101
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Abstract
The functions of coat protein complex II (COPII) coats in cargo packaging and the creation of vesicles at the endoplasmic reticulum are conserved in eukaryotic protein secretion. Standard COPII vesicles, however, cannot handle the secretion of metazoan-specific cargoes such as procollagens, apolipoproteins, and mucins. Metazoans have thus evolved modules centered on proteins like TANGO1 (transport and Golgi organization 1) to engage COPII coats and early secretory pathway membranes to engineer a novel mode of cargo export at the endoplasmic reticulum.
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Affiliation(s)
- I Raote
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain; ,
| | - V Malhotra
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain; , .,Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
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102
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Bisnett BJ, Condon BM, Lamb CH, Georgiou GR, Boyce M. Export Control: Post-transcriptional Regulation of the COPII Trafficking Pathway. Front Cell Dev Biol 2021; 8:618652. [PMID: 33511128 PMCID: PMC7835409 DOI: 10.3389/fcell.2020.618652] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 12/14/2020] [Indexed: 11/13/2022] Open
Abstract
The coat protein complex II (COPII) mediates forward trafficking of protein and lipid cargoes from the endoplasmic reticulum. COPII is an ancient and essential pathway in all eukaryotes and COPII dysfunction underlies a range of human diseases. Despite this broad significance, major aspects of COPII trafficking remain incompletely understood. For example, while the biochemical features of COPII vesicle formation are relatively well characterized, much less is known about how the COPII system dynamically adjusts its activity to changing physiologic cues or stresses. Recently, post-transcriptional mechanisms have emerged as a major mode of COPII regulation. Here, we review the current literature on how post-transcriptional events, and especially post-translational modifications, govern the COPII pathway.
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Affiliation(s)
- Brittany J Bisnett
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
| | - Brett M Condon
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
| | - Caitlin H Lamb
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
| | - George R Georgiou
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
| | - Michael Boyce
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
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103
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Fujioka Y, Noda NN. Biomolecular condensates in autophagy regulation. Curr Opin Cell Biol 2021; 69:23-29. [PMID: 33445149 DOI: 10.1016/j.ceb.2020.12.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/06/2020] [Accepted: 12/12/2020] [Indexed: 12/13/2022]
Abstract
Autophagy is an intracellular degradation system that contributes to cellular homeostasis. Autophagosome formation is a landmark event in autophagy, which sequesters and delivers cytoplasmic components to the lysosome for degradation. Based on selectivity, autophagy can be classified into bulk and selective autophagy, which are mechanistically distinct from each other, especially in the requirement of cargos for autophagosome formation. Recent studies revealed that liquid-like biomolecular condensates, which are formed through liquid-liquid phase separation, regulate the autophagosome formation of both bulk and selective autophagy. Here, we focus on recent findings on the involvement of biomolecular condensates in autophagy regulation and discuss their significance.
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Affiliation(s)
- Yuko Fujioka
- Institute of Microbial Chemistry, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo, 141-0021, Japan.
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104
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Maeda S, Yamamoto H, Kinch LN, Garza CM, Takahashi S, Otomo C, Grishin NV, Forli S, Mizushima N, Otomo T. Structure, lipid scrambling activity and role in autophagosome formation of ATG9A. Nat Struct Mol Biol 2020; 27:1194-1201. [PMID: 33106659 PMCID: PMC7718406 DOI: 10.1038/s41594-020-00520-2] [Citation(s) in RCA: 185] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/22/2020] [Indexed: 01/01/2023]
Abstract
De novo formation of the double-membrane compartment autophagosome is seeded by small vesicles carrying membrane protein autophagy-related 9 (ATG9), the function of which remains unknown. Here we find that ATG9A scrambles phospholipids of membranes in vitro. Cryo-EM structures of human ATG9A reveal a trimer with a solvated central pore, which is connected laterally to the cytosol through the cavity within each protomer. Similarities to ABC exporters suggest that ATG9A could be a transporter that uses the central pore to function. Moreover, molecular dynamics simulation suggests that the central pore opens laterally to accommodate lipid headgroups, thereby enabling lipids to flip. Mutations in the pore reduce scrambling activity and yield markedly smaller autophagosomes, indicating that lipid scrambling by ATG9A is essential for membrane expansion. We propose ATG9A acts as a membrane-embedded funnel to facilitate lipid flipping and to redistribute lipids added to the outer leaflet of ATG9 vesicles, thereby enabling growth into autophagosomes.
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Affiliation(s)
- Shintaro Maeda
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Hayashi Yamamoto
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Lisa N Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Christina M Garza
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Satoru Takahashi
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Chinatsu Otomo
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takanori Otomo
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
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105
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Matoba K, Kotani T, Tsutsumi A, Tsuji T, Mori T, Noshiro D, Sugita Y, Nomura N, Iwata S, Ohsumi Y, Fujimoto T, Nakatogawa H, Kikkawa M, Noda NN. Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion. Nat Struct Mol Biol 2020; 27:1185-1193. [PMID: 33106658 DOI: 10.1038/s41594-020-00518-w] [Citation(s) in RCA: 247] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022]
Abstract
The molecular function of Atg9, the sole transmembrane protein in the autophagosome-forming machinery, remains unknown. Atg9 colocalizes with Atg2 at the expanding edge of the isolation membrane (IM), where Atg2 receives phospholipids from the endoplasmic reticulum (ER). Here we report that yeast and human Atg9 are lipid scramblases that translocate phospholipids between outer and inner leaflets of liposomes in vitro. Cryo-EM of fission yeast Atg9 reveals a homotrimer, with two connected pores forming a path between the two membrane leaflets: one pore, located at a protomer, opens laterally to the cytoplasmic leaflet; the other, at the trimer center, traverses the membrane vertically. Mutation of residues lining the pores impaired IM expansion and autophagy activity in yeast and abolished Atg9's ability to transport phospholipids between liposome leaflets. These results suggest that phospholipids delivered by Atg2 are translocated from the cytoplasmic to the luminal leaflet by Atg9, thereby driving autophagosomal membrane expansion.
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Affiliation(s)
- Kazuaki Matoba
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
| | - Tetsuya Kotani
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Akihisa Tsutsumi
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takuma Tsuji
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | | | | | - Yuji Sugita
- RIKEN Cluster for Pioneering Research, Wako, Japan
- RIKEN Center for Computational Science, Kobe, Japan
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Norimichi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- RIKEN SPring-8 Center, Hyogo, Japan
| | - Yoshinori Ohsumi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Toyoshi Fujimoto
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hitoshi Nakatogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan.
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106
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Wijerathna-Yapa A, Stroeher E, Fenske R, Li L, Duncan O, Millar AH. Proteomics for Autophagy Receptor and Cargo Identification in Plants. J Proteome Res 2020; 20:129-138. [PMID: 33241938 DOI: 10.1021/acs.jproteome.0c00609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Autophagy is a catabolic process facilitating the degradation of cytoplasmic proteins and organelles in a lysosome- or vacuole-dependent manner in plants, animals, and fungi. Proteomic studies have demonstrated that autophagy controls and shapes the proteome and has identified both receptor and cargo proteins inside autophagosomes. In a smaller selection of studies, proteomics has been used for the analysis of post-translational modifications that target proteins for elimination and protein-protein interactions between receptors and cargo, providing a better understanding of the complex regulatory processes controlling autophagy. In this perspective, we highlight how proteomic studies have contributed to our understanding of autophagy in plants against the backdrop of yeast and animal studies. We then provide a framework for how the future application of proteomics in plant autophagy can uncover the mechanisms and outcomes of sculpting organelles during plant development, particularly through the identification of autophagy receptors and cargo in plants.
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Affiliation(s)
- Akila Wijerathna-Yapa
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009 Crawley, Western Australia, Australia
| | - Elke Stroeher
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009 Crawley, Western Australia, Australia
| | - Ricarda Fenske
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009 Crawley, Western Australia, Australia
| | - Lei Li
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009 Crawley, Western Australia, Australia.,Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, 300071 Tianjin, China
| | - Owen Duncan
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009 Crawley, Western Australia, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009 Crawley, Western Australia, Australia
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107
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Secret of Atg9: lipid scramblase activity drives de novo autophagosome biogenesis. Cell Death Differ 2020; 27:3386-3388. [PMID: 33177618 DOI: 10.1038/s41418-020-00663-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 10/27/2020] [Accepted: 10/28/2020] [Indexed: 02/01/2023] Open
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108
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In vitro reconstitution of autophagic processes. Biochem Soc Trans 2020; 48:2003-2014. [PMID: 32897375 DOI: 10.1042/bst20200130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 11/17/2022]
Abstract
Autophagy is a lysosomal degradation system that involves de novo autophagosome formation. A lot of factors are involved in autophagosome formation, including dozens of Atg proteins that form supramolecular complexes, membrane structures including vesicles and organelles, and even membraneless organelles. Because these diverse higher-order structural components cooperate to mediate de novo formation of autophagosomes, it is too complicated to be elaborated only by cell biological approaches. Recent trials to regenerate each step of this phenomenon in vitro have started to elaborate on the molecular mechanisms of such a complicated process by simplification. In this review article, we outline the in vitro reconstitution trials in autophagosome formation, mainly focusing on the reports in the past few years and discussing the molecular mechanisms of autophagosome formation by comparing in vitro and in vivo observations.
