201
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Pfaffenwimmer T, Reiter W, Brach T, Nogellova V, Papinski D, Schuschnig M, Abert C, Ammerer G, Martens S, Kraft C. Hrr25 kinase promotes selective autophagy by phosphorylating the cargo receptor Atg19. EMBO Rep 2014; 15:862-70. [PMID: 24968893 PMCID: PMC4197043 DOI: 10.15252/embr.201438932] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 05/30/2014] [Accepted: 06/10/2014] [Indexed: 01/08/2023] Open
Abstract
Autophagy is the major pathway for the delivery of cytoplasmic material to the vacuole or lysosome. Selective autophagy is mediated by cargo receptors, which link the cargo to the scaffold protein Atg11 and to Atg8 family proteins on the forming autophagosomal membrane. We show that the essential kinase Hrr25 activates the cargo receptor Atg19 by phosphorylation, which is required to link cargo to the Atg11 scaffold, allowing selective autophagy to proceed. We also find that the Atg34 cargo receptor is regulated in a similar manner, suggesting a conserved mechanism.
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Affiliation(s)
| | - Wolfgang Reiter
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Thorsten Brach
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | | | - Daniel Papinski
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | | | - Christine Abert
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Gustav Ammerer
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Sascha Martens
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Claudine Kraft
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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202
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Schuck S, Gallagher CM, Walter P. ER-phagy mediates selective degradation of endoplasmic reticulum independently of the core autophagy machinery. J Cell Sci 2014; 127:4078-88. [PMID: 25052096 PMCID: PMC4163648 DOI: 10.1242/jcs.154716] [Citation(s) in RCA: 191] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Selective autophagy of damaged or redundant organelles is an important mechanism for maintaining cell homeostasis. We found previously that endoplasmic reticulum (ER) stress in the yeast Saccharomyces cerevisiae causes massive ER expansion and triggers the formation of large ER whorls. Here, we show that stress-induced ER whorls are selectively taken up into the vacuole, the yeast lysosome, by a process termed ER-phagy. Import into the vacuole does not involve autophagosomes but occurs through invagination of the vacuolar membrane, indicating that ER-phagy is topologically equivalent to microautophagy. Even so, ER-phagy requires neither the core autophagy machinery nor several other proteins specifically implicated in microautophagy. Thus, autophagy of ER whorls represents a distinct type of organelle-selective autophagy. Finally, we provide evidence that ER-phagy degrades excess ER membrane, suggesting that it contributes to cell homeostasis by controlling organelle size.
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Affiliation(s)
- Sebastian Schuck
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158, USA
| | - Ciara M Gallagher
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158, USA
| | - Peter Walter
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158, USA
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203
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Young CL, Robinson AS. Protein folding and secretion: mechanistic insights advancing recombinant protein production in S. cerevisiae. Curr Opin Biotechnol 2014; 30:168-77. [PMID: 25032908 DOI: 10.1016/j.copbio.2014.06.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 06/19/2014] [Accepted: 06/22/2014] [Indexed: 10/25/2022]
Abstract
The emergence of genomic approaches coupled to recombinant DNA technologies have identified the quality control systems that regulate proteostasis - biological pathways that modulate protein biogenesis, maturation, trafficking, and degradation. The elucidation of these pathways has become of growing importance in therapeutics as loss of proteostasis has been suggested to lead to a number of human diseases including Alzheimer's, Parkinson's Disease and Type II Diabetes. We anticipate that the most successful strategies for protein expression and therapeutics development may involve integration of protein engineering strategies with host manipulation, to exploit the cell's native stress response pathways and trafficking mechanisms. This review will highlight recent findings and mechanistic detail correlated to quality control in the early secretory pathway of Saccharomyces cerevisiae.
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Affiliation(s)
- Carissa L Young
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Anne S Robinson
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA 70118, United States.
