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Wang Y, Xiao T, Zhao C, Li G. The Regulation of Exosome Generation and Function in Physiological and Pathological Processes. Int J Mol Sci 2023; 25:255. [PMID: 38203424 PMCID: PMC10779122 DOI: 10.3390/ijms25010255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/16/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Exosomes, a type of extracellular vesicle with a diameter of approximately 100 nm that is secreted by all cells, regulate the phenotype and function of recipient cells by carrying molecules such as proteins, nucleic acids, and lipids and are important mediators of intercellular communication. Exosomes are involved in various physiological and pathological processes such as immunomodulation, angiogenesis, tumorigenesis, metastasis, and chemoresistance. Due to their excellent properties, exosomes have shown their potential application in the clinical diagnosis and treatment of disease. The functions of exosomes depend on their biogenesis, uptake, and composition. Thus, a deeper understanding of these processes and regulatory mechanisms can help to find new targets for disease diagnosis and therapy. Therefore, this review summarizes and integrates the recent advances in the regulatory mechanisms of the entire biological process of exosomes, starting from the formation of early-sorting endosomes (ESCs) by plasma membrane invagination to the release of exosomes by fusion of multivesicular bodies (MVBs) with the plasma membrane, as well as the regulatory process of the interactions between exosomes and recipient cells. We also describe and discuss the regulatory mechanisms of exosome production in tumor cells and the potential of exosomes used in cancer diagnosis and therapy.
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Affiliation(s)
| | | | | | - Guiying Li
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China; (Y.W.); (T.X.); (C.Z.)
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2
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Shi M, Tang C, Wu JX, Ji BW, Gong BM, Wu XH, Wang X. Mass Spectrometry Detects Sphingolipid Metabolites for Discovery of New Strategy for Cancer Therapy from the Aspect of Programmed Cell Death. Metabolites 2023; 13:867. [PMID: 37512574 PMCID: PMC10384871 DOI: 10.3390/metabo13070867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Sphingolipids, a type of bioactive lipid, play crucial roles within cells, serving as integral components of membranes and exhibiting strong signaling properties that have potential therapeutic implications in anti-cancer treatments. However, due to the diverse group of lipids and intricate mechanisms, sphingolipids still face challenges in enhancing the efficacy of different therapy approaches. In recent decades, mass spectrometry has made significant advancements in uncovering sphingolipid biomarkers and elucidating their impact on cancer development, progression, and resistance. Primary sphingolipids, such as ceramide and sphingosine-1-phosphate, exhibit contrasting roles in regulating cancer cell death and survival. The evasion of cell death is a characteristic hallmark of cancer cells, leading to treatment failure and a poor prognosis. The escape initiates with long-established apoptosis and extends to other programmed cell death (PCD) forms when patients experience chemotherapy, radiotherapy, and/or immunotherapy. Gradually, supportive evidence has uncovered the fundamental molecular mechanisms underlying various forms of PCD leading to the development of innovative molecular, genetic, and pharmacological tools that specifically target sphingolipid signaling nodes. In this study, we provide a comprehensive overview of the sphingolipid biomarkers revealed through mass spectrometry in recent decades, as well as an in-depth analysis of the six main forms of PCD (apoptosis, autophagy, pyroptosis, necroptosis, ferroptosis, and cuproptosis) in aspects of tumorigenesis, metastasis, and tumor response to treatments. We review the corresponding small-molecule compounds associated with these processes and their potential implications in cancer therapy.
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Affiliation(s)
- Ming Shi
- State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Collaborative Innovation Center of Genetics and Development, Institute of Developmental Biology and Molecular Medicine, School of Life Sciences, Fudan University, Shanghai 200438, China
- Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan 523808, China
| | - Chao Tang
- National Clinical Research Center for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Jia-Xing Wu
- SINO-SWISS Institute of Advanced Technology, School of Microelectronics, Shanghai University, Shanghai 200444, China
| | - Bao-Wei Ji
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai 200032, China
| | - Bao-Ming Gong
- State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Collaborative Innovation Center of Genetics and Development, Institute of Developmental Biology and Molecular Medicine, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiao-Hui Wu
- State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Collaborative Innovation Center of Genetics and Development, Institute of Developmental Biology and Molecular Medicine, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xue Wang
- State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Collaborative Innovation Center of Genetics and Development, Institute of Developmental Biology and Molecular Medicine, School of Life Sciences, Fudan University, Shanghai 200438, China
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3
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Vos M, Klein C, Hicks AA. Role of Ceramides and Sphingolipids in Parkinson's Disease. J Mol Biol 2023:168000. [PMID: 36764358 DOI: 10.1016/j.jmb.2023.168000] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/24/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023]
Abstract
Sphingolipids, including the basic ceramide, are a subset of bioactive lipids that consist of many different species. Sphingolipids are indispensable for proper neuronal function, and an increasing number of studies have emerged on the complexity and importance of these lipids in (almost) all biological processes. These include regulation of mitochondrial function, autophagy, and endosomal trafficking, which are affected in Parkinson's disease (PD). PD is the second most common neurodegenerative disorder and is characterized by the loss of dopaminergic neurons. Currently, PD cannot be cured due to the lack of knowledge of the exact pathogenesis. Nonetheless, important advances have identified molecular changes in mitochondrial function, autophagy, and endosomal function. Furthermore, recent studies have identified ceramide alterations in patients suffering from PD, and in PD models, suggesting a critical interaction between sphingolipids and related cellular processes in PD. For instance, autosomal recessive forms of PD cause mitochondrial dysfunction, including energy production or mitochondrial clearance, that is directly influenced by manipulating sphingolipids. Additionally, endo-lysosomal recycling is affected by genes that cause autosomal dominant forms of the disease, such as VPS35 and SNCA. Furthermore, endo-lysosomal recycling is crucial for transporting sphingolipids to different cellular compartments where they will execute their functions. This review will discuss mitochondrial dysfunction, defects in autophagy, and abnormal endosomal activity in PD and the role sphingolipids play in these vital molecular processes.
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Affiliation(s)
- Melissa Vos
- Institute of Neurogenetics, University of Luebeck, 23562 Luebeck, Germany.
| | - Christine Klein
- Institute of Neurogenetics, University of Luebeck, 23562 Luebeck, Germany
| | - Andrew A Hicks
- Institute for Biomedicine (affiliated to the University of Luebeck, Luebeck, Germany), Eurac Research, 39100 Bolzano, Italy. https://twitter.com/andrewhicks
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4
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Pexophagy suppresses ROS-induced damage in leaf cells under high-intensity light. Nat Commun 2022; 13:7493. [PMID: 36470866 PMCID: PMC9722907 DOI: 10.1038/s41467-022-35138-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 11/18/2022] [Indexed: 12/12/2022] Open
Abstract
Although light is essential for photosynthesis, it has the potential to elevate intracellular levels of reactive oxygen species (ROS). Since high ROS levels are cytotoxic, plants must alleviate such damage. However, the cellular mechanism underlying ROS-induced leaf damage alleviation in peroxisomes was not fully explored. Here, we show that autophagy plays a pivotal role in the selective removal of ROS-generating peroxisomes, which protects plants from oxidative damage during photosynthesis. We present evidence that autophagy-deficient mutants show light intensity-dependent leaf damage and excess aggregation of ROS-accumulating peroxisomes. The peroxisome aggregates are specifically engulfed by pre-autophagosomal structures and vacuolar membranes in both leaf cells and isolated vacuoles, but they are not degraded in mutants. ATG18a-GFP and GFP-2×FYVE, which bind to phosphatidylinositol 3-phosphate, preferentially target the peroxisomal membranes and pre-autophagosomal structures near peroxisomes in ROS-accumulating cells under high-intensity light. Our findings provide deeper insights into the plant stress response caused by light irradiation.
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5
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Characterization of Protein-Membrane Interactions in Yeast Autophagy. Cells 2022; 11:cells11121876. [PMID: 35741004 PMCID: PMC9221364 DOI: 10.3390/cells11121876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 02/06/2023] Open
Abstract
Cells rely on autophagy to degrade cytosolic material and maintain homeostasis. During autophagy, content to be degraded is encapsulated in double membrane vesicles, termed autophagosomes, which fuse with the yeast vacuole for degradation. This conserved cellular process requires the dynamic rearrangement of membranes. As such, the process of autophagy requires many soluble proteins that bind to membranes to restructure, tether, or facilitate lipid transfer between membranes. Here, we review the methods that have been used to investigate membrane binding by the core autophagy machinery and additional accessory proteins involved in autophagy in yeast. We also review the key experiments demonstrating how each autophagy protein was shown to interact with membranes.
