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Choi J, Jang H, Xuan Z, Park D. Emerging roles of ATG9/ATG9A in autophagy: implications for cell and neurobiology. Autophagy 2024:1-15. [PMID: 39099167 DOI: 10.1080/15548627.2024.2384349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 07/01/2024] [Accepted: 07/22/2024] [Indexed: 08/06/2024] Open
Abstract
Atg9, the only transmembrane protein among many autophagy-related proteins, was first identified in the year 2000 in yeast. Two homologs of Atg9, ATG9A and ATG9B, have been found in mammals. While ATG9B shows a tissue-specific expression pattern, such as in the placenta and pituitary gland, ATG9A is ubiquitously expressed. Additionally, ATG9A deficiency leads to severe defects not only at the molecular and cellular levels but also at the organismal level, suggesting key and fundamental roles for ATG9A. The subcellular localization of ATG9A on small vesicles and its functional relevance to autophagy have suggested a potential role for ATG9A in the lipid supply during autophagosome biogenesis. Nevertheless, the precise role of ATG9A in the autophagic process has remained a long-standing mystery, especially in neurons. Recent findings, however, including structural, proteomic, and biochemical analyses, have provided new insights into its function in the expansion of the phagophore membrane. In this review, we aim to understand various aspects of ATG9 (in invertebrates and plants)/ATG9A (in mammals), including its localization, trafficking, and other functions, in nonneuronal cells and neurons by comparing recent discoveries related to ATG9/ATG9A and proposing directions for future research.Abbreviation: AP-4: adaptor protein complex 4; ATG: autophagy related; cKO: conditional knockout; CLA-1: CLArinet (functional homolog of cytomatrix at the active zone proteins piccolo and fife); cryo-EM: cryogenic electron microscopy; ER: endoplasmic reticulum; KO: knockout; PAS: phagophore assembly site; PtdIns3K: class III phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate; RB1CC1/FIP200: RB1 inducible coiled-coil 1; SV: synaptic vesicle; TGN: trans-Golgi network; ULK: unc-51 like autophagy activating kinase; WIPI2: WD repeat domain, phosphoinositide interacting 2.
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Affiliation(s)
- Jiyoung Choi
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon, South Korea
- Department of Biotechnology, The Catholic University of Korea, Bucheon, South Korea
| | - Haeun Jang
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon, South Korea
| | - Zhao Xuan
- School of Biology and Ecology, University of Maine, Orono, ME, USA
| | - Daehun Park
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon, South Korea
- Department of Biotechnology, The Catholic University of Korea, Bucheon, South Korea
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2
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Yi S, Wang L, Ho MS, Zhang S. The autophagy protein Atg9 functions in glia and contributes to parkinsonian symptoms in a Drosophila model of Parkinson's disease. Neural Regen Res 2024; 19:1150-1155. [PMID: 37862221 PMCID: PMC10749615 DOI: 10.4103/1673-5374.382259] [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: 03/08/2023] [Revised: 05/31/2023] [Accepted: 07/10/2023] [Indexed: 10/22/2023] Open
Abstract
Parkinson's disease is a progressive neurodegenerative disease characterized by motor deficits, dopaminergic neuron loss, and brain accumulation of α-synuclein aggregates called Lewy bodies. Dysfunction in protein degradation pathways, such as autophagy, has been demonstrated in neurons as a critical mechanism for eliminating protein aggregates in Parkinson's disease. However, it is less well understood how protein aggregates are eliminated in glia, the other cell type in the brain. In the present study, we show that autophagy-related gene 9 (Atg9), the only transmembrane protein in the autophagy machinery, is highly expressed in Drosophila glia from adult brain. Results from immunostaining and live cell imaging analysis reveal that a portion of Atg9 localizes to the trans-Golgi network, autophagosomes, and lysosomes in glia. Atg9 is persistently in contact with these organelles. Lacking glial atg9 reduces the number of omegasomes and autophagosomes, and impairs autophagic substrate degradation. This suggests that glial Atg9 participates in the early steps of autophagy, and hence the control of autophagic degradation. Importantly, loss of glial atg9 induces parkinsonian symptoms in Drosophila including progressive loss of dopaminergic neurons, locomotion deficits, and glial activation. Our findings identify a functional role of Atg9 in glial autophagy and establish a potential link between glial autophagy and Parkinson's disease. These results may provide new insights on the underlying mechanism of Parkinson's disease.
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Affiliation(s)
- Shuanglong Yi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Linfang Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Margaret S. Ho
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Shiping Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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3
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Xiang H, Zhou M, Li Y, Zhou L, Wang R. Drug discovery by targeting the protein-protein interactions involved in autophagy. Acta Pharm Sin B 2023; 13:4373-4390. [PMID: 37969735 PMCID: PMC10638514 DOI: 10.1016/j.apsb.2023.07.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/31/2023] [Accepted: 07/10/2023] [Indexed: 11/17/2023] Open
Abstract
Autophagy is a cellular process in which proteins and organelles are engulfed in autophagosomal vesicles and transported to the lysosome/vacuole for degradation. Protein-protein interactions (PPIs) play a crucial role at many stages of autophagy, which present formidable but attainable targets for autophagy regulation. Moreover, selective regulation of PPIs tends to have a lower risk in causing undesired off-target effects in the context of a complicated biological network. Thus, small-molecule regulators, including peptides and peptidomimetics, targeting the critical PPIs involved in autophagy provide a new opportunity for innovative drug discovery. This article provides general background knowledge of the critical PPIs involved in autophagy and reviews a range of successful attempts on discovering regulators targeting those PPIs. Successful strategies and existing limitations in this field are also discussed.
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Affiliation(s)
- Honggang Xiang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Mi Zhou
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yan Li
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Lu Zhou
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Renxiao Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
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Guo H, Bechtel-Walz W. The Interplay of Autophagy and Oxidative Stress in the Kidney: What Do We Know? Nephron Clin Pract 2023; 147:627-642. [PMID: 37442108 DOI: 10.1159/000531290] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 05/19/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Autophagy, as an indispensable metabolism, plays pivotal roles in maintaining intracellular homeostasis. Nutritional stress, amino acid deficiency, oxidative stress, and hypoxia can trigger its initiation. Oxidative stress in the kidney activates essential signal molecules, like mammalian target of rapamycin (mTOR), adenosine monophosphate-activated protein kinase (AMPK), and silent mating-type information regulation 2 homolog-1 (SIRT1), to stimulate autophagy, ultimately leading to degradation of intracellular oxidative substances and damaged organelles. Growing evidence suggests that autophagy protects the kidney from oxidative stress during acute ischemic kidney injury, chronic kidney disease, and even aging. SUMMARY This review emphasizes the cross talk between reactive oxygen species (ROS) signaling pathways and autophagy during renal homeostasis and chronic kidney disease according to the current latest research and provides therapeutic targets during kidney disorders by adjusting autophagy and suppressing oxidative stress. KEY MESSAGES ROS arise through an imbalance of oxidation and antioxidant defense mechanisms, leading to impaired cellular and organ function. Targeting the overproduction of ROS and reactive nitrogen species, reducing the antioxidant enzyme activity and the recovery of the prooxidative-antioxidative balance provide novel therapeutic regimens to contribute to recovery in acute and chronic renal failure. Although, in recent years, great progress has been made in understanding the molecular mechanisms of oxidative stress and autophagy in acute and chronic renal failure, the focus on clinical therapies is still in its infancy. The growing number of studies on the interactive mechanisms of oxidative stress-mediated autophagy will be of great importance for the future treatment and prevention of kidney diseases.
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Affiliation(s)
- Haihua Guo
- Renal Division, Department of Medicine, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Wibke Bechtel-Walz
- Renal Division, Department of Medicine, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
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Mao B, Yuan W, Wu F, Yan Y, Wang B. Autophagy in hepatic ischemia-reperfusion injury. Cell Death Discov 2023; 9:115. [PMID: 37019879 PMCID: PMC10076300 DOI: 10.1038/s41420-023-01387-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 04/07/2023] Open
Abstract
Hepatic ischemia-reperfusion injury (HIRI) is a major complication of liver resection or liver transplantation that can seriously affect patient's prognosis. There is currently no definitive and effective treatment strategy for HIRI. Autophagy is an intracellular self-digestion pathway initiated to remove damaged organelles and proteins, which maintains cell survival, differentiation, and homeostasis. Recent studies have shown that autophagy is involved in the regulation of HIRI. Numerous drugs and treatments can change the outcome of HIRI by controlling the pathways of autophagy. This review mainly discusses the occurrence and development of autophagy, the selection of experimental models for HIRI, and the specific regulatory pathways of autophagy in HIRI. Autophagy has considerable potential in the treatment of HIRI.
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Affiliation(s)
- Benliang Mao
- College of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Wei Yuan
- Department of General Surgery, Guangzhou Red Cross Hospital affiliated to Jinan University, Guangzhou, China
| | - Fan Wu
- Department of General Surgery, Guangzhou Red Cross Hospital affiliated to Jinan University, Guangzhou, China
| | - Yong Yan
- Department of General Surgery, Guangzhou Red Cross Hospital affiliated to Jinan University, Guangzhou, China
| | - Bailin Wang
- College of Clinical Medicine, Guizhou Medical University, Guiyang, China.
- Department of General Surgery, Guangzhou Red Cross Hospital affiliated to Jinan University, Guangzhou, China.
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Dong L, He J, Luo L, Wang K. Targeting the Interplay of Autophagy and ROS for Cancer Therapy: An Updated Overview on Phytochemicals. Pharmaceuticals (Basel) 2023; 16:ph16010092. [PMID: 36678588 PMCID: PMC9865312 DOI: 10.3390/ph16010092] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/21/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Autophagy is an evolutionarily conserved self-degradation system that recycles cellular components and damaged organelles, which is critical for the maintenance of cellular homeostasis. Intracellular reactive oxygen species (ROS) are short-lived molecules containing unpaired electrons that are formed by the partial reduction of molecular oxygen. It is widely known that autophagy and ROS can regulate each other to influence the progression of cancer. Recently, due to the wide potent anti-cancer effects with minimal side effects, phytochemicals, especially those that can modulate ROS and autophagy, have attracted great interest of researchers. In this review, we afford an overview of the complex regulatory relationship between autophagy and ROS in cancer, with an emphasis on phytochemicals that regulate ROS and autophagy for cancer therapy. We also discuss the effects of ROS/autophagy inhibitors on the anti-cancer effects of phytochemicals, and the challenges associated with harnessing the regulation potential on ROS and autophagy of phytochemicals for cancer therapy.
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Affiliation(s)
- Lixia Dong
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Jingqiu He
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Li Luo
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu 610041, China
- Correspondence: (L.L.); (K.W.)
| | - Kui Wang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
- Correspondence: (L.L.); (K.W.)
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Khan SU, Fatima K, Aisha S, Hamza B, Malik F. Redox balance and autophagy regulation in cancer progression and their therapeutic perspective. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 40:12. [PMID: 36352310 DOI: 10.1007/s12032-022-01871-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/30/2022] [Indexed: 11/10/2022]
Abstract
Cellular ROS production participates in various cellular functions but its accumulation decides the cell fate. Malignant cells have higher levels of ROS and active antioxidant machinery, a characteristic hallmark of cancer with an outcome of activation of stress-induced pathways like autophagy. Autophagy is an intracellular catabolic process that produces alternative raw materials to meet the energy demand of cells and is influenced by the cellular redox state thus playing a definite role in cancer cell fate. Since damaged mitochondria are the main source of ROS in the cell, however, cancer cells remove them by upregulating the process of mitophagy which is known to play a decisive role in tumorigenesis and tumor progression. Chemotherapy exploits cell machinery which results in the accumulation of toxic levels of ROS in cells resulting in cell death by activating either of the pathways like apoptosis, necrosis, ferroptosis or autophagy in them. So understanding these redox and autophagy regulations offers a promising method to design and develop new cancer therapies that can be very effective and durable for years. This review will give a summary of the current therapeutic molecules targeting redox regulation and autophagy for the treatment of cancer. Further, it will highlight various challenges in developing anticancer agents due to autophagy and ROS regulation in the cell and insights into the development of future therapies.
