151
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Mitophagy in Parkinson's disease: From pathogenesis to treatment target. Neurochem Int 2020; 138:104756. [PMID: 32428526 DOI: 10.1016/j.neuint.2020.104756] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/21/2020] [Accepted: 05/10/2020] [Indexed: 12/13/2022]
Abstract
Healthy mitochondria play an essential role in energy metabolism, but dysfunctional mitochondria can cause perturbations in cellular processes which can ultimately lead to cell death. The process which selectively removes and degrades dysfunctional mitochondria, mitophagy, protects against the accumulation of abnormal mitochondria and hence has a protective role in maintaining cell health. Increasing numbers of studies have linked defective mitophagy to a range of diseases, including Parkinson's disease (PD). Whilst current treatment strategies in PD can improve the classical motor symptoms of the disease, they are also associated with often severe side-effects, and generally do not tackle the underlying progressive neurodegeneration seen in the disease. The identification of novel treatment targets, such as mitophagy, are therefore of increasing interest in PD research. This review will begin by outlining the process of mitophagy, before examining evidence implicating mitophagy in both monogenic and sporadic forms of PD, drawing links between mitophagy and wider pathological processes such as protein accumulation and neuroinflammation. Finally, this review will examine the diverse strategies employed to promote mitophagy so far, discuss considerations arising from these studies, and present a framework for eventual assessment of mitophagy-promoting compounds and their viability as a treatment strategy for PD patients.
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152
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Wang L, Lu G, Shen HM. The Long and the Short of PTEN in the Regulation of Mitophagy. Front Cell Dev Biol 2020; 8:299. [PMID: 32478067 PMCID: PMC7237741 DOI: 10.3389/fcell.2020.00299] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/06/2020] [Indexed: 12/11/2022] Open
Abstract
Mitophagy is a key mitochondrial quality control mechanism for effective and selective elimination of damaged mitochondria through the autophagy-lysosome machinery. Defective mitophagy is associated with pathogenesis of important human diseases including neurodegenerative diseases, heart failure, innate immunity, and cancer. In the past two decades, the mechanistic studies of mitophagy have made many breakthroughs with the discoveries of phosphatase and tensin homolog (PTEN)-induced kinase protein 1 (PINK1)-parkin-mediated ubiquitin (Ub)-driven pathway and BCL2/adenovirus E1B 19 kDa protein-interacting proteins 3 (BNIP3)/NIX or FUN14 domain containing 1 (FUNDC1) mitochondrial receptor-mediated pathways. Recently, several isoforms of dual phosphatase PTEN, such as PTEN-long (PTEN-L), have been identified, and some of them are implicated in the mitophagy process via their protein phosphatase activity. In this review, we aim to discuss the regulatory roles of PTEN isoforms in mitophagy. These discoveries may provide new opportunities for development of novel therapeutic strategies for mitophagy-related diseases such as neurodegenerative disorders via targeting PTEN isoforms and mitophagy.
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Affiliation(s)
- Liming Wang
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Guang Lu
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Han-Ming Shen
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Faculty of Health Sciences, University of Macau, Macau, China
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153
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Hoffmann-Conaway S, Brockmann MM, Schneider K, Annamneedi A, Rahman KA, Bruns C, Textoris-Taube K, Trimbuch T, Smalla KH, Rosenmund C, Gundelfinger ED, Garner CC, Montenegro-Venegas C. Parkin contributes to synaptic vesicle autophagy in Bassoon-deficient mice. eLife 2020; 9:56590. [PMID: 32364493 PMCID: PMC7224700 DOI: 10.7554/elife.56590] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/02/2020] [Indexed: 12/18/2022] Open
Abstract
Mechanisms regulating the turnover of synaptic vesicle (SV) proteins are not well understood. They are thought to require poly-ubiquitination and degradation through proteasome, endo-lysosomal or autophagy-related pathways. Bassoon was shown to negatively regulate presynaptic autophagy in part by scaffolding Atg5. Here, we show that increased autophagy in Bassoon knockout neurons depends on poly-ubiquitination and that the loss of Bassoon leads to elevated levels of ubiquitinated synaptic proteins per se. Our data show that Bassoon knockout neurons have a smaller SV pool size and a higher turnover rate as indicated by a younger pool of SV2. The E3 ligase Parkin is required for increased autophagy in Bassoon-deficient neurons as the knockdown of Parkin normalized autophagy and SV protein levels and rescued impaired SV recycling. These data indicate that Bassoon is a key regulator of SV proteostasis and that Parkin is a key E3 ligase in the autophagy-mediated clearance of SV proteins.
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Affiliation(s)
| | - Marisa M Brockmann
- Charité - Universitätsmedizin Berlin, Institute of Neurobiology, Berlin, Germany.,NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Anil Annamneedi
- Leibniz Institute for Neurobiology, Magdeburg, Germany.,Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany.,Institute of Biology (IBIO), Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Kazi Atikur Rahman
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany.,Einstein Center for Neurosciences Berlin, Berlin, Germany
| | - Christine Bruns
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
| | - Kathrin Textoris-Taube
- Charité - Universitätsmedizin Berlin, Institute of Biochemistry, Core Facility High Throughput Mass Spectrometry, Berlin, Germany
| | - Thorsten Trimbuch
- Charité - Universitätsmedizin Berlin, Institute of Neurobiology, Berlin, Germany.,NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Karl-Heinz Smalla
- Leibniz Institute for Neurobiology, Magdeburg, Germany.,Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
| | - Christian Rosenmund
- Charité - Universitätsmedizin Berlin, Institute of Neurobiology, Berlin, Germany.,NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Eckart D Gundelfinger
- Leibniz Institute for Neurobiology, Magdeburg, Germany.,Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany.,Molecular Neurobiology, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Craig Curtis Garner
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany.,Charité - Universitätsmedizin Berlin, Institute of Neurobiology, Berlin, Germany.,NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Carolina Montenegro-Venegas
- Leibniz Institute for Neurobiology, Magdeburg, Germany.,Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany.,Institute for Pharmacology and Toxicology, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
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154
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Liu L, Liao X, Wu H, Li Y, Zhu Y, Chen Q. Mitophagy and Its Contribution to Metabolic and Aging-Associated Disorders. Antioxid Redox Signal 2020; 32:906-927. [PMID: 31969001 DOI: 10.1089/ars.2019.8013] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Significance: Mitochondria are the cellular powerhouses for ATP synthesis through oxidative phosphorylation, and the centers for fatty acid β-oxidation, metabolite synthesis, reactive oxygen species production, innate immunity, and apoptosis. To fulfill these critical functions, mitochondrial quality and homeostasis must be well maintained. Abnormal mitochondrial quality contributes to aging and age-related disorders, such as metabolic syndrome, cancers, and neurodegenerative diseases. Recent Advances: Mitophagy is a cellular process that selectively removes damaged or superfluous mitochondria by autolysosomal degradation and is regarded as one of the major mechanisms responsible for mitochondrial quality control. Critical Issues: To date, distinct mitophagy pathways have been discovered, including receptor-mediated mitophagy and ubiquitin-dependent mitophagy. Emerging knowledge of these pathways shows that they play important roles in sensing mitochondrial stress and signaling for metabolic adaptations. Future Directions: Here, we provide a review on the molecular mechanisms for mitophagy and its interplay with cellular metabolism, with a particular focus on its role in metabolic and age-related disorders.
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Affiliation(s)
- Lei Liu
- The State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xudong Liao
- The State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Hao Wu
- The State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanjun Li
- The State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yushan Zhu
- The State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Quan Chen
- The State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
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155
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Fritsch LE, Moore ME, Sarraf SA, Pickrell AM. Ubiquitin and Receptor-Dependent Mitophagy Pathways and Their Implication in Neurodegeneration. J Mol Biol 2020; 432:2510-2524. [PMID: 31689437 PMCID: PMC7195237 DOI: 10.1016/j.jmb.2019.10.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/14/2019] [Accepted: 10/20/2019] [Indexed: 12/29/2022]
Abstract
Selective autophagy of mitochondria, or mitophagy, refers to the specific removal and degradation of damaged or surplus mitochondria via targeting to the lysosome for destruction. Disruptions in this homeostatic process may contribute to disease. The identification of diverse mitophagic pathways and how selectivity for each of these pathways is conferred is just beginning to be understood. The removal of both damaged and healthy mitochondria under disease and physiological conditions is controlled by either ubiquitin-dependent or receptor-dependent mechanisms. In this review, we will discuss the known types of mitophagy observed in mammals, recent findings related to PINK1/Parkin-mediated mitophagy (which is the most well-studied form of mitophagy), the implications of defective mitophagy to neurodegenerative processes, and unanswered questions inspiring future research that would enhance our understanding of mitochondrial quality control.
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Affiliation(s)
- Lauren E Fritsch
- Translational Biology, Medicine, and Health Graduate Program, Virginia Polytechnic Institute and State University, Roanoke, VA 24016, USA
| | - M Elyse Moore
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Shireen A Sarraf
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alicia M Pickrell
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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156
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Hou X, Watzlawik JO, Fiesel FC, Springer W. Autophagy in Parkinson's Disease. J Mol Biol 2020; 432:2651-2672. [PMID: 32061929 PMCID: PMC7211126 DOI: 10.1016/j.jmb.2020.01.037] [Citation(s) in RCA: 207] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/24/2020] [Accepted: 01/30/2020] [Indexed: 02/07/2023]
Abstract
Impaired protein homeostasis and accumulation of damaged or abnormally modified protein are common disease mechanisms in many neurodegenerative disorders, including Parkinson's disease (PD). As one of the major degradation pathways, autophagy plays a pivotal role in maintaining effective turnover of proteins and damaged organelles in cells. Several decades of research efforts led to insights into the potential contribution of impaired autophagy machinery to α-synuclein accumulation and the degeneration of dopaminergic neurons, two major features of PD pathology. In this review, we summarize recent pathological, genetic, and mechanistic findings that link defective autophagy with PD pathogenesis in human patients, animals, and cellular models and discuss current challenges in the field.
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Affiliation(s)
- Xu Hou
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | | | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA.
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157
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Dar KB, Bhat AH, Amin S, Reshi BA, Zargar MA, Masood A, Ganie SA. Elucidating Critical Proteinopathic Mechanisms and Potential Drug Targets in Neurodegeneration. Cell Mol Neurobiol 2020; 40:313-345. [PMID: 31584139 DOI: 10.1007/s10571-019-00741-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 08/06/2019] [Indexed: 12/18/2022]
Abstract
Neurodegeneration entails progressive loss of neuronal structure as well as function leading to cognitive failure, apathy, anxiety, irregular body movements, mood swing and ageing. Proteomic dysregulation is considered the key factor for neurodegeneration. Mechanisms involving deregulated processing of proteins such as amyloid beta (Aβ) oligomerization; tau hyperphosphorylation, prion misfolding; α-synuclein accumulation/lewy body formation, chaperone deregulation, acetylcholine depletion, adenosine 2A (A2A) receptor hyperactivation, secretase deregulation, leucine-rich repeat kinase 2 (LRRK2) mutation and mitochondrial proteinopathies have deeper implications in neurodegenerative disorders. Better understanding of such pathological mechanisms is pivotal for exploring crucial drug targets. Herein, we provide a comprehensive outlook about the diverse proteomic irregularities in Alzheimer's, Parkinson's and Creutzfeldt Jakob disease (CJD). We explicate the role of key neuroproteomic drug targets notably Aβ, tau, alpha synuclein, prions, secretases, acetylcholinesterase (AchE), LRRK2, molecular chaperones, A2A receptors, muscarinic acetylcholine receptors (mAchR), N-methyl-D-aspartate receptor (NMDAR), glial cell line-derived neurotrophic factor (GDNF) family ligands (GFLs) and mitochondrial/oxidative stress-related proteins for combating neurodegeneration and associated cognitive and motor impairment. Cross talk between amyloidopathy, synucleinopathy, tauopathy and several other proteinopathies pinpoints the need to develop safe therapeutics with ability to strike multiple targets in the aetiology of the neurodegenerative disorders. Therapeutics like microtubule stabilisers, chaperones, kinase inhibitors, anti-aggregation agents and antibodies could serve promising regimens for treating neurodegeneration. However, drugs should be target specific, safe and able to penetrate blood-brain barrier.
