1
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Takeda E, Isoda T, Hosokawa S, Oikawa Y, Hotta-Ren S, May AI, Ohsumi Y. Receptor-mediated cargo hitchhiking on bulk autophagy. EMBO J 2024:10.1038/s44318-024-00091-8. [PMID: 38755257 DOI: 10.1038/s44318-024-00091-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/24/2024] [Accepted: 02/28/2024] [Indexed: 05/18/2024] Open
Abstract
While the molecular mechanism of autophagy is well studied, the cargoes delivered by autophagy remain incompletely characterized. To examine the selectivity of autophagy cargo, we conducted proteomics on isolated yeast autophagic bodies, which are intermediate structures in the autophagy process. We identify a protein, Hab1, that is highly preferentially delivered to vacuoles. The N-terminal 42 amino acid region of Hab1 contains an amphipathic helix and an Atg8-family interacting motif, both of which are necessary and sufficient for the preferential delivery of Hab1 by autophagy. We find that fusion of this region with a cytosolic protein results in preferential delivery of this protein to the vacuole. Furthermore, attachment of this region to an organelle allows for autophagic delivery in a manner independent of canonical autophagy receptor or scaffold proteins. We propose a novel mode of selective autophagy in which a receptor, in this case Hab1, binds directly to forming isolation membranes during bulk autophagy.
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Affiliation(s)
- Eigo Takeda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.
| | - Takahiro Isoda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- School and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
- Frontier Research Center, POLA Chemical Industries Inc., Yokohama, Japan
| | - Sachiko Hosokawa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yu Oikawa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Shukun Hotta-Ren
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Alexander I May
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yoshinori Ohsumi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.
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2
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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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3
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Steffek M, Helgason E, Popovych N, Rougé L, Bruning JM, Li KS, Burdick DJ, Cai J, Crawford T, Xue J, Decurtins W, Fang C, Grubers F, Holliday MJ, Langley A, Petersen A, Satz AL, Song A, Stoffler D, Strebel Q, Tom JYK, Skelton N, Staben ST, Wichert M, Mulvihill MM, Dueber EC. A Multifaceted Hit-Finding Approach Reveals Novel LC3 Family Ligands. Biochemistry 2023; 62:633-644. [PMID: 34985287 DOI: 10.1021/acs.biochem.1c00682] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Autophagy-related proteins (Atgs) drive the lysosome-mediated degradation pathway, autophagy, to enable the clearance of dysfunctional cellular components and maintain homeostasis. In humans, this process is driven by the mammalian Atg8 (mAtg8) family of proteins comprising the LC3 and GABARAP subfamilies. The mAtg8 proteins play essential roles in the formation and maturation of autophagosomes and the capture of specific cargo through binding to the conserved LC3-interacting region (LIR) sequence within target proteins. Modulation of interactions of mAtg8 with its target proteins via small-molecule ligands would enable further interrogation of their function. Here we describe unbiased fragment and DNA-encoded library (DEL) screening approaches for discovering LC3 small-molecule ligands. Both strategies resulted in compounds that bind to LC3, with the fragment hits favoring a conserved hydrophobic pocket in mATG8 proteins, as detailed by LC3A-fragment complex crystal structures. Our findings demonstrate that the malleable LIR-binding surface can be readily targeted by fragments; however, rational design of additional interactions to drive increased affinity proved challenging. DEL libraries, which combine small, fragment-like building blocks into larger scaffolds, yielded higher-affinity binders and revealed an unexpected potential for reversible, covalent ligands. Moreover, DEL hits identified possible vectors for synthesizing fluorescent probes or bivalent molecules for engineering autophagic degradation of specific targets.
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Affiliation(s)
- Micah Steffek
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Elizabeth Helgason
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Nataliya Popovych
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Lionel Rougé
- Structure Biology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - John M Bruning
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Ke Sherry Li
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel J Burdick
- Chemistry Departments, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Jianping Cai
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Terry Crawford
- Chemistry Departments, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Jing Xue
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Willy Decurtins
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Chunlin Fang
- WuXi AppTec (Wuhan) Company, Ltd., No. 666 GaoXin Road, WuHan East Lake High-tech Development Zone, Hubei 430075, China
| | - Felix Grubers
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Michael J Holliday
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Allyson Langley
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Ann Petersen
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Alexander Lee Satz
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Aimin Song
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel Stoffler
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Quentin Strebel
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Jeffrey Y K Tom
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Nicholas Skelton
- Chemistry Departments, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Steven T Staben
- Chemistry Departments, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Moreno Wichert
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Melinda M Mulvihill
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Erin C Dueber
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
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4
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Luo N, Shang D, Tang Z, Mai J, Huang X, Tao LZ, Liu L, Gao C, Qian Y, Xie Q, Li F. Engineered ATG8-binding motif-based selective autophagy to degrade proteins and organelles in planta. THE NEW PHYTOLOGIST 2023; 237:684-697. [PMID: 36263708 DOI: 10.1111/nph.18557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Protein-targeting technologies represent essential approaches in biological research. Protein knockdown tools developed recently in mammalian cells by exploiting natural degradation mechanisms allow for precise determination of protein function and discovery of degrader-type drugs. However, no method to directly target endogenous proteins for degradation is currently available in plants. Here, we describe a novel method for targeted protein clearance by engineering an autophagy receptor with a binder to provide target specificity and an ATG8-binding motif (AIM) to link the targets to nascent autophagosomes, thus harnessing the autophagy machinery for degradation. We demonstrate its specificity and broad potentials by degrading various fluorescence-tagged proteins, including cytosolic mCherry, the nucleus-localized bZIP transcription factor TGA5, and the plasma membrane-anchored brassinosteroid receptor BRI1, as well as fluorescence-coated peroxisomes, using a tobacco-based transient expression system. Stable expression of AIM-based autophagy receptors in Arabidopsis further confirms the feasibility of this approach in selective autophagy of endogenous proteins. With its wide substrate scope and its specificity, our concept of engineered AIM-based selective autophagy could provide a convenient and robust research tool for manipulating endogenous proteins in plants and may open an avenue toward degradation of cytoplasmic components other than proteins in plant research.
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Affiliation(s)
- Na Luo
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Dandan Shang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Zhiwei Tang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jinyan Mai
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xiao Huang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Li-Zhen Tao
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Linchuan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Caiji Gao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yangwen Qian
- WIMI Biotechnology Co. Ltd, Changzhou, 213000, China
| | - Qingjun Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Faqiang Li
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, 510642, China
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5
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Park SW, Jeon P, Yamasaki A, Lee HE, Choi H, Mun JY, Jun YW, Park JH, Lee SH, Lee SK, Lee YK, Song HK, Lazarou M, Cho DH, Komatsu M, Noda NN, Jang DJ, Lee JA. Development of new tools to study membrane-anchored mammalian Atg8 proteins. Autophagy 2022:1-20. [PMID: 36250672 DOI: 10.1080/15548627.2022.2132040] [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: 11/02/2022] Open
Abstract
ABBREVIATIONS A:C autophagic membrane:cytosol; ALS amyotrophic lateral sclerosis; ATG4 autophagy related 4; Atg8 autophagy related 8; BafA1 bafilomycin A1; BNIP3L/Nix BCL2 interacting protein 3 like; CALCOCO2/NDP52 calcium binding and coiled-coil domain 2; EBSS Earle's balanced salt solution; GABARAP GABA type A receptor-associated protein; GST glutathione S transferase; HKO hexa knockout; Kd dissociation constant; LIR LC3-interacting region; MAP1LC3/LC3 microtubule associated protein 1 light chain 3; NLS nuclear localization signal/sequence; PE phosphatidylethanolamine; SpHfl1 Schizosaccharomyces pombeorganic solute transmembrane transporter; SQSTM1/p62 SQSTM1/p62; TARDBP/TDP-43 TAR DNA binding protein; TKO triple knockout.
