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House M, Khadayat K, Trybala TN, Nambiar N, Jones E, Abel SM, Baccile J, Joshi AS. Phosphatidic acid drives spatiotemporal distribution of Pex30 at ER-LD contact sites. J Cell Biol 2025; 224:e202405162. [PMID: 40407416 PMCID: PMC12101077 DOI: 10.1083/jcb.202405162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 03/18/2025] [Accepted: 04/25/2025] [Indexed: 05/26/2025] Open
Abstract
Lipid droplets (LDs) are ubiquitous neutral lipid storage organelles that form at discrete subdomains in the ER bilayer. The assembly of these ER subdomains and the mechanism by which proteins are recruited to them is poorly understood. Here, we investigate the spatiotemporal distribution of Pex30 at the ER-LD membrane contact sites (MCSs). Pex30, an ER membrane-shaping protein, has a reticulon homology domain, a dysferlin (DysF) domain, and a Duf4196 domain. Deletion of SEI1, which codes for seipin, a highly conserved protein required for LD biogenesis, results in accumulation of Pex30 and phosphatidic acid (PA) at ER-LD contact sites. We show that PA recruits Pex30 at ER subdomains by binding to the DysF domain. The distribution of Pex30 as well as PA is also affected by phosphatidylcholine (PC) levels. We propose that PA regulates the spatiotemporal distribution of Pex30 at ER subdomains that plays a critical role in driving the formation of LDs in the ER membrane.
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Affiliation(s)
- Morgan House
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Karan Khadayat
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Thomas N. Trybala
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Nikhil Nambiar
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA
| | - Elizabeth Jones
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Steven M. Abel
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA
| | - Joshua Baccile
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Amit S. Joshi
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
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2
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Yamashita SI, Arai R, Hada H, Padman BS, Lazarou M, Chan DC, Kanki T, Waguri S. The mitophagy receptors BNIP3 and NIX mediate tight attachment and expansion of the isolation membrane to mitochondria. J Cell Biol 2025; 224:e202408166. [PMID: 40358358 PMCID: PMC12071194 DOI: 10.1083/jcb.202408166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2024] [Revised: 03/24/2025] [Accepted: 04/17/2025] [Indexed: 05/15/2025] Open
Abstract
BNIP3 and NIX are the main receptors for mitophagy, but their mechanisms of action remain elusive. Here, we used correlative light EM (CLEM) and electron tomography to reveal the tight attachment of isolation membranes (IMs) to mitochondrial protrusions, often connected with ER via thin tubular and/or linear structures. In BNIP3/NIX-double knockout (DKO) HeLa cells, the ULK1 complex and nascent IM formed on mitochondria, but the IM did not expand. Artificial tethering of LC3B to mitochondria induced mitophagy that was equally efficient in DKO cells and WT cells. BNIP3 and NIX accumulated at the segregated mitochondrial protrusions via binding with LC3 through their LIR motifs but did not require dimer formation. Finally, the average distance between the IM and the mitochondrial surface in receptor-mediated mitophagy was significantly smaller than that in ubiquitin-mediated mitophagy. Collectively, these results indicate that BNIP3 and NIX are required for the tight attachment and expansion of the IM along the mitochondrial surface during mitophagy.
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Affiliation(s)
- Shun-ichi Yamashita
- Department of Cellular Physiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Ritsuko Arai
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Fukushima, Japan
- Division of Biofunctional Sciences, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroshi Hada
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Benjamin Scott Padman
- Telethon Kids Institute, Perth Children’s Hospital, Nedlands, Australia
- The University of Western Australia, Crawley, Australia
| | - Michael Lazarou
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - David C. Chan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tomotake Kanki
- Department of Cellular Physiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Satoshi Waguri
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Fukushima, Japan
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3
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Küng C, Lazarou M, Nguyen TN. Advances in mitophagy initiation mechanisms. Curr Opin Cell Biol 2025; 94:102493. [PMID: 40117675 DOI: 10.1016/j.ceb.2025.102493] [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: 01/20/2025] [Revised: 02/19/2025] [Accepted: 02/20/2025] [Indexed: 03/23/2025]
Abstract
Mitophagy is an important lysosomal degradative pathway that removes damaged or unwanted mitochondria to maintain cellular and organismal homeostasis. The mechanisms behind how mitophagy is initiated to form autophagosomes around mitochondria have gained a lot of interest since they can be potentially targeted by mitophagy-inducing therapeutics. Mitophagy initiation can be driven by various autophagy receptors or adaptors that respond to different cellular and mitochondrial stimuli, ranging from mitochondrial damage to metabolic rewiring. This review will cover recent advances in our understanding of how mitophagy is initiated, and by doing so reveal the mechanistic plasticity of how autophagosome formation can begin.
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Affiliation(s)
- Catharina Küng
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Michael Lazarou
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia; Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia; Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA.
| | - Thanh Ngoc Nguyen
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia; Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia; Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA.
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4
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Wosnitzka E, Gambarotto L, Nikoletopoulou V. Macroautophagy at the service of synapses. Curr Opin Neurobiol 2025; 93:103054. [PMID: 40414166 DOI: 10.1016/j.conb.2025.103054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2024] [Revised: 04/02/2025] [Accepted: 05/02/2025] [Indexed: 05/27/2025]
Abstract
Post-mitotic and highly polarized neurons are dependent on the fitness of their synapses, which are often found a long distance away from the soma. How the synaptic proteome is maintained, dynamically reshaped, and continuously turned over is a topic of intense investigation. Autophagy, a highly conserved, lysosome-mediated degradation pathway has emerged as a vital component of long-term neuronal maintenance, and now more specifically of synaptic homeostasis. Here, we review the most recent findings on how autophagy undergoes both dynamic and local regulation at the synapse, and how it contributes to pre- and post-synaptic proteostasis and function. We also discuss the insights and open questions that this new evidence brings.
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Affiliation(s)
- Erin Wosnitzka
- Department of Fundamental Neurosciences, University of Lausanne, Rue du Bugnon 9, 1005, Lausanne, Switzerland
| | - Lisa Gambarotto
- Department of Fundamental Neurosciences, University of Lausanne, Rue du Bugnon 9, 1005, Lausanne, Switzerland
| | - Vassiliki Nikoletopoulou
- Department of Fundamental Neurosciences, University of Lausanne, Rue du Bugnon 9, 1005, Lausanne, Switzerland.
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5
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Muneshige K, Hatakeyama R. Vacuoles provide the source membrane for TORC1-containing signaling endosomes. J Cell Biol 2025; 224:e202407021. [PMID: 40052923 PMCID: PMC11893502 DOI: 10.1083/jcb.202407021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 12/12/2024] [Accepted: 02/14/2025] [Indexed: 03/14/2025] Open
Abstract
Organelle biogenesis is fundamental to eukaryotic cell biology. Yeast signaling endosomes were recently identified as a signaling platform for the evolutionarily conserved Target of Rapamycin Complex 1 (TORC1) kinase complex. Despite the importance of signaling endosomes for TORC1-mediated control of cellular metabolism, how this organelle is generated has been a mystery. Here, we developed a system to induce synchronized de novo formation of signaling endosomes, enabling real-time monitoring of their biogenesis. Using this system, we identify vacuoles as a membrane source for newly formed signaling endosomes. Membrane supply from vacuoles is mediated by the CROP membrane-cutting complex, consisting of Atg18 PROPPIN and retromer subunits. The formation of signaling endosomes requires TORC1 activity, suggestive of a tightly regulated process. This study unveiled the first mechanistic principles and molecular participants of signaling endosome biogenesis.
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Affiliation(s)
- Kenji Muneshige
- Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - Riko Hatakeyama
- Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
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6
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Zheng W, Pu M, Zeng S, Zhang H, Wang Q, Chen T, Zhou T, Chang C, Neculai D, Liu W. S-palmitoylation modulates ATG2-dependent non-vesicular lipid transport during starvation-induced autophagy. EMBO J 2025; 44:2596-2619. [PMID: 40128367 PMCID: PMC12048663 DOI: 10.1038/s44318-025-00410-7] [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: 09/26/2024] [Revised: 02/22/2025] [Accepted: 03/02/2025] [Indexed: 03/26/2025] Open
Abstract
Lipid transfer proteins mediate the non-vesicular transport of lipids at membrane contact sites to regulate the lipid composition of organelle membranes. Despite significant recent advances in our understanding of the structural basis for lipid transfer, its functional regulation remains unclear. In this study, we report that S-palmitoylation modulates the cellular function of ATG2, a rod-like lipid transfer protein responsible for transporting phospholipids from the endoplasmic reticulum (ER) to phagophores during autophagosome formation. During starvation-induced autophagy, ATG2A undergoes depalmitoylation as the balance between ZDHHC11-mediated palmitoylation and APT1-mediated depalmitoylation. Inhibition of ATG2A depalmitoylation leads to impaired autophagosome formation and disrupted autophagic flux. Further, in cell and in vitro analyses demonstrate that S-palmitoylation at the C-terminus of ATG2A anchors the C-terminus to the ER. Depalmitoylation detaches the C-terminus from the ER membrane, enabling it to interact with phagophores and promoting their growth. These findings elucidate a S-palmitoylation-dependent regulatory mechanism of cellular ATG2, which may represent a broad regulatory strategy for lipid transport mediated by bridge-like transporters within cells.
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Affiliation(s)
- Wenhui Zheng
- Department of Respiratory and Critical Care Medicine, Center for Metabolism Research, The Fourth Affiliated Hospital of Zhejiang University School of Medicine and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China
| | - Maomao Pu
- Department of Respiratory and Critical Care Medicine, Center for Metabolism Research, The Fourth Affiliated Hospital of Zhejiang University School of Medicine and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China
| | - Sai Zeng
- Department of Respiratory and Critical Care Medicine, Center for Metabolism Research, The Fourth Affiliated Hospital of Zhejiang University School of Medicine and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China
| | - Hongtao Zhang
- Department of Respiratory and Critical Care Medicine, Center for Metabolism Research, The Fourth Affiliated Hospital of Zhejiang University School of Medicine and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China
| | - Qian Wang
- Department of Respiratory and Critical Care Medicine, Center for Metabolism Research, The Fourth Affiliated Hospital of Zhejiang University School of Medicine and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China
| | - Tao Chen
- Department of Respiratory and Critical Care Medicine, Center for Metabolism Research, The Fourth Affiliated Hospital of Zhejiang University School of Medicine and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China
| | - Tianhua Zhou
- Department of Respiratory and Critical Care Medicine, Center for Metabolism Research, The Fourth Affiliated Hospital of Zhejiang University School of Medicine and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China
| | - Chunmei Chang
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.
| | - Dante Neculai
- Department of Respiratory and Critical Care Medicine, Center for Metabolism Research, The Fourth Affiliated Hospital of Zhejiang University School of Medicine and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China.
| | - Wei Liu
- Department of Respiratory and Critical Care Medicine, Center for Metabolism Research, The Fourth Affiliated Hospital of Zhejiang University School of Medicine and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China.
- Department of Ultrasound Medicine and State Key laboratory Implantation Device, The Second Affiliated Hospital of Zhejiang University, Hangzhou, China.
