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      Reversible induction of mitophagy by an optogenetic bimodular system

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          Abstract

          Autophagy-mediated degradation of mitochondria (mitophagy) is a key process in cellular quality control. Although mitophagy impairment is involved in several patho-physiological conditions, valuable methods to induce mitophagy with low toxicity in vivo are still lacking. Herein, we describe a new optogenetic tool to stimulate mitophagy, based on light-dependent recruitment of pro-autophagy protein AMBRA1 to mitochondrial surface. Upon illumination, AMBRA1-RFP-sspB is efficiently relocated from the cytosol to mitochondria, where it reversibly mediates mito-aggresome formation and reduction of mitochondrial mass. Finally, as a proof of concept of the biomedical relevance of this method, we induced mitophagy in an in vitro model of neurotoxicity, fully preventing cell death, as well as in human T lymphocytes and in zebrafish in vivo. Given the unique features of this tool, we think it may turn out to be very useful for a wide range of both therapeutic and research applications.

          Abstract

          Autophagic degradation of mitochondria (mitophagy) is a key quality control mechanism in cellular homeostasis, and its misregulation is involved in neurodegenerative diseases. Here the authors develop an optogenetic system for reversible induction of mitophagy and validate its use in cell culture and zebrafish embryos.

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          Most cited references29

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          The mitochondrial deubiquitinase USP30 opposes parkin-mediated mitophagy.

          Cells maintain healthy mitochondria by degrading damaged mitochondria through mitophagy; defective mitophagy is linked to Parkinson's disease. Here we report that USP30, a deubiquitinase localized to mitochondria, antagonizes mitophagy driven by the ubiquitin ligase parkin (also known as PARK2) and protein kinase PINK1, which are encoded by two genes associated with Parkinson's disease. Parkin ubiquitinates and tags damaged mitochondria for clearance. Overexpression of USP30 removes ubiquitin attached by parkin onto damaged mitochondria and blocks parkin's ability to drive mitophagy, whereas reducing USP30 activity enhances mitochondrial degradation in neurons. Global ubiquitination site profiling identified multiple mitochondrial substrates oppositely regulated by parkin and USP30. Knockdown of USP30 rescues the defective mitophagy caused by pathogenic mutations in parkin and improves mitochondrial integrity in parkin- or PINK1-deficient flies. Knockdown of USP30 in dopaminergic neurons protects flies against paraquat toxicity in vivo, ameliorating defects in dopamine levels, motor function and organismal survival. Thus USP30 inhibition is potentially beneficial for Parkinson's disease by promoting mitochondrial clearance and quality control.
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            Coordination of mitophagy and mitochondrial biogenesis during ageing in C. elegans.

            Impaired mitochondrial maintenance in disparate cell types is a shared hallmark of many human pathologies and ageing. How mitochondrial biogenesis coordinates with the removal of damaged or superfluous mitochondria to maintain cellular homeostasis is not well understood. Here we show that mitophagy, a selective type of autophagy targeting mitochondria for degradation, interfaces with mitochondrial biogenesis to regulate mitochondrial content and longevity in Caenorhabditis elegans. We find that DCT-1 is a key mediator of mitophagy and longevity assurance under conditions of stress in C. elegans. Impairment of mitophagy compromises stress resistance and triggers mitochondrial retrograde signalling through the SKN-1 transcription factor that regulates both mitochondrial biogenesis genes and mitophagy by enhancing DCT-1 expression. Our findings reveal a homeostatic feedback loop that integrates metabolic signals to coordinate the biogenesis and turnover of mitochondria. Uncoupling of these two processes during ageing contributes to overproliferation of damaged mitochondria and decline of cellular function.
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              Parkin mediates proteasome-dependent protein degradation and rupture of the outer mitochondrial membrane.

              Upon mitochondrial depolarization, Parkin, a Parkinson disease-related E3 ubiquitin ligase, translocates from the cytosol to mitochondria and promotes their degradation by mitophagy, a selective type of autophagy. Here, we report that in addition to mitophagy, Parkin mediates proteasome-dependent degradation of outer membrane proteins such as Tom20, Tom40, Tom70, and Omp25 of depolarized mitochondria. By contrast, degradation of the inner membrane and matrix proteins largely depends on mitophagy. Furthermore, Parkin induces rupture of the outer membrane of depolarized mitochondria, which also depends on proteasomal activity. Upon induction of mitochondrial depolarization, proteasomes are recruited to mitochondria in the perinuclear region. Neither proteasome-dependent degradation of outer membrane proteins nor outer membrane rupture is required for mitophagy. These results suggest that Parkin regulates degradation of outer and inner mitochondrial membrane proteins differently through proteasome- and mitophagy-dependent pathways.
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                Author and article information

                Contributors
                cecconi@cancer.dk
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                4 April 2019
                4 April 2019
                2019
                : 10
                : 1533
                Affiliations
                [1 ]ISNI 0000 0001 0727 6809, GRID grid.414125.7, Department of Paediatric Haematology, , Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children’s Hospital, ; Piazza Sant’Onofrio 4, 00165 Rome, Italy
                [2 ]ISNI 0000 0001 0692 3437, GRID grid.417778.a, IRCCS Fondazione Santa Lucia, ; Via del Fosso di Fiorano 64, 00143 Rome, Italy
                [3 ]ISNI 0000 0001 2300 0941, GRID grid.6530.0, Department of Biology, , University of Tor Vergata, ; Via della Ricerca Scientifica 1, 00133 Rome, Italy
                [4 ]ISNI 0000 0004 1757 3470, GRID grid.5608.b, Department of Biology, , University of Padova, ; Via Ugo Bassi 58/b, 35131 Padova, Italy
                [5 ]GRID grid.7841.a, Department of Gynecology/Obstetrics and Pediatrics, , Sapienza University of Rome, ; Piazzale Aldo Moro 5, 00185 Rome, Italy
                [6 ]ISNI 0000 0001 2175 6024, GRID grid.417390.8, Unit of Cell Stress and Survival, Danish Cancer Society Research Center, ; Strandboulevarden 49, DK-2100 Copenhagen, Denmark
                Author information
                http://orcid.org/0000-0001-7237-0076
                http://orcid.org/0000-0003-0285-7449
                http://orcid.org/0000-0002-9250-0605
                http://orcid.org/0000-0003-0795-6390
                http://orcid.org/0000-0001-9643-3465
                http://orcid.org/0000-0001-8097-6369
                http://orcid.org/0000-0003-0536-2484
                http://orcid.org/0000-0002-5614-4359
                Article
                9487
                10.1038/s41467-019-09487-1
                6449392
                30948710
                b857643f-06d6-4644-8201-c1b644509e00
                © The Author(s) 2019

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 1 August 2018
                : 12 March 2019
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