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Affiliation(s)
- Sang-Won Park
- Department of Vector Entomology, College of Ecology and Environment, Kyungpook National University, Sangju, Korea
| | - Pureum Jeon
- Department of Biological Sciences and Biotechnology, College of Life Sciences and Nanotechnology, Hannam University, Daejeon, Korea
| | | | - Hye Eun Lee
- Neural circuit research group, Korea Brain Research Institute, Daegu, Korea
| | - Haneul Choi
- Department of Biological Sciences and Biotechnology, College of Life Sciences and Nanotechnology, Hannam University, Daejeon, Korea
| | - Ji Young Mun
- Neural circuit research group, Korea Brain Research Institute, Daegu, Korea
| | - Yong-Woo Jun
- Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, Sangju, Korea
| | - Ju-Hui Park
- Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, Sangju, Korea
| | - Seung-Hwan Lee
- Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, Sangju, Korea
| | - Soo-Kyeong Lee
- Department of Biological Sciences and Biotechnology, College of Life Sciences and Nanotechnology, Hannam University, Daejeon, Korea
| | - You-Kyung Lee
- Department of Biological Sciences and Biotechnology, College of Life Sciences and Nanotechnology, Hannam University, Daejeon, Korea
| | - Hyun Kyu Song
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Michael Lazarou
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Victoria, Australia
| | - Dong-Hyong Cho
- School of Life Sciences, Kyungpook National University, Daegu, Korea
| | - Masaaki Komatsu
- Department of Physiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry, Tokyo, Japan.,Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Deok-Jin Jang
- Department of Vector Entomology, College of Ecology and Environment, Kyungpook National University, Sangju, Korea.,Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, Sangju, Korea
| | - Jin-A Lee
- Department of Biological Sciences and Biotechnology, College of Life Sciences and Nanotechnology, Hannam University, Daejeon, Korea
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6
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Quinet G, Génin P, Ozturk O, Belgareh-Touzé N, Courtot L, Legouis R, Weil R, Cohen MM, Rodriguez MS. Exploring selective autophagy events in multiple biologic models using LC3-interacting regions (LIR)-based molecular traps. Sci Rep 2022; 12:7652. [PMID: 35538106 PMCID: PMC9090809 DOI: 10.1038/s41598-022-11417-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 04/22/2022] [Indexed: 01/18/2023] Open
Abstract
Autophagy is an essential cellular pathway that ensures degradation of a wide range of substrates including damaged organelles or large protein aggregates. Understanding how this proteolytic pathway is regulated would increase our comprehension on its role in cellular physiology and contribute to identify biomarkers or potential drug targets to develop more specific treatments for disease in which autophagy is dysregulated. Here, we report the development of molecular traps based in the tandem disposition of LC3-interacting regions (LIR). The estimated affinity of LC3-traps for distinct recombinant LC3/GABARAP proteins is in the low nanomolar range and allows the capture of these proteins from distinct mammalian cell lines, S. cerevisiae and C. elegans. LC3-traps show preferences for GABARAP/LGG1 or LC3/LGG2 and pull-down substrates targeted to proteaphagy and mitophagy. Therefore, LC3-traps are versatile tools that can be adapted to multiple applications to monitor selective autophagy events in distinct physiologic and pathologic circumstances.
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Affiliation(s)
- Grégoire Quinet
- Laboratoire de Chimie de Coordination (LCC)-CNRS, UPS, 31400, Toulouse, France
| | - Pierre Génin
- Centre d'immunologie et des Maladies Infectieuses (CIMI-Paris)- Faculté de Médecine, Sorbonne Université, 75013, Paris, France
| | - Oznur Ozturk
- Sorbonne Université, CNRS, UMR8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, 75005, Paris, France
| | - Naima Belgareh-Touzé
- Sorbonne Université, CNRS, UMR8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, 75005, Paris, France
| | - Lilas Courtot
- Laboratoire de Chimie de Coordination (LCC)-CNRS, UPS, 31400, Toulouse, France
| | - Renaud Legouis
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France.,INSERM U1280, 91198, Gif-sur-Yvette, France
| | - Robert Weil
- Centre d'immunologie et des Maladies Infectieuses (CIMI-Paris)- Faculté de Médecine, Sorbonne Université, 75013, Paris, France
| | - Mickael M Cohen
- Sorbonne Université, CNRS, UMR8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, 75005, Paris, France
| | - Manuel S Rodriguez
- Laboratoire de Chimie de Coordination (LCC)-CNRS, UPS, 31400, Toulouse, France.
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7
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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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8
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Kliche J, Kuss H, Ali M, Ivarsson Y. Cytoplasmic short linear motifs in ACE2 and integrin β 3 link SARS-CoV-2 host cell receptors to mediators of endocytosis and autophagy. Sci Signal 2021; 14:14/665/eabf1117. [PMID: 33436498 PMCID: PMC7928716 DOI: 10.1126/scisignal.abf1117] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
SARS-CoV-2, the virus that causes COVID-19, enters cells through endocytosis upon binding to the cell surface receptor ACE2 and potentially others, including integrins. Using bioinformatics, Mészáros et al. predicted the presence of short amino acid sequences, called short linear motifs (SLiMs), in the cytoplasmic tails of ACE2 and various integrins that may engage the endocytic and autophagic machinery. Using affinity binding assays, Kliche et al. not only confirmed that many of these predicted SLiMs interacted with target peptides in various components of the endocytosis and autophagy machinery, but also found that these interactions were regulated by the phosphorylation of SLiM-adjacent amino acids. Together, these findings have identified a potential link between autophagy and integrin signaling and could lead to new ways to prevent viral infection. The spike protein of SARS-CoV-2 binds the angiotensin-converting enzyme 2 (ACE2) on the host cell surface and subsequently enters host cells through receptor-mediated endocytosis. Additional cell receptors may be directly or indirectly involved, including integrins. The cytoplasmic tails of ACE2 and integrins contain several predicted short linear motifs (SLiMs) that may facilitate internalization of the virus as well as its subsequent propagation through processes such as autophagy. Here, we measured the binding affinity of predicted interactions between SLiMs in the cytoplasmic tails of ACE2 and integrin β3 with proteins that mediate endocytic trafficking and autophagy. We validated that a class I PDZ-binding motif mediated binding of ACE2 to the scaffolding proteins SNX27, NHERF3, and SHANK, and that a binding site for the clathrin adaptor AP2 μ2 in ACE2 overlaps with a phospho-dependent binding site for the SH2 domains of Src family tyrosine kinases. Furthermore, we validated that an LC3-interacting region (LIR) in integrin β3 bound to the ATG8 domains of the autophagy receptors MAP1LC3 and GABARAP in a manner enhanced by LIR-adjacent phosphorylation. Our results provide molecular links between cell receptors and mediators of endocytosis and autophagy that may facilitate viral entry and propagation.
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Affiliation(s)
- Johanna Kliche
- Department of Chemistry, BMC, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
| | - Hanna Kuss
- Department of Chemistry, BMC, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden.,WWU Münster, Institute for Evolution and Biodiversity, DE-48149 Münster, Germany
| | - Muhammad Ali
- Department of Chemistry, BMC, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
| | - Ylva Ivarsson
- Department of Chemistry, BMC, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden.
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9
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The Kinase Chemogenomic Set (KCGS): An Open Science Resource for Kinase Vulnerability Identification. Int J Mol Sci 2021; 22:ijms22020566. [PMID: 33429995 PMCID: PMC7826789 DOI: 10.3390/ijms22020566] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 12/29/2020] [Indexed: 12/11/2022] Open
Abstract
We describe the assembly and annotation of a chemogenomic set of protein kinase inhibitors as an open science resource for studying kinase biology. The set only includes inhibitors that show potent kinase inhibition and a narrow spectrum of activity when screened across a large panel of kinase biochemical assays. Currently, the set contains 187 inhibitors that cover 215 human kinases. The kinase chemogenomic set (KCGS), current Version 1.0, is the most highly annotated set of selective kinase inhibitors available to researchers for use in cell-based screens.
