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Chakraborty S, Nandi P, Mishra J, Niharika, Roy A, Manna S, Baral T, Mishra P, Mishra PK, Patra SK. Molecular mechanisms in regulation of autophagy and apoptosis in view of epigenetic regulation of genes and involvement of liquid-liquid phase separation. Cancer Lett 2024; 587:216779. [PMID: 38458592 DOI: 10.1016/j.canlet.2024.216779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/19/2024] [Accepted: 02/29/2024] [Indexed: 03/10/2024]
Abstract
Cellular physiology is critically regulated by multiple signaling nexuses, among which cell death mechanisms play crucial roles in controlling the homeostatic landscape at the tissue level within an organism. Apoptosis, also known as programmed cell death, can be induced by external and internal stimuli directing the cells to commit suicide in unfavourable conditions. In contrast, stress conditions like nutrient deprivation, infection and hypoxia trigger autophagy, which is lysosome-mediated processing of damaged cellular organelle for recycling of the degraded products, including amino acids. Apparently, apoptosis and autophagy both are catabolic and tumor-suppressive pathways; apoptosis is essential during development and cancer cell death, while autophagy promotes cell survival under stress. Moreover, autophagy plays dual role during cancer development and progression by facilitating the survival of cancer cells under stressed conditions and inducing death in extreme adversity. Despite having two different molecular mechanisms, both apoptosis and autophagy are interconnected by several crosslinking intermediates. Epigenetic modifications, such as DNA methylation, post-translational modification of histone tails, and miRNA play a pivotal role in regulating genes involved in both autophagy and apoptosis. Both autophagic and apoptotic genes can undergo various epigenetic modifications and promote or inhibit these processes under normal and cancerous conditions. Epigenetic modifiers are uniquely important in controlling the signaling pathways regulating autophagy and apoptosis. Therefore, these epigenetic modifiers of both autophagic and apoptotic genes can act as novel therapeutic targets against cancers. Additionally, liquid-liquid phase separation (LLPS) also modulates the aggregation of misfolded proteins and provokes autophagy in the cytosolic environment. This review deals with the molecular mechanisms of both autophagy and apoptosis including crosstalk between them; emphasizing epigenetic regulation, involvement of LLPS therein, and possible therapeutic approaches against cancers.
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Affiliation(s)
- Subhajit Chakraborty
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Piyasa Nandi
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Jagdish Mishra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Niharika
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Ankan Roy
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Soumen Manna
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Tirthankar Baral
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Prahallad Mishra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Pradyumna Kumar Mishra
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bypass Road, Bhauri, Bhopal, 462 030, MP, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India.
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Egebjerg JM, Szomek M, Thaysen K, Juhl AD, Kozakijevic S, Werner S, Pratsch C, Schneider G, Kapishnikov S, Ekman A, Röttger R, Wüstner D. Automated quantification of vacuole fusion and lipophagy in Saccharomyces cerevisiae from fluorescence and cryo-soft X-ray microscopy data using deep learning. Autophagy 2024; 20:902-922. [PMID: 37908116 PMCID: PMC11062380 DOI: 10.1080/15548627.2023.2270378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023] Open
Abstract
During starvation in the yeast Saccharomyces cerevisiae vacuolar vesicles fuse and lipid droplets (LDs) can become internalized into the vacuole in an autophagic process named lipophagy. There is a lack of tools to quantitatively assess starvation-induced vacuole fusion and lipophagy in intact cells with high resolution and throughput. Here, we combine soft X-ray tomography (SXT) with fluorescence microscopy and use a deep-learning computational approach to visualize and quantify these processes in yeast. We focus on yeast homologs of mammalian NPC1 (NPC intracellular cholesterol transporter 1; Ncr1 in yeast) and NPC2 proteins, whose dysfunction leads to Niemann Pick type C (NPC) disease in humans. We developed a convolutional neural network (CNN) model which classifies fully fused versus partially fused vacuoles based on fluorescence images of stained cells. This CNN, named Deep Yeast Fusion Network (DYFNet), revealed that cells lacking Ncr1 (ncr1∆ cells) or Npc2 (npc2∆ cells) have a reduced capacity for vacuole fusion. Using a second CNN model, we implemented a pipeline named LipoSeg to perform automated instance segmentation of LDs and vacuoles from high-resolution reconstructions of X-ray tomograms. From that, we obtained 3D renderings of LDs inside and outside of the vacuole in a fully automated manner and additionally measured droplet volume, number, and distribution. We find that ncr1∆ and npc2∆ cells could ingest LDs into vacuoles normally but showed compromised degradation of LDs and accumulation of lipid vesicles inside vacuoles. Our new method is versatile and allows for analysis of vacuole fusion, droplet size and lipophagy in intact cells.Abbreviations: BODIPY493/503: 4,4-difluoro-1,3,5,7,8-pentamethyl-4-bora-3a,4a-diaza-s-Indacene; BPS: bathophenanthrolinedisulfonic acid disodium salt hydrate; CNN: convolutional neural network; DHE; dehydroergosterol; npc2∆, yeast deficient in Npc2; DSC, Dice similarity coefficient; EM, electron microscopy; EVs, extracellular vesicles; FIB-SEM, focused ion beam milling-scanning electron microscopy; FM 4-64, N-(3-triethylammoniumpropyl)-4-(6-[4-{diethylamino} phenyl] hexatrienyl)-pyridinium dibromide; LDs, lipid droplets; Ncr1, yeast homolog of human NPC1 protein; ncr1∆, yeast deficient in Ncr1; NPC, Niemann Pick type C; NPC2, Niemann Pick type C homolog; OD600, optical density at 600 nm; ReLU, rectifier linear unit; PPV, positive predictive value; NPV, negative predictive value; MCC, Matthews correlation coefficient; SXT, soft X-ray tomography; UV, ultraviolet; YPD, yeast extract peptone dextrose.
