51
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Beltran S, Nassif M, Vicencio E, Arcos J, Labrador L, Cortes BI, Cortez C, Bergmann CA, Espinoza S, Hernandez MF, Matamala JM, Bargsted L, Matus S, Rojas-Rivera D, Bertrand MJM, Medinas DB, Hetz C, Manque PA, Woehlbier U. Network approach identifies Pacer as an autophagy protein involved in ALS pathogenesis. Mol Neurodegener 2019; 14:14. [PMID: 30917850 PMCID: PMC6437924 DOI: 10.1186/s13024-019-0313-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/11/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a multifactorial fatal motoneuron disease without a cure. Ten percent of ALS cases can be pointed to a clear genetic cause, while the remaining 90% is classified as sporadic. Our study was aimed to uncover new connections within the ALS network through a bioinformatic approach, by which we identified C13orf18, recently named Pacer, as a new component of the autophagic machinery and potentially involved in ALS pathogenesis. METHODS Initially, we identified Pacer using a network-based bioinformatic analysis. Expression of Pacer was then investigated in vivo using spinal cord tissue from two ALS mouse models (SOD1G93A and TDP43A315T) and sporadic ALS patients. Mechanistic studies were performed in cell culture using the mouse motoneuron cell line NSC34. Loss of function of Pacer was achieved by knockdown using short-hairpin constructs. The effect of Pacer repression was investigated in the context of autophagy, SOD1 aggregation, and neuronal death. RESULTS Using an unbiased network-based approach, we integrated all available ALS data to identify new functional interactions involved in ALS pathogenesis. We found that Pacer associates to an ALS-specific subnetwork composed of components of the autophagy pathway, one of the main cellular processes affected in the disease. Interestingly, we found that Pacer levels are significantly reduced in spinal cord tissue from sporadic ALS patients and in tissues from two ALS mouse models. In vitro, Pacer deficiency lead to impaired autophagy and accumulation of ALS-associated protein aggregates, which correlated with the induction of cell death. CONCLUSIONS This study, therefore, identifies Pacer as a new regulator of proteostasis associated with ALS pathology.
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Affiliation(s)
- S Beltran
- Center for Integrative Biology, Faculty of Science, Universidad Mayor, Camino la Piramide 5750, P.O.BOX 70086, Santiago, Chile.,Center for Genomics and Bioinformatics, Faculty of Science, Universidad Mayor, Camino la Piramide, 5750, Santiago, Chile
| | - M Nassif
- Center for Integrative Biology, Faculty of Science, Universidad Mayor, Camino la Piramide 5750, P.O.BOX 70086, Santiago, Chile.,Center for Genomics and Bioinformatics, Faculty of Science, Universidad Mayor, Camino la Piramide, 5750, Santiago, Chile
| | - E Vicencio
- Center for Integrative Biology, Faculty of Science, Universidad Mayor, Camino la Piramide 5750, P.O.BOX 70086, Santiago, Chile.,Center for Genomics and Bioinformatics, Faculty of Science, Universidad Mayor, Camino la Piramide, 5750, Santiago, Chile
| | - J Arcos
- Center for Integrative Biology, Faculty of Science, Universidad Mayor, Camino la Piramide 5750, P.O.BOX 70086, Santiago, Chile.,Center for Genomics and Bioinformatics, Faculty of Science, Universidad Mayor, Camino la Piramide, 5750, Santiago, Chile
| | - L Labrador
- Center for Integrative Biology, Faculty of Science, Universidad Mayor, Camino la Piramide 5750, P.O.BOX 70086, Santiago, Chile.,Center for Genomics and Bioinformatics, Faculty of Science, Universidad Mayor, Camino la Piramide, 5750, Santiago, Chile
