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Phosphorylation of the LIR Domain of SCOC Modulates ATG8 Binding Affinity and Specificity. J Mol Biol 2021; 433:166987. [PMID: 33845085 PMCID: PMC8202330 DOI: 10.1016/j.jmb.2021.166987] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/27/2021] [Accepted: 04/04/2021] [Indexed: 12/15/2022]
Abstract
Autophagy is a highly conserved degradative pathway, essential for cellular homeostasis and implicated in diseases including cancer and neurodegeneration. Autophagy-related 8 (ATG8) proteins play a central role in autophagosome formation and selective delivery of cytoplasmic cargo to lysosomes by recruiting autophagy adaptors and receptors. The LC3-interacting region (LIR) docking site (LDS) of ATG8 proteins binds to LIR motifs present in autophagy adaptors and receptors. LIR-ATG8 interactions can be highly selective for specific mammalian ATG8 family members (LC3A-C, GABARAP, and GABARAPL1-2) and how this specificity is generated and regulated is incompletely understood. We have identified a LIR motif in the Golgi protein SCOC (short coiled-coil protein) exhibiting strong binding to GABARAP, GABARAPL1, LC3A and LC3C. The residues within and surrounding the core LIR motif of the SCOC LIR domain were phosphorylated by autophagy-related kinases (ULK1-3, TBK1) increasing specifically LC3 family binding. More distant flanking residues also contributed to ATG8 binding. Loss of these residues was compensated by phosphorylation of serine residues immediately adjacent to the core LIR motif, indicating that the interactions of the flanking LIR regions with the LDS are important and highly dynamic. Our comprehensive structural, biophysical and biochemical analyses support and provide novel mechanistic insights into how phosphorylation of LIR domain residues regulates the affinity and binding specificity of ATG8 proteins towards autophagy adaptors and receptors.
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Nam SE, Cheung YWS, Nguyen TN, Gong M, Chan S, Lazarou M, Yip CK. Insights on autophagosome-lysosome tethering from structural and biochemical characterization of human autophagy factor EPG5. Commun Biol 2021; 4:291. [PMID: 33674710 PMCID: PMC7935953 DOI: 10.1038/s42003-021-01830-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 02/10/2021] [Indexed: 12/17/2022] Open
Abstract
Pivotal to the maintenance of cellular homeostasis, macroautophagy (hereafter autophagy) is an evolutionarily conserved degradation system that involves sequestration of cytoplasmic material into the double-membrane autophagosome and targeting of this transport vesicle to the lysosome/late endosome for degradation. EPG5 is a large-sized metazoan protein proposed to serve as a tethering factor to enforce autophagosome–lysosome/late endosome fusion specificity, and its deficiency causes a severe multisystem disorder known as Vici syndrome. Here, we show that human EPG5 (hEPG5) adopts an extended “shepherd’s staff” architecture. We find that hEPG5 binds preferentially to members of the GABARAP subfamily of human ATG8 proteins critical to autophagosome–lysosome fusion. The hEPG5–GABARAPs interaction, which is mediated by tandem LIR motifs that exhibit differential affinities, is required for hEPG5 recruitment to mitochondria during PINK1/Parkin-dependent mitophagy. Lastly, we find that the Vici syndrome mutation Gln336Arg does not affect the hEPG5’s overall stability nor its ability to engage in interaction with the GABARAPs. Collectively, results from our studies reveal new insights into how hEPG5 recognizes mature autophagosome and establish a platform for examining the molecular effects of Vici syndrome disease mutations on hEPG5. Nam and Cheung et al. describe the structural and biochemical characterization of human autophagy factor EPG5 that functions in autophagosome–lysosome tethering. They show that hEPG5 adopts an extended shepherd’s staff architecture, binds preferentially to GABARAP proteins, and is recruited to mitochondria during mitophagy.
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Affiliation(s)
- Sung-Eun Nam
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada
| | - Yiu Wing Sunny Cheung
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada
| | - Thanh Ngoc Nguyen
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Michael Gong
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada
| | - Samuel Chan
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada
| | - Michael Lazarou
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Calvin K Yip
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada.
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Jacquet M, Guittaut M, Fraichard A, Despouy G. The functions of Atg8-family proteins in autophagy and cancer: linked or unrelated? Autophagy 2021; 17:599-611. [PMID: 32255730 PMCID: PMC8032235 DOI: 10.1080/15548627.2020.1749367] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 03/09/2020] [Accepted: 03/26/2020] [Indexed: 01/04/2023] Open
Abstract
The Atg8-family proteins are subdivided into two subfamilies: the GABARAP and LC3 subfamilies. These proteins, which are major players of the autophagy pathway, present a conserved glycine in their C-terminus necessary for their association to the autophagosome membrane. This family of proteins present multiple roles from autophagy induction to autophagosome-lysosome fusion and have been described to play a role during cancer progression. Indeed, GABARAPs are described to be downregulated in cancers, and high expression has been linked to a good prognosis. Regarding LC3 s, their expression does not correlate to a particular tumor type or stage. The involvement of Atg8-family proteins during cancer, therefore, remains unclear, and it appears that their anti-tumor role may be associated with their implication in selective protein degradation by autophagy but might also be independent, in some cases, of their conjugation to autophagosomes. In this review, we will then focus on the involvement of GABARAP and LC3 subfamilies during autophagy and cancer and highlight the similarities but also the differences of action of each subfamily member.Abbreviations: AIM: Atg8-interacting motif; AMPK: adenosine monophosphate-associated protein kinase; ATG: autophagy-related; BECN1: beclin 1; BIRC6/BRUCE: baculoviral IAP repeat containing 6; BNIP3L/NIX: BCL2 interacting protein 3 like; GABARAP: GABA type A receptor-associated protein; GABARAPL1/2: GABA type A receptor associated protein like 1/2; GABRA/GABAA: gamma-aminobutyric acid type A receptor subunit; LAP: LC3-associated phagocytosis; LMNB1: lamin B1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MTOR: mechanistic target of rapamycin kinase; PI4K2A/PI4KIIα: phosphatidylinositol 4-kinase type 2 alpha; PLEKHM1: plecktrin homology and RUN domain containing M1; PtdIns3K-C1: class III phosphatidylinositol 3-kinase complex 1; SQSTM1: sequestosome 1; ULK1: unc51-like autophagy activating kinase 1.
