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Lorentzen KC, Prescott AR, Ganley IG. Artificial targeting of autophagy components to mitochondria reveals both conventional and unconventional mitophagy pathways. Autophagy 2024:1-23. [PMID: 39177530 DOI: 10.1080/15548627.2024.2395149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 08/16/2024] [Accepted: 08/18/2024] [Indexed: 08/24/2024] Open
Abstract
Macroautophagy/autophagy enables lysosomal degradation of a diverse array of intracellular material. This process is essential for normal cellular function and its dysregulation is implicated in many diseases. Given this, there is much interest in understanding autophagic mechanisms of action in order to determine how it can be best targeted therapeutically. In mitophagy, the selective degradation of mitochondria via autophagy, mitochondria first need to be primed with signals that allow the recruitment of the core autophagy machinery to drive the local formation of an autophagosome around the target mitochondrion. To determine how the recruitment of different core autophagy components can drive mitophagy, we took advantage of the mito-QC mitophagy assay (an outer mitochondrial membrane-localized tandem mCherry-GFP tag). By tagging autophagy proteins with an anti-mCherry (or anti-GFP) nanobody, we could recruit them to mitochondria and simultaneously monitor levels of mitophagy. We found that targeting ULK1, ATG16L1 and the different Atg8-family proteins was sufficient to induce mitophagy. Mitochondrial recruitment of ULK1 and the Atg8-family proteins induced a conventional mitophagy pathway, requiring RB1CC1/FIP200, PIK3C3/VPS34 activity and ATG5. Surprisingly, the mitophagy pathway upon recruitment of ATG16L1 proceeded independently of ATG5, although it still required RB1CC1 and PIK3C3/VPS34 activity. In this latter pathway, mitochondria were alternatively delivered to lysosomes via uptake into early endosomes.Abbreviation: aGFP: anti-GFP nanobody; amCh: anti-mCherry nanobody; ATG: autophagy related; ATG16L1: autophagy related 16 like 1; AUTAC/AUTOTAC: autophagy-targeting chimera; BafA1: bafilomycin A1; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; CCCP: carbonyl cyanide m-chlorophenylhydrazone; COX4/COX IV: cytochrome c oxidase subunit 4; DFP: deferiprone; DMSO: dimethyl sulfoxide; GABARAP: GABA type A receptor-associated protein; GABARAPL1: GABA type A receptor associated protein like 1; HSPD1/HSP60: heat shock protein family D (Hsp60) member 1; HRP: horseradish peroxidase; HTRA2/OMI: HtrA serine peptidase 2; IB: immunoblotting; IF: immunofluorescence; KO: knockout; LAMP1: lysosomal associated membrane protein 1; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MEF: mouse embryonic fibroblast; NBR1: NBR1 autophagy cargo receptor; OMM: outer mitochondrial membrane; OPA1: OPA1 mitochondrial dynamin like GTPase; OPTN: optineurin; (D)PBS: (Dulbecco's) phosphate-buffered saline; PD: Parkinson disease; PFA: paraformaldehyde; POI: protein of interest; PtdIns3K: class III phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate; RAB: RAB, member RAS oncogene family; RB1CC1/FIP200: RB1 inducible coiled-coil 1; SQSTM1: sequestosome 1; TAX1BP1: Tax1 binding protein 1; ULK: unc-51 like autophagy activating kinase 1; VPS: vacuolar protein sorting; WIPI: WD repeat domain, phosphoinositide interacting.
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Affiliation(s)
- Katharina C Lorentzen
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Alan R Prescott
- Dundee Imaging Facility, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ian G Ganley
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
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2
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Mohan J, Moparthi SB, Girard-Blanc C, Campisi D, Blanchard S, Nugues C, Rama S, Salles A, Pénard E, Vassilopoulos S, Wollert T. ATG16L1 induces the formation of phagophore-like membrane cups. Nat Struct Mol Biol 2024; 31:1448-1459. [PMID: 38834913 DOI: 10.1038/s41594-024-01300-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 03/28/2024] [Indexed: 06/06/2024]
Abstract
The hallmark of non-selective autophagy is the formation of cup-shaped phagophores that capture bulk cytoplasm. The process is accompanied by the conjugation of LC3B to phagophores by an E3 ligase complex comprising ATG12-ATG5 and ATG16L1. Here we combined two complementary reconstitution approaches to reveal the function of LC3B and its ligase complex during phagophore expansion. We found that LC3B forms together with ATG12-ATG5-ATG16L1 a membrane coat that remodels flat membranes into cups that closely resemble phagophores. Mechanistically, we revealed that cup formation strictly depends on a close collaboration between LC3B and ATG16L1. Moreover, only LC3B, but no other member of the ATG8 protein family, promotes cup formation. ATG16L1 truncates that lacked the C-terminal membrane binding domain catalyzed LC3B lipidation but failed to assemble coats, did not promote cup formation and inhibited the biogenesis of non-selective autophagosomes. Our results thus demonstrate that ATG16L1 and LC3B induce and stabilize the characteristic cup-like shape of phagophores.
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Affiliation(s)
- Jagan Mohan
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, Paris, France
| | - Satish B Moparthi
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, Paris, France
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Association Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| | - Christine Girard-Blanc
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, Paris, France
| | - Daniele Campisi
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, Paris, France
| | - Stéphane Blanchard
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, Paris, France
| | - Charlotte Nugues
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, Paris, France
| | - Sowmya Rama
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, Paris, France
| | - Audrey Salles
- Unit of Technology and Service Photonic BioImaging (UTechS PBI), C2RT, Institut Pasteur, Université de Paris, Paris, France
| | - Esthel Pénard
- Ultrastructural BioImaging Core Facility (UBI), C2RT, Institut Pasteur, Université Paris Cité, Paris, France
| | - Stéphane Vassilopoulos
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Association Institut de Myologie, Centre de Recherche en Myologie, Paris, France.
| | - Thomas Wollert
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, Paris, France.
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3
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Lee YM, Vucic D. The role of autophagy in RIP1 mediated cell death and intestinal inflammation. Adv Immunol 2024; 163:1-20. [PMID: 39271257 DOI: 10.1016/bs.ai.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2024]
Abstract
Autophagy, a highly conserved catabolic process that targets various types of cellular cargoes to lysosomal degradation, is one of the most important biological mechanisms critical for cellular homeostasis. Components of these cellular cargoes can range from individual proteins to invading pathogens, and degrading these materials is important for maintaining organismal health and survival. The process of autophagy is carried out by complex molecular mechanisms, and a growing body of evidence indicates that these mechanisms intersect with those involved in the cell death pathways. In this review, we examine several emerging studies elucidating the role of autophagy in RIP1-mediated cell death signaling, with particular emphasis on impaired autophagy caused by ATG16L1 deficiency. We also discuss how autophagy in RIP1-mediated cell death affects intestinal homeostasis in preclinical models, and the implications of the intersection between RIP1 and autophagy for understanding the intestinal pathologies associated with inflammatory bowel disease (IBD). Finally, we highlight the potential benefits of therapeutic targeting of RIP1 and autophagy proteins, while also proposing areas of research that will likely elucidate new links between autophagy and cell death signaling.
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Affiliation(s)
| | - Domagoj Vucic
- Immunology Discovery, Genentech, South San Francisco, CA, United States.
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4
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Chvanov M, Voronina S, Jefferson M, Mayer U, Sutton R, Criddle DN, Wileman T, Tepikin AV. Deletion of the WD40 domain of ATG16L1 exacerbates acute pancreatitis, abolishes LAP-like non-canonical autophagy and slows trypsin degradation. Autophagy 2024:1-13. [PMID: 39216469 DOI: 10.1080/15548627.2024.2392478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 08/07/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024] Open
Abstract
The WD40 domain (WDD) of ATG16L1 plays a pivotal role in non-canonical autophagy. This study examined the role of recently identified LAP-like non-canonical autophagy (LNCA) in acute pancreatitis. LNCA involves rapid single-membrane LC3 conjugation to endocytic vacuoles in pancreatic acinar cells. The rationale for this study was the previously observed presence of trypsin in the organelles undergoing LNCA; aberrant trypsin formation is an important factor in pancreatitis development. Here we report that the deletion of WDD (attained in ATG16L1[E230] mice) eliminated LNCA, aggravated caerulein-induced acute pancreatitis and suppressed the fast trypsin degradation observed in both a rapid caerulein-induced disease model and in caerulein-treated isolated pancreatic acinar cells. These experiments indicate that LNCA is a WDD-dependent mechanism and suggest that it plays not an activating but a protective role in acute pancreatitis. Furthermore, palmitoleic acid, another inducer of experimental acute pancreatitis, strongly inhibited LNCA, suggesting a novel mechanism of pancreatic lipotoxicity.Abbreviation: AMY: amylase; AP: acute pancreatitis; CASM: conjugation of Atg8 to single membranes; CCK: cholecystokinin; FAEE model: fatty acid and ethanol model; IL6: interleukin 6; LA: linoleic acid; LAP: LC3-associated phagocytosis; LMPO: lung myeloperoxidase; LNCA: LAP-like non-canonical autophagy; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MPO: myeloperoxidase; PMPO: pancreatic myeloperoxidase; POA: palmitoleic acid; WDD: WD40 domain; WT: wild type.
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Affiliation(s)
- Michael Chvanov
- Department of Molecular & Clinical Cancer Medicine, Institute of Systems Molecular & Integrative Biology, University of Liverpool, Liverpool, UK
| | - Svetlana Voronina
- Department of Molecular & Clinical Cancer Medicine, Institute of Systems Molecular & Integrative Biology, University of Liverpool, Liverpool, UK
| | - Matthew Jefferson
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Ulrike Mayer
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Robert Sutton
- Department of Molecular & Clinical Cancer Medicine, Institute of Systems Molecular & Integrative Biology, University of Liverpool, Liverpool, UK
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - David N Criddle
- Department of Molecular & Clinical Cancer Medicine, Institute of Systems Molecular & Integrative Biology, University of Liverpool, Liverpool, UK
| | - Thomas Wileman
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Alexei V Tepikin
- Department of Molecular & Clinical Cancer Medicine, Institute of Systems Molecular & Integrative Biology, University of Liverpool, Liverpool, UK
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5
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Wu X, Yang Y, Ru Y, Hao R, Zhao D, Ren R, Lu B, Li Y, Sun S, Zheng H, Wang W. Knockout of the WD40 domain of ATG16L1 enhances foot and mouth disease virus replication. BMC Genomics 2024; 25:796. [PMID: 39179961 PMCID: PMC11342673 DOI: 10.1186/s12864-024-10703-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 08/12/2024] [Indexed: 08/26/2024] Open
Abstract
The WD40 domain is one of the most abundant domains and is among the top interacting domains in eukaryotic genomes. The WD40 domain of ATG16L1 is essential for LC3 recruitment to endolysosomal membranes during non-canonical autophagy, but dispensable for canonical autophagy. Canonical autophagy was utilized by FMDV, while the relationship between FMDV and non-canonical autophagy is still elusive. In the present study, WD40 knockout (KO) PK15 cells were successfully generated via CRISPR/cas9 technology as a tool for studying the effect of non-canonical autophagy on FMDV replication. The results of growth curve analysis, morphological observation and karyotype analysis showed that the WD40 knockout cell line was stable in terms of growth and morphological characteristics. After infection with FMDV, the expression of viral protein, viral titers, and the number of copies of viral RNA in the WD40-KO cells were significantly greater than those in the wild-type PK15 cells. Moreover, RNA‒seq technology was used to sequence WD40-KO cells and wild-type cells infected or uninfected with FMDV. Differentially expressed factors such as Mx1, RSAD2, IFIT1, IRF9, IFITM3, GBP1, CXCL8, CCL5, TNFRSF17 were significantly enriched in the autophagy, NOD-like receptor signaling pathway, RIG-I-like receptor signaling pathway, Toll-like receptor signaling pathway, cytokine-cytokine receptor interaction and TNF signaling pathway, etc. The expression levels of differentially expressed genes were detected via qRT‒PCR, which was consistent with the RNA‒seq data. Here, we experimentally demonstrate for the first time that knockout of the WD40 domain of ATG16L1 enhances FMDV replication by downregulation innate immune factors. In addition, this result also indicates non-canonical autophagy inhibits FMDV replication. In total, our results play an essential role in regulating the replication level of FMDV and providing new insights into virus-host interactions and potential antiviral strategies.
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Affiliation(s)
- Xiuping Wu
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou Veterinary Research Institute, Lanzhou University, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Yang Yang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou Veterinary Research Institute, Lanzhou University, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Yi Ru
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou Veterinary Research Institute, Lanzhou University, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Rongzeng Hao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou Veterinary Research Institute, Lanzhou University, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Dongmei Zhao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou Veterinary Research Institute, Lanzhou University, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Ruifang Ren
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou Veterinary Research Institute, Lanzhou University, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Bingzhou Lu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou Veterinary Research Institute, Lanzhou University, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Yajun Li
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou Veterinary Research Institute, Lanzhou University, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Shengzhen Sun
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou Veterinary Research Institute, Lanzhou University, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Haixue Zheng
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou Veterinary Research Institute, Lanzhou University, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China.
| | - Wenhui Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China.