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7
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Shen H, Xie Y, Wang Y, Xie Y, Wang Y, Su Z, Zhao L, Yao S, Cao X, Liang J, Long J, Zhong R, Tang J, Wang S, Zhang L, Wang X, Stork B, Cui L, Wu W. The ER protein CANX (calnexin)-mediated autophagy protects against alzheimer disease. Autophagy 2025; 21:1096-1115. [PMID: 39813987 PMCID: PMC12013425 DOI: 10.1080/15548627.2024.2447206] [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: 06/23/2024] [Revised: 12/15/2024] [Accepted: 12/22/2024] [Indexed: 01/18/2025] Open
Abstract
Although the relationship between macroautophagy/autophagy and Alzheimer disease (AD) is widely studied, the underlying mechanisms are poorly understood, especially the regulatory role of the initiation signaling of autophagy on AD. Here, we find that the ER transmembrane protein CANX (calnexin) is a novel interaction partner of the autophagy-inducing kinase ULK1 and is required for ULK1 recruitment to the ER under basal or starved conditions. Loss of CANX results in the inactivity of ULK1 kinase and inhibits autophagy flux. In the brains of people with AD and APP-PSEN1 mice, the interaction of CANX and ULK1 declines. In mice, the lack of CANX in hippocampal neurons causes the accumulation of autophagy receptors and neuron damage, which affects the cognitive function of C57BL/6 mice. Conversely, overexpression of CANX in hippocampal neurons enhances autophagy flux and partially contributes to improving cognitive function of APP-PSEN1 mice, but not the CANX variant lacking the interaction domain with ULK1. These findings reveal a novel role of CANX in autophagy activity and cognitive function by cooperating with ULK1.Abbreviation: AD: Alzheimer disease; APEX: ascorbate peroxidase; APP: amyloid beta precursor protein; APP-PSEN1 mice: amyloid beta precursor protein-presenilin 1 transgenic mice; ATG: autophagy related; Aβ: amyloid-β; BiFC: bimolecular fluorescence complementation; CANX: calnexin; EBSS: Earle's balanced salt solution; EM: electron microscopy; IP: immunopurification; KO: knockout; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MWM: Morris water maze; PLA: proximity ligation assay; PtdIns3K: class III phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate; SQSTM1/p62, sequestosome 1.
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Affiliation(s)
- Hongtao Shen
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yuying Xie
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Yan Wang
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Yusheng Xie
- Department of Pharmacology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yongxiang Wang
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- Department of Rehabilitation Medicine, Pingshan General Hospital, Southern Medical University, Shenzhen, China
- Department of Rehabilitation Medicine, Pingshan District Peoples’ Hospital of Shenzhen, Shenzhen, China
| | - Zhenyan Su
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Laixi Zhao
- Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Shi Yao
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Xiaoling Cao
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Jinglan Liang
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Junrui Long
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Rimei Zhong
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Jinfeng Tang
- Clinical Research and Experimental Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Sijie Wang
- Clinical Research and Experimental Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Liangqing Zhang
- Department of Anesthesiology, Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Xiaojing Wang
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Björn Stork
- Institute of Molecular Medicine I, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lili Cui
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- The Marine Biomedical Research Institute of Guangdong, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, China
| | - Wenxian Wu
- Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
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8
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Xun J, Tan JX. Lysosomal Repair in Health and Disease. J Cell Physiol 2025; 240:e70044. [PMID: 40349217 PMCID: PMC12066097 DOI: 10.1002/jcp.70044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2025] [Revised: 04/17/2025] [Accepted: 04/21/2025] [Indexed: 05/14/2025]
Abstract
Lysosomes are essential organelles degrading a wide range of substrates, maintaining cellular homeostasis, and regulating cell growth through nutrient and metabolic signaling. A key vulnerability of lysosomes is their membrane permeabilization (LMP), a process tightly linked to diseases including aging, neurodegeneration, lysosomal storage disorders, and cardiovascular disease. Research progress in the past few years has greatly improved our understanding of lysosomal repair mechanisms. Upon LMP, cells activate multiple membrane remodeling processes to restore lysosomal integrity, such as membrane invagination, tubulation, lipid patching, and membrane stabilization. These repair pathways are critical in preserving cellular stress tolerance and preventing deleterious inflammation and cell death triggered by lysosomal damage. This review focuses on the expanding mechanistic insights of lysosomal repair, highlighting its crucial role in maintaining cellular health and the implications for disease pathogenesis and therapeutic strategies.
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Affiliation(s)
- Jinrui Xun
- Aging InstituteUniversity of Pittsburgh School of Medicine/University of Pittsburgh Medical CenterPittsburghPennsylvaniaUSA
| | - Jay Xiaojun Tan
- Aging InstituteUniversity of Pittsburgh School of Medicine/University of Pittsburgh Medical CenterPittsburghPennsylvaniaUSA
- Department of Cell BiologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
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9
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Gross AS, Raffeiner M, Zeng Y, Üstün S, Dagdas Y. Autophagy in Plant Health and Disease. ANNUAL REVIEW OF PLANT BIOLOGY 2025; 76:197-227. [PMID: 39841933 DOI: 10.1146/annurev-arplant-060324-094912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2025]
Abstract
Autophagy has emerged as an essential quality control pathway in plants that selectively and rapidly removes damaged or unwanted cellular components to maintain cellular homeostasis. It can recycle a broad range of cargoes, including entire organelles, protein aggregates, and even invading microbes. It involves the de novo biogenesis of a new cellular compartment, making it intimately linked to endomembrane trafficking pathways. Autophagy is induced by a wide range of biotic and abiotic stress factors, and autophagy mutant plants are highly sensitive to stress, making it an attractive target for improving plant stress resilience. Here, we critically discuss recent discoveries related to plant autophagy and highlight open questions and future research areas.
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Affiliation(s)
- Angelina S Gross
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria;
- Current affiliation: Department of Applied Genetics and Cell Biology, Institute of Molecular Plant Biology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Margot Raffeiner
- Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Yonglun Zeng
- State Key Laboratory of Plant Diversity and Specialty Crops and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Suayib Üstün
- Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Yasin Dagdas
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria;
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10
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Song JZ, Li H, Yang H, Liu R, Zhang W, He T, Xie MX, Chen C, Cui L, Wu S, Rong Y, Pan LF, Zhu J, Gong Q, Wang J, Qin Z, Xie Z. Recruitment of Atg1 to the phagophore by Atg8 orchestrates autophagy machineries. Nat Struct Mol Biol 2025:10.1038/s41594-025-01546-0. [PMID: 40295771 DOI: 10.1038/s41594-025-01546-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 03/24/2025] [Indexed: 04/30/2025]
Abstract
Autophagy-related (Atg) proteins catalyze autophagosome formation at the phagophore assembly site (PAS). The assembly of Atg proteins at the PAS follows a semihierarchical order, in which Atg8 is thought to be quite downstream but still able to control the size of autophagosomes. Yet, how Atg8 coordinates multiple branches of autophagy machinery to regulate autophagosomal size is not clear. Here, we show that, in yeast, Atg8 positively regulates the autophagy-specific phosphatidylinositol 3-OH kinase complex and the retrograde trafficking of Atg9 vesicles through interaction with Atg1. Mechanistically, Atg8 does not enhance the kinase activity of Atg1; instead, it recruits Atg1 to the surface of the phagophore likely to orient Atg1's activity toward select substrates, leading to efficient phagophore expansion. Artificial tethering of Atg1 kinase domains to Atg8s enhanced autophagy in yeast, human and plant cells and improved muscle performance in worms. We propose that Atg8-mediated relocation of Atg1 from the PAS scaffold to the phagophore is a critical step in positive autophagy regulation.
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Affiliation(s)
- Jing-Zhen Song
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Hui Li
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Haiyan Yang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Rui Liu
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wenting Zhang
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Tianlong He
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Meng-Xi Xie
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chen Chen
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Li Cui
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shian Wu
- School of Life Sciences, Nankai University, Tianjin, China
| | - Yueguang Rong
- School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
| | - Li-Feng Pan
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Jing Zhu
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qingqiu Gong
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Juan Wang
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China.
| | - Zhao Qin
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, School of Medicine, Tongji University, Shanghai, China.
- Collaborative Innovation Center for Brain Science, Tongji University, Shanghai, China.
| | - Zhiping Xie
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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11
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Swan LE. VPS13 and bridge-like lipid transporters, mechanisms, and mysteries. Front Neurosci 2025; 19:1534061. [PMID: 40356703 PMCID: PMC12066543 DOI: 10.3389/fnins.2025.1534061] [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: 11/25/2024] [Accepted: 03/14/2025] [Indexed: 05/15/2025] Open
Abstract
Bridge-like lipid transporters (BLTPs) have recently been revealed as key regulators of intraorganellar lipid trafficking, with their loss being associated with defective synaptic signalling and congenital neurological diseases. This group consists of five protein subfamilies [BLTP1-3, autophagy-related 2 (ATG2), and vacuolar protein sorting 13 (VPS13)], which mediate minimally selective lipid transfer between cellular membranes. Deceptively simple in both structure and presumed function, this review addresses open questions as to how bridge-like transporters work, the functional consequences of bulk lipid transfer on cellular signalling, and summarises some recent studies that have shed light on the surprising level of regulation and specificity found in this family of transporters.
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Affiliation(s)
- Laura Elizabeth Swan
- Department of Biochemistry, Cell and Systems Biology, University of Liverpool, Liverpool, United Kingdom
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12
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Zhang H, Meléndez A. Conserved components of the macroautophagy machinery in Caenorhabditis elegans. Genetics 2025; 229:iyaf007. [PMID: 40180610 PMCID: PMC12005284 DOI: 10.1093/genetics/iyaf007] [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: 03/29/2024] [Accepted: 12/13/2024] [Indexed: 04/05/2025] Open
Abstract
Macroautophagy involves the sequestration of cytoplasmic contents in a double-membrane autophagosome and its subsequent delivery to lysosomes for degradation and recycling. In Caenorhabditis elegans, autophagy participates in diverse processes such as stress resistance, cell fate specification, tissue remodeling, aging, and adaptive immunity. Genetic screens in C. elegans have identified a set of metazoan-specific autophagy genes that form the basis for our molecular understanding of steps unique to the autophagy pathway in multicellular organisms. Suppressor screens have uncovered multiple mechanisms that modulate autophagy activity under physiological conditions. C. elegans also provides a model to investigate how autophagy activity is coordinately controlled at an organismal level. In this chapter, we will discuss the molecular machinery, regulation, and physiological functions of autophagy, and also methods utilized for monitoring autophagy during C. elegans development.