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6
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Sirasanagandla SR, Sofin RS, Al-Huseini I, Das S. Role of Bisphenol A in Autophagy Modulation: Understanding the Molecular Concepts and Therapeutic Options. Mini Rev Med Chem 2022; 22:2213-2223. [DOI: 10.2174/1389557522666220214094055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/05/2021] [Accepted: 12/16/2021] [Indexed: 11/22/2022]
Abstract
Abstract:
Bisphenol A (4,4′-isopropylidenediphenol) is an organic compound, commonly used in the plastic bottles, packaging containers, beverages and resin industry. The adverse effects of bisphenol A were studied in various systems of the body. Autophagy is a lysosomal degradation process meant for the regeneration of new cells. The role of bisphenol A on autophagy modulation in the pathogenesis of diseases is still debatable. Few research studies showed that bisphenol A-induced adverse effects were associated with autophagy dysregulation, while few showed the activation of autophagy by bisphenol A. Such contrasting views make the subject more interesting and debatable. In the present review, we discuss the different steps of autophagy, genes involved, and the effect of bisphenol A in autophagy modulation on different systems of the body. We also discuss the methods for monitoring autophagy and the roles of drugs such as chloroquine, verteporfin, and rapamycin in autophagy. Proper understanding of the role of bisphenol A in the modulation of autophagy may be important for future treatment and drug discovery.
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Affiliation(s)
- Srinivasa Rao Sirasanagandla
- Department of Human and Clinical Anatomy, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Al-Khodh 123, Oman
| | - R.G. Sumesh Sofin
- Department of Physics, College of Science, Sultan Qaboos University, Muscat, Al-Khodh 123, Oman
| | - Isehaq Al-Huseini
- Department of Physiology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Al-Khodh 123, Oman
| | - Srijit Das
- Department of Human and Clinical Anatomy, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Al-Khodh 123, Oman
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7
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Liu H, Wang X, Shen P, Ni Y, Han X. The basic functions of phosphoglycerate kinase 1 and its roles in cancer and other diseases. Eur J Pharmacol 2022; 920:174835. [DOI: 10.1016/j.ejphar.2022.174835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/15/2022] [Indexed: 01/17/2023]
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8
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Zheng Q, Duan L, Zhang Y, Li J, Zhang S, Wang H. A dynamically evolving war between autophagy and pathogenic microorganisms. J Zhejiang Univ Sci B 2022; 23:19-41. [PMID: 35029086 PMCID: PMC8758936 DOI: 10.1631/jzus.b2100285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Autophagy is an intracellular degradation process that maintains cellular homeostasis. It is essential for protecting organisms from environmental stress. Autophagy can help the host to eliminate invading pathogens, including bacteria, viruses, fungi, and parasites. However, pathogens have evolved multiple strategies to interfere with autophagic signaling pathways or inhibit the fusion of autophagosomes with lysosomes to form autolysosomes. Moreover, host cell matrix degradation by different types of autophagy can be used for the proliferation and reproduction of pathogens. Thus, determining the roles and mechanisms of autophagy during pathogen infections will promote understanding of the mechanisms of pathogen‒host interactions and provide new strategies for the treatment of infectious diseases.
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Affiliation(s)
- Qianqian Zheng
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China.,Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China
| | - Liangwei Duan
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China.,Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China
| | - Yang Zhang
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China.,Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China
| | - Jiaoyang Li
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China.,Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China
| | - Shiyu Zhang
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China.,Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China
| | - Hui Wang
- Henan Key Laboratory of Immunology and Targeted Drugs, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China. .,Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China.
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9
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Nitrogen Starvation and Stationary Phase Lipophagy Have Distinct Molecular Mechanisms. Int J Mol Sci 2020; 21:ijms21239094. [PMID: 33260464 PMCID: PMC7730393 DOI: 10.3390/ijms21239094] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 01/06/2023] Open
Abstract
In yeast, the selective autophagy of intracellular lipid droplets (LDs) or lipophagy can be induced by either nitrogen (N) starvation or carbon limitation (e.g., in the stationary (S) phase). We developed the yeast, Komagataella phaffii (formerly Pichia pastoris), as a new lipophagy model and compared the N-starvation and S-phase lipophagy in over 30 autophagy-related mutants using the Erg6-GFP processing assay. Surprisingly, two lipophagy pathways had hardly overlapping stringent molecular requirements. While the N-starvation lipophagy strictly depended on the core autophagic machinery (Atg1-Atg9, Atg18, and Vps15), vacuole fusion machinery (Vam7 and Ypt7), and vacuolar proteolysis (proteinases A and B), only Atg6 and proteinases A and B were essential for the S-phase lipophagy. The rest of the proteins were only partially required in the S-phase. Moreover, we isolated the prl1 (for the positive regulator of lipophagy 1) mutant affected in the S-phase lipophagy, but not N-starvation lipophagy. The prl1 defect was at a stage of delivery of the LDs from the cytoplasm to the vacuole, further supporting the mechanistically different nature of the two lipophagy pathways. Taken together, our results suggest that N-starvation and S-phase lipophagy have distinct molecular mechanisms.
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10
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Soto-Avellaneda A, Morrison BE. Signaling and other functions of lipids in autophagy: a review. Lipids Health Dis 2020; 19:214. [PMID: 32998777 PMCID: PMC7525950 DOI: 10.1186/s12944-020-01389-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/23/2020] [Indexed: 12/19/2022] Open
Abstract
The process of autophagy is integral to cellular function. In this process, proteins, organelles, and metabolites are engulfed in a lipid vesicle and trafficked to a lysosome for degradation. Its central role in protein and organelle homeostasis has piqued interest for autophagy dysfunction as a driver of pathology for a number of diseases including cancer, muscular disorders, neurological disorders, and non-alcoholic fatty liver disease. For much of its history, the study of autophagy has centered around proteins, however, due to advances in mass spectrometry and refined methodologies, the role of lipids in this essential cellular process has become more apparent. This review discusses the diverse endogenous lipid compounds shown to mediate autophagy. Downstream lipid signaling pathways are also reviewed in the context of autophagy regulation. Specific focus is placed upon the Mammalian Target of Rapamycin (mTOR) and Peroxisome Proliferator-Activated Receptor (PPAR) signaling pathways as integration hubs for lipid regulation of autophagy.
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Affiliation(s)
| | - Brad E Morrison
- Biomolecular Sciences Graduate programs, Boise State University, Boise, ID, 83725, USA.
- Department of Biological Sciences, Boise State University, Boise, ID, 83725, USA.
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11
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Mir B, Goettsch C. Extracellular Vesicles as Delivery Vehicles of Specific Cellular Cargo. Cells 2020; 9:cells9071601. [PMID: 32630649 PMCID: PMC7407641 DOI: 10.3390/cells9071601] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 02/06/2023] Open
Abstract
Extracellular vesicles (EVs) mediate cell-to-cell communication via the transfer of biomolecules locally and systemically between organs. It has been elucidated that the specific EV cargo load is fundamental for cellular response upon EV delivery. Therefore, revealing the specific molecular machinery that functionally regulates the precise EV cargo intracellularly is of importance in understanding the role of EVs in physiology and pathophysiology and conveying therapeutic use. The purpose of this review is to summarize recent findings on the general rules, as well as specific modulator motifs governing EV cargo loading. Finally, we address available information on potential therapeutic strategies to alter cargo loading.
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12
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Ye H, Ji C, Guo R, Jiang L. Membrane Contact Sites and Organelles Interaction in Plant Autophagy. FRONTIERS IN PLANT SCIENCE 2020; 11:477. [PMID: 32391037 PMCID: PMC7193052 DOI: 10.3389/fpls.2020.00477] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/30/2020] [Indexed: 05/24/2023]
Abstract
Autophagy is an intracellular trafficking and degradation system for recycling of damaged organelles, mis-folded proteins and cytoplasmic constituents. Autophagy can be divided into non-selective autophagy and selective autophagy according to the cargo specification. Key to the process is the timely formation of the autophagosome, a double-membrane structure which is responsible for the delivery of damaged organelles and proteins to lysosomes or vacuoles for their turnover. Autophagosomes are formed by the closure of cup-shaped phagophore which depends on the proper communication with membrane contributors. The endoplasmic reticulum (ER) is a major membrane source for autophagosome biogenesis whereby the ER connects with phagophore through membrane contact sites (MCSs). MCSs are closely apposed domains between organelle membranes where lipids and signals are exchanged. Lipid transfer proteins (LTPs) are a large family of proteins including Oxysterol-binding protein related proteins (ORP) which can be found at MCSs and mediate lipid transfer in mammals and yeast. In addition, interaction between autophagosomes and other organelles can also be detected in selective autophagy for selection and degradation of various damaged organelles. Selective autophagy is mediated by the binding of a receptor or an adaptor between a cargo and an autophagosome. Here we summarize what we know about the MCS between autophagosomes and other organelles in eukaryotes. We then discuss progress in our understanding about ORPs at MCSs in plants and the underlying mechanisms of selective autophagy in plants with a focus on receptors/adaptors that are involved in the interaction of the autophagosome with other cytoplasmic constituents, including the Neighbor of BRCA1 gene 1 (NBR1), ATG8-interacting protein 1 (ATI1), Regulatory Particle Non-ATPase 10 (RPN10), and Dominant Suppressor of KAR2 (DSK2).