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Affiliation(s)
- Sameer Ullah Khan
- Division of Cancer Pharmacology, CSIR-Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, 190005, Jammu and Kashmir, India.
- Academy of Scientific and Innovative Research (AcSIR), Sanat Nagar, Ghaziabad, 201002, India.
| | - Kaneez Fatima
- Division of Cancer Pharmacology, CSIR-Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, 190005, Jammu and Kashmir, India
- Academy of Scientific and Innovative Research (AcSIR), Sanat Nagar, Ghaziabad, 201002, India
| | - Shariqa Aisha
- Division of Cancer Pharmacology, CSIR-Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, 190005, Jammu and Kashmir, India
| | - Baseerat Hamza
- Division of Cancer Pharmacology, CSIR-Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, 190005, Jammu and Kashmir, India
| | - Fayaz Malik
- Division of Cancer Pharmacology, CSIR-Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, 190005, Jammu and Kashmir, India.
- Academy of Scientific and Innovative Research (AcSIR), Sanat Nagar, Ghaziabad, 201002, India.
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8
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Zhao X, Zhang Q, Zheng R. The interplay between oxidative stress and autophagy in chronic obstructive pulmonary disease. Front Physiol 2022; 13:1004275. [PMID: 36225291 PMCID: PMC9548529 DOI: 10.3389/fphys.2022.1004275] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
Autophagy is a highly conserved process that is indispensable for cell survival, embryonic development, and tissue homeostasis. Activation of autophagy protects cells against oxidative stress and is a major adaptive response to injury. When autophagy is dysregulated by factors such as smoking, environmental insults and aging, it can lead to enhanced formation of aggressors and production of reactive oxygen species (ROS), resulting in oxidative stress and oxidative damage to cells. ROS activates autophagy, which in turn promotes cell adaptation and reduces oxidative damage by degrading and circulating damaged macromolecules and dysfunctional cell organelles. The cellular response triggered by oxidative stress includes changes in signaling pathways that ultimately regulate autophagy. Chronic obstructive pulmonary disease (COPD) is the most common lung disease among the elderly worldwide, with a high mortality rate. As an induced response to oxidative stress, autophagy plays an important role in the pathogenesis of COPD. This review discusses the regulation of oxidative stress and autophagy in COPD, and aims to provide new avenues for future research on target-specific treatments for COPD.
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Affiliation(s)
| | | | - Rui Zheng
- *Correspondence: Qiang Zhang, ; Rui Zheng,
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9
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Baines K, Yoshioka K, Takuwa Y, Lane JD. The ATG5 interactome links clathrin-mediated vesicular trafficking with the autophagosome assembly machinery. AUTOPHAGY REPORTS 2022; 1:88-118. [PMID: 35449600 PMCID: PMC9015699 DOI: 10.1080/27694127.2022.2042054] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Autophagosome formation involves the sequential actions of conserved ATG proteins to coordinate the lipidation of the ubiquitin-like modifier Atg8-family proteins at the nascent phagophore membrane. Although the molecular steps driving this process are well understood, the source of membranes for the expanding phagophore and their mode of delivery are only now beginning to be revealed. Here, we have used quantitative SILAC-based proteomics to identify proteins that associate with the ATG12-ATG5 conjugate, a crucial player during Atg8-family protein lipidation. Our datasets reveal a strong enrichment of regulators of clathrin-mediated vesicular trafficking, including clathrin heavy and light chains, and several clathrin adaptors. Also identified were PIK3C2A (a phosphoinositide 3-kinase involved in clathrin-mediated endocytosis) and HIP1R (a component of clathrin vesicles), and the absence of either of these proteins alters autophagic flux in cell-based starvation assays. To determine whether the ATG12-ATG5 conjugate reciprocally influences trafficking within the endocytic compartment, we captured the cell surface proteomes of autophagy-competent and autophagy-incompetent mouse embryonic fibroblasts under fed and starved conditions. We report changes in the relative proportions of individual cell surface proteins and show that cell surface levels of the SLC7A5-SLC3A2 amino acid transporter are influenced by autophagy capability. Our data provide evidence for direct regulatory coupling between the ATG12-ATG5 conjugate and the clathrin membrane trafficking system and suggest candidate membrane proteins whose trafficking within the cell may be modulated by the autophagy machinery. Abbreviations: ATG, autophagy related; BafA1, bafilomycin A1; GFP, green fluorescent protein; HIP1R, huntingtin interacting protein 1 related; MEF, mouse embryo fibroblast; PIK3C2A, phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 alpha; SILAC, stable isotope labelling with amino acids in culture; SQSTM1, sequestosome 1; STRING, search tool for the retrieval of interacting genes/proteins.
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Affiliation(s)
- Kiren Baines
- Cell Biology Laboratories, School of Biochemistry, University of Bristol, University Walk, Bristol, BS81TD, UK
| | - Kazuaki Yoshioka
- Department of Physiology, Kanazawa University Graduate School of Medical Sciences, 13-1 Takara-machi, Kanazawa Ishikawa920-8640, Japan
| | - Yoh Takuwa
- Department of Physiology, Kanazawa University Graduate School of Medical Sciences, 13-1 Takara-machi, Kanazawa Ishikawa920-8640, Japan
| | - Jon D. Lane
- Cell Biology Laboratories, School of Biochemistry, University of Bristol, University Walk, Bristol, BS81TD, UK
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10
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Yang S, Park D, Manning L, Hill SE, Cao M, Xuan Z, Gonzalez I, Dong Y, Clark B, Shao L, Okeke I, Almoril-Porras A, Bai J, De Camilli P, Colón-Ramos DA. Presynaptic autophagy is coupled to the synaptic vesicle cycle via ATG-9. Neuron 2022; 110:824-840.e10. [PMID: 35065714 PMCID: PMC9017068 DOI: 10.1016/j.neuron.2021.12.031] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 10/20/2021] [Accepted: 12/20/2021] [Indexed: 01/01/2023]
Abstract
Autophagy is a cellular degradation pathway essential for neuronal health and function. Autophagosome biogenesis occurs at synapses, is locally regulated, and increases in response to neuronal activity. The mechanisms that couple autophagosome biogenesis to synaptic activity remain unknown. In this study, we determine that trafficking of ATG-9, the only transmembrane protein in the core autophagy pathway, links the synaptic vesicle cycle with autophagy. ATG-9-positive vesicles in C. elegans are generated from the trans-Golgi network via AP-3-dependent budding and delivered to presynaptic sites. At presynaptic sites, ATG-9 undergoes exo-endocytosis in an activity-dependent manner. Mutations that disrupt endocytosis, including a lesion in synaptojanin 1 associated with Parkinson's disease, result in abnormal ATG-9 accumulation at clathrin-rich synaptic foci and defects in activity-induced presynaptic autophagy. Our findings uncover regulated key steps of ATG-9 trafficking at presynaptic sites and provide evidence that ATG-9 exo-endocytosis couples autophagosome biogenesis at presynaptic sites with the activity-dependent synaptic vesicle cycle.
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Affiliation(s)
- Sisi Yang
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Daehun Park
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Laura Manning
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Sarah E Hill
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Mian Cao
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Zhao Xuan
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Ian Gonzalez
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Yongming Dong
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Benjamin Clark
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Lin Shao
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Ifechukwu Okeke
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Agustin Almoril-Porras
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA
| | - Jihong Bai
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Pietro De Camilli
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA; Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Daniel A Colón-Ramos
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neuroscience and of Cell Biology, Yale University School of Medicine, 260 Whitney Avenue, YSB C167, New Haven, CT 06511, USA; Instituto de Neurobiología José del Castillo, Recinto de Ciencias Médicas, Universidad de Puerto Rico, 201 Boulevard del Valle, San Juan, PR 00901, USA; Wu Tsai Institute, Yale University, New Haven, CT 06510, USA.
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11
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Jung Y, Artan M, Kim N, Yeom J, Hwang AB, Jeong DE, Altintas Ö, Seo K, Seo M, Lee D, Hwang W, Lee Y, Sohn J, Kim EJE, Ju S, Han SK, Nam HJ, Adams L, Ryu Y, Moon DJ, Kang C, Yoo JY, Park SK, Ha CM, Hansen M, Kim S, Lee C, Park SY, Lee SJV. MON-2, a Golgi protein, mediates autophagy-dependent longevity in Caenorhabditis elegans. SCIENCE ADVANCES 2021; 7:eabj8156. [PMID: 34860542 PMCID: PMC8641931 DOI: 10.1126/sciadv.abj8156] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/14/2021] [Indexed: 06/02/2023]
Abstract
The Golgi apparatus plays a central role in trafficking cargoes such as proteins and lipids. Defects in the Golgi apparatus lead to various diseases, but its role in organismal longevity is largely unknown. Using a quantitative proteomic approach, we found that a Golgi protein, MON-2, was up-regulated in long-lived Caenorhabditis elegans mutants with mitochondrial respiration defects and was required for their longevity. Similarly, we showed that DOP1/PAD-1, which acts with MON-2 to traffic macromolecules between the Golgi and endosome, contributed to the longevity of respiration mutants. Furthermore, we demonstrated that MON-2 was required for up-regulation of autophagy, a longevity-associated recycling process, by activating the Atg8 ortholog GABARAP/LGG-1 in C. elegans. Consistently, we showed that mammalian MON2 activated GABARAPL2 through physical interaction, which increased autophagic flux in mammalian cells. Thus, the evolutionarily conserved role of MON2 in trafficking between the Golgi and endosome is an integral part of autophagy-mediated longevity.
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Affiliation(s)
- Yoonji Jung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Murat Artan
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Nari Kim
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Jeonghun Yeom
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Ara B. Hwang
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Dae-Eun Jeong
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Özlem Altintas
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Keunhee Seo
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Mihwa Seo
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Dongyeop Lee
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Wooseon Hwang
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Yujin Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Jooyeon Sohn
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Eun Ji E. Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Sungeun Ju
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Seong Kyu Han
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Hyun-Jun Nam
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Linnea Adams
- Development, Aging, and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Youngjae Ryu
- Research Division and Brain Research Core Facilities of Korea Brain Research Institute, Daegu 41068, South Korea
| | - Dong Jin Moon
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Chanhee Kang
- School of Biological Sciences, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Joo-Yeon Yoo
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Sang Ki Park
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Chang Man Ha
- Research Division and Brain Research Core Facilities of Korea Brain Research Institute, Daegu 41068, South Korea
| | - Malene Hansen
- Development, Aging, and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sanguk Kim
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Seung-Yeol Park
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea
| | - Seung-Jae V. Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
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12
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Shen T, Jiang L, Wang X, Xu Q, Han L, Liu S, Huang T, Li H, Dai L, Li H, Lu K. Function and molecular mechanism of N-terminal acetylation in autophagy. Cell Rep 2021; 37:109937. [PMID: 34788606 DOI: 10.1016/j.celrep.2021.109937] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 08/16/2021] [Accepted: 10/12/2021] [Indexed: 02/08/2023] Open
Abstract
Acetyl ligation to the amino acids in a protein is an important posttranslational modification. However, in contrast to lysine acetylation, N-terminal acetylation is elusive in terms of its cellular functions. Here, we identify Nat3 as an N-terminal acetyltransferase essential for autophagy, a catabolic pathway for bulk transport and degradation of cytoplasmic components. We identify the actin cytoskeleton constituent Act1 and dynamin-like GTPase Vps1 (vacuolar protein sorting 1) as substrates for Nat3-mediated N-terminal acetylation of the first methionine. Acetylated Act1 forms actin filaments and therefore promotes the transport of Atg9 vesicles for autophagosome formation; acetylated Vps1 recruits and facilitates bundling of the SNARE (soluble N-ethylmaleimide-sensitive factor activating protein receptor) complex for autophagosome fusion with vacuoles. Abolishment of the N-terminal acetylation of Act1 and Vps1 is associated with blockage of upstream and downstream steps of the autophagy process. Therefore, our work shows that protein N-terminal acetylation plays a critical role in controlling autophagy by fine-tuning multiple steps in the process.