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Affiliation(s)
- Marine Jacquet
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
| | - Michaël Guittaut
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
- DImaCell Platform, Univ. Bourgogne Franche-Comté, Besançon, France
| | - Annick Fraichard
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
| | - Gilles Despouy
- Univ. Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
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54
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Terešak P, Lapao A, Subic N, Boya P, Elazar Z, Simonsen A. Regulation of PRKN-independent mitophagy. Autophagy 2021; 18:24-39. [PMID: 33570005 DOI: 10.1080/15548627.2021.1888244] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Mitochondria are dynamic, multifunctional cellular organelles that play a fundamental role in maintaining cellular homeostasis. Keeping the quality of mitochondria in check is of essential importance for functioning and survival of the cells. Selective autophagic clearance of flawed mitochondria, a process termed mitophagy, is one of the most prominent mechanisms through which cells maintain a healthy mitochondrial pool. The best-studied pathway through which mitophagy is exerted is the PINK1-PRKN pathway. However, an increasing number of studies have shown an existence of alternative pathways, where different proteins and lipids are able to recruit autophagic machinery independently of PINK1 and PRKN. The significance of PRKN-independent mitophagy pathways is reflected in various physiological and pathophysiological processes, but many questions regarding the regulation and the interplay between these pathways remain open. Here we review the current knowledge and recent progress made in the field of PRKN-independent mitophagy. Particularly we focus on the regulation of various receptors that participate in targeting impaired mitochondria to autophagosomes independently of PRKN.AbbreviationsAMPK: AMP-activated protein kinase; ATP: adenosine triphosphate; BCL2: BCL2 apoptosis regulator; BH: BCL2 homology; CCCP: Carbonyl cyanide m-chlorophenylhydrazone; CL: cardiolipin; ER: endoplasmic reticulum; FCCP: carbonyl cyanide p-trifluoromethoxyphenylhydrazone; IMM: inner mitochondrial membrane; IMS: mitochondrial intermembrane space; LIR: LC3-interacting region; MDVs: mitochondrial-derived vesicles; MTORC1: mechanistic target of rapamycin kinase complex 1; OMM: outer mitochondrial membrane; OXPHOS: oxidative phosphorylation; PD: Parkinson disease; PtdIns3K: phosphatidylinositol 3-kinase; RGC: retinal ganglion cell; RING: really interesting new gene; ROS: reactive oxygen species; SUMO: small ubiquitin like modifier; TBI: traumatic brain injury; TM: transmembrane.
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Affiliation(s)
- Petra Terešak
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Ana Lapao
- Department of Molecular Medicine, Institute of Basic Medical Sciences and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Nemanja Subic
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Patricia Boya
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Zvulun Elazar
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Anne Simonsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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55
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Nieto-Torres JL, Leidal AM, Debnath J, Hansen M. Beyond Autophagy: The Expanding Roles of ATG8 Proteins. Trends Biochem Sci 2021; 46:673-686. [PMID: 33558127 DOI: 10.1016/j.tibs.2021.01.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/10/2021] [Accepted: 01/12/2021] [Indexed: 12/14/2022]
Abstract
The ATG8 family proteins are critical players in autophagy, a cytoprotective process that mediates degradation of cytosolic cargo. During autophagy, ATG8s conjugate to autophagosome membranes to facilitate cargo recruitment, autophagosome biogenesis, transport, and fusion with lysosomes, for cargo degradation. In addition to these canonical functions, recent reports demonstrate that ATG8s are also delivered to single-membrane organelles, which leads to highly divergent degradative or secretory fates, vesicle maturation, and cargo specification. The association of ATG8s with different vesicles involves complex regulatory mechanisms still to be fully elucidated. Whether individual ATG8 family members play unique canonical or non-canonical roles, also remains unclear. This review summarizes the many open molecular questions regarding ATG8s that are only beginning to be unraveled.
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Affiliation(s)
- Jose L Nieto-Torres
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA, USA
| | - Andrew M Leidal
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Jayanta Debnath
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
| | - Malene Hansen
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA, USA.
