1
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Baumann V, Achleitner S, Tulli S, Schuschnig M, Klune L, Martens S. Faa1 membrane binding drives positive feedback in autophagosome biogenesis via fatty acid activation. J Cell Biol 2024; 223:e202309057. [PMID: 38573225 PMCID: PMC10993510 DOI: 10.1083/jcb.202309057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 02/14/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024] Open
Abstract
Autophagy serves as a stress response pathway by mediating the degradation of cellular material within lysosomes. In autophagy, this material is encapsulated in double-membrane vesicles termed autophagosomes, which form from precursors referred to as phagophores. Phagophores grow by lipid influx from the endoplasmic reticulum into Atg9-positive compartments and local lipid synthesis provides lipids for their expansion. How phagophore nucleation and expansion are coordinated with lipid synthesis is unclear. Here, we show that Faa1, an enzyme activating fatty acids, is recruited to Atg9 vesicles by directly binding to negatively charged membranes with a preference for phosphoinositides such as PI3P and PI4P. We define the membrane-binding surface of Faa1 and show that its direct interaction with the membrane is required for its recruitment to phagophores. Furthermore, the physiological localization of Faa1 is key for its efficient catalysis and promotes phagophore expansion. Our results suggest a positive feedback loop coupling phagophore nucleation and expansion to lipid synthesis.
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Affiliation(s)
- Verena Baumann
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
| | - Sonja Achleitner
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
- Vienna BioCenter PhD Program, A Doctoral School of the University of Vienna, Medical University of Vienna, Vienna, Austria
| | - Susanna Tulli
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
| | - Martina Schuschnig
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
| | - Lara Klune
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
| | - Sascha Martens
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
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2
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Boyle KB, Ellison CJ, Elliott PR, Schuschnig M, Grimes K, Dionne MS, Sasakawa C, Munro S, Martens S, Randow F. TECPR1 conjugates LC3 to damaged endomembranes upon detection of sphingomyelin exposure. EMBO J 2023; 42:e113012. [PMID: 37409490 PMCID: PMC10476172 DOI: 10.15252/embj.2022113012] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 06/07/2023] [Accepted: 06/14/2023] [Indexed: 07/07/2023] Open
Abstract
Invasive bacteria enter the cytosol of host cells through initial uptake into bacteria-containing vacuoles (BCVs) and subsequent rupture of the BCV membrane, thereby exposing to the cytosol intraluminal, otherwise shielded danger signals such as glycans and sphingomyelin. The detection of glycans by galectin-8 triggers anti-bacterial autophagy, but how cells sense and respond to cytosolically exposed sphingomyelin remains unknown. Here, we identify TECPR1 (tectonin beta-propeller repeat containing 1) as a receptor for cytosolically exposed sphingomyelin, which recruits ATG5 into an E3 ligase complex that mediates lipid conjugation of LC3 independently of ATG16L1. TECPR1 binds sphingomyelin through its N-terminal DysF domain (N'DysF), a feature not shared by other mammalian DysF domains. Solving the crystal structure of N'DysF, we identified key residues required for the interaction, including a solvent-exposed tryptophan (W154) essential for binding to sphingomyelin-positive membranes and the conjugation of LC3 to lipids. Specificity of the ATG5/ATG12-E3 ligase responsible for the conjugation of LC3 is therefore conferred by interchangeable receptor subunits, that is, the canonical ATG16L1 and the sphingomyelin-specific TECPR1, in an arrangement reminiscent of certain multi-subunit ubiquitin E3 ligases.
