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Lamb CA, Nühlen S, Judith D, Frith D, Snijders AP, Behrends C, Tooze SA. TBC1D14 regulates autophagy via the TRAPP complex and ATG9 traffic. EMBO J 2016; 35:281-301. [PMID: 26711178 PMCID: PMC4741301 DOI: 10.15252/embj.201592695] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 11/25/2015] [Accepted: 11/26/2015] [Indexed: 12/19/2022] Open
Abstract
Macroautophagy requires membrane trafficking and remodelling to form the autophagosome and deliver its contents to lysosomes for degradation. We have previously identified the TBC domain-containing protein, TBC1D14, as a negative regulator of autophagy that controls delivery of membranes from RAB11-positive recycling endosomes to forming autophagosomes. In this study, we identify the TRAPP complex, a multi-subunit tethering complex and GEF for RAB1, as an interactor of TBC1D14. TBC1D14 binds to the TRAPP complex via an N-terminal 103 amino acid region, and overexpression of this region inhibits both autophagy and secretory traffic. TRAPPC8, the mammalian orthologue of a yeast autophagy-specific TRAPP subunit, forms part of a mammalian TRAPPIII-like complex and both this complex and TBC1D14 are needed for RAB1 activation. TRAPPC8 modulates autophagy and secretory trafficking and is required for TBC1D14 to bind TRAPPIII. Importantly, TBC1D14 and TRAPPIII regulate ATG9 trafficking independently of ULK1. We propose a model whereby TBC1D14 and TRAPPIII regulate a constitutive trafficking step from peripheral recycling endosomes to the early Golgi, maintaining the cycling pool of ATG9 required for initiation of autophagy.
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Affiliation(s)
- Christopher A Lamb
- Molecular Cell Biology of Autophagy Group, Francis Crick Institute, London, UK
| | - Stefanie Nühlen
- Institute of Biochemistry II, Medical School Goethe University, Frankfurt, Germany
| | - Delphine Judith
- Molecular Cell Biology of Autophagy Group, Francis Crick Institute, London, UK
| | - David Frith
- The Francis Crick Institute Mass Spectrometry Core Technology Platform Clare Hall Laboratories, Potters Bar, UK
| | - Ambrosius P Snijders
- The Francis Crick Institute Mass Spectrometry Core Technology Platform Clare Hall Laboratories, Potters Bar, UK
| | - Christian Behrends
- Institute of Biochemistry II, Medical School Goethe University, Frankfurt, Germany
| | - Sharon A Tooze
- Molecular Cell Biology of Autophagy Group, Francis Crick Institute, London, UK
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Zhuang X, Cui Y, Gao C, Jiang L. Endocytic and autophagic pathways crosstalk in plants. CURRENT OPINION IN PLANT BIOLOGY 2015; 28:39-47. [PMID: 26453966 DOI: 10.1016/j.pbi.2015.08.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 07/25/2015] [Accepted: 08/30/2015] [Indexed: 05/19/2023]
Abstract
The vacuole is the central site for both storage and metabolism in plant cells and mediates multiple cellular events during plant development and growth. Cargo proteins are usually sequestered into membrane-bound organelles and delivered into the vacuole upon membrane fusion. Two major organelles are responsible for the recognition and transport of cargos targeted to the vacuole: the single-membrane multivesicular body (MVB) or prevacuolar compartment (PVC) and the double-membrane autophagosome. Here, we will highlight recent discoveries about MVB/PVC-mediated and autophagosome-mediated protein trafficking and degradation, and will pay special attention to a possible interplay between the endocytic and autophagic pathways in regulating vacuolar degradation in plants.
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Affiliation(s)
- Xiaohong Zhuang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Yong Cui
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Caiji Gao
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Liwen Jiang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China; CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China.
