2
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Ke PY. Molecular Mechanism of Autophagosome-Lysosome Fusion in Mammalian Cells. Cells 2024; 13:500. [PMID: 38534345 DOI: 10.3390/cells13060500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024] Open
Abstract
In eukaryotes, targeting intracellular components for lysosomal degradation by autophagy represents a catabolic process that evolutionarily regulates cellular homeostasis. The successful completion of autophagy initiates the engulfment of cytoplasmic materials within double-membrane autophagosomes and subsequent delivery to autolysosomes for degradation by acidic proteases. The formation of autolysosomes relies on the precise fusion of autophagosomes with lysosomes. In recent decades, numerous studies have provided insights into the molecular regulation of autophagosome-lysosome fusion. In this review, an overview of the molecules that function in the fusion of autophagosomes with lysosomes is provided. Moreover, the molecular mechanism underlying how these functional molecules regulate autophagosome-lysosome fusion is summarized.
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Affiliation(s)
- Po-Yuan Ke
- Department of Biochemistry & Molecular Biology, Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Liver Research Center, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan
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3
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Broadbent DG, Barnaba C, Perez GI, Schmidt JC. Quantitative analysis of autophagy reveals the role of ATG9 and ATG2 in autophagosome formation. J Cell Biol 2023; 222:e202210078. [PMID: 37115157 PMCID: PMC10148237 DOI: 10.1083/jcb.202210078] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/03/2023] [Accepted: 03/17/2023] [Indexed: 04/29/2023] Open
Abstract
Autophagy is a catabolic pathway required for the recycling of cytoplasmic materials. To define the mechanisms underlying autophagy it is critical to quantitatively characterize the dynamic behavior of autophagy factors in living cells. Using a panel of cell lines expressing HaloTagged autophagy factors from their endogenous loci, we analyzed the abundance, single-molecule dynamics, and autophagosome association kinetics of autophagy proteins involved in autophagosome biogenesis. We demonstrate that autophagosome formation is inefficient and ATG2-mediated tethering to donor membranes is a key commitment step in autophagosome formation. Furthermore, our observations support the model that phagophores are initiated by the accumulation of autophagy factors on mobile ATG9 vesicles, and that the ULK1 complex and PI3-kinase form a positive feedback loop required for autophagosome formation. Finally, we demonstrate that the duration of autophagosome biogenesis is ∼110 s. In total, our work provides quantitative insight into autophagosome biogenesis and establishes an experimental framework to analyze autophagy in human cells.
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Affiliation(s)
- David G. Broadbent
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Carlo Barnaba
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Gloria I. Perez
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Jens C. Schmidt
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- Department of Obstetrics and Gynecology, Michigan State University, East Lansing, MI, USA
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4
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Gundelfinger ED, Karpova A, Pielot R, Garner CC, Kreutz MR. Organization of Presynaptic Autophagy-Related Processes. Front Synaptic Neurosci 2022; 14:829354. [PMID: 35368245 PMCID: PMC8968026 DOI: 10.3389/fnsyn.2022.829354] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/04/2022] [Indexed: 11/13/2022] Open
Abstract
Brain synapses pose special challenges on the quality control of their protein machineries as they are far away from the neuronal soma, display a high potential for plastic adaptation and have a high energy demand to fulfill their physiological tasks. This applies in particular to the presynaptic part where neurotransmitter is released from synaptic vesicles, which in turn have to be recycled and refilled in a complex membrane trafficking cycle. Pathways to remove outdated and damaged proteins include the ubiquitin-proteasome system acting in the cytoplasm as well as membrane-associated endolysosomal and the autophagy systems. Here we focus on the latter systems and review what is known about the spatial organization of autophagy and endolysomal processes within the presynapse. We provide an inventory of which components of these degradative systems were found to be present in presynaptic boutons and where they might be anchored to the presynaptic apparatus. We identify three presynaptic structures reported to interact with known constituents of membrane-based protein-degradation pathways and therefore may serve as docking stations. These are (i) scaffolding proteins of the cytomatrix at the active zone, such as Bassoon or Clarinet, (ii) the endocytic machinery localized mainly at the peri-active zone, and (iii) synaptic vesicles. Finally, we sketch scenarios, how presynaptic autophagic cargos are tagged and recruited and which cellular mechanisms may govern membrane-associated protein turnover in the presynapse.
