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Deretic V, Duque T, Trosdal E, Paddar M, Javed R, Akepati P. Membrane atg8ylation in Canonical and Noncanonical Autophagy. J Mol Biol 2024; 436:168532. [PMID: 38479594 PMCID: PMC11260254 DOI: 10.1016/j.jmb.2024.168532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 04/13/2024]
Abstract
Membrane atg8ylation is a homeostatic process responding to membrane remodeling and stress signals. Membranes are atg8ylated by mammalian ATG8 ubiquitin-like proteins through a ubiquitylation-like cascade. A model has recently been put forward which posits that atg8ylation of membranes is conceptually equivalent to ubiquitylation of proteins. Like ubiquitylation, membrane atg8ylation involves E1, E2 and E3 enzymes. The E3 ligases catalyze the final step of atg8ylation of aminophospholipids in membranes. Until recently, the only known E3 ligase for membrane atg8ylation was ATG16L1 in a noncovalent complex with the ATG12-ATG5 conjugate. ATG16L1 was first identified as a factor in canonical autophagy. During canonical autophagy, the ATG16L1-based E3 ligase complex includes WIPI2, which in turn recognizes phosphatidylinositiol 3-phosphate and directs atg8ylation of autophagic phagophores. As an alternative to WIPIs, binding of ATG16L1 to the proton pump V-ATPase guides atg8ylation of endolysosomal and phagosomal membranes in response to lumenal pH changes. Recently, a new E3 complex containing TECPR1 instead of ATG16L1, has been identified that responds to sphingomyelin's presence on the cytofacial side of perturbed endolysosomal membranes. In present review, we cover the principles of membrane atg8ylation, catalog its various presentations, and provide a perspective on the growing repertoire of E3 ligase complexes directing membrane atg8ylation at diverse locations.
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Affiliation(s)
- Vojo Deretic
- Autophagy Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA; Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA.
| | - Thabata Duque
- Autophagy Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA; Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Einar Trosdal
- Autophagy Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA; Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Masroor Paddar
- Autophagy Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA; Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Ruheena Javed
- Autophagy Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA; Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Prithvi Akepati
- Gastroenterology Division, Department of Internal Medicine, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
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2
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Hickey K, Şahin Y, Turner G, Nazarov T, Jitkov V, Pumphrey M, Smertenko A. Genotype-Specific Activation of Autophagy during Heat Wave in Wheat. Cells 2024; 13:1226. [PMID: 39056807 PMCID: PMC11274669 DOI: 10.3390/cells13141226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/04/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Recycling of unnecessary or dysfunctional cellular structures through autophagy plays a critical role in cellular homeostasis and environmental resilience. Therefore, the autophagy trait may have been unintentionally selected in wheat breeding programs for higher yields in arid climates. This hypothesis was tested by measuring the response of three common autophagy markers, ATG7, ATG8, and NBR1, to a heat wave under reduced soil moisture content in 16 genetically diverse spring wheat landraces originating from different geographical locations. We observed in the greenhouse trials that ATG8 and NBR1 exhibited genotype-specific responses to a 1 h, 40 °C heat wave, while ATG7 did not show a consistent response. Three genotypes from Uruguay, Mozambique, and Afghanistan showed a pattern consistent with higher autophagic activity: decreased or stable abundance of both ATG8 and NBR1 proteins, coupled with increased transcription of ATG8 and NBR1. In contrast, three genotypes from Pakistan, Ethiopia, and Egypt exhibited elevated ATG8 protein levels alongside reduced or unaltered ATG8 transcript levels, indicating a potential suppression or no change in autophagic activity. Principal component analysis demonstrated a correlation between lower abundance of ATG8 and NBR1 proteins and higher yield in the field trials. We found that (i) the combination of heat and drought activated autophagy only in several genotypes, suggesting that despite being a resilience mechanism, autophagy is a heat-sensitive process; (ii) higher autophagic activity correlates positively with greater yield; (iii) the lack of autophagic activity in some high-yielding genotypes suggests contribution of alternative stress-resilient mechanisms; and (iv) enhanced autophagic activity in response to heat and drought was independently selected by wheat breeding programs in different geographic locations.
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Affiliation(s)
- Kathleen Hickey
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99163, USA (Y.Ş.); (G.T.); (T.N.)
| | - Yunus Şahin
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99163, USA (Y.Ş.); (G.T.); (T.N.)
| | - Glenn Turner
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99163, USA (Y.Ş.); (G.T.); (T.N.)
| | - Taras Nazarov
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99163, USA (Y.Ş.); (G.T.); (T.N.)
| | - Vadim Jitkov
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA; (V.J.); (M.P.)
| | - Mike Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA; (V.J.); (M.P.)
| | - Andrei Smertenko
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99163, USA (Y.Ş.); (G.T.); (T.N.)
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3
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Chen J, Zhao H, Liu M, Chen L. A new perspective on the autophagic and non-autophagic functions of the GABARAP protein family: a potential therapeutic target for human diseases. Mol Cell Biochem 2024; 479:1415-1441. [PMID: 37440122 DOI: 10.1007/s11010-023-04800-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/24/2023] [Indexed: 07/14/2023]
Abstract
Mammalian autophagy-related protein Atg8, including the LC3 subfamily and GABARAP subfamily. Atg8 proteins play a vital role in autophagy initiation, autophagosome formation and transport, and autophagy-lysosome fusion. GABARAP subfamily proteins (GABARAPs) share a high degree of homology with LC3 family proteins, and their unique roles are often overlooked. GABARAPs are as indispensable as LC3 in autophagy. Deletion of GABARAPs fails autophagy flux induction and autophagy lysosomal fusion, which leads to the failure of autophagy. GABARAPs are also involved in the transport of selective autophagy receptors. They are engaged in various particular autophagy processes, including mitochondrial autophagy, endoplasmic reticulum autophagy, Golgi autophagy, centrosome autophagy, and dorphagy. Furthermore, GABARAPs are closely related to the transport and delivery of the inhibitory neurotransmitter γ-GABAA and the angiotensin II AT1 receptor (AT1R), tumor growth, metastasis, and prognosis. GABARAPs also have been confirmed to be involved in various diseases, such as cancer, cardiovascular disease, and neurodegenerative diseases. In order to better understand the role and therapeutic potential of GABARAPs, this article comprehensively reviews the autophagic and non-autophagic functions of GABARAPs, as well as the research progress of the role and mechanism of GABARAPs in cancer, cardiovascular diseases and neurodegenerative diseases. It emphasizes the significance of GABARAPs in the clinical prevention and treatment of diseases, and may provide new therapeutic ideas and targets for human diseases. GABARAP and GABARAPL1 in the serum of cancer patients are positively correlated with the prognosis of patients, which can be used as a clinical biomarker, predictor and potential therapeutic target.
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Affiliation(s)
- Jiawei Chen
- Central Laboratory of Yan'nan Hospital Affiliated to Kunming, Medical University, Key Laboratory of Cardiovascular Diseases of Yunnan Province, Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, No. 245, Renmin East Road, Kunming, 650000, Yunnan, China
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Hong Zhao
- Central Laboratory of Yan'nan Hospital Affiliated to Kunming, Medical University, Key Laboratory of Cardiovascular Diseases of Yunnan Province, Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, No. 245, Renmin East Road, Kunming, 650000, Yunnan, China
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
- School of Nursing, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Meiqing Liu
- Central Laboratory of Yan'nan Hospital Affiliated to Kunming, Medical University, Key Laboratory of Cardiovascular Diseases of Yunnan Province, Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, No. 245, Renmin East Road, Kunming, 650000, Yunnan, China.
| | - Linxi Chen
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
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4
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Sakuma C, Shizukuishi S, Ogawa M, Honjo Y, Takeyama H, Guan JL, Weiser J, Sasai M, Yamamoto M, Ohnishi M, Akeda Y. Individual Atg8 paralogs and a bacterial metabolite sequentially promote hierarchical CASM-xenophagy induction and transition. Cell Rep 2024; 43:114131. [PMID: 38656870 DOI: 10.1016/j.celrep.2024.114131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/06/2024] [Accepted: 04/04/2024] [Indexed: 04/26/2024] Open
Abstract
Atg8 paralogs, consisting of LC3A/B/C and GBRP/GBRPL1/GATE16, function in canonical autophagy; however, their function is controversial because of functional redundancy. In innate immunity, xenophagy and non-canonical single membranous autophagy called "conjugation of Atg8s to single membranes" (CASM) eliminate bacteria in various cells. Previously, we reported that intracellular Streptococcus pneumoniae can induce unique hierarchical autophagy comprised of CASM induction, shedding, and subsequent xenophagy. However, the molecular mechanisms underlying these processes and the biological significance of transient CASM induction remain unknown. Herein, we profile the relationship between Atg8s, autophagy receptors, poly-ubiquitin, and Atg4 paralogs during pneumococcal infection to understand the driving principles of hierarchical autophagy and find that GATE16 and GBRP sequentially play a pivotal role in CASM shedding and subsequent xenophagy induction, respectively, and LC3A and GBRPL1 are involved in CASM/xenophagy induction. Moreover, we reveal ingenious bacterial tactics to gain intracellular survival niches by manipulating CASM-xenophagy progression by generating intracellular pneumococci-derived H2O2.
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Affiliation(s)
- Chisato Sakuma
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Sayaka Shizukuishi
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Michinaga Ogawa
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
| | - Yuko Honjo
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan; Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Haruko Takeyama
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-0072, Japan; Research Organization for Nano & Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan; Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Jun-Lin Guan
- Department of Cancer Biology, University of Cincinnati College of Medicine, CARE/Crawley Building, Suite E-870 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Jeffery Weiser
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Miwa Sasai
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Laboratory of Immunoparasitology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan; Department of Immunoparasitology, Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masahiro Yamamoto
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Laboratory of Immunoparasitology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan; Department of Immunoparasitology, Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
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5
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Jian F, Wang S, Tian R, Wang Y, Li C, Li Y, Wang S, Fang C, Ma C, Rong Y. The STX17-SNAP47-VAMP7/VAMP8 complex is the default SNARE complex mediating autophagosome-lysosome fusion. Cell Res 2024; 34:151-168. [PMID: 38182888 PMCID: PMC10837459 DOI: 10.1038/s41422-023-00916-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/11/2023] [Indexed: 01/07/2024] Open
Abstract
Autophagosome-lysosome fusion mediated by SNARE complexes is an essential step in autophagy. Two SNAP29-containing SNARE complexes have been extensively studied in starvation-induced bulk autophagy, while the relevant SNARE complexes in other types of autophagy occurring under non-starvation conditions have been overlooked. Here, we found that autophagosome-lysosome fusion in selective autophagy under non-starvation conditions does not require SNAP29-containing SNARE complexes, but requires the STX17-SNAP47-VAMP7/VAMP8 SNARE complex. Further, the STX17-SNAP47-VAMP7/VAMP8 SNARE complex also functions in starvation-induced autophagy. SNAP47 is recruited to autophagosomes following concurrent detection of ATG8s and PI(4,5)P2 via its Pleckstrin homology domain. By contrast, SNAP29-containing SNAREs are excluded from selective autophagy due to inactivation by O-GlcNAcylation under non-starvation conditions. These findings depict a previously unknown, default SNARE complex responsible for autophagosome-lysosome fusion in both selective and bulk autophagy, which could guide research and therapeutic development in autophagy-related diseases.
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Affiliation(s)
- Fenglei Jian
- School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonostic Infectious Disease, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shen Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Rui Tian
- School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonostic Infectious Disease, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yufen Wang
- School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonostic Infectious Disease, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chuangpeng Li
- School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonostic Infectious Disease, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yan Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shixuan Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chao Fang
- School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonostic Infectious Disease, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Cong Ma
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Yueguang Rong
- School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonostic Infectious Disease, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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6
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Rogov VV, Nezis IP, Tsapras P, Zhang H, Dagdas Y, Noda NN, Nakatogawa H, Wirth M, Mouilleron S, McEwan DG, Behrends C, Deretic V, Elazar Z, Tooze SA, Dikic I, Lamark T, Johansen T. Atg8 family proteins, LIR/AIM motifs and other interaction modes. AUTOPHAGY REPORTS 2023; 2:27694127.2023.2188523. [PMID: 38214012 PMCID: PMC7615515 DOI: 10.1080/27694127.2023.2188523] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
The Atg8 family of ubiquitin-like proteins play pivotal roles in autophagy and other processes involving vesicle fusion and transport where the lysosome/vacuole is the end station. Nuclear roles of Atg8 proteins are also emerging. Here, we review the structural and functional features of Atg8 family proteins and their protein-protein interaction modes in model organisms such as yeast, Arabidopsis, C. elegans and Drosophila to humans. Although varying in number of homologs, from one in yeast to seven in humans, and more than ten in some plants, there is a strong evolutionary conservation of structural features and interaction modes. The most prominent interaction mode is between the LC3 interacting region (LIR), also called Atg8 interacting motif (AIM), binding to the LIR docking site (LDS) in Atg8 homologs. There are variants of these motifs like "half-LIRs" and helical LIRs. We discuss details of the binding modes and how selectivity is achieved as well as the role of multivalent LIR-LDS interactions in selective autophagy. A number of LIR-LDS interactions are known to be regulated by phosphorylation. New methods to predict LIR motifs in proteins have emerged that will aid in discovery and analyses. There are also other interaction surfaces than the LDS becoming known where we presently lack detailed structural information, like the N-terminal arm region and the UIM-docking site (UDS). More interaction modes are likely to be discovered in future studies.