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Affiliation(s)
- Keith B Boyle
- Division of Protein and Nucleic Acid ChemistryMRC Laboratory of Molecular BiologyCambridgeUK
| | - Cara J Ellison
- Division of Protein and Nucleic Acid ChemistryMRC Laboratory of Molecular BiologyCambridgeUK
- Present address:
Department of BiochemistryUniversity of OxfordOxfordUK
| | - Paul R Elliott
- Division of Protein and Nucleic Acid ChemistryMRC Laboratory of Molecular BiologyCambridgeUK
- Present address:
Department of BiochemistryUniversity of OxfordOxfordUK
| | - Martina Schuschnig
- Max Perutz Labs, Vienna BioCenter (VBC)University of ViennaViennaAustria
| | - Krista Grimes
- MRC Centre for Molecular Bacteriology and InfectionImperial College LondonLondonUK
| | - Marc S Dionne
- MRC Centre for Molecular Bacteriology and InfectionImperial College LondonLondonUK
| | - Chihiro Sasakawa
- Medical Mycology Research CenterChiba UniversityChibaJapan
- Nippon Institute for Biological ScienceOmeJapan
| | - Sean Munro
- Division of Protein and Nucleic Acid ChemistryMRC Laboratory of Molecular BiologyCambridgeUK
| | - Sascha Martens
- Max Perutz Labs, Vienna BioCenter (VBC)University of ViennaViennaAustria
- Center for Molecular Biology, Department of Biochemistry and Cell BiologyUniversity of ViennaViennaAustria
| | - Felix Randow
- Division of Protein and Nucleic Acid ChemistryMRC Laboratory of Molecular BiologyCambridgeUK
- Department of Medicine, Addenbrooke's HospitalUniversity of CambridgeCambridgeUK
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3
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Jensen LE, Rao S, Schuschnig M, Cada AK, Martens S, Hummer G, Hurley JH. Membrane curvature sensing and stabilization by the autophagic LC3 lipidation machinery. Sci Adv 2022; 8:eadd1436. [PMID: 36516251 PMCID: PMC9750143 DOI: 10.1126/sciadv.add1436] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 11/10/2022] [Indexed: 05/28/2023]
Abstract
How the highly curved phagophore membrane is stabilized during autophagy initiation is a major open question in autophagosome biogenesis. Here, we use in vitro reconstitution on membrane nanotubes and molecular dynamics simulations to investigate how core autophagy proteins in the LC3 (Microtubule-associated proteins 1A/1B light chain 3) lipidation cascade interact with curved membranes, providing insight into their possible roles in regulating membrane shape during autophagosome biogenesis. ATG12(Autophagy-related 12)-ATG5-ATG16L1 was up to 100-fold enriched on highly curved nanotubes relative to flat membranes. At high surface density, ATG12-ATG5-ATG16L1 binding increased the curvature of the nanotubes. While WIPI2 (WD repeat domain phosphoinositide-interacting protein 2) binding directs membrane recruitment, the amphipathic helix α2 of ATG16L1 is responsible for curvature sensitivity. Molecular dynamics simulations revealed that helix α2 of ATG16L1 inserts shallowly into the membrane, explaining its curvature-sensitive binding to the membrane. These observations show how the binding of the ATG12-ATG5-ATG16L1 complex to the early phagophore rim could stabilize membrane curvature and facilitate autophagosome growth.
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Affiliation(s)
- Liv E. Jensen
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Shanlin Rao
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Martina Schuschnig
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - A. King Cada
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - Sascha Martens
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Gerhard Hummer
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main 60438, Germany
| | - James H. Hurley
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
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4
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Coudevylle N, Banaś B, Baumann V, Schuschnig M, Zawadzka-Kazimierczuk A, Koźmiński W, Martens S. Mechanism of Atg9 recruitment by Atg11 in the cytoplasm-to-vacuole targeting pathway. J Biol Chem 2022; 298:101573. [PMID: 35007534 PMCID: PMC8814668 DOI: 10.1016/j.jbc.2022.101573] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/22/2022] Open
Abstract
Autophagy is a lysosomal degradation pathway for the removal of damaged and superfluous cytoplasmic material. This is achieved by the sequestration of this cargo material within double-membrane vesicles termed autophagosomes. Autophagosome formation is mediated by the conserved autophagy machinery. In selective autophagy, this machinery including the transmembrane protein Atg9 is recruited to specific cargo material via cargo receptors and the Atg11/FIP200 scaffold protein. The molecular details of the interaction between Atg11 and Atg9 are unclear, and it is still unknown how the recruitment of Atg9 is regulated. Here we employ NMR spectroscopy of the N-terminal disordered domain of Atg9 (Atg9-NTD) to map its interaction with Atg11 revealing that it involves two short peptides both containing a PLF motif. We show that the Atg9-NTD binds to Atg11 with an affinity of about 1 μM and that both PLF motifs contribute to the interaction. Mutation of the PLF motifs abolishes the interaction of the Atg9-NTD with Atg11, reduces the recruitment of Atg9 to the precursor aminopeptidase 1 (prApe1) cargo, and blocks prApe1 transport into the vacuole by the selective autophagy-like cytoplasm-to-vacuole (Cvt) targeting pathway while not affecting bulk autophagy. Our results provide mechanistic insights into the interaction of the Atg11 scaffold with the Atg9 transmembrane protein in selective autophagy and suggest a model where only clustered Atg11 when bound to the prApe1 cargo is able to efficiently recruit Atg9 vesicles.
