151
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Methods to Monitor and Quantify Autophagy in the Social Amoeba Dictyostelium discoideum. Cells 2017; 6:cells6030018. [PMID: 28671610 PMCID: PMC5617964 DOI: 10.3390/cells6030018] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/27/2017] [Accepted: 06/28/2017] [Indexed: 12/30/2022] Open
Abstract
Autophagy is a eukaryotic catabolic pathway that degrades and recycles cellular components to maintain homeostasis. It can target protein aggregates, superfluous biomolecular complexes, dysfunctional and damaged organelles, as well as pathogenic intracellular microbes. Autophagy is a dynamic process in which the different stages from initiation to final degradation of cargo are finely regulated. Therefore, the study of this process requires the use of a palette of techniques, which are continuously evolving and whose interpretation is not trivial. Here, we present the social amoeba Dictyostelium discoideum as a relevant model to study autophagy. Several methods have been developed based on the tracking and observation of autophagosomes by microscopy, analysis of changes in expression of autophagy genes and proteins, and examination of the autophagic flux with various techniques. In this review, we discuss the pros and cons of the currently available techniques to assess autophagy in this organism.
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152
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Galluzzi L, Baehrecke EH, Ballabio A, Boya P, Bravo-San Pedro JM, Cecconi F, Choi AM, Chu CT, Codogno P, Colombo MI, Cuervo AM, Debnath J, Deretic V, Dikic I, Eskelinen EL, Fimia GM, Fulda S, Gewirtz DA, Green DR, Hansen M, Harper JW, Jäättelä M, Johansen T, Juhasz G, Kimmelman AC, Kraft C, Ktistakis NT, Kumar S, Levine B, Lopez-Otin C, Madeo F, Martens S, Martinez J, Melendez A, Mizushima N, Münz C, Murphy LO, Penninger JM, Piacentini M, Reggiori F, Rubinsztein DC, Ryan KM, Santambrogio L, Scorrano L, Simon AK, Simon HU, Simonsen A, Tavernarakis N, Tooze SA, Yoshimori T, Yuan J, Yue Z, Zhong Q, Kroemer G. Molecular definitions of autophagy and related processes. EMBO J 2017; 36:1811-1836. [PMID: 28596378 PMCID: PMC5494474 DOI: 10.15252/embj.201796697] [Citation(s) in RCA: 1220] [Impact Index Per Article: 152.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 03/21/2017] [Accepted: 03/22/2017] [Indexed: 12/15/2022] Open
Abstract
Over the past two decades, the molecular machinery that underlies autophagic responses has been characterized with ever increasing precision in multiple model organisms. Moreover, it has become clear that autophagy and autophagy-related processes have profound implications for human pathophysiology. However, considerable confusion persists about the use of appropriate terms to indicate specific types of autophagy and some components of the autophagy machinery, which may have detrimental effects on the expansion of the field. Driven by the overt recognition of such a potential obstacle, a panel of leading experts in the field attempts here to define several autophagy-related terms based on specific biochemical features. The ultimate objective of this collaborative exchange is to formulate recommendations that facilitate the dissemination of knowledge within and outside the field of autophagy research.
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Affiliation(s)
- Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
- Université Paris Descartes/Paris V, Paris, France
| | - Eric H Baehrecke
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Medical Genetics, Department of Pediatrics, Federico II University, Naples, Italy
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Patricia Boya
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - José Manuel Bravo-San Pedro
- Université Paris Descartes/Paris V, Paris, France
- Université Pierre et Marie Curie/Paris VI, Paris, France
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
- INSERM, U1138, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France
| | - Francesco Cecconi
- Department of Biology, University of Tor Vergata, Rome, Italy
- Unit of Cell Stress and Survival, Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Pediatric Hematology and Oncology, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Augustine M Choi
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Charleen T Chu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Patrice Codogno
- Université Paris Descartes/Paris V, Paris, France
- Institut Necker-Enfants Malades (INEM), Paris, France
- INSERM, U1151, Paris, France
- CNRS, UMR8253, Paris, France
| | - Maria Isabel Colombo
- Laboratorio de Biología Celular y Molecular, Instituto de Histología y Embriología (IHEM)-CONICET, Mendoza, Argentina
- Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Ana Maria Cuervo
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jayanta Debnath
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Vojo Deretic
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Ivan Dikic
- Institute of Biochemistry II, School of Medicine, Goethe University Frankfurt, Frankfurt, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt Main, Germany
- Department of Immunology and Medical Genetics, University of Split School of Medicine, Split, Croatia
| | | | - Gian Maria Fimia
- National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
| | - Simone Fulda
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University, Frankfurt, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David A Gewirtz
- Department of Pharmacology and Toxicology and Medicine, Virginia Commonwealth University, Richmond, VA, USA
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Malene Hansen
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Marja Jäättelä
- Cell Death and Metabolism Unit, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Terje Johansen
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Gabor Juhasz
- Department of Anatomy, Cell and Developmental Biology, Eotvos Lorand University, Budapest, Hungary
- Institute of Genetics, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Alec C Kimmelman
- Department of Radiation Oncology, Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY, USA
| | - Claudine Kraft
- Max F. Perutz Laboratories, Department of Biochemistry and Cell Biology, Vienna Biocenter, University of Vienna, Vienna, Austria
| | | | - Sharad Kumar
- Centre for Cancer Biology, University of South Australia, Adelaide, SA, Australia
| | - Beth Levine
- Center for Autophagy Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute (HHMI), Dallas, TX, USA
| | - Carlos Lopez-Otin
- Department de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
- Centro de Investigación en Red de Cáncer, Oviedo, Spain
| | - Frank Madeo
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Sascha Martens
- Max F. Perutz Laboratories, Department of Biochemistry and Cell Biology, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Jennifer Martinez
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Alicia Melendez
- Department of Biology, Queens College, Queens, NY, USA
- Graduate Center, City University of New York, New York, NY, USA
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Christian Münz
- Viral Immunobiology, Institute of Experimental Immunology, University of Zürich, Zurich, Switzerland
| | - Leon O Murphy
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Campus Vienna BioCentre, Vienna, Austria
| | - Mauro Piacentini
- Department of Biology, University of Tor Vergata, Rome, Italy
- National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
| | - Fulvio Reggiori
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - David C Rubinsztein
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Kevin M Ryan
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Laura Santambrogio
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Luca Scorrano
- Department of Biology, University of Padova, Padova, Italy
- Venetian Institute of Molecular Medicine, Padova, Italy
| | - Anna Katharina Simon
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Hans-Uwe Simon
- Institute of Pharmacology, University of Bern, Bern, Switzerland
| | - Anne Simonsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
- Department of Basic Sciences, Faculty of Medicine, University of Crete, Heraklion, Greece
| | - Sharon A Tooze
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, London, UK
| | - Tamotsu Yoshimori
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences Osaka University, Osaka, Japan
| | - Junying Yuan
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Ludwig Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Zhenyu Yue
- Department of Neurology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Qing Zhong
- Center for Autophagy Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guido Kroemer
- Université Paris Descartes/Paris V, Paris, France
- Université Pierre et Marie Curie/Paris VI, Paris, France
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
- INSERM, U1138, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France
- Department of Women's and Children's Health, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
- Pôle de Biologie, Hopitâl Européen George Pompidou, AP-HP, Paris, France
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153
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Bakula D, Müller AJ, Zuleger T, Takacs Z, Franz-Wachtel M, Thost AK, Brigger D, Tschan MP, Frickey T, Robenek H, Macek B, Proikas-Cezanne T. WIPI3 and WIPI4 β-propellers are scaffolds for LKB1-AMPK-TSC signalling circuits in the control of autophagy. Nat Commun 2017; 8:15637. [PMID: 28561066 PMCID: PMC5460038 DOI: 10.1038/ncomms15637] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 04/13/2017] [Indexed: 12/31/2022] Open
Abstract
Autophagy is controlled by AMPK and mTOR, both of which associate with ULK1 and control the production of phosphatidylinositol 3-phosphate (PtdIns3P), a prerequisite for autophagosome formation. Here we report that WIPI3 and WIPI4 scaffold the signal control of autophagy upstream of PtdIns3P production and have a role in the PtdIns3P effector function of WIPI1-WIPI2 at nascent autophagosomes. In response to LKB1-mediated AMPK stimulation, WIPI4-ATG2 is released from a WIPI4-ATG2/AMPK-ULK1 complex and translocates to nascent autophagosomes, controlling their size, to which WIPI3, in complex with FIP200, also contributes. Upstream, WIPI3 associates with AMPK-activated TSC complex at lysosomes, regulating mTOR. Our WIPI interactome analysis reveals the scaffold functions of WIPI proteins interconnecting autophagy signal control and autophagosome formation. Our functional kinase screen uncovers a novel regulatory link between LKB1-mediated AMPK stimulation that produces a direct signal via WIPI4, and we show that the AMPK-related kinases NUAK2 and BRSK2 regulate autophagy through WIPI4. During autophagy, AMPK and mTOR associate with ULK1 and regulate phosphatidylinositol 3-phosphate (PtdIns3P) production that mediates autophagosome formation via WIPI proteins. Here the authors show WIPI3 and WIPI4 have a scaffolding function upstream of PtdIns3P production and have a role in the PtdIns3P effector function of WIPI1-WIPI2 at nascent autophagosomes.