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Affiliation(s)
- Jacob Marcus Egebjerg
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense M, Denmark
| | - Maria Szomek
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Katja Thaysen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Alice Dupont Juhl
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Suzana Kozakijevic
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Stephan Werner
- Department of X‑Ray Microscopy, Helmholtz-Zentrum Berlin, Germany and Humboldt-Universität zu Berlin, Institut für Physik, Berlin, Germany
| | - Christoph Pratsch
- Department of X‑Ray Microscopy, Helmholtz-Zentrum Berlin, Germany and Humboldt-Universität zu Berlin, Institut für Physik, Berlin, Germany
| | - Gerd Schneider
- Department of X‑Ray Microscopy, Helmholtz-Zentrum Berlin, Germany and Humboldt-Universität zu Berlin, Institut für Physik, Berlin, Germany
| | - Sergey Kapishnikov
- SiriusXT, 9A Holly Ave. Stillorgan Industrial Park, Blackrock, Co, Dublin, Ireland
| | - Axel Ekman
- Department of Biological and Environmental Science and Nanoscience Centre, University of Jyväskylä, Jyväskylä, Finland
| | - Richard Röttger
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense M, Denmark
| | - Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
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Sakai Y, Oku M. ATG and ESCRT control multiple modes of microautophagy. FEBS Lett 2024; 598:48-58. [PMID: 37857501 DOI: 10.1002/1873-3468.14760] [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: 07/20/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 10/21/2023]
Abstract
The discovery of microautophagy, the direct engulfment of cytoplasmic material by the lysosome, dates back to 1966 in a morphological study of mammalian cells by Christian de Duve. Since then, studies on microautophagy have shifted toward the elucidation of the physiological significance of the process. However, in contrast to macroautophagy, studies on the molecular mechanisms of microautophagy have been limited. Only recent studies revealed that ATG proteins involved in macroautophagy are also operative in several types of microautophagy and that ESCRT proteins, responsible for the multivesicular body pathway, play a central role in most microautophagy processes. In this review, we summarize our current knowledge on the function of ATG and ESCRT proteins in microautophagy.
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Affiliation(s)
- Yasuyoshi Sakai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Japan
| | - Masahide Oku
- Department of Bioscience and Biotechnology, Faculty of Bioenvironmental Sciences, Kyoto University of Advanced Science, Kameoka, Japan
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Kuchitsu Y, Taguchi T. Lysosomal microautophagy: an emerging dimension in mammalian autophagy. Trends Cell Biol 2023:S0962-8924(23)00238-6. [PMID: 38104013 DOI: 10.1016/j.tcb.2023.11.005] [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: 08/23/2023] [Revised: 11/08/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023]
Abstract
Autophagy is a self-catabolic process through which cellular components are delivered to lysosomes for degradation. There are three types of autophagy, i.e., macroautophagy, chaperone-mediated autophagy (CMA), and microautophagy. In macroautophagy, a portion of the cytoplasm is wrapped by the autophagosome, which then fuses with lysosomes and delivers the engulfed cytoplasm for degradation. In CMA, the translocation of cytosolic substrates to the lysosomal lumen is directly across the limiting membrane of lysosomes. In microautophagy, lytic organelles, including endosomes or lysosomes, take up a portion of the cytoplasm directly. Although macroautophagy has been investigated extensively, microautophagy has received much less attention. Nonetheless, it has become evident that microautophagy plays a variety of cellular roles from yeast to mammals. Here we review the very recent updates of microautophagy. In particular, we focus on the feature of the degradative substrates and the molecular machinery that mediates microautophagy.
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Affiliation(s)
- Yoshihiko Kuchitsu
- Laboratory of Organelle Pathophysiology, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
| | - Tomohiko Taguchi
- Laboratory of Organelle Pathophysiology, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
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Tian R, Yuan L, Huang Y, Zhang R, Lyu H, Xiao S, Guo D, Ali DW, Michalak M, Chen XZ, Zhou C, Tang J. Perturbed autophagy intervenes systemic lupus erythematosus by active ingredients of traditional Chinese medicine. Front Pharmacol 2023; 13:1053602. [PMID: 36733375 PMCID: PMC9887156 DOI: 10.3389/fphar.2022.1053602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/05/2022] [Indexed: 01/19/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is a common multisystem, multiorgan heterozygous autoimmune disease. The main pathological features of the disease are autoantibody production and immune complex deposition. Autophagy is an important mechanism to maintain cell homeostasis. Autophagy functional abnormalities lead to the accumulation of apoptosis and induce the autoantibodies that result in immune disorders. Therefore, improving autophagy may alleviate the development of SLE. For SLE, glucocorticoids or immunosuppressive agents are commonly used in clinical treatment, but long-term use of these drugs causes serious side effects in humans. Immunosuppressive agents are expensive. Traditional Chinese medicines (TCMs) are widely used for immune diseases due to their low toxicity and few side effects. Many recent studies found that TCM and its active ingredients affected the pathological development of SLE by regulating autophagy. This article explains how autophagy interferes with immune system homeostasis and participates in the occurrence and development of SLE. It also summarizes several studies on TCM-regulated autophagy intervention in SLE to generate new ideas for basic research, the development of novel medications, and the clinical treatment of SLE.