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Affiliation(s)
- Khalid Bashir Dar
- Department of Clinical Biochemistry, Faculty of Biological Sciences, University of Kashmir, Srinagar, India
- Department of Biochemistry, Faculty of Biological Sciences, University of Kashmir, Srinagar, India
| | - Aashiq Hussain Bhat
- Department of Clinical Biochemistry, Faculty of Biological Sciences, University of Kashmir, Srinagar, India
- Department of Biochemistry, Faculty of Biological Sciences, University of Kashmir, Srinagar, India
| | - Shajrul Amin
- Department of Biochemistry, Faculty of Biological Sciences, University of Kashmir, Srinagar, India
| | - Bilal Ahmad Reshi
- Department of Biotechnology, Faculty of Biological Sciences, University of Kashmir, Srinagar, India
| | - Mohammad Afzal Zargar
- Department of Clinical Biochemistry, Faculty of Biological Sciences, University of Kashmir, Srinagar, India
| | - Akbar Masood
- Department of Biochemistry, Faculty of Biological Sciences, University of Kashmir, Srinagar, India
| | - Showkat Ahmad Ganie
- Department of Clinical Biochemistry, Faculty of Biological Sciences, University of Kashmir, Srinagar, India.
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158
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Ke PY. Mitophagy in the Pathogenesis of Liver Diseases. Cells 2020; 9:cells9040831. [PMID: 32235615 PMCID: PMC7226805 DOI: 10.3390/cells9040831] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 02/07/2023] Open
Abstract
Autophagy is a catabolic process involving vacuolar sequestration of intracellular components and their targeting to lysosomes for degradation, thus supporting nutrient recycling and energy regeneration. Accumulating evidence indicates that in addition to being a bulk, nonselective degradation mechanism, autophagy may selectively eliminate damaged mitochondria to promote mitochondrial turnover, a process termed “mitophagy”. Mitophagy sequesters dysfunctional mitochondria via ubiquitination and cargo receptor recognition and has emerged as an important event in the regulation of liver physiology. Recent studies have shown that mitophagy may participate in the pathogenesis of various liver diseases, such as liver injury, liver steatosis/fatty liver disease, hepatocellular carcinoma, viral hepatitis, and hepatic fibrosis. This review summarizes the current knowledge on the molecular regulations and functions of mitophagy in liver physiology and the roles of mitophagy in the development of liver-related diseases. Furthermore, the therapeutic implications of targeting hepatic mitophagy to design a new strategy to cure liver diseases are discussed.
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Affiliation(s)
- Po-Yuan Ke
- Department of Biochemistry & Molecular Biology and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; ; Tel.: +886-3-211-8800 (ext. 5115); Fax: +886-3-211-8700
- Liver Research Center, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan
- Division of Allergy, Immunology, and Rheumatology, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan
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159
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Sun Y, Lu F, Yu X, Wang B, Chen J, Lu F, Peng S, Sun X, Yu M, Chen H, Wang Y, Zhang L, Liu N, Du H, Zhao D, Zhang W. Exogenous H 2S Promoted USP8 Sulfhydration to Regulate Mitophagy in the Hearts of db/db Mice. Aging Dis 2020; 11:269-285. [PMID: 32257541 PMCID: PMC7069468 DOI: 10.14336/ad.2019.0524] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/24/2019] [Indexed: 01/06/2023] Open
Abstract
Hydrogen sulfide (H2S), an important gasotransmitter, regulates cardiovascular functions. Mitochondrial damage induced by the overproduction of reactive oxygen species (ROS) results in myocardial injury with a diabetic state. The purpose of this study was to investigate the effects of exogenous H2S on mitophagy formation in diabetic cardiomyopathy. In this study, we found that exogenous H2S could improve cardiac functions, reduce mitochondrial fragments and ROS levels, enhance mitochondrial respiration chain activities and inhibit mitochondrial apoptosis in the hearts of db/db mice. Our results showed that exogenous H2S facilitated parkin translocation into mitochondria and promoted mitophagy formation in the hearts of db/db mice. Our studies further revealed that the ubiquitination level of cytosolic parkin was increased and the expression of USP8, a deubiquitinating enzyme, was decreased in db/db cardiac tissues. S-sulfhydration is a novel posttranslational modification of specific cysteine residues on target proteins by H2S. Our results showed that the S-sulfhydration level of USP8 was obviously decreased in vivo and in vitro under hyperglycemia and hyperlipidemia, however, exogenous H2S could reverse this effect and promote USP8/parkin interaction. Dithiothreitol, a reducing agent that reverses sulfhydration-mediated covalent modification, increased the ubiquitylation level of parkin, abolished the effects of exogenous H2S on USP8 deubiquitylation and suppressed the interaction of USP8 with parkin in neonatal rat cardiomyocytes treated with high glucose, oleate and palmitate. Our findings suggested that H2S promoted mitophagy formation by increasing S-sulfhydration of USP8, which enhanced deubiquitination of parkin through the recruitment of parkin in mitochondria.
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Affiliation(s)
- Yu Sun
- 1Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Fanghao Lu
- 1Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Xiangjing Yu
- 1Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Bingzhu Wang
- 1Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Jian Chen
- 1Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Fangping Lu
- 1Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Shuo Peng
- 1Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Xiaojiao Sun
- 1Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Miao Yu
- 1Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - He Chen
- 2Department of Forensic Medicine, Harbin Medical University, Harbin, China
| | - Yan Wang
- 3Department of Urologic Surgery, First affiliated hospital of Harbin Medical University, Harbin, China
| | - Linxue Zhang
- 1Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Ning Liu
- 1Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Haining Du
- 1Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Dechao Zhao
- 4Department of Cardiology, First affiliated hospital of Harbin Medical University, Harbin, China
| | - Weihua Zhang
- 1Department of Pathophysiology, Harbin Medical University, Harbin, China.,5Key Laboratory of Cardiovascular Medicine Research (Harbin Medical University), Ministry of Education, Harbin, China
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160
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PINK1/Parkin Mediated Mitophagy, Ca 2+ Signalling, and ER-Mitochondria Contacts in Parkinson's Disease. Int J Mol Sci 2020; 21:ijms21051772. [PMID: 32150829 PMCID: PMC7084677 DOI: 10.3390/ijms21051772] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 12/19/2022] Open
Abstract
Endoplasmic reticulum (ER)–mitochondria contact sites are critical structures for cellular function. They are implicated in a plethora of cellular processes, including Ca2+ signalling and mitophagy, the selective degradation of damaged mitochondria. Phosphatase and tensin homolog (PTEN)-induced kinase (PINK) and Parkin proteins, whose mutations are associated with familial forms of Parkinson’s disease, are two of the best characterized mitophagy players. They accumulate at ER–mitochondria contact sites and modulate organelles crosstalk. Alterations in ER–mitochondria tethering are a common hallmark of many neurodegenerative diseases including Parkinson’s disease. Here, we summarize the current knowledge on the involvement of PINK1 and Parkin at the ER–mitochondria contact sites and their role in the modulation of Ca2+ signalling and mitophagy.
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161
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Ubiquitin-specific protease 8 (USP8/UBPy): a prototypic multidomain deubiquitinating enzyme with pleiotropic functions. Biochem Soc Trans 2020; 47:1867-1879. [PMID: 31845722 PMCID: PMC6925526 DOI: 10.1042/bst20190527] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/29/2019] [Accepted: 12/02/2019] [Indexed: 01/07/2023]
Abstract
Protein modification by ubiquitin is one of the most versatile posttranslational regulations and counteracted by almost 100 deubiquitinating enzymes (DUBs). USP8 was originally identified as a growth regulated ubiquitin-specific protease and is like many other DUBs characterized by its multidomain architecture. Besides the catalytic domain, specific protein-protein interaction modules were characterized which contribute to USP8 substrate recruitment, regulation and targeting to distinct protein complexes. Studies in mice and humans impressively showed the physiological relevance and non-redundant function of USP8 within the context of the whole organism. USP8 knockout (KO) mice exhibit early embryonic lethality while induced deletion in adult animals rapidly causes lethal liver failure. Furthermore, T-cell specific ablation disturbs T-cell development and function resulting in fatal autoimmune inflammatory bowel disease. In human patients, somatic mutations in USP8 were identified as the underlying cause of adrenocorticotropic hormone (ACTH) releasing pituitary adenomas causing Cushing's disease (CD). Here we provide an overview of the versatile molecular, cellular and pathology associated function and regulation of USP8 which appears to depend on specific protein binding partners, substrates and the cellular context.
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162
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Zhang Z, Wang D, Wang P, Zhao Y, You F. OTUD1 Negatively Regulates Type I IFN Induction by Disrupting Noncanonical Ubiquitination of IRF3. THE JOURNAL OF IMMUNOLOGY 2020; 204:1904-1918. [DOI: 10.4049/jimmunol.1900305] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 01/15/2020] [Indexed: 12/21/2022]
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163
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Pathways of protein synthesis and degradation in PD pathogenesis. PROGRESS IN BRAIN RESEARCH 2020; 252:217-270. [PMID: 32247365 DOI: 10.1016/bs.pbr.2020.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Since the discovery of protein aggregates in the brains of individuals with Parkinson's disease (PD) in the early 20th century, the scientific community has been interested in the role of dysfunctional protein metabolism in PD etiology. Recent advances in the field have implicated defective protein handling underlying PD through genetic, in vitro, and in vivo studies incorporating many disease models alongside neuropathological evidence. Here, we discuss the existing body of research focused on understanding cellular pathways of protein synthesis and degradation, and how aberrations in either system could engender PD pathology with special attention to α-synuclein-related consequences. We consider transcription, translation, and post-translational modification to constitute protein synthesis, and protein degradation to encompass proteasome-, lysosome- and endoplasmic reticulum-dependent mechanisms. Novel findings connecting each of these steps in protein metabolism to development of PD indicate that deregulation of protein production and turnover remains an exciting area in PD research.
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164
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Abdrakhmanov A, Gogvadze V, Zhivotovsky B. To Eat or to Die: Deciphering Selective Forms of Autophagy. Trends Biochem Sci 2020; 45:347-364. [PMID: 32044127 DOI: 10.1016/j.tibs.2019.11.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 11/09/2019] [Accepted: 11/18/2019] [Indexed: 12/23/2022]
Abstract
Autophagy is an evolutionarily conserved process whereby damaged and redundant components of the cell are degraded in structures called autophagolysosomes. Currently, three main types of autophagy are recognized: macroautophagy, microautophagy, and chaperone-mediated autophagy (CMA). However, we still know little about some specific types of autophagy that are linked to various intracellular compartments and their roles in the physiology of the whole organism and connections to various diseases. Here, we aim to shed light on the latest insights on and mechanisms of several selective forms of autophagy.