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Affiliation(s)
- Hong Zhang
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P.R. China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Alicia Meléndez
- Department of Biology, Queens College, City University of New York, Flushing, NY 11367, USA
- Molecular, Cellular and Developmental Biology and Biochemistry Ph.D. Programs, The Graduate Center of the City University of New York, New York, NY 10016, USA
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13
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Hanna MG, Rodriguez Cruz HO, Fujise K, Wu Y, Xu CS, Pang S, Li Z, Monetti M, De Camilli P. BLTP3A is associated with membranes of the late endocytic pathway and is an effector of CASM. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.09.28.615015. [PMID: 39386594 PMCID: PMC11463362 DOI: 10.1101/2024.09.28.615015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Recent studies have identified a family of rod-shaped proteins thought to mediate lipid transfer at intracellular membrane contacts by a bridge-like mechanism. We show one such protein, bridge-like lipid transfer protein 3A (BLTP3A)/UHRF1BP1 binds VAMP7 vesicles via its C-terminal region and anchors them to lysosomes via its chorein domain containing N-terminal region to Rab7. Upon lysosome damage, BLTP3A-positive vesicles rapidly (within minutes) dissociate from lysosomes. Lysosome damage is known to activate the CASM (Conjugation of ATG8 to Single Membranes) pathway leading to lipidation and recruitment to lysosomes of mammalian ATG8 (mATG8) proteins. We find that this process drives the reassociation of BLTP3A with damaged lysosomes via an interaction of its LIR motif with mATG8 which coincides with a dissociation from the vesicles. Our findings reveal that BLTP3A is an effector of CASM, potentially as part of a mechanism to help repair or minimize lysosome damage.
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Affiliation(s)
- Michael G. Hanna
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Hely O. Rodriguez Cruz
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Kenshiro Fujise
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Yumei Wu
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - C. Shan Xu
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT
| | - Song Pang
- Yale University School of Medicine, New Haven, CT
| | - Zhuonging Li
- Proteomics Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mara Monetti
- Proteomics Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pietro De Camilli
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
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14
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Neuman SD, Thakur RS, Gratz SJ, O'Connor-Giles KM, Bashirullah A. Neurodegenerative and Neurodevelopmental Roles for Bulk Lipid Transporters VPS13A and BLTP2. Mov Disord 2025. [PMID: 40152532 DOI: 10.1002/mds.30178] [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: 12/19/2024] [Revised: 02/27/2025] [Accepted: 03/06/2025] [Indexed: 03/29/2025] Open
Abstract
BACKGROUND Bridge-like lipid transfer proteins (BLTPs) mediate bulk lipid transport at membrane contact sites. Mutations in BLTPs are linked to both early-onset neurodevelopmental and later-onset neurodegenerative diseases, including movement disorders. The tissue specificity and temporal requirements of BLTPs in disease pathogenesis remain poorly understood. OBJECTIVE The objective of this study was to determine tissue-specific and aging-dependent roles for VPS13A and BLTP2 using Drosophila models. METHODS We generated tissue-specific knockdowns of the VPS13A ortholog (Vps13) and the BLTP2 ortholog (hobbit) in neurons and muscles of Drosophila. We analyzed age-dependent locomotor behavior, neurodegeneration, and synapse development and function. RESULTS Neuron-specific loss of the VPS13A ortholog caused neurodegeneration followed by aging-dependent movement deficits and reduced lifespan, whereas muscle-specific loss affected only lifespan. In contrast, neuronal loss of the BLTP2 ortholog resulted in severe early-onset locomotor defects without neurodegeneration, whereas muscle loss impaired synaptogenesis and neurotransmission at the neuromuscular junction. CONCLUSIONS VPS13A maintains neuronal survival, whereas BLTP2 orchestrates synaptic development. The phenotypic specificity of BLTP function provides mechanistic insights into distinct disease trajectories for BLTP-associated disorders. © 2025 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Sarah D Neuman
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Rajan S Thakur
- Department of Neuroscience, Brown University, Providence, Rhode Island, USA
| | - Scott J Gratz
- Department of Neuroscience, Brown University, Providence, Rhode Island, USA
| | - Kate M O'Connor-Giles
- Department of Neuroscience, Brown University, Providence, Rhode Island, USA
- Carney Institute for Brain Science, Brown University, Providence, Rhode Island, USA
| | - Arash Bashirullah
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
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15
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Fuller DM, Wu Y, Schueder F, Rasool B, Nag S, Korfhage JL, Garcia-Milian R, Melnyk KD, Bewersdorf J, De Camilli P, Melia TJ. ATG2A engages Rab1a and ARFGAP1 positive membranes during autophagosome biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.24.645038. [PMID: 40196537 PMCID: PMC11974814 DOI: 10.1101/2025.03.24.645038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
Abstract
Autophagosomes form from seed membranes that expand through bulk-lipid transport via the bridge-like lipid transporter ATG2. The origins of the seed membranes and their relationship to the lipid transport machinery are poorly understood. Using proximity labeling and a variety of fluorescence microscopy techniques, we show that ATG2A localizes to extra-Golgi ARFGAP1 puncta during autophagosome biogenesis. ARFGAP1 itself is dispensable during macroautophagy, but among other proteins associating to these membranes, we find that Rab1 is essential. ATG2A co-immunoprecipitates strongly with Rab1a, and siRNA-mediated depletion of Rab1 blocks autophagy downstream of LC3B lipidation, similar to ATG2A depletion. Further, when either autophagosome formation or the early secretory pathway is perturbed, ARFGAP1 and Rab1a accumulate at ectopic locations with autophagic machinery. Our results suggest that ATG2A engages a Rab1a complex on select early secretory membranes at an early stage in autophagosome biogenesis.
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Affiliation(s)
- Devin M. Fuller
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, 20 MD
| | - Yumei Wu
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, 20 MD
- Department of Neuroscience, Yale University School of Medicine, New Haven CT
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT
- Program in Cellular Neuroscience Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
| | - Florian Schueder
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
| | - Burha Rasool
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
| | - Shanta Nag
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
| | - Justin L. Korfhage
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
| | - Rolando Garcia-Milian
- Bioinformatics Support Hub, Yale Medical Library, Yale School of Medicine, 333 Cedar St, New Haven, CT 06510
| | - Katerina D. Melnyk
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Department of Physics, Yale University, New Haven, CT, USA
| | - Pietro De Camilli
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, 20 MD
- Department of Neuroscience, Yale University School of Medicine, New Haven CT
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT
- Program in Cellular Neuroscience Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
| | - Thomas J. Melia
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, 20 MD
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16
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Zheng Z, Ji C, Zhao H, Zhao YG. ATG2A acts as a tether to regulate autophagosome-lysosome fusion in neural cells. Autophagy 2025:1-12. [PMID: 40083067 DOI: 10.1080/15548627.2025.2479427] [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: 10/03/2024] [Revised: 03/06/2025] [Accepted: 03/11/2025] [Indexed: 03/16/2025] Open
Abstract
The macroautophagy/autophagy proteins ATG2A and ATG2B transfer lipids for phagophore membrane growth. They also form stable complexes with WDR45 and WDR45B. Our previous study demonstrated that WDR45 and WDR45B mediate autophagosome-lysosome fusion in neural cells. Given the defective autophagosome formation in cells lacking both ATG2s, their role in later autophagy stages is hard to explore. Here, we report that in neuroblastoma-derived Neuro-2a (N2a) cells, knocking down (KD) Atg2a, but not Atg2b, results in significant accumulation of SQSTM1/p62 and MAP1LC3-II/LC3-II, indicating impaired autophagy. Atg2a deficiency does not affect autophagosome formation, but reduces colocalization of autophagosomal LC3 with late endosomal/lysosomal RFP-RAB7, suggesting impaired autophagosome-lysosome fusion. ATG2A interacts with the SNARE proteins STX17, SNAP29, and VAMP8, facilitating their assembly. Overexpression of ATG2A partially rescues the autophagosome-lysosome fusion defects in Wdr45- and Wdr45b-deficient cells. ATG2 and another tether protein, EPG5, function partially redundantly in mediating autophagosome-lysosome fusion. Thus, ATG2A plays a key role in neural autophagy by tethering autophagosomes with lysosomes for fusion.Abbreviations: AAV: adeno-associated virus; ATG2Ar: RNAi-resistant ATG2A; Baf: bafilomycin A1; co-IP: co-immunoprecipitation; CQ: chloroquine; DKD: double knockdown; DKO: double knockout; ER: endoplasmic reticulum; KD: knockdown; KO: knockout; MIL: membrane-impermeable Halo ligand; MPL: membrane-permeable Halo ligand; N2a: Neuro-2a; NC negative control; PG: phagophore; PtdIns3K: phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate; TEM: Transmission electron microscopy; TM: transmembrane domain; WT: wild-type.
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Affiliation(s)
- Ze Zheng
- Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, P.R. China
| | - Cuicui Ji
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
- Department of Biology, College of Chemistry and Life Science, Beijing University of Technology, Beijing, P.R. China
| | - Hongyu Zhao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
| | - Yan G Zhao
- Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, P.R. China
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17
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Moreno TM, Nieto-Torres JL, Kumsta C. Monitoring Autophagy in Human Aging: Key Cell Models and Insights. FRONT BIOSCI-LANDMRK 2025; 30:27091. [PMID: 40152379 PMCID: PMC12042822 DOI: 10.31083/fbl27091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2024] [Revised: 11/08/2024] [Accepted: 11/22/2024] [Indexed: 03/29/2025]
Abstract
Autophagy, a key cellular degradation and recycling pathway, is critical for maintaining cellular homeostasis and responding to metabolic and environmental stress. Evidence for age-related autophagic dysfunction and its implications in chronic age-related diseases including neurodegeneration is accumulating. However, as a complex, multi-step process, autophagy can be challenging to measure, particularly in humans and human aging- and disease-relevant models. This review describes the links between macroautophagy, aging, and chronic age-related diseases. We present three novel human cell models, peripheral blood mononuclear cells (PBMCs), primary dermal fibroblasts (PDFs), and induced neurons (iNs), which serve as essential tools for studying autophagy flux and assessing its potential as a biomarker for aging. Unlike traditional models, these cell models retain age- and disease-associated molecular signatures, enhancing their relevance for human studies. The development of robust tools and methodologies for measuring autophagy flux in human cell models holds promise for advancing our understanding of autophagy's role in aging and age-related diseases, ultimately facilitating the discovery of therapies to enhance health outcomes.
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Affiliation(s)
- Tatiana M. Moreno
- Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Jose L. Nieto-Torres
- Department of Biomedical Sciences, School of Health Sciences, Universidad Cardenal Herrera-CEU, CEU Universities, 46115 Valencia, Spain
| | - Caroline Kumsta
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
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18
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Das SK, Khasbage S, Mishra A, Jee B. Prognostic and clinicopathological roles of circular RNA expression in chemoresistance in head and neck squamous cell carcinoma: a systematic review. Front Pharmacol 2025; 16:1502107. [PMID: 40176914 PMCID: PMC11962432 DOI: 10.3389/fphar.2025.1502107] [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: 09/26/2024] [Accepted: 02/18/2025] [Indexed: 04/05/2025] Open
Abstract
Background Characterized by a poor prognosis and survivability, head and neck squamous cell carcinoma (HNSCC) is an aggressive neoplastic condition with a propensity for recurrence where the development of chemoresistance adversely affects the prognostic outcome. Recently, it was shown that circular RNAs (circRNAs) augment the cellular survivability and chemoresistance of malignant cells. Hence, biomarkers for early detection of chemoresistance in these patients can significantly aid in preventing a poor prognostic outcome. Objective The present study aimed to systematically identify circRNAs that play a vital role in the development of chemoresistance in HNSCC and understand their mechanisms of action in HNSCC chemoresistance. Methods The protocol was prospectively registered on PROSPERO with protocol no. CRD42024532291. A six-stage methodological and PRISMA recommendations were followed for the review. Results and Discussion 13 studies were identified which yielded 13 circRNAs which have been investigated for their role in the chemoresistance in HNSCC. Of these, 11 circRNAs were reported to be upregulated while only 2 circRNAs were found to be downregulated. Moreover, we found that circRNAs can modulate autophagy (circPARD3, circPKD2, circAP1M2 and circPGAM1), apoptosis (circ-ILF2, circANKS1B, circTPST2, circPUM1 and circ_0001971), drug efflux (circ-ILF2, has_circ_0005033 and circTPST2), EMT (circANKS1B, circCRIM1, circ_0001971), tumor microenvironment (circ-ILF2. circ-ILF2, circCRIM1 and circTPST2), DNA damage (circTPST2) and malignant potential (hsa_circ_0000190 and hg19_ circ_0005033). Conclusion The present study identified 13 circRNAs which may serve as biomarkers for prognosis as well as response to chemotherapy in HNSCC. Systematic Review Registration PROSPERO, identifier CRD42024532291.
