1
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Rasool S, Shomali T, Truong L, Croteau N, Veyron S, Bustillos BA, Springer W, Fiesel FC, Trempe JF. Identification and structural characterization of small molecule inhibitors of PINK1. Sci Rep 2024; 14:7739. [PMID: 38565869 PMCID: PMC10987619 DOI: 10.1038/s41598-024-58285-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/27/2024] [Indexed: 04/04/2024] Open
Abstract
Mutations in PINK1 and Parkin cause early-onset Parkinson's Disease (PD). PINK1 is a kinase which functions as a mitochondrial damage sensor and initiates mitochondrial quality control by accumulating on the damaged organelle. There, it phosphorylates ubiquitin, which in turn recruits and activates Parkin, an E3 ubiquitin ligase. Ubiquitylation of mitochondrial proteins leads to the autophagic degradation of the damaged organelle. Pharmacological modulation of PINK1 constitutes an appealing avenue to study its physiological function and develop therapeutics. In this study, we used a thermal shift assay with insect PINK1 to identify small molecules that inhibit ATP hydrolysis and ubiquitin phosphorylation. PRT062607, an SYK inhibitor, is the most potent inhibitor in our screen and inhibits both insect and human PINK1, with an IC50 in the 0.5-3 µM range in HeLa cells and dopaminergic neurons. The crystal structures of insect PINK1 bound to PRT062607 or CYC116 reveal how the compounds interact with the ATP-binding pocket. PRT062607 notably engages with the catalytic aspartate and causes a destabilization of insert-2 at the autophosphorylation dimer interface. While PRT062607 is not selective for PINK1, it provides a scaffold for the development of more selective and potent inhibitors of PINK1 that could be used as chemical probes.
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Affiliation(s)
- Shafqat Rasool
- Department of Pharmacology & Therapeutics, Centre de Recherche en Biologie Structurale, and Structural Genomics Consortium, McGill University, 3655 Prom Sir William Osler, Montréal, QC, H3G 1Y6, Canada
| | - Tara Shomali
- Department of Pharmacology & Therapeutics, Centre de Recherche en Biologie Structurale, and Structural Genomics Consortium, McGill University, 3655 Prom Sir William Osler, Montréal, QC, H3G 1Y6, Canada
| | - Luc Truong
- Department of Pharmacology & Therapeutics, Centre de Recherche en Biologie Structurale, and Structural Genomics Consortium, McGill University, 3655 Prom Sir William Osler, Montréal, QC, H3G 1Y6, Canada
| | - Nathalie Croteau
- Department of Pharmacology & Therapeutics, Centre de Recherche en Biologie Structurale, and Structural Genomics Consortium, McGill University, 3655 Prom Sir William Osler, Montréal, QC, H3G 1Y6, Canada
| | - Simon Veyron
- Department of Pharmacology & Therapeutics, Centre de Recherche en Biologie Structurale, and Structural Genomics Consortium, McGill University, 3655 Prom Sir William Osler, Montréal, QC, H3G 1Y6, Canada
| | | | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, 32224, USA
| | - Fabienne C Fiesel
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, 32224, USA
| | - Jean-François Trempe
- Department of Pharmacology & Therapeutics, Centre de Recherche en Biologie Structurale, and Structural Genomics Consortium, McGill University, 3655 Prom Sir William Osler, Montréal, QC, H3G 1Y6, Canada.
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2
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Gan ZY, Callegari S, Nguyen TN, Kirk NS, Leis A, Lazarou M, Dewson G, Komander D. Interaction of PINK1 with nucleotides and kinetin. SCIENCE ADVANCES 2024; 10:eadj7408. [PMID: 38241364 PMCID: PMC10798554 DOI: 10.1126/sciadv.adj7408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/21/2023] [Indexed: 01/21/2024]
Abstract
The ubiquitin kinase PINK1 accumulates on damaged mitochondria to trigger mitophagy, and PINK1 loss-of-function mutations cause early onset Parkinson's disease. Nucleotide analogs such as kinetin triphosphate (KTP) were reported to enhance PINK1 activity and may represent a therapeutic strategy for the treatment of Parkinson's disease. Here, we investigate the interaction of PINK1 with nucleotides, including KTP. We establish a cryo-EM platform exploiting the dodecamer assembly of Pediculus humanus corporis (Ph) PINK1 and determine PINK1 structures bound to AMP-PNP and ADP, revealing conformational changes in the kinase N-lobe that help establish PINK1's ubiquitin binding site. Notably, we find that KTP is unable to bind PhPINK1 or human (Hs) PINK1 due to a steric clash with the kinase "gatekeeper" methionine residue, and mutation to Ala or Gly is required for PINK1 to bind and use KTP as a phosphate donor in ubiquitin phosphorylation and mitophagy. HsPINK1 M318G can be used to conditionally uncouple PINK1 stabilization and activity on mitochondria.
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Affiliation(s)
- Zhong Yan Gan
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Sylvie Callegari
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Thanh N. Nguyen
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Nicholas S. Kirk
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew Leis
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Michael Lazarou
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Grant Dewson
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - David Komander
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
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3
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Lo HH, Chen YJ, Jiang CH, Tseng CH, Yang CN. A molecular simulation study of the clinical G409V mutant in PINK1 associated with early-onset Parkinson's disease. Int J Biol Macromol 2024; 254:127566. [PMID: 37865376 DOI: 10.1016/j.ijbiomac.2023.127566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 10/06/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023]
Abstract
The serine/threonine kinase PINK1 is responsible for phosphorylating a ubiquitin (Ub)-like domain in an E3 Ub ligase Parkin protein and a Parkin-bound Ub. PINK1 works as a mitochondrial quality control by phosphorylating and activating the E3 ubiquitin ligase Parkin. Recent medicinal study has reported that mutations of Parkin and PINK1 cause defects in mitophagy and induce early-onset Parkinson's disease (EOPD). In this study, we conducted molecular dynamics simulations to investigate the structural discrepancy caused by a clinical G409V mutation in PINK1 kinase domain's A-loop. The Ub phosphorylation begins with PINK1 D362 deprotonating the hydroxyl group of the substrate Ub's S65' and PINK1's A-loop is responsible for coordinating S65'. On contrary to G409 offering structural plasticity, the replaced, bulky V409 interferes with the alignment of D362-S65', seriously hampering Ub phosphorylation, leading to the accumulation of damaged mitochondria, and ultimately EOPD. In this study, we predicted the hPINK1WT-UbWT binding mode and detected the structural impact brought by G409V replacement. It is expected the concluded remarks to be beneficial for developing cures to alleviate structural interference and restore PINK1 function.
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Affiliation(s)
- Hsuan-Hsuan Lo
- Institute of Precision Medicine, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Ya-Jyun Chen
- Institute of Precision Medicine, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Cheng-Han Jiang
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung, Taiwan
| | - Chih-Hua Tseng
- Department of Fragrance and Cosmetic Science, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chia-Ning Yang
- Institute of Precision Medicine, National Sun Yat-sen University, Kaohsiung, Taiwan.
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4
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Mehellou Y. Parkinson's Disease: Are PINK1 Activators Inching Closer to the Clinic? ACS Med Chem Lett 2023; 14:870-874. [PMID: 37465300 PMCID: PMC10350934 DOI: 10.1021/acsmedchemlett.3c00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/31/2023] [Indexed: 07/20/2023] Open
Abstract
The activation of PINK1 by small molecules has emerged as a promising strategy in treating Parkinson's disease (PD). Recent progress in this area has raised excitement around PINK1 activators as PD treatments, and herein we offer insight into these developments and their potential to deliver much needed novel PD treatments.
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5
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Akabane S, Watanabe K, Kosako H, Yamashita SI, Nishino K, Kato M, Sekine S, Kanki T, Matsuda N, Endo T, Oka T. TIM23 facilitates PINK1 activation by safeguarding against OMA1-mediated degradation in damaged mitochondria. Cell Rep 2023:112454. [PMID: 37160114 DOI: 10.1016/j.celrep.2023.112454] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 02/24/2023] [Accepted: 04/16/2023] [Indexed: 05/11/2023] Open
Abstract
PINK1 is activated by autophosphorylation and forms a high-molecular-weight complex, thereby initiating the selective removal of damaged mitochondria by autophagy. Other than translocase of the outer mitochondrial membrane complexes, members of PINK1-containing protein complexes remain obscure. By mass spectrometric analysis of PINK1 co-immunoprecipitates, we identify the inner membrane protein TIM23 as a component of the PINK1 complex. TIM23 downregulation decreases PINK1 levels and significantly delays autophosphorylation, indicating that TIM23 promotes PINK1 accumulation in response to depolarization. Moreover, inactivation of the mitochondrial protease OMA1 not only enhances PINK1 accumulation but also represses the reduction in PINK1 levels induced by TIM23 downregulation, suggesting that TIM23 facilitates PINK1 activation by safeguarding against degradation by OMA1. Indeed, deficiencies of pathogenic PINK1 mutants that fail to interact with TIM23 are partially restored by OMA1 inactivation. These findings indicate that TIM23 plays a distinct role in activating mitochondrial autophagy by protecting PINK1.
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Affiliation(s)
- Shiori Akabane
- Department of Life Science, Rikkyo University, Tokyo 171-8501, Japan; Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Kiyona Watanabe
- Department of Life Science, Rikkyo University, Tokyo 171-8501, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Shun-Ichi Yamashita
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Kohei Nishino
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Masahiro Kato
- Department of Life Science, Rikkyo University, Tokyo 171-8501, Japan
| | - Shiori Sekine
- Aging Institute, Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Tomotake Kanki
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Noriyuki Matsuda
- Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan; Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Toshihiko Oka
- Department of Life Science, Rikkyo University, Tokyo 171-8501, Japan.
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6
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Trempe JF, Gehring K. Structural mechanisms of mitochondrial quality control mediated by PINK1 and parkin. J Mol Biol 2023:168090. [PMID: 37054910 DOI: 10.1016/j.jmb.2023.168090] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/31/2023] [Accepted: 04/05/2023] [Indexed: 04/15/2023]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease and represents a looming public health crisis as the global population ages. While the etiology of the more common, idiopathic form of the disease remains unknown, the last ten years have seen a breakthrough in our understanding of the genetic forms related to two proteins that regulate a quality control system for the removal of damaged or non-functional mitochondria. Here, we review the structure of these proteins, PINK1, a protein kinase, and parkin, a ubiquitin ligase with an emphasis on the molecular mechanisms responsible for their recognition of dysfunctional mitochondria and control of the subsequent ubiquitination cascade. Recent atomic structures have revealed the basis of PINK1 substrate specificity and the conformational changes responsible for activation of PINK1 and parkin catalytic activity. Progress in understanding the molecular basis of mitochondrial quality control promises to open new avenues for therapeutic interventions in PD.
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Affiliation(s)
- Jean-François Trempe
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada; Centre de Recherche en Biologie Structurale
| | - Kalle Gehring
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada; Centre de Recherche en Biologie Structurale
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7
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Biswas S, Bagchi A. Analysis of the structural dynamics of the mutations in the kinase domain of PINK1 protein associated with Parkinson's disease. Gene 2023; 857:147183. [PMID: 36623675 DOI: 10.1016/j.gene.2023.147183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/19/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023]
Abstract
Parkinson's disease (PD) is a very common neurodegenerative disorder and is considered to be one of the most severe disorders worldwide. Mutations in some PD causing genes are responsible for the early onset of the disease. Pathogenic variants in parkin, PINK1 and DJ1 genes can cause early-onset of PD. Many PINK1 gene mutations have been reported, but not all variants are pathogenic. The gene product of PINK1, also known as PINK1 protein, has 581 amino acid residues in it. Several different mutations are present throughout the kinase domain of PINK1 protein. In this work, we used in silico approaches to analyze the different types of mutations that are distributed in the kinase domain of the PINK1 protein. Based on our results, we categorized the mutations as high, moderate and low pathogenic variants. Furthermore, we performed molecular dynamics simulations of the pathogenic PINK1 variants to decipher their possible impacts on the structure and made a comparison with the wild type PINK1. In conclusion, we suggested the possible mechanistic roles of the pathogenic variants of PINK1 kinase domain that can affect its function. These pathogenic variants are the causative agents of early onset of PD called autosomal recessive Parkinson disease.