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Affiliation(s)
- Vladimir V. Rogov
- Institute for Pharmaceutical Chemistry, Department of Biochemistry, Chemistry and Pharmacy, Goethe University, 60438 Frankfurt, am Main, and Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Ioannis P. Nezis
- School of Life Sciences, University of Warwick, CV4 7AL Coventry, UK
| | | | - Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China and College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yasin Dagdas
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Nobuo N. Noda
- Institute for Genetic Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo 060-0815, Japan
| | - Hitoshi Nakatogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Martina Wirth
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Stephane Mouilleron
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | | | - Christian Behrends
- Munich Cluster of Systems Neurology, Ludwig-Maximilians-Universität München, München, Germany
| | - Vojo Deretic
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM and Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Zvulun Elazar
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Sharon A. Tooze
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Ivan Dikic
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt am Main, and Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Trond Lamark
- Autophagy Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Terje Johansen
- Autophagy Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
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7
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Sathiyaseelan P, Chittaranjan S, Kalloger SE, Chan J, Go NE, Jardon MA, Ho CJ, Hui T, Xu J, Chow C, Gao D, Johnson FD, Lockwood WW, Morin GB, Renouf DJ, Schaeffer DF, Gorski SM. Loss of ATG4B and ATG4A results in two-stage cell cycle defects in pancreatic ductal adenocarcinoma cells. J Cell Sci 2023; 136:jcs260644. [PMID: 37701987 PMCID: PMC10617609 DOI: 10.1242/jcs.260644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 07/17/2023] [Indexed: 09/14/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) exhibits elevated levels of autophagy, which promote tumor progression and treatment resistance. ATG4B is an autophagy-related cysteine protease under consideration as a potential therapeutic target, but it is largely unexplored in PDAC. Here, we investigated the clinical and functional relevance of ATG4B expression in PDAC. Using two PDAC patient cohorts, we found that low ATG4B mRNA or protein expression is associated with worse patient survival outcomes, poorly differentiated PDAC tumors and a lack of survival benefit from adjuvant chemotherapy. In PDAC cell lines, ATG4B knockout reduced proliferation, abolished processing of LC3B (also known as MAP1LC3B), and reduced GABARAP and GABARAPL1 levels, but increased ATG4A levels. ATG4B and ATG4A double knockout lines displayed a further reduction in proliferation, characterized by delays in G1-S phase transition and mitosis. Pro-LC3B accumulated aberrantly at the centrosome with a concomitant increase in centrosomal proteins PCM1 and CEP131, which was rescued by exogenous ATG4B. The two-stage cell cycle defects following ATG4B and ATG4A loss have important therapeutic implications for PDAC.
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Affiliation(s)
- Paalini Sathiyaseelan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Suganthi Chittaranjan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | - Steve E. Kalloger
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Pancreas Centre BC, Vancouver, BC, V5Z 1L8, Canada
| | - Jennifer Chan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Nancy E. Go
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | - Mario A. Jardon
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | - Cally J. Ho
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Theodore Hui
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Jing Xu
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | - Christine Chow
- Genetic Pathology Evaluation Centre, Vancouver, BC, V6H 3Z6, Canada
| | - Dongxia Gao
- Genetic Pathology Evaluation Centre, Vancouver, BC, V6H 3Z6, Canada
| | - Fraser D. Johnson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
- Department of Integrative Oncology, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | - William W. Lockwood
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
- Department of Integrative Oncology, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | - Gregg B. Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Daniel J. Renouf
- Pancreas Centre BC, Vancouver, BC, V5Z 1L8, Canada
- Division of Medical Oncology, BC Cancer, Vancouver, BC, V5Z 4E6, Canada
| | - David F. Schaeffer
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
- Pancreas Centre BC, Vancouver, BC, V5Z 1L8, Canada
- Division of Anatomical Pathology, Vancouver General Hospital, Vancouver, BC, V5Z 1M9, Canada
| | - Sharon M. Gorski
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
- Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
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8
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Zhou J, Ma J, Yang C, Zhu X, Li J, Zheng X, Li X, Chen S, Feng L, Wang P, Ho MI, Ma W, Liao J, Li F, Wang C, Zhuang X, Jiang L, Kang BH, Gao C. A non-canonical role of ATG8 in Golgi recovery from heat stress in plants. NATURE PLANTS 2023; 9:749-765. [PMID: 37081290 DOI: 10.1038/s41477-023-01398-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
Above-optimal growth temperatures, usually referred to as heat stress (HS), pose a challenge to organisms' survival as they interfere with essential physiological functions and disrupt cellular organization. Previous studies have elucidated the complex transcriptional regulatory networks involved in plant HS responses, but the mechanisms of organellar remodelling and homeostasis during plant HS adaptations remain elusive. Here we report a non-canonical function of ATG8 in regulating the restoration of plant Golgi damaged by HS. Short-term acute HS causes vacuolation of the Golgi apparatus and translocation of ATG8 to the dilated Golgi membrane. The inactivation of the ATG conjugation system, but not of the upstream autophagic initiators, abolishes the targeting of ATG8 to the swollen Golgi, causing a delay in Golgi recovery after HS. Using TurboID-based proximity labelling, we identified CLATHRIN LIGHT CHAIN 2 (CLC2) as an interacting partner of ATG8 via the AIM-LDS interface. CLC2 is recruited to the cisternal membrane by ATG8 to facilitate Golgi reassembly. Collectively, our study reveals a hitherto unanticipated process of Golgi stack recovery from HS in plant cells and uncovers a previously unknown mechanism of organelle resilience involving ATG8.
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Affiliation(s)
- Jun Zhou
- MOE Key Laboratory & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China.
| | - Juncai Ma
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong, China
| | - Chao Yang
- MOE Key Laboratory & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xiu Zhu
- MOE Key Laboratory & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jing Li
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong, China
| | - Xuanang Zheng
- MOE Key Laboratory & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xibao Li
- MOE Key Laboratory & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Siyu Chen
- MOE Key Laboratory & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Lei Feng
- MOE Key Laboratory & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong, China
| | - Pengfei Wang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong, China
| | - Man Ip Ho
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong, China
| | - Wenlong Ma
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong, China
| | - Jun Liao
- MOE Key Laboratory & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Faqiang Li
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Chao Wang
- College of Life Sciences, Shaoxing University, Shaoxing, China
| | - Xiaohong Zhuang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong, China
| | - Liwen Jiang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong, China
| | - Byung-Ho Kang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong, China.
| | - Caiji Gao
- MOE Key Laboratory & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China.
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9
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Walczak M, Meister TR, Nguyen HM, Zhu Y, Besteiro S, Yeh E. Structure-Function Relationship for a Divergent Atg8 Protein Required for a Nonautophagic Function in Apicomplexan Parasites. mBio 2023; 14:e0364221. [PMID: 36625582 PMCID: PMC9973341 DOI: 10.1128/mbio.03642-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Atg8 family proteins are highly conserved eukaryotic proteins with diverse autophagy and nonautophagic functions in eukaryotes. While the structural features required for conserved autophagy functions of Atg8 are well established, little is known about the molecular changes that facilitated acquisition of divergent, nonautophagic functions of Atg8. The malaria parasite Plasmodium falciparum offers a unique opportunity to study nonautophagic functions of Atg8 family proteins because it encodes a single Atg8 homolog whose only essential function is in the inheritance of an unusual secondary plastid called the apicoplast. Here, we used functional complementation to investigate the structure-function relationship for this divergent Atg8 protein. We showed that the LC3-interacting region (LIR) docking site (LDS), the major interaction interface of the Atg8 protein family, is required for P. falciparum Atg8 (PfAtg8) apicoplast localization and function, likely via Atg8 lipidation. On the other hand, another region previously implicated in canonical Atg8 interactions, the N-terminal helix, is not required for apicoplast-specific PfAtg8 function. Finally, our investigations at the cellular level demonstrate that the unique apicomplexan-specific loop, previously implicated in interaction with membrane conjugation machinery in recombinant protein-based in vitro assays, is not required for membrane conjugation nor for the apicoplast-specific effector function of Atg8 in both P. falciparum and related Apicomplexa member Toxoplasma gondii. These results suggest that the effector function of apicomplexan Atg8 is mediated by structural features distinct from those previously identified for macroautophagy and selective autophagy functions. IMPORTANCE The most extensively studied role of Atg8 proteins is in autophagy. However, it is clear that they have other nonautophagic functions critical to cell function and disease pathogenesis that are so far understudied compared to their canonical role in autophagy. Mammalian cells contain multiple Atg8 paralogs that have diverse, specialized functions. Gaining molecular insight into their nonautophagic functions is difficult because of redundancy between the homologs and their role in both autophagy and nonautophagic pathways. Malaria parasites such as Plasmodium falciparum are a unique system to study a novel, nonautophagic function of Atg8 separate from its role in autophagy: they have only one Atg8 protein whose only essential function is in the inheritance of the apicoplast, a unique secondary plastid organelle. Insights into the molecular basis of PfAtg8's function in apicoplast biogenesis will have important implications for the evolution of diverse nonautophagic functions of the Atg8 protein family.
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Affiliation(s)
- Marta Walczak
- Department of Pathology, Stanford School of Medicine, Stanford, California, USA
| | - Thomas R. Meister
- Department of Molecular and Cellular Physiology, Stanford School of Medicine, Stanford, California, USA
| | - Hoa Mai Nguyen
- LPHI UMR5235, University of Montpellier, CNRS, Montpellier, France
| | - Yili Zhu
- Department of Pathology, Stanford School of Medicine, Stanford, California, USA
| | | | - Ellen Yeh
- Department of Pathology, Stanford School of Medicine, Stanford, California, USA
- Department of Microbiology & Immunology, Stanford School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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10
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Varga VB, Keresztes F, Sigmond T, Vellai T, Kovács T. The evolutionary and functional divergence of the Atg8 autophagy protein superfamily. Biol Futur 2022; 73:375-384. [PMID: 35731422 DOI: 10.1007/s42977-022-00123-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/28/2022] [Indexed: 01/27/2023]
Abstract
Autophagy is a highly conserved self-degradation process of eukaryotic cells which is required for the effective elimination of damaged and unnecessary cytosolic constituents. Defects in the process can cause the intracellular accumulation of such damages, thereby leading to the senescence and subsequent loss of the affected cell. Defective autophagy hence is implicated in the development of various degenerative processes, including cancer, neurodegenerative diseases, diabetes, tissue atrophy and fibrosis, and immune deficiency, as well as in accelerated aging. The autophagic process is mediated by numerous autophagy-related (ATG) proteins, among which the ATG8/LC3/GABARAP (Microtubule-associated protein 1A/1B-light chain 3/Gammaaminobutyric acid receptor-associated protein) superfamily has a pivotal role in the formation and maturation of autophagosome, a key (macro) autophagic structure (the autophagosome sequesters parts of the cytoplasm which are destined for breakdown). While in the unicellular yeast there is only a single ATG8 protein, metazoan systems usually contain more ATG8 paralogs. ATG8 paralogs generally display tissue-specific expression patterns and their functions are not strictly restricted to autophagy. For example, GABARAP proteins also play a role in intracellular vesicle transport, and, in addition to autophagosome formation, ATG8 also functions in selective autophagy. In this review, we summarize the functional diversity of ATG8/LC3/GABARAP proteins, using tractable genetic models applied in autophagy research.
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Affiliation(s)
- Virginia B Varga
- Department of Genetics, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, H-1117, Hungary
| | - Fanni Keresztes
- Department of Genetics, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, H-1117, Hungary
| | - Tímea Sigmond
- Department of Genetics, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, H-1117, Hungary
| | - Tibor Vellai
- Department of Genetics, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, H-1117, Hungary.,ELKH-ELTE Genetics Research Group, Pázmány Péter sétány 1/C, Budapest, H-1117, Hungary
| | - Tibor Kovács
- Department of Genetics, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, H-1117, Hungary.
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11
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Ding Y, Xing D, Fei Y, Lu B. Emerging degrader technologies engaging lysosomal pathways. Chem Soc Rev 2022; 51:8832-8876. [PMID: 36218065 PMCID: PMC9620493 DOI: 10.1039/d2cs00624c] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Indexed: 08/24/2023]
Abstract
Targeted protein degradation (TPD) provides unprecedented opportunities for drug discovery. While the proteolysis-targeting chimera (PROTAC) technology has already entered clinical trials and changed the landscape of small-molecule drugs, new degrader technologies harnessing alternative degradation machineries, especially lysosomal pathways, have emerged and broadened the spectrum of degradable targets. We have recently proposed the concept of autophagy-tethering compounds (ATTECs) that hijack the autophagy protein microtubule-associated protein 1A/1B light chain 3 (LC3) for targeted degradation. Other groups also reported degrader technologies engaging lysosomal pathways through different mechanisms including AUTACs, AUTOTACs, LYTACs and MoDE-As. In this review, we analyse and discuss ATTECs along with other lysosomal-relevant degrader technologies. Finally, we will briefly summarize the current status of these degrader technologies and envision possible future studies.
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Affiliation(s)
- Yu Ding
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, School of Life Sciences, Fudan University, Shanghai, China.
| | - Dong Xing
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.
| | - Yiyan Fei
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai, China.
| | - Boxun Lu
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, School of Life Sciences, Fudan University, Shanghai, China.
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12
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Chan JCY, Gorski SM. Unlocking the gate to GABARAPL2. Biol Futur 2022; 73:157-169. [PMID: 35486231 DOI: 10.1007/s42977-022-00119-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/08/2022] [Indexed: 10/18/2022]
Abstract
GABARAPL2 was initially characterized for its involvement in protein transport and membrane fusion events, but has since gained notoriety for its role in autophagy. GABARAPL2 is frequently studied alongside its GABARAP subfamily members, GABARAP and GABARAPL1. Although functional redundancy exists among the subfamily members, a complex network of molecular interactions, physiological processes and pathologies can be primarily related to GABARAPL2. GABARAPL2 has a multifaceted role, ranging from cellular differentiation to intracellular degradation. Much of what we know about GABARAPL2 is gained through identifying its interacting partners-a list that is constantly growing. In this article, we review both the autophagy-dependent and autophagy-independent roles of GABARAPL2, and emphasize their implications for both health and disease.