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Affiliation(s)
- Sayan Kumar Das
- Department of Pharmacology, Manipal Tata Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Sameer Khasbage
- Department of Pharmacology, People’s College of Medical Sciences and Research, Bhopal, India
| | - Ashim Mishra
- Department of Forensic Medicine, Manipal Tata Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Babban Jee
- Department of Research, Manipal Tata Medical College, Manipal Academy of Higher Education, Manipal, India
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19
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Dziurdzik SK, Sridhar V, Eng H, Neuman SD, Yan J, Davey M, Taubert S, Bashirullah A, Conibear E. Hoi1 targets the yeast BLTP2 protein to ER-PM contact sites to regulate lipid homeostasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.11.637747. [PMID: 39990326 PMCID: PMC11844476 DOI: 10.1101/2025.02.11.637747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/25/2025]
Abstract
Membrane contact sites between organelles are important for maintaining cellular lipid homeostasis. Members of the recently identified family of bridge-like lipid transfer proteins (BLTPs) span opposing membranes at these contact sites to enable the rapid transfer of bulk lipids between organelles. While the VPS13 and ATG2 family members use organelle-specific adaptors for membrane targeting, the mechanisms that regulate other bridge-like transporters remain unknown. Here, we identify the conserved protein Ybl086c, which we name Hoi1 (Hob interactor 1), as an adaptor that targets the yeast BLTP2-like proteins Fmp27/Hob1 and Hob2 to ER-PM contact sites. Two separate Hoi1 domains interface with alpha-helical projections that decorate the central hydrophobic channel on Fmp27, and loss of these interactions disrupts cellular sterol homeostasis. The mutant phenotypes of BLTP2 and HOI1 orthologs indicate these proteins act in a shared pathway in worms and flies. Together, this suggests that Hoi1-mediated recruitment of BLTP2-like proteins represents an evolutionarily conserved mechanism for regulating lipid transport at membrane contact sites.
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Affiliation(s)
- Samantha K. Dziurdzik
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, Canada V5Z 4H4
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada V6H 3N1
| | - Vaishnavi Sridhar
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, Canada V5Z 4H4
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada V6H 3N1
| | - Hailey Eng
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, Canada V5Z 4H4
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada V6H 3N1
| | - Sarah D. Neuman
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI 53705-2222, USA
| | - Junran Yan
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, Canada V5Z 4H4
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada V6H 3N1
| | - Michael Davey
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, Canada V5Z 4H4
| | - Stefan Taubert
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, Canada V5Z 4H4
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada V6H 3N1
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada V6H 3N1
| | - Arash Bashirullah
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI 53705-2222, USA
| | - Elizabeth Conibear
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, Canada V5Z 4H4
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada V6H 3N1
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada V6H 3N1
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20
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Javed R, Mari M, Trosdal E, Duque T, Paddar MA, Allers L, Mudd MH, Claude-Taupin A, Akepati PR, Hendrix E, He Y, Salemi M, Phinney B, Uchiyama Y, Reggiori F, Deretic V. ATG9A facilitates the closure of mammalian autophagosomes. J Cell Biol 2025; 224:e202404047. [PMID: 39745851 PMCID: PMC11694768 DOI: 10.1083/jcb.202404047] [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: 04/17/2024] [Revised: 08/29/2024] [Accepted: 11/11/2024] [Indexed: 01/04/2025] Open
Abstract
Canonical autophagy captures within specialized double-membrane organelles, termed autophagosomes, an array of cytoplasmic components destined for lysosomal degradation. An autophagosome is completed when the growing phagophore undergoes ESCRT-dependent membrane closure, a prerequisite for its subsequent fusion with endolysosomal organelles and degradation of the sequestered cargo. ATG9A, a key integral membrane protein of the autophagy pathway, is best known for its role in the formation and expansion of phagophores. Here, we report a hitherto unappreciated function of mammalian ATG9A in directing autophagosome closure. ATG9A partners with IQGAP1 and key ESCRT-III component CHMP2A to facilitate this final stage in autophagosome formation. Thus, ATG9A is a central hub governing all major aspects of autophagosome membrane biogenesis, from phagophore formation to its closure, and is a unique ATG factor with progressive functionalities affecting the physiological outputs of autophagy.
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Affiliation(s)
- Ruheena Javed
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Muriel Mari
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Einar Trosdal
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Thabata Duque
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Masroor Ahmad Paddar
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Lee Allers
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Michal H. Mudd
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Aurore Claude-Taupin
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Prithvi Reddy Akepati
- Gastroenterology Division, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Emily Hendrix
- Department of Chemistry and Chemical Biology, The University of New Mexico, Albuquerque, NM, USA
| | - Yi He
- Department of Chemistry and Chemical Biology, The University of New Mexico, Albuquerque, NM, USA
| | - Michelle Salemi
- Proteomics Core Facility, UC Davis Genome Center, University of California, Davis, Davis, CA, USA
| | - Brett Phinney
- Proteomics Core Facility, UC Davis Genome Center, University of California, Davis, Davis, CA, USA
| | - Yasuo Uchiyama
- Department of Cellular and Molecular Neuropathology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Fulvio Reggiori
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Vojo Deretic
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, USA
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21
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Wu Y, Xu R, Zhuang X. Multifaceted Roles of the ATG8 Protein Family in Plant Autophagy: From Autophagosome Biogenesis to Cargo Recognition. J Mol Biol 2025:168981. [PMID: 39909236 DOI: 10.1016/j.jmb.2025.168981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2024] [Revised: 01/25/2025] [Accepted: 01/30/2025] [Indexed: 02/07/2025]
Abstract
In plant cells, autophagy is an essential quality control process by forming a double-membrane structure named the autophagosome, which envelopes and transports the cargoes to the vacuole for degradation/recycling. Autophagy-related (ATG) 8, a key regulator in autophagy, exerts multifunctional roles during autophagy. ATG8 anchors on the phagophore membrane through the ATG8 conjugation system and participates in different steps during autophagosome formation. Accumulating evidence has demonstrated that ATG8 cooperates with other ATG or non-ATG proteins in autophagosome biogenesis. Meanwhile, ATG8 plays an important role in cargo recognition, which is mainly attributed by the specific interactions between ATG8 and the selective autophagy receptors (SARs) or cargos for selective autophagy. Emerging roles of ATG8 in non-canonical autophagy have been recently reported in plants for different stress adaptations. Here, we review the diverse functions of ATG8 in plants, focusing on autophagosome biogenesis and cargo recognition in canonical and non-canonical autophagy.
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Affiliation(s)
- Yixin Wu
- AoE Centre for Organelle Biogenesis and Function, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Rui Xu
- AoE Centre for Organelle Biogenesis and Function, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xiaohong Zhuang
- AoE Centre for Organelle Biogenesis and Function, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
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22
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Mishra AK, Tripathi MK, Kumar D, Gupta SP. Neurons Specialize in Presynaptic Autophagy: A Perspective to Ameliorate Neurodegeneration. Mol Neurobiol 2025; 62:2626-2640. [PMID: 39141193 DOI: 10.1007/s12035-024-04399-8] [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: 05/06/2024] [Accepted: 07/24/2024] [Indexed: 08/15/2024]
Abstract
The efficient and prolonged neurotransmission is reliant on the coordinated action of numerous synaptic proteins in the presynaptic compartment that remodels synaptic vesicles for neurotransmitter packaging and facilitates their exocytosis. Once a cycle of neurotransmission is completed, membranes and associated proteins are endocytosed into the cytoplasm for recycling or degradation. Both exocytosis and endocytosis are closely regulated in a timely and spatially constrained manner. Recent research demonstrated the impact of dysfunctional synaptic vesicle retrieval in causing retrograde degeneration of midbrain neurons and has highlighted the importance of such endocytic proteins, including auxilin, synaptojanin1 (SJ1), and endophilin A (EndoA) in neurodegenerative diseases. Additionally, the role of other associated proteins, including leucine-rich repeat kinase 2 (LRRK2), adaptor proteins, and retromer proteins, is being investigated for their roles in regulating synaptic vesicle recycling. Research suggests that the degradation of defective vesicles via presynaptic autophagy, followed by their recycling, not only revitalizes them in the active zone but also contributes to strengthening synaptic plasticity. The presynaptic autophagy rejuvenating terminals and maintaining neuroplasticity is unique in autophagosome formation. It involves several synaptic proteins to support autophagosome construction in tiny compartments and their retrograde trafficking toward the cell bodies. Despite having a comprehensive understanding of ATG proteins in autophagy, we still lack a framework to explain how autophagy is triggered and potentiated in compact presynaptic compartments. Here, we reviewed synaptic proteins' involvement in forming presynaptic autophagosomes and in retrograde trafficking of terminal cargos. The review also discusses the status of endocytic proteins and endocytosis-regulating proteins in neurodegenerative diseases and strategies to combat neurodegeneration.
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Affiliation(s)
- Abhishek Kumar Mishra
- Department of Zoology, Government Shaheed Gendsingh College, Charama, Uttar Bastar Kanker, 494 337, Chhattisgarh, India.
| | - Manish Kumar Tripathi
- School of Pharmacy, Faculty of Medicine, Institute for Drug Research, The Hebrew University of Jerusalem, 91120, Jerusalem, Israel
| | - Dipak Kumar
- Department of Zoology, Munger University, Munger, Bihar, India
| | - Satya Prakash Gupta
- Department of Biochemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221 005, India
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23
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Acheson J, Joanisse S, Sale C, Hodson N. Recycle, repair, recover: the role of autophagy in modulating skeletal muscle repair and post-exercise recovery. Biosci Rep 2025; 45:1-30. [PMID: 39670455 PMCID: PMC12096956 DOI: 10.1042/bsr20240137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2024] [Revised: 12/03/2024] [Accepted: 12/11/2024] [Indexed: 12/14/2024] Open
Abstract
Skeletal muscle is a highly plastic tissue that can adapt relatively rapidly to a range of stimuli. In response to novel mechanical loading, e.g. unaccustomed resistance exercise, myofibers are disrupted and undergo a period of ultrastructural remodeling to regain full physiological function, normally within 7 days. The mechanisms that underpin this remodeling are believed to be a combination of cellular processes including ubiquitin-proteasome/calpain-mediated degradation, immune cell infiltration, and satellite cell proliferation/differentiation. A relatively understudied system that has the potential to be a significant contributing mechanism to repair and recovery is the autophagolysosomal system, an intracellular process that degrades damaged and redundant cellular components to provide constituent metabolites for the resynthesis of new organelles and cellular structures. This review summarizes our current understanding of the autophagolysosomal system in the context of skeletal muscle repair and recovery. In addition, we also provide hypothetical models of how this system may interact with other processes involved in skeletal muscle remodeling and provide avenues for future research to improve our understanding of autophagy in human skeletal muscle.
