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Deol KK, Eyles SJ, Strieter ER. Quantitative Middle-Down MS Analysis of Parkin-Mediated Ubiquitin Chain Assembly. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1132-1139. [PMID: 32297515 PMCID: PMC7333183 DOI: 10.1021/jasms.0c00058] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Misregulation of the E3 ubiquitin ligase Parkin and the kinase PINK1 underlie both inherited and idiopathic Parkinson's disease-associated neurodegeneration. Parkin and PINK1 work together to catalyze the assembly of ubiquitin chains on substrates located on the outer mitochondrial membrane to facilitate autophagic removal of damaged mitochondria through a process termed mitophagy. Quantitative measurements of Parkin-mediated chain assembly, both in vitro and on mitochondria, have revealed that chains are composed of Lys6, Lys11, Lys48, and Lys63 linkages. The combinatorial nature of these chains is further expanded by the ability of PINK1 to phosphorylate individual subunits. The precise architecture of chains produced by the coordinated action of PINK1 and Parkin, however, are unknown. Here, we demonstrate that quantitative middle-down mass spectrometry using uniformly 15N-labeled ubiquitin variants as internal standards informs on the extent of chain branching. We find that Parkin is a prolific branching enzyme in vitro. Quantitative middle-down mass spectrometry also reveals that phospho-Ser65-ubiquitin (pSer65-Ub)-a key activator of Parkin-is not incorporated into chains to a significant extent. Our results suggest that Parkin-mediated chain branching is "on-pathway", and branch points are the principal targets of the deubiquitinase USP30.
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Affiliation(s)
- Kirandeep K Deol
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Stephen J Eyles
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Eric R Strieter
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
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102
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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: 55] [Impact Index Per Article: 13.8] [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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103
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Zhao B, Tsai YC, Jin B, Wang B, Wang Y, Zhou H, Carpenter T, Weissman AM, Yin J. Protein Engineering in the Ubiquitin System: Tools for Discovery and Beyond. Pharmacol Rev 2020; 72:380-413. [PMID: 32107274 PMCID: PMC7047443 DOI: 10.1124/pr.118.015651] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ubiquitin (UB) transfer cascades consisting of E1, E2, and E3 enzymes constitute a complex network that regulates a myriad of biologic processes by modifying protein substrates. Deubiquitinating enzymes (DUBs) reverse UB modifications or trim UB chains of diverse linkages. Additionally, many cellular proteins carry UB-binding domains (UBDs) that translate the signals encoded in UB chains to target proteins for degradation by proteasomes or in autophagosomes, as well as affect nonproteolytic outcomes such as kinase activation, DNA repair, and transcriptional regulation. Dysregulation of the UB transfer pathways and malfunctions of DUBs and UBDs play causative roles in the development of many diseases. A greater understanding of the mechanism of UB chain assembly and the signals encoded in UB chains should aid in our understanding of disease pathogenesis and guide the development of novel therapeutics. The recent flourish of protein-engineering approaches such as unnatural amino acid incorporation, protein semisynthesis by expressed protein ligation, and high throughput selection by phage and yeast cell surface display has generated designer proteins as powerful tools to interrogate cell signaling mediated by protein ubiquitination. In this study, we highlight recent achievements of protein engineering on mapping, probing, and manipulating UB transfer in the cell. SIGNIFICANCE STATEMENT: The post-translational modification of proteins with ubiquitin alters the fate and function of proteins in diverse ways. Protein engineering is fundamentally transforming research in this area, providing new mechanistic insights and allowing for the exploration of concepts that can potentially be applied to therapeutic intervention.
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Affiliation(s)
- Bo Zhao
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Yien Che Tsai
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Bo Jin
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Bufan Wang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Yiyang Wang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Han Zhou
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Tomaya Carpenter
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Allan M Weissman
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Jun Yin
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
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104
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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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105
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Ge P, Dawson VL, Dawson TM. PINK1 and Parkin mitochondrial quality control: a source of regional vulnerability in Parkinson's disease. Mol Neurodegener 2020; 15:20. [PMID: 32169097 PMCID: PMC7071653 DOI: 10.1186/s13024-020-00367-7] [Citation(s) in RCA: 243] [Impact Index Per Article: 60.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/13/2020] [Indexed: 02/06/2023] Open
Abstract
That certain cell types in the central nervous system are more likely to undergo neurodegeneration in Parkinson's disease is a widely appreciated but poorly understood phenomenon. Many vulnerable subpopulations, including dopamine neurons in the substantia nigra pars compacta, have a shared phenotype of large, widely distributed axonal networks, dense synaptic connections, and high basal levels of neural activity. These features come at substantial bioenergetic cost, suggesting that these neurons experience a high degree of mitochondrial stress. In such a context, mechanisms of mitochondrial quality control play an especially important role in maintaining neuronal survival. In this review, we focus on understanding the unique challenges faced by the mitochondria in neurons vulnerable to neurodegeneration in Parkinson's and summarize evidence that mitochondrial dysfunction contributes to disease pathogenesis and to cell death in these subpopulations. We then review mechanisms of mitochondrial quality control mediated by activation of PINK1 and Parkin, two genes that carry mutations associated with autosomal recessive Parkinson's disease. We conclude by pinpointing critical gaps in our knowledge of PINK1 and Parkin function, and propose that understanding the connection between the mechanisms of sporadic Parkinson's and defects in mitochondrial quality control will lead us to greater insights into the question of selective vulnerability.
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Affiliation(s)
- Preston Ge
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Department of Neurology, Department of Physiology, Solomon H. Snyder Department of Neuroscience, Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 733 North Broadway, Suite 731, Baltimore, MD 21205 USA
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130 USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130 USA
- Present address: Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Present address: Picower Institute for Learning and Memory, Cambridge, MA 02139 USA
- Present address: Harvard-MIT MD/PhD Program, Harvard Medical School, Boston, MA 02115 USA
| | - Valina L. Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Department of Neurology, Department of Physiology, Solomon H. Snyder Department of Neuroscience, Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 733 North Broadway, Suite 731, Baltimore, MD 21205 USA
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130 USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130 USA
| | - Ted M. Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Department of Neurology, Department of Physiology, Solomon H. Snyder Department of Neuroscience, Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 733 North Broadway, Suite 731, Baltimore, MD 21205 USA
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130 USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130 USA
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106
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The 'dark matter' of ubiquitin-mediated processes: opportunities and challenges in the identification of ubiquitin-binding domains. Biochem Soc Trans 2020; 47:1949-1962. [PMID: 31829417 DOI: 10.1042/bst20190869] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/05/2019] [Accepted: 11/28/2019] [Indexed: 12/19/2022]
Abstract
Ubiquitin modifications of target proteins act to localise, direct and specify a diverse range of cellular processes, many of which are biomedically relevant. To allow this diversity, ubiquitin modifications exhibit remarkable complexity, determined by a combination of polyubiquitin chain length, linkage type, numbers of ubiquitin chains per target, and decoration of ubiquitin with other small modifiers. However, many questions remain about how different ubiquitin signals are specifically recognised and transduced by the decoding ubiquitin-binding domains (UBDs) within ubiquitin-binding proteins. This review briefly outlines our current knowledge surrounding the diversity of UBDs, identifies key challenges in their discovery and considers recent structural studies with implications for the increasing complexity of UBD function and identification. Given the comparatively low numbers of functionally characterised polyubiquitin-selective UBDs relative to the ever-expanding variety of polyubiquitin modifications, it is possible that many UBDs have been overlooked, in part due to limitations of current approaches used to predict their presence within the proteome. Potential experimental approaches for UBD discovery are considered; web-based informatic analyses, Next-Generation Phage Display, deubiquitinase-resistant diubiquitin, proximity-dependent biotinylation and Ubiquitin-Phototrap, including possible advantages and limitations. The concepts discussed here work towards identifying new UBDs which may represent the 'dark matter' of the ubiquitin system.
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107
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Kulek AR, Anzell A, Wider JM, Sanderson TH, Przyklenk K. Mitochondrial Quality Control: Role in Cardiac Models of Lethal Ischemia-Reperfusion Injury. Cells 2020; 9:cells9010214. [PMID: 31952189 PMCID: PMC7016592 DOI: 10.3390/cells9010214] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/10/2020] [Accepted: 01/12/2020] [Indexed: 02/07/2023] Open
Abstract
The current standard of care for acute myocardial infarction or 'heart attack' is timely restoration of blood flow to the ischemic region of the heart. While reperfusion is essential for the salvage of ischemic myocardium, re-introduction of blood flow paradoxically kills (rather than rescues) a population of previously ischemic cardiomyocytes-a phenomenon referred to as 'lethal myocardial ischemia-reperfusion (IR) injury'. There is long-standing and exhaustive evidence that mitochondria are at the nexus of lethal IR injury. However, during the past decade, the paradigm of mitochondria as mediators of IR-induced cardiomyocyte death has been expanded to include the highly orchestrated process of mitochondrial quality control. Our aims in this review are to: (1) briefly summarize the current understanding of the pathogenesis of IR injury, and (2) incorporating landmark data from a broad spectrum of models (including immortalized cells, primary cardiomyocytes and intact hearts), provide a critical discussion of the emerging concept that mitochondrial dynamics and mitophagy (the components of mitochondrial quality control) may contribute to the pathogenesis of cardiomyocyte death in the setting of ischemia-reperfusion.
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Affiliation(s)
- Andrew R. Kulek
- Cardiovascular Research Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA; (A.R.K.); (A.A.); (T.H.S.)
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Anthony Anzell
- Cardiovascular Research Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA; (A.R.K.); (A.A.); (T.H.S.)
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Departments of Emergency Medicine and Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA;
| | - Joseph M. Wider
- Departments of Emergency Medicine and Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA;
| | - Thomas H. Sanderson
- Cardiovascular Research Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA; (A.R.K.); (A.A.); (T.H.S.)
- Departments of Emergency Medicine and Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA;
| | - Karin Przyklenk
- Cardiovascular Research Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA; (A.R.K.); (A.A.); (T.H.S.)