| | - B I Cortes
- Center for Integrative Biology, Faculty of Science, Universidad Mayor, Camino la Piramide 5750, P.O.BOX 70086, Santiago, Chile.,Center for Genomics and Bioinformatics, Faculty of Science, Universidad Mayor, Camino la Piramide, 5750, Santiago, Chile
| | - C Cortez
- Center for Genomics and Bioinformatics, Faculty of Science, Universidad Mayor, Camino la Piramide, 5750, Santiago, Chile
| | - C A Bergmann
- Center for Integrative Biology, Faculty of Science, Universidad Mayor, Camino la Piramide 5750, P.O.BOX 70086, Santiago, Chile.,Center for Genomics and Bioinformatics, Faculty of Science, Universidad Mayor, Camino la Piramide, 5750, Santiago, Chile
| | - S Espinoza
- Center for Integrative Biology, Faculty of Science, Universidad Mayor, Camino la Piramide 5750, P.O.BOX 70086, Santiago, Chile
| | - M F Hernandez
- Center for Integrative Biology, Faculty of Science, Universidad Mayor, Camino la Piramide 5750, P.O.BOX 70086, Santiago, Chile.,Center for Genomics and Bioinformatics, Faculty of Science, Universidad Mayor, Camino la Piramide, 5750, Santiago, Chile
| | - J M Matamala
- Department of Neurological Sciences, Faculty of Medicine, University of Chile, Santiago, Chile.,Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Independencia, 1027, Santiago, Chile
| | - L Bargsted
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Independencia, 1027, Santiago, Chile
| | - S Matus
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Independencia, 1027, Santiago, Chile.,Fundación Ciencia & Vida, Zañartu 1482, 7780272, Santiago, Chile.,Neurounion Biomedical Foundation, 7780272, Santiago, Chile.,Center for Geroscience, Brain Health and Metabolism (GERO), Santiago, Chile
| | - D Rojas-Rivera
- Center for Integrative Biology, Faculty of Science, Universidad Mayor, Camino la Piramide 5750, P.O.BOX 70086, Santiago, Chile.,VIB Center for Inflammation Research, Technologiepark 927, Zwijnaarde, 9052, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, Zwijnaarde, 9052, Ghent, Belgium
| | - M J M Bertrand
- VIB Center for Inflammation Research, Technologiepark 927, Zwijnaarde, 9052, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, Zwijnaarde, 9052, Ghent, Belgium
| | - D B Medinas
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Independencia, 1027, Santiago, Chile.,Center for Geroscience, Brain Health and Metabolism (GERO), Santiago, Chile.,Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Independencia, 1027, Santiago, Chile
| | - C Hetz
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Independencia, 1027, Santiago, Chile.,Center for Geroscience, Brain Health and Metabolism (GERO), Santiago, Chile.,Buck Institute for Research on Aging, Novato, CA, 94945, USA.,Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Independencia, 1027, Santiago, Chile.,Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, 02115, USA
| | - P A Manque
- Center for Integrative Biology, Faculty of Science, Universidad Mayor, Camino la Piramide 5750, P.O.BOX 70086, Santiago, Chile. .,Center for Genomics and Bioinformatics, Faculty of Science, Universidad Mayor, Camino la Piramide, 5750, Santiago, Chile. .,Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, 23298, USA.
| | - U Woehlbier
- Center for Integrative Biology, Faculty of Science, Universidad Mayor, Camino la Piramide 5750, P.O.BOX 70086, Santiago, Chile. .,Center for Genomics and Bioinformatics, Faculty of Science, Universidad Mayor, Camino la Piramide, 5750, Santiago, Chile.