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56
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Liu F, Hu W, Li F, Marshall RS, Zarza X, Munnik T, Vierstra RD. AUTOPHAGY-RELATED14 and Its Associated Phosphatidylinositol 3-Kinase Complex Promote Autophagy in Arabidopsis. THE PLANT CELL 2020; 32:3939-3960. [PMID: 33004618 PMCID: PMC7721316 DOI: 10.1105/tpc.20.00285] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/24/2020] [Accepted: 09/29/2020] [Indexed: 05/20/2023]
Abstract
Phosphatidylinositol 3-phosphate (PI3P) is an essential membrane signature for both autophagy and endosomal sorting that is synthesized in plants by the class III phosphatidylinositol 3-kinase (PI3K) complex, consisting of the VPS34 kinase, together with ATG6, VPS15, and either VPS38 or ATG14 as the fourth subunit. Although Arabidopsis (Arabidopsis thaliana) plants missing the three core subunits are infertile, vps38 mutants are viable but have aberrant leaf, root, and seed development, Suc sensing, and endosomal trafficking, suggesting that VPS38 and ATG14 are nonredundant. Here, we evaluated the role of ATG14 through a collection of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 and T-DNA insertion mutants disrupting the two Arabidopsis paralogs. atg14a atg14b double mutants were relatively normal phenotypically but displayed pronounced autophagy defects, including reduced accumulation of autophagic bodies and cargo delivery during nutrient stress. Unexpectedly, homozygous atg14a atg14b vps38 triple mutants were viable but showed severely compromised rosette development and reduced fecundity, pollen germination, and autophagy, consistent with a need for both ATG14 and VPS38 to fully actuate PI3P biology. However, the triple mutants still accumulated PI3P, but they were hypersensitive to the PI3K inhibitor wortmannin, indicating that the ATG14/VPS38 component is not essential for PI3P synthesis. Collectively, the ATG14/VPS38 mutant collection now permits the study of plants altered in specific aspects of PI3P biology.
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Affiliation(s)
- Fen Liu
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Weiming Hu
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Faqiang Li
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Richard S Marshall
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Xavier Zarza
- Department of Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 Amsterdam, The Netherlands
| | - Teun Munnik
- Department of Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 Amsterdam, The Netherlands
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
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57
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Dudley LJ, Makar AN, Gammoh N. Membrane targeting of core autophagy players during autophagosome biogenesis. FEBS J 2020; 287:4806-4821. [PMID: 32301577 DOI: 10.1111/febs.15334] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/27/2020] [Accepted: 04/14/2020] [Indexed: 12/18/2022]
Abstract
Autophagosomes are vital organelles required to facilitate the lysosomal degradation of cytoplasmic cargo, thereby playing an important role in maintaining cellular homeostasis. A number of autophagy-related (ATG) protein complexes are recruited to the site of autophagosome biogenesis where they act to facilitate membrane growth and maturation. Regulated recruitment of ATG complexes to autophagosomal membranes is essential for their autophagic activities and is required to ensure the efficient engulfment of cargo destined for lysosomal degradation. In this review, we discuss our current understanding of the spatiotemporal hierarchy between ATG proteins, examining the mechanisms underlying their recruitment to membranes. A particular focus is placed on the relevance of phosphatidylinositol 3-phosphate and the extent to which the core autophagy players are reliant on this lipid for their localisation to autophagic membranes. In addition, open questions and potential future research directions regarding the membrane recruitment and displacement of ATG proteins are discussed here.
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Affiliation(s)
- Leo J Dudley
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
| | - Agata N Makar
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
| | - Noor Gammoh
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
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58
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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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59
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López-Pérez Ó, Badiola JJ, Bolea R, Ferrer I, Llorens F, Martín-Burriel I. An Update on Autophagy in Prion Diseases. Front Bioeng Biotechnol 2020; 8:975. [PMID: 32984276 PMCID: PMC7481332 DOI: 10.3389/fbioe.2020.00975] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/27/2020] [Indexed: 12/18/2022] Open
Abstract
Autophagy is a dynamic intracellular mechanism involved in protein and organelle turnover through lysosomal degradation. When properly regulated, autophagy supports normal cellular and developmental processes, whereas defects in autophagic degradation have been associated with several pathologies, including prion diseases. Prion diseases, or transmissible spongiform encephalopathies (TSE), are a group of fatal neurodegenerative disorders characterized by the accumulation of the pathological misfolded isoform (PrPSc) of the physiological cellular prion protein (PrPc) in the central nervous system. Autophagic vacuoles have been described in experimental models of TSE and in the natural disease in humans. The precise connection of this process with prion-related neuropathology, or even whether autophagy is completely beneficial or pathogenic during neurodegeneration, is poorly understood. Thus, the biological role of autophagy in these diseases is still open to debate. During the last years, researchers have used a wide range of morphological, genetic and biochemical methods to monitor and manipulate the autophagic pathway and thus determine the specific role of this process in TSE. It has been suggested that PrPc could play a crucial role in modulating the autophagic pathway in neuronal cells, and the presence of abnormal autophagic activity has been frequently observed in several models of TSE both in vitro and in vivo, as well as in human prion diseases. Altogether, these findings suggest that autophagy is implicated in prion neuropathology and points to an impairment or failure of the process, potentially contributing to the pathogenesis of the disease. Additionally, autophagy is now emerging as a host defense response in controlling prion infection that plays a protective role by facilitating the clearance of aggregation-prone proteins accumulated within neurons. Since autophagy is one of the pathways of PrPSc degradation, and drug-induced stimulation of autophagic flux (the dynamic process of autophagic degradation activity) produces anti-prion effects, new treatments based on its activation have been tested to develop therapeutic strategies for prion diseases. In this review, we summarize previous and recent findings concerning the role of autophagy in TSE.