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Department of Emergency Medicine, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Correspondence: ; Tel.: +1-313-577-9047
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108
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Evans CS, Holzbaur EL. Degradation of engulfed mitochondria is rate-limiting in Optineurin-mediated mitophagy in neurons. eLife 2020; 9:50260. [PMID: 31934852 PMCID: PMC6959996 DOI: 10.7554/elife.50260] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/19/2019] [Indexed: 12/19/2022] Open
Abstract
Mitophagy, the selective removal of damaged mitochondria, is thought to be critical to maintain neuronal homeostasis. Mutations of proteins in the pathway cause neurodegenerative diseases, suggesting defective mitochondrial turnover contributes to neurodegeneration. In primary rat hippocampal neurons, we developed a mitophagy induction paradigm where mild oxidative stress induced low levels of mitochondrial damage. Mitophagy-associated proteins were sequentially recruited to depolarized mitochondria followed by sequestration into autophagosomes. The localization of these mitophagy events had a robust somal bias. In basal and induced conditions, engulfed mitochondria remained in non-acidified organelles for hours to days, illustrating efficient autophagosome sequestration but delayed lysosomal fusion or acidification. Furthermore, expression of an ALS-linked mutation in the pathway disrupted mitochondrial network integrity and this effect was exacerbated by oxidative stress. Thus, age-related decline in neuronal health or expression of disease-associated mutations in the pathway may exacerbate the slow kinetics of neuronal mitophagy, leading to neurodegeneration.
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Affiliation(s)
- Chantell S Evans
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Erika Lf Holzbaur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
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109
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Mendes ML, Fougeras MR, Dittmar G. Analysis of ubiquitin signaling and chain topology cross-talk. J Proteomics 2020; 215:103634. [PMID: 31918034 DOI: 10.1016/j.jprot.2020.103634] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/13/2019] [Accepted: 01/05/2020] [Indexed: 12/12/2022]
Abstract
Protein ubiquitination is a powerful post-translational modification implicated in many cellular processes. Although ubiquitination is associated with protein degradation, depending on the topology of polyubiquitin chains, protein ubiquitination is connected to non-degradative events in DNA damage response, cell cycle control, immune response, trafficking, intracellular localization, and vesicle fusion events. It has been shown that a ubiquitin chain can contain two or more topologies at the same time. These branched chains add another level of complexity to ubiquitin signaling, increasing its versatility and specificity. Mass spectrometry-based proteomics has been playing an important role in the identification of all types of ubiquitin chains and linkages. This review aims to provide an overview of ubiquitin chain topology and associated signaling pathways and discusses the MS-based proteomic methodologies used to determine such topologies. SIGNIFICANCE: Ubiquitination plays important roles in many cellular processes. Proteins can be monoubiquitinated or polyubiquitinated forming non-branched or branched chains in a high number of possible combinations, each associated with different cellular processes. The detection and the topology of ubiquitin chains is thus of extreme importance in order to explain such processes. Advances in mass spectrometry based proteomics allowed for the discovery and topology mapping of many ubiquitin chains. This review revisits the state of the art in ubiquitin chain identification by mass spectrometry and gives an insight on the implication of such chains in many cellular processes.
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Affiliation(s)
- Marta L Mendes
- Proteomics of Cellular Signaling, Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Miriam R Fougeras
- Proteomics of Cellular Signaling, Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg; Faculty of Science, Technology and Communication, University of Luxembourg, 2 avenue de l'Université, 4365, Esch-sur-Alzette, Luxembourg
| | - Gunnar Dittmar
- Proteomics of Cellular Signaling, Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg; Faculty of Science, Technology and Communication, University of Luxembourg, 2 avenue de l'Université, 4365, Esch-sur-Alzette, Luxembourg.
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110
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Herhaus L, Bhaskara RM, Lystad AH, Gestal‐Mato U, Covarrubias‐Pinto A, Bonn F, Simonsen A, Hummer G, Dikic I. TBK1-mediated phosphorylation of LC3C and GABARAP-L2 controls autophagosome shedding by ATG4 protease. EMBO Rep 2020; 21:e48317. [PMID: 31709703 PMCID: PMC6945063 DOI: 10.15252/embr.201948317] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 10/08/2019] [Accepted: 10/15/2019] [Indexed: 12/22/2022] Open
Abstract
Autophagy is a highly conserved catabolic process through which defective or otherwise harmful cellular components are targeted for degradation via the lysosomal route. Regulatory pathways, involving post-translational modifications such as phosphorylation, play a critical role in controlling this tightly orchestrated process. Here, we demonstrate that TBK1 regulates autophagy by phosphorylating autophagy modifiers LC3C and GABARAP-L2 on surface-exposed serine residues (LC3C S93 and S96; GABARAP-L2 S87 and S88). This phosphorylation event impedes their binding to the processing enzyme ATG4 by destabilizing the complex. Phosphorylated LC3C/GABARAP-L2 cannot be removed from liposomes by ATG4 and are thus protected from ATG4-mediated premature removal from nascent autophagosomes. This ensures a steady coat of lipidated LC3C/GABARAP-L2 throughout the early steps in autophagosome formation and aids in maintaining a unidirectional flow of the autophagosome to the lysosome. Taken together, we present a new regulatory mechanism of autophagy, which influences the conjugation and de-conjugation of LC3C and GABARAP-L2 to autophagosomes by TBK1-mediated phosphorylation.
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Affiliation(s)
- Lina Herhaus
- Institute of Biochemistry IISchool of MedicineGoethe UniversityFrankfurt am MainGermany
| | - Ramachandra M Bhaskara
- Department of Theoretical BiophysicsMax Planck Institute of BiophysicsFrankfurt am MainGermany
| | - Alf Håkon Lystad
- Department of Molecular MedicineFaculty of MedicineInstitute of Basic Medical Sciences and Centre for Cancer Cell ReprogrammingInstitute of Clinical MedicineUniversity of OsloOsloNorway
| | - Uxía Gestal‐Mato
- Institute of Biochemistry IISchool of MedicineGoethe UniversityFrankfurt am MainGermany
| | | | - Florian Bonn
- Institute of Biochemistry IISchool of MedicineGoethe UniversityFrankfurt am MainGermany
- Present address:
Immundiagnostik AGBensheimGermany
| | - Anne Simonsen
- Department of Molecular MedicineFaculty of MedicineInstitute of Basic Medical Sciences and Centre for Cancer Cell ReprogrammingInstitute of Clinical MedicineUniversity of OsloOsloNorway
| | - Gerhard Hummer
- Department of Theoretical BiophysicsMax Planck Institute of BiophysicsFrankfurt am MainGermany
- Institute for BiophysicsGoethe UniversityFrankfurt am MainGermany
| | - Ivan Dikic
- Institute of Biochemistry IISchool of MedicineGoethe UniversityFrankfurt am MainGermany
- Buchmann Institute for Molecular Life SciencesRiedberg Campus, Goethe University FrankfurtFrankfurt am MainGermany
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111
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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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112
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Mathur S, Fletcher AJ, Branigan E, Hay RT, Virdee S. Photocrosslinking Activity-Based Probes for Ubiquitin RING E3 Ligases. Cell Chem Biol 2019; 27:74-82.e6. [PMID: 31859248 PMCID: PMC6963778 DOI: 10.1016/j.chembiol.2019.11.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/13/2019] [Accepted: 11/20/2019] [Indexed: 12/13/2022]
Abstract
Activity-based protein profiling is an invaluable technique for studying enzyme biology and facilitating the development of therapeutics. Ubiquitin E3 ligases (E3s) are one of the largest enzyme families and regulate a host of (patho)physiological processes. The largest subtype are the RING E3s of which there are >600 members. RING E3s have adaptor-like activity that can be subject to diverse regulatory mechanisms and have become attractive drug targets. Activity-based probes (ABPs) for measuring RING E3 activity do not exist. Here we re-engineer ubiquitin-charged E2 conjugating enzymes to produce photocrosslinking ABPs. We demonstrate activity-dependent profiling of two divergent cancer-associated RING E3s, RNF4 and c-Cbl, in response to their native activation signals. We also demonstrate profiling of endogenous RING E3 ligase activation in response to epidermal growth factor (EGF) stimulation. These photocrosslinking ABPs should advance E3 ligase research and the development of selective modulators against this important class of enzymes. Photoactivated activity-based probes developed for large class of ubiquitin E3 ligases ABPs are compatible with divergent RING E3 activation mechanisms Parallelized E3 profiling and detection of growth factor-induced E3 activation
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Affiliation(s)
- Sunil Mathur
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK
| | - Adam J Fletcher
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK
| | - Emma Branigan
- Division of Gene Regulation and Expression, University of Dundee, Scotland, UK
| | - Ronald T Hay
- Division of Gene Regulation and Expression, University of Dundee, Scotland, UK
| | - Satpal Virdee
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK.
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113
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Bhatia D, Chung KP, Nakahira K, Patino E, Rice MC, Torres LK, Muthukumar T, Choi AM, Akchurin OM, Choi ME. Mitophagy-dependent macrophage reprogramming protects against kidney fibrosis. JCI Insight 2019; 4:132826. [PMID: 31639106 DOI: 10.1172/jci.insight.132826] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 10/16/2019] [Indexed: 12/27/2022] Open
Abstract
Mitophagy, by maintaining mitochondrial quality control, plays a key role in maintaining kidney function and is impaired in pathologic states. Macrophages are well known for their pathogenic role in kidney fibrosis. Here, we report that PINK1/Parkin-mediated mitophagy in macrophages is compromised in experimental and human kidney fibrosis. We demonstrate downregulation of mitophagy regulators mitofusin-2 (MFN2) and Parkin downstream of PINK1 in kidney fibrosis. Loss of either Pink1 or Prkn promoted renal extracellular matrix accumulation and frequency of profibrotic/M2 macrophages. Pink1-/- or Prkn-/- BM-derived macrophages (BMDMs) showed enhanced expression of rictor. Mitochondria from TGF-β1-treated Pink1-/- BMDMs exhibited increased superoxide levels, along with reduced respiration and ATP production. In addition, mitophagy in macrophages involves PINK1-mediated phosphorylation of downstream MFN2, MFN2-facilitated recruitment of Parkin to damaged mitochondria, and macrophage-specific deletion of Mfn2 aggravates kidney fibrosis. Moreover, mitophagy regulators were downregulated in human CKD kidney and TGF-β1-treated human renal macrophages, whereas Mdivi1 treatment suppressed mitophagy mediators and promoted fibrotic response. Taken together, our study is the first to our knowledge to demonstrate that macrophage mitophagy plays a protective role against kidney fibrosis via regulating the PINK1/MFN2/Parkin-mediated pathway.