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6
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Wei F, Wang Y, Yao J, Mei L, Huang X, Kong H, Chen J, Chen X, Liu L, Wang Z, Wang J, Song J, Kong E, Yang A. ZDHHC7-mediated S-palmitoylation of ATG16L1 facilitates LC3 lipidation and autophagosome formation. Autophagy 2024:1-19. [PMID: 39087410 DOI: 10.1080/15548627.2024.2386915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/14/2024] [Accepted: 07/29/2024] [Indexed: 08/02/2024] Open
Abstract
Macroautophagy/autophagy is a fundamental cellular catabolic process that delivers cytoplasmic components into double-membrane vesicles called autophagosomes, which then fuse with lysosomes and their contents are degraded. Autophagy recycles cytoplasmic components, including misfolded proteins, dysfunctional organelles and even microbial invaders, thereby playing an essential role in development, immunity and cell death. Autophagosome formation is the main step in autophagy, which is governed by a set of ATG (autophagy related) proteins. ATG16L1 interacts with ATG12-ATG5 conjugate to form an ATG12-ATG5-ATG16L1 complex. The complex acts as a ubiquitin-like E3 ligase that catalyzes the lipidation of MAP1LC3/LC3 (microtubule associated protein 1 light chain 3), which is crucial for autophagosome formation. In the present study, we found that ATG16L1 was subject to S-palmitoylation on cysteine 153, which was catalyzed by ZDHHC7 (zinc finger DHHC-type palmitoyltransferase 7). We observed that re-expressing ATG16L1 but not the S-palmitoylation-deficient mutant ATG16L1C153S rescued a defect in the lipidation of LC3 and the formation of autophagosomes in ATG16L1-KO (knockout) HeLa cells. Furthermore, increasing ATG16L1 S-palmitoylation by ZDHHC7 expression promoted the production of LC3-II, whereas reducing ATG16L1 S-palmitoylation by ZDHHC7 deletion inhibited the LC3 lipidation process and autophagosome formation. Mechanistically, the addition of a hydrophobic 16-carbon palmitoyl group on Cys153 residue of ATG16L1 enhances the formation of ATG16L1-WIPI2B complex and ATG16L1-RAB33B complex on phagophore, thereby facilitating the LC3 lipidation process and autophagosome formation. In conclusion, S-palmitoylation of ATG16L1 is essential for the lipidation process of LC3 and the formation of autophagosomes. Our research uncovers a new regulatory mechanism of ATG16L1 function in autophagy.Abbreviation: ABE: acyl-biotin exchange; ATG: autophagy related; Baf-A1: bafilomycin A1; 2-BP: 2-bromopalmitate; CCD: coiled-coil domain; co-IP: co-immunoprecipitation; CQ: chloroquine; EBSS: Earle's balanced salt solution; HAM: hydroxylamine; KO: knockout; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; NP-40: Nonidet P-40; PBS: phosphate-buffered saline; PE: phosphatidylethanolamine; PtdIns3K-C1: class III phosphatidylinositol 3-kinase complex I; PTM: post-translational modification; RAB33B: RAB33B, member RAS oncogene family; RB1CC1/FIP200: RB1 inducible coiled-coil 1; SDS: sodium dodecyl sulfate; SQSTM1/p62: sequestosome 1; TEM: transmission electron microscope; WD: tryptophan and aspartic acid; WIPI2B: WD repeat domain, phosphoinositide interacting 2B; WT: wild-type; ZDHHC: zinc finger DHHC-type.
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Affiliation(s)
- Fujing Wei
- School of Life Sciences, Chongqing University, Chongqing, China
- Medical Research Institute, Southwest University, Chongqing, China
| | - Yu Wang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Jia Yao
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Ligang Mei
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xue Huang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Hesheng Kong
- Institute of Psychiatry and Neuroscience, Xinxiang Key Laboratory of Protein Palmitoylation and Major Human Diseases, Henan Health Commission Key Laboratory of Gastrointestinal Cancer Prevention and Treatment, Xinxiang Medical University, Xinxiang, China
| | - Jing Chen
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xiaorong Chen
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Lu Liu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Zhuolin Wang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Jiaxin Wang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Jiong Song
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Eryan Kong
- Institute of Psychiatry and Neuroscience, Xinxiang Key Laboratory of Protein Palmitoylation and Major Human Diseases, Henan Health Commission Key Laboratory of Gastrointestinal Cancer Prevention and Treatment, Xinxiang Medical University, Xinxiang, China
| | - Aimin Yang
- School of Life Sciences, Chongqing University, Chongqing, China
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7
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Timimi L, Wrobel AG, Chiduza GN, Maslen SL, Torres-Méndez A, Montaner B, Davis C, Minckley T, Hole KL, Serio A, Devine MJ, Skehel JM, Rubinstein JL, Schreiber A, Beale R. The V-ATPase/ATG16L1 axis is controlled by the V 1H subunit. Mol Cell 2024; 84:2966-2983.e9. [PMID: 39089251 DOI: 10.1016/j.molcel.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 05/15/2024] [Accepted: 07/05/2024] [Indexed: 08/03/2024]
Abstract
Defects in organellar acidification indicate compromised or infected compartments. Recruitment of the autophagy-related ATG16L1 complex to pathologically neutralized organelles targets ubiquitin-like ATG8 molecules to perturbed membranes. How this process is coupled to proton gradient disruption is unclear. Here, we reveal that the V1H subunit of the vacuolar ATPase (V-ATPase) proton pump binds directly to ATG16L1. The V1H/ATG16L1 interaction only occurs within fully assembled V-ATPases, allowing ATG16L1 recruitment to be coupled to increased V-ATPase assembly following organelle neutralization. Cells lacking V1H fail to target ATG8s during influenza infection or after activation of the immune receptor stimulator of interferon genes (STING). We identify a loop within V1H that mediates ATG16L1 binding. A neuronal V1H isoform lacks this loop and is associated with attenuated ATG8 targeting in response to ionophores in primary murine and human iPSC-derived neurons. Thus, V1H controls ATG16L1 recruitment following proton gradient dissipation, suggesting that the V-ATPase acts as a cell-intrinsic damage sensor.
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Affiliation(s)
- Lewis Timimi
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Division of Medicine, University College London, London WC1E 6JF, UK
| | - Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - George N Chiduza
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Sarah L Maslen
- Proteomics STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Antonio Torres-Méndez
- Neural Circuits & Evolution Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Beatriz Montaner
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Colin Davis
- Cellular Degradation Systems Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Taylor Minckley
- Neural Circuit Bioengineering and Disease Modelling Laboratory, The Francis Crick Institute, London NW1 1AT, UK; UK Dementia Research Institute at King's College London, London SE5 9RX, UK; Department of Basic and Clinical Neuroscience, Institute of Psychiatry Psychology & Neuroscience, King's College London, London SE5 9RX, UK
| | - Katriona L Hole
- Mitochondrial Neurobiology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Andrea Serio
- Neural Circuit Bioengineering and Disease Modelling Laboratory, The Francis Crick Institute, London NW1 1AT, UK; UK Dementia Research Institute at King's College London, London SE5 9RX, UK; Department of Basic and Clinical Neuroscience, Institute of Psychiatry Psychology & Neuroscience, King's College London, London SE5 9RX, UK
| | - Michael J Devine
- Mitochondrial Neurobiology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - J Mark Skehel
- Proteomics STP, The Francis Crick Institute, London NW1 1AT, UK
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Medical Biophysics, The University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Anne Schreiber
- Cellular Degradation Systems Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Division of Medicine, University College London, London WC1E 6JF, UK.
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8
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Üffing A, Weiergräber OH, Schwarten M, Hoffmann S, Willbold D. GABARAP interacts with EGFR - supporting the unique role of this hAtg8 protein during receptor trafficking. FEBS Lett 2024. [PMID: 39160442 DOI: 10.1002/1873-3468.14997] [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: 05/14/2024] [Revised: 07/02/2024] [Accepted: 07/24/2024] [Indexed: 08/21/2024]
Abstract
The human Atg8 family member GABARAP is involved in numerous autophagy-related and -unrelated processes. We recently observed that specifically the deficiency of GABARAP enhances epidermal growth factor receptor (EGFR) degradation upon ligand stimulation. Here, we report on two putative LC3-interacting regions (LIRs) within EGFR, the first of which (LIR1) is selected as a GABARAP binding site in silico. Indeed, in vitro interaction studies reveal preferential binding of LIR1 to GABARAP and GABARAPL1. Our X-ray data demonstrate interaction of core LIR1 residues FLPV with both hydrophobic pockets of GABARAP suggesting canonical binding. Although LIR1 occupies the LIR docking site, GABARAP Y49 and L50 appear dispensable in this case. Our data support the hypothesis that GABARAP affects the fate of EGFR at least in part through direct binding.
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Affiliation(s)
- Alina Üffing
- Heinrich-Heine-Universität Düsseldorf, Mathematisch-Naturwissenschaftliche Fakultät, Institut für Physikalische Biologie, Düsseldorf, Germany
- Forschungszentrum Jülich, Institut für Biologische Informationsprozesse: Strukturbiochemie (IBI-7), Jülich, Germany
| | - Oliver H Weiergräber
- Heinrich-Heine-Universität Düsseldorf, Mathematisch-Naturwissenschaftliche Fakultät, Institut für Physikalische Biologie, Düsseldorf, Germany
- Forschungszentrum Jülich, Institut für Biologische Informationsprozesse: Strukturbiochemie (IBI-7), Jülich, Germany
| | - Melanie Schwarten
- Forschungszentrum Jülich, Institut für Biologische Informationsprozesse: Strukturbiochemie (IBI-7), Jülich, Germany
| | - Silke Hoffmann
- Forschungszentrum Jülich, Institut für Biologische Informationsprozesse: Strukturbiochemie (IBI-7), Jülich, Germany
| | - Dieter Willbold
- Heinrich-Heine-Universität Düsseldorf, Mathematisch-Naturwissenschaftliche Fakultät, Institut für Physikalische Biologie, Düsseldorf, Germany
- Forschungszentrum Jülich, Institut für Biologische Informationsprozesse: Strukturbiochemie (IBI-7), Jülich, Germany
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9
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Deretic V, Duque T, Trosdal E, Paddar M, Javed R, Akepati P. Membrane atg8ylation in Canonical and Noncanonical Autophagy. J Mol Biol 2024; 436:168532. [PMID: 38479594 PMCID: PMC11260254 DOI: 10.1016/j.jmb.2024.168532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 04/13/2024]
Abstract
Membrane atg8ylation is a homeostatic process responding to membrane remodeling and stress signals. Membranes are atg8ylated by mammalian ATG8 ubiquitin-like proteins through a ubiquitylation-like cascade. A model has recently been put forward which posits that atg8ylation of membranes is conceptually equivalent to ubiquitylation of proteins. Like ubiquitylation, membrane atg8ylation involves E1, E2 and E3 enzymes. The E3 ligases catalyze the final step of atg8ylation of aminophospholipids in membranes. Until recently, the only known E3 ligase for membrane atg8ylation was ATG16L1 in a noncovalent complex with the ATG12-ATG5 conjugate. ATG16L1 was first identified as a factor in canonical autophagy. During canonical autophagy, the ATG16L1-based E3 ligase complex includes WIPI2, which in turn recognizes phosphatidylinositiol 3-phosphate and directs atg8ylation of autophagic phagophores. As an alternative to WIPIs, binding of ATG16L1 to the proton pump V-ATPase guides atg8ylation of endolysosomal and phagosomal membranes in response to lumenal pH changes. Recently, a new E3 complex containing TECPR1 instead of ATG16L1, has been identified that responds to sphingomyelin's presence on the cytofacial side of perturbed endolysosomal membranes. In present review, we cover the principles of membrane atg8ylation, catalog its various presentations, and provide a perspective on the growing repertoire of E3 ligase complexes directing membrane atg8ylation at diverse locations.
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Affiliation(s)
- Vojo Deretic
- Autophagy Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA; Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA.
| | - Thabata Duque
- Autophagy Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA; Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Einar Trosdal
- Autophagy Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA; Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Masroor Paddar
- Autophagy Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA; Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Ruheena Javed
- Autophagy Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA; Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Prithvi Akepati
- Gastroenterology Division, Department of Internal Medicine, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
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10
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Figueras-Novoa C, Timimi L, Marcassa E, Ulferts R, Beale R. Conjugation of ATG8s to single membranes at a glance. J Cell Sci 2024; 137:jcs261031. [PMID: 39145464 PMCID: PMC11361636 DOI: 10.1242/jcs.261031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024] Open
Abstract
Autophagy refers to a set of degradative mechanisms whereby cytoplasmic contents are targeted to the lysosome. This is best described for macroautophagy, where a double-membrane compartment (autophagosome) is generated to engulf cytoplasmic contents. Autophagosomes are decorated with ubiquitin-like ATG8 molecules (ATG8s), which are recruited through covalent lipidation, catalysed by the E3-ligase-like ATG16L1 complex. LC3 proteins are ATG8 family members that are often used as a marker for autophagosomes. In contrast to canonical macroautophagy, conjugation of ATG8s to single membranes (CASM) describes a group of non-canonical autophagy processes in which ATG8s are targeted to pre-existing single-membrane compartments. CASM occurs in response to disrupted intracellular pH gradients, when the V-ATPase proton pump recruits ATG16L1 in a process called V-ATPase-ATG16L1-induced LC3 lipidation (VAIL). Recent work has demonstrated a parallel, alternative axis for CASM induction, triggered when the membrane recruitment factor TECPR1 recognises sphingomyelin exposed on the cytosolic face of a membrane and forms an alternative E3-ligase-like complex. This sphingomyelin-TECPR1-induced LC3 lipidation (STIL) is independent of the V-ATPase and ATG16L1. In light of these discoveries, this Cell Science at a Glance article summarises these two mechanisms of CASM to highlight how they differ from canonical macroautophagy, and from each other.
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Affiliation(s)
- Carmen Figueras-Novoa
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Lewis Timimi
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
- Division of Medicine, University College London, London NW1 1AT, UK
| | - Elena Marcassa
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Rachel Ulferts
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK
- Division of Medicine, University College London, London NW1 1AT, UK
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11
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Wang Y, Wu L, Van Kaer L. Role of canonical and noncanonical autophagy pathways in shaping the life journey of B cells. Front Immunol 2024; 15:1426204. [PMID: 39139569 PMCID: PMC11319164 DOI: 10.3389/fimmu.2024.1426204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 07/16/2024] [Indexed: 08/15/2024] Open
Abstract
Autophagy is a regulated intracellular catabolic process by which invading pathogens, damaged organelles, aggregated proteins, and other macromolecules are degraded in lysosomes. It has been widely appreciated that autophagic activity plays an important role in regulating the development, fate determination, and function of cells in the immune system, including B lymphocytes. Autophagy encompasses several distinct pathways that have been linked to B cell homeostasis and function. While B cell presentation of major histocompatibility complex (MHC) class II-restricted cytosolic antigens to T cells involves both macroautophagy and chaperone-mediated autophagy (CMA), plasma cells and memory B cells mainly rely on macroautophagy for their survival. Emerging evidence indicates that core autophagy factors also participate in processes related to yet clearly distinct from classical autophagy. These autophagy-related pathways, referred to as noncanonical autophagy or conjugation of ATG8 to single membranes (CASM), contribute to B cell homeostasis and functions, including MHC class II-restricted antigen presentation to T cells, germinal center formation, plasma cell differentiation, and recall responses. Dysregulation of B cell autophagy has been identified in several autoimmune and autoinflammatory diseases such as systemic lupus erythematosus, rheumatoid arthritis, and inflammatory bowel disease. In this review, we discuss recent advances in understanding the role of canonical and noncanonical autophagy in B cells, including B cell development and maturation, antigen processing and presentation, pathogen-specific antibody responses, cytokine secretion, and autoimmunity. Unraveling the molecular mechanisms of canonical and noncanonical autophagy in B cells will improve our understanding of B cell biology, with implications for the development of autophagy-based immunotherapies.
