101
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Valverde DP, Yu S, Boggavarapu V, Kumar N, Lees JA, Walz T, Reinisch KM, Melia TJ. ATG2 transports lipids to promote autophagosome biogenesis. J Cell Biol 2019; 218:1787-1798. [PMID: 30952800 PMCID: PMC6548141 DOI: 10.1083/jcb.201811139] [Citation(s) in RCA: 384] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/05/2019] [Accepted: 03/28/2019] [Indexed: 02/07/2023] Open
Abstract
Valverde et al. show that the autophagy protein ATG2 functions in autophagosome biogenesis by transferring lipids at ER–autophagosome contact sites. During macroautophagic stress, autophagosomes can be produced continuously and in high numbers. Many different organelles have been reported as potential donor membranes for this sustained autophagosome growth, but specific machinery to support the delivery of lipid to the growing autophagosome membrane has remained unknown. Here we show that the autophagy protein, ATG2, without a clear function since its discovery over 20 yr ago, is in fact a lipid-transfer protein likely operating at the ER–autophagosome interface. ATG2A can bind tens of glycerophospholipids at once and transfers lipids robustly in vitro. An N-terminal fragment of ATG2A that supports lipid transfer in vitro is both necessary and fully sufficient to rescue blocked autophagosome biogenesis in ATG2A/ATG2B KO cells, implying that regulation of lipid homeostasis is the major autophagy-dependent activity of this protein and, by extension, that protein-mediated lipid transfer across contact sites is a principal contributor to autophagosome formation.
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Affiliation(s)
- Diana P Valverde
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
| | - Shenliang Yu
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
| | - Venkata Boggavarapu
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY
| | - Nikit Kumar
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
| | - Joshua A Lees
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY
| | - Karin M Reinisch
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
| | - Thomas J Melia
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
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102
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Chung T. How phosphoinositides shape autophagy in plant cells. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 281:146-158. [PMID: 30824047 DOI: 10.1016/j.plantsci.2019.01.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 01/10/2019] [Accepted: 01/19/2019] [Indexed: 05/06/2023]
Abstract
Plant cells use autophagy to degrade their own cytoplasm in vacuoles, thereby not only recycling their breakdown products, but also ensuring the homeostasis of essential cytoplasmic constituents and organelles. Plants and other eukaryotes have a conserved set of core Autophagy-related (ATG) genes involved in the biogenesis of the autophagosome, the main autophagic compartment destined for the lytic vacuole. In the past decade, the core ATG genes were isolated from several plant species. The core ATG proteins include the components of the VACUOLAR PROTEIN SORTING 34 (VPS34) complex that is responsible for the local production of phosphatidylinositol 3-phosphate (PI3P) at the site of autophagosome formation. Dissecting the roles of PI3P and its effectors in autophagy is challenging, because of the multi-faceted links between autophagosomal and endosomal systems. This review highlights recent studies on putative plant PI3P effectors involved in autophagosome dynamics. Molecular mechanisms underlying the requirement of PI3P for autophagosome biogenesis and trafficking are also discussed.
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Affiliation(s)
- Taijoon Chung
- Department of Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea.
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103
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Atg2 mediates direct lipid transfer between membranes for autophagosome formation. Nat Struct Mol Biol 2019; 26:281-288. [PMID: 30911189 DOI: 10.1038/s41594-019-0203-4] [Citation(s) in RCA: 325] [Impact Index Per Article: 54.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 02/15/2019] [Indexed: 12/30/2022]
Abstract
A key event in autophagy is autophagosome formation, whereby the newly synthesized isolation membrane (IM) expands to form a complete autophagosome using endomembrane-derived lipids. Atg2 physically links the edge of the expanding IM with the endoplasmic reticulum (ER), a role that is essential for autophagosome formation. However, the molecular function of Atg2 during ER-IM contact remains unclear, as does the mechanism of lipid delivery to the IM. Here we show that the conserved amino-terminal region of Schizosaccharomyces pombe Atg2 includes a lipid-transfer-protein-like hydrophobic cavity that accommodates phospholipid acyl chains. Atg2 bridges highly curved liposomes, thereby facilitating efficient phospholipid transfer in vitro, a function that is inhibited by mutations that impair autophagosome formation in vivo. These results suggest that Atg2 acts as a lipid-transfer protein that supplies phospholipids for autophagosome formation.
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104
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Ktistakis NT. ER platforms mediating autophagosome generation. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1865:158433. [PMID: 30890442 DOI: 10.1016/j.bbalip.2019.03.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 12/12/2022]
Abstract
The origin of the autophagosomal membrane started to be debated by scientists working in the field within one year of the modern definition of autophagy in 1963. There is now converging evidence from older and newer studies that the endoplasmic reticulum is involved in formation of autophagosomes. Thus, it is possible to trace from early morphological work - done without the benefit of molecular descriptions - to recent studies - dissecting how specific proteins nucleate autophagosome biogenesis - a long series of experimental findings that are beginning to answer the 55-year old question with some confidence. The view that has emerged is that specialised regions of the endoplasmic reticulum, in dynamic cross talk with most intracellular organelles via membrane contact sites, provide a platform for autophagosome biogenesis.
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105
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Kurokawa K, Osakada H, Kojidani T, Waga M, Suda Y, Asakawa H, Haraguchi T, Nakano A. Visualization of secretory cargo transport within the Golgi apparatus. J Cell Biol 2019; 218:1602-1618. [PMID: 30858192 PMCID: PMC6504898 DOI: 10.1083/jcb.201807194] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 12/31/2018] [Accepted: 02/04/2019] [Indexed: 01/09/2023] Open
Abstract
Kurokawa et al. visualize the transport of secretory cargo in the Golgi apparatus in living yeast cells. Cargo stays in the cisterna, whose property changes from cis to trans and further to the trans-Golgi network, but shows a dynamic behavior between the early and the late zones within the maturing cisterna. To describe trafficking of secretory cargo within the Golgi apparatus, the cisternal maturation model predicts that Golgi cisternae change their properties from cis to trans while cargo remains in the cisternae. Cisternal change has been demonstrated in living yeast Saccharomyces cerevisiae; however, the behavior of cargo has yet to be examined directly. In this study, we conducted simultaneous three-color and four-dimensional visualization of secretory transmembrane cargo together with early and late Golgi resident proteins. We show that cargo stays in a Golgi cisterna during maturation from cis-Golgi to trans-Golgi and further to the trans-Golgi network (TGN), which involves dynamic mixing and segregation of two zones of the earlier and later Golgi resident proteins. The location of cargo changes from the early to the late zone within the cisterna during the progression of maturation. In addition, cargo shows an interesting behavior during the maturation to the TGN. After most cargo has reached the TGN zone, a small amount of cargo frequently reappears in the earlier zone.
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Affiliation(s)
- Kazuo Kurokawa
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Saitama, Japan
| | - Hiroko Osakada
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Tomoko Kojidani
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan.,Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Tokyo, Japan
| | - Miho Waga
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Saitama, Japan
| | - Yasuyuki Suda
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Saitama, Japan.,Laboratory of Molecular Cell Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Haruhiko Asakawa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Tokuko Haraguchi
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Akihiko Nakano
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Saitama, Japan
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106
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Brier LW, Ge L, Stjepanovic G, Thelen AM, Hurley JH, Schekman R. Regulation of LC3 lipidation by the autophagy-specific class III phosphatidylinositol-3 kinase complex. Mol Biol Cell 2019; 30:1098-1107. [PMID: 30811270 PMCID: PMC6724508 DOI: 10.1091/mbc.e18-11-0743] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Autophagy is a conserved eukaryotic pathway critical for cellular adaptation to changes in nutrition levels and stress. The class III phosphatidylinositol (PI)3-kinase complexes I and II (PI3KC3-C1 and -C2) are essential for autophagosome initiation and maturation, respectively, from highly curved vesicles. We used a cell-free reaction that reproduces a key autophagy initiation step, LC3 lipidation, as a biochemical readout to probe the role of autophagy-related gene (ATG)14, a PI3KC3-C1-specific subunit implicated in targeting the complex to autophagy initiation sites. We reconstituted LC3 lipidation with recombinant PI3KC3-C1, -C2, or various mutant derivatives added to extracts derived from a CRISPR/Cas9-generated ATG14-knockout cell line. Both complexes C1 and C2 require the C-terminal helix of VPS34 for activity on highly curved membranes. However, only complex C1 supports LC3 lipidation through the curvature-targeting amphipathic lipid packing sensor (ALPS) motif of ATG14. Furthermore, the ALPS motif and VPS34 catalytic activity are required for downstream recruitment of WD-repeat domain phosphoinositide-interacting protein (WIPI)2, a protein that binds phosphatidylinositol 3-phosphate and its product phosphatidylinositol 3, 5-bisphosphate, and a WIPI-binding protein, ATG2A, but do not affect membrane association of ATG3 and ATG16L1, enzymes contributing directly to LC3 lipidation. These data reveal the nuanced role of the ATG14 ALPS in membrane curvature sensing, suggesting that the ALPS has additional roles in supporting LC3 lipidation.
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Affiliation(s)
- Livia W Brier
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94270.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94270
| | - Liang Ge
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94270.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94270
| | - Goran Stjepanovic
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94270.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94270.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Ashley M Thelen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94270
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94270.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94270.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Randy Schekman
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94270.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94270
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107
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Shima T, Kirisako H, Nakatogawa H. COPII vesicles contribute to autophagosomal membranes. J Cell Biol 2019; 218:1503-1510. [PMID: 30787039 PMCID: PMC6504894 DOI: 10.1083/jcb.201809032] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 01/11/2019] [Accepted: 02/05/2019] [Indexed: 01/03/2023] Open
Abstract
The membrane dynamics underlying the biogenesis of autophagosomes, including the origin of the autophagosomal membrane, are still elusive. Shima et al. use a recently developed COPII vesicle–labeling system to show that COPII vesicles are a membrane source in autophagosome formation. A hallmark of autophagy is the de novo formation of double-membrane vesicles called autophagosomes, which sequester various cellular constituents for degradation in lysosomes or vacuoles. The membrane dynamics underlying the biogenesis of autophagosomes, including the origin of the autophagosomal membrane, are still elusive. Although previous studies suggested that COPII vesicles are closely associated with autophagosome biogenesis, it remains unclear whether these vesicles serve as a source of the autophagosomal membrane. Using a recently developed COPII vesicle–labeling system in fluorescence and immunoelectron microscopy in the budding yeast Saccharomyces cerevisiae, we show that the transmembrane cargo Axl2 is loaded into COPII vesicles in the ER. Axl2 is then transferred to autophagosome intermediates, ultimately becoming part of autophagosomal membranes. This study provides a definitive answer to a long-standing, fundamental question regarding the mechanisms of autophagosome formation by implicating COPII vesicles as a membrane source for autophagosomes.
