1
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Basak B, Holzbaur ELF. Mitophagy in Neurons: Mechanisms Regulating Mitochondrial Turnover and Neuronal Homeostasis. J Mol Biol 2025:169161. [PMID: 40268233 DOI: 10.1016/j.jmb.2025.169161] [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: 01/10/2025] [Revised: 04/14/2025] [Accepted: 04/15/2025] [Indexed: 04/25/2025]
Abstract
Mitochondrial quality control is instrumental in regulating neuronal health and survival. The receptor-mediated clearance of damaged mitochondria by autophagy, known as mitophagy, plays a key role in controlling mitochondrial homeostasis. Mutations in genes that regulate mitophagy are causative for familial forms of neurological disorders including Parkinson's disease (PD) and Amyotrophic lateral sclerosis (ALS). PINK1/Parkin-dependent mitophagy is the best studied mitophagy pathway, while more recent work has brought to light additional mitochondrial quality control mechanisms that operate either in parallel to or independent of PINK1/Parkin mitophagy. Here, we discuss our current understanding of mitophagy mechanisms operating in neurons to govern mitochondrial homeostasis. We also summarize progress in our understanding of the links between mitophagic dysfunction and neurodegeneration, and highlight the potential for therapeutic interventions to maintain mitochondrial health and neuronal function.
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Affiliation(s)
- Bishal Basak
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Erika L F Holzbaur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
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2
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Matsuhisa K, Sato S, Kaneko M. Identification of E3 Ubiquitin Ligase Substrates Using Biotin Ligase-Based Proximity Labeling Approaches. Biomedicines 2025; 13:854. [PMID: 40299435 PMCID: PMC12024899 DOI: 10.3390/biomedicines13040854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2025] [Revised: 03/05/2025] [Accepted: 03/06/2025] [Indexed: 04/30/2025] Open
Abstract
Ubiquitylation is a post-translational modification originally identified as the first step in protein degradation by the ubiquitin-proteasome system. Ubiquitylation is also known to regulate many cellular processes without degrading the ubiquitylated proteins. Substrate proteins are specifically recognized and ubiquitylated by ubiquitin ligases. It is necessary to identify the substrates for each ubiquitin ligase to understand the physiological and pathological roles of ubiquitylation. Recently, a promiscuous mutant of a biotin ligase derived from Escherichia coli, BioID, and its variants have been utilized to analyze protein-protein interaction. In this review, we summarize the current knowledge regarding the molecular mechanisms underlying ubiquitylation, BioID-based approaches for interactome studies, and the application of BirA and its variants for the identification of ubiquitin ligase substrates.
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Affiliation(s)
- Koji Matsuhisa
- Lee Kong Chian School of Medicine, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore;
| | - Shinya Sato
- Department of Pharmacology and Therapeutic Innovation, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8521, Japan;
| | - Masayuki Kaneko
- Department of Pharmacology and Therapeutic Innovation, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8521, Japan;
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3
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Antico O, Thompson PW, Hertz NT, Muqit MMK, Parton LE. Targeting mitophagy in neurodegenerative diseases. Nat Rev Drug Discov 2025; 24:276-299. [PMID: 39809929 DOI: 10.1038/s41573-024-01105-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2024] [Indexed: 01/16/2025]
Abstract
Mitochondrial dysfunction is a hallmark of idiopathic neurodegenerative diseases, including Parkinson disease, amyotrophic lateral sclerosis, Alzheimer disease and Huntington disease. Familial forms of Parkinson disease and amyotrophic lateral sclerosis are often characterized by mutations in genes associated with mitophagy deficits. Therefore, enhancing the mitophagy pathway may represent a novel therapeutic approach to targeting an underlying pathogenic cause of neurodegenerative diseases, with the potential to deliver neuroprotection and disease modification, which is an important unmet need. Accumulating genetic, molecular and preclinical model-based evidence now supports targeting mitophagy in neurodegenerative diseases. Despite clinical development challenges, small-molecule-based approaches for selective mitophagy enhancement - namely, USP30 inhibitors and PINK1 activators - are entering phase I clinical trials for the first time.
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Affiliation(s)
- Odetta Antico
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Paul W Thompson
- Mission Therapeutics Ltd, Babraham Research Campus, Cambridge, UK
| | | | - Miratul M K Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Laura E Parton
- Mission Therapeutics Ltd, Babraham Research Campus, Cambridge, UK.
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4
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Wang X, Li Y, Li Y, Wang X, Song H, Wang Y, Huang C, Mao C, Wang L, Zhong C, Yu D, Xia Z, Feng Y, Duan J, Liu Y, Ou J, Luo C, Mai W, Hong H, Cai W, Zheng L, Trempe JF, Fon EA, Liao J, Yi W, Chen J. AMPK-dependent Parkin activation suppresses macrophage antigen presentation to promote tumor progression. SCIENCE ADVANCES 2025; 11:eadn8402. [PMID: 40117357 PMCID: PMC11927615 DOI: 10.1126/sciadv.adn8402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/18/2025] [Indexed: 03/23/2025]
Abstract
The constrained cross-talk between myeloid cells and T cells in the tumor immune microenvironment (TIME) restricts cancer immunotherapy efficacy, whereas the underlying mechanism remains elusive. Parkin, an E3 ubiquitin ligase renowned for mitochondrial quality control, has emerged as a regulator of immune response. Here, we show that both systemic and macrophage-specific ablations of Parkin in mice lead to attenuated tumor progression and prolonged mouse survival. By single-cell RNA-seq and flow cytometry, we demonstrate that Parkin deficiency reshapes the TIME through activating both innate and adaptive immunities to control tumor progression and recurrence. Mechanistically, Parkin activation by AMP-activated protein kinase rather than PTEN-induced kinase 1 mediated major histocompatibility complex I down-regulation on macrophages via Autophagy related 5-dependent autophagy. Furthermore, Parkin deletion synergizes with immune checkpoint blockade treatment and Park2-/- signature aids in predicting the prognosis of patients with solid tumor. Our findings uncover Parkin's involvement in suppressing macrophage antigen presentation for coordinating the cross-talk between macrophages and T cells.
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Affiliation(s)
- Xinyu Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Jinfeng Laboratory, Chongqing, China
| | - Yiyi Li
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yan Li
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiumei Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Jinfeng Laboratory, Chongqing, China
| | - Hongrui Song
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yingzhao Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chunliu Huang
- Nasopharyngeal Carcinoma Center, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Zhuhai, China
| | - Chengzhou Mao
- Department of Anatomy and Histology, Shenzhen University Medical School, Shenzhen, China
| | - Lixiang Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Jinfeng Laboratory, Chongqing, China
| | - Cheng Zhong
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Di Yu
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Ian Frazer Centre for Children’s Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Zijin Xia
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yongyi Feng
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jingjing Duan
- Department of Anatomy and Neurobiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yujia Liu
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Juanjuan Ou
- Yu-Yue Pathology Research Center, Chongqing, China
- Centre for Translational Research in Cancer, Sichuan Cancer Hospital & Institute, University of Electronic Science and Technology of China, No. 55 South Renmin Road, Third Inpatient Building, Chengdu, China
- Department of Oncology, Fuling Central Hospital of Chongqing City, Chongqing, China
| | - Congzhou Luo
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Wenhao Mai
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hai Hong
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control of the Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Weibin Cai
- Guangdong Engineering & Technology Research Center for Disease-Model Animals, Laboratory Animal Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Limin Zheng
- Ministry of Education Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jean-François Trempe
- Department of Pharmacology & Therapeutics and Centre de Recherche en Biologie Structurale, McGill University, Montréal, Canada
| | - Edward A. Fon
- McGill Parkinson Program, Neurodegenerative Diseases Group, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Jing Liao
- GMU-GIBH Joint School of Life Sciences, Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, China
| | - Wei Yi
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Jun Chen
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Jinfeng Laboratory, Chongqing, China
- Key Laboratory of Tropical Disease Control of the Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Guangdong Engineering & Technology Research Center for Disease-Model Animals, Laboratory Animal Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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5
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Yamada T, Ikeda A, Murata D, Wang H, Zhang C, Khare P, Adachi Y, Ito F, Quirós PM, Blackshaw S, López-Otín C, Langer T, Chan DC, Le A, Dawson VL, Dawson TM, Iijima M, Sesaki H. Dual regulation of mitochondrial fusion by Parkin-PINK1 and OMA1. Nature 2025; 639:776-783. [PMID: 39972141 DOI: 10.1038/s41586-025-08590-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 01/03/2025] [Indexed: 02/21/2025]
Abstract
Mitochondrial stress pathways protect mitochondrial health from cellular insults1-8. However, their role under physiological conditions is largely unknown. Here, using 18 single, double and triple whole-body and tissue-specific knockout and mutant mice, along with systematic mitochondrial morphology analysis, untargeted metabolomics and RNA sequencing, we discovered that the synergy between two stress-responsive systems-the ubiquitin E3 ligase Parkin and the metalloprotease OMA1-safeguards mitochondrial structure and genome by mitochondrial fusion, mediated by the outer membrane GTPase MFN1 and the inner membrane GTPase OPA1. Whereas the individual loss of Parkin or OMA1 does not affect mitochondrial integrity, their combined loss results in small body size, low locomotor activity, premature death, mitochondrial abnormalities and innate immune responses. Thus, our data show that Parkin and OMA1 maintain a dual regulatory mechanism that controls mitochondrial fusion at the two membranes, even in the absence of extrinsic stress.
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Affiliation(s)
- Tatsuya Yamada
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Arisa Ikeda
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daisuke Murata
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hu Wang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cissy Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Gigantest, Inc., Baltimore, MD, USA
| | - Pratik Khare
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Gigantest, Inc., Baltimore, MD, USA
| | - Yoshihiro Adachi
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fumiya Ito
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Pedro M Quirós
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - Seth Blackshaw
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
- Centre de Recherche des Cordeliers, Inserm U1138, Université Paris Cité, Sorbonne Université, Paris, France
- Facultad de Ciencias de la Vida y la Naturaleza, Universidad Nebrija, Madrid, Spain
| | - Thomas Langer
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - David C Chan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Anne Le
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Gigantest, Inc., Baltimore, MD, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA
| | - Miho Iijima
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Hiromi Sesaki
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA.
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6
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Kovacheva E, Gevezova M, Mehterov N, Kazakova M, Sarafian V. The Intersection of Mitophagy and Autism Spectrum Disorder: A Systematic Review. Int J Mol Sci 2025; 26:2217. [PMID: 40076836 PMCID: PMC11899999 DOI: 10.3390/ijms26052217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2025] [Revised: 02/27/2025] [Accepted: 02/28/2025] [Indexed: 03/14/2025] Open
Abstract
Autism spectrum disorder (ASD) is a group of neurodevelopmental and biobehavioral conditions that arises from complex interactions between environmental factors and physiological development in genetically predisposed individuals. Among the most frequently observed metabolic abnormalities in ASD is mitochondrial dysfunction. Mitochondria respond to cellular stress by altering their dynamics or initiating mitophagy. In neurons, the buildup of dysfunctional mitochondria and reactive oxygen species (ROS) poses a significant risk, as these cells cannot regenerate through division. To safeguard mitochondrial health, cells rely on an efficient "clean-up mechanism" to remove compromised organelles. Mitophagy, a specific form of autophagy, is responsible for regulating the turnover of flawed and non-functional mitochondria. Impairments in this process result in the accumulation of defective mitochondria in neurons, a characteristic of several neurodegenerative disorders associated with behavioral abnormalities. This systematic review offers an in-depth summary of the present knowledge of mitophagy and underscores its pivotal role in the pathogenesis of ASD.
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Affiliation(s)
- Eleonora Kovacheva
- Department of Medical Biology, Faculty of Medicine, Medical University—Plovdiv, 4000 Plovdiv, Bulgaria; (E.K.); (M.G.); (N.M.); (M.K.)
- Research Institute, Medical University—Plovdiv, 4000 Plovdiv, Bulgaria
| | - Maria Gevezova
- Department of Medical Biology, Faculty of Medicine, Medical University—Plovdiv, 4000 Plovdiv, Bulgaria; (E.K.); (M.G.); (N.M.); (M.K.)
- Research Institute, Medical University—Plovdiv, 4000 Plovdiv, Bulgaria
| | - Nikolay Mehterov
- Department of Medical Biology, Faculty of Medicine, Medical University—Plovdiv, 4000 Plovdiv, Bulgaria; (E.K.); (M.G.); (N.M.); (M.K.)
- Research Institute, Medical University—Plovdiv, 4000 Plovdiv, Bulgaria
| | - Maria Kazakova
- Department of Medical Biology, Faculty of Medicine, Medical University—Plovdiv, 4000 Plovdiv, Bulgaria; (E.K.); (M.G.); (N.M.); (M.K.)
- Research Institute, Medical University—Plovdiv, 4000 Plovdiv, Bulgaria
| | - Victoria Sarafian
- Department of Medical Biology, Faculty of Medicine, Medical University—Plovdiv, 4000 Plovdiv, Bulgaria; (E.K.); (M.G.); (N.M.); (M.K.)
- Research Institute, Medical University—Plovdiv, 4000 Plovdiv, Bulgaria
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7
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Yang P, Shuai W, Wang X, Hu X, Zhao M, Wang A, Wu Y, Ouyang L, Wang G. Mitophagy in Neurodegenerative Diseases: Mechanisms of Action and the Advances of Drug Discovery. J Med Chem 2025; 68:3970-3994. [PMID: 39908485 DOI: 10.1021/acs.jmedchem.4c01779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2025]
Abstract
Neurodegenerative diseases (NDDs), such as Parkinson's disease (PD) and Alzheimer's disease (AD), are devastating brain diseases and are incurable at the moment. Increasing evidence indicates that NDDs are associated with mitochondrial dysfunction. Mitophagy removes defective or redundant mitochondria to maintain cell homeostasis, whereas deficient mitophagy accelerates the accumulation of damaged mitochondria to mediate the pathologies of NDDs. Therefore, targeting mitophagy has become a valuable therapeutic pathway for the treatment of NDDs. Several mitophagy modulators have been shown to ameliorate neurodegeneration in PD and AD. However, it remains to be further investigated for other NDDs. Here, we describe the mechanism and key signaling pathway of mitophagy and summarize the roles of defective mitophagy on the pathogenesis of NDDs. Further, we underline the development advances of mitophagy modulators for PD and AD therapy, discuss the therapeutic challenges and limitations of the existing modulators, and provide guidelines for mitophagy mechanism exploration and drug design.
