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      Phosphorylation of Mitochondrial Polyubiquitin by PINK1 Promotes Parkin Mitochondrial Tethering

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          Abstract

          The kinase PINK1 and the E3 ubiquitin (Ub) ligase Parkin participate in mitochondrial quality control. The phosphorylation of Ser65 in Parkin's ubiquitin-like (UBl) domain by PINK1 stimulates Parkin activation and translocation to damaged mitochondria, which induces mitophagy generating polyUb chain. However, Parkin Ser65 phosphorylation is insufficient for Parkin mitochondrial translocation. Here we report that Ser65 in polyUb chain is also phosphorylated by PINK1, and that phosphorylated polyUb chain on mitochondria tethers Parkin at mitochondria. The expression of Tom70 MTS-4xUb SE, which mimics phospho-Ser65 polyUb chains on the mitochondria, activated Parkin E3 activity and its mitochondrial translocation. An E3-dead form of Parkin translocated to mitochondria with reduced membrane potential in the presence of Tom70 MTS-4xUb SE, whereas non-phospho-polyUb mutant Tom70 MTS-4xUb SA abrogated Parkin translocation. Parkin binds to the phospho-polyUb chain through its RING1-In-Between-RING (IBR) domains, but its RING0-linker is also required for mitochondrial translocation. Moreover, the expression of Tom70 MTS-4xUb SE improved mitochondrial degeneration in PINK1-deficient, but not Parkin-deficient, Drosophila. Our study suggests that the phosphorylation of mitochondrial polyUb by PINK1 is implicated in both Parkin activation and mitochondrial translocation, predicting a chain reaction mechanism of mitochondrial phospho-polyUb production by which rapid translocation of Parkin is achieved.

          Author Summary

          Parkinson's disease is a neurodegenerative disorder caused by degeneration of the midbrain dopaminergic system in addition to other nervous systems. PINK1 and parkin, which encode mitochondrial protein kinase and cytosolic Ub ligase, respectively, were identified as the genes responsible for the autosomal recessive form of juvenile Parkinson's disease. Activation of PINK1 upon reduction of mitochondrial membrane potential recruits Parkin from the cytosol activating its Ub ligase activity, which ensures removal of damaged mitochondria through mitophagy. However, how PINK1 recruits Parkin to the damaged mitochondria remained unclear. Here, we describe that the phosphorylation of polyUb chain by PINK1 is a key event to recruit Parkin on the mitochondria. Parkin binds to, and is activated by, phospho-polyUb generated by Parkin in collaboration with PINK1. Expression of a phospho-polyUb mimetic protein on mitochondria rescued mitochondrial degeneration caused by loss of PINK1 in Drosophila. Our study suggests the existence of an amplification cascade of Parkin activation and mitochondrial translocation, in which a ‘seed' of phosphorylated polyUb on the mitochondria, generated by PINK1 and Parkin, triggers a chain reaction of Parkin recruitment and activation.

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          Most cited references26

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          A probability-based approach for high-throughput protein phosphorylation analysis and site localization.

          Data analysis and interpretation remain major logistical challenges when attempting to identify large numbers of protein phosphorylation sites by nanoscale reverse-phase liquid chromatography/tandem mass spectrometry (LC-MS/MS) (Supplementary Figure 1 online). In this report we address challenges that are often only addressable by laborious manual validation, including data set error, data set sensitivity and phosphorylation site localization. We provide a large-scale phosphorylation data set with a measured error rate as determined by the target-decoy approach, we demonstrate an approach to maximize data set sensitivity by efficiently distracting incorrect peptide spectral matches (PSMs), and we present a probability-based score, the Ascore, that measures the probability of correct phosphorylation site localization based on the presence and intensity of site-determining ions in MS/MS spectra. We applied our methods in a fully automated fashion to nocodazole-arrested HeLa cell lysate where we identified 1,761 nonredundant phosphorylation sites from 491 proteins with a peptide false-positive rate of 1.3%.
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            PINK1 is activated by mitochondrial membrane potential depolarization and stimulates Parkin E3 ligase activity by phosphorylating Serine 65