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Affiliation(s)
- Takayuki Shima
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hiromi Kirisako
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hitoshi Nakatogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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108
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Understanding phosphoinositides: rare, dynamic, and essential membrane phospholipids. Biochem J 2019; 476:1-23. [PMID: 30617162 DOI: 10.1042/bcj20180022] [Citation(s) in RCA: 177] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 12/03/2018] [Accepted: 12/07/2018] [Indexed: 12/15/2022]
Abstract
Polyphosphoinositides (PPIs) are essential phospholipids located in the cytoplasmic leaflet of eukaryotic cell membranes. Despite contributing only a small fraction to the bulk of cellular phospholipids, they make remarkable contributions to practically all aspects of a cell's life and death. They do so by recruiting cytoplasmic proteins/effectors or by interacting with cytoplasmic domains of membrane proteins at the membrane-cytoplasm interface to organize and mold organelle identity. The present study summarizes aspects of our current understanding concerning the metabolism, manipulation, measurement, and intimate roles these lipids play in regulating membrane homeostasis and vital cell signaling reactions in health and disease.
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109
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Spatially Distinct Pools of TORC1 Balance Protein Homeostasis. Mol Cell 2019; 73:325-338.e8. [DOI: 10.1016/j.molcel.2018.10.040] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/03/2018] [Accepted: 10/25/2018] [Indexed: 11/19/2022]
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110
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Norizuki T, Kanazawa T, Minamino N, Tsukaya H, Ueda T. Marchantia polymorpha, a New Model Plant for Autophagy Studies. FRONTIERS IN PLANT SCIENCE 2019; 10:935. [PMID: 31379911 PMCID: PMC6652269 DOI: 10.3389/fpls.2019.00935] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/03/2019] [Indexed: 05/18/2023]
Abstract
Autophagy is a catabolic process for bulk and selective degradation of cytoplasmic components in the vacuole/lysosome. In Saccharomyces cerevisiae, ATG genes were identified as essential genes for autophagy, and most ATG genes are highly conserved among eukaryotes, including plants. Although reverse genetic analyses have revealed that autophagy is involved in responses to abiotic and biotic stresses in land plants, our knowledge of its molecular mechanism remains limited. This limitation is partly because of the multiplication of some ATG genes, including ATG8, in widely used model plants such as Arabidopsis thaliana, which adds complexity to functional studies. Furthermore, due to limited information on the composition and functions of the ATG genes in basal land plants and charophytes, it remains unclear whether multiplication of ATG genes is associated with neofunctionalization of these genes. To gain insight into the diversification of ATG genes during plant evolution, we compared the composition of ATG genes in plants with a special focus on a liverwort and two charophytes, which have not previously been analyzed. Our results showed that the liverwort Marchantia polymorpha and the charophytes Klebsormidium nitens and Chara braunii harbor fundamental sets of ATG genes with low redundancy compared with those of A. thaliana and the moss Physcomitrella patens, suggesting that multiplication of ATG genes occurred during land plant evolution. We also attempted to establish an experimental system for analyzing autophagy in M. polymorpha. We generated transgenic plants expressing fluorescently tagged MpATG8 to observe its dynamics in M. polymorpha and produced autophagy-defective mutants by genome editing using the CRISPR/Cas9 system. These tools allowed us to demonstrate that MpATG8 is transported into the vacuole in an MpATG2-, MpATG5-, and MpATG7-dependent manner, suggesting that fluorescently tagged MpATG8 can be used as an autophagosome marker in M. polymorpha. M. polymorpha can provide a powerful system for studying the mechanisms and evolution of autophagy in plants.
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Affiliation(s)
- Takuya Norizuki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Japan
| | - Takehiko Kanazawa
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
| | - Naoki Minamino
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Japan
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
- *Correspondence: Takashi Ueda,
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111
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Osawa T, Alam JM, Noda NN. Membrane-binding domains in autophagy. Chem Phys Lipids 2019; 218:1-9. [DOI: 10.1016/j.chemphyslip.2018.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/31/2018] [Accepted: 11/07/2018] [Indexed: 02/07/2023]
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112
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Otomo T, Chowdhury S, Lander GC. The rod-shaped ATG2A-WIPI4 complex tethers membranes in vitro. ACTA ACUST UNITED AC 2018; 1. [PMID: 30766969 DOI: 10.1177/2515256418819936] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The autophagosome precursor membrane, termed the "isolation membrane" or "phagophore," emerges adjacent to a PI3P-enriched transient subdomain of the ER called the "omegasome," thereafter expanding to engulf cytoplasmic content. Uncovering the molecular events that occur in the vicinity of the omegasome during phagophore biogenesis is imperative for understanding the mechanisms involved in this critical step of the autophagy pathway. We recently characterized the ATG2A-WIPI4 complex, one of the factors that localize to the omegasome and play a critical role in mediating phagophore expansion. Our structural and biochemical studies revealed that ATG2A is a rod-shaped protein with membrane-interacting properties at each end, endowing ATG2A with membrane-tethering capability. Association of the PI3P-binding protein WIPI4 at one of the ATG2A tips enables the ATG2A-WIPI4 complex to specifically tether PI3P-containing membranes to non-PI3P-containing membranes. We proposed models for the ATG2A-WIPI4 complex-mediated membrane associations between the omegasome and surrounding membranes, including the phagophore edge, the ER, ATG9 vesicles, and COPII vesicles.
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Affiliation(s)
- Takanori Otomo
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Saikat Chowdhury
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Present address: Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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113
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Xu P, Damschroder D, Zhang M, Ryall KA, Adler PN, Saucerman JJ, Wessells RJ, Yan Z. Atg2, Atg9 and Atg18 in mitochondrial integrity, cardiac function and healthspan in Drosophila. J Mol Cell Cardiol 2018; 127:116-124. [PMID: 30571977 DOI: 10.1016/j.yjmcc.2018.12.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 11/12/2018] [Accepted: 12/15/2018] [Indexed: 12/25/2022]
Abstract
In yeast, the Atg2-Atg18 complex regulates Atg9 recycling from phagophore assembly site during autophagy; their function in higher eukaryotes remains largely unknown. In a targeted screening in Drosophila melanogaster, we show that Mef2-GAL4-RNAi-mediated knockdown of Atg2, Atg9 or Atg18 in the heart and indirect flight muscles led to shortened healthspan (declined locomotive function) and lifespan. These flies displayed an accelerated age-dependent loss of cardiac function along with cardiac hypertrophy (increased heart tube wall thickness) and structural abnormality (distortion of the lumen surface). Using the Mef2-GAL4-MitoTimer mitochondrial reporter system and transmission electron microscopy, we observed significant elongation of mitochondria and reduced number of lysosome-targeted autophagosomes containing mitochondria in the heart tube but exaggerated mitochondrial fragmentation and reduced mitochondrial density in indirect flight muscles. These findings provide the first direct evidence of the importance of Atg2-Atg18/Atg9 autophagy complex in the maintenance of mitochondrial integrity and, regulation of heart and muscle functions in Drosophila, raising the possibility of augmenting Atg2-Atg18/Atg9 activity in promoting mitochondrial health and, muscle and heart function.
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Affiliation(s)
- Peng Xu
- Department of Medicine, University of Virginia, Charlottesville, VA 22908, United States; Center for Skeletal Muscle Research at Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA 22908, United States
| | - Deena Damschroder
- Department of Physiology, Wayne State School of Medicine, Detroit, MI 48201, United States
| | - Mei Zhang
- Department of Medicine, University of Virginia, Charlottesville, VA 22908, United States; Center for Skeletal Muscle Research at Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA 22908, United States
| | - Karen A Ryall
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, United States
| | - Paul N Adler
- Department of Biology, University of Virginia, Charlottesville, VA 22908, United States
| | - Jeffrey J Saucerman
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, United States
| | - Robert J Wessells
- Department of Physiology, Wayne State School of Medicine, Detroit, MI 48201, United States.
| | - Zhen Yan
- Department of Medicine, University of Virginia, Charlottesville, VA 22908, United States; Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, United States; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, United States; Center for Skeletal Muscle Research at Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA 22908, United States.
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114
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Trejo-Solís C, Serrano-Garcia N, Escamilla-Ramírez Á, Castillo-Rodríguez RA, Jimenez-Farfan D, Palencia G, Calvillo M, Alvarez-Lemus MA, Flores-Nájera A, Cruz-Salgado A, Sotelo J. Autophagic and Apoptotic Pathways as Targets for Chemotherapy in Glioblastoma. Int J Mol Sci 2018; 19:ijms19123773. [PMID: 30486451 PMCID: PMC6320836 DOI: 10.3390/ijms19123773] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/14/2018] [Accepted: 11/21/2018] [Indexed: 01/07/2023] Open
Abstract
Glioblastoma multiforme is the most malignant and aggressive type of brain tumor, with a mean life expectancy of less than 15 months. This is due in part to the high resistance to apoptosis and moderate resistant to autophagic cell death in glioblastoma cells, and to the poor therapeutic response to conventional therapies. Autophagic cell death represents an alternative mechanism to overcome the resistance of glioblastoma to pro-apoptosis-related therapies. Nevertheless, apoptosis induction plays a major conceptual role in several experimental studies to develop novel therapies against brain tumors. In this review, we outline the different components of the apoptotic and autophagic pathways and explore the mechanisms of resistance to these cell death pathways in glioblastoma cells. Finally, we discuss drugs with clinical and preclinical use that interfere with the mechanisms of survival, proliferation, angiogenesis, migration, invasion, and cell death of malignant cells, favoring the induction of apoptosis and autophagy, or the inhibition of the latter leading to cell death, as well as their therapeutic potential in glioma, and examine new perspectives in this promising research field.
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Affiliation(s)
- Cristina Trejo-Solís
- Departamento de Neuroinmunología, Laboratorio de Neurobiología Molecular y Celular, Laboratorio Experimental de Enfermedades Neurodegenerativas del Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", C.P. 14269 Ciudad de México, Mexico.
| | - Norma Serrano-Garcia
- Departamento de Neuroinmunología, Laboratorio de Neurobiología Molecular y Celular, Laboratorio Experimental de Enfermedades Neurodegenerativas del Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", C.P. 14269 Ciudad de México, Mexico.
| | - Ángel Escamilla-Ramírez
- Departamento de Neuroinmunología, Laboratorio de Neurobiología Molecular y Celular, Laboratorio Experimental de Enfermedades Neurodegenerativas del Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", C.P. 14269 Ciudad de México, Mexico.