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Affiliation(s)
- Sima Biswas
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani - 741235, Nadia, West Bengal, India
| | - Angshuman Bagchi
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani - 741235, Nadia, West Bengal, India.
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8
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Hayashida R, Kikuchi R, Imai K, Kojima W, Yamada T, Iijima M, Sesaki H, Tanaka K, Matsuda N, Yamano K. Elucidation of ubiquitin-conjugating enzymes that interact with RBR-type ubiquitin ligases using a liquid-liquid phase separation-based method. J Biol Chem 2022; 299:102822. [PMID: 36563856 PMCID: PMC9860496 DOI: 10.1016/j.jbc.2022.102822] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/08/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
RING-between RING (RBR)-type ubiquitin (Ub) ligases (E3s) such as Parkin receive Ub from Ub-conjugating enzymes (E2s) in response to ligase activation. However, the specific E2s that transfer Ub to each RBR-type ligase are largely unknown because of insufficient methods for monitoring their interaction. To address this problem, we have developed a method that detects intracellular interactions between E2s and activated Parkin. Fluorescent homotetramer Azami-Green fused with E2 and oligomeric Ash (Assembly helper) fused with Parkin form a liquid-liquid phase separation (LLPS) in cells only when E2 and Parkin interact. Using this method, we identified multiple E2s interacting with activated Parkin on damaged mitochondria during mitophagy. Combined with in vitro ubiquitination assays and bioinformatics, these findings revealed an underlying consensus sequence for E2 interactions with activated Parkin. Application of this method to other RBR-type E3s including HOIP, HHARI, and TRIAD1 revealed that HOIP forms an LLPS with its substrate NEMO in response to a proinflammatory cytokine and that HHARI and TRIAD1 form a cytosolic LLPS independent of Ub-like protein NEDD8. Since an E2-E3 interaction is a prerequisite for RBR-type E3 activation and subsequent substrate ubiquitination, the method we have established here can be an in-cell tool to elucidate the potentially novel mechanisms involved in RBR-type E3s.
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Affiliation(s)
- Ryota Hayashida
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Reika Kikuchi
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan; Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kenichiro Imai
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Waka Kojima
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan; Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tatsuya Yamada
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Miho Iijima
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hiromi Sesaki
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Keiji Tanaka
- Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Noriyuki Matsuda
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan; Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
| | - Koji Yamano
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan; Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
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9
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Panicker N, Kam TI, Wang H, Neifert S, Chou SC, Kumar M, Brahmachari S, Jhaldiyal A, Hinkle JT, Akkentli F, Mao X, Xu E, Karuppagounder SS, Hsu ET, Kang SU, Pletnikova O, Troncoso J, Dawson VL, Dawson TM. Neuronal NLRP3 is a parkin substrate that drives neurodegeneration in Parkinson's disease. Neuron 2022; 110:2422-2437.e9. [PMID: 35654037 PMCID: PMC9357148 DOI: 10.1016/j.neuron.2022.05.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 04/09/2022] [Accepted: 05/12/2022] [Indexed: 02/09/2023]
Abstract
Parkinson's disease (PD) is mediated, in part, by intraneuronal accumulation of α-synuclein aggregates andsubsequent death of dopamine (DA) neurons in the substantia nigra pars compacta (SNpc). Microglial hyperactivation of the NOD-like receptor protein 3 (NLRP3) inflammasome has been well-documented in various neurodegenerative diseases, including PD. We show here that loss of parkin activity in mouse and human DA neurons results in spontaneous neuronal NLRP3 inflammasome assembly, leading to DA neuron death. Parkin normally inhibits inflammasome priming by ubiquitinating and targeting NLRP3 for proteasomal degradation. Loss of parkin activity also contributes to the assembly of an active NLRP3 inflammasome complex via mitochondrial-derived reactive oxygen species (mitoROS) generation through the accumulation of another parkin ubiquitination substrate, ZNF746/PARIS. Inhibition of neuronal NLRP3 inflammasome assembly prevents degeneration of DA neurons in familial and sporadic PD models. Strategies aimed at limiting neuronal NLRP3 inflammasome activation hold promise as a disease-modifying therapy for PD.
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Affiliation(s)
- Nikhil Panicker
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tae-In Kam
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130, USA
| | - Hu Wang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130, USA
| | - Stewart Neifert
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130, USA; Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130, USA
| | - Shih-Ching Chou
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Manoj Kumar
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Saurav Brahmachari
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Aanishaa Jhaldiyal
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jared T Hinkle
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Fatih Akkentli
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130, USA; Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130, USA
| | - Xiaobo Mao
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Enquan Xu
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Senthilkumar S Karuppagounder
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Eric T Hsu
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sung-Ung Kang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Olga Pletnikova
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Juan Troncoso
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130, USA; Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130, USA.
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130, USA; Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130, USA.
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10
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De Novo Development of Mitochondria-Targeted Molecular Probes Targeting Pink1. Int J Mol Sci 2022; 23:ijms23116076. [PMID: 35682755 PMCID: PMC9181014 DOI: 10.3390/ijms23116076] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/23/2022] [Accepted: 05/25/2022] [Indexed: 12/10/2022] Open
Abstract
Mitochondria play central roles in maintaining cellular metabolic homeostasis, cell survival and cell death, and generate most of the cell’s energy. Mitochondria maintain their homeostasis by dynamic (fission and fusion) and quality control mechanisms, including mitophagy, the removal of damaged mitochondria that is mediated mainly by the Pink1/Parkin pathway. Pink1 is a serine/threonine kinase which regulates mitochondrial function, hitherto many molecular mechanisms underlying Pink1 activity in mitochondrial homeostasis and cell fate remain unknown. Peptides are vital biological mediators that demonstrate remarkable potency, selectivity, and low toxicity, yet they have two major limitations, low oral bioavailability and poor stability. Herein, we rationally designed a linear peptide that targets Pink1 and, using straightforward chemistry, we developed molecular probes with drug-like properties to further characterize Pink1. Initially, we conjugated a cell-penetrating peptide and a cross-linker to map Pink1’s 3D structure and its interaction sites. Next, we conjugated a fluorescent dye for cell-imaging. Finally, we developed cyclic peptides with improved stability and binding affinity. Overall, we present a facile approach to converting a non-permeable linear peptide into a research tool possessing important properties for therapeutics. This is a general approach using straightforward chemistry that can be tailored for various applications by numerous laboratories.
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11
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Kakade P, Ojha H, Raimi OG, Shaw A, Waddell AD, Ault JR, Burel S, Brockmann K, Kumar A, Ahangar MS, Krysztofinska EM, Macartney T, Bayliss R, Fitzgerald JC, Muqit MMK. Mapping of a N-terminal α-helix domain required for human PINK1 stabilization, Serine228 autophosphorylation and activation in cells. Open Biol 2022; 12:210264. [PMID: 35042401 PMCID: PMC8767193 DOI: 10.1098/rsob.210264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/25/2021] [Indexed: 12/11/2022] Open
Abstract
Autosomal recessive mutations in the PINK1 gene are causal for Parkinson's disease (PD). PINK1 encodes a mitochondrial localized protein kinase that is a master-regulator of mitochondrial quality control pathways. Structural studies to date have elaborated the mechanism of how mutations located within the kinase domain disrupt PINK1 function; however, the molecular mechanism of PINK1 mutations located upstream and downstream of the kinase domain is unknown. We have employed mutagenesis studies to define the minimal region of human PINK1 required for optimal ubiquitin phosphorylation, beginning at residue Ile111. Inspection of the AlphaFold human PINK1 structure model predicts a conserved N-terminal α-helical extension (NTE) domain forming an intramolecular interaction with the C-terminal extension (CTE), which we corroborate using hydrogen/deuterium exchange mass spectrometry of recombinant insect PINK1 protein. Cell-based analysis of human PINK1 reveals that PD-associated mutations (e.g. Q126P), located within the NTE : CTE interface, markedly inhibit stabilization of PINK1; autophosphorylation at Serine228 (Ser228) and Ubiquitin Serine65 (Ser65) phosphorylation. Furthermore, we provide evidence that NTE and CTE domain mutants disrupt PINK1 stabilization at the mitochondrial Translocase of outer membrane complex. The clinical relevance of our findings is supported by the demonstration of defective stabilization and activation of endogenous PINK1 in human fibroblasts of a patient with early-onset PD due to homozygous PINK1 Q126P mutations. Overall, we define a functional role of the NTE : CTE interface towards PINK1 stabilization and activation and show that loss of NTE : CTE interactions is a major mechanism of PINK1-associated mutations linked to PD.
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Affiliation(s)
- Poonam Kakade
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, UK
| | - Hina Ojha
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, UK
| | - Olawale G. Raimi
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, UK
| | - Andrew Shaw
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, UK
| | - Andrew D. Waddell
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, UK
| | - James R. Ault
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Sophie Burel
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, UK
| | - Kathrin Brockmann
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- The German Centre for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Atul Kumar
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, UK
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Mohd Syed Ahangar
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Ewelina M. Krysztofinska
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, UK
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, UK
| | - Thomas Macartney
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, UK
| | - Richard Bayliss
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Julia C. Fitzgerald
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Miratul M. K. Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, UK
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12
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Abstract
Mutations in the protein kinase PINK1 lead to defects in mitophagy and cause autosomal recessive early onset Parkinson's disease1,2. PINK1 has many unique features that enable it to phosphorylate ubiquitin and the ubiquitin-like domain of Parkin3-9. Structural analysis of PINK1 from diverse insect species10-12 with and without ubiquitin provided snapshots of distinct structural states yet did not explain how PINK1 is activated. Here we elucidate the activation mechanism of PINK1 using crystallography and cryo-electron microscopy (cryo-EM). A crystal structure of unphosphorylated Pediculus humanus corporis (Ph; human body louse) PINK1 resolves an N-terminal helix, revealing the orientation of unphosphorylated yet active PINK1 on the mitochondria. We further provide a cryo-EM structure of a symmetric PhPINK1 dimer trapped during the process of trans-autophosphorylation, as well as a cryo-EM structure of phosphorylated PhPINK1 undergoing a conformational change to an active ubiquitin kinase state. Structures and phosphorylation studies further identify a role for regulatory PINK1 oxidation. Together, our research delineates the complete activation mechanism of PINK1, illuminates how PINK1 interacts with the mitochondrial outer membrane and reveals how PINK1 activity may be modulated by mitochondrial reactive oxygen species.
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13
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Ganesan S, Parvathi VD. Deconstructing the molecular genetics behind the PINK1/Parkin axis in Parkinson’s disease using Drosophila melanogaster as a model organism. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2021. [DOI: 10.1186/s43042-021-00208-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Abstract
Background
Parkinson’s disease (PD) is a multifactorial neurodegenerative disorder marked by the death of nigrostriatal dopaminergic neurons in response to the compounding effects of oxidative stress, mitochondrial dysfunction and protein aggregation. Transgenic Drosophila models have been used extensively to decipher the underlying genetic interactions that exacerbate neural health in PD. Autosomal recessive forms of the disease have been linked to mutations in the serine/threonine kinase PINK1(PTEN-Induced Putative Kinase 1) and E3 ligase Parkin, which function in an axis that is conserved in flies. This review aims to probe the current understanding of PD pathogenesis via the PINK1/Parkin axis while underscoring the importance of several molecular and pharmacologic rescues brought to light through studies in Drosophila.