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Affiliation(s)
- Alibek Abdrakhmanov
- Faculty of Medicine, MV Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vladimir Gogvadze
- Faculty of Medicine, MV Lomonosov Moscow State University, 119991 Moscow, Russia; Division of Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 210, 17177 Stockholm, Sweden
| | - Boris Zhivotovsky
- Faculty of Medicine, MV Lomonosov Moscow State University, 119991 Moscow, Russia; Division of Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 210, 17177 Stockholm, Sweden.
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165
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Huang Q, Zhang X. Emerging Roles and Research Tools of Atypical Ubiquitination. Proteomics 2020; 20:e1900100. [PMID: 31930661 DOI: 10.1002/pmic.201900100] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 12/02/2019] [Indexed: 12/19/2022]
Abstract
Ubiquitination is a posttranslational modification characterized by the covalent attachment of ubiquitin molecules to protein substrates. The ubiquitination modification process is reversible, dynamic, and involved in the regulation of various biological processes, such as autophagy, inflammatory responses, and DNA damage responses. The forms of ubiquitin modification are very diverse, incorporating either a single ubiquitin molecule or a complicated ubiquitin polymer, and different types of ubiquitination usually elicit corresponding cellular responses. The development of research tools and strategies has afforded more detailed insight into atypical ubiquitin signaling pathways that were previously poorly understood. Here, an update on the understanding of atypical ubiquitin chain signaling pathways is provided and the recent development of representative research tools for ubiquitin systems is discussed. In addition, the future challenges in ubiquitin research are reflected on and summarized.
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Affiliation(s)
- Qiuling Huang
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Xiaofei Zhang
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510530, China
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166
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Garza-Lombó C, Pappa A, Panayiotidis MI, Franco R. Redox homeostasis, oxidative stress and mitophagy. Mitochondrion 2020; 51:105-117. [PMID: 31972372 DOI: 10.1016/j.mito.2020.01.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 12/21/2019] [Accepted: 01/03/2020] [Indexed: 02/07/2023]
Abstract
Autophagy is a ubiquitous homeostatic mechanism for the degradation or turnover of cellular components. Degradation of mitochondria via autophagy (mitophagy) is involved in a number of physiological processes including cellular homeostasis, differentiation and aging. Upon stress or injury, mitophagy prevents the accumulation of damaged mitochondria and the increased steady state levels of reactive oxygen species leading to oxidative stress and cell death. A number of human diseases, particularly neurodegenerative disorders, have been linked to the dysregulation of mitophagy. In this mini-review, we aimed to review the molecular mechanisms involved in the regulation of mitophagy and their relationship with redox signaling and oxidative stress.
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Affiliation(s)
- Carla Garza-Lombó
- Redox Biology Center and School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, United States.
| | - Aglaia Pappa
- Department of Molecular Biology & Genetics, Democritus University of Thrace, Alexandroupolis 68100, Greece
| | | | - Rodrigo Franco
- Redox Biology Center and School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, United States.
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167
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Autophagy as a Cellular Stress Response Mechanism in the Nervous System. J Mol Biol 2020; 432:2560-2588. [PMID: 31962122 DOI: 10.1016/j.jmb.2020.01.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/11/2019] [Accepted: 01/10/2020] [Indexed: 12/13/2022]
Abstract
Cells of an organism face with various types of insults during their lifetime. Exposure to toxins, metabolic problems, ischaemia/reperfusion, physical trauma, genetic diseases, neurodegenerative diseases are among the conditions that trigger cellular stress responses. In this context, autophagy is one of the mechanisms that supports cell survival under stressful conditions. Autophagic vesicle engulfs the cargo and transports it to lysosome for degradation and turnover. As such, autophagy eliminates abnormal proteins, clears damaged organelles, limits oxidative stress and helps to improve metabolic balance. Nervous system cells and particularly postmitotic neurons are highly sensitive to a spectrum of insults, and autophagy emerges as one of the key stress response mechanism, ensuring health and survival of these vulnerable cell types. In this review, we will overview mechanisms through which cells cope with stress, and how these stress responses regulate autophagy, with a special focus on the nervous system.
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168
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Wang L, Qi H, Tang Y, Shen HM. Post-translational Modifications of Key Machinery in the Control of Mitophagy. Trends Biochem Sci 2020; 45:58-75. [DOI: 10.1016/j.tibs.2019.08.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/05/2019] [Accepted: 08/16/2019] [Indexed: 12/12/2022]
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169
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Feng ST, Wang ZZ, Yuan YH, Wang XL, Sun HM, Chen NH, Zhang Y. Dynamin-related protein 1: A protein critical for mitochondrial fission, mitophagy, and neuronal death in Parkinson’s disease. Pharmacol Res 2020; 151:104553. [DOI: 10.1016/j.phrs.2019.104553] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/14/2019] [Accepted: 11/16/2019] [Indexed: 01/14/2023]
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170
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Sharma A, Trivedi AK. Regulation of apoptosis by E3 ubiquitin ligases in ubiquitin proteasome system. Cell Biol Int 2019; 44:721-734. [PMID: 31814188 DOI: 10.1002/cbin.11277] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/06/2019] [Indexed: 11/10/2022]
Abstract
Apoptosis is an organised ATP-dependent programmed cell death that organisms have evolved to maintain homoeostatic cell numbers and eliminate unnecessary or unhealthy cells from the system. Dysregulation of apoptosis can have serious manifestations culminating into various diseases, especially cancer. Accurate control of apoptosis requires regulation of a wide range of growth enhancing as well as anti-oncogenic factors. Appropriate regulation of magnitude and temporal expression of key proteins is vital to maintain functional apoptotic signalling. Controlled protein turnover is thus critical to the unhindered operation of the apoptotic machinery, disruption of which can have severe consequences, foremost being oncogenic transformation of cells. The ubiquitin proteasome system (UPS) is one such major cellular pathway that maintains homoeostatic protein levels. Recent studies have found interesting links between these two fundamental cellular processes, wherein UPS depending on the cue can either inhibit or promote apoptosis. A diverse range of E3 ligases are involved in regulating the turnover of key proteins of the apoptotic pathway. This review summarises an overview of key E3 ubiquitin ligases involved in the regulation of the fundamental proteins involved in apoptosis, linking UPS to apoptosis and attempts to emphasize the significance of this relationship in context of cancer.
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Affiliation(s)
- Akshay Sharma
- LSS008, Division of Cancer Biology, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow, 226031, India
| | - Arun K Trivedi
- LSS008, Division of Cancer Biology, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow, 226031, India
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171
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De Snoo ML, Friesen EL, Zhang YT, Earnshaw R, Dorval G, Kapadia M, O'Hara DM, Agapova V, Chau H, Pellerito O, Tang MY, Wang X, Schmitt-Ulms G, Durcan TM, Fon EA, Kalia LV, Kalia SK. Bcl-2-associated athanogene 5 (BAG5) regulates Parkin-dependent mitophagy and cell death. Cell Death Dis 2019; 10:907. [PMID: 31787745 PMCID: PMC6885512 DOI: 10.1038/s41419-019-2132-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 10/20/2019] [Accepted: 11/11/2019] [Indexed: 01/06/2023]
Abstract
As pathogenic Parkin mutations result in the defective clearance of damaged mitochondria, Parkin-dependent mitophagy is thought to be protective against the dopaminergic neurodegeneration observed in Parkinson’s disease. Recent studies, however, have demonstrated that Parkin can promote cell death in the context of severe mitochondrial damage by degrading the pro-survival Bcl-2 family member, Mcl-1. Therefore, Parkin may act as a ‘switch’ that can shift the balance between protective or pro-death pathways depending on the degree of mitochondrial damage. Here, we report that the Parkin interacting protein, Bcl-2-associated athanogene 5 (BAG5), impairs mitophagy by suppressing Parkin recruitment to damaged mitochondria and reducing the movement of damaged mitochondria into the lysosomes. BAG5 also enhanced Parkin-mediated Mcl-1 degradation and cell death following severe mitochondrial insult. These results suggest that BAG5 may regulate the bi-modal activity of Parkin, promoting cell death by suppressing Parkin-dependent mitophagy and enhancing Parkin-mediated Mcl-1 degradation.
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Affiliation(s)
- Mitchell L De Snoo
- Krembil Research Institute, Toronto Western Hospital, University Health Network, 60 Leonard Avenue, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, ON, Canada
| | - Erik L Friesen
- Krembil Research Institute, Toronto Western Hospital, University Health Network, 60 Leonard Avenue, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, ON, Canada
| | - Yu Tong Zhang
- Krembil Research Institute, Toronto Western Hospital, University Health Network, 60 Leonard Avenue, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, ON, Canada
| | - Rebecca Earnshaw
- Krembil Research Institute, Toronto Western Hospital, University Health Network, 60 Leonard Avenue, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, ON, Canada
| | - Geneviève Dorval
- McGill Parkinson Program, Department of Neurology & Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Minesh Kapadia
- Krembil Research Institute, Toronto Western Hospital, University Health Network, 60 Leonard Avenue, Toronto, ON, Canada
| | - Darren M O'Hara
- Krembil Research Institute, Toronto Western Hospital, University Health Network, 60 Leonard Avenue, Toronto, ON, Canada
| | - Victoria Agapova
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, ON, Canada
| | - Hien Chau
- Krembil Research Institute, Toronto Western Hospital, University Health Network, 60 Leonard Avenue, Toronto, ON, Canada
| | - Ornella Pellerito
- Krembil Research Institute, Toronto Western Hospital, University Health Network, 60 Leonard Avenue, Toronto, ON, Canada
| | - Matthew Y Tang
- McGill Parkinson Program, Department of Neurology & Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Xinzhu Wang
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
| | - Gerold Schmitt-Ulms
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
| | - Thomas M Durcan
- McGill Parkinson Program, Department of Neurology & Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Edward A Fon
- McGill Parkinson Program, Department of Neurology & Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Lorraine V Kalia
- Krembil Research Institute, Toronto Western Hospital, University Health Network, 60 Leonard Avenue, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, ON, Canada.,Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada.,Morton and Gloria Shulman Movement Disorders Clinic and the Edmond J. Safra Program in Parkinson's Disease, Division of Neurology, Department of Medicine, Toronto Western Hospital, University Health Network, 399 Bathurst Street, Toronto, ON, Canada
| | - Suneil K Kalia
- Krembil Research Institute, Toronto Western Hospital, University Health Network, 60 Leonard Avenue, Toronto, ON, Canada. .,Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, ON, Canada. .,Division of Neurosurgery, Department of Surgery, University of Toronto, 149 College Street, Toronto, ON, Canada.