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Affiliation(s)
- Hao Ye
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Changyang Ji
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Rongfang Guo
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 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, Hong Kong, China
- CUHK Shenzhen Research Institute, Shenzhen, China
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Li M, Russo M, Pirozzi F, Tocchetti CG, Ghigo A. Autophagy and cancer therapy cardiotoxicity: From molecular mechanisms to therapeutic opportunities. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118493. [DOI: 10.1016/j.bbamcr.2019.06.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/31/2019] [Accepted: 06/15/2019] [Indexed: 11/25/2022]
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14
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Ktistakis NT. ER platforms mediating autophagosome generation. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1865:158433. [PMID: 30890442 DOI: 10.1016/j.bbalip.2019.03.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 12/12/2022]
Abstract
The origin of the autophagosomal membrane started to be debated by scientists working in the field within one year of the modern definition of autophagy in 1963. There is now converging evidence from older and newer studies that the endoplasmic reticulum is involved in formation of autophagosomes. Thus, it is possible to trace from early morphological work - done without the benefit of molecular descriptions - to recent studies - dissecting how specific proteins nucleate autophagosome biogenesis - a long series of experimental findings that are beginning to answer the 55-year old question with some confidence. The view that has emerged is that specialised regions of the endoplasmic reticulum, in dynamic cross talk with most intracellular organelles via membrane contact sites, provide a platform for autophagosome biogenesis.
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15
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Autophagy: An Essential Degradation Program for Cellular Homeostasis and Life. Cells 2018; 7:cells7120278. [PMID: 30572663 PMCID: PMC6315530 DOI: 10.3390/cells7120278] [Citation(s) in RCA: 226] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 12/18/2018] [Accepted: 12/18/2018] [Indexed: 12/21/2022] Open
Abstract
Autophagy is a lysosome-dependent cellular degradation program that responds to a variety of environmental and cellular stresses. It is an evolutionarily well-conserved and essential pathway to maintain cellular homeostasis, therefore, dysfunction of autophagy is closely associated with a wide spectrum of human pathophysiological conditions including cancers and neurodegenerative diseases. The discovery and characterization of the kingdom of autophagy proteins have uncovered the molecular basis of the autophagy process. In addition, recent advances on the various post-translational modifications of autophagy proteins have shed light on the multiple layers of autophagy regulatory mechanisms, and provide novel therapeutic targets for the treatment of the diseases.
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16
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Nakanishi T, Tokunaga T, Ishida T, Kobayashi I, Katahama Y, Yano A, Erickson L, Kawahara S. Changes in expression of the autophagy-related genes microtubule-associated protein 1 light chain 3β and autophagy related 7 in skeletal muscle of fattening Japanese Black cattle: a pilot study. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018; 32:592-598. [PMID: 30208695 PMCID: PMC6409458 DOI: 10.5713/ajas.18.0370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 09/03/2018] [Indexed: 12/15/2022]
Abstract
Objective Autophagy is a bulk degradation system for intracellular proteins which contributes to skeletal muscle homeostasis, according to previous studies in humans and rodents. However, there is a lack of information on the physiological role of autophagy in the skeletal muscle of meat animals. This study was planned as a pilot study to investigate changes in expression of two major autophagy-related genes, microtubule-associated protein 1 light chain 3β (MAP1LC3B) and autophagy related 7 (ATG7) in fattening beef cattle, and to compare them with skeletal muscle growth. Methods Six castrated Japanese Black cattle (initial body weight: 503±20 kg) were enrolled in this study and fattened for 7 months. Three skeletal muscles, M. longissimus, M. gluteus medius, and M. semimembranosus, were collected by needle biopsy three times during the observation period, and mRNA levels of MAP1LC3B and ATG7 were determined by quantitative reverse-transcription polymerase chain reaction. The expression levels of genes associated with the ubiquitin-proteasome system, another proteolytic mechanism, were also analyzed for comparison with autophagy-related genes. In addition, ultrasonic scanning was repeatedly performed to measure M. longissimus area as an index of muscle growth. Results Our results showed that both MAP1LC3B and ATG7 expression increased over the observation period in all three skeletal muscles. Interestingly, the increase in expression of these two genes in M. longissimus was highly correlated with ultrasonic M. longissimus area and body weight. On the other hand, the expression of genes associated with the ubiquitin-proteasome system was unchanged during the same period. Conclusion These findings suggest that autophagy plays an important role in the growth of skeletal muscle of fattening beef cattle and imply that autophagic activity affects meat productivity.
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Affiliation(s)
- Tomonori Nakanishi
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Tadaaki Tokunaga
- Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Takafumi Ishida
- Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Ikuo Kobayashi
- Sumiyoshi Livestock Science Station, Field Science Center, University of Miyazaki, Miyazaki 880-0121, Japan
| | - Yuta Katahama
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Azusa Yano
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Laurie Erickson
- Department of Biology, Harold Washington City College of Chicago, Chicago IL 60601, USA.,Department of Health Sciences, Blitstein Institute of Hebrew Theological College, Chicago IL 60645, USA
| | - Satoshi Kawahara
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
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17
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Yan Q, Wang J, Fu ZQ, Chen W. Endocytosis of AtRGS1 Is Regulated by the Autophagy Pathway after D-Glucose Stimulation. FRONTIERS IN PLANT SCIENCE 2017; 8:1229. [PMID: 28747924 PMCID: PMC5506085 DOI: 10.3389/fpls.2017.01229] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/29/2017] [Indexed: 05/21/2023]
Abstract
Sugar, as a signal molecule, has significant functions in signal transduction in which the seven-transmembrane regulator of G-protein signaling (RGS1) protein participates. D-Glucose causes endocytosis of the AtRGS1, leading to the physical uncoupling of AtRGS1 from AtGPA1 and thus a release of the GAP activity and concomitant sustained activation of G-protein signaling. Autophagy involves in massive degradation and recycling of cytoplasmic components to survive environmental stresses. The function of autophagy in AtRGS1 endocytosis during D-glucose stimulation has not been elucidated. In this study, we investigate the relationship between autophagy and AtRGS1 in response to D-glucose. Our findings demonstrated that AtRGS1 mediated the activation of autophagy by affecting the activities of the five functional groups of protein complexes and promoted the formation of autophagosomes under D-glucose application. When the autophagy pathway was interrupted, AtRGS1 recovery increased and endocytosis of ATRGS1 was inhibited, indicating that autophagy pathway plays an important role in regulating the endocytosis and recovery of AtRGS1 after D-glucose stimulation.
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Affiliation(s)
- Quanquan Yan
- Ministry of Education Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal UniversityGuangzhou, China
| | - Jingchun Wang
- Ministry of Education Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal UniversityGuangzhou, China
| | - Zheng Qing Fu
- Department of Biological Sciences, University of South Carolina, ColumbiaSC, United States
| | - Wenli Chen
- Ministry of Education Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal UniversityGuangzhou, China
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18
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Chen L, Zhang X, Wang W, Geng X, Shi Y, Na R, Dou D, Li H. Network and role analysis of autophagy in Phytophthora sojae. Sci Rep 2017; 7:1879. [PMID: 28500315 PMCID: PMC5431975 DOI: 10.1038/s41598-017-01988-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 04/05/2017] [Indexed: 12/17/2022] Open
Abstract
Autophagy is an evolutionarily conserved mechanism in eukaryotes with roles in development and the virulence of plant fungal pathogens. However, few reports on autophagy in oomycete species have been published. Here, we identified 26 autophagy-related genes (ATGs) belonging to 20 different groups in Phytophthora sojae using a genome-wide survey, and core ATGs in oomycetes were used to construct a preliminary autophagy pathway model. Expression profile analysis revealed that these ATGs are broadly expressed and that the majority of them significantly increase during infection stages, suggesting a central role for autophagy in virulence. Autophagy in P. sojae was detected using a GFP-PsAtg8 fusion protein and the fluorescent dye MDC during rapamycin and starvation treatment. In addition, autophagy was significantly induced during sporangium formation and cyst germination. Silencing PsAtg6a in P. sojae significantly reduced sporulation and pathogenicity. Furthermore, a PsAtg6a-silenced strain showed haustorial formation defects. These results suggested that autophagy might play essential roles in both the development and infection mechanism of P. sojae.
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Affiliation(s)
- Linlin Chen
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiong Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wen Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xuejing Geng
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yan Shi
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Risong Na
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Honglian Li
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, 450002, China.