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Affiliation(s)
- Jennifer C Y Chan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.,Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | - Sharon M Gorski
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada. .,Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, V5Z 1L3, Canada. .,Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
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13
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Brennan A, Layfield R, Long J, Williams HEL, Oldham NJ, Scott D, Searle MS. An ALS-associated variant of the autophagy receptor SQSTM1/p62 reprograms binding selectivity toward the autophagy-related hATG8 proteins. J Biol Chem 2022; 298:101514. [PMID: 34929165 PMCID: PMC8762078 DOI: 10.1016/j.jbc.2021.101514] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 11/29/2022] Open
Abstract
Recognition of human autophagy-related 8 (hATG8) proteins by autophagy receptors represents a critical step within this cellular quality control system. Autophagy impairment is known to be a pathogenic mechanism in the motor neuron disorder amyotrophic lateral sclerosis (ALS). Overlapping but specific roles of hATG8 proteins belonging to the LC3 and GABARAP subfamilies are incompletely understood, and binding selectivity is typically overlooked. We previously showed that an ALS-associated variant of the SQSTM1/p62 (p62) autophagy receptor bearing an L341V mutation within its ATG8-interacting motif (AIM) impairs recognition of LC3B in vitro, yielding an autophagy-deficient phenotype. Improvements in understanding of hATG8 recognition by AIMs now distinguish LC3-interaction and GABARAP-interaction motifs and predict the effects of L341V substitution may extend beyond loss of function to biasing AIM binding preference. Through biophysical analyses, we confirm impaired binding of the L341V-AIM mutant to LC3A, LC3B, GABARAP, and GABARAPL1. In contrast, p62 AIM interactions with LC3C and GABARAPL2 are unaffected by this mutation. Isothermal titration calorimetry and NMR investigations provided insights into the entropy-driven GABARAPL2/p62 interaction and how the L341V mutation may be tolerated. Competition binding demonstrated reduced association of the L341V-AIM with one hATG8 manifests as a relative increase in association with alternate hATG8s, indicating effective reprogramming of hATG8 selectivity. These data highlight how a single AIM peptide might compete for binding with different hATG8s and suggest that the L341V-AIM mutation may be neomorphic, representative of a disease mechanism that likely extends into other human disorders.
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Affiliation(s)
- Andrew Brennan
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham, UK
| | - Robert Layfield
- School of Life Sciences, University of Nottingham Medical School, Nottingham, UK.
| | - Jed Long
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham, UK
| | - Huw E L Williams
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham, UK
| | - Neil J Oldham
- School of Chemistry, University Park, University of Nottingham, Nottingham, UK
| | - Daniel Scott
- School of Life Sciences, University of Nottingham Medical School, Nottingham, UK.
| | - Mark S Searle
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham, UK.
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14
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Does GEC1 Enhance Expression and Forward Trafficking of the Kappa Opioid Receptor (KOR) via Its Ability to Interact with NSF Directly? Handb Exp Pharmacol 2022; 271:83-96. [PMID: 33404775 PMCID: PMC9126001 DOI: 10.1007/164_2020_398] [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: 01/03/2023]
Abstract
We reported previously that GEC1 (glandular epithelial cell 1), a member of microtubule-associated proteins (MAPs), interacted directly with the C-tail of KOR (KCT) and tubulin and enhanced cell surface expression of KOR in CHO cells by facilitating its trafficking along the export pathway. Two GEC1 analogs (GABARAP and GATE16) were also shown to increase KOR expression. In addition, to understand the underlying mechanism, we demonstrated that N-ethylmaleimide-sensitive factor (NSF), an essential component for membrane fusion, co-immunoprecipitated with GEC1 from brain extracts. In this study, using pull-down techniques, we have found that (1) GEC1 interacts with NSF directly and prefers the ADP-bound NSF to the ATP-bound NSF; (2) D1 and/or D2 domain(s) of NSF interact with GEC1, but the N domain of NSF does not; (3) NSF does not interact with KCT directly, but forms a protein complex with KCT via GEC1; (4) NSF and/or α-SNAP do not affect KCT-GEC1 interaction. Thus, GEC1 (vs the α-SNAP/SNAREs complex) binds to NSF in distinctive ways in terms of the ADP- or ATP-bound form and domains of NSF involved. In conclusion, GEC1 may, via its direct interactions with KOR, NSF, and tubulin, enhance trafficking and fusion of KOR-containing vesicles selectively along the export pathway, which leads to increase in surface expression of KOR. GABARAP and GATE16 may enhance KOR expression in a similar way.
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15
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Jung Y, Artan M, Kim N, Yeom J, Hwang AB, Jeong DE, Altintas Ö, Seo K, Seo M, Lee D, Hwang W, Lee Y, Sohn J, Kim EJE, Ju S, Han SK, Nam HJ, Adams L, Ryu Y, Moon DJ, Kang C, Yoo JY, Park SK, Ha CM, Hansen M, Kim S, Lee C, Park SY, Lee SJV. MON-2, a Golgi protein, mediates autophagy-dependent longevity in Caenorhabditis elegans. SCIENCE ADVANCES 2021; 7:eabj8156. [PMID: 34860542 PMCID: PMC8641931 DOI: 10.1126/sciadv.abj8156] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/14/2021] [Indexed: 06/02/2023]
Abstract
The Golgi apparatus plays a central role in trafficking cargoes such as proteins and lipids. Defects in the Golgi apparatus lead to various diseases, but its role in organismal longevity is largely unknown. Using a quantitative proteomic approach, we found that a Golgi protein, MON-2, was up-regulated in long-lived Caenorhabditis elegans mutants with mitochondrial respiration defects and was required for their longevity. Similarly, we showed that DOP1/PAD-1, which acts with MON-2 to traffic macromolecules between the Golgi and endosome, contributed to the longevity of respiration mutants. Furthermore, we demonstrated that MON-2 was required for up-regulation of autophagy, a longevity-associated recycling process, by activating the Atg8 ortholog GABARAP/LGG-1 in C. elegans. Consistently, we showed that mammalian MON2 activated GABARAPL2 through physical interaction, which increased autophagic flux in mammalian cells. Thus, the evolutionarily conserved role of MON2 in trafficking between the Golgi and endosome is an integral part of autophagy-mediated longevity.
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Affiliation(s)
- Yoonji Jung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Murat Artan
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Nari Kim
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Jeonghun Yeom
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Ara B. Hwang
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Dae-Eun Jeong
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Özlem Altintas
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Keunhee Seo
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Mihwa Seo
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Dongyeop Lee
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Wooseon Hwang
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Yujin Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Jooyeon Sohn
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Eun Ji E. Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Sungeun Ju
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Seong Kyu Han
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Hyun-Jun Nam
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Linnea Adams
- Development, Aging, and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Youngjae Ryu
- Research Division and Brain Research Core Facilities of Korea Brain Research Institute, Daegu 41068, South Korea
| | - Dong Jin Moon
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Chanhee Kang
- School of Biological Sciences, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Joo-Yeon Yoo
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Sang Ki Park
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Chang Man Ha
- Research Division and Brain Research Core Facilities of Korea Brain Research Institute, Daegu 41068, South Korea
| | - Malene Hansen
- Development, Aging, and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sanguk Kim
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Seung-Yeol Park
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Seung-Jae V. Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
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16
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Jacquet M, Hervouet E, Baudu T, Herfs M, Parratte C, Feugeas JP, Perez V, Reynders C, Ancion M, Vigneron M, Baguet A, Guittaut M, Fraichard A, Despouy G. GABARAPL1 Inhibits EMT Signaling through SMAD-Tageted Negative Feedback. BIOLOGY 2021; 10:biology10100956. [PMID: 34681055 PMCID: PMC8533302 DOI: 10.3390/biology10100956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/10/2021] [Accepted: 09/14/2021] [Indexed: 12/03/2022]
Abstract
Simple Summary Epithelial–mesenchymal transition (EMT) is involved in metastasis formation, chemoresistance, apoptosis resistance, and acquisition of stem cell properties, making this process an attractive target in cancer. However, direct targeting of EMT remains challenging. Autophagy—an intracellular mechanism—has been noted to be involved in the regulation of EMT—mainly by its involvement in the degradation of EMT actors, explaining why understanding of how autophagy could regulate EMT might be promising in the development of new cancer therapies. Here, we found that GABARAPL1—an autophagy-related gene—was increased in human NSCLC mesenchymal tumors compared to epithelial tumors, and induction of EMT in an A549 lung cancer cell line by TGF-β/TNF-α cytokines also led to an increase in GABARAPL1 expression. This regulation could involve the EMT-related transcription factors of the SMAD family. To understand the role of GABARAPL1 in EMT regulation in lung cancer cells, A549 KO GABARAPL1 were designed and used to investigate whether GABARAPL1 could inhibit EMT via its involvement in SMAD degradation. The results indicate that GABARAPL1-mediated autophagic degradation could intervene as a negative EMT-regulatory loop. Abstract The pathway of selective autophagy, leading to a targeted elimination of specific intracellular components, is mediated by the ATG8 proteins, and has been previously suggested to be involved in the regulation of the Epithelial–mesenchymal transition (EMT) during cancer’s etiology. However, the molecular factors and steps of selective autophagy occurring during EMT remain unclear. We therefore analyzed a cohort of lung adenocarcinoma tumors using transcriptome analysis and immunohistochemistry, and found that the expression of ATG8 genes is correlated with that of EMT-related genes, and that GABARAPL1 protein levels are increased in EMT+ tumors compared to EMT- ones. Similarly, the induction of EMT in the A549 lung adenocarcinoma cell line using TGF-β/TNF-α led to a high increase in GABARAPL1 expression mediated by the EMT-related transcription factors of the SMAD family, whereas the other ATG8 genes were less modified. To determine the role of GABARAPL1 during EMT, we used the CRISPR/Cas9 technology in A549 and ACHN kidney adenocarcinoma cell lines to deplete GABARAPL1. We then observed that GABARAPL1 knockout induced EMT linked to a defect of GABARAPL1-mediated degradation of the SMAD proteins. These findings suggest that, during EMT, GABARAPL1 might intervene in an EMT-regulatory loop. Indeed, induction of EMT led to an increase in GABARAPL1 levels through the activation of the SMAD signaling pathway, and then GABARAPL1 induced the autophagy-selective degradation of SMAD proteins, leading to EMT inhibition.
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Affiliation(s)
- Marine Jacquet
- Université Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, F-25000 Besançon, France; (M.J.); (E.H.); (T.B.); (C.P.); (J.-P.F.); (V.P.); (A.B.); (M.G.); (A.F.)
| | - Eric Hervouet
- Université Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, F-25000 Besançon, France; (M.J.); (E.H.); (T.B.); (C.P.); (J.-P.F.); (V.P.); (A.B.); (M.G.); (A.F.)
- DImaCellplatform, Université Bourgogne Franche-Comté, F-25000 Besançon, France
- EPIGENExp, Université Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Timothée Baudu
- Université Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, F-25000 Besançon, France; (M.J.); (E.H.); (T.B.); (C.P.); (J.-P.F.); (V.P.); (A.B.); (M.G.); (A.F.)
| | - Michaël Herfs
- Laboratory of Experimental Pathology, GIGA-Cancer, University of Liege, 4000 Liege, Belgium; (M.H.); (C.R.); (M.A.)
| | - Chloé Parratte
- Université Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, F-25000 Besançon, France; (M.J.); (E.H.); (T.B.); (C.P.); (J.-P.F.); (V.P.); (A.B.); (M.G.); (A.F.)
| | - Jean-Paul Feugeas
- Université Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, F-25000 Besançon, France; (M.J.); (E.H.); (T.B.); (C.P.); (J.-P.F.); (V.P.); (A.B.); (M.G.); (A.F.)
| | - Valérie Perez
- Université Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, F-25000 Besançon, France; (M.J.); (E.H.); (T.B.); (C.P.); (J.-P.F.); (V.P.); (A.B.); (M.G.); (A.F.)
| | - Célia Reynders
- Laboratory of Experimental Pathology, GIGA-Cancer, University of Liege, 4000 Liege, Belgium; (M.H.); (C.R.); (M.A.)
| | - Marie Ancion
- Laboratory of Experimental Pathology, GIGA-Cancer, University of Liege, 4000 Liege, Belgium; (M.H.); (C.R.); (M.A.)
| | - Marc Vigneron
- Team Replisome Dynamics and Cancer, UMR7242 Biotechnologie et Signalisation Cellulaire, Ecole Supérieure de Biotechnologie de Strasbourg, CNRS-Université de Strasbourg, F-67412 Illkirch, France;
| | - Aurélie Baguet
- Université Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, F-25000 Besançon, France; (M.J.); (E.H.); (T.B.); (C.P.); (J.-P.F.); (V.P.); (A.B.); (M.G.); (A.F.)
| | - Michaël Guittaut
- Université Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, F-25000 Besançon, France; (M.J.); (E.H.); (T.B.); (C.P.); (J.-P.F.); (V.P.); (A.B.); (M.G.); (A.F.)
- DImaCellplatform, Université Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Annick Fraichard
- Université Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, F-25000 Besançon, France; (M.J.); (E.H.); (T.B.); (C.P.); (J.-P.F.); (V.P.); (A.B.); (M.G.); (A.F.)
| | - Gilles Despouy
- Université Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, F-25000 Besançon, France; (M.J.); (E.H.); (T.B.); (C.P.); (J.-P.F.); (V.P.); (A.B.); (M.G.); (A.F.)