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Affiliation(s)
- Jordan Acheson
- Department of Sport and Exercise Sciences, Manchester Metropolitan University, Institute of Sport, Manchester, U.K.
| | - Sophie Joanisse
- School of Life Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, U.K.
| | - Craig Sale
- Department of Sport and Exercise Sciences, Manchester Metropolitan University, Institute of Sport, Manchester, U.K.
| | - Nathan Hodson
- Department of Sport and Exercise Sciences, Manchester Metropolitan University, Institute of Sport, Manchester, U.K.
- Faculty of Kinesiology and Physical Education, University of Toronto, Toronto, Ontario, Canada
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Paddar MA, Wang F, Trosdal ES, Hendrix E, He Y, Salemi MR, Mudd M, Jia J, Duque T, Javed R, Phinney BS, Deretic V. Noncanonical roles of ATG5 and membrane atg8ylation in retromer assembly and function. eLife 2025; 13:RP100928. [PMID: 39773872 PMCID: PMC11706607 DOI: 10.7554/elife.100928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2025] Open
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, University of New Mexico School of MedicineAlbuquerqueUnited States
- Department of Molecular Genetics and Microbiology, University of New Mexico School of MedicineAlbuquerqueUnited States
| | - Fulong Wang
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico School of MedicineAlbuquerqueUnited States
- Department of Molecular Genetics and Microbiology, University of New Mexico School of MedicineAlbuquerqueUnited States
| | - Einar S Trosdal
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico School of MedicineAlbuquerqueUnited States
- Department of Molecular Genetics and Microbiology, University of New Mexico School of MedicineAlbuquerqueUnited States
| | - Emily Hendrix
- Department of Chemistry & Chemical Biology, The University of New MexicoAlbuquerqueUnited States
| | - Yi He
- Department of Chemistry & Chemical Biology, The University of New MexicoAlbuquerqueUnited States
| | - Michelle R Salemi
- Proteomics Core Facility, University of California, DavisDavisUnited States
| | - Michal Mudd
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico School of MedicineAlbuquerqueUnited States
- Department of Molecular Genetics and Microbiology, University of New Mexico School of MedicineAlbuquerqueUnited States
| | - Jingyue Jia
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico School of MedicineAlbuquerqueUnited States
- Department of Molecular Genetics and Microbiology, University of New Mexico School of MedicineAlbuquerqueUnited States
| | - Thabata Duque
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico School of MedicineAlbuquerqueUnited States
- Department of Molecular Genetics and Microbiology, University of New Mexico School of MedicineAlbuquerqueUnited States
| | - Ruheena Javed
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico School of MedicineAlbuquerqueUnited States
- Department of Molecular Genetics and Microbiology, University of New Mexico School of MedicineAlbuquerqueUnited States
| | - Brett S Phinney
- Proteomics Core Facility, University of California, DavisDavisUnited States
| | - Vojo Deretic
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico School of MedicineAlbuquerqueUnited States
- Department of Molecular Genetics and Microbiology, University of New Mexico School of MedicineAlbuquerqueUnited States
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25
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Zhuang H, Ma X. Advances in Aggrephagy: Mechanisms, Disease Implications, and Therapeutic Strategies. J Cell Physiol 2025; 240:e31512. [PMID: 39749851 DOI: 10.1002/jcp.31512] [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: 10/09/2024] [Revised: 11/28/2024] [Accepted: 12/10/2024] [Indexed: 01/04/2025]
Abstract
The accumulation of misfolded proteins within cells leads to the formation of protein aggregates that disrupt normal cellular functions and contribute to a range of human pathologies, notably neurodegenerative disorders. Consequently, the investigation into the mechanisms of aggregate formation and their subsequent clearance is of considerable importance for the development of therapeutic strategies. The clearance of protein aggregates is predominantly achieved via the autophagy-lysosomal pathway, a process known as aggrephagy. In this pathway, autophagosome biogenesis and lysosomal digestion provide necessary conditions for the clearance of protein aggregates, while autophagy receptors such as P62, NBR1, TAX1BP1, TOLLIP, and CCT2 facilitate the recognition of protein aggregates by the autophagy machinery, playing a pivotal role in their degradation. This review will introduce the mechanisms of aggregate formation, progression, and degradation, with particular emphasis on advances in aggrephagy, providing insights for aggregates-related diseases and the development of novel therapeutic strategies.
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Affiliation(s)
- Haixia Zhuang
- Department of Anesthesiology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xinyu Ma
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
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26
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Yu S. Determining ATG2 Localization During Autophagosome Formation in Mammalian Cells. Methods Mol Biol 2025; 2888:193-200. [PMID: 39699732 DOI: 10.1007/978-1-0716-4318-1_13] [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: 12/20/2024]
Abstract
This chapter describes two imaging-based approaches for examining the localization of bridge-like lipid transfer proteins at membrane contact sites during native biological processes. These approaches use multi-color fluorescence imaging, enabling high spatial and temporal resolution and overcoming the limitations of biochemical methods. The first approach involves immunofluorescence in fixed cells, while the second utilizes time-lapse imaging in live cells. These methods are showcased through the example of ATG2, an essential autophagy-related protein, and demonstrate the ability to overcome technical difficulties such as large protein size, lack of high-quality antibodies, and imaging highly dynamic subcellular structures. These described methods provide a powerful tool for understanding protein function and biological processes and can be widely applied to various research questions in cell biology.
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Affiliation(s)
- Shenliang Yu
- Department of Physiology, University of California, San Francisco, San Francisco, CA, USA.
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27
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Wang Y, Dahmane S, Ti R, Mai X, Zhu L, Carlson LA, Stjepanovic G. Structural basis for lipid transfer by the ATG2A-ATG9A complex. Nat Struct Mol Biol 2025; 32:35-47. [PMID: 39174844 DOI: 10.1038/s41594-024-01376-6] [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: 01/11/2023] [Accepted: 07/23/2024] [Indexed: 08/24/2024]
Abstract
Autophagy is characterized by the formation of double-membrane vesicles called autophagosomes. Autophagy-related proteins (ATGs) 2A and 9A have an essential role in autophagy by mediating lipid transfer and re-equilibration between membranes for autophagosome formation. Here we report the cryo-electron microscopy structures of human ATG2A in complex with WD-repeat protein interacting with phosphoinositides 4 (WIPI4) at 3.2 Å and the ATG2A-WIPI4-ATG9A complex at 7 Å global resolution. On the basis of molecular dynamics simulations, we propose a mechanism of lipid extraction from the donor membranes. Our analysis revealed 3:1 stoichiometry of the ATG9A-ATG2A complex, directly aligning the ATG9A lateral pore with ATG2A lipid transfer cavity, and an interaction of the ATG9A trimer with both the N-terminal and the C-terminal tip of rod-shaped ATG2A. Cryo-electron tomography of ATG2A liposome-binding states showed that ATG2A tethers lipid vesicles at different orientations. In summary, this study provides a molecular basis for the growth of the phagophore membrane and lends structural insights into spatially coupled lipid transport and re-equilibration during autophagosome formation.
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Affiliation(s)
- Yang Wang
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China
| | - Selma Dahmane
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Rujuan Ti
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China
| | - Xinyi Mai
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China
| | - Lizhe Zhu
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China.
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China.
| | - Lars-Anders Carlson
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden.
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden.
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.
| | - Goran Stjepanovic
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, China.
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FUJIOKA Y, N. NODA N. Mechanisms of autophagosome formation. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2025; 101:32-40. [PMID: 39805588 PMCID: PMC11808202 DOI: 10.2183/pjab.101.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2024] [Accepted: 10/25/2024] [Indexed: 01/16/2025]
Abstract
The formation of autophagosomes is a pivotal step in autophagy, a lysosomal degradation system that plays a crucial role in maintaining cellular homeostasis. After autophagy induction, phase separation of the autophagy-related (Atg) 1 complex occurs, facilitating the gathering of Atg proteins and organizes the autophagosome formation site, where the initial isolation membrane (IM)/phagophore is generated. The IM then expands after receiving phospholipids from endomembranes such as the endoplasmic reticulum. This process is driven by the collaboration of lipid transfer (Atg2) and scrambling (Atg9) proteins. The IM assumes a cup shaped morphology and undergoes closure, resulting in the formation of a double membrane-bound autophagosome. The Atg8 lipidation system is hypothesized to be a pivotal factor in this process. This review presents an overview of the current understanding of these processes and discusses the basic mechanisms of autophagosome formation.
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Affiliation(s)
- Yuko FUJIOKA
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Nobuo N. NODA
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
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29
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Neuman SD, Thakur RS, Gratz SJ, O'Connor-Giles KM, Bashirullah A. Neurodegenerative and neurodevelopmental roles for bulk lipid transporters VPS13A and BLTP2 in movement disorders. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.30.630795. [PMID: 39803515 PMCID: PMC11722402 DOI: 10.1101/2024.12.30.630795] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2025]
Abstract
Background Bridge-like lipid transfer proteins (BLTPs) mediate bulk lipid transport at membrane contact sites. Mutations in BLTPs are linked to both early-onset neurodevelopmental and later-onset neurodegenerative diseases, including movement disorders. The tissue specificity and temporal requirements of BLTPs in disease pathogenesis remain poorly understood. Objectives To determine the age-of-onset and tissue-specific roles of VPS13A and BLTP2 in movement disorder pathogenesis using Drosophila models. Methods We generated tissue-specific knockdowns of the VPS13A ortholog ( Vps13 ) and the BLTP2 ortholog ( hobbit ) in neurons and muscles of Drosophila . We analyzed age-dependent locomotor behavior, neurodegeneration, and synapse development and function. Results Neuron-specific loss of the VPS13A ortholog caused neurodegeneration followed by age- onset movement deficits and reduced lifespan, while muscle-specific loss affected only lifespan, revealing neurodegeneration and myopathy as independent comorbidities in VPS13A disease. In contrast, neuronal loss of the BLTP2 ortholog resulted in severe early-onset locomotor defects without neurodegeneration, while muscle loss impaired synaptogenesis and neurotransmission at the neuromuscular junction (NMJ). Conclusions VPS13A maintains neuronal survival, while BLTP2 orchestrates synaptic development. VPS13A function in muscle does not play a role in movement defects. The phenotypic specificity of BLTP function provides mechanistic insights into distinct disease trajectories for BLTP-associated movement disorders.