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Affiliation(s)
| | - Bartłomiej Banaś
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Verena Baumann
- Max Perutz Laboratories, University of Vienna, Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | | | | | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Sascha Martens
- Max Perutz Laboratories, University of Vienna, Vienna, Austria.
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5
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Turco E, Savova A, Gere F, Ferrari L, Romanov J, Schuschnig M, Martens S. Reconstitution defines the roles of p62, NBR1 and TAX1BP1 in ubiquitin condensate formation and autophagy initiation. Nat Commun 2021; 12:5212. [PMID: 34471133 PMCID: PMC8410870 DOI: 10.1038/s41467-021-25572-w] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 08/13/2021] [Indexed: 01/02/2023] Open
Abstract
The autophagic degradation of misfolded and ubiquitinated proteins is important for cellular homeostasis. In this process, which is governed by cargo receptors, ubiquitinated proteins are condensed into larger structures and subsequently become targets for the autophagy machinery. Here we employ in vitro reconstitution and cell biology to define the roles of the human cargo receptors p62/SQSTM1, NBR1 and TAX1BP1 in the selective autophagy of ubiquitinated substrates. We show that p62 is the major driver of ubiquitin condensate formation. NBR1 promotes condensate formation by equipping the p62-NBR1 heterooligomeric complex with a high-affinity UBA domain. Additionally, NBR1 recruits TAX1BP1 to the ubiquitin condensates formed by p62. While all three receptors interact with FIP200, TAX1BP1 is the main driver of FIP200 recruitment and thus the autophagic degradation of p62–ubiquitin condensates. In summary, our study defines the roles of all three receptors in the selective autophagy of ubiquitin condensates. Misfolded proteins are ubquitinated and subsequently condensed by cargo receptors for selective autophagy. Here, the authors use in vitro reconstitution to elegantly dissect how the receptors p62/SQSTM1, NBR1 and TAX1BP1 contribute to p62-ubiquitin condensate formation and degradation by autophagy.
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Affiliation(s)
- Eleonora Turco
- Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC), Vienna, Austria.
| | - Adriana Savova
- Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Flora Gere
- Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Luca Ferrari
- Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Julia Romanov
- Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Martina Schuschnig
- Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Sascha Martens
- Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC), Vienna, Austria.
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6
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Sawa-Makarska J, Baumann V, Coudevylle N, von Bülow S, Nogellova V, Abert C, Schuschnig M, Graef M, Hummer G, Martens S. Reconstitution of autophagosome nucleation defines Atg9 vesicles as seeds for membrane formation. Science 2020; 369:369/6508/eaaz7714. [PMID: 32883836 DOI: 10.1126/science.aaz7714] [Citation(s) in RCA: 136] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 05/16/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022]
Abstract
Autophagosomes form de novo in a manner that is incompletely understood. Particularly enigmatic are autophagy-related protein 9 (Atg9)-containing vesicles that are required for autophagy machinery assembly but do not supply the bulk of the autophagosomal membrane. In this study, we reconstituted autophagosome nucleation using recombinant components from yeast. We found that Atg9 proteoliposomes first recruited the phosphatidylinositol 3-phosphate kinase complex, followed by Atg21, the Atg2-Atg18 lipid transfer complex, and the E3-like Atg12-Atg5-Atg16 complex, which promoted Atg8 lipidation. Furthermore, we found that Atg2 could transfer lipids for Atg8 lipidation. In selective autophagy, these reactions could potentially be coupled to the cargo via the Atg19-Atg11-Atg9 interactions. We thus propose that Atg9 vesicles form seeds that establish membrane contact sites to initiate lipid transfer from compartments such as the endoplasmic reticulum.