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Affiliation(s)
| | | | - Luc Van Kaer
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, United States
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12
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Paddar MA, Wang F, Trosdal ES, Hendrix E, He Y, Salemi M, Mudd M, Jia J, Duque TLA, Javed R, Phinney B, Deretic V. Noncanonical roles of ATG5 and membrane atg8ylation in retromer assembly and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.602886. [PMID: 39026874 PMCID: PMC11257513 DOI: 10.1101/2024.07.10.602886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
ATG5 is one of the core autophagy proteins with additional functions such as noncanonical membrane atg8ylation, which among a growing number of biological outputs includes control of tuberculosis in animal models. Here we show that ATG5 associates with retromer's core components VPS26, VPS29 and VPS35 and modulates retromer function. Knockout of ATG5 blocked trafficking of a key glucose transporter sorted by the retromer, GLUT1, to the plasma membrane. Knockouts of other genes essential for membrane atg8ylation, of which ATG5 is a component, affected GLUT1 sorting, indicating that membrane atg8ylation as a process affects retromer function and endosomal sorting. The contribution of membrane atg8ylation to retromer function in GLUT1 sorting was independent of canonical autophagy. These findings expand the scope of membrane atg8ylation to specific sorting processes in the cell dependent on the retromer and its known interactors.
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Affiliation(s)
- Masroor Ahmad Paddar
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Fulong Wang
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Einar S Trosdal
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Emily Hendrix
- Department of Chemistry & Chemical Biology, The University of New Mexico, Albuquerque, NM, USA
| | - Yi He
- Department of Chemistry & Chemical Biology, The University of New Mexico, Albuquerque, NM, USA
| | - Michelle Salemi
- Proteomics Core Facility, UC Davis Genome Center, University of California, Davis, CA 95616, USA
| | - Michal Mudd
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Jingyue Jia
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Thabata L A Duque
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Ruheena Javed
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Brett Phinney
- Proteomics Core Facility, UC Davis Genome Center, University of California, Davis, CA 95616, USA
| | - Vojo Deretic
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
- Lead Contact
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13
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Ben-Hur S, Sernik S, Afar S, Kolpakova A, Politi Y, Gal L, Florentin A, Golani O, Sivan E, Dezorella N, Morgenstern D, Pietrokovski S, Schejter E, Yacobi-Sharon K, Arama E. Egg multivesicular bodies elicit an LC3-associated phagocytosis-like pathway to degrade paternal mitochondria after fertilization. Nat Commun 2024; 15:5715. [PMID: 38977659 PMCID: PMC11231261 DOI: 10.1038/s41467-024-50041-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 06/27/2024] [Indexed: 07/10/2024] Open
Abstract
Mitochondria are maternally inherited, but the mechanisms underlying paternal mitochondrial elimination after fertilization are far less clear. Using Drosophila, we show that special egg-derived multivesicular body vesicles promote paternal mitochondrial elimination by activating an LC3-associated phagocytosis-like pathway, a cellular defense pathway commonly employed against invading microbes. Upon fertilization, these egg-derived vesicles form extended vesicular sheaths around the sperm flagellum, promoting degradation of the sperm mitochondrial derivative and plasma membrane. LC3-associated phagocytosis cascade of events, including recruitment of a Rubicon-based class III PI(3)K complex to the flagellum vesicular sheaths, its activation, and consequent recruitment of Atg8/LC3, are all required for paternal mitochondrial elimination. Finally, lysosomes fuse with strings of large vesicles derived from the flagellum vesicular sheaths and contain degrading fragments of the paternal mitochondrial derivative. Given reports showing that in some mammals, the paternal mitochondria are also decorated with Atg8/LC3 and surrounded by multivesicular bodies upon fertilization, our findings suggest that a similar pathway also mediates paternal mitochondrial elimination in other flagellated sperm-producing organisms.
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Affiliation(s)
- Sharon Ben-Hur
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Shoshana Sernik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sara Afar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Alina Kolpakova
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yoav Politi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Liron Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Anat Florentin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Microbiology and Molecular Genetics, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ofra Golani
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ehud Sivan
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Nili Dezorella
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - David Morgenstern
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalised Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Shmuel Pietrokovski
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Eyal Schejter
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Keren Yacobi-Sharon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Eli Arama
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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14
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Jin X, Jin W, Tong L, Zhao J, Zhang L, Lin N. Therapeutic strategies of targeting non-apoptotic regulated cell death (RCD) with small-molecule compounds in cancer. Acta Pharm Sin B 2024; 14:2815-2853. [PMID: 39027232 PMCID: PMC11252466 DOI: 10.1016/j.apsb.2024.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/29/2024] [Accepted: 03/18/2024] [Indexed: 07/20/2024] Open
Abstract
Regulated cell death (RCD) is a controlled form of cell death orchestrated by one or more cascading signaling pathways, making it amenable to pharmacological intervention. RCD subroutines can be categorized as apoptotic or non-apoptotic and play essential roles in maintaining homeostasis, facilitating development, and modulating immunity. Accumulating evidence has recently revealed that RCD evasion is frequently the primary cause of tumor survival. Several non-apoptotic RCD subroutines have garnered attention as promising cancer therapies due to their ability to induce tumor regression and prevent relapse, comparable to apoptosis. Moreover, they offer potential solutions for overcoming the acquired resistance of tumors toward apoptotic drugs. With an increasing understanding of the underlying mechanisms governing these non-apoptotic RCD subroutines, a growing number of small-molecule compounds targeting single or multiple pathways have been discovered, providing novel strategies for current cancer therapy. In this review, we comprehensively summarized the current regulatory mechanisms of the emerging non-apoptotic RCD subroutines, mainly including autophagy-dependent cell death, ferroptosis, cuproptosis, disulfidptosis, necroptosis, pyroptosis, alkaliptosis, oxeiptosis, parthanatos, mitochondrial permeability transition (MPT)-driven necrosis, entotic cell death, NETotic cell death, lysosome-dependent cell death, and immunogenic cell death (ICD). Furthermore, we focused on discussing the pharmacological regulatory mechanisms of related small-molecule compounds. In brief, these insightful findings may provide valuable guidance for investigating individual or collaborative targeting approaches towards different RCD subroutines, ultimately driving the discovery of novel small-molecule compounds that target RCD and significantly enhance future cancer therapeutics.
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Affiliation(s)
- Xin Jin
- Department of Ultrasound, Department of Medical Oncology and Department of Hematology, the First Hospital of China Medical University, China Medical University, Shenyang 110001, China
| | - Wenke Jin
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Linlin Tong
- Department of Ultrasound, Department of Medical Oncology and Department of Hematology, the First Hospital of China Medical University, China Medical University, Shenyang 110001, China
| | - Jia Zhao
- Department of Ultrasound, Department of Medical Oncology and Department of Hematology, the First Hospital of China Medical University, China Medical University, Shenyang 110001, China
| | - Lan Zhang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Na Lin
- Department of Ultrasound, Department of Medical Oncology and Department of Hematology, the First Hospital of China Medical University, China Medical University, Shenyang 110001, China
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15
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Kolli S, Kline CJ, Rad KM, Wehman AM. Phagolysosomes break down the membrane of a non-apoptotic corpse independent of macroautophagy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.19.599770. [PMID: 38948720 PMCID: PMC11212964 DOI: 10.1101/2024.06.19.599770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Cell corpses must be cleared in an efficient manner to maintain tissue homeostasis and regulate immune responses. Ubiquitin-like Atg8/LC3 family proteins promote the degradation of membranes and internal cargo during both macroautophagy and corpse clearance, raising the question how macroautophagy contributes to corpse clearance. Studying the clearance of non-apoptotic dying polar bodies in Caenorhabditis elegans embryos, we show that the LC3 ortholog LGG-2 is enriched in the polar body phagolysosome independent of membrane association or autophagosome formation. We demonstrate that ATG-16.1 and ATG-16.2, which promote membrane association of lipidated Atg8/LC3 proteins, redundantly promote polar body membrane breakdown in phagolysosomes independent of their role in macroautophagy. We also show that the lipid scramblase ATG-9 is needed for autophagosome formation in early embryos but is dispensable for timely polar body membrane breakdown or protein cargo degradation. These findings demonstrate that macroautophagy is not required to promote polar body degradation, in contrast to recent findings with apoptotic corpse clearance in C. elegans embryos. Determining how membrane association of Atg8/LC3 promotes the breakdown of different types of cell corpses in distinct cell types or metabolic states is likely to give insights into the mechanisms of immunoregulation during normal development, physiology, and disease.
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Affiliation(s)
- Shruti Kolli
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Cassidy J. Kline
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Kimya M. Rad
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Ann M. Wehman
- Department of Biological Sciences, University of Denver, Denver, CO, USA
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16
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Cui X, Wang YT. Function of autophagy genes in innate immune defense against mucosal pathogens. Curr Opin Microbiol 2024; 79:102456. [PMID: 38554450 DOI: 10.1016/j.mib.2024.102456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 04/01/2024]
Abstract
Mucosal immunity is posed to constantly interact with commensal microbes and invading pathogens. As a fundamental cell biological pathway affecting immune response, autophagy regulates the interaction between mucosal immunity and microbes through multiple mechanisms, including direct elimination of microbes, control of inflammation, antigen presentation and lymphocyte homeostasis, and secretion of immune mediators. Some of these physiologically important functions do not involve canonical degradative autophagy but rely on certain autophagy genes and their 'autophagy gene-specific functions.' Here, we review the relationship between autophagy and important mucosal pathogens, including influenza virus, Mycobacterium tuberculosis, Salmonella enterica, Citrobacter rodentium, norovirus, and herpes simplex virus, with a particular focus on distinguishing the canonical versus gene-specific mechanisms of autophagy genes.
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Affiliation(s)
- Xiaoyan Cui
- Center for Infectious Disease Research, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Ya-Ting Wang
- Center for Infectious Disease Research, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China.
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17
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Bindschedler A, Schmuckli-Maurer J, Buchser S, Fischer TD, Wacker R, Davalan T, Brunner J, Heussler VT. LC3B labeling of the parasitophorous vacuole membrane of Plasmodium berghei liver stage parasites depends on the V-ATPase and ATG16L1. Mol Microbiol 2024; 121:1095-1111. [PMID: 38574236 DOI: 10.1111/mmi.15259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 04/06/2024]
Abstract
The protozoan parasite Plasmodium, the causative agent of malaria, undergoes an obligatory stage of intra-hepatic development before initiating a blood-stage infection. Productive invasion of hepatocytes involves the formation of a parasitophorous vacuole (PV) generated by the invagination of the host cell plasma membrane. Surrounded by the PV membrane (PVM), the parasite undergoes extensive replication. During intracellular development in the hepatocyte, the parasites provoke the Plasmodium-associated autophagy-related (PAAR) response. This is characterized by a long-lasting association of the autophagy marker protein, and ATG8 family member, LC3B with the PVM. LC3B localization at the PVM does not follow the canonical autophagy pathway since upstream events specific to canonical autophagy are dispensable. Here, we describe that LC3B localization at the PVM of Plasmodium parasites requires the V-ATPase and its interaction with ATG16L1. The WD40 domain of ATG16L1 is crucial for its recruitment to the PVM. Thus, we provide new mechanistic insight into the previously described PAAR response targeting Plasmodium liver stage parasites.
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Affiliation(s)
- Annina Bindschedler
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | | | - Sophie Buchser
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Tara D Fischer
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Rahel Wacker
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Tim Davalan
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Jessica Brunner
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Volker T Heussler
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
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18
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Jassey A, Jackson WT. Viruses and autophagy: bend, but don't break. Nat Rev Microbiol 2024; 22:309-321. [PMID: 38102460 DOI: 10.1038/s41579-023-00995-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2023] [Indexed: 12/17/2023]
Abstract
Autophagy is a constitutive cellular process of degradation required to maintain homeostasis and turn over spent organelles and aggregated proteins. For some viruses, the process can be antiviral, degrading viral proteins or virions themselves. For many other viruses, the induction of the autophagic process provides a benefit and promotes viral replication. In this Review, we survey the roles that the autophagic pathway plays in the replication of viruses. Most viruses that benefit from autophagic induction block autophagic degradation, which is a 'bend, but don't break' strategy initiating but limiting a potentially antiviral response. In almost all cases, it is other effects of the redirected autophagic machinery that benefit these viruses. This rapid mechanism to generate small double-membraned vesicles can be usurped to shape membranes for viral genome replication and virion maturation. However, data suggest that autophagic maintenance of cellular homeostasis is crucial for the initiation of infection, as viruses have evolved to replicate in normal, healthy cells. Inhibition of autophagic degradation is important once infection has initiated. Although true degradative autophagy is probably a negative for most viruses, initiating nondegradative autophagic membranes benefits a wide variety of viruses.
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Affiliation(s)
- Alagie Jassey
- Department of Microbiology and Immunology and Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - William T Jackson
- Department of Microbiology and Immunology and Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA.
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19
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Xu Y, Qian C, Wang Q, Song L, He Z, Liu W, Wan W. Deacetylation of ATG7 drives the induction of macroautophagy and LC3-associated microautophagy. Autophagy 2024; 20:1134-1146. [PMID: 37999993 PMCID: PMC11135844 DOI: 10.1080/15548627.2023.2287932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023] Open
Abstract
LC3 lipidation plays an important role in the regulation of macroautophagy and LC3-associated microautophagy. The E1-like enzyme ATG7 is one of the core components that are directly involved in LC3 lipidation reaction. Here, we provide evidence showing that acetylation of ATG7 tightly controls its enzyme activity to regulate the induction of macroautophagy and LC3-associated microautophagy. Mechanistically, acetylation of ATG7 disrupts its interaction with the E2-like enzyme ATG3, leading to an inhibition of LC3 lipidation in vitro and in vivo. Functionally, in response to various different stimuli, cellular ATG7 undergoes deacetylation to induce macroautophagy and LC3-associated microautophagy, which are necessary for cells to eliminate cytoplasmic DNA and degrade lysosome membrane proteins, respectively. Taken together, these findings reveal that ATG7 acetylation acts as a critical rheostat in controlling LC3 lipidation and related cellular processes.Abbreviations: AMPK: AMP-activated protein kinase; ATG: autophagy-related; cGAMP: cyclic GMP-AMP; CGAS: cyclic GMP-AMP synthase; CREBBP/CBP: CREB binding protein; EGF: epidermal growth factor; EGFR: epidermal growth factor receptor; EP300/p300: E1A binding protein p300; IFNB1: interferon beta 1; ISD: interferon stimulatory DNA; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MCOLN1/TRPML1: mucolipin TRP cation channel 1; MEF: mouse embryonic fibroblast; MTOR: mechanistic target of rapamycin kinase; NAM: nicotinamide; PE: phosphatidylethanolamine; PTM: post-translational modification; RB1CC1/FIP200: RB1 inducible coiled-coil 1; SIRT: sirtuin; SQSTM1/p62: sequestosome 1; STING1: stimulator of interferon response cGAMP interactor 1; TSA: trichostatin A; ULK1: unc-51 like autophagy activating kinase 1; WIPI2: WD repeat domain, phosphoinositide interacting 2; WT: wild-type.