- Hospital Regional de Alta Especialidad de Oaxaca, Secretaria de Salud, C.P. 71256 Oaxaca, Mexico.
| | | | - Dolores Jimenez-Farfan
- Laboratorio de Inmunología, División de Estudios de Posgrado e Investigación, Facultad de Odontología, Universidad Nacional Autónoma de México, C.P. 04510 Ciudad de México, Mexico.
| | - Guadalupe Palencia
- Departamento de Neuroinmunología, Laboratorio de Neurobiología Molecular y Celular, Laboratorio Experimental de Enfermedades Neurodegenerativas del Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", C.P. 14269 Ciudad de México, Mexico.
| | - Minerva Calvillo
- Departamento de Neuroinmunología, Laboratorio de Neurobiología Molecular y Celular, Laboratorio Experimental de Enfermedades Neurodegenerativas del Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", C.P. 14269 Ciudad de México, Mexico.
| | - Mayra A Alvarez-Lemus
- División Académica de Ingeniería y Arquitectura, Universidad Juárez Autónoma de Tabasco, C.P. 86040 Tabasco, Mexico.
| | - Athenea Flores-Nájera
- Departamento de Cirugía Experimental, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Secretaria de Salud, 14000 Ciudad de México, Mexico.
| | - Arturo Cruz-Salgado
- Departamento de Neuroinmunología, Laboratorio de Neurobiología Molecular y Celular, Laboratorio Experimental de Enfermedades Neurodegenerativas del Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", C.P. 14269 Ciudad de México, Mexico.
| | - Julio Sotelo
- Departamento de Neuroinmunología, Laboratorio de Neurobiología Molecular y Celular, Laboratorio Experimental de Enfermedades Neurodegenerativas del Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", C.P. 14269 Ciudad de México, Mexico.
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Moparthi SB, Wollert T. Reconstruction of destruction – in vitro reconstitution methods in autophagy research. J Cell Sci 2018; 132:132/4/jcs223792. [DOI: 10.1242/jcs.223792] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
ABSTRACT
Autophagy is one of the most elaborative membrane remodeling systems in eukaryotic cells. Its major function is to recycle cytoplasmic material by delivering it to lysosomes for degradation. To achieve this, a membrane cisterna is formed that gradually captures cargo such as organelles or protein aggregates. The diversity of cargo requires autophagy to be highly versatile to adapt the shape of the phagophore to its substrate. Upon closure of the phagophore, a double-membrane-surrounded autophagosome is formed that eventually fuses with lysosomes. In response to environmental cues such as cytotoxicity or starvation, bulk cytoplasm can be captured and delivered to lysosomes. Autophagy thus supports cellular survival under adverse conditions. During the past decades, groundbreaking genetic and cell biological studies have identified the core machinery involved in the process. In this Review, we are focusing on in vitro reconstitution approaches to decipher the details and spatiotemporal control of autophagy, and how such studies contributed to our current understanding of the pathways in yeast and mammals. We highlight studies that revealed the function of the autophagy machinery at a molecular level with respect to its capacity to remodel membranes.
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Affiliation(s)
- Satish Babu Moparthi
- Membrane Biochemistry and Transport, Institute Pasteur, 28 rue du Dr Roux, 75015 Paris, France
| | - Thomas Wollert
- Membrane Biochemistry and Transport, Institute Pasteur, 28 rue du Dr Roux, 75015 Paris, France
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Baba M, Tomonaga S, Suzuki M, Gen M, Takeda E, Matsuura A, Kamada Y, Baba N. A nuclear membrane-derived structure associated with Atg8 is involved in the sequestration of selective cargo, the Cvt complex, during autophagosome formation in yeast. Autophagy 2018; 15:423-437. [PMID: 30238844 DOI: 10.1080/15548627.2018.1525475] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Macroautophagy (hereafter autophagy) is a conserved intracellular degradation mechanism required for cell survival. A double-membrane structure, the phagophore, is generated to sequester cytosolic cargos destined for degradation in the vacuole. The mechanism involved in the biogenesis of the phagophore is still an open question. We focused on 4 autophagy-related (Atg) proteins (Atg2, Atg9, Atg14, and Atg18), which are involved in the formation of the phagophore in order to gain a more complete understanding of the membrane dynamics that occur during formation of the autophagosome. The corresponding mutants, while defective in autophagy, nonetheless generate the membrane-bound form of Atg8, allowing us to use this protein as a marker for the nascent autophagosome precursor membrane. Using electron microscopy (EM), we discovered in these atg mutants a novel single-membrane structure (~120 to 150 nm in size). Electron tomography revealed that this structure originates from a part of the nuclear membrane, and we have named it the alphasome. Our data suggest that the alphasome is associated with Atg8, and sequesters selective cargo, the Cvt complex, during autophagy. Abbreviations: 3D: three-dimensional; AB: autophagic body; AP: autophagosome; Atg: autophagy-related; Cvt: cytoplasm-to-vacuole targeting; EM: electron microscopy; IEM: immunoelectron microscopy; L: lipid droplet; N: nucleus; NM: nuclear membrane; PAS: phagophore assembly site; PE: phosphatidylethanolamine; prApe1: precursor aminopeptidase I; rER: rough endoplasmic reticulum; TEM: transmission electron microscopy; V: vacuole; VLP: virus-like particle.
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Affiliation(s)
- Misuzu Baba
- a Research Institute for Science and Technology , Kogakuin University , Hachioji, Tokyo , Japan
| | - Sachihiko Tomonaga
- b Major of Informatics , Graduate School, Kogakuin University , Hachioji, Tokyo , Japan
| | - Masato Suzuki
- b Major of Informatics , Graduate School, Kogakuin University , Hachioji, Tokyo , Japan
| | - Maeda Gen
- b Major of Informatics , Graduate School, Kogakuin University , Hachioji, Tokyo , Japan
| | - Eigo Takeda
- c Department of Nanobiology , Graduate School of Advanced Integration Science, Chiba University , Inage-ku, Chiba , Japan
| | - Akira Matsuura
- c Department of Nanobiology , Graduate School of Advanced Integration Science, Chiba University , Inage-ku, Chiba , Japan.,d Department of Biology , Graduate School of Science, Chiba University , Inage-ku, Chiba , Japan
| | - Yoshiaki Kamada
- e Laboratory of Biological Diversity , National Institute for Basic Biology, and School of Life Science, Graduate School of Advanced Studies , Myodaiji Okazaki, Aichi , Japan
| | - Norio Baba
- a Research Institute for Science and Technology , Kogakuin University , Hachioji, Tokyo , Japan.,b Major of Informatics , Graduate School, Kogakuin University , Hachioji, Tokyo , Japan
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The Atg2-Atg18 complex tethers pre-autophagosomal membranes to the endoplasmic reticulum for autophagosome formation. Proc Natl Acad Sci U S A 2018; 115:10363-10368. [PMID: 30254161 DOI: 10.1073/pnas.1806727115] [Citation(s) in RCA: 218] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The biogenesis of double-membrane vesicles called autophagosomes, which sequester and transport intracellular material for degradation in lysosomes or vacuoles, is a central event in autophagy. This process requires a unique set of factors called autophagy-related (Atg) proteins. The Atg proteins assemble to organize the preautophagosomal structure (PAS), at which a cup-shaped membrane, the isolation membrane (or phagophore), forms and expands to become the autophagosome. The molecular mechanism of autophagosome biogenesis remains poorly understood. Previous studies have shown that Atg2 forms a complex with the phosphatidylinositol 3-phosphate (PI3P)-binding protein Atg18 and localizes to the PAS to initiate autophagosome biogenesis; however, the molecular function of Atg2 remains unknown. In this study, we show that Atg2 has two membrane-binding domains in the N- and C-terminal regions and acts as a membrane tether during autophagosome formation in the budding yeast Saccharomyces cerevisiae An amphipathic helix in the C-terminal region binds to membranes and facilitates Atg18 binding to PI3P to target the Atg2-Atg18 complex to the PAS. The N-terminal region of Atg2 is also involved in the membrane binding of this protein but is dispensable for the PAS targeting of the Atg2-Atg18 complex. Our data suggest that this region associates with the endoplasmic reticulum (ER) and is responsible for the formation of the isolation membrane at the PAS. Based on these results, we propose that the Atg2-Atg18 complex tethers the PAS to the ER to initiate membrane expansion during autophagosome formation.
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Insights into autophagosome biogenesis from structural and biochemical analyses of the ATG2A-WIPI4 complex. Proc Natl Acad Sci U S A 2018; 115:E9792-E9801. [PMID: 30185561 DOI: 10.1073/pnas.1811874115] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Autophagy is an enigmatic cellular process in which double-membrane compartments, called "autophagosomes, form de novo adjacent to the endoplasmic reticulum (ER) and package cytoplasmic contents for delivery to lysosomes. Expansion of the precursor membrane phagophore requires autophagy-related 2 (ATG2), which localizes to the PI3P-enriched ER-phagophore junction. We combined single-particle electron microscopy, chemical cross-linking coupled with mass spectrometry, and biochemical analyses to characterize human ATG2A in complex with the PI3P effector WIPI4. ATG2A is a rod-shaped protein that can bridge neighboring vesicles through interactions at each of its tips. WIPI4 binds to one of the tips, enabling the ATG2A-WIPI4 complex to tether a PI3P-containing vesicle to another PI3P-free vesicle. These data suggest that the ATG2A-WIPI4 complex mediates ER-phagophore association and/or tethers vesicles to the ER-phagophore junction, establishing the required organization for phagophore expansion via the transfer of lipid membranes from the ER and/or the vesicles to the phagophore.
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Liu F, Marshall RS, Li F. Understanding and exploiting the roles of autophagy in plants through multi-omics approaches. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 274:146-152. [PMID: 30080598 PMCID: PMC6082170 DOI: 10.1016/j.plantsci.2018.05.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/15/2018] [Accepted: 05/15/2018] [Indexed: 05/20/2023]
Abstract
Autophagy is a highly conserved pathway in eukaryotes that promotes nutrient recycling and cellular homeostasis through the degradation of excess or damaged cytoplasmic constituents. In plants, autophagy is increasingly recognized as a key contributor to development, reproduction, metabolism, leaf senescence, endosperm and grain development, pathogen defense, and tolerance to abiotic and biotic stresses. Characterizing the functional transcriptomic, proteomic, and metabolomic networks relating to autophagy in plants subjected to various extra- and intra-cellular stimuli may help to identify components associated with the pathway. As such, the integration of multi-omics approaches (i.e., transcriptomics, proteomics and metabolomics), along with cellular, genetic and functional analyses, could provide a global perspective regarding the effects of autophagy on plant metabolism, development and stress responses. In this mini-review, recent research progress in plant autophagy is discussed, highlighting the importance of high-throughput omics approaches for defining the underpinning molecular mechanisms of autophagy and understanding its associated regulatory network.
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Affiliation(s)
- Fen Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Richard S Marshall
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Faqiang Li
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
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Gómez-Sánchez R, Rose J, Guimarães R, Mari M, Papinski D, Rieter E, Geerts WJ, Hardenberg R, Kraft C, Ungermann C, Reggiori F. Atg9 establishes Atg2-dependent contact sites between the endoplasmic reticulum and phagophores. J Cell Biol 2018; 217:2743-2763. [PMID: 29848619 PMCID: PMC6080931 DOI: 10.1083/jcb.201710116] [Citation(s) in RCA: 202] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 03/07/2018] [Accepted: 05/02/2018] [Indexed: 11/22/2022] Open
Abstract
The autophagy-related (Atg) proteins play a key role in the formation of autophagosomes, the hallmark of autophagy. The function of the cluster composed by Atg2, Atg18, and transmembrane Atg9 is completely unknown despite their importance in autophagy. In this study, we provide insights into the molecular role of these proteins by identifying and characterizing Atg2 point mutants impaired in Atg9 binding. We show that Atg2 associates to autophagosomal membranes through lipid binding and independently from Atg9. Its interaction with Atg9, however, is key for Atg2 confinement to the growing phagophore extremities and subsequent association of Atg18. Assembly of the Atg9-Atg2-Atg18 complex is important to establish phagophore-endoplasmic reticulum (ER) contact sites. In turn, disruption of the Atg2-Atg9 interaction leads to an aberrant topological distribution of both Atg2 and ER contact sites on forming phagophores, which severely impairs autophagy. Altogether, our data shed light in the interrelationship between Atg9, Atg2, and Atg18 and highlight the possible functional relevance of the phagophore-ER contact sites in phagophore expansion.