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204
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Le Bars R, Marion J, Le Borgne R, Satiat-Jeunemaitre B, Bianchi MW. ATG5 defines a phagophore domain connected to the endoplasmic reticulum during autophagosome formation in plants. Nat Commun 2014; 5:4121. [PMID: 24947672 DOI: 10.1038/ncomms5121] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 05/14/2014] [Indexed: 02/03/2023] Open
Abstract
Autophagosomes are the organelles responsible for macroautophagy and arise, in yeast and animals, from the sealing of a cup-shaped double-membrane precursor, the phagophore. How the phagophore is generated and grows into a sealed autophagosome is still not clear in detail, and unknown in plants. This is due, in part, to the scarcity of structurally informative, real-time imaging data of the required protein machinery at the phagophore formation site. Here we find that in intact living Arabidopsis tissue, autophagy-related protein ATG5, which is essential for autophagosome formation, is present at the phagophore site from early, sub-resolution stages and later defines a torus-shaped structure on a flat cisternal early phagophore. Movement and expansion of this structure are accompanied by the underlying endoplasmic reticulum, suggesting tight connections between the two compartments. Detailed real-time and 3D imaging of the growing phagophore are leveraged to propose a model for autophagosome formation in plants.
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Affiliation(s)
- Romain Le Bars
- Laboratoire Dynamique de la Compartimentation Cellulaire, CNRS UPR2355, Institut des Sciences du Végétal, Centre de Recherche de Gif (FRC3115), Saclay Plant Sciences, 91198 Gif-sur-Yvette, France
| | - Jessica Marion
- Laboratoire Dynamique de la Compartimentation Cellulaire, CNRS UPR2355, Institut des Sciences du Végétal, Centre de Recherche de Gif (FRC3115), Saclay Plant Sciences, 91198 Gif-sur-Yvette, France
| | - Rémi Le Borgne
- 1] Laboratoire Dynamique de la Compartimentation Cellulaire, CNRS UPR2355, Institut des Sciences du Végétal, Centre de Recherche de Gif (FRC3115), Saclay Plant Sciences, 91198 Gif-sur-Yvette, France [2] Pôle de Biologie Cellulaire, Imagif, Centre de Recherche de Gif, (FRC3115), Saclay Plant Sciences, CNRS, 91198 Gif-sur-Yvette, France
| | - Béatrice Satiat-Jeunemaitre
- 1] Laboratoire Dynamique de la Compartimentation Cellulaire, CNRS UPR2355, Institut des Sciences du Végétal, Centre de Recherche de Gif (FRC3115), Saclay Plant Sciences, 91198 Gif-sur-Yvette, France [2] Pôle de Biologie Cellulaire, Imagif, Centre de Recherche de Gif, (FRC3115), Saclay Plant Sciences, CNRS, 91198 Gif-sur-Yvette, France
| | - Michele Wolfe Bianchi
- 1] Laboratoire Dynamique de la Compartimentation Cellulaire, CNRS UPR2355, Institut des Sciences du Végétal, Centre de Recherche de Gif (FRC3115), Saclay Plant Sciences, 91198 Gif-sur-Yvette, France [2] UFR Sciences et Technologie, Université Paris-Est Créteil Val de Marne (UPEC), 61 av. Général de Gaulle, 94010 Créteil, France
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205
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Jin M, Klionsky DJ. Regulation of autophagy: modulation of the size and number of autophagosomes. FEBS Lett 2014; 588:2457-63. [PMID: 24928445 DOI: 10.1016/j.febslet.2014.06.015] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/02/2014] [Accepted: 06/03/2014] [Indexed: 10/25/2022]
Abstract
Autophagy as a conserved degradation and recycling process in eukaryotic cells, occurs constitutively, but is induced by stress. A fine regulation of autophagy in space, time, and intensity is critical for maintaining normal energy homeostasis and metabolism, and to allow for its therapeutic modulation in various autophagy-related human diseases. Autophagy activity is regulated in both transcriptional and post-translational manners. In this review, we summarize the cytosolic regulation of autophagy via its molecular machinery, and nuclear regulation by transcription factors. Specifically, we consider Ume6-ATG8 and Pho23-ATG9 transcriptional regulation in detail, as examples of how nuclear transcription factors and cytosolic machinery cooperate to determine autophagosome size and number, which are the two main mechanistic factors through which autophagy activity is regulated.
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Affiliation(s)
- Meiyan Jin
- Life Sciences Institute, and the Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Daniel J Klionsky
- Life Sciences Institute, and the Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, United States.