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Affiliation(s)
- Tianyun Shen
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and The Research Units of West China, Chinese Academy of Medical Sciences, Chengdu 610041, China
| | - Lan Jiang
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and The Research Units of West China, Chinese Academy of Medical Sciences, Chengdu 610041, China
| | - Xinyuan Wang
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Qingjia Xu
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and The Research Units of West China, Chinese Academy of Medical Sciences, Chengdu 610041, China
| | - Lu Han
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and The Research Units of West China, Chinese Academy of Medical Sciences, Chengdu 610041, China
| | - Shiyan Liu
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and The Research Units of West China, Chinese Academy of Medical Sciences, Chengdu 610041, China
| | - Ting Huang
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and The Research Units of West China, Chinese Academy of Medical Sciences, Chengdu 610041, China
| | - Hongyan Li
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China.
| | - Huihui Li
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and The Research Units of West China, Chinese Academy of Medical Sciences, Chengdu 610041, China; West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China.
| | - Kefeng Lu
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and The Research Units of West China, Chinese Academy of Medical Sciences, Chengdu 610041, China.
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13
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Focus on the Small GTPase Rab1: A Key Player in the Pathogenesis of Parkinson's Disease. Int J Mol Sci 2021; 22:ijms222112087. [PMID: 34769517 PMCID: PMC8584362 DOI: 10.3390/ijms222112087] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 12/19/2022] Open
Abstract
Parkinson’s disease (PD) is the second most frequent neurodegenerative disease. It is characterized by the loss of dopaminergic neurons in the substantia nigra and the formation of large aggregates in the survival neurons called Lewy bodies, which mainly contain α-synuclein (α-syn). The cause of cell death is not known but could be due to mitochondrial dysfunction, protein homeostasis failure, and alterations in the secretory/endolysosomal/autophagic pathways. Survival nigral neurons overexpress the small GTPase Rab1. This protein is considered a housekeeping Rab that is necessary to support the secretory pathway, the maintenance of the Golgi complex structure, and the regulation of macroautophagy from yeast to humans. It is also involved in signaling, carcinogenesis, and infection for some pathogens. It has been shown that it is directly linked to the pathogenesis of PD and other neurodegenerative diseases. It has a protective effect against α–σψν toxicity and has recently been shown to be a substrate of LRRK2, which is the most common cause of familial PD and the risk of sporadic disease. In this review, we analyze the key aspects of Rab1 function in dopamine neurons and its implications in PD neurodegeneration/restauration. The results of the current and former research support the notion that this GTPase is a good candidate for therapeutic strategies.
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14
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Guardia CM, Jain A, Mattera R, Friefeld A, Li Y, Bonifacino JS. RUSC2 and WDR47 oppositely regulate kinesin-1-dependent distribution of ATG9A to the cell periphery. Mol Biol Cell 2021; 32:ar25. [PMID: 34432492 PMCID: PMC8693955 DOI: 10.1091/mbc.e21-06-0295] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/10/2021] [Accepted: 08/18/2021] [Indexed: 01/12/2023] Open
Abstract
Autophagy-related protein 9 (ATG9) is a transmembrane protein component of the autophagy machinery that cycles between the trans-Golgi network (TGN) in the perinuclear area and other compartments in the peripheral area of the cell. In mammalian cells, export of the ATG9A isoform from the TGN into ATG9A-containing vesicles is mediated by the adaptor protein 4 (AP-4) complex. However, the mechanisms responsible for the subsequent distribution of these vesicles to the cell periphery are unclear. Herein we show that the AP-4-accessory protein RUSC2 couples ATG9A-containing vesicles to the plus-end-directed microtubule motor kinesin-1 via an interaction between a disordered region of RUSC2 and the kinesin-1 light chain. This interaction is counteracted by the microtubule-associated protein WDR47. These findings uncover a mechanism for the peripheral distribution of ATG9A-containing vesicles involving the function of RUSC2 as a kinesin-1 adaptor and WDR47 as a negative regulator of this function.
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Affiliation(s)
- Carlos M. Guardia
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development
| | - Akansha Jain
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development
| | - Rafael Mattera
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development
| | - Alex Friefeld
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892
| | - Juan S. Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development
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15
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Wu MY, Wang EJ, Feng D, Li M, Ye RD, Lu JH. Pharmacological insights into autophagy modulation in autoimmune diseases. Acta Pharm Sin B 2021; 11:3364-3378. [PMID: 34900523 PMCID: PMC8642426 DOI: 10.1016/j.apsb.2021.03.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/08/2021] [Accepted: 02/16/2021] [Indexed: 12/21/2022] Open
Abstract
As a cellular bulk degradation and survival mechanism, autophagy is implicated in diverse biological processes. Genome-wide association studies have revealed the link between autophagy gene polymorphisms and susceptibility of autoimmune diseases including systemic lupus erythematosus (SLE) and inflammatory bowel disease (IBD), indicating that autophagy dysregulation may be involved in the development of autoimmune diseases. A series of autophagy modulators have displayed protective effects on autoimmune disease models, highlighting the emerging role of autophagy modulators in treating autoimmune diseases. This review explores the roles of autophagy in the autoimmune diseases, with emphasis on four major autoimmune diseases [SLE, rheumatoid arthritis (RA), IBD, and experimental autoimmune encephalomyelitis (EAE)]. More importantly, the therapeutic potentials of small molecular autophagy modulators (including autophagy inducers and inhibitors) on autoimmune diseases are comprehensively analyzed.
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Affiliation(s)
- Ming-Yue Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau 9999078, China
| | - Er-Jin Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau 9999078, China
| | - Du Feng
- Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, College of Basic Medical Science, Guangzhou Medical University, Guangzhou 510000, China
| | - Min Li
- School of Pharmaceutical Sciences, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510000, China
| | - Richard D. Ye
- Kobilka Institute of Innovative Drug Discovery, School of Life and Health Sciences, the Chinese University of Hong Kong, Shenzhen 518000, China
| | - Jia-Hong Lu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau 9999078, China
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16
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Meyer N, Henkel L, Linder B, Zielke S, Tascher G, Trautmann S, Geisslinger G, Münch C, Fulda S, Tegeder I, Kögel D. Autophagy activation, lipotoxicity and lysosomal membrane permeabilization synergize to promote pimozide- and loperamide-induced glioma cell death. Autophagy 2021; 17:3424-3443. [PMID: 33461384 PMCID: PMC8632287 DOI: 10.1080/15548627.2021.1874208] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 01/06/2021] [Indexed: 12/22/2022] Open
Abstract
Increasing evidence suggests that induction of lethal macroautophagy/autophagy carries potential significance for the treatment of glioblastoma (GBM). In continuation of previous work, we demonstrate that pimozide and loperamide trigger an ATG5- and ATG7 (autophagy related 5 and 7)-dependent type of cell death that is significantly reduced with cathepsin inhibitors and the lipid reactive oxygen species (ROS) scavenger α-tocopherol in MZ-54 GBM cells. Global proteomic analysis after treatment with both drugs also revealed an increase of proteins related to lipid and cholesterol metabolic processes. These changes were accompanied by a massive accumulation of cholesterol and other lipids in the lysosomal compartment, indicative of impaired lipid transport/degradation. In line with these observations, pimozide and loperamide treatment were associated with a pronounced increase of bioactive sphingolipids including ceramides, glucosylceramides and sphingoid bases measured by targeted lipidomic analysis. Furthermore, pimozide and loperamide inhibited the activity of SMPD1/ASM (sphingomyelin phosphodiesterase 1) and promoted induction of lysosomal membrane permeabilization (LMP), as well as release of CTSB (cathepsin B) into the cytosol in MZ-54 wild-type (WT) cells. Whereas LMP and cell death were significantly attenuated in ATG5 and ATG7 knockout (KO) cells, both events were enhanced by depletion of the lysophagy receptor VCP (valosin containing protein), supporting a pro-survival function of lysophagy under these conditions. Collectively, our data suggest that pimozide and loperamide-driven autophagy and lipotoxicity synergize to induce LMP and cell death. The results also support the notion that simultaneous overactivation of autophagy and induction of LMP represents a promising approach for the treatment of GBM.Abbreviations: ACD: autophagic cell death; AKT1: AKT serine/threonine kinase 1; ATG5: autophagy related 5; ATG7: autophagy related 7; ATG14: autophagy related 14; CERS1: ceramide synthase 1; CTSB: cathepsin B; CYBB/NOX2: cytochrome b-245 beta chain; ER: endoplasmatic reticulum; FBS: fetal bovine serum; GBM: glioblastoma; GO: gene ontology; HTR7/5-HT7: 5-hydroxytryptamine receptor 7; KD: knockdown; KO: knockout; LAMP1: lysosomal associated membrane protein 1; LAP: LC3-associated phagocytosis; LMP: lysosomal membrane permeabilization; MAP1LC3B: microtubule associated protein 1 light chain 3 beta; MTOR: mechanistic target of rapamycin kinase; RB1CC1: RB1 inducible coiled-coil 1; ROS: reactive oxygen species; RPS6: ribosomal protein S6; SMPD1/ASM: sphingomyelin phosphodiesterase 1; VCP/p97: valosin containing protein; WT: wild-type.