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Affiliation(s)
- Óscar López-Pérez
- Laboratorio de Genética Bioquímica (LAGENBIO), Instituto Agroalimentario de Aragón-IA2, Instituto de Investigación Sanitaria Aragón-IISA, Universidad de Zaragoza, Zaragoza, Spain.,Centro de Encefalopatías y Enfermedades Transmisibles Emergentes (CEETE), Instituto Agroalimentario de Aragón-IA2, Instituto de Investigación Sanitaria Aragón-IISA, Universidad de Zaragoza, Zaragoza, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain.,Instituto de Investigación Biomédica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Juan José Badiola
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes (CEETE), Instituto Agroalimentario de Aragón-IA2, Instituto de Investigación Sanitaria Aragón-IISA, Universidad de Zaragoza, Zaragoza, Spain
| | - Rosa Bolea
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes (CEETE), Instituto Agroalimentario de Aragón-IA2, Instituto de Investigación Sanitaria Aragón-IISA, Universidad de Zaragoza, Zaragoza, Spain
| | - Isidro Ferrer
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain.,Instituto de Investigación Biomédica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.,Departamento de Patología y Terapéutica Experimental, Universidad de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Franc Llorens
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain.,Instituto de Investigación Biomédica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.,Department of Neurology, Clinical Dementia Center and National Reference Center for CJD Surveillance, University Medical School, Göttingen, Germany
| | - Inmaculada Martín-Burriel
- Laboratorio de Genética Bioquímica (LAGENBIO), Instituto Agroalimentario de Aragón-IA2, Instituto de Investigación Sanitaria Aragón-IISA, Universidad de Zaragoza, Zaragoza, Spain.,Centro de Encefalopatías y Enfermedades Transmisibles Emergentes (CEETE), Instituto Agroalimentario de Aragón-IA2, Instituto de Investigación Sanitaria Aragón-IISA, Universidad de Zaragoza, Zaragoza, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto Carlos III, Zaragoza, Spain
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60
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Ohashi Y, Tremel S, Masson GR, McGinney L, Boulanger J, Rostislavleva K, Johnson CM, Niewczas I, Clark J, Williams RL. Membrane characteristics tune activities of endosomal and autophagic human VPS34 complexes. eLife 2020; 9:58281. [PMID: 32602837 PMCID: PMC7326497 DOI: 10.7554/elife.58281] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 06/04/2020] [Indexed: 12/14/2022] Open
Abstract
The lipid kinase VPS34 orchestrates diverse processes, including autophagy, endocytic sorting, phagocytosis, anabolic responses and cell division. VPS34 forms various complexes that help adapt it to specific pathways, with complexes I and II being the most prominent ones. We found that physicochemical properties of membranes strongly modulate VPS34 activity. Greater unsaturation of both substrate and non-substrate lipids, negative charge and curvature activate VPS34 complexes, adapting them to their cellular compartments. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) of complexes I and II on membranes elucidated structural determinants that enable them to bind membranes. Among these are the Barkor/ATG14L autophagosome targeting sequence (BATS), which makes autophagy-specific complex I more active than the endocytic complex II, and the Beclin1 BARA domain. Interestingly, even though Beclin1 BARA is common to both complexes, its membrane-interacting loops are critical for complex II, but have only a minor role for complex I.
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Affiliation(s)
- Yohei Ohashi
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Shirley Tremel
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Glenn Robert Masson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Lauren McGinney
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Jerome Boulanger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Ksenia Rostislavleva
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Christopher M Johnson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | | | | | - Roger L Williams
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
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61
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Damiano V, Spessotto P, Vanin G, Perin T, Maestro R, Santarosa M. The Autophagy Machinery Contributes to E-cadherin Turnover in Breast Cancer. Front Cell Dev Biol 2020; 8:545. [PMID: 32714931 PMCID: PMC7344152 DOI: 10.3389/fcell.2020.00545] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/09/2020] [Indexed: 12/19/2022] Open
Abstract
Autophagy is an intracellular catabolic process that is increasingly being recognized as a crucial factor in several human diseases including cancers. Mounting evidence suggests that autophagy allows tumor cells to overcome otherwise fatal stresses and to increase dissemination. Nevertheless, how autophagy controls these processes and in particular how it impinges on cell-cell adhesion is still poorly understood. Here, we investigate the role of autophagy in the turnover of the epithelial adhesion molecule E-cadherin in the context of breast cancer. We demonstrated in breast cancer cell lines that autophagy impinges on E-cadherin expression and in the configuration of adherens junctions. Besides, we showed that E-cadherin colocalizes with LC3B and SQSTM1/p62, two components of the autophagosome machinery. Pull down and immunoprecipitation analyses provided evidence that E-cadherin and SQSTM1/p62 physically interact. Moreover, the physical closeness of E-cadherin and SQSTM1/p62 was demonstrated by proximity ligation assays in breast cancer cell lines and primary tumors. Finally, we proved that the silencing of SQSTM1/p62 diminished the E-cadherin/LC3B colocalization, further supporting the role of SQSTM1/p62 in E-cadherin delivery to autophagosomes. These findings suggest that the activation of autophagy, reported in breast cancers with poor prognosis and in dormant breast cancer cells, may contribute to the control of tumor progression via downmodulation of E-cadherin protein levels.