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206
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Mulakkal NC, Nagy P, Takats S, Tusco R, Juhász G, Nezis IP. Autophagy in Drosophila: from historical studies to current knowledge. BIOMED RESEARCH INTERNATIONAL 2014; 2014:273473. [PMID: 24949430 PMCID: PMC4052151 DOI: 10.1155/2014/273473] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/17/2014] [Indexed: 12/17/2022]
Abstract
The discovery of evolutionarily conserved Atg genes required for autophagy in yeast truly revolutionized this research field and made it possible to carry out functional studies on model organisms. Insects including Drosophila are classical and still popular models to study autophagy, starting from the 1960s. This review aims to summarize past achievements and our current knowledge about the role and regulation of autophagy in Drosophila, with an outlook to yeast and mammals. The basic mechanisms of autophagy in fruit fly cells appear to be quite similar to other eukaryotes, and the role that this lysosomal self-degradation process plays in Drosophila models of various diseases already made it possible to recognize certain aspects of human pathologies. Future studies in this complete animal hold great promise for the better understanding of such processes and may also help finding new research avenues for the treatment of disorders with misregulated autophagy.
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Affiliation(s)
- Nitha C. Mulakkal
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Peter Nagy
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Szabolcs Takats
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Radu Tusco
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Gábor Juhász
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Ioannis P. Nezis
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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207
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Papanikou E, Glick BS. Golgi compartmentation and identity. Curr Opin Cell Biol 2014; 29:74-81. [PMID: 24840895 DOI: 10.1016/j.ceb.2014.04.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 04/07/2014] [Accepted: 04/24/2014] [Indexed: 10/25/2022]
Abstract
Recent work supports the idea that cisternae of the Golgi apparatus can be assigned to three classes, which correspond to discrete stages of cisternal maturation. Each stage has a unique pattern of membrane traffic. At the first stage, cisternae form in association with the ER at multifunctional membrane assembly stations. At the second stage, cisternae synthesize carbohydrates while exchanging material via COPI vesicles. At the third stage, cisternae of the trans-Golgi network segregate into domains and produce transport carriers with the aid of specific lipids and the actin cytoskeleton. These processes are coordinated by cascades of Rab and Arf/Arl GTPases.
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Affiliation(s)
- Effrosyni Papanikou
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, United States
| | - Benjamin S Glick
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, United States.
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208
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209
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Shin KD, Lee HN, Chung T. A revised assay for monitoring autophagic flux in Arabidopsis thaliana reveals involvement of AUTOPHAGY-RELATED9 in autophagy. Mol Cells 2014; 37:399-405. [PMID: 24805779 PMCID: PMC4044311 DOI: 10.14348/molcells.2014.0042] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 03/30/2014] [Accepted: 04/08/2014] [Indexed: 01/29/2023] Open
Abstract
Autophagy targets cytoplasmic cargo to a lytic compartment for degradation. Autophagy-related (Atg) proteins, including the transmembrane protein Atg9, are involved in different steps of autophagy in yeast and mammalian cells. Functional classification of core Atg proteins in plants has not been clearly confirmed, partly because of the limited availability of reliable assays for monitoring autophagic flux. By using proUBQ10-GFP-ATG8a as an autophagic marker, we showed that autophagic flux is reduced but not completely compromised in Arabidopsis thaliana atg9 mutants. In contrast, we confirmed full inhibition of autophagic flux in atg7 and that the difference in autophagy was consistent with the differences in mutant phenotypes such as hypersensitivity to nutrient stress and selective autophagy. Autophagic flux is also reduced by an inhibitor of phosphatidylinositol kinase. Our data indicated that atg9 is phenotypically distinct from atg7 and atg2 in Arabidopsis, and we proposed that ATG9 and phosphatidylinositol kinase activity contribute to efficient autophagy in Arabidopsis.