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Affiliation(s)
- Panpan Yang
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Wen Shuai
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Xin Wang
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Xiuying Hu
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Min Zhao
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Aoxue Wang
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Yongya Wu
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Liang Ouyang
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Guan Wang
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, China
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8
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Cinviz ZN, Sensoy O. Computational Study of the Activation Mechanism of Wild-Type Parkin and Its Clinically Relevant Mutant. ACS Chem Neurosci 2025; 16:417-427. [PMID: 39865619 DOI: 10.1021/acschemneuro.4c00630] [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: 01/28/2025] Open
Abstract
Parkinson's disease (PD) is the second most prevalent neurodegenerative disorder. It impairs the control of movement and balance. Parkin mutations worsen the symptoms in sporadic cases and cause the early onset of the disease. Therefore, recent efforts have focused on the rescue of defective parkin by engineered proteins or small-molecule activators to enhance parkin activation. These attempts require holistic understanding of the multistep activation mechanism and molecular effects of disease-associated mutations. Hereby, we provided a comprehensive analysis of the activation mechanism of parkin and a clinically relevant mutant, parkinS167N, using molecular dynamics simulations based on the following crystal structures: (1) parkin, (2) parkin/pUb (phosphorylated Ubiquitin), (3) pparkin/pUb, and (4) pparkin/pUb/UbcH7-Ub. Each of these represents an individual step in the activation process. We showed that the mutation impacted the dynamics of not only the RING0 domain, where it is localized, but also the RING2, Ubl, and IBR domains. We identified residues participating in the allosteric interaction network involved in parkin activation. Some of them are mutated in PD-associated parkin variants. The RING0 domain provides a binding interface with various proteins, so understanding problems associated with the mutation paves the way to the discovery of effective engineered proteins or small molecules that activate mutant parkin.
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Affiliation(s)
- Zeynep Nur Cinviz
- Graduate School of Engineering and Natural Sciences, Istanbul Medipol University, Istanbul 34810, Turkey
| | - Ozge Sensoy
- Graduate School of Engineering and Natural Sciences, Istanbul Medipol University, Istanbul 34810, Turkey
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul 34810, Turkey
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9
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Kiraly S, Stanley J, Eden ER. Lysosome-Mitochondrial Crosstalk in Cellular Stress and Disease. Antioxidants (Basel) 2025; 14:125. [PMID: 40002312 PMCID: PMC11852311 DOI: 10.3390/antiox14020125] [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: 11/26/2024] [Revised: 12/23/2024] [Accepted: 01/11/2025] [Indexed: 02/27/2025] Open
Abstract
The perception of lysosomes and mitochondria as entirely separate and independent entities that degrade material and produce ATP, respectively, has been challenged in recent years as not only more complex roles for both organelles, but also an unanticipated level of interdependence are being uncovered. Coupled lysosome and mitochondrial function and dysfunction involve complex crosstalk between the two organelles which goes beyond mitochondrial quality control and lysosome-mediated clearance of damaged mitochondria through mitophagy. Our understanding of crosstalk between these two essential metabolic organelles has been transformed by major advances in the field of membrane contact sites biology. We now know that membrane contact sites between lysosomes and mitochondria play central roles in inter-organelle communication. This importance of mitochondria-lysosome contacts (MLCs) in cellular homeostasis, evinced by the growing number of diseases that have been associated with their dysregulation, is starting to be appreciated. How MLCs are regulated and how their coordination with other pathways of lysosome-mitochondria crosstalk is achieved are the subjects of ongoing scrutiny, but this review explores the current understanding of the complex crosstalk governing the function of the two organelles and its impact on cellular stress and disease.
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Affiliation(s)
| | | | - Emily R. Eden
- UCL Institute of Ophthalmology, London EC1V 9EL, UK; (S.K.); (J.S.)
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10
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Kochańczyk T, Fishman M, Lima CD. Chemical Tools for Probing the Ub/Ubl Conjugation Cascades. Chembiochem 2025; 26:e202400659. [PMID: 39313481 PMCID: PMC11727022 DOI: 10.1002/cbic.202400659] [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: 08/07/2024] [Revised: 09/23/2024] [Accepted: 09/23/2024] [Indexed: 09/25/2024]
Abstract
Conjugation of ubiquitin (Ub) and structurally related ubiquitin-like proteins (Ubls), essential for many cellular processes, employs multi-step reactions orchestrated by specific E1, E2 and E3 enzymes. The E1 enzyme activates the Ub/Ubl C-terminus in an ATP-dependent process that results in the formation of a thioester linkage with the E1 active site cysteine. The thioester-activated Ub/Ubl is transferred to the active site of an E2 enzyme which then interacts with an E3 enzyme to promote conjugation to the target substrate. The E1-E2-E3 enzymatic cascades utilize labile intermediates, extensive conformational changes, and vast combinatorial diversity of short-lived protein-protein complexes to conjugate Ub/Ubl to various substrates in a regulated manner. In this review, we discuss various chemical tools and methods used to study the consecutive steps of Ub/Ubl activation and conjugation, which are often too elusive for direct studies. We focus on methods developed to probe enzymatic activities and capture and characterize stable mimics of the transient intermediates and transition states, thereby providing insights into fundamental mechanisms in the Ub/Ubl conjugation pathways.
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Affiliation(s)
- Tomasz Kochańczyk
- Structural Biology ProgramSloan Kettering Institute1275 York AvenueNew York, New York10065USA
| | - Michael Fishman
- Structural Biology ProgramSloan Kettering Institute1275 York AvenueNew York, New York10065USA
| | - Christopher D. Lima
- Structural Biology ProgramSloan Kettering Institute1275 York AvenueNew York, New York10065USA
- Howard Hughes Medical Institute1275 York AvenueNew York, New York10065USA
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11
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Zheng C, Nguyen KK, Vishnivetskiy SA, Gurevich VV, Gurevich EV. Arrestin-3 binds parkin and enhances parkin-dependent mitophagy. J Neurochem 2025; 169:e16043. [PMID: 38196269 PMCID: PMC11231064 DOI: 10.1111/jnc.16043] [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: 05/08/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 01/11/2024]
Abstract
Arrestins were discovered for their role in homologous desensitization of G-protein-coupled receptors (GPCRs). Later non-visual arrestins were shown to regulate several signaling pathways. Some of these pathways require arrestin binding to GPCRs, the regulation of others is receptor independent. Here, we demonstrate that arrestin-3 binds the E3 ubiquitin ligase parkin via multiple sites, preferentially interacting with its RING0 domain. Identification of the parkin domains involved suggests that arrestin-3 likely relieves parkin autoinhibition and/or stabilizes the enzymatically active "open" conformation of parkin. Arrestin-3 binding enhances ubiquitination by parkin of the mitochondrial protein mitofusin-1 and facilitates parkin-mediated mitophagy in HeLa cells. Furthermore, arrestin-3 and its mutant with enhanced parkin binding rescue mitofusin-1 ubiquitination and mitophagy in the presence of the Parkinson's disease-associated R275W parkin mutant, which is defective in both functions. Thus, modulation of parkin activity via arrestin-3 might be a novel strategy of anti-parkinsonian therapy.
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Affiliation(s)
- Chen Zheng
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
| | - Kevin K. Nguyen
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
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12
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Wagner JP, Sauvé V, Saran A, Gehring K. Structural basis for the pathogenicity of parkin catalytic domain mutants. J Biol Chem 2025; 301:108051. [PMID: 39631693 PMCID: PMC11742612 DOI: 10.1016/j.jbc.2024.108051] [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: 07/30/2024] [Revised: 11/21/2024] [Accepted: 11/26/2024] [Indexed: 12/07/2024] Open
Abstract
Mutations in the E3 ubiquitin ligase parkin cause a familial form of Parkinson's disease. Parkin and the mitochondrial kinase PTEN-induced kinase 1 assure quality control of mitochondria through selective autophagy of mitochondria (mitophagy). Whereas numerous parkin mutations have been functionally and structurally characterized, several Parkinson's disease mutations found in the catalytic Rcat domain of parkin remain poorly understood. Here, we characterize two pathogenic Rcat mutants, T415N and P437L. We demonstrate that both mutants exhibit impaired activity using autoubiquitination and ubiquitin vinyl sulfone assays. We determine the minimal ubiquitin-binding segment and show that both mutants display impaired binding of ubiquitin charged on the E2 enzyme. Finally, we use AlphaFold 3 to predict a model of the phospho-parkin:phospho-ubiquitin:ubiquitin-charged E2 complex. The model shows the repressor element of parkin and the N-terminal residues of the catalytic domain form a helix to position ubiquitin for transfer from the E2 to parkin. Our results rationalize the pathogenicity of the parkin mutations and deepen our understanding of the active parkin:E2∼Ub complex.
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Affiliation(s)
- Julian P Wagner
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada; Centre de Recherche en Biologie Structurale, McGill University, Montreal, Quebec, Canada
| | - Véronique Sauvé
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada; Centre de Recherche en Biologie Structurale, McGill University, Montreal, Quebec, Canada
| | - Anshu Saran
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada; Centre de Recherche en Biologie Structurale, McGill University, Montreal, Quebec, Canada
| | - Kalle Gehring
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada; Centre de Recherche en Biologie Structurale, McGill University, Montreal, Quebec, Canada.
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13
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Safreena N, Nair IC, Chandra G. Therapeutic potential of Parkin and its regulation in Parkinson's disease. Biochem Pharmacol 2024; 230:116600. [PMID: 39500382 DOI: 10.1016/j.bcp.2024.116600] [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: 07/25/2024] [Revised: 10/05/2024] [Accepted: 10/28/2024] [Indexed: 11/14/2024]
Abstract
Parkinson's disease (PD) is a debilitating neurodegenerative disorder characterized by the progressive loss of dopaminergic neurons in the midbrain substantia nigra, resulting in motor and non-motor symptoms. While the exact etiology of PD remains elusive, a growing body of evidence suggests that dysfunction in the parkin protein plays a pivotal role in the pathogenesis of the disease. Parkin is an E3 ubiquitin ligase that ubiquitinates substrate proteins to control a number of crucial cellular processes including protein catabolism, immune response, and cellular apoptosis.While autosomal recessive mutations in the PARK2 gene, which codes for parkin, are linked to an inherited form of early-onset PD, heterozygous mutations in PARK2 have also been reported in the more commonly occurring sporadic PD cases. Impairment of parkin's E3 ligase activity is believed to play a pathogenic role in both familial and sporadic forms of PD.This article provides an overview of the current understanding of the mechanistic basis of parkin's E3 ligase activity, its major physiological role in controlling cellular functions, and how these are disrupted in familial and sporadic PD. The second half of the manuscript explores the currently available and potential therapeutic strategies targeting parkin structure and/or function in order to slow down or mitigate the progressive neurodegeneration in PD.
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Affiliation(s)
- Narukkottil Safreena
- Cell Biology Laboratory, Center for Development and Aging Research, Inter University Center for Biomedical Research & Super Specialty Hospital, Mahatma Gandhi University Campus at Thalappady, Rubber Board PO, Kottayam 686009, Kerala, India
| | - Indu C Nair
- SAS SNDP Yogam College, Konni, Pathanamthitta 689691, Kerala, India
| | - Goutam Chandra
- Cell Biology Laboratory, Center for Development and Aging Research, Inter University Center for Biomedical Research & Super Specialty Hospital, Mahatma Gandhi University Campus at Thalappady, Rubber Board PO, Kottayam 686009, Kerala, India.
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14
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Lenka DR, Chaurasiya S, Ratnakar L, Kumar A. Mechanism of phospho-Ubls' specificity and conformational changes that regulate Parkin activity. Structure 2024; 32:2107-2122.e3. [PMID: 39368463 DOI: 10.1016/j.str.2024.09.012] [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: 03/23/2024] [Revised: 07/24/2024] [Accepted: 09/10/2024] [Indexed: 10/07/2024]
Abstract
PINK1 and Parkin mutations lead to the early onset of Parkinson's disease. PINK1-mediated phosphorylation of ubiquitin (Ub), ubiquitin-like protein (NEDD8), and ubiquitin-like (Ubl) domain of Parkin activate autoinhibited Parkin E3 ligase. The mechanism of various phospho-Ubls' specificity and conformational changes leading to Parkin activation remain elusive. Herein, we show that compared to Ub, NEDD8 is a more robust binder and activator of Parkin. Structures and biophysical/biochemical data reveal specific recognition and underlying mechanisms of pUb/pNEDD8 and pUbl domain binding to the RING1 and RING0 domains, respectively. Also, pUb/pNEDD8 binding in the RING1 pocket promotes allosteric conformational changes in Parkin's catalytic domain (RING2), leading to Parkin activation. Furthermore, Parkinson's disease mutation K211N in the RING0 domain was believed to perturb Parkin activation due to loss of pUb binding. However, our data reveal allosteric conformational changes due to N211 that lock RING2 with RING0 to inhibit Parkin activity without disrupting pNEDD8/pUb binding.
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Affiliation(s)
- Dipti Ranjan Lenka
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal 462066, India
| | - Shradha Chaurasiya
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal 462066, India
| | - Loknath Ratnakar
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal 462066, India
| | - Atul Kumar
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal 462066, India.
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15
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Kusch S, Frantzeskakis L, Lassen BD, Kümmel F, Pesch L, Barsoum M, Walden KD, Panstruga R. A fungal plant pathogen overcomes mlo-mediated broad-spectrum disease resistance by rapid gene loss. THE NEW PHYTOLOGIST 2024; 244:962-979. [PMID: 39155769 DOI: 10.1111/nph.20063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 08/03/2024] [Indexed: 08/20/2024]
Abstract
Hosts and pathogens typically engage in a coevolutionary arms race. This also applies to phytopathogenic powdery mildew fungi, which can rapidly overcome plant resistance and perform host jumps. Using experimental evolution, we show that the powdery mildew pathogen Blumeria hordei is capable of breaking the agriculturally important broad-spectrum resistance conditioned by barley loss-of-function mlo mutants. Partial mlo virulence of evolved B. hordei isolates is correlated with a distinctive pattern of adaptive mutations, including small-sized (c. 8-40 kb) deletions, of which one is linked to the de novo insertion of a transposable element. Occurrence of the mutations is associated with a transcriptional induction of effector protein-encoding genes that is absent in mlo-avirulent isolates on mlo mutant plants. The detected mutational spectrum comprises the same loci in at least two independently isolated mlo-virulent isolates, indicating convergent multigenic evolution. The mutational events emerged in part early (within the first five asexual generations) during experimental evolution, likely generating a founder population in which incipient mlo virulence was later stabilized by additional events. This work highlights the rapid dynamic genome evolution of an obligate biotrophic plant pathogen with a transposon-enriched genome.