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Affiliation(s)
| | - Kuei-Pin Chung
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York, USA.,National Taiwan University Hospital, Taipei, Taiwan
| | - Kiichi Nakahira
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | | | | | - Lisa K Torres
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Thangamani Muthukumar
- Division of Nephrology and Hypertension and.,NewYork-Presbyterian Hospital, New York, New York, USA
| | - Augustine Mk Choi
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York, USA.,NewYork-Presbyterian Hospital, New York, New York, USA
| | - Oleh M Akchurin
- NewYork-Presbyterian Hospital, New York, New York, USA.,Division of Pediatric Nephrology, Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA
| | - Mary E Choi
- Division of Nephrology and Hypertension and.,NewYork-Presbyterian Hospital, New York, New York, USA
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114
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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: 65] [Impact Index Per Article: 13.0] [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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115
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Choi YS, Lian S, Cohen RE. Fluorescent Sensors That Enable a General Method To Quantify Affinities of Receptor Proteins for Polyubiquitin Ligands. ACS Sens 2019; 4:2908-2914. [PMID: 31599572 DOI: 10.1021/acssensors.9b01240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In all eukaryotic cells, modifications of proteins by polymers of ubiquitin (polyUb) are signals used in diverse biological processes. To better understand how polyUb signals are read and promote their different functions, quantitative measurements of their interactions with receptor proteins are needed. However, affinities and selectivities of different forms of polyUb with various receptors have been difficult to determine because the availability of well-defined polyUb chains can be limiting and there is a lack of general, sensitive methods to assay their interactions. We have addressed this challenge by developing a series of fluorescent protein sensors for polyUb; by competition of the sensors against receptor proteins in vitro for limiting amounts of polyUb, receptor·polyUb affinities can be quantified. Due to the high affinities of the polyUb sensors (Kd ∼ 10-9 M), binding assays using this competition format require much less polyUb (<0.1%) than would be needed in direct titrations of the polyUb ligands. Furthermore, the high sensitivity and large dynamic range of the sensor fluorescence readout allow for precise measurements even for very tight interactions (i.e., nanomolar Kd). Importantly, as demonstrated here with Ub2 and Ub3 ligands, the assay does not require labeling of either the receptor protein or the polyUb, and it can be used with polyUb ligands composed of virtually any Ub-Ub linkage type.
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Affiliation(s)
- Yun-Seok Choi
- Department of Biochemistry and Molecular Biology, Colorado State University, 1870 Campus Delivery, Fort Collins, Colorado 80523, United States
- School of Natural Sciences, Black Hills State University, Spearfish, South Dakota 57799, United States
| | - Sharon Lian
- Department of Biochemistry and Molecular Biology, Colorado State University, 1870 Campus Delivery, Fort Collins, Colorado 80523, United States
| | - Robert E. Cohen
- Department of Biochemistry and Molecular Biology, Colorado State University, 1870 Campus Delivery, Fort Collins, Colorado 80523, United States
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116
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Boyman L, Karbowski M, Lederer WJ. Regulation of Mitochondrial ATP Production: Ca 2+ Signaling and Quality Control. Trends Mol Med 2019; 26:21-39. [PMID: 31767352 DOI: 10.1016/j.molmed.2019.10.007] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/16/2019] [Accepted: 10/23/2019] [Indexed: 02/06/2023]
Abstract
Cardiac ATP production primarily depends on oxidative phosphorylation in mitochondria and is dynamically regulated by Ca2+ levels in the mitochondrial matrix as well as by cytosolic ADP. We discuss mitochondrial Ca2+ signaling and its dysfunction which has recently been linked to cardiac pathologies including arrhythmia and heart failure. Similar dysfunction in other excitable and long-lived cells including neurons is associated with neurodegenerative diseases such as Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), and Parkinson's disease (PD). Central to this new understanding is crucial Ca2+ regulation of both mitochondrial quality control and ATP production. Mitochondria-associated membrane (MAM) signaling from the sarcoplasmic reticulum (SR) and the endoplasmic reticulum (ER) to mitochondria is discussed. We propose future research directions that emphasize a need to define quantitatively the physiological roles of MAMs, as well as mitochondrial quality control and ATP production.
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Affiliation(s)
- Liron Boyman
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Mariusz Karbowski
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - W Jonathan Lederer
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
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117
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Heo JM, Harper NJ, Paulo JA, Li M, Xu Q, Coughlin M, Elledge SJ, Harper JW. Integrated proteogenetic analysis reveals the landscape of a mitochondrial-autophagosome synapse during PARK2-dependent mitophagy. SCIENCE ADVANCES 2019; 5:eaay4624. [PMID: 31723608 PMCID: PMC6834391 DOI: 10.1126/sciadv.aay4624] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/16/2019] [Indexed: 05/08/2023]
Abstract
The PINK1 protein kinase activates the PARK2 ubiquitin ligase to promote mitochondrial ubiquitylation and recruitment of ubiquitin-binding mitophagy receptors typified by OPTN and TAX1BP1. Here, we combine proximity biotinylation of OPTN and TAX1BP1 with CRISPR-Cas9-based screens for mitophagic flux to develop a spatial proteogenetic map of PARK2-dependent mitophagy. Proximity labeling of OPTN allowed visualization of a "mitochondrial-autophagosome synapse" upon mitochondrial depolarization. Proximity proteomics of OPTN and TAX1BP1 revealed numerous proteins at the synapse, including both PARK2 substrates and autophagy components. Parallel mitophagic flux screens identified proteins with roles in autophagy, vesicle formation and fusion, as well as PARK2 targets, many of which were also identified via proximity proteomics. One protein identified in both approaches, HK2, promotes assembly of a high-molecular weight complex of PINK1 and phosphorylation of ubiquitin in response to mitochondrial damage. This work provides a resource for understanding the spatial and molecular landscape of PARK2-dependent mitophagy.
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Affiliation(s)
- Jin-Mi Heo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Nathan J. Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mamie Li
- Department of Genetics, Harvard Medical School, Howard Hughes Medical Institute; Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Qikai Xu
- Department of Genetics, Harvard Medical School, Howard Hughes Medical Institute; Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Margaret Coughlin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Stephen J. Elledge
- Department of Genetics, Harvard Medical School, Howard Hughes Medical Institute; Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - J. Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Corresponding author.
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118
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Kappler L, Lehmann R. Mass-spectrometric multi-omics linked to function – State-of-the-art investigations of mitochondria in systems medicine. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115635] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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119
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Tang C, Zhang WP. How Phosphorylation by PINK1 Remodels the Ubiquitin System: A Perspective from Structure and Dynamics. Biochemistry 2019; 59:26-33. [PMID: 31503455 DOI: 10.1021/acs.biochem.9b00715] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Ubiquitin is an important signaling protein in cells. It functions by covalent attachment to substrate proteins and by noncovalent interactions with target proteins. Ubiquitins are also concatenated, and the resulting polyubiquitins recognize target proteins multivalently with enhanced specificity. The function of ubiquitin is enabled by the conformational dynamics of ubiquitin and polyubiquitins, which spans over 12 orders of magnitude in a time scale. Recently, it was found that ubiquitin can be phosphorylated by PINK1 at residues S65 and T66. Only sparsely populated for the unmodified ubiquitin, a C-terminally retracted conformation is stabilized for phosphorylated ubiquitin and is further enriched at an increasing pH. The modulation of tertiary structure further impacts the quaternary arrangements of ubiquitin subunits in polyubiquitins. Additionally, ubiquitin phosphorylation inhibits the activities of many enzymes responsible for attaching and removing polyubiquitins, thus remodeling the composition and length of polyubiquitins. The phosphorylation-remolded polyubiquitins can then recognize different target proteins. As PINK1 and ubiquitin phosphorylation levels are up-regulated under certain pathophysiological conditions, the remodeled ubiquitin system may be involved in the divergence of cell fate.
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Affiliation(s)
- Chun Tang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan , Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences , Wuhan , Hubei 430071 , China
| | - Wei-Ping Zhang
- Department of Pharmacology, Key Laboratory of Medical Neurobiology of Ministry of Health of China , Zhejiang University School of Medicine , Hangzhou , Zhejiang 310058 , China
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120
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Carter FE, Moore ME, Pickrell AM. Methods to detect mitophagy in neurons during disease. J Neurosci Methods 2019; 325:108351. [PMID: 31299189 PMCID: PMC6688849 DOI: 10.1016/j.jneumeth.2019.108351] [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] [Received: 06/05/2019] [Revised: 07/05/2019] [Accepted: 07/06/2019] [Indexed: 01/29/2023]
Abstract
Mitophagy is the selective degradation of mitochondria by autophagy. Methods to study mitophagy in neurons is of increasing importance as neurodegenerative diseases such as Parkinson's and Alzheimer's display disrupted mitophagy as part of their pathogenesis. Since the last decade, researchers have determined how selective mitophagy pathways such as PINK1/Parkin and Mul1 function at the cellular level. Thus, advances in techniques to study these pathways specifically in neurons and glia have arisen. This review will introduce mitophagy pathways studied in neurons and evaluate current techniques available to investigate mitophagy.
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Affiliation(s)
- Faith E. Carter
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA,Virginia Tech Post-Baccalaureate Program, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA,Present address: Graduate Program in Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - M. Elyse Moore
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Alicia M. Pickrell
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA,Correspondence should be addressed to: Alicia M. Pickrell, 970 Washington Street SW, Life Science I Room 217, Blacksburg, VA 24061, Tel: 540-232-8465; Fax: 540-231-1475;
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121
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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: 144] [Impact Index Per Article: 28.8] [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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122
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Jacoupy M, Hamon-Keromen E, Ordureau A, Erpapazoglou Z, Coge F, Corvol JC, Nosjean O, Mannoury la Cour C, Millan MJ, Boutin JA, Harper JW, Brice A, Guedin D, Gautier CA, Corti O. The PINK1 kinase-driven ubiquitin ligase Parkin promotes mitochondrial protein import through the presequence pathway in living cells. Sci Rep 2019; 9:11829. [PMID: 31413265 PMCID: PMC6694185 DOI: 10.1038/s41598-019-47352-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 05/28/2019] [Indexed: 01/05/2023] Open
Abstract
Most of over a thousand mitochondrial proteins are encoded by nuclear genes and must be imported from the cytosol. Little is known about the cytosolic events regulating mitochondrial protein import, partly due to the lack of appropriate tools for its assessment in living cells. We engineered an inducible biosensor for monitoring the main presequence-mediated import pathway with a quantitative, luminescence-based readout. This tool was used to explore the regulation of mitochondrial import by the PINK1 kinase-driven Parkin ubiquitin ligase, which is dysfunctional in autosomal recessive Parkinson's disease. We show that mitochondrial import was stimulated by Parkin, but not by disease-causing Parkin variants. This effect was dependent on Parkin activation by PINK1 and accompanied by an increase in the abundance of K11 ubiquitin chains on mitochondria and by ubiquitylation of subunits of the translocase of outer mitochondrial membrane. Mitochondrial import efficiency was abnormally low in cells from patients with PINK1- and PARK2-linked Parkinson's disease and was restored by phosphomimetic ubiquitin in cells with residual Parkin activity. Altogether, these findings uncover a role of ubiquitylation in mitochondrial import regulation and suggest that loss of this regulatory loop may underlie the pathophysiology of Parkinson's disease, providing novel opportunities for therapeutic intervention.