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Affiliation(s)
- Nina Meyer
- Experimental Neurosurgery, Goethe University Hospital Frankfurt/Main, Frankfurt, Germany
| | - Lisa Henkel
- Experimental Neurosurgery, Goethe University Hospital Frankfurt/Main, Frankfurt, Germany
| | - Benedikt Linder
- Experimental Neurosurgery, Goethe University Hospital Frankfurt/Main, Frankfurt, Germany
| | - Svenja Zielke
- Experimental Cancer Research in Pediatrics, Goethe University Hospital Frankfurt/Main, Frankfurt, Germany
| | - Georg Tascher
- Institute of Biochemistry II, Goethe University Hospital Frankfurt/Main, Frankfurt, Germany
| | - Sandra Trautmann
- Institute of Clinical Pharmacology, Goethe University Hospital Frankfurt/Main, Frankfurt, Germany
| | - Gerd Geisslinger
- Institute of Clinical Pharmacology, Goethe University Hospital Frankfurt/Main, Frankfurt, Germany
| | - Christian Münch
- Institute of Biochemistry II, Goethe University Hospital Frankfurt/Main, Frankfurt, Germany
| | - Simone Fulda
- Experimental Cancer Research in Pediatrics, Goethe University Hospital Frankfurt/Main, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt, Frankfurt, Germany
| | - Irmgard Tegeder
- Institute of Clinical Pharmacology, Goethe University Hospital Frankfurt/Main, Frankfurt, Germany
| | - Donat Kögel
- Experimental Neurosurgery, Goethe University Hospital Frankfurt/Main, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt, Frankfurt, Germany
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17
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Yang Y, Zheng L, Zheng X, Ge L. Autophagosomal Membrane Origin and Formation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1208:17-42. [PMID: 34260019 DOI: 10.1007/978-981-16-2830-6_2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Autophagosome formation is a regulated membrane remodeling process, which involves the generation of autophagosomal membrane precursors (vesicles), the assembly of the autophagosomal membrane precursors to form the phagophore, and phagophore elongation to complete the autophagosome. The sources of the autophagosomal membrane precursors are endomembrane compartments, such as the endoplasmic reticulum (ER), the ER-Golgi intermediate compartment (ERGIC), ER-exit sites (ERES), and endosomes. In response to stress, these structures are remodeled, to generate the early autophagosomal membrane precursors. The phagophore assembly site (PAS), which mainly localizes on the ER, harbors the site for autophagosomal membrane assembly, elongation, and completion. ATG proteins, membrane remodeling factors, and autophagic membranes follow a precise choreography to complete the overall process. In this chapter, we briefly discuss our current knowledge on the membrane origins of the autophagosome, as well as autophagosomal precursor generation, assembly, and expansion.
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Affiliation(s)
- Yi Yang
- Hangzhou Normal University, Hangzhou, Zhejiang, China.
| | - Li Zheng
- School of Life Sciences, Tsinghua University, Beijing, China
| | | | - Liang Ge
- School of Life Sciences, Tsinghua University, Beijing, China.
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18
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Claude-Taupin A, Morel E. Phosphoinositides: Functions in autophagy-related stress responses. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:158903. [PMID: 33578048 DOI: 10.1016/j.bbalip.2021.158903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/29/2021] [Accepted: 02/06/2021] [Indexed: 01/02/2023]
Abstract
Phosphoinositides are key lipids in eukaryotes, regulating organelles' identity and function. Their synthesis and turnover require specific phosphorylation/dephosphorylation events that are ensured by dedicated lipid kinases and phosphatases, which modulate the structure of the inositol ring by adding or removing phosphates on positions 3, 4 or 5. Beside their implication in intracellular signalization and cytoskeleton dynamics, phosphoinositides are essential for vesicular transport along intracellular trafficking routes, by providing molecular scaffolds to membrane related events such as budding, fission or fusion. Robust and detailed literature demonstrated that some members of the phosphoinositides family are crucial for the autophagy pathway, acting as fine tuners and regulators. In this review, we discuss the known functions of phosphoinositides in autophagy canonical processes, such as during autophagosome formation, as well as the importance of phosphoinositides in organelle-based processes directly connected to the autophagic machinery, such as endosomal dynamics, ciliogenesis and innate immunity.
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Affiliation(s)
- Aurore Claude-Taupin
- Institut Necker Enfants-Malades (INEM), INSERM U1151-CNRS UMR 8253, Université de Paris, Paris, France
| | - Etienne Morel
- Institut Necker Enfants-Malades (INEM), INSERM U1151-CNRS UMR 8253, Université de Paris, Paris, France.
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19
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Varusai TM, Jupe S, Sevilla C, Matthews L, Gillespie M, Stein L, Wu G, D’Eustachio P, Metzakopian E, Hermjakob H. Using Reactome to build an autophagy mechanism knowledgebase. Autophagy 2021; 17:1543-1554. [PMID: 32486891 PMCID: PMC8204961 DOI: 10.1080/15548627.2020.1761659] [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: 01/07/2020] [Revised: 04/16/2020] [Accepted: 04/21/2020] [Indexed: 10/26/2022] Open
Abstract
The 21st century has revealed much about the fundamental cellular process of autophagy. Autophagy controls the catabolism and recycling of various cellular components both as a constitutive process and as a response to stress and foreign material invasion. There is considerable knowledge of the molecular mechanisms of autophagy, and this is still growing as new modalities emerge. There is a need to investigate autophagy mechanisms reliably, comprehensively and conveniently. Reactome is a freely available knowledgebase that consists of manually curated molecular events (reactions) organized into cellular pathways (https://reactome.org/). Pathways/reactions in Reactome are hierarchically structured, graphically presented and extensively annotated. Data analysis tools, such as pathway enrichment, expression data overlay and species comparison, are also available. For customized analysis, information can also be programmatically queried. Here, we discuss the curation and annotation of the molecular mechanisms of autophagy in Reactome. We also demonstrate the value that Reactome adds to research by reanalyzing a previously published work on genome-wide CRISPR screening of autophagy components.Abbreviations: CMA: chaperone-mediated autophagy; GO: Gene Ontology; MA: macroautophagy; MI: microautophagy; MTOR: mechanistic target of rapamycin kinase; SQSTM1: sequestosome 1.
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Affiliation(s)
- Thawfeek Mohamed Varusai
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
- Open Targets, Wellcome Genome Campus, Cambridgeshire, UK
| | - Steven Jupe
- COSMIC, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Cristoffer Sevilla
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Lisa Matthews
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY, USA
| | - Marc Gillespie
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Pharmaceutical Sciences, St.John’s University, Queens, NY, USA
| | - Lincoln Stein
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Guanming Wu
- Department of Medical Informatics and Clinical Epidemiology, School of Medicine, Oregon Health and Science University, Oregon, Portland, OR, USA
| | - Peter D’Eustachio
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY, USA
| | - Emmanouil Metzakopian
- UK Dementia Research Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, National Center for Protein Sciences, Beijing, China
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20
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Peng D, Ruan C, Fu S, He C, Song J, Li H, Tu Y, Tang D, Yao L, Lin S, Shi Y, Zhang W, Zhou H, Zhu L, Ma C, Chang C, Ma J, Xie Z, Wang C, Xue Y. Atg9-centered multi-omics integration reveals new autophagy regulators in Saccharomyces cerevisiae. Autophagy 2021; 17:4453-4476. [PMID: 33722159 DOI: 10.1080/15548627.2021.1898749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
In Saccharomyces cerevisiae, Atg9 is an important autophagy-related (Atg) protein, and interacts with hundreds of other proteins. How many Atg9-interacting proteins are involved in macroautophagy/autophagy is unclear. Here, we conducted a multi-omic profiling of Atg9-dependent molecular landscapes during nitrogen starvation-induced autophagy, and identified 290 and 256 genes to be markedly regulated by ATG9 in transcriptional and translational levels, respectively. Unexpectedly, we found most of known Atg proteins and autophagy regulators that interact with Atg9 were not significantly changed in the mRNA or protein level during autophagy. Based on a hypothesis that proteins with similar molecular characteristics might have similar functions, we developed a new method named inference of functional interacting partners (iFIP) to integrate the transcriptomic, proteomic and interactomic data, and predicted 42 Atg9-interacting proteins to be potentially involved in autophagy, including 15 known Atg proteins or autophagy regulators. We validated 2 Atg9-interacting partners, Glo3 and Scs7, to be functional in both bulk and selective autophagy. The mRNA and protein expressions but not subcellular localizations of Glo3 and Scs7 were affected with or without ATG9 during autophagy, whereas the colocalizations of the 2 proteins and Atg9 were markedly enhanced at early stages of the autophagic process. Further analyses demonstrated that Glo3 but not Scs7 regulates the retrograde transport of Atg9 during autophagy. A working model was illustrated to highlight the importance of the Atg9 interactome. Taken together, our study not only provided a powerful method for analyzing the multi-omics data, but also revealed 2 new players that regulate autophagy.Abbreviations: ALP: alkaline phosphatase; Arf1: ADP-ribosylation factor 1; Atg: autophagy-related; Co-IP: co-immunoprecipitation; Cvt: cytoplasm-to-vacuole targeting; DEM: differentially expressed mRNA; DEP: differentially expressed protein; DIC: differential interference contrast; E-ratio: enrichment ratio; ER: endoplasmic reticulum; ES: enrichment score; FC: fold change; FPKM: fragments per kilobase of exon per million fragments mapped; GAP: GTPase-activating protein; GFP: green fluorescent protein; GO: gene ontology; GSEA: gene set enrichment analysis; GST: glutathione S-transferase; HA: hemagglutinin; iFIP: inference of functional interacting partners; KO: knockout; LR: logistic regression; OE: over-expression; PAS: phagophore assembly site; PPI: protein-protein interaction; RFP: red fluorescence protein; RNA-seq: RNA sequencing; RT-PCR: real-time polymerase chain reaction; SCC: Spearman's correlation coefficient; SD-N: synthetic minimal medium lacking nitrogen; THANATOS: The Autophagy, Necrosis, ApopTosis OrchestratorS; Vsn: variance stabilization normalization; WT: wild-type.
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Affiliation(s)
- Di Peng
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei China.,Nanjing University Institute of Artificial Intelligence Biomedicine, Nanjing, Jiangsu China
| | - Chen Ruan
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei China
| | - Shanshan Fu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei China
| | - Chengwen He
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai China
| | - Jingzhen Song
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai China
| | - Hui Li
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai China
| | - Yiran Tu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei China
| | - Dachao Tang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei China
| | - Lan Yao
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei China
| | - Shaofeng Lin
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei China
| | - Ying Shi
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei China
| | - Weizhi Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei China
| | - Hao Zhou
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei China
| | - Le Zhu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei China
| | - Cong Ma
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei China
| | - Cheng Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing China
| | - Jie Ma
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing China
| | - Zhiping Xie
- State Key Laboratory of Microbial Metabolism & Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai China
| | - Chenwei Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei China
| | - Yu Xue
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei China.,Nanjing University Institute of Artificial Intelligence Biomedicine, Nanjing, Jiangsu China
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21
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Terešak P, Lapao A, Subic N, Boya P, Elazar Z, Simonsen A. Regulation of PRKN-independent mitophagy. Autophagy 2021; 18:24-39. [PMID: 33570005 DOI: 10.1080/15548627.2021.1888244] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Mitochondria are dynamic, multifunctional cellular organelles that play a fundamental role in maintaining cellular homeostasis. Keeping the quality of mitochondria in check is of essential importance for functioning and survival of the cells. Selective autophagic clearance of flawed mitochondria, a process termed mitophagy, is one of the most prominent mechanisms through which cells maintain a healthy mitochondrial pool. The best-studied pathway through which mitophagy is exerted is the PINK1-PRKN pathway. However, an increasing number of studies have shown an existence of alternative pathways, where different proteins and lipids are able to recruit autophagic machinery independently of PINK1 and PRKN. The significance of PRKN-independent mitophagy pathways is reflected in various physiological and pathophysiological processes, but many questions regarding the regulation and the interplay between these pathways remain open. Here we review the current knowledge and recent progress made in the field of PRKN-independent mitophagy. Particularly we focus on the regulation of various receptors that participate in targeting impaired mitochondria to autophagosomes independently of PRKN.AbbreviationsAMPK: AMP-activated protein kinase; ATP: adenosine triphosphate; BCL2: BCL2 apoptosis regulator; BH: BCL2 homology; CCCP: Carbonyl cyanide m-chlorophenylhydrazone; CL: cardiolipin; ER: endoplasmic reticulum; FCCP: carbonyl cyanide p-trifluoromethoxyphenylhydrazone; IMM: inner mitochondrial membrane; IMS: mitochondrial intermembrane space; LIR: LC3-interacting region; MDVs: mitochondrial-derived vesicles; MTORC1: mechanistic target of rapamycin kinase complex 1; OMM: outer mitochondrial membrane; OXPHOS: oxidative phosphorylation; PD: Parkinson disease; PtdIns3K: phosphatidylinositol 3-kinase; RGC: retinal ganglion cell; RING: really interesting new gene; ROS: reactive oxygen species; SUMO: small ubiquitin like modifier; TBI: traumatic brain injury; TM: transmembrane.