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30
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Lee M, Son S, Lim HJ, Song H. The differential expression patterns of Atg9a and Atg9b in cells of the reproductive organs. Clin Exp Reprod Med 2024; 51:301-308. [PMID: 38757275 PMCID: PMC11617914 DOI: 10.5653/cerm.2023.06737] [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: 12/02/2023] [Revised: 02/26/2024] [Accepted: 03/12/2024] [Indexed: 05/18/2024] Open
Abstract
OBJECTIVE Autophagy is a major intracellular catabolic pathway governed by the sequential actions of proteins encoded by autophagy-related genes (Atg). ATG9, the only transmembrane protein involved in this process, regulates phospholipid translocation to autophagosomes during the early phases of autophagy. In mammals, two Atg9 isoforms have been reported: Atg9a and Atg9b. In this study, we examined whether the molecular and cellular characteristics of these two isoforms differed in mice. METHODS Whole uteri were collected on days 1, 4, and 8 of pregnancy and from ovariectomized mice injected with vehicle, progesterone, or 17β-estradiol. Cells from reproductive tissues, such as granulosa cells, uterine epithelial cells (UECs), uterine stromal cells (USCs), and oocytes were collected. Two human uterine cell lines were also used in this analysis. Reverse transcription-polymerase chain reaction tests, Western blotting, and immunofluorescence staining were performed. Serum starvation conditions were used to induce autophagy in primary cells. RESULTS Atg9a and Atg9b were expressed in multiple mouse tissues and reproductive cells. Neither Atg9A nor Atg9B significantly changed in response to steroid hormones. Immunofluorescence staining of the UECs and USCs showed that ATG9A was distributed in a punctate-like pattern, whereas ATG9B exhibited a pattern of elongated tubular shapes in the cytoplasm. In human cancer cell lines, ATG9B was undetectable, whereas ATG9A was found in all cell types examined. CONCLUSION The Atg9 isoforms exhibited distinct subcellular localizations in UECs and may play different roles in autophagy. Notably, human uterine cells exhibited reduced ATG9B expression, suggesting that this suppression may be due to epigenetic regulation.
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Affiliation(s)
- Minseo Lee
- Department of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Sujin Son
- Department of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Hyunjung J. Lim
- Department of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Haengseok Song
- Department of Biomedical Science, CHA University, Seongnam, Republic of Korea
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31
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Hamaï A, Drin G. Specificity of lipid transfer proteins: An in vitro story. Biochimie 2024; 227:85-110. [PMID: 39304019 DOI: 10.1016/j.biochi.2024.09.007] [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: 06/04/2024] [Revised: 09/06/2024] [Accepted: 09/17/2024] [Indexed: 09/22/2024]
Abstract
Lipids, which are highly diverse, are finely distributed between organelle membranes and the plasma membrane (PM) of eukaryotic cells. As a result, each compartment has its own lipid composition and molecular identity, which is essential for the functional fate of many proteins. This distribution of lipids depends on two main processes: lipid synthesis, which takes place in different subcellular regions, and the transfer of these lipids between and across membranes. This review will discuss the proteins that carry lipids throughout the cytosol, called LTPs (Lipid Transfer Proteins). More than the modes of action or biological roles of these proteins, we will focus on the in vitro strategies employed during the last 60 years to address a critical question: What are the lipid ligands of these LTPs? We will describe the extent to which these strategies, combined with structural data and investigations in cells, have made it possible to discover proteins, namely ORPs, Sec14, PITPs, STARDs, Ups/PRELIs, START-like, SMP-domain containing proteins, and bridge-like LTPs, which compose some of the main eukaryotic LTP families, and their lipid ligands. We will see how these approaches have played a central role in cell biology, showing that LTPs can connect distant metabolic branches, modulate the composition of cell membranes, and even create new subcellular compartments.
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Affiliation(s)
- Amazigh Hamaï
- Université Côte d'Azur, CNRS and Inserm, Institut de Pharmacologie Moléculaire et Cellulaire, UMR 7275, 660 route des lucioles, 06560, Valbonne Sophia Antipolis, France
| | - Guillaume Drin
- Université Côte d'Azur, CNRS and Inserm, Institut de Pharmacologie Moléculaire et Cellulaire, UMR 7275, 660 route des lucioles, 06560, Valbonne Sophia Antipolis, France.
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32
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Lyu J, Zhang H, Wang C, Pan M. New insight in treating autoimmune diseases by targeting autophagy. Autoimmunity 2024; 57:2351872. [PMID: 38739691 DOI: 10.1080/08916934.2024.2351872] [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: 01/22/2024] [Accepted: 04/28/2024] [Indexed: 05/16/2024]
Abstract
Autophagy is a highly conserved biological process in eukaryotes, which degrades cellular misfolded proteins, damaged organelles and invasive pathogens in the lysosome-dependent manner. Autoimmune diseases caused by genetic elements, environments and aberrant immune responses severely impact patients' living quality and even threaten life. Recently, numerous studies have reported autophagy can regulate immune responses, and play an important role in autoimmune diseases. In this review, we summarised the features of autophagy and autophagy-related genes, enumerated some autophagy-related genes involved in autoimmune diseases, and further overviewed how to treat autoimmune diseases through targeting autophagy. Finally, we outlooked the prospect of relieving and curing autoimmune diseases by targeting autophagy pathway.
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Affiliation(s)
- Jiao Lyu
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Hongqian Zhang
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Chaoyang Wang
- The Key Medical Laboratory for Chemical Poison Detection of Henan Province, The Third People's Hospital of Henan Province, Zhengzhou, China
- Department of Biomedical Science, City University of Hong Kong, Hong Kong, China
| | - Mingyu Pan
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
- Department of Biomedical Science, City University of Hong Kong, Hong Kong, China
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33
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Wei Z, Hu X, Wu Y, Zhou L, Zhao M, Lin Q. Molecular Mechanisms Underlying Initiation and Activation of Autophagy. Biomolecules 2024; 14:1517. [PMID: 39766224 PMCID: PMC11673044 DOI: 10.3390/biom14121517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Revised: 11/15/2024] [Accepted: 11/26/2024] [Indexed: 01/11/2025] Open
Abstract
Autophagy is an important catabolic process to maintain cellular homeostasis and antagonize cellular stresses. The initiation and activation are two of the most important aspects of the autophagic process. This review focuses on mechanisms underlying autophagy initiation and activation and signaling pathways regulating the activation of autophagy found in recent years. These findings include autophagy initiation by liquid-liquid phase separation (LLPS), autophagy initiation in the endoplasmic reticulum (ER) and Golgi apparatus, and the signaling pathways mediated by the ULK1 complex, the mTOR complex, the AMPK complex, and the PI3KC3 complex. Through the review, we attempt to present current research progress in autophagy regulation and forward our understanding of the regulatory mechanisms and signaling pathways of autophagy initiation and activation.
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Affiliation(s)
| | | | | | | | | | - Qiong Lin
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China; (Z.W.); (X.H.); (Y.W.); (L.Z.); (M.Z.)
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Lee Y, Tuan NM, Lee GJ, Kim B, Park JH, Lee CH. Regulatory Mechanisms Governing the Autophagy-Initiating VPS34 Complex and Its inhibitors. Biomol Ther (Seoul) 2024; 32:723-735. [PMID: 39370737 PMCID: PMC11535298 DOI: 10.4062/biomolther.2024.094] [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: 06/07/2024] [Accepted: 06/26/2024] [Indexed: 10/08/2024] Open
Abstract
VPS34 is a crucial protein in cells, essential for handling cellular stress through its involvement in autophagy and endocytosis. This protein functions as a Class III phosphatidylinositol 3-kinase, producing phosphatidylinositol 3-phosphate, which is necessary for autophagy and vesicle trafficking. Additionally, VPS34 forms two mutually exclusive complexes, each playing a vital role in autophagy and endocytic sorting. These complexes share common subunits, including VPS15, VPS34, and Beclin 1, with complex I having ATG14 as a specific subunit. Due to its association with various human diseases, regulation of the VPS34 complex I has garnered significant interest, emerging as a potential therapeutic target for drug discovery. Summaries of the structure, function of VPS34 complexes, and developed VPS34 inhibitors have been provided, along with discussions on the regulation mechanism of VPS34, particularly in relation to the initiation complex I of autophagy. This offers valuable insights for treating autophagy-related diseases.
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Affiliation(s)
- Yongook Lee
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Seoul 04620, Republic of Korea
| | - Nguyen Minh Tuan
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Seoul 04620, Republic of Korea
| | - Gi Jeong Lee
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Seoul 04620, Republic of Korea
| | - Boram Kim
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Seoul 04620, Republic of Korea
| | - Jung Ho Park
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Seoul 04620, Republic of Korea
| | - Chang Hoon Lee
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Seoul 04620, Republic of Korea
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Norell PN, Campisi D, Mohan J, Wollert T. Biogenesis of omegasomes and autophagosomes in mammalian autophagy. Biochem Soc Trans 2024; 52:2145-2155. [PMID: 39392358 PMCID: PMC11555699 DOI: 10.1042/bst20240015] [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: 10/12/2024]
Abstract
Autophagy is a highly conserved catabolic pathway that maintains cellular homeostasis by promoting the degradation of damaged or superfluous cytoplasmic material. A hallmark of autophagy is the generation of membrane cisternae that sequester autophagic cargo. Expansion of these structures allows cargo to be engulfed in a highly selective and exclusive manner. Cytotoxic stress or starvation induces the formation of autophagosomes that sequester bulk cytoplasm instead of selected cargo. This rather nonselective pathway is essential for maintaining vital cellular functions during adverse conditions and is thus a major stress response pathway. Both selective and nonselective autophagy rely on the same molecular machinery. However, due to the different nature of cargo to be sequestered, the involved molecular mechanisms are fundamentally different. Although intense research over the past decades has advanced our understanding of autophagy, fundamental questions remain to be addressed. This review will focus on molecular principles and open questions regarding the formation of omegasomes and phagophores in nonselective mammalian autophagy.
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Affiliation(s)
- Puck N. Norell
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, UMR3691 CNRS, 75015 Paris, France
| | - Daniele Campisi
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, UMR3691 CNRS, 75015 Paris, France
| | - Jagan Mohan
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, UMR3691 CNRS, 75015 Paris, France
| | - Thomas Wollert
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, UMR3691 CNRS, 75015 Paris, France
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36
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Liu J, Ma H, Wu Z, Ji Y, Liang Y. The Knowns and Unknowns of Membrane Features and Changes During Autophagosome-Lysosome/Vacuole Fusion. Int J Mol Sci 2024; 25:11160. [PMID: 39456939 PMCID: PMC11508585 DOI: 10.3390/ijms252011160] [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: 08/06/2024] [Revised: 10/04/2024] [Accepted: 10/14/2024] [Indexed: 10/28/2024] Open
Abstract
Autophagosome (AP)-lysosome/vacuole fusion is one of the hallmarks of macroautophagy. Membrane features and changes during the fusion process have mostly been described using two-dimensional (2D) models with one AP and one lysosome/vacuole. The outer membrane (OM) of a closed mature AP has been suggested to fuse with the lysosomal/vacuolar membrane. However, the descriptions in some studies for fusion-related issues are questionable or incomplete. The correct membrane features of APs and lysosomes/vacuoles are the prerequisite for describing the fusion process. We searched the literature for representative membrane features of AP-related structures based on electron microscopy (EM) graphs of both animal and yeast cells and re-evaluated the findings. We also summarized the main 2D models describing the membrane changes during AP-lysosome/vacuole fusion in the literature. We used three-dimensional (3D) models to characterize the known and unknown membrane changes during and after fusion of the most plausible 2D models. The actual situation is more complex, since multiple lysosomes may fuse with the same AP in mammalian cells, multiple APs may fuse with the same vacuole in yeast cells, and in some mutant cells, phagophores (unclosed APs) fuse with lysosomes/vacuoles. This review discusses the membrane features and highly dynamic changes during AP (phagophore)-lysosome/vacuole fusion. The resulting information will improve the understanding of AP-lysosome/vacuole fusion and direct the future research on AP-lysosome/vacuole fusion and regeneration.