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Affiliation(s)
- Stefan Kusch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Lamprinos Frantzeskakis
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Birthe D Lassen
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Florian Kümmel
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Lina Pesch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Mirna Barsoum
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Kim D Walden
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
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16
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Ye X, Kotaru S, Lopes R, Cravens S, Lasagna M, Wand AJ. Cooperative Substructure and Energetics of Allosteric Regulation of the Catalytic Core of the E3 Ubiquitin Ligase Parkin by Phosphorylated Ubiquitin. Biomolecules 2024; 14:1338. [PMID: 39456270 PMCID: PMC11506642 DOI: 10.3390/biom14101338] [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: 08/20/2024] [Revised: 10/13/2024] [Accepted: 10/14/2024] [Indexed: 10/28/2024] Open
Abstract
Mutations in the parkin gene product Parkin give rise to autosomal recessive juvenile parkinsonism. Parkin is an E3 ubiquitin ligase that is a critical participant in the process of mitophagy. Parkin has a complex structure that integrates several allosteric signals to maintain precise control of its catalytic activity. Though its allosterically controlled structural reorganization has been extensively characterized by crystallography, the energetics and mechanisms of allosteric regulation of Parkin are much less well understood. Allostery is fundamentally linked to the energetics of the cooperative (sub)structure of the protein. Herein, we examine the mechanism of allosteric activation by phosphorylated ubiquitin binding to the enzymatic core of Parkin, which lacks the antagonistic Ubl domain. In this way, the allosteric effects of the agonist phosphorylated ubiquitin can be isolated. Using native-state hydrogen exchange monitored by mass spectrometry, we find that the five structural domains of the core of Parkin are energetically distinct. Nevertheless, association of phosphorylated ubiquitin destabilizes structural elements that bind the ubiquitin-like domain antagonist while promoting the dissociation of the catalytic domain and energetically poises the protein for transition to the fully activated structure.
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Affiliation(s)
- Xiang Ye
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843, USA
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sravya Kotaru
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rosana Lopes
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Shannen Cravens
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Chemistry and Biochemistry, Gonzaga University, Spokane, WA 99258, USA
| | - Mauricio Lasagna
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - A. Joshua Wand
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843, USA
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
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17
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Han R, Wang Q, Xiong X, Chen X, Tu Z, Li B, Zhang F, Chen C, Pan M, Xu T, Chen L, Wang Z, Liu Y, He D, Guo X, He F, Wu P, Yin P, Liu Y, Yan X, Li S, Li XJ, Yang W. Deficiency of parkin causes neurodegeneration and accumulation of pathological α-synuclein in monkey models. J Clin Invest 2024; 134:e179633. [PMID: 39403921 PMCID: PMC11473153 DOI: 10.1172/jci179633] [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: 01/22/2024] [Accepted: 08/26/2024] [Indexed: 10/19/2024] Open
Abstract
Parkinson's disease (PD) is characterized by age-dependent neurodegeneration and the accumulation of toxic phosphorylated α-synuclein (pS129-α-syn). The mechanisms underlying these crucial pathological changes remain unclear. Mutations in parkin RBR E3 ubiquitin protein ligase (PARK2), the gene encoding parkin that is phosphorylated by PTEN-induced putative kinase 1 (PINK1) to participate in mitophagy, cause early onset PD. However, current parkin-KO mouse and pig models do not exhibit neurodegeneration. In the current study, we utilized CRISPR/Cas9 technology to establish parkin-deficient monkey models at different ages. We found that parkin deficiency leads to substantia nigra neurodegeneration in adult monkey brains and that parkin phosphorylation decreases with aging, primarily due to increased insolubility of parkin. Phosphorylated parkin is important for neuroprotection and the reduction of pS129-α-syn. Consistently, overexpression of WT parkin, but not a mutant form that cannot be phosphorylated by PINK1, reduced the accumulation of pS129-α-syn. These findings identify parkin phosphorylation as a key factor in PD pathogenesis and suggest it as a promising target for therapeutic interventions.
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Affiliation(s)
- Rui Han
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of Non-human Primate Research, GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Qi Wang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of Non-human Primate Research, GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Xin Xiong
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of Non-human Primate Research, GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Xiusheng Chen
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of Non-human Primate Research, GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Zhuchi Tu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of Non-human Primate Research, GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Bang Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of Non-human Primate Research, GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Fei Zhang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of Non-human Primate Research, GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Chunyu Chen
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of Non-human Primate Research, GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Mingtian Pan
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of Non-human Primate Research, GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Ting Xu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of Non-human Primate Research, GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Laiqiang Chen
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of Non-human Primate Research, GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Zhifu Wang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of Non-human Primate Research, GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Yanting Liu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of Non-human Primate Research, GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Dajian He
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of Non-human Primate Research, GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Xiangyu Guo
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of Non-human Primate Research, GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Feng He
- Hubei Topgene Biotechnological Research Institute Co., Ltd. Wuhan, China
| | - Peng Wu
- Hubei Topgene Biotechnological Research Institute Co., Ltd. Wuhan, China
| | - Peng Yin
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of Non-human Primate Research, GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Yunbo Liu
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoxin Yan
- Department of Anatomy and Neurobiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Shihua Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of Non-human Primate Research, GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Xiao-Jiang Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of Non-human Primate Research, GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Weili Yang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of Non-human Primate Research, GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China
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18
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Narendra DP, Youle RJ. The role of PINK1-Parkin in mitochondrial quality control. Nat Cell Biol 2024; 26:1639-1651. [PMID: 39358449 DOI: 10.1038/s41556-024-01513-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 08/22/2024] [Indexed: 10/04/2024]
Abstract
Mitophagy mediated by the recessive Parkinson's disease genes PINK1 and Parkin responds to mitochondrial damage to preserve mitochondrial function. In the pathway, PINK1 is the damage sensor, probing the integrity of the mitochondrial import pathway, and activating Parkin when import is blocked. Parkin is the effector, selectively marking damaged mitochondria with ubiquitin for mitophagy and other quality-control processes. This selective mitochondrial quality-control pathway may be especially critical for dopamine neurons affected in Parkinson's disease, in which the mitochondrial network is widely distributed throughout a highly branched axonal arbor. Here we review the current understanding of the role of PINK1-Parkin in the quality control of mitophagy, including sensing of mitochondrial distress by PINK1, activation of Parkin by PINK1 to induce mitophagy, and the physiological relevance of the PINK1-Parkin pathway.
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Affiliation(s)
- Derek P Narendra
- Mitochondrial Biology and Neurodegeneration Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
| | - Richard J Youle
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
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19
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Sun X, Ye G, Li J, Yuan L, Bai G, Xu YJ, Zhang J. The tumor suppressor Parkin exerts anticancer effects through regulating mitochondrial GAPDH activity. Oncogene 2024; 43:3215-3226. [PMID: 39285229 DOI: 10.1038/s41388-024-03157-3] [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: 04/17/2024] [Revised: 08/23/2024] [Accepted: 09/03/2024] [Indexed: 09/19/2024]
Abstract
Cancer cells preferentially utilize glycolysis for energy production, and GAPDH is a critical enzyme in glycolysis. Parkin is a tumor suppressor and a key protein involved in mitophagy regulation. However, the tumor suppression mechanism of Parkin has still not been elucidated. In this study, we identified mitochondrial GAPDH as a new substrate of the E3 ubiquitin ligase Parkin, which mediated GAPDH ubiquitination in human cervical cancer. The translocation of GAPDH into mitochondria was driven by the PINK1 kinase, and either PINK1 or GAPDH mutation prevented the accumulation of GAPDH in mitochondria. Parkin caused the ubiquitination of GAPDH at multiple sites (K186, K215, and K219) located within the enzyme-catalyzed binding domain of the GAPDH protein. GAPDH ubiquitination was required for mitophagy, and stimulation of mitophagy suppressed cervical cancer cell growth, indicating that mitophagy serves as a type of cell death. Mechanistically, PHB2 served as a key mediator in GAPDH ubiquitination-induced mitophagy through stabilizing PINK1 protein and GAPDH mutation resulted in the reduced distribution of PHB2 in mitophagic vacuole. In addition, ubiquitination of GAPDH decreased its phosphorylation level and enzyme activity and inhibited the glycolytic pathway in cervical cancer cells. The results of in vivo experiments also showed that the GAPDH mutation increased glycolysis in cervical cancer cells and accelerated tumorigenesis. Thus, we concluded that Parkin may exert its anticancer function by ubiquitinating GAPDH in mitochondria. Taken together, our study further clarified the molecular mechanism of tumor suppression by Parkin through the regulation of energy metabolism, which provides an experimental basis for the development of new drugs for the treatment of human cervical cancer.
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Affiliation(s)
- Xin Sun
- Cancer Center, Department of Medical Oncology, Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Key Laboratory for Diagnosis and Treatment of Upper Limb Edema and Stasis of Breast Cancer, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Guiqin Ye
- Department of Clinical Laboratory, Yuhuan People's Hospital, Taizhou, China
| | - Jiuzhou Li
- Department of Neurosurgery, Binzhou People's Hospital, Binzhou, China
| | - Liyang Yuan
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Gongxun Bai
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou, China.
| | - Yong-Jiang Xu
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Jiangnan University, Wuxi, China.
| | - Jianbin Zhang
- Cancer Center, Department of Medical Oncology, Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Key Laboratory for Diagnosis and Treatment of Upper Limb Edema and Stasis of Breast Cancer, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China.
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20
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Sauvé V, Stefan E, Croteau N, Goiran T, Fakih R, Bansal N, Hadzipasic A, Fang J, Murugan P, Chen S, Fon EA, Hirst WD, Silvian LF, Trempe JF, Gehring K. Activation of parkin by a molecular glue. Nat Commun 2024; 15:7707. [PMID: 39300082 PMCID: PMC11412986 DOI: 10.1038/s41467-024-51889-3] [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: 04/03/2024] [Accepted: 08/16/2024] [Indexed: 09/22/2024] Open
Abstract
Mutations in parkin and PINK1 cause early-onset Parkinson's disease (EOPD). The ubiquitin ligase parkin is recruited to damaged mitochondria and activated by PINK1, a kinase that phosphorylates ubiquitin and the ubiquitin-like domain of parkin. Activated phospho-parkin then ubiquitinates mitochondrial proteins to target the damaged organelle for degradation. Here, we present the mechanism of activation of a new class of small molecule allosteric modulators that enhance parkin activity. The compounds act as molecular glues to enhance the ability of phospho-ubiquitin (pUb) to activate parkin. Ubiquitination assays and isothermal titration calorimetry with the most active compound (BIO-2007817) identify the mechanism of action. We present the crystal structure of a closely related compound (BIO-1975900) bound to a complex of parkin and two pUb molecules. The compound binds next to pUb on RING0 and contacts both proteins. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) experiments confirm that activation occurs through release of the catalytic Rcat domain. In organello and mitophagy assays demonstrate that BIO-2007817 partially rescues the activity of parkin EOPD mutants, R42P and V56E, offering a basis for the design of activators as therapeutics for Parkinson's disease.
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Affiliation(s)
- Véronique Sauvé
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montreal, QC, Canada
| | - Eric Stefan
- Biotherapeutics and Medicinal Sciences, Biogen, Cambridge, MA, USA
| | - Nathalie Croteau
- Centre de Recherche en Biologie Structurale, McGill University, Montreal, QC, Canada
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada
- Structural Genomics Consortium, McGill University, Montreal, QC, Canada
- Brain Repair and Integrative Neuroscience (BRaIN) Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Thomas Goiran
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Rayan Fakih
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montreal, QC, Canada
| | - Nupur Bansal
- Biotherapeutics and Medicinal Sciences, Biogen, Cambridge, MA, USA
| | - Adelajda Hadzipasic
- Biotherapeutics and Medicinal Sciences, Biogen, Cambridge, MA, USA
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Jing Fang
- Biotherapeutics and Medicinal Sciences, Biogen, Cambridge, MA, USA
- Aura Biosciences, Boston, MA, USA
| | - Paramasivam Murugan
- Biotherapeutics and Medicinal Sciences, Biogen, Cambridge, MA, USA
- Bristol-Myers Squibb, New York, NY, USA
| | - Shimin Chen
- Biotherapeutics and Medicinal Sciences, Biogen, Cambridge, MA, USA
- Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Edward A Fon
- Structural Genomics Consortium, McGill University, Montreal, QC, Canada
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Warren D Hirst
- Neurodegenerative Disease Research Unit, Biogen, Cambridge, MA, USA
- DaCapo Brainscience, North Cambridge, MA, USA
| | - Laura F Silvian
- Biotherapeutics and Medicinal Sciences, Biogen, Cambridge, MA, USA.
| | - Jean-François Trempe
- Centre de Recherche en Biologie Structurale, McGill University, Montreal, QC, Canada
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada
- Structural Genomics Consortium, McGill University, Montreal, QC, Canada
- Brain Repair and Integrative Neuroscience (BRaIN) Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Kalle Gehring
- Department of Biochemistry, McGill University, Montreal, QC, Canada.
- Centre de Recherche en Biologie Structurale, McGill University, Montreal, QC, Canada.
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21
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Lenka DR, Dahe SV, Antico O, Sahoo P, Prescott AR, Muqit MMK, Kumar A. Additional feedforward mechanism of Parkin activation via binding of phospho-UBL and RING0 in trans. eLife 2024; 13:RP96699. [PMID: 39221915 PMCID: PMC11368401 DOI: 10.7554/elife.96699] [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] [Indexed: 09/04/2024] Open
Abstract
Loss-of-function Parkin mutations lead to early-onset of Parkinson's disease. Parkin is an auto-inhibited ubiquitin E3 ligase activated by dual phosphorylation of its ubiquitin-like (Ubl) domain and ubiquitin by the PINK1 kinase. Herein, we demonstrate a competitive binding of the phospho-Ubl and RING2 domains towards the RING0 domain, which regulates Parkin activity. We show that phosphorylated Parkin can complex with native Parkin, leading to the activation of autoinhibited native Parkin in trans. Furthermore, we show that the activator element (ACT) of Parkin is required to maintain the enzyme kinetics, and the removal of ACT slows the enzyme catalysis. We also demonstrate that ACT can activate Parkin in trans but less efficiently than when present in the cis molecule. Furthermore, the crystal structure reveals a donor ubiquitin binding pocket in the linker connecting REP and RING2, which plays a crucial role in Parkin activity.