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10
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Novel Insights into the Cellular Localization and Regulation of the Autophagosomal Proteins LC3A, LC3B and LC3C. Cells 2020; 9:cells9102315. [PMID: 33081014 PMCID: PMC7603224 DOI: 10.3390/cells9102315] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022] Open
Abstract
Macroautophagy is a conserved degradative process for maintaining cellular homeostasis and plays a key role in aging and various human disorders. The microtubule-associated protein 1A/1B light chain 3B (MAP1LC3B or LC3B) is commonly analyzed as a key marker for autophagosomes and as a proxy for autophagic flux. Three paralogues of the LC3 gene exist in humans: LC3A, LC3B and LC3C. The molecular function, regulation and cellular localization of LC3A and LC3C have not been investigated frequently, even if a similar function to that described for LC3B appears likely. Here, we have selectively decapacitated LC3B by three separate strategies in primary human fibroblasts and analyzed the evoked effects on LC3A, LC3B and LC3C in terms of their cellular distribution and co-localization with p62, a ubiquitin and autophagy receptor. First, treatment with pharmacological sirtuin 1 (SIRT1) inhibitors to prevent the translocation of LC3B from the nucleus into the cytosol induced an increase in cytosolic LC3C, a heightened co-localization of LC3C with p62, and an increase LC3C-dependent autophagic flux as assessed by protein lipidation. Cytosolic LC3A, however, was moderately reduced, but also more co-localized with p62. Second, siRNA-based knock-down of SIRT1 broadly reproduced these findings and increased the co-localization of LC3A and particularly LC3C with p62 in presumed autophagosomes. These effects resembled the effects of pharmacological sirtuin inhibition under normal and starvation conditions. Third, siRNA-based knock-down of total LC3B in cytosol and nucleus also induced a redistribution of LC3C as if to replace LC3B in the nucleus, but only moderately affected LC3A. Total protein expression of LC3A, LC3B, LC3C, GABARAP and GABARAP-L1 following LC3B decapacitation was unaltered. Our data indicate that nuclear trapping and other causes of LC3B functional loss in the cytosol are buffered by LC3A and actively compensated by LC3C, but not by GABARAPs. The biological relevance of the potential functional compensation of LC3B decapacitation by LC3C and LC3A warrants further study.
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Eck F, Phuyal S, Smith MD, Kaulich M, Wilkinson S, Farhan H, Behrends C. ACSL3 is a novel GABARAPL2 interactor that links ufmylation and lipid droplet biogenesis. J Cell Sci 2020; 133:jcs243477. [PMID: 32843575 DOI: 10.1242/jcs.243477] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 08/10/2020] [Indexed: 12/12/2022] Open
Abstract
While studies of the autophagy-related (ATG) genes in knockout models have led to an explosion of knowledge about the functions of autophagy components, the exact roles of LC3 and GABARAP family proteins (human ATG8 equivalents) are still poorly understood. A major drawback in understanding their roles is that the available interactome data has largely been acquired using overexpression systems. To overcome these limitations, we employed CRISPR/Cas9-based genome-editing to generate a panel of cells in which human ATG8 genes were tagged at their natural chromosomal locations with an N-terminal affinity epitope. This cellular resource was employed to map endogenous GABARAPL2 protein complexes using interaction proteomics. This approach identified the ER-associated protein and lipid droplet (LD) biogenesis factor ACSL3 as a stabilizing GABARAPL2-binding partner. GABARAPL2 bound ACSL3 in a manner dependent on its LC3-interacting regions, whose binding site in GABARAPL2 was required to recruit the latter to the ER. Through this interaction, the UFM1-activating enzyme UBA5 became anchored at the ER. Furthermore, ACSL3 depletion and LD induction affected the abundance of several ufmylation components and ER-phagy. Together these data allow us to define ACSL3 as a novel regulator of the enigmatic UFM1 conjugation pathway.
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Affiliation(s)
- Franziska Eck
- Munich Cluster for Systems Neurology (SyNergy), Medical Faculty, Ludwig-Maximilians-University München, Feodor-Lynen Strasse 17, 81377 Munich, Germany
| | - Santosh Phuyal
- Institute of Basic Medical Sciences, Department of Molecular Medicine, University of Oslo, Sognsvannsveien 9, 0372 Oslo, Norway
| | - Matthew D Smith
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Manuel Kaulich
- Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Simon Wilkinson
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Hesso Farhan
- Institute of Basic Medical Sciences, Department of Molecular Medicine, University of Oslo, Sognsvannsveien 9, 0372 Oslo, Norway
| | - Christian Behrends
- Munich Cluster for Systems Neurology (SyNergy), Medical Faculty, Ludwig-Maximilians-University München, Feodor-Lynen Strasse 17, 81377 Munich, Germany
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12
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Wesch N, Kirkin V, Rogov VV. Atg8-Family Proteins-Structural Features and Molecular Interactions in Autophagy and Beyond. Cells 2020; 9:E2008. [PMID: 32882854 PMCID: PMC7564214 DOI: 10.3390/cells9092008] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 12/25/2022] Open
Abstract
Autophagy is a common name for a number of catabolic processes, which keep the cellular homeostasis by removing damaged and dysfunctional intracellular components. Impairment or misbalance of autophagy can lead to various diseases, such as neurodegeneration, infection diseases, and cancer. A central axis of autophagy is formed along the interactions of autophagy modifiers (Atg8-family proteins) with a variety of their cellular counter partners. Besides autophagy, Atg8-proteins participate in many other pathways, among which membrane trafficking and neuronal signaling are the most known. Despite the fact that autophagy modifiers are well-studied, as the small globular proteins show similarity to ubiquitin on a structural level, the mechanism of their interactions are still not completely understood. A thorough analysis and classification of all known mechanisms of Atg8-protein interactions could shed light on their functioning and connect the pathways involving Atg8-proteins. In this review, we present our views of the key features of the Atg8-proteins and describe the basic principles of their recognition and binding by interaction partners. We discuss affinity and selectivity of their interactions as well as provide perspectives for discovery of new Atg8-interacting proteins and therapeutic approaches to tackle major human diseases.
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Affiliation(s)
- Nicole Wesch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany;
| | - Vladimir Kirkin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research London, Sutton SM2 5NG, UK;
| | - Vladimir V. Rogov
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany;
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany
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13
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Ueno T, Komatsu M. Monitoring Autophagy Flux and Activity: Principles and Applications. Bioessays 2020; 42:e2000122. [DOI: 10.1002/bies.202000122] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/03/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Takashi Ueno
- Laboratory of Proteomics and Biomolecular Science Juntendo University Graduate School of Medicine 2‐1‐1 Hongo, Bunkyo‐ku Tokyo 113‐8421 Japan
| | - Masaaki Komatsu
- Department of Physiology Juntendo University Graduate School of Medicine 2‐1‐1 Hongo, Bunkyo‐ku Tokyo 113‐8421 Japan
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14
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Maculins T, Garcia-Pardo J, Skenderovic A, Gebel J, Putyrski M, Vorobyov A, Busse P, Varga G, Kuzikov M, Zaliani A, Rahighi S, Schaeffer V, Parnham MJ, Sidhu SS, Ernst A, Dötsch V, Akutsu M, Dikic I. Discovery of Protein-Protein Interaction Inhibitors by Integrating Protein Engineering and Chemical Screening Platforms. Cell Chem Biol 2020; 27:1441-1451.e7. [PMID: 32726587 DOI: 10.1016/j.chembiol.2020.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/24/2020] [Accepted: 07/09/2020] [Indexed: 02/06/2023]
Abstract
Protein-protein interactions (PPIs) govern intracellular life, and identification of PPI inhibitors is challenging. Roadblocks in assay development stemming from weak binding affinities of natural PPIs impede progress in this field. We postulated that enhancing binding affinity of natural PPIs via protein engineering will aid assay development and hit discovery. This proof-of-principle study targets PPI between linear ubiquitin chains and NEMO UBAN domain, which activates NF-κB signaling. Using phage display, we generated ubiquitin variants that bind to the functional UBAN epitope with high affinity, act as competitive inhibitors, and structurally maintain the existing PPI interface. When utilized in assay development, variants enable generation of robust cell-based assays for chemical screening. Top compounds identified using this approach directly bind to UBAN and dampen NF-κB signaling. This study illustrates advantages of integrating protein engineering and chemical screening in hit identification, a development that we anticipate will have wide application in drug discovery.