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53
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Ypt1 and COPII vesicles act in autophagosome biogenesis and the early secretory pathway. Biochem Soc Trans 2015; 43:92-6. [PMID: 25619251 DOI: 10.1042/bst20140247] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The GTPase Ypt1, Rab1 in mammals functions on multiple intracellular trafficking pathways. Ypt1 has an established role on the early secretory pathway in targeting coat protein complex II (COPII) coated vesicles to the cis-Golgi. Additionally, Ypt1 functions during the initial stages of macroautophagy, a process of cellular degradation induced during periods of cell stress. In the present study, we discuss the role of Ypt1 and other secretory machinery during macroautophagy, highlighting commonalities between these two pathways.
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Hierro A, Gershlick DC, Rojas AL, Bonifacino JS. Formation of Tubulovesicular Carriers from Endosomes and Their Fusion to the trans-Golgi Network. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 318:159-202. [PMID: 26315886 DOI: 10.1016/bs.ircmb.2015.05.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Endosomes undergo extensive spatiotemporal rearrangements as proteins and lipids flux through them in a series of fusion and fission events. These controlled changes enable the concentration of cargo for eventual degradation while ensuring the proper recycling of other components. A growing body of studies has now defined multiple recycling pathways from endosomes to the trans-Golgi network (TGN) which differ in their molecular machineries. The recycling process requires specific sets of lipids, coats, adaptors, and accessory proteins that coordinate cargo selection with membrane deformation and its association with the cytoskeleton. Specific tethering factors and SNARE (SNAP (Soluble NSF Attachment Protein) Receptor) complexes are then required for the docking and fusion with the acceptor membrane. Herein, we summarize some of the current knowledge of the machineries that govern the retrograde transport from endosomes to the TGN.
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Affiliation(s)
- Aitor Hierro
- Structural Biology Unit, CIC bioGUNE, Derio, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - David C Gershlick
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | | | - Juan S Bonifacino
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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55
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Chi RJ, Harrison MS, Burd CG. Biogenesis of endosome-derived transport carriers. Cell Mol Life Sci 2015; 72:3441-3455. [PMID: 26022064 DOI: 10.1007/s00018-015-1935-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 05/18/2015] [Accepted: 05/21/2015] [Indexed: 01/29/2023]
Abstract
Sorting of macromolecules within the endosomal system is vital for physiological control of nutrient homeostasis, cell motility, and proteostasis. Trafficking routes that export macromolecules from the endosome via vesicle and tubule transport carriers constitute plasma membrane recycling and retrograde endosome-to-Golgi pathways. Proteins of the sorting nexin family have been discovered to function at nearly every step of endosomal transport carrier biogenesis and it is becoming increasingly clear that they form the core machineries of cargo-specific transport pathways that are closely integrated with cellular physiology. Here, we summarize recent progress in elucidating the pathways that mediate the biogenesis of endosome-derived transport carriers.
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Affiliation(s)
- Richard J Chi
- Department of Cell Biology, Yale School of Medicine, SHM C425B, 333 Cedar Street, New Haven, CT 06520, USA
| | - Megan S Harrison
- Department of Cell Biology, Yale School of Medicine, SHM C425B, 333 Cedar Street, New Haven, CT 06520, USA
| | - Christopher G Burd
- Department of Cell Biology, Yale School of Medicine, SHM C425B, 333 Cedar Street, New Haven, CT 06520, USA
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56
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Segarra VA, Boettner DR, Lemmon SK. Atg27 tyrosine sorting motif is important for its trafficking and Atg9 localization. Traffic 2015; 16:365-78. [PMID: 25557545 DOI: 10.1111/tra.12253] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 12/22/2014] [Accepted: 12/22/2014] [Indexed: 02/04/2023]
Abstract
During autophagy, the transmembrane protein Atg27 facilitates transport of the major autophagy membrane protein Atg9 to the preautophagosomal structure (PAS). To better understand the function of Atg27 and its relationship with Atg9, Atg27 trafficking and localization were examined. Atg27 localized to endosomes and the vacuolar membrane, in addition to previously described PAS, Golgi and Atg9-positive structures. Atg27 vacuolar membrane localization was dependent on the adaptor AP-3, which mediates direct transport from the trans-Golgi to the vacuole. The four C-terminal amino acids (YSAV) of Atg27 comprise a tyrosine sorting motif. Mutation of the YSAV abrogated Atg27 transport to the vacuolar membrane and affected its distribution in TGN/endosomal compartments, while PAS localization was normal. Also, in atg27(ΔYSAV) or AP-3 mutants, accumulation of Atg9 in the vacuolar lumen was observed upon autophagy induction. Nevertheless, PAS localization of Atg9 was normal in atg27(ΔYSAV) cells. The vacuole lumen localization of Atg9 was dependent on transport through the multivesicular body, as Atg9 accumulated in the class E compartment and vacuole membrane in atg27(ΔYSAV) vps4Δ but not in ATG27 vps4Δ cells. We suggest that Atg27 has an additional role to retain Atg9 in endosomal reservoirs that can be mobilized during autophagy.