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Affiliation(s)
- Kwang Deok Shin
- Department of Biological Sciences, Pusan National University, Busan 609-735,
Korea
| | - Han Nim Lee
- Department of Biological Sciences, Pusan National University, Busan 609-735,
Korea
| | - Taijoon Chung
- Department of Biological Sciences, Pusan National University, Busan 609-735,
Korea
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210
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Hurley JH, Schulman BA. Atomistic autophagy: the structures of cellular self-digestion. Cell 2014; 157:300-311. [PMID: 24725401 PMCID: PMC4038036 DOI: 10.1016/j.cell.2014.01.070] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 01/28/2014] [Accepted: 01/28/2014] [Indexed: 01/06/2023]
Abstract
Autophagy is directed by numerous distinct autophagy-related (Atg) proteins. These transmit starvation-induced signals to lipids and regulatory proteins and assemble a double-membrane autophagosome sequestering bulk cytoplasm and/or selected cargos destined for degradation upon autophagosome fusion with a vacuole or lysosome. This Review discusses the structural mechanisms by which Atg proteins sense membrane curvature, mediate a PI(3)P-signaling cascade, and utilize autophagy-specific ubiquitin-like protein cascades to tether proteins to autophagosomal membranes. Recent elucidation of molecular interactions enabling vesicle nucleation, elongation, and cargo recruitment provides insights into how dynamic protein-protein and protein-membrane interactions may dictate size, shape, and contents of autophagosomes.
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Affiliation(s)
- James H Hurley
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA.
| | - Brenda A Schulman
- Department of Structural Biology and Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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211
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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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212
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Saleh AA, Bhadra AK, Roy I. Cytotoxicity of mutant huntingtin fragment in yeast can be modulated by the expression level of wild type huntingtin fragment. ACS Chem Neurosci 2014; 5:205-15. [PMID: 24377263 PMCID: PMC3963126 DOI: 10.1021/cn400171d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 12/26/2013] [Indexed: 12/23/2022] Open
Abstract
Conflicting reports exist in the literature regarding the role of wild-type huntingtin in determining the toxicity of the aggregated, mutant huntingtin in Huntington's disease (HD). Some studies report the amelioration of toxicity of the mutant protein in the presence of the wild-type protein, while others indicate sequestration of the wild-type protein by mutant huntingtin. Over the years, yeast has been established as a valid model organism to study molecular changes associated with HD, especially at the protein level. We have used an inducible system to express human huntingtin fragments harboring normal (25Q) and pathogenic (103Q) polyglutamine lengths under the control of a galactose promoter in a yeast model of HD. We show that the relative expression level of each allele (wild-type/mutant) decides the cellular phenotype. When the expression level of wild-type huntingtin is high, an increase in the solubility of the mutant protein is observed. Fluorescence-recovery-after-photobleaching (FRAP) studies show that solubility reaches ∼94% in these cells. This leads to reduction in oxidative stress and cytotoxicity, and increases cell viability. In-cell FRET studies show that interaction between these proteins does not require the presence of a mediator. When the expression of wild-type huntingtin is low, it is sequestered into aggregates by the mutant protein. Even under these conditions, cytotoxicity is attenuated. Our findings indicate that the presence of wild-type huntingtin has a beneficial role even when its relative expression level is lower than that of the mutant protein.
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Affiliation(s)
- Aliabbas Ahmedbhai Saleh
- Department of Biotechnology, National Institute
of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Ankan Kumar Bhadra
- Department of Biotechnology, National Institute
of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute
of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India
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213
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Umemiya-Shirafuji R, Galay RL, Maeda H, Kawano S, Tanaka T, Fukumoto S, Suzuki H, Tsuji N, Fujisaki K. Expression analysis of autophagy-related genes in the hard tick Haemaphysalis longicornis. Vet Parasitol 2014; 201:169-75. [DOI: 10.1016/j.vetpar.2014.01.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 01/14/2014] [Accepted: 01/24/2014] [Indexed: 12/16/2022]
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214
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Böckler S, Westermann B. Mitochondrial ER contacts are crucial for mitophagy in yeast. Dev Cell 2014; 28:450-8. [PMID: 24530295 DOI: 10.1016/j.devcel.2014.01.012] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 12/20/2013] [Accepted: 01/13/2014] [Indexed: 10/25/2022]
Abstract
Damaged and superfluous mitochondria are removed from the cell by selective autophagy, a process termed mitophagy. This serves to maintain the proper quantity and quality of the organelle. Mitophagy is executed by an evolutionarily conserved pathway, many components of which were first discovered and characterized in yeast. In a systematic screen of a yeast deletion collection, we identified ERMES, a complex connecting mitochondria and the endoplasmic reticulum (ER), as an important factor contributing to the selective degradation of mitochondria. We show that efficient mitophagy depends on mitochondrial ER tethering. ERMES colocalizes with sites of mitophagosome biogenesis and affects the formation of the isolation membrane that engulfs the organelles destined for degradation. These results provide insights into the cellular mechanisms that govern organelle homeostasis.