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Affiliation(s)
- Daniela Bakula
- Department of Molecular Biology, Interfaculty Institute of Cell Biology, Eberhard Karls University Tuebingen, D-72076 Tuebingen, Germany.,International Max Planck Research School 'From Molecules to Organisms', Max Planck Institute for Developmental Biology and Eberhard Karls University Tuebingen, D-72076 Tuebingen, Germany
| | - Amelie J Müller
- Department of Molecular Biology, Interfaculty Institute of Cell Biology, Eberhard Karls University Tuebingen, D-72076 Tuebingen, Germany.,International Max Planck Research School 'From Molecules to Organisms', Max Planck Institute for Developmental Biology and Eberhard Karls University Tuebingen, D-72076 Tuebingen, Germany
| | - Theresia Zuleger
- Department of Molecular Biology, Interfaculty Institute of Cell Biology, Eberhard Karls University Tuebingen, D-72076 Tuebingen, Germany
| | - Zsuzsanna Takacs
- Department of Molecular Biology, Interfaculty Institute of Cell Biology, Eberhard Karls University Tuebingen, D-72076 Tuebingen, Germany.,International Max Planck Research School 'From Molecules to Organisms', Max Planck Institute for Developmental Biology and Eberhard Karls University Tuebingen, D-72076 Tuebingen, Germany
| | - Mirita Franz-Wachtel
- Proteome Center Tuebingen, Interfaculty Institute of Cell Biology, Eberhard Karls University Tuebingen, D-72076 Tuebingen, Germany
| | - Ann-Katrin Thost
- Department of Molecular Biology, Interfaculty Institute of Cell Biology, Eberhard Karls University Tuebingen, D-72076 Tuebingen, Germany
| | - Daniel Brigger
- Division of Experimental Pathology, Institute of Pathology, University of Bern, CH-3008 Bern, Switzerland
| | - Mario P Tschan
- Division of Experimental Pathology, Institute of Pathology, University of Bern, CH-3008 Bern, Switzerland
| | - Tancred Frickey
- Department of Biology, Applied Bioinformatics, Konstanz University, D-78457 Konstanz, Germany
| | - Horst Robenek
- Institute of Experimental Musculoskeletal Medicine, University Hospital Muenster, D-48149 Muenster, Germany
| | - Boris Macek
- International Max Planck Research School 'From Molecules to Organisms', Max Planck Institute for Developmental Biology and Eberhard Karls University Tuebingen, D-72076 Tuebingen, Germany.,Proteome Center Tuebingen, Interfaculty Institute of Cell Biology, Eberhard Karls University Tuebingen, D-72076 Tuebingen, Germany
| | - Tassula Proikas-Cezanne
- Department of Molecular Biology, Interfaculty Institute of Cell Biology, Eberhard Karls University Tuebingen, D-72076 Tuebingen, Germany.,International Max Planck Research School 'From Molecules to Organisms', Max Planck Institute for Developmental Biology and Eberhard Karls University Tuebingen, D-72076 Tuebingen, Germany
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154
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Vanhauwaert R, Kuenen S, Masius R, Bademosi A, Manetsberger J, Schoovaerts N, Bounti L, Gontcharenko S, Swerts J, Vilain S, Picillo M, Barone P, Munshi ST, de Vrij FM, Kushner SA, Gounko NV, Mandemakers W, Bonifati V, Meunier FA, Soukup SF, Verstreken P. The SAC1 domain in synaptojanin is required for autophagosome maturation at presynaptic terminals. EMBO J 2017; 36:1392-1411. [PMID: 28331029 DOI: 10.15252/embj.201695773] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 02/25/2017] [Accepted: 03/01/2017] [Indexed: 11/09/2022] Open
Abstract
Presynaptic terminals are metabolically active and accrue damage through continuous vesicle cycling. How synapses locally regulate protein homeostasis is poorly understood. We show that the presynaptic lipid phosphatase synaptojanin is required for macroautophagy, and this role is inhibited by the Parkinson's disease mutation R258Q. Synaptojanin drives synaptic endocytosis by dephosphorylating PI(4,5)P2, but this function appears normal in SynaptojaninRQ knock-in flies. Instead, R258Q affects the synaptojanin SAC1 domain that dephosphorylates PI(3)P and PI(3,5)P2, two lipids found in autophagosomal membranes. Using advanced imaging, we show that SynaptojaninRQ mutants accumulate the PI(3)P/PI(3,5)P2-binding protein Atg18a on nascent synaptic autophagosomes, blocking autophagosome maturation at fly synapses and in neurites of human patient induced pluripotent stem cell-derived neurons. Additionally, we observe neurodegeneration, including dopaminergic neuron loss, in SynaptojaninRQ flies. Thus, synaptojanin is essential for macroautophagy within presynaptic terminals, coupling protein turnover with synaptic vesicle cycling and linking presynaptic-specific autophagy defects to Parkinson's disease.
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Affiliation(s)
- Roeland Vanhauwaert
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), KU Leuven, Leuven, Belgium
| | - Sabine Kuenen
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), KU Leuven, Leuven, Belgium
| | - Roy Masius
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Adekunle Bademosi
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Julia Manetsberger
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), KU Leuven, Leuven, Belgium
| | - Nils Schoovaerts
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), KU Leuven, Leuven, Belgium
| | - Laura Bounti
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), KU Leuven, Leuven, Belgium
| | - Serguei Gontcharenko
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), KU Leuven, Leuven, Belgium
| | - Jef Swerts
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), KU Leuven, Leuven, Belgium
| | - Sven Vilain
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), KU Leuven, Leuven, Belgium
| | - Marina Picillo
- Department of Medicine and Surgery, Center for Neurodegenerative Diseases (CEMAND), University of Salerno, Salerno, Italy
| | - Paolo Barone
- Department of Medicine and Surgery, Center for Neurodegenerative Diseases (CEMAND), University of Salerno, Salerno, Italy
| | | | - Femke Ms de Vrij
- Department of Psychiatry, Erasmus MC, Rotterdam, The Netherlands
| | - Steven A Kushner
- Department of Psychiatry, Erasmus MC, Rotterdam, The Netherlands
| | - Natalia V Gounko
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), KU Leuven, Leuven, Belgium.,Electron Microscopy Platform, VIB Bio-Imaging Core, Leuven, Belgium
| | - Wim Mandemakers
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Vincenzo Bonifati
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Frederic A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Sandra-Fausia Soukup
- VIB Center for Brain & Disease Research, Leuven, Belgium .,Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), KU Leuven, Leuven, Belgium
| | - Patrik Verstreken
- VIB Center for Brain & Disease Research, Leuven, Belgium .,Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), KU Leuven, Leuven, Belgium
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155
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De Craene JO, Bertazzi DL, Bär S, Friant S. Phosphoinositides, Major Actors in Membrane Trafficking and Lipid Signaling Pathways. Int J Mol Sci 2017; 18:ijms18030634. [PMID: 28294977 PMCID: PMC5372647 DOI: 10.3390/ijms18030634] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/02/2017] [Accepted: 03/06/2017] [Indexed: 11/30/2022] Open
Abstract
Phosphoinositides are lipids involved in the vesicular transport of proteins and lipids between the different compartments of eukaryotic cells. They act by recruiting and/or activating effector proteins and thus are involved in regulating various cellular functions, such as vesicular budding, membrane fusion and cytoskeleton dynamics. Although detected in small concentrations in membranes, their role is essential to cell function, since imbalance in their concentrations is a hallmark of many cancers. Their synthesis involves phosphorylating/dephosphorylating positions D3, D4 and/or D5 of their inositol ring by specific lipid kinases and phosphatases. This process is tightly regulated and specific to the different intracellular membranes. Most enzymes involved in phosphoinositide synthesis are conserved between yeast and human, and their loss of function leads to severe diseases (cancer, myopathy, neuropathy and ciliopathy).