Main body
Mutations in PINK1 and Parkin have been shown to affect the axonal transport of mitochondria within dopaminergic neurons and perturb the balance between mitochondrial fusion/fission resulting in abnormal mitochondrial morphology. As per studies in flies, ectopic expression of Fwd kinase and Atg-1 to promote fission and mitophagy while suppressing fusion via MUL1 E3 ligase may aid to halt mitochondrial aggregation and prolong the survival of dopaminergic neurons. Furthermore, upregulation of Hsp70/Hsp90 chaperone systems (Trap1, CHIP) to target misfolded mitochondrial respiratory complexes may help to preserve their bioenergetic capacity. Accumulation of reactive oxygen species as a consequence of respiratory complex dysfunction or antioxidant enzyme deficiency further escalates neural death by inducing apoptosis, lipid peroxidation and DNA damage. Fly studies have reported the induction of canonical Wnt signalling to enhance the activity of transcriptional co-activators (PGC1α, FOXO) which induce the expression of antioxidant enzymes. Enhancing the clearance of free radicals via uncoupling proteins (UCP4) has also been reported to ameliorate oxidative stress-induced cell death in PINK1/Parkin mutants.
Conclusion
While these novel mechanisms require validation through mammalian studies, they offer several explanations for the factors propagating dopaminergic death as well as promising insights into the therapeutic importance of transgenic fly models in PD.
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14
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Yamano K, Kojima W. Molecular functions of autophagy adaptors upon ubiquitin-driven mitophagy. Biochim Biophys Acta Gen Subj 2021; 1865:129972. [PMID: 34332032 DOI: 10.1016/j.bbagen.2021.129972] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/16/2021] [Accepted: 07/21/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Perturbations in organellar health can lead to an accumulation of unwanted and/or damaged organelles that are toxic to the cell and which can contribute to the onset of neurodegenerative diseases such as Parkinson's disease. Mitochondrial health is particularly critical given the indispensable role the organelle has not only in adenosine triphosphate production but also other metabolic processes. Byproducts of oxidative respiration, such as reactive oxygen species, however, can negatively impact mitochondrial fitness. Consequently, selective degradation of damaged mitochondria, which occurs via a specific autophagic process termed mitophagy, is essential for normal cell maintenance. SCOPE OF REVIEW Recent accumulating evidence has shown that autophagy adaptors (also referred to as autophagy receptors) play critical roles in connecting ubiquitinated mitochondria with the autophagic machinery of the autophagy-lysosome pathway that is required for degradation. In this review, we focus on our current understanding of the autophagy adaptor mechanisms underlying PINK1/Parkin-driven mitophagy. MAJOR CONCLUSIONS Although autophagy adaptors are canonically defined as proteins that possess ubiquitin-binding domains and ATG8s-binding motifs, the recent identification of novel binding partners has contributed to the development of a more sophisticated model for how autophagy adaptors contribute to the molecular hub that organizes autophagic cargo-degradation. GENERAL SIGNIFICANCE Although mitophagy is recognized as one of the selective autophagy pathways that removes dysfunctional mitochondria, a more nuanced understanding of the interactions connecting autophagy adaptors and their associated proteins is needed to gain deeper insights into the fundamental biological processes underlying human diseases, including neurodegenerative disorders. This review is part of a Special Issue entitled Mitophagy.
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Affiliation(s)
- Koji Yamano
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.
| | - Waka Kojima
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
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15
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Gonçalves FB, Morais VA. PINK1: A Bridge between Mitochondria and Parkinson's Disease. Life (Basel) 2021; 11:life11050371. [PMID: 33919398 PMCID: PMC8143285 DOI: 10.3390/life11050371] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 12/31/2022] Open
Abstract
Mitochondria are known as highly dynamic organelles essential for energy production. Intriguingly, in the recent years, mitochondria have revealed the ability to maintain cell homeostasis and ultimately regulate cell fate. This regulation is achieved by evoking mitochondrial quality control pathways that are capable of sensing the overall status of the cellular environment. In a first instance, actions to maintain a robust pool of mitochondria take place; however, if unsuccessful, measures that lead to overall cell death occur. One of the central key players of these mitochondrial quality control pathways is PINK1 (PTEN-induce putative kinase), a mitochondrial targeted kinase. PINK1 is known to interact with several substrates to regulate mitochondrial functions, and not only is responsible for triggering mitochondrial clearance via mitophagy, but also participates in maintenance of mitochondrial functions and homeostasis, under healthy conditions. Moreover, PINK1 has been associated with the familial form of Parkinson’s disease (PD). Growing evidence has strongly linked mitochondrial homeostasis to the central nervous system (CNS), a system that is replenished with high energy demanding long-lasting neuronal cells. Moreover, sporadic cases of PD have also revealed mitochondrial impairments. Thus, one could speculate that mitochondrial homeostasis is the common denominator in these two forms of the disease, and PINK1 may play a central role in maintaining mitochondrial homeostasis. In this review, we will discuss the role of PINK1 in the mitochondrial physiology and scrutinize its role in the cascade of PD pathology.
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16
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Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disorder resulting from the death of dopamine neurons in the substantia nigra pars compacta. Our understanding of PD biology has been enriched by the identification of genes involved in its rare, inheritable forms, termed PARK genes. These genes encode proteins including α-syn, LRRK2, VPS35, parkin, PINK1, and DJ1, which can cause monogenetic PD when mutated. Investigating the cellular functions of these proteins has been instrumental in identifying signaling pathways that mediate pathology in PD and neuroprotective mechanisms active during homeostatic and pathological conditions. It is now evident that many PD-associated proteins perform multiple functions in PD-associated signaling pathways in neurons. Furthermore, several PARK proteins contribute to non-cell-autonomous mechanisms of neuron death, such as neuroinflammation. A comprehensive understanding of cell-autonomous and non-cell-autonomous pathways involved in PD is essential for developing therapeutics that may slow or halt its progression.
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Affiliation(s)
- Nikhil Panicker
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Preston Ge
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD.,Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA.,Diana Helis Henry Medical Research Foundation, New Orleans, LA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD.,Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD.,Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA.,Diana Helis Henry Medical Research Foundation, New Orleans, LA
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17
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Patoli D, Mignotte F, Deckert V, Dusuel A, Dumont A, Rieu A, Jalil A, Van Dongen K, Bourgeois T, Gautier T, Magnani C, Le Guern N, Mandard S, Bastin J, Djouadi F, Schaeffer C, Guillaumot N, Narce M, Nguyen M, Guy J, Dargent A, Quenot JP, Rialland M, Masson D, Auwerx J, Lagrost L, Thomas C. Inhibition of mitophagy drives macrophage activation and antibacterial defense during sepsis. J Clin Invest 2021; 130:5858-5874. [PMID: 32759503 DOI: 10.1172/jci130996] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 07/29/2020] [Indexed: 12/26/2022] Open
Abstract
Mitochondria have emerged as key actors of innate and adaptive immunity. Mitophagy has a pivotal role in cell homeostasis, but its contribution to macrophage functions and host defense remains to be delineated. Here, we showed that lipopolysaccharide (LPS) in combination with IFN-γ inhibited PINK1-dependent mitophagy in macrophages through a STAT1-dependent activation of the inflammatory caspases 1 and 11. In addition, we demonstrated that the inhibition of mitophagy triggered classical macrophage activation in a mitochondrial ROS-dependent manner. In a murine model of polymicrobial infection (cecal ligature and puncture), adoptive transfer of Pink1-deficient bone marrow or pharmacological inhibition of mitophagy promoted macrophage activation, which favored bactericidal clearance and led to a better survival rate. Reciprocally, mitochondrial uncouplers that promote mitophagy reversed LPS/IFN-γ-mediated activation of macrophages and led to immunoparalysis with impaired bacterial clearance and lowered survival. In critically ill patients, we showed that mitophagy was inhibited in blood monocytes of patients with sepsis as compared with nonseptic patients. Overall, this work demonstrates that the inhibition of mitophagy is a physiological mechanism that contributes to the activation of myeloid cells and improves the outcome of sepsis.
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Affiliation(s)
- Danish Patoli
- Université de Bourgogne Franche-Comté (UBFC), UMR 1231, INSERM/AgroSup Dijon/Université de Bourgogne, Dijon, France.,LipSTIC LabEx, Dijon, France
| | - Franck Mignotte
- Université de Bourgogne Franche-Comté (UBFC), UMR 1231, INSERM/AgroSup Dijon/Université de Bourgogne, Dijon, France.,LipSTIC LabEx, Dijon, France
| | - Valérie Deckert
- Université de Bourgogne Franche-Comté (UBFC), UMR 1231, INSERM/AgroSup Dijon/Université de Bourgogne, Dijon, France.,LipSTIC LabEx, Dijon, France
| | - Alois Dusuel
- Université de Bourgogne Franche-Comté (UBFC), UMR 1231, INSERM/AgroSup Dijon/Université de Bourgogne, Dijon, France.,LipSTIC LabEx, Dijon, France
| | - Adélie Dumont
- Université de Bourgogne Franche-Comté (UBFC), UMR 1231, INSERM/AgroSup Dijon/Université de Bourgogne, Dijon, France.,LipSTIC LabEx, Dijon, France
| | - Aurélie Rieu
- UBFC, UMR PAM A 02.102, AgroSup Dijon/ Université de Bourgogne, Dijon, France
| | - Antoine Jalil
- Université de Bourgogne Franche-Comté (UBFC), UMR 1231, INSERM/AgroSup Dijon/Université de Bourgogne, Dijon, France.,LipSTIC LabEx, Dijon, France
| | - Kevin Van Dongen
- Université de Bourgogne Franche-Comté (UBFC), UMR 1231, INSERM/AgroSup Dijon/Université de Bourgogne, Dijon, France.,LipSTIC LabEx, Dijon, France
| | - Thibaut Bourgeois
- Université de Bourgogne Franche-Comté (UBFC), UMR 1231, INSERM/AgroSup Dijon/Université de Bourgogne, Dijon, France.,LipSTIC LabEx, Dijon, France
| | - Thomas Gautier
- Université de Bourgogne Franche-Comté (UBFC), UMR 1231, INSERM/AgroSup Dijon/Université de Bourgogne, Dijon, France.,LipSTIC LabEx, Dijon, France
| | - Charlène Magnani
- Université de Bourgogne Franche-Comté (UBFC), UMR 1231, INSERM/AgroSup Dijon/Université de Bourgogne, Dijon, France.,LipSTIC LabEx, Dijon, France
| | - Naig Le Guern
- Université de Bourgogne Franche-Comté (UBFC), UMR 1231, INSERM/AgroSup Dijon/Université de Bourgogne, Dijon, France.,LipSTIC LabEx, Dijon, France
| | - Stéphane Mandard
- Université de Bourgogne Franche-Comté (UBFC), UMR 1231, INSERM/AgroSup Dijon/Université de Bourgogne, Dijon, France.,LipSTIC LabEx, Dijon, France
| | - Jean Bastin
- Centre de Recherche des Cordeliers, INSERM, Université Sorbonne-Paris-Cité, Paris, France
| | - Fatima Djouadi
- Centre de Recherche des Cordeliers, INSERM, Université Sorbonne-Paris-Cité, Paris, France
| | | | - Nina Guillaumot
- Université de Strasbourg, CNRS, UMR 7178, LSMBO, Strasbourg, France
| | - Michel Narce
- Université de Bourgogne Franche-Comté (UBFC), UMR 1231, INSERM/AgroSup Dijon/Université de Bourgogne, Dijon, France.,LipSTIC LabEx, Dijon, France
| | - Maxime Nguyen
- Université de Bourgogne Franche-Comté (UBFC), UMR 1231, INSERM/AgroSup Dijon/Université de Bourgogne, Dijon, France.,LipSTIC LabEx, Dijon, France.,Department of Anesthesiology and Intensive Care
| | | | - Auguste Dargent
- Université de Bourgogne Franche-Comté (UBFC), UMR 1231, INSERM/AgroSup Dijon/Université de Bourgogne, Dijon, France.,LipSTIC LabEx, Dijon, France.,Department of Intensive Care, University Hospital François Mitterrand, Dijon, France
| | - Jean-Pierre Quenot
- Université de Bourgogne Franche-Comté (UBFC), UMR 1231, INSERM/AgroSup Dijon/Université de Bourgogne, Dijon, France.,LipSTIC LabEx, Dijon, France.,Department of Intensive Care, University Hospital François Mitterrand, Dijon, France.,Clinical Epidemiology, INSERM CIC 1432 and University of Burgundy, Dijon, France
| | - Mickaël Rialland
- Université de Bourgogne Franche-Comté (UBFC), UMR 1231, INSERM/AgroSup Dijon/Université de Bourgogne, Dijon, France.,LipSTIC LabEx, Dijon, France
| | - David Masson
- Université de Bourgogne Franche-Comté (UBFC), UMR 1231, INSERM/AgroSup Dijon/Université de Bourgogne, Dijon, France.,LipSTIC LabEx, Dijon, France.,Clinical Biochemistry Department, University Hospital François Mitterrand, Dijon, France
| | - Johan Auwerx
- Laboratory for Integrative Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Laurent Lagrost
- Université de Bourgogne Franche-Comté (UBFC), UMR 1231, INSERM/AgroSup Dijon/Université de Bourgogne, Dijon, France.,LipSTIC LabEx, Dijon, France.,Clinical Biochemistry Department, University Hospital François Mitterrand, Dijon, France
| | - Charles Thomas
- Université de Bourgogne Franche-Comté (UBFC), UMR 1231, INSERM/AgroSup Dijon/Université de Bourgogne, Dijon, France.,LipSTIC LabEx, Dijon, France
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18
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Onishi M, Yamano K, Sato M, Matsuda N, Okamoto K. Molecular mechanisms and physiological functions of mitophagy. EMBO J 2021; 40:e104705. [PMID: 33438778 PMCID: PMC7849173 DOI: 10.15252/embj.2020104705] [Citation(s) in RCA: 521] [Impact Index Per Article: 173.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 08/03/2020] [Accepted: 10/02/2020] [Indexed: 12/12/2022] Open
Abstract
Degradation of mitochondria via a selective form of autophagy, named mitophagy, is a fundamental mechanism conserved from yeast to humans that regulates mitochondrial quality and quantity control. Mitophagy is promoted via specific mitochondrial outer membrane receptors, or ubiquitin molecules conjugated to proteins on the mitochondrial surface leading to the formation of autophagosomes surrounding mitochondria. Mitophagy-mediated elimination of mitochondria plays an important role in many processes including early embryonic development, cell differentiation, inflammation, and apoptosis. Recent advances in analyzing mitophagy in vivo also reveal high rates of steady-state mitochondrial turnover in diverse cell types, highlighting the intracellular housekeeping role of mitophagy. Defects in mitophagy are associated with various pathological conditions such as neurodegeneration, heart failure, cancer, and aging, further underscoring the biological relevance. Here, we review our current molecular understanding of mitophagy, and its physiological implications, and discuss how multiple mitophagy pathways coordinately modulate mitochondrial fitness and populations.