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Affiliation(s)
- Stefan Böckler
- Institut für Zellbiologie, Universität Bayreuth, 95440 Bayreuth, Germany
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215
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Papinski D, Schuschnig M, Reiter W, Wilhelm L, Barnes CA, Maiolica A, Hansmann I, Pfaffenwimmer T, Kijanska M, Stoffel I, Lee SS, Brezovich A, Lou JH, Turk BE, Aebersold R, Ammerer G, Peter M, Kraft C. Early steps in autophagy depend on direct phosphorylation of Atg9 by the Atg1 kinase. Mol Cell 2014; 53:471-83. [PMID: 24440502 PMCID: PMC3978657 DOI: 10.1016/j.molcel.2013.12.011] [Citation(s) in RCA: 262] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 11/11/2013] [Accepted: 12/11/2013] [Indexed: 11/25/2022]
Abstract
Bulk degradation of cytoplasmic material is mediated by a highly conserved intracellular trafficking pathway termed autophagy. This pathway is characterized by the formation of double-membrane vesicles termed autophagosomes engulfing the substrate and transporting it to the vacuole/lysosome for breakdown and recycling. The Atg1/ULK1 kinase is essential for this process; however, little is known about its targets and the means by which it controls autophagy. Here we have screened for Atg1 kinase substrates using consensus peptide arrays and identified three components of the autophagy machinery. The multimembrane-spanning protein Atg9 is a direct target of this kinase essential for autophagy. Phosphorylated Atg9 is then required for the efficient recruitment of Atg8 and Atg18 to the site of autophagosome formation and subsequent expansion of the isolation membrane, a prerequisite for a functioning autophagy pathway. These findings show that the Atg1 kinase acts early in autophagy by regulating the outgrowth of autophagosomal membranes.
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Affiliation(s)
- Daniel Papinski
- Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | | | - Wolfgang Reiter
- Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | - Larissa Wilhelm
- Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | - Christopher A Barnes
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Wolfgang Pauli Strasse 16, 8093 Zürich, Switzerland
| | - Alessio Maiolica
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Wolfgang Pauli Strasse 16, 8093 Zürich, Switzerland
| | - Isabella Hansmann
- Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | | | - Monika Kijanska
- Institute of Biochemistry, Department of Biology, ETH Zürich, Schafmattstrasse 18, 8093 Zürich, Switzerland
| | - Ingrid Stoffel
- Institute of Biochemistry, Department of Biology, ETH Zürich, Schafmattstrasse 18, 8093 Zürich, Switzerland
| | - Sung Sik Lee
- Institute of Biochemistry, Department of Biology, ETH Zürich, Schafmattstrasse 18, 8093 Zürich, Switzerland
| | - Andrea Brezovich
- Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | - Jane Hua Lou
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Wolfgang Pauli Strasse 16, 8093 Zürich, Switzerland
| | - Gustav Ammerer
- Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | - Matthias Peter
- Institute of Biochemistry, Department of Biology, ETH Zürich, Schafmattstrasse 18, 8093 Zürich, Switzerland
| | - Claudine Kraft
- Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria.
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216
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Tamura N, Oku M, Sakai Y. Atg21 regulates pexophagy via its PI(3)P-binding activity in Pichia pastoris. FEMS Yeast Res 2014; 14:435-44. [PMID: 24373415 DOI: 10.1111/1567-1364.12132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 11/19/2013] [Accepted: 12/16/2013] [Indexed: 01/28/2023] Open
Abstract
Pexophagy is a selective degradation pathway of peroxisomes. In the present study, we revealed that PpAtg21 was required for pexophagy in the methylotrophic yeast Pichia pastoris. PpAtg21 was essential for efficient lipidation of Atg8 and for de novo synthesis of pexophagic membranes. In contrast to PpAtg18, PpAtg21 was not necessary for vacuolar fission nor invagination during micropexophagy. PpAtg21 specifically bound to PI(3)P, but not to PI(3,5)P2 in vitro, and the localization analyses matched with this phosphoinositide-binding specificity. The mutant which lost the lipid-binding activity showed defect in pexophagy, suggesting that PI(3)P-binding activity of PpAtg21 was required for pexophagy.