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Affiliation(s)
- Justyna Sawa-Makarska
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria.
| | - Verena Baumann
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Nicolas Coudevylle
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Sören von Bülow
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Veronika Nogellova
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Christine Abert
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Martina Schuschnig
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Martin Graef
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Institute for Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Sascha Martens
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria.
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7
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Turco E, Witt M, Abert C, Bock-Bierbaum T, Su MY, Trapannone R, Sztacho M, Danieli A, Shi X, Zaffagnini G, Gamper A, Schuschnig M, Fracchiolla D, Bernklau D, Romanov J, Hartl M, Hurley JH, Daumke O, Martens S. How RB1CC1/FIP200 claws its way to autophagic engulfment of SQSTM1/p62-ubiquitin condensates. Autophagy 2019; 15:1475-1477. [PMID: 31066340 DOI: 10.1080/15548627.2019.1615306] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Macroautophagy/autophagy mediates the degradation of ubiquitinated aggregated proteins within lysosomes in a process known as aggrephagy. The cargo receptor SQSTM1/p62 condenses aggregated proteins into larger structures and links them to the nascent autophagosomal membrane (phagophore). How the condensation reaction and autophagosome formation are coupled is unclear. We recently discovered that a region of SQSTM1 containing its LIR motif directly interacts with RB1CC1/FIP200, a protein acting at early stages of autophagosome formation. Determination of the structure of the C-terminal region of RB1CC1 revealed a claw-shaped domain. Using a structure-function approach, we show that the interaction of SQSTM1 with the RB1CC1 claw domain is crucial for the productive recruitment of the autophagy machinery to ubiquitin-positive condensates and their subsequent degradation by autophagy. We also found that concentrated Atg8-family proteins on the phagophore displace RB1CC1 from SQSTM1, suggesting an intrinsic directionality in the process of autophagosome formation. Ultimately, our study reveals how the interplay of SQSTM1 and RB1CC1 couples cargo condensation to autophagosome formation.
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Affiliation(s)
- Eleonora Turco
- a Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL) , University of Vienna, Vienna BioCenter , Vienna , Austria
| | - Marie Witt
- b Crystallography , Max-Delbrück-Center for Molecular Medicine , Berlin , Germany.,c Institute of Chemistry and Biochemistry , Freie Universität Berlin , Berlin , Germany
| | - Christine Abert
- a Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL) , University of Vienna, Vienna BioCenter , Vienna , Austria
| | - Tobias Bock-Bierbaum
- b Crystallography , Max-Delbrück-Center for Molecular Medicine , Berlin , Germany
| | - Ming-Yuan Su
- d Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences , University of California , Berkeley , CA , USA.,e Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , CA , USA
| | - Riccardo Trapannone
- a Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL) , University of Vienna, Vienna BioCenter , Vienna , Austria
| | - Martin Sztacho
- a Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL) , University of Vienna, Vienna BioCenter , Vienna , Austria
| | - Alberto Danieli
- a Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL) , University of Vienna, Vienna BioCenter , Vienna , Austria
| | - Xiaoshan Shi
- d Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences , University of California , Berkeley , CA , USA
| | - Gabriele Zaffagnini
- a Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL) , University of Vienna, Vienna BioCenter , Vienna , Austria
| | - Annamaria Gamper
- a Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL) , University of Vienna, Vienna BioCenter , Vienna , Austria
| | - Martina Schuschnig
- a Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL) , University of Vienna, Vienna BioCenter , Vienna , Austria
| | - Dorotea Fracchiolla
- a Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL) , University of Vienna, Vienna BioCenter , Vienna , Austria
| | - Daniel Bernklau
- a Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL) , University of Vienna, Vienna BioCenter , Vienna , Austria
| | - Julia Romanov
- a Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL) , University of Vienna, Vienna BioCenter , Vienna , Austria