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Affiliation(s)
- Mashun Onishi
- Laboratory of Mitochondrial DynamicsGraduate School of Frontier BiosciencesOsaka UniversitySuitaJapan
| | - Koji Yamano
- The Ubiquitin ProjectTokyo Metropolitan Institute of Medical ScienceTokyoJapan
| | - Miyuki Sato
- Laboratory of Molecular Membrane BiologyInstitute for Molecular and Cellular RegulationGunma UniversityMaebashiJapan
| | - Noriyuki Matsuda
- The Ubiquitin ProjectTokyo Metropolitan Institute of Medical ScienceTokyoJapan
| | - Koji Okamoto
- Laboratory of Mitochondrial DynamicsGraduate School of Frontier BiosciencesOsaka UniversitySuitaJapan
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19
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Lin J, Chen K, Chen W, Yao Y, Ni S, Ye M, Zhuang G, Hu M, Gao J, Gao C, Liu Y, Yang M, Zhang Z, Zhang X, Huang J, Chen F, Sun L, Zhang X, Yu S, Chen Y, Jiang Y, Wang S, Yang X, Liu K, Zhou HM, Ji Z, Deng H, Haque ME, Li J, Mi LZ, Li Y, Yang Y. Paradoxical Mitophagy Regulation by PINK1 and TUFm. Mol Cell 2020; 80:607-620.e12. [PMID: 33113344 DOI: 10.1016/j.molcel.2020.10.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/25/2020] [Accepted: 10/06/2020] [Indexed: 01/19/2023]
Abstract
Aberrant mitophagy has been implicated in a broad spectrum of disorders. PINK1, Parkin, and ubiquitin have pivotal roles in priming mitophagy. However, the entire regulatory landscape and the precise control mechanisms of mitophagy remain to be elucidated. Here, we uncover fundamental mitophagy regulation involving PINK1 and a non-canonical role of the mitochondrial Tu translation elongation factor (TUFm). The mitochondrion-cytosol dual-localized TUFm interacts with PINK1 biochemically and genetically, which is an evolutionarily conserved Parkin-independent route toward mitophagy. A PINK1-dependent TUFm phosphoswitch at Ser222 determines conversion from activating to suppressing mitophagy. PINK1 modulates differential translocation of TUFm because p-S222-TUFm is restricted predominantly to the cytosol, where it inhibits mitophagy by impeding Atg5-Atg12 formation. The self-antagonizing feature of PINK1/TUFm is critical for the robustness of mitophagy regulation, achieved by the unique kinetic parameters of p-S222-TUFm, p-S65-ubiquitin, and their common kinase PINK1. Our findings provide new mechanistic insights into mitophagy and mitophagy-associated disorders.
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Affiliation(s)
- Jingjing Lin
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Kai Chen
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Wenfeng Chen
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Yizhou Yao
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Shiwei Ni
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Meina Ye
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Guifeng Zhuang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Minhuang Hu
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Jun Gao
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Caixi Gao
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Yan Liu
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Mingjuan Yang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Zhenkun Zhang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Xiaohui Zhang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Jiexiang Huang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Fei Chen
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Ling Sun
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Xi Zhang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Suhong Yu
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Yuling Chen
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yating Jiang
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Shujuan Wang
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Xiaozhen Yang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Ke Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Hai-Meng Zhou
- Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Zhejiang Jiaxing 314006, China
| | - Zhiliang Ji
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - M Emdadul Haque
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, PO Box 17666, United Arab Emirates
| | - Junxiang Li
- AgeCode R&D Center, Yangtze Delta Region Institute of Tsinghua University, Zhejiang Jiaxing 314006, China
| | - Li-Zhi Mi
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Yuexi Li
- Huadong Research Institute for Medicine and Biotechniques, 293 East Zhongshan Road, Nanjing 210002, China.
| | - Yufeng Yang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China.
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20
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Han H, Tan J, Wang R, Wan H, He Y, Yan X, Guo J, Gao Q, Li J, Shang S, Chen F, Tian R, Liu W, Liao L, Tang B, Zhang Z. PINK1 phosphorylates Drp1 S616 to regulate mitophagy-independent mitochondrial dynamics. EMBO Rep 2020; 21:e48686. [PMID: 32484300 PMCID: PMC7403662 DOI: 10.15252/embr.201948686] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 04/20/2020] [Accepted: 05/05/2020] [Indexed: 11/09/2022] Open
Abstract
Impairment of PINK1/parkin-mediated mitophagy is currently proposed to be the molecular basis of mitochondrial abnormality in Parkinson's disease (PD). We here demonstrate that PINK1 directly phosphorylates Drp1 on S616. Drp1S616 phosphorylation is significantly reduced in cells and mouse tissues deficient for PINK1, but unaffected by parkin inactivation. PINK1-mediated mitochondrial fission is Drp1S616 phosphorylation dependent. Overexpression of either wild-type Drp1 or of the phosphomimetic mutant Drp1S616D , but not a dephosphorylation-mimic mutant Drp1S616A , rescues PINK1 deficiency-associated phenotypes in Drosophila. Moreover, Drp1 restores PINK1-dependent mitochondrial fission in ATG5-null cells and ATG7-null Drosophila. Reduced Drp1S616 phosphorylation is detected in fibroblasts derived from 4 PD patients harboring PINK1 mutations and in 4 out of 7 sporadic PD cases. Taken together, we have identified Drp1 as a substrate of PINK1 and a novel mechanism how PINK1 regulates mitochondrial fission independent of parkin and autophagy. Our results further link impaired PINK1-mediated Drp1S616 phosphorylation with the pathogenesis of both familial and sporadic PD.
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Affiliation(s)
- Hailong Han
- Key Laboratory of Molecular Precision Medicine of Hunan Province and Center for Medical GeneticsInstitute of Molecular Precision MedicineXiangya HospitalCentral South UniversityChangshaChina
- Department of NeurologyXiangya HospitalCentral South UniversityChangshaChina
| | - Jieqiong Tan
- Key Laboratory of Molecular Precision Medicine of Hunan Province and Center for Medical GeneticsInstitute of Molecular Precision MedicineXiangya HospitalCentral South UniversityChangshaChina
- Department of NeurologyXiangya HospitalCentral South UniversityChangshaChina
| | - Ruoxi Wang
- Key Laboratory of Molecular Precision Medicine of Hunan Province and Center for Medical GeneticsInstitute of Molecular Precision MedicineXiangya HospitalCentral South UniversityChangshaChina
- Department of NeurologyXiangya HospitalCentral South UniversityChangshaChina
| | - Huida Wan
- Shanghai Key Laboratory of Regulatory BiologySchool of Life SciencesEast China Normal UniversityShanghaiChina
| | - Yaohui He
- Fujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiamenChina
| | - Xinxiang Yan
- Department of NeurologyXiangya HospitalCentral South UniversityChangshaChina
| | - Jifeng Guo
- Department of NeurologyXiangya HospitalCentral South UniversityChangshaChina
| | - Qingtao Gao
- Key Laboratory of Molecular Precision Medicine of Hunan Province and Center for Medical GeneticsInstitute of Molecular Precision MedicineXiangya HospitalCentral South UniversityChangshaChina
- Department of NeurologyXiangya HospitalCentral South UniversityChangshaChina
| | - Jie Li
- Key Laboratory of Molecular Precision Medicine of Hunan Province and Center for Medical GeneticsInstitute of Molecular Precision MedicineXiangya HospitalCentral South UniversityChangshaChina
- Department of NeurologyXiangya HospitalCentral South UniversityChangshaChina
| | - Shuai Shang
- Key Laboratory of Molecular Precision Medicine of Hunan Province and Center for Medical GeneticsInstitute of Molecular Precision MedicineXiangya HospitalCentral South UniversityChangshaChina
- Department of NeurologyXiangya HospitalCentral South UniversityChangshaChina
| | - Fang Chen
- Key Laboratory of Molecular Precision Medicine of Hunan Province and Center for Medical GeneticsInstitute of Molecular Precision MedicineXiangya HospitalCentral South UniversityChangshaChina
- Department of NeurologyXiangya HospitalCentral South UniversityChangshaChina
| | - Runyi Tian
- Key Laboratory of Molecular Precision Medicine of Hunan Province and Center for Medical GeneticsInstitute of Molecular Precision MedicineXiangya HospitalCentral South UniversityChangshaChina
- Department of NeurologyXiangya HospitalCentral South UniversityChangshaChina
| | - Wen Liu
- Fujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiamenChina
| | - Lujian Liao
- Shanghai Key Laboratory of Regulatory BiologySchool of Life SciencesEast China Normal UniversityShanghaiChina
| | - Beisha Tang
- Department of NeurologyXiangya HospitalCentral South UniversityChangshaChina
| | - Zhuohua Zhang
- Key Laboratory of Molecular Precision Medicine of Hunan Province and Center for Medical GeneticsInstitute of Molecular Precision MedicineXiangya HospitalCentral South UniversityChangshaChina
- Department of NeurologyXiangya HospitalCentral South UniversityChangshaChina
- Department of NeurosciencesUniversity of South China Medical SchoolHengyangChina
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21
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Abstract
In 2004, PINK1 was established as a gene linked to early onset of autosomal recessive juvenile Parkinsonism. Since then, tremendous efforts allowed involving the gene product in diverse events but with a strong focus on its partnership with the protein Parkin for the degradation of damaged mitochondria through mitophagy. Yet, it is now clear that the importance of PINK1 encompasses a wider spectrum of intracellular processes. In this minireview, we highlight some of the PINK1 interplays and recent advances, including its growing involvement in immunity and also its emerging place in this era of mitochondria-organelles contact sites.