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172
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Bayne AN, Trempe JF. Mechanisms of PINK1, ubiquitin and Parkin interactions in mitochondrial quality control and beyond. Cell Mol Life Sci 2019; 76:4589-4611. [PMID: 31254044 PMCID: PMC11105328 DOI: 10.1007/s00018-019-03203-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/13/2019] [Accepted: 06/19/2019] [Indexed: 12/20/2022]
Abstract
Parkinson's disease (PD) is a degenerative movement disorder resulting from the loss of specific neuron types in the midbrain. Early environmental and pathophysiological studies implicated mitochondrial damage and protein aggregation as the main causes of PD. These findings are now vindicated by the characterization of more than 20 genes implicated in rare familial forms of the disease. In particular, two proteins encoded by the Parkin and PINK1 genes, whose mutations cause early-onset autosomal recessive PD, function together in a mitochondrial quality control pathway. In this review, we will describe recent development in our understanding of their mechanisms of action, structure, and function. We explain how PINK1 acts as a mitochondrial damage sensor via the regulated proteolysis of its N-terminus and the phosphorylation of ubiquitin tethered to outer mitochondrial membrane proteins. In turn, phospho-ubiquitin recruits and activates Parkin via conformational changes that increase its ubiquitin ligase activity. We then describe how the formation of polyubiquitin chains on mitochondria triggers the recruitment of the autophagy machinery or the formation of mitochondria-derived vesicles. Finally, we discuss the evidence for the involvement of these mechanisms in physiological processes such as immunity and inflammation, as well as the links to other PD genes.
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Affiliation(s)
- Andrew N Bayne
- Department of Pharmacology and Therapeutics and Centre for Structural Biology, McGill University, 3655 Prom Sir William Osler, Montreal, QC, H3G 1Y6, Canada
| | - Jean-François Trempe
- Department of Pharmacology and Therapeutics and Centre for Structural Biology, McGill University, 3655 Prom Sir William Osler, Montreal, QC, H3G 1Y6, Canada.
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173
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Yang X, Pan W, Xu G, Chen L. Mitophagy: A crucial modulator in the pathogenesis of chronic diseases. Clin Chim Acta 2019; 502:245-254. [PMID: 31730816 DOI: 10.1016/j.cca.2019.11.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 10/31/2019] [Accepted: 11/04/2019] [Indexed: 02/07/2023]
Abstract
Mitophagy is an autophagic process through which damaged or dysfunctional mitochondria are specifically degraded to maintain cellular homeostasis. It is highly regulated by various signaling pathways such as the PTEN-induced putative kinase 1 (PINK1)/Parkin and NIP3-like protein X (NIX)/BNIP3 pathways. Additionally, it plays a crucial role in inducing some pathological processes. Notably, some evidence suggesting the association of mitophagy with the occurrence of chronic diseases such as Parkinson's disease (PD), cancer, diabetes, atherosclerosis (AS), and myocardial ischemia reperfusion (MIR) injury is available. Particularly, it has been reported that mitophagy could hinder the development of PD by activating the PINK1/Parkin pathway and acting as a defense mechanism against the induction of diabetes. Conversely, the induction of mitophagy plays dual roles in driving the process of cancer, AS, and MIR injury. In this review, we have explained the role and regulatory mechanisms through which mitophagy plays a role in these chronic pathologies. Importantly, the pharmacological targeting of mitophagy might prove to be a potential alternative for the treatment of these chronic diseases.
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Affiliation(s)
- Xiao Yang
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drugs Study, University of South China, Hengyang 421001, China
| | - Weinan Pan
- Hunan Food and Drug Vocational College, No.345 Bachelor's Road, Yue Lu Science and Technology Industrial Park, Changsha City, Hunan Province, China
| | - Gaosheng Xu
- Department of Breast Surgery, Yueyang Maternal and Child Health-Care Hospital, Yueyang 414000, Hunan Province, China.
| | - Linxi Chen
- Institute of Pharmacy and Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drugs Study, University of South China, Hengyang 421001, China.
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174
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Geisler S, Jäger L, Golombek S, Nakanishi E, Hans F, Casadei N, Terradas AL, Linnemann C, Kahle PJ. Ubiquitin-specific protease USP36 knockdown impairs Parkin-dependent mitophagy via downregulation of Beclin-1-associated autophagy-related ATG14L. Exp Cell Res 2019; 384:111641. [DOI: 10.1016/j.yexcr.2019.111641] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 09/19/2019] [Accepted: 09/20/2019] [Indexed: 01/18/2023]
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175
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Mennerich D, Kubaichuk K, Kietzmann T. DUBs, Hypoxia, and Cancer. Trends Cancer 2019; 5:632-653. [PMID: 31706510 DOI: 10.1016/j.trecan.2019.08.005] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/24/2019] [Accepted: 08/27/2019] [Indexed: 02/08/2023]
Abstract
Alterations in protein ubiquitylation and hypoxia are commonly associated with cancer. Ubiquitylation is carried out by three sequentially acting ubiquitylating enzymes and can be opposed by deubiquitinases (DUBs), which have emerged as promising drug targets. Apart from protein localization and activity, ubiquitylation regulates degradation of proteins, among them hypoxia-inducible factors (HIFs). Thereby, various E3 ubiquitin ligases and DUBs regulate HIF abundance. Conversely, several E3s and DUBs are regulated by hypoxia. While hypoxia is a powerful HIF regulator, less is known about hypoxia-regulated DUBs and their impact on HIFs. Here, we review current knowledge about the relationship of E3s, DUBs, and hypoxia signaling. We also discuss the reciprocal regulation of DUBs by hypoxia and use of DUB-specific drugs in cancer.
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Affiliation(s)
- Daniela Mennerich
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, 90570, Finland
| | - Kateryna Kubaichuk
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, 90570, Finland
| | - Thomas Kietzmann
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, 90570, Finland; Biocenter Oulu, University of Oulu, Oulu, 90570, Finland.
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176
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Fung TS, Ji WK, Higgs HN, Chakrabarti R. Two distinct actin filament populations have effects on mitochondria, with differences in stimuli and assembly factors. J Cell Sci 2019; 132:jcs234435. [PMID: 31413070 PMCID: PMC6765187 DOI: 10.1242/jcs.234435] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 08/07/2019] [Indexed: 12/12/2022] Open
Abstract
Recent studies show that mitochondria and actin filaments work together in two contexts: (1) increased cytoplasmic calcium induces cytoplasmic actin polymerization that stimulates mitochondrial fission and (2) mitochondrial depolarization causes actin assembly around mitochondria, with roles in mitophagy. It is unclear whether these two processes utilize similar actin assembly mechanisms. Here, we show that these are distinct actin assembly mechanisms in the acute phase after treatment (<10 min). Calcium-induced actin assembly is INF2 dependent and Arp2/3 complex independent, whereas depolarization-induced actin assembly is Arp2/3 complex dependent and INF2 independent. The two types of actin polymerization are morphologically distinct, with calcium-induced filaments throughout the cytosol and depolarization-induced filaments as 'clouds' around depolarized mitochondria. We have previously shown that calcium-induced actin stimulates increases in both mitochondrial calcium and recruitment of the dynamin GTPase Drp1 (also known as DNM1L). In contrast, depolarization-induced actin is temporally associated with extensive mitochondrial dynamics that do not result in mitochondrial fission, but in circularization of the inner mitochondrial membrane (IMM). These dynamics are dependent on the protease OMA1 and independent of Drp1. Actin cloud inhibition causes increased IMM circularization, suggesting that actin clouds limit these dynamics.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Tak Shun Fung
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Wei-Ke Ji
- Department of Biochemistry and Molecular Biology, School of Basic Medicine and the Collaborative Innovation Center for Brain Science, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Henry N Higgs
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Rajarshi Chakrabarti
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
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177
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Shin S, Kim K, Kim HR, Ylaya K, Do SI, Hewitt SM, Park HS, Roe JS, Chung JY, Song J. Deubiquitylation and stabilization of Notch1 intracellular domain by ubiquitin-specific protease 8 enhance tumorigenesis in breast cancer. Cell Death Differ 2019; 27:1341-1354. [PMID: 31527799 DOI: 10.1038/s41418-019-0419-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 07/31/2019] [Accepted: 09/04/2019] [Indexed: 12/13/2022] Open
Abstract
Notch, an essential factor in tissue development and homoeostasis, has been reported to play an oncogenic function in a variety of cancers. Here, we report ubiquitin-specific protease 8 (USP8) as a novel deubiquitylase of Notch1 intracellular domain (NICD). USP8 specifically stabilizes and deubiquitylates NICD through a direct interaction. The inhibition of USP8 downregulated the Notch signalling pathway via NICD destabilization, resulting in the retardation of cellular growth, wound closure, and colony forming ability of breast cancer cell lines. These phenomena were restored by the reconstitution of NICD or USP8, supporting the direct interaction between these two proteins. The expression levels of NICD and USP8 proteins were positively correlated in patients with advanced breast cancer. Taken together, our results suggest that USP8 functions as a positive regulator of Notch signalling, offering a therapeutic target for breast cancer.
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Affiliation(s)
- Soyeon Shin
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Kyungeun Kim
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, 03181, Republic of Korea
| | - Hwa-Ryeon Kim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Kris Ylaya
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sung-Im Do
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, 03181, Republic of Korea
| | - Stephen M Hewitt
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hee-Sae Park
- Hormone Research Center, School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea
| | - Jae-Seok Roe
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Joon-Yong Chung
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jaewhan Song
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
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178
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Liang H, Su X, Wu Q, Shan H, Lv L, Yu T, Zhao X, Sun J, Yang R, Zhang L, Yan H, Zhou Y, Li X, Du Z, Shan H. LncRNA 2810403D21Rik/Mirf promotes ischemic myocardial injury by regulating autophagy through targeting Mir26a. Autophagy 2019; 16:1077-1091. [PMID: 31512556 DOI: 10.1080/15548627.2019.1659610] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
More evidence is emerging of the roles long non-coding RNAs (lncRNAs) play as regulatory factors in a variety of biological processes, but the mechanisms underlying the function of lncRNAs in acute myocardial infarction (AMI) have not been explicitly delineated. The present study identified the lncRNA 2810403D21Rik/AK007586/Mirf (myocardial infarction-regulatory factor), that inhibited macroautophagy/autophagy by modulating Mir26a (microRNA 26a). Inhibition of Mir26a led to cardiac injury both in vitro and in vivo, whereas overexpression of Mir26a attenuated ischemic stress-induced cell death by activating autophagy through targeting Usp15 (ubiquitin specific peptidase 15). More importantly, 2810403D21Rik/Mirf acted as a competitive endogenous RNA (ceRNA) of Mir26a; forced expression of 2810403D21Rik/Mirf downregulated Mir26a to inhibit autophagy. In contrast, loss of 2810403D21Rik/Mirf resulted in upregulation of Mir26a to promote autophagy and alleviate cardiac injury, which in turn improved cardiac function in MI mice. This study identified a lncRNA 2810403D21Rik/Mirf that functions as an anti-autophagic molecule via ceRNA activity toward Mir26a. Our findings suggest that knockdown of 2810403D21Rik/Mirf might be a novel therapeutic approach for cardiac diseases associated with autophagy. ABBREVIATIONS 3-MA: 3-methyladenine; AAV-9: adenovirus associated virus-9; agoMir26a: cholesterol-conjugated Mir26a mimic; AMI: acute myocardial infarction; AMO-26a: Mir26a inhibitor; ATG: autophagy related; BECN1: beclin 1; ceRNA: competitive endogenous RNAs; EF: ejection fraction; f-2810403D21Rik/Mirf: fragment encompassing the Mir26a binding site; FS: fraction shortening; GFP-mRFP: a plasmid expressing green fluorescent protein-monomeric red fluorescent protein; lncRNA: long non-coding RNA; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; Mirf: myocardial infarction-regulatory factor; miRNAs: microRNAs; NC: negative control; NMCMs: neonatal mice cardiomyocytes; shRNA: short hairpin RNA; siRNA: small interfering RNA; SQSTM1/p62: sequestosome 1; TEM: transmission electron microscopy; Usp15: ubiquitin specific peptidase 15.