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109
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Chou HY, Lee YT, Lin YJ, Wen JK, Peng WH, Hsieh PL, Lin SY, Hung CC, Chen GC. PTPN9-mediated dephosphorylation of VTI1B promotes ATG16L1 precursor fusion and autophagosome formation. Autophagy 2020; 17:2750-2765. [PMID: 33112705 DOI: 10.1080/15548627.2020.1838117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Macroautophagy/autophagy is an evolutionarily conserved intracellular pathway for the degradation of cytoplasmic materials. Under stress conditions, autophagy is upregulated and double-membrane autophagosomes are formed by the expansion of phagophores. The ATG16L1 precursor fusion contributes to development of phagophore structures and is critical for the biogenesis of autophagosomes. Here, we discovered a novel role of the protein tyrosine phosphatase PTPN9 in the regulation of homotypic ATG16L1 vesicle fusion and early autophagosome formation. Depletion of PTPN9 and its Drosophila homolog Ptpmeg2 impaired autophagosome formation and autophagic flux. PTPN9 colocalized with ATG16L1 and was essential for homotypic fusion of ATG16L1+ vesicles during starvation-induced autophagy. We further identified the Q-SNARE VTI1B as a substrate target of PTPN9 phosphatase. Like PTPN9, the VTI1B nonphosphorylatable mutant but not the phosphomimetic mutant enhanced SNARE complex assembly and autophagic flux. Our findings highlight the important role of PTPN9 in the regulation of ATG16L1+ autophagosome precursor fusion and autophagosome biogenesis through modulation of VTI1B phosphorylation status.Abbreviations: csw: corkscrew; EBSS: Earle's balanced salt solution; ERGIC: ER-Golgi intermediate compartment; ESCRT: endosomal sorting complexes required for transport; mop: myopic; NSF: N-ethylmaleimide-sensitive factor; PAS: phagophore assembly site; PolyQ: polyglutamine; PtdIns3P: phosphatidylinositol-3-phosphate; PTK: protein tyrosine kinase; PTM: posttranslational modification; PTP: protein tyrosine phosphatase; PTPN23/HD-PTP: protein tyrosine phosphatase non-receptor type 23; SNARE: soluble N-ethylmaleimide sensitive factor attachment protein receptor; STX7: syntaxin 7; STX8: syntaxin 8; STX17: syntaxin 17; VAMP3: vesicle associated membrane protein 3; VAMP7: vesicle associated membrane protein 7; VTI1B: vesicle transport through interaction with t-SNAREs 1B; YKT6: YKT6 v-SNARE homolog; ZFYVE1/DFCP1: zinc finger FYVE-type containing 1.
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Affiliation(s)
- He-Yen Chou
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yi-Tang Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yuchieh Jay Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan.,Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Jung-Kun Wen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Wen-Hsin Peng
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Pei-Lien Hsieh
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Shu-Yu Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chin-Chun Hung
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Guang-Chao Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan.,Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
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110
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Miyata T, Hagiwara D, Hodai Y, Miwata T, Kawaguchi Y, Kurimoto J, Ozaki H, Mitsumoto K, Takagi H, Suga H, Kobayashi T, Sugiyama M, Onoue T, Ito Y, Iwama S, Banno R, Matsumoto M, Kawakami N, Ohno N, Sakamoto H, Arima H. Degradation of Mutant Protein Aggregates within the Endoplasmic Reticulum of Vasopressin Neurons. iScience 2020; 23:101648. [PMID: 33103081 PMCID: PMC7578753 DOI: 10.1016/j.isci.2020.101648] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/08/2020] [Accepted: 10/02/2020] [Indexed: 12/20/2022] Open
Abstract
Misfolded or unfolded proteins in the ER are said to be degraded only after translocation or isolation from the ER. Here, we describe a mechanism by which mutant proteins are degraded within the ER. Aggregates of mutant arginine vasopressin (AVP) precursor were confined to ER-associated compartments (ERACs) connected to the ER in AVP neurons of a mouse model of familial neurohypophysial diabetes insipidus. The ERACs were enclosed by membranes, an ER chaperone and marker protein of phagophores and autophagosomes were expressed around the aggregates, and lysosomes fused with the ERACs. Moreover, lysosome-related molecules were present within the ERACs, and aggregate degradation within the ERACs was dependent on autophagic-lysosomal activity. Thus, we demonstrate that protein aggregates can be degraded by autophagic-lysosomal machinery within specialized compartments of the ER. Mutant AVP precursors are confined to ERACs connected to the ER of FNDI AVP neurons Lysosomes fuse with ERACs surrounded by phagophore-like membranes Lysosome-related molecules are localized within ERACs Rapamycin reduces and chloroquine increases protein aggregate accumulation in ERACs
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Affiliation(s)
- Takashi Miyata
- Department of Endocrinology and Diabetes, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Daisuke Hagiwara
- Department of Endocrinology and Diabetes, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Yuichi Hodai
- Department of Endocrinology and Diabetes, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Tsutomu Miwata
- Department of Endocrinology and Diabetes, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Yohei Kawaguchi
- Department of Endocrinology and Diabetes, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Junki Kurimoto
- Department of Endocrinology and Diabetes, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Hajime Ozaki
- Department of Endocrinology and Diabetes, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Kazuki Mitsumoto
- Department of Endocrinology and Diabetes, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Hiroshi Takagi
- Department of Endocrinology and Diabetes, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Hidetaka Suga
- Department of Endocrinology and Diabetes, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Tomoko Kobayashi
- Department of Endocrinology and Diabetes, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Mariko Sugiyama
- Department of Endocrinology and Diabetes, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Takeshi Onoue
- Department of Endocrinology and Diabetes, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Yoshihiro Ito
- Department of Endocrinology and Diabetes, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Shintaro Iwama
- Department of Endocrinology and Diabetes, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Ryoichi Banno
- Department of Endocrinology and Diabetes, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan.,Research Center of Health, Physical Fitness and Sports, Nagoya University, Nagoya 464-8601, Japan
| | - Mami Matsumoto
- Section of Electron Microscopy, Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki 444-8787, Japan
| | - Natsuko Kawakami
- Ushimado Marine Institute, Graduate School of Natural Science and Technology, Okayama University, Setouchi 701-4303, Japan
| | - Nobuhiko Ohno
- Department of Anatomy, Division of Histology and Cell Biology, Jichi Medical University, School of Medicine, Shimotsuke 329-0498, Japan.,Division of Ultrastructural Research, National Institute for Physiological Sciences, Okazaki 444-8787, Japan
| | - Hirotaka Sakamoto
- Ushimado Marine Institute, Graduate School of Natural Science and Technology, Okayama University, Setouchi 701-4303, Japan
| | - Hiroshi Arima
- Department of Endocrinology and Diabetes, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
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111
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Yamamoto YH, Noda T. Autophagosome formation in relation to the endoplasmic reticulum. J Biomed Sci 2020; 27:97. [PMID: 33087127 PMCID: PMC7579975 DOI: 10.1186/s12929-020-00691-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/02/2020] [Indexed: 02/08/2023] Open
Abstract
Autophagy is a process in which a myriad membrane structures called autophagosomes are formed de novo in a single cell, which deliver the engulfed substrates into lysosomes for degradation. The size of the autophagosomes is relatively uniform in non-selective autophagy and variable in selective autophagy. It has been recently established that autophagosome formation occurs near the endoplasmic reticulum (ER). In this review, we have discussed recent advances in the relationship between autophagosome formation and endoplasmic reticulum. Autophagosome formation occurs near the ER subdomain enriched with phospholipid synthesizing enzymes like phosphatidylinositol synthase (PIS)/CDP-diacylglycerol-inositol 3-phosphatidyltransferase (CDIPT) and choline/ethanolamine phosphotransferase 1 (CEPT1). Autophagy-related protein 2 (Atg2), which is involved in autophagosome formation has a lipid transfer capacity and is proposed to directly transfer the lipid molecules from the ER to form autophagosomes. Vacuole membrane protein 1 (VMP1) and transmembrane protein 41b (TMEM41b) are ER membrane proteins that are associated with the formation of the subdomain. Recently, we have reported that an uncharacterized ER membrane protein possessing the DNAJ domain, called ERdj8/DNAJC16, is associated with the regulation of the size of autophagosomes. The localization of ERdj8/DNAJC16 partially overlaps with the PIS-enriched ER subdomain, thereby implying its association with autophagosome size determination.
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Affiliation(s)
- Yo-Hei Yamamoto
- Center for Frontier Oral Sciences, Graduate School of Dentistry, Osaka University Graduate School, 1-8 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takeshi Noda
- Center for Frontier Oral Sciences, Graduate School of Dentistry, Osaka University Graduate School, 1-8 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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112
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Gao J, Kurre R, Rose J, Walter S, Fröhlich F, Piehler J, Reggiori F, Ungermann C. Function of the SNARE Ykt6 on autophagosomes requires the Dsl1 complex and the Atg1 kinase complex. EMBO Rep 2020; 21:e50733. [PMID: 33025734 PMCID: PMC7726795 DOI: 10.15252/embr.202050733] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/04/2020] [Accepted: 09/14/2020] [Indexed: 12/11/2022] Open
Abstract
The mechanism and regulation of fusion between autophagosomes and lysosomes/vacuoles are still only partially understood in both yeast and mammals. In yeast, this fusion step requires SNARE proteins, the homotypic vacuole fusion and protein sorting (HOPS) tethering complex, the RAB7 GTPase Ypt7, and its guanine nucleotide exchange factor (GEF) Mon1‐Ccz1. We and others recently identified Ykt6 as the autophagosomal SNARE protein. However, it has not been resolved when and how lipid‐anchored Ykt6 is recruited onto autophagosomes. Here, we show that Ykt6 is recruited at an early stage of the formation of these carriers through a mechanism that depends on endoplasmic reticulum (ER)‐resident Dsl1 complex and COPII‐coated vesicles. Importantly, Ykt6 activity on autophagosomes is regulated by the Atg1 kinase complex, which inhibits Ykt6 through direct phosphorylation. Thus, our findings indicate that the Ykt6 pool on autophagosomal membranes is kept inactive by Atg1 phosphorylation, and once an autophagosome is ready to fuse with vacuole, Ykt6 dephosphorylation allows its engagement in the fusion event.