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Affiliation(s)
- Edgar Djaha Yoboue
- IRCCS Mondino Foundation, Pavia, Italy; Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Enza Maria Valente
- IRCCS Mondino Foundation, Pavia, Italy; Department of Molecular Medicine, University of Pavia, Pavia, Italy.
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22
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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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23
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Hill BG, Shiva S, Ballinger S, Zhang J, Darley-Usmar VM. Bioenergetics and translational metabolism: implications for genetics, physiology and precision medicine. Biol Chem 2019; 401:3-29. [PMID: 31815377 PMCID: PMC6944318 DOI: 10.1515/hsz-2019-0268] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 06/24/2019] [Indexed: 12/25/2022]
Abstract
It is now becoming clear that human metabolism is extremely plastic and varies substantially between healthy individuals. Understanding the biochemistry that underlies this physiology will enable personalized clinical interventions related to metabolism. Mitochondrial quality control and the detailed mechanisms of mitochondrial energy generation are central to understanding susceptibility to pathologies associated with aging including cancer, cardiac and neurodegenerative diseases. A precision medicine approach is also needed to evaluate the impact of exercise or caloric restriction on health. In this review, we discuss how technical advances in assessing mitochondrial genetics, cellular bioenergetics and metabolomics offer new insights into developing metabolism-based clinical tests and metabolotherapies. We discuss informatics approaches, which can define the bioenergetic-metabolite interactome and how this can help define healthy energetics. We propose that a personalized medicine approach that integrates metabolism and bioenergetics with physiologic parameters is central for understanding the pathophysiology of diseases with a metabolic etiology. New approaches that measure energetics and metabolomics from cells isolated from human blood or tissues can be of diagnostic and prognostic value to precision medicine. This is particularly significant with the development of new metabolotherapies, such as mitochondrial transplantation, which could help treat complex metabolic diseases.
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Affiliation(s)
- Bradford G. Hill
- Envirome Institute, Diabetes and Obesity Center, Department of Medicine, University of Louisville, Louisville, KY 40202
| | - Sruti Shiva
- Department of Pharmacology & Chemical Biology, Vascular Medicine Institute, Center for Metabolism & Mitochondrial Medicine, University of Pittsburgh, Pittsburgh, PA 15143
| | - Scott Ballinger
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294
- Mitochondrial Medicine Laboratory, University of Alabama at Birmingham, Birmingham, AL 35294
- Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Jianhua Zhang
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294
- Mitochondrial Medicine Laboratory, University of Alabama at Birmingham, Birmingham, AL 35294
- Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL 35294
- Department of Veteran Affairs Medical Center, Birmingham, AL 35294
| | - Victor M. Darley-Usmar
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294
- Mitochondrial Medicine Laboratory, University of Alabama at Birmingham, Birmingham, AL 35294
- Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL 35294
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24
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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: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/13/2019] [Accepted: 06/19/2019] [Indexed: 12/20/2022]
Abstract
Parkinson's disease (PD) is a degenerative movement disorder resulting from the loss of specific neuron types in the midbrain. Early environmental and pathophysiological studies implicated mitochondrial damage and protein aggregation as the main causes of PD. These findings are now vindicated by the characterization of more than 20 genes implicated in rare familial forms of the disease. In particular, two proteins encoded by the Parkin and PINK1 genes, whose mutations cause early-onset autosomal recessive PD, function together in a mitochondrial quality control pathway. In this review, we will describe recent development in our understanding of their mechanisms of action, structure, and function. We explain how PINK1 acts as a mitochondrial damage sensor via the regulated proteolysis of its N-terminus and the phosphorylation of ubiquitin tethered to outer mitochondrial membrane proteins. In turn, phospho-ubiquitin recruits and activates Parkin via conformational changes that increase its ubiquitin ligase activity. We then describe how the formation of polyubiquitin chains on mitochondria triggers the recruitment of the autophagy machinery or the formation of mitochondria-derived vesicles. Finally, we discuss the evidence for the involvement of these mechanisms in physiological processes such as immunity and inflammation, as well as the links to other PD genes.
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Affiliation(s)
- Andrew N Bayne
- Department of Pharmacology and Therapeutics and Centre for Structural Biology, McGill University, 3655 Prom Sir William Osler, Montreal, QC, H3G 1Y6, Canada
| | - Jean-François Trempe
- Department of Pharmacology and Therapeutics and Centre for Structural Biology, McGill University, 3655 Prom Sir William Osler, Montreal, QC, H3G 1Y6, Canada.
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25
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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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26
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SerThr-PhosphoProteome of Brain from Aged PINK1-KO+A53T-SNCA Mice Reveals pT1928-MAP1B and pS3781-ANK2 Deficits, as Hub between Autophagy and Synapse Changes. Int J Mol Sci 2019; 20:ijms20133284. [PMID: 31277379 PMCID: PMC6651490 DOI: 10.3390/ijms20133284] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/30/2019] [Accepted: 07/02/2019] [Indexed: 02/08/2023] Open
Abstract
Hereditary Parkinson’s disease (PD) can be triggered by an autosomal dominant overdose of alpha-Synuclein (SNCA) as stressor or the autosomal recessive deficiency of PINK1 Serine/Threonine-phosphorylation activity as stress-response. We demonstrated the combination of PINK1-knockout with overexpression of SNCAA53T in double mutant (DM) mice to exacerbate locomotor deficits and to reduce lifespan. To survey posttranslational modifications of proteins underlying the pathology, brain hemispheres of old DM mice underwent quantitative label-free global proteomic mass spectrometry, focused on Ser/Thr-phosphorylations. As an exceptionally strong effect, we detected >300-fold reductions of phosphoThr1928 in MAP1B, a microtubule-associated protein, and a similar reduction of phosphoSer3781 in ANK2, an interactor of microtubules. MAP1B depletion is known to trigger perturbations of microtubular mitochondria trafficking, neurite extension, and synaptic function, so it was noteworthy that relevantly decreased phosphorylation was also detected for other microtubule and microfilament factors, namely MAP2S1801, MARK1S394, MAP1AT1794, KIF1AS1537, 4.1NS541, 4.1GS86, and ADD2S528. While the MAP1B heavy chain supports regeneration and growth cones, its light chain assists DAPK1-mediated autophagy. Interestingly, relevant phosphorylation decreases of DAPK2S299, VPS13DS2429, and VPS13CS2480 in the DM brain affected regulators of autophagy, which are implicated in PD. Overall, significant downregulations were enriched for PFAM C2 domains, other kinases, and synaptic transmission factors upon automated bioinformatics, while upregulations were not enriched for selective motifs or pathways. Validation experiments confirmed the change of LC3 processing as reflection of excessive autophagy in DM brain, and dependence of ANK2/MAP1B expression on PINK1 levels. Our new data provide independent confirmation in a mouse model with combined PARK1/PARK4/PARK6 pathology that MAP1B/ANK2 phosphorylation events are implicated in Parkinsonian neurodegeneration. These findings expand on previous observations in Drosophila melanogaster that the MAP1B ortholog futsch in the presynapse is a primary target of the PARK8 protein LRRK2, and on a report that MAP1B is a component of the pathological Lewy body aggregates in PD patient brains. Similarly, ANK2 gene locus variants are associated with the risk of PD, ANK2 interacts with PINK1/Parkin-target proteins such as MIRO1 or ATP1A2, and ANK2-derived peptides are potent inhibitors of autophagy.
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27
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Miller S, Muqit MMK. Therapeutic approaches to enhance PINK1/Parkin mediated mitophagy for the treatment of Parkinson's disease. Neurosci Lett 2019; 705:7-13. [PMID: 30995519 DOI: 10.1016/j.neulet.2019.04.029] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/07/2019] [Accepted: 04/12/2019] [Indexed: 11/30/2022]
Abstract
The discovery of rare familial monogenic forms of early-onset Parkinson's disease has led to the identification of a mitochondrial quality control process as a key player in this disease. Loss-of-function mutations in the genes encoding PINK1 or Parkin result in insufficient removal of dysfunctional mitochondria through autophagy, a process termed mitophagy. Understanding the mechanism of this process and the function of its two key players, PINK1 and Parkin, has led to the discovery of new therapeutic approaches. Small molecule activators of mitophagy, either activating PINK1 or Parkin directly or inhibiting Parkin's counterplayer, the ubiquitin-specific protease USP30, are in preclinical development. To enable clinical success of future small molecule mitophagy enhancers, biomarkers for mitochondrial integrity and mitophagy are being developed. Only a few years after the discovery of mitophagy deficits in Parkinson's disease, research of the underlying mechanisms, drug discovery of modulators for this mechanism and identification of biomarkers provide new avenues towards the development of disease-modifying therapies.
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Affiliation(s)
- Silke Miller
- Neuroscience Department, Amgen Research, 360 Binney St., Cambridge, MA, 02142, USA.
| | - Miratul M K Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, United Kingdom
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28
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Adamski Z, Bufo SA, Chowański S, Falabella P, Lubawy J, Marciniak P, Pacholska-Bogalska J, Salvia R, Scrano L, Słocińska M, Spochacz M, Szymczak M, Urbański A, Walkowiak-Nowicka K, Rosiński G. Beetles as Model Organisms in Physiological, Biomedical and Environmental Studies - A Review. Front Physiol 2019; 10:319. [PMID: 30984018 PMCID: PMC6447812 DOI: 10.3389/fphys.2019.00319] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 03/11/2019] [Indexed: 12/13/2022] Open
Abstract
Model organisms are often used in biological, medical and environmental research. Among insects, Drosophila melanogaster, Galleria mellonella, Apis mellifera, Bombyx mori, Periplaneta americana, and Locusta migratoria are often used. However, new model organisms still appear. In recent years, an increasing number of insect species has been suggested as model organisms in life sciences research due to their worldwide distribution and environmental significance, the possibility of extrapolating research studies to vertebrates and the relatively low cost of rearing. Beetles are the largest insect order, with their representative - Tribolium castaneum - being the first species with a completely sequenced genome, and seem to be emerging as new potential candidates for model organisms in various studies. Apart from T. castaneum, additional species representing various Coleoptera families, such as Nicrophorus vespilloides, Leptinotarsa decemlineata, Coccinella septempunctata, Poecilus cupreus, Tenebrio molitor and many others, have been used. They are increasingly often included in two major research aspects: biomedical and environmental studies. Biomedical studies focus mainly on unraveling mechanisms of basic life processes, such as feeding, neurotransmission or activity of the immune system, as well as on elucidating the mechanism of different diseases (neurodegenerative, cardiovascular, metabolic, or immunological) using beetles as models. Furthermore, pharmacological bioassays for testing novel biologically active substances in beetles have also been developed. It should be emphasized that beetles are a source of compounds with potential antimicrobial and anticancer activity. Environmental-based studies focus mainly on the development and testing of new potential pesticides of both chemical and natural origin. Additionally, beetles are used as food or for their valuable supplements. Different beetle families are also used as bioindicators. Another important research area using beetles as models is behavioral ecology studies, for instance, parental care. In this paper, we review the current knowledge regarding beetles as model organisms and their practical application in various fields of life science.