| | - Markus Hartl
- a Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL) , University of Vienna, Vienna BioCenter , Vienna , Austria
| | - James H Hurley
- d Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences , University of California , Berkeley , CA , USA.,e Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , CA , USA
| | - Oliver Daumke
- b Crystallography , Max-Delbrück-Center for Molecular Medicine , Berlin , Germany.,c Institute of Chemistry and Biochemistry , Freie Universität Berlin , Berlin , Germany
| | - Sascha Martens
- a Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL) , University of Vienna, Vienna BioCenter , Vienna , Austria
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8
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Bas L, Papinski D, Licheva M, Torggler R, Rohringer S, Schuschnig M, Kraft C. Reconstitution reveals Ykt6 as the autophagosomal SNARE in autophagosome-vacuole fusion. J Cell Biol 2018; 217:3656-3669. [PMID: 30097514 PMCID: PMC6168255 DOI: 10.1083/jcb.201804028] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 06/12/2018] [Accepted: 07/05/2018] [Indexed: 11/22/2022] Open
Abstract
Autophagy mediates the bulk degradation of cytoplasmic material, particularly during starvation. Upon the induction of autophagy, autophagosomes form a sealed membrane around cargo, fuse with a lytic compartment, and release the cargo for degradation. The mechanism of autophagosome-vacuole fusion is poorly understood, although factors that mediate other cellular fusion events have been implicated. In this study, we developed an in vitro reconstitution assay that enables systematic discovery and dissection of the players involved in autophagosome-vacuole fusion. We found that this process requires the Atg14-Vps34 complex to generate PI3P and thus recruit the Ypt7 module to autophagosomes. The HOPS-tethering complex, recruited by Ypt7, is required to prepare SNARE proteins for fusion. Furthermore, we discovered that fusion requires the R-SNARE Ykt6 on the autophagosome, together with the Q-SNAREs Vam3, Vam7, and Vti1 on the vacuole. These findings shed new light on the mechanism of autophagosome-vacuole fusion and reveal that the R-SNARE Ykt6 is required for this process.
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Affiliation(s)
- Levent Bas
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Daniel Papinski
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Mariya Licheva
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research , Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Raffaela Torggler
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria.,Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research , Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Sabrina Rohringer
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Martina Schuschnig
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Claudine Kraft
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, Vienna, Austria .,Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research , Faculty of Medicine, University of Freiburg, Freiburg, Germany
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9
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Torggler R, Papinski D, Brach T, Bas L, Schuschnig M, Pfaffenwimmer T, Rohringer S, Matzhold T, Schweida D, Brezovich A, Kraft C. Two Independent Pathways within Selective Autophagy Converge to Activate Atg1 Kinase at the Vacuole. Mol Cell 2017; 64:221-235. [PMID: 27768871 DOI: 10.1016/j.molcel.2016.09.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 08/15/2016] [Accepted: 09/07/2016] [Indexed: 12/22/2022]
Abstract
Autophagy is a potent cellular degradation pathway, and its activation needs to be tightly controlled. Cargo receptors mediate selectivity during autophagy by bringing cargo to the scaffold protein Atg11 and, in turn, to the autophagic machinery, including the central autophagy kinase Atg1. Here we show how selective autophagy is tightly regulated in space and time to prevent aberrant Atg1 kinase activation and autophagy induction. We established an induced bypass approach (iPass) that combines genetic deletion with chemically induced dimerization to evaluate the roles of Atg13 and cargo receptors in Atg1 kinase activation and selective autophagy progression. We show that Atg1 activation does not require cargo receptors, cargo-bound Atg11, or Atg13 per se. Rather, these proteins function in two independent pathways that converge to activate Atg1 at the vacuole. This pathway architecture underlies the spatiotemporal control of Atg1 kinase activity, thereby preventing inappropriate autophagosome formation.