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52
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Nakamura S, Oba M, Suzuki M, Takahashi A, Yamamuro T, Fujiwara M, Ikenaka K, Minami S, Tabata N, Yamamoto K, Kubo S, Tokumura A, Akamatsu K, Miyazaki Y, Kawabata T, Hamasaki M, Fukui K, Sango K, Watanabe Y, Takabatake Y, Kitajima TS, Okada Y, Mochizuki H, Isaka Y, Antebi A, Yoshimori T. Suppression of autophagic activity by Rubicon is a signature of aging. Nat Commun 2019; 10:847. [PMID: 30783089 PMCID: PMC6381146 DOI: 10.1038/s41467-019-08729-6] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 01/11/2019] [Indexed: 12/23/2022] Open
Abstract
Autophagy, an evolutionarily conserved cytoplasmic degradation system, has been implicated as a convergent mechanism in various longevity pathways. Autophagic activity decreases with age in several organisms, but the underlying mechanism is unclear. Here, we show that the expression of Rubicon, a negative regulator of autophagy, increases in aged worm, fly and mouse tissues at transcript and/or protein levels, suggesting that an age-dependent increase in Rubicon impairs autophagy over time, and thereby curtails animal healthspan. Consistent with this idea, knockdown of Rubicon extends worm and fly lifespan and ameliorates several age-associated phenotypes. Tissue-specific experiments reveal that Rubicon knockdown in neurons has the greatest effect on lifespan. Rubicon knockout mice exhibits reductions in interstitial fibrosis in kidney and reduced α-synuclein accumulation in the brain. Rubicon is suppressed in several long-lived worms and calorie restricted mice. Taken together, our results suggest that suppression of autophagic activity by Rubicon is one of signatures of aging.
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Affiliation(s)
- Shuhei Nakamura
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan
- Institute for Advanced Co-Creation Studies, Osaka University, Osaka, 565-0871, Japan
| | - Masaki Oba
- Diabetic Neuropathy Project, Department of Sensory and Motor Systems, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, 156-8506, Japan
- Department of Bioscience and Engineering, Shibaura Institute of Technology, Saitama, 337-8570, Japan
| | - Mari Suzuki
- Diabetic Neuropathy Project, Department of Sensory and Motor Systems, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, 156-8506, Japan
| | - Atsushi Takahashi
- Department of Nephrology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Tadashi Yamamuro
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Mari Fujiwara
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Kensuke Ikenaka
- Department of Neurology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Satoshi Minami
- Department of Nephrology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Namine Tabata
- Laboratory for Chromosome Segregation, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, Japan
- Laboratory of Molecular Cell Biology and Development, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
- Laboratory of Biomolecular Informatics, Graduate School of Science, Osaka University, Osaka, 560-0043, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Sayaka Kubo
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan
| | - Ayaka Tokumura
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Kanako Akamatsu
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Yumi Miyazaki
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan
| | - Tsuyoshi Kawabata
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
- Department of Stem Cell Biology, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, 852-8523, Japan
| | - Maho Hamasaki
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan
| | - Koji Fukui
- Department of Bioscience and Engineering, Shibaura Institute of Technology, Saitama, 337-8570, Japan
| | - Kazunori Sango
- Diabetic Neuropathy Project, Department of Sensory and Motor Systems, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, 156-8506, Japan
| | - Yoshihisa Watanabe
- Department of Basic Geriatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Yoshitsugu Takabatake
- Institute for Advanced Co-Creation Studies, Osaka University, Osaka, 565-0871, Japan
| | - Tomoya S Kitajima
- Laboratory for Chromosome Segregation, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, Japan
- Laboratory of Molecular Cell Biology and Development, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
- Laboratory of Biomolecular Informatics, Graduate School of Science, Osaka University, Osaka, 560-0043, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Hideki Mochizuki
- Department of Neurology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Yoshitaka Isaka
- Department of Nephrology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Adam Antebi
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, Cologne, 50931, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, 50931, Germany
| | - Tamotsu Yoshimori
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan.
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan.