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Affiliation(s)
- Petra Terešak
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Ana Lapao
- Department of Molecular Medicine, Institute of Basic Medical Sciences and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Nemanja Subic
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Patricia Boya
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Zvulun Elazar
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Anne Simonsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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22
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Tamargo-Gómez I, Fernández ÁF, Mariño G. Pathogenic Single Nucleotide Polymorphisms on Autophagy-Related Genes. Int J Mol Sci 2020; 21:ijms21218196. [PMID: 33147747 PMCID: PMC7672651 DOI: 10.3390/ijms21218196] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 02/06/2023] Open
Abstract
In recent years, the study of single nucleotide polymorphisms (SNPs) has gained increasing importance in biomedical research, as they can either be at the molecular origin of a determined disorder or directly affect the efficiency of a given treatment. In this regard, sequence variations in genes involved in pro-survival cellular pathways are commonly associated with pathologies, as the alteration of these routes compromises cellular homeostasis. This is the case of autophagy, an evolutionarily conserved pathway that counteracts extracellular and intracellular stressors by mediating the turnover of cytosolic components through lysosomal degradation. Accordingly, autophagy dysregulation has been extensively described in a wide range of human pathologies, including cancer, neurodegeneration, or inflammatory alterations. Thus, it is not surprising that pathogenic gene variants in genes encoding crucial effectors of the autophagosome/lysosome axis are increasingly being identified. In this review, we present a comprehensive list of clinically relevant SNPs in autophagy-related genes, highlighting the scope and relevance of autophagy alterations in human disease.
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Affiliation(s)
- Isaac Tamargo-Gómez
- Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain;
- Departamento de Biología Funcional, Universidad de Oviedo, 33011 Oviedo, Spain
| | - Álvaro F. Fernández
- Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain;
- Departamento de Biología Funcional, Universidad de Oviedo, 33011 Oviedo, Spain
- Correspondence: (Á.F.F.); (G.M.); Tel.: +34-985652416 (G.M.)
| | - Guillermo Mariño
- Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain;
- Departamento de Biología Funcional, Universidad de Oviedo, 33011 Oviedo, Spain
- Correspondence: (Á.F.F.); (G.M.); Tel.: +34-985652416 (G.M.)
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23
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Dudley LJ, Makar AN, Gammoh N. Membrane targeting of core autophagy players during autophagosome biogenesis. FEBS J 2020; 287:4806-4821. [PMID: 32301577 DOI: 10.1111/febs.15334] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/27/2020] [Accepted: 04/14/2020] [Indexed: 12/18/2022]
Abstract
Autophagosomes are vital organelles required to facilitate the lysosomal degradation of cytoplasmic cargo, thereby playing an important role in maintaining cellular homeostasis. A number of autophagy-related (ATG) protein complexes are recruited to the site of autophagosome biogenesis where they act to facilitate membrane growth and maturation. Regulated recruitment of ATG complexes to autophagosomal membranes is essential for their autophagic activities and is required to ensure the efficient engulfment of cargo destined for lysosomal degradation. In this review, we discuss our current understanding of the spatiotemporal hierarchy between ATG proteins, examining the mechanisms underlying their recruitment to membranes. A particular focus is placed on the relevance of phosphatidylinositol 3-phosphate and the extent to which the core autophagy players are reliant on this lipid for their localisation to autophagic membranes. In addition, open questions and potential future research directions regarding the membrane recruitment and displacement of ATG proteins are discussed here.
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Affiliation(s)
- Leo J Dudley
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
| | - Agata N Makar
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
| | - Noor Gammoh
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
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24
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In vitro reconstitution of autophagic processes. Biochem Soc Trans 2020; 48:2003-2014. [PMID: 32897375 DOI: 10.1042/bst20200130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 11/17/2022]
Abstract
Autophagy is a lysosomal degradation system that involves de novo autophagosome formation. A lot of factors are involved in autophagosome formation, including dozens of Atg proteins that form supramolecular complexes, membrane structures including vesicles and organelles, and even membraneless organelles. Because these diverse higher-order structural components cooperate to mediate de novo formation of autophagosomes, it is too complicated to be elaborated only by cell biological approaches. Recent trials to regenerate each step of this phenomenon in vitro have started to elaborate on the molecular mechanisms of such a complicated process by simplification. In this review article, we outline the in vitro reconstitution trials in autophagosome formation, mainly focusing on the reports in the past few years and discussing the molecular mechanisms of autophagosome formation by comparing in vitro and in vivo observations.
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25
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Cheung YWS, Nam SE, Yip CK. Recent Advances in Single-Particle Electron Microscopic Analysis of Autophagy Degradation Machinery. Int J Mol Sci 2020; 21:E8051. [PMID: 33126766 PMCID: PMC7663694 DOI: 10.3390/ijms21218051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/25/2020] [Accepted: 10/25/2020] [Indexed: 12/31/2022] Open
Abstract
Macroautophagy (also known as autophagy) is a major pathway for selective degradation of misfolded/aggregated proteins and damaged organelles and non-selective degradation of cytoplasmic constituents for the generation of power during nutrient deprivation. The multi-step degradation process, from sequestering cytoplasmic cargo into the double-membrane vesicle termed autophagosome to the delivery of the autophagosome to the lysosome or lytic vacuole for breakdown, is mediated by the core autophagy machinery composed of multiple Atg proteins, as well as the divergent sequence family of selective autophagy receptors. Single-particle electron microscopy (EM) is a molecular imaging approach that has become an increasingly important tool in the structural characterization of proteins and macromolecular complexes. This article summarizes the contributions single-particle EM have made in advancing our understanding of the core autophagy machinery and selective autophagy receptors. We also discuss current technical challenges and roadblocks, as well as look into the future of single-particle EM in autophagy research.
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Affiliation(s)
| | | | - Calvin K. Yip
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (Y.W.S.C.); (S.-E.N.)
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26
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Yamamoto YH, Noda T. Autophagosome formation in relation to the endoplasmic reticulum. J Biomed Sci 2020; 27:97. [PMID: 33087127 PMCID: PMC7579975 DOI: 10.1186/s12929-020-00691-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/02/2020] [Indexed: 02/08/2023] Open
Abstract
Autophagy is a process in which a myriad membrane structures called autophagosomes are formed de novo in a single cell, which deliver the engulfed substrates into lysosomes for degradation. The size of the autophagosomes is relatively uniform in non-selective autophagy and variable in selective autophagy. It has been recently established that autophagosome formation occurs near the endoplasmic reticulum (ER). In this review, we have discussed recent advances in the relationship between autophagosome formation and endoplasmic reticulum. Autophagosome formation occurs near the ER subdomain enriched with phospholipid synthesizing enzymes like phosphatidylinositol synthase (PIS)/CDP-diacylglycerol-inositol 3-phosphatidyltransferase (CDIPT) and choline/ethanolamine phosphotransferase 1 (CEPT1). Autophagy-related protein 2 (Atg2), which is involved in autophagosome formation has a lipid transfer capacity and is proposed to directly transfer the lipid molecules from the ER to form autophagosomes. Vacuole membrane protein 1 (VMP1) and transmembrane protein 41b (TMEM41b) are ER membrane proteins that are associated with the formation of the subdomain. Recently, we have reported that an uncharacterized ER membrane protein possessing the DNAJ domain, called ERdj8/DNAJC16, is associated with the regulation of the size of autophagosomes. The localization of ERdj8/DNAJC16 partially overlaps with the PIS-enriched ER subdomain, thereby implying its association with autophagosome size determination.
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Affiliation(s)
- Yo-Hei Yamamoto
- Center for Frontier Oral Sciences, Graduate School of Dentistry, Osaka University Graduate School, 1-8 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takeshi Noda
- Center for Frontier Oral Sciences, Graduate School of Dentistry, Osaka University Graduate School, 1-8 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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27
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Ornatowski W, Lu Q, Yegambaram M, Garcia AE, Zemskov EA, Maltepe E, Fineman JR, Wang T, Black SM. Complex interplay between autophagy and oxidative stress in the development of pulmonary disease. Redox Biol 2020; 36:101679. [PMID: 32818797 PMCID: PMC7451718 DOI: 10.1016/j.redox.2020.101679] [Citation(s) in RCA: 196] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/20/2020] [Accepted: 08/04/2020] [Indexed: 12/16/2022] Open
Abstract
The autophagic pathway involves the encapsulation of substrates in double-membraned vesicles, which are subsequently delivered to the lysosome for enzymatic degradation and recycling of metabolic precursors. Autophagy is a major cellular defense against oxidative stress, or related conditions that cause accumulation of damaged proteins or organelles. Selective forms of autophagy can maintain organelle populations or remove aggregated proteins. Dysregulation of redox homeostasis under pathological conditions results in excessive generation of reactive oxygen species (ROS), leading to oxidative stress and the associated oxidative damage of cellular components. Accumulating evidence indicates that autophagy is necessary to maintain redox homeostasis. ROS activates autophagy, which facilitates cellular adaptation and diminishes oxidative damage by degrading and recycling intracellular damaged macromolecules and dysfunctional organelles. The cellular responses triggered by oxidative stress include the altered regulation of signaling pathways that culminate in the regulation of autophagy. Current research suggests a central role for autophagy as a mammalian oxidative stress response and its interrelationship to other stress defense systems. Altered autophagy phenotypes have been observed in lung diseases such as chronic obstructive lung disease, acute lung injury, cystic fibrosis, idiopathic pulmonary fibrosis, and pulmonary arterial hypertension, and asthma. Understanding the mechanisms by which ROS regulate autophagy will provide novel therapeutic targets for lung diseases. This review highlights our current understanding on the interplay between ROS and autophagy in the development of pulmonary disease.
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Affiliation(s)
- Wojciech Ornatowski
- Department of Medicine, The University of Arizona Health Sciences, Tucson, AZ, USA
| | - Qing Lu
- Department of Medicine, The University of Arizona Health Sciences, Tucson, AZ, USA
| | | | - Alejandro E Garcia
- Department of Medicine, The University of Arizona Health Sciences, Tucson, AZ, USA
| | - Evgeny A Zemskov
- Department of Medicine, The University of Arizona Health Sciences, Tucson, AZ, USA
| | - Emin Maltepe
- Department of Pediatrics, The University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey R Fineman
- Department of Pediatrics, The University of California, San Francisco, San Francisco, CA, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Ting Wang
- Department of Internal Medicine, The University of Arizona Health Sciences, Phoenix, AZ, USA
| | - Stephen M Black
- Department of Medicine, The University of Arizona Health Sciences, Tucson, AZ, USA.