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Affiliation(s)
- Yinfeng Xu
- Laboratory of Basic Biology, Hunan First Normal University, Changsha, Hunan, China
| | - Chuying Qian
- Department of Biochemistry, and Department of Thoracic Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qian Wang
- Department of Biochemistry, and Department of Thoracic Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lijiang Song
- Department of Biochemistry, and Department of Thoracic Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhengfu He
- Department of Biochemistry, and Department of Thoracic Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Wei Liu
- Department of Metabolic Medicine, International Institutes of Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Wei Wan
- Department of Biochemistry, and Department of Thoracic Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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20
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Hollingsworth LR, Veeraraghavan P, Paulo JA, Harper JW, Rauch I. Spatiotemporal proteomic profiling of cellular responses to NLRP3 agonists. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590338. [PMID: 38659763 PMCID: PMC11042255 DOI: 10.1101/2024.04.19.590338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Nucleotide-binding domain and leucine-rich repeat pyrin-domain containing protein 3 (NLRP3) is an innate immune sensor that forms an inflammasome in response to various cellular stressors. Gain-of-function mutations in NLRP3 cause autoinflammatory diseases and NLRP3 signalling itself exacerbates the pathogenesis of many other human diseases. Despite considerable therapeutic interest, the primary drivers of NLRP3 activation remain controversial due to the diverse array of signals that are integrated through NLRP3. Here, we mapped subcellular proteome changes to lysosomes, mitochondrion, EEA1-positive endosomes, and Golgi caused by the NLRP3 inflammasome agonists nigericin and CL097. We identified several common disruptions to retrograde trafficking pathways, including COPI and Shiga toxin-related transport, in line with recent studies. We further characterized mouse NLRP3 trafficking throughout its activation using temporal proximity proteomics, which supports a recent model of NLRP3 recruitment to endosomes during inflammasome activation. Collectively, these findings provide additional granularity to our understanding of the molecular events driving NLRP3 activation and serve as a valuable resource for cell biological research. We have made our proteomics data accessible through an open-access Shiny browser to facilitate future research within the community, available at: https://harperlab.connect.hms.harvard.edu/inflame/. We will display anonymous peer review for this manuscript on pubpub.org (https://harperlab.pubpub.org/pub/nlrp3/) rather than a traditional journal. Moreover, we invite community feedback on the pubpub version of this manuscript, and we will address criticisms accordingly.
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Affiliation(s)
- L. Robert Hollingsworth
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | | | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - J. Wade Harper
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Isabella Rauch
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University
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21
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Tang J, Fang D, Zhong J, Li M. Missing WD40 Repeats in ATG16L1 Delays Canonical Autophagy and Inhibits Noncanonical Autophagy. Int J Mol Sci 2024; 25:4493. [PMID: 38674078 PMCID: PMC11050548 DOI: 10.3390/ijms25084493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Canonical autophagy is an evolutionarily conserved process that forms double-membrane structures and mediates the degradation of long-lived proteins (LLPs). Noncanonical autophagy (NCA) is an important alternative pathway involving the formation of microtubule-associated protein 1 light chain 3 (LC3)-positive structures that are independent of partial core autophagy proteins. NCA has been defined by the conjugation of ATG8s to single membranes (CASM). During canonical autophagy and NCA/CASM, LC3 undergoes a lipidation modification, and ATG16L1 is a crucial protein in this process. Previous studies have reported that the WDR domain of ATG16L1 is not necessary for canonical autophagy. However, our study found that WDR domain deficiency significantly impaired LLP degradation in basal conditions and slowed down LC3-II accumulation in canonical autophagy. We further demonstrated that the observed effect was due to a reduced interaction between ATG16L1 and FIP200/WIPI2, without affecting lysosome function or fusion. Furthermore, we also found that the WDR domain of ATG16L1 is crucial for chemical-induced NCA/CASM. The results showed that removing the WDR domain or introducing the K490A mutation in ATG16L1 significantly inhibited the NCA/CASM, which interrupted the V-ATPase-ATG16L1 axis. In conclusion, this study highlights the significance of the WDR domain of ATG16L1 for both canonical autophagy and NCA functions, improving our understanding of its role in autophagy.
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Affiliation(s)
- Jiuge Tang
- State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, Guangzhou 510006, China
| | - Dongmei Fang
- State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, Guangzhou 510006, China
| | - Jialing Zhong
- State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, Guangzhou 510006, China
| | - Min Li
- State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, Guangzhou 510006, China
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22
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Schmid M, Fischer P, Engl M, Widder J, Kerschbaum-Gruber S, Slade D. The interplay between autophagy and cGAS-STING signaling and its implications for cancer. Front Immunol 2024; 15:1356369. [PMID: 38660307 PMCID: PMC11039819 DOI: 10.3389/fimmu.2024.1356369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
Autophagy is an intracellular process that targets various cargos for degradation, including members of the cGAS-STING signaling cascade. cGAS-STING senses cytosolic double-stranded DNA and triggers an innate immune response through type I interferons. Emerging evidence suggests that autophagy plays a crucial role in regulating and fine-tuning cGAS-STING signaling. Reciprocally, cGAS-STING pathway members can actively induce canonical as well as various non-canonical forms of autophagy, establishing a regulatory network of feedback mechanisms that alter both the cGAS-STING and the autophagic pathway. The crosstalk between autophagy and the cGAS-STING pathway impacts a wide variety of cellular processes such as protection against pathogenic infections as well as signaling in neurodegenerative disease, autoinflammatory disease and cancer. Here we provide a comprehensive overview of the mechanisms involved in autophagy and cGAS-STING signaling, with a specific focus on the interactions between the two pathways and their importance for cancer.
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Affiliation(s)
- Maximilian Schmid
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- MedAustron Ion Therapy Center, Wiener Neustadt, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Patrick Fischer
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- MedAustron Ion Therapy Center, Wiener Neustadt, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Magdalena Engl
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Joachim Widder
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Sylvia Kerschbaum-Gruber
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- MedAustron Ion Therapy Center, Wiener Neustadt, Austria
| | - Dea Slade
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- MedAustron Ion Therapy Center, Wiener Neustadt, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
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23
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Eguchi T, Sakurai M, Wang Y, Saito C, Yoshii G, Wileman T, Mizushima N, Kuwahara T, Iwatsubo T. The V-ATPase-ATG16L1 axis recruits LRRK2 to facilitate the lysosomal stress response. J Cell Biol 2024; 223:e202302067. [PMID: 38227290 PMCID: PMC10791558 DOI: 10.1083/jcb.202302067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 10/13/2023] [Accepted: 12/11/2023] [Indexed: 01/17/2024] Open
Abstract
Leucine-rich repeat kinase 2 (LRRK2), a Rab kinase associated with Parkinson's disease and several inflammatory diseases, has been shown to localize to stressed lysosomes and get activated to regulate lysosomal homeostasis. However, the mechanisms of LRRK2 recruitment and activation have not been well understood. Here, we found that the ATG8 conjugation system regulates the recruitment of LRRK2 as well as LC3 onto single membranes of stressed lysosomes/phagosomes. This recruitment did not require FIP200-containing autophagy initiation complex, nor did it occur on double-membrane autophagosomes, suggesting independence from canonical autophagy. Consistently, LRRK2 recruitment was regulated by the V-ATPase-ATG16L1 axis, which requires the WD40 domain of ATG16L1 and specifically mediates ATG8 lipidation on single membranes. This mechanism was also responsible for the lysosomal stress-induced activation of LRRK2 and the resultant regulation of lysosomal secretion and enlargement. These results indicate that the V-ATPase-ATG16L1 axis serves a novel non-autophagic role in the maintenance of lysosomal homeostasis by recruiting LRRK2.
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Affiliation(s)
- Tomoya Eguchi
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Maria Sakurai
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yingxue Wang
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Chieko Saito
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Gen Yoshii
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Thomas Wileman
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomoki Kuwahara
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takeshi Iwatsubo
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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24
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Deretic V, Klionsky DJ. An expanding repertoire of E3 ligases in membrane Atg8ylation. Nat Cell Biol 2024; 26:307-308. [PMID: 38225349 PMCID: PMC11164235 DOI: 10.1038/s41556-023-01329-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Affiliation(s)
- Vojo Deretic
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence and Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, USA.
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25
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Shariq M, Khan MF, Raj R, Ahsan N, Kumar P. PRKAA2, MTOR, and TFEB in the regulation of lysosomal damage response and autophagy. J Mol Med (Berl) 2024; 102:287-311. [PMID: 38183492 DOI: 10.1007/s00109-023-02411-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 12/07/2023] [Accepted: 12/18/2023] [Indexed: 01/08/2024]
Abstract
Lysosomes function as critical signaling hubs that govern essential enzyme complexes. LGALS proteins (LGALS3, LGALS8, and LGALS9) are integral to the endomembrane damage response. If ESCRT fails to rectify damage, LGALS-mediated ubiquitination occurs, recruiting autophagy receptors (CALCOCO2, TRIM16, and SQSTM1) and VCP/p97 complex containing UBXN6, PLAA, and YOD1, initiating selective autophagy. Lysosome replenishment through biogenesis is regulated by TFEB. LGALS3 interacts with TFRC and TRIM16, aiding ESCRT-mediated repair and autophagy-mediated removal of damaged lysosomes. LGALS8 inhibits MTOR and activates TFEB for ATG and lysosomal gene transcription. LGALS9 inhibits USP9X, activates PRKAA2, MAP3K7, ubiquitination, and autophagy. Conjugation of ATG8 to single membranes (CASM) initiates damage repair mediated by ATP6V1A, ATG16L1, ATG12, ATG5, ATG3, and TECPR1. ATG8ylation or CASM activates the MERIT system (ESCRT-mediated repair, autophagy-mediated clearance, MCOLN1 activation, Ca2+ release, RRAG-GTPase regulation, MTOR modulation, TFEB activation, and activation of GTPase IRGM). Annexins ANAX1 and ANAX2 aid damage repair. Stress granules stabilize damaged membranes, recruiting FLCN-FNIP1/2, G3BP1, and NUFIP1 to inhibit MTOR and activate TFEB. Lysosomes coordinate the synergistic response to endomembrane damage and are vital for innate and adaptive immunity. Future research should unveil the collaborative actions of ATG proteins, LGALSs, TRIMs, autophagy receptors, and lysosomal proteins in lysosomal damage response.
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Affiliation(s)
- Mohd Shariq
- Quantlase Imaging Laboratory, Quantlase Lab LLC, Unit 1-8, Masdar City, Abu Dhabi, UAE.
| | - Mohammad Firoz Khan
- Quantlase Imaging Laboratory, Quantlase Lab LLC, Unit 1-8, Masdar City, Abu Dhabi, UAE.
| | - Reshmi Raj
- Quantlase Imaging Laboratory, Quantlase Lab LLC, Unit 1-8, Masdar City, Abu Dhabi, UAE
| | - Nuzhat Ahsan
- Quantlase Imaging Laboratory, Quantlase Lab LLC, Unit 1-8, Masdar City, Abu Dhabi, UAE
| | - Pramod Kumar
- Quantlase Imaging Laboratory, Quantlase Lab LLC, Unit 1-8, Masdar City, Abu Dhabi, UAE
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26
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Yousefi P, Tabibzadeh A, Jawaziri AK, Mehrjoo M, Akhavan M, Allahqoli L, Salehiniya H. Autophagy-related genes polymorphism in hepatitis B virus-associated hepatocellular carcinoma: A systematic review. Immun Inflamm Dis 2024; 12:e1182. [PMID: 38353395 PMCID: PMC10865419 DOI: 10.1002/iid3.1182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 01/19/2024] [Accepted: 01/27/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Chronic hepatitis B (CHB) virus is the most common risk factor for developing liver malignancy. Autophagy is an essential element in human cell maintenance. Several studies have demonstrated that autophagy plays a vital role in liver cancer at different stages. In this systematic review, we intend to investigate the role of polymorphism and mutations of autophagy-related genes (ATGs) in the pathogenesis and carcinogenesis of the hepatitis B virus (HBV). MATERIALS AND METHODS The search was conducted in online databases (Web of Science, PubMed, and Scopus) using Viruses, Infections, Polymorphism, Autophagy, and ATG. The study was conducted based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses criteria. RESULTS The primary search results led to 422 studies. By screening and eligibility evaluation, only four studies were relevant. The most important polymorphisms in hepatocellular carcinoma were rs2241880 in ATG16L1, rs77859116, rs510432, and rs548234 in ATG5. Furthermore, some polymorphisms are associated with an increased risk of HBV infection including, rs2241880 in ATG16L1 and rs6568431 in ATG5. CONCLUSION The current study highlights the importance of rs2241880 in ATG16L1 and rs77859116, rs510432, and rs548234 in ATG5 for HBV-induced HCC. Additionally, some mutations in ATG16L1 and ATG5 were important in risk of HBV infection. The study highlights the gap of knowledge in the field of ATG polymorphisms in HBV infection and HBV-induced HCC.