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Affiliation(s)
- Haihai Liang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University , Harbin, Heilongjiang, P. R. China.,Northern Translational Medicine Research and Cooperation Center, Heilongjiang Academy of Medical Sciences, Harbin Medical University , Harbin, Heilongjiang, P. R. China
| | - Xiaomin Su
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University , Harbin, Heilongjiang, P. R. China.,Northern Translational Medicine Research and Cooperation Center, Heilongjiang Academy of Medical Sciences, Harbin Medical University , Harbin, Heilongjiang, P. R. China
| | - Qiuxia Wu
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University , Harbin, Heilongjiang, P. R. China.,Northern Translational Medicine Research and Cooperation Center, Heilongjiang Academy of Medical Sciences, Harbin Medical University , Harbin, Heilongjiang, P. R. China
| | - Huitong Shan
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University , Harbin, Heilongjiang, P. R. China.,Northern Translational Medicine Research and Cooperation Center, Heilongjiang Academy of Medical Sciences, Harbin Medical University , Harbin, Heilongjiang, P. R. China
| | - Lifang Lv
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University , Harbin, Heilongjiang, P. R. China
| | - Tong Yu
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University , Harbin, Heilongjiang, P. R. China.,Northern Translational Medicine Research and Cooperation Center, Heilongjiang Academy of Medical Sciences, Harbin Medical University , Harbin, Heilongjiang, P. R. China
| | - Xiaoguang Zhao
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University , Harbin, Heilongjiang, P. R. China.,Northern Translational Medicine Research and Cooperation Center, Heilongjiang Academy of Medical Sciences, Harbin Medical University , Harbin, Heilongjiang, P. R. China
| | - Jian Sun
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University , Harbin, Heilongjiang, P. R. China.,Northern Translational Medicine Research and Cooperation Center, Heilongjiang Academy of Medical Sciences, Harbin Medical University , Harbin, Heilongjiang, P. R. China
| | - Rui Yang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University , Harbin, Heilongjiang, P. R. China
| | - Lu Zhang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University , Harbin, Heilongjiang, P. R. China.,Northern Translational Medicine Research and Cooperation Center, Heilongjiang Academy of Medical Sciences, Harbin Medical University , Harbin, Heilongjiang, P. R. China
| | - He Yan
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University , Harbin, Heilongjiang, P. R. China.,Northern Translational Medicine Research and Cooperation Center, Heilongjiang Academy of Medical Sciences, Harbin Medical University , Harbin, Heilongjiang, P. R. China
| | - Yuhong Zhou
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University , Harbin, Heilongjiang, P. R. China
| | - Xuelian Li
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University , Harbin, Heilongjiang, P. R. China
| | - Zhimin Du
- Institute of Clinical Pharmacy, The 2nd Affiliated Hospital, Harbin Medical University , Harbin, Heilongjiang, P. R. China
| | - Hongli Shan
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University , Harbin, Heilongjiang, P. R. China.,Northern Translational Medicine Research and Cooperation Center, Heilongjiang Academy of Medical Sciences, Harbin Medical University , Harbin, Heilongjiang, P. R. China
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179
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Niu K, Fang H, Chen Z, Zhu Y, Tan Q, Wei D, Li Y, Balajee AS, Zhao Y. USP33 deubiquitinates PRKN/parkin and antagonizes its role in mitophagy. Autophagy 2019; 16:724-734. [PMID: 31432739 DOI: 10.1080/15548627.2019.1656957] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
PRKN/parkin activation through phosphorylation of its ubiquitin and ubiquitin-like domain by PINK1 is critical in mitophagy induction for eliminating the damaged mitochondria. Deubiquitinating enzymes (DUBs) functionally reversing PRKN ubiquitination are critical in controlling the magnitude of PRKN-mediated mitophagy process. However, potential DUBs that directly target PRKN and antagonize its pro-mitophagy effect remains to be identified and characterized. Here, we demonstrated that USP33/VDU1 is localized at the outer membrane of mitochondria and serves as a PRKN DUB through their interaction. Cellular and in vitro assays illustrated that USP33 deubiquitinates PRKN in a DUB activity-dependent manner. USP33 prefers to remove K6, K11, K48 and K63-linked ubiquitin conjugates from PRKN, and deubiquitinates PRKN mainly at Lys435. Mutation of this site leads to a significantly decreased level of K63-, but not K48-linked PRKN ubiquitination. USP33 deficiency enhanced both K48- and K63-linked PRKN ubiquitination, but only K63-linked PRKN ubiquitination was significantly increased under mitochondrial depolarization. Further, USP33 knockdown increased both PRKN protein stabilization and its translocation to depolarized mitochondria leading to the enhancement of mitophagy. Moreover, USP33 silencing protects SH-SY5Y human neuroblastoma cells from the neurotoxin MPTP-induced apoptotic cell death. Our findings convincingly demonstrate that USP33 is a novel PRKN deubiquitinase antagonizing its regulatory roles in mitophagy and SH-SY5Y neuron-like cell survival. Thus, USP33 inhibition may represents an attractive new therapeutic strategy for PD patients.Abbreviations: CCCP: carbonyl cyanide 3-chlorophenylhydrazone; DUB: deubiquitinating enzymes; MPTP: 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine; OMM: outer mitochondrial membrane; PD: Parkinson disease; PINK1: PTEN induced kinase 1; PRKN/PARK2: parkin RBR E3 ubiquitin protein ligase; ROS: reactive oxygen species; TM: transmembrane; Ub: ubiquitin; UBA1: ubiquitin like modifier activating enzyme 1; UBE2L3/UbcH7: ubiquitin conjugating enzyme E2 L3; USP33: ubiquitin specific peptidase 33; WT: wild type.
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Affiliation(s)
- Kaifeng Niu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hongbo Fang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Zixiang Chen
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuqi Zhu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qunsong Tan
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Di Wei
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yueyang Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Adayabalam S Balajee
- REAC/TS, Oak Ridge Associated Universities, Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Yongliang Zhao
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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180
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Insights into ubiquitin chain architecture using Ub-clipping. Nature 2019; 572:533-537. [PMID: 31413367 DOI: 10.1038/s41586-019-1482-y] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 07/17/2019] [Indexed: 01/17/2023]
Abstract
Protein ubiquitination is a multi-functional post-translational modification that affects all cellular processes. Its versatility arises from architecturally complex polyubiquitin chains, in which individual ubiquitin moieties may be ubiquitinated on one or multiple residues, and/or modified by phosphorylation and acetylation1-3. Advances in mass spectrometry have enabled the mapping of individual ubiquitin modifications that generate the ubiquitin code; however, the architecture of polyubiquitin signals has remained largely inaccessible. Here we introduce Ub-clipping as a methodology by which to understand polyubiquitin signals and architectures. Ub-clipping uses an engineered viral protease, Lbpro∗, to incompletely remove ubiquitin from substrates and leave the signature C-terminal GlyGly dipeptide attached to the modified residue; this simplifies the direct assessment of protein ubiquitination on substrates and within polyubiquitin. Monoubiquitin generated by Lbpro∗ retains GlyGly-modified residues, enabling the quantification of multiply GlyGly-modified branch-point ubiquitin. Notably, we find that a large amount (10-20%) of ubiquitin in polymers seems to exist as branched chains. Moreover, Ub-clipping enables the assessment of co-existing ubiquitin modifications. The analysis of depolarized mitochondria reveals that PINK1/parkin-mediated mitophagy predominantly exploits mono- and short-chain polyubiquitin, in which phosphorylated ubiquitin moieties are not further modified. Ub-clipping can therefore provide insight into the combinatorial complexity and architecture of the ubiquitin code.
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181
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Bowling JL, Skolfield MC, Riley WA, Nolin AP, Wolf LC, Nelson DE. Temporal integration of mitochondrial stress signals by the PINK1:Parkin pathway. BMC Mol Cell Biol 2019; 20:33. [PMID: 31412778 PMCID: PMC6694515 DOI: 10.1186/s12860-019-0220-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/08/2019] [Indexed: 11/10/2022] Open
Abstract
Background The PINK1:Parkin pathway regulates the autophagic removal of damaged and dysfunctional mitochondria. While the response of this pathway to complete loss of ΔΨm, as caused by high concentrations of mitochondrial ionophores, has been well characterized, it remains unclear how the pathway makes coherent decisions about whether to keep or purge mitochondria in situations where ΔΨm is only partially lost or exhibits fluctuations, as has been observed in response to certain types of cellular stress. Results To investigate the responses of the PINK1:Parkin pathway to mitochondrial insults of different magnitude and duration, controlled titration of the mitochondrial protonophore, CCCP, was used to manipulate ΔΨm in live cells, and the dynamics of PINK1 and Parkin recruitment was measured by fluorescence microscopy. In contrast to the stable accumulation of PINK1 and Parkin seen at completely depolarized mitochondria, partial depolarization produced a transient pulse of PINK1 stabilization and rapid loss, which was driven by small fluctuations in ΔΨm. As the rate of Parkin dissociation from the mitochondria and phospho-polyubiquitin chain removal was comparatively slow, repetitive pulses of PINK1 were able to drive a slow step-wise accumulation of Parkin and phospho-polyubiquitin leading to deferred mitophagy. Conclusion These data suggest that the PINK1:Parkin mitophagy pathway is able to exhibit distinct dynamic responses to complete and partial mitochondrial depolarization. In this way, the pathway is able to differentiate between irretrievably damaged mitochondria and those showing signs of dysfunction, promoting either rapid or delayed autophagy, respectively. Electronic supplementary material The online version of this article (10.1186/s12860-019-0220-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- J Logan Bowling
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | | | - Wesley A Riley
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Andrew P Nolin
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Larissa C Wolf
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - David E Nelson
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA.
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182
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Kovalchuke L, Mosharov EV, Levy OA, Greene LA. Stress-induced phospho-ubiquitin formation causes parkin degradation. Sci Rep 2019; 9:11682. [PMID: 31406131 PMCID: PMC6690910 DOI: 10.1038/s41598-019-47952-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 07/26/2019] [Indexed: 12/21/2022] Open
Abstract
Mutations in the E3 ubiquitin ligase parkin are the most common known cause of autosomal recessive Parkinson’s disease (PD), and parkin depletion may play a role in sporadic PD. Here, we sought to elucidate the mechanisms by which stress decreases parkin protein levels using cultured neuronal cells and the PD-relevant stressor, L-DOPA. We find that L-DOPA causes parkin loss through both oxidative stress-independent and oxidative stress-dependent pathways. Characterization of the latter reveals that it requires both the kinase PINK1 and parkin’s interaction with phosphorylated ubiquitin (phospho-Ub) and is mediated by proteasomal degradation. Surprisingly, autoubiquitination and mitophagy do not appear to be required for such loss. In response to stress induced by hydrogen peroxide or CCCP, parkin degradation also requires its association with phospho-Ub, indicating that this mechanism is broadly generalizable. As oxidative stress, metabolic dysfunction and phospho-Ub levels are all elevated in PD, we suggest that these changes may contribute to a loss of parkin expression.
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Affiliation(s)
| | - Eugene V Mosharov
- Departments of Psychiatry, Neurology, and Pharmacology, Columbia University: Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, USA
| | - Oren A Levy
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Lloyd A Greene
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA.