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Affiliation(s)
- Raffaela Torggler
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Daniel Papinski
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Thorsten Brach
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Levent Bas
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Martina Schuschnig
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Thaddäus Pfaffenwimmer
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Sabrina Rohringer
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Tamara Matzhold
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - David Schweida
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Andrea Brezovich
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Claudine Kraft
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria.
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10
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Sánchez-Wandelmer J, Kriegenburg F, Rohringer S, Schuschnig M, Gómez-Sánchez R, Zens B, Abreu S, Hardenberg R, Hollenstein D, Gao J, Ungermann C, Martens S, Kraft C, Reggiori F. Atg4 proteolytic activity can be inhibited by Atg1 phosphorylation. Nat Commun 2017; 8:295. [PMID: 28821724 PMCID: PMC5562703 DOI: 10.1038/s41467-017-00302-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 06/19/2017] [Indexed: 11/09/2022] Open
Abstract
The biogenesis of autophagosomes depends on the conjugation of Atg8-like proteins with phosphatidylethanolamine. Atg8 processing by the cysteine protease Atg4 is required for its covalent linkage to phosphatidylethanolamine, but it is also necessary for Atg8 deconjugation from this lipid to release it from membranes. How these two cleavage steps are coordinated is unknown. Here we show that phosphorylation by Atg1 inhibits Atg4 function, an event that appears to exclusively occur at the site of autophagosome biogenesis. These results are consistent with a model where the Atg8-phosphatidylethanolamine pool essential for autophagosome formation is protected at least in part by Atg4 phosphorylation by Atg1 while newly synthesized cytoplasmic Atg8 remains susceptible to constitutive Atg4 processing.The protease Atg4 mediates Atg8 lipidation, required for autophagosome biogenesis, but also triggers Atg8 release from the membranes, however is unclear how these steps are coordinated. Here the authors show that phosphorylation by Atg1 inhibits Atg4 at autophagosome formation sites.
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Affiliation(s)
- Jana Sánchez-Wandelmer
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Heidelberglaan 100, 8564 CX, Utrecht, The Netherlands
| | - Franziska Kriegenburg
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Heidelberglaan 100, 8564 CX, Utrecht, The Netherlands
| | - Sabrina Rohringer
- Max F. Perutz Laboratories, University of Vienna, 1030, Vienna, Austria
| | | | - Rubén Gómez-Sánchez
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Heidelberglaan 100, 8564 CX, Utrecht, The Netherlands
| | - Bettina Zens
- Max F. Perutz Laboratories, University of Vienna, 1030, Vienna, Austria
| | - Susana Abreu
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Heidelberglaan 100, 8564 CX, Utrecht, The Netherlands
| | - Ralph Hardenberg
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - David Hollenstein
- Max F. Perutz Laboratories, University of Vienna, 1030, Vienna, Austria
| | - Jieqiong Gao
- University of Osnabrück, Department of Biology/Chemistry, Biochemistry section, Barbarastrasse 13, 49076, Osnabrück, Germany
| | - Christian Ungermann
- University of Osnabrück, Department of Biology/Chemistry, Biochemistry section, Barbarastrasse 13, 49076, Osnabrück, Germany
| | - Sascha Martens
- Max F. Perutz Laboratories, University of Vienna, 1030, Vienna, Austria
| | - Claudine Kraft
- Max F. Perutz Laboratories, University of Vienna, 1030, Vienna, Austria
| | - Fulvio Reggiori
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands. .,Department of Cell Biology, University Medical Center Utrecht, Heidelberglaan 100, 8564 CX, Utrecht, The Netherlands.