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Affiliation(s)
- M Jacoupy
- Inserm, U1127, F-75013, Paris, France.,CNRS, UMR 7225, F-75013, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - E Hamon-Keromen
- Inserm, U1127, F-75013, Paris, France.,CNRS, UMR 7225, F-75013, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - A Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Z Erpapazoglou
- Inserm, U1127, F-75013, Paris, France.,CNRS, UMR 7225, F-75013, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - F Coge
- Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France.,Laboratoire de Chémogénétique Servier, F-75013, Paris, France.,Institut de Recherches Servier, Croissy-sur-Seine, France
| | - J-C Corvol
- Inserm, U1127, F-75013, Paris, France.,CNRS, UMR 7225, F-75013, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France.,Assistance-Publique Hôpitaux de Paris, Inserm, CIC-1422, Department of Neurology, Hôpital Pitié-Salpêtrière, F-75013, Paris, France
| | - O Nosjean
- Institut de Recherches Servier, Croissy-sur-Seine, France
| | | | - M J Millan
- Institut de Recherches Servier, Croissy-sur-Seine, France
| | - J A Boutin
- Institut de Recherches Servier, Croissy-sur-Seine, France
| | - J W Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - A Brice
- Inserm, U1127, F-75013, Paris, France.,CNRS, UMR 7225, F-75013, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - D Guedin
- Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France.,Laboratoire de Chémogénétique Servier, F-75013, Paris, France.,Institut de Recherches Servier, Croissy-sur-Seine, France
| | - C A Gautier
- Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France. .,Laboratoire de Chémogénétique Servier, F-75013, Paris, France. .,Institut de Recherches Servier, Croissy-sur-Seine, France.
| | - O Corti
- Inserm, U1127, F-75013, Paris, France. .,CNRS, UMR 7225, F-75013, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France. .,Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France.
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123
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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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124
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Padmanabhan S, Polinski NK, Menalled LB, Baptista MAS, Fiske BK. The Michael J. Fox Foundation for Parkinson's Research Strategy to Advance Therapeutic Development of PINK1 and Parkin. Biomolecules 2019; 9:biom9080296. [PMID: 31344817 PMCID: PMC6723155 DOI: 10.3390/biom9080296] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/16/2019] [Accepted: 07/19/2019] [Indexed: 01/01/2023] Open
Abstract
The role of mitochondria in Parkinson's disease (PD) has been investigated since the 1980s and is gaining attention with recent advances in PD genetics research. Mutations in PRKN and PTEN-Induced Putative Kinase 1 (PINK1) are well-established causes of autosomal recessive early-onset PD. Genetic and biochemical studies have revealed that PINK1 and Parkin proteins function together in the same biological pathway to govern mitochondrial quality control. These proteins have also been implicated in the regulation of innate and adaptive immunity and other mitochondrial functions. Additionally, structural studies on Parkin have delineated an activation mechanism and have identified druggable regions that are currently being explored by academic and industry groups. To de-risk therapeutic development for these genetic targets, The Michael J. Fox Foundation for Parkinson's Research (MJFF) has deployed a strategic funding and enabling framework that brings together the research community to discuss important breakthroughs and challenges in research on PINK1-Parkin biology, supports collaborative initiatives to further our understanding within this field and develops high-quality research tools and assays that are widely available to all researchers. The Foundation's efforts are leading to significant advances in understanding of the underlying biology of these genes, proteins and pathways and in the development of Parkinson's therapies.
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Affiliation(s)
- Shalini Padmanabhan
- The Michael J. Fox Foundation for Parkinson's Research, Grand Central Station, P.O. Box 4777, New York, NY 10120, USA.
| | - Nicole K Polinski
- The Michael J. Fox Foundation for Parkinson's Research, Grand Central Station, P.O. Box 4777, New York, NY 10120, USA
| | - Liliana B Menalled
- The Michael J. Fox Foundation for Parkinson's Research, Grand Central Station, P.O. Box 4777, New York, NY 10120, USA
| | - Marco A S Baptista
- The Michael J. Fox Foundation for Parkinson's Research, Grand Central Station, P.O. Box 4777, New York, NY 10120, USA
| | - Brian K Fiske
- The Michael J. Fox Foundation for Parkinson's Research, Grand Central Station, P.O. Box 4777, New York, NY 10120, USA
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High-affinity free ubiquitin sensors for quantifying ubiquitin homeostasis and deubiquitination. Nat Methods 2019; 16:771-777. [PMID: 31308549 PMCID: PMC6669086 DOI: 10.1038/s41592-019-0469-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 05/21/2019] [Indexed: 02/07/2023]
Abstract
Ubiquitin (Ub) conjugation is an essential post-translational modification that affects nearly all proteins in eukaryotes. The functions and mechanisms of ubiquitination are areas of extensive study, and yet the dynamics and regulation of even free (i.e., unconjugated) Ub are poorly understood. A major impediment has been the lack of simple and robust techniques to quantify Ub levels in cells and to monitor Ub release from conjugates. Here we describe avidity-based fluorescent sensors that address this need. The sensors bind specifically to free Ub, have Kd values down to 60 pM, and, in concert with a newly developed workflow, allow us to distinguish and quantify the pools of free, protein-conjugated, and thioesterified forms of Ub from cell lysates. Alternatively, free Ub in fixed cells can be visualized microscopically by staining with a sensor. Real-time assays using the sensors afford unprecedented flexibility and precision to measure deubiquitination of virtually any (poly)Ub conjugate.
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Wright JN, Benavides GA, Johnson MS, Wani W, Ouyang X, Zou L, Collins HE, Zhang J, Darley-Usmar V, Chatham JC. Acute increases in O-GlcNAc indirectly impair mitochondrial bioenergetics through dysregulation of LonP1-mediated mitochondrial protein complex turnover. Am J Physiol Cell Physiol 2019; 316:C862-C875. [PMID: 30865517 PMCID: PMC6620580 DOI: 10.1152/ajpcell.00491.2018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/19/2019] [Accepted: 03/09/2019] [Indexed: 12/26/2022]
Abstract
The attachment of O-linked β-N-acetylglucosamine (O-GlcNAc) to the serine and threonine residues of proteins in distinct cellular compartments is increasingly recognized as an important mechanism regulating cellular function. Importantly, the O-GlcNAc modification of mitochondrial proteins has been identified as a potential mechanism to modulate metabolism under stress with both potentially beneficial and detrimental effects. This suggests that temporal and dose-dependent changes in O-GlcNAcylation may have different effects on mitochondrial function. In the current study, we found that acutely augmenting O-GlcNAc levels by inhibiting O-GlcNAcase with Thiamet-G for up to 6 h resulted in a time-dependent decrease in cellular bioenergetics and decreased mitochondrial complex I, II, and IV activities. Under these conditions, mitochondrial number was unchanged, whereas an increase in the protein levels of the subunits of several electron transport complex proteins was observed. However, the observed bioenergetic changes appeared not to be due to direct increased O-GlcNAc modification of complex subunit proteins. Increases in O-GlcNAc were also associated with an accumulation of mitochondrial ubiquitinated proteins; phosphatase and tensin homolog induced kinase 1 (PINK1) and p62 protein levels were also significantly increased. Interestingly, the increase in O-GlcNAc levels was associated with a decrease in the protein levels of the mitochondrial Lon protease homolog 1 (LonP1), which is known to target complex IV subunits and PINK1, in addition to other mitochondrial proteins. These data suggest that impaired bioenergetics associated with short-term increases in O-GlcNAc levels could be due to impaired, LonP1-dependent, mitochondrial complex protein turnover.
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Affiliation(s)
- JaLessa N Wright
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama , Birmingham, Alabama
| | - Gloria A Benavides
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama , Birmingham, Alabama
| | - Michelle S Johnson
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama , Birmingham, Alabama
| | - Willayat Wani
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama , Birmingham, Alabama
| | - Xiaosen Ouyang
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama , Birmingham, Alabama
| | - Luyun Zou
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama , Birmingham, Alabama
| | - Helen E Collins
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama , Birmingham, Alabama
| | - Jianhua Zhang
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama , Birmingham, Alabama
- Birmingham VA Medical Center, University of Alabama , Birmingham, Alabama
| | - Victor Darley-Usmar
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama , Birmingham, Alabama
| | - John C Chatham
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama , Birmingham, Alabama
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Kang C, Badr MA, Kyrychenko V, Eskelinen EL, Shirokova N. Deficit in PINK1/PARKIN-mediated mitochondrial autophagy at late stages of dystrophic cardiomyopathy. Cardiovasc Res 2019; 114:90-102. [PMID: 29036556 DOI: 10.1093/cvr/cvx201] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 10/04/2017] [Indexed: 01/09/2023] Open
Abstract
Aims Duchenne muscular dystrophy (DMD) is an inherited devastating muscle disease with severe and often lethal cardiac complications. Emerging evidence suggests that the evolution of the pathology in DMD is accompanied by the accumulation of mitochondria with defective structure and function. Here, we investigate whether defects in the housekeeping autophagic pathway contribute to mitochondrial and metabolic dysfunctions in dystrophic cardiomyopathy. Methods and results We employed various biochemical and imaging techniques to assess mitochondrial structure and function as well as to evaluate autophagy, and specific mitochondrial autophagy (mitophagy), in hearts of mdx mice, an animal model of DMD. Our results indicate substantial structural damage of mitochondria and a significant decrease in ATP production in hearts of mdx animals, which developed cardiomyopathy. In these hearts, we also detected enhanced autophagy but paradoxically, mitophagy appeared to be suppressed. In addition, we found decreased levels of several proteins involved in the PINK1/PARKIN mitophagy pathway as well as an insignificant amount of PARKIN protein phosphorylation at the S65 residue upon induction of mitophagy. Conclusions Our results suggest faulty mitophagy in dystrophic hearts due to defects in the PINK1/PARKIN pathway.