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Affiliation(s)
- Rubén Gómez-Sánchez
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Jaqueline Rose
- Department of Biology/Chemistry, Biochemistry Section, University of Osnabrück, Osnabrück, Germany
| | - Rodrigo Guimarães
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Cell Biology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Muriel Mari
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Daniel Papinski
- Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Ester Rieter
- Department of Cell Biology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Willie J Geerts
- Biomolecular Imaging, Bijvoet Center, Utrecht University, Utrecht, Netherlands
| | - Ralph Hardenberg
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Claudine Kraft
- Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
- Institute of Biochemistry and Molecular Biology, Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christian Ungermann
- Department of Biology/Chemistry, Biochemistry Section, University of Osnabrück, Osnabrück, Germany
| | - Fulvio Reggiori
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Cell Biology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
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Liu W, Duan X, Fang X, Shang W, Tong C. Mitochondrial protein import regulates cytosolic protein homeostasis and neuronal integrity. Autophagy 2018; 14:1293-1309. [PMID: 29909722 DOI: 10.1080/15548627.2018.1474991] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Neurodegeneration is characterized by protein aggregate deposits and mitochondrial malfunction. Reduction in Tom40 (translocase of outer membrane 40) expression, a key subunit of the translocase of the outer mitochondrial membrane complex, led to accumulation of ubiquitin (Ub)-positive protein aggregates engulfed by Atg8a-positive membranes. Other macroautophagy markers were also abnormally accumulated. Autophagy was induced but the majority of autophagosomes failed to fuse with lysosomes when Tom40 was downregulated. In Tom40 RNAi tissues, autophagosome-like (AL) structures, often not sealed, were 10 times larger than starvation induced autophagosomes. Atg5 downregulation abolished Tom40 RNAi induced AL structure formation, but the Ub-positive aggregates remained, whereas knock down of Syx17, a gene required for autophagosome-lysosome fusion, led to the disappearance of giant AL structures and accumulation of small autophagosomes and phagophores near the Ub-positive aggregates. The protein aggregates contained many mitochondrial preproteins, cytosolic proteins, and proteasome subunits. Proteasome activity and ATP levels were reduced and the ROS levels was increased in Tom40 RNAi tissues. The simultaneous inhibition of proteasome activity, reduction in ATP production, and increase in ROS, but none of these conditions alone, can mimic the imbalanced proteostasis phenotypes observed in Tom40 RNAi cells. Knockdown of ref(2)P or ectopic expression of Pink1 and park greatly reduced aggregate formation in Tom40 RNAi tissues. In nerve tissues, reduction in Tom40 activity leads to aggregate formation and neurodegeneration. Rather than diminishing the neurodegenerative phenotypes, overexpression of Pink1 enhanced them. We proposed that defects in mitochondrial protein import may be the key to linking imbalanced proteostasis and mitochondrial defects. ABBREVIATIONS AL: autophagosome-like; Atg12: Autophagy-related 12; Atg14: Autophagy-related 14; Atg16: Autophagy-related 16; Atg5: Autophagy-related 5; Atg6: Autophagy-related 6; Atg8a: Autophagy-related 8a; Atg9: Autophagy-related 9; ATP: adenosine triphosphate; Cas9: CRISPR associated protein 9; cDNA: complementary DNA; COX4: Cytochrome c oxidase subunit 4; CRISPR: clustered regularly interspaced short palindromic repeats; Cyt-c1: Cytochrome c1; DAPI: 4,6-diamidino-2-phenylindole dihydrochloride; Dcr-2: Dicer-2; FLP: Flippase recombination enzyme; FRT: FLP recombination target; GFP: green fluorescent protein; GO: gene ontology; gRNA: guide RNA; Hsp60: Heat shock protein 60A; HDAC6: Histone deacetylase 6; htt: huntingtin; Idh: Isocitrate dehydrogenase; IFA: immunofluorescence assay; Irp-1A: Iron regulatory protein 1A; kdn: knockdown; Marf: Mitochondrial assembly regulatory factor; MitoGFP: Mitochondrial-GFP; MS: mass spectrometry; MTPAP: mitochondrial poly(A) polymerase; Nmnat: Nicotinamide mononucleotide adenylyltransferase; OE: overexpression; Pink1/PINK1: PTEN-induced putative kinase 1; polyQ: polyglutamine; PRKN: parkin RBR E3 ubiquitin protein ligase; Prosα4: proteasome α4 subunit; Prosβ1: proteasome β1 subunit; Prosβ5: proteasome β5 subunit; Prosβ7: proteasome β7 subunit; ref(2)P: refractory to sigma P; RFP: red fluorescent protein; RNAi: RNA interference; ROS: reactive oxygen species; Rpn11: Regulatory particle non-ATPase 11; Rpt2: Regulatory particle triple-A ATPase 2; scu: scully; sicily: severe impairment of CI with lengthened youth; sesB: stress-sensitive B; Syx17: Syntaxin17; TEM: transmission electron microscopy; ttm50: tiny tim 50; Tom: translocase of the outer membrane; Tom20: translocase of outer membrane 20; Tom40: translocase of outer membrane 40; Tom70: translocase of outer membrane 70; UAS: upstream active sequence; Ub: ubiquitin; VNC: ventral nerve cord; ZFYVE1: zinc finger FYVE-type containing 1.
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Affiliation(s)
- Wei Liu
- a Life Sciences Institute and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , China
| | - Xiuying Duan
- a Life Sciences Institute and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , China
| | - Xuefei Fang
- a Life Sciences Institute and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , China
| | - Weina Shang
- a Life Sciences Institute and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , China
| | - Chao Tong
- a Life Sciences Institute and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , China
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123
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van Leeuwen W, van der Krift F, Rabouille C. Modulation of the secretory pathway by amino-acid starvation. J Cell Biol 2018; 217:2261-2271. [PMID: 29669743 PMCID: PMC6028531 DOI: 10.1083/jcb.201802003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/28/2018] [Accepted: 03/29/2018] [Indexed: 12/30/2022] Open
Abstract
As a major anabolic pathway, the secretory pathway needs to adapt to the demands of the surrounding environment and responds to different exogenous signals and stimuli. In this context, the transport in the early secretory pathway from the endoplasmic reticulum (ER) to the Golgi apparatus appears particularly regulated. For instance, protein export from the ER is critically stimulated by growth factors. Conversely, nutrient starvation also modulates functions of the early secretory pathway in multiple ways. In this review, we focus on amino-acid starvation and how the function of the early secretory pathway is redirected to fuel autophagy, how the ER exit sites are remodeled into novel cytoprotective stress assemblies, and how secretion is modulated in vivo in starving organisms. With the increasingly exciting knowledge on mechanistic target of rapamycin complex 1 (mTORC1), the major nutrient sensor, it is also a good moment to establish how the modulation of the secretory pathway by amino-acid restriction intersects with this major signaling hub.
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Affiliation(s)
- Wessel van Leeuwen
- Hubrecht Institute of the Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, Netherlands
| | - Felix van der Krift
- Hubrecht Institute of the Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, Netherlands
| | - Catherine Rabouille
- Hubrecht Institute of the Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, Netherlands .,Department of Cell Biology, University Medical Center Groningen, Groningen, Netherlands
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124
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Nguyen HM, Liu S, Daher W, Tan F, Besteiro S. Characterisation of two Toxoplasma PROPPINs homologous to Atg18/WIPI suggests they have evolved distinct specialised functions. PLoS One 2018; 13:e0195921. [PMID: 29659619 PMCID: PMC5901921 DOI: 10.1371/journal.pone.0195921] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/02/2018] [Indexed: 01/20/2023] Open
Abstract
Toxoplasma gondii is a parasitic protist possessing a limited set of proteins involved in the autophagy pathway, a self-degradative machinery for protein and organelle recycling. This distant eukaryote has even repurposed part of this machinery, centered on protein ATG8, for a non-degradative function related to the maintenance of the apicoplast, a parasite-specific organelle. However, some evidence also suggest Toxoplasma is able to generate autophagic vesicles upon stress, and that some autophagy-related proteins, such as ATG9, might be involved solely in the canonical autophagy function. Here, we have characterised TgPROP1 and TgPROP2, two Toxoplasma proteins containing WD-40 repeat that can bind lipids for their recruitment to vesicular structures upon stress. They belong to the PROPPIN family and are homologues to ATG18/WIPI, which are known to be important for the autophagic process. We conducted a functional analysis of these two Toxoplasma PROPPINs. One of them is dispensable for normal in vitro growth, although it may play a role for parasite survival in specific stress conditions or for parasite fitness in the host, through a canonical autophagy-related function. The other, however, seems important for parasite viability in normal growth conditions and could be primarily involved in a non-canonical function. These divergent roles for two proteins from the same family illustrate the functional versatility of the autophagy-related machinery in Toxoplasma.
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Affiliation(s)
- Hoa Mai Nguyen
- DIMNP, UMR5235 CNRS - Université de Montpellier, Montpellier, France
| | - Shuxian Liu
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, People’s Republic of China
| | - Wassim Daher
- DIMNP, UMR5235 CNRS - Université de Montpellier, Montpellier, France
| | - Feng Tan
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, People’s Republic of China
- * E-mail: (FT); (SB)
| | - Sébastien Besteiro
- DIMNP, UMR5235 CNRS - Université de Montpellier, Montpellier, France
- * E-mail: (FT); (SB)
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Lin MG, Schöneberg J, Davies CW, Ren X, Hurley JH. The dynamic Atg13-free conformation of the Atg1 EAT domain is required for phagophore expansion. Mol Biol Cell 2018. [PMID: 29540529 PMCID: PMC5935072 DOI: 10.1091/mbc.e17-04-0258] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Yeast macroautophagy begins with the de novo formation of a double-membrane phagophore at the preautophagosomal structure/phagophore assembly site (PAS), followed by its expansion into the autophagosome responsible for cargo engulfment. The kinase Atg1 is recruited to the PAS by Atg13 through interactions between the EAT domain of the former and the tMIM motif of the latter. Mass-spectrometry data have shown that, in the absence of Atg13, the EAT domain structure is strikingly dynamic, but the function of this Atg13-free dynamic state has been unclear. We used structure-based mutational analysis and quantitative and superresolution microscopy to show that Atg1 is present on autophagic puncta at, on average, twice the stoichiometry of Atg13. Moreover, Atg1 colocalizes with the expanding autophagosome in a manner dependent on Atg8 but not Atg13. We used isothermal titration calorimetry and crystal structure information to design an EAT domain mutant allele ATG1DD that selectively perturbs the function of the Atg13-free state. Atg1DD shows reduced PAS formation and does not support phagophore expansion, showing that the EAT domain has an essential function that is separate from its Atg13-dependent role in autophagy initiation.