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Affiliation(s)
- Jieqiong Gao
- Department of Biology/Chemistry, Biochemistry Section, University of Osnabrück, Osnabrück, Germany
| | - Rainer Kurre
- Center of Cellular Nanoanalytics Osnabrück (CellNanOs), University of Osnabrück, Osnabrück, Germany.,Center of Cellular Nanoanalytics, Integrated Bioimaging Facility, University of Osnabrück, Osnabrück, Germany
| | - Jaqueline Rose
- Department of Biology/Chemistry, Biochemistry Section, University of Osnabrück, Osnabrück, Germany
| | - Stefan Walter
- Center of Cellular Nanoanalytics Osnabrück (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Florian Fröhlich
- Department of Biology/Chemistry, Molecular Membrane Biology Group, University of Osnabrück, Osnabrück, Germany
| | - Jacob Piehler
- Center of Cellular Nanoanalytics Osnabrück (CellNanOs), University of Osnabrück, Osnabrück, Germany.,Center of Cellular Nanoanalytics, Integrated Bioimaging Facility, University of Osnabrück, Osnabrück, Germany.,Department of Biology/Chemistry, Biophysics Section, University of Osnabrück, Osnabrück, Germany
| | - Fulvio Reggiori
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Christian Ungermann
- Department of Biology/Chemistry, Biochemistry Section, University of Osnabrück, Osnabrück, Germany.,Center of Cellular Nanoanalytics Osnabrück (CellNanOs), University of Osnabrück, Osnabrück, Germany
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113
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Sakai Y, Koyama-Honda I, Tachikawa M, Knorr RL, Mizushima N. Modeling Membrane Morphological Change during Autophagosome Formation. iScience 2020; 23:101466. [PMID: 32891055 PMCID: PMC7479497 DOI: 10.1016/j.isci.2020.101466] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/21/2020] [Accepted: 08/12/2020] [Indexed: 11/23/2022] Open
Abstract
Autophagy is an intracellular degradation process that is mediated by de novo formation of autophagosomes. Autophagosome formation involves dynamic morphological changes; a disk-shaped membrane cisterna grows, bends to become a cup-shaped structure, and finally develops into a spherical autophagosome. We have constructed a theoretical model that integrates the membrane morphological change and entropic partitioning of putative curvature generators, which we have used to investigate the autophagosome formation process quantitatively. We show that the membrane curvature and the distribution of the curvature generators stabilize disk- and cup-shaped intermediate structures during autophagosome formation, which is quantitatively consistent with in vivo observations. These results suggest that various autophagy proteins with membrane curvature-sensing properties control morphological change by stabilizing these intermediate structures. Our model provides a framework for understanding autophagosome formation.
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Affiliation(s)
- Yuji Sakai
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS) Program, RIKEN, Wako, Saitama 351-0198, Japan
| | - Ikuko Koyama-Honda
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masashi Tachikawa
- Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS) Program, RIKEN, Wako, Saitama 351-0198, Japan
- Institute for Frontier Life and Medical Sciences, Kyoto University, Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507 Japan
| | - Roland L. Knorr
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Max Planck Institute of Colloids and Interfaces, Department of Theory & Bio-Systems, 14424 Potsdam, Germany
- Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology, 14424 Potsdam, Germany
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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114
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Sawa-Makarska J, Baumann V, Coudevylle N, von Bülow S, Nogellova V, Abert C, Schuschnig M, Graef M, Hummer G, Martens S. Reconstitution of autophagosome nucleation defines Atg9 vesicles as seeds for membrane formation. Science 2020; 369:eaaz7714. [PMID: 32883836 PMCID: PMC7610778 DOI: 10.1126/science.aaz7714] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 05/16/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022]
Abstract
Autophagosomes form de novo in a manner that is incompletely understood. Particularly enigmatic are autophagy-related protein 9 (Atg9)-containing vesicles that are required for autophagy machinery assembly but do not supply the bulk of the autophagosomal membrane. In this study, we reconstituted autophagosome nucleation using recombinant components from yeast. We found that Atg9 proteoliposomes first recruited the phosphatidylinositol 3-phosphate kinase complex, followed by Atg21, the Atg2-Atg18 lipid transfer complex, and the E3-like Atg12-Atg5-Atg16 complex, which promoted Atg8 lipidation. Furthermore, we found that Atg2 could transfer lipids for Atg8 lipidation. In selective autophagy, these reactions could potentially be coupled to the cargo via the Atg19-Atg11-Atg9 interactions. We thus propose that Atg9 vesicles form seeds that establish membrane contact sites to initiate lipid transfer from compartments such as the endoplasmic reticulum.
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Affiliation(s)
- Justyna Sawa-Makarska
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria.
| | - Verena Baumann
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Nicolas Coudevylle
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Sören von Bülow
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Veronika Nogellova
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Christine Abert
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Martina Schuschnig
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Martin Graef
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
- Institute for Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Sascha Martens
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria.
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115
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Li D, Yang SG, He CW, Zhang ZT, Liang Y, Li H, Zhu J, Su X, Gong Q, Xie Z. Excess diacylglycerol at the endoplasmic reticulum disrupts endomembrane homeostasis and autophagy. BMC Biol 2020; 18:107. [PMID: 32859196 PMCID: PMC7453538 DOI: 10.1186/s12915-020-00837-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/24/2020] [Indexed: 01/22/2023] Open
Abstract
Background When stressed, eukaryotic cells produce triacylglycerol (TAG) to store nutrients and mobilize autophagy to combat internal damage. We and others previously reported that in yeast, elimination of TAG synthesizing enzymes inhibits autophagy under nitrogen starvation, yet the underlying mechanism has remained elusive. Results Here, we show that disruption of TAG synthesis led to diacylglycerol (DAG) accumulation and its relocation from the vacuolar membrane to the endoplasmic reticulum (ER). We further show that, beyond autophagy, ER-accumulated DAG caused severe defects in the endomembrane system, including disturbing the balance of ER-Golgi protein trafficking, manifesting in bulging of ER and loss of the Golgi apparatus. Genetic or chemical manipulations that increase consumption or decrease supply of DAG reversed these defects. In contrast, increased amounts of precursors of glycerolipid synthesis, including phosphatidic acid and free fatty acids, did not replicate the effects of excess DAG. We also provide evidence that the observed endomembrane defects do not rely on Golgi-produced DAG, Pkc1 signaling, or the unfolded protein response. Conclusions This work identifies DAG as the critical lipid molecule responsible for autophagy inhibition under condition of defective TAG synthesis and demonstrates the disruption of ER and Golgi function by excess DAG as the potential cause of the autophagy defect.
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Affiliation(s)
- Dan Li
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, #800 Dong-Chuan Road, Shanghai, 200240, People's Republic of China
| | - Shu-Gao Yang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, People's Republic of China
| | - Cheng-Wen He
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, #800 Dong-Chuan Road, Shanghai, 200240, People's Republic of China
| | - Zheng-Tan Zhang
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, #800 Dong-Chuan Road, Shanghai, 200240, People's Republic of China
| | - Yongheng Liang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, People's Republic of China
| | - Hui Li
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, #800 Dong-Chuan Road, Shanghai, 200240, People's Republic of China
| | - Jing Zhu
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, #800 Dong-Chuan Road, Shanghai, 200240, People's Republic of China
| | - Xiong Su
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, People's Republic of China.
| | - Qingqiu Gong
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, #800 Dong-Chuan Road, Shanghai, 200240, People's Republic of China.
| | - Zhiping Xie
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, #800 Dong-Chuan Road, Shanghai, 200240, People's Republic of China.
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116
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Bomfim L, Ramos I. Deficiency of ULK1/ATG1 in the follicle cells disturbs ER homeostasis and causes defective chorion deposition in the vector Rhodnius prolixus. FASEB J 2020; 34:13561-13572. [PMID: 32844451 DOI: 10.1096/fj.202001396r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/20/2020] [Accepted: 07/27/2020] [Indexed: 12/27/2022]
Abstract
In insects, synthesis and deposition of the chorion (eggshell) are performed by the professional secretory follicle cells (FCs) that surround the oocytes in the course of oogenesis. Here, we found that ULK1/ATG1, an autophagy-related protein, is highly expressed in the FCs of the Chagas-Disease vector Rhodnius prolixus, and that parental RNAi silencing of ULK1/ATG1 results in oocytes with abnormal chorion ultrastructure and FCs presenting expanded rough ER membranes as well as increased expression of the ER chaperone BiP3, both indicatives of ER stress. Silencing of LC3/ATG8, another essential autophagy protein, did not replicate the ULK1/ATG1 phenotypes, whereas silencing of SEC16A, a known partner of the noncanonical ULK1/ATG1 function in the ER exit sites phenocopied the silencing of ULK1/ATG1. Our findings point to a cooperated function of ULK1/ATG1 and SEC16A in the FCs to complete choriogenesis and provide additional in vivo phenotype-based evidence to the literature of the role of ULK1/ATG1 in the ER in a professional secretory cell.