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183
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Liu J, Liu W, Li R, Yang H. Mitophagy in Parkinson's Disease: From Pathogenesis to Treatment. Cells 2019; 8:cells8070712. [PMID: 31336937 PMCID: PMC6678174 DOI: 10.3390/cells8070712] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/07/2019] [Accepted: 07/10/2019] [Indexed: 01/20/2023] Open
Abstract
Parkinson’s disease (PD) is the second most common neurodegenerative disease. The pathogenesis of PD is complicated and remains obscure, but growing evidence suggests the involvement of mitochondrial and lysosomal dysfunction. Mitophagy, the process of removing damaged mitochondria, is compromised in PD patients and models, and was found to be associated with accelerated neurodegeneration. Several PD-related proteins are known to participate in the regulation of mitophagy, including PINK1 and Parkin. In addition, mutations in several PD-related genes are known to cause mitochondrial defects and neurotoxicity by disturbing mitophagy, indicating that mitophagy is a critical component of PD pathogenesis. Therefore, it is crucial to understand how these genes are involved in mitochondrial quality control or mitophagy regulation in the study of PD pathogenesis and the development of novel treatment strategies. In this review, we will discuss the critical roles of mitophagy in PD pathogenesis, highlighting the potential therapeutic implications of mitophagy regulation.
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Affiliation(s)
- Jia Liu
- Department of Neurobiology School of Basic Medical Sciences, Beijing Institute for Brain Disorders, Capital Medical University, Beijing 100069, China
| | - Weijin Liu
- Department of Neurobiology School of Basic Medical Sciences, Beijing Institute for Brain Disorders, Capital Medical University, Beijing 100069, China
| | - Ruolin Li
- Department of Neurobiology School of Basic Medical Sciences, Beijing Institute for Brain Disorders, Capital Medical University, Beijing 100069, China
| | - Hui Yang
- Department of Neurobiology School of Basic Medical Sciences, Beijing Institute for Brain Disorders, Capital Medical University, Beijing 100069, China.
- Center of Parkinson's Disease Beijing Key Laboratory of Neural Regeneration and Repair, Beijing Key Laboratory on Parkinson's Disease, Key Laboratory for Neurodegenerative Disease of the Ministry of Education, Beijing 100069, China.
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184
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Peng H, Yang F, Hu Q, Sun J, Peng C, Zhao Y, Huang C. The ubiquitin-specific protease USP8 directly deubiquitinates SQSTM1/p62 to suppress its autophagic activity. Autophagy 2019; 16:698-708. [PMID: 31241013 DOI: 10.1080/15548627.2019.1635381] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
SQSTM1/p62 (sequestosome 1) is a critical macroautophagy/autophagy receptor that promotes the formation and degradation of ubiquitinated aggregates. SQSTM1 can be modified by ubiquitination, and this modification modulates its autophagic activity. However, the molecular mechanisms underpinning its reversible deubiquitination have never been described. Here we report that USP8 (ubiquitin specific peptidase 8) directly interacted with and deubiquitinated SQSTM1. USP8 preferentially removed the lysine 11 (K11)-linked ubiquitin chains from SQSTM1. Moreover, USP8 deubiquitinated SQSTM1 principally at K420 within its ubiquitin-association (UBA) domain. Finally, USP8 inhibited SQSTM1 degradation and autophagic influx in cells with wild-type SQSTM1, but not its mutant with substitution of K420 with an arginine. Taken together, USP8 acts as a negative regulator of autophagy by deubiquitinating SQSTM1 at K420.Abbreviations: BafA1: bafilomycin A1; BAP1: BRCA1 associated protein 1; DUB: deubiquitinating enzyme; ESCRT: endosomal sorting complex required for transport; HTT: huntingtin; K: lysine; KEAP1: kelch like ECH associated protein 1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MEF: mouse embryonic fibroblast; shRNA: short hairpin RNA; SQSTM1: sequestosome 1; Ub: ubiquitin; UBA: ubiquitin-association; UBE2D2: ubiquitin conjugating enzyme E2 D2; UBE2D3: ubiquitin conjugating enzyme E2 D3; USP: ubiquitin specific peptidase; WT: wild-type.
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Affiliation(s)
- Hong Peng
- Shanghai Institute of Immunology & Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Laboratory of Medical Virology, School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Fang Yang
- Shanghai Institute of Immunology & Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qianwen Hu
- Shanghai Institute of Immunology & Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Sun
- Department of Breast Surgery, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Cheng Peng
- Shanghai Institute of Immunology & Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yao Zhao
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chuanxin Huang
- Shanghai Institute of Immunology & Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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185
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Liu X, Hebron M, Shi W, Lonskaya I, Moussa CEH. Ubiquitin specific protease-13 independently regulates parkin ubiquitination and alpha-synuclein clearance in alpha-synucleinopathies. Hum Mol Genet 2019; 28:548-560. [PMID: 30329047 DOI: 10.1093/hmg/ddy365] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/09/2018] [Indexed: 12/22/2022] Open
Abstract
Ubiquitin specific proteases (USPs) are de-ubiquitinases (DUBs) that control protein ubiquitination cycle. The role of DUBs is poorly understood in neurodegenerative diseases. We found that USP13 is overexpressed in post-mortem Parkinson's disease (PD) brains. We investigated whether changes in USP13 levels can affect two molecules, parkin and alpha-synuclein, that are implicated in PD pathogenesis. Parkin is an E3 ubiquitin ligase that is regulated by ubiquitination and targets certain proteins for degradation, and alpha-synuclein may be ubiquitinated and recycled in the normal brain. We found that USP13 independently regulates parkin and alpha-synuclein ubiquitination in models of alpha-synucleinopathies. USP13 shRNA knockdown increases alpha-synuclein ubiquitination and clearance, in a parkin-independent manner. Furthermore, USP13 overexpression counteracts the effects of a tyrosine kinase inhibitor, Nilotinib, while USP13 knockdown facilitates Nilotinib effects on alpha-synculein clearance, suggesting that alpha-synuclein ubiquitnation is important for its clearance. These studies provide novel evidence of USP13 effects on parkin and alpha-synuclein metabolism and suggest that USP13 is a potential therapeutic target in the alpha-synucleinopathies.
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Affiliation(s)
- Xiaoguang Liu
- Department of Neurology, Laboratory for Dementia and Parkinsonism, Translational Neurotherapeutics Program, National Parkinson's Foundation Center of Excellence, Lewy Body Dementia Research Center of Excellence, Georgetown University Medical Center, N.W. Washington D.C., USA
| | - Michaeline Hebron
- Department of Neurology, Laboratory for Dementia and Parkinsonism, Translational Neurotherapeutics Program, National Parkinson's Foundation Center of Excellence, Lewy Body Dementia Research Center of Excellence, Georgetown University Medical Center, N.W. Washington D.C., USA
| | - Wangke Shi
- Department of Neurology, Laboratory for Dementia and Parkinsonism, Translational Neurotherapeutics Program, National Parkinson's Foundation Center of Excellence, Lewy Body Dementia Research Center of Excellence, Georgetown University Medical Center, N.W. Washington D.C., USA
| | - Irina Lonskaya
- Department of Neurology, Laboratory for Dementia and Parkinsonism, Translational Neurotherapeutics Program, National Parkinson's Foundation Center of Excellence, Lewy Body Dementia Research Center of Excellence, Georgetown University Medical Center, N.W. Washington D.C., USA
| | - Charbel E-H Moussa
- Department of Neurology, Laboratory for Dementia and Parkinsonism, Translational Neurotherapeutics Program, National Parkinson's Foundation Center of Excellence, Lewy Body Dementia Research Center of Excellence, Georgetown University Medical Center, N.W. Washington D.C., USA
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186
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Chakraborty J, von Stockum S, Marchesan E, Caicci F, Ferrari V, Rakovic A, Klein C, Antonini A, Bubacco L, Ziviani E. USP14 inhibition corrects an in vivo model of impaired mitophagy. EMBO Mol Med 2019; 10:emmm.201809014. [PMID: 30249595 PMCID: PMC6220287 DOI: 10.15252/emmm.201809014] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Mitochondrial autophagy or mitophagy is a key process that allows selective sequestration and degradation of dysfunctional mitochondria to prevent excessive reactive oxygen species, and activation of cell death. Recent studies revealed that ubiquitin–proteasome complex activity and mitochondrial membrane rupture are key steps preceding mitophagy, in combination with the ubiquitination of specific outer mitochondrial membrane (OMM) proteins. The deubiquitinating enzyme ubiquitin‐specific peptidase 14 (USP14) has been shown to modulate both proteasome activity and autophagy. Here, we report that genetic and pharmacological inhibition of USP14 promotes mitophagy, which occurs in the absence of the well‐characterised mediators of mitophagy, PINK1 and Parkin. Critical to USP14‐induced mitophagy is the exposure of the LC3 receptor Prohibitin 2 by mitochondrial fragmentation and mitochondrial membrane rupture. Genetic or pharmacological inhibition of USP14 in vivo corrected mitochondrial dysfunction and locomotion behaviour of PINK1/Parkin mutant Drosophila model of Parkinson's disease, an age‐related progressive neurodegenerative disorder that is correlated with diminished mitochondrial quality control. Our study identifies a novel therapeutic target that ameliorates mitochondrial dysfunction and in vivo PD‐related symptoms.
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Affiliation(s)
| | | | | | | | - Vanni Ferrari
- Department of Biology, University of Padova, Padova, Italy
| | | | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Angelo Antonini
- Department of Neuroscience, University of Padova, Padova, Italy
| | - Luigi Bubacco
- Department of Biology, University of Padova, Padova, Italy
| | - Elena Ziviani
- Department of Biology, University of Padova, Padova, Italy .,Fondazione Ospedale San Camillo IRCCS, Venezia, Italia
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187
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Involvement of E3 Ligases and Deubiquitinases in the Control of HIF-α Subunit Abundance. Cells 2019; 8:cells8060598. [PMID: 31208103 PMCID: PMC6627837 DOI: 10.3390/cells8060598] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/07/2019] [Accepted: 06/13/2019] [Indexed: 12/21/2022] Open
Abstract
The ubiquitin and hypoxia-inducible factor (HIF) pathways are cellular processes involved in the regulation of a variety of cellular functions. Enzymes called ubiquitin E3 ligases perform protein ubiquitylation. The action of these enzymes can be counteracted by another group of enzymes called deubiquitinases (DUBs), which remove ubiquitin from target proteins. The balanced action of these enzymes allows cells to adapt their protein content to a variety of cellular and environmental stress factors, including hypoxia. While hypoxia appears to be a powerful regulator of the ubiquitylation process, much less is known about the impact of DUBs on the HIF system and hypoxia-regulated DUBs. Moreover, hypoxia and DUBs play crucial roles in many diseases, such as cancer. Hence, DUBs are considered to be promising targets for cancer cell-specific treatment. Here, we review the current knowledge about the role DUBs play in the control of HIFs, the regulation of DUBs by hypoxia, and their implication in cancer progression.