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Affiliation(s)
- Johan-Owen De Craene
- Department of Molecular and Cellular Genetics, Université de Strasbourg, CNRS, GMGM UMR 7156, F-67000 Strasbourg, France.
| | - Dimitri L Bertazzi
- Department of Molecular and Cellular Genetics, Université de Strasbourg, CNRS, GMGM UMR 7156, F-67000 Strasbourg, France.
| | - Séverine Bär
- Department of Molecular and Cellular Genetics, Université de Strasbourg, CNRS, GMGM UMR 7156, F-67000 Strasbourg, France.
| | - Sylvie Friant
- Department of Molecular and Cellular Genetics, Université de Strasbourg, CNRS, GMGM UMR 7156, F-67000 Strasbourg, France.
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156
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Hasegawa J, Strunk BS, Weisman LS. PI5P and PI(3,5)P 2: Minor, but Essential Phosphoinositides. Cell Struct Funct 2017; 42:49-60. [PMID: 28302928 DOI: 10.1247/csf.17003] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In most eukaryotes, phosphoinositides (PIs) have crucial roles in multiple cellular functions. Although the cellular levels of phosphatidylinositol 5-phosphate (PI5P) and phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) are extremely low relative to some other PIs, emerging evidence demonstrates that both lipids are crucial for the endocytic pathway, intracellular signaling, and adaptation to stress. Mutations that causes defects in the biosynthesis of PI5P and PI(3,5)P2 are linked to human diseases including neurodegenerative disorders. Here, we review recent findings on cellular roles of PI5P and PI(3,5)P2, as well as the pathophysiological importance of these lipids.Key words: Phosphoinositides, Membrane trafficking, Endocytosis, Vacuoles/Lysosomes, Fab1/PIKfyve.
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157
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Wang L, Huang J, Pang S, Qin X, Qi Z, Hawley RG, Yan B. Genetic analysis of the ATG16L1 gene promoter in sporadic Parkinson's disease. Neurosci Lett 2017; 646:30-35. [PMID: 28279708 DOI: 10.1016/j.neulet.2017.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/03/2017] [Indexed: 11/25/2022]
Abstract
Parkinson's disease (PD) is a common and progressive neurodegenerative disease in which the majority of cases arise sporadically. Sporadic PD is caused by the interactions of genetic and environmental factors. To date, genetic causes for sporadic PD remain largely unknown. Autophagy, a highly conserved cellular process, has been implicated in PD pathogenesis. We speculated that genetic variants in autophagy-related genes (ATG) that regulate gene expression may contribute to PD development. In our previous studies, we have identified several functional DNA sequence variants (DSVs) in the ATG5, ATG7 and LC3 genes in sporadic PD patients. In this study, we further genetically and functionally analyzed the promoter of the ATG16L1 gene, a critical gene for autophagosome formation, in groups of sporadic PD patients and ethnic-matched healthy controls. One novel heterozygous DSV, 233251432C>T, was found in one PD patient. Functionally, this DSV did not affect the transcriptional activity of the ATG16L1 gene promoter in human dopaminergic SH-SY5Y cells. Two heterozygous DSVs including one SNP, 233251286G>A (rs539735288) and 233251582C>T, were found only in controls. In addition, five other SNPs were found in both PD patients and controls. Taken together, the data suggested that genetic variants within the ATG16L1 gene promoter were not a risk factor for sporadic PD development.
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Affiliation(s)
- Lixia Wang
- Center for Reproductive Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong 272029, China
| | - Jian Huang
- Shandong Provincial Sino-US Cooperation Center for Translational Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, 272029, China
| | - Shuchao Pang
- Shandong Provincial Sino-US Cooperation Center for Translational Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, 272029, China
| | - Xianyun Qin
- Shandong Provincial Sino-US Cooperation Center for Translational Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, 272029, China
| | - Ziyou Qi
- Division of Neurology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong 272029, China
| | - Robert G Hawley
- Shandong Provincial Sino-US Cooperation Center for Translational Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, 272029, China; Department of Anatomy and Regenerative Biology, The George Washington University, 2300 Eye Street, NW, Washington, DC 20037, USA.
| | - Bo Yan
- Shandong Provincial Sino-US Cooperation Center for Translational Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, 272029, China; Department of Anatomy and Regenerative Biology, The George Washington University, 2300 Eye Street, NW, Washington, DC 20037, USA.
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158
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Fluorescence-Based Assays to Analyse Phosphatidylinositol 5-Phosphate in Autophagy. Methods Enzymol 2017. [PMID: 28253963 DOI: 10.1016/bs.mie.2016.09.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Autophagosome formation is stimulated by VPS34-dependent PI(3)P formation and by alternative VPS34-independent pathways. We recently described that PI(5)P regulates autophagosome biogenesis and rescues autophagy in VPS34-inactivated cells, suggesting that PI(5)P contributes to canonical autophagy. Our analysis revealed a hitherto unknown functional interplay between PIKfyve and PIPK type II in controlling PI(5)P levels in the context of autophagy. Among phosphoinositides, visualization of PI(5)P in intact cells has remained difficult. While PI(5)P has been implicated in signaling pathways, chromatin organization, bacterial invasion, and cytoskeletal remodeling, our study is the first report showing PI(5)P localization on autophagosomes and early autophagosomal structures when autophagy is induced by nutrient deprivation (amino acids or glucose starvation). We provided a detailed analysis of PI(5)P distribution by the use of super-resolution structured illuminated microscopy. Here, we present a set of tools for detection of PI(5)P during autophagy by confocal microscopy, live-cell imaging, and super-resolution microscopy.
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159
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Yakhine-Diop S, Martínez-Chacón G, González-Polo R, Fuentes J, Niso-Santano M. Fluorescent FYVE Chimeras to Quantify PtdIns3P Synthesis During Autophagy. Methods Enzymol 2017; 587:257-269. [DOI: 10.1016/bs.mie.2016.09.060] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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160
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Schoijet AC, Sternlieb T, Alonso GD. The Phosphatidylinositol 3-kinase Class III Complex Containing TcVps15 and TcVps34 Participates in Autophagy in Trypanosoma cruzi. J Eukaryot Microbiol 2016; 64:308-321. [PMID: 27603757 DOI: 10.1111/jeu.12367] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 08/26/2016] [Accepted: 08/26/2016] [Indexed: 01/05/2023]
Abstract
Autophagy is a degradative process by which eukaryotic cells digest their own components to provide aminoacids that may function as energy source under nutritional stress conditions. There is experimental evidence for autophagy in parasitic protists belonging to the family Trypanosomatidae. However, few proteins implicated in this process have been characterized so far in these parasites. Moreover, it has been shown that autophagy is involved in Trypanosoma cruzi differentiation and thus might have a role in pathogenicity. Here, we report the cloning and biochemical characterization of TcVps15. In addition, we demonstrate that TcVps15 interact with the PI3K TcVps34 and that both proteins associate with cellular membranes. Under nutritional stress conditions, TcVps15 and TcVps34 modify their subcellular distribution showing a partial co-localization in autophagosomes with TcAtg8.1 and using an active site TcVps15-mutated version (TcVps15-K219D-HA) we demonstrated that this relocalization depends on the TcVps15 catalytic activity. Overexpression of TcVps15-HA and TcVps15-K219D-HA also leads to increased accumulation of monodansylcadaverine (MDC) in autophagic vacuoles under nutritional stress conditions compared to wild-type cells. In addition, the MDC-specific activity shows to be significantly higher in TcVps15-HA overexpressing cells when compared with TcVps15-K219D-HA. Our results reveal for the first time a role of TcVps15 as a key regulator of TcVps34 enzymatic activity and implicate the TcVps15-Vps34 complex in autophagy in T. cruzi, exposing a new key pathway to explore novel chemotherapeutic targets.