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Affiliation(s)
- Zbigniew Adamski
- Department of Animal Physiology and Development, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
- Laboratory of Electron and Confocal Microscopy, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Sabino A. Bufo
- Department of Sciences, University of Basilicata, Potenza, Italy
- Department of Geography, Environmental Management & Energy Studies, University of Johannesburg, Johannesburg, South Africa
| | - Szymon Chowański
- Department of Animal Physiology and Development, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | | | - Jan Lubawy
- Department of Animal Physiology and Development, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Paweł Marciniak
- Department of Animal Physiology and Development, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Joanna Pacholska-Bogalska
- Department of Animal Physiology and Development, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Rosanna Salvia
- Department of Sciences, University of Basilicata, Potenza, Italy
| | - Laura Scrano
- Department of European and Mediterranean Cultures, University of Basilicata, Matera, Italy
| | - Małgorzata Słocińska
- Department of Animal Physiology and Development, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Marta Spochacz
- Department of Animal Physiology and Development, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Monika Szymczak
- Department of Animal Physiology and Development, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Arkadiusz Urbański
- Department of Animal Physiology and Development, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Karolina Walkowiak-Nowicka
- Department of Animal Physiology and Development, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Grzegorz Rosiński
- Department of Animal Physiology and Development, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
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29
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Zhang C, Wang R, Liu Z, Bunker E, Lee S, Giuntini M, Chapnick D, Liu X. The plant triterpenoid celastrol blocks PINK1-dependent mitophagy by disrupting PINK1's association with the mitochondrial protein TOM20. J Biol Chem 2019; 294:7472-7487. [PMID: 30885942 DOI: 10.1074/jbc.ra118.006506] [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: 11/01/2018] [Revised: 03/05/2019] [Indexed: 12/31/2022] Open
Abstract
A critical function of the PTEN-induced kinase 1 (PINK1)-Parkin pathway is to mediate the clearing of unhealthy or damaged mitochondria via mitophagy. Loss of either PINK1 or Parkin protein expression is associated with Parkinson's disease. Here, using a high-throughput screening approach along with recombinant protein expression and kinase, immunoblotting, and immunofluorescence live-cell imaging assays, we report that celastrol, a pentacyclic triterpenoid isolated from extracts of the medicinal plant Tripterygium wilfordii, blocks recruitment pof Parkin to mitochondria, preventing mitophagy in response to mitochondrial depolarization induced by carbonyl cyanide m-chlorophenylhydrazone or to gamitrinib-induced inhibition of mitochondrial heat shock protein 90 (HSP90). Celastrol's effect on mitophagy was independent of its known role in microtubule disruption. Instead, we show that celastrol suppresses Parkin recruitment by inactivating PINK1 and preventing it from phosphorylating Parkin and also ubiquitin. We also observed that PINK1 directly and strongly associates with TOM20, a component of the translocase of outer mitochondrial membrane (TOM) machinery and relatively weak binding to another TOM subunit, TOM70. Moreover, celastrol disrupted binding between PINK1 and TOM20 both in vitro and in vivo but did not affect binding between TOM20 and TOM70. Using native gel analysis, we also show that celastrol disrupts PINK1 complex formation upon mitochondrial depolarization and sequesters PINK1 to high-molecular-weight protein aggregates. These results reveal that celastrol regulates the mitochondrial quality control pathway by interfering with PINK1-TOM20 binding.
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Affiliation(s)
- Conggang Zhang
- From the Department of Biochemistry, JSCBB, University of Colorado, Boulder, Colorado 80303 and
| | - Rongchun Wang
- From the Department of Biochemistry, JSCBB, University of Colorado, Boulder, Colorado 80303 and.,the Biology Institute, Qilu University of Technology, Shandong Academy of Sciences, 28789 East Jinshi Street, Licheng District, Jinan 250103, China
| | - Zeyu Liu
- From the Department of Biochemistry, JSCBB, University of Colorado, Boulder, Colorado 80303 and
| | - Eric Bunker
- From the Department of Biochemistry, JSCBB, University of Colorado, Boulder, Colorado 80303 and
| | - Schuyler Lee
- From the Department of Biochemistry, JSCBB, University of Colorado, Boulder, Colorado 80303 and
| | - Michelle Giuntini
- From the Department of Biochemistry, JSCBB, University of Colorado, Boulder, Colorado 80303 and
| | - Douglas Chapnick
- From the Department of Biochemistry, JSCBB, University of Colorado, Boulder, Colorado 80303 and
| | - Xuedong Liu
- From the Department of Biochemistry, JSCBB, University of Colorado, Boulder, Colorado 80303 and
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30
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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: 6] [Impact Index Per Article: 1.0] [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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31
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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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32
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Okatsu K, Sato Y, Yamano K, Matsuda N, Negishi L, Takahashi A, Yamagata A, Goto-Ito S, Mishima M, Ito Y, Oka T, Tanaka K, Fukai S. Structural insights into ubiquitin phosphorylation by PINK1. Sci Rep 2018; 8:10382. [PMID: 29991771 PMCID: PMC6039469 DOI: 10.1038/s41598-018-28656-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 05/31/2018] [Indexed: 11/09/2022] Open
Abstract
Mutations of PTEN-induced putative kinase 1 (PINK1) and the E3 ubiquitin (Ub) ligase parkin can cause familial parkinsonism. These two proteins are essential for ubiquitylation of damaged mitochondria and subsequent degradation. PINK1 phosphorylates Ser65 of Ub and the Ub-like (UBL) domain of parkin to allosterically relieve the autoinhibition of parkin. To understand the structural mechanism of the Ub/UBL-specific phosphorylation by PINK1, we determined the crystal structure of Tribolium castaneum PINK1 kinase domain (TcPINK1) in complex with a nonhydrolyzable ATP analogue at 2.5 Å resolution. TcPINK1 consists of the N- and C-terminal lobes with the PINK1-specific extension. The ATP analogue is bound in the cleft between the N- and C-terminal lobes. The adenine ring of the ATP analogue is bound to a hydrophobic pocket, whereas the triphosphate group of the ATP analogue and two coordinated Mg ions interact with the catalytic hydrophilic residues. Comparison with protein kinases A and C (PKA and PKC, respectively) unveils a putative Ub/UBL-binding groove, which is wider than the peptide-binding groove of PKA or PKC to accommodate the globular head of Ub or UBL. Further crosslinking analyses suggested a PINK1-interacting surface of Ub. Structure-guided mutational analyses support the findings from the present structural analysis of PINK1.
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Affiliation(s)
- Kei Okatsu
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Yusuke Sato
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan
| | - Koji Yamano
- Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Noriyuki Matsuda
- Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan.,PRESTO, Japan Science and Technology Agency, Saitama, 332-0012, Japan
| | - Lumi Negishi
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Akiko Takahashi
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Atsushi Yamagata
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan
| | - Sakurako Goto-Ito
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Masaki Mishima
- Graduate School of Science & Engineering, Tokyo Metropolitan University, Tokyo, 192-0397, Japan
| | - Yutaka Ito
- Graduate School of Science & Engineering, Tokyo Metropolitan University, Tokyo, 192-0397, Japan
| | - Toshihiko Oka
- Department of Life Science, Rikkyo University, Tokyo, 171-8501, Japan
| | - Keiji Tanaka
- Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Shuya Fukai
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan. .,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan. .,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan.
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Baltussen LL, Rosianu F, Ultanir SK. Kinases in synaptic development and neurological diseases. Prog Neuropsychopharmacol Biol Psychiatry 2018; 84:343-352. [PMID: 29241837 DOI: 10.1016/j.pnpbp.2017.12.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 12/08/2017] [Accepted: 12/09/2017] [Indexed: 10/18/2022]
Abstract
Neuronal morphogenesis and synapse development is essential for building a functioning nervous system, and defects in these processes are associated with neurological disorders. Our understanding of molecular components and signalling events that contribute to neuronal development and pathogenesis is limited. Genes associated with neurodevelopmental and neurodegenerative diseases provide entry points for elucidating molecular events that contribute to these conditions. Several protein kinases, enzymes that regulate protein function by phosphorylating their substrates, are genetically linked to neurological disorders. Identifying substrates of these kinases is key to discovering their function and providing insight for possible therapies. In this review, we describe how various methods for kinase-substrate identification helped elucidate kinase signalling pathways important for neuronal development and function. We describe recent advances on roles of kinases TAOK2, TNIK and CDKL5 in neuronal development and the converging pathways of LRRK2, PINK1 and GAK in Parkinson's Disease.
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Affiliation(s)
- Lucas L Baltussen
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Flavia Rosianu
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Sila K Ultanir
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom.
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Course MM, Scott AI, Schoor C, Hsieh CH, Papakyrikos AM, Winter D, Cowan TM, Wang X. Phosphorylation of MCAD selectively rescues PINK1 deficiencies in behavior and metabolism. Mol Biol Cell 2018; 29:1219-1227. [PMID: 29563254 PMCID: PMC5935071 DOI: 10.1091/mbc.e18-03-0155] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PTEN-induced putative kinase 1 (PINK1) is a mitochondria-targeted kinase whose mutations are a cause of Parkinson’s disease. We set out to better understand PINK1’s effects on mitochondrial proteins in vivo. Using an unbiased phosphoproteomic screen in Drosophila, we found that PINK1 mediates the phosphorylation of MCAD, a mitochondrial matrix protein critical to fatty acid metabolism. By mimicking phosphorylation of this protein in a PINK1 null background, we restored PINK1 null’s climbing, flight, thorax, and wing deficiencies. Owing to MCAD’s role in fatty acid metabolism, we examined the metabolic profile of PINK1 null flies, where we uncovered significant disruptions in both acylcarnitines and amino acids. Some of these disruptions were rescued by phosphorylation of MCAD, consistent with MCAD’s rescue of PINK1 null’s organismal phenotypes. Our work validates and extends the current knowledge of PINK1, identifies a novel function of MCAD, and illuminates the need for and effectiveness of metabolic profiling in models of neurodegenerative disease.
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Affiliation(s)
- Meredith M Course
- Department of Neurosurgery, Stanford University, Stanford, CA 94305.,Neurosciences Graduate Program, Stanford University, Stanford, CA 94305
| | - Anna I Scott
- Department of Pathology, Stanford University, Stanford, CA 94305
| | - Carmen Schoor
- Institute for Biochemistry and Molecular Biology, University of Bonn, 53115 Bonn, Germany
| | - Chung-Han Hsieh
- Department of Neurosurgery, Stanford University, Stanford, CA 94305
| | - Amanda M Papakyrikos
- Department of Neurosurgery, Stanford University, Stanford, CA 94305.,Developmental Biology Graduate Program, Stanford University, Stanford, CA 94305
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, University of Bonn, 53115 Bonn, Germany
| | - Tina M Cowan
- Department of Pathology, Stanford University, Stanford, CA 94305
| | - Xinnan Wang
- Department of Neurosurgery, Stanford University, Stanford, CA 94305
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35
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Aguirre JD, Dunkerley KM, Lam R, Rusal M, Shaw GS. Impact of altered phosphorylation on loss of function of juvenile Parkinsonism-associated genetic variants of the E3 ligase parkin. J Biol Chem 2018. [PMID: 29530980 PMCID: PMC5925814 DOI: 10.1074/jbc.ra117.000605] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Autosomal recessive juvenile Parkinsonism (ARJP) is an inherited neurodegenerative disease in which 50% of affected individuals harbor mutations in the gene encoding the E3 ligase parkin. Parkin regulates the mitochondrial recycling pathway, which is induced by oxidative stress. In its native state, parkin is auto-inhibited by its N-terminal ubiquitin-like (Ubl) domain, which blocks the binding site for an incoming E2∼ubiquitin conjugate, needed for parkin's ubiquitination activity. Parkin is activated via phosphorylation of Ser-65 in its Ubl domain by PTEN-induced putative kinase 1 (PINK1) and a ubiquitin molecule phosphorylated at a position equivalent to Ser-65 in parkin. Here we have examined the underlying molecular mechanism of phosphorylation of parkin's Ubl domain carrying ARJP-associated substitutions and how altered phosphorylation modulates parkin activation and ubiquitination. We found that three substitutions in the Ubl domain (G12R, R33Q, and R42P) significantly decrease PINK1's ability to phosphorylate the Ubl domain. We noted that two basic loss-of-function substitutions (R33Q and R42P) are close to acidic patches in the proposed PINK1–parkin interface, indicating that ionic interactions at this site may be important for efficient parkin phosphorylation. Increased auto-ubiquitination with unique ubiquitin chain patterns was observed for two other Ubl domain substitutions (G12R and T55I), suggesting that these substitutions, along with phosphorylation, increase parkin degradation. Moreover, Ubl domain phosphorylation decreased its affinity for the potential effector protein ataxin-3, which edits ubiquitin chain building by parkin. Overall, our work provides a framework for the mechanisms of parkin's loss-of-function, indicating an interplay between ARJP-associated substitutions and phosphorylation of its Ubl domain.