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188
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Corti O. Neuronal Mitophagy: Lessons from a Pathway Linked to Parkinson's Disease. Neurotox Res 2019; 36:292-305. [PMID: 31102068 DOI: 10.1007/s12640-019-00060-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 04/17/2019] [Accepted: 05/06/2019] [Indexed: 02/06/2023]
Abstract
Neurons are specialized cells with complex and extended architecture and high energy requirements. Energy in the form of adenosine triphosphate, produced essentially by mitochondrial respiration, is necessary to preserve neuronal morphology, maintain resting potential, fire action potentials, and ensure neurotransmission. Pools of functional mitochondria are required in all neuronal compartments, including cell body and dendrites, nodes of Ranvier, growth cones, axons, and synapses. The mechanisms by which old or damaged mitochondria are removed and replaced in neurons remain to be fully understood. Mitophagy has gained considerable interest since the discovery of familial forms of Parkinson's disease caused by dysfunction of PINK1 and Parkin, two multifunctional proteins cooperating in the regulation of this process. Over the past 10 years, the molecular mechanisms by which PINK1 and Parkin jointly promote the degradation of defective mitochondria by autophagy have been dissected. However, our understanding of the relevance of mitophagy to mitochondrial homeostasis in neurons remains poor. Insight has been recently gained thanks to the development of fluorescent reporter systems for tracking mitochondria in the acidic compartment of the lysosome. Using these tools, mitophagy events have been visualized in primary neurons in culture and in vivo, under basal conditions and in response to toxic insults. Despite these advances, whether PINK1 and Parkin play a major role in promoting neuronal mitophagy under physiological conditions in adult animals and during aging remains a matter of debate. Future studies will have to clarify in how far dysfunction of neuronal mitophagy is central to the pathophysiology of Parkinson's disease.
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Affiliation(s)
- Olga Corti
- Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France.
- Inserm, U1127, F-75013, Paris, France.
- CNRS, UMR 7225, F-75013, Paris, France.
- Sorbonne Universités, F-75013, Paris, France.
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189
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Pearson G, Soleimanpour SA. Visualization of Endogenous Mitophagy Complexes In Situ in Human Pancreatic Beta Cells Utilizing Proximity Ligation Assay. J Vis Exp 2019. [PMID: 31107439 DOI: 10.3791/59398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Mitophagy is an essential mitochondrial quality control pathway, which is crucial for pancreatic islet beta cell bioenergetics to fuel glucose-stimulated insulin release. Assessment of mitophagy is challenging and often requires genetic reporters or multiple complementary techniques not easily utilized in tissue samples, such as primary human pancreatic islets. Here we demonstrate a robust approach to visualize and quantify formation of key endogenous mitophagy complexes in primary human pancreatic islets. Utilizing the sensitive proximity ligation assay technique to detect interaction of the mitophagy regulators NRDP1 and USP8, we are able to specifically quantify formation of essential mitophagy complexes in situ. By coupling this approach to counterstaining for the transcription factor PDX1, we can quantify mitophagy complexes, and the factors that can impair mitophagy, specifically within beta cells. The methodology we describe overcomes the need for large quantities of cellular extracts required for other protein-protein interaction studies, such as immunoprecipitation (IP) or mass spectrometry, and is ideal for precious human islet samples generally not available in sufficient quantities for these approaches. Further, this methodology obviates the need for flow sorting techniques to purify beta cells from a heterogeneous islet population for downstream protein applications. Thus, we describe a valuable protocol for visualization of mitophagy highly compatible for use in heterogeneous and limited cell populations.
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Affiliation(s)
- Gemma Pearson
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor
| | - Scott A Soleimanpour
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor; VA Ann Arbor Healthcare System;
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190
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von Stockum S, Sanchez-Martinez A, Corrà S, Chakraborty J, Marchesan E, Locatello L, Da Rè C, Cusumano P, Caicci F, Ferrari V, Costa R, Bubacco L, Rasotto MB, Szabo I, Whitworth AJ, Scorrano L, Ziviani E. Inhibition of the deubiquitinase USP8 corrects a Drosophila PINK1 model of mitochondria dysfunction. Life Sci Alliance 2019; 2:2/2/e201900392. [PMID: 30988163 PMCID: PMC6467245 DOI: 10.26508/lsa.201900392] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 04/04/2019] [Accepted: 04/05/2019] [Indexed: 02/02/2023] Open
Abstract
Aberrant mitochondrial dynamics disrupts mitochondrial function and contributes to disease conditions. A targeted RNA interference screen for deubiquitinating enzymes (DUBs) affecting protein levels of multifunctional mitochondrial fusion protein Mitofusin (MFN) identified USP8 prominently influencing MFN levels. Genetic and pharmacological inhibition of USP8 normalized the elevated MFN protein levels observed in PINK1 and Parkin-deficient models. This correlated with improved mitochondrial function, locomotor performance and life span, and prevented dopaminergic neurons loss in Drosophila PINK1 KO flies. We identified a novel target antagonizing pathologically elevated MFN levels, mitochondrial dysfunction, and dopaminergic neuron loss of a Drosophila model of mitochondrial dysfunction.
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Affiliation(s)
| | | | - Samantha Corrà
- Department of Biology, University of Padova, Padova, Italy,Neurogenetics and Behavior of Drosophila Lab, Department of Biology, University of Padova, Padova, Italy
| | | | | | - Lisa Locatello
- Department of Biology, University of Padova, Padova, Italy
| | - Caterina Da Rè
- Department of Biology, University of Padova, Padova, Italy,Neurogenetics and Behavior of Drosophila Lab, Department of Biology, University of Padova, Padova, Italy
| | - Paola Cusumano
- Department of Biology, University of Padova, Padova, Italy,Neurogenetics and Behavior of Drosophila Lab, Department of Biology, University of Padova, Padova, Italy
| | | | - Vanni Ferrari
- Department of Biology, University of Padova, Padova, Italy
| | - Rodolfo Costa
- Department of Biology, University of Padova, Padova, Italy,Neurogenetics and Behavior of Drosophila Lab, Department of Biology, University of Padova, Padova, Italy
| | - Luigi Bubacco
- Department of Biology, University of Padova, Padova, Italy
| | | | - Ildiko Szabo
- Department of Biology, University of Padova, Padova, Italy
| | | | - Luca Scorrano
- Department of Biology, University of Padova, Padova, Italy,Dulbecco-Telethon Institute, Venetian Institute of Molecular Medicine, Padova, Italy
| | - Elena Ziviani
- Fondazione Ospedale San Camillo, IRCCS, Venezia, Italy,Department of Biology, University of Padova, Padova, Italy,Correspondence:
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191
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Miller S, Muqit MMK. Therapeutic approaches to enhance PINK1/Parkin mediated mitophagy for the treatment of Parkinson's disease. Neurosci Lett 2019; 705:7-13. [PMID: 30995519 DOI: 10.1016/j.neulet.2019.04.029] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/07/2019] [Accepted: 04/12/2019] [Indexed: 11/30/2022]
Abstract
The discovery of rare familial monogenic forms of early-onset Parkinson's disease has led to the identification of a mitochondrial quality control process as a key player in this disease. Loss-of-function mutations in the genes encoding PINK1 or Parkin result in insufficient removal of dysfunctional mitochondria through autophagy, a process termed mitophagy. Understanding the mechanism of this process and the function of its two key players, PINK1 and Parkin, has led to the discovery of new therapeutic approaches. Small molecule activators of mitophagy, either activating PINK1 or Parkin directly or inhibiting Parkin's counterplayer, the ubiquitin-specific protease USP30, are in preclinical development. To enable clinical success of future small molecule mitophagy enhancers, biomarkers for mitochondrial integrity and mitophagy are being developed. Only a few years after the discovery of mitophagy deficits in Parkinson's disease, research of the underlying mechanisms, drug discovery of modulators for this mechanism and identification of biomarkers provide new avenues towards the development of disease-modifying therapies.
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Affiliation(s)
- Silke Miller
- Neuroscience Department, Amgen Research, 360 Binney St., Cambridge, MA, 02142, USA.
| | - Miratul M K Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, United Kingdom
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192
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Gu H, Shi X, Liu C, Wang C, Sui N, Zhao Y, Gong J, Wang F, Zhang H, Li W, Zhao T. USP8 maintains embryonic stem cell stemness via deubiquitination of EPG5. Nat Commun 2019; 10:1465. [PMID: 30931944 PMCID: PMC6443784 DOI: 10.1038/s41467-019-09430-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 03/05/2019] [Indexed: 02/07/2023] Open
Abstract
Embryonic stem cells (ESCs) can propagate in an undifferentiated state indefinitely in culture and retain the potential to differentiate into any somatic lineage as well as germ cells. The catabolic process autophagy has been reported to be involved in ESC identity regulation, but the underlying mechanism is still largely unknown. Here we show that EPG5, a eukaryotic-specific autophagy regulator which mediates autophagosome/lysosome fusion, is highly expressed in ESCs and contributes to ESC identity maintenance. We identify that the deubiquitinating enzyme USP8 binds to the Coiled-coil domain of EPG5. Mechanistically, USP8 directly removes non-classical K63-linked ubiquitin chains from EPG5 at Lysine 252, leading to enhanced interaction between EPG5 and LC3. We propose that deubiquitination of EPG5 by USP8 guards the autophagic flux in ESCs to maintain their stemness. This work uncovers a novel crosstalk pathway between ubiquitination and autophagy through USP8-EPG5 interaction to regulate the stemness of ESCs.
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Affiliation(s)
- Haifeng Gu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xingxing Shi
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chaoqun Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Qufu Normal University, Qufu, 273165, China
| | - Ning Sui
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Qufu Normal University, Qufu, 273165, China
| | - Yu Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiaqi Gong
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fuping Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Hebei University, Baoding, 071002, China
| | - Hong Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Tongbiao Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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193
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Dharadhar S, Kim RQ, Uckelmann M, Sixma TK. Quantitative analysis of USP activity in vitro. Methods Enzymol 2019; 618:281-319. [PMID: 30850056 DOI: 10.1016/bs.mie.2018.12.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Ubiquitin-specific proteases (USPs) are an important class of deubiquitinating enzymes (DUBs) that carry out critical roles in cellular physiology and are regulated at multiple levels. Quantitative characterization of USP activity is crucial for mechanistic understanding of USP function and regulation. This requires kinetic analysis using in vitro activity assays on minimal and natural substrates with purified proteins. In this chapter we give advice for efficient design of USP constructs and their optimal expression, followed by a series of purification strategies. We then present protocols for studying USP activity quantitatively on minimal and more natural substrates, and we discuss how to include possible regulatory elements such as internal USP domains or external interacting proteins. Lastly, we examine different binding assays for studying USP interactions and discuss how these can be included in full kinetic analyses.
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Affiliation(s)
- Shreya Dharadhar
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Robbert Q Kim
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Michael Uckelmann
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Titia K Sixma
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.
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194
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Novel Approaches for the Treatment of Alzheimer's and Parkinson's Disease. Int J Mol Sci 2019; 20:ijms20030719. [PMID: 30743990 PMCID: PMC6386829 DOI: 10.3390/ijms20030719] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 01/18/2019] [Accepted: 02/03/2019] [Indexed: 12/19/2022] Open
Abstract
Neurodegenerative disorders affect around one billion people worldwide. They can arise from a combination of genomic, epigenomic, metabolic, and environmental factors. Aging is the leading risk factor for most chronic illnesses of old age, including Alzheimer’s and Parkinson’s diseases. A progressive neurodegenerative process and neuroinflammation occur, and no current therapies can prevent, slow, or halt disease progression. To date, no novel disease-modifying therapies have been shown to provide significant benefit for patients who suffer from these devastating disorders. Therefore, early diagnosis and the discovery of new targets and novel therapies are of upmost importance. Neurodegenerative diseases, like in other age-related disorders, the progression of pathology begins many years before the onset of symptoms. Many efforts in this field have led to the conclusion that exits some similar events among these diseases that can explain why the aging brain is so vulnerable to suffer neurodegenerative diseases. This article reviews the current knowledge about these diseases by summarizing the most common features of major neurodegenerative disorders, their causes and consequences, and the proposed novel therapeutic approaches.