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Affiliation(s)
- Dipti Ranjan Lenka
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) BhopalBhopalIndia
| | - Shakti Virendra Dahe
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) BhopalBhopalIndia
| | - Odetta Antico
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Pritiranjan Sahoo
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) BhopalBhopalIndia
| | - Alan R Prescott
- Division of Cell Signalling and Immunology, Dundee Imaging Facility, School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Miratul MK Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Atul Kumar
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) BhopalBhopalIndia
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22
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Zhong Y, Xia S, Wang G, Liu Q, Ma F, Yu Y, Zhang Y, Qian L, Hu L, Xie J. The interplay between mitophagy and mitochondrial ROS in acute lung injury. Mitochondrion 2024; 78:101920. [PMID: 38876297 DOI: 10.1016/j.mito.2024.101920] [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: 01/17/2024] [Revised: 04/27/2024] [Accepted: 06/11/2024] [Indexed: 06/16/2024]
Abstract
Mitochondria orchestrate the production of new mitochondria and the removal of damaged ones to dynamically maintain mitochondrial homeostasis through constant biogenesis and clearance mechanisms. Mitochondrial quality control particularly relies on mitophagy, defined as selective autophagy with mitochondria-targeting specificity. Most ROS are derived from mitochondria, and the physiological concentration of mitochondrial ROS (mtROS) is no longer considered a useless by-product, as it has been proven to participate in immune and autophagy pathway regulation. However, excessive mtROS appears to be a pathogenic factor in several diseases, including acute lung injury (ALI). The interplay between mitophagy and mtROS is complex and closely related to ALI. Here, we review the pathways of mitophagy, the intricate relationship between mitophagy and mtROS, the role of mtROS in the pathogenesis of ALI, and their effects and related progression in ALI induced by different conditions.
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Affiliation(s)
- Yizhi Zhong
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, No.3 East Qingchun Road, Jianggan District, Hangzhou 310016, China
| | - Siwei Xia
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, No.3 East Qingchun Road, Jianggan District, Hangzhou 310016, China
| | - Gaojian Wang
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, No.3 East Qingchun Road, Jianggan District, Hangzhou 310016, China
| | - Qinxue Liu
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, No.3 East Qingchun Road, Jianggan District, Hangzhou 310016, China
| | - Fengjie Ma
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, No.3 East Qingchun Road, Jianggan District, Hangzhou 310016, China
| | - Yijin Yu
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, No.3 East Qingchun Road, Jianggan District, Hangzhou 310016, China
| | - Yaping Zhang
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, No.3 East Qingchun Road, Jianggan District, Hangzhou 310016, China
| | - Lu Qian
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, No.3 East Qingchun Road, Jianggan District, Hangzhou 310016, China
| | - Li Hu
- Department of Anesthesiology, Second Affiliated Hospital of Jiaxing University, No.1518 North Huancheng Road, Nanhu District, Jiaxing 314000, China
| | - Junran Xie
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, No.3 East Qingchun Road, Jianggan District, Hangzhou 310016, China.
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23
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Huq TS, Luo J, Fakih R, Sauvé V, Gehring K. Naturally occurring hyperactive variants of human parkin. Commun Biol 2024; 7:961. [PMID: 39117722 PMCID: PMC11310320 DOI: 10.1038/s42003-024-06656-x] [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: 12/12/2023] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease in the world. Although most cases are sporadic and occur later in life, 10-15% of cases are genetic. Loss-of-function mutations in the ring-between-ring E3 ubiquitin ligase parkin, encoded by the PRKN gene, cause autosomal recessive forms of early onset PD. Together with the kinase PINK1, parkin forms a mitochondrial quality control pathway that tags damaged mitochondria for clearance. Under basal conditions, parkin is inhibited and compounds that increase its activity have been proposed as a therapy for PD. Recently, several naturally occurring hyperactive parkin variants were identified, which increased mitophagy in cultured cells. Here, we validate the hyperactivities of these variants in vitro and compare the levels of activity of the variants to those of the wild-type and the well-characterized hyperactive variant, W403A. We also study the effects of mutating the parkin ACT (activating element) on parkin activity in vitro. This work advances our understanding of the pathogenicity of parkin variants and is an important first step in the design of molecules to increase parkin activity.
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Affiliation(s)
- Tahrima Saiha Huq
- Department of Biochemistry, McGill University, Montréal, Canada
- Centre de recherche en biologie structurale, McGill University, Montréal, Canada
- North South University, Dhaka, Bangladesh
| | - Jean Luo
- Department of Biochemistry, McGill University, Montréal, Canada
- Centre de recherche en biologie structurale, McGill University, Montréal, Canada
- Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Rayan Fakih
- Department of Biochemistry, McGill University, Montréal, Canada
- Centre de recherche en biologie structurale, McGill University, Montréal, Canada
| | - Véronique Sauvé
- Department of Biochemistry, McGill University, Montréal, Canada
- Centre de recherche en biologie structurale, McGill University, Montréal, Canada
| | - Kalle Gehring
- Department of Biochemistry, McGill University, Montréal, Canada.
- Centre de recherche en biologie structurale, McGill University, Montréal, Canada.
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24
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Connelly EM, Rintala-Dempsey AC, Gundogdu M, Freeman EA, Koszela J, Aguirre JD, Zhu G, Kämäräinen O, Tadayon R, Walden H, Shaw GS. Capturing the catalytic intermediates of parkin ubiquitination. Proc Natl Acad Sci U S A 2024; 121:e2403114121. [PMID: 39078678 PMCID: PMC11317638 DOI: 10.1073/pnas.2403114121] [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: 02/13/2024] [Accepted: 06/24/2024] [Indexed: 07/31/2024] Open
Abstract
Parkin is an E3 ubiquitin ligase implicated in early-onset forms of Parkinson's disease. It catalyzes a transthiolation reaction by accepting ubiquitin (Ub) from an E2 conjugating enzyme, forming a short-lived thioester intermediate, and transfers Ub to mitochondrial membrane substrates to signal mitophagy. A major impediment to the development of Parkinsonism therapeutics is the lack of structural and mechanistic detail for the essential, short-lived transthiolation intermediate. It is not known how Ub is recognized by the catalytic Rcat domain in parkin that enables Ub transfer from an E2~Ub conjugate to the catalytic site and the structure of the transthiolation complex is undetermined. Here, we capture the catalytic intermediate for the Rcat domain of parkin in complex with ubiquitin (Rcat-Ub) and determine its structure using NMR-based chemical shift perturbation experiments. We show that a previously unidentified α-helical region near the Rcat domain is unmasked as a recognition motif for Ub and guides the C-terminus of Ub toward the parkin catalytic site. Further, we apply a combination of guided AlphaFold modeling, chemical cross-linking, and single turnover assays to establish and validate a model of full-length parkin in complex with UbcH7, its donor Ub, and phosphoubiquitin, trapped in the process of transthiolation. Identification of this catalytic intermediate and orientation of Ub with respect to the Rcat domain provides important structural insights into Ub transfer by this E3 ligase and explains how the previously enigmatic Parkinson's pathogenic mutation T415N alters parkin activity.
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Affiliation(s)
- Elizabeth M. Connelly
- Department of Biochemistry, The University of Western Ontario, London, ONN6A 5C1, Canada
| | | | - Mehmet Gundogdu
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, GlasgowG12 8QQ, UK
| | - E. Aisha Freeman
- Department of Biochemistry, The University of Western Ontario, London, ONN6A 5C1, Canada
| | - Joanna Koszela
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, GlasgowG12 8QQ, UK
| | - Jacob D. Aguirre
- Department of Biochemistry, The University of Western Ontario, London, ONN6A 5C1, Canada
| | - Grace Zhu
- Department of Biochemistry, The University of Western Ontario, London, ONN6A 5C1, Canada
| | - Outi Kämäräinen
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, GlasgowG12 8QQ, UK
| | - Roya Tadayon
- Department of Biochemistry, The University of Western Ontario, London, ONN6A 5C1, Canada
| | - Helen Walden
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, GlasgowG12 8QQ, UK
| | - Gary S. Shaw
- Department of Biochemistry, The University of Western Ontario, London, ONN6A 5C1, Canada
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25
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Gąssowska-Dobrowolska M, Olech-Kochańczyk G, Culmsee C, Adamczyk A. Novel Insights into Parkin-Mediated Mitochondrial Dysfunction and "Mito-Inflammation" in α-Synuclein Toxicity. The Role of the cGAS-STING Signalling Pathway. J Inflamm Res 2024; 17:4549-4574. [PMID: 39011416 PMCID: PMC11249072 DOI: 10.2147/jir.s468609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 06/22/2024] [Indexed: 07/17/2024] Open
Abstract
The prevalence of age-related neurodegenerative diseases, such as Parkinson's disease (PD) and related disorders continues to grow worldwide. Increasing evidence links intracellular inclusions of misfolded alpha-synuclein (α-syn) aggregates, so-called Lewy bodies (LB) and Lewy neuritis, to the progressive pathology of PD and other synucleinopathies. Our previous findings established that α-syn oligomers induce S-nitrosylation and deregulation of the E3-ubiquitin ligase Parkin, leading to mitochondrial disturbances in neuronal cells. The accumulation of damaged mitochondria as a consequence, together with the release of mitochondrial-derived damage-associated molecular patterns (mtDAMPs) could activate the innate immune response and induce neuroinflammation ("mito-inflammation"), eventually accelerating neurodegeneration. However, the molecular pathways that transmit pro-inflammatory signals from damaged mitochondria are not well understood. One of the proposed pathways could be the cyclic GMP-AMP synthase (cGAS) - stimulator of interferon genes (STING) (cGAS-STING) pathway, which plays a pivotal role in modulating the innate immune response. It has recently been suggested that cGAS-STING deregulation may contribute to the development of various pathological conditions. Especially, its excessive engagement may lead to neuroinflammation and appear to be essential for the development of neurodegenerative brain diseases, including PD. However, the precise molecular mechanisms underlying cGAS-STING pathway activation in PD and other synucleinopathies are not fully understood. This review focuses on linking mitochondrial dysfunction to neuroinflammation in these disorders, particularly emphasizing the role of the cGAS-STING signaling. We propose the cGAS-STING pathway as a critical driver of inflammation in α-syn-dependent neurodegeneration and hypothesize that cGAS-STING-driven "mito-inflammation" may be one of the key mechanisms promoting the neurodegeneration in PD. Understanding the molecular mechanisms of α-syn-induced cGAS-STING-associated "mito-inflammation" in PD and related synucleinopathies may contribute to the identification of new targets for the treatment of these disorders.
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Affiliation(s)
| | - Gabriela Olech-Kochańczyk
- Department of Cellular Signalling, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Carsten Culmsee
- Institute of Pharmacology and Clinical Pharmacy, University of Marburg, Marburg, Germany
- Center for Mind Brain and Behavior - CMBB, University of Marburg, Marburg, Germany
| | - Agata Adamczyk
- Department of Cellular Signalling, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
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26
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Iacono D, Murphy EK, Stimpson CD, Perl DP, Day RM. Low-dose radiation decreases Lrrk2 levels in the striatum of large mammalian brains: New venues to treat Parkinson's disease? Parkinsonism Relat Disord 2024; 124:107024. [PMID: 38843617 DOI: 10.1016/j.parkreldis.2024.107024] [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: 01/24/2024] [Revised: 05/29/2024] [Accepted: 06/01/2024] [Indexed: 07/05/2024]
Abstract
INTRODUCTION Among gene mutations and variants linked to an increased risk of PD, mutations of leucine-rich repeat kinase 2 gene (LRRK2) are among the most frequently associated with early- and late-onset PD. Clinical and neuropathological characteristics of idiopathic-PD (iPD) and LRRK2-PD are similar, and these similarities suggest that the pathomechanisms between these two conditions are shared. LRRK2 mutations determine a gain-of-function and yield higher levels of lrrk2 across body tissues, including brain. On another side, recent animal studies supported the potential use of low dose radiation (LDR) to modify the pathomechanisms of diseases such as Alzheimer's disease (AD). METHODS We assessed if a single total-body LDR (sLDR) exposure in normal swine could alter expression levels of the following PD-associated molecules: alpha-synuclein (α-syn), phosphorylated-α-synuclein (pα-syn), parkin, tyrosine hydroxylase (th), lrrk2, phosphorylated-lrrk2 (pS935-lrrk2), and some LRRK2 substrates (Rab8a, Rab12) across different brain regions. These proteins were measured in frontal cortex, hippocampus, striatum, thalamus/hypothalamus, and cerebellum of 9 radiated (RAD) vs. 6 sham (SH) swine after 28 days from a sLDR of 1.79Gy exposure. RESULTS Western Blot analyses showed lowered lrrk2 levels in the striatum of RAD vs. SH swine (p < 0.05), with no differences across the remaining brain regions. None of the other protein levels differed between RAD and SH swine in any examined brain regions. No lrrk2 and p-lrrk2 (S935) levels differed in the lungs of RAD vs. SH swine. CONCLUSIONS These findings show a specific striatal lrrk2 lowering effect due to LDR and support the potential use of LDR to interfere with the pathomechanisms of PD.