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Affiliation(s)
- Alejandra C Schoijet
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres", Vuelta de Obligado 2490, Buenos Aires, C1428ADN, Argentina.,Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Intendente Güiraldes 2160, C1428EGA CABA, Argentina
| | - Tamara Sternlieb
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres", Vuelta de Obligado 2490, Buenos Aires, C1428ADN, Argentina
| | - Guillermo D Alonso
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres", Vuelta de Obligado 2490, Buenos Aires, C1428ADN, Argentina.,Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Intendente Güiraldes 2160, C1428EGA CABA, Argentina
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161
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Botti-Millet J, Nascimbeni AC, Dupont N, Morel E, Codogno P. Fine-tuning autophagy: from transcriptional to posttranslational regulation. Am J Physiol Cell Physiol 2016; 311:C351-62. [DOI: 10.1152/ajpcell.00129.2016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 06/20/2016] [Indexed: 12/13/2022]
Abstract
Macroautophagy (hereafter called autophagy) is a vacuolar lysosomal pathway for degradation of intracellular material in eukaryotic cells. Autophagy plays crucial roles in tissue homeostasis, in adaptation to stress situations, and in immune and inflammatory responses. Alteration of autophagy is associated with cancer, diabetes and obesity, cardiovascular disease, neurodegenerative disease, autoimmune disease, infection, and chronic inflammatory disease. Autophagy is controlled by autophagy-related (ATG) proteins that act in a coordinated manner to build up the initial autophagic vacuole named the autophagosome. It is now known that the activities of ATG proteins are modulated by posttranslational modifications such as phosphorylation, ubiquitination, and acetylation. Moreover, transcriptional and epigenetic controls are involved in the regulation of autophagy in stress situations. Here we summarize and discuss how posttranslational modifications and transcriptional and epigenetic controls regulate the involvement of autophagy in the proteostasis network.
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Affiliation(s)
- Joëlle Botti-Millet
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151-Centre National de la Recherche Scientifique UMR 8253, Paris, France
- Université Paris Diderot-Sorbonne Paris Cité, Paris, France; and
| | - Anna Chiara Nascimbeni
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151-Centre National de la Recherche Scientifique UMR 8253, Paris, France
- Université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Nicolas Dupont
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151-Centre National de la Recherche Scientifique UMR 8253, Paris, France
- Université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Etienne Morel
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151-Centre National de la Recherche Scientifique UMR 8253, Paris, France
- Université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Patrice Codogno
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151-Centre National de la Recherche Scientifique UMR 8253, Paris, France
- Université Paris Descartes-Sorbonne Paris Cité, Paris, France
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162
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Shatz O, Holland P, Elazar Z, Simonsen A. Complex Relations Between Phospholipids, Autophagy, and Neutral Lipids. Trends Biochem Sci 2016; 41:907-923. [PMID: 27595473 DOI: 10.1016/j.tibs.2016.08.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/28/2016] [Accepted: 08/01/2016] [Indexed: 11/27/2022]
Abstract
Research in the past decade has established the importance of autophagy to a large number of physiological processes and pathophysiological conditions. Originally characterized as a pathway responsible for protein turnover and recycling of amino acids in times of starvation, it has been recently recognized as a major regulator of lipid metabolism. Different lipid species play various roles in the regulation of autophagosomal biogenesis, both as membrane constituents and as signaling platforms. Distinct types of autophagy, in turn, facilitate specific steps in metabolic pathways of different lipid classes, best exemplified in recent studies on neutral lipid dynamics. We review the emerging notion of intricate links between phospholipids, autophagy, and neutral lipids.
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Affiliation(s)
- Oren Shatz
- Department of Biomolecular Sciences, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Petter Holland
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
| | - Zvulun Elazar
- Department of Biomolecular Sciences, Weizmann Institute of Science, 76100 Rehovot, Israel.
| | - Anne Simonsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway.
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163
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Ktistakis NT, Tooze SA. Digesting the Expanding Mechanisms of Autophagy. Trends Cell Biol 2016; 26:624-635. [PMID: 27050762 DOI: 10.1016/j.tcb.2016.03.006] [Citation(s) in RCA: 271] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/03/2016] [Accepted: 03/14/2016] [Indexed: 12/17/2022]
Abstract
Autophagy is a catabolic 'self-eating' pathway that is emerging as a crucial integration point in cell physiology. With its own set of genes, the autophagy pathway communicates with virtually all signalling networks and organelles. Recent advances have been made in understanding the origin of the autophagosomal membrane, novel regulators, and the mechanisms by which specific intracellular membranes become autophagy substrates. New studies on noncanonical autophagy, mediated by subsets of autophagy proteins, and the role of autophagy proteins in non-autophagy pathways are also emerging in many different biological contexts. Our understanding of canonical autophagy, including membrane origin and autophagy proteins, needs to be considered together with emerging noncanonical pathways.
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Affiliation(s)
| | - Sharon A Tooze
- Molecular Cell Biology of Autophagy, Francis Crick Institute, London, UK.
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164
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Peralta S, Garcia S, Yin HY, Arguello T, Diaz F, Moraes CT. Sustained AMPK activation improves muscle function in a mitochondrial myopathy mouse model by promoting muscle fiber regeneration. Hum Mol Genet 2016; 25:3178-3191. [PMID: 27288451 PMCID: PMC5179920 DOI: 10.1093/hmg/ddw167] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/22/2016] [Accepted: 05/23/2016] [Indexed: 12/25/2022] Open
Abstract
Acute pharmacological activation of adenosine monophosphate (AMP)-kinase using 5-aminoimidazole-4-carboxamide-1-b-D-ribofuranoside (AICAR) has been shown to improve muscle mitochondrial function by increasing mitochondrial biogenesis. We asked whether prolonged AICAR treatment is beneficial in a mouse model of slowly progressing mitochondrial myopathy (Cox10-Mef2c-Cre), and whether the compensatory mechanism is indeed an increase in mitochondrial biogenesis. We treated the animals for 3 months and found that sustained AMP-dependent kinase activation improved cytochrome c oxidase activity, rescued the motor phenotype and delayed the onset of the myopathy. This improvement was observed whether treatment started before or after the onset of the disease. We found that AICAR increased skeletal muscle regeneration thereby decreasing the levels of deleted Cox10-floxed alleles. We conclude that although increase in mitochondrial biogenesis and other pathways may contribute, the main mechanism by which AICAR improves the myopathy phenotype is by promoting muscle regeneration.
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Affiliation(s)
| | | | | | | | | | - Carlos T Moraes
- Department of Neurology
- Genetics Graduate Program
- Department of Cell Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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165
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Lystad AH, Simonsen A. Phosphoinositide-binding proteins in autophagy. FEBS Lett 2016; 590:2454-68. [PMID: 27391591 DOI: 10.1002/1873-3468.12286] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 06/28/2016] [Accepted: 07/05/2016] [Indexed: 12/21/2022]
Abstract
Phosphoinositides represent a very small fraction of membrane phospholipids, having fast turnover rates and unique subcellular distributions, which make them perfect for initiating local temporal effects. Seven different phosphoinositide species are generated through reversible phosphorylation of the inositol ring of phosphatidylinositol (PtdIns). The negative charge generated by the phosphates provides specificity for interaction with various protein domains that commonly contain a cluster of basic residues. Examples of domains that bind phosphoinositides include PH domains, WD40 repeats, PX domains, and FYVE domains. Such domains often display specificity toward a certain species or subset of phosphoinositides. Here we will review the current literature of different phosphoinositide-binding proteins involved in autophagy.
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Affiliation(s)
- Alf Håkon Lystad
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Norway
| | - Anne Simonsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Norway
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166
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Nakashima M, Takano K, Tsuyusaki Y, Yoshitomi S, Shimono M, Aoki Y, Kato M, Aida N, Mizuguchi T, Miyatake S, Miyake N, Osaka H, Saitsu H, Matsumoto N. WDR45 mutations in three male patients with West syndrome. J Hum Genet 2016; 61:653-661. [PMID: 27030146 DOI: 10.1038/jhg.2016.27] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 02/23/2016] [Accepted: 02/27/2016] [Indexed: 01/06/2023]
Abstract
West syndrome is an early-onset epileptic encephalopathy characterized by clustered spasms with hypsarrhythmia seen on electroencephalogram (EEG). West syndrome is genetically heterogeneous, and its genetic causes have not been fully elucidated. WD Repeat Domain 45 (WDR45) resides on Xp11.23, and encodes a member of the WD repeat protein interacting with phosphoinositides (WIPI) family, which is crucial in the macroautophagy pathway. De novo mutations in WDR45 cause beta-propeller protein-associated neurodegeneration characterized by iron accumulation in the basal ganglia. In this study, we performed whole exome sequencing of individuals with West syndrome and identified three WDR45 mutations in three independent males (patients 1, 2 and 3). Two novel mutations occurred de novo (patients 1 and 2) and the remaining mutation detected in a male patient (patient 3) and his affected sister was inherited from the mother, harboring the somatic mutation. The three male patients showed early-onset intractable seizures, profound intellectual disability and developmental delay. Their brain magnetic resonance imaging scans showed cerebral atrophy. We found no evidence of somatic mosaicism in the three male patients. Our findings indicate that hemizygous WDR45 mutations in males lead to severe epileptic encephalopathy.
