] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/08/2021] [Accepted: 02/15/2021] [Indexed: 12/18/2022]
Abstract
OTU domain-containing ubiquitin aldehyde-binding proteins Otubain1 (OTUB1) and Otubain2 (OTUB2) were initially identified as OTU deubiquitinases (DUBs). Recently, Otubains have emerged as essential regulators of diverse physiological processes, such as immune signaling and DNA damage response. Dysregulation of those processes is likely to increase the risk in multiple aspects of aging-related diseases, including cancers, neurodegenerative disorders, chronic kidney diseases, bone dysplasia and pulmonary fibrosis. Consistently, Otubains are aberrantly expressed in cancers and have been identified to be both tumor suppressors and tumor promoters in different types of cancers. Therefore, the regulatory mechanism of the activity and expression of Otubains is very important for better understanding of Otubains-associated biological networks and human diseases. This review provides a comprehensive description of functions and regulatory axis of Otubains, highlighting experimental evidences indicating Otubains as potential therapeutic targets against aging-related disorders.
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Affiliation(s)
- Qiong Zhu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 100850, China
| | - Yesheng Fu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 100850, China
| | - Lei Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 100850, China
| | - Cui Hua Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology (Chinese Academy of Sciences), Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100101, China.
| | - Lingqiang Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 100850, China.
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17
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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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18
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Le Guerroué F, Youle RJ. Ubiquitin signaling in neurodegenerative diseases: an autophagy and proteasome perspective. Cell Death Differ 2020; 28:439-454. [PMID: 33208890 DOI: 10.1038/s41418-020-00667-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 12/13/2022] Open
Abstract
Ubiquitin signaling is a sequence of events driving the fate of a protein based on the type of ubiquitin modifications attached. In the case of neurodegenerative diseases, ubiquitin signaling is mainly associated with degradation signals to process aberrant proteins, which form aggregates often fatal for the brain cells. This signaling is often perturbed by the aggregates themselves and leads to the accumulation of toxic aggregates and inclusion bodies that are deleterious due to a toxic gain of function. Decrease in quality control pathways is often seen with age and is a critical onset for the development of neurodegeneration. Many aggregates are now thought to propagate in a prion-like manner, where mutated proteins acting like seeds are transitioning from cell to cell, converting normal proteins to toxic aggregates. Modulation of ubiquitin signaling, by stimulating ubiquitin ligase activation, is a potential therapeutic strategy to treat patients with neurodegeneration diseases.
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Affiliation(s)
- François Le Guerroué
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Richard J Youle
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA.
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Celebi G, Kesim H, Ozer E, Kutlu O. The Effect of Dysfunctional Ubiquitin Enzymes in the Pathogenesis of Most Common Diseases. Int J Mol Sci 2020; 21:ijms21176335. [PMID: 32882786 PMCID: PMC7503467 DOI: 10.3390/ijms21176335] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/17/2020] [Accepted: 07/18/2020] [Indexed: 12/14/2022] Open
Abstract
Ubiquitination is a multi-step enzymatic process that involves the marking of a substrate protein by bonding a ubiquitin and protein for proteolytic degradation mainly via the ubiquitin–proteasome system (UPS). The process is regulated by three main types of enzymes, namely ubiquitin-activating enzymes (E1), ubiquitin-conjugating enzymes (E2), and ubiquitin ligases (E3). Under physiological conditions, ubiquitination is highly reversible reaction, and deubiquitinases or deubiquitinating enzymes (DUBs) can reverse the effect of E3 ligases by the removal of ubiquitin from substrate proteins, thus maintaining the protein quality control and homeostasis in the cell. The dysfunction or dysregulation of these multi-step reactions is closely related to pathogenic conditions; therefore, understanding the role of ubiquitination in diseases is highly valuable for therapeutic approaches. In this review, we first provide an overview of the molecular mechanism of ubiquitination and UPS; then, we attempt to summarize the most common diseases affecting the dysfunction or dysregulation of these mechanisms.
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Affiliation(s)
- Gizem Celebi
- Faculty of Engineering and Natural Sciences, Molecular Biology, Genetics, and Bioengineering Program, Sabanci University, Istanbul 34956, Turkey; (G.C.); (H.K.); (E.O.)
| | - Hale Kesim
- Faculty of Engineering and Natural Sciences, Molecular Biology, Genetics, and Bioengineering Program, Sabanci University, Istanbul 34956, Turkey; (G.C.); (H.K.); (E.O.)
| | - Ebru Ozer
- Faculty of Engineering and Natural Sciences, Molecular Biology, Genetics, and Bioengineering Program, Sabanci University, Istanbul 34956, Turkey; (G.C.); (H.K.); (E.O.)
| | - Ozlem Kutlu
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Istanbul 34956, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano Diagnostics (EFSUN), Sabanci University, Istanbul 34956, Turkey
- Correspondence: ; Tel.: +90-216-483-9000 (ext. 2413)
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