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Affiliation(s)
- Diego Iacono
- DoD/USU Brain Tissue Repository & Neuropathology Program, Uniformed Services University (USU), Bethesda, MD, USA; Department of Neurology, F. Edward Hébert School of Medicine, Uniformed Services University (USU), Bethesda, MD, USA; Department of Pathology, F. Edward Hébert School of Medicine, Uniformed Services University (USU), Bethesda, MD, USA; Neuroscience Program, Department of Anatomy, Physiology & Genetics, Uniformed Services University (USU), Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine (HJF) Inc., Bethesda, MD, USA.
| | - Erin K Murphy
- DoD/USU Brain Tissue Repository & Neuropathology Program, Uniformed Services University (USU), Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine (HJF) Inc., Bethesda, MD, USA
| | - Cheryl D Stimpson
- DoD/USU Brain Tissue Repository & Neuropathology Program, Uniformed Services University (USU), Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine (HJF) Inc., Bethesda, MD, USA
| | - Daniel P Perl
- DoD/USU Brain Tissue Repository & Neuropathology Program, Uniformed Services University (USU), Bethesda, MD, USA; Department of Pathology, F. Edward Hébert School of Medicine, Uniformed Services University (USU), Bethesda, MD, USA
| | - Regina M Day
- Department of Pharmacology and Molecular Therapeutics, F. Edward Hébert School of Medicine, Uniformed Services University (USU), Bethesda, MD, USA
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27
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Trease AJ, Totusek S, Lichter EZ, Stauch KL, Fox HS. Mitochondrial DNA Instability Supersedes Parkin Mutations in Driving Mitochondrial Proteomic Alterations and Functional Deficits in Polg Mutator Mice. Int J Mol Sci 2024; 25:6441. [PMID: 38928146 PMCID: PMC11203920 DOI: 10.3390/ijms25126441] [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: 04/19/2024] [Revised: 05/30/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Mitochondrial quality control is essential in mitochondrial function. To examine the importance of Parkin-dependent mechanisms in mitochondrial quality control, we assessed the impact of modulating Parkin on proteome flux and mitochondrial function in a context of reduced mtDNA fidelity. To accomplish this, we crossed either the Parkin knockout mouse or ParkinW402A knock-in mouse lines to the Polg mitochondrial mutator line to generate homozygous double mutants. In vivo longitudinal isotopic metabolic labeling was followed by isolation of liver mitochondria and synaptic terminals from the brain, which are rich in mitochondria. Mass spectrometry and bioenergetics analysis were assessed. We demonstrate that slower mitochondrial protein turnover is associated with loss of mtDNA fidelity in liver mitochondria but not synaptic terminals, and bioenergetic function in both tissues is impaired. Pathway analysis revealed loss of mtDNA fidelity is associated with disturbances of key metabolic pathways, consistent with its association with metabolic disorders and neurodegeneration. Furthermore, we find that loss of Parkin leads to exacerbation of Polg-driven proteomic consequences, though it may be bioenergetically protective in tissues exhibiting rapid mitochondrial turnover. Finally, we provide evidence that, surprisingly, dis-autoinhibition of Parkin (ParkinW402A) functionally resembles Parkin knockout and fails to rescue deleterious Polg-driven effects. Our study accomplishes three main outcomes: (1) it supports recent studies suggesting that Parkin dependence is low in response to an increased mtDNA mutational load, (2) it provides evidence of a potential protective role of Parkin insufficiency, and (3) it draws into question the therapeutic attractiveness of enhancing Parkin function.
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Affiliation(s)
- Andrew J. Trease
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA; (A.J.T.); (S.T.); (K.L.S.)
| | - Steven Totusek
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA; (A.J.T.); (S.T.); (K.L.S.)
| | - Eliezer Z. Lichter
- Computational Biomedicine Section, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA;
| | - Kelly L. Stauch
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA; (A.J.T.); (S.T.); (K.L.S.)
| | - Howard S. Fox
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA; (A.J.T.); (S.T.); (K.L.S.)
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28
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Koszela J, Rintala-Dempsey A, Salzano G, Pimenta V, Kamarainen O, Gabrielsen M, Parui AL, Shaw GS, Walden H. A substrate-interacting region of Parkin directs ubiquitination of the mitochondrial GTPase Miro1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597144. [PMID: 38895334 PMCID: PMC11185606 DOI: 10.1101/2024.06.03.597144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Mutations in the gene encoding for the E3 ubiquitin ligase Parkin have been linked to early-onset Parkinson's disease. Besides many other cellular roles, Parkin is involved in clearance of damaged mitochondria via mitophagy - a process of particular importance in dopaminergic neurons. Upon mitochondrial damage, Parkin accumulates at the outer mitochondrial membrane and is activated, leading to ubiquitination of many mitochondrial substrates and recruitment of mitophagy effectors. While the activation mechanisms of autoinhibited Parkin have been extensively studied, it remains unknown how Parkin recognises its substrates for ubiquitination, and no substrate interaction site in Parkin has been reported. Here, we identify a conserved region in the flexible linker between the Ubl and RING0 domains of Parkin, which is indispensable for Parkin interaction with the mitochondrial GTPase Miro1. Our results explain the preferential targeting and ubiquitination of Miro1 by Parkin and provide a biochemical explanation for the presence of Parkin at the mitochondrial membrane prior to activation induced by mitochondrial damage. Our findings are important for understanding mitochondrial homeostasis and may inspire new therapeutic avenues for Parkinson's disease.
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Affiliation(s)
- Joanna Koszela
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Anne Rintala-Dempsey
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
| | | | - Viveka Pimenta
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
| | - Outi Kamarainen
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Mads Gabrielsen
- Integrated Protein Analysis, Shared Research Facilities, University of Glasgow, Glasgow, UK
| | - Aasna L Parui
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Gary S Shaw
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
| | - Helen Walden
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
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29
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Clausen L, Okarmus J, Voutsinos V, Meyer M, Lindorff-Larsen K, Hartmann-Petersen R. PRKN-linked familial Parkinson's disease: cellular and molecular mechanisms of disease-linked variants. Cell Mol Life Sci 2024; 81:223. [PMID: 38767677 PMCID: PMC11106057 DOI: 10.1007/s00018-024-05262-8] [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: 02/27/2024] [Revised: 04/25/2024] [Accepted: 05/02/2024] [Indexed: 05/22/2024]
Abstract
Parkinson's disease (PD) is a common and incurable neurodegenerative disorder that arises from the loss of dopaminergic neurons in the substantia nigra and is mainly characterized by progressive loss of motor function. Monogenic familial PD is associated with highly penetrant variants in specific genes, notably the PRKN gene, where homozygous or compound heterozygous loss-of-function variants predominate. PRKN encodes Parkin, an E3 ubiquitin-protein ligase important for protein ubiquitination and mitophagy of damaged mitochondria. Accordingly, Parkin plays a central role in mitochondrial quality control but is itself also subject to a strict protein quality control system that rapidly eliminates certain disease-linked Parkin variants. Here, we summarize the cellular and molecular functions of Parkin, highlighting the various mechanisms by which PRKN gene variants result in loss-of-function. We emphasize the importance of high-throughput assays and computational tools for the clinical classification of PRKN gene variants and how detailed insights into the pathogenic mechanisms of PRKN gene variants may impact the development of personalized therapeutics.
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Affiliation(s)
- Lene Clausen
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Justyna Okarmus
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, 5230, Odense, Denmark
| | - Vasileios Voutsinos
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Morten Meyer
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, 5230, Odense, Denmark
- Department of Neurology, Odense University Hospital, 5000, Odense, Denmark
- Department of Clinical Research, BRIDGE, Brain Research Inter Disciplinary Guided Excellence, University of Southern Denmark, 5230, Odense, Denmark
| | - Kresten Lindorff-Larsen
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Rasmus Hartmann-Petersen
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200, Copenhagen, Denmark.
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Filograna R, Gerlach J, Choi HN, Rigoni G, Barbaro M, Oscarson M, Lee S, Tiklova K, Ringnér M, Koolmeister C, Wibom R, Riggare S, Nennesmo I, Perlmann T, Wredenberg A, Wedell A, Motori E, Svenningsson P, Larsson NG. PARKIN is not required to sustain OXPHOS function in adult mammalian tissues. NPJ Parkinsons Dis 2024; 10:93. [PMID: 38684669 PMCID: PMC11058849 DOI: 10.1038/s41531-024-00707-0] [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: 09/12/2023] [Accepted: 04/11/2024] [Indexed: 05/02/2024] Open
Abstract
Loss-of-function variants in the PRKN gene encoding the ubiquitin E3 ligase PARKIN cause autosomal recessive early-onset Parkinson's disease (PD). Extensive in vitro and in vivo studies have reported that PARKIN is involved in multiple pathways of mitochondrial quality control, including mitochondrial degradation and biogenesis. However, these findings are surrounded by substantial controversy due to conflicting experimental data. In addition, the existing PARKIN-deficient mouse models have failed to faithfully recapitulate PD phenotypes. Therefore, we have investigated the mitochondrial role of PARKIN during ageing and in response to stress by employing a series of conditional Parkin knockout mice. We report that PARKIN loss does not affect oxidative phosphorylation (OXPHOS) capacity and mitochondrial DNA (mtDNA) levels in the brain, heart, and skeletal muscle of aged mice. We also demonstrate that PARKIN deficiency does not exacerbate the brain defects and the pro-inflammatory phenotype observed in mice carrying high levels of mtDNA mutations. To rule out compensatory mechanisms activated during embryonic development of Parkin-deficient mice, we generated a mouse model where loss of PARKIN was induced in adult dopaminergic (DA) neurons. Surprisingly, also these mice did not show motor impairment or neurodegeneration, and no major transcriptional changes were found in isolated midbrain DA neurons. Finally, we report a patient with compound heterozygous PRKN pathogenic variants that lacks PARKIN and has developed PD. The PARKIN deficiency did not impair OXPHOS activities or induce mitochondrial pathology in skeletal muscle from the patient. Altogether, our results argue that PARKIN is dispensable for OXPHOS function in adult mammalian tissues.
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Affiliation(s)
- Roberta Filograna
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| | - Jule Gerlach
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Hae-Na Choi
- Institute for Biochemistry, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Giovanni Rigoni
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Michela Barbaro
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Mikael Oscarson
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Seungmin Lee
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Katarina Tiklova
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Markus Ringnér
- Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Camilla Koolmeister
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Rolf Wibom
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Sara Riggare
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Inger Nennesmo
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Thomas Perlmann
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Anna Wredenberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Wedell
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Elisa Motori
- Institute for Biochemistry, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Per Svenningsson
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, Stockholm, Sweden
| | - Nils-Göran Larsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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31
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Yu J, Zhao Z, Li Y, Chen J, Huang N, Luo Y. Role of NLRP3 in Parkinson's disease: Specific activation especially in dopaminergic neurons. Heliyon 2024; 10:e28838. [PMID: 38596076 PMCID: PMC11002585 DOI: 10.1016/j.heliyon.2024.e28838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/11/2024] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder with motor symptoms like bradykinesia, tremors, and balance issues. The pathology is recognized by progressively degenerative nigrostriatal dopaminergic neurons (DANs) loss. Its exact pathogenesis is unclear. Numerous studies have shown that nucleotide-binding oligomerization domain-like receptor protein 3 (NLRP3) contributes to the pathogenesis of PD. Previous studies have demonstrated that the over-activation of NLRP3 inflammasome in microglia indirectly leads to the loss of DANs, which can worsen PD. In recent years, autopsy analyses of PD patients and studies in PD models have revealed upregulation of NLRP3 expression within DANs and demonstrated that activation of NLRP3 inflammasome in neurons is sufficient to drive neuronal loss, whereas microglial activation occurs after neuronal death, and that inhibition of intraneuronal NLRP3 inflammasome prevents degeneration of DANs. In this review, we provide research evidence related to NLRP3 inflammasome in DANs in PD as well as focus on possible mechanisms of NLRP3 inflammasome activation in neurons, aiming to provide a new way of thinking about the pathogenesis and prevention of PD.
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Affiliation(s)
- Juan Yu
- Department of Neurology, Third Affiliated Hospital of Zunyi Medical University (The First People's Hospital of Zunyi), Zunyi, 563000, China
| | - Zhanghong Zhao
- Department of Neurology, Third Affiliated Hospital of Zunyi Medical University (The First People's Hospital of Zunyi), Zunyi, 563000, China
| | - Yuanyuan Li
- National Drug Clinical Trial Institution, Third Affiliated Hospital of Zunyi Medical University (The First People's Hospital of Zunyi), Zunyi, Guizhou, China
| | - Jian Chen
- Department of Neurology, Third Affiliated Hospital of Zunyi Medical University (The First People's Hospital of Zunyi), Zunyi, 563000, China
| | - Nanqu Huang
- National Drug Clinical Trial Institution, Third Affiliated Hospital of Zunyi Medical University (The First People's Hospital of Zunyi), Zunyi, Guizhou, China
| | - Yong Luo
- Department of Neurology, Third Affiliated Hospital of Zunyi Medical University (The First People's Hospital of Zunyi), Zunyi, 563000, China
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Kaushik A, Parashar S, Ambasta RK, Kumar P. Ubiquitin E3 ligases assisted technologies in protein degradation: Sharing pathways in neurodegenerative disorders and cancer. Ageing Res Rev 2024; 96:102279. [PMID: 38521359 DOI: 10.1016/j.arr.2024.102279] [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: 01/10/2024] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 03/25/2024]
Abstract
E3 ligases, essential components of the ubiquitin-proteasome-mediated protein degradation system, play a critical role in cellular regulation. By covalently attaching ubiquitin (Ub) molecules to target proteins, these ligases mark them for degradation, influencing various bioprocesses. With over 600 E3 ligases identified, there is a growing realization of their potential as therapeutic candidates for addressing proteinopathies in cancer and neurodegenerative disorders (NDDs). Recent research has highlighted the need to delve deeper into the intricate roles of E3 ligases as nexus points in the pathogenesis of both cancer and NDDs. Their dysregulation is emerging as a common thread linking these seemingly disparate diseases, necessitating a comprehensive understanding of their molecular intricacies. Herein, we have discussed (i) the fundamental mechanisms through which different types of E3 ligases actively participate in selective protein degradation in cancer and NDDs, followed by an examination of common E3 ligases playing pivotal roles in both situations, emphasising common players. Moving to, (ii) the functional domains and motifs of E3 ligases involved in ubiquitination, we have explored their interactions with specific substrates in NDDs and cancer. Additionally, (iii) we have explored techniques like PROTAC, molecular glues, and other state-of-the-art methods for hijacking neurotoxic and oncoproteins. Lastly, (iv) we have provided insights into ongoing clinical trials, offering a glimpse into the evolving landscape of E3-based therapeutics for cancer and NDDs. Unravelling the intricate network of E3 ligase-mediated regulation holds the key to unlocking targeted therapies that address the specific molecular signatures of individual patients, heralding a new era in personalized medicines.
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Affiliation(s)
- Aastha Kaushik
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Delhi 110042, India
| | - Somya Parashar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Delhi 110042, India
| | - Rashmi K Ambasta
- Department of Biotechnology and Microbiology, SRM University-Sonepat, Haryana, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Delhi 110042, India.