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53
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Pacer Is a Mediator of mTORC1 and GSK3-TIP60 Signaling in Regulation of Autophagosome Maturation and Lipid Metabolism. Mol Cell 2019; 73:788-802.e7. [PMID: 30704899 DOI: 10.1016/j.molcel.2018.12.017] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 07/18/2018] [Accepted: 12/19/2018] [Indexed: 01/01/2023]
Abstract
mTORC1 and GSK3 play critical roles in early stages of (macro)autophagy, but how they regulate late steps of autophagy remains poorly understood. Here we show that mTORC1 and GSK3-TIP60 signaling converge to modulate autophagosome maturation through Pacer, an autophagy regulator that was identified in our recent study. Hepatocyte-specific Pacer knockout in mice results in impaired autophagy flux, glycogen and lipid accumulation, and liver fibrosis. Under nutrient-rich conditions, mTORC1 phosphorylates Pacer at serine157 to disrupt the association of Pacer with Stx17 and the HOPS complex and thus abolishes Pacer-mediated autophagosome maturation. Importantly, dephosphorylation of Pacer under nutrient-deprived conditions promotes TIP60-mediated Pacer acetylation, which facilitates HOPS complex recruitment and is required for autophagosome maturation and lipid droplet clearance. This work not only identifies Pacer as a regulator in hepatic autophagy and liver homeostasis in vivo but also reveals a signal integration mechanism involved in late stages of autophagy and lipid metabolism.
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54
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Chang C, Young LN, Morris KL, von Bülow S, Schöneberg J, Yamamoto-Imoto H, Oe Y, Yamamoto K, Nakamura S, Stjepanovic G, Hummer G, Yoshimori T, Hurley JH. Bidirectional Control of Autophagy by BECN1 BARA Domain Dynamics. Mol Cell 2019; 73:339-353.e6. [PMID: 30581147 PMCID: PMC6450660 DOI: 10.1016/j.molcel.2018.10.035] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 09/15/2018] [Accepted: 10/19/2018] [Indexed: 12/11/2022]
Abstract
Membrane targeting of the BECN1-containing class III PI 3-kinase (PI3KC3) complexes is pivotal to the regulation of autophagy. The interaction of PI3KC3 complex II and its ubiquitously expressed inhibitor, Rubicon, was mapped to the first β sheet of the BECN1 BARA domain and the UVRAG BARA2 domain by hydrogen-deuterium exchange and cryo-EM. These data suggest that the BARA β sheet 1 unfolds to directly engage the membrane. This mechanism was confirmed using protein engineering, giant unilamellar vesicle assays, and molecular simulations. Using this mechanism, a BECN1 β sheet-1 derived peptide activates both PI3KC3 complexes I and II, while HIV-1 Nef inhibits complex II. These data reveal how BECN1 switches on and off PI3KC3 binding to membranes. The observations explain how PI3KC3 inhibition by Rubicon, activation by autophagy-inducing BECN1 peptides, and inhibition by HIV-1 Nef are mediated by the switchable ability of the BECN1 BARA domain to partially unfold and insert into membranes.
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Affiliation(s)
- Chunmei Chang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Lindsey N Young
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kyle L Morris
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Sören von Bülow
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt/M, Germany
| | - Johannes Schöneberg
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hitomi Yamamoto-Imoto
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Yukako Oe
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Kentaro Yamamoto
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Shuhei Nakamura
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Goran Stjepanovic
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt/M, Germany; Institute of Biophysics, Goethe University, 60438 Frankfurt/M, Germany
| | - Tamotsu Yoshimori
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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55
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Zhao YG, Zhang H. Autophagosome maturation: An epic journey from the ER to lysosomes. J Cell Biol 2018; 218:757-770. [PMID: 30578282 PMCID: PMC6400552 DOI: 10.1083/jcb.201810099] [Citation(s) in RCA: 225] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/05/2018] [Accepted: 12/05/2018] [Indexed: 12/23/2022] Open
Abstract
Macroautophagy involves the sequestration of cytoplasmic contents in a double-membrane autophagosome and their delivery to lysosomes for degradation. In multicellular organisms, nascent autophagosomes fuse with vesicles originating from endolysosomal compartments before forming degradative autolysosomes, a process known as autophagosome maturation. ATG8 family members, tethering factors, Rab GTPases, and SNARE proteins act coordinately to mediate fusion of autophagosomes with endolysosomal vesicles. The machinery mediating autophagosome maturation is under spatiotemporal control and provides regulatory nodes to integrate nutrient availability with autophagy activity. Dysfunction of autophagosome maturation is associated with various human diseases, including neurodegenerative diseases, Vici syndrome, cancer, and lysosomal storage disorders. Understanding the molecular mechanisms underlying autophagosome maturation will provide new insights into the pathogenesis and treatment of these diseases.