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Affiliation(s)
- Mitsuko Nakashima
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kyoko Takano
- Division of Neurology, Kanagawa Children's Medical Center, Yokohama, Japan
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Yu Tsuyusaki
- Division of Neurology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Shinsaku Yoshitomi
- Department of Pediatrics, Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Masayuki Shimono
- Department of Pediatrics, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Yoshihiro Aoki
- Department of Pediatrics, Asahi General Hospital, Asahi, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Yamagata University Faculty of Medicine, Yamagata, Japan
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Noriko Aida
- Department of Radiology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hitoshi Osaka
- Division of Neurology, Kanagawa Children's Medical Center, Yokohama, Japan
- Department of Pediatrics, Jichi Medical University, Tochigi, Japan
| | - Hirotomo Saitsu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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167
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Porcine Circovirus Type 2 Activates CaMMKβ to Initiate Autophagy in PK-15 Cells by Increasing Cytosolic Calcium. Viruses 2016; 8:v8050135. [PMID: 27213427 PMCID: PMC4885090 DOI: 10.3390/v8050135] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 12/25/2022] Open
Abstract
Porcine circovirus type 2 (PCV2) induces autophagy via the 5′ adenosine monophosphate-activated protein kinase (AMPK)/extracellular signal-regulated kinase (ERK)/tuberous sclerosis complex 2 (TSC2)/mammalian target of rapamycin (mTOR) pathway in pig kidney PK-15 cells. However, the underlying mechanisms of AMPK activation in autophagy induction remain unknown. With specific inhibitors and RNA interference (RNAi), we show that PCV2 infection upregulated calcium/calmodulin-dependent protein kinase kinase-beta (CaMKKβ) by increasing cytosolic Ca2+ via inositol 1,4,5-trisphosphate receptor (IP3R). Elevation of cytosolic calcium ion (Ca2+) did not seem to involve inositol 1,4,5-trisphosphate (IP3) release from phosphatidylinositol 4,5-bisphosphate (PIP2) by phosphoinositide phospholipase C-gamma (PLC-γ). CaMKKβ then activated both AMPK and calcium/calmodulin-dependent protein kinase I (CaMKI). PCV2 employed CaMKI and Trp-Asp (WD) repeat domain phosphoinositide-interacting protein 1 (WIPI1) as another pathway additional to AMPK signaling in autophagy initiation. Our findings could help better understanding of the signaling pathways of autophagy induction as part of PCV2 pathogenesis. Further research is warranted to study if PCV2 interacts directly with IP3R or indirectly with the molecules that antagonize IP3R activity responsible for increased cytosolic Ca2+ both in PK-15 cells and PCV2-targeted primary cells from pigs.
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168
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Advances in Autophagy Regulatory Mechanisms. Cells 2016; 5:cells5020024. [PMID: 27187479 PMCID: PMC4931673 DOI: 10.3390/cells5020024] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 04/20/2016] [Accepted: 05/05/2016] [Indexed: 12/19/2022] Open
Abstract
Autophagy plays a critical role in cell metabolism by degrading and recycling internal components when challenged with limited nutrients. This fundamental and conserved mechanism is based on a membrane trafficking pathway in which nascent autophagosomes engulf cytoplasmic cargo to form vesicles that transport their content to the lysosome for degradation. Based on this simple scheme, autophagy modulates cellular metabolism and cytoplasmic quality control to influence an unexpectedly wide range of normal mammalian physiology and pathophysiology. In this review, we summarise recent advancements in three broad areas of autophagy regulation. We discuss current models on how autophagosomes are initiated from endogenous membranes. We detail how the uncoordinated 51-like kinase (ULK) complex becomes activated downstream of mechanistic target of rapamycin complex 1 (MTORC1). Finally, we summarise the upstream signalling mechanisms that can sense amino acid availability leading to activation of MTORC1.
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169
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Behl C. Breaking BAG: The Co-Chaperone BAG3 in Health and Disease. Trends Pharmacol Sci 2016; 37:672-688. [PMID: 27162137 DOI: 10.1016/j.tips.2016.04.007] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/11/2016] [Accepted: 04/12/2016] [Indexed: 01/01/2023]
Abstract
Human BAG (Bcl-2-associated athanogene) proteins form a family of antiapoptotic proteins that currently consists of six members (BAG1-6) all sharing the BAG protein domain from which the name arises. Via this domain, BAG proteins bind to the heat shock protein 70 (Hsp70), thereby acting as a co-chaperone regulating the activity of Hsp70. In addition to their antiapoptotic activity, all human BAG proteins have distinct functions in health and disease, and BAG3 in particular is the focus of many investigations. BAG3 has a modular protein domain composition offering the possibility for manifold interactions with other proteins. Various BAG3 functions are implicated in disorders including cancer, myopathies, and neurodegeneration. The discovery of its role in selective autophagy and the description of BAG3-mediated selective macroautophagy as an adaptive mechanism to maintain cellular homeostasis, under stress as well as during aging, make BAG3 a highly interesting target for future pharmacological interventions.
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Affiliation(s)
- Christian Behl
- Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
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170
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Chen HY, Liu CC, Chen RH. Cul3-KLHL20 ubiquitin ligase: physiological functions, stress responses, and disease implications. Cell Div 2016; 11:5. [PMID: 27042198 PMCID: PMC4818519 DOI: 10.1186/s13008-016-0017-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 03/16/2016] [Indexed: 01/01/2023] Open
Abstract
Cullin-RING ubiquitin ligases are the largest Ubiquitin ligase family in eukaryotes and are multi-protein complexes. In these complexes, the Cullin protein serves as a scaffold to connect two functional modules of the ligases, the catalytic subunit and substrate-binding subunit. KLHL20 is a substrate-binding subunit of Cullin3 (Cul3) ubiquitin ligase. Recent studies have identified a number of substrates of KLHL20-based ubiquitin ligase. Through ubiquitination of these substrates, KLHL20 elicits diverse cellular functions, some of which are associated with human diseases. Furthermore, the functions, subcellular localizations, and expression of KLHL20 are regulated by several physiological and stressed signals, which allow KLHL20 to preferentially act on certain substrates to response to these signals. Here, we provide a summary of the functions and regulations of KLHL20 in several physiological processes and stress responses and its disease implications.
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Affiliation(s)
- Hsin-Yi Chen
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Chin-Chih Liu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan ; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Ruey-Hwa Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan ; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
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171
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Mechanistically Dissecting Autophagy: Insights from In Vitro Reconstitution. J Mol Biol 2016; 428:1700-13. [PMID: 26946034 DOI: 10.1016/j.jmb.2016.02.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 02/19/2016] [Accepted: 02/19/2016] [Indexed: 12/13/2022]
Abstract
Autophagy is a fundamental cellular mechanism responsible for bulk turnover of cytoplasmic components. It is broadly related to many cellular activities, physiological processes, and pathological conditions. Autophagy entails a spatiotemporal interaction between cytosolic factors and membranes that are remodeled to encapsulate autophagic cargo within an autophagosome. Although majority of the factors [autophagy-related gene (Atg) proteins] involved in autophagy have been identified by genetic studies, the mechanism accounting for how these factors act upon the membrane to remodel it and efficiently recruit cargo for degradation is unclear. In vitro reconstitution of several different aspects of autophagy has provided important insights into the understanding of the mechanistic details underlying autophagic membrane remodeling and cargo recruitment. Here, we highlight these efforts toward studying autophagy through in vitro approaches.
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172
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Abstract
Bilayered phospholipid membranes are vital to the organization of the living cell. Based on fundamental principles of polarity, membranes create borders allowing defined spaces to be encapsulated. This compartmentalization is a prerequisite for the complex functional design of the eukaryotic cell, yielding localities that can differ in composition and operation. During macroautophagy, cytoplasmic components become enclosed by a growing double bilayered membrane, which upon closure creates a separate compartment, the autophagosome. The autophagosome is then primed for fusion with endosomal and lysosomal compartments, leading to degradation of the captured material. A large number of proteins have been found to be essential for autophagy, but little is known about the specific lipids that constitute the autophagic membranes and the membrane modeling events that are responsible for regulation of autophagosome shape and size. In this Commentary, we review the recent progress in our understanding of the membrane shaping and remodeling events that are required at different steps of the autophagy pathway. This article is part of a Focus on Autophagosome biogenesis. For further reading, please see related articles: 'ERES: sites for autophagosome biogenesis and maturation?' by Jana Sanchez-Wandelmer et al. (J. Cell Sci. 128, 185-192) and 'WIPI proteins: essential PtdIns3P effectors at the nascent autophagosome' by Tassula Proikas-Cezanne et al. (J. Cell Sci. 128, 207-217).