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Affiliation(s)
- Valentina Damiano
- Unit of Oncogenetics and Functional Oncogenomics, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Paola Spessotto
- Unit of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Giulia Vanin
- Unit of Oncogenetics and Functional Oncogenomics, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Tiziana Perin
- Pathology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Roberta Maestro
- Unit of Oncogenetics and Functional Oncogenomics, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Manuela Santarosa
- Unit of Oncogenetics and Functional Oncogenomics, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
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62
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Sora V, Kumar M, Maiani E, Lambrughi M, Tiberti M, Papaleo E. Structure and Dynamics in the ATG8 Family From Experimental to Computational Techniques. Front Cell Dev Biol 2020; 8:420. [PMID: 32587856 PMCID: PMC7297954 DOI: 10.3389/fcell.2020.00420] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/06/2020] [Indexed: 12/31/2022] Open
Abstract
Autophagy is a conserved and essential intracellular mechanism for the removal of damaged components. Since autophagy deregulation is linked to different kinds of pathologies, it is fundamental to gain knowledge on the fine molecular and structural details related to the core proteins of the autophagy machinery. Among these, the family of human ATG8 proteins plays a central role in recruiting other proteins to the different membrane structures involved in the autophagic pathway. Several experimental structures are available for the members of the ATG8 family alone or in complex with their different biological partners, including disordered regions of proteins containing a short linear motif called LC3 interacting motif. Recently, the first structural details of the interaction of ATG8 proteins with biological membranes came into light. The availability of structural data for human ATG8 proteins has been paving the way for studies on their structure-function-dynamic relationship using biomolecular simulations. Experimental and computational structural biology can help to address several outstanding questions on the mechanism of human ATG8 proteins, including their specificity toward different interactors, their association with membranes, the heterogeneity of their conformational ensemble, and their regulation by post-translational modifications. We here summarize the main results collected so far and discuss the future perspectives within the field and the knowledge gaps. Our review can serve as a roadmap for future structural and dynamics studies of the ATG8 family members in health and disease.
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Affiliation(s)
- Valentina Sora
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Mukesh Kumar
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Emiliano Maiani
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Matteo Lambrughi
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Matteo Tiberti
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Elena Papaleo
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
- Translational Disease System Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
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63
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Emerging roles of ATG proteins and membrane lipids in autophagosome formation. Cell Discov 2020; 6:32. [PMID: 32509328 PMCID: PMC7248066 DOI: 10.1038/s41421-020-0161-3] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/21/2020] [Indexed: 12/12/2022] Open
Abstract
Autophagosome biogenesis is a dynamic membrane event, which is executed by the sequential function of autophagy-related (ATG) proteins. Upon autophagy induction, a cup-shaped membrane structure appears in the cytoplasm, then elongates sequestering cytoplasmic materials, and finally forms a closed double membrane autophagosome. However, how this complex vesicle formation event is strictly controlled and achieved is still enigmatic. Recently, there is accumulating evidence showing that some ATG proteins have the ability to directly interact with membranes, transfer lipids between membranes and regulate lipid metabolism. A novel role for various membrane lipids in autophagosome formation is also emerging. Here, we highlight past and recent key findings on the function of ATG proteins related to autophagosome biogenesis and consider how ATG proteins control this dynamic membrane formation event to organize the autophagosome by collaborating with membrane lipids.
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64
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Birgisdottir ÅB, Johansen T. Autophagy and endocytosis – interconnections and interdependencies. J Cell Sci 2020; 133:133/10/jcs228114. [DOI: 10.1242/jcs.228114] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
ABSTRACT
Autophagy and endocytosis are membrane-vesicle-based cellular pathways for degradation and recycling of intracellular and extracellular components, respectively. These pathways have a common endpoint at the lysosome, where their cargo is degraded. In addition, the two pathways intersect at different stages during vesicle formation, fusion and trafficking, and share parts of the molecular machinery. Accumulating evidence shows that autophagy is dependent upon endocytosis and vice versa. The emerging joint network of autophagy and endocytosis is of vital importance for cellular metabolism and signaling, and thus also highly relevant in disease settings. In this Review, we will discuss examples of how the autophagy machinery impacts on endocytosis and cell signaling, and highlight how endocytosis regulates the different steps in autophagy in mammalian cells. Finally, we will focus on the interplay of these pathways in the quality control of their common endpoint, the lysosome.
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Affiliation(s)
- Åsa B. Birgisdottir
- The Heart and Lung Clinic, University Hospital of North Norway, 9037 Tromsø, Norway
- Clinical Cardiovascular Research Group, Department of Clinical Medicine, University of Tromsø –The Arctic University of Norway, 9037 Tromsø, Norway
| | - Terje Johansen
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø–The Arctic University of Norway, 9037 Tromsø, Norway
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65
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Martens S, Fracchiolla D. Activation and targeting of ATG8 protein lipidation. Cell Discov 2020; 6:23. [PMID: 32377373 PMCID: PMC7198486 DOI: 10.1038/s41421-020-0155-1] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/03/2020] [Indexed: 12/19/2022] Open
Abstract
ATG8 family proteins are evolutionary conserved ubiquitin-like modifiers, which become attached to the headgroup of the membrane lipid phosphatidylethanolamine in a process referred to as lipidation. This reaction is carried out analogous to the conjugation of ubiquitin to its target proteins, involving the E1-like ATG7, the E2-like ATG3 and the E3-like ATG12-ATG5-ATG16 complex, which determines the site of lipidation. ATG8 lipidation is a hallmark of autophagy where these proteins are involved in autophagosome formation, the fusion of autophagosomes with lysosomes and cargo selection. However, it has become evident that ATG8 lipidation also occurs in processes that are not directly related to autophagy. Here we discuss recent insights into the targeting of ATG8 lipidation in autophagy and other pathways with special emphasis on the recruitment and activation of the E3-like complex.