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Affiliation(s)
- Yan G Zhao
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Hong Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China .,National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
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56
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Ohashi Y, Tremel S, Williams RL. VPS34 complexes from a structural perspective. J Lipid Res 2018; 60:229-241. [PMID: 30397185 PMCID: PMC6358306 DOI: 10.1194/jlr.r089490] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/24/2018] [Indexed: 02/07/2023] Open
Abstract
VPS34 phosphorylates phosphatidylinositol to produce PtdIns3P and is the progenitor of the phosphoinositide 3-kinase (PI3K) family. VPS34 has a simpler domain organization than class I PI3Ks, which belies the complexity of its quaternary organization, with the enzyme always functioning within larger assemblies. PtdIns3P recruits specific recognition modules that are common in protein-sorting pathways, such as autophagy and endocytic sorting. It is best characterized in two heterotetramers, complexes I and II. Complex I is composed of VPS34, VPS15, Beclin 1, and autophagy-related gene (ATG)14L, whereas complex II replaces ATG14L with UVRAG. Because VPS34 can form a component of several distinct complexes, it enables independent regulation of various pathways that are controlled by PtdIns3P. Complexes I and II are critical for early events in autophagy and endocytic sorting, respectively. Autophagy has a complex association with cancer. In early stages, it inhibits tumorigenesis, but in later stages, it acts as a survival factor for tumors. Recently, various disease-associated somatic mutations were found in genes encoding complex I and II subunits. Lipid kinase activities of the complexes are also influenced by posttranslational modifications (PTMs). Mapping PTMs and somatic mutations on three-dimensional models of the complexes suggests mechanisms for how these affect VPS34 activity.
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Affiliation(s)
- Yohei Ohashi
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Shirley Tremel
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Roger L Williams
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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57
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Corona AK, Jackson WT. Finding the Middle Ground for Autophagic Fusion Requirements. Trends Cell Biol 2018; 28:869-881. [PMID: 30115558 PMCID: PMC6197918 DOI: 10.1016/j.tcb.2018.07.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/29/2018] [Accepted: 07/06/2018] [Indexed: 12/26/2022]
Abstract
Autophagosome/amphisome-lysosome fusion is a highly regulated process at the protein, lipid, and biochemical level. Each primary component of fusion, such as the core SNAREs, HOPS complex, or physical positioning by microtubule-associated dynein motors, are regulated at multiple points to ensure optimum conditions for autophagic flux to proceed. With the complexity of the membrane fusion system, it is not difficult to imagine how autophagic flux defect-related disorders, such as Huntington's disease, non-familial Alzheimer's disease, and Vici syndrome develop. Each membrane fusion step is regulated at the protein, lipid, and ion level. This review aims to discuss the recent developments toward understanding the regulation of autophagosome, amphisome, and lysosome fusion requirements for successful autophagic flux.
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Affiliation(s)
- Abigail K Corona
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 685 W. Baltimore Avenue, Baltimore, MD 21201, USA
| | - William T Jackson
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 685 W. Baltimore Avenue, Baltimore, MD 21201, USA.