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Affiliation(s)
- Timurs Maculins
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany.
| | - Javier Garcia-Pardo
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | | | - Jakob Gebel
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Strasse 9, 60438 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, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Andrew Vorobyov
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Philipp Busse
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Gabor Varga
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Maria Kuzikov
- Fraunhofer Institute for Molecular Biology and Applied Ecology Screening Port, Hamburg, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Molecular Biology and Applied Ecology Screening Port, Hamburg, Germany
| | - Simin Rahighi
- Chapman University School of Pharmacy (CUSP), Harry and Diane Rinker Health Science Campus, Chapman University, Irvine, CA 92618, USA
| | | | - Michael J Parnham
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Sachdev S Sidhu
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Andreas Ernst
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
| | - Masato Akutsu
- Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany.
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15
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Russell KL, Gorgulho CM, Allen A, Vakaki M, Wang Y, Facciabene A, Lee D, Roy P, Buchser WJ, Appleman LJ, Maranchie J, Storkus WJ, Lotze MT. Inhibiting Autophagy in Renal Cell Cancer and the Associated Tumor Endothelium. ACTA ACUST UNITED AC 2020; 25:165-177. [PMID: 31135523 PMCID: PMC10395074 DOI: 10.1097/ppo.0000000000000374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The clear cell subtype of kidney cancer encompasses most renal cell carcinoma cases and is associated with the loss of von Hippel-Lindau gene function or expression. Subsequent loss or mutation of the other allele influences cellular stress responses involving nutrient and hypoxia sensing. Autophagy is an important regulatory process promoting the disposal of unnecessary or degraded cellular components, tightly linked to almost all cellular processes. Organelles and proteins that become damaged or that are no longer needed in the cell are sequestered and digested in autophagosomes upon fusing with lysosomes, or alternatively, released via vesicular exocytosis. Tumor development tends to disrupt the regulation of the balance between this process and apoptosis, permitting prolonged cell survival and increased replication. Completed trials of autophagic inhibitors using hydroxychloroquine in combination with other anticancer agents including rapalogues and high-dose interleukin 2 have now been reported. The complex nature of autophagy and the unique biology of clear cell renal cell carcinoma warrant further understanding to better develop the next generation of relevant anticancer agents.
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Affiliation(s)
| | | | - Abigail Allen
- Bioengineering, University of Pittsburgh, Pittsburgh, PA
| | | | | | - Andrea Facciabene
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA
| | | | - Partha Roy
- Bioengineering, University of Pittsburgh, Pittsburgh, PA
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16
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Putyrski M, Vakhrusheva O, Bonn F, Guntur S, Vorobyov A, Brandts C, Dikic I, Ernst A. Disrupting the LC3 Interaction Region (LIR) Binding of Selective Autophagy Receptors Sensitizes AML Cell Lines to Cytarabine. Front Cell Dev Biol 2020; 8:208. [PMID: 32296703 PMCID: PMC7137635 DOI: 10.3389/fcell.2020.00208] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/10/2020] [Indexed: 12/26/2022] Open
Abstract
Short linear motifs (SLiMs) located in disordered regions of multidomain proteins are important for the organization of protein-protein interaction networks. By dynamic association with their binding partners, SLiMs enable assembly of multiprotein complexes, pivotal for the regulation of various aspects of cell biology in higher organisms. Despite their importance, there is a paucity of molecular tools to study SLiMs of endogenous proteins in live cells. LC3 interacting regions (LIRs), being quintessential for orchestrating diverse stages of autophagy, are a prominent example of SLiMs and mediate binding to the ubiquitin-like LC3/GABARAP family of proteins. The role of LIRs ranges from the posttranslational processing of their binding partners at early stages of autophagy to the binding of selective autophagy receptors (SARs) to the autophagosome. In order to generate tools to study LIRs in cells, we engineered high affinity binders of LIR motifs of three archetypical SARs: OPTN, p62, and NDP52. In an array of in vitro and cellular assays, the engineered binders were shown to have greatly improved affinity and specificity when compared with the endogenous LC3/GABARAP family of proteins, thus providing a unique possibility for modulating LIR interactions in living systems. We exploited these novel tools to study the impact of LIR inhibition on the fitness and the responsiveness to cytarabine treatment of THP-1 cells - a model for studying acute myeloid leukemia (AML). Our results demonstrate that inhibition of LIR of a single autophagy receptor is insufficient to sensitize the cells to cytarabine, while simultaneous inhibition of three LIR motifs in three distinct SARs reduces the IC50 of the chemotherapeutic.
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Affiliation(s)
- Mateusz Putyrski
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt, Germany.,Project Group Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Frankfurt, Germany
| | - Olesya Vakhrusheva
- Department of Medicine, Hematology/Oncology, Goethe-University, Frankfurt, Germany
| | - Florian Bonn
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt, Germany
| | - Suchithra Guntur
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt, Germany
| | - Andrew Vorobyov
- Project Group Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Frankfurt, Germany
| | - Christian Brandts
- Department of Medicine, Hematology/Oncology, Goethe-University, Frankfurt, Germany.,German Cancer Consortium and German Cancer Research Center, Heidelberg, Germany.,University Cancer Center Frankfurt, Goethe-University, Frankfurt, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Frankfurt, Germany
| | - Andreas Ernst
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt, Germany.,Project Group Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Frankfurt, Germany
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17
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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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18
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Kirkin V. History of the Selective Autophagy Research: How Did It Begin and Where Does It Stand Today? J Mol Biol 2020; 432:3-27. [PMID: 31082435 PMCID: PMC6971693 DOI: 10.1016/j.jmb.2019.05.010] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 02/07/2023]
Abstract
Autophagy, self-eating, is a pivotal catabolic mechanism that ensures homeostasis and survival of the cell in the face of stressors as different as starvation, infection, or protein misfolding. The importance of the research in this field was recognized by the general public after the Nobel Prize for Physiology or Medicine was awarded in 2016 to Yoshinori Ohsumi for discoveries of the mechanisms of autophagy using yeast as a model organism. One of the seminal findings of Ohsumi was on the role ubiquitin-like proteins (UBLs)-Atg5, Atg12, and Atg8-play in the formation of the double-membrane vesicle autophagosome, which is the functional unit of autophagy. Subsequent work by several groups demonstrated that, like the founding member of the UBL family ubiquitin, these small but versatile protein and lipid modifiers interact with a plethora of proteins, which either directly regulate autophagosome formation, for example, components of the Atg1/ULK1 complex, or are involved in cargo recognition, for example, Atg19 and p62/SQSTM1. By tethering the cargo to the UBLs present on the forming autophagosome, the latter proteins were proposed to effectively act as selective autophagy receptors. The discovery of the selective autophagy receptors brought a breakthrough in the autophagy field, supplying the mechanistic underpinning for the formation of an autophagosome selectively around the cytosolic cargo, that is, a protein aggregate, a mitochondrion, or a cytosolic bacterium. In this historical overview, I highlight key steps that the research into selective autophagy has been taking over the past 20 years. I comment on their significance and discuss current challenges in developing more detailed knowledge of the mechanisms of selective autophagy. I will conclude by introducing the new directions that this dynamic research field is taking into its third decade.
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Affiliation(s)
- Vladimir Kirkin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK.
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19
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Mizushima N. The ATG conjugation systems in autophagy. Curr Opin Cell Biol 2019; 63:1-10. [PMID: 31901645 DOI: 10.1016/j.ceb.2019.12.001] [Citation(s) in RCA: 259] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/31/2019] [Accepted: 12/02/2019] [Indexed: 02/08/2023]
Abstract
Autophagosome formation and maturation involve the two ubiquitin-like systems: The ATG8 and ATG12 systems. ATG8 (LC3s and gamma-aminobutyric acid receptor-associated proteins in mammals) and ATG12 are covalently conjugated to phosphatidylethanolamine and ATG5, respectively. Although the ATG12 and ATG8 systems were discovered more than 20 years ago, their molecular functions are not fully understood. The aim of this review is to summarize recent findings related to ATG conjugation systems, focusing on current controversies regarding the genetic hierarchy of these systems, interpretation of conjugation-independent alternative macroautophagy, the differences in roles between LC3s and gamma-aminobutyric acid receptor-associated proteins in autophagosome formation and cargo recognition, and evolution of these systems.