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Affiliation(s)
- Chifei Kang
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, 185 South Orange Avenue, Newark, NJ 07103, USA
| | - Myriam A Badr
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, 185 South Orange Avenue, Newark, NJ 07103, USA
| | - Viktoriia Kyrychenko
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, 185 South Orange Avenue, Newark, NJ 07103, USA
| | - Eeva-Liisa Eskelinen
- Division of Biochemistry and Biotechnology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Natalia Shirokova
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, 185 South Orange Avenue, Newark, NJ 07103, USA
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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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Matsumoto ML, Castellanos ER, Zeng YJ, Kirkpatrick DS. Interpreting the Language of Polyubiquitin with Linkage-Specific Antibodies and Mass Spectrometry. Methods Mol Biol 2019; 1844:385-400. [PMID: 30242722 DOI: 10.1007/978-1-4939-8706-1_24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
Posttranslational modification of cellular proteins by ubiquitin serves a variety of functions. Among the multitude of ubiquitin substrates, ubiquitin itself is the most prevalent. For many years, the direct detection of polyubiquitin chains attached to cellular substrates was not practical, with cell biologists relegated to indirect approaches involving site-directed mutagenesis or in vitro biochemistry. Recent advances in two technologies-polyubiquitin linkage-specific antibodies and mass spectrometry proteomics, have overcome that limitation. Using one or both of these, the direct analysis of polyubiquitin chain linkages on cellular substrate proteins may be performed. This paper describes the complimentary nature of linkage-specific antibodies and mass spectrometry proteomics for the characterization of complex ubiquitin signals using lessons learned in early development of both technologies.
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Affiliation(s)
- Marissa L Matsumoto
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA, USA.
| | - Erick R Castellanos
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Yi Jimmy Zeng
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South San Francisco, CA, USA
| | - Donald S Kirkpatrick
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South San Francisco, CA, USA.
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Affiliation(s)
- Karl W Barber
- Department of Cellular and Molecular Physiology and the Systems Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Jesse Rinehart
- Department of Cellular and Molecular Physiology and the Systems Biology Institute, Yale University, West Haven, Connecticut, USA
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Key J, Mueller AK, Gispert S, Matschke L, Wittig I, Corti O, Münch C, Decher N, Auburger G. Ubiquitylome profiling of Parkin-null brain reveals dysregulation of calcium homeostasis factors ATP1A2, Hippocalcin and GNA11, reflected by altered firing of noradrenergic neurons. Neurobiol Dis 2019; 127:114-130. [PMID: 30763678 DOI: 10.1016/j.nbd.2019.02.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/05/2018] [Accepted: 02/08/2019] [Indexed: 02/06/2023] Open
Abstract
Parkinson's disease (PD) is the second most frequent neurodegenerative disorder in the old population. Among its monogenic variants, a frequent cause is a mutation in the Parkin gene (Prkn). Deficient function of Parkin triggers ubiquitous mitochondrial dysfunction and inflammation in the brain, but it remains unclear how selective neural circuits become vulnerable and finally undergo atrophy. We attempted to go beyond previous work, mostly done in peripheral tumor cells, which identified protein targets of Parkin activity, an ubiquitin E3 ligase. Thus, we now used aged Parkin-knockout (KO) mouse brain for a global quantification of ubiquitylated peptides by mass spectrometry (MS). This approach confirmed the most abundant substrate to be VDAC3, a mitochondrial outer membrane porin that modulates calcium flux, while uncovering also >3-fold dysregulations for neuron-specific factors. Ubiquitylation decreases were prominent for Hippocalcin (HPCA), Calmodulin (CALM1/CALML3), Pyruvate Kinase (PKM2), sodium/potassium-transporting ATPases (ATP1A1/2/3/4), the Rab27A-GTPase activating protein alpha (TBC1D10A) and an ubiquitin ligase adapter (DDB1), while strong increases occurred for calcium transporter ATP2C1 and G-protein subunits G(i)/G(o)/G(Tr). Quantitative immunoblots validated elevated abundance for the electrogenic pump ATP1A2, for HPCA as neuron-specific calcium sensor, which stimulates guanylate cyclases and modifies axonal slow afterhyperpolarization (sAHP), and for the calcium-sensing G-protein GNA11. We assessed if compensatory molecular regulations become insufficient over time, leading to functional deficits. Patch clamp experiments in acute Parkin-KO brain slices indeed revealed alterations of the electrophysiological properties in aged noradrenergic locus coeruleus (LC) neurons. LC neurons of aged Parkin-KO brain showed an acceleration of the spontaneous pacemaker frequency, a reduction in sAHP and shortening of action potential duration, without modulation of KCNQ potassium currents. These findings indicate altered calcium-dependent excitability in a PARK2 model of PD, mediated by diminished turnover of potential Parkin targets such as ATP1A2 and HPCA. The data also identified further novel Parkin substrate candidates like SIRT2, OTUD7B and CUL5. Our elucidation of neuron-specific mechanisms of PD pathogenesis helps to explain the known exceptional susceptibility of noradrenergic and dopaminergic projections to alterations of calcium homeostasis and its mitochondrial buffering.
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Affiliation(s)
- J Key
- Exp. Neurology, Goethe University Medical School, 60590 Frankfurt am Main, Germany
| | - A K Mueller
- Institute for Physiology and Pathophysiology, Vegetative Physiology and Marburg Center for Mind, Brain and Behavior - MCMBB; Clinic for Neurology, Philipps-University Marburg, 35037 Marburg, Germany
| | - S Gispert
- Exp. Neurology, Goethe University Medical School, 60590 Frankfurt am Main, Germany
| | - L Matschke
- Institute for Physiology and Pathophysiology, Vegetative Physiology and Marburg Center for Mind, Brain and Behavior - MCMBB; Clinic for Neurology, Philipps-University Marburg, 35037 Marburg, Germany
| | - I Wittig
- Functional Proteomics, SFB 815 Core Unit, Goethe University Medical School, 60590 Frankfurt am Main, Germany
| | - O Corti
- Institut du Cerveau et de la Moelle épinière, ICM, Paris, F-75013, France; Inserm, U1127, Paris, F-75013, France; CNRS, UMR 7225, Paris, F-75013, France; Sorbonne Universités, Paris, F-75013, France
| | - C Münch
- Institute of Biochemistry II, Goethe University Medical School, 60590 Frankfurt am Main, Germany
| | - N Decher
- Institute for Physiology and Pathophysiology, Vegetative Physiology and Marburg Center for Mind, Brain and Behavior - MCMBB; Clinic for Neurology, Philipps-University Marburg, 35037 Marburg, Germany.
| | - G Auburger
- Exp. Neurology, Goethe University Medical School, 60590 Frankfurt am Main, Germany.
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132
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Xiong W, Hua J, Liu Z, Cai W, Bai Y, Zhan Q, Lai W, Zeng Q, Ren H, Xu D. PTEN induced putative kinase 1 (PINK1) alleviates angiotensin II-induced cardiac injury by ameliorating mitochondrial dysfunction. Int J Cardiol 2019; 266:198-205. [PMID: 29887448 DOI: 10.1016/j.ijcard.2018.03.054] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 02/17/2018] [Accepted: 03/12/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND Mitochondrial quality control is crucial to the development of angiotensin II (AngII)-induced cardiac hypertrophy. PTEN induced putative kinase 1 (PINK1) is rapidly degraded in normal mitochondria but accumulates in damaged mitochondria, triggering autophagy to protect cells. PINK1 mediates mitophagy in general, but whether PINK1 mediates AngII-induced mitophagy and the effects of PINK1 on AngII-induced injury are unknown. This study was designed to investigate the function of PINK1 in an AngII stimulation model and its regulation of AngII-induced mitophagy. METHODS We studied the function of PINK1 in mitochondrial homeostasis in AngII-stimulated cardiomyocytes via RNA interference-mediated knockdown and adenovirus-mediated overexpression of the PINK1 protein. Mitochondrial membrane potential (MMP), reactive oxygen species (ROS) production, adenosine triphosphate (ATP) content, cell apoptosis rates and cardiomyocyte hypertrophy were measured. The expression of LC3B, Beclin1 and p62 was measured. Mitochondrial morphology was examined via electron microscopy. Mitophagy was detected by confocal microscopy based on the co-localization of lysosomes and mitochondria. Additionally, endogenous PINK1, phosphorylated PINK1, mito-PINK1, total Parkin, cyto-Parkin, mito-Parkin and phosphorylated Parkin protein levels were measured. RESULTS Cardiomyocytes untreated by AngII had very low levels of total and phosphorylated PINK1. However, in the AngII stimulation model, the MMP was decreased, and the levels of total and phosphorylated PINK1 were increased. After PINK1 was knocked down, Parkin translocation to the mitochondria was inhibited. Moreover, levels of phosphorylated Parkin were reduced, and autophagy markers were downregulated. MMP and ATP contents were further reduced, ROS production and the apoptotic rate were further increased, and myocardial hypertrophy was further aggravated compared with those in the AngII group. However, PINK1 overexpression promoted Parkin translocation and phosphorylation, autophagy markers were upregulated, and myocardial injury was reduced. In addition, the effects of PINK1 overexpression were reversed by autophagy inhibitors. CONCLUSION Decreased MMP induced by AngII maintains the stability of PINK1, causing PINK1 autophosphorylation. PINK1 activation promotes Parkin translocation and phosphorylation and increases autophagy to clear damaged mitochondria. Thus, PINK1/Parkin-mediated mitophagy has a compensatory, protective role in AngII-induced cytotoxicity.