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Affiliation(s)
- Larissa Bomfim
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Isabela Ramos
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,INCT-EM/CNPq, Rio de Janeiro, Brazil
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117
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Shi X, Chang C, Yokom AL, Jensen LE, Hurley JH. The autophagy adaptor NDP52 and the FIP200 coiled-coil allosterically activate ULK1 complex membrane recruitment. eLife 2020; 9:59099. [PMID: 32773036 PMCID: PMC7447430 DOI: 10.7554/elife.59099] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/09/2020] [Indexed: 12/21/2022] Open
Abstract
The selective autophagy pathways of xenophagy and mitophagy are initiated when the adaptor NDP52 recruits the ULK1 complex to autophagic cargo. Hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) was used to map the membrane and NDP52 binding sites of the ULK1 complex to unique regions of the coiled coil of the FIP200 subunit. Electron microscopy of the full-length ULK1 complex shows that the FIP200 coiled coil projects away from the crescent-shaped FIP200 N-terminal domain dimer. NDP52 allosterically stimulates membrane-binding by FIP200 and the ULK1 complex by promoting a more dynamic conformation of the membrane-binding portion of the FIP200 coiled coil. Giant unilamellar vesicle (GUV) reconstitution confirmed that membrane recruitment by the ULK1 complex is triggered by NDP52 engagement. These data reveal how the allosteric linkage between NDP52 and the ULK1 complex could drive the first membrane recruitment event of phagophore biogenesis in xenophagy and mitophagy.
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Affiliation(s)
- Xiaoshan Shi
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
| | - Chunmei Chang
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
| | - Adam L Yokom
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
| | - Liv E Jensen
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
| | - James H Hurley
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
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118
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Hollenstein DM, Kraft C. Autophagosomes are formed at a distinct cellular structure. Curr Opin Cell Biol 2020; 65:50-57. [PMID: 32203894 PMCID: PMC7588827 DOI: 10.1016/j.ceb.2020.02.012] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/13/2020] [Accepted: 02/20/2020] [Indexed: 11/09/2022]
Abstract
Autophagy is characterized by the formation of double-membrane vesicles called autophagosomes, which deliver bulk cytoplasmic material to the lytic compartment of the cell for degradation. Autophagosome formation is initiated by assembly and recruitment of the core autophagy machinery to distinct cellular sites, referred to as phagophore assembly sites (PAS) in yeast or autophagosome formation sites in other organisms. A large number of autophagy proteins involved in the formation of autophagosomes has been identified; however, how the individual components of the PAS are assembled and how they function to generate autophagosomes remains a fundamental question. Here, we highlight recent studies that provide molecular insights into PAS organization and the role of the endoplasmic reticulum and the vacuole in autophagosome formation.
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Affiliation(s)
- David M Hollenstein
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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119
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Mookherjee D, Das S, Mukherjee R, Bera M, Jana SC, Chakrabarti S, Chakrabarti O. RETREG1/FAM134B mediated autophagosomal degradation of AMFR/GP78 and OPA1 -a dual organellar turnover mechanism. Autophagy 2020; 17:1729-1752. [PMID: 32559118 DOI: 10.1080/15548627.2020.1783118] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Turnover of cellular organelles, including endoplasmic reticulum (ER) and mitochondria, is orchestrated by an efficient cellular surveillance system. We have identified a mechanism for dual regulation of ER and mitochondria under stress. It is known that AMFR, an ER E3 ligase and ER-associated degradation (ERAD) regulator, degrades outer mitochondrial membrane (OMM) proteins, MFNs (mitofusins), via the proteasome and triggers mitophagy. We show that destabilized mitochondria are almost devoid of the OMM and generate "mitoplasts". This brings the inner mitochondrial membrane (IMM) in the proximity of the ER. When AMFR levels are high and the mitochondria are stressed, the reticulophagy regulatory protein RETREG1 participates in the formation of the mitophagophore by interacting with OPA1. Interestingly, OPA1 and other IMM proteins exhibit similar RETREG1-dependent autophagosomal degradation as AMFR, unlike most of the OMM proteins. The "mitoplasts" generated are degraded by reticulo-mito-phagy - simultaneously affecting dual organelle turnover.Abbreviations: AMFR/GP78: autocrine motility factor receptor; BAPTA: 1,2-bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid; BFP: blue fluorescent protein; CCCP: carbonyl cyanide m-chlorophenyl hydrazone; CNBr: cyanogen bromide; ER: endoplasmic reticulum; ERAD: endoplasmic-reticulum-associated protein degradation; FL: fluorescence, GFP: green fluorescent protein; HA: hemagglutinin; HEPES: 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid; IMM: inner mitochondrial membrane; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MFN: mitofusin, MGRN1: mahogunin ring finger 1; NA: numerical aperature; OMM: outer mitochondrial membrane; OPA1: OPA1 mitochondrial dynamin like GTPase; PRNP/PrP: prion protein; RER: rough endoplasmic reticulum; RETREG1/FAM134B: reticulophagy regulator 1; RFP: red fluorescent protein; RING: really interesting new gene; ROI: region of interest; RTN: reticulon; SEM: standard error of the mean; SER: smooth endoplasmic reticulum; SIM: structured illumination microscopy; SQSTM1/p62: sequestosome 1; STED: stimulated emission depletion; STOML2: stomatin like 2; TOMM20: translocase of outer mitochondrial membrane 20; UPR: unfolded protein response.
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Affiliation(s)
- Debdatto Mookherjee
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Subhrangshu Das
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Rukmini Mukherjee
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India.,Buchmann Institute for Molecular Life Sciences, Frankfurt Am Main, Germany
| | - Manindra Bera
- Laboratory of Cell Biology, the Rockefeller University, New York, USA
| | | | - Saikat Chakrabarti
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Oishee Chakrabarti
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India.,Homi Bhabha National Institute, Mumbai, India
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120
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Rossini M, Pizzo P, Filadi R. Better to keep in touch: investigating inter‐organelle cross‐talk. FEBS J 2020; 288:740-755. [DOI: 10.1111/febs.15451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/28/2020] [Accepted: 06/11/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Michela Rossini
- Department of Biomedical Sciences University of Padua Padua Italy
| | - Paola Pizzo
- Department of Biomedical Sciences University of Padua Padua Italy
- Neuroscience Institute National Research Council (CNR) Padua Italy
| | - Riccardo Filadi
- Department of Biomedical Sciences University of Padua Padua Italy
- Neuroscience Institute National Research Council (CNR) Padua Italy
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121
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Nicolas V, Lievin-Le Moal V. Small Trafficking Inhibitor Retro-2 Disrupts the Microtubule-Dependent Trafficking of Autophagic Vacuoles. Front Cell Dev Biol 2020; 8:464. [PMID: 32626708 PMCID: PMC7314991 DOI: 10.3389/fcell.2020.00464] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/19/2020] [Indexed: 12/13/2022] Open
Abstract
Autophagy is a catabolic recycling process by which a cell degrades its own constituents to contribute to cell homeostasis or survival. We report that the small trafficking inhibitor Retro-2 impairs microtubule-dependent vacuolar trafficking in autophagy. Retro-2 induced autophagy and promoted the dramatic cytoplasmic accumulation of large autophagosomes. Moreover, Retro-2 decreased the spreading of autophagosomes within the cytoplasm of nutrient-starved cells. In addition, Retro-2 abolished autolysosomes formation. We show that these effects arise from hitherto unsuspected disassembly activity of the small molecule on the cellular microtubule network, which is known to act as a key regulator of vacuolar trafficking of the autophagy pathway.
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Affiliation(s)
- Valérie Nicolas
- Université Paris-Saclay, Institut Paris-Saclay d'Innovation Thérapeutique (IPSIT), Microscope Facility (MIPSIT), UMS-US31-UMS3679, Châtenay-Malabry, France
| | - Vanessa Lievin-Le Moal
- University Paris-Saclay, Inserm, UMR-S 996 Inflammation, Microbiome and Immunosurveillance, Clamart, France
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122
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Lei Y, Klionsky DJ. Scission, a critical step in autophagosome formation. Autophagy 2020; 16:1363-1365. [PMID: 32544363 DOI: 10.1080/15548627.2020.1779468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
A key feature of macroautophagy (hereafter autophagy) is the formation of the phagophore, a double-membrane compartment sequestering cargos and finally maturing into a vesicle termed an autophagosome; however, where these membranes originate from is not clear. In a previous study, researchers from the Rubinsztein lab proposed a model in which the autophagosome can evolve from the RAB11A-positive recycling endosome. In their recent paper, they determine that DNM2 (dynamin 2) functions in scission of the recycling endosome, and the release of the autophagosome precursor. These findings explain how the centronuclear myopathy (CNM) mutation in DNM2 results in the accumulation of immature autophagic structures.
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Affiliation(s)
- Yuchen Lei
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan , Ann Arbor, MI, USA
| | - Daniel J Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan , Ann Arbor, MI, USA
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123
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Abstract
Autophagy is a conserved vacuole/lysosome-mediated degradation pathway for clearing and recycling cellular components including cytosol, macromolecules, and dysfunctional organelles. In recent years, autophagy has emerged to play important roles in plant-pathogen interactions. It acts as an antiviral defense mechanism in plants. Moreover, increasing evidence shows that plant viruses can manipulate, hijack, or even exploit the autophagy pathway to promote pathogenesis, demonstrating the pivotal role of autophagy in the evolutionary arms race between hosts and viruses. In this review, we discuss recent findings about the antiviral and proviral roles of autophagy in plant-virus interactions.