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Affiliation(s)
- Jacob D Aguirre
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Karen M Dunkerley
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Rica Lam
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Michele Rusal
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Gary S Shaw
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
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36
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Tsai PI, Lin CH, Hsieh CH, Papakyrikos AM, Kim MJ, Napolioni V, Schoor C, Couthouis J, Wu RM, Wszolek ZK, Winter D, Greicius MD, Ross OA, Wang X. PINK1 Phosphorylates MIC60/Mitofilin to Control Structural Plasticity of Mitochondrial Crista Junctions. Mol Cell 2018; 69:744-756.e6. [DOI: 10.1016/j.molcel.2018.01.026] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 12/07/2017] [Accepted: 01/19/2018] [Indexed: 01/05/2023]
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37
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Rasool S, Soya N, Truong L, Croteau N, Lukacs GL, Trempe JF. PINK1 autophosphorylation is required for ubiquitin recognition. EMBO Rep 2018; 19:embr.201744981. [PMID: 29475881 DOI: 10.15252/embr.201744981] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 01/26/2018] [Accepted: 02/01/2018] [Indexed: 11/09/2022] Open
Abstract
Mutations in PINK1 cause autosomal recessive Parkinson's disease (PD), a neurodegenerative movement disorder. PINK1 is a kinase that acts as a sensor of mitochondrial damage and initiates Parkin-mediated clearance of the damaged organelle. PINK1 phosphorylates Ser65 in both ubiquitin and the ubiquitin-like (Ubl) domain of Parkin, which stimulates its E3 ligase activity. Autophosphorylation of PINK1 is required for Parkin activation, but how this modulates the ubiquitin kinase activity is unclear. Here, we show that autophosphorylation of Tribolium castaneum PINK1 is required for substrate recognition. Using enzyme kinetics and NMR spectroscopy, we reveal that PINK1 binds the Parkin Ubl with a 10-fold higher affinity than ubiquitin via a conserved interface that is also implicated in RING1 and SH3 binding. The interaction requires phosphorylation at Ser205, an invariant PINK1 residue (Ser228 in human). Using mass spectrometry, we demonstrate that PINK1 rapidly autophosphorylates in trans at Ser205. Small-angle X-ray scattering and hydrogen-deuterium exchange experiments provide insights into the structure of the PINK1 catalytic domain. Our findings suggest that multiple PINK1 molecules autophosphorylate first prior to binding and phosphorylating ubiquitin and Parkin.
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Affiliation(s)
- Shafqat Rasool
- Department of Pharmacology & Therapeutics and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, QC, Canada.,Department of Biochemistry, McGill University, Montréal, QC, Canada
| | - Naoto Soya
- Department of Physiology and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, QC, Canada
| | - Luc Truong
- Department of Pharmacology & Therapeutics and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, QC, Canada
| | - Nathalie Croteau
- Department of Pharmacology & Therapeutics and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, QC, Canada
| | - Gergely L Lukacs
- Department of Biochemistry, McGill University, Montréal, QC, Canada.,Department of Physiology and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, QC, Canada
| | - Jean-François Trempe
- Department of Pharmacology & Therapeutics and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, QC, Canada
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38
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Barini E, Miccoli A, Tinarelli F, Mulholland K, Kadri H, Khanim F, Stojanovski L, Read KD, Burness K, Blow JJ, Mehellou Y, Muqit MMK. The Anthelmintic Drug Niclosamide and Its Analogues Activate the Parkinson's Disease Associated Protein Kinase PINK1. Chembiochem 2018; 19:425-429. [PMID: 29226533 PMCID: PMC5901409 DOI: 10.1002/cbic.201700500] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Indexed: 01/08/2023]
Abstract
Mutations in PINK1, which impair its catalytic kinase activity, are causal for autosomal recessive early‐onset Parkinson's disease (PD). Various studies have indicated that the activation of PINK1 could be a useful strategy in treating neurodegenerative diseases, such as PD. Herein, it is shown that the anthelmintic drug niclosamide and its analogues are capable of activating PINK1 in cells through the reversible impairment of the mitochondrial membrane potential. With these compounds, for the first time, it is demonstrated that the PINK1 pathway is active and detectable in primary neurons. These findings suggest that niclosamide and its analogues are robust compounds for the study of the PINK1 pathway and may hold promise as a therapeutic strategy in PD and related disorders.
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Affiliation(s)
- Erica Barini
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Ageo Miccoli
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff, CF10 3NB, UK
| | - Federico Tinarelli
- Centre for Gene Regulation and Expression, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Katie Mulholland
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Hachemi Kadri
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff, CF10 3NB, UK
| | - Farhat Khanim
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Laste Stojanovski
- Drug Discovery Unit, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Kevin D Read
- Drug Discovery Unit, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Kerry Burness
- MRC PPU Reagents and Services, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Julian J Blow
- Centre for Gene Regulation and Expression, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Youcef Mehellou
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff, CF10 3NB, UK
| | - Miratul M K Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.,School of Medicine, University of Dundee, Dow Street, Dundee, DD1 9SY, UK
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39
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Wan H, Tang B, Liao X, Zeng Q, Zhang Z, Liao L. Analysis of neuronal phosphoproteome reveals PINK1 regulation of BAD function and cell death. Cell Death Differ 2017; 25:904-917. [PMID: 29234155 DOI: 10.1038/s41418-017-0027-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 10/24/2017] [Accepted: 10/25/2017] [Indexed: 11/09/2022] Open
Abstract
PINK1 mutations that disrupt its kinase activity cause autosomal recessive early onset Parkinson's disease (PD). Although research in recent years has elucidated a PINK1-Parkin pathway of mitophagy activation that requires PINK1 kinase activity, mitophagy-independent functions of PINK1 and their possible roles in PD pathogenesis have been proposed. Using an unbiased quantitative mass spectrometry approach to analyze the phosphoproteome in primary neurons from wild type and Pink1 knockout mice after mitochondrial depolarization, we uncovered PINK1-regulated phosphorylation sites, which involve coordinated activation of multiple signaling pathways that control cellular response to stress. We further identified the pro-apoptotic protein BAD as a potential mitochondrial substrate of PINK1 both in vitro and in vivo, and found that cells more susceptible to a12poptosis induced by mitochondrial damage can be rescued by phosphorylation mimic BAD. Our results thus suggest that PINK1 kinase activity is important for pro-apoptotic protein function in regulation of cell death.
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Affiliation(s)
- Huida Wan
- Key Laboratory of Brain Functional Genomics of Ministry of Education, Shanghai Key Laboratory of Brain Functional Genomics, and Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Bin Tang
- Key Laboratory of Brain Functional Genomics of Ministry of Education, Shanghai Key Laboratory of Brain Functional Genomics, and Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Xun Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Qiufang Zeng
- Key Laboratory of Brain Functional Genomics of Ministry of Education, Shanghai Key Laboratory of Brain Functional Genomics, and Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Zhuohua Zhang
- Institute of Precision Medicine, State key laboratory of Medical Genetics, the Xiangya Hospital and the Xiangya Medical School, Central South University, Changsha, Hunan, 410078, China
| | - Lujian Liao
- Key Laboratory of Brain Functional Genomics of Ministry of Education, Shanghai Key Laboratory of Brain Functional Genomics, and Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China.
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40
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41
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Schubert AF, Gladkova C, Pardon E, Wagstaff JL, Freund SM, Steyaert J, Maslen SL, Komander D. Structure of PINK1 in complex with its substrate ubiquitin. Nature 2017; 552:51-56. [PMID: 29160309 PMCID: PMC6020998 DOI: 10.1038/nature24645] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 10/20/2017] [Indexed: 12/28/2022]
Abstract
Autosomal-recessive juvenile Parkinsonism (AR-JP) is caused by mutations in a number of PARK genes, in particular the genes encoding the E3 ubiquitin ligase Parkin (PARK2, also known as PRKN) and its upstream protein kinase PINK1 (also known as PARK6). PINK1 phosphorylates both ubiquitin and the ubiquitin-like domain of Parkin on structurally protected Ser65 residues, triggering mitophagy. Here we report a crystal structure of a nanobody-stabilized complex containing Pediculus humanus corporis (Ph)PINK1 bound to ubiquitin in the 'C-terminally retracted' (Ub-CR) conformation. The structure reveals many peculiarities of PINK1, including the architecture of the C-terminal region, and reveals how the N lobe of PINK1 binds ubiquitin via a unique insertion. The flexible Ser65 loop in the Ub-CR conformation contacts the activation segment, facilitating placement of Ser65 in a phosphate-accepting position. The structure also explains how autophosphorylation in the N lobe stabilizes structurally and functionally important insertions, and reveals the molecular basis of AR-JP-causing mutations, some of which disrupt ubiquitin binding.
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Affiliation(s)
- Alexander F. Schubert
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Christina Gladkova
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Els Pardon
- VIB-VUB Center for Structural Biology, VIB, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Jane L. Wagstaff
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Stefan M.V. Freund
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Jan Steyaert
- VIB-VUB Center for Structural Biology, VIB, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Sarah L. Maslen
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - David Komander
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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42
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Gladkova C, Schubert AF, Wagstaff JL, Pruneda JN, Freund SM, Komander D. An invisible ubiquitin conformation is required for efficient phosphorylation by PINK1. EMBO J 2017; 36:3555-3572. [PMID: 29133469 PMCID: PMC5730886 DOI: 10.15252/embj.201797876] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/16/2017] [Accepted: 10/18/2017] [Indexed: 11/09/2022] Open
Abstract
The Ser/Thr protein kinase PINK1 phosphorylates the well-folded, globular protein ubiquitin (Ub) at a relatively protected site, Ser65. We previously showed that Ser65 phosphorylation results in a conformational change in which Ub adopts a dynamic equilibrium between the known, common Ub conformation and a distinct, second conformation wherein the last β-strand is retracted to extend the Ser65 loop and shorten the C-terminal tail. We show using chemical exchange saturation transfer (CEST) nuclear magnetic resonance experiments that a similar, C-terminally retracted (Ub-CR) conformation also exists at low population in wild-type Ub. Point mutations in the moving β5 and neighbouring β-strands shift the Ub/Ub-CR equilibrium. This enabled functional studies of the two states, and we show that while the Ub-CR conformation is defective for conjugation, it demonstrates improved binding to PINK1 through its extended Ser65 loop, and is a superior PINK1 substrate. Together our data suggest that PINK1 utilises a lowly populated yet more suitable Ub-CR conformation of Ub for efficient phosphorylation. Our findings could be relevant for many kinases that phosphorylate residues in folded protein domains.
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Affiliation(s)
| | | | - Jane L Wagstaff
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Stefan Mv Freund
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - David Komander
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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43
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Hauser DN, Primiani CT, Cookson MR. The Effects of Variants in the Parkin, PINK1, and DJ-1 Genes along with Evidence for their Pathogenicity. Curr Protein Pept Sci 2017; 18:702-714. [PMID: 26965687 DOI: 10.2174/1389203717666160311121954] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 09/15/2016] [Accepted: 06/30/2016] [Indexed: 12/13/2022]
Abstract
Early onset Parkinson's disease can be caused by variants in the PINK1, Parkin, and DJ-1 genes. Since their initial discoveries, hundreds of variants have been found in these genes that are associated with a Parkinsonian phenotype. This review will briefly discuss the functions of the protein products of the three genes, then focus on the effects that disease associated variants have on these functions. We will also discuss how experimental findings can help decide whether individual variants are pathogenic or not.