- Correspondence:
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Kumar S, Jia J, Deretic V. Atg8ylation as a general membrane stress and remodeling response. Cell Stress 2021; 5:128-142. [PMID: 34527862 PMCID: PMC8404385 DOI: 10.15698/cst2021.09.255] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/26/2021] [Accepted: 07/30/2021] [Indexed: 12/30/2022] Open
Abstract
The yeast Atg8 protein and its paralogs in mammals, mammalian Atg8s (mAtg8s), have been primarily appreciated for their participation in autophagy. However, lipidated mAtg8s, including the most frequently used autophagosomal membrane marker LC3B, are found on cellular membranes other than autophagosomes. Here we put forward a hypothesis that the lipidation of mAtg8s, termed 'Atg8ylation', is a general membrane stress and remodeling response analogous to the role that ubiquitylation plays in tagging proteins. Ubiquitin and mAtg8s are related in sequence and structure, and the lipidation of mAtg8s occurs on its C-terminal glycine, akin to the C-terminal glycine of ubiquitin. Conceptually, we propose that mAtg8s and Atg8ylation are to membranes what ubiquitin and ubiquitylation are to proteins, and that, like ubiquitylation, Atg8ylation has a multitude of downstream effector outputs, one of which is autophagy.
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Affiliation(s)
- Suresh Kumar
- Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Jingyue Jia
- Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Vojo Deretic
- Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
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Interaction of Poliovirus Capsid Proteins with the Cellular Autophagy Pathway. Viruses 2021; 13:v13081587. [PMID: 34452452 PMCID: PMC8402707 DOI: 10.3390/v13081587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/28/2021] [Accepted: 08/10/2021] [Indexed: 12/23/2022] Open
Abstract
The capsid precursor P1 constitutes the N-terminal part of the enterovirus polyprotein. It is processed into VP0, VP3, and VP1 by the viral proteases, and VP0 is cleaved autocatalytically into VP4 and VP2. We observed that poliovirus VP0 is recognized by an antibody against a cellular autophagy protein, LC3A. The LC3A-like epitope overlapped the VP4/VP2 cleavage site. Individually expressed VP0-EGFP and P1 strongly colocalized with a marker of selective autophagy, p62/SQSTM1. To assess the role of capsid proteins in autophagy development we infected different cells with poliovirus or encapsidated polio replicon coding for only the replication proteins. We analyzed the processing of LC3B and p62/SQSTM1, markers of the initiation and completion of the autophagy pathway and investigated the association of the viral antigens with these autophagy proteins in infected cells. We observed cell-type-specific development of autophagy upon infection and found that only the virion signal strongly colocalized with p62/SQSTM1 early in infection. Collectively, our data suggest that activation of autophagy is not required for replication, and that capsid proteins contain determinants targeting them to p62/SQSTM1-dependent sequestration. Such a strategy may control the level of capsid proteins so that viral RNAs are not removed from the replication/translation pool prematurely.
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Pesaola F, Quassollo G, Venier AC, De Paul AL, Noher I, Bisbal M. The neuronal ceroid lipofuscinosis-related protein CLN8 regulates endo-lysosomal dynamics and dendritic morphology. Biol Cell 2021; 113:419-437. [PMID: 34021618 DOI: 10.1111/boc.202000016] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/18/2021] [Accepted: 05/22/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND INFORMATION The endo-lysosomal system (ELS) comprises a set of membranous organelles responsible for transporting intracellular and extracellular components within cells. Defects in lysosomal proteins usually affect a large variety of processes and underlie many diseases, most of them with a strong neuronal impact. Mutations in the endoplasmic reticulum-resident CLN8 protein cause CLN8 disease. This condition is one of the 14 known neuronal ceroid lipofuscinoses (NCLs), a group of inherited diseases characterised by accumulation of lipofuscin-like pigments within lysosomes. Besides mediating the transport of soluble lysosomal proteins, recent research suggested a role for CLN8 in the transport of vesicles and lipids, and autophagy. However, the consequences of CLN8 deficiency on ELS structure and activity, as well as the potential impact on neuronal development, remain poorly characterised. Therefore, we performed CLN8 knockdown in neuronal and non-neuronal cell models to analyse structural, dynamic and functional changes in the ELS and to assess the impact of CLN8 deficiency on axodendritic development. RESULTS CLN8 knockdown increased the size of the Golgi apparatus, the number of mobile vesicles and the speed of endo-lysosomes. Using the fluorescent fusion protein mApple-LAMP1-pHluorin, we detected significant lysosomal alkalisation in CLN8-deficient cells. In turn, experiments in primary rat hippocampal neurons showed that CLN8 deficiency decreased the complexity and size of the somatodendritic compartment. CONCLUSIONS Our results suggest the participation of CLN8 in vesicular distribution, lysosomal pH and normal development of the dendritic tree. We speculate that the defects triggered by CLN8 deficiency on ELS structure and dynamics underlie morphological alterations in neurons, which ultimately lead to the characteristic neurodegeneration observed in this NCL. SIGNIFICANCE This is, to our knowledge, the first characterisation of the effects of CLN8 dysfunction on the structure and dynamics of the ELS. Moreover, our findings suggest a novel role for CLN8 in somatodendritic development, which may account at least in part for the neuropathological manifestations associated with CLN8 disease.
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Affiliation(s)
- Favio Pesaola
- Programa de Investigación Translacional de Lipofuscinosis Ceroidea Neuronal, Hospital de Niños de Córdoba, Córdoba, 5014, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones Médicas "Mercedes y Martin Ferreyra"- IMMF-UNC-CONICET, Laboratorio de Neurobiología, Av. Friuli 2434, 5016 Córdoba, Argentina, Universidad Nacional de Córdoba, Córdoba, 5000, Argentina
| | - Gonzalo Quassollo
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones Médicas "Mercedes y Martin Ferreyra"- IMMF-UNC-CONICET, Laboratorio de Neurobiología, Av. Friuli 2434, 5016 Córdoba, Argentina, Universidad Nacional de Córdoba, Córdoba, 5000, Argentina
| | - Ana Clara Venier
- Programa de Investigación Translacional de Lipofuscinosis Ceroidea Neuronal, Hospital de Niños de Córdoba, Córdoba, 5014, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigación en Ciencias de la Salud (INICSA), Bv. de la Reforma y Enfermera Gordillo, Ciudad Universitaria, Córdoba, 5016, Argentina
| | - Ana Lucía De Paul
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigación en Ciencias de la Salud (INICSA), Bv. de la Reforma y Enfermera Gordillo, Ciudad Universitaria, Córdoba, 5016, Argentina.,Universidad Nacional de Córdoba, Facultad de Ciencias Médicas, Centro de Microscopía Electrónica, Bv. de la Reforma y Enfermera Gordillo, Ciudad Universitaria, Córdoba, 5016, Argentina
| | - Ines Noher
- Programa de Investigación Translacional de Lipofuscinosis Ceroidea Neuronal, Hospital de Niños de Córdoba, Córdoba, 5014, Argentina
| | - Mariano Bisbal
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones Médicas "Mercedes y Martin Ferreyra"- IMMF-UNC-CONICET, Laboratorio de Neurobiología, Av. Friuli 2434, 5016 Córdoba, Argentina, Universidad Nacional de Córdoba, Córdoba, 5000, Argentina.,Instituto Universitario de Ciencias Biomédicas Córdoba, Córdoba, 5016, Argentina
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20
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Jacquet M, Guittaut M, Fraichard A, Despouy G. The functions of Atg8-family proteins in autophagy and cancer: linked or unrelated? Autophagy 2021; 17:599-611. [PMID: 32255730 PMCID: PMC8032235 DOI: 10.1080/15548627.2020.1749367] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 03/09/2020] [Accepted: 03/26/2020] [Indexed: 01/04/2023] Open
Abstract
The Atg8-family proteins are subdivided into two subfamilies: the GABARAP and LC3 subfamilies. These proteins, which are major players of the autophagy pathway, present a conserved glycine in their C-terminus necessary for their association to the autophagosome membrane. This family of proteins present multiple roles from autophagy induction to autophagosome-lysosome fusion and have been described to play a role during cancer progression. Indeed, GABARAPs are described to be downregulated in cancers, and high expression has been linked to a good prognosis. Regarding LC3 s, their expression does not correlate to a particular tumor type or stage. The involvement of Atg8-family proteins during cancer, therefore, remains unclear, and it appears that their anti-tumor role may be associated with their implication in selective protein degradation by autophagy but might also be independent, in some cases, of their conjugation to autophagosomes. In this review, we will then focus on the involvement of GABARAP and LC3 subfamilies during autophagy and cancer and highlight the similarities but also the differences of action of each subfamily member.Abbreviations: AIM: Atg8-interacting motif; AMPK: adenosine monophosphate-associated protein kinase; ATG: autophagy-related; BECN1: beclin 1; BIRC6/BRUCE: baculoviral IAP repeat containing 6; BNIP3L/NIX: BCL2 interacting protein 3 like; GABARAP: GABA type A receptor-associated protein; GABARAPL1/2: GABA type A receptor associated protein like 1/2; GABRA/GABAA: gamma-aminobutyric acid type A receptor subunit; LAP: LC3-associated phagocytosis; LMNB1: lamin B1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MTOR: mechanistic target of rapamycin kinase; PI4K2A/PI4KIIα: phosphatidylinositol 4-kinase type 2 alpha; PLEKHM1: plecktrin homology and RUN domain containing M1; PtdIns3K-C1: class III phosphatidylinositol 3-kinase complex 1; SQSTM1: sequestosome 1; ULK1: unc51-like autophagy activating kinase 1.
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Affiliation(s)
- Marine Jacquet
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
| | - Michaël Guittaut
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
- DImaCell Platform, Univ. Bourgogne Franche-Comté, Besançon, France
| | - Annick Fraichard
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
| | - Gilles Despouy
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
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Sanwald JL, Dobner J, Simons IM, Poschmann G, Stühler K, Üffing A, Hoffmann S, Willbold D. Lack of GABARAP-Type Proteins Is Accompanied by Altered Golgi Morphology and Surfaceome Composition. Int J Mol Sci 2020; 22:E85. [PMID: 33374830 PMCID: PMC7795684 DOI: 10.3390/ijms22010085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/18/2020] [Accepted: 12/22/2020] [Indexed: 02/06/2023] Open
Abstract
GABARAP (γ-aminobutyric acid type A receptor-associated protein) and its paralogues GABARAPL1 and GABARAPL2 comprise a subfamily of autophagy-related Atg8 proteins. They are studied extensively regarding their roles during autophagy. Originally, however, especially GABARAPL2 was discovered to be involved in intra-Golgi transport and homotypic fusion of post-mitotic Golgi fragments. Recently, a broader function of mammalian Atg8s on membrane trafficking through interaction with various soluble N-ethylmaleimide-sensitive factor-attachment protein receptors SNAREs was suggested. By immunostaining and microscopic analysis of the Golgi network, we demonstrate the importance of the presence of individual GABARAP-type proteins on Golgi morphology. Furthermore, triple knockout (TKO) cells lacking the whole GABARAP subfamily showed impaired Golgi-dependent vesicular trafficking as assessed by imaging of fluorescently labelled ceramide. With the Golgi apparatus being central within the secretory pathway, we sought to investigate the role of the GABARAP-type proteins for cell surface protein trafficking. By analysing the surfaceome compositionofTKOs, we identified a subset of cell surface proteins with altered plasma membrane localisation. Taken together, we provide novel insights into an underrated aspect of autophagy-independent functions of the GABARAP subfamily and recommend considering the potential impact of GABARAP subfamily proteins on a plethora of processes during experimental analysis of GABARAP-deficient cells not only in the autophagic context.
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Affiliation(s)
- Julia L. Sanwald
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany; (J.L.S.); (J.D.); (I.M.S.); (A.Ü.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Leo-Brandt-Straße, 52428 Jülich, Germany
| | - Jochen Dobner
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany; (J.L.S.); (J.D.); (I.M.S.); (A.Ü.)
| | - Indra M. Simons
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany; (J.L.S.); (J.D.); (I.M.S.); (A.Ü.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Leo-Brandt-Straße, 52428 Jülich, Germany
| | - Gereon Poschmann
- Institute of Molecular Medicine I, Proteome Research, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany; (G.P.); (K.S.)
| | - Kai Stühler
- Institute of Molecular Medicine I, Proteome Research, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany; (G.P.); (K.S.)
- Molecular Proteomics Laboratory, Biologisch-Medizinisches Forschungszentrum (BMFZ), Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Alina Üffing
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany; (J.L.S.); (J.D.); (I.M.S.); (A.Ü.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Leo-Brandt-Straße, 52428 Jülich, Germany
| | - Silke Hoffmann
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Leo-Brandt-Straße, 52428 Jülich, Germany
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany; (J.L.S.); (J.D.); (I.M.S.); (A.Ü.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Leo-Brandt-Straße, 52428 Jülich, Germany
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Autophagy-Related Protein MAP1LC3C Plays a Crucial Role in Odontogenic Differentiation of Human Dental Pulp Cells. Tissue Eng Regen Med 2020; 18:265-277. [PMID: 33230801 DOI: 10.1007/s13770-020-00310-3] [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: 08/19/2020] [Revised: 09/27/2020] [Accepted: 10/13/2020] [Indexed: 10/22/2022] Open
Abstract
BACKGROUND Autophagy plays important roles in odontogenic differentiation of dental pulp cells (DPCs) in the developmental stage of tooth bud. Few studies have reported the role of autophagy during reparative dentin formation process. The objective of this study was to discover gene expression pattern correlated to autophagy and their role during odontogenic differentiation process in DPCs. METHODS After tooth cavities were prepared on the mesial surface of lower first molar crown of rats. Odontogenic differentiation and reparative dentin formation were assessed based on detection of morphology change with hematoxylin and eosin staining. RESULTS After tooth cavities were prepared on the mesial surface of lower first molar crown of rats, odontogenic differentiation and reparative dentin formation were assessed based on detection of morphology change with hematoxylin and eosin staining and dentin sialophosphoprotein (DSPP), whereas autophagy inhibitor 3-methyladenine (3MA) reversed. Results of quantitative polymerized chain reaction array of autophagosome formation related genes revealed that GABARAPL2 was prominently upregulated while expression of other ATG8 family members were moderately increased after tooth cavity preparation. In addition, human DPCs incubated in differentiation medium predominantly upregulated MAP1LC3C, which selectively decreased by 3MA but not by autophagy enhancer trehalose. Knock-down of MAP1LC3C using shRNA resulted in strong downregulation of dentin matrix protein 1 and DSPP as well-known odontogenic marker compared to knock-down of MAP1LC3B during odontogenic differentiation process of human DPCs. CONCLUSION Our results suggest that MAP1LC3C plays a crucial role in odontogenic differentiation of human DPCs via regulating autophagic flux.