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195
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Clague MJ, Urbé S, Komander D. Breaking the chains: deubiquitylating enzyme specificity begets function. Nat Rev Mol Cell Biol 2019; 20:338-352. [DOI: 10.1038/s41580-019-0099-1] [Citation(s) in RCA: 315] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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196
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Dzimianski JV, Beldon BS, Daczkowski CM, Goodwin OY, Scholte FEM, Bergeron É, Pegan SD. Probing the impact of nairovirus genomic diversity on viral ovarian tumor domain protease (vOTU) structure and deubiquitinase activity. PLoS Pathog 2019; 15:e1007515. [PMID: 30629698 PMCID: PMC6343935 DOI: 10.1371/journal.ppat.1007515] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/23/2019] [Accepted: 12/09/2018] [Indexed: 01/27/2023] Open
Abstract
Post-translational modification of host and viral proteins by ubiquitin (Ub) and Ub-like proteins, such as interferon stimulated gene product 15 (ISG15), plays a key role in response to infection. Viruses have been increasingly identified that contain proteases possessing deubiquitinase (DUB) and/or deISGylase functions. This includes viruses in the Nairoviridae family that encode a viral homologue of the ovarian tumor protease (vOTU). vOTU activity was recently demonstrated to be critical for replication of the often-fatal Crimean-Congo hemorrhagic fever virus, with DUB activity suppressing the type I interferon responses and deISGylase activity broadly removing ISG15 conjugated proteins. There are currently about 40 known nairoviruses classified into fourteen species. Recent genomic characterization has revealed a high degree of diversity, with vOTUs showing less than 25% amino acids identities within the family. Previous investigations have been limited to only a few closely related nairoviruses, leaving it unclear what impact this diversity has on vOTU function. To probe the effects of vOTU diversity on enzyme activity and specificity, we assessed representative vOTUs spanning the Nairoviridae family towards Ub and ISG15 fluorogenic substrates. This revealed great variation in enzymatic activity and specific substrate preferences. A subset of the vOTUs were further assayed against eight biologically relevant di-Ub substrates, uncovering both common trends and distinct preferences of poly-Ub linkages by vOTUs. Four novel X-ray crystal structures were obtained that provide a biochemical rationale for vOTU substrate preferences and elucidate structural features that distinguish the vOTUs, including a motif in the Hughes orthonairovirus species that has not been previously observed in OTU domains. Additionally, structure-informed mutagenesis provided the first direct evidence of a second site involved in di-Ub binding for vOTUs. These results provide new insight into nairovirus evolution and pathogenesis, and further enhances the development of tools for therapeutic purposes. Viruses utilize a variety of mechanisms to manipulate and suppress host responses to infection. One specific mechanism used by nairoviruses is the production of a deubiquitinating enzyme, termed the vOTU, that disrupts the innate immune response. This enzyme has been shown to play a key role in efficient replication of Crimean-Congo hemorrhagic fever virus (CCHFV), a severe human pathogen causing outbreaks with high case fatality rates. Recent genomic studies have revealed a high degree of sequence variation for the vOTU among nairoviruses, but knowledge relating to the functional impact of this diversity is lacking. Here we investigated the effects of this diversity on the structure and function of vOTUs from a wide range of nairoviruses. This revealed that vOTUs from different nairoviruses possess distinct preferences for certain host proteins. In addition, we found that different vOTUs possess distinguishing structural features, including a unique motif present in one that was previously undescribed. Utilizing this information, we were able to provide a rational basis for the observed differences in the vOTUs. This work provides a foundation to understand nairovirus evolution by providing insight into a mechanism that influences virus host adaptation and pathogenesis.
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Affiliation(s)
- John V. Dzimianski
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Brianna S. Beldon
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Courtney M. Daczkowski
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Octavia Y. Goodwin
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Florine E. M. Scholte
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Éric Bergeron
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Scott D. Pegan
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
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197
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Gustafsson ÅB, Dorn GW. Evolving and Expanding the Roles of Mitophagy as a Homeostatic and Pathogenic Process. Physiol Rev 2019; 99:853-892. [PMID: 30540226 PMCID: PMC6442924 DOI: 10.1152/physrev.00005.2018] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 08/10/2018] [Accepted: 09/29/2018] [Indexed: 02/07/2023] Open
Abstract
The central functions fulfilled by mitochondria as both energy generators essential for tissue homeostasis and gateways to programmed apoptotic and necrotic cell death mandate tight control over the quality and quantity of these ubiquitous endosymbiotic organelles. Mitophagy, the targeted engulfment and destruction of mitochondria by the cellular autophagy apparatus, has conventionally been considered as the mechanism primarily responsible for mitochondrial quality control. However, our understanding of how, why, and under what specific conditions mitophagy is activated has grown tremendously over the past decade. Evidence is accumulating that nonmitophagic mitochondrial quality control mechanisms are more important to maintaining normal tissue homeostasis whereas mitophagy is an acute tissue stress response. Moreover, previously unrecognized mitophagic regulation of mitochondrial quantity control, metabolic reprogramming, and cell differentiation suggests that the mechanisms linking genetic or acquired defects in mitophagy to neurodegenerative and cardiovascular diseases or cancer are more complex than simple failure of normal mitochondrial quality control. Here, we provide a comprehensive overview of mitophagy in cellular homeostasis and disease and examine the most revolutionary concepts in these areas. In this context, we discuss evidence that atypical mitophagy and nonmitophagic pathways play central roles in mitochondrial quality control, functioning that was previously considered to be the primary domain of mitophagy.
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Affiliation(s)
- Åsa B Gustafsson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , La Jolla, California ; and Washington University School of Medicine, St. Louis, Missouri
| | - Gerald W Dorn
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , La Jolla, California ; and Washington University School of Medicine, St. Louis, Missouri
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198
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Wang P, Gong P, Wang W, Li J, Ai Y, Zhang X. An Eimeria acervulina OTU protease exhibits linkage-specific deubiquitinase activity. Parasitol Res 2018; 118:47-55. [PMID: 30415394 DOI: 10.1007/s00436-018-6113-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 10/07/2018] [Indexed: 02/03/2023]
Abstract
Ubiquitination is an important post-translational modification process that regulates many cellular processes. Proteins can be modified at single or multiple lysine residues by a single ubiquitin protein or by ubiquitin oligomers. It is important to note that the type of ubiquitin chains determines the functional outcome of the modification. Ubiquitin or ubiquitin chains can be removed by deubiquitinases (DUBs). In our previous study, the Eimeria tenella ovarian tumour (Et-OTU) DUB was shown to regulate the telomerase activity of E. tenella and affect E. tenella proliferation. The amino acid sequences of Et-OTU (GenBank: XP_013229759.1) and Eimeria acervulina (E. acervulina) ovarian tumour (Ea-OTUD3) DUB (XP_013250378.1) are 74% identical. Although Et-OTU may regulate E. tenella telomerase activity, whether Ea-OTUD3 affects E. acervulina growth and reproduction remains unclear. We show here that Ea-OTUD3 belongs to the OTU domain class of cysteine protease deubiquitinating enzymes. Ea-OTUD3 is highly linkage-specific, cleaving K48 (Lys48)-, K63-, and K6-linked diubiquitin but not K29-, K33-, and K11-linked diubiquitin. The precise linkage preference of Ea-OTUD3 among these three nonlinear diubiquitin chains is K6 > K48 > K63. Recombinant Ea-OTUD3, but not its catalytic-site mutant Ea-OTUD3 (C247A), exhibits activity against diubiquitin. Ea-OTUD3 removes ubiquitin from the K48-, but to a lesser extent from the K63-linked ubiquitinated E. acervulina proteins of the modified target protein, thereby exhibiting the characteristics of deubiquitinase. This study reveals that the Ea-OTUD3 is a novel functional deubiquitinating enzyme. Furthermore, the Ea-OTUD3 protein may regulate the stability of some K48-linked ubiquitinated E. acervulina proteins.
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Affiliation(s)
- Pu Wang
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Pengtao Gong
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Weirong Wang
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Jianhua Li
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Yongxing Ai
- College of Animal Science, Jilin University, Changchun, 130062, China.
| | - Xichen Zhang
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
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199
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Zhu T, Chen JL, Wang Q, Shao W, Qi B. Modulation of Mitochondrial Dynamics in Neurodegenerative Diseases: An Insight Into Prion Diseases. Front Aging Neurosci 2018; 10:336. [PMID: 30455640 PMCID: PMC6230661 DOI: 10.3389/fnagi.2018.00336] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/05/2018] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial dysfunction is a common and prominent feature of prion diseases and other neurodegenerative disorders. Mitochondria are dynamic organelles that constantly fuse with one another and subsequently break apart. Defective or superfluous mitochondria are usually eliminated by a form of autophagy, referred to as mitophagy, to maintain mitochondrial homeostasis. Mitochondrial dynamics are tightly regulated by processes including fusion and fission. Dysfunction of mitochondrial dynamics can lead to the accumulation of abnormal mitochondria and contribute to cellular damage. Neurons are among the cell types that consume the most energy, have a highly complex morphology, and are particularly dependent on mitochondrial functions and dynamics. In this review article, we summarize the molecular mechanisms underlying the mitochondrial dynamics and the regulation of mitophagy and discuss the dysfunction of these processes in the progression of prion diseases and other neurodegenerative disorders. We have also provided an overview of mitochondrial dynamics as a therapeutic target for neurodegenerative diseases.
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Affiliation(s)
- Ting Zhu
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ji-Long Chen
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qingsen Wang
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenhan Shao
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Baomin Qi
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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200
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Kocaturk NM, Gozuacik D. Crosstalk Between Mammalian Autophagy and the Ubiquitin-Proteasome System. Front Cell Dev Biol 2018; 6:128. [PMID: 30333975 PMCID: PMC6175981 DOI: 10.3389/fcell.2018.00128] [Citation(s) in RCA: 275] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/13/2018] [Indexed: 12/16/2022] Open
Abstract
Autophagy and the ubiquitin-proteasome system (UPS) are the two major intracellular quality control and recycling mechanisms that are responsible for cellular homeostasis in eukaryotes. Ubiquitylation is utilized as a degradation signal by both systems, yet, different mechanisms are in play. The UPS is responsible for the degradation of short-lived proteins and soluble misfolded proteins whereas autophagy eliminates long-lived proteins, insoluble protein aggregates and even whole organelles (e.g., mitochondria, peroxisomes) and intracellular parasites (e.g., bacteria). Both the UPS and selective autophagy recognize their targets through their ubiquitin tags. In addition to an indirect connection between the two systems through ubiquitylated proteins, recent data indicate the presence of connections and reciprocal regulation mechanisms between these degradation pathways. In this review, we summarize these direct and indirect interactions and crosstalks between autophagy and the UPS, and their implications for cellular stress responses and homeostasis.
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Affiliation(s)
- Nur Mehpare Kocaturk
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Devrim Gozuacik
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano Diagnostics (EFSUN), Sabanci University, Istanbul, Turkey
- Nanotechnology Research and Application Center (SUNUM), Sabanci University, Istanbul, Turkey
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