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11
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Abreu S, Kriegenburg F, Gómez-Sánchez R, Mari M, Sánchez-Wandelmer J, Skytte Rasmussen M, Soares Guimarães R, Zens B, Schuschnig M, Hardenberg R, Peter M, Johansen T, Kraft C, Martens S, Reggiori F. Conserved Atg8 recognition sites mediate Atg4 association with autophagosomal membranes and Atg8 deconjugation. EMBO Rep 2017; 18:765-780. [PMID: 28330855 DOI: 10.15252/embr.201643146] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 02/12/2017] [Accepted: 02/20/2017] [Indexed: 12/12/2022] Open
Abstract
Deconjugation of the Atg8/LC3 protein family members from phosphatidylethanolamine (PE) by Atg4 proteases is essential for autophagy progression, but how this event is regulated remains to be understood. Here, we show that yeast Atg4 is recruited onto autophagosomal membranes by direct binding to Atg8 via two evolutionarily conserved Atg8 recognition sites, a classical LC3-interacting region (LIR) at the C-terminus of the protein and a novel motif at the N-terminus. Although both sites are important for Atg4-Atg8 interaction in vivo, only the new N-terminal motif, close to the catalytic center, plays a key role in Atg4 recruitment to autophagosomal membranes and specific Atg8 deconjugation. We thus propose a model where Atg4 activity on autophagosomal membranes depends on the cooperative action of at least two sites within Atg4, in which one functions as a constitutive Atg8 binding module, while the other has a preference toward PE-bound Atg8.
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Affiliation(s)
- Susana Abreu
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Franziska Kriegenburg
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rubén Gómez-Sánchez
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Muriel Mari
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jana Sánchez-Wandelmer
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mads Skytte Rasmussen
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Rodrigo Soares Guimarães
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bettina Zens
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Martina Schuschnig
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Ralph Hardenberg
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Matthias Peter
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Terje Johansen
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Claudine Kraft
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Sascha Martens
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Fulvio Reggiori
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands .,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
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12
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Brezovich A, Schuschnig M, Ammerer G, Kraft C. An in vivo detection system for transient and low-abundant protein interactions and their kinetics in budding yeast. Yeast 2015; 32:355-65. [PMID: 25582094 PMCID: PMC4949564 DOI: 10.1002/yea.3063] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/22/2014] [Accepted: 12/24/2014] [Indexed: 11/20/2022] Open
Abstract
Methylation tracking (M‐Track) is a protein‐proximity assay in Saccharomyces cerevisiae, allowing the detection of transient protein–protein interactions in living cells. The bait protein is fused to a histone lysine methyl transferase and the prey protein to a methylation acceptor peptide derived from histone 3. Upon interaction, the histone 3 fragment is stably methylated on lysine 9 and can be detected by methylation‐specific antibodies. Since methylation marking is irreversible in budding yeast and only takes place in living cells, the occurrence of artifacts during cell lysate preparation is greatly reduced, leading to a more accurate representation of native interactions. So far, this method has been limited to highly abundant or overexpressed proteins. However, many proteins of interest are low‐abundant, and overexpression of proteins may interfere with their function, leading to an artificial situation. Here we report the generation of a toolbox including a novel cleavage‐enrichment system for the analysis of very low‐abundant proteins at their native expression levels. In addition, we developed a system for the parallel analysis of two prey proteins in a single cell, as well as an inducible methylation system. The inducible system allows precise control over the time during which the interaction is detected and can be used to determine interaction kinetics. Furthermore, we generated a set of constructs facilitating the cloning‐free genomic tagging of proteins at their endogenous locus by homologous recombination, and their expression from centromeric plasmids. GenBank submissions: pCK900; KM407502, pCK901; KM407503, pCK902; KM407504, pCK903; KM407505, pCK904; KM407506, pCK905; KM407507, pCK906; KM407508, pCK907; KM407509, pCK908; KM407510, pCK909; KM407511, pCK910; KM407512, pCK911; KM407513. © 2015 The Authors. Yeast published by John Wiley & Sons Ltd.
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Affiliation(s)
- Andrea Brezovich
- Max F. Perutz Laboratories, University of Vienna, Vienna, A-1030, Austria
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13
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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 DOI: 10.15252/embr.201438932] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [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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14
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Papinski D, Schuschnig M, Reiter W, Wilhelm L, Barnes C, Maiolica A, Hansmann I, Pfaffenwimmer T, Kijanska M, Stoffel I, Lee S, Brezovich A, Lou J, Turk B, 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. [PMCID: PMC4077220 DOI: 10.1016/j.molcel.2014.01.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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15
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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: 231] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [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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