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Affiliation(s)
- Wenjun Xiong
- State Key Laboratory of Organ Failure Research, Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, China; Key Laboratory for Organ Failure Research, Ministry of Education of the People's Republic of China, Guangzhou, China
| | - Jinghai Hua
- State Key Laboratory of Organ Failure Research, Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, China; Key Laboratory for Organ Failure Research, Ministry of Education of the People's Republic of China, Guangzhou, China
| | - Zuheng Liu
- State Key Laboratory of Organ Failure Research, Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, China; Key Laboratory for Organ Failure Research, Ministry of Education of the People's Republic of China, Guangzhou, China
| | - Wanqiang Cai
- State Key Laboratory of Organ Failure Research, Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, China; Key Laboratory for Organ Failure Research, Ministry of Education of the People's Republic of China, Guangzhou, China
| | - Yujia Bai
- State Key Laboratory of Organ Failure Research, Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, China; Key Laboratory for Organ Failure Research, Ministry of Education of the People's Republic of China, Guangzhou, China
| | - Qiong Zhan
- State Key Laboratory of Organ Failure Research, Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, China; Key Laboratory for Organ Failure Research, Ministry of Education of the People's Republic of China, Guangzhou, China
| | - Wenyan Lai
- State Key Laboratory of Organ Failure Research, Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, China; Key Laboratory for Organ Failure Research, Ministry of Education of the People's Republic of China, Guangzhou, China
| | - Qingchun Zeng
- State Key Laboratory of Organ Failure Research, Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, China; Key Laboratory for Organ Failure Research, Ministry of Education of the People's Republic of China, Guangzhou, China
| | - Hao Ren
- Key Laboratory for Organ Failure Research, Ministry of Education of the People's Republic of China, Guangzhou, China; Department of Rheumatology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Dingli Xu
- State Key Laboratory of Organ Failure Research, Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, China; Key Laboratory for Organ Failure Research, Ministry of Education of the People's Republic of China, Guangzhou, China.
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Autophagy in Mitochondrial Quality Control. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1206:421-434. [DOI: 10.1007/978-981-15-0602-4_19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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134
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Meza-Gutierrez F, Simsek D, Toczyski DP. A genetic approach to study polyubiquitination in Saccharomyces cerevisiae. Methods Enzymol 2019; 618:49-72. [DOI: 10.1016/bs.mie.2018.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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135
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Kappler L, Kollipara L, Lehmann R, Sickmann A. Investigating the Role of Mitochondria in Type 2 Diabetes - Lessons from Lipidomics and Proteomics Studies of Skeletal Muscle and Liver. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1158:143-182. [PMID: 31452140 DOI: 10.1007/978-981-13-8367-0_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mitochondrial dysfunction is discussed as a key player in the pathogenesis of type 2 diabetes mellitus (T2Dm), a highly prevalent disease rapidly developing as one of the greatest global health challenges of this century. Data however about the involvement of mitochondria, central hubs in bioenergetic processes, in the disease development are still controversial. Lipid and protein homeostasis are under intense discussion to be crucial for proper mitochondrial function. Consequently proteomics and lipidomics analyses might help to understand how molecular changes in mitochondria translate to alterations in energy transduction as observed in the healthy and metabolic diseases such as T2Dm and other related disorders. Mitochondrial lipids integrated in a tool covering proteomic and functional analyses were up to now rarely investigated, although mitochondrial lipids might provide a possible lynchpin in the understanding of type 2 diabetes development and thereby prevention. In this chapter state-of-the-art analytical strategies, pre-analytical aspects, potential pitfalls as well as current proteomics and lipidomics-based knowledge about the pathophysiological role of mitochondria in the pathogenesis of type 2 diabetes will be discussed.
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Affiliation(s)
- Lisa Kappler
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Laxmikanth Kollipara
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
| | - Rainer Lehmann
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany.,Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Centre Munich at the University of Tuebingen, Tuebingen, Germany.,German Center for Diabetes Research (DZD e.V.), Tuebingen, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany. .,Medical Proteome Centre, Ruhr Universität Bochum, Bochum, Germany. .,Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, UK.
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136
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Drake JC, Laker RC, Wilson RJ, Zhang M, Yan Z. Exercise-induced mitophagy in skeletal muscle occurs in the absence of stabilization of Pink1 on mitochondria. Cell Cycle 2018; 18:1-6. [PMID: 30558471 DOI: 10.1080/15384101.2018.1559556] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Maintenance of mitochondrial quality is essential for skeletal muscle function and overall health. Exercise training elicits profound adaptations to mitochondria to improve mitochondrial quality in skeletal muscle. We have recently demonstrated that acute exercise promotes removal of damaged/dysfunctional mitochondria via mitophagy in skeletal muscle during recovery through the Ampk-Ulk1 signaling cascade. In this Extra View, we explore whether Pink1 is stabilized on mitochondria following exercise as the signal for mitophagy. We observed no discernable presence of Pink1 in isolated mitochondria from skeletal muscle at any time point following acute exercise, in contrast to clear evidence of stabilization of Pink1 on mitochondria in HeLa cells following treatment with the uncoupler carbonyl cyanide m-chlorophenyl hydrazone (CCCP). Taken together, we conclude that Pink1 is not involved in exercise-induced mitophagy in skeletal muscle.
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Affiliation(s)
- Joshua C Drake
- a Departments of Medicine , University of Virginia School of Medicine , Charlottesville , VA , USA.,b Center for Skeletal Muscle Research at Robert M. Berne Cardiovascular Research Center , University of Virginia School of Medicine , Charlottesville , VA , USA
| | - Rhianna C Laker
- a Departments of Medicine , University of Virginia School of Medicine , Charlottesville , VA , USA.,b Center for Skeletal Muscle Research at Robert M. Berne Cardiovascular Research Center , University of Virginia School of Medicine , Charlottesville , VA , USA
| | - Rebecca J Wilson
- a Departments of Medicine , University of Virginia School of Medicine , Charlottesville , VA , USA.,b Center for Skeletal Muscle Research at Robert M. Berne Cardiovascular Research Center , University of Virginia School of Medicine , Charlottesville , VA , USA
| | - Mei Zhang
- a Departments of Medicine , University of Virginia School of Medicine , Charlottesville , VA , USA.,b Center for Skeletal Muscle Research at Robert M. Berne Cardiovascular Research Center , University of Virginia School of Medicine , Charlottesville , VA , USA
| | - Zhen Yan
- a Departments of Medicine , University of Virginia School of Medicine , Charlottesville , VA , USA.,b Center for Skeletal Muscle Research at Robert M. Berne Cardiovascular Research Center , University of Virginia School of Medicine , Charlottesville , VA , USA.,c Pharmacology , University of Virginia School of Medicine , Charlottesville , VA , USA.,d Molecular Physiology and Biological Physics , University of Virginia School of Medicine , Charlottesville , VA , USA
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Meza Gutierrez F, Simsek D, Mizrak A, Deutschbauer A, Braberg H, Johnson J, Xu J, Shales M, Nguyen M, Tamse-Kuehn R, Palm C, Steinmetz LM, Krogan NJ, Toczyski DP. Genetic analysis reveals functions of atypical polyubiquitin chains. eLife 2018; 7:42955. [PMID: 30547882 PMCID: PMC6305200 DOI: 10.7554/elife.42955] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 11/30/2018] [Indexed: 12/27/2022] Open
Abstract
Although polyubiquitin chains linked through all lysines of ubiquitin exist, specific functions are well-established only for lysine-48 and lysine-63 linkages in Saccharomyces cerevisiae. To uncover pathways regulated by distinct linkages, genetic interactions between a gene deletion library and a panel of lysine-to-arginine ubiquitin mutants were systematically identified. The K11R mutant had strong genetic interactions with threonine biosynthetic genes. Consistently, we found that K11R mutants import threonine poorly. The K11R mutant also exhibited a strong genetic interaction with a subunit of the anaphase-promoting complex (APC), suggesting a role in cell cycle regulation. K11-linkages are important for vertebrate APC function, but this was not previously described in yeast. We show that the yeast APC also modifies substrates with K11-linkages in vitro, and that those chains contribute to normal APC-substrate turnover in vivo. This study reveals comprehensive genetic interactomes of polyubiquitin chains and characterizes the role of K11-chains in two biological pathways.
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Affiliation(s)
- Fernando Meza Gutierrez
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | | | - Arda Mizrak
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | | | - Hannes Braberg
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Jeffrey Johnson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Jiewei Xu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Michael Shales
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Michelle Nguyen
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Raquel Tamse-Kuehn
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Curt Palm
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Lars M Steinmetz
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - David P Toczyski
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
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138
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Safiulina D, Kuum M, Choubey V, Gogichaishvili N, Liiv J, Hickey MA, Cagalinec M, Mandel M, Zeb A, Liiv M, Kaasik A. Miro proteins prime mitochondria for Parkin translocation and mitophagy. EMBO J 2018; 38:embj.201899384. [PMID: 30504269 PMCID: PMC6331716 DOI: 10.15252/embj.201899384] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 10/11/2018] [Accepted: 10/23/2018] [Indexed: 11/12/2022] Open
Abstract
The Parkinson's disease‐associated protein kinase PINK1 and ubiquitin ligase Parkin coordinate the ubiquitination of mitochondrial proteins, which marks mitochondria for degradation. Miro1, an atypical GTPase involved in mitochondrial trafficking, is one of the substrates tagged by Parkin after mitochondrial damage. Here, we demonstrate that a small pool of Parkin interacts with Miro1 before mitochondrial damage occurs. This interaction does not require PINK1, does not involve ubiquitination of Miro1 and also does not disturb Miro1 function. However, following mitochondrial damage and PINK1 accumulation, this initial pool of Parkin becomes activated, leading to the ubiquitination and degradation of Miro1. Knockdown of Miro proteins reduces Parkin translocation to mitochondria and suppresses mitophagic removal of mitochondria. Moreover, we demonstrate that Miro1 EF‐hand domains control Miro1's ubiquitination and Parkin recruitment to damaged mitochondria, and they protect neurons from glutamate‐induced mitophagy. Together, our results suggest that Miro1 functions as a calcium‐sensitive docking site for Parkin on mitochondria.