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19
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De Craene JO, Bertazzi DL, Bär S, Friant S. Phosphoinositides, Major Actors in Membrane Trafficking and Lipid Signaling Pathways. Int J Mol Sci 2017; 18:ijms18030634. [PMID: 28294977 PMCID: PMC5372647 DOI: 10.3390/ijms18030634] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/02/2017] [Accepted: 03/06/2017] [Indexed: 11/30/2022] Open
Abstract
Phosphoinositides are lipids involved in the vesicular transport of proteins and lipids between the different compartments of eukaryotic cells. They act by recruiting and/or activating effector proteins and thus are involved in regulating various cellular functions, such as vesicular budding, membrane fusion and cytoskeleton dynamics. Although detected in small concentrations in membranes, their role is essential to cell function, since imbalance in their concentrations is a hallmark of many cancers. Their synthesis involves phosphorylating/dephosphorylating positions D3, D4 and/or D5 of their inositol ring by specific lipid kinases and phosphatases. This process is tightly regulated and specific to the different intracellular membranes. Most enzymes involved in phosphoinositide synthesis are conserved between yeast and human, and their loss of function leads to severe diseases (cancer, myopathy, neuropathy and ciliopathy).
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Affiliation(s)
- Johan-Owen De Craene
- Department of Molecular and Cellular Genetics, Université de Strasbourg, CNRS, GMGM UMR 7156, F-67000 Strasbourg, France.
| | - Dimitri L Bertazzi
- Department of Molecular and Cellular Genetics, Université de Strasbourg, CNRS, GMGM UMR 7156, F-67000 Strasbourg, France.
| | - Séverine Bär
- Department of Molecular and Cellular Genetics, Université de Strasbourg, CNRS, GMGM UMR 7156, F-67000 Strasbourg, France.
| | - Sylvie Friant
- Department of Molecular and Cellular Genetics, Université de Strasbourg, CNRS, GMGM UMR 7156, F-67000 Strasbourg, France.
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20
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Nascimbeni AC, Codogno P, Morel E. Phosphatidylinositol-3-phosphate in the regulation of autophagy membrane dynamics. FEBS J 2017; 284:1267-1278. [PMID: 27973739 DOI: 10.1111/febs.13987] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 11/15/2016] [Accepted: 12/07/2016] [Indexed: 12/30/2022]
Abstract
Phosphatidylinositol-3-phosphate (PI3P) is a key player in membrane dynamics and trafficking regulation. Most PI3P is associated with endosomal membranes and with the autophagosome preassembly machinery, presumably at the endoplasmic reticulum. The enzyme responsible for most PI3P synthesis, VPS34 and proteins such as Beclin1 and ATG14L that regulate PI3P levels are positive modulators of autophagy initiation. It had been assumed that a local PI3P pool was present at autophagosomes and preautophagosomal structures, such as the omegasome and the phagophore. This was recently confirmed by the demonstration that PI3P-binding proteins participate in the complex sequence of signalling that results in autophagosome assembly and activity. Here we summarize the historical discoveries of PI3P lipid kinase involvement in autophagy, and we discuss the proposed role of PI3P during autophagy, notably during the autophagosome biogenesis sequence.
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Affiliation(s)
- Anna Chiara Nascimbeni
- Institut Necker-Enfants Malades (INEM), INSERM U1151-CNRS UMR 8253, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, France
| | - Patrice Codogno
- Institut Necker-Enfants Malades (INEM), INSERM U1151-CNRS UMR 8253, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, France
| | - Etienne Morel
- Institut Necker-Enfants Malades (INEM), INSERM U1151-CNRS UMR 8253, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, France
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21
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Kaminska J, Rzepnikowska W, Polak A, Flis K, Soczewka P, Bala K, Sienko M, Grynberg M, Kaliszewski P, Urbanek A, Ayscough K, Zoladek T. Phosphatidylinositol-3-phosphate regulates response of cells to proteotoxic stress. Int J Biochem Cell Biol 2016; 79:494-504. [PMID: 27498190 DOI: 10.1016/j.biocel.2016.08.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 07/29/2016] [Accepted: 08/03/2016] [Indexed: 12/22/2022]
Abstract
Human Nedd4 ubiquitin ligase, or its variants, inhibit yeast cell growth by disturbing the actin cytoskeleton organization and dynamics, and lead to an increase in levels of ubiquitinated proteins. In a screen for multicopy suppressors which rescue growth of yeast cells producing Nedd4 ligase with an inactive WW4 domain (Nedd4w4), we identified a fragment of ATG2 gene encoding part of the Atg2 core autophagy protein. Expression of the Atg2-C1 fragment (aa 1074-1447) improved growth, actin cytoskeleton organization, but did not significantly change the levels of ubiquitinated proteins in these cells. The GFP-Atg2-C1 protein in Nedd4w4-producing cells primarily localized to a single defined structure adjacent to the vacuole, surrounded by an actin filament ring, containing Hsp42 and Hsp104 chaperones. This localization was not affected in several atg deletion mutants, suggesting that it might be distinct from the phagophore assembly site (PAS). However, deletion of ATG18 encoding a phosphatidylinositol-3-phosphate (PI3P)-binding protein affected the morphology of the GFP-Atg2-C1 structure while deletion of ATG14 encoding a subunit of PI3 kinase suppressed toxicity of Nedd4w4 independently of GFP-Atg2-C1. Further analysis of the Atg2-C1 revealed that it contains an APT1 domain of previously uncharacterized function. Most importantly, we showed that this domain is able to bind phosphatidylinositol phosphates, especially PI3P, which is abundant in the PAS and endosomes. Together our results suggest that human Nedd4 ubiquitinates proteins in yeast and causes proteotoxic stress and, with some Atg proteins, leads to formation of a perivacuolar structure, which may be involved in sequestration, aggregation or degradation of proteins.
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Affiliation(s)
- Joanna Kaminska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Weronika Rzepnikowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Anna Polak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Krzysztof Flis
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Piotr Soczewka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Katarzyna Bala
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Marzena Sienko
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Marcin Grynberg
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Pawel Kaliszewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Agnieszka Urbanek
- Department of Biomedical Science, University of Sheffield, Sheffield, UK
| | - Kathryn Ayscough
- Department of Biomedical Science, University of Sheffield, Sheffield, UK
| | - Teresa Zoladek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
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22
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Edens BM, Miller N, Ma YC. Impaired Autophagy and Defective Mitochondrial Function: Converging Paths on the Road to Motor Neuron Degeneration. Front Cell Neurosci 2016; 10:44. [PMID: 26973461 PMCID: PMC4776126 DOI: 10.3389/fncel.2016.00044] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/08/2016] [Indexed: 12/12/2022] Open
Abstract
Selective motor neuron degeneration is a hallmark of amyotrophic lateral sclerosis (ALS). Around 10% of all cases present as familial ALS (FALS), while sporadic ALS (SALS) accounts for the remaining 90%. Diverse genetic mutations leading to FALS have been identified, but the underlying causes of SALS remain largely unknown. Despite the heterogeneous and incompletely understood etiology, different types of ALS exhibit overlapping pathology and common phenotypes, including protein aggregation and mitochondrial deficiencies. Here, we review the current understanding of mechanisms leading to motor neuron degeneration in ALS as they pertain to disrupted cellular clearance pathways, ATP biogenesis, calcium buffering and mitochondrial dynamics. Through focusing on impaired autophagic and mitochondrial functions, we highlight how the convergence of diverse cellular processes and pathways contributes to common pathology in motor neuron degeneration.
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Affiliation(s)
- Brittany M. Edens
- Departments of Pediatrics, Neurology, and Physiology, Northwestern University Feinberg School of MedicineChicago, IL, USA
- Lurie Children’s Hospital of ChicagoChicago, IL, USA
| | - Nimrod Miller
- Departments of Pediatrics, Neurology, and Physiology, Northwestern University Feinberg School of MedicineChicago, IL, USA
- Lurie Children’s Hospital of ChicagoChicago, IL, USA
| | - Yong-Chao Ma
- Departments of Pediatrics, Neurology, and Physiology, Northwestern University Feinberg School of MedicineChicago, IL, USA
- Lurie Children’s Hospital of ChicagoChicago, IL, USA
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23
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Lai JKF, Sam IC, Chan YF. The Autophagic Machinery in Enterovirus Infection. Viruses 2016; 8:v8020032. [PMID: 26828514 PMCID: PMC4776187 DOI: 10.3390/v8020032] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 01/13/2016] [Accepted: 01/19/2016] [Indexed: 02/07/2023] Open
Abstract
The Enterovirus genus of the Picornaviridae family comprises many important human pathogens, including polioviruses, rhinovirus, enterovirus A71, and enterovirus D68. They cause a wide variety of diseases, ranging from mild to severe life-threatening diseases. Currently, no effective vaccine is available against enteroviruses except for poliovirus. Enteroviruses subvert the autophagic machinery to benefit their assembly, maturation, and exit from host. Some enteroviruses spread between cells via a process described as autophagosome-mediated exit without lysis (AWOL). The early and late phases of autophagy are regulated through various lipids and their metabolizing enzymes. Some of these lipids and enzymes are specifically regulated by enteroviruses. In the present review, we summarize the current understanding of the regulation of autophagic machinery by enteroviruses, and provide updates on recent developments in this field.