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Affiliation(s)
- Mary G Lin
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720
| | - Johannes Schöneberg
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720
| | - Christopher W Davies
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720
| | - Xuefeng Ren
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720
| | - James H Hurley
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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Park SH, Kang MK, Choi YJ, Kim YH, Antika LD, Kim DY, Lee EJ, Lim SS, Kang YH. α-Asarone blocks 7β-hydroxycholesterol-exposed macrophage injury through blocking elF2α phosphorylation and prompting beclin-1-dependent autophagy. Oncotarget 2018; 8:7370-7383. [PMID: 28088783 PMCID: PMC5352328 DOI: 10.18632/oncotarget.14566] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 01/02/2017] [Indexed: 12/27/2022] Open
Abstract
Macrophage apoptosis is salient in advanced atherosclerotic lesions and is induced by several stimuli including endoplasmic reticulum (ER) stress. This study examined that a-asarone present in purple perilla abrogated macrophage injury caused by oxysterols via ER stress- and autophagy-mediated mechanisms. Nontoxic a-asarone at 1-20 M attenuated 7β-hydroxycholesterol-induced activation of eukaryotic initiation factor 2a in macrophages leading to C/EBP homologous protein (CHOP) expression and apoptosis due to sustained ER stress. The a-asarone treatment increased the formation of autophagolysosomes localizing in perinuclear regions of 7β-hydroxycholesterol-exposed macrophages. Consistently, this compound promoted the induction of the key autophagic proteins of beclin-1, vacuolar protein sorting 34 and p150 responsible for vesicle nucleation, and prompted the conversion of microtubule-associated protein 1A/1B-light chain 3 and the induction of p62, neighbor of BRCA1 and autophagy-related (Atg) 12-Atg5-Atg16L conjugate involved in phagophore expansion and autophagosome formation. Additionally, a-asarone increased ER phosphorylation of bcl-2 facilitating beclin-1 entry to autophagic process. Furthermore, the deletion of Atg5 or beclin-1 gene enhanced apoptotic CHOP induction. Collectively, a-asarone-stimulated autophagy may be potential multi-targeted therapeutic avenues in treating ER stress-associated macrophage apoptosis.
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Affiliation(s)
- Sin-Hye Park
- Department of Food Science and Nutrition, Hallym University, Chuncheon, Korea
| | - Min-Kyung Kang
- Department of Food Science and Nutrition, Hallym University, Chuncheon, Korea
| | - Yean-Jung Choi
- Department of Food Science and Nutrition, Hallym University, Chuncheon, Korea
| | - Yun-Ho Kim
- Department of Food Science and Nutrition, Hallym University, Chuncheon, Korea
| | - Lucia Dwi Antika
- Department of Food Science and Nutrition, Hallym University, Chuncheon, Korea
| | - Dong Yeon Kim
- Department of Food Science and Nutrition, Hallym University, Chuncheon, Korea
| | - Eun-Jung Lee
- Department of Food Science and Nutrition, Hallym University, Chuncheon, Korea
| | - Soon Sung Lim
- Department of Food Science and Nutrition, Hallym University, Chuncheon, Korea
| | - Young-Hee Kang
- Department of Food Science and Nutrition, Hallym University, Chuncheon, Korea
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Graef M. Lipid droplet-mediated lipid and protein homeostasis in budding yeast. FEBS Lett 2018; 592:1291-1303. [PMID: 29397034 PMCID: PMC5947121 DOI: 10.1002/1873-3468.12996] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 01/24/2018] [Accepted: 01/25/2018] [Indexed: 12/25/2022]
Abstract
Lipid droplets are conserved specialized organelles that store neutral lipids. Our view on this unique organelle has evolved from a simple fat deposit to a highly dynamic and functionally diverse hub—one that mediates the buffering of fatty acid stress and the adaptive reshaping of lipid metabolism to promote membrane and organelle homeostasis and the integrity of central proteostasis pathways, including autophagy, which ensure stress resistance and cell survival. This Review will summarize the recent developments in the budding yeast Saccharomyces cerevisiae, as this model organism has been instrumental in deciphering the fundamental mechanisms and principles of lipid droplet biology and interconnecting lipid droplets with many unanticipated cellular functions applicable to many other cell systems.
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Affiliation(s)
- Martin Graef
- Max Planck Institute for Biology of Ageing, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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128
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Gao J, Langemeyer L, Kümmel D, Reggiori F, Ungermann C. Molecular mechanism to target the endosomal Mon1-Ccz1 GEF complex to the pre-autophagosomal structure. eLife 2018; 7:31145. [PMID: 29446751 PMCID: PMC5841931 DOI: 10.7554/elife.31145] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 02/12/2018] [Indexed: 11/13/2022] Open
Abstract
During autophagy, a newly formed double membrane surrounds its cargo to generate the so-called autophagosome, which then fuses with a lysosome after closure. Previous work implicated that endosomal Rab7/Ypt7 associates to autophagosomes prior to their fusion with lysosomes. Here, we unravel how the Mon1-Ccz1 guanosine exchange factor (GEF) acting upstream of Ypt7 is specifically recruited to the pre-autophagosomal structure under starvation conditions. We find that Mon1-Ccz1 directly binds to Atg8, the yeast homolog of the members of the mammalian LC3 protein family. This requires at least one LIR motif in the Ccz1 C-terminus, which is essential for autophagy but not for endosomal transport. In agreement, only wild-type, but not LIR-mutated Mon1-Ccz1 promotes Atg8-dependent activation of Ypt7. Our data reveal how GEF targeting can specify the fate of a newly formed organelle and provide new insights into the regulation of autophagosome-lysosome fusion. Autophagy is a word derived from the Greek for “self-eating”. It describes a biological process in which a living cell breaks down its own material to release their chemical building blocks that can then be used to make new molecules. Autophagy is often triggered when a cell becomes damaged or when nutrients are in short supply. The hallmark of autophagy is the formation of structures called autophagosomes. These structures capture the cellular material, fuse with other compartments in the cell – namely endosomes in animals and vacuoles in yeast – and then deliver the material inside, ready to be broken down. For an autophagosome to fuse to an endosome or a vacuole, small proteins of the Rab protein family must be located on the surface of the autophagosome. Rab proteins are recruited to this surface by enzymes known as GEFs. However it remains unclear how most GEFs get to the surface of a compartment within the cell to begin with. The Mon1-Ccz1 complex is a GEF that occurs in yeast and animals, including fruit flies and humans. It is found on endosomes, and was recently shown to also localize to autophagosomes. Now, Gao et al. report that, in yeast, the Mon1-Ccz1 complex binds directly to a protein named Atg8. This protein is anchored on to the surface of autophagosomes, and is closely related to other proteins in animal cells. Gao et al. discovered that this specific GEF binds to Atg8 via at least one binding site on its Ccz1 component. This binding site is only needed for the GEF to localize to the autophagosomes; the Mon1-Czz1 complex can still bind to endosomes without it. Blocking the GEF from binding to Atg8 stopped the autophagosomes from fusing with vacuoles. These findings reveal how a GEF can be targeted to two distinct compartments in the cell: endosomes and autophagosomes. Further work is now needed to understand how this process is regulated by the availability of nutrients or damage to the cell, to ensure that autophagy is only triggered under the right conditions. Also, because cancer cells often rely on autophagy to survive, the molecules that regulate this process could represent possible targets for new anticancer drugs.
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Affiliation(s)
- Jieqiong Gao
- Biochemistry Section, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Lars Langemeyer
- Biochemistry Section, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Daniel Kümmel
- Structural Biology Section, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Fulvio Reggiori
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Christian Ungermann
- Biochemistry Section, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
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Takahashi Y, Tsotakos N, Liu Y, Young MM, Serfass J, Tang Z, Abraham T, Wang HG. The Bif-1-Dynamin 2 membrane fission machinery regulates Atg9-containing vesicle generation at the Rab11-positive reservoirs. Oncotarget 2018; 7:20855-68. [PMID: 26980706 PMCID: PMC4991497 DOI: 10.18632/oncotarget.8028] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 02/15/2016] [Indexed: 01/08/2023] Open
Abstract
Atg9 is a multispanning transmembrane protein that is required for autophagosome formation. During autophagy, vesicles containing Atg9 are generated through an unknown mechanism and delivered to the autophagosome formation sites. We have previously reported that Atg9-containing membranes undergo continuous tubulation and fission during nutrient starvation in a manner dependent on the curvature-inducing protein Bif-1/Sh3glb1. Here, we identify Dynamin 2 (DNM2) as a Bif-1-interacting protein that mediates the fission of Atg9-containing membranes during autophagy. The interaction of Bif-1 and DNM2 is enhanced upon nutrient starvation, and Bif-1 and DNM2 cooperatively induce the generation of Atg9-containing vesicles. Inhibition of the GTPase activity of DNM2 results in the accumulation of Atg9-positive tubular structures that originate from a Rab11-positive reservoir. Although Atg9 seems to be constitutively trafficked to the reservoir regardless of Bif-1 expression, membrane tubulation from the Atg9 reservoir is dependent on Bif-1 and is strongly induced upon nutrient starvation. These findings suggest that the generation of Atg9 vesicles from a Rab11-positive reservoir is tightly controlled by the Bif-1-DNM2 membrane fission machinery in response to cellular demand for autophagy.
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Affiliation(s)
- Yoshinori Takahashi
- Department of Pediatrics, Penn State University College of Medicine, Hershey, PA 17033, USA.,Penn State Cancer Institute, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Nikolaos Tsotakos
- Department of Pediatrics, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Ying Liu
- Department of Pharmacology, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Megan M Young
- Department of Pediatrics, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Jacob Serfass
- Department of Pharmacology, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Zhenyuan Tang
- Department of Pharmacology, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Thomas Abraham
- Department of Neural and Behavioral Science and the Microscopy Imaging Facility, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Hong-Gang Wang
- Department of Pediatrics, Penn State University College of Medicine, Hershey, PA 17033, USA.,Department of Pharmacology, Penn State University College of Medicine, Hershey, PA 17033, USA.,Penn State Cancer Institute, Penn State University College of Medicine, Hershey, PA 17033, USA
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130
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Kawaoka T, Ohnuki S, Ohya Y, Suzuki K. Morphometric analysis of autophagy-related structures in Saccharomyces cerevisiae. Autophagy 2017; 13:2104-2110. [PMID: 28980865 DOI: 10.1080/15548627.2017.1384888] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
When macroautophagy (autophagy) is induced by nutrient starvation or rapamycin treatment, Atg (autophagy-related) proteins are assembled at a restricted region close to the vacuole. Subsequently, the phagophore expands to form a closed autophagosome. In Saccharomyces cerevisiae cells overexpressing precursor Ape1 (prApe1), a specific autophagosome cargo protein, the phagophore can be visualized as a cup-shaped structure labeled with green fluorescent protein (GFP)-tagged Atg8. Previously, our group has shown that the maximum length of GFP-Atg8-labeled structures reflects the magnitude of bulk autophagy. In that study, the morphological parameters of the autophagy-related structures were extracted manually, requiring a great deal of time. Moreover, only well-expanded phagophores were subjected to further analysis. Here we report Qautas (Quantitative autophagy-related structure analysis system), a high-throughput and comprehensive system for morphological analysis of autophagy-related structures using a combination of image processing and machine learning. We describe both the manual method and Qautas in detail.