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Finethy R, Dockterman J, Kutsch M, Orench‐Rivera N, Wallace GD, Piro AS, Luoma S, Haldar AK, Hwang S, Martinez J, Kuehn MJ, Taylor GA, Coers J. Dynamin-related Irgm proteins modulate LPS-induced caspase-11 activation and septic shock. EMBO Rep 2020; 21:e50830. [PMID: 33124745 PMCID: PMC7645254 DOI: 10.15252/embr.202050830] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/08/2020] [Accepted: 09/25/2020] [Indexed: 12/15/2022] Open
Abstract
Inflammation associated with gram-negative bacterial infections is often instigated by the bacterial cell wall component lipopolysaccharide (LPS). LPS-induced inflammation and resulting life-threatening sepsis are mediated by the two distinct LPS receptors TLR4 and caspase-11 (caspase-4/-5 in humans). Whereas the regulation of TLR4 activation by extracellular and phago-endosomal LPS has been studied in great detail, auxiliary host factors that specifically modulate recognition of cytosolic LPS by caspase-11 are largely unknown. This study identifies autophagy-related and dynamin-related membrane remodeling proteins belonging to the family of Immunity-related GTPases M clade (IRGM) as negative regulators of caspase-11 activation in macrophages. Phagocytes lacking expression of mouse isoform Irgm2 aberrantly activate caspase-11-dependent inflammatory responses when exposed to extracellular LPS, bacterial outer membrane vesicles, or gram-negative bacteria. Consequently, Irgm2-deficient mice display increased susceptibility to caspase-11-mediated septic shock in vivo. This Irgm2 phenotype is partly reversed by the simultaneous genetic deletion of the two additional Irgm paralogs Irgm1 and Irgm3, indicating that dysregulated Irgm isoform expression disrupts intracellular LPS processing pathways that limit LPS availability for caspase-11 activation.
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Affiliation(s)
- Ryan Finethy
- Department of Molecular Genetics and MicrobiologyDuke University Medical CenterDurhamNCUSA
| | - Jacob Dockterman
- Department of ImmunologyDuke University Medical CenterDurhamNCUSA
| | - Miriam Kutsch
- Department of Molecular Genetics and MicrobiologyDuke University Medical CenterDurhamNCUSA
| | | | - Graham D Wallace
- Department of Molecular Genetics and MicrobiologyDuke University Medical CenterDurhamNCUSA
| | - Anthony S Piro
- Department of Molecular Genetics and MicrobiologyDuke University Medical CenterDurhamNCUSA
| | - Sarah Luoma
- Department of Molecular Genetics and MicrobiologyDuke University Medical CenterDurhamNCUSA
| | - Arun K Haldar
- Department of Molecular Genetics and MicrobiologyDuke University Medical CenterDurhamNCUSA
- Present address:
Division of BiochemistryCentral Drug Research Institute (CDRI)Council of Scientific and Industrial Research (CSIR)LucknowIndia
| | - Seungmin Hwang
- Department of PathologyThe University of ChicagoChicagoILUSA
- Present address:
VIR BiotechnologySan FranciscoCAUSA
| | - Jennifer Martinez
- Immunity, Inflammation, and Disease LaboratoryNational Institute of Environmental Health SciencesNational Institutes of HealthResearch Triangle ParkNCUSA
| | - Meta J Kuehn
- Department of BiochemistryDuke University Medical CenterDurhamNCUSA
| | - Gregory A Taylor
- Department of Molecular Genetics and MicrobiologyDuke University Medical CenterDurhamNCUSA
- Department of ImmunologyDuke University Medical CenterDurhamNCUSA
- Division of GeriatricsDepartment of MedicineCenter for the Study of Aging and Human DevelopmentDuke University Medical CenterDurhamNCUSA
- Geriatric Research, Education, and Clinical Center, VA Medical CenterDurhamNCUSA
| | - Jörn Coers
- Department of Molecular Genetics and MicrobiologyDuke University Medical CenterDurhamNCUSA
- Department of ImmunologyDuke University Medical CenterDurhamNCUSA
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24
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Eren E, Planès R, Bagayoko S, Bordignon P, Chaoui K, Hessel A, Santoni K, Pinilla M, Lagrange B, Burlet‐Schiltz O, Howard JC, Henry T, Yamamoto M, Meunier E. Irgm2 and Gate-16 cooperatively dampen Gram-negative bacteria-induced caspase-11 response. EMBO Rep 2020; 21:e50829. [PMID: 33124769 PMCID: PMC7645206 DOI: 10.15252/embr.202050829] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/11/2020] [Accepted: 09/25/2020] [Indexed: 12/20/2022] Open
Abstract
Inflammatory caspase-11 (rodent) and caspases-4/5 (humans) detect the Gram-negative bacterial component LPS within the host cell cytosol, promoting activation of the non-canonical inflammasome. Although non-canonical inflammasome-induced pyroptosis and IL-1-related cytokine release are crucial to mount an efficient immune response against various bacteria, their unrestrained activation drives sepsis. This suggests that cellular components tightly control the threshold level of the non-canonical inflammasome in order to ensure efficient but non-deleterious inflammatory responses. Here, we show that the IFN-inducible protein Irgm2 and the ATG8 family member Gate-16 cooperatively counteract Gram-negative bacteria-induced non-canonical inflammasome activation, both in cultured macrophages and in vivo. Specifically, the Irgm2/Gate-16 axis dampens caspase-11 targeting to intracellular bacteria, which lowers caspase-11-mediated pyroptosis and cytokine release. Deficiency in Irgm2 or Gate16 induces both guanylate binding protein (GBP)-dependent and GBP-independent routes for caspase-11 targeting to intracellular bacteria. Our findings identify molecular effectors that fine-tune bacteria-activated non-canonical inflammasome responses and shed light on the understanding of the immune pathways they control.
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Affiliation(s)
- Elif Eren
- Institute of Pharmacology and Structural Biology (IPBS)CNRS, UMR5089University of ToulouseToulouseFrance
| | - Rémi Planès
- Institute of Pharmacology and Structural Biology (IPBS)CNRS, UMR5089University of ToulouseToulouseFrance
| | - Salimata Bagayoko
- Institute of Pharmacology and Structural Biology (IPBS)CNRS, UMR5089University of ToulouseToulouseFrance
| | - Pierre‐Jean Bordignon
- Institute of Pharmacology and Structural Biology (IPBS)CNRS, UMR5089University of ToulouseToulouseFrance
| | - Karima Chaoui
- Institute of Pharmacology and Structural Biology (IPBS)CNRS, UMR5089University of ToulouseToulouseFrance
- Mass Spectrometry Core FacilityInstitute of Pharmacology and Structural Biology (IPBS)CNRS, UMR5089University of ToulouseToulouseFrance
| | - Audrey Hessel
- Institute of Pharmacology and Structural Biology (IPBS)CNRS, UMR5089University of ToulouseToulouseFrance
| | - Karin Santoni
- Institute of Pharmacology and Structural Biology (IPBS)CNRS, UMR5089University of ToulouseToulouseFrance
| | - Miriam Pinilla
- Institute of Pharmacology and Structural Biology (IPBS)CNRS, UMR5089University of ToulouseToulouseFrance
| | - Brice Lagrange
- CIRI, Centre International de Recherche en InfectiologieInserm, U1111CNRS, UMR5308École Normale Supérieure de LyonUniversité Claude Bernard Lyon 1Univ LyonLyonFrance
| | - Odile Burlet‐Schiltz
- Institute of Pharmacology and Structural Biology (IPBS)CNRS, UMR5089University of ToulouseToulouseFrance
- Mass Spectrometry Core FacilityInstitute of Pharmacology and Structural Biology (IPBS)CNRS, UMR5089University of ToulouseToulouseFrance
| | - Jonathan C Howard
- Fundação Calouste GulbenkianInstituto Gulbenkian de CiênciaOeirasPortugal
| | - Thomas Henry
- CIRI, Centre International de Recherche en InfectiologieInserm, U1111CNRS, UMR5308École Normale Supérieure de LyonUniversité Claude Bernard Lyon 1Univ LyonLyonFrance
| | - Masahiro Yamamoto
- Department of ImmunoparasitologyResearch Institute for Microbial DiseasesOsaka UniversityOsakaJapan
- Laboratory of ImmunoparasitologyWPI Immunology Frontier Research CenterOsaka UniversityOsakaJapan
| | - Etienne Meunier
- Institute of Pharmacology and Structural Biology (IPBS)CNRS, UMR5089University of ToulouseToulouseFrance
- Present address:
Institute of Pharmacology and Structural Biology (IPBS)CNRSToulouseFrance
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25
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Sakaguchi N, Sasai M, Bando H, Lee Y, Pradipta A, Ma JS, Yamamoto M. Role of Gate-16 and Gabarap in Prevention of Caspase-11-Dependent Excess Inflammation and Lethal Endotoxic Shock. Front Immunol 2020; 11:561948. [PMID: 33042141 PMCID: PMC7522336 DOI: 10.3389/fimmu.2020.561948] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/18/2020] [Indexed: 12/03/2022] Open
Abstract
Sepsis is a life-threating multi-organ disease induced by host innate immunity to pathogen-derived endotoxins including lipopolysaccharide (LPS). Direct sensing of LPS by caspase-11 activates inflammasomes and causes lethal sepsis in mice. Inhibition of caspase-11 inflammasomes is important for the prevention of LPS-induced septic shock; however, whether a caspase-11 inflammasome-specific suppressive mechanism exists is unclear. Here we show that deficiency of GABARAP autophagy-related proteins results in over-activation of caspase-11 inflammasomes but not of canonical inflammasomes. Gate-16−/−Gabarap−/− macrophages exhibited elevated guanylate binding protein 2 (GBP2)-dependent caspase-11 activation and inflammatory responses. Deficiency of GABARAPs resulted in formation of GBP2-containing aggregates that promote IL-1β production. High mortality after low dose LPS challenge in Gate-16−/−Gabarap−/− mice primed with poly(I:C) or polymicrobial sepsis was ameliorated by compound GBP2 deficiency. These results reveal a critical function of Gate-16 and Gabarap to suppress GBP2-dependent caspase-11-induced inflammation and septic shock.
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Affiliation(s)
- Naoya Sakaguchi
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Laboratory of Immunoparasitology, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Miwa Sasai
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Laboratory of Immunoparasitology, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Hironori Bando
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Laboratory of Immunoparasitology, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Youngae Lee
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Laboratory of Immunoparasitology, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Ariel Pradipta
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Ji Su Ma
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Laboratory of Immunoparasitology, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Masahiro Yamamoto
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Laboratory of Immunoparasitology, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
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26
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Bu F, Yang M, Guo X, Huang W, Chen L. Multiple Functions of ATG8 Family Proteins in Plant Autophagy. Front Cell Dev Biol 2020; 8:466. [PMID: 32596242 PMCID: PMC7301642 DOI: 10.3389/fcell.2020.00466] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/19/2020] [Indexed: 11/13/2022] Open
Abstract
Autophagy is a major degradation process of cytoplasmic components in eukaryotes, and executes both bulk and selective degradation of targeted cargos. A set of autophagy-related (ATG) proteins participate in various stages of the autophagic process. Among ATGs, ubiquitin-like protein ATG8 plays a central role in autophagy. The ATG8 protein is conjugated to the membrane lipid phosphatidylethanolamine in a ubiquitin-like conjugation reaction that is essential for autophagosome formation. In addition, ATG8 interacts with various adaptor/receptor proteins to recruit specific cargos for degradation by selective autophagy. The ATG8-interacting proteins usually contain the ATG8-interacting motif (AIM) or the ubiquitin-interacting motif (UIM) for ATG8 binding. Unlike a single ATG8 gene in yeast, multiple ATG8 orthologs have been identified in the plant kingdom. The large diversity within the ATG8 family may explain the various functions of selective autophagy in plants. Here, we discuss and summarize the current view of the structure and function of ATG8 proteins in plants.
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Affiliation(s)
- Fan Bu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Mingkang Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Xu Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Wei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Liang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
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27
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Martens S, Fracchiolla D. Activation and targeting of ATG8 protein lipidation. Cell Discov 2020; 6:23. [PMID: 32377373 PMCID: PMC7198486 DOI: 10.1038/s41421-020-0155-1] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/03/2020] [Indexed: 12/19/2022] Open
Abstract
ATG8 family proteins are evolutionary conserved ubiquitin-like modifiers, which become attached to the headgroup of the membrane lipid phosphatidylethanolamine in a process referred to as lipidation. This reaction is carried out analogous to the conjugation of ubiquitin to its target proteins, involving the E1-like ATG7, the E2-like ATG3 and the E3-like ATG12-ATG5-ATG16 complex, which determines the site of lipidation. ATG8 lipidation is a hallmark of autophagy where these proteins are involved in autophagosome formation, the fusion of autophagosomes with lysosomes and cargo selection. However, it has become evident that ATG8 lipidation also occurs in processes that are not directly related to autophagy. Here we discuss recent insights into the targeting of ATG8 lipidation in autophagy and other pathways with special emphasis on the recruitment and activation of the E3-like complex.