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Affiliation(s)
- Sascha Martens
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/5, 1030 Vienna, Austria
| | - Dorotea Fracchiolla
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/5, 1030 Vienna, Austria
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66
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Bozic M, van den Bekerom L, Milne BA, Goodman N, Roberston L, Prescott AR, Macartney TJ, Dawe N, McEwan DG. A conserved ATG2-GABARAP family interaction is critical for phagophore formation. EMBO Rep 2020; 21:e48412. [PMID: 32009292 PMCID: PMC7054675 DOI: 10.15252/embr.201948412] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 12/16/2019] [Accepted: 12/23/2019] [Indexed: 01/08/2023] Open
Abstract
The intracellular trafficking pathway, macroautophagy, is a recycling and disposal service that can be upregulated during periods of stress to maintain cellular homeostasis. An essential phase is the elongation and closure of the phagophore to seal and isolate unwanted cargo prior to lysosomal degradation. Human ATG2A and ATG2B proteins, through their interaction with WIPI proteins, are thought to be key players during phagophore elongation and closure, but little mechanistic detail is known about their function. We have identified a highly conserved motif driving the interaction between human ATG2 and GABARAP proteins that is in close proximity to the ATG2‐WIPI4 interaction site. We show that the ATG2A‐GABARAP interaction mutants are unable to form and close phagophores resulting in blocked autophagy, similar to ATG2A/ATG2B double‐knockout cells. In contrast, the ATG2A‐WIPI4 interaction mutant fully restored phagophore formation and autophagy flux, similar to wild‐type ATG2A. Taken together, we provide new mechanistic insights into the requirements for ATG2 function at the phagophore and suggest that an ATG2‐GABARAP/GABARAP‐L1 interaction is essential for phagophore formation, whereas ATG2‐WIPI4 interaction is dispensable.
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Affiliation(s)
- Mihaela Bozic
- Division of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, Dundee, UK.,Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Luuk van den Bekerom
- Division of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, Dundee, UK.,MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Beth A Milne
- Division of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Nicola Goodman
- Division of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, Dundee, UK.,MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Lisa Roberston
- Division of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Alan R Prescott
- Dundee Imaging Facility, School of Life Sciences, University of Dundee, Dundee, UK
| | - Thomas J Macartney
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Nina Dawe
- Division of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - David G McEwan
- Division of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, Dundee, UK.,Cancer Research UK Beatson Institute, Glasgow, UK
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67
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Yu ZQ, Sun LL, Jiang ZD, Liu XM, Zhao D, Wang HT, He WZ, Dong MQ, Du LL. Atg38-Atg8 interaction in fission yeast establishes a positive feedback loop to promote autophagy. Autophagy 2020; 16:2036-2051. [PMID: 31941401 PMCID: PMC7595586 DOI: 10.1080/15548627.2020.1713644] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Macroautophagy (autophagy) is driven by the coordinated actions of core autophagy-related (Atg) proteins. Atg8, the core Atg protein generally considered acting most downstream, has recently been shown to interact with other core Atg proteins via their Atg8-family-interacting motifs (AIMs). However, the extent, functional consequence, and evolutionary conservation of such interactions remain inadequately understood. Here, we show that, in the fission yeast Schizosaccharomyces pombe, Atg38, a subunit of the phosphatidylinositol 3-kinase (PtdIns3K) complex I, interacts with Atg8 via an AIM, which is highly conserved in Atg38 proteins of fission yeast species, but not conserved in Atg38 proteins of other species. This interaction recruits Atg38 to Atg8 on the phagophore assembly site (PAS) and consequently enhances PAS accumulation of the PtdIns3K complex I and Atg proteins acting downstream of the PtdIns3K complex I, including Atg8. The disruption of the Atg38-Atg8 interaction leads to the reduction of autophagosome size and autophagic flux. Remarkably, the loss of this interaction can be compensated by an artificial Atg14-Atg8 interaction. Our findings demonstrate that the Atg38-Atg8 interaction in fission yeast establishes a positive feedback loop between Atg8 and the PtdIns3K complex I to promote efficient autophagosome formation, underscore the prevalence and diversity of AIM-mediated connections within the autophagic machinery, and reveal unforeseen flexibility of such connections. Abbreviations: AIM: Atg8-family-interacting motif; AP-MS: affinity purification coupled with mass spectrometry; Atg: autophagy-related; FLIP: fluorescence loss in photobleaching; PAS: phagophore assembly site; PB: piggyBac; PE: phosphatidylethanolamine; PtdIns3K: phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol 3-phosphate.