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Affiliation(s)
- Naoki Tamura
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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217
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Kaufmann A, Beier V, Franquelim H, Wollert T. Molecular Mechanism of Autophagic Membrane-Scaffold Assembly and Disassembly. Cell 2014; 156:469-81. [DOI: 10.1016/j.cell.2013.12.022] [Citation(s) in RCA: 171] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 11/07/2013] [Accepted: 11/14/2013] [Indexed: 12/21/2022]
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218
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Stanley RE, Ragusa MJ, Hurley JH. The beginning of the end: how scaffolds nucleate autophagosome biogenesis. Trends Cell Biol 2014; 24:73-81. [PMID: 23999079 PMCID: PMC3877172 DOI: 10.1016/j.tcb.2013.07.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 07/24/2013] [Accepted: 07/25/2013] [Indexed: 10/26/2022]
Abstract
Autophagy is a conserved mechanism that is essential for cell survival in starvation. Moreover, autophagy maintains cellular health by clearing unneeded or harmful materials from cells. Autophagy proceeds by the engulfment of bulk cytosol and organelles by a cup-shaped double-membrane sheet known as the phagophore. The phagophore closes on itself to form the autophagosome, which delivers its contents to the vacuole or lysosome for degradation. A multiprotein complex comprising the protein kinase autophagy-related protein 1 (Atg1) together with Atg13, Atg17, Atg29, and Atg31 (ULK1, ATG13, FIP200, and ATG101 in humans) has a pivotal role in the earliest steps of this process. This review summarizes recent structural and ultrastructural analysis of the earliest step in autophagosome biogenesis and discusses a model in which the Atg1 complex clusters high-curvature vesicles containing the integral membrane protein Atg9, thereby initiating the phagophore.
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Affiliation(s)
- Robin E Stanley
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael J Ragusa
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - James H Hurley
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA.
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219
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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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220
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Lamb CA, Yoshimori T, Tooze SA. The autophagosome: origins unknown, biogenesis complex. Nat Rev Mol Cell Biol 2013; 14:759-74. [PMID: 24201109 DOI: 10.1038/nrm3696] [Citation(s) in RCA: 1038] [Impact Index Per Article: 86.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Healthy cells use autophagy as a general 'housekeeping' mechanism and to survive stress, including stress induced by nutrient deprivation. Autophagy is initiated at the isolation membrane (originally termed the phagophore), and the coordinated action of ATG (autophagy-related) proteins results in the expansion of this membrane to form the autophagosome. Although the biogenesis of the isolation membrane and the autophagosome is complex and incompletely understood, insight has been gained into the molecular processes involved in initiating the isolation membrane, the source from which this originates (for example, it was recently proposed that the isolation membrane forms from the mitochondria-associated endoplasmic reticulum (ER) membrane (MAM)) and the role of ATG proteins and the vesicular trafficking machinery in autophagosome formation.
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221
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The EM structure of the TRAPPIII complex leads to the identification of a requirement for COPII vesicles on the macroautophagy pathway. Proc Natl Acad Sci U S A 2013; 110:19432-7. [PMID: 24218626 DOI: 10.1073/pnas.1316356110] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The transport protein particle (TRAPP) III complex, comprising the TRAPPI complex and additional subunit Trs85, is an autophagy-specific guanine nucleotide exchange factor for the Rab GTPase Ypt1 that is recruited to the phagophore assembly site when macroautophagy is induced. We present the single-particle electron microscopy structure of TRAPPIII, which reveals that the dome-shaped Trs85 subunit associates primarily with the Trs20 subunit of TRAPPI. We further demonstrate that TRAPPIII binds the coat protein complex (COP) II coat subunit Sec23. The COPII coat facilitates the budding and targeting of ER-derived vesicles with their acceptor compartment. We provide evidence that COPII-coated vesicles and the ER-Golgi fusion machinery are needed for macroautophagy. Our results imply that TRAPPIII binds to COPII vesicles at the phagophore assembly site and that COPII vesicles may provide one of the membrane sources used in autophagosome formation. These events are conserved in yeast to mammals.