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Affiliation(s)
| | | | | | | | - Yongheng Liang
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (J.L.); (H.M.); (Z.W.); (Y.J.)
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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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Mohammed WH, Sulaiman GM, Abomughaid MM, Klionsky DJ, Abu-Alghayth MH. The dual role of autophagy in suppressing and promoting hepatocellular carcinoma. Front Cell Dev Biol 2024; 12:1472574. [PMID: 39463763 PMCID: PMC11502961 DOI: 10.3389/fcell.2024.1472574] [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: 08/01/2024] [Accepted: 09/25/2024] [Indexed: 10/29/2024] Open
Abstract
The 5-year survival rate for hepatocellular carcinoma (HCC), a deadly form of liver cancer, is quite low. Although drug therapy is successful, patients with advanced liver cancer frequently develop resistance because of the significant phenotypic and genetic heterogeneity of these cells. The overexpression of drug efflux transporters, downstream adaptive responses, malfunctioning DNA damage repair, epigenetic modification, the tumor microenvironment, and the extracellular matrix can all be linked to drug resistance. The evolutionary process of autophagy, which is in charge of intracellular breakdown, is intimately linked to medication resistance in HCC. Autophagy is involved in both the promotion and suppression of cancer by influencing treatment resistance, metastasis, carcinogenesis, and the viability of stem cells. Certain autophagy regulators are employed in anticancer treatment; however, because of the dual functions of autophagy, their use is restricted, and therapeutic failure is increased. By focusing on autophagy, it is possible to reduce HCC expansion and metastasis, and enhance tumor cell reactivity to treatment. Macroautophagy, the best-characterized type of autophagy, involves the formation of a sequestering compartment termed a phagophore, which surrounds and encloses aberrant or superfluous components. The phagophore matures into a double-membrane autophagosome that delivers the cargo to the lysosome; lysosomes and autophagosomes fuse to degrade and recycle the cargo. Macroautophagy plays dual functions in both promoting and suppressing cancer in a variety of cancer types.
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Affiliation(s)
- Wasnaa H. Mohammed
- Department of Biotechnology, College of Applied Sciences, University of Technology, Baghdad, Iraq
| | - Ghassan M. Sulaiman
- Department of Biotechnology, College of Applied Sciences, University of Technology, Baghdad, Iraq
| | - Mosleh M. Abomughaid
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, Bisha, Saudi Arabia
| | - Daniel J. Klionsky
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States
| | - Mohammed H. Abu-Alghayth
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, Bisha, Saudi Arabia
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39
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Kang Y, Pogany J, Nagy PD. Proviral role of ATG2 autophagy related protein in tomato bushy stunt virus replication through bulk phospholipid transfer into the viral replication organelle. Mol Biol Cell 2024; 35:ar124. [PMID: 39110527 PMCID: PMC11481700 DOI: 10.1091/mbc.e24-05-0236] [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: 06/03/2024] [Accepted: 07/30/2024] [Indexed: 09/21/2024] Open
Abstract
Subversion of cellular membranes and membrane proliferation are used by positive-strand RNA viruses to build viral replication organelles (VROs) that support virus replication. The biogenesis of the membranous VROs requires major changes in lipid metabolism and lipid transfer in infected cells. In this work, we show that tomato bushy stunt virus (TBSV) hijacks Atg2 autophagy related protein with bulk lipid transfer activity into VROs via interaction with TBSV p33 replication protein. Deletion of Atg2 in yeast and knockdown of Atg2 in Nicotiana benthamiana resulted in decreased TBSV replication. We found that subversion of Atg2 by TBSV was important to enrich VRO membranes with phosphatidylethanolamine (PE), phosphatidylserine (PS) and PI(3)P phosphoinositide. Interestingly, inhibition of autophagy did not affect the efficient recruitment of Atg2 into VROs, and overexpression of Atg2 enhanced TBSV replication, indicating autophagy-independent subversion of Atg2 by TBSV. These findings suggest that the proviral function of Atg2 lipid transfer protein is in VRO membrane proliferation. In addition, we find that Atg2 interacting partner Atg9 with membrane lipid-scramblase activity is also coopted for tombusvirus replication. Altogether, the subversion of Atg2 bridge-type lipid transfer protein provides a new mechanism for tombusviruses to greatly expand VRO membranes to support robust viral replication.
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Affiliation(s)
- Yuanrong Kang
- Department of Plant Pathology, University of Kentucky, Plant Science Building, Lexington, KY 40546
| | - Judit Pogany
- Department of Plant Pathology, University of Kentucky, Plant Science Building, Lexington, KY 40546
| | - Peter D. Nagy
- Department of Plant Pathology, University of Kentucky, Plant Science Building, Lexington, KY 40546
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40
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Filali-Mouncef Y, Leytens A, Vargas Duarte P, Zampieri M, Dengjel J, Reggiori F. An APEX2-based proximity-dependent biotinylation assay with temporal specificity to study protein interactions during autophagy in the yeast Saccharomyces cerevisiae. Autophagy 2024; 20:2323-2337. [PMID: 38958087 PMCID: PMC11423678 DOI: 10.1080/15548627.2024.2366749] [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: 12/03/2023] [Revised: 05/30/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024] Open
Abstract
Autophagosome biogenesis is a complex process orchestrated by dynamic interactions between Atg (autophagy-related) proteins and characterized by the turnover of specific cargoes, which can differ over time and depending on how autophagy is stimulated. Proteomic analyses are central to uncover protein-protein interaction networks and when combined with proximity-dependent biotinylation or proximity labeling (PL) approaches, they also permit to detect transient and weak interactions. However, current PL procedures for yeast Saccharomyces cerevisiae, one of the leading models for the study of autophagy, do not allow to keep temporal specificity and thus identify interactions and cargoes at a precise time point upon autophagy induction. Here, we present a new ascorbate peroxidase 2 (APEX2)-based PL protocol adapted to yeast that preserves temporal specificity and allows uncovering neighbor proteins by either western blot or proteomics. As a proof of concept, we applied this new method to identify Atg8 and Atg9 interactors and detected known binding partners as well as potential uncharacterized ones in rich and nitrogen starvation conditions. Also, as a proof of concept, we confirmed the spatial proximity interaction between Atg8 and Faa1. We believe that this protocol will be a new important experimental tool for all those researchers studying the mechanism and roles of autophagy in yeast, but also other cellular pathways in this model organism.Abbreviations: APEX2, ascorbate peroxidase 2, Atg, autophagy-related; BP, biotin phenol; Cvt, cytoplasm-to-vacuole targeting; ER, endoplasmic reticulum; LN2, liquid nitrogen; MS, mass spectrometry; PAS, phagophore assembly site; PL, proximity labeling; PE, phosphatidylethanolamine; PPINs, protein-protein interaction networks; PPIs, protein-protein interactions; RT, room temperature; SARs, selective autophagy receptors; WT, wild-type.
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Affiliation(s)
- Yasmina Filali-Mouncef
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, AV, The Netherlands
| | - Alexandre Leytens
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | - Mattia Zampieri
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Fulvio Reggiori
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, AV, The Netherlands
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
- Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Aarhus C, Denmark
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41
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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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Knupp J, Chen YJ, Wang E, Arvan P, Tsai B. Sigma-1 receptor recruits LC3 mRNA to ER-associated omegasomes to promote localized LC3 translation enabling functional autophagy. Cell Rep 2024; 43:114619. [PMID: 39128005 PMCID: PMC11376464 DOI: 10.1016/j.celrep.2024.114619] [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: 01/16/2024] [Revised: 05/14/2024] [Accepted: 07/25/2024] [Indexed: 08/13/2024] Open
Abstract
Autophagosome formation initiated on the endoplasmic reticulum (ER)-associated omegasome requires LC3. Translational regulation of LC3 biosynthesis is unexplored. Here we demonstrate that LC3 mRNA is recruited to omegasomes by directly binding to the ER transmembrane Sigma-1 receptor (S1R). Cell-based and in vitro reconstitution experiments show that S1R interacts with the 3' UTR of LC3 mRNA and ribosomes to promote LC3 translation. Strikingly, the 3' UTR of LC3 is also required for LC3 protein lipidation, thereby linking the mRNA-3' UTR to LC3 function. An autophagy-defective S1R mutant responsible for amyotrophic lateral sclerosis cannot bind LC3 mRNA or induce LC3 translation. We propose a model wherein S1R de-represses LC3 mRNA via its 3' UTR at the ER, enabling LC3 biosynthesis and lipidation. Because several other LC3-related proteins use the same mechanism, our data reveal a conserved pathway for localized translation essential for autophagosome biogenesis with insights illuminating the molecular basis of a neurodegenerative disease.
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Affiliation(s)
- Jeffrey Knupp
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, BSRB 3043, Ann Arbor, MI 48109, USA; Cellular and Molecular Biology Program, University of Michigan Medical School, 1135 Catherine Street, Ann Arbor, MI 48109 USA
| | - Yu-Jie Chen
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, BSRB 3043, Ann Arbor, MI 48109, USA
| | - Emily Wang
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, BSRB 3043, Ann Arbor, MI 48109, USA
| | - Peter Arvan
- Cellular and Molecular Biology Program, University of Michigan Medical School, 1135 Catherine Street, Ann Arbor, MI 48109 USA; Division of Metabolism Endocrinology & Diabetes, University of Michigan Medical School, 1000 Wall Street, Ann Arbor, MI 48105, USA.
| | - Billy Tsai
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, BSRB 3043, Ann Arbor, MI 48109, USA; Cellular and Molecular Biology Program, University of Michigan Medical School, 1135 Catherine Street, Ann Arbor, MI 48109 USA.
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Pareek G, Kundu M. Physiological functions of ULK1/2. J Mol Biol 2024; 436:168472. [PMID: 38311233 PMCID: PMC11382334 DOI: 10.1016/j.jmb.2024.168472] [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: 12/19/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
UNC-51-like kinases 1 and 2 (ULK1/2) are serine/threonine kinases that are best known for their evolutionarily conserved role in the autophagy pathway. Upon sensing the nutrient status of a cell, ULK1/2 integrate signals from upstream cellular energy sensors such as mTOR and AMPK and relay them to the downstream components of the autophagy machinery. ULK1/2 also play indispensable roles in the selective autophagy pathway, removing damaged mitochondria, invading pathogens, and toxic protein aggregates. Additional functions of ULK1/2 have emerged beyond autophagy, including roles in protein trafficking, RNP granule dynamics, and signaling events impacting innate immunity, axon guidance, cellular homeostasis, and cell fate. Therefore, it is no surprise that alterations in ULK1/2 expression and activity have been linked with pathophysiological processes, including cancer, neurological disorders, and cardiovascular diseases. Growing evidence suggests that ULK1/2 function as biological rheostats, tuning cellular functions to intra and extra-cellular cues. Given their broad physiological relevance, ULK1/2 are candidate targets for small molecule activators or inhibitors that may pave the way for the development of therapeutics for the treatment of diseases in humans.