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Affiliation(s)
- Meng Yang
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China;
| | - Asigul Ismayil
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China;
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China;
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124
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Munzel L, Neumann P, Otto FB, Krick R, Metje-Sprink J, Kroppen B, Karedla N, Enderlein J, Meinecke M, Ficner R, Thumm M. Atg21 organizes Atg8 lipidation at the contact of the vacuole with the phagophore. Autophagy 2020; 17:1458-1478. [PMID: 32515645 DOI: 10.1080/15548627.2020.1766332] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Coupling of Atg8 to phosphatidylethanolamine is crucial for the expansion of the crescent-shaped phagophore during cargo engulfment. Atg21, a PtdIns3P-binding beta-propeller protein, scaffolds Atg8 and its E3-like complex Atg12-Atg5-Atg16 during lipidation. The crystal structure of Atg21, in complex with the Atg16 coiled-coil domain, showed its binding at the bottom side of the Atg21 beta-propeller. Our structure allowed detailed analyses of the complex formation of Atg21 with Atg16 and uncovered the orientation of the Atg16 coiled-coil domain with respect to the membrane. We further found that Atg21 was restricted to the phagophore edge, near the vacuole, known as the vacuole isolation membrane contact site (VICS). We identified a specialized vacuolar subdomain at the VICS, typical of organellar contact sites, where the membrane protein Vph1 was excluded, while Vac8 was concentrated. Furthermore, Vac8 was required for VICS formation. Our results support a specialized organellar contact involved in controlling phagophore elongation. Abbreviations: FCCS: fluorescence cross correlation spectroscopy; NVJ: nucleus-vacuole junction; PAS: phagophore assembly site; PE: phosphatidylethanolamine; PROPPIN: beta-propeller that binds phosphoinositides; PtdIns3P: phosphatidylinositol- 3-phosphate; VICS: vacuole isolation membrane contact site.
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Affiliation(s)
- Lena Munzel
- Department of Cellular Biochemistry, University Medicine, Goettingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Florian B Otto
- Department of Cellular Biochemistry, University Medicine, Goettingen, Germany
| | - Roswitha Krick
- Department of Cellular Biochemistry, University Medicine, Goettingen, Germany
| | - Janina Metje-Sprink
- Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Benjamin Kroppen
- Department of Cellular Biochemistry, University Medicine, Goettingen, Germany
| | - Narain Karedla
- Physics Department III, University of Goettingen, Goettingen, Germany
| | - Jörg Enderlein
- Physics Department III, University of Goettingen, Goettingen, Germany
| | - Michael Meinecke
- Department of Cellular Biochemistry, University Medicine, Goettingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Michael Thumm
- Department of Cellular Biochemistry, University Medicine, Goettingen, Germany
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125
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Emerging roles of ATG proteins and membrane lipids in autophagosome formation. Cell Discov 2020; 6:32. [PMID: 32509328 PMCID: PMC7248066 DOI: 10.1038/s41421-020-0161-3] [Citation(s) in RCA: 153] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/21/2020] [Indexed: 12/12/2022] Open
Abstract
Autophagosome biogenesis is a dynamic membrane event, which is executed by the sequential function of autophagy-related (ATG) proteins. Upon autophagy induction, a cup-shaped membrane structure appears in the cytoplasm, then elongates sequestering cytoplasmic materials, and finally forms a closed double membrane autophagosome. However, how this complex vesicle formation event is strictly controlled and achieved is still enigmatic. Recently, there is accumulating evidence showing that some ATG proteins have the ability to directly interact with membranes, transfer lipids between membranes and regulate lipid metabolism. A novel role for various membrane lipids in autophagosome formation is also emerging. Here, we highlight past and recent key findings on the function of ATG proteins related to autophagosome biogenesis and consider how ATG proteins control this dynamic membrane formation event to organize the autophagosome by collaborating with membrane lipids.
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126
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A current view of molecular dissection in autophagy machinery. J Physiol Biochem 2020; 76:357-372. [DOI: 10.1007/s13105-020-00746-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/14/2020] [Indexed: 02/06/2023]
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127
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Kohler V, Aufschnaiter A, Büttner S. Closing the Gap: Membrane Contact Sites in the Regulation of Autophagy. Cells 2020; 9:E1184. [PMID: 32397538 PMCID: PMC7290522 DOI: 10.3390/cells9051184] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 04/29/2020] [Accepted: 05/07/2020] [Indexed: 12/14/2022] Open
Abstract
In all eukaryotic cells, intracellular organization and spatial separation of incompatible biochemical processes is established by individual cellular subcompartments in form of membrane-bound organelles. Virtually all of these organelles are physically connected via membrane contact sites (MCS), allowing interorganellar communication and a functional integration of cellular processes. These MCS coordinate the exchange of diverse metabolites and serve as hubs for lipid synthesis and trafficking. While this of course indirectly impacts on a plethora of biological functions, including autophagy, accumulating evidence shows that MCS can also directly regulate autophagic processes. Here, we focus on the nexus between interorganellar contacts and autophagy in yeast and mammalian cells, highlighting similarities and differences. We discuss MCS connecting the ER to mitochondria or the plasma membrane, crucial for early steps of both selective and non-selective autophagy, the yeast-specific nuclear-vacuolar tethering system and its role in microautophagy, the emerging function of distinct autophagy-related proteins in organellar tethering as well as novel MCS transiently emanating from the growing phagophore and mature autophagosome.
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Affiliation(s)
- Verena Kohler
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden;
| | - Andreas Aufschnaiter
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden;
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden;
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
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128
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Nakatogawa H. Mechanisms governing autophagosome biogenesis. Nat Rev Mol Cell Biol 2020; 21:439-458. [PMID: 32372019 DOI: 10.1038/s41580-020-0241-0] [Citation(s) in RCA: 457] [Impact Index Per Article: 114.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2020] [Indexed: 12/20/2022]
Abstract
Autophagosomes are double-membrane vesicles newly formed during autophagy to engulf a wide range of intracellular material and transport this autophagic cargo to lysosomes (or vacuoles in yeasts and plants) for subsequent degradation. Autophagosome biogenesis responds to a plethora of signals and involves unique and dynamic membrane processes. Autophagy is an important cellular mechanism allowing the cell to meet various demands, and its disruption compromises homeostasis and leads to various diseases, including metabolic disorders, neurodegeneration and cancer. Thus, not surprisingly, the elucidation of the molecular mechanisms governing autophagosome biogenesis has attracted considerable interest. Key molecules and organelles involved in autophagosome biogenesis, including autophagy-related (ATG) proteins and the endoplasmic reticulum, have been discovered, and their roles and relationships have been investigated intensely. However, several fundamental questions, such as what supplies membranes/lipids to build the autophagosome and how the membrane nucleates, expands, bends into a spherical shape and finally closes, have proven difficult to address. Nonetheless, owing to recent studies with new approaches and technologies, we have begun to unveil the mechanisms underlying these processes on a molecular level. We now know that autophagosome biogenesis is a highly complex process, in which multiple proteins and lipids from various membrane sources, supported by the formation of membrane contact sites, cooperate with biophysical phenomena, including membrane shaping and liquid-liquid phase separation, to ensure seamless segregation of the autophagic cargo. Together, these studies pave the way to obtaining a holistic view of autophagosome biogenesis.
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Affiliation(s)
- Hitoshi Nakatogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.
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129
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Li Z, Huang W, Wang W. Multifaceted roles of COPII subunits in autophagy. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118627. [DOI: 10.1016/j.bbamcr.2019.118627] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 12/09/2019] [Accepted: 12/14/2019] [Indexed: 01/06/2023]
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130
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Abstract
Autophagy is a conserved catabolic process critical for cell homeostasis with broad implications for aging and age-associated diseases. A defining feature of autophagy is the
de novo formation of a specialized transient organelle, the double-membrane autophagosome. Autophagosomes originate from small vesicular precursors after rapid membrane expansion resulting in the engulfment of a broad spectrum of cytoplasmic cargoes within a few minutes for vacuolar or lysosomal degradation. Recent advances have provided exciting new insights into the molecular mechanisms underlying the assembly of autophagic membranes during autophagosome biogenesis. Specifically, the phospholipid biosynthesis activity of the endoplasmic reticulum and a dedicated membrane-tethering complex between nascent autophagosomes and the endoplasmic reticulum have emerged as key factors in autophagosome formation.
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Affiliation(s)
- Martin Graef
- Max Planck Institute for Biology of Ageing, Cologne, 50931, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, 50931, Germany
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131
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Multifarious roles of lipid droplets in autophagy - Target, product, and what else? Semin Cell Dev Biol 2020; 108:47-54. [PMID: 32169402 DOI: 10.1016/j.semcdb.2020.02.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/12/2020] [Accepted: 02/29/2020] [Indexed: 01/09/2023]
Abstract
Lipid droplets (LDs) are not an inert storage of excessive lipids, but play various roles in cellular lipid metabolism. Autophagy involves several mechanisms for the degradation of cellular components, and is related to many aspects of lipid metabolism. LD and autophagic membranes often distribute in proximity, but their relationship is complex. LDs can be degraded by autophagy, but LDs are also generated as a result of autophagy or support the execution of autophagy. Moreover, several proteins crucial for autophagy were shown to affect different aspects of LD formation. This article aims to categorize this multifaceted and seemingly entangled LD-autophagy relationship and to discuss unresolved issues.
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132
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Eickhorst C, Licheva M, Kraft C. Scaffold proteins in bulk and selective autophagy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 172:15-35. [PMID: 32620241 DOI: 10.1016/bs.pmbts.2020.01.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Autophagy is a crucial cellular degradation and recycling pathway. During autophagy double-membrane vesicles, called autophagosomes, encapsulate cellular components and deliver their cargo to the lytic compartment for degradation. Formation of autophagosomes is regulated by the Atg1 kinase complex in yeast and the homologous ULK1 kinase complex in mammals. While research on Atg1 and ULK1 has advanced our understanding of how these protein kinases function in autophagy, the other Atg1/ULK1 kinase complex members have received much less attention. Here, we focus on the functions of the Atg1 kinase complex members Atg11 and Atg17 as well as the ULK1 kinase complex member FIP200 in autophagy. These three proteins act as scaffolds in their respective complexes. Recent studies have made it evident that they have similar but also distinct functions. In this article, we review our current understanding of how these scaffold proteins function from autophagosome formation to fusion and also discuss their possible roles in diseases.