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Affiliation(s)
- Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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20
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Park SW, Jeon P, Jun YW, Park JH, Lee SH, Lee S, Lee JA, Jang DJ. Monitoring LC3- or GABARAP-positive autophagic membranes using modified RavZ-based probes. Sci Rep 2019; 9:16593. [PMID: 31719622 PMCID: PMC6851389 DOI: 10.1038/s41598-019-53372-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/25/2019] [Indexed: 11/27/2022] Open
Abstract
Xenophagy is a selective lysosomal degradation pathway for invading pathogens in host cells. However, invading bacteria also develop survival mechanisms to inhibit host autophagy. RavZ is a protein secreted by Legionella that irreversibly delipidates mammalian autophagy-related protein 8 (mATG8) on autophagic membranes in host cells via efficient autophagic membrane targeting. In this study, we leveraged the autophagic membrane-targeting mechanism of RavZ and generated a new autophagosome probe by replacing the catalytic domain of RavZ with GFP. This probe is efficiently localized to mATG8-positive autophagic membranes via a synergistic combination between mATG8 protein-binding mediated by the LC3-interacting region (LIR) motifs and phosphoinositide-3-phosphate (PI3P) binding mediated by the membrane-targeting (MT) domain. Furthermore, the membrane association activity of this new probe with an MT domain was more efficient than that of probes with a hydrophobic domain that were previously used in LIR-based autophagosome sensors. Finally, by substituting the LIR motifs of RavZ with selective LIR motifs from Fyco1 or ULK2, we developed new probes for detecting LC3A/B- or GABARAP subfamily-positive autophagic membranes, respectively. We propose that these new RavZ-based sensors will be useful for monitoring and studying the function of mATG8-positive autophagic membranes in different cellular contexts for autophagy research.
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Affiliation(s)
- Sang-Won Park
- Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, 2559, Gyeongsang-daero, Sangju-si, Gyeongsangbuk-do, 37224, Republic of Korea
| | - Pureum Jeon
- Department of Biological Science and Biotechnology, College of Life Science and Nano Technology, Hannam University, 1646, Yuseong-daero, Yuseong-gu, Daejeon, 34054, Republic of Korea
| | - Yong-Woo Jun
- Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, 2559, Gyeongsang-daero, Sangju-si, Gyeongsangbuk-do, 37224, Republic of Korea
| | - Ju-Hui Park
- Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, 2559, Gyeongsang-daero, Sangju-si, Gyeongsangbuk-do, 37224, Republic of Korea
| | - Seung-Hwan Lee
- Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, 2559, Gyeongsang-daero, Sangju-si, Gyeongsangbuk-do, 37224, Republic of Korea
| | - Sangkyu Lee
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
| | - Jin-A Lee
- Department of Biological Science and Biotechnology, College of Life Science and Nano Technology, Hannam University, 1646, Yuseong-daero, Yuseong-gu, Daejeon, 34054, Republic of Korea.
| | - Deok-Jin Jang
- Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, 2559, Gyeongsang-daero, Sangju-si, Gyeongsangbuk-do, 37224, Republic of Korea.
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21
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Lystad AH, Simonsen A. Mechanisms and Pathophysiological Roles of the ATG8 Conjugation Machinery. Cells 2019; 8:E973. [PMID: 31450711 PMCID: PMC6769624 DOI: 10.3390/cells8090973] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/18/2022] Open
Abstract
Since their initial discovery around two decades ago, the yeast autophagy-related (Atg)8 protein and its mammalian homologues of the light chain 3 (LC3) and γ-aminobutyric acid receptor associated proteins (GABARAP) families have been key for the tremendous expansion of our knowledge about autophagy, a process in which cytoplasmic material become targeted for lysosomal degradation. These proteins are ubiquitin-like proteins that become directly conjugated to a lipid in the autophagy membrane upon induction of autophagy, thus providing a marker of the pathway, allowing studies of autophagosome biogenesis and maturation. Moreover, the ATG8 proteins function to recruit components of the core autophagy machinery as well as cargo for selective degradation. Importantly, comprehensive structural and biochemical in vitro studies of the machinery required for ATG8 protein lipidation, as well as their genetic manipulation in various model organisms, have provided novel insight into the molecular mechanisms and pathophysiological roles of the mATG8 proteins. Recently, it has become evident that the ATG8 proteins and their conjugation machinery are also involved in intracellular pathways and processes not related to autophagy. This review focuses on the molecular functions of ATG8 proteins and their conjugation machinery in autophagy and other pathways, as well as their links to disease.
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Affiliation(s)
- Alf Håkon Lystad
- Department of Molecular Medicine, Institute of Basic Medical Sciences and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 1112 Blindern, 0317 Oslo, Norway.
| | - Anne Simonsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 1112 Blindern, 0317 Oslo, Norway.
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22
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Atkinson JM, Ye Y, Gebru MT, Liu Q, Zhou S, Young MM, Takahashi Y, Lin Q, Tian F, Wang HG. Time-resolved FRET and NMR analyses reveal selective binding of peptides containing the LC3-interacting region to ATG8 family proteins. J Biol Chem 2019; 294:14033-14042. [PMID: 31362979 DOI: 10.1074/jbc.ra119.008723] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/24/2019] [Indexed: 11/06/2022] Open
Abstract
Selective autophagy sequesters cytoplasmic cargo for lysosomal degradation via the binding of autophagy receptors to Atg8 (autophagy-related 8) family proteins on the autophagic membrane. The sole yeast Atg8 gene has six mAtg8 (mammalian Atg8) homologs, including the MAP1LC3 (microtubule-associated protein-1 light chain 3) family and the GABA receptor-associated proteins. Selective autophagy receptors interact with two conserved hydrophobic pockets (termed the W-site and L-site) of mATG8 proteins through a linear motif called the LC3-interacting region (LIR) with the general composition (W/F/Y)XX(I/L/V). To address a lack in our knowledge regarding LIR peptide specificity toward each mATG8 homolog, here we used competitive time-resolved FRET to sensitively and quantitatively characterize the interactions between LIRs and mAtg8. We report that 14 representative LIR-containing peptides display differential binding affinities toward the mAtg8 proteins and identified the LIR domain peptide of TP53INP1 as exhibiting high affinity for all six mATG8 proteins. Using peptide truncation studies, we found that both N- and C-terminal acidic residues, as well as the C-terminal Cys residue of the TP53INP1 LIR peptide, are required for its high-affinity binding to LC3A and LC3B, whereas binding to the GABARAP subfamily proteins was facilitated by residues either N-terminal or C-terminal to the core motif. Finally, we used NMR chemical shift perturbation analysis to gain molecular insights into these findings. Collectively, our results may aid in the development of molecules that selectively disrupt specific mATG8-LIR interactions to dissect the biological roles of the six mATG8 homologs for potential therapeutic applications.