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Affiliation(s)
- Verónica A Segarra
- Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL, USA
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Wani W, Boyer-Guittaut M, Dodson M, Chatham J, Darley-Usmar V, Zhang J. Regulation of autophagy by protein post-translational modification. J Transl Med 2015; 95:14-25. [PMID: 25365205 PMCID: PMC4454381 DOI: 10.1038/labinvest.2014.131] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 08/14/2014] [Indexed: 12/11/2022] Open
Abstract
Autophagy is a lysosome-mediated intracellular protein degradation process that involves about 38 autophagy-related genes as well as key signaling pathways that sense cellular metabolic and redox status, and has an important role in quality control of macromolecules and organelles. As with other major cellular pathways, autophagy proteins are subjected to regulatory post-translational modification. Phosphorylation is so far the most intensively studied post-translational modification in the autophagy process, followed by ubiquitination and acetylation. An interesting and new area is also now emerging, which appears to complement these more traditional mechanisms, and includes O-GlcNAcylation and redox regulation at thiol residues. Identification of the full spectrum of post-translational modifications of autophagy proteins, and determination of their impact on autophagy will be crucial for a better understanding of autophagy regulation, its deficits in diseases, and how to exploit this process for disease therapies.
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Affiliation(s)
- Willayat Wani
- Center for Free Radical Biology, University of Alabama at Birmingham,Department of Pathology, University of Alabama at Birmingham
| | - Michaël Boyer-Guittaut
- Université de Franche-Comté, Laboratoire de Biochimie, EA3922, SFR IBCT FED4234, Sciences et Techniques, 16 route de Gray, 25030 Besançon Cedex, France
| | - Matthew Dodson
- Center for Free Radical Biology, University of Alabama at Birmingham,Department of Pathology, University of Alabama at Birmingham
| | - John Chatham
- Center for Free Radical Biology, University of Alabama at Birmingham,Department of Pathology, University of Alabama at Birmingham
| | - Victor Darley-Usmar
- Center for Free Radical Biology, University of Alabama at Birmingham,Department of Pathology, University of Alabama at Birmingham
| | - Jianhua Zhang
- Center for Free Radical Biology, University of Alabama at Birmingham,Department of Pathology, University of Alabama at Birmingham,Department of Veterans Affairs, Birmingham VA Medical Center
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Abstract
Membrane trafficking depends on transport vesicles and carriers docking and fusing with the target organelle for the delivery of cargo. Membrane tethers and small guanosine triphosphatases (GTPases) mediate the docking of transport vesicles/carriers to enhance the efficiency of the subsequent SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor)-mediated fusion event with the target membrane bilayer. Different classes of membrane tethers and their specific intracellular location throughout the endomembrane system are now well defined. Recent biochemical and structural studies have led to a deeper understanding of the mechanism by which membrane tethers mediate docking of membrane carriers as well as an appreciation of the role of tethers in coordinating the correct SNARE complex and in regulating the organization of membrane compartments. This review will summarize the properties and roles of membrane tethers of both secretory and endocytic systems.