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Affiliation(s)
- Parastoo Yousefi
- Department of Virology, School of MedicineIran University of Medical SciencesTehranIran
| | - Alireza Tabibzadeh
- Department of Virology, School of MedicineIran University of Medical SciencesTehranIran
| | | | - Mohsen Mehrjoo
- Department of Biochemistry and Genetics, School of MedicineLorestan University of Medical SciencesKhorramabadIran
| | - Mandana Akhavan
- Department of Microbiology, Faculty of Medical SciencesIslamic Azad University, Arak BranchArakIran
| | - Leila Allahqoli
- Department of MidwiferyMinistry of Health and Medical EducationTehranIran
| | - Hamid Salehiniya
- Department of Epidemiology and Biostatistics, School of Health, Social Determinants of Health Research CenterBirjand University of Medical SciencesBirjandIran
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27
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Yang Y, Arnold ML, Lange CM, Sun LH, Broussalian M, Doroodian S, Ebata H, Choy EH, Poon K, Moreno TM, Singh A, Driscoll M, Kumsta C, Hansen M. Autophagy protein ATG-16.2 and its WD40 domain mediate the beneficial effects of inhibiting early-acting autophagy genes in C. elegans neurons. NATURE AGING 2024; 4:198-212. [PMID: 38177330 PMCID: PMC11022750 DOI: 10.1038/s43587-023-00548-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 11/27/2023] [Indexed: 01/06/2024]
Abstract
While autophagy genes are required for lifespan of long-lived animals, their tissue-specific roles in aging remain unclear. Here, we inhibited autophagy genes in Caenorhabditis elegans neurons, and found that knockdown of early-acting autophagy genes, except atg-16.2, increased lifespan, and decreased neuronal PolyQ aggregates, independently of autophagosomal degradation. Neurons can secrete protein aggregates via vesicles called exophers. Inhibiting neuronal early-acting autophagy genes, except atg-16.2, increased exopher formation and exopher events extended lifespan, suggesting exophers promote organismal fitness. Lifespan extension, reduction in PolyQ aggregates and increase in exophers were absent in atg-16.2 null mutants, and restored by full-length ATG-16.2 expression in neurons, but not by ATG-16.2 lacking its WD40 domain, which mediates noncanonical functions in mammalian systems. We discovered a neuronal role for C. elegans ATG-16.2 and its WD40 domain in lifespan, proteostasis and exopher biogenesis. Our findings suggest noncanonical functions for select autophagy genes in both exopher formation and in aging.
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Affiliation(s)
- Yongzhi Yang
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Scripps Research Institute, La Jolla, CA, USA
| | - Meghan Lee Arnold
- Rutgers, The State University of New Jersey, Nelson Biological Labs, Piscataway, NJ, USA
| | - Caitlin M Lange
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Ling-Hsuan Sun
- Buck Institute for Aging Research, Novato, CA, USA
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | | | | | | | - Elizabeth H Choy
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Karie Poon
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Tatiana M Moreno
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Anupama Singh
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Monica Driscoll
- Rutgers, The State University of New Jersey, Nelson Biological Labs, Piscataway, NJ, USA
| | - Caroline Kumsta
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
| | - Malene Hansen
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
- Buck Institute for Aging Research, Novato, CA, USA.
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28
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Zhai H, Wang T, Liu D, Pan L, Sun Y, Qiu HJ. Autophagy as a dual-faced host response to viral infections. Front Cell Infect Microbiol 2023; 13:1289170. [PMID: 38125906 PMCID: PMC10731275 DOI: 10.3389/fcimb.2023.1289170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/10/2023] [Indexed: 12/23/2023] Open
Abstract
Autophagy selectively degrades viral particles or cellular components, either facilitating or inhibiting viral replication. Conversely, most viruses have evolved strategies to escape or exploit autophagy. Moreover, autophagy collaborates with the pattern recognition receptor signaling, influencing the expression of adaptor molecules involved in the innate immune response and regulating the expression of interferons (IFNs). The intricate relationship between autophagy and IFNs plays a critical role in the host cell defense against microbial invasion. Therefore, it is important to summarize the interactions between viral infections, autophagy, and the host defense mechanisms against viruses. This review specifically focuses on the interactions between autophagy and IFN pathways during viral infections, providing a comprehensive summary of the molecular mechanisms utilized or evaded by different viruses.
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Affiliation(s)
| | | | | | | | - Yuan Sun
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hua-Ji Qiu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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29
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Cross J, Durgan J, McEwan DG, Tayler M, Ryan KM, Florey O. Lysosome damage triggers direct ATG8 conjugation and ATG2 engagement via non-canonical autophagy. J Cell Biol 2023; 222:e202303078. [PMID: 37796195 PMCID: PMC10561555 DOI: 10.1083/jcb.202303078] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 07/14/2023] [Accepted: 09/07/2023] [Indexed: 10/06/2023] Open
Abstract
Cells harness multiple pathways to maintain lysosome integrity, a central homeostatic process. Damaged lysosomes can be repaired or targeted for degradation by lysophagy, a selective autophagy process involving ATG8/LC3. Here, we describe a parallel ATG8/LC3 response to lysosome damage, mechanistically distinct from lysophagy. Using a comprehensive series of biochemical, pharmacological, and genetic approaches, we show that lysosome damage induces non-canonical autophagy and Conjugation of ATG8s to Single Membranes (CASM). Following damage, ATG8s are rapidly and directly conjugated onto lysosome membranes, independently of ATG13/WIPI2, lipidating to PS (and PE), a molecular hallmark of CASM. Lysosome damage drives V-ATPase V0-V1 association, direct recruitment of ATG16L1 via its WD40-domain/K490A, and is sensitive to Salmonella SopF. Lysosome damage-induced CASM is associated with formation of dynamic, LC3A-positive tubules, and promotes robust LC3A engagement with ATG2, a lipid transfer protein central to lysosome repair. Together, our data identify direct ATG8 conjugation as a rapid response to lysosome damage, with important links to lipid transfer and dynamics.
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Affiliation(s)
- Jake Cross
- Signalling Programme, Babraham Institute, Cambridge, UK
| | - Joanne Durgan
- Signalling Programme, Babraham Institute, Cambridge, UK
| | - David G. McEwan
- Tumour Cell Death and Autophagy Laboratory, Cancer Research UK Beatson Institute, Glasgow, UK
| | | | - Kevin M. Ryan
- Tumour Cell Death and Autophagy Laboratory, Cancer Research UK Beatson Institute, Glasgow, UK
| | - Oliver Florey
- Signalling Programme, Babraham Institute, Cambridge, UK
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30
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Sun Y, Wang X, Yang X, Wang L, Ding J, Wang CC, Zhang H, Wang X. V-ATPase recruitment to ER exit sites switches COPII-mediated transport to lysosomal degradation. Dev Cell 2023; 58:2761-2775.e5. [PMID: 37922908 DOI: 10.1016/j.devcel.2023.10.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 08/23/2023] [Accepted: 10/12/2023] [Indexed: 11/07/2023]
Abstract
Endoplasmic reticulum (ER)-phagy is crucial to regulate the function and homeostasis of the ER via lysosomal degradation, but how it is initiated is unclear. Here we discover that Z-AAT, a disease-causing mutant of α1-antitrypsin, induces noncanonical ER-phagy at ER exit sites (ERESs). Accumulation of misfolded Z-AAT at the ERESs impairs coat protein complex II (COPII)-mediated ER-to-Golgi transport and retains V0 subunits that further assemble V-ATPase at the arrested ERESs. V-ATPase subsequently recruits ATG16L1 onto ERESs to mediate in situ lipidation of LC3C. FAM134B-II is then recruited by LC3C via its LIR motif and elicits ER-phagy leading to efficient lysosomal degradation of Z-AAT. Activation of this ER-phagy mediated by the V-ATPase-ATG16L1-LC3C axis (EVAC) is also triggered by blocking ER export. Our findings identify a pathway which switches COPII-mediated transport to lysosomal degradation for ER quality control.
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Affiliation(s)
- Yiwei Sun
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xi'e Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaotong Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingjin Ding
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chih-Chen Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xi Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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Zheng Z, Zhao M, Shan H, Fang D, Jin Z, Tang J, Liu Z, Hong L, Liu P, Li M. Noncanonical autophagy is a new strategy to inhibit HSV-1 through STING1 activation. Autophagy 2023; 19:3096-3112. [PMID: 37471002 PMCID: PMC10621258 DOI: 10.1080/15548627.2023.2237794] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 07/06/2023] [Accepted: 07/13/2023] [Indexed: 07/21/2023] Open
Abstract
STING1 (stimulator of interferon response cGAMP interactor 1) plays an essential role in immune responses for virus inhibition via inducing the production of type I interferon, inflammatory factors and macroautophagy/autophagy. In this study, we found that STING1 activation could induce not only canonical autophagy but also non-canonical autophagy (NCA) which is independent of the ULK1 or BECN1 complexes to form MAP1LC3/LC3-positive structures. Whether STING1-induced NCA has similar characters and physiological functions to canonical autophagy is totally unknown. Different from canonical autophagy, NCA could increase single-membrane structures and failed to degrade long-lived proteins, and could be strongly suppressed by interrupting vacuolar-type H+-translocating ATPase (V-ATPase) activity. Importantly, STING1-induced NCA could effectively inhibit DNA virus HSV-1 in cell model. Moreover, STING1 [1-340], a STING1 mutant lacking immunity and inflammatory response due to deletion of the tail end of STING1, could degrade virus through NCA alone, suggesting that the antiviral effect of activated STING1 could be separately mediated by inherent immunity, canonical autophagy, and NCA. In addition, the translocation and dimerization of STING1 do not rely on its immunity function and autophagy pathway. Similar to canonical autophagy, LC3-positive structures of NCA induced by STING1 could finally fuse with lysosomes, and the degradation of HSV-1 could be reverted by inhibition of lysosome function, suggesting that the elimination of DNA virus via NCA still requires the lysosome pathway. Collectively, we proved that besides its classical immunity function and canonical autophagy pathway, STING1-induced NCA is also an efficient antiviral pathway for the host cell.Abbreviations: ATG: autophagy related; Baf: bafilomycin A1; CASM: conjugation of LC3 to a single membrane; CGAS: cyclic GMP-AMP synthase; cGAMP: cyclic GMP-AMP; CQ: chloroquine; CTD: C-terminal domain; CTT: C-terminal tail; ER: endoplasmic reticulum; ERGIC: ER-Golgi intermediate compartment; HSV-1: herpes simplex virus 1; IRF3: interferon regulatory factor 3; IFNs: interferons; LAMP1: lysosomal associated membrane protein 1; LAP: LC3-associated phagocytosis; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MOI: multiplicity of infection; RB1CC1/FIP200: RB1 inducible coiled-coil 1; STING1: stimulator of interferon response cGAMP interactor 1; TBK1: TANK binding kinase 1; TGOLN2/TGN46: trans-golgi network protein 2; ULK1: unc-51 like autophagy activating kinase 1; V-ATPase: vacuolar-type H+-translocating ATPase; VSV: vesicular stomatitis virus.
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Affiliation(s)
- Zhihua Zheng
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, National and Local Joint Engineering Laboratory of Druggability and New Drugs Evaluation, Sun Yat-Sen University, Guangzhou, Guangdong, China
- School of Pharmaceutical Sciences, Jinan University, Guangzhou, Guangdong, China
| | - Man Zhao
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, National and Local Joint Engineering Laboratory of Druggability and New Drugs Evaluation, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Hao Shan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, National and Local Joint Engineering Laboratory of Druggability and New Drugs Evaluation, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Dongmei Fang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, National and Local Joint Engineering Laboratory of Druggability and New Drugs Evaluation, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zuyi Jin
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, National and Local Joint Engineering Laboratory of Druggability and New Drugs Evaluation, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jiuge Tang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, National and Local Joint Engineering Laboratory of Druggability and New Drugs Evaluation, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zhiping Liu
- School of Pharmaceutical Sciences, Jinan University, Guangzhou, Guangdong, China
| | - Liang Hong
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, National and Local Joint Engineering Laboratory of Druggability and New Drugs Evaluation, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Peiqing Liu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, National and Local Joint Engineering Laboratory of Druggability and New Drugs Evaluation, Sun Yat-Sen University, Guangzhou, Guangdong, China
- School of Pharmaceutical Sciences, Jinan University, Guangzhou, Guangdong, China
| | - Min Li
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, National and Local Joint Engineering Laboratory of Druggability and New Drugs Evaluation, Sun Yat-Sen University, Guangzhou, Guangdong, China
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Yang T, Qu X, Wang X, Xu D, Sheng M, Lin Y, Ke M, Song C, Xia Q, Jiang L, Li J, Farmer DG, Ke B. The macrophage STING-YAP axis controls hepatic steatosis by promoting the autophagic degradation of lipid droplets. Hepatology 2023:01515467-990000000-00616. [PMID: 37870294 PMCID: PMC11035483 DOI: 10.1097/hep.0000000000000638] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/19/2023] [Indexed: 10/24/2023]
Abstract
BACKGROUND AND AIMS The hallmark of NAFLD or hepatic steatosis is characterized by lipid droplet (LD) accumulation in hepatocytes. Autophagy may have profound effects on lipid metabolism and innate immune response. However, how innate immune activation may regulate the autophagic degradation of intracellular LDs remains elusive. APPROACH AND RESULTS A mouse model of a high-fat diet-induced NASH was used in the myeloid-specific stimulator of interferon genes (STING) knockout or STING/yes-associated protein (YAP) double knockout mice. Liver injury, lipid accumulation, lipid droplet proteins, autophagic genes, chromatin immunoprecipitation coupled with massively parallel sequencing, and RNA-Seq were assessed in vivo and in vitro . We found that high-fat diet-induced oxidative stress activates STING and YAP pathways in hepatic macrophages. The acrophage STING deficiency (myeloid-specific STING knockout) enhances nuclear YAP activity, reduces lipid accumulation, and increases autophagy-related proteins ATG5, ATG7, and light chain 3B but diminishes LD protein perilipin 2 expression. However, disruption of STING and YAP (myeloid STING and YAP double knockout) increases serum alanine aminotransferase and triglyceride levels and reduces β-fatty acid oxidation gene expression but augments perilipin 2 levels, exacerbating high-fat diet-induced lipid deposition. Chromatin immunoprecipitation coupled with massively parallel sequencing reveals that macrophage YAP targets transmembrane protein 205 and activates AMP-activated protein kinase α, which interacts with hepatocyte mitofusin 2 and induces protein disulfide isomerase activation. Protein disulfide isomerase activates hypoxia-inducible factor-1α signaling, increases autophagosome colocalization with LDs, and promotes the degradation of perilipin 2 by interacting with chaperone-mediated autophagy chaperone HSC70. CONCLUSIONS The macrophage STING-YAP axis controls hepatic steatosis by reprogramming lipid metabolism in a transmembrane protein 205/mitofusin 2/protein disulfide isomerase-dependent pathway. These findings highlight the regulatory mechanism of the macrophage STING-driven YAP activity on lipid control.