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Affiliation(s)
- Sascha Martens
- 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
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28
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Huber J, Obata M, Gruber J, Akutsu M, Löhr F, Rogova N, Güntert P, Dikic I, Kirkin V, Komatsu M, Dötsch V, Rogov VV. An atypical LIR motif within UBA5 (ubiquitin like modifier activating enzyme 5) interacts with GABARAP proteins and mediates membrane localization of UBA5. Autophagy 2020; 16:256-270. [PMID: 30990354 PMCID: PMC6984602 DOI: 10.1080/15548627.2019.1606637] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 03/15/2019] [Accepted: 03/27/2019] [Indexed: 12/15/2022] Open
Abstract
Short linear motifs, known as LC3-interacting regions (LIRs), interact with mactoautophagy/autophagy modifiers (Atg8/LC3/GABARAP proteins) via a conserved universal mechanism. Typically, this includes the occupancy of 2 hydrophobic pockets on the surface of Atg8-family proteins by 2 specific aromatic and hydrophobic residues within the LIR motifs. Here, we describe an alternative mechanism of Atg8-family protein interaction with the non-canonical UBA5 LIR, an E1-like enzyme of the ufmylation pathway that preferentially interacts with GABARAP but not LC3 proteins. By solving the structures of both GABARAP and GABARAPL2 in complex with the UBA5 LIR, we show that in addition to the binding to the 2 canonical hydrophobic pockets (HP1 and HP2), a conserved tryptophan residue N-terminal of the LIR core sequence binds into a novel hydrophobic pocket on the surface of GABARAP proteins, which we term HP0. This mode of action is unique for UBA5 and accompanied by large rearrangements of key residues including the side chains of the gate-keeping K46 and the adjacent K/R47 in GABARAP proteins. Swapping mutations in LC3B and GABARAPL2 revealed that K/R47 is the key residue in the specific binding of GABARAP proteins to UBA5, with synergetic contributions of the composition and dynamics of the loop L3. Finally, we elucidate the physiological relevance of the interaction and show that GABARAP proteins regulate the localization and function of UBA5 on the endoplasmic reticulum membrane in a lipidation-independent manner.Abbreviations: ATG: AuTophaGy-related; EGFP: enhanced green fluorescent protein; GABARAP: GABA-type A receptor-associated protein; ITC: isothermal titration calorimetry; KO: knockout; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; NMR: nuclear magnetic resonance; RMSD: root-mean-square deviation of atomic positions; TKO: triple knockout; UBA5: ubiquitin like modifier activating enzyme 5.
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Affiliation(s)
- Jessica Huber
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Miki Obata
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Jens Gruber
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Masato Akutsu
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt am Main, Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Natalia Rogova
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Peter Güntert
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
- Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Ivan Dikic
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt am Main, Germany
- Institute of Biochemistry II, School of Medicine, Frankfurt am Main, Germany
| | - Vladimir Kirkin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Masaaki Komatsu
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- Department of Physiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Vladimir V. Rogov
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
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29
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Taniguchi S, Toyoshima M, Takamatsu T, Mima J. Curvature-sensitive trans-assembly of human Atg8-family proteins in autophagy-related membrane tethering. Protein Sci 2020; 29:1387-1400. [PMID: 31960529 DOI: 10.1002/pro.3828] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/15/2020] [Accepted: 01/15/2020] [Indexed: 12/18/2022]
Abstract
In macroautophagy, de novo formation of the double membrane-bound organelles, termed autophagosomes, is essential for engulfing and sequestering the cytoplasmic contents to be degraded in the lytic compartments such as vacuoles and lysosomes. Atg8-family proteins have been known to be responsible for autophagosome formation via membrane tethering and fusion events of precursor membrane structures. Nevertheless, how Atg8 proteins act directly upon autophagosome formation still remains enigmatic. Here, to further gain molecular insights into Atg8-mediated autophagic membrane dynamics, we study the two representative human Atg8 orthologs, LC3B and GATE-16, by quantitatively evaluating their intrinsic potency to physically tether lipid membranes in a chemically defined reconstitution system using purified Atg8 proteins and synthetic liposomes. Both LC3B and GATE-16 retained the capacities to trigger efficient membrane tethering at the protein-to-lipid molar ratios ranging from 1:100 to 1:5,000. These human Atg8-mediated membrane-tethering reactions require trans-assembly between the membrane-anchored forms of LC3B and GATE-16 and can be reversibly and strictly controlled by the membrane attachment and detachment cycles. Strikingly, we further uncovered distinct membrane curvature dependences of LC3B- and GATE-16-mediated membrane tethering reactions: LC3B can drive tethering more efficiently than GATE-16 for highly curved small vesicles (e.g., 50 nm in diameter), although GATE-16 turns out to be a more potent tether than LC3B for flatter large vesicles (e.g., 200 and 400 nm in diameter). Our findings establish curvature-sensitive trans-assembly of human Atg8-family proteins in reconstituted membrane tethering, which recapitulates an essential subreaction of the biogenesis of autophagosomes in vivo.
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Affiliation(s)
- Saki Taniguchi
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | | | - Tomoyo Takamatsu
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Joji Mima
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
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30
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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: 61] [Impact Index Per Article: 15.3] [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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31
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Gu Y, Princely Abudu Y, Kumar S, Bissa B, Choi SW, Jia J, Lazarou M, Eskelinen E, Johansen T, Deretic V. Mammalian Atg8 proteins regulate lysosome and autolysosome biogenesis through
SNARE
s. EMBO J 2019; 38. [DOI: https:/doi.org/10.15252/embj.2019101994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 09/13/2019] [Indexed: 12/19/2023] Open
Affiliation(s)
- Yuexi Gu
- Autophagy, Inflammation and Metabolism (AIM) Center of Biomedical Research Excellence University of New Mexico Health Sciences Center Albuquerque NM USA
- Department of Molecular Genetics and Microbiology University of New Mexico Health Sciences Center Albuquerque NM USA
| | - Yakubu Princely Abudu
- Molecular Cancer Research Group Institute of Medical Biology University of Tromsø‐The Arctic University of Norway Tromsø Norway
| | - Suresh Kumar
- Autophagy, Inflammation and Metabolism (AIM) Center of Biomedical Research Excellence University of New Mexico Health Sciences Center Albuquerque NM USA
- Department of Molecular Genetics and Microbiology University of New Mexico Health Sciences Center Albuquerque NM USA
| | - Bhawana Bissa
- Autophagy, Inflammation and Metabolism (AIM) Center of Biomedical Research Excellence University of New Mexico Health Sciences Center Albuquerque NM USA
- Department of Molecular Genetics and Microbiology University of New Mexico Health Sciences Center Albuquerque NM USA
| | - Seong Won Choi
- Department of Molecular Genetics and Microbiology University of New Mexico Health Sciences Center Albuquerque NM USA
| | - Jingyue Jia
- Autophagy, Inflammation and Metabolism (AIM) Center of Biomedical Research Excellence University of New Mexico Health Sciences Center Albuquerque NM USA
- Department of Molecular Genetics and Microbiology University of New Mexico Health Sciences Center Albuquerque NM USA
| | - Michael Lazarou
- Department of Biochemistry and Molecular Biology Biomedicine Discovery Institute Monash University Melbourne Australia
| | | | - Terje Johansen
- Molecular Cancer Research Group Institute of Medical Biology University of Tromsø‐The Arctic University of Norway Tromsø Norway
| | - Vojo Deretic
- Autophagy, Inflammation and Metabolism (AIM) Center of Biomedical Research Excellence University of New Mexico Health Sciences Center Albuquerque NM USA
- Department of Molecular Genetics and Microbiology University of New Mexico Health Sciences Center Albuquerque NM USA
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32
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Gu Y, Princely Abudu Y, Kumar S, Bissa B, Choi SW, Jia J, Lazarou M, Eskelinen E, Johansen T, Deretic V. Mammalian Atg8 proteins regulate lysosome and autolysosome biogenesis through SNAREs. EMBO J 2019; 38:e101994. [PMID: 31625181 PMCID: PMC6856626 DOI: 10.15252/embj.2019101994] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 09/07/2019] [Accepted: 09/13/2019] [Indexed: 12/14/2022] Open
Abstract
Mammalian homologs of yeast Atg8 protein (mAtg8s) are important in autophagy, but their exact mode of action remains ill-defined. Syntaxin 17 (Stx17), a SNARE with major roles in autophagy, was recently shown to bind mAtg8s. Here, we identified LC3-interacting regions (LIRs) in several SNAREs that broaden the landscape of the mAtg8-SNARE interactions. We found that Syntaxin 16 (Stx16) and its cognate SNARE partners all have LIR motifs and bind mAtg8s. Knockout of Stx16 caused defects in lysosome biogenesis, whereas a Stx16 and Stx17 double knockout completely blocked autophagic flux and decreased mitophagy, pexophagy, xenophagy, and ribophagy. Mechanistic analyses revealed that mAtg8s and Stx16 control several properties of lysosomal compartments including their function as platforms for active mTOR. These findings reveal a broad direct interaction of mAtg8s with SNAREs with impact on membrane remodeling in eukaryotic cells and expand the roles of mAtg8s to lysosome biogenesis.
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Affiliation(s)
- Yuexi Gu
- Autophagy, Inflammation and Metabolism (AIM) Center of Biomedical Research ExcellenceUniversity of New Mexico Health Sciences CenterAlbuquerqueNMUSA
- Department of Molecular Genetics and MicrobiologyUniversity of New Mexico Health Sciences CenterAlbuquerqueNMUSA
| | - Yakubu Princely Abudu
- Molecular Cancer Research GroupInstitute of Medical BiologyUniversity of Tromsø‐The Arctic University of NorwayTromsøNorway
| | - Suresh Kumar
- Autophagy, Inflammation and Metabolism (AIM) Center of Biomedical Research ExcellenceUniversity of New Mexico Health Sciences CenterAlbuquerqueNMUSA
- Department of Molecular Genetics and MicrobiologyUniversity of New Mexico Health Sciences CenterAlbuquerqueNMUSA
| | - Bhawana Bissa
- Autophagy, Inflammation and Metabolism (AIM) Center of Biomedical Research ExcellenceUniversity of New Mexico Health Sciences CenterAlbuquerqueNMUSA
- Department of Molecular Genetics and MicrobiologyUniversity of New Mexico Health Sciences CenterAlbuquerqueNMUSA
| | - Seong Won Choi
- Department of Molecular Genetics and MicrobiologyUniversity of New Mexico Health Sciences CenterAlbuquerqueNMUSA
| | - Jingyue Jia
- Autophagy, Inflammation and Metabolism (AIM) Center of Biomedical Research ExcellenceUniversity of New Mexico Health Sciences CenterAlbuquerqueNMUSA
- Department of Molecular Genetics and MicrobiologyUniversity of New Mexico Health Sciences CenterAlbuquerqueNMUSA
| | - Michael Lazarou
- Department of Biochemistry and Molecular BiologyBiomedicine Discovery InstituteMonash UniversityMelbourneAustralia
| | | | - Terje Johansen
- Molecular Cancer Research GroupInstitute of Medical BiologyUniversity of Tromsø‐The Arctic University of NorwayTromsøNorway
| | - Vojo Deretic
- Autophagy, Inflammation and Metabolism (AIM) Center of Biomedical Research ExcellenceUniversity of New Mexico Health Sciences CenterAlbuquerqueNMUSA
- Department of Molecular Genetics and MicrobiologyUniversity of New Mexico Health Sciences CenterAlbuquerqueNMUSA
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Li W, Zhang L. Regulation of ATG and Autophagy Initiation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1206:41-65. [PMID: 31776979 DOI: 10.1007/978-981-15-0602-4_2] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
ATG is involved in multiple processes of autophagosome formation, including the initial phase of autophagy. The mammalian autophagy complex-ULK1 complex is composed of ULK1, FIP200, ATG13 and ATG101, and the yeast autophagy initiation complex-ATG1 complex is composed of ATG1, ATG13, ATG17, ATG29 and ATG31. After this complex is activated, it binds and phosphorylates ATG9 on the vesicles. Then PI3KC3-C1 (yeast: ATG34: ATG15: ATG6: ATG14 or mammal animal: ATG34: ATG15: BECN1: ATG14L) is recruited to the PAS. Further, ATG12-ATG5-ATG16 complex is localized on PAS (Yeast) or localized on the outer surface of the membrane (mammal) and makes binding of ATG8 (LC3) with PE to form ATG8-PE complex, promoting autophagic membrane elongation, closure and formation autophagosome and autophagosome lysosome.
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Affiliation(s)
- Wen Li
- Department of Immunology, School of Basic Medical Science, Shandong University, 44# Wenhua Xi Road, Jinan, 250012, China
| | - Lining Zhang
- Department of Immunology, School of Basic Medical Science, Shandong University, 44# Wenhua Xi Road, Jinan, 250012, China.
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Mohan J, Wollert T. Human ubiquitin-like proteins as central coordinators in autophagy. Interface Focus 2018; 8:20180025. [PMID: 30443326 DOI: 10.1098/rsfs.2018.0025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2018] [Indexed: 02/07/2023] Open
Abstract
Autophagy is one of the most versatile recycling systems of eukaryotic cells. It degrades diverse cytoplasmic components such as organelles, protein aggregates, ribosomes and multi-enzyme complexes. Not surprisingly, any failure of autophagy or reduced activity of the pathway contributes to the onset of various pathologies, including neurodegeneration, cancer and metabolic disorders such as diabetes or immune diseases. Furthermore, autophagy contributes to the innate immune response and combats bacterial or viral pathogens. The hallmark of macroautophagy is the formation of a membrane sack that sequesters cytoplasmic cargo and delivers it to lysosomes for degradation. More than 40 autophagy-related (ATG) proteins have so far been identified. A unique protein-conjugation system represents one of the core components of this highly elaborate machinery. It conjugates six homologous ATG8 family proteins to the autophagic membrane. In this review, we summarize the current knowledge regarding the various functions of ATG8 proteins in autophagy and briefly discuss how physical approaches and in vitro reconstitution contributed in deciphering their function.