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28
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O'Loughlin T, Kruppa AJ, Ribeiro ALR, Edgar JR, Ghannam A, Smith AM, Buss F. OPTN recruitment to a Golgi-proximal compartment regulates immune signalling and cytokine secretion. J Cell Sci 2020; 133:jcs239822. [PMID: 32376785 PMCID: PMC7328155 DOI: 10.1242/jcs.239822] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 04/14/2020] [Indexed: 12/14/2022] Open
Abstract
Optineurin (OPTN) is a multifunctional protein involved in autophagy and secretion, as well as nuclear factor κB (NF-κB) and IRF3 signalling, and OPTN mutations are associated with several human diseases. Here, we show that, in response to viral RNA, OPTN translocates to foci in the perinuclear region, where it negatively regulates NF-κB and IRF3 signalling pathways and downstream pro-inflammatory cytokine secretion. These OPTN foci consist of a tight cluster of small membrane vesicles, which are positive for ATG9A. Disease mutations in OPTN linked to primary open-angle glaucoma (POAG) cause aberrant foci formation in the absence of stimuli, which correlates with the ability of OPTN to inhibit signalling. By using proximity labelling proteomics, we identify the linear ubiquitin assembly complex (LUBAC), CYLD and TBK1 as part of the OPTN interactome and show that these proteins are recruited to this OPTN-positive perinuclear compartment. Our work uncovers a crucial role for OPTN in dampening NF-κB and IRF3 signalling through the sequestration of LUBAC and other positive regulators in this viral RNA-induced compartment, leading to altered pro-inflammatory cytokine secretion.
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Affiliation(s)
- Thomas O'Loughlin
- Cambridge Institute for Medical Research, The Keith Peters Building, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA 94158, USA
| | - Antonina J Kruppa
- Cambridge Institute for Medical Research, The Keith Peters Building, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Andre L R Ribeiro
- Microbial Diseases, Eastman Dental Institute, University College London, London WC1X 8LD, UK
- Department of Oral and Maxillofacial Surgery, University Centre of Pará, Belém, Brazil
| | - James R Edgar
- Cambridge Institute for Medical Research, The Keith Peters Building, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Abdulaziz Ghannam
- Microbial Diseases, Eastman Dental Institute, University College London, London WC1X 8LD, UK
| | - Andrew M Smith
- Microbial Diseases, Eastman Dental Institute, University College London, London WC1X 8LD, UK
| | - Folma Buss
- Cambridge Institute for Medical Research, The Keith Peters Building, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
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29
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Birgisdottir ÅB, Johansen T. Autophagy and endocytosis – interconnections and interdependencies. J Cell Sci 2020; 133:133/10/jcs228114. [DOI: 10.1242/jcs.228114] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
ABSTRACT
Autophagy and endocytosis are membrane-vesicle-based cellular pathways for degradation and recycling of intracellular and extracellular components, respectively. These pathways have a common endpoint at the lysosome, where their cargo is degraded. In addition, the two pathways intersect at different stages during vesicle formation, fusion and trafficking, and share parts of the molecular machinery. Accumulating evidence shows that autophagy is dependent upon endocytosis and vice versa. The emerging joint network of autophagy and endocytosis is of vital importance for cellular metabolism and signaling, and thus also highly relevant in disease settings. In this Review, we will discuss examples of how the autophagy machinery impacts on endocytosis and cell signaling, and highlight how endocytosis regulates the different steps in autophagy in mammalian cells. Finally, we will focus on the interplay of these pathways in the quality control of their common endpoint, the lysosome.
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Affiliation(s)
- Åsa B. Birgisdottir
- The Heart and Lung Clinic, University Hospital of North Norway, 9037 Tromsø, Norway
- Clinical Cardiovascular Research Group, Department of Clinical Medicine, University of Tromsø –The Arctic University of Norway, 9037 Tromsø, Norway
| | - Terje Johansen
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø–The Arctic University of Norway, 9037 Tromsø, Norway
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30
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Garza-Lombó C, Pappa A, Panayiotidis MI, Franco R. Redox homeostasis, oxidative stress and mitophagy. Mitochondrion 2020; 51:105-117. [PMID: 31972372 DOI: 10.1016/j.mito.2020.01.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 12/21/2019] [Accepted: 01/03/2020] [Indexed: 02/07/2023]
Abstract
Autophagy is a ubiquitous homeostatic mechanism for the degradation or turnover of cellular components. Degradation of mitochondria via autophagy (mitophagy) is involved in a number of physiological processes including cellular homeostasis, differentiation and aging. Upon stress or injury, mitophagy prevents the accumulation of damaged mitochondria and the increased steady state levels of reactive oxygen species leading to oxidative stress and cell death. A number of human diseases, particularly neurodegenerative disorders, have been linked to the dysregulation of mitophagy. In this mini-review, we aimed to review the molecular mechanisms involved in the regulation of mitophagy and their relationship with redox signaling and oxidative stress.
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Affiliation(s)
- Carla Garza-Lombó
- Redox Biology Center and School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, United States.
| | - Aglaia Pappa
- Department of Molecular Biology & Genetics, Democritus University of Thrace, Alexandroupolis 68100, Greece
| | | | - Rodrigo Franco
- Redox Biology Center and School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, United States.
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31
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Lai LTF, Ye H, Zhang W, Jiang L, Lau WCY. Structural Biology and Electron Microscopy of the Autophagy Molecular Machinery. Cells 2019; 8:E1627. [PMID: 31842460 PMCID: PMC6952983 DOI: 10.3390/cells8121627] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/06/2019] [Accepted: 12/10/2019] [Indexed: 12/30/2022] Open
Abstract
Autophagy is a highly regulated bulk degradation process that plays a key role in the maintenance of cellular homeostasis. During autophagy, a double membrane-bound compartment termed the autophagosome is formed through de novo nucleation and assembly of membrane sources to engulf unwanted cytoplasmic components and targets them to the lysosome or vacuole for degradation. Central to this process are the autophagy-related (ATG) proteins, which play a critical role in plant fitness, immunity, and environmental stress response. Over the past few years, cryo-electron microscopy (cryo-EM) and single-particle analysis has matured into a powerful and versatile technique for the structural determination of protein complexes at high resolution and has contributed greatly to our current understanding of the molecular mechanisms underlying autophagosome biogenesis. Here we describe the plant-specific ATG proteins and summarize recent structural and mechanistic studies on the protein machinery involved in autophagy initiation with an emphasis on those by single-particle analysis.
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Affiliation(s)
- Louis Tung Faat Lai
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Hao Ye
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Wenxin Zhang
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Liwen Jiang
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
- CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
| | - Wilson Chun Yu Lau
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
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32
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Hu G, Rios L, Yan Z, Jasper AM, Luera D, Luo S, Rao H. Autophagy regulator Atg9 is degraded by the proteasome. Biochem Biophys Res Commun 2019; 522:254-258. [PMID: 31759633 DOI: 10.1016/j.bbrc.2019.11.089] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 11/14/2019] [Indexed: 01/10/2023]
Abstract
Autophagy is a highly conserved biological process essential to protein, cellular and organismal homeostasis. As autophagy plays a critical role in cellular responses to various external and internal stimuli, it is important to understand the mechanism underlying autophagy regulation. Here, we monitor the stability of 17 key autophagy factors in the yeast S. cerevisiae and show that Atg9 and Atg14 are degraded under normal growth conditions. Whereas Atg14 is regulated by both the proteasome and autophagy, Atg9 turnover is normally mediated by the proteasome but impeded upon starvation or rapamycin treatment. Interestingly, distinct segments of Atg9 confer instability, suggesting that multiple pathways are involved in Atg9 degradation. Our results provide the foundation to further elucidate the physiological significance of Atg9 turnover and also the interplay between two major proteolytic systems (i.e., autophagy and the proteasome).
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Affiliation(s)
- Guohui Hu
- Center for Experimental Medicine, the First Affiliated Hospital, Nanchang University, Nanchang, China; Department of General Medicine, the First Affiliated Hospital, Nanchang University, Nanchang, China
| | - Lizette Rios
- Department of Molecular Medicine, the University of Texas Health, San Antonio, TX, 78229, USA
| | - Zhengwei Yan
- Center for Experimental Medicine, the First Affiliated Hospital, Nanchang University, Nanchang, China
| | - Angela M Jasper
- Department of Molecular Medicine, the University of Texas Health, San Antonio, TX, 78229, USA
| | - Dezzarae Luera
- Department of Molecular Medicine, the University of Texas Health, San Antonio, TX, 78229, USA
| | - Shiwen Luo
- Center for Experimental Medicine, the First Affiliated Hospital, Nanchang University, Nanchang, China
| | - Hai Rao
- Department of Molecular Medicine, the University of Texas Health, San Antonio, TX, 78229, USA.
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33
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Chen RH, Chen YH, Huang TY. Ubiquitin-mediated regulation of autophagy. J Biomed Sci 2019; 26:80. [PMID: 31630678 PMCID: PMC6802350 DOI: 10.1186/s12929-019-0569-y] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/01/2019] [Indexed: 02/01/2023] Open
Abstract
Autophagy is a major degradation pathway that utilizes lysosome hydrolases to degrade cellular constituents and is often induced under cellular stress conditions to restore cell homeostasis. Another prime degradation pathway in the cells is ubiquitin-proteasome system (UPS), in which proteins tagged by certain types of polyubiquitin chains are selectively recognized and removed by proteasome. Although the two degradation pathways are operated independently with different sets of players, recent studies have revealed reciprocal cross talks between UPS and autophagy at multiple layers. In this review, we summarize the roles of protein ubiquitination and deubiquitination in controlling the initiation, execution, and termination of bulk autophagy as well as the role of ubiquitination in signaling certain types of selective autophagy. We also highlight how dysregulation of ubiquitin-mediated autophagy pathways is associated with a number of human diseases and the potential of targeting these pathways for disease intervention.
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Affiliation(s)
- Ruey-Hwa Chen
- Academia Sinica, Institute of Biological Chemistry, Taipei, 115, Taiwan. .,Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, 100, Taiwan.
| | - Yu-Hsuan Chen
- Academia Sinica, Institute of Biological Chemistry, Taipei, 115, Taiwan.,Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, 100, Taiwan
| | - Tzu-Yu Huang
- Academia Sinica, Institute of Biological Chemistry, Taipei, 115, Taiwan.,Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, 100, Taiwan
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34
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Sequential formation of different layers of dystrophic neurites in Alzheimer's brains. Mol Psychiatry 2019; 24:1369-1382. [PMID: 30899091 PMCID: PMC7204504 DOI: 10.1038/s41380-019-0396-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/08/2019] [Accepted: 02/14/2019] [Indexed: 12/19/2022]
Abstract
Alzheimer's disease (AD) is characterized by the presence of neuritic plaques in which dystrophic neurites (DNs) are typical constituents. We recently showed that DNs labeled by antibodies to the tubular endoplasmic reticulum (ER) protein reticulon-3 (RTN3) are enriched with clustered tubular ER. However, multi-vesicle bodies are also found in DNs, suggesting that different populations of DNs exist in brains of AD patients. To understand how different DNs evolve to surround core amyloid plaques, we monitored the growth of DNs in AD mouse brains (5xFAD and APP/PS1ΔE9 mice) by multiple approaches, including two-dimensional and three-dimensional (3D) electron microscopy (EM). We discovered that a pre-autophagosome protein ATG9A was enriched in DNs when a plaque was just beginning to develop. ATG9A-positive DNs were often closer to the core amyloid plaque, whereas RTN3 immunoreactive DNs were mostly located in the outer layers of ATG9A-positive DNs. Proteins such as RAB7 and LC3 appeared in DNs at later stages during plaque growth, likely accumulated as a part of large autophagy vesicles, and were distributed relatively furthest from the core amyloid plaque. Reconstructing the 3D structure of different morphologies of DNs revealed that DNs in AD mouse brains were constituted in three layers that are distinct by enriching different types of vesicles, as validated by immune-EM methods. Collectively, our results provide the first evidence that DNs evolve from dysfunctions of pre-autophagosomes, tubular ER, mature autophagosomes, and the ubiquitin proteasome system during plaque growth.