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Menon PJ, Sambin S, Criniere-Boizet B, Courtin T, Tesson C, Casse F, Ferrien M, Mariani LL, Carvalho S, Lejeune FX, Rebbah S, Martet G, Houot M, Lanore A, Mangone G, Roze E, Vidailhet M, Aasly J, Gan Or Z, Yu E, Dauvilliers Y, Zimprich A, Tomantschger V, Pirker W, Álvarez I, Pastor P, Di Fonzo A, Bhatia KP, Magrinelli F, Houlden H, Real R, Quattrone A, Limousin P, Korlipara P, Foltynie T, Grosset D, Williams N, Narendra D, Lin HP, Jovanovic C, Svetel M, Lynch T, Gallagher A, Vandenberghe W, Gasser T, Brockmann K, Morris HR, Borsche M, Klein C, Corti O, Brice A, Lesage S, Corvol JC. Genotype-phenotype correlation in PRKN-associated Parkinson's disease. NPJ Parkinsons Dis 2024; 10:72. [PMID: 38553467 PMCID: PMC10980707 DOI: 10.1038/s41531-024-00677-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 03/07/2024] [Indexed: 04/02/2024] Open
Abstract
Bi-allelic pathogenic variants in PRKN are the most common cause of autosomal recessive Parkinson's disease (PD). 647 patients with PRKN-PD were included in this international study. The pathogenic variants present were characterised and investigated for their effect on phenotype. Clinical features and progression of PRKN-PD was also assessed. Among 133 variants in index cases (n = 582), there were 58 (43.6%) structural variants, 34 (25.6%) missense, 20 (15%) frameshift, 10 splice site (7.5%%), 9 (6.8%) nonsense and 2 (1.5%) indels. The most frequent variant overall was an exon 3 deletion (n = 145, 12.3%), followed by the p.R275W substitution (n = 117, 10%). Exon3, RING0 protein domain and the ubiquitin-like protein domain were mutational hotspots with 31%, 35.4% and 31.7% of index cases presenting mutations in these regions respectively. The presence of a frameshift or structural variant was associated with a 3.4 ± 1.6 years or a 4.7 ± 1.6 years earlier age at onset of PRKN-PD respectively (p < 0.05). Furthermore, variants located in the N-terminus of the protein, a region enriched with frameshift variants, were associated with an earlier age at onset. The phenotype of PRKN-PD was characterised by slow motor progression, preserved cognition, an excellent motor response to levodopa therapy and later development of motor complications compared to early-onset PD. Non-motor symptoms were however common in PRKN-PD. Our findings on the relationship between the type of variant in PRKN and the phenotype of the disease may have implications for both genetic counselling and the design of precision clinical trials.
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Affiliation(s)
- Poornima Jayadev Menon
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France.
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Hôpital Pitié-Salpêtrière, Paris, France.
- School of Postgraduate Studies, Royal College of Surgeons in Ireland, Dublin, Ireland.
| | - Sara Sambin
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Hôpital Pitié-Salpêtrière, Paris, France
| | - Baptiste Criniere-Boizet
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Thomas Courtin
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
- Assistance Publique Hôpitaux de Paris, Department of Genetics, Hôpital Pitié-Salpêtrière, Paris, France
| | - Christelle Tesson
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Fanny Casse
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Melanie Ferrien
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Louise-Laure Mariani
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Hôpital Pitié-Salpêtrière, Paris, France
| | - Stephanie Carvalho
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Francois-Xavier Lejeune
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Sana Rebbah
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Gaspard Martet
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Marion Houot
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Hôpital Pitié-Salpêtrière, Paris, France
- Centre of Excellence of Neurodegenerative Disease (CoEN), AP-HP, Pitié-Salpêtrière Hospital, Paris, France
- Institute of Memory and Alzheimer's Disease (IM2A), Department of Neurology, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Aymeric Lanore
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Hôpital Pitié-Salpêtrière, Paris, France
| | - Graziella Mangone
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Hôpital Pitié-Salpêtrière, Paris, France
- Department of Neurology, Movement Disorder Division, Rush University Medical Center, 1725 W. Harrison Street, Chicago, IL, USA
| | - Emmanuel Roze
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Hôpital Pitié-Salpêtrière, Paris, France
| | - Marie Vidailhet
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Hôpital Pitié-Salpêtrière, Paris, France
| | - Jan Aasly
- Department of Neurology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ziv Gan Or
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Eric Yu
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Yves Dauvilliers
- Department of Neurology, Gui-de-Chauliac Hospital, CHU Montpellier, University of Montpellier, Institute for Neurosciences of Montpellier (INM), INSERM, Montpellier, France
| | | | | | - Walter Pirker
- Department of Neurology, Ottakring Clinic, Vienna, Austria
| | - Ignacio Álvarez
- Department of Neurology, Hospital Universitari Mutua de Terrassa, and Fundació per a la Recerca Biomèdica i Social Mútua de Terrassa, Terrassa, Barcelona, Spain
| | - Pau Pastor
- Unit of Neurodegenerative diseases, Department of Neurology, University Hospital Germans Trias i Pujol and The Germans Trias i Pujol Research Institute (IGTP) Badalona, Barcelona, Spain
| | - Alessio Di Fonzo
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Kailash P Bhatia
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Francesca Magrinelli
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Raquel Real
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
- UCL Movement Disorders Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Andrea Quattrone
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
- Institute of Neurology, Department of Medical and Surgical Sciences, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Patricia Limousin
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Prasad Korlipara
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Thomas Foltynie
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Donald Grosset
- Institute of Neurological Sciences, University of Glasgow, Glasgow, UK
| | - Nigel Williams
- Department of Psychological Medicine and Neurology, Cardiff University, Cardiff, UK
| | - Derek Narendra
- Inherited Disorders Unit, Neurogenetics Branch, Division of Intramural Research, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Hsin-Pin Lin
- Inherited Disorders Unit, Neurogenetics Branch, Division of Intramural Research, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Carna Jovanovic
- University Clinical Center of Serbia, Neurology Clinic, Belgrade, Serbia
| | - Marina Svetel
- University Clinical Center of Serbia, Neurology Clinic, Belgrade, Serbia
| | - Timothy Lynch
- The Dublin Neurological Institute at the Mater Misericordiae University Hospital, Dublin Ireland and University College Dublin, Dublin, Ireland
| | - Amy Gallagher
- The Dublin Neurological Institute at the Mater Misericordiae University Hospital, Dublin Ireland and University College Dublin, Dublin, Ireland
| | - Wim Vandenberghe
- Department of Neurology, University Hospitals Leuven; Department of Neurosciences, KU Leuven; Leuven Brain Institute, Leuven, Belgium
| | - Thomas Gasser
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- DZNE, German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Kathrin Brockmann
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- DZNE, German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Huw R Morris
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Max Borsche
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Olga Corti
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Alexis Brice
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
- Assistance Publique Hôpitaux de Paris, Department of Genetics, Hôpital Pitié-Salpêtrière, Paris, France
| | - Suzanne Lesage
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Jean Christophe Corvol
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Hôpital Pitié-Salpêtrière, Paris, France
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Islam NN, Weber CA, Coban M, Cocker LT, Fiesel FC, Springer W, Caulfield TR. In Silico Investigation of Parkin-Activating Mutations Using Simulations and Network Modeling. Biomolecules 2024; 14:365. [PMID: 38540783 PMCID: PMC10968616 DOI: 10.3390/biom14030365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 05/05/2024] Open
Abstract
Complete loss-of-function mutations in the PRKN gene are a major cause of early-onset Parkinson's disease (PD). PRKN encodes the Parkin protein, an E3 ubiquitin ligase that works in conjunction with the ubiquitin kinase PINK1 in a distinct quality control pathway to tag damaged mitochondria for autophagic clearance, i.e., mitophagy. According to previous structural investigations, Parkin protein is typically kept in an inactive conformation via several intramolecular, auto-inhibitory interactions. Here, we performed molecular dynamics simulations (MDS) to provide insights into conformational changes occurring during the de-repression of Parkin and the gain of catalytic activity. We analyzed four different Parkin-activating mutations that are predicted to disrupt certain aspects of its auto-inhibition. All four variants showed greater conformational motions compared to wild-type protein, as well as differences in distances between domain interfaces and solvent-accessible surface area, which are thought to play critical roles as Parkin gains catalytic activity. Our findings reveal that the studied variants exert a notable influence on Parkin activation as they alter the opening of its closed inactive structure, a finding that is supported by recent structure- and cell-based studies. These findings not only helped further characterize the hyperactive variants but overall improved our understanding of Parkin's catalytic activity and nominated targets within Parkin's structure for potential therapeutic designs.
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Affiliation(s)
- Naeyma N. Islam
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA; (N.N.I.); (C.A.W.); (M.C.); (F.C.F.)
| | - Caleb A. Weber
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA; (N.N.I.); (C.A.W.); (M.C.); (F.C.F.)
| | - Matt Coban
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA; (N.N.I.); (C.A.W.); (M.C.); (F.C.F.)
| | - Liam T. Cocker
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA; (N.N.I.); (C.A.W.); (M.C.); (F.C.F.)
| | - Fabienne C. Fiesel
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA; (N.N.I.); (C.A.W.); (M.C.); (F.C.F.)
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA; (N.N.I.); (C.A.W.); (M.C.); (F.C.F.)
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Thomas R. Caulfield
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA; (N.N.I.); (C.A.W.); (M.C.); (F.C.F.)
- Department of Neurosurgery, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA
- Department of Biochemistry & Molecular Biology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA
- Department of Computational Biology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA
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35
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Wu D, Zhang K, Khan FA, Pandupuspitasari NS, Guan K, Sun F, Huang C. A comprehensive review on signaling attributes of serine and serine metabolism in health and disease. Int J Biol Macromol 2024; 260:129607. [PMID: 38253153 DOI: 10.1016/j.ijbiomac.2024.129607] [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: 09/24/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/24/2024]
Abstract
Serine is a metabolite with ever-expanding metabolic and non-metabolic signaling attributes. By providing one‑carbon units for macromolecule biosynthesis and functional modifications, serine and serine metabolism largely impinge on cellular survival and function. Cancer cells frequently have a preference for serine metabolic reprogramming to create a conducive metabolic state for survival and aggressiveness, making intervention of cancer-associated rewiring of serine metabolism a promising therapeutic strategy for cancer treatment. Beyond providing methyl donors for methylation in modulation of innate immunity, serine metabolism generates formyl donors for mitochondrial tRNA formylation which is required for mitochondrial function. Interestingly, fully developed neurons lack the machinery for serine biosynthesis and rely heavily on astrocytic l-serine for production of d-serine to shape synaptic plasticity. Here, we recapitulate recent discoveries that address the medical significance of serine and serine metabolism in malignancies, mitochondrial-associated disorders, and neurodegenerative pathologies. Metabolic control and epigenetic- and posttranslational regulation of serine metabolism are also discussed. Given the metabolic similarities between cancer cells, neurons and germ cells, we further propose the relevance of serine metabolism in testicular homeostasis. Our work provides valuable hints for future investigations that will lead to a deeper understanding of serine and serine metabolism in cellular physiology and pathology.
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Affiliation(s)
- Di Wu
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong 226001, China
| | - Kejia Zhang
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong 226001, China
| | - Faheem Ahmed Khan
- Research Center for Animal Husbandry, National Research and Innovation Agency, Jakarta Pusat 10340, Indonesia
| | | | - Kaifeng Guan
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China.
| | - Fei Sun
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong 226001, China.
| | - Chunjie Huang
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong 226001, China.
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36
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Sheng X, Xia Z, Yang H, Hu R. The ubiquitin codes in cellular stress responses. Protein Cell 2024; 15:157-190. [PMID: 37470788 PMCID: PMC10903993 DOI: 10.1093/procel/pwad045] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/04/2023] [Indexed: 07/21/2023] Open
Abstract
Ubiquitination/ubiquitylation, one of the most fundamental post-translational modifications, regulates almost every critical cellular process in eukaryotes. Emerging evidence has shown that essential components of numerous biological processes undergo ubiquitination in mammalian cells upon exposure to diverse stresses, from exogenous factors to cellular reactions, causing a dazzling variety of functional consequences. Various forms of ubiquitin signals generated by ubiquitylation events in specific milieus, known as ubiquitin codes, constitute an intrinsic part of myriad cellular stress responses. These ubiquitination events, leading to proteolytic turnover of the substrates or just switch in functionality, initiate, regulate, or supervise multiple cellular stress-associated responses, supporting adaptation, homeostasis recovery, and survival of the stressed cells. In this review, we attempted to summarize the crucial roles of ubiquitination in response to different environmental and intracellular stresses, while discussing how stresses modulate the ubiquitin system. This review also updates the most recent advances in understanding ubiquitination machinery as well as different stress responses and discusses some important questions that may warrant future investigation.
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Affiliation(s)
- Xiangpeng Sheng
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- State Key Laboratory of Animal Disease Control, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Zhixiong Xia
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hanting Yang
- Department of Neurology, State Key Laboratory of Medical Neurobiology, Institute for Translational Brain Research, MOE Frontiers Center for Brain Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Ronggui Hu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
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37
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Traynor R, Moran J, Stevens M, Antico O, Knebel A, Behrouz B, Merchant K, Hastie CJ, Davies P, Muqit MMK, De Cesare V. Design and high-throughput implementation of MALDI-TOF/MS-based assays for Parkin E3 ligase activity. CELL REPORTS METHODS 2024; 4:100712. [PMID: 38382522 PMCID: PMC10921019 DOI: 10.1016/j.crmeth.2024.100712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 10/11/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024]
Abstract
Parkinson's disease (PD) is a progressive neurological disorder that manifests clinically as alterations in movement as well as multiple non-motor symptoms including but not limited to cognitive and autonomic abnormalities. Loss-of-function mutations in the gene encoding the ubiquitin E3 ligase Parkin are causal for familial and juvenile PD. Among several therapeutic approaches being explored to treat or improve the prognosis of patients with PD, the use of small molecules able to reinstate or boost Parkin activity represents a potential pharmacological treatment strategy. A major barrier is the lack of high-throughput platforms for the robust and accurate quantification of Parkin activity in vitro. Here, we present two different and complementary Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF/MS)-based approaches for the quantification of Parkin E3 ligase activity in vitro. Both approaches are scalable for high-throughput primary screening to facilitate the identification of Parkin modulators.