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Affiliation(s)
- Jennifer M Atkinson
- Department of Pediatrics, Penn State College of Medicine, Hershey, Pennsylvania 17033
| | - Yansheng Ye
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033
| | - Melat T Gebru
- Department of Pediatrics, Penn State College of Medicine, Hershey, Pennsylvania 17033
| | - Qiang Liu
- Department of Pediatrics, Penn State College of Medicine, Hershey, Pennsylvania 17033
| | - Shouhao Zhou
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania 17033
| | - Megan M Young
- Department of Pediatrics, Penn State College of Medicine, Hershey, Pennsylvania 17033
| | - Yoshinori Takahashi
- Department of Pediatrics, Penn State College of Medicine, Hershey, Pennsylvania 17033
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260
| | - Fang Tian
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033
| | - Hong-Gang Wang
- Department of Pediatrics, Penn State College of Medicine, Hershey, Pennsylvania 17033
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23
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Jatana N, Ascher DB, Pires DEV, Gokhale RS, Thukral L. Human LC3 and GABARAP subfamily members achieve functional specificity via specific structural modulations. Autophagy 2019; 16:239-255. [PMID: 30982432 DOI: 10.1080/15548627.2019.1606636] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Autophagy is a conserved adaptive cellular pathway essential to maintain a variety of physiological functions. Core components of this machinery are the six human Atg8 orthologs that initiate formation of appropriate protein complexes. While these proteins are routinely used as indicators of autophagic flux, it is presently not possible to discern their individual biological functions due to our inability to predict specific binding partners. In our attempts towards determining downstream effector functions, we developed a computational pipeline to define structural determinants of human Atg8 family members that dictate functional diversity. We found a clear evolutionary separation between human LC3 and GABARAP subfamilies and also defined a novel sequence motif responsible for their specificity. By analyzing known protein structures, we observed that functional modules or microclusters reveal a pattern of intramolecular network, including distinct hydrogen bonding of key residues (F52/Y49; a subset of HP2) that may directly modulate their interaction preferences. Multiple molecular dynamics simulations were performed to characterize how these proteins interact with a common protein binding partner, PLEKHM1. Our analysis showed remarkable differences in binding modes via intrinsic protein dynamics, with PLEKHM1-bound GABARAP complexes showing less fluctuations and higher number of contacts. We further mapped 373 genomic variations and demonstrated that distinct cancer-related mutations are likely to lead to significant structural changes. Our findings present a quantitative framework to establish factors underlying exquisite specificity of human Atg8 proteins, and thus facilitate the design of precise modulators.Abbreviations: Atg: autophagy-related; ECs: evolutionary constraints; GABARAP: GABA type A receptor-associated protein; HsAtg8: human Atg8; HP: hydrophobic pocket; KBTBD6: kelch repeat and BTB domain containing 6; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MD: molecular dynamics; HIV-1 Nef: human immunodeficiency virus type 1 negative regulatory factor; PLEKHM1: pleckstrin homology and RUN domain containing M1; RMSD: root mean square deviation; SQSTM1/p62: sequestosome 1; WDFY3/ALFY: WD repeat and FYVE domain containing 3.
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Affiliation(s)
- Nidhi Jatana
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - David B Ascher
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.,Department of Biochemistry, University of Cambridge, Cambridgeshire, UK.,Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Douglas E V Pires
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.,Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Rajesh S Gokhale
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,National Institute of Immunology, New Delhi, India
| | - Lipi Thukral
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR- Institute of Genomics and Integrative Biology, New Delhi, India.,Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany
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24
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Jeon P, Park JH, Jun YW, Lee YK, Jang DJ, Lee JA. Development of GABARAP family protein-sensitive LIR-based probes for neuronal autophagy. Mol Brain 2019; 12:33. [PMID: 30961647 PMCID: PMC6454701 DOI: 10.1186/s13041-019-0458-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 04/01/2019] [Indexed: 11/10/2022] Open
Abstract
Autophagy allows for lysosomal cellular degradation of cytosolic components. In particular, neuronal autophagy is essential for cellular homeostasis and neuronal survival and is tightly regulated by several autophagy-related (ATG) proteins in post-mitotic neurons. Among these ATG proteins, the LC3/GABARAP proteins are known to regulate autophagosome biogenesis/maturation and cargo recognition. However, little is known about the role of GABARAP family proteins in neuronal autophagy despite their abundant expression in post-mitotic neurons. We have previously developed HyD (Hydrophobic Domain)-LIR (LC3-interacting region)-based autophagosome markers. In this study, to monitor GABARAP family proteins in autophagosomes of post-mitotic neurons, we improved the sensitivity of the probes for specifically detecting endogenous GABARAP family proteins by adding one more LIR motif to the LIR probes. We have tested the efficiency of two different LIRs, from ULK2 and Stbd1, in regard to their cellular localization to autophagosomes. HyD-2xLIR(ULK2)-GFP and HyD-2xLIR(Stbd1)-GFP demonstrated specific localization to GABARAP-positive autophagosomes relative to LC3B-positive autophagosomes in MEF/HeLa cells in an autophagy-dependent manner. Indeed, HyD-2xLIR(Stbd1)-GFP could efficiently detect GABARAP-positive autophagosomes in cultured cortical neurons. Our improved GABARAP-sensitive probes will contribute toward understanding the specific role of GABARAP family proteins in regard to neuronal autophagy.
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Affiliation(s)
- Pureum Jeon
- Department of Biological Sciences and Biotechnology, College of Life Sciences and Nanotechnology, Hannam University, 461-6 Jeonmin-dong, Yuseong-gu, Daejeon, 34054, Republic of Korea
| | - Ju-Hui Park
- Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, 386, Gajang-dong, Sangju-si, Kyungbuk, 37224, South Korea
| | - Yong-Woo Jun
- Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, 386, Gajang-dong, Sangju-si, Kyungbuk, 37224, South Korea
| | - You-Kyung Lee
- Department of Biological Sciences and Biotechnology, College of Life Sciences and Nanotechnology, Hannam University, 461-6 Jeonmin-dong, Yuseong-gu, Daejeon, 34054, Republic of Korea
| | - Deok-Jin Jang
- Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, 386, Gajang-dong, Sangju-si, Kyungbuk, 37224, South Korea.
| | - Jin-A Lee
- Department of Biological Sciences and Biotechnology, College of Life Sciences and Nanotechnology, Hannam University, 461-6 Jeonmin-dong, Yuseong-gu, Daejeon, 34054, Republic of Korea.
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25
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The highly GABARAP specific rat monoclonal antibody 8H5 visualizes GABARAP in immunofluorescence imaging at endogenous levels. Sci Rep 2019; 9:526. [PMID: 30679523 PMCID: PMC6346085 DOI: 10.1038/s41598-018-36717-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 11/25/2018] [Indexed: 12/16/2022] Open
Abstract
The determination of unique functions of GABARAP (gamma-aminobutyric acid type A receptor-associated protein), a member of the highly conserved protein family of mammalian autophagy-related 8 protein (mATG8), within diverse cellular processes remains challenging. Because available anti-GABARAP antibodies perform inadequate, especially within various microscopy-based applications, we aimed to develop an antibody that targets GABARAP but not its close orthologs. Following the latest recommendations for antibody validation including fluorescence protein tagging, genetic and orthogonal strategies, we characterized the resulting anti-GABARAP (8H5) antibody during confocal immunofluorescence imaging in-depth. We compared the antibody staining pattern with that obtained for fluorescence protein tagged GABARAP, GABARAPL1 or GABARAPL2 each ectopically expressed in GABARAP knockout cells. Furthermore, we imaged cells expressing all mATG8 family members at endogenous levels and checked GABARAP knockout cells for unspecific staining under fed or macroautophagy-inducing conditions. Finally, we simultaneously stained cells for endogenous GABARAP and the common autophagosomal marker LC3B. Summarized, the presented antibody shows high specificity for GABARAP without cross-reactivity to other mATG8 family members in immunofluorescence imaging making it a valuable tool for the identification of unique GABARAP functions.
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26
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Moparthi SB, Wollert T. Reconstruction of destruction – in vitro reconstitution methods in autophagy research. J Cell Sci 2018; 132:132/4/jcs223792. [DOI: 10.1242/jcs.223792] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
ABSTRACT
Autophagy is one of the most elaborative membrane remodeling systems in eukaryotic cells. Its major function is to recycle cytoplasmic material by delivering it to lysosomes for degradation. To achieve this, a membrane cisterna is formed that gradually captures cargo such as organelles or protein aggregates. The diversity of cargo requires autophagy to be highly versatile to adapt the shape of the phagophore to its substrate. Upon closure of the phagophore, a double-membrane-surrounded autophagosome is formed that eventually fuses with lysosomes. In response to environmental cues such as cytotoxicity or starvation, bulk cytoplasm can be captured and delivered to lysosomes. Autophagy thus supports cellular survival under adverse conditions. During the past decades, groundbreaking genetic and cell biological studies have identified the core machinery involved in the process. In this Review, we are focusing on in vitro reconstitution approaches to decipher the details and spatiotemporal control of autophagy, and how such studies contributed to our current understanding of the pathways in yeast and mammals. We highlight studies that revealed the function of the autophagy machinery at a molecular level with respect to its capacity to remodel membranes.