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35
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Zhou FL, Li SC, Zhu Y, Guo WJ, Shao LJ, Nelson J, Simpkins S, Yang DH, Liu Q, Yashiroda Y, Xu JB, Fan YY, Yue JM, Yoshida M, Xia T, Myers CL, Boone C, Wang MW. Integrating yeast chemical genomics and mammalian cell pathway analysis. Acta Pharmacol Sin 2019; 40:1245-1255. [PMID: 31138898 PMCID: PMC6786357 DOI: 10.1038/s41401-019-0231-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/14/2019] [Indexed: 12/27/2022] Open
Abstract
Chemical genomics has been applied extensively to evaluate small molecules that modulate biological processes in Saccharomyces cerevisiae. Here, we use yeast as a surrogate system for studying compounds that are active against metazoan targets. Large-scale chemical-genetic profiling of thousands of synthetic and natural compounds from the Chinese National Compound Library identified those with high-confidence bioprocess target predictions. To discover compounds that have the potential to function like therapeutic agents with known targets, we also analyzed a reference library of approved drugs. Previously uncharacterized compounds with chemical-genetic profiles resembling existing drugs that modulate autophagy and Wnt/β-catenin signal transduction were further examined in mammalian cells, and new modulators with specific modes of action were validated. This analysis exploits yeast as a general platform for predicting compound bioactivity in mammalian cells.
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Affiliation(s)
- Fu-Lai Zhou
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sheena C Li
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, 3510198, Japan
| | - Yue Zhu
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wan-Jing Guo
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Jun Shao
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Justin Nelson
- Bioinformatics and Computational Biology Program, University of Minnesota-Twin Cities, Minneapolis, Minnesota, 55455, USA
| | - Scott Simpkins
- Bioinformatics and Computational Biology Program, University of Minnesota-Twin Cities, Minneapolis, Minnesota, 55455, USA
| | - De-Hua Yang
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, 201203, China
| | - Qing Liu
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, 201203, China
| | - Yoko Yashiroda
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, 3510198, Japan
| | - Jin-Biao Xu
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yao-Yue Fan
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Jian-Min Yue
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Minoru Yoshida
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, 3510198, Japan
- Department of Biology, The University of Tokyo, Bunkyo-ku, Tokyo, 1138657, Japan
- Collaborative Research for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, 1138657, Japan
| | - Tian Xia
- Department of Electronics and Information Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Chad L Myers
- Bioinformatics and Computational Biology Program, University of Minnesota-Twin Cities, Minneapolis, Minnesota, 55455, USA.
| | - Charles Boone
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, 3510198, Japan.
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, Ontario, M5S 3E1, Canada.
| | - Ming-Wei Wang
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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36
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Lai LTF, Yu C, Wong JSK, Lo HS, Benlekbir S, Jiang L, Lau WCY. Subnanometer resolution cryo-EM structure of Arabidopsis thaliana ATG9. Autophagy 2019; 16:575-583. [PMID: 31276439 DOI: 10.1080/15548627.2019.1639300] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Macroautophagy/autophagy is an essential process for the maintenance of cellular homeostasis by recycling macromolecules under normal and stress conditions. ATG9 (autophagy related 9) is the only integral membrane protein in the autophagy core machinery and has a central role in mediating autophagosome formation. In cells, ATG9 exists on mobile vesicles that traffic to the growing phagophore, providing an essential membrane source for the formation of autophagosomes. Here we report the three-dimensional structure of ATG9 from Arabidopsis thaliana at 7.8 Å resolution, determined by single particle cryo-electron microscopy. ATG9 organizes into a homotrimer, with each protomer contributing at least six transmembrane α-helices. At the center of the trimer, the protomers interact via their membrane-embedded and C-terminal cytoplasmic regions. Combined with prediction of protein contacts using sequence co-evolutionary information, the structure provides molecular insights into the ATG9 architecture and testable hypotheses for the molecular mechanism of autophagy progression regulated by ATG9.Abbreviations: 2D: 2-dimensional; 3D: 3-dimensional; AtATG9: Arabidopsis ATG9; Atg: autophagy-related; ATG9: autophagy-related protein 9; cryo-EM: cryo-electron microscopy; DDM: dodecyl maltoside; GraDeR: gradient-based detergent removal; LMNG: lauryl maltose-neopentyl glycol; PAS: phagophore assembly site; PtdIns3K: phosphatidylinositol 3-kinase.
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Affiliation(s)
- Louis Tung Faat Lai
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Chuanyang Yu
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Jan Siu Kei Wong
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Ho Sing Lo
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Samir Benlekbir
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Canada
| | - Liwen Jiang
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, China.,CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Wilson Chun Yu Lau
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
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37
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Abstract
Macroautophagy is an intracellular degradation system that delivers diverse cytoplasmic materials to lysosomes via autophagosomes. Recent advances have enabled identification of several selective autophagy substrates and receptors, greatly expanding our understanding of the cellular functions of autophagy. In this review, we describe the diverse cellular functions of macroautophagy, including its essential contribution to metabolic adaptation and cellular homeostasis. We also discuss emerging findings on the mechanisms and functions of various types of selective autophagy.
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Affiliation(s)
- Hideaki Morishita
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; ,
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; ,
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38
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Kerins MJ, Liu P, Tian W, Mannheim W, Zhang DD, Ooi A. Genome-Wide CRISPR Screen Reveals Autophagy Disruption as the Convergence Mechanism That Regulates the NRF2 Transcription Factor. Mol Cell Biol 2019; 39:e00037-19. [PMID: 31010806 PMCID: PMC6580702 DOI: 10.1128/mcb.00037-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/13/2019] [Accepted: 04/14/2019] [Indexed: 02/06/2023] Open
Abstract
The nuclear factor (erythroid 2)-like 2 (NRF2 or NFE2L2) transcription factor regulates the expression of many genes that are critical in maintaining cellular homeostasis. Its deregulation has been implicated in many diseases, including cancer and metabolic and neurodegenerative diseases. While several mechanisms by which NRF2 can be activated have gradually been identified over time, a more complete regulatory network of NRF2 is still lacking. Here we show through a genome-wide clustered regularly interspaced short palindromic repeat (CRISPR) screen that a total of 273 genes, when knocked out, will lead to sustained NRF2 activation. Pathway analysis revealed a significant overrepresentation of genes (18 of the 273 genes) involved in autophagy. Molecular validation of a subset of the enriched genes identified 8 high-confidence genes that negatively regulate NRF2 activity irrespective of cell type: ATG12, ATG7, GOSR1, IFT172, NRXN2, RAB6A, VPS37A, and the well-known negative regulator of NRF2, KEAP1 Of these, ATG12, ATG7, KEAP1, and VPS37A are known to be involved in autophagic processes. Our results present a comprehensive list of NRF2 negative regulators and reveal an intimate link between autophagy and NRF2 regulation.
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Affiliation(s)
- Michael J Kerins
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona, USA
| | - Pengfei Liu
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona, USA
| | - Wang Tian
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona, USA
| | - William Mannheim
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona, USA
| | - Donna D Zhang
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona, USA
- University of Arizona Cancer Center, University of Arizona, Tucson, Arizona, USA
| | - Aikseng Ooi
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona, USA
- University of Arizona Cancer Center, University of Arizona, Tucson, Arizona, USA
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39
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Chakraborty D, Felzen V, Hiebel C, Stürner E, Perumal N, Manicam C, Sehn E, Grus F, Wolfrum U, Behl C. Enhanced autophagic-lysosomal activity and increased BAG3-mediated selective macroautophagy as adaptive response of neuronal cells to chronic oxidative stress. Redox Biol 2019; 24:101181. [PMID: 30959460 PMCID: PMC6454062 DOI: 10.1016/j.redox.2019.101181] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 01/05/2023] Open
Abstract
Oxidative stress and a disturbed cellular protein homeostasis (proteostasis) belong to the most important hallmarks of aging and of neurodegenerative disorders. The proteasomal and autophagic-lysosomal degradation pathways are key measures to maintain proteostasis. Here, we report that hippocampal cells selected for full adaptation and resistance to oxidative stress induced by hydrogen peroxide (oxidative stress-resistant cells, OxSR cells) showed a massive increase in the expression of components of the cellular autophagic-lysosomal network and a significantly higher overall autophagic activity. A comparative expression analysis revealed that distinct key regulators of autophagy are upregulated in OxSR cells. The observed adaptive autophagic response was found to be independent of the upstream autophagy regulator mTOR but is accompanied by a significant upregulation of further downstream components of the canonical autophagy network such as Beclin1, WIPI1 and the transmembrane ATG9 proteins. Interestingly, the expression of the HSP70 co-chaperone BAG3, mediator of BAG3-mediated selective macroautophagy and highly relevant for the clearance of aggregated proteins in cells, was found to be increased in OxSR cells that were consequently able to effectively overcome proteotoxic stress. Overexpression of BAG3 in oxidative stress-sensitive HT22 wildtype cells partly established the vesicular phenotype and the enhanced autophagic flux seen in OxSR cells suggesting that BAG3 takes over an important part in the adaptation process. A full proteome analysis demonstrated additional changes in the expression of mitochondrial proteins, metabolic enzymes and different pathway regulators in OxSR cells as consequence of the adaptation to oxidative stress in addition to autophagy-related proteins. Taken together, this analysis revealed a wide variety of pathways and players that act as adaptive response to chronic redox stress in neuronal cells.
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Affiliation(s)
- Debapriya Chakraborty
- Institute of Pathobiochemistry, University Medical Center Mainz of the Johannes Gutenberg University, 55099, Mainz, Germany.
| | - Vanessa Felzen
- Institute of Pathobiochemistry, University Medical Center Mainz of the Johannes Gutenberg University, 55099, Mainz, Germany.
| | - Christof Hiebel
- Institute of Pathobiochemistry, University Medical Center Mainz of the Johannes Gutenberg University, 55099, Mainz, Germany.
| | - Elisabeth Stürner
- Institute of Pathobiochemistry, University Medical Center Mainz of the Johannes Gutenberg University, 55099, Mainz, Germany.
| | - Natarajan Perumal
- Experimental and Translational Ophthalmology, University Medical Center Mainz, 55131, Mainz, Germany.
| | - Caroline Manicam
- Experimental and Translational Ophthalmology, University Medical Center Mainz, 55131, Mainz, Germany.
| | - Elisabeth Sehn
- Institute for Molecular Physiology, Johannes Gutenberg University, 55128, Mainz, Germany.
| | - Franz Grus
- Experimental and Translational Ophthalmology, University Medical Center Mainz, 55131, Mainz, Germany.
| | - Uwe Wolfrum
- Institute for Molecular Physiology, Johannes Gutenberg University, 55128, Mainz, Germany.
| | - Christian Behl
- Institute of Pathobiochemistry, University Medical Center Mainz of the Johannes Gutenberg University, 55099, Mainz, Germany.
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40
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Abstract
ATG9 vesicles are crucial for autophagy, yet the role of ATG9 remains unclear. In this issue, Judith et al. (2019. J. Cell Biol. https://doi.org/10.1083/jcb.201901115) implicate the BAR protein Arfaptin2 in the loading of PI4-kinase IIIβ onto ATG9 vesicles for recruitment of ATG13 to the site of autophagosome biogenesis.