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Affiliation(s)
- Tatsuya Kawaoka
- a Department of Integrated Biosciences , Graduate School of Frontier Sciences , University of Tokyo , Kashiwa , Chiba , Japan
| | - Shinsuke Ohnuki
- a Department of Integrated Biosciences , Graduate School of Frontier Sciences , University of Tokyo , Kashiwa , Chiba , Japan
| | - Yoshikazu Ohya
- a Department of Integrated Biosciences , Graduate School of Frontier Sciences , University of Tokyo , Kashiwa , Chiba , Japan
| | - Kuninori Suzuki
- a Department of Integrated Biosciences , Graduate School of Frontier Sciences , University of Tokyo , Kashiwa , Chiba , Japan.,b Bioimaging Center , Graduate School of Frontier Sciences , University of Tokyo , Kashiwa , Chiba , Japan
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131
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Lussignol M, Esclatine A. Herpesvirus and Autophagy: "All Right, Everybody Be Cool, This Is a Robbery!". Viruses 2017; 9:v9120372. [PMID: 29207540 PMCID: PMC5744147 DOI: 10.3390/v9120372] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 11/26/2017] [Accepted: 11/27/2017] [Indexed: 12/20/2022] Open
Abstract
Autophagy is an essential vacuolar process of the cell, leading to lysosomal degradation and recycling of proteins and organelles, which is extremely important in maintaining homeostasis. Multiple roles have been now associated with autophagy, in particular a pro-survival role in nutrient starvation or in stressful environments, a role in life span extension, in development, or in innate and adaptive immunity. This cellular process can also take over microorganisms or viral proteins inside autophagosomes and degrade them directly in autolysosomes and is then called xenophagy and virophagy, respectively. Several Herpesviruses have developed strategies to escape this degradation, by expression of specific anti-autophagic proteins. However, we are increasingly discovering that Herpesviruses hijack autophagy, rather than just fight it. This beneficial effect is obvious since inhibition of autophagy will lead to decreased viral titers for human cytomegalovirus (HCMV), Epstein-Barr virus (EBV) or Varicella-Zoster virus (VZV), for example. Conversely, autophagy stimulation will improve viral multiplication. The autophagic machinery can be used in whole or in part, and can optimize viral propagation or persistence. Some viruses block maturation of autophagosomes to avoid the degradation step, then autophagosomal membranes are used to contribute to the envelopment and/or the egress of viral particles. On the other hand, VZV stimulates the whole process of autophagy to subvert it in order to use vesicles containing ATG (autophagy-related) proteins and resembling amphisomes for their transport in the cytoplasm. During latency, autophagy can also be activated by latent proteins encoded by different oncogenic Herpesviruses to promote cell survival and achieve long term viral persistence in vivo. Finally, reactivation of gammaherpesvirus Murid Herpesvirus 68 (MHV68) in mice appears to be positively modulated by autophagy, in order to control the level of inflammation. Therefore, Herpesviruses appear to behave more like thieves than fugitives.
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Affiliation(s)
- Marion Lussignol
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.
| | - Audrey Esclatine
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.
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132
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Sánchez-Wandelmer J, Reggiori F. Atg4 in autophagosome biogenesis. Oncotarget 2017; 8:108290-108291. [PMID: 29312531 PMCID: PMC5752444 DOI: 10.18632/oncotarget.22714] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/24/2017] [Indexed: 12/26/2022] Open
Affiliation(s)
- Jana Sánchez-Wandelmer
- Fulvio Reggiori: Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Fulvio Reggiori
- Fulvio Reggiori: Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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133
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Autophagy in the context of the cellular membrane-trafficking system: the enigma of Atg9 vesicles. Biochem Soc Trans 2017; 45:1323-1331. [PMID: 29150528 PMCID: PMC5730941 DOI: 10.1042/bst20170128] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 10/11/2017] [Accepted: 10/16/2017] [Indexed: 12/15/2022]
Abstract
Macroautophagy is an intracellular degradation system that involves the de novo formation of membrane structures called autophagosomes, although the detailed process by which membrane lipids are supplied during autophagosome formation is yet to be elucidated. Macroautophagy is thought to be associated with canonical membrane trafficking, but several mechanistic details are still missing. In this review, the current understanding and potential mechanisms by which membrane trafficking participates in macroautophagy are described, with a focus on the enigma of the membrane protein Atg9, for which the proximal mechanisms determining its movement are disputable, despite its key role in autophagosome formation.
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134
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Scacioc A, Schmidt C, Hofmann T, Urlaub H, Kühnel K, Pérez-Lara Á. Structure based biophysical characterization of the PROPPIN Atg18 shows Atg18 oligomerization upon membrane binding. Sci Rep 2017; 7:14008. [PMID: 29070817 PMCID: PMC5656675 DOI: 10.1038/s41598-017-14337-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 09/19/2017] [Indexed: 11/29/2022] Open
Abstract
PROPPINs (β-propellers that bind polyphosphoinositides) are PtdIns3P and PtdIns(3,5)P2 binding autophagy related proteins. They contain two phosphatidylinositolphosphate (PIP) binding sites and a conserved FRRG motif is essential for PIP binding. Here we present the 2.0 Å resolution crystal structure of the PROPPIN Atg18 from Pichia angusta. We designed cysteine mutants for labelling with the fluorescence dyes to probe the distances of the mutants to the membrane. These measurements support a model for PROPPIN-membrane binding, where the PROPPIN sits in a perpendicular or slightly tilted orientation on the membrane. Stopped-flow measurements suggest that initial PROPPIN-membrane binding is driven by non-specific PIP interactions. The FRRG motif then retains the protein in the membrane by binding two PIP molecules as evident by a lower dissociation rate for Atg18 in comparison with its PIP binding deficient FTTG mutant. We demonstrate that the amine-specific cross-linker Bis(sulfosuccinimidyl)suberate (BS3), which is used for protein-protein cross-linking can also be applied for cross-linking proteins and phosphatidylethanolamine (PE). Cross-linking experiments with liposome bound Atg18 yielded several PE cross-linked peptides. We also observed intermolecular cross-linked peptides, which indicated Atg18 oligomerization. FRET-based stopped-flow measurements revealed that Atg18 rapidly oligomerizes upon membrane binding while it is mainly monomeric in solution.
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Affiliation(s)
- Andreea Scacioc
- Research Group Autophagy, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Carla Schmidt
- Interdisciplinary research center HALOmem, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle, Germany. .,Bioanalytical Mass Spectrometry Group, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany.
| | - Tommy Hofmann
- Interdisciplinary research center HALOmem, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany.,Bioanalytics Group, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075, Göttingen, Germany
| | - Karin Kühnel
- Research Group Autophagy, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany. .,Nature Communications, 4 Crinan Street, London, N1 9XW, United Kingdom.
| | - Ángel Pérez-Lara
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany.
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135
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Gopaldass N, Fauvet B, Lashuel H, Roux A, Mayer A. Membrane scission driven by the PROPPIN Atg18. EMBO J 2017; 36:3274-3291. [PMID: 29030482 DOI: 10.15252/embj.201796859] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 09/07/2017] [Accepted: 09/08/2017] [Indexed: 12/14/2022] Open
Abstract
Sorting, transport, and autophagic degradation of proteins in endosomes and lysosomes, as well as the division of these organelles, depend on scission of membrane-bound tubulo-vesicular carriers. How scission occurs is poorly understood, but family proteins bind these membranes. Here, we show that the yeast PROPPIN Atg18 carries membrane scission activity. Purified Atg18 drives tubulation and scission of giant unilamellar vesicles. Upon membrane contact, Atg18 folds its unstructured CD loop into an amphipathic α-helix that inserts into the bilayer. This allows the protein to engage its two lipid binding sites for PI3P and PI(3,5)P2 PI(3,5)P2 induces Atg18 oligomerization, which should concentrate lipid-inserted α-helices in the outer membrane leaflet and drive membrane tubulation and scission. The scission activity of Atg18 is compatible with its known roles in endo-lysosomal protein trafficking, autophagosome biogenesis, and vacuole fission. Key features required for membrane tubulation and scission by Atg18 are shared by other PROPPINs, suggesting that membrane scission may be a generic function of this protein family.
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Affiliation(s)
- Navin Gopaldass
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Bruno Fauvet
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Hilal Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Aurélien Roux
- Department of Biochemistry, University of Geneva, Geneva, Switzerland.,Swiss National Centre for Competence in Research Program Chemical Biology, Geneva, Switzerland
| | - Andreas Mayer
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
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136
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Long non-coding RNAs involved in autophagy regulation. Cell Death Dis 2017; 8:e3073. [PMID: 28981093 PMCID: PMC5680586 DOI: 10.1038/cddis.2017.464] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 08/14/2017] [Accepted: 08/17/2017] [Indexed: 01/17/2023]
Abstract
Autophagy degrades non-functioning or damaged proteins and organelles to maintain cellular homeostasis in a physiological or pathological context. Autophagy can be protective or detrimental, depending on its activation status and other conditions. Therefore, autophagy has a crucial role in a myriad of pathophysiological processes. From the perspective of autophagy-related (ATG) genes, the molecular dissection of autophagy process and the regulation of its level have been largely unraveled. However, the discovery of long non-coding RNAs (lncRNAs) provides a new paradigm of gene regulation in almost all important biological processes, including autophagy. In this review, we highlight recent advances in autophagy-associated lncRNAs and their specific autophagic targets, as well as their relevance to human diseases such as cancer, cardiovascular disease, diabetes and cerebral ischemic stroke.
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137
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Farhan H, Kundu M, Ferro-Novick S. The link between autophagy and secretion: a story of multitasking proteins. Mol Biol Cell 2017; 28:1161-1164. [PMID: 28468940 PMCID: PMC5415012 DOI: 10.1091/mbc.e16-11-0762] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 02/28/2017] [Accepted: 03/02/2017] [Indexed: 01/01/2023] Open
Abstract
The secretory and autophagy pathways can be thought of as the biosynthetic (i.e., anabolic) and degradative (i.e., catabolic) branches of the endomembrane system. In analogy to anabolic and catabolic pathways in metabolism, there is mounting evidence that the secretory and autophagy pathways are intimately linked and that certain regulatory elements are shared between them. Here we highlight the parallels and points of intersection between these two evolutionarily highly conserved and fundamental endomembrane systems. The intersection of these pathways may play an important role in remodeling membranes during cellular stress.