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Affiliation(s)
- Ryan Traynor
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Jennifer Moran
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Michael Stevens
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Odetta Antico
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Bahareh Behrouz
- Vincere Biosciences, Inc., 245 Main St. Fl 2, Cambridge, MA 02142, USA
| | - Kalpana Merchant
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - C James Hastie
- MRC Protein Phosphorylation and Ubiquitylation Unit Reagents and Services, School of Life Sciences, University of Dundee, Dow St., Dundee DD1 5EH, Scotland, UK
| | - Paul Davies
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Miratul M K Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK.
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38
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Clausen L, Voutsinos V, Cagiada M, Johansson KE, Grønbæk-Thygesen M, Nariya S, Powell RL, Have MKN, Oestergaard VH, Stein A, Fowler DM, Lindorff-Larsen K, Hartmann-Petersen R. A mutational atlas for Parkin proteostasis. Nat Commun 2024; 15:1541. [PMID: 38378758 PMCID: PMC10879094 DOI: 10.1038/s41467-024-45829-4] [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: 07/05/2023] [Accepted: 02/01/2024] [Indexed: 02/22/2024] Open
Abstract
Proteostasis can be disturbed by mutations affecting folding and stability of the encoded protein. An example is the ubiquitin ligase Parkin, where gene variants result in autosomal recessive Parkinsonism. To uncover the pathological mechanism and provide comprehensive genotype-phenotype information, variant abundance by massively parallel sequencing (VAMP-seq) is leveraged to quantify the abundance of Parkin variants in cultured human cells. The resulting mutational map, covering 9219 out of the 9300 possible single-site amino acid substitutions and nonsense Parkin variants, shows that most low abundance variants are proteasome targets and are located within the structured domains of the protein. Half of the known disease-linked variants are found at low abundance. Systematic mapping of degradation signals (degrons) reveals an exposed degron region proximal to the so-called "activation element". This work provides examples of how missense variants may cause degradation either via destabilization of the native protein, or by introducing local signals for degradation.
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Affiliation(s)
- Lene Clausen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Vasileios Voutsinos
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Matteo Cagiada
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristoffer E Johansson
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Martin Grønbæk-Thygesen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Snehal Nariya
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Rachel L Powell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Magnus K N Have
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Amelie Stein
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Rasmus Hartmann-Petersen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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Marchesan E, Nardin A, Mauri S, Bernardo G, Chander V, Di Paola S, Chinellato M, von Stockum S, Chakraborty J, Herkenne S, Basso V, Schrepfer E, Marin O, Cendron L, Medina DL, Scorrano L, Ziviani E. Activation of Ca 2+ phosphatase Calcineurin regulates Parkin translocation to mitochondria and mitophagy in flies. Cell Death Differ 2024; 31:217-238. [PMID: 38238520 PMCID: PMC10850161 DOI: 10.1038/s41418-023-01251-9] [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: 12/05/2022] [Revised: 11/23/2023] [Accepted: 12/05/2023] [Indexed: 02/09/2024] Open
Abstract
Selective removal of dysfunctional mitochondria via autophagy is crucial for the maintenance of cellular homeostasis. This event is initiated by the translocation of the E3 ubiquitin ligase Parkin to damaged mitochondria, and it requires the Serine/Threonine-protein kinase PINK1. In a coordinated set of events, PINK1 operates upstream of Parkin in a linear pathway that leads to the phosphorylation of Parkin, Ubiquitin, and Parkin mitochondrial substrates, to promote ubiquitination of outer mitochondrial membrane proteins. Ubiquitin-decorated mitochondria are selectively recruiting autophagy receptors, which are required to terminate the organelle via autophagy. In this work, we show a previously uncharacterized molecular pathway that correlates the activation of the Ca2+-dependent phosphatase Calcineurin to Parkin translocation and Parkin-dependent mitophagy. Calcineurin downregulation or genetic inhibition prevents Parkin translocation to CCCP-treated mitochondria and impairs stress-induced mitophagy, whereas Calcineurin activation promotes Parkin mitochondrial recruitment and basal mitophagy. Calcineurin interacts with Parkin, and promotes Parkin translocation in the absence of PINK1, but requires PINK1 expression to execute mitophagy in MEF cells. Genetic activation of Calcineurin in vivo boosts basal mitophagy in neurons and corrects locomotor dysfunction and mitochondrial respiratory defects of a Drosophila model of impaired mitochondrial functions. Our study identifies Calcineurin as a novel key player in the regulation of Parkin translocation and mitophagy.
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Affiliation(s)
| | - Alice Nardin
- Department of Biology, University of Padova, Padova, Italy
| | - Sofia Mauri
- Department of Biology, University of Padova, Padova, Italy
| | - Greta Bernardo
- Department of Biology, University of Padova, Padova, Italy
| | - Vivek Chander
- Department of Biology, University of Padova, Padova, Italy
| | - Simone Di Paola
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
- Institute for Experimental Endocrinology and Oncology (IEOS), National Research Council (CNR), Napoli, Italy
| | | | | | | | | | | | - Emilie Schrepfer
- Department of Biology, University of Padova, Padova, Italy
- Dulbecco-Telethon Institute, Venetian Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Oriano Marin
- Department of Biomedical Sciences (DSB), University of Padova, Padova, Italy
| | - Laura Cendron
- Department of Biology, University of Padova, Padova, Italy
| | - Diego L Medina
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
- Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy
| | - Luca Scorrano
- Department of Biology, University of Padova, Padova, Italy
- Dulbecco-Telethon Institute, Venetian Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Elena Ziviani
- Department of Biology, University of Padova, Padova, Italy.
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40
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Zanon A, Guida M, Lavdas AA, Corti C, Castelo Rueda MP, Negro A, Pramstaller PP, Domingues FS, Hicks AA, Pichler I. Intracellular delivery of Parkin-RING0-based fragments corrects Parkin-induced mitochondrial dysfunction through interaction with SLP-2. J Transl Med 2024; 22:59. [PMID: 38229174 PMCID: PMC10790385 DOI: 10.1186/s12967-024-04850-3] [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: 07/03/2023] [Accepted: 01/02/2024] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Loss-of-function mutations in the PRKN gene, encoding Parkin, are the most common cause of autosomal recessive Parkinson's disease (PD). We have previously identified mitoch ondrial Stomatin-like protein 2 (SLP-2), which functions in the assembly of respiratory chain proteins, as a Parkin-binding protein. Selective knockdown of either Parkin or SLP-2 led to reduced mitochondrial and neuronal function in neuronal cells and Drosophila, where a double knockdown led to a further worsening of Parkin-deficiency phenotypes. Here, we investigated the minimal Parkin region involved in the Parkin-SLP-2 interaction and explored the ability of Parkin-fragments and peptides from this minimal region to restore mitochondrial function. METHODS In fibroblasts, human induced pluripotent stem cell (hiPSC)-derived neurons, and neuroblastoma cells the interaction between Parkin and SLP-2 was investigated, and the Parkin domain responsible for the binding to SLP-2 was mapped. High resolution respirometry, immunofluorescence analysis and live imaging were used to analyze mitochondrial function. RESULTS Using a proximity ligation assay, we quantitatively assessed the Parkin-SLP-2 interaction in skin fibroblasts and hiPSC-derived neurons. When PD-associated PRKN mutations were present, we detected a significantly reduced interaction between the two proteins. We found a preferential binding of SLP-2 to the N-terminal part of Parkin, with a highest affinity for the RING0 domain. Computational modeling based on the crystal structure of Parkin protein predicted several potential binding sites for SLP-2 within the Parkin RING0 domain. Amongst these, three binding sites were observed to overlap with natural PD-causing missense mutations, which we demonstrated interfere substantially with the binding of Parkin to SLP-2. Finally, delivery of the isolated Parkin RING0 domain and a Parkin mini-peptide, conjugated to cell-permeant and mitochondrial transporters, rescued compromised mitochondrial function in Parkin-deficient neuroblastoma cells and hiPSC-derived neurons with endogenous, disease causing PRKN mutations. CONCLUSIONS These findings place further emphasis on the importance of the protein-protein interaction between Parkin and SLP-2 for the maintenance of optimal mitochondrial function. The possibility of restoring an abolished binding to SLP-2 by delivering the Parkin RING0 domain or the Parkin mini-peptide involved in this specific protein-protein interaction into cells might represent a novel organelle-specific therapeutic approach for correcting mitochondrial dysfunction in Parkin-linked PD.
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Affiliation(s)
- Alessandra Zanon
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Marianna Guida
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Alexandros A Lavdas
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Corrado Corti
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | | | - Alessandro Negro
- Department of Biomedical Sciences, University of Padova, Padua, Italy
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
- Department of Neurology, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Francisco S Domingues
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Andrew A Hicks
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Irene Pichler
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.
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41
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Luo S, Wang D, Zhang Z. Post-translational modification and mitochondrial function in Parkinson's disease. Front Mol Neurosci 2024; 16:1329554. [PMID: 38273938 PMCID: PMC10808367 DOI: 10.3389/fnmol.2023.1329554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease with currently no cure. Most PD cases are sporadic, and about 5-10% of PD cases present a monogenic inheritance pattern. Mutations in more than 20 genes are associated with genetic forms of PD. Mitochondrial dysfunction is considered a prominent player in PD pathogenesis. Post-translational modifications (PTMs) allow rapid switching of protein functions and therefore impact various cellular functions including those related to mitochondria. Among the PD-associated genes, Parkin, PINK1, and LRRK2 encode enzymes that directly involved in catalyzing PTM modifications of target proteins, while others like α-synuclein, FBXO7, HTRA2, VPS35, CHCHD2, and DJ-1, undergo substantial PTM modification, subsequently altering mitochondrial functions. Here, we summarize recent findings on major PTMs associated with PD-related proteins, as enzymes or substrates, that are shown to regulate important mitochondrial functions and discuss their involvement in PD pathogenesis. We will further highlight the significance of PTM-regulated mitochondrial functions in understanding PD etiology. Furthermore, we emphasize the potential for developing important biomarkers for PD through extensive research into PTMs.
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Affiliation(s)
- Shishi Luo
- Institute for Future Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Key Laboratory of Rare Pediatric Diseases, Ministry of Education, Hengyang, Hunan, China
- The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, Hunan, China
| | - Danling Wang
- Institute for Future Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Key Laboratory of Rare Pediatric Diseases, Ministry of Education, Hengyang, Hunan, China
- The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, Hunan, China
| | - Zhuohua Zhang
- Institute for Future Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Key Laboratory of Rare Pediatric Diseases, Ministry of Education, Hengyang, Hunan, China
- Institute of Molecular Precision Medicine, Xiangya Hospital, Key Laboratory of Molecular Precision Medicine of Hunan Province and Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
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42
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Zhao G, Zhang T, Li J, Li L, Chen P, Zhang C, Li K, Cui C. Parkin-mediated mitophagy is a potential treatment for oxaliplatin-induced peripheral neuropathy. Am J Physiol Cell Physiol 2024; 326:C214-C228. [PMID: 38073486 PMCID: PMC11192483 DOI: 10.1152/ajpcell.00276.2023] [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: 06/26/2023] [Revised: 10/17/2023] [Accepted: 10/29/2023] [Indexed: 01/06/2024]
Abstract
Oxaliplatin-induced peripheral nerve pain (OIPNP) is a common chemotherapy-related complication, but the mechanism is complex. Mitochondria are vital for cellular homeostasis and regulating oxidative stress. Parkin-mediated mitophagy is a cellular process that removes damaged mitochondria, exhibiting a protective effect in various diseases; however, its role in OIPNP remains unclear. In this study, we found that Parkin-mediated mitophagy was decreased, and reactive oxygen species (ROS) was upregulated in OIPNP rat dorsal root ganglion (DRG) in vivo and in PC12 cells stimulated with oxaliplatin (OXA) in vitro. Overexpression of Parkin indicated that OXA might cause mitochondrial and cell damage by inhibiting mitophagy. We also showed that salidroside (SAL) upregulated Parkin-mediated mitophagy to eliminate damaged mitochondria and promote PC12 cell survival. Knockdown of Parkin indicated that mitophagy is crucial for apoptosis and mitochondrial homeostasis in PC12 cells. In vivo study also demonstrated that SAL enhances Parkin-mediated mitophagy in the DRG and alleviates peripheral nerve injury and pain. These results suggest that Parkin-mediated mitophagy is involved in the pathogenesis of OIPNP and may be a potential therapeutic target for OIPNP.NEW & NOTEWORTHY This article discusses the effects and mechanisms of Parkin-mediated mitophagy in oxaliplatin-induced peripheral nerve pain (OIPNP) from both in vivo and in vitro. We believe that our study makes a significant contribution to the literature because OIPNP has always been the focus of clinical medicine, and mitochondrial quality regulation mechanisms especially Parkin-mediated mitophagy, have been deeply studied in recent years. We use a variety of molecular biological techniques and animal experiments to support our argument.
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Affiliation(s)
- Guoqing Zhao
- Anesthesiology Department, China-Japan Union Hospital of Jilin University, Changchun, People's Republic of China
| | - Te Zhang
- Anesthesiology Department, China-Japan Union Hospital of Jilin University, Changchun, People's Republic of China
| | - Jiannan Li
- Department of Plastic and Reconstructive Microsurgery, China-Japan Union Hospital of Jilin University, Changchun, People's Republic of China
| | - Longyun Li
- Anesthesiology Department, China-Japan Union Hospital of Jilin University, Changchun, People's Republic of China
| | - Peng Chen
- Anesthesiology Department, China-Japan Union Hospital of Jilin University, Changchun, People's Republic of China
| | - Chunlu Zhang
- Anesthesiology Department, China-Japan Union Hospital of Jilin University, Changchun, People's Republic of China
| | - Kai Li
- Anesthesiology Department, China-Japan Union Hospital of Jilin University, Changchun, People's Republic of China
| | - Cancan Cui
- Radiology Department, China-Japan Union Hospital of Jilin University, Changchun, People's Republic of China
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43
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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: 1.5] [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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44
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Yang X, Zhang Y, Luo JX, Zhu T, Ran Z, Mu BR, Lu MH. Targeting mitophagy for neurological disorders treatment: advances in drugs and non-drug approaches. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2023; 396:3503-3528. [PMID: 37535076 DOI: 10.1007/s00210-023-02636-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 07/18/2023] [Indexed: 08/04/2023]
Abstract
Mitochondria serve as a vital energy source for nerve cells. The mitochondrial network also acts as a defense mechanism against external stressors that can threaten the stability of the nervous system. However, excessive accumulation of damaged mitochondria can lead to neuronal death. Mitophagy is an essential pathway in the mitochondrial quality control system and can protect neurons by selectively removing damaged mitochondria. In most neurological disorders, dysfunctional mitochondria are a common feature, and drugs that target mitophagy can improve symptoms. Here, we reviewed the role of mitophagy in Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, Huntington's disease, stroke, and traumatic brain injuries. We also summarized drug and non-drug approaches to promote mitophagy and described their therapeutic role in neurological disorders in order to provide valuable insight into the potential therapeutic agents available for neurological disease treatment. However, most studies on mitophagy regulation are based on preclinical research using cell and animal models, which may not accurately reflect the effects in humans. This poses a challenge to the clinical application of drugs targeting mitophagy. Additionally, these drugs may carry the risk of intolerable side effects and toxicity. Future research should focus on the development of safer and more targeted drugs for mitophagy.