            Summary Missense mutations in PTEN-induced kinase 1 (PINK1) cause autosomal-recessive inherited Parkinson's disease (PD). We have exploited our recent discovery that recombinant insect PINK1 is catalytically active to test whether PINK1 directly phosphorylates 15 proteins encoded by PD-associated genes as well as proteins reported to bind PINK1. We have discovered that insect PINK1 efficiently phosphorylates only one of these proteins, namely the E3 ligase Parkin. We have mapped the phosphorylation site to a highly conserved residue within the Ubl domain of Parkin at Ser65. We show that human PINK1 is specifically activated by mitochondrial membrane potential (Δψm) depolarization, enabling it to phosphorylate Parkin at Ser65. We further show that phosphorylation of Parkin at Ser65 leads to marked activation of its E3 ligase activity that is prevented by mutation of Ser65 or inactivation of PINK1. We provide evidence that once activated, PINK1 autophosphorylates at several residues, including Thr257, which is accompanied by an electrophoretic mobility band-shift. These results provide the first evidence that PINK1 is activated following Δψm depolarization and suggest that PINK1 directly phosphorylates and activates Parkin. Our findings indicate that monitoring phosphorylation of Parkin at Ser65 and/or PINK1 at Thr257 represent the first biomarkers for examining activity of the PINK1-Parkin signalling pathway in vivo. Our findings also suggest that small molecule activators of Parkin that mimic the effect of PINK1 phosphorylation may confer therapeutic benefit for PD.
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              Mitochondrial pathology and muscle and dopaminergic neuron degeneration caused by inactivation of Drosophila Pink1 is rescued by Parkin.

              Mutations in Pink1, a gene encoding a Ser/Thr kinase with a mitochondrial-targeting signal, are associated with Parkinson's disease (PD), the most common movement disorder characterized by selective loss of dopaminergic neurons. The mechanism by which loss of Pink1 leads to neurodegeneration is not understood. Here we show that inhibition of Drosophila Pink1 (dPink1) function results in energy depletion, shortened lifespan, and degeneration of select indirect flight muscles and dopaminergic neurons. The muscle pathology was preceded by mitochondrial enlargement and disintegration. These phenotypes could be rescued by the wild type but not the pathogenic C-terminal deleted form of human Pink1 (hPink1). The muscle and dopaminergic phenotypes associated with dPink1 inactivation show similarity to that seen in parkin mutant flies and could be suppressed by the overexpression of Parkin but not DJ-1. Consistent with the genetic rescue results, we find that, in dPink1 RNA interference (RNAi) animals, the level of Parkin protein is significantly reduced. Together, these results implicate Pink1 and Parkin in a common pathway that regulates mitochondrial physiology and cell survival in Drosophila.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS Genet
                PLoS Genet
                plos
                plosgen
                PLoS Genetics
                Public Library of Science (San Francisco, USA )
                1553-7390
                1553-7404
                December 2014
                4 December 2014
                : 10
                : 12
                : e1004861
                Affiliations
                [1 ]Department of Neurology, Juntendo University Graduate School of Medicine, Tokyo, Japan
                [2 ]Department of Research for Parkinson's Disease, Juntendo University Graduate School of Medicine, Tokyo, Japan
                [3 ]Department of Neuroscience for Neurodegenerative Disorders, Juntendo University Graduate School of Medicine, Tokyo, Japan
                [4 ]Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
                [5 ]Department of Life Science, University of Seoul, Seoul, Korea
                Stanford University School of Medicine, United States of America
                Author notes

                The authors have declared that no competing interests exist.

                Conceived and designed the experiments: KSF YIm. Performed the experiments: KSF TA GM TI SY YIm. Analyzed the data: KSF TA GM TI SY YIs YIm. Contributed reagents/materials/analysis tools: KYR NN. Wrote the paper: NH YIm.

                Article
                PGENETICS-D-14-01720
                10.1371/journal.pgen.1004861
                4256268
                25474007
                797a17c4-8db2-4bce-9837-fef03ee08e40
                Copyright @ 2014

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 26 June 2014
                : 29 October 2014
                Page count
                Pages: 18
                Funding
                This study was supported by the Takeda Science Foundation (YIm), the Life Science Foundation of Japan (YIm), the Daiichi-Sankyo Foundation for Life Science (YIm), the Mochida Memorial Foundation for Medical and Pharmaceutical Research (YIm), and Otsuka Pharmaceutical (NH, YIm), the Grant-in-Aid for Scientific Research 26461280 (KSF) and 26293070 (YIm) from MEXT in Japan, and a Grant-in-Aid for Scientific Research on Innovative Areas 23111003 (NH) and 26117727 (YIm). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Biochemistry
                Bioenergetics
                Energy-Producing Organelles
                Mitochondria
                Mitochondrial Membrane
                Proteins
                Post-Translational Modification
                Ubiquitination
                Cell Biology
                Cellular Structures and Organelles
                Subcellular Localization
                Signal Transduction
                Cell Signaling
                Signaling Cascades
                Protein Kinase Signaling Cascade
                Molecular Cell Biology
                Genetics
                Animal Genetics
                Invertebrate Genetics
                Molecular Genetics
                Molecular Biology
                Research and Analysis Methods
                Bioassays and Physiological Analysis
                Biochemical Analysis
                Enzyme Assays
                In Vitro Kinase Assay
                Custom metadata
                The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its Supporting Information files.

                Genetics
                Genetics

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