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Affiliation(s)
- Tao Yang
- The Dumont-UCLA Transplant Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Department of Infectious Diseases, the First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Xiaoye Qu
- The Dumont-UCLA Transplant Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Department of Liver Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiao Wang
- The Dumont-UCLA Transplant Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Department of Infectious Diseases, the First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Dongwei Xu
- The Dumont-UCLA Transplant Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Department of Liver Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Mingwei Sheng
- The Dumont-UCLA Transplant Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Yuanbang Lin
- The Dumont-UCLA Transplant Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Michael Ke
- The Dumont-UCLA Transplant Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Ci Song
- Department of Epidemiology, Nanjing Medical University, Nanjing, China
| | - Qiang Xia
- Department of Liver Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Longfeng Jiang
- The Dumont-UCLA Transplant Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Department of Infectious Diseases, the First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Jun Li
- Department of Infectious Diseases, the First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Douglas G. Farmer
- The Dumont-UCLA Transplant Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Bibo Ke
- The Dumont-UCLA Transplant Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
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Fischer TD, Bunker EN, Zhu PP, Le Guerroué F, Dominguez-Martin E, Scavone F, Cohen R, Yao T, Wang Y, Werner A, Youle RJ. STING induces LUBAC-mediated synthesis of linear ubiquitin chains to stimulate innate immune signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.14.562349. [PMID: 37873486 PMCID: PMC10592814 DOI: 10.1101/2023.10.14.562349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
STING activation by cyclic dinucleotides in mammals induces interferon- and NFκB -related gene expression, and the lipidation of LC3B at Golgi membranes. While mechanisms of the interferon response are well understood, the mechanisms of NFκB activation mediated by STING remain unclear. We report that STING activation induces K63- and M1-linked/linear ubiquitin chain formation at LC3B-associated Golgi membranes. Loss of the LUBAC E3 ubiquitin ligase prevents formation of linear, but not K63-linked ubiquitin chains or STING activation and inhibits STING-induced NFκB and IRF3-mediated signaling in monocytic THP1 cells. The proton channel activity of STING is also important for both K63 and linear ubiquitin chain formation, and NFκB- and interferon-related gene expression. Thus, LUBAC synthesis of linear ubiquitin chains regulates STING-mediated innate immune signaling.
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Affiliation(s)
- Tara D. Fischer
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Bethesda, MD, USA
| | - Eric N. Bunker
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Bethesda, MD, USA
| | - Peng-Peng Zhu
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Bethesda, MD, USA
| | - François Le Guerroué
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Bethesda, MD, USA
| | - Eunice Dominguez-Martin
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Bethesda, MD, USA
| | - Francesco Scavone
- Department of Biochemistry and Molecular Biology, Colorado State University; Fort Collins, CO, USA
| | - Robert Cohen
- Department of Biochemistry and Molecular Biology, Colorado State University; Fort Collins, CO, USA
| | - Tingting Yao
- Department of Biochemistry and Molecular Biology, Colorado State University; Fort Collins, CO, USA
| | - Yan Wang
- Mass Spectrometry, National Institute of Dental and Craniofacial Research, National Institutes of Health; Bethesda, MD, USA
| | - Achim Werner
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health; Bethesda, MD, USA
| | - Richard J. Youle
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Bethesda, MD, USA
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Meng X, Chi H, Zhang Z, Li Q, Sheng X, Tang X, Xing J, Zhan W. Transcriptome Analysis of Peritoneal Cells Reveals the Early Immune Response of Flounder ( Paralichthys olivaceus) to Inactivated Vibrio anguillarum Immunization. Vaccines (Basel) 2023; 11:1603. [PMID: 37897005 PMCID: PMC10611026 DOI: 10.3390/vaccines11101603] [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: 09/06/2023] [Revised: 10/12/2023] [Accepted: 10/14/2023] [Indexed: 10/29/2023] Open
Abstract
Vibrio anguillarum (V. anguillarum) is a bacterium that seriously harms flounder and other aquaculture species. Vaccination is an effective means of preventing vibriosis and is mainly administered by intraperitoneal injection. Effective antigen processing at the initial stage of immunization is essential to elicit adaptive immune responses and improve vaccine efficacy. To understand the early immune response of flounder caused by inactivated V. anguillarum, we detected the transcriptome profiles of the cells in the peritoneal cavity (PoPerCs) after inactivated V. anguillarum immunization. More than 10 billion high-quality reads were obtained, of which about 89.33% were successfully mapped to the reference genome of flounder. A total of 1985, 3072, 4001, and 5476 differentially expressed genes were captured at 6, 12, 24, and 48 h post immunization, respectively. The hub module correlated with the immunization time was identified by WGCNA. GO and KEGG analysis showed that hub module genes were abundantly expressed in various immune-related aspects, including the response to stimuli, the immune system process, signal transducer activity, autophagy, the NOD-like receptor signaling pathway, the toll-like receptor signaling pathway, the T cell receptor signaling pathway, and Th17 cell differentiation. Additionally, genes related to Th cell differentiation are presented as heatmaps. These genes constitute a complex immune regulatory network, mainly involved in pathogen recognition, antigen processing and presentation, and Th cell differentiation. The results of this study provide the first transcriptome profile of PoPerCs associated with inactivated V. anguillarum immunity and lay a solid foundation for further studies on effective V. anguillarum vaccines.
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Affiliation(s)
- Xianghu Meng
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao 266003, China; (X.M.); (Q.L.); (X.S.); (X.T.); (J.X.); (W.Z.)
| | - Heng Chi
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao 266003, China; (X.M.); (Q.L.); (X.S.); (X.T.); (J.X.); (W.Z.)
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Zuobing Zhang
- College of Life Sciences, Shanxi University, Taiyuan 030006, China;
| | - Qian Li
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao 266003, China; (X.M.); (Q.L.); (X.S.); (X.T.); (J.X.); (W.Z.)
| | - Xiuzhen Sheng
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao 266003, China; (X.M.); (Q.L.); (X.S.); (X.T.); (J.X.); (W.Z.)
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Xiaoqian Tang
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao 266003, China; (X.M.); (Q.L.); (X.S.); (X.T.); (J.X.); (W.Z.)
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Jing Xing
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao 266003, China; (X.M.); (Q.L.); (X.S.); (X.T.); (J.X.); (W.Z.)
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Wenbin Zhan
- Laboratory of Pathology and Immunology of Aquatic Animals, KLMME, Ocean University of China, Qingdao 266003, China; (X.M.); (Q.L.); (X.S.); (X.T.); (J.X.); (W.Z.)
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
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Florey O. TECPR1 helps bridge the CASM during lysosome damage. EMBO J 2023; 42:e115210. [PMID: 37638605 PMCID: PMC10548167 DOI: 10.15252/embj.2023115210] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 08/15/2023] [Indexed: 08/29/2023] Open
Abstract
Maintaining the integrity of the endolysosomal system is of great importance for cellular homeostasis. Recent work published in The EMBO Journal and EMBO Reports reveals a novel role for the protein TECPR1 as a sensor for stressed membranes and regulator of lysosomal membrane repair.
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36
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Heron R, Amato C, Wood W, Davidson AJ. Understanding the diversity and dynamics of in vivo efferocytosis: Insights from the fly embryo. Immunol Rev 2023; 319:27-44. [PMID: 37589239 PMCID: PMC10952863 DOI: 10.1111/imr.13266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/18/2023] [Indexed: 08/18/2023]
Abstract
The clearance of dead and dying cells, termed efferocytosis, is a rapid and efficient process and one that is critical for organismal health. The extraordinary speed and efficiency with which dead cells are detected and engulfed by immune cells within tissues presents a challenge to researchers who wish to unravel this fascinating process, since these fleeting moments of uptake are almost impossible to catch in vivo. In recent years, the fruit fly (Drosophila melanogaster) embryo has emerged as a powerful model to circumvent this problem. With its abundance of dying cells, specialist phagocytes and relative ease of live imaging, the humble fly embryo provides a unique opportunity to catch and study the moment of cell engulfment in real-time within a living animal. In this review, we explore the recent advances that have come from studies in the fly, and how live imaging and genetics have revealed a previously unappreciated level of diversity in the efferocytic program. A variety of efferocytic strategies across the phagocytic cell population ensure efficient and rapid clearance of corpses wherever death is encountered within the varied and complex setting of a multicellular living organism.
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Affiliation(s)
- Rosalind Heron
- Institute for Regeneration and RepairUniversity of EdinburghEdinburghUK
| | - Clelia Amato
- Institute for Regeneration and RepairUniversity of EdinburghEdinburghUK
| | - Will Wood
- Institute for Regeneration and RepairUniversity of EdinburghEdinburghUK
| | - Andrew J. Davidson
- Institute for Regeneration and RepairUniversity of EdinburghEdinburghUK
- School of Cancer SciencesWolfson Wohl Cancer Research Centre, University of GlasgowGlasgowUK
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37
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Kaur N, de la Ballina LR, Haukaas HS, Torgersen ML, Radulovic M, Munson MJ, Sabirsh A, Stenmark H, Simonsen A, Carlsson SR, Lystad AH. TECPR1 is activated by damage-induced sphingomyelin exposure to mediate noncanonical autophagy. EMBO J 2023; 42:e113105. [PMID: 37409525 PMCID: PMC10476171 DOI: 10.15252/embj.2022113105] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 05/30/2023] [Accepted: 06/07/2023] [Indexed: 07/07/2023] Open
Abstract
Cells use noncanonical autophagy, also called conjugation of ATG8 to single membranes (CASM), to label damaged intracellular compartments with ubiquitin-like ATG8 family proteins in order to signal danger caused by pathogens or toxic compounds. CASM relies on E3 complexes to sense membrane damage, but so far, only the mechanism to activate ATG16L1-containing E3 complexes, associated with proton gradient loss, has been described. Here, we show that TECPR1-containing E3 complexes are key mediators of CASM in cells treated with a variety of pharmacological drugs, including clinically relevant nanoparticles, transfection reagents, antihistamines, lysosomotropic compounds, and detergents. Interestingly, TECPR1 retains E3 activity when ATG16L1 CASM activity is obstructed by the Salmonella Typhimurium pathogenicity factor SopF. Mechanistically, TECPR1 is recruited by damage-induced sphingomyelin (SM) exposure using two DysF domains, resulting in its activation and ATG8 lipidation. In vitro assays using purified human TECPR1-ATG5-ATG12 complex show direct activation of its E3 activity by SM, whereas SM has no effect on ATG16L1-ATG5-ATG12. We conclude that TECPR1 is a key activator of CASM downstream of SM exposure.
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Affiliation(s)
- Namrita Kaur
- Centre for Cancer Cell Reprogramming, Faculty of MedicineUniversity of OsloOsloNorway
- Department of Molecular Cell Biology, Institute for Cancer ResearchOslo University HospitalOsloNorway
| | - Laura Rodriguez de la Ballina
- Centre for Cancer Cell Reprogramming, Faculty of MedicineUniversity of OsloOsloNorway
- Department of Molecular Medicine, Institute of Basic Medical SciencesUniversity of OsloOsloNorway
| | - Håvard Styrkestad Haukaas
- Centre for Cancer Cell Reprogramming, Faculty of MedicineUniversity of OsloOsloNorway
- Department of Molecular Cell Biology, Institute for Cancer ResearchOslo University HospitalOsloNorway
| | - Maria Lyngaas Torgersen
- Centre for Cancer Cell Reprogramming, Faculty of MedicineUniversity of OsloOsloNorway
- Department of Molecular Cell Biology, Institute for Cancer ResearchOslo University HospitalOsloNorway
| | - Maja Radulovic
- Centre for Cancer Cell Reprogramming, Faculty of MedicineUniversity of OsloOsloNorway
- Department of Molecular Cell Biology, Institute for Cancer ResearchOslo University HospitalOsloNorway
| | - Michael J Munson
- Advanced Drug Delivery, Pharmaceutical SciencesBiopharmaceuticals R&D, AstraZenecaGothenburgSweden
| | - Alan Sabirsh
- Advanced Drug Delivery, Pharmaceutical SciencesBiopharmaceuticals R&D, AstraZenecaGothenburgSweden
| | - Harald Stenmark
- Centre for Cancer Cell Reprogramming, Faculty of MedicineUniversity of OsloOsloNorway
- Department of Molecular Cell Biology, Institute for Cancer ResearchOslo University HospitalOsloNorway
| | - Anne Simonsen
- Centre for Cancer Cell Reprogramming, Faculty of MedicineUniversity of OsloOsloNorway
- Department of Molecular Cell Biology, Institute for Cancer ResearchOslo University HospitalOsloNorway
- Department of Molecular Medicine, Institute of Basic Medical SciencesUniversity of OsloOsloNorway
| | - Sven R Carlsson
- Department of Medical Biochemistry and BiophysicsUniversity of UmeåUmeåSweden
| | - Alf Håkon Lystad
- Centre for Cancer Cell Reprogramming, Faculty of MedicineUniversity of OsloOsloNorway
- Department of Molecular Cell Biology, Institute for Cancer ResearchOslo University HospitalOsloNorway
- Department of Molecular Medicine, Institute of Basic Medical SciencesUniversity of OsloOsloNorway
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Nieto-Torres JL, Zaretski S, Liu T, Adams PD, Hansen M. Post-translational modifications of ATG8 proteins - an emerging mechanism of autophagy control. J Cell Sci 2023; 136:jcs259725. [PMID: 37589340 PMCID: PMC10445744 DOI: 10.1242/jcs.259725] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023] Open
Abstract
Autophagy is a recycling mechanism involved in cellular homeostasis with key implications for health and disease. The conjugation of the ATG8 family proteins, which includes LC3B (also known as MAP1LC3B), to autophagosome membranes, constitutes a hallmark of the canonical autophagy process. After ATG8 proteins are conjugated to the autophagosome membranes via lipidation, they orchestrate a plethora of protein-protein interactions that support key steps of the autophagy process. These include binding to cargo receptors to allow cargo recruitment, association with proteins implicated in autophagosome transport and autophagosome-lysosome fusion. How these diverse and critical protein-protein interactions are regulated is still not well understood. Recent reports have highlighted crucial roles for post-translational modifications of ATG8 proteins in the regulation of ATG8 functions and the autophagy process. This Review summarizes the main post-translational regulatory events discovered to date to influence the autophagy process, mostly described in mammalian cells, including ubiquitylation, acetylation, lipidation and phosphorylation, as well as their known contributions to the autophagy process, physiology and disease.