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Affiliation(s)
- Hesso Farhan
- Institute of Basic Medical Sciences, University of Oslo, 3072 Oslo, Norway
| | - Mondira Kundu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Susan Ferro-Novick
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093
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138
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Abstract
Macroautophagy is an intracellular pathway used for targeting of cellular components to the lysosome for their degradation and involves sequestration of cytoplasmic material into autophagosomes formed from a double membrane structure called the phagophore. The nucleation and elongation of the phagophore is tightly regulated by several autophagy-related (ATG) proteins, but also involves vesicular trafficking from different subcellular compartments to the forming autophagosome. Such trafficking must be tightly regulated by various intra- and extracellular signals to respond to different cellular stressors and metabolic states, as well as the nature of the cargo to become degraded. We are only starting to understand the interconnections between different membrane trafficking pathways and macroautophagy. This review will focus on the membrane trafficking machinery found to be involved in delivery of membrane, lipids, and proteins to the forming autophagosome and in the subsequent autophagosome fusion with endolysosomal membranes. The role of RAB proteins and their regulators, as well as coat proteins, vesicle tethers, and SNARE proteins in autophagosome biogenesis and maturation will be discussed.
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139
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Torggler R, Papinski D, Brach T, Bas L, Schuschnig M, Pfaffenwimmer T, Rohringer S, Matzhold T, Schweida D, Brezovich A, Kraft C. Two Independent Pathways within Selective Autophagy Converge to Activate Atg1 Kinase at the Vacuole. Mol Cell 2017; 64:221-235. [PMID: 27768871 DOI: 10.1016/j.molcel.2016.09.008] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 08/15/2016] [Accepted: 09/07/2016] [Indexed: 12/22/2022]
Abstract
Autophagy is a potent cellular degradation pathway, and its activation needs to be tightly controlled. Cargo receptors mediate selectivity during autophagy by bringing cargo to the scaffold protein Atg11 and, in turn, to the autophagic machinery, including the central autophagy kinase Atg1. Here we show how selective autophagy is tightly regulated in space and time to prevent aberrant Atg1 kinase activation and autophagy induction. We established an induced bypass approach (iPass) that combines genetic deletion with chemically induced dimerization to evaluate the roles of Atg13 and cargo receptors in Atg1 kinase activation and selective autophagy progression. We show that Atg1 activation does not require cargo receptors, cargo-bound Atg11, or Atg13 per se. Rather, these proteins function in two independent pathways that converge to activate Atg1 at the vacuole. This pathway architecture underlies the spatiotemporal control of Atg1 kinase activity, thereby preventing inappropriate autophagosome formation.
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Affiliation(s)
- Raffaela Torggler
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Daniel Papinski
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Thorsten Brach
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Levent Bas
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Martina Schuschnig
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Thaddäus Pfaffenwimmer
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Sabrina Rohringer
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Tamara Matzhold
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - David Schweida
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Andrea Brezovich
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria
| | - Claudine Kraft
- Max F. Perutz Laboratories, Vienna Biocenter, University of Vienna, 1030 Vienna, Austria.
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140
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The ER-Localized Transmembrane Protein EPG-3/VMP1 Regulates SERCA Activity to Control ER-Isolation Membrane Contacts for Autophagosome Formation. Mol Cell 2017; 67:974-989.e6. [PMID: 28890335 DOI: 10.1016/j.molcel.2017.08.005] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/23/2017] [Accepted: 08/08/2017] [Indexed: 01/27/2023]
Abstract
During autophagosome formation in mammalian cells, isolation membranes (IMs; autophagosome precursors) dynamically contact the ER. Here, we demonstrated that the ER-localized metazoan-specific autophagy protein EPG-3/VMP1 controls ER-IM contacts. Loss of VMP1 causes stable association of IMs with the ER, thus blocking autophagosome formation. Interaction of WIPI2 with the ULK1/FIP200 complex and PI(3)P contributes to the formation of ER-IM contacts, and these interactions are enhanced by VMP1 depletion. VMP1 controls contact formation by promoting SERCA (sarco[endo]plasmic reticulum calcium ATPase) activity. VMP1 interacts with SERCA and prevents formation of the SERCA/PLN/SLN inhibitory complex. VMP1 also modulates ER contacts with lipid droplets, mitochondria, and endosomes. These ER contacts are greatly elevated by the SERCA inhibitor thapsigargin. Calmodulin acts as a sensor/effector to modulate the ER contacts mediated by VMP1/SERCA. Our study provides mechanistic insights into the establishment and disassociation of ER-IM contacts and reveals that VMP1 modulates SERCA activity to control ER contacts.
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141
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Joo JH, Wang B, Frankel E, Ge L, Xu L, Iyengar R, Li-Harms X, Wright C, Shaw TI, Lindsten T, Green DR, Peng J, Hendershot LM, Kilic F, Sze JY, Audhya A, Kundu M. The Noncanonical Role of ULK/ATG1 in ER-to-Golgi Trafficking Is Essential for Cellular Homeostasis. Mol Cell 2017; 62:491-506. [PMID: 27203176 DOI: 10.1016/j.molcel.2016.04.020] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/07/2016] [Accepted: 04/19/2016] [Indexed: 01/08/2023]
Abstract
ULK1 and ULK2 are thought to be essential for initiating autophagy, and Ulk1/2-deficient mice die perinatally of autophagy-related defects. Therefore, we used a conditional knockout approach to investigate the roles of ULK1/2 in the brain. Although the mice showed neuronal degeneration, the neurons showed no accumulation of P62(+)/ubiquitin(+) inclusions or abnormal membranous structures, which are observed in mice lacking other autophagy genes. Rather, neuronal death was associated with activation of the unfolded protein response (UPR) pathway. An unbiased proteomics approach identified SEC16A as an ULK1/2 interaction partner. ULK-mediated phosphorylation of SEC16A regulated the assembly of endoplasmic reticulum (ER) exit sites and ER-to-Golgi trafficking of specific cargo, and did not require other autophagy proteins (e.g., ATG13). The defect in ER-to-Golgi trafficking activated the UPR pathway in ULK-deficient cells; both processes were reversed upon expression of SEC16A with a phosphomimetic substitution. Thus, the regulation of ER-to-Golgi trafficking by ULK1/2 is essential for cellular homeostasis.
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Affiliation(s)
- Joung Hyuck Joo
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Bo Wang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Integrated Biomedical Sciences Program, the University of Tennessee Health Science Center, Memphis, TN, USA
| | - Elisa Frankel
- Department of Biomolecular Chemistry, University of Wisconsin-Madison Medical School, Madison, WI, USA
| | - Liang Ge
- Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, CA, USA
| | - Lu Xu
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rekha Iyengar
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - XiuJie Li-Harms
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Christopher Wright
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Timothy I Shaw
- St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tullia Lindsten
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Junmin Peng
- St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, TN, USA.,Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Linda M Hendershot
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Fusun Kilic
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ji Ying Sze
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Anjon Audhya
- Department of Biomolecular Chemistry, University of Wisconsin-Madison Medical School, Madison, WI, USA
| | - Mondira Kundu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
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142
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Mishra P, Dauphinee AN, Ward C, Sarkar S, Gunawardena AHLAN, Manjithaya R. Discovery of pan autophagy inhibitors through a high-throughput screen highlights macroautophagy as an evolutionarily conserved process across 3 eukaryotic kingdoms. Autophagy 2017; 13:1556-1572. [PMID: 28792845 PMCID: PMC5612355 DOI: 10.1080/15548627.2017.1339002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Due to the involvement of macroautophagy/autophagy in different pathophysiological conditions such as infections, neurodegeneration and cancer, identification of novel small molecules that modulate the process is of current research and clinical interest. In this work, we developed a luciferase-based sensitive and robust kinetic high-throughput screen (HTS) of small molecules that modulate autophagic degradation of peroxisomes in the budding yeast Saccharomyces cerevisiae. Being a pathway-specific rather than a target-driven assay, we identified small molecule modulators that acted at key steps of autophagic flux. Two of the inhibitors, Bay11 and ZPCK, obtained from the screen were further characterized using secondary assays in yeast. Bay11 inhibited autophagy at a step before fusion with the vacuole whereas ZPCK inhibited the cargo degradation inside the vacuole. Furthermore, we demonstrated that these molecules altered the process of autophagy in mammalian cells as well. Strikingly, these molecules also modulated autophagic flux in a novel model plant, Aponogeton madagascariensis. Thus, using small molecule modulators identified by using a newly developed HTS autophagy assay, our results support that macroautophagy is a conserved process across fungal, animal and plant kingdoms.
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Affiliation(s)
- Piyush Mishra
- a Molecular Biology and Genetics Unit , Jawaharlal Nehru Centre for Advanced Scientific Research , Jakkur, Bangalore , India
| | - Adrian N Dauphinee
- b Biology Department, Life Sciences Centre , Dalhousie University , Halifax , NS , Canada
| | - Carl Ward
- c Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences , University of Birmingham , Edgbaston, Birmingham , UK
| | - Sovan Sarkar
- c Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences , University of Birmingham , Edgbaston, Birmingham , UK
| | | | - Ravi Manjithaya
- a Molecular Biology and Genetics Unit , Jawaharlal Nehru Centre for Advanced Scientific Research , Jakkur, Bangalore , India
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143
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Ge L, Zhang M, Kenny SJ, Liu D, Maeda M, Saito K, Mathur A, Xu K, Schekman R. Remodeling of ER-exit sites initiates a membrane supply pathway for autophagosome biogenesis. EMBO Rep 2017; 18:1586-1603. [PMID: 28754694 DOI: 10.15252/embr.201744559] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/27/2017] [Accepted: 06/28/2017] [Indexed: 01/14/2023] Open
Abstract
Autophagosomes are double-membrane vesicles generated during autophagy. Biogenesis of the autophagosome requires membrane acquisition from intracellular compartments, the mechanisms of which are unclear. We previously found that a relocation of COPII machinery to the ER-Golgi intermediate compartment (ERGIC) generates ERGIC-derived COPII vesicles which serve as a membrane precursor for the lipidation of LC3, a key membrane component of the autophagosome. Here we employed super-resolution microscopy to show that starvation induces the enlargement of ER-exit sites (ERES) positive for the COPII activator, SEC12, and the remodeled ERES patches along the ERGIC A SEC12 binding protein, CTAGE5, is required for the enlargement of ERES, SEC12 relocation to the ERGIC, and modulates autophagosome biogenesis. Moreover, FIP200, a subunit of the ULK protein kinase complex, facilitates the starvation-induced enlargement of ERES independent of the other subunits of this complex and associates via its C-terminal domain with SEC12. Our data indicate a pathway wherein FIP200 and CTAGE5 facilitate starvation-induced remodeling of the ERES, a prerequisite for the production of COPII vesicles budded from the ERGIC that contribute to autophagosome formation.