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Affiliation(s)
- Christopher Eickhorst
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Mariya Licheva
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany; CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
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133
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ER-Phagy: Quality Control and Turnover of Endoplasmic Reticulum. Trends Cell Biol 2020; 30:384-398. [PMID: 32302550 DOI: 10.1016/j.tcb.2020.02.001] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/30/2020] [Accepted: 02/03/2020] [Indexed: 12/11/2022]
Abstract
The endoplasmic reticulum (ER) is the largest organelle in cells and has fundamental functions, such as folding, processing, and trafficking of proteins, cellular metabolism, and ion storage. To maintain its function, it is turned over constitutively, and even more actively under certain stress conditions. Quality control of the ER is mediated primarily by two pathways: the ubiquitin-proteasome system and autophagy (termed 'ER-phagy'). The identification of ER-phagy adaptor molecules has shed light on the mechanisms and physiological significance of ER-phagy. Here, we describe recent findings on various types of ER-phagy and present unanswered questions related to their mechanism and regulation.
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134
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Hale A, Merchant M, White M. Detection and analysis of autophagy in the American alligator (Alligator mississippiensis). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 334:192-207. [PMID: 32061056 DOI: 10.1002/jez.b.22936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 01/10/2020] [Accepted: 01/28/2020] [Indexed: 11/07/2022]
Abstract
In response to environmental temperature depression in the fall and winter, American alligators (Alligator mississippiensis) brumate. Brumation is characterized by lethargy, fasting, decreased metabolism, and decreased body temperature. During brumation, alligators will periodically emerge for basking or other encounters when environmental conditions permit. This sporadic activity and lack of nutrient intake may place strain on nutrient reserves. Nutrient scarcity, at the cellular and/or organismal level, promotes autophagy, a well-conserved subcellular catabolic process used to maintain energy homeostasis during periods of metabolic or hypoxic stress. An analysis of the putative alligator autophagy-related proteins has been conducted, and the results will be used to investigate the physiological role of autophagy during the brumation period. Using published genomic data, we have determined that autophagy is highly conserved, and alligator amino acid sequences exhibit a high percentage of identity with human homologs. Transcriptome analysis conducted using liver tissue derived from alligators confirmed the expression of one or more isoforms of each of the 34 autophagy initiation and elongation genes assayed. Five autophagy-related proteins (ATG5, ATG9A, BECN1, ATG16L1, and MAP1-LC3B), with functions spanning the major stages of autophagy, have been detected in alligator liver tissue by western blot analysis. In addition, ATG5 was detected in alligator liver tissue by immunohistochemistry. This is the first characterization of autophagy in crocodylians, and the first description of autophagy-related protein expression in whole blood.
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Affiliation(s)
- Amber Hale
- Department of Biology, McNeese State University, Lake Charles, Louisiana
| | - Mark Merchant
- Department of Chemistry and Physics, McNeese State University, Lake Charles, Louisiana
| | - Mary White
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, Louisiana
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135
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Abstract
Nucleophagy, the mechanism for autophagic degradation of nuclear material, occurs in both a macro- and micronucleophagic manner. Upon nitrogen deprivation, we observed, in an in-depth fluorescence microscopy study, the formation of micronuclei: small parts of superfluous nuclear components surrounded by perinuclear ER. We identified two types of micronuclei associated with a corresponding autophagic mode. Our results showed that macronucleophagy degraded these smaller micronuclei. Engulfed in Atg8-positive phagophores and containing cargo receptor Atg39, macronucleophagic structures revealed finger-like extensions when observed in 3-dimensional reconstitutions of fluorescence microscopy images, suggesting directional growth. Interestingly, in the late stages of phagophore elongation, the adjacent vacuolar membrane showed a reduction of integral membrane protein Pho8. This change in membrane composition could indicate the formation of a specialized vacuolar domain, required for autophagosomal fusion. Significantly larger micronuclei formed at nucleus vacuole junctions and were identified as a substrate of piecemeal microautophagy of the nucleus (PMN), by the presence of the integral membrane protein Nvj1. Micronuclei sequestered by vacuolar invaginations also contained Atg39. A detailed investigation revealed that both Atg39 and Atg8 accumulated between the vacuolar tips. These findings suggest a role for Atg39 in micronucleophagy. Indeed, following the degradation of Nvj1, an exclusive substrate of PMN, in immunoblots, we could confirm the essential role of Atg39 for PMN. Our study thus details the involvement of Atg8 in both macronucleophagy and PMN and identifies Atg39 as the general cargo receptor for nucleophagic processes.Abbreviations: DIC: Differential interference contrast, FWHM: Full width at half maximum, IQR: Interquartile range, MIPA: Micropexophagy-specific membrane apparatus, NLS: Nuclear localization signal, NVJ: Nucleus vacuole junction, PMN: Piecemeal microautophagy of the nucleus, pnER: Perinuclear ER.
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Affiliation(s)
- Florian B Otto
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Michael Thumm
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
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136
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Germain K, Kim PK. Pexophagy: A Model for Selective Autophagy. Int J Mol Sci 2020; 21:ijms21020578. [PMID: 31963200 PMCID: PMC7013971 DOI: 10.3390/ijms21020578] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/09/2020] [Accepted: 01/13/2020] [Indexed: 01/03/2023] Open
Abstract
The removal of damaged or superfluous organelles from the cytosol by selective autophagy is required to maintain organelle function, quality control and overall cellular homeostasis. Precisely how substrate selectivity is achieved, and how individual substrates are degraded during selective autophagy in response to both extracellular and intracellular cues is not well understood. The aim of this review is to highlight pexophagy, the autophagic degradation of peroxisomes, as a model for selective autophagy. Peroxisomes are dynamic organelles whose abundance is rapidly modulated in response to metabolic demands. Peroxisomes are routinely turned over by pexophagy for organelle quality control yet can also be degraded by pexophagy in response to external stimuli such as amino acid starvation or hypoxia. This review discusses the molecular machinery and regulatory mechanisms governing substrate selectivity during both quality-control pexophagy and pexophagy in response to external stimuli, in yeast and mammalian systems. We draw lessons from pexophagy to infer how the cell may coordinate the degradation of individual substrates by selective autophagy across different cellular cues.
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Affiliation(s)
- Kyla Germain
- Cell Biology Program, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada;
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Peter K. Kim
- Cell Biology Program, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada;
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
- Correspondence: ; Tel.: +1-416-813-5983
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137
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Turco E, Fracchiolla D, Martens S. Recruitment and Activation of the ULK1/Atg1 Kinase Complex in Selective Autophagy. J Mol Biol 2020; 432:123-134. [PMID: 31351898 PMCID: PMC6971721 DOI: 10.1016/j.jmb.2019.07.027] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/19/2019] [Accepted: 07/21/2019] [Indexed: 01/26/2023]
Abstract
Autophagy is a major cellular degradation pathway, which mediates the delivery of cytoplasmic cargo material into lysosomes. This is achieved by the specific sequestration of the cargo within double-membrane vesicles, the autophagosomes, which form de novo around this material. Autophagosome formation requires the action of a conserved set of factors, which act in hierarchical manner. The ULK1/Atg1 kinase complex is one of the most upstream acting components of the autophagy machinery. Here we discuss recent insights into the mechanisms of ULK1/Atg1 recruitment and activation at the cargo during selective autophagy. In particular, we will focus on the role of cargo receptors such as p62 and NDP52 during this process and discuss the emerging concept that cargo receptors act upstream of the autophagy machinery during cargo-induced selective autophagy.
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Affiliation(s)
- Eleonora Turco
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/5, 1030 Vienna, Austria.
| | - Dorotea Fracchiolla
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/5, 1030 Vienna, Austria.
| | - Sascha Martens
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/5, 1030 Vienna, Austria.
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138
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Mechanisms of Autophagy in Metabolic Stress Response. J Mol Biol 2020; 432:28-52. [DOI: 10.1016/j.jmb.2019.09.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/06/2019] [Accepted: 09/06/2019] [Indexed: 01/17/2023]
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139
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Prinz WA, Toulmay A, Balla T. The functional universe of membrane contact sites. Nat Rev Mol Cell Biol 2020; 21:7-24. [PMID: 31732717 PMCID: PMC10619483 DOI: 10.1038/s41580-019-0180-9] [Citation(s) in RCA: 358] [Impact Index Per Article: 89.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2019] [Indexed: 12/13/2022]
Abstract
Organelles compartmentalize eukaryotic cells, enhancing their ability to respond to environmental and developmental changes. One way in which organelles communicate and integrate their activities is by forming close contacts, often called 'membrane contact sites' (MCSs). Interest in MCSs has grown dramatically in the past decade as it is has become clear that they are ubiquitous and have a much broader range of critical roles in cells than was initially thought. Indeed, functions for MCSs in intracellular signalling (particularly calcium signalling, reactive oxygen species signalling and lipid signalling), autophagy, lipid metabolism, membrane dynamics, cellular stress responses and organelle trafficking and biogenesis have now been reported.