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Affiliation(s)
- Eckart D. Gundelfinger
- Research Group Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany
- Institute of Pharmacology and Toxicology, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
- Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
| | - Anna Karpova
- Research Group Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany
- Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
| | - Rainer Pielot
- Institute of Pharmacology and Toxicology, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
- Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
| | - Craig C. Garner
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
- Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Michael R. Kreutz
- Research Group Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany
- Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
- Center for Molecular Neurobiology (ZMNH), University Hospital Hamburg-Eppendorf, Hamburg, Germany
- German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany
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5
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Yang S, Park D, Manning L, Hill SE, Cao M, Xuan Z, Gonzalez I, Dong Y, Clark B, Shao L, Okeke I, Almoril-Porras A, Bai J, De Camilli P, Colón-Ramos DA. Presynaptic autophagy is coupled to the synaptic vesicle cycle via ATG-9. Neuron 2022; 110:824-840.e10. [PMID: 35065714 PMCID: PMC9017068 DOI: 10.1016/j.neuron.2021.12.031] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 10/20/2021] [Accepted: 12/20/2021] [Indexed: 01/01/2023]
Abstract
Autophagy is a cellular degradation pathway essential for neuronal health and function. Autophagosome biogenesis occurs at synapses, is locally regulated, and increases in response to neuronal activity. The mechanisms that couple autophagosome biogenesis to synaptic activity remain unknown. In this study, we determine that trafficking of ATG-9, the only transmembrane protein in the core autophagy pathway, links the synaptic vesicle cycle with autophagy. ATG-9-positive vesicles in C. elegans are generated from the trans-Golgi network via AP-3-dependent budding and delivered to presynaptic sites. At presynaptic sites, ATG-9 undergoes exo-endocytosis in an activity-dependent manner. Mutations that disrupt endocytosis, including a lesion in synaptojanin 1 associated with Parkinson's disease, result in abnormal ATG-9 accumulation at clathrin-rich synaptic foci and defects in activity-induced presynaptic autophagy. Our findings uncover regulated key steps of ATG-9 trafficking at presynaptic sites and provide evidence that ATG-9 exo-endocytosis couples autophagosome biogenesis at presynaptic sites with the activity-dependent synaptic vesicle cycle.
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Affiliation(s)
- Sisi Yang
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Daehun Park
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Laura Manning
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Sarah E Hill
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Mian Cao
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Zhao Xuan
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Ian Gonzalez
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Yongming Dong
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Benjamin Clark
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Lin Shao
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Ifechukwu Okeke
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Agustin Almoril-Porras
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Jihong Bai
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Pietro De Camilli
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA; Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Daniel A Colón-Ramos
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA; Instituto de Neurobiología José del Castillo, Recinto de Ciencias Médicas, Universidad de Puerto Rico, 201 Boulevard del Valle, San Juan, PR 00901, USA; Wu Tsai Institute, Yale University, New Haven, CT 06510, USA.
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6
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Egea PF. Mechanisms of Non-Vesicular Exchange of Lipids at Membrane Contact Sites: Of Shuttles, Tunnels and, Funnels. Front Cell Dev Biol 2021; 9:784367. [PMID: 34912813 PMCID: PMC8667587 DOI: 10.3389/fcell.2021.784367] [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: 09/27/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Eukaryotic cells are characterized by their exquisite compartmentalization resulting from a cornucopia of membrane-bound organelles. Each of these compartments hosts a flurry of biochemical reactions and supports biological functions such as genome storage, membrane protein and lipid biosynthesis/degradation and ATP synthesis, all essential to cellular life. Acting as hubs for the transfer of matter and signals between organelles and throughout the cell, membrane contacts sites (MCSs), sites of close apposition between membranes from different organelles, are essential to cellular homeostasis. One of the now well-acknowledged function of MCSs involves the non-vesicular trafficking of lipids; its characterization answered one long-standing question of eukaryotic cell biology revealing how some organelles receive and distribute their membrane lipids in absence of vesicular trafficking. The endoplasmic reticulum (ER) in synergy with the mitochondria, stands as the nexus for the biosynthesis and distribution of phospholipids (PLs) throughout the cell by contacting nearly all other organelle types. MCSs create and maintain lipid fluxes and gradients essential to the functional asymmetry and polarity of biological membranes throughout the cell. Membrane apposition is mediated by proteinaceous tethers some of which function as lipid transfer proteins (LTPs). We summarize here the current state of mechanistic knowledge of some of the major classes of LTPs and tethers based on the available atomic to near-atomic resolution structures of several "model" MCSs from yeast but also in Metazoans; we describe different models of lipid transfer at MCSs and analyze the determinants of their specificity and directionality. Each of these systems illustrate fundamental principles and mechanisms for the non-vesicular exchange of lipids between eukaryotic membrane-bound organelles essential to a wide range of cellular processes such as at PL biosynthesis and distribution, lipid storage, autophagy and organelle biogenesis.