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Affiliation(s)
- Sven R Carlsson
- Department of Medical Biochemistry and Biophysics, University of Umeå, SE-901 87 Umeå, Sweden
| | - Anne Simonsen
- Institute of Basic Medical Sciences, University of Oslo, NO-0317 Oslo, Norway
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173
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Marat AL, Haucke V. Phosphatidylinositol 3-phosphates-at the interface between cell signalling and membrane traffic. EMBO J 2016; 35:561-79. [PMID: 26888746 DOI: 10.15252/embj.201593564] [Citation(s) in RCA: 191] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 01/26/2016] [Indexed: 12/31/2022] Open
Abstract
Phosphoinositides (PIs) form a minor class of phospholipids with crucial functions in cell physiology, ranging from cell signalling and motility to a role as signposts of compartmental membrane identity. Phosphatidylinositol 3-phosphates are present at the plasma membrane and within the endolysosomal system, where they serve as key regulators of both cell signalling and of intracellular membrane traffic. Here, we provide an overview of the metabolic pathways that regulate cellular synthesis of PI 3-phosphates at distinct intracellular sites and discuss the mechanisms by which these lipids regulate cell signalling and membrane traffic. Finally, we provide a framework for how PI 3-phosphate metabolism is integrated into the cellular network.
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Affiliation(s)
- Andrea L Marat
- Leibniz Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Volker Haucke
- Leibniz Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
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174
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Liu CC, Lin YC, Chen YH, Chen CM, Pang LY, Chen HA, Wu PR, Lin MY, Jiang ST, Tsai TF, Chen RH. Cul3-KLHL20 Ubiquitin Ligase Governs the Turnover of ULK1 and VPS34 Complexes to Control Autophagy Termination. Mol Cell 2016; 61:84-97. [DOI: 10.1016/j.molcel.2015.11.001] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/19/2015] [Accepted: 10/30/2015] [Indexed: 12/17/2022]
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175
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Pillich H, Puri M, Chakraborty T. ActA of Listeria monocytogenes and Its Manifold Activities as an Important Listerial Virulence Factor. Curr Top Microbiol Immunol 2016; 399:113-132. [PMID: 27726006 DOI: 10.1007/82_2016_30] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Listeria monocytogenes is a ubiquitously occurring gram-positive bacterium in the environment that causes listeriosis, one of the deadliest foodborne infections known today. It is a versatile facultative intracellular pathogen capable of growth within the host's cytosolic compartment. Following entry into the host cell, L. monocytogenes escapes from vacuolar compartments to the cytosol, where the bacterium begins a remarkable journey within the host cytoplasm, culminating in bacterial spread from cell to cell, to deeper tissues and organs. This dissemination process depends on the ability of the bacterium to harness central components of the host cell actin cytoskeleton using the surface bound bacterial factor ActA (actin assembly inducing protein). Hence ActA plays a major role in listerial virulence, and its absence renders bacteria intracellularly immotile and essentially non-infectious. As the bacterium, moving by building a network of filamentous actin behind itself that is often referred to as its actin tail, encounters cell-cell contacts it forms double-vacuolar protrusions that allow it to enter the neighboring cell where the cycle then continues. Recent studies have now implicated ActA in other stages of the life cycle of L. monocytogenes. These include extracellular properties of aggregation and biofilm formation to mediate colonization of the gut lumen, promotion and enhancement of bacterial host cell entry, evasion of autophagy, vacuolar exit, as well as nuclear factor of kappa light polypeptide gene enhancer in B-cells (NF-κB) activation. These novel properties provide a new view of ActA and help explain its role as an essential virulence factor of L. monocytogenes.
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Affiliation(s)
- Helena Pillich
- Institute of Medical Microbiology, Justus-Liebig University Giessen, Schubertstrasse 81, 35392, Giessen, Germany
| | - Madhu Puri
- Institute of Medical Microbiology, Justus-Liebig University Giessen, Schubertstrasse 81, 35392, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus-Liebig University Giessen, Schubertstrasse 81, 35392, Giessen, Germany.
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176
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Yoon MS. Vps34 and PLD1 take center stage in nutrient signaling: their dual roles in regulating autophagy. Cell Commun Signal 2015; 13:44. [PMID: 26589724 PMCID: PMC4654845 DOI: 10.1186/s12964-015-0122-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 11/18/2015] [Indexed: 02/08/2023] Open
Abstract
Autophagy is a critical pathway leading to lysosomal degradation of cellular components in response to changes in nutrient availability. Autophagy includes the biogenesis of autophagosomes and their sequential maturation through fusion with endo-lysosomes. The class III PI3 kinase Vps34 and its product phosphatidylinositol-3-phosphate (PI(3)P) play a critical role in this process, and enable the amino acid-mediated activation of mammalian target of rapamycin (mTOR), a suppressor of autophagy. Recent studies have shown that phospholipase PLD1, a downstream regulator of Vps34, is also closely involved in both mTOR activation and autophagy. This mini review summarizes recent findings in the regulation of Vps34 and PLD1 and highlights the role of these lipid-metabolizing enzymes in both mTOR activation and autophagy.
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Affiliation(s)
- Mee-Sup Yoon
- Department of Molecular Medicine, School of Medicine, Gachon University, Incheon, 406-840, Korea.
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177
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Viaud J, Payrastre B. [Phosphoinositides: the lipids coordinating cell dynamics]. Med Sci (Paris) 2015; 31:996-1005. [PMID: 26576607 DOI: 10.1051/medsci/20153111014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Within the glycerophospholipid family, phosphoinositides, which are minor components of eukaryotic cell membranes, play a critical role as spatiotemporal organizers of cell dynamics. By specifically interacting with proteins, they coordinate the formation and the organization of multiprotein complexes involved in cell signaling, intracellular trafficking and cytoskeleton rearrangement. The highly precise spatiotemporal dynamics of phosphoinositides-regulated mechanisms is ensured by kinases and phosphatases that specifically produce, hydrolyze and control the interconversion of these lipids. The direct implication of these enzymes in human pathologies such as genetic diseases, cancer or infectious pathologies, and the recent arrival of inhibitors targeting some phosphoinositide kinases in clinic, illustrate the mandatory functions of these fascinating lipids.
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Affiliation(s)
- Julien Viaud
- Inserm UMR 1048, institut des maladies métaboliques et cardiovasculaires (I2MC), université Toulouse III Paul-Sabatier, 1, avenue Jean Poulhès, BP 84225, 31432 Toulouse cedex 04, France
| | - Bernard Payrastre
- Inserm UMR 1048, institut des maladies métaboliques et cardiovasculaires (I2MC), université Toulouse III Paul-Sabatier, 1, avenue Jean Poulhès, BP 84225, 31432 Toulouse cedex 04, France - Centre hospitalier universitaire de Toulouse, laboratoire d'hématologie, 31059 Toulouse Cedex 03, France
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178
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Rey-Jurado E, Riedel CA, González PA, Bueno SM, Kalergis AM. Contribution of autophagy to antiviral immunity. FEBS Lett 2015; 589:3461-70. [PMID: 26297829 PMCID: PMC7094639 DOI: 10.1016/j.febslet.2015.07.047] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Revised: 07/20/2015] [Accepted: 07/29/2015] [Indexed: 12/22/2022]
Abstract
Although identified in the 1960's, interest in autophagy has significantly increased in the past decade with notable research efforts oriented at understanding as to how this multi-protein complex operates and is regulated. Autophagy is commonly defined as a "self-eating" process evolved by eukaryotic cells to recycle senescent organelles and expired proteins, which is significantly increased during cellular stress responses. In addition, autophagy can also play important roles during human diseases, such as cancer, neurodegenerative and autoimmune disorders. Furthermore, novel findings suggest that autophagy contributes to the host defense against microbial infections. In this article, we review the role of macroautophagy in antiviral immune responses and discuss molecular mechanisms evolved by viral pathogens to evade this process. A role for autophagy as an effector mechanism used both, by innate and adaptive immunity is also discussed.
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Affiliation(s)
- Emma Rey-Jurado
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Claudia A Riedel
- Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas y Facultad de Medicina, Universidad Andrés Bello, Santiago, Chile
| | - Pablo A González
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Susan M Bueno
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexis M Kalergis
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile; Departamento de Inmunología Clínica y Reumatología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile; INSERM U1064, Nantes, France.