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Affiliation(s)
- William A Prinz
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Alexandre Toulmay
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tamas Balla
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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140
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Local Fatty Acid Channeling into Phospholipid Synthesis Drives Phagophore Expansion during Autophagy. Cell 2019; 180:135-149.e14. [PMID: 31883797 DOI: 10.1016/j.cell.2019.12.005] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 10/29/2019] [Accepted: 12/04/2019] [Indexed: 12/21/2022]
Abstract
Autophagy is a conserved catabolic homeostasis process central for cellular and organismal health. During autophagy, small single-membrane phagophores rapidly expand into large double-membrane autophagosomes to encapsulate diverse cargoes for degradation. It is thought that autophagic membranes are mainly derived from preformed organelle membranes. Instead, here we delineate a pathway that expands the phagophore membrane by localized phospholipid synthesis. Specifically, we find that the conserved acyl-CoA synthetase Faa1 accumulates on nucleated phagophores and locally activates fatty acids (FAs) required for phagophore elongation and autophagy. Strikingly, using isotopic FA tracing, we directly show that Faa1 channels activated FAs into the synthesis of phospholipids and promotes their assembly into autophagic membranes. Indeed, the first committed steps of de novo phospholipid synthesis at the ER, which forms stable contacts with nascent autophagosomes, are essential for autophagy. Together, our work illuminates how cells spatially tune synthesis and flux of phospholipids for autophagosome biogenesis during autophagy.
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141
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Yorimitsu T, Sato K. Sec16 function in ER export and autophagy is independent of its phosphorylation in Saccharomyces cerevisiae. Mol Biol Cell 2019; 31:149-156. [PMID: 31851588 PMCID: PMC7001475 DOI: 10.1091/mbc.e19-08-0477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Coat protein complex II (COPII) protein assembles at the endoplasmic reticulum exit site (ERES) to form vesicle carrier for transport from the ER to the Golgi apparatus. Sec16 has a critical role in COPII assembly to form ERES. Sec16∆565N mutant, which lacks the N-terminal 565 amino acids, is defective in ERES formation and ER export. Several phosphoproteomic studies have identified 108 phosphorylated Ser/Thr/Tyr residues in Sec16 of Saccharomyces cerevisiae, of which 30 residues are located in the truncated part of Sec16∆565N. The exact role of the phosphorylation in Sec16 function remains to be determined. Therefore, we analyzed nonphosphorylatable Sec16 mutants, in which all identified phosphorylation sites are substituted with Ala. These mutants show ERES and ER export comparable to those of wild-type Sec16, although the nonphosphorylatable mutant binds the COPII subunit Sec23 more efficiently than the wild-type protein. Because nutrient starvation–induced autophagy depends on Sec16, Sec16∆565N impairs autophagy, whereas the nonphosphorylatable mutants do not affect autophagy. We conclude that Sec16 phosphorylation is not essential for its function.
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Affiliation(s)
- Tomohiro Yorimitsu
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Tokyo 153-8902, Japan
| | - Ken Sato
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Tokyo 153-8902, Japan
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142
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Lai LTF, Ye H, Zhang W, Jiang L, Lau WCY. Structural Biology and Electron Microscopy of the Autophagy Molecular Machinery. Cells 2019; 8:E1627. [PMID: 31842460 PMCID: PMC6952983 DOI: 10.3390/cells8121627] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/06/2019] [Accepted: 12/10/2019] [Indexed: 12/30/2022] Open
Abstract
Autophagy is a highly regulated bulk degradation process that plays a key role in the maintenance of cellular homeostasis. During autophagy, a double membrane-bound compartment termed the autophagosome is formed through de novo nucleation and assembly of membrane sources to engulf unwanted cytoplasmic components and targets them to the lysosome or vacuole for degradation. Central to this process are the autophagy-related (ATG) proteins, which play a critical role in plant fitness, immunity, and environmental stress response. Over the past few years, cryo-electron microscopy (cryo-EM) and single-particle analysis has matured into a powerful and versatile technique for the structural determination of protein complexes at high resolution and has contributed greatly to our current understanding of the molecular mechanisms underlying autophagosome biogenesis. Here we describe the plant-specific ATG proteins and summarize recent structural and mechanistic studies on the protein machinery involved in autophagy initiation with an emphasis on those by single-particle analysis.
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Affiliation(s)
- Louis Tung Faat Lai
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Hao Ye
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Wenxin Zhang
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Liwen Jiang
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
- CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
| | - Wilson Chun Yu Lau
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
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143
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COPII Vesicle Transport Is Required for Rotavirus NSP4 Interaction with the Autophagy Protein LC3 II and Trafficking to Viroplasms. J Virol 2019; 94:JVI.01341-19. [PMID: 31597778 DOI: 10.1128/jvi.01341-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/03/2019] [Indexed: 11/20/2022] Open
Abstract
Many viruses that replicate in the cytoplasm dramatically remodel and stimulate the accumulation of host cell membranes for efficient replication by poorly understood mechanisms. For rotavirus, a critical step in virion assembly requires the accumulation of membranes adjacent to virus replication centers called viroplasms. Early electron microscopy studies describe viroplasm-associated membranes as "swollen" endoplasmic reticulum (ER). We previously demonstrated that rotavirus infection initiates cellular autophagy and that membranes containing the autophagy marker protein LC3 and the rotavirus ER-synthesized transmembrane glycoprotein NSP4 traffic to viroplasms, suggesting that NSP4 must exit the ER. This study aimed to address the mechanism of NSP4 exit from the ER and determine whether the viroplasm-associated membranes are ER derived. We report that (i) NSP4 exits the ER in COPII vesicles, resulting in disrupted COPII vesicle transport and ER exit sites; (ii) COPII vesicles are hijacked by LC3 II, which interacts with NSP4; and (iii) NSP4/LC3 II-containing membranes accumulate adjacent to viroplasms. In addition, the ER transmembrane proteins SERCA and calnexin were not detected in viroplasm-associated membranes, providing evidence that the rotavirus maturation process of "budding" occurs through autophagy-hijacked COPII vesicle membranes. These findings reveal a new mechanism for rotavirus maturation dependent on intracellular host protein transport and autophagy for the accumulation of membranes required for virus replication.IMPORTANCE In a morphogenic step that is exceedingly rare for nonenveloped viruses, immature rotavirus particles assemble in replication centers called viroplasms, and bud through cytoplasmic cellular membranes to acquire the outer capsid proteins for infectious particle assembly. Historically, the intracellular membranes used for particle budding were thought to be endoplasmic reticulum (ER) because the rotavirus nonstructural protein NSP4, which interacts with the immature particles to trigger budding, is synthesized as an ER transmembrane protein. This present study shows that NSP4 exits the ER in COPII vesicles and that the NSP4-containing COPII vesicles are hijacked by the cellular autophagy machinery, which mediates the trafficking of NSP4 to viroplasms. Changing the paradigm for rotavirus maturation, we propose that the cellular membranes required for immature rotavirus particle budding are not an extension of the ER but are COPII-derived autophagy isolation membranes.
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144
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Osawa T, Ishii Y, Noda NN. Human ATG2B possesses a lipid transfer activity which is accelerated by negatively charged lipids and WIPI4. Genes Cells 2019; 25:65-70. [PMID: 31721365 DOI: 10.1111/gtc.12733] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/11/2019] [Accepted: 11/11/2019] [Indexed: 11/30/2022]
Abstract
Atg2 is one of the essential factors for autophagy. Recent advance of structural and biochemical study on yeast Atg2 proposed that Atg2 tethers the edge of the isolation membrane (IM) to the endoplasmic reticulum and mediates direct lipid transfer (LT) from ER to IM for IM expansion. In mammals, two Atg2 orthologs, ATG2A and ATG2B, participate in autophagic process. Here we showed that human ATG2B possesses the membrane tethering (MT) and LT activity that was promoted by negatively charged membranes and an Atg18 ortholog WIPI4. By contrast, negatively charged membranes reduced the yeast Atg2 activities in the absence of Atg18. These results suggest that the MT/LT activity of Atg2 is evolutionally conserved although their regulation differs among species.
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Affiliation(s)
- Takuo Osawa
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
| | - Yuki Ishii
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
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145
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Zeng Y, Li B, Lin Y, Jiang L. The interplay between endomembranes and autophagy in plants. CURRENT OPINION IN PLANT BIOLOGY 2019; 52:14-22. [PMID: 31344498 DOI: 10.1016/j.pbi.2019.05.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/08/2019] [Accepted: 05/22/2019] [Indexed: 06/10/2023]
Abstract
Autophagosomes are unique double-membrane organelles that enclose a portion of intracellular components for lysosome/vacuole delivery to maintain cellular homeostasis in eukaryotic cells. Genetic screening has revealed the requirement of autophagy-related proteins for autophagosome formation, although the origin of the autophagosome membrane remains elusive. The endomembrane system is a series of membranous organelles maintained by dynamic membrane flow between various compartments. In plants, there is accumulating evidence pointing to a link between autophagy and the endomembrane system, in particular between the endoplasmic reticulum and autophagosome. Here, we highlight and discuss about recent findings on plant autophagosome formation. We also look into the functional roles of endomembrane machineries in regard to the autophagy pathway in plants.
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Affiliation(s)
- Yonglun Zeng
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
| | - Baiying Li
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
| | - Youshun Lin
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Liwen Jiang
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong; The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China.