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Affiliation(s)
- Jeffrey K F Lai
- Department of Medical Microbiology, Faculty of Medicine, University Malaya, 50603 Kuala Lumpur, Malaysia.
| | - I-Ching Sam
- Department of Medical Microbiology, Faculty of Medicine, University Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Yoke Fun Chan
- Department of Medical Microbiology, Faculty of Medicine, University Malaya, 50603 Kuala Lumpur, Malaysia.
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24
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Abstract
Maintenance of cellular homeostasis requires tight and coordinated control of numerous metabolic pathways, which are governed by interconnected networks of signaling pathways and energy-sensing regulators. Autophagy, a lysosomal degradation pathway by which the cell self-digests its own components, has over the past decade been recognized as an essential part of metabolism. Autophagy not only rids the cell of excessive or damaged organelles, misfolded proteins, and invading microorganisms, it also provides nutrients to maintain crucial cellular functions. Besides serving as essential structural moieties of biomembranes, lipids including sphingolipids are increasingly being recognized as central regulators of a number of important cellular processes, including autophagy. In the present review we describe how sphingolipids, with special emphasis on ceramides and sphingosine-1-phosphate, can act as physiological regulators of autophagy in relation to cellular and organismal growth, survival, and aging.
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Affiliation(s)
- Eva Bang Harvald
- Villum Center for Bioanalytical Sciences, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
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25
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Wesselborg S, Stork B. Autophagy signal transduction by ATG proteins: from hierarchies to networks. Cell Mol Life Sci 2015; 72:4721-57. [PMID: 26390974 PMCID: PMC4648967 DOI: 10.1007/s00018-015-2034-8] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 08/13/2015] [Accepted: 08/31/2015] [Indexed: 02/07/2023]
Abstract
Autophagy represents an intracellular degradation process which is involved in both cellular homeostasis and disease settings. In the last two decades, the molecular machinery governing this process has been characterized in detail. To date, several key factors regulating this intracellular degradation process have been identified. The so-called autophagy-related (ATG) genes and proteins are central to this process. However, several additional molecules contribute to the outcome of an autophagic response. Several review articles describing the molecular process of autophagy have been published in the recent past. In this review article we would like to add the most recent findings to this knowledge, and to give an overview of the network character of the autophagy signaling machinery.
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Affiliation(s)
- Sebastian Wesselborg
- Institute of Molecular Medicine I, Heinrich-Heine-University, Universitätsstr. 1, Building 23.12, 40225, Düsseldorf, Germany
| | - Björn Stork
- Institute of Molecular Medicine I, Heinrich-Heine-University, Universitätsstr. 1, Building 23.12, 40225, Düsseldorf, Germany.
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26
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Daher W, Morlon-Guyot J, Sheiner L, Lentini G, Berry L, Tawk L, Dubremetz JF, Wengelnik K, Striepen B, Lebrun M. Lipid kinases are essential for apicoplast homeostasis in Toxoplasma gondii. Cell Microbiol 2014; 17:559-78. [PMID: 25329540 DOI: 10.1111/cmi.12383] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 09/26/2014] [Accepted: 10/10/2014] [Indexed: 12/25/2022]
Abstract
Phosphoinositides regulate numerous cellular processes by recruiting cytosolic effector proteins and acting as membrane signalling entities. The cellular metabolism and localization of phosphoinositides are tightly regulated by distinct lipid kinases and phosphatases. Here, we identify and characterize a unique phosphatidylinositol 3 kinase (PI3K) in Toxoplasma gondii, a protozoan parasite belonging to the phylum Apicomplexa. Conditional depletion of this enzyme and subsequently of its product, PI(3)P, drastically alters the morphology and inheritance of the apicoplast, an endosymbiotic organelle of algal origin that is a unique feature of many Apicomplexa. We searched the T. gondii genome for PI(3)P-binding proteins and identified in total six PX and FYVE domain-containing proteins including a PIKfyve lipid kinase, which phosphorylates PI(3)P into PI(3,5)P2 . Although depletion of putative PI(3)P-binding proteins shows that they are not essential for parasite growth and apicoplast biology, conditional disruption of PIKfyve induces enlarged apicoplasts, as observed upon loss of PI(3)P. A similar defect of apicoplast homeostasis was also observed by knocking down the PIKfyve regulatory protein ArPIKfyve, suggesting that in T. gondii, PI(3)P-related function for the apicoplast might mainly be to serve as a precursor for the synthesis of PI(3,5)P2 . Accordingly, PI3K is conserved in all apicomplexan parasites whereas PIKfyve and ArPIKfyve are absent in Cryptosporidium species that lack an apicoplast, supporting a direct role of PI(3,5)P2 in apicoplast homeostasis. This study enriches the already diverse functions attributed to PI(3,5)P2 in eukaryotic cells and highlights these parasite lipid kinases as potential drug targets.
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Affiliation(s)
- Wassim Daher
- Dynamique des Interactions Membranaires Normales et Pathologiques, UMR5235 CNRS, Université de Montpellier 1 et 2, Montpellier, France
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27
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Calvo-Garrido J, King JS, Muñoz-Braceras S, Escalante R. Vmp1 regulates PtdIns3P signaling during autophagosome formation in Dictyostelium discoideum. Traffic 2014; 15:1235-46. [PMID: 25131297 DOI: 10.1111/tra.12210] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 08/13/2014] [Accepted: 08/13/2014] [Indexed: 01/08/2023]
Abstract
Generation and turnover of phosphatidylinositol 3-phosphate (PtdIns3P) signaling is essential for autophagosome formation and other membrane traffic processes. In both Dictyostelium discoideum and mammalian cells, autophagosomes are formed from specialized regions of the endoplasmic reticulum (ER), called omegasomes, which are enriched in the signaling lipid PtdIns3P. Vacuole membrane protein 1 (Vmp1) is a multispanning membrane protein localized at the ER that is required for autophagosome formation. There are conflicting reports in the literature as to whether Vmp1 is strictly required or not for autophagy-related PtdIns3P signaling and its hierarchical relationship with Atg1 and PI3K. We have now addressed these questions in the Dictyostelium model. We show that Dictyostelium cells lacking Vmp1 have elevated and aberrant PtdIns3P signaling on the ER, resulting in an increased and persistent recruitment of Atg18 and other autophagic proteins. This indicates that Vmp1 is not strictly essential for the generation of PtdIns3P signaling but rather suggests a role in the correct turnover or modulation of this signaling. Of interest, these PtdIns3P-enriched regions of the ER surround ubiquitinated protein aggregates but are unable to form functional autophagosomes. vmp1 null cells also have additional defects in macropinocytosis and growth, which are not shared by other autophagy mutants. Remarkably, we show that these defects and also the aberrant PtdIns3P distribution are largely suppressed by the concomitant loss of Atg1, indicating that aberrant autophagic signaling on the ER inhibits macropinocytosis. These results suggest that Atg1 functions upstream of Vmp1 in this signaling pathway and demonstrates a previously unappreciated link between abnormal autophagy signaling and macropinocytosis.
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Affiliation(s)
- Javier Calvo-Garrido
- Instituto de Investigaciones Biomédicas Alberto Sols, C.S.I.C./U.A.M., Madrid, 28029, Spain
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28
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Pfisterer SG, Bakula D, Frickey T, Cezanne A, Brigger D, Tschan MP, Robenek H, Proikas-Cezanne T. Lipid droplet and early autophagosomal membrane targeting of Atg2A and Atg14L in human tumor cells. J Lipid Res 2014; 55:1267-78. [PMID: 24776541 DOI: 10.1194/jlr.m046359] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Indexed: 12/26/2022] Open
Abstract
Autophagy is a lysosomal bulk degradation pathway for cytoplasmic cargo, such as long-lived proteins, lipids, and organelles. Induced upon nutrient starvation, autophagic degradation is accomplished by the concerted actions of autophagy-related (ATG) proteins. Here we demonstrate that two ATGs, human Atg2A and Atg14L, colocalize at cytoplasmic lipid droplets (LDs) and are functionally involved in controlling the number and size of LDs in human tumor cell lines. We show that Atg2A is targeted to cytoplasmic ADRP-positive LDs that migrate bidirectionally along microtubules. The LD localization of Atg2A was found to be independent of the autophagic status. Further, Atg2A colocalized with Atg14L under nutrient-rich conditions when autophagy was not induced. Upon nutrient starvation and dependent on phosphatidylinositol 3-phosphate [PtdIns(3)P] generation, both Atg2A and Atg14L were also specifically targeted to endoplasmic reticulum-associated early autophagosomal membranes, marked by the PtdIns(3)P effectors double-FYVE containing protein 1 (DFCP1) and WD-repeat protein interacting with phosphoinositides 1 (WIPI-1), both of which function at the onset of autophagy. These data provide evidence for additional roles of Atg2A and Atg14L in the formation of early autophagosomal membranes and also in lipid metabolism.