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Affiliation(s)
- Rui Tian
- National “111’’ Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education and Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China,Membrane Protein Disease Research Group, Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada,College of Biological Science and Technology, Hubei MinZu University, Enshi, China
| | - Lin Yuan
- Hubei Provincial Key Laboratory of Occurrence and Intervention of Rheumatic Diseases, Enshi, China
| | - Yuan Huang
- National “111’’ Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education and Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Rui Zhang
- National “111’’ Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education and Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Hao Lyu
- National “111’’ Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education and Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Shuai Xiao
- National “111’’ Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education and Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Dong Guo
- National “111’’ Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education and Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Declan William Ali
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Marek Michalak
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Xing-Zhen Chen
- Membrane Protein Disease Research Group, Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada,*Correspondence: Xing-Zhen Chen, ; Cefan Zhou, ; Jingfeng Tang,
| | - Cefan Zhou
- National “111’’ Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education and Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China,*Correspondence: Xing-Zhen Chen, ; Cefan Zhou, ; Jingfeng Tang,
| | - Jingfeng Tang
- National “111’’ Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education and Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China,Lead Contact, Wuhan, China,*Correspondence: Xing-Zhen Chen, ; Cefan Zhou, ; Jingfeng Tang,
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Yin Y, Zhou Y, Yang X, Xu Z, Yang B, Luo P, Yan H, He Q. The participation of non-canonical autophagic proteins in the autophagy process and their potential as therapeutic targets. Expert Opin Ther Targets 2023; 27:71-86. [PMID: 36735300 DOI: 10.1080/14728222.2023.2177151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
INTRODUCTION Autophagy is a conserved catabolic process that helps recycle intracellular components to maintain homeostasis. The completion of autophagy requires the synergistic effect of multiple canonical autophagic proteins. Defects in autophagy machinery have been reported to promote diseases, rendering autophagy a bone fide health-modifying agent. However, the clinical implication of canonical pan-autophagic activators or inhibitors has often led to undesirable side effects, making it urgent to find a safer autophagy-related therapeutic target. The discovery of non-canonical autophagic proteins has been found to specifically affect the development of diseases without causing a universal impact on autophagy and has shed light on finding a safer way to utilize autophagy in the therapeutic context. AREAS COVERED This review summarizes recently discovered non-canonical autophagic proteins, how these proteins influence autophagy, and their potential therapeutic role in the disease due to their interaction with autophagy. EXPERT OPINION Several therapies have been studied thus far and continued research is needed to identify the potential that non-canonical autophagic proteins have for treating certain diseases. In the meantime, continue to uncover new non-canonical autophagic proteins and examine which are likely to have therapeutic implications.
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Affiliation(s)
- Yiming Yin
- College of Pharmaceutical Sciences, Center for Drug Safety Evaluation and Research of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yourong Zhou
- College of Pharmaceutical Sciences, Center for Drug Safety Evaluation and Research of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaochun Yang
- College of Pharmaceutical Sciences, Center for Drug Safety Evaluation and Research of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhifei Xu
- College of Pharmaceutical Sciences, Center for Drug Safety Evaluation and Research of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang, China
| | - Bo Yang
- Institute of Pharmacology & Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Peihua Luo
- College of Pharmaceutical Sciences, Center for Drug Safety Evaluation and Research of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Pharmacology and Toxicology, Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hao Yan
- College of Pharmaceutical Sciences, Center for Drug Safety Evaluation and Research of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qiaojun He
- College of Pharmaceutical Sciences, Center for Drug Safety Evaluation and Research of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang, China.,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, Zhejiang, China
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Gómez-Virgilio L, Silva-Lucero MDC, Flores-Morelos DS, Gallardo-Nieto J, Lopez-Toledo G, Abarca-Fernandez AM, Zacapala-Gómez AE, Luna-Muñoz J, Montiel-Sosa F, Soto-Rojas LO, Pacheco-Herrero M, Cardenas-Aguayo MDC. Autophagy: A Key Regulator of Homeostasis and Disease: An Overview of Molecular Mechanisms and Modulators. Cells 2022; 11:cells11152262. [PMID: 35892559 PMCID: PMC9329718 DOI: 10.3390/cells11152262] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 01/18/2023] Open
Abstract
Autophagy is a highly conserved lysosomal degradation pathway active at basal levels in all cells. However, under stress conditions, such as a lack of nutrients or trophic factors, it works as a survival mechanism that allows the generation of metabolic precursors for the proper functioning of the cells until the nutrients are available. Neurons, as post-mitotic cells, depend largely on autophagy to maintain cell homeostasis to get rid of damaged and/or old organelles and misfolded or aggregated proteins. Therefore, the dysfunction of this process contributes to the pathologies of many human diseases. Furthermore, autophagy is highly active during differentiation and development. In this review, we describe the current knowledge of the different pathways, molecular mechanisms, factors that induce it, and the regulation of mammalian autophagy. We also discuss its relevant role in development and disease. Finally, here we summarize several investigations demonstrating that autophagic abnormalities have been considered the underlying reasons for many human diseases, including liver disease, cardiovascular, cerebrovascular diseases, neurodegenerative diseases, neoplastic diseases, cancers, and, more recently, infectious diseases, such as SARS-CoV-2 caused COVID-19 disease.
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Affiliation(s)
- Laura Gómez-Virgilio
- Laboratory of Cellular Reprogramming, Departamento de Fisiología, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City 04510, Mexico; (L.G.-V.); (M.-d.-C.S.-L.); (D.-S.F.-M.); (J.G.-N.); (G.L.-T.); (A.-M.A.-F.)
| | - Maria-del-Carmen Silva-Lucero
- Laboratory of Cellular Reprogramming, Departamento de Fisiología, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City 04510, Mexico; (L.G.-V.); (M.-d.-C.S.-L.); (D.-S.F.-M.); (J.G.-N.); (G.L.-T.); (A.-M.A.-F.)
| | - Diego-Salvador Flores-Morelos
- Laboratory of Cellular Reprogramming, Departamento de Fisiología, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City 04510, Mexico; (L.G.-V.); (M.-d.-C.S.-L.); (D.-S.F.-M.); (J.G.-N.); (G.L.-T.); (A.-M.A.-F.)