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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 92037, USA
- Department of Biomedical Sciences, School of Health Sciences and Veterinary, Universidad Cardenal Herrera-CEU, CEU Universities, 46113 Moncada, Spain
| | - Sviatlana Zaretski
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
| | - Tianhui Liu
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
| | - Peter D. Adams
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
| | - Malene Hansen
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
- The Buck Institute for Aging Research, Novato, CA 94945, USA
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Costa-Laparra I, Juárez-Escoto E, Vicario C, Moratalla R, García-Sanz P. APOE ε4 allele, along with G206D- PSEN1 mutation, alters mitochondrial networks and their degradation in Alzheimer's disease. Front Aging Neurosci 2023; 15:1087072. [PMID: 37455931 PMCID: PMC10340123 DOI: 10.3389/fnagi.2023.1087072] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction Alzheimer's disease remains the most common neurodegenerative disorder, depicted mainly by memory loss and the presence in the brain of senile plaques and neurofibrillary tangles. This disease is related to several cellular alterations like the loss of synapses, neuronal death, disruption of lipid homeostasis, mitochondrial fragmentation, or raised oxidative stress. Notably, changes in the autophagic pathway have turned out to be a key factor in the early development of the disease. The aim of this research is to determine the impact of the APOE allele ε4 and G206D-PSEN1 on the underlying mechanisms of Alzheimer's disease. Methods Fibroblasts from Alzheimer's patients with APOE 3/4 + G206D-PSEN1 mutation and homozygous APOE ε4 were used to study the effects of APOE polymorphism and PSEN1 mutation on the autophagy pathway, mitochondrial network fragmentation, superoxide anion levels, lysosome clustering, and p62/SQSTM1 levels. Results We observed that the APOE allele ε4 in homozygosis induces mitochondrial network fragmentation that correlates with an increased colocalization with p62/SQSTM1, probably due to an inefficient autophagy. Moreover, G206D-PSEN1 mutation causes an impairment of the integrity of mitochondrial networks, triggering high superoxide anion levels and thus making APOE 3/4 + PSEN1 fibroblasts more vulnerable to cell death induced by oxidative stress. Of note, PSEN1 mutation induces accumulation and clustering of lysosomes that, along with an increase of global p62/SQSTM1, could compromise lysosomal function and, ultimately, its degradation. Conclusion The findings suggest that all these modifications could eventually contribute to the neuronal degeneration that underlies the pathogenesis of Alzheimer's disease. Further research in this area may help to develop targeted therapies for the treatment of Alzheimer's disease.
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Affiliation(s)
- Irene Costa-Laparra
- Neurobiology of the Basal Ganglia Laboratory, Department of Functional Systems and Neurobiology, Instituto Cajal, Spanish National Research Council (CSIC), Madrid, Spain
| | - Elena Juárez-Escoto
- Neurobiology of the Basal Ganglia Laboratory, Department of Functional Systems and Neurobiology, Instituto Cajal, Spanish National Research Council (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Vicario
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Stem Cells, Neurogenesis and Neurodegeneration Laboratory, Department of Molecular, Cellular and Developmental Neurobiology, Cajal Institute, Spanish National Research Council (CSIC), Madrid, Spain
| | - Rosario Moratalla
- Neurobiology of the Basal Ganglia Laboratory, Department of Functional Systems and Neurobiology, Instituto Cajal, Spanish National Research Council (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Patricia García-Sanz
- Neurobiology of the Basal Ganglia Laboratory, Department of Functional Systems and Neurobiology, Instituto Cajal, Spanish National Research Council (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
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Szabó Á, Vincze V, Chhatre AS, Jipa A, Bognár S, Varga KE, Banik P, Harmatos-Ürmösi A, Neukomm LJ, Juhász G. LC3-associated phagocytosis promotes glial degradation of axon debris after injury in Drosophila models. Nat Commun 2023; 14:3077. [PMID: 37248218 DOI: 10.1038/s41467-023-38755-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 05/09/2023] [Indexed: 05/31/2023] Open
Abstract
Glial engulfment of neuron-derived debris after trauma, during development, and in neurodegenerative diseases supports nervous system functions. However, mechanisms governing the efficiency of debris degradation in glia have remained largely unexplored. Here we show that LC3-associated phagocytosis (LAP), an engulfment pathway assisted by certain autophagy factors, promotes glial phagosome maturation in the Drosophila wing nerve. A LAP-specific subset of autophagy-related genes is required in glia for axon debris clearance, encoding members of the Atg8a (LC3) conjugation system and the Vps34 lipid kinase complex including UVRAG and Rubicon. Phagosomal Rubicon and Atg16 WD40 domain-dependent conjugation of Atg8a mediate proper breakdown of internalized axon fragments, and Rubicon overexpression in glia accelerates debris elimination. Finally, LAP promotes survival following traumatic brain injury. Our results reveal a role of glial LAP in the clearance of neuronal debris in vivo, with potential implications for the recovery of the injured nervous system.
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Affiliation(s)
- Áron Szabó
- Biological Research Center, Institute of Genetics, Eötvös Loránd Research Network (ELKH), Szeged, H-6726, Hungary.
| | - Virág Vincze
- Biological Research Center, Institute of Genetics, Eötvös Loránd Research Network (ELKH), Szeged, H-6726, Hungary
| | - Aishwarya Sanjay Chhatre
- Biological Research Center, Institute of Genetics, Eötvös Loránd Research Network (ELKH), Szeged, H-6726, Hungary
- Doctoral School of Biology, University of Szeged, Szeged, Hungary
| | - András Jipa
- Biological Research Center, Institute of Genetics, Eötvös Loránd Research Network (ELKH), Szeged, H-6726, Hungary
| | - Sarolta Bognár
- Biological Research Center, Institute of Genetics, Eötvös Loránd Research Network (ELKH), Szeged, H-6726, Hungary
| | - Katalin Eszter Varga
- Biological Research Center, Institute of Genetics, Eötvös Loránd Research Network (ELKH), Szeged, H-6726, Hungary
| | - Poulami Banik
- Biological Research Center, Institute of Genetics, Eötvös Loránd Research Network (ELKH), Szeged, H-6726, Hungary
| | - Adél Harmatos-Ürmösi
- Biological Research Center, Institute of Genetics, Eötvös Loránd Research Network (ELKH), Szeged, H-6726, Hungary
| | - Lukas J Neukomm
- Department of Fundamental Neurosciences, University of Lausanne, CH-1005, Lausanne, Switzerland
| | - Gábor Juhász
- Biological Research Center, Institute of Genetics, Eötvös Loránd Research Network (ELKH), Szeged, H-6726, Hungary.
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, H-1117, Hungary.
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Zhou J, Ma J, Yang C, Zhu X, Li J, Zheng X, Li X, Chen S, Feng L, Wang P, Ho MI, Ma W, Liao J, Li F, Wang C, Zhuang X, Jiang L, Kang BH, Gao C. A non-canonical role of ATG8 in Golgi recovery from heat stress in plants. NATURE PLANTS 2023; 9:749-765. [PMID: 37081290 DOI: 10.1038/s41477-023-01398-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
Above-optimal growth temperatures, usually referred to as heat stress (HS), pose a challenge to organisms' survival as they interfere with essential physiological functions and disrupt cellular organization. Previous studies have elucidated the complex transcriptional regulatory networks involved in plant HS responses, but the mechanisms of organellar remodelling and homeostasis during plant HS adaptations remain elusive. Here we report a non-canonical function of ATG8 in regulating the restoration of plant Golgi damaged by HS. Short-term acute HS causes vacuolation of the Golgi apparatus and translocation of ATG8 to the dilated Golgi membrane. The inactivation of the ATG conjugation system, but not of the upstream autophagic initiators, abolishes the targeting of ATG8 to the swollen Golgi, causing a delay in Golgi recovery after HS. Using TurboID-based proximity labelling, we identified CLATHRIN LIGHT CHAIN 2 (CLC2) as an interacting partner of ATG8 via the AIM-LDS interface. CLC2 is recruited to the cisternal membrane by ATG8 to facilitate Golgi reassembly. Collectively, our study reveals a hitherto unanticipated process of Golgi stack recovery from HS in plant cells and uncovers a previously unknown mechanism of organelle resilience involving ATG8.
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Affiliation(s)
- Jun Zhou
- MOE Key Laboratory & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China.
| | - Juncai Ma
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong, China
| | - Chao Yang
- MOE Key Laboratory & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xiu Zhu
- MOE Key Laboratory & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jing Li
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong, China
| | - Xuanang Zheng
- MOE Key Laboratory & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xibao Li
- MOE Key Laboratory & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Siyu Chen
- MOE Key Laboratory & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Lei Feng
- MOE Key Laboratory & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong, China
| | - Pengfei Wang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong, China
| | - Man Ip Ho
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong, China
| | - Wenlong Ma
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong, China
| | - Jun Liao
- MOE Key Laboratory & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Faqiang Li
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Chao Wang
- College of Life Sciences, Shaoxing University, Shaoxing, China
| | - Xiaohong Zhuang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong, China
| | - Liwen Jiang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong, China
| | - Byung-Ho Kang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong, China.
| | - Caiji Gao
- MOE Key Laboratory & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China.
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Wan W, Qian C, Wang Q, Li J, Zhang H, Wang L, Pu M, Huang Y, He Z, Zhou T, Shen H, Liu W. STING directly recruits WIPI2 for autophagosome formation during STING-induced autophagy. EMBO J 2023; 42:e112387. [PMID: 36872914 PMCID: PMC10106988 DOI: 10.15252/embj.2022112387] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 03/07/2023] Open
Abstract
The cGAS-STING pathway plays an important role in host defense by sensing pathogen DNA, inducing type I IFNs, and initiating autophagy. However, the molecular mechanism of autophagosome formation in cGAS-STING pathway-induced autophagy is still unclear. Here, we report that STING directly interacts with WIPI2, which is the key protein for LC3 lipidation in autophagy. Binding to WIPI2 is necessary for STING-induced autophagosome formation but does not affect STING activation and intracellular trafficking. In addition, the specific interaction between STING and the PI3P-binding motif of WIPI2 leads to the competition of WIPI2 binding between STING and PI3P, and mutual inhibition between STING-induced autophagy and canonical PI3P-dependent autophagy. Furthermore, we show that the STING-WIPI2 interaction is required for the clearance of cytoplasmic DNA and the attenuation of cGAS-STING signaling. Thus, the direct interaction between STING and WIPI2 enables STING to bypass the canonical upstream machinery to induce LC3 lipidation and autophagosome formation.
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Affiliation(s)
- Wei Wan
- Department of Biochemistry, and Department of Thoracic Surgery of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
| | - Chuying Qian
- Department of Biochemistry, and Department of Thoracic Surgery of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
| | - Qian Wang
- Department of Biochemistry, and Department of Thoracic Surgery of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
| | - Jin Li
- Department of Biochemistry, and Department of Thoracic Surgery of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
| | - Hongtao Zhang
- Department of Biochemistry, and Department of Thoracic Surgery of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
| | - Lei Wang
- Department of Biochemistry, and Department of Thoracic Surgery of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
| | - Maomao Pu
- Department of Metabolic Medicine, International Institutes of Medicine, the Fourth Affiliated HospitalZhejiang University School of MedicineYiwuChina
| | - Yewei Huang
- Department of Metabolic Medicine, International Institutes of Medicine, the Fourth Affiliated HospitalZhejiang University School of MedicineYiwuChina
| | - Zhengfu He
- Department of Biochemistry, and Department of Thoracic Surgery of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
| | - Tianhua Zhou
- Department of Biochemistry, and Department of Thoracic Surgery of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
| | - Han‐Ming Shen
- Faculty of Health SciencesUniversity of MacauMacauChina
| | - Wei Liu
- Department of Biochemistry, and Department of Thoracic Surgery of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
- Department of Metabolic Medicine, International Institutes of Medicine, the Fourth Affiliated HospitalZhejiang University School of MedicineYiwuChina
- Joint Institute of Genetics and Genomics Medicine between Zhejiang University and University of TorontoHangzhouChina
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Bhattacharya A, Mukherjee R, Kuncha SK, Brunstein ME, Rathore R, Junek S, Münch C, Dikic I. A lysosome membrane regeneration pathway depends on TBC1D15 and autophagic lysosomal reformation proteins. Nat Cell Biol 2023; 25:685-698. [PMID: 37024685 DOI: 10.1038/s41556-023-01125-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 03/07/2023] [Indexed: 04/08/2023]
Abstract
Acute lysosomal membrane damage reduces the cellular population of functional lysosomes. However, these damaged lysosomes have a remarkable recovery potential independent of lysosomal biogenesis and remain unaffected in cells depleted in TFEB and TFE3. We combined proximity-labelling-based proteomics, biochemistry and high-resolution microscopy to unravel a lysosomal membrane regeneration pathway that depends on ATG8, the lysosomal membrane protein LIMP2, the RAB7 GTPase-activating protein TBC1D15 and proteins required for autophagic lysosomal reformation, including dynamin-2, kinesin-5B and clathrin. Following lysosomal damage, LIMP2 acts as a lysophagy receptor to bind ATG8, which in turn recruits TBC1D15 to damaged membranes. TBC1D15 interacts with ATG8 proteins on damaged lysosomes and provides a scaffold to assemble and stabilize the autophagic lysosomal reformation machinery. This potentiates the formation of lysosomal tubules and subsequent dynamin-2-dependent scission. TBC1D15-mediated lysosome regeneration was also observed in a cell culture model of oxalate nephropathy.
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Affiliation(s)
- Anshu Bhattacharya
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | - Rukmini Mukherjee
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
- Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Santosh Kumar Kuncha
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | | | - Rajeshwari Rathore
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany
| | - Stephan Junek
- Max Planck Institute of Biophysics, Frankfurt, Germany
- Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Christian Münch
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany.
- Max Planck Institute of Biophysics, Frankfurt, Germany.
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Frankfurt, Germany.
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Fu J, Zhao L, Pang Y, Chen H, Yamamoto H, Chen Y, Li Z, Mizushima N, Jia H. Apicoplast biogenesis mediated by ATG8 requires the ATG12-ATG5-ATG16L and SNAP29 complexes in Toxoplasma gondii. Autophagy 2023; 19:1258-1276. [PMID: 36095096 PMCID: PMC10012919 DOI: 10.1080/15548627.2022.2123639] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 11/02/2022] Open
Abstract
In apicomplexan parasites, the macroautophagy/autophagy machinery is repurposed to maintain the plastid-like organelle apicoplast. Previously, we showed that in Toxoplasma and Plasmodium, ATG12 interacts with ATG5 in a non-covalent manner, in contrast to the covalent interaction in most organisms. However, it remained unknown whether apicomplexan parasites have functional orthologs of ATG16L1, a protein that is essential for the function of the covalent ATG12-ATG5 complex in vivo in other organisms. Furthermore, the mechanism used by the autophagy machinery to maintain the apicoplast is unclear. We report that the ATG12-ATG5-ATG16L complex exists in Toxoplasma gondii (Tg). This complex is localized on isolated structures at the periphery of the apicoplast dependent on TgATG16L. Inducible depletion of TgATG12, TgATG5, or TgATG16L caused loss of the apicoplast and affected parasite growth. We found that a putative soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) protein, synaptosomal-associated protein 29 (TgSNAP29, Qbc SNARE), is required to maintain the apicoplast in T. gondii. TgSNAP29 depletion disrupted TgATG8 localization at the apicoplast. Additionally, we identified a putative ubiquitin-interacting motif-docking site (UDS) of TgATG8. Mutation of the UDS site abolished TgATG8 localization on the apicoplast but not lipidation. These findings suggest that the TgATG12-TgATG5-TgATG16L complex is required for biogenesis of the apicoplast, in which TgATG8 is translocated to the apicoplast via vesicles in a SNARE -dependent manner in T. gondii.Abbreviations: AID: auxin-inducible degron; CCD: coiled-coil domain; HFF: human foreskin fibroblast; IAA: indole-3-acetic acid; LAP: LC3-associated phagocytosis; NAA: 1-naphthaleneacetic acid; PtdIns3P: phosphatidylinositol-3-phosphate; SNARE: soluble N-ethylmaleimide sensitive factor attachment protein receptor; UDS: ubiquitin-interacting motif-docking site; UIM: ubiquitin-interacting motif.