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Affiliation(s)
- Simon G Pfisterer
- Autophagy Laboratory, Department of Molecular Biology, Interfaculty Institute for Cell Biology, Eberhard Karls University Tuebingen, Tuebingen, Germany
| | - Daniela Bakula
- Autophagy Laboratory, Department of Molecular Biology, Interfaculty Institute for Cell Biology, Eberhard Karls University Tuebingen, Tuebingen, Germany International Max Planck Research School 'From Molecules to Organisms', Max Planck Institute for Developmental Biology and Eberhard Karls University Tuebingen, Tuebingen, Germany
| | - Tancred Frickey
- Applied Bioinformatics Laboratory, University of Konstanz, Konstanz, Germany
| | - Alice Cezanne
- Autophagy Laboratory, Department of Molecular Biology, Interfaculty Institute for Cell Biology, Eberhard Karls University Tuebingen, Tuebingen, Germany
| | - Daniel Brigger
- Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland
| | - Mario P Tschan
- Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland
| | - Horst Robenek
- Leibniz Institute for Arteriosklerosis Research, University of Muenster, Muenster, Germany
| | - Tassula Proikas-Cezanne
- Autophagy Laboratory, Department of Molecular Biology, Interfaculty Institute for Cell Biology, Eberhard Karls University Tuebingen, Tuebingen, Germany International Max Planck Research School 'From Molecules to Organisms', Max Planck Institute for Developmental Biology and Eberhard Karls University Tuebingen, Tuebingen, Germany
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29
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Araki Y, Ku WC, Akioka M, May AI, Hayashi Y, Arisaka F, Ishihama Y, Ohsumi Y. Atg38 is required for autophagy-specific phosphatidylinositol 3-kinase complex integrity. ACTA ACUST UNITED AC 2013; 203:299-313. [PMID: 24165940 PMCID: PMC3812978 DOI: 10.1083/jcb.201304123] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Atg38 provides a physical linkage between the Vps15–Vps34 and Atg14–Vps30 subcomplexes to facilitate PI3-kinase complex I formation. Autophagy is a conserved eukaryotic process of protein and organelle self-degradation within the vacuole/lysosome. Autophagy is characterized by the formation of an autophagosome, for which Vps34-dervied phosphatidylinositol 3-phosphate (PI3P) is essential. In yeast, Vps34 forms two distinct protein complexes: complex I, which functions in autophagy, and complex II, which is involved in protein sorting to the vacuole. Here we identify and characterize Atg38 as a stably associated subunit of complex I. In atg38Δ cells, autophagic activity was significantly reduced and PI3-kinase complex I dissociated into the Vps15–Vps34 and Atg14–Vps30 subcomplexes. We find that Atg38 physically interacted with Atg14 and Vps34 via its N terminus. Further biochemical analyses revealed that Atg38 homodimerizes through its C terminus and that this homodimer formation is indispensable for the integrity of complex I. These data suggest that the homodimer of Atg38 functions as a physical linkage between the Vps15–Vps34 and Atg14–Vps30 subcomplexes to facilitate complex I formation.
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Affiliation(s)
- Yasuhiro Araki
- Frontier Research Center, Tokyo Institute of Technology, Yokohama 226-8503, Japan
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30
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Voigt O, Herzog B, Jakobshagen A, Pöggeler S. Autophagic kinases SmVPS34 and SmVPS15 are required for viability in the filamentous ascomycete Sordaria macrospora. Microbiol Res 2013; 169:128-38. [PMID: 23953726 DOI: 10.1016/j.micres.2013.07.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 07/17/2013] [Accepted: 07/18/2013] [Indexed: 10/26/2022]
Abstract
Autophagy is a tightly controlled degradation process of all eukaryotes. It includes the sequestration of cytoplasmic contents and organelles within a double-membraned autophagosome. Autophagy involves core autophagy related (atg) genes as well as genes regulating vesicle trafficking. Previously, we analyzed the impact of proteins of the core autophagic machinery SmATG7, SmATG8 and SmATG4 on the sexual and vegetative development of the filamentous ascomycete Sordaria macrospora. While deletion of Smatg8 and Smatg4 abolished fruiting-body formation and impaired vegetative growth, Smatg7 is required for viability. In yeast, the phosphatidylinositol 3-kinase vacuolar protein sorting 34 (Vps34) and its myristoylated membrane targeting unit, the protein kinase Vps15 have been shown to be important regulators of autophagy and vacuolar protein sorting. However, their exact role in filamentous ascomycetes remains elusive. To determine the function of Smvps34 and Smvps15 we isolated genes with high sequence similarity to Saccharomyces cerevisiae VPS34 and VPS15. For both genes we were not able to generate a homokaryotic knockout mutant in S. macrospora, suggesting that Smvps34 and Smvps15 are required for viability. Furthermore, we analyzed the repertoire of vps genes encoded by S. macrospora and could identify putative homologs of nearly all of the 61 VPS genes of S. cerevisiae.
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Affiliation(s)
- Oliver Voigt
- Institute of Microbiology and Genetics, Department of Genetics of Eukaryotic Microorganisms, Georg-August-University, Göttingen, Germany
| | - Britta Herzog
- Institute of Microbiology and Genetics, Department of Genetics of Eukaryotic Microorganisms, Georg-August-University, Göttingen, Germany
| | - Antonia Jakobshagen
- Institute of Microbiology and Genetics, Department of Genetics of Eukaryotic Microorganisms, Georg-August-University, Göttingen, Germany
| | - Stefanie Pöggeler
- Institute of Microbiology and Genetics, Department of Genetics of Eukaryotic Microorganisms, Georg-August-University, Göttingen, Germany.
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Abstract
Autophagy is a catabolic pathway in which the cell sequesters cytoplasmic material, including long-lived proteins, lipids and organelles, in specialized double-membrane vesicles, called autophagosomes. Subsequently, autophagosomes communicate with the lysosomal compartment and acquire acidic hydrolases for final cargo degradation. This process of partial self-eating secures the survival of eukaryotic cells during starvation periods and is critically regulated by mTORC1 (mammalian target of rapamycin complex 1). Under nutrient-poor conditions, inhibited mTORC1 permits localized PtdIns(3)P production at particular membranes that contribute to autophagosome formation. Members of the human WIPI (WD-repeat protein interacting with phosphoinositides) family fulfil an essential role as PtdIns(3)P effectors at the initiation step of autophagosome formation. In the present article, we discuss the role of human WIPIs in autophagy, and the identification of evolutionarily conserved amino acids of WIPI-1 that confer PtdIns(3)P binding downstream of mTORC1 inhibition. We also discuss the PtdIns(3)P effector function of WIPIs in the context of longevity and autophagy-related human diseases, such as cancer and neurodegeneration.
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Dall'Armi C, Devereaux KA, Di Paolo G. The role of lipids in the control of autophagy. Curr Biol 2013; 23:R33-45. [PMID: 23305670 DOI: 10.1016/j.cub.2012.10.041] [Citation(s) in RCA: 211] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Macroautophagy is an essential cellular pathway mediating the lysosomal degradation of defective organelles, long-lived proteins and a variety of protein aggregates. Similar to other intracellular trafficking pathways, macroautophagy involves a complex sequence of membrane remodeling and trafficking events. These include the biogenesis of autophagosomes, which engulf portions of cytoplasm at specific subcellular locations, and their subsequent maturation into autophagolysosomes through fusion with the endo-lysosomal compartment. Although the formation and maturation of autophagosomes are controlled by molecular reactions occurring at the membrane-cytosol interface, little is known about the role of lipids and their metabolizing enzymes in this process. Historically dominated by studies on class III phosphatidylinositol 3-kinase (also known as Vps34) and its product phosphatidylinositol-3-phosphate, as well as on the lipidation of Atg8/LC3-like proteins, this area of research has recently expanded, implicating a variety of other lipids, such as phosphatidic acid and diacylglycerol, and their metabolizing enzymes in macroautophagy. This review summarizes this progress and highlights the role of specific lipids in the various steps of macroautophagy, including the signaling processes underlying macroautophagy initiation, autophagosome biogenesis and maturation.