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39070, Guerrero, Mexico;
| | - Jazmin Gallardo-Nieto
- Laboratory of Cellular Reprogramming, Departamento de Fisiología, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City 04510, Mexico; (L.G.-V.); (M.-d.-C.S.-L.); (D.-S.F.-M.); (J.G.-N.); (G.L.-T.); (A.-M.A.-F.)
- Biotechnology Engeniering, Universidad Politécnica de Quintana Roo, Cancún 77500, Quintana Roo, Mexico
| | - Gustavo Lopez-Toledo
- Laboratory of Cellular Reprogramming, Departamento de Fisiología, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City 04510, Mexico; (L.G.-V.); (M.-d.-C.S.-L.); (D.-S.F.-M.); (J.G.-N.); (G.L.-T.); (A.-M.A.-F.)
| | - Arminda-Mercedes Abarca-Fernandez
- Laboratory of Cellular Reprogramming, Departamento de Fisiología, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City 04510, Mexico; (L.G.-V.); (M.-d.-C.S.-L.); (D.-S.F.-M.); (J.G.-N.); (G.L.-T.); (A.-M.A.-F.)
- Biotechnology Engeniering, Universidad Politécnica de Quintana Roo, Cancún 77500, Quintana Roo, Mexico
| | - Ana-Elvira Zacapala-Gómez
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39070, Guerrero, Mexico;
| | - José Luna-Muñoz
- National Dementia BioBank, Ciencias Biológicas, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlan Izcalli 53150, Estado de México, Mexico; (J.L.-M.); (F.M.-S.)
- Banco Nacional de Cerebros-UNPHU, Universidad Nacional Pedro Henríquez Ureña, Santo Domingo 11805, Dominican Republic
| | - Francisco Montiel-Sosa
- National Dementia BioBank, Ciencias Biológicas, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlan Izcalli 53150, Estado de México, Mexico; (J.L.-M.); (F.M.-S.)
| | - Luis O. Soto-Rojas
- Laboratorio de Patogénesis Molecular, Laboratorio 4, Edificio A4, Carrera Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Estado de México, Mexico;
- Red MEDICI, Carrera Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Estado de México, Mexico
| | - Mar Pacheco-Herrero
- Neuroscience Research Laboratory, Faculty of Health Sciences, Pontificia Universidad Católica Madre y Maestra, Santiago de los Caballeros 51000, Dominican Republic;
| | - Maria-del-Carmen Cardenas-Aguayo
- Laboratory of Cellular Reprogramming, Departamento de Fisiología, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City 04510, Mexico; (L.G.-V.); (M.-d.-C.S.-L.); (D.-S.F.-M.); (J.G.-N.); (G.L.-T.); (A.-M.A.-F.)
- Correspondence: ; Tel.: +52-55-2907-0937
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Cell Autophagy in NASH and NASH-Related Hepatocellular Carcinoma. Int J Mol Sci 2022; 23:ijms23147734. [PMID: 35887082 PMCID: PMC9322157 DOI: 10.3390/ijms23147734] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/10/2022] [Accepted: 07/11/2022] [Indexed: 12/21/2022] Open
Abstract
Autophagy, a cellular self-digestion process, involves the degradation of targeted cell components such as damaged organelles, unfolded proteins, and intracellular pathogens by lysosomes. It is a major quality control system of the cell and plays an important role in cell differentiation, survival, development, and homeostasis. Alterations in the cell autophagic machinery have been implicated in several disease conditions, including neurodegeneration, autoimmunity, cancer, infection, inflammatory diseases, and aging. In non-alcoholic fatty liver disease, including its inflammatory form, non-alcoholic steatohepatitis (NASH), a decrease in cell autophagic activity, has been implicated in the initial development and progression of steatosis to NASH and hepatocellular carcinoma (HCC). We present an overview of autophagy as it occurs in mammalian cells with an insight into the emerging understanding of the role of autophagy in NASH and NASH-related HCC.
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Takuma T, Ushimaru T. Vacuolar fragmentation promotes fluxes of microautophagy and micronucleophagy but not of macroautophagy. Biochem Biophys Res Commun 2022; 614:161-168. [PMID: 35597153 DOI: 10.1016/j.bbrc.2022.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/07/2022] [Indexed: 11/17/2022]
Abstract
Vacuoles and lysosomes are organelles involved in the degradation of cytoplasmic proteins and organelles. Vacuolar morphology is dynamically regulated by fission and fusion in budding yeast. Vacuolar fusion is elicited in nutrient-depleted conditions and mediated by inactivation of target of rapamycin complex 1 (TORC1) protein kinase. However, it is unknown whether and how vacuolar morphology affects macroautophagy and microautophagy, which are induced by nutrient starvation and TORC1 inactivation. Here, we developed a system to control vacuolar fission in budding yeast. Vacuolar fragmentation promoted microautophagy but not macroautophagy. Vacuolar fragmentation caused multiple nucleus-vacuole junctions. Multiple vacuoles caused by vacuolar fragmentation also improved micronucleophagy (microautophagic degradation of a portion of the nucleus). However, vacuolar morphology did not impact nucleolar remodeling, condensation of the rDNA (rRNA gene) region, or separation of ribosomal DNA from nucleolar proteins, which is evoked by TORC1 inactivation. Thus, this study provides insights into the impacts of vacuolar/lysosomal morphology on macroautophagy and microautophagy.