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Affiliation(s)
- Zhong-Qiu Yu
- National Institute of Biological Sciences , Beijing, China.,PTN Graduate Program, School of Life Sciences, Peking University , Beijing, China
| | - Ling-Ling Sun
- National Institute of Biological Sciences , Beijing, China
| | - Zhao-Di Jiang
- National Institute of Biological Sciences , Beijing, China
| | - Xiao-Man Liu
- National Institute of Biological Sciences , Beijing, China
| | - Dan Zhao
- National Institute of Biological Sciences , Beijing, China
| | - Hai-Tao Wang
- National Institute of Biological Sciences , Beijing, China
| | - Wan-Zhong He
- National Institute of Biological Sciences , Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences , Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University , Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences , Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University , Beijing, China
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68
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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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69
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Gu Y, Princely Abudu Y, Kumar S, Bissa B, Choi SW, Jia J, Lazarou M, Eskelinen E, Johansen T, Deretic V. Mammalian Atg8 proteins regulate lysosome and autolysosome biogenesis through
SNARE
s. EMBO J 2019; 38. [DOI: https:/doi.org/10.15252/embj.2019101994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 09/13/2019] [Indexed: 12/19/2023] Open
Affiliation(s)
- Yuexi Gu
- Autophagy, Inflammation and Metabolism (AIM) Center of Biomedical Research Excellence University of New Mexico Health Sciences Center Albuquerque NM USA
- Department of Molecular Genetics and Microbiology University of New Mexico Health Sciences Center Albuquerque NM USA
| | - Yakubu Princely Abudu
- Molecular Cancer Research Group Institute of Medical Biology University of Tromsø‐The Arctic University of Norway Tromsø Norway
| | - Suresh Kumar
- Autophagy, Inflammation and Metabolism (AIM) Center of Biomedical Research Excellence University of New Mexico Health Sciences Center Albuquerque NM USA
- Department of Molecular Genetics and Microbiology University of New Mexico Health Sciences Center Albuquerque NM USA
| | - Bhawana Bissa
- Autophagy, Inflammation and Metabolism (AIM) Center of Biomedical Research Excellence University of New Mexico Health Sciences Center Albuquerque NM USA
- Department of Molecular Genetics and Microbiology University of New Mexico Health Sciences Center Albuquerque NM USA
| | - Seong Won Choi
- Department of Molecular Genetics and Microbiology University of New Mexico Health Sciences Center Albuquerque NM USA
| | - Jingyue Jia
- Autophagy, Inflammation and Metabolism (AIM) Center of Biomedical Research Excellence University of New Mexico Health Sciences Center Albuquerque NM USA
- Department of Molecular Genetics and Microbiology University of New Mexico Health Sciences Center Albuquerque NM USA
| | - Michael Lazarou
- Department of Biochemistry and Molecular Biology Biomedicine Discovery Institute Monash University Melbourne Australia
| | | | - Terje Johansen
- Molecular Cancer Research Group Institute of Medical Biology University of Tromsø‐The Arctic University of Norway Tromsø Norway
| | - Vojo Deretic
- Autophagy, Inflammation and Metabolism (AIM) Center of Biomedical Research Excellence University of New Mexico Health Sciences Center Albuquerque NM USA
- Department of Molecular Genetics and Microbiology University of New Mexico Health Sciences Center Albuquerque NM USA
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70
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Colhado Rodrigues BL, Lallo MA, Perez EC. The Controversial Role of Autophagy in Tumor Development: A Systematic Review. Immunol Invest 2019; 49:386-396. [PMID: 31726897 DOI: 10.1080/08820139.2019.1682600] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Autophagy is a natural regulatory mechanism of the cell that eliminates unnecessary and dysfunctional cellular components to maintain homeostasis. Several authors have demonstrated that this mechanism can be induced by pathological conditions as cancer. However, their role in tumor development is still a controversial issue in cancer research. Here, we discussed the most relevant findings concerning autophagy in tumor development. In this critical review performed with studies published between 2002 and 2018, we found that the main pathway involved in the autophagy process is the PI3K/AKT/mTOR intracellular signaling pathway. Regarding their role in cancer development, breast cancer is the main study target, followed by lung, prostate and colon cancer. In these issues, 46% of the works consulted suggesting that autophagy inhibits tumor progression by favor a better antitumor response, 4% suggest that favors growth and tumor progression and, 50% of the authors failed to establish whether autophagy inhibits or favors tumor development. Herein, we concluded that depending on the study model, autophagy may favor or inhibits growth and cancer progression.
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Affiliation(s)
- Bridilla Luiza Colhado Rodrigues
- Programa de Pós-Graduação em Patologia Ambiental e Experimental, Universidade Paulista, São Paulo, Brazil.,Laboratório de Imunogenética, Instituto Butantan, São Paulo, Brazil
| | - Maria Anete Lallo
- Programa de Pós-Graduação em Patologia Ambiental e Experimental, Universidade Paulista, São Paulo, Brazil
| | - Elizabeth Cristina Perez
- Programa de Pós-Graduação em Patologia Ambiental e Experimental, Universidade Paulista, São Paulo, Brazil
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71
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Gu Y, Princely Abudu Y, Kumar S, Bissa B, Choi SW, Jia J, Lazarou M, Eskelinen EL, Johansen T, Deretic V. Mammalian Atg8 proteins regulate lysosome and autolysosome biogenesis through SNAREs. EMBO J 2019; 38:e101994. [PMID: 31625181 DOI: 10.15252/embj.2019101994] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 09/07/2019] [Accepted: 09/13/2019] [Indexed: 12/14/2022] Open
Abstract
Mammalian homologs of yeast Atg8 protein (mAtg8s) are important in autophagy, but their exact mode of action remains ill-defined. Syntaxin 17 (Stx17), a SNARE with major roles in autophagy, was recently shown to bind mAtg8s. Here, we identified LC3-interacting regions (LIRs) in several SNAREs that broaden the landscape of the mAtg8-SNARE interactions. We found that Syntaxin 16 (Stx16) and its cognate SNARE partners all have LIR motifs and bind mAtg8s. Knockout of Stx16 caused defects in lysosome biogenesis, whereas a Stx16 and Stx17 double knockout completely blocked autophagic flux and decreased mitophagy, pexophagy, xenophagy, and ribophagy. Mechanistic analyses revealed that mAtg8s and Stx16 control several properties of lysosomal compartments including their function as platforms for active mTOR. These findings reveal a broad direct interaction of mAtg8s with SNAREs with impact on membrane remodeling in eukaryotic cells and expand the roles of mAtg8s to lysosome biogenesis.