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146
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Hollenstein DM, Gómez-Sánchez R, Ciftci A, Kriegenburg F, Mari M, Torggler R, Licheva M, Reggiori F, Kraft C. Vac8 spatially confines autophagosome formation at the vacuole in S. cerevisiae. J Cell Sci 2019; 132:jcs.235002. [PMID: 31649143 PMCID: PMC6899017 DOI: 10.1242/jcs.235002] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/01/2019] [Indexed: 01/02/2023] Open
Abstract
Autophagy is initiated by the formation of a phagophore assembly site (PAS), the precursor of autophagosomes. In mammals, autophagosome formation sites form throughout the cytosol in specialized subdomains of the endoplasmic reticulum (ER). In yeast, the PAS is also generated close to the ER, but always in the vicinity of the vacuole. How the PAS is anchored to the vacuole and the functional significance of this localization are unknown. Here, we investigated the role of the PAS–vacuole connection for bulk autophagy in the yeast Saccharomyces cerevisiae. We show that Vac8 constitutes a vacuolar tether that stably anchors the PAS to the vacuole throughout autophagosome biogenesis via the PAS component Atg13. S. cerevisiae lacking Vac8 show inefficient autophagosome–vacuole fusion, and form fewer and smaller autophagosomes that often localize away from the vacuole. Thus, the stable PAS–vacuole connection established by Vac8 creates a confined space for autophagosome biogenesis between the ER and the vacuole, and allows spatial coordination of autophagosome formation and autophagosome–vacuole fusion. These findings reveal that the spatial regulation of autophagosome formation at the vacuole is required for efficient bulk autophagy. Highlighted Article: Vac8 tethers the phagophore assembly site to the vacuole, which creates a confined space for autophagosome biogenesis and coordinates autophagosome formation with vacuolar fusion.
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Affiliation(s)
- David M Hollenstein
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Rubén Gómez-Sánchez
- Department of Biomedical Sciences of Cells & Systems, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Akif Ciftci
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Franziska Kriegenburg
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Muriel Mari
- Department of Biomedical Sciences of Cells & Systems, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Raffaela Torggler
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Mariya Licheva
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Fulvio Reggiori
- Department of Biomedical Sciences of Cells & Systems, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany .,CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg
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147
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Park S, Zuber C, Roth J. Selective autophagy of cytosolic protein aggregates involves ribosome-free rough endoplasmic reticulum. Histochem Cell Biol 2019; 153:89-99. [PMID: 31720797 DOI: 10.1007/s00418-019-01829-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2019] [Indexed: 10/25/2022]
Abstract
Autophagy is a degradative cellular process that can be both non-selective and selective and begins with the formation of a unique smooth double-membrane phagophore which wraps around a portion of the cytoplasm. Excess and damaged organelles and cytoplasmic protein aggregates are degraded by selective autophagy. Previously, we reported that in fed HepG2 cells, cytoplasmic aggregates of EDEM1 and surplus fibrinogen Aα-γ assembly intermediates are targets of selective autophagy receptors and become degraded by a selective autophagy called aggrephagy. Here, we show by multiple confocal immunofluorescence and colocalization panels the codistribution of cytoplasmic protein aggregates with the selective autophagy receptors p62/SQSTM1 and NBR1 and with the phagophore marker LC3, and that phagophores induced by vinblastine treatment contain complexes of protein aggregates and selective autophagy receptors. By combined serial ultrathin section analysis and immunoelectron microscopy, we found that in fed HepG2 cells, a basically ribosome-free subdomain of rough endoplasmic reticulum (RER) cisternae forms a cradle that engulfs the cytoplasmic protein aggregates. This RER subdomain appears structurally different from omegasomes formed by the RER, which were suggested to provide a membrane platform from which the phagophore is derived in starvation-induced autophagy. Taken together, our observations provide further evidence for the importance of RER subdomains as a site and membrane source for phagophore formation and show their involvement in selective autophagy.
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Affiliation(s)
- Sujin Park
- Biozentrum, University of Basel, 4056, Basel, Switzerland.,Department of Integrated OMICS for Biomedical Science, WCU Program of Graduate School, Yonsei University, Seoul, 120-749, South Korea
| | - Christian Zuber
- Division of Cell and Molecular Pathology, Department of Pathology, University of Zurich, 8091, Zurich, Switzerland
| | - Jürgen Roth
- Department of Integrated OMICS for Biomedical Science, WCU Program of Graduate School, Yonsei University, Seoul, 120-749, South Korea. .,Division of Cell and Molecular Pathology, Department of Pathology, University of Zurich, 8091, Zurich, Switzerland.
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148
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Staiano L, Zappa F. Hijacking intracellular membranes to feed autophagosomal growth. FEBS Lett 2019; 593:3120-3134. [PMID: 31603532 DOI: 10.1002/1873-3468.13637] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/02/2019] [Accepted: 10/03/2019] [Indexed: 12/21/2022]
Abstract
Autophagy is widely considered as a housekeeping mechanism that enables cells to survive stress conditions and, in particular, nutrient deprivation. Autophagy begins with the formation of the phagophore that expands and closes around cytosolic material and damaged organelles destined for degradation. The execution of this complex machinery is guaranteed by the coordinated action of more than 40 ATG (autophagy-related) proteins that control the entire process at different stages from the biogenesis of the autophagosome to cargo sequestration and fusion with lysosomes. Autophagosome biogenesis occurs at multiple intracellular sites, such as the endoplasmic reticulum (ER) and the plasma membrane. Soon after the formation of the phagophore, the nascent autophagosome progressively grows in size and ultimately closes by recruiting intracellular membranes. In this review, we focus on the contribution of three membrane sources - the ER, the ER-Golgi intermediate compartment, and the Golgi complex - to autophagosome biogenesis and expansion. We also highlight the interplay between the secretory pathway and autophagy in cells when nutrients are scarce.
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Affiliation(s)
- Leopoldo Staiano
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy
| | - Francesca Zappa
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy.,Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
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149
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Mamidi AS, Ray A, Surolia N. Structural Analysis of PfSec62-Autophagy Interacting Motifs (AIM) and PfAtg8 Interactions for Its Implications in RecovER-phagy in Plasmodium falciparum. Front Bioeng Biotechnol 2019; 7:240. [PMID: 31608276 PMCID: PMC6773812 DOI: 10.3389/fbioe.2019.00240] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 09/11/2019] [Indexed: 11/27/2022] Open
Abstract
Autophagy is a degradative pathway associated with many pathological and physiological processes crucial for cell survival. During ER stress, while selective autophagy occurs via ER-phagy, the re-establishment of physiologic ER homeostasis upon resolution of a transient ER stress is mediated by recovER-phagy. Recent studies demonstrated that recovER-phagy is governed via association of Sec62 as an ER-resident autophagy receptor through its autophagy interacting motifs (AIM)/LC3-interacting region (LIR) toAtg8/LC3. Atg8 is an autophagy protein, which is central to autophagosome formation and maturation. Plasmodium falciparum Atg8 (PfAtg8) has both autophagic and non-autophagic functions critical for parasite survival. Since Plasmodium also has Sec62 in the ER membrane and is prone to ER stress due to drastic transformation during their complex intraerythrocytic cycle; hence, we initiated the studies to check whether recovER-phagy occurs in the parasite. To achieve this, a comprehensive study based on the computational approaches was carried out. This study embarks upon identification of AIM sequences in PfSec62 by carrying out peptide-protein docking simulations and comparing the interactions of these AIMs with PfAtg8, based on the molecular dynamic simulations. Detailed analysis is based on electrostatic surface complementarity, peptide-protein interaction strength, mapping of non-covalent bond interactions and rupture force calculated from steered MD simulations. Potential mean forces and unbinding free energies (ΔGdissociation) using Jarzynski's equality were also computed for the AIM/LIR motif complexes with PfAtg8/HsLC3 autophagy proteins to understand their dissociation free energy profiles and thereby their binding affinities and stability of the peptide-protein complexes. Through this study, we predict Sec62 mediated recovER-phagy in Plasmodium falciparum, which might open new avenues to explore novel drug targets for antimalarial drug discovery.
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Affiliation(s)
- Ashalatha Sreshty Mamidi
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.,Division of Biological Sciences, Indian Institute of Petroleum and Energy, Visakhapatnam, India
| | - Ananya Ray
- Molecular Biology and Genetics Laboratory, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Namita Surolia
- Molecular Biology and Genetics Laboratory, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
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150
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Autophagy differentially regulates macrophage lipid handling depending on the lipid substrate (oleic acid vs. acetylated-LDL) and inflammatory activation state. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:158527. [PMID: 31520777 DOI: 10.1016/j.bbalip.2019.158527] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/01/2019] [Accepted: 09/08/2019] [Indexed: 12/17/2022]
Abstract
The regulation of lipid droplet (LD) dynamics by autophagy in naïve macrophages is complex: Inhibiting autophagosome initiation steps attenuates oleic acid (OA) induced LD (OA-LD) biogenesis, whereas interfering with later-autophagosome maturation/lysosomal steps accelerates OA-LD biogenesis rate, but not OA-LD degradation. Here we hypothesized that regulation of macrophage lipid handling by autophagy may be lipid-substrate and activation-state-specific. Using automated quantitative live-cell imaging, initial LD biogenesis rate was ~30% slower when the lipid source was acetylated low density lipoprotein (acLDL) compared to OA. Yet, both were similarly affected by triacsin-C, an inhibitor of acyl-CoA synthase, which inhibited, and etomoxir, an inhibitor of acylcarnitine palmitoyl transferase (fatty acid oxidation), which augmented, LD biogenesis rates. An autophagy inducing peptide, Tat-Beclin1, enhanced the degradation, and inhibited (by 37%) the biogenesis of acLDL induced LD (acLDL-LD). Yet, Tat-Beclin1 increased OA-LD biogenesis rate by 70%. When macrophages were pre-activated with LPS + INFG they exhibited increased autophagosome number and area, and reduced BECN1 and ATG14 protein levels, which associated with a markedly attenuated autophagic flux. Concomitantly, OA-LD and acLDL-LD biogenesis rates increased 3 and 7.4-fold, respectively, but could not be further modulated by Tat-Beclin1, as observed in non-activated/naïve macrophages. We propose that macrophage autophagy, and/or components of its machinery, differentially regulate LD/foam-cell biogenesis depending on the lipid-source, and that inflammatory activation uncouples autophagy from LD biogenesis.
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