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Affiliation(s)
- Tsuneyuki Takuma
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan
| | - Takashi Ushimaru
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan; Research Institute of Green Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan.
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10
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Ding X, Zhang X, Paez-Valencia J, McLoughlin F, Reyes FC, Morohashi K, Grotewold E, Vierstra RD, Otegui MS. Microautophagy Mediates Vacuolar Delivery of Storage Proteins in Maize Aleurone Cells. FRONTIERS IN PLANT SCIENCE 2022; 13:833612. [PMID: 35251104 PMCID: PMC8894768 DOI: 10.3389/fpls.2022.833612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
The molecular machinery orchestrating microautophagy, whereby eukaryotic cells sequester autophagic cargo by direct invagination of the vacuolar/lysosomal membrane, is still largely unknown, especially in plants. Here, we demonstrate microautophagy of storage proteins in the maize aleurone cells of the endosperm and analyzed proteins with potential regulatory roles in this process. Within the cereal endosperm, starchy endosperm cells accumulate storage proteins (mostly prolamins) and starch whereas the peripheral aleurone cells store oils, storage proteins, and specialized metabolites. Although both cell types synthesize prolamins, they employ different pathways for their subcellular trafficking. Starchy endosperm cells accumulate prolamins in protein bodies within the endoplasmic reticulum (ER), whereas aleurone cells deliver prolamins to vacuoles via an autophagic mechanism, which we show is by direct association of ER prolamin bodies with the tonoplast followed by engulfment via microautophagy. To identify candidate proteins regulating this process, we performed RNA-seq transcriptomic comparisons of aleurone and starchy endosperm tissues during seed development and proteomic analysis on tonoplast-enriched fractions of aleurone cells. From these datasets, we identified 10 candidate proteins with potential roles in membrane modification and/or microautophagy, including phospholipase-Dα5 and a possible EUL-like lectin. We found that both proteins increased the frequency of tonoplast invaginations when overexpressed in Arabidopsis leaf protoplasts and are highly enriched at the tonoplast surface surrounding ER protein bodies in maize aleurone cells, thus supporting their potential connections to microautophagy. Collectively, this candidate list now provides useful tools to study microautophagy in plants.
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Affiliation(s)
- Xinxin Ding
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States
| | - Xiaoguo Zhang
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States
| | - Julio Paez-Valencia
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States
| | - Fionn McLoughlin
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Francisca C. Reyes
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
| | - Kengo Morohashi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Richard D. Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Marisa S. Otegui
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States
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11
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Tasnin MN, Ito K, Katsuta H, Takuma T, Sharmin T, Ushimaru T. The PI3 Kinase Complex II-PI3P-Vps27 Axis on Vacuolar Membranes is Critical for Microautophagy Induction and Nutrient Stress Adaptation. J Mol Biol 2021; 434:167360. [PMID: 34798133 DOI: 10.1016/j.jmb.2021.167360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 12/27/2022]
Abstract
Phosphatidylinositol 3-phosphate (PI3P), a scaffold of membrane-associated proteins required for diverse cellular events, is produced by Vps34-containing phosphatidylinositol 3-kinase (PI3K). PI3K complex I (PI3KCI)-generated PI3P is required for macroautophagy, whereas PI3K complex II (PI3KCII)-generated PI3P is required for endosomal sorting complex required for transport (ESCRT)-mediated multi-vesicular body (MVB) formation in late endosomes. ESCRT also promotes vacuolar membrane remodeling in microautophagy after nutrient starvation and inactivation of target of rapamycin complex 1 (TORC1) protein kinase in budding yeast. Whereas PI3KCI and macroautophagy are critical for the nutrient starvation response, the physiological roles of PI3KCII and microautophagy during starvation are largely unknown. Here, we showed that PI3KCII-produced PI3P on vacuolar membranes is required for microautophagy induction and survival in nutrient-stressed conditions. PI3KCII is required for Vps27 (an ESCRT-0 component) recruitment and ESCRT-0 complex formation on vacuolar surfaces after TORC1 inactivation. Forced recruitment of Vps27 onto vacuolar membranes rescued the defect in microautophagy induction in PI3KCII-deficient cells, indicating that a critical role of PI3P on microautophagy induction is Vps27 recruitment onto vacuolar surfaces. Finally, vacuolar membrane-associated Vps27 was able to recover survival during nutrient starvation in cells lacking PI3KCII or Vps27. This study revealed that the PI3KCII-PI3P-Vps27 axis on vacuolar membranes is critical for ESCRT-mediated microautophagy induction and nutrient stress adaptation.
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Affiliation(s)
- Most Naoshia Tasnin
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Kisara Ito
- Department of Bioscience, Faculty of Science, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Haruko Katsuta
- Course of Biological Science, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Tsuneyuki Takuma
- Course of Biological Science, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Tasnuva Sharmin
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Takashi Ushimaru
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan; Department of Bioscience, Faculty of Science, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan; Course of Biological Science, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan.