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Affiliation(s)
- Dzhamilja Safiulina
- Department of Pharmacology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Malle Kuum
- Department of Pharmacology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Vinay Choubey
- Department of Pharmacology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Nana Gogichaishvili
- Department of Pharmacology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Joanna Liiv
- Department of Pharmacology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Miriam A Hickey
- Department of Pharmacology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Michal Cagalinec
- Department of Pharmacology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Merle Mandel
- Department of Pharmacology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Akbar Zeb
- Department of Pharmacology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Mailis Liiv
- Department of Pharmacology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Allen Kaasik
- Department of Pharmacology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
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139
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Condos TE, Dunkerley KM, Freeman EA, Barber KR, Aguirre JD, Chaugule VK, Xiao Y, Konermann L, Walden H, Shaw GS. Synergistic recruitment of UbcH7~Ub and phosphorylated Ubl domain triggers parkin activation. EMBO J 2018; 37:embj.2018100014. [PMID: 30446597 PMCID: PMC6276879 DOI: 10.15252/embj.2018100014] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 12/05/2022] Open
Abstract
The E3 ligase parkin ubiquitinates outer mitochondrial membrane proteins during oxidative stress and is linked to early‐onset Parkinson's disease. Parkin is autoinhibited but is activated by the kinase PINK1 that phosphorylates ubiquitin leading to parkin recruitment, and stimulates phosphorylation of parkin's N‐terminal ubiquitin‐like (pUbl) domain. How these events alter the structure of parkin to allow recruitment of an E2~Ub conjugate and enhanced ubiquitination is an unresolved question. We present a model of an E2~Ub conjugate bound to the phospho‐ubiquitin‐loaded C‐terminus of parkin, derived from NMR chemical shift perturbation experiments. We show the UbcH7~Ub conjugate binds in the open state whereby conjugated ubiquitin binds to the RING1/IBR interface. Further, NMR and mass spectrometry experiments indicate the RING0/RING2 interface is re‐modelled, remote from the E2 binding site, and this alters the reactivity of the RING2(Rcat) catalytic cysteine, needed for ubiquitin transfer. Our experiments provide evidence that parkin phosphorylation and E2~Ub recruitment act synergistically to enhance a weak interaction of the pUbl domain with the RING0 domain and rearrange the location of the RING2(Rcat) domain to drive parkin activity.
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Affiliation(s)
- Tara Ec Condos
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
| | - Karen M Dunkerley
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
| | - E Aisha Freeman
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
| | - Kathryn R Barber
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
| | - Jacob D Aguirre
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
| | - Viduth K Chaugule
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow, UK
| | - Yiming Xiao
- Department of Chemistry, The University of Western Ontario, London, ON, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, ON, Canada
| | - Helen Walden
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow, UK
| | - Gary S Shaw
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
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140
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Lambourne OA, Mehellou Y. Chemical Strategies for Activating PINK1, a Protein Kinase Mutated in Parkinson's Disease. Chembiochem 2018; 19:2433-2437. [PMID: 30248222 DOI: 10.1002/cbic.201800497] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Indexed: 12/20/2022]
Abstract
PINK1 is a ubiquitously expressed mitochondrial serine/threonine protein kinase that has emerged as a key player in mitochondrial quality control. This protein kinase came to prominence in the mid-2000s, when PINK1 mutations were found to cause early onset Parkinson's disease (PD). As most of the PD-related mutations occurred in the kinase domain and impaired PINK1's catalytic activity, it was suggested that small molecules that activated PINK1 would maintain mitochondrial quality control and, as a result, have neuroprotective effects. Working on this hypothesis, a few small-molecule PINK1 activators that offer critical insights and distinct approaches for activating PINK1 have been discovered. Herein, we briefly highlight the discovery of these small molecules and offer insight into the future development of small-molecule PINK1 activators as potential treatments for PD.
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Affiliation(s)
- Olivia A Lambourne
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Redwood Building, Cardiff, CF10 3NB, UK
| | - Youcef Mehellou
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Redwood Building, Cardiff, CF10 3NB, UK
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141
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McWilliams TG, Barini E, Pohjolan-Pirhonen R, Brooks SP, Singh F, Burel S, Balk K, Kumar A, Montava-Garriga L, Prescott AR, Hassoun SM, Mouton-Liger F, Ball G, Hills R, Knebel A, Ulusoy A, Di Monte DA, Tamjar J, Antico O, Fears K, Smith L, Brambilla R, Palin E, Valori M, Eerola-Rautio J, Tienari P, Corti O, Dunnett SB, Ganley IG, Suomalainen A, Muqit MMK. Phosphorylation of Parkin at serine 65 is essential for its activation in vivo. Open Biol 2018; 8:rsob.180108. [PMID: 30404819 PMCID: PMC6282074 DOI: 10.1098/rsob.180108] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mutations in PINK1 and Parkin result in autosomal recessive Parkinson's disease (PD). Cell culture and in vitro studies have elaborated the PINK1-dependent regulation of Parkin and defined how this dyad orchestrates the elimination of damaged mitochondria via mitophagy. PINK1 phosphorylates ubiquitin at serine 65 (Ser65) and Parkin at an equivalent Ser65 residue located within its N-terminal ubiquitin-like domain, resulting in activation; however, the physiological significance of Parkin Ser65 phosphorylation in vivo in mammals remains unknown. To address this, we generated a Parkin Ser65Ala (S65A) knock-in mouse model. We observe endogenous Parkin Ser65 phosphorylation and activation in mature primary neurons following mitochondrial depolarization and reveal this is disrupted in Parkin S65A/S65A neurons. Phenotypically, Parkin S65A/S65A mice exhibit selective motor dysfunction in the absence of any overt neurodegeneration or alterations in nigrostriatal mitophagy. The clinical relevance of our findings is substantiated by the discovery of homozygous PARKIN (PARK2) p.S65N mutations in two unrelated patients with PD. Moreover, biochemical and structural analysis demonstrates that the ParkinS65N/S65N mutant is pathogenic and cannot be activated by PINK1. Our findings highlight the central role of Parkin Ser65 phosphorylation in health and disease.
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Affiliation(s)
- Thomas G McWilliams
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK .,Research Programs Unit, Molecular Neurology, University of Helsinki, 00290 Helsinki, Finland
| | - Erica Barini
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Risto Pohjolan-Pirhonen
- Research Programs Unit, Molecular Neurology, University of Helsinki, 00290 Helsinki, Finland.,Neuroscience Center, University of Helsinki, 00290 Helsinki, Finland.,Helsinki University Hospital, 00290 Helsinki, Finland
| | - Simon P Brooks
- The Brain Repair Group, Division of Neuroscience, School of Biosciences, Cardiff University, Wales CF10 3AX, UK
| | - François Singh
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Sophie Burel
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Kristin Balk
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Atul Kumar
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Lambert Montava-Garriga
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Alan R Prescott
- Dundee Imaging Facility, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | | | | | - Graeme Ball
- Dundee Imaging Facility, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Rachel Hills
- The Brain Repair Group, Division of Neuroscience, School of Biosciences, Cardiff University, Wales CF10 3AX, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Ayse Ulusoy
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Jevgenia Tamjar
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Odetta Antico
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Kyle Fears
- The Brain Repair Group, Division of Neuroscience, School of Biosciences, Cardiff University, Wales CF10 3AX, UK
| | - Laura Smith
- The Brain Repair Group, Division of Neuroscience, School of Biosciences, Cardiff University, Wales CF10 3AX, UK
| | - Riccardo Brambilla
- Neuroscience & Mental Health Institute, Neuroscience Division, School of Biosciences, Hadyn Ellis Building, Maindy Road, Cardiff CF24 4HQ, UK
| | - Eino Palin
- Research Programs Unit, Molecular Neurology, University of Helsinki, 00290 Helsinki, Finland.,Neuroscience Center, University of Helsinki, 00290 Helsinki, Finland.,Helsinki University Hospital, 00290 Helsinki, Finland
| | - Miko Valori
- Research Programs Unit, Molecular Neurology, University of Helsinki, 00290 Helsinki, Finland.,Neuroscience Center, University of Helsinki, 00290 Helsinki, Finland.,Helsinki University Hospital, 00290 Helsinki, Finland
| | - Johanna Eerola-Rautio
- Research Programs Unit, Molecular Neurology, University of Helsinki, 00290 Helsinki, Finland.,Neuroscience Center, University of Helsinki, 00290 Helsinki, Finland.,Helsinki University Hospital, 00290 Helsinki, Finland.,Department of Neurology, Helsinki University Hospital, Haartmaninkatu 4, Helsinki, FI 00290, Finland
| | - Pentti Tienari
- Research Programs Unit, Molecular Neurology, University of Helsinki, 00290 Helsinki, Finland.,Neuroscience Center, University of Helsinki, 00290 Helsinki, Finland.,Helsinki University Hospital, 00290 Helsinki, Finland
| | | | - Stephen B Dunnett
- The Brain Repair Group, Division of Neuroscience, School of Biosciences, Cardiff University, Wales CF10 3AX, UK
| | - Ian G Ganley
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Anu Suomalainen
- Research Programs Unit, Molecular Neurology, University of Helsinki, 00290 Helsinki, Finland.,Neuroscience Center, University of Helsinki, 00290 Helsinki, Finland.,Helsinki University Hospital, 00290 Helsinki, Finland
| | - Miratul M K Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK .,School of Medicine, University of Dundee, Dundee DD1 9SY, UK
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142
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Junqueira SC, Centeno EGZ, Wilkinson KA, Cimarosti H. Post-translational modifications of Parkinson's disease-related proteins: Phosphorylation, SUMOylation and Ubiquitination. Biochim Biophys Acta Mol Basis Dis 2018; 1865:2001-2007. [PMID: 30412791 DOI: 10.1016/j.bbadis.2018.10.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/12/2018] [Accepted: 10/19/2018] [Indexed: 12/11/2022]
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder characterized by loss of dopaminergic neurons in the nigrostriatal pathway. The etiology of PD remains unclear and most cases are sporadic, however genetic mutations in more than 20 proteins have been shown to cause inherited forms of PD. Many of these proteins are linked to mitochondrial function, defects in which are a central characteristic of PD. Post-translational modifications (PTMs) allow rapid and reversible control over protein function. Largely focussing on mitochondrial dysfunction in PD, here we review findings on the PTMs phosphorylation, SUMOylation and ubiquitination that have been shown to affect PD-related proteins.
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Affiliation(s)
- Stella C Junqueira
- Department of Pharmacology, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Eduarda G Z Centeno
- Department of Pharmacology, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Kevin A Wilkinson
- School of Biochemistry, Centre for Synaptic Plasticity, University of Bristol, Bristol, UK.
| | - Helena Cimarosti
- Department of Pharmacology, Federal University of Santa Catarina, Florianopolis, Brazil.