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Affiliation(s)
- Xiong Yang
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yu Zhang
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Jia-Xin Luo
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Tao Zhu
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Zhao Ran
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Ben-Rong Mu
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Mei-Hong Lu
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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45
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Waters CS, Angenent SB, Altschuler SJ, Wu LF. A PINK1 input threshold arises from positive feedback in the PINK1/Parkin mitophagy decision circuit. Cell Rep 2023; 42:113260. [PMID: 37851575 PMCID: PMC10668033 DOI: 10.1016/j.celrep.2023.113260] [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: 11/11/2022] [Revised: 08/25/2023] [Accepted: 09/28/2023] [Indexed: 10/20/2023] Open
Abstract
Mechanisms that prevent accidental activation of the PINK1/Parkin mitophagy circuit on healthy mitochondria are poorly understood. On the surface of damaged mitochondria, PINK1 accumulates and acts as the input signal to a positive feedback loop of Parkin recruitment, which in turn promotes mitochondrial degradation via mitophagy. However, PINK1 is also present on healthy mitochondria, where it could errantly recruit Parkin and thereby activate this positive feedback loop. Here, we explore emergent properties of the PINK1/Parkin circuit by quantifying the relationship between mitochondrial PINK1 concentrations and Parkin recruitment dynamics. We find that Parkin is recruited to mitochondria only if PINK1 levels exceed a threshold and then only after a delay that is inversely proportional to PINK1 levels. Furthermore, these two regulatory properties arise from the input-coupled positive feedback topology of the PINK1/Parkin circuit. These results outline an intrinsic mechanism by which the PINK1/Parkin circuit can avoid errant activation on healthy mitochondria.
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Affiliation(s)
- Christopher S Waters
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sigurd B Angenent
- Mathematics Department, University of Wisconsin Madison, Madison, WI 53706, USA
| | - Steven J Altschuler
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Lani F Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
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Suresh K, Mattern M, Goldberg MS, Butt TR. The Ubiquitin Proteasome System as a Therapeutic Area in Parkinson's Disease. Neuromolecular Med 2023; 25:313-329. [PMID: 36739586 DOI: 10.1007/s12017-023-08738-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/28/2023] [Indexed: 02/06/2023]
Abstract
Parkinson's disease (PD) is the most common neurodegenerative movement disorder. There are no available therapeutics that slow or halt the progressive loss of dopamine-producing neurons, which underlies the primary clinical symptoms. Currently approved PD drugs can provide symptomatic relief by increasing brain dopamine content or activity; however, the alleviation is temporary, and the effectiveness diminishes with the inevitable progression of neurodegeneration. Discovery and development of disease-modifying neuroprotective therapies has been hampered by insufficient understanding of the root cause of PD-related neurodegeneration. The etiology of PD involves a combination of genetic and environmental factors. Although a single cause has yet to emerge, genetic, cell biological and neuropathological evidence implicates mitochondrial dysfunction and protein aggregation. Postmortem PD brains show pathognomonic Lewy body intraneuronal inclusions composed of aggregated α-synuclein, indicative of failure to degrade misfolded protein. Mutations in the genes that code for α-synuclein, as well as the E3 ubiquitin ligase Parkin, cause rare inherited forms of PD. While many ubiquitin ligases label proteins with ubiquitin chains to mark proteins for degradation by the proteasome, Parkin has been shown to mark dysfunctional mitochondria for degradation by mitophagy. The ubiquitin proteasome system participates in several aspects of the cell's response to mitochondrial damage, affording numerous therapeutic opportunities to augment mitophagy and potentially stop PD progression. This review examines the role and therapeutic potential of such UPS modulators, exemplified by both ubiquitinating and deubiquitinating enzymes.
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Affiliation(s)
- Kumar Suresh
- Progenra Inc., 271A Great Valley Parkway, Malvern, PA, 19355, USA.
| | - Michael Mattern
- Progenra Inc., 271A Great Valley Parkway, Malvern, PA, 19355, USA
| | - Matthew S Goldberg
- Department of Neurology, The University of Alabama at Birmingham, Birmingham, AL, USA
- Center for Neurodegeneration and Experimental Therapeutics, The University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Neurobiology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tauseef R Butt
- Progenra Inc., 271A Great Valley Parkway, Malvern, PA, 19355, USA
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Jin K, Shi Y, Zhang H, Zhangyuan G, Wang F, Li S, Chen C, Zhang J, Wang H, Zhang W, Sun B. A TNFα/Miz1-positive feedback loop inhibits mitophagy in hepatocytes and propagates non-alcoholic steatohepatitis. J Hepatol 2023; 79:403-416. [PMID: 37040844 DOI: 10.1016/j.jhep.2023.03.039] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/13/2023]
Abstract
BACKGROUND & AIMS Non-alcoholic steatohepatitis (NASH) is a chronic inflammatory disease that can further progress to cirrhosis and hepatocellular carcinoma. However, the key molecular mechanisms behind this process have not been clarified. METHODS We analyzed human NASH and normal liver tissue samples by RNA-sequencing and liquid chromatography-mass spectrometry, identifying hepatocyte cytosolic protein Myc-interacting zinc-finger protein 1 (Miz1) as a potential target in NASH progression. We established a Western diet+fructose-induced NASH model in hepatocyte-specific Miz1 knockout and adeno-associated virus type 8-overexpressing mice. Human NASH liver organoids were used to confirm the mechanism, and immunoprecipitation and mass spectrometry were used to detect proteins that could interact with Miz1. RESULTS We demonstrate that Miz1 is reduced in hepatocytes in human NASH. Miz1 is shown to bind to peroxiredoxin 6 (PRDX6), retaining it in the cytosol, blocking its interaction with mitochondrial Parkin at Cys431, and inhibiting Parkin-mediated mitophagy. In NASH livers, loss of hepatocyte Miz1 results in PRDX6-mediated inhibition of mitophagy, increased dysfunctional mitochondria in hepatocytes, and production of proinflammatory cytokines, including TNFα, by hepatic macrophages. Crucially, the increased production of TNFα results in a further reduction in hepatocyte Miz1 by E3-ubiquitination. This produces a positive feedback loop of TNFα-mediated hepatocyte Miz1 degradation, resulting in PRDX6-mediated inhibition of hepatocyte mitophagy, with the accumulation of dysfunctional mitochondria in hepatocytes and increased macrophage TNFα production. CONCLUSIONS Our study identified hepatocyte Miz1 as a suppressor of NASH progression via its role in mitophagy; we also identified a positive feedback loop by which TNFα production induces degradation of cytosolic Miz1, which inhibits mitophagy and thus leads to increased macrophage TNFα production. Interruption of this positive feedback loop could be a strategy to inhibit the progression of NASH. IMPACT AND IMPLICATIONS Non-alcoholic steatohepatitis (NASH) is a chronic inflammatory disease that can further develop into cirrhosis and hepatocellular carcinoma. However, the key molecular mechanism of this process has not been fully clarified. Herein, we identified a positive feedback loop of macrophage TNFα-mediated hepatocyte Miz1 degradation, resulting in PRDX6-mediated inhibition of hepatocyte mitophagy, aggravation of mitochondrial damage and increased macrophage TNFα production. Our findings not only provide mechanistic insight into NASH progression but also provide potential therapeutic targets for patients with NASH. Our human NASH liver organoid culture is therefore a useful platform for exploring treatment strategies for NASH development.
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Affiliation(s)
- Kangpeng Jin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University & Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing 210008, Jiangsu Province, China
| | - Yuze Shi
- Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing 210008, Jiangsu Province, China
| | - Haitian Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University & Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing 210008, Jiangsu Province, China
| | - Guangyan Zhangyuan
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Fei Wang
- Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing 210008, Jiangsu Province, China
| | - Shuo Li
- Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210008, Jiangsu Province, China
| | - Chen Chen
- Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing 210008, Jiangsu Province, China
| | - Jinyao Zhang
- Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Peking Union Medical College Graduate School, Nanjing 210008, Jiangsu Province, China
| | - Hua Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University & Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing 210008, Jiangsu Province, China
| | - Wenjie Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University & Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing 210008, Jiangsu Province, China; Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing 210008, Jiangsu Province, China.
| | - Beicheng Sun
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University & Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing 210008, Jiangsu Province, China; Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing 210008, Jiangsu Province, China.
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Peng W, Schröder LF, Song P, Wong YC, Krainc D. Parkin regulates amino acid homeostasis at mitochondria-lysosome (M/L) contact sites in Parkinson's disease. SCIENCE ADVANCES 2023; 9:eadh3347. [PMID: 37467322 PMCID: PMC10355824 DOI: 10.1126/sciadv.adh3347] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/15/2023] [Indexed: 07/21/2023]
Abstract
Mutations in the E3 ubiquitin ligase parkin are the most common cause of early-onset Parkinson's disease (PD). Although parkin modulates mitochondrial and endolysosomal homeostasis during cellular stress, whether parkin regulates mitochondrial and lysosomal cross-talk under physiologic conditions remains unresolved. Using transcriptomics, metabolomics and super-resolution microscopy, we identify amino acid metabolism as a disrupted pathway in iPSC-derived dopaminergic neurons from patients with parkin PD. Compared to isogenic controls, parkin mutant neurons exhibit decreased mitochondria-lysosome contacts via destabilization of active Rab7. Subcellular metabolomics in parkin mutant neurons reveals amino acid accumulation in lysosomes and their deficiency in mitochondria. Knockdown of the Rab7 GTPase-activating protein TBC1D15 restores mitochondria-lysosome tethering and ameliorates cellular and subcellular amino acid profiles in parkin mutant neurons. Our data thus uncover a function of parkin in promoting mitochondrial and lysosomal amino acid homeostasis through stabilization of mitochondria-lysosome contacts and suggest that modulation of interorganelle contacts may serve as a potential target for ameliorating amino acid dyshomeostasis in disease.
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Affiliation(s)
| | - Leonie F. Schröder
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Pingping Song
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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49
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Moehlman AT, Kanfer G, Youle RJ. Loss of STING in parkin mutant flies suppresses muscle defects and mitochondria damage. PLoS Genet 2023; 19:e1010828. [PMID: 37440574 PMCID: PMC10368295 DOI: 10.1371/journal.pgen.1010828] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 07/25/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023] Open
Abstract
The early pathogenesis and underlying molecular causes of motor neuron degeneration in Parkinson's Disease (PD) remains unresolved. In the model organism Drosophila melanogaster, loss of the early-onset PD gene parkin (the ortholog of human PRKN) results in impaired climbing ability, damage to the indirect flight muscles, and mitochondrial fragmentation with swelling. These stressed mitochondria have been proposed to activate innate immune pathways through release of damage associated molecular patterns (DAMPs). Parkin-mediated mitophagy is hypothesized to suppress mitochondrial damage and subsequent activation of the cGAS/STING innate immunity pathway, but the relevance of this interaction in the fly remains unresolved. Using a combination of genetics, immunoassays, and RNA sequencing, we investigated a potential role for STING in the onset of parkin-null phenotypes. Our findings demonstrate that loss of Drosophila STING in flies rescues the thorax muscle defects and the climbing ability of parkin-/- mutants. Loss of STING also suppresses the disrupted mitochondrial morphology in parkin-/- flight muscles, suggesting unexpected feedback of STING on mitochondria integrity or activation of a compensatory mitochondrial pathway. In the animals lacking both parkin and sting, PINK1 is activated and cell death pathways are suppressed. These findings support a unique, non-canonical role for Drosophila STING in the cellular and organismal response to mitochondria stress.
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Affiliation(s)
- Andrew T. Moehlman
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
- Postdoctoral Research Associate Training Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Gil Kanfer
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Richard J. Youle
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
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50
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Stevens MU, Croteau N, Eldeeb MA, Antico O, Zeng ZW, Toth R, Durcan TM, Springer W, Fon EA, Muqit MM, Trempe JF. Structure-based design and characterization of Parkin-activating mutations. Life Sci Alliance 2023; 6:e202201419. [PMID: 36941054 PMCID: PMC10027901 DOI: 10.26508/lsa.202201419] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/22/2023] Open
Abstract
Autosomal recessive mutations in the Parkin gene cause Parkinson's disease. Parkin encodes an ubiquitin E3 ligase that functions together with the kinase PINK1 in a mitochondrial quality control pathway. Parkin exists in an inactive conformation mediated by autoinhibitory domain interfaces. Thus, Parkin has become a target for the development of therapeutics that activate its ligase activity. Yet, the extent to which different regions of Parkin can be targeted for activation remained unknown. Here, we have used a rational structure-based approach to design new activating mutations in both human and rat Parkin across interdomain interfaces. Out of 31 mutations tested, we identified 11 activating mutations that all cluster near the RING0:RING2 or REP:RING1 interfaces. The activity of these mutants correlates with reduced thermal stability. Furthermore, three mutations V393D, A401D, and W403A rescue a Parkin S65A mutant, defective in mitophagy, in cell-based studies. Overall our data extend previous analysis of Parkin activation mutants and suggests that small molecules that would mimic RING0:RING2 or REP:RING1 destabilisation offer therapeutic potential for Parkinson's disease patients harbouring select Parkin mutations.
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Affiliation(s)
- Michael U Stevens
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Nathalie Croteau
- Department of Pharmacology & Therapeutics, McGill University, Montréal, Canada
- Centre de Recherche en Biologie Structurale, Montpellier, France
| | - Mohamed A Eldeeb
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Odetta Antico
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Zhi Wei Zeng
- Department of Pharmacology & Therapeutics, McGill University, Montréal, Canada
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Thomas M Durcan
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Edward A Fon
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Miratul Mk Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Jean-François Trempe
- Department of Pharmacology & Therapeutics, McGill University, Montréal, Canada
- Centre de Recherche en Biologie Structurale, Montpellier, France
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