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12
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Robert G, Yagyu M, Lascano HR, Masclaux-Daubresse C, Yoshimoto K. A proposed role for endomembrane trafficking processes in regulating tonoplast content and vacuole dynamics under ammonium stress conditions in Arabidopsis root cells. PLANT SIGNALING & BEHAVIOR 2021; 16:1924977. [PMID: 33955336 PMCID: PMC8280891 DOI: 10.1080/15592324.2021.1924977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
Ammonium (NH4+) stress has multiple effects on plant physiology, therefore, plant responses are complex, and multiple mechanisms are involved in NH4+ sensitivity and tolerance in plants. Root growth inhibition is an important quantitative readout of the effects of NH4+ stress on plant physiology, and cell elongation appear as the principal growth inhibition target. We recently proposed autophagy as a relevant physiological mechanisms underlying NH4+ sensitivity response in Arabidopsis. In a brief overview, the impaired macro-autophagic flux observed under NH4+ stress conditions has a detrimental impact on the cellular energetic balance, and therefore on the energy-demanding plant growth. In contrast to its inhibitory effect on the autophagosomes flux to vacuole, NH4+ toxicity induced a micro-autophagy-like process. Consistent with the reduced membrane flux to the vacuole related to macro-autophagy inhibition and the increased tonoplast degradation due to enhanced micro-autophagy, the vacuoles of the root cells of the NH4+-stressed plants showed lower tonoplast content and a decreased perimeter/area ratio. As the endosome-to-vacuole trafficking is another important process that contributes to membrane flux toward the vacuole, we evaluated the effects of NH4+ stress on this process. This allows us to propose that autophagy could contribute to vacuole development as well as possible avenues to follow for future studies.
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Affiliation(s)
- Germán Robert
- Plant Stress Biology Group, Unidad de Doble Dependencia INTA-CONICET (UDEA), Córdoba, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV), Córdoba, Argentina
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Mako Yagyu
- Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa, Japan
| | - Hernán Ramiro Lascano
- Plant Stress Biology Group, Unidad de Doble Dependencia INTA-CONICET (UDEA), Córdoba, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV), Córdoba, Argentina
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | | | - Kohki Yoshimoto
- Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa, Japan
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13
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Zhang X, Deibert CP, Kim WJ, Jaman E, Rao AV, Lotze MT, Amankulor NM. Autophagy inhibition is the next step in the treatment of glioblastoma patients following the Stupp era. Cancer Gene Ther 2021; 28:971-983. [PMID: 32759988 DOI: 10.1038/s41417-020-0205-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 01/30/2023]
Abstract
It has now been nearly 15 years since the last major advance in the treatment of patients with glioma. "The addition of temozolomide to radiotherapy for newly diagnosed glioblastoma resulted in a clinically meaningful and statistically significant survival benefit with minimal additional toxicity". Autophagy is primarily a survival pathway, literally self-eating, that is utilized in response to stress (such as radiation and chemotherapy), enabling clearance of effete protein aggregates and multimolecular assemblies. Promising results have been observed in patients with glioma for over a decade now when autophagy inhibition with chloroquine derivatives coupled with conventional therapy. The application of autophagy inhibitors, the role of immune cell-induced autophagy, and the potential role of novel cellular and gene therapies, should now be considered for development as part of this well-established regimen.
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Affiliation(s)
- Xiaoran Zhang
- Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Christopher P Deibert
- Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Wi-Jin Kim
- Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Emade Jaman
- Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Aparna V Rao
- Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Michael T Lotze
- Department of Surgery, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Nduka M Amankulor
- Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
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14
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Rahman MA, Kumar R, Sanchez E, Nazarko TY. Lipid Droplets and Their Autophagic Turnover via the Raft-Like Vacuolar Microdomains. Int J Mol Sci 2021; 22:8144. [PMID: 34360917 PMCID: PMC8348048 DOI: 10.3390/ijms22158144] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 01/01/2023] Open
Abstract
Although once perceived as inert structures that merely serve for lipid storage, lipid droplets (LDs) have proven to be the dynamic organelles that hold many cellular functions. The LDs' basic structure of a hydrophobic core consisting of neutral lipids and enclosed in a phospholipid monolayer allows for quick lipid accessibility for intracellular energy and membrane production. Whereas formed at the peripheral and perinuclear endoplasmic reticulum, LDs are degraded either in the cytosol by lipolysis or in the vacuoles/lysosomes by autophagy. Autophagy is a regulated breakdown of dysfunctional, damaged, or surplus cellular components. The selective autophagy of LDs is called lipophagy. Here, we review LDs and their degradation by lipophagy in yeast, which proceeds via the micrometer-scale raft-like lipid domains in the vacuolar membrane. These vacuolar microdomains form during nutrient deprivation and facilitate internalization of LDs via the vacuolar membrane invagination and scission. The resultant intra-vacuolar autophagic bodies with LDs inside are broken down by vacuolar lipases and proteases. This type of lipophagy is called microlipophagy as it resembles microautophagy, the type of autophagy when substrates are sequestered right at the surface of a lytic compartment. Yeast microlipophagy via the raft-like vacuolar microdomains is a great model system to study the role of lipid domains in microautophagic pathways.
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Affiliation(s)
- Muhammad Arifur Rahman
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (M.A.R.); (E.S.)
| | - Ravinder Kumar
- Department of Obstetrics, Gynecology and Reproductive Science, University of California, San Francisco, CA 94143, USA;
| | - Enrique Sanchez
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (M.A.R.); (E.S.)
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Taras Y. Nazarko
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (M.A.R.); (E.S.)