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Affiliation(s)
- Oren Shatz
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Zvulun Elazar
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
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41
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Tettamanti G, Carata E, Montali A, Dini L, Fimia GM. Autophagy in development and regeneration: role in tissue remodelling and cell survival. EUROPEAN ZOOLOGICAL JOURNAL 2019. [DOI: 10.1080/24750263.2019.1601271] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- G. Tettamanti
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - E. Carata
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
| | - A. Montali
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - L. Dini
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - G. M. Fimia
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
- Department of Epidemiology and Preclinical Research, National Institute for Infectious Diseases IRCCS “Lazzaro Spallanzani”, Rome, Italy
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42
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Delcour C, Amazit L, Patino LC, Magnin F, Fagart J, Delemer B, Young J, Laissue P, Binart N, Beau I. ATG7 and ATG9A loss-of-function variants trigger autophagy impairment and ovarian failure. Genet Med 2019; 21:930-938. [PMID: 30224786 DOI: 10.1038/s41436-018-0287-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 08/17/2018] [Indexed: 12/11/2022] Open
Abstract
PURPOSE Primary ovarian insufficiency (POI) is a frequent disorder that affects ~1% of women under 40 years of age. POI, which is characterized by the premature depletion of ovarian follicles and elevated plasma levels of follicle-stimulating hormone (FSH), leads to infertility. Although various etiological factors have been described, including chromosomal abnormalities and gene variants, most cases remain idiopathic. The aim of the present study was to identify and validate functionally new sequence variants in ATG (autophagy-related genes) leading to POI. METHODS We have reanalyzed, in silico, the exome sequencing data from a previously reported work performed in 69 unrelated POI women. Functional experiments using a classical hallmark of autophagy, the microtubule-associated protein 1 light chain 3β (LC3), were then used to link these genes to this lysosomal degradation pathway. RESULTS We venture a functional link between ATG7 and ATG9A variants and POI. We demonstrated that variant ATG7 and ATG9A led to a decrease in autophagosome biosynthesis and consequently to an impairment of autophagy, a key biological process implicated in the preservation of the primordial follicles forming the ovarian reserve. CONCLUSION Our results unveil that impaired autophagy is a novel pathophysiological mechanism involved in human POI.
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Affiliation(s)
- Clémence Delcour
- Inserm U1185, Faculté de Médecine Paris Sud, Le Kremlin-Bicêtre, France
- Univ Paris Sud, Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Larbi Amazit
- Inserm U1185, Faculté de Médecine Paris Sud, Le Kremlin-Bicêtre, France
- Univ Paris Sud, Université Paris-Saclay, Le Kremlin-Bicêtre, France
- Institut Biomédical de Bicêtre, UMS-32, Le Kremlin-Bicêtre, France
| | - Liliana C Patino
- Center For Research in Genetics and Genomics (CIGGUR), GENIUROS Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, DC, Colombia
| | - Françoise Magnin
- Inserm U1185, Faculté de Médecine Paris Sud, Le Kremlin-Bicêtre, France
- Univ Paris Sud, Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Jérôme Fagart
- Inserm U1185, Faculté de Médecine Paris Sud, Le Kremlin-Bicêtre, France
- Univ Paris Sud, Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Brigitte Delemer
- Service d'Endocrinologie-Diabète-Nutrition, CHU de Reims-Hôpital Robert-Debré, Reims, France
| | - Jacques Young
- Inserm U1185, Faculté de Médecine Paris Sud, Le Kremlin-Bicêtre, France
- Univ Paris Sud, Université Paris-Saclay, Le Kremlin-Bicêtre, France
- Service d'Endocrinologie et des Maladies de la Reproduction, APHP, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | - Paul Laissue
- Center For Research in Genetics and Genomics (CIGGUR), GENIUROS Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, DC, Colombia
| | - Nadine Binart
- Inserm U1185, Faculté de Médecine Paris Sud, Le Kremlin-Bicêtre, France
- Univ Paris Sud, Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Isabelle Beau
- Inserm U1185, Faculté de Médecine Paris Sud, Le Kremlin-Bicêtre, France.
- Univ Paris Sud, Université Paris-Saclay, Le Kremlin-Bicêtre, France.
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43
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Rab7a and Mitophagosome Formation. Cells 2019; 8:cells8030224. [PMID: 30857122 PMCID: PMC6468461 DOI: 10.3390/cells8030224] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 02/27/2019] [Accepted: 03/01/2019] [Indexed: 12/14/2022] Open
Abstract
The small GTPase, Rab7a, and the regulators of its GDP/GTP-binding status were shown to have roles in both endocytic membrane traffic and autophagy. Classically known to regulate endosomal retrograde transport and late endosome-lysosome fusion, earlier work has indicated a role for Rab7a in autophagosome-lysosome fusion as well as autolysosome maturation. However, as suggested by recent findings on PTEN-induced kinase 1 (PINK1)-Parkin-mediated mitophagy, Rab7a and its regulators are critical for the correct targeting of Atg9a-bearing vesicles to effect autophagosome formation around damaged mitochondria. This mitophagosome formation role for Rab7a is dependent on an intact Rab cycling process mediated by the Rab7a-specific guanine nucleotide exchange factor (GEF) and GTPase activating proteins (GAPs). Rab7a activity in this regard is also dependent on the retromer complex, as well as phosphorylation by the TRAF family-associated NF-κB activator binding kinase 1 (TBK1). Here, we discuss these recent findings and broadened perspectives on the role of the Rab7a network in PINK1-Parkin mediated mitophagy.
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44
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Springhorn A, Hoppe T. Western blot analysis of the autophagosomal membrane protein LGG-1/LC3 in Caenorhabditis elegans. Methods Enzymol 2019; 619:319-336. [DOI: 10.1016/bs.mie.2018.12.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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45
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Gassen NC, Rein T. Is There a Role of Autophagy in Depression and Antidepressant Action? Front Psychiatry 2019; 10:337. [PMID: 31156481 PMCID: PMC6529564 DOI: 10.3389/fpsyt.2019.00337] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 04/29/2019] [Indexed: 12/12/2022] Open
Abstract
Autophagy has been recognized as evolutionary conserved intracellular pathway that ensures energy, organelle, and protein homeostasis through lysosomal degradation of damaged macromolecules and organelles. It is activated under various stress situations, e.g., food deprivation or proteotoxic conditions. Autophagy has been linked to several diseases, more recently also including stress-related diseases such as depression. A growing number of publications report on the role of autophagy in neurons, also referred to as "neuronal autophagy" on the one hand, and several studies describe effects of antidepressants-or of compounds that exert antidepressant-like actions-on autophagy on the other hand. This minireview highlights the emerging evidence for the involvement of autophagy in the pathology and treatment of depression and discusses current limitations as well as potential avenues for future research.
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Affiliation(s)
- Nils C Gassen
- Department of Psychiatry, Bonn Clinical Center, Bonn, Germany.,Max Planck Institute of Psychiatry, Munich, Germany
| | - Theo Rein
- Max Planck Institute of Psychiatry, Munich, Germany
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46
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Mizushima N. A brief history of autophagy from cell biology to physiology and disease. Nat Cell Biol 2018; 20:521-527. [PMID: 29686264 DOI: 10.1038/s41556-018-0092-5] [Citation(s) in RCA: 472] [Impact Index Per Article: 78.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 03/20/2018] [Indexed: 02/06/2023]
Abstract
The field of autophagy research has developed rapidly since the first description of the process in the 1960s and the identification of autophagy genes in the 1990s. Autophagy is now increasingly studied at the level of organismal pathophysiology and is being connected to the medical sciences. This Historical Perspective describes a brief history of autophagy and discusses unanswered cell biological questions in the field.
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Affiliation(s)
- Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan.
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Swart AL, Harrison CF, Eichinger L, Steinert M, Hilbi H. Acanthamoeba and Dictyostelium as Cellular Models for Legionella Infection. Front Cell Infect Microbiol 2018; 8:61. [PMID: 29552544 PMCID: PMC5840211 DOI: 10.3389/fcimb.2018.00061] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 02/13/2018] [Indexed: 12/20/2022] Open
Abstract
Environmental bacteria of the genus Legionella naturally parasitize free-living amoebae. Upon inhalation of bacteria-laden aerosols, the opportunistic pathogens grow intracellularly in alveolar macrophages and can cause a life-threatening pneumonia termed Legionnaires' disease. Intracellular replication in amoebae and macrophages takes place in a unique membrane-bound compartment, the Legionella-containing vacuole (LCV). LCV formation requires the bacterial Icm/Dot type IV secretion system, which translocates literally hundreds of "effector" proteins into host cells, where they modulate crucial cellular processes for the pathogen's benefit. The mechanism of LCV formation appears to be evolutionarily conserved, and therefore, amoebae are not only ecologically significant niches for Legionella spp., but also useful cellular models for eukaryotic phagocytes. In particular, Acanthamoeba castellanii and Dictyostelium discoideum emerged over the last years as versatile and powerful models. Using genetic, biochemical and cell biological approaches, molecular interactions between amoebae and Legionella pneumophila have recently been investigated in detail with a focus on the role of phosphoinositide lipids, small and large GTPases, autophagy components and the retromer complex, as well as on bacterial effectors targeting these host factors.
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Affiliation(s)
- A Leoni Swart
- Institute of Medical Microbiology, Medical Faculty, University of Zurich, Zurich, Switzerland
| | - Christopher F Harrison
- Max von Pettenkofer Institute, Medical Faculty, Ludwig-Maximilians University Munich, Munich, Germany
| | - Ludwig Eichinger
- Institute for Biochemistry I, Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Michael Steinert
- Department of Life Sciences, Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Hubert Hilbi
- Institute of Medical Microbiology, Medical Faculty, University of Zurich, Zurich, Switzerland
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Üstün S, Hafrén A, Liu Q, Marshall RS, Minina EA, Bozhkov PV, Vierstra RD, Hofius D. Bacteria Exploit Autophagy for Proteasome Degradation and Enhanced Virulence in Plants. THE PLANT CELL 2018; 30:668-685. [PMID: 29500318 PMCID: PMC5894834 DOI: 10.1105/tpc.17.00815] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 02/09/2018] [Accepted: 03/01/2018] [Indexed: 05/21/2023]
Abstract
Autophagy and the ubiquitin-proteasome system (UPS) are two major protein degradation pathways implicated in the response to microbial infections in eukaryotes. In animals, the contribution of autophagy and the UPS to antibacterial immunity is well documented and several bacteria have evolved measures to target and exploit these systems to the benefit of infection. In plants, the UPS has been established as a hub for immune responses and is targeted by bacteria to enhance virulence. However, the role of autophagy during plant-bacterial interactions is less understood. Here, we have identified both pro- and antibacterial functions of autophagy mechanisms upon infection of Arabidopsis thaliana with virulent Pseudomonas syringae pv tomato DC3000 (Pst). We show that Pst activates autophagy in a type III effector (T3E)-dependent manner and stimulates the autophagic removal of proteasomes (proteaphagy) to support bacterial proliferation. We further identify the T3E Hrp outer protein M1 (HopM1) as a principle mediator of autophagy-inducing activities during infection. In contrast to the probacterial effects of Pst-induced proteaphagy, NEIGHBOR OF BRCA1-dependent selective autophagy counteracts disease progression and limits the formation of HopM1-mediated water-soaked lesions. Together, we demonstrate that distinct autophagy pathways contribute to host immunity and bacterial pathogenesis during Pst infection and provide evidence for an intimate crosstalk between proteasome and autophagy in plant-bacterial interactions.
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Affiliation(s)
- Suayib Üstün
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Anders Hafrén
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Qinsong Liu
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Richard S Marshall
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Elena A Minina
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Daniel Hofius
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
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