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Affiliation(s)
- Jagan Mohan
- Membrane Biochemistry and Transport, Institute Pasteur, 28 rue du Dr Roux, 75015 Paris, France
| | - Thomas Wollert
- Membrane Biochemistry and Transport, Institute Pasteur, 28 rue du Dr Roux, 75015 Paris, France
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35
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Zientara-Rytter K, Subramani S. AIM/LIR-based fluorescent sensors-new tools to monitor mAtg8 functions. Autophagy 2018; 14:1074-1078. [PMID: 29749795 DOI: 10.1080/15548627.2018.1454238] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
Abstract
Macroautophagy/autophagy, a catabolic process by which cytoplasmic materials are degraded and recycled in lysosomes/vacuoles, remains a rapidly expanding research topic with the need for constantly improved methodologies to study each step of this pathway. Recently Lee and colleagues, as well as Stolz et al., independently reported the development of new AIM/LIR-based fluorescent sensors, which mark individual endogenous mammalian Atg8-family (mAtg8) proteins without affecting the autophagic flux. When expressed in cells, each sensor selectively recognizes individual mAtg8 isoforms and distinguishes mammalian MAP1LC3/LC3 proteins from the related GABARAPs. Such selectivity was achieved by using various LC3-interacting regions with high binding affinity to either a subgroup, or a specific, mAtg8 isoform as part of the sensor. Here we discuss the utility of these sensors in autophagy research and highlight their strengths, weaknesses and future directions.
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Affiliation(s)
- Katarzyna Zientara-Rytter
- a Section of Molecular Biology, Division of Biological Sciences , University of California San Diego , La Jolla , CA , USA
| | - Suresh Subramani
- a Section of Molecular Biology, Division of Biological Sciences , University of California San Diego , La Jolla , CA , USA
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36
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Dutta P, Dargahi L, O'Connell KE, Bolia A, Ozkan B, Sailer AW, Dev KK. A novel modelling mechanism of PAEL receptor and GABARAPL2 interaction involved in Parkinson's disease. Neurosci Lett 2018; 673:12-18. [PMID: 29496607 DOI: 10.1016/j.neulet.2018.02.055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 01/30/2018] [Accepted: 02/25/2018] [Indexed: 11/18/2022]
Abstract
Parkin associated endothelin like receptor (PAELR) is G-protein coupled and ubiquitinated by parkin, promoting its degradation. In autosomal recessive Parkinson's disease, mutations in parkin lead to PAELR aggregation in the endoplasmic reticulum (ER), ER stress, neurotoxicity and cell death. We have identified previously that the protein kinase C interacting protein (PICK1) interacts with and regulates the expression and cell toxicity of PAELR. Here, we experimentally identify and provide in-silico modelling of a novel interaction between PAELR and GABARAPL2 (γ-aminobutyrate type A receptor associated protein like 2), which is an autophagosome-specific Ub-like protein implicated in vesicle trafficking and autophagy. We show that the family of GABARAPs interact with the carboxy terminal (ct) of PAELR and find the cysteine rich region (-CCCCCC-EEC) of ct-PAELR interacts with the GABAA binding site of GABARAPL2. This interaction is modelled by in-slico analysis and confirmed using affinity chromatography, showing Myc-tagged GABARAPL2 is retained by a GST fusion of the ct-PAELR. We also demonstrate that transient transfection of GABARAPL2 in HEK293 cells reduces PAELR expression. This study supports the idea that protein levels of PAELR are likely regulated by a multitude of proteins including parkin, PICK1 and GABARAPL2 via mechanisms that include ubiquitination, proteasomal degradagtion and autophagy.
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Affiliation(s)
- Priyanka Dutta
- Drug Development, School of Medicine, Trinity College Dublin, Ireland
| | - Leila Dargahi
- Drug Development, School of Medicine, Trinity College Dublin, Ireland
| | - Kara E O'Connell
- Drug Development, School of Medicine, Trinity College Dublin, Ireland
| | - Ashini Bolia
- Department of Physics, Center for Biological Physics, Arizona State University, Tempe, AZ, USA
| | - Banu Ozkan
- Department of Physics, Center for Biological Physics, Arizona State University, Tempe, AZ, USA
| | - Andreas W Sailer
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Kumlesh K Dev
- Drug Development, School of Medicine, Trinity College Dublin, Ireland.
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ATG8 Is Essential Specifically for an Autophagy-Independent Function in Apicoplast Biogenesis in Blood-Stage Malaria Parasites. mBio 2018; 9:mBio.02021-17. [PMID: 29295911 PMCID: PMC5750400 DOI: 10.1128/mbio.02021-17] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Plasmodium parasites and related pathogens contain an essential nonphotosynthetic plastid organelle, the apicoplast, derived from secondary endosymbiosis. Intriguingly, a highly conserved eukaryotic protein, autophagy-related protein 8 (ATG8), has an autophagy-independent function in the apicoplast. Little is known about the novel apicoplast function of ATG8 and its importance in blood-stage Plasmodium falciparum Using a P. falciparum strain in which ATG8 expression was conditionally regulated, we showed that P. falciparum ATG8 (PfATG8) is essential for parasite replication. Significantly, growth inhibition caused by the loss of PfATG8 was reversed by addition of isopentenyl pyrophosphate (IPP), which was previously shown to rescue apicoplast defects in P. falciparum Parasites deficient in PfATG8, but whose growth was rescued by IPP, had lost their apicoplast. We designed a suite of functional assays, including a new fluorescence in situ hybridization (FISH) method for detection of the low-copy-number apicoplast genome, to interrogate specific steps in apicoplast biogenesis and detect apicoplast defects which preceded the block in parasite replication. Though protein import and membrane expansion of the apicoplast were unaffected, the apicoplast was not inherited by daughter parasites. Our findings demonstrate that, though multiple autophagy-dependent and independent functions have been proposed for PfATG8, only its role in apicoplast biogenesis is essential in blood-stage parasites. We propose that PfATG8 is required for fission or segregation of the apicoplast during parasite replication.IMPORTANCEPlasmodium parasites, which cause malaria, and related apicomplexan parasites are important human and veterinary pathogens. They are evolutionarily distant from traditional model organisms and possess a unique plastid organelle, the apicoplast, acquired by an unusual eukaryote-eukaryote endosymbiosis which established novel protein/lipid import and organelle inheritance pathways in the parasite cell. Though the apicoplast is essential for parasite survival in all stages of its life cycle, little is known about these novel biogenesis pathways. We show that malaria parasites have adapted a highly conserved protein required for macroautophagy in yeast and mammals to function specifically in apicoplast inheritance. Our finding elucidates a novel mechanism of organelle biogenesis, essential for pathogenesis, in this divergent branch of pathogenic eukaryotes.
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Poillet-Perez L, Jacquet M, Hervouet E, Gauthier T, Fraichard A, Borg C, Pallandre JR, Gonzalez BJ, Ramdani Y, Boyer-Guittaut M, Delage-Mourroux R, Despouy G. GABARAPL1 tumor suppressive function is independent of its conjugation to autophagosomes in MCF-7 breast cancer cells. Oncotarget 2017; 8:55998-56020. [PMID: 28915569 PMCID: PMC5593540 DOI: 10.18632/oncotarget.19639] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 07/18/2017] [Indexed: 12/19/2022] Open
Abstract
The GABARAPL1 protein belongs to the ATG8 family whose members are involved in autophagy. Our laboratory previously demonstrated that GABARAPL1 associates with autophagic vesicles, regulates autophagic flux and acts as a tumor suppressor protein in breast cancer. In this study, we aimed to determine whether GABARAPL1 conjugation to autophagosomes is necessary for its tumor suppressive functions using the MCF-7 breast cancer cell line overexpressing GABARAPL1 or a G116A mutant, which is unable to be lipidated and associated to autophagosomes. We show that the G116A mutation impaired GABARAPL1 function in autophagosome/lysosome fusion and inhibited lysosome activity but did not alter MTOR and ULK1 activities or tumor growth in vivo. Our results demonstrate for the first time that GABARAPL1 plays different regulatory functions during early and late stages of autophagy, independently or not of its conjugation to autophagosomes, but its tumor suppressive function appeared to be independent of its conjugation to autophagic vesicles.
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Affiliation(s)
- Laura Poillet-Perez
- Unité Mixte de Recherche, Interactions Hôte-Greffon-Tumeur, Ingénierie Cellulaire et Génique, Université Bourgogne Franche-Comté, Besançon, France.,Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Marine Jacquet
- Unité Mixte de Recherche, Interactions Hôte-Greffon-Tumeur, Ingénierie Cellulaire et Génique, Université Bourgogne Franche-Comté, Besançon, France
| | - Eric Hervouet
- Unité Mixte de Recherche, Interactions Hôte-Greffon-Tumeur, Ingénierie Cellulaire et Génique, Université Bourgogne Franche-Comté, Besançon, France
| | - Thierry Gauthier
- Unité Mixte de Recherche, Interactions Hôte-Greffon-Tumeur, Ingénierie Cellulaire et Génique, Université Bourgogne Franche-Comté, Besançon, France
| | - Annick Fraichard
- Unité Mixte de Recherche, Interactions Hôte-Greffon-Tumeur, Ingénierie Cellulaire et Génique, Université Bourgogne Franche-Comté, Besançon, France
| | - Christophe Borg
- Unité Mixte de Recherche, Interactions Hôte-Greffon-Tumeur, Ingénierie Cellulaire et Génique, Université Bourgogne Franche-Comté, Besançon, France
| | - Jean-René Pallandre
- Unité Mixte de Recherche, Interactions Hôte-Greffon-Tumeur, Ingénierie Cellulaire et Génique, Université Bourgogne Franche-Comté, Besançon, France
| | - Bruno J Gonzalez
- Microvascular Endothelium and Neonatal Brain Lesions, Université de Normandie, UFR de Médecine et de Pharmacie, Rouen, France
| | - Yasmina Ramdani
- Microvascular Endothelium and Neonatal Brain Lesions, Université de Normandie, UFR de Médecine et de Pharmacie, Rouen, France
| | - Michaël Boyer-Guittaut
- Unité Mixte de Recherche, Interactions Hôte-Greffon-Tumeur, Ingénierie Cellulaire et Génique, Université Bourgogne Franche-Comté, Besançon, France
| | - Régis Delage-Mourroux
- Unité Mixte de Recherche, Interactions Hôte-Greffon-Tumeur, Ingénierie Cellulaire et Génique, Université Bourgogne Franche-Comté, Besançon, France
| | - Gilles Despouy
- Unité Mixte de Recherche, Interactions Hôte-Greffon-Tumeur, Ingénierie Cellulaire et Génique, Université Bourgogne Franche-Comté, Besançon, France
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Direct binding to GABARAP family members is essential for HIV-1 Nef plasma membrane localization. Sci Rep 2017; 7:5979. [PMID: 28729737 PMCID: PMC5519724 DOI: 10.1038/s41598-017-06319-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/12/2017] [Indexed: 12/29/2022] Open
Abstract
HIV-1 Nef is an important pathogenic factor for HIV/AIDS pathogenesis. Studies have shown that the association of Nef with the inner leaflet of the plasma membrane and with endocytic and perinuclear vesicles is essential for most activities of Nef. Using purified recombinant proteins in pull-down assays and by co-immunoprecipitation assays we demonstrate that Nef binds directly and specifically to all GABARAP family members, but not to LC3 family members. Based on nuclear magnetic resonance (NMR) experiments we showed that Nef binds to GABARAP via two surface exposed hydrophobic pockets. S53 and F62 of GABARAP were identified as key residues for the interaction with Nef. During live-cell fluorescence microscopy an accumulation of Nef and all GABARAP family members in vesicular structures throughout the cytoplasm and at the plasma membrane was observed. This plasma membrane accumulation was significantly reduced after knocking down GABARAP, GABARAPL1 and GABARAPL2 with respective siRNAs. We identified GABARAPs as the first known direct interaction partners of Nef that are essential for its plasma membrane localization.
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40
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Wang B, Kundu M. Canonical and noncanonical functions of ULK/Atg1. Curr Opin Cell Biol 2017; 45:47-54. [PMID: 28292700 DOI: 10.1016/j.ceb.2017.02.011] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 02/09/2017] [Accepted: 02/17/2017] [Indexed: 02/07/2023]
Abstract
Mammalian Unc-51-like kinases 1 and 2 (ULK1 and ULK2) belong to the ULK/Atg1 family of serine/threonine kinases, which are conserved from yeast to mammals. Although ULK/Atg1 is best known for regulating flux through the autophagy pathway, it has evolutionarily conserved noncanonical functions in protein trafficking that are essential for maintaining cellular homeostasis. As a direct target of energy- and nutrient-sensing kinases, ULK/Atg1 is positioned to regulate the distribution and use of cellular resources in response to metabolic cues. In this review, we provide an overview of the molecular mechanisms through which ULK/Atg1 carries out its canonical and noncanonical functions and the signaling pathways that link its function to metabolism. We also highlight potential contributions of ULK/Atg1 in human diseases, including cancer and neurodegeneration.
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Affiliation(s)
- Bo Wang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States
| | - Mondira Kundu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States.