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15
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Lemus L, Matić Z, Gal L, Fadel A, Schuldiner M, Goder V. Post-ER degradation of misfolded GPI-anchored proteins is linked with microautophagy. Curr Biol 2021; 31:4025-4037.e5. [PMID: 34314677 DOI: 10.1016/j.cub.2021.06.078] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/07/2021] [Accepted: 06/25/2021] [Indexed: 01/08/2023]
Abstract
Glycosylphosphatidylinositol-anchored proteins (GPI-APs) are membrane-conjugated cell-surface proteins with diverse structural, developmental, and signaling functions and clinical relevance. Typically, after biosynthesis and attachment to the preassembled GPI anchor, GPI-APs rapidly leave the endoplasmic reticulum (ER) and rely on post-ER quality control. Terminally misfolded GPI-APs end up inside the vacuole/lysosome for degradation, but their trafficking itinerary to this organelle and the processes linked to their uptake by the vacuole/lysosome remain uncharacterized. In a yeast mutant that is lacking Pep4, a key vacuolar protease, several misfolded model GPI-APs accumulated in the vacuolar membrane. In the same mutant, macroautophagy and the multi-vesicular body (MVB) pathway were intact, hinting at a hitherto-unknown trafficking pathway for the degradation of misfolded GPI-APs. To unravel it, we used a genome-wide screen coupled to high-throughput fluorescence microscopy and followed the fate of the misfolded GPI-AP: Gas1∗. We found that components of the early secretory and endocytic pathways are involved in its targeting to the vacuole and that vacuolar transporter chaperones (VTCs), with roles in microautophagy, negatively affect the vacuolar uptake of Gas1∗. In support, we demonstrate that Gas1∗ internalizes from vacuolar membranes into membrane-bound intravacuolar vesicles prior to degradation. Our data link post-ER degradation with microautophagy.
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Affiliation(s)
- Leticia Lemus
- Department of Genetics, University of Seville, Ave Reina Mercedes, 6, 41012 Seville, Spain.
| | - Zrinka Matić
- Department of Genetics, University of Seville, Ave Reina Mercedes, 6, 41012 Seville, Spain
| | - Lihi Gal
- Department of Molecular Genetics, Meyer Bldg. Room 122, Weizmann Institute of Sciences, 76100 Rehovot, Israel
| | - Amir Fadel
- Department of Molecular Genetics, Meyer Bldg. Room 122, Weizmann Institute of Sciences, 76100 Rehovot, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Meyer Bldg. Room 122, Weizmann Institute of Sciences, 76100 Rehovot, Israel
| | - Veit Goder
- Department of Genetics, University of Seville, Ave Reina Mercedes, 6, 41012 Seville, Spain.
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16
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Sharmin T, Morshed S, Tasnin MN, Takuma T, Ushimaru T. Cdc14 phosphatase downmodulates ESCRT-0 complex formation on vacuolar membranes and microautophagy after TORC1 inactivation. Biochem Biophys Res Commun 2021; 561:158-164. [PMID: 34023781 DOI: 10.1016/j.bbrc.2021.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 05/08/2021] [Indexed: 11/19/2022]
Abstract
Remodeling of vacuolar membranes mediated by endosomal sorting complex required for transport (ESCRT) is critical for microautophagy induction in budding yeast. Nutrient depletion and inactivation of target of rapamycin complex 1 (TORC1) protein kinase elicit recruitment of the ESCRT-0 complex (Vps27-Hse1) onto vacuolar membranes and ESCRT-mediated microautophagy induction. Mitotic protein phosphatase Cdc14 antagonizes TORC1-mediated phosphorylation in macroautophagy induction after nutrient starvation and TORC1 inactivation. Here, we report that Cdc14 downregulates microautophagy induction after TORC1 inactivation. Cdc14 dysfunction stimulated the vacuolar membrane recruitment of Hse1, but not Vps27, after TORC1 inactivation, promoting ESCRT-0 complex formation. Conversely, overexpression of CDC14 compromises Hse1 recruitment on vacuolar membranes and microautophagy induction after TORC1 inactivation. Thus, Cdc14 phosphatase regulates the fluxes of two types of autophagy in the opposite directions, namely, it elicits macroautophagy and attenuates microautophagy.
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Affiliation(s)
- Tasnuva Sharmin
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan
| | - Shamsul Morshed
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan
| | - Most Naoshia Tasnin
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan
| | - Tsuneyuki Takuma
- Course of Bioscience, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan
| | - Takashi Ushimaru
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan; Course of Bioscience, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan.
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17
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Kaur S, Sharma N, Kapoor P, Chunduri V, Pandey AK, Garg M. Spotlight on the overlapping routes and partners for anthocyanin transport in plants. PHYSIOLOGIA PLANTARUM 2021; 171:868-881. [PMID: 33639001 DOI: 10.1111/ppl.13378] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 02/12/2021] [Accepted: 02/26/2021] [Indexed: 05/27/2023]
Abstract
Secondary metabolites are produced by plants and are classified based on their chemical structure or the biosynthetic routes through which they are synthesized. Among them, flavonoids, including anthocyanins and pro-anthocyanidins (PAs), are abundant in leaves, flowers, fruits, and seed coats in plants. The anthocyanin biosynthetic pathway has been intensively studied, but the molecular mechanism of anthocyanin transport from the synthesis site to the storage site needs attention. Although the major transporters are well defined yet, the redundancy of these transporters for structurally similar or dis-similar anthocyanins motivates additional research. Herein, we reviewed the role of membrane transporters involved in anthocyanin transport, including ATP-binding cassette, multidrug and toxic compound extrusion (MATE), Bilitranslocase-homolog (BTL), and vesicle-mediated transport. We also highlight the ability of transporters to cater distinct anthocyanins or their chemically-modified forms with overlapping transport mechanisms and sequestration into the vacuoles. Our understanding of the anthocyanin transporters could provide anthocyanin-rich crops and fruits with a benefit on human health at a large scale.