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179
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Moruno Manchon JF, Uzor NE, Dabaghian Y, Furr-Stimming EE, Finkbeiner S, Tsvetkov AS. Cytoplasmic sphingosine-1-phosphate pathway modulates neuronal autophagy. Sci Rep 2015; 5:15213. [PMID: 26477494 PMCID: PMC4609990 DOI: 10.1038/srep15213] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/21/2015] [Indexed: 12/13/2022] Open
Abstract
Autophagy is an important homeostatic mechanism that eliminates long-lived proteins, protein aggregates and damaged organelles. Its dysregulation is involved in many neurodegenerative disorders. Autophagy is therefore a promising target for blunting neurodegeneration. We searched for novel autophagic pathways in primary neurons and identified the cytosolic sphingosine-1-phosphate (S1P) pathway as a regulator of neuronal autophagy. S1P, a bioactive lipid generated by sphingosine kinase 1 (SK1) in the cytoplasm, is implicated in cell survival. We found that SK1 enhances flux through autophagy and that S1P-metabolizing enzymes decrease this flux. When autophagy is stimulated, SK1 relocalizes to endosomes/autophagosomes in neurons. Expression of a dominant-negative form of SK1 inhibits autophagosome synthesis. In a neuron model of Huntington’s disease, pharmacologically inhibiting S1P-lyase protected neurons from mutant huntingtin-induced neurotoxicity. These results identify the S1P pathway as a novel regulator of neuronal autophagy and provide a new target for developing therapies for neurodegenerative disorders.
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Affiliation(s)
| | - Ndidi-Ese Uzor
- Department of Neurobiology and Anatomy, University of Texas Medical School, Houston, TX 77030.,The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030
| | - Yuri Dabaghian
- The Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030.,Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005
| | | | - Steven Finkbeiner
- Gladstone Institute of Neurological Disease and the Taube/Koret Center for Neurodegenerative Disease Research, San Francisco, CA 94158.,Departments of Neurology and Physiology, University of California, San Francisco, CA 94143
| | - Andrey S Tsvetkov
- Department of Neurobiology and Anatomy, University of Texas Medical School, Houston, TX 77030.,The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030
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180
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Amaya C, Fader CM, Colombo MI. Autophagy and proteins involved in vesicular trafficking. FEBS Lett 2015; 589:3343-53. [PMID: 26450776 DOI: 10.1016/j.febslet.2015.09.021] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 09/19/2015] [Accepted: 09/22/2015] [Indexed: 12/16/2022]
Abstract
Autophagy is an intracellular degradation system that, as a basic mechanism it delivers cytoplasmic components to the lysosomes in order to maintain adequate energy levels and cellular homeostasis. This complex cellular process is activated by low cellular nutrient levels and other stress situations such as low ATP levels, the accumulation of damaged proteins or organelles, or pathogen invasion. Autophagy as a multistep process involves vesicular transport events leading to tethering and fusion of autophagic vesicles with several intracellular compartments. This review summarizes our current understanding of the autophagic pathway with emphasis in the trafficking machinery (i.e. Rabs GTPases and SNAP receptors (SNAREs)) involved in specific steps of the pathway.
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Affiliation(s)
- Celina Amaya
- Laboratorio de Biología Celular y Molecular, Instituto de Histología y Embriología (IHEM)-CONICET, Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Casilla de Correo 56, Centro Universitario, Parque General San Martín, 5500 Mendoza, Argentina
| | - Claudio Marcelo Fader
- Laboratorio de Biología Celular y Molecular, Instituto de Histología y Embriología (IHEM)-CONICET, Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Casilla de Correo 56, Centro Universitario, Parque General San Martín, 5500 Mendoza, Argentina
| | - María Isabel Colombo
- Laboratorio de Biología Celular y Molecular, Instituto de Histología y Embriología (IHEM)-CONICET, Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Casilla de Correo 56, Centro Universitario, Parque General San Martín, 5500 Mendoza, Argentina.
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181
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Viaud J, Mansour R, Antkowiak A, Mujalli A, Valet C, Chicanne G, Xuereb JM, Terrisse AD, Séverin S, Gratacap MP, Gaits-Iacovoni F, Payrastre B. Phosphoinositides: Important lipids in the coordination of cell dynamics. Biochimie 2015; 125:250-8. [PMID: 26391221 DOI: 10.1016/j.biochi.2015.09.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/02/2015] [Indexed: 01/21/2023]
Abstract
By interacting specifically with proteins, phosphoinositides organize the spatiotemporal formation of protein complexes involved in the control of intracellular signaling, vesicular trafficking and cytoskeleton dynamics. A set of specific kinases and phosphatases ensures the production, degradation and inter-conversion of phosphoinositides to achieve a high level of precision in the regulation of cellular dynamics coordinated by these lipids. The direct involvement of these enzymes in cancer, genetic or infectious diseases, and the recent arrival of inhibitors targeting specific phosphoinositide kinases in clinic, emphasize the importance of these lipids and their metabolism in the biomedical field.
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Affiliation(s)
- Julien Viaud
- INSERM UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III Paul Sabatier, 1 Avenue Jean Poulhès, BP84225, 31432 Toulouse Cedex 04, France.
| | - Rana Mansour
- INSERM UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III Paul Sabatier, 1 Avenue Jean Poulhès, BP84225, 31432 Toulouse Cedex 04, France
| | - Adrien Antkowiak
- INSERM UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III Paul Sabatier, 1 Avenue Jean Poulhès, BP84225, 31432 Toulouse Cedex 04, France
| | - Abdulrahman Mujalli
- INSERM UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III Paul Sabatier, 1 Avenue Jean Poulhès, BP84225, 31432 Toulouse Cedex 04, France
| | - Colin Valet
- INSERM UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III Paul Sabatier, 1 Avenue Jean Poulhès, BP84225, 31432 Toulouse Cedex 04, France
| | - Gaëtan Chicanne
- INSERM UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III Paul Sabatier, 1 Avenue Jean Poulhès, BP84225, 31432 Toulouse Cedex 04, France
| | - Jean-Marie Xuereb
- INSERM UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III Paul Sabatier, 1 Avenue Jean Poulhès, BP84225, 31432 Toulouse Cedex 04, France
| | - Anne-Dominique Terrisse
- INSERM UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III Paul Sabatier, 1 Avenue Jean Poulhès, BP84225, 31432 Toulouse Cedex 04, France
| | - Sonia Séverin
- INSERM UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III Paul Sabatier, 1 Avenue Jean Poulhès, BP84225, 31432 Toulouse Cedex 04, France
| | - Marie-Pierre Gratacap
- INSERM UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III Paul Sabatier, 1 Avenue Jean Poulhès, BP84225, 31432 Toulouse Cedex 04, France
| | - Frédérique Gaits-Iacovoni
- INSERM UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III Paul Sabatier, 1 Avenue Jean Poulhès, BP84225, 31432 Toulouse Cedex 04, France
| | - Bernard Payrastre
- INSERM UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III Paul Sabatier, 1 Avenue Jean Poulhès, BP84225, 31432 Toulouse Cedex 04, France; Centre Hospitalier Universitaire de Toulouse, Laboratoire d'Hématologie, 31059 Toulouse Cedex 03, France.
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182
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Mi N, Chen Y, Wang S, Chen M, Zhao M, Yang G, Ma M, Su Q, Luo S, Shi J, Xu J, Guo Q, Gao N, Sun Y, Chen Z, Yu L. CapZ regulates autophagosomal membrane shaping by promoting actin assembly inside the isolation membrane. Nat Cell Biol 2015; 17:1112-23. [DOI: 10.1038/ncb3215] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 07/01/2015] [Indexed: 12/16/2022]
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183
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Abstract
Autophagy is an intracellular catabolic pathway essential for the recycling of proteins and larger substrates such as aggregates, apoptotic corpses, or long-lived and superfluous organelles whose accumulation could be toxic for cells. Because of its unique feature to engulf part of cytoplasm in double-membrane cup-shaped structures, which further fuses with lysosomes, autophagy is also involved in the elimination of host cell invaders and takes an active part of the innate and adaptive immune response. Its pivotal role in maintenance of the inflammatory balance makes dysfunctions of the autophagy process having important pathological consequences. Indeed, defects in autophagy are associated with a wide range of human diseases including metabolic disorders (diabetes and obesity), inflammatory bowel disease (IBD), and cancer. In this review, we will focus on interrelations that exist between inflammation and autophagy. We will discuss in particular how mediators of inflammation can regulate autophagy activity and, conversely, how autophagy shapes the inflammatory response. Impact of genetic polymorphisms in autophagy-related gene on inflammatory bowel disease will be also discussed.