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Affiliation(s)
- Satish Babu Moparthi
- Membrane Biochemistry and Transport, Institute Pasteur, 28 rue du Dr Roux, 75015 Paris, France
| | - Thomas Wollert
- Membrane Biochemistry and Transport, Institute Pasteur, 28 rue du Dr Roux, 75015 Paris, France
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27
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Fecal Microbiota Transplantation Beneficially Regulates Intestinal Mucosal Autophagy and Alleviates Gut Barrier Injury. mSystems 2018; 3:mSystems00137-18. [PMID: 30320222 PMCID: PMC6178585 DOI: 10.1128/msystems.00137-18] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/11/2018] [Indexed: 02/07/2023] Open
Abstract
The gut microbiota plays a crucial role in human and animal health, and its disorder causes multiple diseases. Over the past decade, FMT has gained increasing attention due to the success in treating Clostridium difficile infection (CDI) and inflammatory bowel disease (IBD). Although FMT appears to be effective, how FMT functions in the recipient remains unknown. Whether FMT exerts this beneficial effect through a series of changes in the host organism caused by alteration of gut microbial structure is also not known. In the present study, newborn piglets and E. coli K88-infected piglets were selected as models to explore the interplay between host and gut microbiota following FMT. Our results showed that FMT triggered intestinal mucosal autophagy and alleviated gut barrier injury caused by E. coli K88. This report provides a theoretical basis for the use of FMT as a viable therapeutic method for gut microbial regulation. Fecal microbiota transplantation (FMT) is one of the most effective ways to regulate the gut microbiota. Here, we investigated the effect of exogenous fecal microbiota on gut function from the perspective of analysis of the mucosal proteomes in a piglet model. A total of 289 differentially expressed proteins were annotated with 4,068 gene ontology (GO) function entries in the intestinal mucosa, and the levels of autophagy-related proteins in the forkhead box O (FoxO) signaling pathway were increased whereas the levels of proteins related to inflammation response were decreased in the recipient. Then, to assess the alleviation of epithelial injury in the Escherichia coli K88-infected piglets following FMT, intestinal microbiome-metabolome responses were determined. 16S rRNA gene sequencing showed that the abundances of beneficial bacteria, such as Lactobacillus and Succinivibrio, were increased whereas those of Enterobacteriaceae and Proteobacteria bacteria were decreased in the infected piglets following FMT. Metabolomic analysis revealed that levels of 58 metabolites, such as lactic acid and succinic acid, were enhanced in the intestinal lumen and that seven metabolic pathways, such as branched-chain amino acid metabolism pathways, were upregulated in the infected piglets following FMT. In concordance with the metabolome data, results of metagenomics prediction analysis also demonstrated that FMT modulated the metabolic functions of gut microbiota associated with linoleic acid metabolism. In addition, intestinal morphology was improved, a result that coincided with the decrease of intestinal permeability and the enhancement of mucins and mucosal expression of tight junction proteins in the recipient. Taken together, the results showed that FMT triggered intestinal mucosal protective autophagy and alleviated gut barrier injury through alteration of the gut microbial structure. IMPORTANCE The gut microbiota plays a crucial role in human and animal health, and its disorder causes multiple diseases. Over the past decade, FMT has gained increasing attention due to the success in treating Clostridium difficile infection (CDI) and inflammatory bowel disease (IBD). Although FMT appears to be effective, how FMT functions in the recipient remains unknown. Whether FMT exerts this beneficial effect through a series of changes in the host organism caused by alteration of gut microbial structure is also not known. In the present study, newborn piglets and E. coli K88-infected piglets were selected as models to explore the interplay between host and gut microbiota following FMT. Our results showed that FMT triggered intestinal mucosal autophagy and alleviated gut barrier injury caused by E. coli K88. This report provides a theoretical basis for the use of FMT as a viable therapeutic method for gut microbial regulation.
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28
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Di Rita A, Peschiaroli A, D Acunzo P, Strobbe D, Hu Z, Gruber J, Nygaard M, Lambrughi M, Melino G, Papaleo E, Dengjel J, El Alaoui S, Campanella M, Dötsch V, Rogov VV, Strappazzon F, Cecconi F. HUWE1 E3 ligase promotes PINK1/PARKIN-independent mitophagy by regulating AMBRA1 activation via IKKα. Nat Commun 2018; 9:3755. [PMID: 30217973 PMCID: PMC6138665 DOI: 10.1038/s41467-018-05722-3] [Citation(s) in RCA: 179] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 06/27/2018] [Indexed: 01/18/2023] Open
Abstract
The selective removal of undesired or damaged mitochondria by autophagy, known as mitophagy, is crucial for cellular homoeostasis, and prevents tumour diffusion, neurodegeneration and ageing. The pro-autophagic molecule AMBRA1 (autophagy/beclin-1 regulator-1) has been defined as a novel regulator of mitophagy in both PINK1/PARKIN-dependent and -independent systems. Here, we identified the E3 ubiquitin ligase HUWE1 as a key inducing factor in AMBRA1-mediated mitophagy, a process that takes place independently of the main mitophagy receptors. Furthermore, we show that mitophagy function of AMBRA1 is post-translationally controlled, upon HUWE1 activity, by a positive phosphorylation on its serine 1014. This modification is mediated by the IKKα kinase and induces structural changes in AMBRA1, thus promoting its interaction with LC3/GABARAP (mATG8) proteins and its mitophagic activity. Altogether, these results demonstrate that AMBRA1 regulates mitophagy through a novel pathway, in which HUWE1 and IKKα are key factors, shedding new lights on the regulation of mitochondrial quality control and homoeostasis in mammalian cells. Mitophagy is crucial for mitochondrial quality control and maintenance of cellular homeostasis. Here the authors identify an E3 ubiquitin ligase, HUWE1, that collaborates with LC3-interacting protein AMBRA1 to induce mitochondrial clearance.
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Affiliation(s)
- Anthea Di Rita
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy.,Department of Paediatric Haematology, Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Rome, Italy.,IRCCS FONDAZIONE SANTA LUCIA, 00143, Rome, Italy
| | - Angelo Peschiaroli
- National Research Council of Italy (CNR), Institute of Translational Pharmacology IFT, Via Fosso del Cavaliere 100, 00133, Rome, Italy
| | - Pasquale D Acunzo
- Department of Paediatric Haematology, Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Daniela Strobbe
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy.,IRCCS- Regina Elena, National Cancer Institute, 00133, Rome, Italy
| | - Zehan Hu
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Jens Gruber
- Institute of Biophysical and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, Germany
| | - Mads Nygaard
- Computational Biology Laboratory, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Matteo Lambrughi
- Computational Biology Laboratory, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Gerry Melino
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | - Michelangelo Campanella
- IRCCS- Regina Elena, National Cancer Institute, 00133, Rome, Italy.,Department of Comparative Biomedical Sciences, Royal Veterinary College, London, NW1 0TU, UK.,University College London Consortium for Mitochondrial Research, University College London, London, WC1 6BT, UK
| | - Volker Dötsch
- Institute of Biophysical and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, Germany
| | - Vladimir V Rogov
- Institute of Biophysical and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, Germany
| | - Flavie Strappazzon
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy. .,IRCCS FONDAZIONE SANTA LUCIA, 00143, Rome, Italy.
| | - Francesco Cecconi
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy. .,Department of Paediatric Haematology, Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Rome, Italy. .,Unit of Cell Stress and Survival, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark.