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222
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O Farrell F, Rusten TE, Stenmark H. Phosphoinositide 3-kinases as accelerators and brakes of autophagy. FEBS J 2013; 280:6322-37. [PMID: 23953235 DOI: 10.1111/febs.12486] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 08/06/2013] [Accepted: 08/07/2013] [Indexed: 12/27/2022]
Abstract
Degradation of cytoplasmic material by autophagy plays a key role in protein homeostasis and metabolic control, as well as in the removal of intracellular protein aggregates, pathogens and damaged organelles. The concept of up- or down-regulating this pathway pharmacologically in neurodegenerative diseases, infections, inflammation and cancer is therefore attractive. Among the key pharmacological targets in regulation of autophagy are the phosphoinositide 3-kinases (PI3Ks), which mediate the phosphorylation of phosphatidylinositol (PtdIns) or PtdIns 4,5-bisphosphate in the 3-position of the (phospho)inositol headgroup. The catalytic products, PtdIns 3-phosphate (PtdIns3P) and PtdIns 3,4,5-trisphosphate [PtdIns(3,4,5)P3 ], respectively, have opposing roles in autophagy. PtdIns3P, the product of class II and III PI3Ks, mediates the recruitment of specific autophagic effectors to the sites of origin of autophagic membranes and thereby plays an essential role in canonical autophagy. By contrast, PtdIns(3,4,5)P3 , the product of class I PI3Ks, triggers the target of rapamycin signalling pathway, which inhibits autophagy. In this review, we discuss the functions of class I, II and III PI3Ks in autophagy and describe the protein effectors of PtdIns3P and PtdIns(3,4,5)P3 that promote or inhibit autophagy, respectively. We also provide examples of how PI3K-mediated control of autophagy is relevant to an understanding of tumour suppression and progression.
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Affiliation(s)
- Fergal O Farrell
- Centre for Cancer Biomedicine, Faculty of Medicine, Oslo University Hospital, Montebello, Norway; Department of Biochemistry, Institute for Cancer Research, Oslo University Hospital, Montebello, Norway
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223
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Hain AUP, Bosch J. Autophagy in Plasmodium, a multifunctional pathway? Comput Struct Biotechnol J 2013; 8:e201308002. [PMID: 24688742 PMCID: PMC3962217 DOI: 10.5936/csbj.201308002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 07/18/2013] [Accepted: 07/24/2013] [Indexed: 11/23/2022] Open
Abstract
Autophagy is a catabolic process that normally utilizes the lysosome. The far-reaching implications of this system in disease are being increasingly understood. Studying autophagy is complicated by its role in cell survival and programmed cell death and the involvement of the canonical marker of autophagy, Atg8/LC3, in numerous non-autophagic roles. The malaria parasite, Plasmodium, has conserved certain aspects of the autophagic machinery but for what purpose has long remained a mystery. Major advances have recently been gained and suggest a role for Atg8 in apicoplast maintenance, degradation of heme inside the food vacuole, and possibly trafficking of proteins or organelles outside the parasite membrane. Autophagy may also participate in programmed cell death under drug treatment or as a selective tool to limit parasite load. We review the current findings and discuss discrepancies in the field of autophagy in the Plasmodium parasite.