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143
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Heo JM, Ordureau A, Swarup S, Paulo JA, Shen K, Sabatini DM, Harper JW. RAB7A phosphorylation by TBK1 promotes mitophagy via the PINK-PARKIN pathway. SCIENCE ADVANCES 2018; 4:eaav0443. [PMID: 30627666 PMCID: PMC6314648 DOI: 10.1126/sciadv.aav0443] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 10/19/2018] [Indexed: 05/09/2023]
Abstract
Removal of damaged mitochondria is orchestrated by a pathway involving the PINK1 kinase and the PARKIN ubiquitin ligase. Ubiquitin chains assembled by PARKIN on the mitochondrial outer membrane recruit autophagy cargo receptors in complexes with TBK1 protein kinase. While TBK1 is known to phosphorylate cargo receptors to promote ubiquitin binding, it is unknown whether TBK1 phosphorylates other proteins to promote mitophagy. Using global quantitative proteomics, we identified S72 in RAB7A, a RAB previously linked with mitophagy, as a dynamic target of TBK1 upon mitochondrial depolarization. TBK1 directly phosphorylates RAB7AS72, but not several other RABs known to be phosphorylated on the homologous residue by LRRK2, in vitro, and this modification requires PARKIN activity in vivo. Interaction proteomics using nonphosphorylatable and phosphomimetic RAB7A mutants revealed loss of association of RAB7AS72E with RAB GDP dissociation inhibitor and increased association with the DENN domain-containing heterodimer FLCN-FNIP1. FLCN-FNIP1 is recruited to damaged mitochondria, and this process is inhibited in cells expressing RAB7AS72A. Moreover, nonphosphorylatable RAB7A failed to support efficient mitophagy, as well as recruitment of ATG9A-positive vesicles to damaged mitochondria. These data reveal a novel function for TBK1 in mitophagy, which parallels that of LRRK2-mediated phosphorylation of the homologous site in distinct RABs to control membrane trafficking.
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Affiliation(s)
- J.-M. Heo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - A. Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - S. Swarup
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - J. A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - K. Shen
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - D. M. Sabatini
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - J. W. Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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144
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Zhou ZD, Lee JCT, Tan EK. Pathophysiological mechanisms linking F-box only protein 7 (FBXO7) and Parkinson's disease (PD). MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 778:72-78. [PMID: 30454685 DOI: 10.1016/j.mrrev.2018.10.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/11/2018] [Accepted: 10/12/2018] [Indexed: 12/12/2022]
Abstract
Mutations of F-box only protein 7 (FBXO7) gene are associated with a severe form of autosomal recessive juvenile Parkinson's disease (PD) (PARK15) with clinical features of Parkinsonian-Pyramidal syndrome (PPS). FBXO7 is an adaptor protein in SCFFBXO7 ubiquitin E3 ligase complex that recognizes and mediates degradative or non-degradative ubiquitination of substrates. The FBXO7 protein can regulate cell cycle, proliferation, mitochondrial and proteasome functions via interactions with multiple target proteins. Five PARK15-linked FBXO7 gene mutations and several PD-associated single nucleotide polymorphisms (SNP) have been identified so far. WT FBXO7 proteins possess dual protective and deleterious functions, whereas PARK15-linked FBXO7 mutants are toxic. FBXO7 is a stress response protein and stress challenges can promote translocation of FBXO7 protein from nucleus into mitochondria and even form deleterious protein aggregate in mitochondria. FBXO7 mutants aggravate protein aggregation in mitochondria and inhibit mitophagy. The pathological mechanisms concerning FBXO7-relevant protein aggregation, mitochondria impairment, reactive oxygen species (ROS) generation and mitophagy modulation in PARK15 pathogenesis are highlighted and discussed in the current review.
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Affiliation(s)
- Zhi Dong Zhou
- Department of Research, National Neuroscience Institute, 11 Jalan Tan Tock Seng, 308433, Singapore; Signature Research Program in Neuroscience and Behavioural Disorders, Duke-NUS Medical School, 8 College Road, 169857, Singapore.
| | - Ji Chao Tristan Lee
- Department of Research, National Neuroscience Institute, 11 Jalan Tan Tock Seng, 308433, Singapore.
| | - Eng King Tan
- Department of Research, National Neuroscience Institute, 11 Jalan Tan Tock Seng, 308433, Singapore; Department of Neurology, Singapore General Hospital, Outram Road, 169608, Singapore; Signature Research Program in Neuroscience and Behavioural Disorders, Duke-NUS Medical School, 8 College Road, 169857, Singapore.
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145
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Rasool S, Trempe JF. New insights into the structure of PINK1 and the mechanism of ubiquitin phosphorylation. Crit Rev Biochem Mol Biol 2018; 53:515-534. [PMID: 30238821 DOI: 10.1080/10409238.2018.1491525] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Mutations in PINK1 cause early-onset recessive Parkinson's disease. This gene encodes a protein kinase implicated in mitochondrial quality control via ubiquitin phosphorylation and activation of the E3 ubiquitin ligase Parkin. Here, we review and analyze functional features emerging from recent crystallographic, nuclear magnetic resonance (NMR) and mass spectrometry studies of PINK1. We compare the apo and ubiquitin-bound PINK1 structures and reveal an allosteric switch, regulated by autophosphorylation, which modulates substrate recognition. We critically assess the conformational changes taking place in ubiquitin and the Parkin ubiquitin-like domain in relation to its binding to PINK1. Finally, we discuss the implications of these biophysical findings in our understanding of the role of PINK1 in mitochondrial function, and analyze the potential for structure-based drug design.
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Affiliation(s)
- Shafqat Rasool
- a Department of Biochemistry , McGill University , Montréal , Canada.,b Groupe de Recherche Axé sur la Structure des Protéines (GRASP) , Montréal , Canada
| | - Jean-François Trempe
- b Groupe de Recherche Axé sur la Structure des Protéines (GRASP) , Montréal , Canada.,c Department of Pharmacology & Therapeutics , McGill University , Montréal , Canada
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146
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High-content analysis for mitophagy response to nanoparticles: A potential sensitive biomarker for nanosafety assessment. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2018; 15:59-69. [PMID: 30244083 DOI: 10.1016/j.nano.2018.09.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 08/20/2018] [Accepted: 09/03/2018] [Indexed: 12/28/2022]
Abstract
Mitophagy, a selective autophagy of mitochondria, clears up damaged mitochondria to maintain cell homeostasis. We performed high-content analysis (HCA) to detect the increase of PINK1, an essential protein controlling mitophagy, in hepatic cells treated with several nanoparticles (NPs). PINK1 immunofluorescence-based HCA was more sensitive than assays and detections for cell viability and mitochondrial functions. Of which, superparamagnetic iron oxide (SPIO)-NPs or graphene oxide-quantum dots (GO-QDs) was selected as representatives for positive or negative inducer of mitophagy. SPIO-NPs, but not GO-QDs, activated PINK1-dependent mitophagy as demonstrated by recruitment of PARKIN to mitochondria and degradation of injured mitochondria. SPIO-NPs caused the loss of mitochondrial membrane potential, decrease in ATP, and increase in mitochondrial reactive oxide species and Ca2+. Blocking mitophagy with PARKIN siRNA aggravated the cytotoxicity of SPIO-NPs. Taken together, PINK1 immunofluorescence-based HCA is considered to be an early, sensitive, and reliable approach to evaluate the bioimpacts of NPs.
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147
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Abstract
Ubiquitylation is an essential posttranslational modification that controls cell division, differentiation, and survival in all eukaryotes. By combining multiple E3 ligases (writers), ubiquitin-binding effectors (readers), and de-ubiquitylases (erasers) with functionally distinct ubiquitylation tags, the ubiquitin system constitutes a powerful signaling network that is employed in similar ways from yeast to humans. Here, we discuss conserved principles of ubiquitin-dependent signaling that illustrate how this posttranslational modification shapes intracellular signaling networks to establish robust development and homeostasis throughout the eukaryotic kingdom.
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Affiliation(s)
- Eugene Oh
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA; .,Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - David Akopian
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Michael Rape
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA; .,Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
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148
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Foote PK, Statsyuk AV. Monitoring PARKIN RBR Ubiquitin Ligase Activation States with UbFluor. ACTA ACUST UNITED AC 2018; 10:e45. [PMID: 30063295 DOI: 10.1002/cpch.45] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PARKIN is a RING-Between-RING (RBR) E3 ligase, which ubiquitinates mitochondrial proteins in response to mitochondrial damage. Ser65 of PARKIN is phosphorylated by kinase PINK1 (pPARKIN), which causes partial PARKIN activation. PINK1 also phosphorylates Ser65 of ubiquitin (pUb), which further activates pPARKIN. Due to the lack of precise and quantitative assays to quantify the activity of PARKIN, there were many conflicting reports on the role of pUb as a PARKIN activator, whether S65E PARKIN is a true phosphomimetic of pPARKIN, and the effect of substrate of PARKIN turnover was also not known. This protocol provides a step-by-step guide on the use of the UbFluor probe to precisely quantitate changes in the activity of PARKIN in response to phosphorylation, allosteric activation by pUb, protein substrates, and activating structural mutations. These results pave the way to discover PARKIN activators and to precisely quantify the activity of other RBR E3s. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Peter K Foote
- Department of Chemistry, Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois
| | - Alexander V Statsyuk
- Department of Chemistry, Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois.,The Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, Texas
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149
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Gianazza E, Banfi C. Post-translational quantitation by SRM/MRM: applications in cardiology. Expert Rev Proteomics 2018; 15:477-502. [DOI: 10.1080/14789450.2018.1484283] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Erica Gianazza
- Unit of Proteomics, Centro Cardiologico Monzino IRCCS, Milan, Italy
| | - Cristina Banfi
- Unit of Proteomics, Centro Cardiologico Monzino IRCCS, Milan, Italy
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150
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Mechanism of parkin activation by phosphorylation. Nat Struct Mol Biol 2018; 25:623-630. [PMID: 29967542 DOI: 10.1038/s41594-018-0088-7] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 06/12/2018] [Indexed: 12/25/2022]
Abstract
Mutations in the ubiquitin ligase parkin are responsible for a familial form of Parkinson's disease. Parkin and the PINK1 kinase regulate a quality-control system for mitochondria. PINK1 phosphorylates ubiquitin on the outer membrane of damaged mitochondria, thus leading to recruitment and activation of parkin via phosphorylation of its ubiquitin-like (Ubl) domain. Here, we describe the mechanism of parkin activation by phosphorylation. The crystal structure of phosphorylated Bactrocera dorsalis (oriental fruit fly) parkin in complex with phosphorylated ubiquitin and an E2 ubiquitin-conjugating enzyme reveals that the key activating step is movement of the Ubl domain and release of the catalytic RING2 domain. Hydrogen/deuterium exchange and NMR experiments with the various intermediates in the activation pathway confirm and extend the interpretation of the crystal structure to mammalian parkin. Our results rationalize previously unexplained Parkinson's disease mutations and the presence of internal linkers that allow large domain movements in parkin.
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