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Affiliation(s)
- Liang Ge
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Min Zhang
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Samuel J Kenny
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Dawei Liu
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Miharu Maeda
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan
| | - Kota Saito
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan
| | - Anandita Mathur
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Randy Schekman
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
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144
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Pro- and Antioxidant Functions of the Peroxisome-Mitochondria Connection and Its Impact on Aging and Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:9860841. [PMID: 28811869 PMCID: PMC5546064 DOI: 10.1155/2017/9860841] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/27/2017] [Indexed: 12/13/2022]
Abstract
Peroxisomes and mitochondria are the main intracellular sources for reactive oxygen species. At the same time, both organelles are critical for the maintenance of a healthy redox balance in the cell. Consequently, failure in the function of both organelles is causally linked to oxidative stress and accelerated aging. However, it has become clear that peroxisomes and mitochondria are much more intimately connected both physiologically and structurally. Both organelles share common fission components to dynamically respond to environmental cues, and the autophagic turnover of both peroxisomes and mitochondria is decisive for cellular homeostasis. Moreover, peroxisomes can physically associate with mitochondria via specific protein complexes. Therefore, the structural and functional connection of both organelles is a critical and dynamic feature in the regulation of oxidative metabolism, whose dynamic nature will be revealed in the future. In this review, we will focus on fundamental aspects of the peroxisome-mitochondria interplay derived from simple models such as yeast and move onto discussing the impact of an impaired peroxisomal and mitochondrial homeostasis on ROS production, aging, and disease in humans.
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145
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Torggler R, Papinski D, Kraft C. Assays to Monitor Autophagy in Saccharomyces cerevisiae. Cells 2017; 6:cells6030023. [PMID: 28703742 PMCID: PMC5617969 DOI: 10.3390/cells6030023] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/04/2017] [Accepted: 07/09/2017] [Indexed: 12/18/2022] Open
Abstract
Autophagy is an intracellular process responsible for the degradation and recycling of cytoplasmic components. It selectively removes harmful cellular material and enables the cell to survive starvation by mobilizing nutrients via the bulk degradation of cytoplasmic components. While research over the last decades has led to the discovery of the key factors involved in autophagy, the pathway is not yet completely understood. The first studies of autophagy on a molecular level were conducted in the yeast Saccharomyces cerevisiae. Building up on these studies, many homologs have been found in higher eukaryotes. Yeast remains a highly relevant model organism for studying autophagy, with a wide range of established methods to elucidate the molecular details of the autophagy pathway. In this review, we provide an overview of methods to study both selective and bulk autophagy, including intermediate steps in the yeast Saccharomyces cerevisiae. We compare different assays, discuss their advantages and limitations and list potential applications.
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Affiliation(s)
- Raffaela Torggler
- Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Daniel Papinski
- Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria.
| | - Claudine Kraft
- Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria.
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146
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Hirata E, Ohya Y, Suzuki K. Atg4 plays an important role in efficient expansion of autophagic isolation membranes by cleaving lipidated Atg8 in Saccharomyces cerevisiae. PLoS One 2017; 12:e0181047. [PMID: 28704456 PMCID: PMC5509253 DOI: 10.1371/journal.pone.0181047] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 06/26/2017] [Indexed: 12/11/2022] Open
Abstract
Autophagy, an intracellular degradation system, is highly conserved among eukaryotes from yeast to mammalian cells. In the yeast Saccharomyces cerevisiae, most Atg (autophagy-related) proteins, which are essential for autophagosome formation, are recruited to a restricted region close to the vacuole, termed the vacuole-isolation membrane contact site (VICS), upon induction of autophagy. Subsequently, the isolation membrane (IM) expands and sequesters cytoplasmic materials to become a closed autophagosome. In S. cerevisiae, the ubiquitin-like protein Atg8 is C-terminally conjugated to the phospholipid phosphatidylethanolamine (PE) to generate Atg8-PE. During autophagosome formation, Atg8-PE is cleaved by Atg4 to release delipidated Atg8 (Atg8G116) and PE. Although delipidation of Atg8-PE is important for autophagosome formation, it remains controversial whether the delipidation reaction is required for targeting of Atg8 to the VICS or for subsequent IM expansion. We used an IM visualization technique to clearly demonstrate that delipidation of Atg8-PE is dispensable for targeting of Atg8 to the VICS, but required for IM expansion. Moreover, by overexpressing Atg8G116, we showed that the delipidation reaction of Atg8-PE by Atg4 plays an important role in efficient expansion of the IM other than supplying unlipidated Atg8G116. Finally, we suggested the existence of biological membranes at the Atg8-labeled structures in Atg8-PE delipidation-defective cells, but not at those in atg2Δ cells. Taken together, it is likely that Atg2 is involved in localization of biological membranes to the VICS, where Atg4 is responsible for IM expansion.
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Affiliation(s)
- Eri Hirata
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Kuninori Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
- Bioimaging Center, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
- * E-mail:
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147
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Davis S, Wang J, Ferro-Novick S. Crosstalk between the Secretory and Autophagy Pathways Regulates Autophagosome Formation. Dev Cell 2017; 41:23-32. [PMID: 28399396 DOI: 10.1016/j.devcel.2017.03.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 02/26/2017] [Accepted: 03/16/2017] [Indexed: 12/26/2022]
Abstract
The induction of autophagy by nutrient deprivation leads to a rapid increase in the formation of autophagosomes, unique organelles that replenish the cellular pool of nutrients by sequestering cytoplasmic material for degradation. The urgent need for membranes to form autophagosomes during starvation to maintain homeostasis leads to a dramatic rearrangement of intracellular membranes. Here we discuss recent findings that have begun to uncover how different parts of the secretory pathway directly and indirectly contribute to autophagosome formation during starvation.
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Affiliation(s)
- Saralin Davis
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093-0668, USA
| | - Juan Wang
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093-0668, USA
| | - Susan Ferro-Novick
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093-0668, USA.
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148
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Rzepnikowska W, Flis K, Kaminska J, Grynberg M, Urbanek A, Ayscough KR, Zoladek T. Amino acid substitution equivalent to human chorea-acanthocytosis I2771R in yeast Vps13 protein affects its binding to phosphatidylinositol 3-phosphate. Hum Mol Genet 2017; 26:1497-1510. [PMID: 28334785 PMCID: PMC5393151 DOI: 10.1093/hmg/ddx054] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 02/09/2017] [Indexed: 12/16/2022] Open
Abstract
The rare human disorder chorea-acanthocytosis (ChAc) is caused by mutations in hVPS13A gene. The hVps13A protein interacts with actin and regulates the level of phosphatidylinositol 4-phosphate (PI4P) in the membranes of neuronal cells. Yeast Vps13 is involved in vacuolar protein transport and, like hVps13A, participates in PI4P metabolism. Vps13 proteins are conserved in eukaryotes, but their molecular function remains unknown. One of the mutations found in ChAc patients causes amino acids substitution I2771R which affects the localization of hVps13A in skeletal muscles. To dissect the mechanism of pathogenesis of I2771R, we created and analyzed a yeast strain carrying the equivalent mutation. Here we show that in yeast, substitution I2749R causes dysfunction of Vps13 protein in endocytosis and vacuolar transport, although the level of the protein is not affected, suggesting loss of function. We also show that Vps13, like hVps13A, influences actin cytoskeleton organization and binds actin in immunoprecipitation experiments. Vps13-I2749R binds actin, but does not function in the actin cytoskeleton organization. Moreover, we show that Vps13 binds phospholipids, especially phosphatidylinositol 3-phosphate (PI3P), via its SHR_BD and APT1 domains. Substitution I2749R attenuates this ability. Finally, the localization of Vps13-GFP is altered when cellular levels of PI3P are decreased indicating its trafficking within the endosomal membrane system. These results suggest that PI3P regulates the functioning of Vps13, both in protein trafficking and actin cytoskeleton organization. Attenuation of PI3P-binding ability in the mutant hVps13A protein may be one of the reasons for its mislocalization and disrupted function in cells of patients suffering from ChAc.
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Affiliation(s)
- Weronika Rzepnikowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Krzysztof Flis
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Joanna Kaminska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Marcin Grynberg
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Agnieszka Urbanek
- Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
| | - Kathryn R Ayscough
- Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
| | - Teresa Zoladek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
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149
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Chen L, Zhang X, Wang W, Geng X, Shi Y, Na R, Dou D, Li H. Network and role analysis of autophagy in Phytophthora sojae. Sci Rep 2017; 7:1879. [PMID: 28500315 PMCID: PMC5431975 DOI: 10.1038/s41598-017-01988-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 04/05/2017] [Indexed: 12/17/2022] Open
Abstract
Autophagy is an evolutionarily conserved mechanism in eukaryotes with roles in development and the virulence of plant fungal pathogens. However, few reports on autophagy in oomycete species have been published. Here, we identified 26 autophagy-related genes (ATGs) belonging to 20 different groups in Phytophthora sojae using a genome-wide survey, and core ATGs in oomycetes were used to construct a preliminary autophagy pathway model. Expression profile analysis revealed that these ATGs are broadly expressed and that the majority of them significantly increase during infection stages, suggesting a central role for autophagy in virulence. Autophagy in P. sojae was detected using a GFP-PsAtg8 fusion protein and the fluorescent dye MDC during rapamycin and starvation treatment. In addition, autophagy was significantly induced during sporangium formation and cyst germination. Silencing PsAtg6a in P. sojae significantly reduced sporulation and pathogenicity. Furthermore, a PsAtg6a-silenced strain showed haustorial formation defects. These results suggested that autophagy might play essential roles in both the development and infection mechanism of P. sojae.
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Affiliation(s)
- Linlin Chen
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiong Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wen Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xuejing Geng
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yan Shi
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Risong Na
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Honglian Li
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, 450002, China.
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150
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Nishimura T, Tamura N, Kono N, Shimanaka Y, Arai H, Yamamoto H, Mizushima N. Autophagosome formation is initiated at phosphatidylinositol synthase-enriched ER subdomains. EMBO J 2017; 36:1719-1735. [PMID: 28495679 DOI: 10.15252/embj.201695189] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 03/28/2017] [Accepted: 04/11/2017] [Indexed: 11/09/2022] Open
Abstract
The autophagosome, a double-membrane structure mediating degradation of cytoplasmic materials by macroautophagy, is formed in close proximity to the endoplasmic reticulum (ER). However, how the ER membrane is involved in autophagy initiation and to which membrane structures the autophagy-initiation complex is localized have not been fully characterized. Here, we were able to biochemically analyze autophagic intermediate membranes and show that the autophagy-initiation complex containing ULK and FIP200 first associates with the ER membrane. To further characterize the ER subdomain, we screened phospholipid biosynthetic enzymes and found that the autophagy-initiation complex localizes to phosphatidylinositol synthase (PIS)-enriched ER subdomains. Then, the initiation complex translocates to the ATG9A-positive autophagosome precursors in a PI3P-dependent manner. Depletion of phosphatidylinositol (PI) by targeting bacterial PI-specific phospholipase C to the PIS domain impairs recruitment of downstream autophagy factors and autophagosome formation. These findings suggest that the autophagy-initiation complex, the PIS-enriched ER subdomain, and ATG9A vesicles together initiate autophagosome formation.
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Affiliation(s)
- Taki Nishimura
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Norito Tamura
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Nozomu Kono
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuta Shimanaka
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Arai
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.,AMED-CREST, Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Hayashi Yamamoto
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
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