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Settembre C, Cinque L, Bartolomeo R, Di Malta C, De Leonibus C, Forrester A. Defective collagen proteostasis and matrix formation in the pathogenesis of lysosomal storage disorders. Matrix Biol 2018; 71-72:283-293. [DOI: 10.1016/j.matbio.2018.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 12/14/2022]
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59
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Hikita H, Sakane S, Takehara T. Mechanisms of the autophagosome-lysosome fusion step and its relation to non-alcoholic fatty liver disease. LIVER RESEARCH 2018. [DOI: 10.1016/j.livres.2018.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
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60
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Chen Q, Kang J, Fu C. The independence of and associations among apoptosis, autophagy, and necrosis. Signal Transduct Target Ther 2018; 3:18. [PMID: 29967689 PMCID: PMC6026494 DOI: 10.1038/s41392-018-0018-5] [Citation(s) in RCA: 198] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 05/02/2018] [Accepted: 05/14/2018] [Indexed: 12/12/2022] Open
Abstract
Cell death is an essential biological process for physiological growth and development. Three classical forms of cell death-apoptosis, autophagy, and necrosis-display distinct morphological features by activating specific signaling pathways. With recent research advances, we have started to appreciate that these cell death processes can cross-talk through interconnecting, even overlapping, signaling pathways, and the final cell fate is the result of the interplay of different cell death programs. This review provides an insight into the independence of and associations among these three types of cell death and explores the significance of cell death under the specific conditions of human diseases, particularly neurodegenerative diseases and cancer.
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Affiliation(s)
- Qi Chen
- 1College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018 China.,Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Hangzhou, 310018 China
| | - Jian Kang
- 3Cancer Signalling Laboratory, Oncogenic Signalling and Growth Control Program, Peter MacCallum Cancer Centre, 305 Grattan street, Melbourne, VIC 3000 Australia
| | - Caiyun Fu
- 1College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018 China.,Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Hangzhou, 310018 China.,4Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Blvd. South, San Francisco, CA 94158 USA.,Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Hangzhou, 310014 China
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Shi L, Gao X, Yuan W, Xu L, Deng H, Wu C, Yang J, Jin X, Zhang C, Zhu X. Endoplasmic Reticulum-Targeted Fluorescent Nanodot with Large Stokes Shift for Vesicular Transport Monitoring and Long-Term Bioimaging. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1800223. [PMID: 29782699 DOI: 10.1002/smll.201800223] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/31/2018] [Indexed: 06/08/2023]
Abstract
Herein, a highly stable aggregation-induced emission (AIE) fluorescent nanodot assembled by an amphiphilic quinoxalinone derivative-peptide conjugate, namely Quino-1-Fmoc-RACR (also termed as Q1-PEP), which exhibits large Stokes shift and an endoplasmic reticulum (ER)-targeting capacity for bioimaging is reported. It is found that the resulting nanodot can effectively enter the ER with high fluorescent emission. As the ER is mainly involved in the transport of synthesized proteins in vesicles to the Golgi or lysosomes, the Q1-PEP nanodot with ER-targeting capacity can be used to monitor vesicular transport inside the cells. Compared to conventional fluorescent dyes with small Stokes shifts, the self-assembled fluorescent nanodot shows superior resistance to photobleaching and aggregation-induced fluorescence quenching, and elimination of the spectra overlap with autofluorescence of biosubstrate owning to their AIE-active and red fluorescence emission characteristics. All these optical properties make the fluorescent nanodot suitable for noninvasive and long-term imaging both in vitro and in vivo.