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Affiliation(s)
- Gautam Pareek
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mondira Kundu
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, TN, USA.
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Eickhorst C, Babic R, Rush-Kittle J, Lucya L, Imam FL, Sánchez-Martín P, Hollenstein DM, Michaelis J, Münch C, Meisinger C, Slade D, Gámez-Díaz L, Kraft C. FIP200 Phosphorylation Regulates Late Steps in Mitophagy. J Mol Biol 2024; 436:168631. [PMID: 38821350 DOI: 10.1016/j.jmb.2024.168631] [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: 01/27/2024] [Revised: 05/18/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024]
Abstract
Mitophagy is a specific type of autophagy responsible for the selective elimination of dysfunctional or superfluous mitochondria, ensuring the maintenance of mitochondrial quality control. The initiation of mitophagy is coordinated by the ULK1 kinase complex, which engages mitophagy receptors via its FIP200 subunit. Whether FIP200 performs additional functions in the subsequent later phases of mitophagy beyond this initial step and how its regulation occurs, remains unclear. Our findings reveal that multiple phosphorylation events on FIP200 differentially control the early and late stages of mitophagy. Furthermore, these phosphorylation events influence FIP200's interaction with ATG16L1. In summary, our results highlight the necessity for precise and dynamic regulation of FIP200, underscoring its importance in the progression of mitophagy.
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Affiliation(s)
- Christopher Eickhorst
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
| | - Riccardo Babic
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Jorrell Rush-Kittle
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany; Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Faculty of Medicine, University Medical Center Freiburg, 79106 Freiburg, Germany
| | - Leon Lucya
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Fatimah Lami Imam
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Pablo Sánchez-Martín
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - David M Hollenstein
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Department for Biochemistry and Cell Biology, University of Vienna, Center for Molecular Biology, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria; Mass Spectrometry Facility, Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Jonas Michaelis
- Institute of Molecular Systems Medicine, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Christian Münch
- Institute of Molecular Systems Medicine, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Chris Meisinger
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Dea Slade
- Department of Radiation Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria; Comprehensive Cancer Center, Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria; Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Laura Gámez-Díaz
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Faculty of Medicine, University Medical Center Freiburg, 79106 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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45
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Isola D, Elazar Z. Phospholipid Supply for Autophagosome Biogenesis. J Mol Biol 2024; 436:168691. [PMID: 38944336 DOI: 10.1016/j.jmb.2024.168691] [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: 04/09/2024] [Revised: 06/10/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024]
Abstract
Autophagy is a cellular degradation pathway where double-membrane autophagosomes form de novo to engulf cytoplasmic material destined for lysosomal degradation. This process requires regulated membrane remodeling, beginning with the initial autophagosomal precursor and progressing to its elongation and maturation into a fully enclosed, fusion-capable vesicle. While the core protein machinery involved in autophagosome formation has been extensively studied over the past two decades, the role of phospholipids in this process has only recently been studied. This review focuses on the phospholipid composition of the phagophore membrane and the mechanisms that supply lipids to expand this unique organelle.
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Affiliation(s)
- Damilola Isola
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Zvulun Elazar
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel.
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46
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Selarka K, Shravage BV. Illuminating intercellular autophagy: A comprehensive review of cell non-autonomous autophagy. Biochem Biophys Res Commun 2024; 716:150024. [PMID: 38701555 DOI: 10.1016/j.bbrc.2024.150024] [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: 03/31/2024] [Accepted: 04/26/2024] [Indexed: 05/05/2024]
Abstract
Macro-autophagy (autophagy hereafter) is an evolutionarily conserved cellular process that has long been recognized as an intracellular mechanism for maintaining cellular homeostasis. It involves the formation of a membraned structure called the autophagosome, which carries cargo that includes toxic protein aggregates and dysfunctional organelles to the lysosome for degradation and recycling. Autophagy is primarily considered and studied as a cell-autonomous mechanism. However, recent studies have illuminated an underappreciated facet of autophagy, i.e., non-autonomously regulated autophagy. Non-autonomously regulated autophagy involves the degradation of autophagic components, including organelles, cargo, and signaling molecules, and is induced in neighboring cells by signals from primary adjacent or distant cells/tissues/organs. This review provides insight into the complex molecular mechanisms governing non-autonomously regulated autophagy, highlighting the dynamic interplay between cells within tissue/organ or distinct cell types in different tissues/organs. Emphasis is placed on modes of intercellular communication that include secreted molecules, including microRNAs, and their regulatory roles in orchestrating this phenomenon. Furthermore, we explore the multidimensional roles of non-autonomously regulated autophagy in various physiological contexts, spanning tissue development and aging, as well as its importance in diverse pathological conditions, including cancer and neurodegeneration. By studying the complexities of non-autonomously regulated autophagy, we hope to gain insights into the sophisticated intercellular dynamics within multicellular organisms, including mammals. These studies will uncover novel avenues for therapeutic intervention to modulate intercellular autophagic pathways in altered human physiology.
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Affiliation(s)
- Karan Selarka
- Developmental Biology Group, MACS-Agharkar Research Institute, Pune, India; Department of Biotechnology, Savitribai Phule Pune University, Pune, India
| | - Bhupendra V Shravage
- Developmental Biology Group, MACS-Agharkar Research Institute, Pune, India; Department of Biotechnology, Savitribai Phule Pune University, Pune, India; Department of Zoology, Savitribai Phule Pune University, Pune, India.
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47
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Baumann V, Achleitner S, Tulli S, Schuschnig M, Klune L, Martens S. Faa1 membrane binding drives positive feedback in autophagosome biogenesis via fatty acid activation. J Cell Biol 2024; 223:e202309057. [PMID: 38573225 PMCID: PMC10993510 DOI: 10.1083/jcb.202309057] [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: 09/09/2023] [Revised: 02/14/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024] Open
Abstract
Autophagy serves as a stress response pathway by mediating the degradation of cellular material within lysosomes. In autophagy, this material is encapsulated in double-membrane vesicles termed autophagosomes, which form from precursors referred to as phagophores. Phagophores grow by lipid influx from the endoplasmic reticulum into Atg9-positive compartments and local lipid synthesis provides lipids for their expansion. How phagophore nucleation and expansion are coordinated with lipid synthesis is unclear. Here, we show that Faa1, an enzyme activating fatty acids, is recruited to Atg9 vesicles by directly binding to negatively charged membranes with a preference for phosphoinositides such as PI3P and PI4P. We define the membrane-binding surface of Faa1 and show that its direct interaction with the membrane is required for its recruitment to phagophores. Furthermore, the physiological localization of Faa1 is key for its efficient catalysis and promotes phagophore expansion. Our results suggest a positive feedback loop coupling phagophore nucleation and expansion to lipid synthesis.
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Affiliation(s)
- Verena Baumann
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
| | - Sonja Achleitner
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
- Vienna BioCenter PhD Program, A Doctoral School of the University of Vienna, Medical University of Vienna, Vienna, Austria
| | - Susanna Tulli
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
| | - Martina Schuschnig
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
| | - Lara Klune
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
| | - Sascha Martens
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
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48
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Gopaldass N, Mayer A. PROPPINs and membrane fission in the endo-lysosomal system. Biochem Soc Trans 2024; 52:1233-1241. [PMID: 38747700 DOI: 10.1042/bst20230897] [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: 02/27/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 06/27/2024]
Abstract
PROPPINs constitute a conserved protein family with multiple members being expressed in many eukaryotes. PROPPINs have mainly been investigated for their role in autophagy, where they co-operate with several core factors for autophagosome formation. Recently, novel functions of these proteins on endo-lysosomal compartments have emerged. PROPPINs support the division of these organelles and the formation of tubulo-vesicular cargo carriers that mediate protein exit from them, such as those generated by the Retromer coat. In both cases, PROPPINs provide membrane fission activity. Integrating information from yeast and human cells this review summarizes the most important molecular features that allow these proteins to facilitate membrane fission and thus provide a critical element to endo-lysosomal protein traffic.
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Affiliation(s)
- Navin Gopaldass
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - Andreas Mayer
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
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49
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Nähse V, Stenmark H, Schink KO. Omegasomes control formation, expansion, and closure of autophagosomes. Bioessays 2024; 46:e2400038. [PMID: 38724256 DOI: 10.1002/bies.202400038] [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: 02/15/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 05/28/2024]
Abstract
Autophagy, an essential cellular process for maintaining cellular homeostasis and eliminating harmful cytoplasmic objects, involves the de novo formation of double-membraned autophagosomes that engulf and degrade cellular debris, protein aggregates, damaged organelles, and pathogens. Central to this process is the phagophore, which forms from donor membranes rich in lipids synthesized at various cellular sites, including the endoplasmic reticulum (ER), which has emerged as a primary source. The ER-associated omegasomes, characterized by their distinctive omega-shaped structure and accumulation of phosphatidylinositol 3-phosphate (PI3P), play a pivotal role in autophagosome formation. Omegasomes are thought to serve as platforms for phagophore assembly by recruiting essential proteins such as DFCP1/ZFYVE1 and facilitating lipid transfer to expand the phagophore. Despite the critical importance of phagophore biogenesis, many aspects remain poorly understood, particularly the complete range of proteins involved in omegasome dynamics, and the detailed mechanisms of lipid transfer and membrane contact site formation.
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Affiliation(s)
- Viola Nähse
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Harald Stenmark
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Kay O Schink
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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50
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Zhang Y, Lin C. Lipid osmosis, membrane tension, and other mechanochemical driving forces of lipid flow. Curr Opin Cell Biol 2024; 88:102377. [PMID: 38823338 PMCID: PMC11193448 DOI: 10.1016/j.ceb.2024.102377] [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: 01/10/2024] [Revised: 05/12/2024] [Accepted: 05/13/2024] [Indexed: 06/03/2024]
Abstract
Nonvesicular lipid transport among different membranes or membrane domains plays crucial roles in lipid homeostasis and organelle biogenesis. However, the forces that drive such lipid transport are not well understood. We propose that lipids tend to flow towards the membrane area with a higher membrane protein density in a process termed lipid osmosis. This process lowers the membrane tension in the area, resulting in a membrane tension difference called osmotic membrane tension. We examine the thermodynamic basis and experimental evidence of lipid osmosis and osmotic membrane tension. We predict that lipid osmosis can drive bulk lipid flows between different membrane regions through lipid transfer proteins, scramblases, or similar barriers that selectively pass lipids but not membrane proteins. We also speculate on the biological functions of lipid osmosis. Finally, we explore other driving forces for lipid transfer and describe potential methods and systems to further test our theory.
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Affiliation(s)
- Yongli Zhang
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.
| | - Chenxiang Lin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA; Nanobiology Institute, Yale University, West Haven, CT 06516, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
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