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41
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Lee YK, Lee JA. Role of the mammalian ATG8/LC3 family in autophagy: differential and compensatory roles in the spatiotemporal regulation of autophagy. BMB Rep 2017; 49:424-30. [PMID: 27418283 PMCID: PMC5070729 DOI: 10.5483/bmbrep.2016.49.8.081] [Citation(s) in RCA: 231] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Indexed: 12/04/2022] Open
Abstract
Autophagy, an evolutionarily conserved cellular degradation pathway of the lysosome, is associated with many physiological and pathological processes. The hallmark of autophagy is the formation of the autophagosome that engulfs and degrades cytosolic components via its fusion with the lysosome, in either a selective or a non-selective manner. Autophagy is tightly regulated by proteins encoded by autophagy-related (atg) genes. Among these proteins, ATG8/LC3 is essential for autophagosome biogenesis/maturation and it also functions as an adaptor protein for selective autophagy. In mammalian cells, several homologs of yeast Atg8 such as MAP1LC3, GABARAP, and GABARAPL 1/2 have been identified. However, the biological relevance of this gene diversity in higher eukaryotes, and their specific roles, are largely unknown. In this review, we describe the mammalian ATG8/LC3 family and discuss recent advancements in understanding their roles in the autophagic process. [BMB Reports 2016; 49(8): 424-430]
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Affiliation(s)
- You-Kyung Lee
- Department of Biological Sciences and Biotechnology, College of Life Sciences and Nanotechnology, Hannam University, Daejeon 34054, Korea
| | - Jin-A Lee
- Department of Biological Sciences and Biotechnology, College of Life Sciences and Nanotechnology, Hannam University, Daejeon 34054, Korea
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42
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Ryabovol VV, Minibayeva FV. Molecular Mechanisms of Autophagy in Plants: Role of ATG8 Proteins in Formation and Functioning of Autophagosomes. BIOCHEMISTRY (MOSCOW) 2017; 81:348-63. [PMID: 27293092 DOI: 10.1134/s0006297916040052] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Autophagy is an efficient way of degradation and removal of unwanted or damaged intracellular components in plant cells. It plays an important role in recycling of intracellular structures (during starvation, removal of cell components formed during plant development or damaged by various stress factors) and in programmed cell death. Morphologically, autophagy is characterized by the formation of double-membrane vesicles called autophagosomes, which are essential for the isolation and degradation of cytoplasmic components. Among autophagic (ATG) proteins, ATG8 from the ubiquitin-like protein family plays a key role in autophagosome formation. ATG8 is also involved in selective autophagy, fusion of autophagosome with the vacuole, and some other intracellular processes not associated with autophagy. In contrast to yeasts that carry a single ATG8 gene, plants have multigene ATG8 families. The reason for such great ATG8 diversity in plants remains unclear. It is also unknown whether all members of the ATG8 family are involved in the formation and functioning of autophagosomes. To answer these questions, the identification of the structure and the possible functions of plant proteins from ATG8 family is required. In this review, we analyze the structures of ATG8 proteins from plants and their homologs from yeast and animal cells, interactions of ATG8 proteins with functional ligands, and involvement of ATG8 proteins in different metabolic processes in eukaryotes.
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Affiliation(s)
- V V Ryabovol
- Kazan Institute of Biochemistry and Biophysics, Russian Academy of Sciences, Kazan, 420111, Russia
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43
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Stolz A, Putyrski M, Kutle I, Huber J, Wang C, Major V, Sidhu SS, Youle RJ, Rogov VV, Dötsch V, Ernst A, Dikic I. Fluorescence-based ATG8 sensors monitor localization and function of LC3/GABARAP proteins. EMBO J 2016; 36:549-564. [PMID: 28028054 DOI: 10.15252/embj.201695063] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 11/23/2016] [Accepted: 11/27/2016] [Indexed: 12/25/2022] Open
Abstract
Autophagy is a cellular surveillance pathway that balances metabolic and energy resources and transports specific cargos, including damaged mitochondria, other broken organelles, or pathogens for degradation to the lysosome. Central components of autophagosomal biogenesis are six members of the LC3 and GABARAP family of ubiquitin-like proteins (mATG8s). We used phage display to isolate peptides that possess bona fide LIR (LC3-interacting region) properties and are selective for individual mATG8 isoforms. Sensitivity of the developed sensors was optimized by multiplication, charge distribution, and fusion with a membrane recruitment (FYVE) or an oligomerization (PB1) domain. We demonstrate the use of the engineered peptides as intracellular sensors that recognize specifically GABARAP, GABL1, GABL2, and LC3C, as well as a bispecific sensor for LC3A and LC3B. By using an LC3C-specific sensor, we were able to monitor recruitment of endogenous LC3C to Salmonella during xenophagy, as well as to mitochondria during mitophagy. The sensors are general tools to monitor the fate of mATG8s and will be valuable in decoding the biological functions of the individual LC3/GABARAPs.
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Affiliation(s)
- Alexandra Stolz
- Institute of Biochemistry II Goethe University, Frankfurt am Main, Germany
| | - Mateusz Putyrski
- Institute of Biochemistry II Goethe University, Frankfurt am Main, Germany.,Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine and Pharmacology TMP, Frankfurt am Main, Germany
| | - Ivana Kutle
- Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Jessica Huber
- Institute of Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Chunxin Wang
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Viktória Major
- Institute of Biochemistry II Goethe University, Frankfurt am Main, Germany
| | - Sachdev S Sidhu
- Banting and Best Department of Medical Research, The Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Richard J Youle
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Vladimir V Rogov
- Institute of Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Andreas Ernst
- Institute of Biochemistry II Goethe University, Frankfurt am Main, Germany .,Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine and Pharmacology TMP, Frankfurt am Main, Germany
| | - Ivan Dikic
- Institute of Biochemistry II Goethe University, Frankfurt am Main, Germany .,Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
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44
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Schaaf MBE, Keulers TG, Vooijs MA, Rouschop KMA. LC3/GABARAP family proteins: autophagy-(un)related functions. FASEB J 2016; 30:3961-3978. [PMID: 27601442 DOI: 10.1096/fj.201600698r] [Citation(s) in RCA: 413] [Impact Index Per Article: 51.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 08/22/2016] [Indexed: 01/01/2023]
Abstract
From yeast to mammals, autophagy is an important mechanism for sustaining cellular homeostasis through facilitating the degradation and recycling of aged and cytotoxic components. During autophagy, cargo is captured in double-membraned vesicles, the autophagosomes, and degraded through lysosomal fusion. In yeast, autophagy initiation, cargo recognition, cargo engulfment, and vesicle closure is Atg8 dependent. In higher eukaryotes, Atg8 has evolved into the LC3/GABARAP protein family, consisting of 7 family proteins [LC3A (2 splice variants), LC3B, LC3C, GABARAP, GABARAPL1, and GABARAPL2]. LC3B, the most studied family protein, is associated with autophagosome development and maturation and is used to monitor autophagic activity. Given the high homology, the other LC3/GABARAP family proteins are often presumed to fulfill similar functions. Nevertheless, substantial evidence shows that the LC3/GABARAP family proteins are unique in function and important in autophagy-independent mechanisms. In this review, we discuss the current knowledge and functions of the LC3/GABARAP family proteins. We focus on processing of the individual family proteins and their role in autophagy initiation, cargo recognition, vesicle closure, and trafficking, a complex and tightly regulated process that requires selective presentation and recruitment of these family proteins. In addition, functions unrelated to autophagy of the LC3/GABARAP protein family members are discussed.-Schaaf, M. B. E., Keulers, T. G, Vooijs, M. A., Rouschop, K. M. A. LC3/GABARAP family proteins: autophagy-(un)related functions.
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Affiliation(s)
- Marco B E Schaaf
- Department of Radiation Oncology (Maastro Lab), GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Tom G Keulers
- Department of Radiation Oncology (Maastro Lab), GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Marc A Vooijs
- Department of Radiation Oncology (Maastro Lab), GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Kasper M A Rouschop
- Department of Radiation Oncology (Maastro Lab), GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
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45
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Joachim J, Jefferies HBJ, Razi M, Frith D, Snijders AP, Chakravarty P, Judith D, Tooze SA. Activation of ULK Kinase and Autophagy by GABARAP Trafficking from the Centrosome Is Regulated by WAC and GM130. Mol Cell 2015; 60:899-913. [PMID: 26687599 PMCID: PMC4691241 DOI: 10.1016/j.molcel.2015.11.018] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 08/18/2015] [Accepted: 11/12/2015] [Indexed: 11/16/2022]
Abstract
Starvation-induced autophagy requires activation of the ULK complex at the phagophore. Two Golgi proteins, WAC and GM130, regulate autophagy, however their mechanism of regulation is unknown. In search of novel interaction partners of WAC, we found that GM130 directly interacts with WAC, and this interaction is required for autophagy. WAC is bound to the Golgi by GM130. WAC and GM130 interact with the Atg8 homolog GABARAP and regulate its subcellular localization. GABARAP is on the pericentriolar matrix, and this dynamic pool contributes to autophagosome formation. Tethering of GABARAP to the Golgi by GM130 inhibits autophagy, demonstrating an unexpected role for a golgin. WAC suppresses GM130 binding to GABARAP, regulating starvation-induced centrosomal GABARAP delivery to the phagophore. GABARAP, unlipidated and lipidated, but not LC3B, GABARAPL1, and GATE-16, specifically promotes ULK kinase activation dependent on the ULK1 LIR motif, elucidating a unique non-hierarchical role for GABARAP in starvation-induced activation of autophagy.
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Affiliation(s)
- Justin Joachim
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Harold B J Jefferies
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Minoo Razi
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - David Frith
- Mass Spectrometry, The Francis Crick Institute, Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Ambrosius P Snijders
- Mass Spectrometry, The Francis Crick Institute, Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Probir Chakravarty
- Bioinformatics Core, The Francis Crick Institute, Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Delphine Judith
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Sharon A Tooze
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3LY, UK.
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Fernández ÁF, López-Otín C. The functional and pathologic relevance of autophagy proteases. J Clin Invest 2015; 125:33-41. [PMID: 25654548 DOI: 10.1172/jci73940] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Autophagy is a well-conserved catabolic process essential for cellular homeostasis. First described in yeast as an adaptive response to starvation, this pathway is also present in higher eukaryotes, where it is triggered by stress signals such as damaged organelles or pathogen infection. Autophagy is characterized at the cellular level by the engulfment of portions of the cytoplasm in double-membrane structures called autophagosomes. Autophagosomes fuse with lysosomes, resulting in degradation of the inner autophagosomal membrane and luminal content. This process is coordinated by complex molecular systems, including the ATG8 ubiquitin-like conjugation system and the ATG4 cysteine proteases, which are implicated in the formation, elongation, and fusion of these autophagic vesicles. In this Review, we focus on the diverse functional roles of the autophagins, a protease family formed by the four mammalian orthologs of yeast Atg4. We also address the dysfunctional expression of these proteases in several pathologic conditions such as cancer and inflammation and discuss potential therapies based on their modulation.
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Hiyama M, Kusakabe KT, Takeshita A, Sugi S, Kuniyoshi N, Imai H, Kano K, Kiso Y. Nutrient starvation affects expression of LC3 family at the feto-maternal interface during murine placentation. J Vet Med Sci 2014; 77:305-11. [PMID: 25421500 PMCID: PMC4383776 DOI: 10.1292/jvms.14-0490] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
LC3 - the mammalian homolog of Atg8 - was found as autophagosome membrane binding protein in mammals and widely used as an autophagosomal marker. LC3A, B and C show different expression patterns in each tissue. The aim of this study was to reveal the differences of expression patterns among LC3 families in mouse placenta under normal condition and nutrient starving condition. LC3A and B were highly expressed in decidual cells. LC3A and B were increased in D14 compared with D12 and D16 in mouse placenta, while LC3C was decreased. Starvation induced increase in LC3B expression specifically. Immunohistochemistry showed different expression patterns among LC3A, B and C. LC3A expression in syncytiotrophoblast was vanished by starvation. The results of real time RT-PCR suggested differences between D12 and D16 in autophagic cascade induced by starvation. Taken together, this study suggests that autophagy could play a role in placental invasion system and that nutrient starvation affects LC3B expression.
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Affiliation(s)
- Masato Hiyama
- Laboratory of Basic Veterinary Science, The United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi 753-8515, Japan
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Tanida I, Ueno T, Kominami E. In vitro assays of lipidation of Mammalian Atg8 homologs. CURRENT PROTOCOLS IN CELL BIOLOGY 2014; 64:11.20.1-13. [PMID: 25181299 DOI: 10.1002/0471143030.cb1120s64] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Atg8 modifier in yeast is conjugated to phosphatidylethanolamine via ubiquitylation-like reactions essential for autophagy. Mammalian Atg8 homologs (Atg8s) including LC3, GABARAP, and GATE-16, are also ubiquitin-like modifiers. The carboxyl termini of mammalian Atg8 homologs are cleaved by Atg4B, a cysteine protease, to expose carboxyl terminal Gly which is essential for this ubiquitylation-like reaction. Thereafter, the Atg8 homologs are activated by Atg7, an E1-like enzyme, to form unstable Atg7-Atg8 E1-substrate intermediates via a thioester bond. The activated Atg8 homologs are transferred to mammalian Atg3, an E2-like enzyme, to form unstable Atg3-Atg8 E2-substrate intermediates via a thioester bond. Finally, Atg8 homologs are conjugated to phospholipids, phosphatidylethanolamine, and phosphatidylserine. Here, we describe a protocol for the reconstituted conjugation systems for mammalian Atg8 homologs in vitro using purified recombinant Atg proteins and liposomes.
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Affiliation(s)
- Isei Tanida
- Department of Cell Biology and Biochemistry, National Institute of Infectious Diseases, Tokyo, Japan; Laboratory of Proteomics and Biomolecular Science, Juntendo University Graduate School of Medicine, Tokyo, Japan
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Abstract
Selective autophagy is a quality control pathway through which cellular components are sequestered into double-membrane vesicles and delivered to specific intracellular compartments. This process requires autophagy receptors that link cargo to growing autophagosomal membranes. Selective autophagy is also implicated in various membrane trafficking events. Here we discuss the current view on how cargo selection and transport are achieved during selective autophagy, and point out molecular mechanisms that are congruent between autophagy and vesicle trafficking pathways.
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Bellouze S, Schäfer MK, Buttigieg D, Baillat G, Rabouille C, Haase G. Golgi fragmentation in pmn mice is due to a defective ARF1/TBCE cross-talk that coordinates COPI vesicle formation and tubulin polymerization. Hum Mol Genet 2014; 23:5961-75. [DOI: 10.1093/hmg/ddu320] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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