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Affiliation(s)
- Jiawen Fu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, HeilongjiangChina
| | - Lin Zhao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, HeilongjiangChina
| | - Yu Pang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, HeilongjiangChina
| | - Heming Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, HeilongjiangChina
| | - Hayashi Yamamoto
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuntong Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, HeilongjiangChina
| | - Zhaoran Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, HeilongjiangChina
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Honglin Jia
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, HeilongjiangChina
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Chen T, Tu S, Ding L, Jin M, Chen H, Zhou H. The role of autophagy in viral infections. J Biomed Sci 2023; 30:5. [PMID: 36653801 PMCID: PMC9846652 DOI: 10.1186/s12929-023-00899-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/10/2023] [Indexed: 01/20/2023] Open
Abstract
Autophagy is an evolutionarily conserved catabolic cellular process that exerts antiviral functions during a viral invasion. However, co-evolution and co-adaptation between viruses and autophagy have armed viruses with multiple strategies to subvert the autophagic machinery and counteract cellular antiviral responses. Specifically, the host cell quickly initiates the autophagy to degrade virus particles or virus components upon a viral infection, while cooperating with anti-viral interferon response to inhibit the virus replication. Degraded virus-derived antigens can be presented to T lymphocytes to orchestrate the adaptive immune response. Nevertheless, some viruses have evolved the ability to inhibit autophagy in order to evade degradation and immune responses. Others induce autophagy, but then hijack autophagosomes as a replication site, or hijack the secretion autophagy pathway to promote maturation and egress of virus particles, thereby increasing replication and transmission efficiency. Interestingly, different viruses have unique strategies to counteract different types of selective autophagy, such as exploiting autophagy to regulate organelle degradation, metabolic processes, and immune responses. In short, this review focuses on the interaction between autophagy and viruses, explaining how autophagy serves multiple roles in viral infection, with either proviral or antiviral functions.
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Affiliation(s)
- Tong Chen
- grid.35155.370000 0004 1790 4137State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430030 China ,grid.35155.370000 0004 1790 4137Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430030 China
| | - Shaoyu Tu
- grid.35155.370000 0004 1790 4137State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430030 China ,grid.35155.370000 0004 1790 4137Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430030 China
| | - Ling Ding
- grid.35155.370000 0004 1790 4137State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430030 China ,grid.35155.370000 0004 1790 4137Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430030 China
| | - Meilin Jin
- grid.35155.370000 0004 1790 4137State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430030 China ,grid.35155.370000 0004 1790 4137Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430030 China
| | - Huanchun Chen
- grid.35155.370000 0004 1790 4137State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430030 China ,grid.35155.370000 0004 1790 4137Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430030 China
| | - Hongbo Zhou
- grid.35155.370000 0004 1790 4137State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430030 China ,grid.35155.370000 0004 1790 4137Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430030 China
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46
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Abstract
Macroautophagy and microautophagy are highly conserved eukaryotic cellular processes that degrade cytoplasmic material in lysosomes. Both pathways involve characteristic membrane dynamics regulated by autophagy-related proteins and other molecules, some of which are shared between the two pathways. Over the past few years, the application of new technologies, such as cryo-electron microscopy, coevolution-based structural prediction and in vitro reconstitution, has revealed the functions of individual autophagy gene products, especially in autophagy induction, membrane reorganization and cargo recognition. Concomitantly, mutations in autophagy genes have been linked to human disorders, particularly neurodegenerative diseases, emphasizing the potential pathogenic implications of autophagy defects. Accumulating genome data have also illuminated the evolution of autophagy genes within eukaryotes as well as their transition from possible ancestral elements in prokaryotes.
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Affiliation(s)
- Hayashi Yamamoto
- grid.26999.3d0000 0001 2151 536XDepartment of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan ,grid.410821.e0000 0001 2173 8328Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Sidi Zhang
- grid.26999.3d0000 0001 2151 536XDepartment of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Noboru Mizushima
- grid.26999.3d0000 0001 2151 536XDepartment of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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47
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Kumar AV, Mills J. Non-canonical autophagy in aging and age-related diseases. Front Cell Dev Biol 2023; 11:1137870. [PMID: 36910139 PMCID: PMC9995962 DOI: 10.3389/fcell.2023.1137870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/13/2023] [Indexed: 02/25/2023] Open
Abstract
Autophagy, one of the arms of proteostasis, influences aging and age-related diseases. Recently, the discovery of additional roles of autophagy-related proteins in non-canonical degradation and secretion has revealed alternative fates of autophagic cargo. Some of these non-canonical pathways have been linked to neurodegenerative diseases and improving the understanding of this link is crucial for their potential targetability in aging and age-related diseases. This review discusses recent investigations of the involvement of non-canonical autophagy players and pathways in age-related diseases that are now beginning to be discovered. Unraveling these pathways and their relation to classical autophagy could unearth a fascinating new layer of proteostasis regulation during normal aging and in longevity.
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Affiliation(s)
- Anita V Kumar
- Molecular Biology, Cell Biology and Biochemistry Department, Brown University, Providence, RI, United States
| | - Joslyn Mills
- Molecular Biology, Cell Biology and Biochemistry Department, Brown University, Providence, RI, United States.,Wheaton College, Biology Department, Norton, MA, United States
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48
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Reid SE, Kolapalli SP, Nielsen TM, Frankel LB. Canonical and non-canonical roles for ATG8 proteins in autophagy and beyond. Front Mol Biosci 2022; 9:1074701. [PMID: 36601581 PMCID: PMC9806848 DOI: 10.3389/fmolb.2022.1074701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
During autophagy, the ATG8 family proteins have several well-characterized roles in facilitating early, mid, and late steps of autophagy, including autophagosome expansion, cargo recruitment and autophagosome-lysosome fusion. Their discovery has importantly allowed for precise experimental monitoring of the pathway, bringing about a huge expansion of research in the field over the last decades. In this review, we discuss both canonical and non-canonical roles of the autophagic lipidation machinery, with particular focus on the ATG8 proteins, their post-translational modifications and their increasingly uncovered alternative roles mediated through their anchoring at different membranes. These include endosomes, macropinosomes, phagosomes and the plasma membrane, to which ATG8 proteins can bind through canonical or alternative lipidation. Beyond new ATG8 binding partners and cargo types, we also explore several open questions related to alternative outcomes of autophagic machinery engagement beyond degradation. These include their roles in plasma membrane repair and secretion of selected substrates as well as the physiological implications hereof in health and disease.
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Affiliation(s)
| | | | | | - Lisa B. Frankel
- Danish Cancer Society Research Center, Copenhagen, Denmark,Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark,*Correspondence: Lisa B. Frankel,
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49
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Serramito-Gómez I, Terraza-Silvestre E, Fernández-Cabrera Á, Villamuera R, Pimentel-Muiños FX. ATG16L1 WD40 domain-dependent IL10R (interleukin 10 receptor) signaling is insensitive to the T300A Crohn disease risk polymorphism. Autophagy 2022; 18:3023-3030. [PMID: 35311452 PMCID: PMC9673950 DOI: 10.1080/15548627.2022.2054241] [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: 12/15/2022] Open
Abstract
A coding allele of ATG16L1 that increases the risk of Crohn disease (T300A; rs2241880) impairs the interaction between the C-terminal WD40 domain (WDD) and proteins containing a WDD-binding motif, thus specifically inhibiting the unconventional autophagic activities of ATG16L1. In a recent publication we described a novel atypical role of ATG16L1 in the regulation of IL10R (interleukin 10 receptor) trafficking and signaling, an activity that involves direct interaction between the WDD and a target motif present in IL10RB (interleukin 10 receptor subunit beta). Here we show that, unexpectedly, neither the ability of ATG16L1 to interact with IL10RB nor its role in supporting IL10 signaling are altered by the T300A mutation. These results indicate that the ATG16L1T300A allele selectively impairs the interaction between the WDD and a subset of WDD-binding motif versions, suggesting that only a fraction of the unconventional activities mediated by ATG16L1 are required to prevent Crohn disease.Abbreviations: ATG, autophagy related; ATG16L1, autophagy related 16 like 1; BMDMs, bone marrow-derived macrophages; CRISPR, clustered regularly interspaced short palindromic repeats; CSF1/M-CSF, colony stimulating factor 1; FBS, fetal bovine serum; GSH, glutathione; IL10, interleukin 10; IL10R, interleukin 10 receptor; LPS, lipopolysaccharide; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; MEFs, mouse embryonic fibroblasts; PMA, phorbol myristate acetate; p-STAT3: phosphorylated STAT3; qPCR, quantitative polymerase chain reaction; SDS, sodium dodecyl sulfate; sgRNA, single guide RNA; TMEM59, transmembrane protein 59; TNF, tumor necrosis factor; TNFAIP3/A20, TNF alpha induced protein 3; WDD, WD40 domain; WIPI2, WD repeat domain, phosphoinositide interacting 2.
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Affiliation(s)
- Inmaculada Serramito-Gómez
- Instituto de Biología Molecular y Celular del CáncerCentro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Elena Terraza-Silvestre
- Instituto de Biología Molecular y Celular del CáncerCentro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Álvaro Fernández-Cabrera
- Instituto de Biología Molecular y Celular del CáncerCentro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Raquel Villamuera
- Instituto de Biología Molecular y Celular del CáncerCentro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Felipe X. Pimentel-Muiños
- Instituto de Biología Molecular y Celular del CáncerCentro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain,CONTACT Felipe X. Pimentel-Muiños ;Instituto de Biología Molecular y Celular del Cáncer. Centro de Investigación del Cáncer, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera, 1. Salamanca, Madrid, 28049, Spain
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50
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Xu J, Yang KC, Go NE, Colborne S, Ho CJ, Hosseini-Beheshti E, Lystad AH, Simonsen A, Guns ET, Morin GB, Gorski SM. Chloroquine treatment induces secretion of autophagy-related proteins and inclusion of Atg8-family proteins in distinct extracellular vesicle populations. Autophagy 2022; 18:2547-2560. [PMID: 35220892 PMCID: PMC9629075 DOI: 10.1080/15548627.2022.2039535] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Chloroquine (CQ), a lysosomotropic agent, is commonly used to inhibit lysosomal degradation and macroautophagy/autophagy. Here we investigated the cell-extrinsic effects of CQ on secretion. We showed that lysosomal and autophagy inhibition by CQ altered the secretome, and induced the release of Atg8 orthologs and autophagy receptors. Atg8-family proteins, in particular, were secreted inside small extracellular vesicles (sEVs) in a lipidation-dependent manner. CQ treatment enhanced the release of Atg8-family proteins inside sEVs. Using full-length ATG16L1 and an ATG16L1 mutant that enables Atg8-family protein lipidation on double but not on single membranes, we demonstrated that LC3B is released in two distinct sEV populations: one enriched with SDCBP/Syntenin-1, CD63, and endosomal lipidated LC3B, and another that contains LC3B but is not enriched with SDCBP/Syntenin-1 or CD63, and which our data supports as originating from a double-membrane source. Our findings underscore the context-dependency of sEV heterogeneity and composition, and illustrate the integration of autophagy and sEV composition in response to lysosomal inhibition.Abbreviations: ACTB: actin beta; ANOVA: analysis of variance; ATG4B: autophagy related 4B cysteine peptidase; Atg8: autophagy related 8; ATG16L1: autophagy related 16 like 1; ATP5F1A/ATP5a: ATP synthase F1 subunit alpha; CALCOCO2: calcium binding and coiled-coil domain 2; CASP3: caspase 3; CASP7: caspase 7; CQ: chloroquine; CD9: CD9 molecule; CD63: CD63 molecule; DAPI: 4',6-diamidino-2-phenylindole; DQ-BSA: dye quenched-bovine serum albumin; ER: endoplasmic reticulum; ERN1/IRE1a: endoplasmic reticulum to nucleus signaling 1; EV: extracellular vesicles; FBS: fetal bovine serum; FDR: false discovery rate; GABARAP: GABA type A receptor-associated protein; GABARAPL2: GABA type A receptor associated protein like 2; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFP: green fluorescent protein; GO: gene ontology; HCQ: hydroxychloroquine; HSP90AA1: heat shock protein 90 alpha family class A member 1; IP: immunoprecipitation; KO: knockout; LAMP2: lysosomal associated membrane protein 2; LIR: LC3-interacting region; LMNA: lamin A/C; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MS: mass spectrometry; NBR1: NBR1 autophagy cargo receptor; NCOA4: nuclear receptor coactivator 4; NTA: nanoparticle tracking analysis; PE: phosphatidylethanolamine; PECA: probe-level expression change averaging; SDCBP/syntenin-1: syndecan binding protein; SD: standard deviation; SE: secreted; sEV: small extracellular vesicles; SQSTM1/p62: sequestosome 1; TAX1BP1: Tax1 binding protein 1; TEM: transmission electron microscopy; TMT: tandem-mass tag; TSG101: tumor susceptibility 101; ULK1: unc-51 like autophagy activating kinase 1; WC: whole cell.
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Affiliation(s)
- Jing Xu
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Kevin C Yang
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Nancy Erro Go
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Shane Colborne
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Cally J Ho
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Elham Hosseini-Beheshti
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney NSWAustralia
| | - Alf H Lystad
- 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, 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, Norway,Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, Norway
| | - Emma Tomlinson Guns
- The Vancouver Prostate Centre, Vancouver, BC, Canada,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Gregg B Morin
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Sharon M Gorski
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, BC, Canada,CONTACT Sharon M Gorski Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, Canada
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