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Affiliation(s)
- David N Hauser
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, MD, United States
| | - Christopher T Primiani
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, MD, United States
| | - Mark R Cookson
- Cell Biology and Gene Expression Section, NIA, Building 35, Room 1A116, 5 Convent Drive, MSC 3707, Bethesda, MD 20892-3707, United States
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44
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Kumar A, Tamjar J, Waddell AD, Woodroof HI, Raimi OG, Shaw AM, Peggie M, Muqit MM, van Aalten DM. Structure of PINK1 and mechanisms of Parkinson's disease-associated mutations. eLife 2017; 6:29985. [PMID: 28980524 PMCID: PMC5679756 DOI: 10.7554/elife.29985] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/04/2017] [Indexed: 12/28/2022] Open
Abstract
Mutations in the human kinase PINK1 (hPINK1) are associated with autosomal recessive early-onset Parkinson's disease (PD). hPINK1 activates Parkin E3 ligase activity, involving phosphorylation of ubiquitin and the Parkin ubiquitin-like (Ubl) domain via as yet poorly understood mechanisms. hPINK1 is unusual amongst kinases due to the presence of three loop insertions of unknown function. We report the structure of Tribolium castaneum PINK1 (TcPINK1), revealing several unique extensions to the canonical protein kinase fold. The third insertion, together with autophosphorylation at residue Ser205, contributes to formation of a bowl-shaped binding site for ubiquitin. We also define a novel structural element within the second insertion that is held together by a distal loop that is critical for TcPINK1 activity. The structure of TcPINK1 explains how PD-linked mutations that lie within the kinase domain result in hPINK1 loss-of-function and provides a platform for the exploration of small molecule modulators of hPINK1.
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Affiliation(s)
- Atul Kumar
- Division of Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom.,MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, United Kingdom
| | - Jevgenia Tamjar
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, United Kingdom
| | - Andrew D Waddell
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, United Kingdom
| | - Helen I Woodroof
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, United Kingdom
| | - Olawale G Raimi
- Division of Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - Andrew M Shaw
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, United Kingdom
| | - Mark Peggie
- Division of Signal Transduction Therapy, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Miratul Mk Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, United Kingdom.,School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Daan Mf van Aalten
- Division of Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
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45
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Activation mechanisms of the E3 ubiquitin ligase parkin. Biochem J 2017; 474:3075-3086. [PMID: 28860335 DOI: 10.1042/bcj20170476] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/24/2017] [Accepted: 07/31/2017] [Indexed: 12/31/2022]
Abstract
Monogenetic, familial forms of Parkinson's disease (PD) only account for 5-10% of the total number of PD cases, but analysis of the genes involved therein is invaluable to understanding PD-associated neurodegenerative signaling. One such gene, parkin, encodes a 465 amino acid E3 ubiquitin ligase. Of late, there has been considerable interest in the role of parkin signaling in PD and in identifying its putative substrates, as well as the elucidation of the mechanisms through which parkin itself is activated. Its dysfunction underlies both inherited and idiopathic PD-associated neurodegeneration. Here, we review recent literature that provides a model of activation of parkin in the setting of mitochondrial damage that involves PINK1 (PTEN-induced kinase-1) and phosphoubiquitin. We note that neuronal parkin is primarily a cytosolic protein (with various non-mitochondrial functions), and discuss potential cytosolic parkin activation mechanisms.
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46
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Kumar A, Chaugule VK, Condos TEC, Barber KR, Johnson C, Toth R, Sundaramoorthy R, Knebel A, Shaw GS, Walden H. Parkin-phosphoubiquitin complex reveals cryptic ubiquitin-binding site required for RBR ligase activity. Nat Struct Mol Biol 2017; 24:475-483. [PMID: 28414322 PMCID: PMC5420311 DOI: 10.1038/nsmb.3400] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 03/16/2017] [Indexed: 12/20/2022]
Abstract
RING-between-RING (RBR) E3 ligases are a class of ubiquitin ligases distinct from RING or HECT E3 ligases. An important RBR ligase is Parkin, mutations in which lead to early-onset hereditary Parkinsonism. Parkin and other RBR ligases share a catalytic RBR module but are usually autoinhibited and activated via distinct mechanisms. Recent insights into Parkin regulation predict large, unknown conformational changes during Parkin activation. However, current data on active RBR ligases reflect the absence of regulatory domains. Therefore, it remains unclear how individual RBR ligases are activated, and whether they share a common mechanism. We now report the crystal structure of a human Parkin-phosphoubiquitin complex, which shows that phosphoubiquitin binding induces movement in the 'in-between RING' (IBR) domain to reveal a cryptic ubiquitin-binding site. Mutation of this site negatively affects Parkin's activity. Furthermore, ubiquitin binding promotes cooperation between Parkin molecules, which suggests a role for interdomain association in the RBR ligase mechanism.
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Affiliation(s)
- Atul Kumar
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Viduth K Chaugule
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Tara E C Condos
- Department of Biochemistry, Schulich School of Medicine and
Dentistry, University of Western Ontario, London, ON, Canada
| | - Kathryn R Barber
- Department of Biochemistry, Schulich School of Medicine and
Dentistry, University of Western Ontario, London, ON, Canada
| | - Clare Johnson
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | | | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
| | - Gary S Shaw
- Department of Biochemistry, Schulich School of Medicine and
Dentistry, University of Western Ontario, London, ON, Canada
| | - Helen Walden
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences University of Dundee, Dundee, UK
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47
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Osgerby L, Lai YC, Thornton PJ, Amalfitano J, Le Duff CS, Jabeen I, Kadri H, Miccoli A, Tucker JHR, Muqit MMK, Mehellou Y. Kinetin Riboside and Its ProTides Activate the Parkinson's Disease Associated PTEN-Induced Putative Kinase 1 (PINK1) Independent of Mitochondrial Depolarization. J Med Chem 2017; 60:3518-3524. [PMID: 28323427 PMCID: PMC5410652 DOI: 10.1021/acs.jmedchem.6b01897] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
Since loss of function
mutations of PINK1 lead to early onset Parkinson’s
disease, there has been growing interest in the discovery of small
molecules that amplify the kinase activity of PINK1. We herein report
the design, synthesis, serum stability, and hydrolysis of four kinetin
riboside ProTides. These ProTides, along with kinetin riboside, activated
PINK1 in cells independent of mitochondrial depolarization. This highlights
the potential of modified nucleosides and their phosphate prodrugs
as treatments for neurodegenerative diseases.
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Affiliation(s)
- Laura Osgerby
- School of Chemistry, University of Birmingham , Birmingham, B15 2TT, U.K
| | - Yu-Chiang Lai
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee , Dundee DD1 5EH, U.K
| | - Peter J Thornton
- School of Pharmacy, University of Birmingham , Birmingham, B15 2TT, U.K
| | - Joseph Amalfitano
- School of Chemistry, University of Birmingham , Birmingham, B15 2TT, U.K
| | - Cécile S Le Duff
- School of Chemistry, University of Birmingham , Birmingham, B15 2TT, U.K
| | - Iqra Jabeen
- School of Chemistry, University of Birmingham , Birmingham, B15 2TT, U.K
| | - Hachemi Kadri
- School of Pharmacy, University of Birmingham , Birmingham, B15 2TT, U.K
| | - Ageo Miccoli
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University , Cardiff CF10 3NB, U.K
| | - James H R Tucker
- School of Chemistry, University of Birmingham , Birmingham, B15 2TT, U.K
| | - Miratul M K Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee , Dundee DD1 5EH, U.K.,School of Medicine, University of Dundee , Dundee, DD1 9SY, U.K
| | - Youcef Mehellou
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University , Cardiff CF10 3NB, U.K
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48
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Lee Y, Stevens DA, Kang SU, Jiang H, Lee YI, Ko HS, Scarffe LA, Umanah GE, Kang H, Ham S, Kam TI, Allen K, Brahmachari S, Kim JW, Neifert S, Yun SP, Fiesel FC, Springer W, Dawson VL, Shin JH, Dawson TM. PINK1 Primes Parkin-Mediated Ubiquitination of PARIS in Dopaminergic Neuronal Survival. Cell Rep 2017; 18:918-932. [PMID: 28122242 PMCID: PMC5312976 DOI: 10.1016/j.celrep.2016.12.090] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 11/08/2016] [Accepted: 12/27/2016] [Indexed: 02/03/2023] Open
Abstract
Mutations in PTEN-induced putative kinase 1 (PINK1) and parkin cause autosomal-recessive Parkinson's disease through a common pathway involving mitochondrial quality control. Parkin inactivation leads to accumulation of the parkin interacting substrate (PARIS, ZNF746) that plays an important role in dopamine cell loss through repression of proliferator-activated receptor gamma coactivator-1-alpha (PGC-1α) promoter activity. Here, we show that PARIS links PINK1 and parkin in a common pathway that regulates dopaminergic neuron survival. PINK1 interacts with and phosphorylates serines 322 and 613 of PARIS to control its ubiquitination and clearance by parkin. PINK1 phosphorylation of PARIS alleviates PARIS toxicity, as well as repression of PGC-1α promoter activity. Conditional knockdown of PINK1 in adult mouse brains leads to a progressive loss of dopaminergic neurons in the substantia nigra that is dependent on PARIS. Altogether, these results uncover a function of PINK1 to direct parkin-PARIS-regulated PGC-1α expression and dopaminergic neuronal survival.
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Affiliation(s)
- Yunjong Lee
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Division of Pharmacology, Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Samsung Biomedical Research Institute, Suwon 440-746, South Korea
| | - Daniel A Stevens
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sung-Ung Kang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA; Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Haisong Jiang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA; Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Yun-Il Lee
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Han Seok Ko
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA; Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Leslie A Scarffe
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - George E Umanah
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hojin Kang
- Division of Pharmacology, Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Samsung Biomedical Research Institute, Suwon 440-746, South Korea
| | - Sangwoo Ham
- Division of Pharmacology, Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Samsung Biomedical Research Institute, Suwon 440-746, South Korea
| | - Tae-In Kam
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kathleen Allen
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA; Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Saurav Brahmachari
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Jungwoo Wren Kim
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Stewart Neifert
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA; Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Seung Pil Yun
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Fabienne C Fiesel
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA; Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA; Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA; Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA.
| | - Joo-Ho Shin
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Division of Pharmacology, Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Samsung Biomedical Research Institute, Suwon 440-746, South Korea.
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA; Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA.
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49
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Structure of phosphorylated UBL domain and insights into PINK1-orchestrated parkin activation. Proc Natl Acad Sci U S A 2016; 114:298-303. [PMID: 28007983 DOI: 10.1073/pnas.1613040114] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mutations in PARK2 and PARK6 genes are responsible for the majority of hereditary Parkinson's disease cases. These genes encode the E3 ubiquitin ligase parkin and the protein kinase PTEN-induced kinase 1 (PINK1), respectively. Together, parkin and PINK1 regulate the mitophagy pathway, which recycles damaged mitochondria following oxidative stress. Native parkin is inactive and exists in an autoinhibited state mediated by its ubiquitin-like (UBL) domain. PINK1 phosphorylation of serine 65 in parkin's UBL and serine 65 of ubiquitin fully activate ubiquitin ligase activity; however, a structural rationale for these observations is not clear. Here, we report the structure of the phosphorylated UBL domain from parkin. We find that destabilization of the UBL results from rearrangements to hydrophobic core packing that modify its structure. Altered surface electrostatics from the phosphoserine group disrupt its intramolecular association, resulting in poorer autoinhibition in phosphorylated parkin. Further, we show that phosphorylation of both the UBL domain and ubiquitin are required to activate parkin by releasing the UBL domain, forming an extended structure needed to facilitate E2-ubiquitin binding. Together, the results underscore the importance of parkin activation by the PINK1 phosphorylation signal and provide a structural picture of the unraveling of parkin's ubiquitin ligase potential.
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50
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Protein Kinases and Parkinson's Disease. Int J Mol Sci 2016; 17:ijms17091585. [PMID: 27657053 PMCID: PMC5037850 DOI: 10.3390/ijms17091585] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 08/09/2016] [Accepted: 09/01/2016] [Indexed: 01/09/2023] Open
Abstract
Currently, the lack of new drug candidates for the treatment of major neurological disorders such as Parkinson’s disease has intensified the search for drugs that can be repurposed or repositioned for such treatment. Typically, the search focuses on drugs that have been approved and are used clinically for other indications. Kinase inhibitors represent a family of popular molecules for the treatment and prevention of various cancers, and have emerged as strong candidates for such repurposing because numerous serine/threonine and tyrosine kinases have been implicated in the pathobiology of Parkinson’s disease. This review focuses on various kinase-dependent pathways associated with the expression of Parkinson’s disease pathology, and evaluates how inhibitors of these pathways might play a major role as effective therapeutic molecules.
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