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184
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Structure of the Atg101-Atg13 complex reveals essential roles of Atg101 in autophagy initiation. Nat Struct Mol Biol 2015; 22:572-80. [PMID: 26030876 DOI: 10.1038/nsmb.3036] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/29/2015] [Indexed: 12/18/2022]
Abstract
Atg101 is an essential component of the autophagy-initiating ULK complex in higher eukaryotes, but it is absent from the functionally equivalent Atg1 complex in budding yeast. Here, we report the crystal structure of the fission yeast Atg101-Atg13 complex. Atg101 has a Hop1, Rev7 and Mad2 (HORMA) architecture similar to that of Atg13. Mad2 HORMA has two distinct conformations (O-Mad2 and C-Mad2), and, intriguingly, Atg101 resembles O-Mad2 rather than the C-Mad2-like Atg13. Atg13 HORMA from higher eukaryotes possesses an inherently unstable fold, which is stabilized by Atg101 via interactions analogous to those between O-Mad2 and C-Mad2. Mutational studies revealed that Atg101 is responsible for recruiting downstream factors to the autophagosome-formation site in mammals via a newly identified WF finger. These data define the molecular functions of Atg101, providing a basis for elucidating the molecular mechanisms of mammalian autophagy initiation by the ULK complex.
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185
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Grimmel M, Backhaus C, Proikas-Cezanne T. WIPI-Mediated Autophagy and Longevity. Cells 2015; 4:202-17. [PMID: 26010754 PMCID: PMC4493456 DOI: 10.3390/cells4020202] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/17/2015] [Accepted: 05/17/2015] [Indexed: 01/20/2023] Open
Abstract
Autophagy is a lysosomal degradation process for cytoplasmic components, including organelles, membranes, and proteins, and critically secures eukaryotic cellular homeostasis and survival. Moreover, autophagy-related (ATG) genes are considered essential for longevity control in model organisms. Central to the regulatory relationship between autophagy and longevity is the control of insulin/insulin-like growth factor receptor-driven activation of mTOR (mechanistic target of rapamycin), which inhibits WIPI (WD repeat protein interacting with phosphoinositides)-mediated autophagosome formation. Release of the inhibitory mTOR action on autophagy permits the production of PI3P (phosphatidylinositol-3 phosphate), predominantly at the endoplasmic reticulum, to function as an initiation signal for the formation of autophagosomes. WIPI proteins detect this pool of newly produced PI3P and function as essential PI3P effector proteins that recruit downstream autophagy-related (ATG) proteins. The important role of WIPI proteins in autophagy is highlighted by functional knockout of the WIPI homologues ATG-18 and EPG-6 in Caenorhabditis elegans (C. elegans). Adult lifespan is significantly reduced in ATG-18 mutant animals, demonstrating that longevity as such is crucially determined by essential autophagy factors. In this review we summarize the role of WIPI proteins and their C. elegans homologues with regard to the molecular basis of aging. As the development of strategies on how to increase health span in humans is increasingly appreciated, we speculate that targeting WIPI protein function might represent a therapeutic opportunity to fight and delay the onset of age-related human diseases.
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Affiliation(s)
- Mona Grimmel
- Autophagy Laboratory, Department of Molecular Biology, Interfaculty Institute of Cell Biology, Faculty of Science, Eberhard Karls University Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany
| | - Charlotte Backhaus
- Autophagy Laboratory, Department of Molecular Biology, Interfaculty Institute of Cell Biology, Faculty of Science, Eberhard Karls University Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany
| | - Tassula Proikas-Cezanne
- Autophagy Laboratory, Department of Molecular Biology, Interfaculty Institute of Cell Biology, Faculty of Science, Eberhard Karls University Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany.
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186
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Müller AJ, Proikas-Cezanne T. Function of human WIPI proteins in autophagosomal rejuvenation of endomembranes? FEBS Lett 2015; 589:1546-51. [PMID: 25980605 DOI: 10.1016/j.febslet.2015.05.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 04/30/2015] [Accepted: 05/05/2015] [Indexed: 12/28/2022]
Abstract
Despite the availability of a large pool of experimental approaches and hypothetical considerations, the hunt for the enigmatic membrane origin of autophagosomes is still on. In mammalian cells proposed scenarios for the formation of the autophagosomal membrane include both de novo assembly, and rearrangements plus maturation of pre-existing membrane sections from the endoplasmic reticulum (ER), plasma membrane, Golgi or mitochondria. Earlier, we identified the human WD-repeat protein interacting with phosphoinositides (WIPI) family and showed that WIPI proteins function as essential phosphatidylinositol 3-phosphate (PtdIns3P) effectors at the nascent autophagosome. Interestingly, WIPI proteins localize to both pre-existing endomembranes and nascent autophagosomes. In this context, and on the basis of historical records on the formation of autophagosomes, we discuss with appropriate modesty an alternative perspective on the membrane origin of autophagosomes.
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Affiliation(s)
- Amelie Johanna Müller
- Autophagy Laboratory, Department of Molecular Biology, Interfaculty Institute of Cell Biology, Eberhard Karls University Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany
| | - Tassula Proikas-Cezanne
- Autophagy Laboratory, Department of Molecular Biology, Interfaculty Institute of Cell Biology, Eberhard Karls University Tuebingen, Auf der Morgenstelle 15, 72076 Tuebingen, Germany.
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187
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Vicinanza M, Rubinsztein DC. Mirror image phosphoinositides regulate autophagy. Mol Cell Oncol 2015; 3:e1019974. [PMID: 27308581 PMCID: PMC4905334 DOI: 10.1080/23723556.2015.1019974] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 02/10/2015] [Accepted: 02/11/2015] [Indexed: 12/15/2022]
Abstract
Autophagosome formation is stimulated by canonical VPS34-dependent formation of phosphatidylinositol 3-phosphate [PI(3)P], which recruits effectors such as WIPI2. However, non-canonical VPS34-independent autophagy has also been proposed. We recently described that PI(5)P regulates autophagosome biogenesis, recruits WIPI2, and rescues autophagy in VPS34-inactivated cells. These alternative autophagy-initiating pathways reveal new druggable targets for treating neurodegeneration and cancer.
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Affiliation(s)
- Mariella Vicinanza
- Department of Medical Genetics; Cambridge Institute for Medical Research ; Cambridge, UK
| | - David C Rubinsztein
- Department of Medical Genetics; Cambridge Institute for Medical Research ; Cambridge, UK
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188
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Sanchez-Wandelmer J, Ktistakis NT, Reggiori F. ERES: sites for autophagosome biogenesis and maturation? J Cell Sci 2015; 128:185-92. [PMID: 25568152 DOI: 10.1242/jcs.158758] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
Autophagosomes are the hallmark of autophagy, but despite their central role in this degradative pathway that involves vesicle transport to lysosomes or vacuoles, the mechanism underlying their biogenesis still remains largely unknown. Our current concepts about autophagosome biogenesis are based on models suggesting that a small autonomous cisterna grows into an autophagosome through expansion at its extremities. Recent findings have revealed that endoplasmic reticulum (ER) exit sites (ERES), specialized ER regions where proteins are sorted into the secretory system, are key players in the formation of autophagosomes. Owing to the morphological connection of nascent autophagosomes with the ER, this has raised several questions that challenge our current perception of autophagosome biogenesis, such as are ERES the compartments where autophagosome formation takes place? What is the functional relevance of this connection? Are these compartments providing essential molecules for the generation of autophagosomes and/or are they structural platforms where these vesicles emerge? In this Hypothesis, we discuss recent data that have implicated the ERES in autophagosome biogenesis and we propose two models to describe the possible role of this compartment at different steps in the process of autophagosome biogenesis. This article is part of a Focus on Autophagosome biogenesis. For further reading, please see related articles: 'Membrane dynamics in autophagosome biogenesis' by Sven R. Carlsson and Anne Simonsen (J. Cell Sci. 128, 193-205) and 'WIPI proteins: essential PtdIns3P effectors at the nascent autophagosome' by Tassula Proikas-Cezanne et al. (J. Cell Sci. 128, 207-217).
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Affiliation(s)
- Jana Sanchez-Wandelmer
- Department of Cell Biology, Center for Molecular Medicine, University Medical Centre Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | | | - Fulvio Reggiori
- Department of Cell Biology, Center for Molecular Medicine, University Medical Centre Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
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