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Affiliation(s)
- Claudia Dall'Armi
- Department of Pathology and Cell Biology, Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
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ULK1 induces autophagy by phosphorylating Beclin-1 and activating VPS34 lipid kinase. Nat Cell Biol 2013; 15:741-50. [PMID: 23685627 PMCID: PMC3885611 DOI: 10.1038/ncb2757] [Citation(s) in RCA: 1156] [Impact Index Per Article: 105.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 04/15/2013] [Indexed: 12/13/2022]
Abstract
Autophagy is the primary cellular catabolic program activated in response to nutrient starvation. Initiation of autophagy, particularly by amino acid withdrawal, requires the ULK kinases. Despite its pivotal role in autophagy initiation, little is known about the mechanisms by which ULK promotes autophagy. Here we describe a molecular mechanism linking ULK to the pro-autophagic lipid kinase VPS34. Upon amino acid starvation or mTOR inhibition the activated ULK1 phosphorylates Beclin-1 on S14, thereby, enhancing the activity of the ATG14L-containing VPS34 complexes. The Beclin-1 S14 phosphorylation by ULK is required for full autophagic induction in mammals and this requirement is conserved in C. elegans. Our study reveals a molecular link from ULK1 to activation of the autophagy specific VPS34 complex and autophagy induction.
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34
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Kim J, Kim YC, Fang C, Russell RC, Kim JH, Fan W, Liu R, Zhong Q, Guan KL. Differential regulation of distinct Vps34 complexes by AMPK in nutrient stress and autophagy. Cell 2013; 152:290-303. [PMID: 23332761 DOI: 10.1016/j.cell.2012.12.016] [Citation(s) in RCA: 594] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 11/13/2012] [Accepted: 12/12/2012] [Indexed: 12/14/2022]
Abstract
Autophagy is a stress response protecting cells from unfavorable conditions, such as nutrient starvation. The class III phosphatidylinositol-3 kinase, Vps34, forms multiple complexes and regulates both intracellular vesicle trafficking and autophagy induction. Here, we show that AMPK plays a key role in regulating different Vps34 complexes. AMPK inhibits the nonautophagy Vps34 complex by phosphorylating T163/S165 in Vps34 and therefore suppresses overall PI(3)P production and protects cells from starvation. In parallel, AMPK activates the proautophagy Vps34 complex by phosphorylating S91/S94 in Beclin1 to induce autophagy. Atg14L, an autophagy-essential gene present only in the proautophagy Vps34 complex, inhibits Vps34 phosphorylation but increases Beclin1 phosphorylation by AMPK. As such, Atg14L dictates the differential regulation (either inhibition or activation) of different Vps34 complexes in response to glucose starvation. Our study reveals an intricate molecular regulation of Vps34 complexes by AMPK in nutrient stress response and autophagy.
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Affiliation(s)
- Joungmok Kim
- Department of Oral Biochemistry and Molecular Biology, Research Center for Tooth and Periodontal Tissue Regeneration, School of Dentistry, Kyung Hee University, Seoul 130-701, Korea
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Chen J, Chen MX, Fogo AB, Harris RC, Chen JK. mVps34 deletion in podocytes causes glomerulosclerosis by disrupting intracellular vesicle trafficking. J Am Soc Nephrol 2013; 24:198-207. [PMID: 23291473 PMCID: PMC3559479 DOI: 10.1681/asn.2012010101] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 11/06/2012] [Indexed: 01/07/2023] Open
Abstract
Recent studies have suggested that autophagy is a key mechanism in maintaining the integrity of podocytes. The mammalian homologue of yeast vacuolar protein sorting defective 34 (mVps34) has been implicated in the regulation of autophagy, but its role in podocytes is unknown. We generated a line of podocyte-specific mVps34-knockout (mVps34(pdKO)) mice, which were born at Mendelian ratios. These mice appeared grossly normal at 2 weeks of age but exhibited growth retardation and were significantly smaller than control mice by 6 weeks of age, with no difference in ratios of kidney to body weight. mVps34(pdKO) mice developed significant proteinuria by 3 weeks of age, developed severe kidney lesions by 5-6 weeks of age, and died before 9 weeks of age. There was striking podocyte vacuolization and proteinaceous casts, with marked glomerulosclerosis and interstitial fibrosis by 6 weeks of age. Electron microscopy revealed numerous enlarged vacuoles and increased autophagosomes in the podocytes, with complete foot process effacement and irregular and thickened glomerular basement membranes. Immunoblotting of isolated glomerular lysates revealed markedly elevated markers specific for lysosomes (LAMP1 and LAMP2) and autophagosomes (LC3-II/I). Immunofluorescence staining confirmed that the enlarged vacuoles originated from lysosomes. In conclusion, these results demonstrate an indispensable role for mVps34 in the trafficking of intracellular vesicles to protect the normal cellular metabolism, structure, and function of podocytes.
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Affiliation(s)
- Jianchun Chen
- Department of Medicine, Department of Pathology, and Department of Microbiology & Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, and
| | - Mystie X. Chen
- Department of Medicine, Department of Pathology, and Department of Microbiology & Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, and
| | - Agnes B. Fogo
- Department of Medicine, Department of Pathology, and Department of Microbiology & Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, and
| | - Raymond C. Harris
- Department of Medicine, Department of Pathology, and Department of Microbiology & Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, and
| | - Jian-Kang Chen
- Section of Experimental Medicine, Department of Medicine, Georgia Regents University, Augusta, Georgia
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Abstract
Phosphoinositide 3-kinases (PI3Ks) control many important aspects of immune cell development, differentiation, and function. Mammals have eight PI3K catalytic subunits that are divided into three classes based on similarities in structure and function. Specific roles for the class I PI3Ks have been broadly investigated and are relatively well understood, as is the function of their corresponding phosphatases. More recently, specific roles for the class II and class III PI3Ks have emerged. Through vertebrate evolution and in parallel with the evolution of adaptive immunity, there has been a dramatic increase not only in the genes for PI3K subunits but also in genes for phosphatases that act on 3-phosphoinositides and in 3-phosphoinositide-binding proteins. Our understanding of the PI3Ks in immunity is guided by fundamental discoveries made in simpler model organisms as well as by appreciating new adaptations of this signaling module in mammals in general and in immune cells in particular.
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Affiliation(s)
- Klaus Okkenhaug
- Laboratory of Lymphocyte Signaling and Development, The Babraham Institute, Cambridge, CB22 3AT, United Kingdom.
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Li Y, Zhao Y, Hu J, Xiao J, Qu L, Wang Z, Ma D, Chen Y. A novel ER-localized transmembrane protein, EMC6, interacts with RAB5A and regulates cell autophagy. Autophagy 2012. [PMID: 23182941 DOI: 10.4161/auto.22742] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Autophagy is mediated by a unique organelle, the autophagosome, which encloses a portion of the cytoplasm for delivery to the lysosome. Phosphatidylinositol 3-phosphate (PtdIns3P) produced by the class III phosphatidylinositol 3-kinase (PtdIns3K) complex is essential for canonical autophagosome formation. RAB5A, a small GTPase localized to early endosomes, has been shown to associate with the class III PtdIns3K complex, regulate its activity and promote autophagosome formation. However, little is known about how endosome-localized RAB5A functions with the class III PtdIns3K complex. Here we identified a novel endoplasmic reticulum (ER)-localized transmembrane protein, ER membrane protein complex subunit 6 (EMC6), which interacted with both RAB5A and BECN1/Beclin 1 and colocalized with the omegasome marker ZFYVE1/DFCP1. It was shown to regulate autophagosome formation, and its deficiency caused the accumulation of autophagosomal precursor structures and impaired autophagy. Our study showed for the first time that EMC6 is a novel regulator involved in autophagy.