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Affiliation(s)
- Pei Zhi Cheryl Chia
- National Institute of Dental and Craniofacial Research, National Institutes of Health30 Convent Drive, Bethesda, MD 20892-4340USA
| | - Paul A. Gleeson
- The Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute30 Flemington Road, The University of Melbourne, Victoria 3010Australia
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Abstract
Autophagy is the main cellular catabolic process responsible for degrading organelles and large protein aggregates. It is initiated by the formation of a unique membrane structure, the phagophore, which engulfs part of the cytoplasm and forms a double-membrane vesicle termed the autophagosome. Fusion of the outer autophagosomal membrane with the lysosome and degradation of the inner membrane contents complete the process. The extent of autophagy must be tightly regulated to avoid destruction of proteins and organelles essential for cell survival. Autophagic activity is thus regulated by external and internal cues, which initiate the formation of well-defined autophagy-related protein complexes that mediate autophagosome formation and selective cargo recruitment into these organelles. Autophagosome formation and the signaling pathways that regulate it have recently attracted substantial attention. In this review, we analyze the different signaling pathways that regulate autophagy and discuss recent progress in our understanding of autophagosome biogenesis.
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Affiliation(s)
- Adi Abada
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Zvulun Elazar
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
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60
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Lipatova Z, Segev N. Ypt/Rab GTPases regulate two intersections of the secretory and the endosomal/lysosomal pathways. CELLULAR LOGISTICS 2014; 4:e954870. [PMID: 25610722 DOI: 10.4161/21592780.2014.954870] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Accepted: 08/07/2014] [Indexed: 11/19/2022]
Abstract
A prevailing question in the Ypt/Rab field is whether these conserved GTPases are specific to cellular compartments. The established role for Ypt1 and its human homolog Rab1 is in endoplasmic reticulum (ER)-to-Golgi transport. More recently these regulators were implicated also in autophagy. Two different TRAPP complexes, I and III, were identified as the guanine-nucleotide-exchange factors (GEFs) of Ypt1 in ER-to-Golgi transport and autophagy, respectively. Confusingly, Ypt1 and TRAPP III were also suggested to regulate endosome-to-Golgi transport, implying that they function at multiple cellular compartments, and bringing into question the nature of Ypt/Rab specificity. Recently, we showed that the role of TRAPP III and Ypt1 in autophagy occurs at the ER and that they do not regulate endosome-to-Golgi transport. Here, we discuss the significance of this conclusion to the idea that Ypt/Rabs are specific to cellular compartments. We postulate that Ypt1 regulates 2 alternative routes emanating from the ER toward the Golgi and the lysosome/vacuole. We further propose that the secretory and endocytic/lysosomal pathways intersect in 2 junctures, and 2 Ypts, Ypt1 and Ypt31, coordinate transport in the 2 intersections: Ypt1 links ER-to-Golgi and ER-to-autophagy transport, whereas Ypt31 links Golgi-to-plasma membrane (PM) transport with PM-to-Golgi recycling through endosomes.