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Affiliation(s)
- Adelaide U P Hain
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins Malaria Research Institute, Baltimore, MD 21205, United States
| | - Jürgen Bosch
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins Malaria Research Institute, Baltimore, MD 21205, United States
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224
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Sun LL, Li M, Suo F, Liu XM, Shen EZ, Yang B, Dong MQ, He WZ, Du LL. Global analysis of fission yeast mating genes reveals new autophagy factors. PLoS Genet 2013; 9:e1003715. [PMID: 23950735 PMCID: PMC3738441 DOI: 10.1371/journal.pgen.1003715] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 06/25/2013] [Indexed: 01/20/2023] Open
Abstract
Macroautophagy (autophagy) is crucial for cell survival during starvation and plays important roles in animal development and human diseases. Molecular understanding of autophagy has mainly come from the budding yeast Saccharomyces cerevisiae, and it remains unclear to what extent the mechanisms are the same in other organisms. Here, through screening the mating phenotype of a genome-wide deletion collection of the fission yeast Schizosaccharomyces pombe, we obtained a comprehensive catalog of autophagy genes in this highly tractable organism, including genes encoding three heretofore unidentified core Atg proteins, Atg10, Atg14, and Atg16, and two novel factors, Ctl1 and Fsc1. We systematically examined the subcellular localization of fission yeast autophagy factors for the first time and characterized the phenotypes of their mutants, thereby uncovering both similarities and differences between the two yeasts. Unlike budding yeast, all three Atg18/WIPI proteins in fission yeast are essential for autophagy, and we found that they play different roles, with Atg18a uniquely required for the targeting of the Atg12–Atg5·Atg16 complex. Our investigation of the two novel factors revealed unforeseen autophagy mechanisms. The choline transporter-like protein Ctl1 interacts with Atg9 and is required for autophagosome formation. The fasciclin domain protein Fsc1 localizes to the vacuole membrane and is required for autophagosome-vacuole fusion but not other vacuolar fusion events. Our study sheds new light on the evolutionary diversity of the autophagy machinery and establishes the fission yeast as a useful model for dissecting the mechanisms of autophagy. Autophagy is a eukaryotic cellular process that transports cytoplasmic contents into lysosomes/vacuoles for degradation. It has been linked to multiple human diseases, including cancer and neurodegenerative disorders. The molecular machinery of autophagy was first identified and has been best characterized in the budding yeast Saccharomyces cerevisiae, but little is known about the autophagy machinery in another important unicellular model organism, the fission yeast Schizosaccharomyces pombe. In this study, we performed an unbiased and comprehensive screening of the fission yeast autophagy genes by profiling the mating phenotypes of nearly 3000 deletion strains. Following up on the screening results, we systematically characterized both previously known and newly identified fission yeast autophagy factors by examining their localization and the phenotype of their mutants. Our analysis increased the number of experimentally defined fission yeast autophagy factors from 14 to 23, including two novel factors that act in ways different from all previously known autophagy proteins. Together, our data reveal unexpected evolutionary divergence of autophagy mechanisms and establish a new model system for unraveling the molecular details of the autophagy process.
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Affiliation(s)
- Ling-Ling Sun
- National Institute of Biological Sciences, Beijing, China
| | - Ming Li
- National Institute of Biological Sciences, Beijing, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing, China
| | - Xiao-Man Liu
- National Institute of Biological Sciences, Beijing, China
| | - En-Zhi Shen
- National Institute of Biological Sciences, Beijing, China
| | - Bing Yang
- National Institute of Biological Sciences, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China
| | - Wan-Zhong He
- National Institute of Biological Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
- * E-mail:
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225
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Graef M, Friedman JR, Graham C, Babu M, Nunnari J. ER exit sites are physical and functional core autophagosome biogenesis components. Mol Biol Cell 2013; 24:2918-31. [PMID: 23904270 PMCID: PMC3771953 DOI: 10.1091/mbc.e13-07-0381] [Citation(s) in RCA: 296] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
ERES function is required for assembly of the autophagy machinery immediately downstream of the Atg1 kinase complex and is associated with formation of autophagosomes at every stage of the process. ERES are core components of the autophagy machinery for the biogenesis of autophagosomes. Autophagy is a central homeostasis and stress response pathway conserved in all eukaryotes. One hallmark of autophagy is the de novo formation of autophagosomes. These double-membrane vesicular structures form around and deliver cargo for degradation by the vacuole/lysosome. Where and how autophagosomes form are outstanding questions. Here we show, using proteomic, cytological, and functional analyses, that autophagosomes are spatially, physically, and functionally linked to endoplasmic reticulum exit sites (ERES), which are specialized regions of the endoplasmic reticulum where COPII transport vesicles are generated. Our data demonstrate that ERES are core autophagosomal biogenesis components whose function is required for the hierarchical assembly of the autophagy machinery immediately downstream of the Atg1 kinase complex at phagophore assembly sites.
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Affiliation(s)
- Martin Graef
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616 Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
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226
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Abstract
The 3rd EMBO Conference on, "Autophagy: Molecular mechanism, physiology and pathology" organized by Anne Simonsen and Sharon Tooze, was held in May 2013 on a sea cruise along the Norwegian coastline from Bergen to Tromsø. Researchers from all corners of the world presented work covering autophagosome biogenesis, physiological regulation of autophagy, selective autophagy and disease.
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Affiliation(s)
- Sascha Martens
- Max F. Perutz Laboratories; University of Vienna; Campus Vienna Biocenter; Vienna, Austria
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