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Affiliation(s)
- Pascal F Egea
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
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9
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Smith D, Kannan G, Coppens I, Wang F, Nguyen HM, Cerutti A, Olafsson EB, Rimple PA, Schultz TL, Mercado Soto NM, Di Cristina M, Besteiro S, Carruthers VB. Toxoplasma TgATG9 is critical for autophagy and long-term persistence in tissue cysts. eLife 2021; 10:e59384. [PMID: 33904393 PMCID: PMC8128441 DOI: 10.7554/elife.59384] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 04/27/2021] [Indexed: 12/29/2022] Open
Abstract
Many of the world's warm-blooded species are chronically infected with Toxoplasma gondii tissue cysts, including an estimated one-third of the global human population. The cellular processes that permit long-term persistence within the cyst are largely unknown for T. gondii and related coccidian parasites that impact human and animal health. Herein, we show that genetic ablation of TgATG9 substantially reduces canonical autophagy and compromises bradyzoite viability. Transmission electron microscopy revealed numerous structural abnormalities occurring in ∆atg9 bradyzoites. Intriguingly, abnormal mitochondrial networks were observed in TgATG9-deficient bradyzoites, some of which contained numerous different cytoplasmic components and organelles. ∆atg9 bradyzoite fitness was drastically compromised in vitro and in mice, with very few brain cysts identified in mice 5 weeks post-infection. Taken together, our data suggests that TgATG9, and by extension autophagy, is critical for cellular homeostasis in bradyzoites and is necessary for long-term persistence within the cyst of this coccidian parasite.
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Affiliation(s)
- David Smith
- Department of Microbiology and Immunology, University of Michigan Medical SchoolAnn ArborUnited States
| | - Geetha Kannan
- Department of Microbiology and Immunology, University of Michigan Medical SchoolAnn ArborUnited States
| | - Isabelle Coppens
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public HealthBaltimoreUnited States
| | - Fengrong Wang
- Department of Microbiology and Immunology, University of Michigan Medical SchoolAnn ArborUnited States
| | - Hoa Mai Nguyen
- Laboratory of PathogenHost Interactions, UMR 5235, CNRS, Université de MontpellierMontpellierFrance
| | - Aude Cerutti
- Laboratory of PathogenHost Interactions, UMR 5235, CNRS, Université de MontpellierMontpellierFrance
| | - Einar B Olafsson
- Department of Microbiology and Immunology, University of Michigan Medical SchoolAnn ArborUnited States
| | - Patrick A Rimple
- Department of Microbiology and Immunology, University of Michigan Medical SchoolAnn ArborUnited States
| | - Tracey L Schultz
- Department of Microbiology and Immunology, University of Michigan Medical SchoolAnn ArborUnited States
| | - Nayanna M Mercado Soto
- Department of Microbiology and Immunology, University of Michigan Medical SchoolAnn ArborUnited States
| | - Manlio Di Cristina
- Department of Microbiology and Immunology, University of Michigan Medical SchoolAnn ArborUnited States
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di PerugiaPerugiaItaly
| | - Sébastien Besteiro
- Laboratory of PathogenHost Interactions, UMR 5235, CNRS, Université de MontpellierMontpellierFrance
| | - Vern B Carruthers
- Department of Microbiology and Immunology, University of Michigan Medical SchoolAnn ArborUnited States
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