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Affiliation(s)
- Leilei Shi
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Xihui Gao
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Wangzhang Yuan
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Li Xu
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Hongping Deng
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Chenwei Wu
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jiapei Yang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Xin Jin
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Chuan Zhang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Xinyuan Zhu
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
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Bartolomeo R, Cinque L, De Leonibus C, Forrester A, Salzano AC, Monfregola J, De Gennaro E, Nusco E, Azario I, Lanzara C, Serafini M, Levine B, Ballabio A, Settembre C. mTORC1 hyperactivation arrests bone growth in lysosomal storage disorders by suppressing autophagy. J Clin Invest 2017; 127:3717-3729. [PMID: 28872463 DOI: 10.1172/jci94130] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 07/18/2017] [Indexed: 11/17/2022] Open
Abstract
The mammalian target of rapamycin complex 1 (mTORC1) kinase promotes cell growth by activating biosynthetic pathways and suppressing catabolic pathways, particularly that of macroautophagy. A prerequisite for mTORC1 activation is its translocation to the lysosomal surface. Deregulation of mTORC1 has been associated with the pathogenesis of several diseases, but its role in skeletal disorders is largely unknown. Here, we show that enhanced mTORC1 signaling arrests bone growth in lysosomal storage disorders (LSDs). We found that lysosomal dysfunction induces a constitutive lysosomal association and consequent activation of mTORC1 in chondrocytes, the cells devoted to bone elongation. mTORC1 hyperphosphorylates the protein UV radiation resistance-associated gene (UVRAG), reducing the activity of the associated Beclin 1-Vps34 complex and thereby inhibiting phosphoinositide production. Limiting phosphoinositide production leads to a blockage of the autophagy flux in LSD chondrocytes. As a consequence, LSD chondrocytes fail to properly secrete collagens, the main components of the cartilage extracellular matrix. In mouse models of LSD, normalization of mTORC1 signaling or stimulation of the Beclin 1-Vps34-UVRAG complex rescued the autophagy flux, restored collagen levels in cartilage, and ameliorated the bone phenotype. Taken together, these data unveil a role for mTORC1 and autophagy in the pathogenesis of skeletal disorders and suggest potential therapeutic approaches for the treatment of LSDs.
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Affiliation(s)
- Rosa Bartolomeo
- Telethon Institute of Genetics and Medicine (TIGEM), and.,Dulbecco Telethon Institute, Pozzuoli, Naples, Italy
| | - Laura Cinque
- Telethon Institute of Genetics and Medicine (TIGEM), and.,Dulbecco Telethon Institute, Pozzuoli, Naples, Italy
| | - Chiara De Leonibus
- Telethon Institute of Genetics and Medicine (TIGEM), and.,Dulbecco Telethon Institute, Pozzuoli, Naples, Italy
| | - Alison Forrester
- Telethon Institute of Genetics and Medicine (TIGEM), and.,Dulbecco Telethon Institute, Pozzuoli, Naples, Italy.,Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy
| | - Anna Chiara Salzano
- Telethon Institute of Genetics and Medicine (TIGEM), and.,Dulbecco Telethon Institute, Pozzuoli, Naples, Italy
| | | | | | - Edoardo Nusco
- Telethon Institute of Genetics and Medicine (TIGEM), and
| | - Isabella Azario
- Department of Pediatrics, Dulbecco Telethon Institute at Centro Ricerca Tettamanti, University of Milano-Bicocca, Monza, Italy
| | | | - Marta Serafini
- Department of Pediatrics, Dulbecco Telethon Institute at Centro Ricerca Tettamanti, University of Milano-Bicocca, Monza, Italy
| | - Beth Levine
- Center for Autophagy Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), and.,Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy.,Department of Molecular and Human Genetics, Baylor College of Medicine, and.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
| | - Carmine Settembre
- Telethon Institute of Genetics and Medicine (TIGEM), and.,Dulbecco Telethon Institute, Pozzuoli, Naples, Italy.,Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy
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63
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Su H, Yang F, Wang Q, Shen Q, Huang J, Peng C, Zhang Y, Wan W, Wong CCL, Sun Q, Wang F, Zhou T, Liu W. VPS34 Acetylation Controls Its Lipid Kinase Activity and the Initiation of Canonical and Non-canonical Autophagy. Mol Cell 2017; 67:907-921.e7. [PMID: 28844862 DOI: 10.1016/j.molcel.2017.07.024] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 06/13/2017] [Accepted: 07/26/2017] [Indexed: 12/13/2022]
Abstract
The class III phosphoinositide 3-kinase VPS34 plays a key role in the regulation of vesicular trafficking and macroautophagy. So far, we know little about the molecular mechanism of VPS34 activation besides its interaction with regulatory proteins to form complexes. Here, we report that VPS34 is specifically acetylated by the acetyltransferase p300, and p300-mediated acetylation represses VPS34 activity. Acetylation at K771 directly diminishes the affinity of VPS34 for its substrate PI, while acetylation at K29 hinders the VPS34-Beclin 1 core complex formation. Inactivation of p300 induces VPS34 deacetylation, PI3P production, and autophagy, even in AMPK-/-, TSC2-/-, or ULK1-/- cells. In fasting mice, liver autophagy correlates well with p300 inactivation/VPS34 deacetylation, which facilitates the clearance of lipid droplets in hepatocytes. Thus, p300-dependent VPS34 acetylation/deacetylation is the physiological key to VPS34 activation, which controls the initiation of canonical autophagy and of non-canonical autophagy in which the upstream kinases of VPS34 can be bypassed.