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Affiliation(s)
- Yuexi Gu
- Autophagy, Inflammation and Metabolism (AIM) Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.,Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Yakubu Princely Abudu
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Suresh Kumar
- Autophagy, Inflammation and Metabolism (AIM) Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.,Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Bhawana Bissa
- Autophagy, Inflammation and Metabolism (AIM) Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.,Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Seong Won Choi
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Jingyue Jia
- Autophagy, Inflammation and Metabolism (AIM) Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.,Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Michael Lazarou
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | | | - Terje Johansen
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Vojo Deretic
- Autophagy, Inflammation and Metabolism (AIM) Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.,Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
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72
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Kirkin V, Rogov VV. A Diversity of Selective Autophagy Receptors Determines the Specificity of the Autophagy Pathway. Mol Cell 2019; 76:268-285. [PMID: 31585693 DOI: 10.1016/j.molcel.2019.09.005] [Citation(s) in RCA: 296] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/03/2019] [Accepted: 09/06/2019] [Indexed: 12/21/2022]
Abstract
The clearance of surplus, broken, or dangerous components is key for maintaining cellular homeostasis. The failure to remove protein aggregates, damaged organelles, or intracellular pathogens leads to diseases, including neurodegeneration, cancer, and infectious diseases. Autophagy is the evolutionarily conserved pathway that sequesters cytoplasmic components in specialized vesicles, autophagosomes, which transport the cargo to the degradative compartments (vacuoles or lysosomes). Research during the past few decades has elucidated how autophagosomes engulf their substrates selectively. This type of autophagy involves a growing number of selective autophagy receptors (SARs) (e.g., Atg19 in yeasts, p62/SQSTM1 in mammals), which bind to the cargo and simultaneously engage components of the core autophagic machinery via direct interaction with the ubiquitin-like proteins (UBLs) of the Atg8/LC3/GABARAP family and adaptors, Atg11 (in yeasts) or FIP200 (in mammals). In this Review, we critically discuss the biology of the SARs with special emphasis on their interactions with UBLs.
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Affiliation(s)
- 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, Max-von-Laue Strasse 9, 60438 Frankfurt am Main, Germany.
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73
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de la Ballina LR, Munson MJ, Simonsen A. Lipids and Lipid-Binding Proteins in Selective Autophagy. J Mol Biol 2019; 432:135-159. [PMID: 31202884 DOI: 10.1016/j.jmb.2019.05.051] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 02/07/2023]
Abstract
Eukaryotic cells have the capacity to degrade intracellular components through a lysosomal degradation pathway called macroautophagy (henceforth referred to as autophagy) in which superfluous or damaged cytosolic entities are engulfed and separated from the rest of the cell constituents into double membraned vesicles known as autophagosomes. Autophagosomes then fuse with endosomes and lysosomes, where cargo is broken down into basic building blocks that are released to the cytoplasm for the cell to reuse. Autophagic degradation can target either cytoplasmic material in bulk (non-selective autophagy) or particular cargo in what is called selective autophagy. Proper autophagic turnover requires the orchestrated participation of several players that need to be tightly and temporally coordinated. Whereas a large number of autophagy-related (ATG) proteins have been identified and their functions and regulation are starting to be understood, there is substantially less knowledge regarding the specific lipids constituting the autophagic membranes as well as their role in initiating, enabling or regulating the autophagic process. This review focuses on lipids and their corresponding binding proteins that are crucial in the process of selective autophagy.
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Affiliation(s)
- Laura R de la Ballina
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Michael J Munson
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anne Simonsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
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74
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Wirth M, Zhang W, Razi M, Nyoni L, Joshi D, O'Reilly N, Johansen T, Tooze SA, Mouilleron S. Molecular determinants regulating selective binding of autophagy adapters and receptors to ATG8 proteins. Nat Commun 2019; 10:2055. [PMID: 31053714 PMCID: PMC6499816 DOI: 10.1038/s41467-019-10059-6] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 04/15/2019] [Indexed: 02/07/2023] Open
Abstract
Autophagy is an essential recycling and quality control pathway. Mammalian ATG8 proteins drive autophagosome formation and selective removal of protein aggregates and organelles by recruiting autophagy receptors and adaptors that contain a LC3-interacting region (LIR) motif. LIR motifs can be highly selective for ATG8 subfamily proteins (LC3s/GABARAPs), however the molecular determinants regulating these selective interactions remain elusive. Here we show that residues within the core LIR motif and adjacent C-terminal region as well as ATG8 subfamily-specific residues in the LIR docking site are critical for binding of receptors and adaptors to GABARAPs. Moreover, rendering GABARAP more LC3B-like impairs autophagy receptor degradation. Modulating LIR binding specificity of the centriolar satellite protein PCM1, implicated in autophagy and centrosomal function, alters its dynamics in cells. Our data provides new mechanistic insight into how selective binding of LIR motifs to GABARAPs is achieved, and elucidate the overlapping and distinct functions of ATG8 subfamily proteins.
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Affiliation(s)
- Martina Wirth
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| | - Wenxin Zhang
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Structural Biology Science Technology Platforms, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Minoo Razi
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Lynet Nyoni
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Structural Biology Science Technology Platforms, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Dhira Joshi
- Peptide Chemistry Science Technology Platforms, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Nicola O'Reilly
- Peptide Chemistry Science Technology Platforms, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Terje Johansen
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, 9037, Tromsø, Norway
| | - Sharon A Tooze
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| | - Stéphane Mouilleron
- Structural Biology Science Technology Platforms, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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Que Y, Xue J. Propofol activates autophagic activity of vascular endothelial cells by inhibiting SENP1 expression and attenuates vascular endothelial injury induced by ischemia-reperfusion in orthopedic surgery. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1673208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Yuanyuan Que
- Department of Anesthesiology, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, People's Republic of China
| | - Jinpei Xue
- Department of Anesthesiology, Longgang Orthopedics Hospital of Shenzhen, Shenzhen, Guangdong, People's Republic of China
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