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Affiliation(s)
- Yanjun Li
- Key Laboratory of Medical Immunology, Ministry of Health, Peking University Health Science Center, Beijing, China
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Gaugel A, Bakula D, Hoffmann A, Proikas-Cezanne T. Defining regulatory and phosphoinositide-binding sites in the human WIPI-1 β-propeller responsible for autophagosomal membrane localization downstream of mTORC1 inhibition. J Mol Signal 2012; 7:16. [PMID: 23088497 PMCID: PMC3543385 DOI: 10.1186/1750-2187-7-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 09/24/2012] [Indexed: 12/15/2022] Open
Abstract
UNLABELLED BACKGROUND Autophagy is a cytoprotective, lysosomal degradation system regulated upon induced phosphatidylinositol 3-phosphate (PtdIns(3)P) generation by phosphatidylinositol 3-kinase class III (PtdIns3KC3) downstream of mTORC1 inhibition. The human PtdIns(3)P-binding β-propeller protein WIPI-1 accumulates at the initiation site for autophagosome formation (phagophore), functions upstream of the Atg12 and LC3 conjugation systems, and localizes at both the inner and outer membrane of generated autophagosomes. In addition, to a minor degree WIPI-1 also binds PtdIns(3,5)P2. By homology modelling we earlier identified 24 evolutionarily highly conserved amino acids that cluster at two opposite sites of the open Velcro arranged WIPI-1 β-propeller. RESULTS By alanine scanning mutagenesis of 24 conserved residues in human WIPI-1 we define the PtdIns-binding site of human WIPI-1 to critically include S203, S205, G208, T209, R212, R226, R227, G228, S251, T255, H257. These amino acids confer PtdIns(3)P or PtdIns(3,5)P2 binding. In general, WIPI-1 mutants unable to bind PtdIns(3)P/PtdIns(3,5)P2 lost their potential to localize at autophagosomal membranes, but WIPI-1 mutants that retained PtdIns(3)P/PtdIns(3,5)P2 binding localized at Atg12-positive phagophores upon mTORC1 inhibition. Both, downregulation of mTOR by siRNA or cellular PtdIns(3)P elevation upon PIKfyve inhibition by YM201636 significantly increased the localization of WIPI-1 at autophagosomal membranes. Further, we identified regulatory amino acids that influence the membrane recruitment of WIPI-1. Exceptional, WIPI-1 R110A localization at Atg12-positive membranes was independent of autophagy stimulation and insensitive to wortmannin. R112A and H185A mutants were unable to bind PtdIns(3)P/PtdIns(3,5)P2 but localized at autophagosomal membranes, although in a significant reduced number of cells when compared to wild-type WIPI-1. CONCLUSIONS We identified amino acids of the WIPI-1 β-propeller that confer PtdIns(3)P or PtdIns(3,5)P2 binding (S203, S205, G208, T209, R212, R226, R227, G228, S251, T255, H257), and that regulate the localization at autophagosomal membranes (R110, R112, H185) downstream of mTORC1 inhibition.
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Affiliation(s)
- Anja Gaugel
- From the Autophagy Laboratory, Department of Molecular Biology, Interfaculty Institute of Cell Biology, Eberhard Karls University Tuebingen, Auf der Morgenstelle 15, 72076, Tuebingen, Germany.
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Taylor R, Chen PH, Chou CC, Patel J, Jin SV. KCS1 deletion in Saccharomyces cerevisiae leads to a defect in translocation of autophagic proteins and reduces autophagosome formation. Autophagy 2012; 8:1300-11. [PMID: 22889849 DOI: 10.4161/auto.20681] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Inositol phosphates are implicated in the regulation of autophagy; however, the exact role of each inositol phosphate species is unclear. In this study, we systematically analyzed the highly conserved inositol polyphosphate synthesis pathway in S. cerevisiae for its role in regulating autophagy. Using yeast mutants that harbored a deletion in each of the genes within the inositol polyphosphate synthesis pathway, we found that deletion of KCS1, and to a lesser degree IPK2, led to a defect in autophagy. KCS1 encodes an inositol hexakisphosphate/heptakisposphate kinase that synthesizes 5-IP(7) and IP(8); and IPK2 encodes an inositol polyphosphate multikinase required for synthesis of IP(4) and IP(5). We characterized the kcs1Δ mutant strain in detail. The kcs1Δ yeast exhibited reduced autophagic flux, which might be caused by both the reduction in autophagosome number and autophagosome size as observed under nitrogen starvation. The autophagy defect in kcs1Δ strain was associated with mislocalization of the phagophore assembly site (PAS) and a defect in Atg18 release from the vacuole membrane under nitrogen deprivation conditions. Interestingly, formation of autophagosome-like vesicles was commonly observed to originate from the plasma membrane in the kcs1Δ strain. Our results indicate that lack of KCS1 interferes with proper localization of the PAS, leads to reduction of autophagosome formation, and causes the formation of autophagosome-like structure in abnormal subcellular locations.
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Affiliation(s)
- Robert Taylor
- Department of Pharmacology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, NJ, USA
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LC3-Associated Phagocytosis (LAP): Connections with Host Autophagy. Cells 2012; 1:396-408. [PMID: 24710482 PMCID: PMC3901117 DOI: 10.3390/cells1030396] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 07/21/2012] [Accepted: 07/23/2012] [Indexed: 01/03/2023] Open
Abstract
Autophagy is an intracellular degradative process with a number of roles, one of which can be the protection of eukaryotic cells from invading microbes. Microtubule-associated protein light-chain 3 (LC3) is a key autophagy-related protein that is recruited to the double-membrane autophagosome responsible for sequestering material intended for delivery to lysosomes. GFP-LC3 is widely used as a marker of autophagosome formation as denoted by the formation of green puncta when viewed by fluorescence microscopy. Recently, it has been demonstrated that LC3 can be recruited to other membranes including single-membrane phagosomes, in a process termed LC3-associated phagocytosis (LAP). Thus, the observation of green puncta in cells can no longer, by itself, be taken as evidence of autophagy. This review will clarify those features of LAP which serve to distinguish it from autophagy and that make connections with host autophagic responses in terms of infection by microbial pathogens. More specifically, it will refer to concurrent studies of the mechanism by which LAP is triggered in comparison to autophagy.
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How phosphoinositide 3-phosphate controls growth downstream of amino acids and autophagy downstream of amino acid withdrawal. Biochem Soc Trans 2012; 40:37-43. [PMID: 22260663 DOI: 10.1042/bst20110684] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The simple phosphoinositide PtdIns3P has been shown to control cell growth downstream of amino acid signalling and autophagy downstream of amino acid withdrawal. These opposing effects depend in part on the existence of distinct complexes of Vps34 (vacuolar protein sorting 34), the kinase responsible for the majority of PtdIns3P synthesis in cells: one complex is activated after amino acid withdrawal to induce autophagy and another regulates mTORC1 (mammalian target of rapamycin complex 1) activation when amino acids are present. However, lipid-dependent signalling almost always exhibits a spatial dimension, related to the site of formation of the lipid signal. In the case of PtdIns3P-regulated autophagy induction, recent data suggest that PtdIns3P accumulates in a membrane compartment dynamically connected to the endoplasmic reticulum that constitutes a platform for the formation of some autophagosomes. For PtdIns3P-regulated mTORC1 activity, a spatial context is not yet known: several possibilities can be envisaged based on the known effects of PtdIns3P on the endocytic system and on recent data suggesting that activation of mTORC1 depends on its localization on lysosomes.
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Pexophagy: the selective degradation of peroxisomes. Int J Cell Biol 2012; 2012:512721. [PMID: 22536249 PMCID: PMC3320016 DOI: 10.1155/2012/512721] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2011] [Accepted: 11/23/2011] [Indexed: 12/18/2022] Open
Abstract
Peroxisomes are single-membrane-bounded organelles present in the majority of eukaryotic cells. Despite the existence of great diversity among different species, cell types, and under different environmental conditions, peroxisomes contain enzymes involved in β-oxidation of fatty acids and the generation, as well as detoxification, of hydrogen peroxide. The exigency of all eukaryotic cells to quickly adapt to different environmental factors requires the ability to precisely and efficiently control peroxisome number and functionality. Peroxisome homeostasis is achieved by the counterbalance between organelle biogenesis and degradation. The selective degradation of superfluous or damaged peroxisomes is facilitated by several tightly regulated pathways. The most prominent peroxisome degradation system uses components of the general autophagy core machinery and is therefore referred to as “pexophagy.” In this paper we focus on recent developments in pexophagy and provide an overview of current knowledge and future challenges in the field. We compare different modes of pexophagy and mention shared and distinct features of pexophagy in yeast model systems, mammalian cells, and other organisms.
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Atg14: a key player in orchestrating autophagy. Int J Cell Biol 2011; 2011:713435. [PMID: 22013444 PMCID: PMC3195510 DOI: 10.1155/2011/713435] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 07/28/2011] [Indexed: 01/06/2023] Open
Abstract
Phosphorylation of phosphatidylinositol (PtdIns) by a PtdIns 3-kinase is an essential process in autophagy. Atg14, a specific subunit of one of the PtdIns 3-kinase complexes, targets the complex to the probable site of autophagosome formation, thereby, sorting the complex to function specifically in autophagy. The N-terminal half of Atg14, containing coiled-coil domains, is required to form the PtdIns 3-kinase complex and target it to the proper site. The C-terminal half of yeast Atg14 is suggested to be involved in the formation of a normal-sized autophagosome. The C-terminal half of mammalian Atg14 contains the Barkor/Atg14(L) autophagosome-targeting sequence (BATS) domain that preferentially binds to the highly curved membranes containing PtdIns(3)P and is proposed to target the PtdIns 3-kinase complex efficiently to the isolation membrane. Thus, the N- and C-terminal halves of Atg14 are likely to have an essential core function and a regulatory role, respectively.
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