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29
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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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30
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Li J, Zhu R, Chen K, Zheng H, Zhao H, Yuan C, Zhang H, Wang C, Zhang M. Potent and specific Atg8-targeting autophagy inhibitory peptides from giant ankyrins. Nat Chem Biol 2018; 14:778-787. [PMID: 29867141 DOI: 10.1038/s41589-018-0082-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 04/23/2018] [Indexed: 02/03/2023]
Abstract
The mammalian Atg8 family proteins are central drivers of autophagy and contain six members, classified into the LC3 and GABARAP subfamilies. Due to their high sequence similarity and consequent functional overlaps, it is difficult to delineate specific functions of Atg8 proteins in autophagy. Here we discover a super-strong GABARAP-selective inhibitory peptide harbored in 270/480 kDa ankyrin-G and a super-potent pan-Atg8 inhibitory peptide from 440 kDa ankyrin-B. Structural studies elucidate the mechanism governing the Atg8 binding potency and selectivity of the peptides, reveal a general Atg8-binding sequence motif, and allow development of a more GABARAP-selective inhibitory peptide. These peptides effectively blocked autophagy when expressed in cultured cells. Expression of these ankyrin-derived peptides in Caenorhabditis elegans also inhibited autophagy, causing accumulation of the p62 homolog SQST-1, delayed development and shortened life span. Thus, these genetically encodable autophagy inhibitory peptides can be used to occlude autophagy spatiotemporally in living animals.
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Affiliation(s)
- Jianchao Li
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Ruichi Zhu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Keyu Chen
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Hui Zheng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hongyu Zhao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chongzhen Yuan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Chao Wang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. .,Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.
| | - Mingjie Zhang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. .,Center of Systems Biology and Human Health, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
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31
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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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32
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Evolution of tools and methods for monitoring autophagic flux in mammalian cells. Biochem Soc Trans 2018; 46:97-110. [DOI: 10.1042/bst20170102] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 12/06/2017] [Accepted: 12/11/2017] [Indexed: 01/07/2023]
Abstract
Autophagy is an evolutionarily conserved lysosome-mediated degradation and recycling process, which functions in cellular homeostasis and stress adaptation. The process is highly dynamic and involves autophagosome synthesis, cargo recognition and transport, autophagosome–lysosome fusion, and cargo degradation. The multistep nature of autophagy makes it challenging to quantify, and it is important to consider not only the number of autophagosomes within a cell but also the autophagic degradative activity. The rate at which cargos are recognized, segregated, and degraded through the autophagy pathway is defined as autophagic flux. In practice, methods to measure autophagic flux typically evaluate the lysosome-mediated cargo degradation step by leveraging known autophagy markers such as MAP1LC3B (microtubule-associated proteins 1A/1B light chain 3 beta) or lysosome-dependent fluorescent agents. In this review, we summarize the tools and methods used in mammalian cultured cells pertaining to these two approaches, and highlight innovations that have led to their evolution in recent years. We also discuss the potential limitations of these approaches and recommend using a combination of strategies and multiple different autophagy markers to reliably evaluate autophagic flux in mammalian cells.
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Systematic Analysis of Human Cells Lacking ATG8 Proteins Uncovers Roles for GABARAPs and the CCZ1/MON1 Regulator C18orf8/RMC1 in Macroautophagic and Selective Autophagic Flux. Mol Cell Biol 2017; 38:MCB.00392-17. [PMID: 29038162 DOI: 10.1128/mcb.00392-17] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/04/2017] [Indexed: 12/26/2022] Open
Abstract
Selective autophagy and macroautophagy sequester specific organelles/substrates or bulk cytoplasm, respectively, inside autophagosomes as cargo for delivery to lysosomes. The mammalian ATG8 orthologues (MAP1LC3A/B/C and GABARAP/L1/L2) are ubiquitin (UB)-like proteins conjugated to the autophagosome membrane and are thought to facilitate cargo receptor recruitment, vesicle maturation, and lysosomal fusion. To elucidate the molecular functions of the ATG8 proteins, we engineered cells lacking genes for each subfamily as well as all six mammalian ATG8s. Loss of GABARAPs alone attenuates autophagic flux basally and in response to macroautophagic or selective autophagic stimuli, including parkin-dependent mitophagy, and cells lacking all ATG8 proteins accumulate cytoplasmic UB aggregates, which are resolved following ectopic expression of individual GABARAPs. Autophagosomes from cells lacking GABARAPs had reduced lysosomal content by quantitative proteomics, consistent with fusion defects, but accumulated regulators of late endosome (LE)/autophagosome maturation. Through interaction proteomics of proteins accumulating in GABARAP/L1/L2-deficient cells, we identified C18orf8/RMC1 as a new subunit of the CCZ1-MON1 RAB7 guanine exchange factor (GEF) that positively regulates RAB7 recruitment to LE/autophagosomes. This work defines unique roles for GABARAP and LC3 subfamilies in macroautophagy and selective autophagy and demonstrates how analysis of autophagic machinery in the absence of flux can identify new regulatory circuits.
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Le Guerroué F, Eck F, Jung J, Starzetz T, Mittelbronn M, Kaulich M, Behrends C. Autophagosomal Content Profiling Reveals an LC3C-Dependent Piecemeal Mitophagy Pathway. Mol Cell 2017; 68:786-796.e6. [DOI: 10.1016/j.molcel.2017.10.029] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 08/01/2017] [Accepted: 10/20/2017] [Indexed: 10/18/2022]
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35
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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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36
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Lee YK, Jun YW, Choi HE, Huh YH, Kaang BK, Jang DJ, Lee JA. Development of LC3/GABARAP sensors containing a LIR and a hydrophobic domain to monitor autophagy. EMBO J 2017; 36:1100-1116. [PMID: 28320742 DOI: 10.15252/embj.201696315] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 03/03/2017] [Accepted: 03/03/2017] [Indexed: 01/07/2023] Open
Abstract
Macroautophagy allows for bulk degradation of cytosolic components in lysosomes. Overexpression of GFP/RFP-LC3/GABARAP is commonly used to monitor autophagosomes, a hallmark of autophagy, despite artifacts related to their overexpression. Here, we developed new sensors that detect endogenous LC3/GABARAP proteins at the autophagosome using an LC3-interacting region (LIR) and a short hydrophobic domain (HyD). Among HyD-LIR-GFP sensors harboring LIR motifs of 34 known LC3-binding proteins, HyD-LIR(TP)-GFP using the LIR motif from TP53INP2 allowed detection of all LC3/GABARAPs-positive autophagosomes. However, HyD-LIR(TP)-GFP preferentially localized to GABARAP/GABARAPL1-positive autophagosomes in a LIR-dependent manner. In contrast, HyD-LIR(Fy)-GFP using the LIR motif from FYCO1 specifically detected LC3A/B-positive autophagosomes. HyD-LIR(TP)-GFP and HyD-LIR(Fy)-GFP efficiently localized to autophagosomes in the presence of endogenous LC3/GABARAP levels and without affecting autophagic flux. Both sensors also efficiently localized to MitoTracker-positive damaged mitochondria upon mitophagy induction. HyD-LIR(TP)-GFP allowed live-imaging of dynamic autophagosomes upon autophagy induction. These novel autophagosome sensors can thus be widely used in autophagy research.
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Affiliation(s)
- You-Kyung Lee
- Department of Biological Sciences and Biotechnology, College of Life Sciences and Nanotechnology, Hannam University, Daejeon, Korea
| | - Yong-Woo Jun
- Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, Sangju, Korea
| | - Ha-Eun Choi
- Department of Biological Sciences and Biotechnology, College of Life Sciences and Nanotechnology, Hannam University, Daejeon, Korea
| | - Yang Hoon Huh
- Center for Electron Microscopy Research, Korea Basic Science Institute, Daejeon, Korea
| | - Bong-Kiun Kaang
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, Korea
| | - Deok-Jin Jang
- Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, Sangju, Korea
| | - Jin-A Lee
- Department of Biological Sciences and Biotechnology, College of Life Sciences and Nanotechnology, Hannam University, Daejeon, Korea
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37
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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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