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Affiliation(s)
- Hua Su
- Department of Biochemistry and Molecular Biology, Program in Molecular and Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Fei Yang
- Department of Biochemistry and Molecular Biology, Program in Molecular and Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Qiuting Wang
- Department of Biochemistry and Molecular Biology, Program in Molecular and Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Qiuhong Shen
- Department of Biochemistry and Molecular Biology, Program in Molecular and Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jingtao Huang
- Department of Biochemistry and Molecular Biology, Program in Molecular and Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Chao Peng
- National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yi Zhang
- Department of Biochemistry and Molecular Biology, Program in Molecular and Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Wei Wan
- Department of Biochemistry and Molecular Biology, Program in Molecular and Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Catherine C L Wong
- National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qiming Sun
- Department of Biochemistry and Molecular Biology, Program in Molecular and Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Fudi Wang
- Department of Biochemistry and Molecular Biology, Program in Molecular and Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Tianhua Zhou
- Department of Biochemistry and Molecular Biology, Program in Molecular and Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Wei Liu
- Department of Biochemistry and Molecular Biology, Program in Molecular and Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.
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64
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Stjepanovic G, Baskaran S, Lin MG, Hurley JH. Vps34 Kinase Domain Dynamics Regulate the Autophagic PI 3-Kinase Complex. Mol Cell 2017; 67:528-534.e3. [PMID: 28757208 DOI: 10.1016/j.molcel.2017.07.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 05/16/2017] [Accepted: 06/30/2017] [Indexed: 12/29/2022]
Abstract
The class III phosphatidylinositol 3-kinase complex I (PI3KC3-C1) is required for the initiation of essentially all macroautophagic processes. PI3KC3-C1 consists of the lipid kinase catalytic subunit VPS34, the VPS15 scaffold, and the regulatory BECN1 and ATG14 subunits. The VPS34 catalytic domain and BECN1:ATG14 subcomplex do not touch, and it is unclear how allosteric signals are transmitted to VPS34. We used EM and crosslinking mass spectrometry to dissect five conformational substates of the complex, including one in which the VPS34 catalytic domain is dislodged from the complex but remains tethered by an intrinsically disordered linker. A "leashed" construct prevented dislodging without interfering with the other conformations, blocked enzyme activity in vitro, and blocked autophagy induction in yeast cells. This pinpoints the dislodging and tethering of the VPS34 catalytic domain, and its regulation by VPS15, as a master allosteric switch in autophagy induction.
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Affiliation(s)
- Goran Stjepanovic
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sulochanadevi Baskaran
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mary G Lin
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - James H Hurley
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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65
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Regulation of Mitochondrial Dynamics and Autophagy by the Mitochondria-Associated Membrane. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 997:33-47. [DOI: 10.1007/978-981-10-4567-7_3] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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