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Affiliation(s)
- Zhanna Lipatova
- Department of Biochemistry and Molecular Genetics; University of Illinois at Chicago ; Chicago, IL USA
| | - Nava Segev
- Department of Biochemistry and Molecular Genetics; University of Illinois at Chicago ; Chicago, IL USA
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61
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Kira S, Tabata K, Shirahama-Noda K, Nozoe A, Yoshimori T, Noda T. Reciprocal conversion of Gtr1 and Gtr2 nucleotide-binding states by Npr2-Npr3 inactivates TORC1 and induces autophagy. Autophagy 2014; 10:1565-78. [PMID: 25046117 PMCID: PMC4206535 DOI: 10.4161/auto.29397] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Autophagy is an intracellular degradation process that delivers cytosolic material to
lysosomes and vacuoles. To investigate the mechanisms that regulate autophagy, we
performed a genome-wide screen using a yeast deletion-mutant collection, and found that
Npr2 and Npr3 mutants were defective in autophagy. Their mammalian homologs, NPRL2 and
NPRL3, were also involved in regulation of autophagy. Npr2-Npr3 function upstream of
Gtr1-Gtr2, homologs of the mammalian RRAG GTPase complex, which is crucial for TORC1
regulation. Both npr2∆ mutants and a GTP-bound Gtr1 mutant suppressed
autophagy and increased Tor1 vacuole localization. Furthermore, Gtr2 binds to the TORC1
subunit Kog1. A GDP-bound Gtr1 mutant induced autophagy even under nutrient-rich
conditions, and this effect was dependent on the direct binding of Gtr2 to Kog1. These
results revealed that 2 molecular mechanisms, Npr2-Npr3-dependent GTP hydrolysis of Gtr1
and direct binding of Gtr2 to Kog1, are involved in TORC1 inactivation and autophagic
induction.
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Affiliation(s)
- Shintaro Kira
- Center for Frontier Oral Science; Graduate School of Dentistry; Osaka University, Osaka, Japan; Graduate School of Frontier Bioscience; Osaka University; Osaka, Japan
| | - Keisuke Tabata
- Laboratory of Viral Infection; International Research Center for Infectious Diseases; Research Institute for Microbial Diseases; Osaka University; Osaka, Japan
| | - Kanae Shirahama-Noda
- Center for Frontier Oral Science; Graduate School of Dentistry; Osaka University, Osaka, Japan
| | - Akiko Nozoe
- Graduate School of Medicine, Osaka University; Osaka, Japan
| | - Tamotsu Yoshimori
- Graduate School of Frontier Bioscience; Osaka University; Osaka, Japan; Graduate School of Medicine, Osaka University; Osaka, Japan
| | - Takeshi Noda
- Center for Frontier Oral Science; Graduate School of Dentistry; Osaka University, Osaka, Japan; Graduate School of Frontier Bioscience; Osaka University; Osaka, Japan
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62
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Ge L, Baskaran S, Schekman R, Hurley JH. The protein-vesicle network of autophagy. Curr Opin Cell Biol 2014; 29:18-24. [PMID: 24681112 DOI: 10.1016/j.ceb.2014.02.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 02/28/2014] [Indexed: 10/25/2022]
Abstract
The biogenesis of autophagosomes entails the nucleation and growth of a double-membrane sheet, the phagophore, which engulfs cytosol for delivery to the lysosome. Genetic studies have identified a class of Atg proteins that are essential for the process, yet the molecular mechanism of autophagosome biogenesis has been elusive. Proteomic, structural, super-resolution imaging, and biochemical reconstitution experiments have begun to fill in some of the gaps. This review describes progress and prospects for obtaining a four-dimensional network model of the nucleation and growth of the phagophore.
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Affiliation(s)
- Liang Ge
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, United States
| | - Sulochanadevi Baskaran
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, United States
| | - Randy Schekman
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, United States
| | - James H Hurley
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, United States.
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Abstract
Autophagy is a bulk degradation system induced by cellular stresses such as nutrient starvation. Its function relies on the formation of double-membrane vesicles called autophagosomes. Unlike other organelles that appear to stably exist in the cell, autophagosomes are formed on demand, and once their formation is initiated, it proceeds surprisingly rapidly. How and where this dynamic autophagosome formation takes place has been a long-standing question, but the discovery of Atg proteins in the 1990's significantly accelerated our understanding of autophagosome biogenesis. In this review, we will briefly introduce each Atg functional unit in relation to autophagosome biogenesis, and then discuss the origin of the autophagosomal membrane with an introduction to selected recent studies addressing this problem.
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