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Affiliation(s)
- Satveer Kaur
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
| | - Natasha Sharma
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
| | - Payal Kapoor
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
| | - Venkatesh Chunduri
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
| | - Ajay K Pandey
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
| | - Monika Garg
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Mohali, India
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18
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Robert G, Yagyu M, Koizumi T, Naya L, Masclaux-Daubresse C, Yoshimoto K. Ammonium stress increases microautophagic activity while impairing macroautophagic flux in Arabidopsis roots. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1083-1097. [PMID: 33222335 DOI: 10.1111/tpj.15091] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 06/11/2023]
Abstract
Plant responses to NH4+ stress are complex, and multiple mechanisms underlying NH4+ sensitivity and tolerance in plants may be involved. Here, we demonstrate that macro- and microautophagic activities are oppositely affected in plants grown under NH4+ toxicity conditions. When grown under NH4+ stress conditions, macroautophagic activity was impaired in roots. Root cells accumulated autophagosomes in the cytoplasm, but showed less autophagic flux, indicating that late steps of the macroautophagy process are affected under NH4+ stress conditions. Under this scenario, we also found that the CCZ1-MON1 complex, a critical factor for vacuole delivery pathways, functions in the late step of the macroautophagic pathway in Arabidopsis. In contrast, an accumulation of tonoplast-derived vesicles was observed in vacuolar lumens of root cells of NH4+ -stressed plants, suggesting the induction of a microautophagy-like process. In this sense, some SYP22-, but mainly VAMP711-positive vesicles were observed inside vacuole in roots of NH4+ -stressed plants. Consistent with the increased tonoplast degradation and the reduced membrane flow to the vacuole due to the impaired macroautophagic flux, the vacuoles of root cells of NH4+ -stressed plants showed a simplified structure and lower tonoplast content. Taken together, this study presents evidence that postulates late steps of the macroautophagic process as a relevant physiological mechanism underlying the NH4+ sensitivity response in Arabidopsis, and additionally provides insights into the molecular tools for studying microautophagy in plants.
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Affiliation(s)
- Germán Robert
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
- Instituto Nacional de Tecnología Agropecuaria (INTA) - Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV), Av. 11 de Septiembre, Córdoba, 4755-X5020ICA, Argentina
- Unidad de doble dependencia INTA-CONICET (UDEA), Av. 11 de Septiembre, Córdoba, 4755-X5020ICA, Argentina
| | - Mako Yagyu
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki-shi, Kanagawa, 214-8571, Japan
| | - Takaya Koizumi
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki-shi, Kanagawa, 214-8571, Japan
| | - Loreto Naya
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Céline Masclaux-Daubresse
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Kohki Yoshimoto
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki-shi, Kanagawa, 214-8571, Japan
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19
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Wildburger NC, Hartke AS, Schidlitzki A, Richter F. Current Evidence for a Bidirectional Loop Between the Lysosome and Alpha-Synuclein Proteoforms. Front Cell Dev Biol 2020; 8:598446. [PMID: 33282874 PMCID: PMC7705175 DOI: 10.3389/fcell.2020.598446] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/28/2020] [Indexed: 12/28/2022] Open
Abstract
Cumulative evidence collected in recent decades suggests that lysosomal dysfunction contributes to neurodegenerative diseases, especially if amyloid proteins are involved. Among these, alpha-synuclein (aSyn) that progressively accumulates and aggregates in Lewy bodies is undisputedly a main culprit in Parkinson disease (PD) pathogenesis. Lysosomal dysfunction is evident in brains of PD patients, and mutations in lysosomal enzymes are a major risk factor of PD. At first glance, the role of protein-degrading lysosomes in a disease with pathological protein accumulation seems obvious and should guide the development of straightforward and rational therapeutic targets. However, our review demonstrates that the story is more complicated for aSyn. The protein can possess diverse posttranslational modifications, aggregate formations, and truncations, all of which contribute to a growing known set of proteoforms. These interfere directly or indirectly with lysosome function, reducing their own degradation, and thereby accelerating the protein aggregation and disease process. Conversely, unbalanced lysosomal enzymatic processes can produce truncated aSyn proteoforms that may be more toxic and prone to aggregation. This highlights the possibility of enhancing lysosomal function as a treatment for PD, if it can be confirmed that this approach effectively reduces harmful aSyn proteoforms and does not produce novel, toxic proteoforms.
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Affiliation(s)
- Norelle C Wildburger
- Department of Pharmacology, Toxicology, and Pharmacy, University of Veterinary Medicine, Hanover, Germany.,Center for Systems Neuroscience, Hanover, Germany
| | - Anna-Sophia Hartke
- Department of Pharmacology, Toxicology, and Pharmacy, University of Veterinary Medicine, Hanover, Germany
| | - Alina Schidlitzki
- Department of Pharmacology, Toxicology, and Pharmacy, University of Veterinary Medicine, Hanover, Germany
| | - Franziska Richter
- Department of Pharmacology, Toxicology, and Pharmacy, University of Veterinary Medicine, Hanover, Germany.,Center for Systems Neuroscience, Hanover, Germany
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20
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Garcia EJ, Liao PC, Tan G, Vevea JD, Sing CN, Tsang CA, McCaffery JM, Boldogh IR, Pon LA. Membrane dynamics and protein targets of lipid droplet microautophagy during ER stress-induced proteostasis in the budding yeast, Saccharomyces cerevisiae. Autophagy 2020. [PMID: 33021864 DOI: 10.1080/15548627.2020.1826691.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2022] Open
Abstract
Our previous studies reveal a mechanism for lipid droplet (LD)-mediated proteostasis in the endoplasmic reticulum (ER) whereby unfolded proteins that accumulate in the ER in response to lipid imbalance-induced ER stress are removed by LDs and degraded by microlipophagy (µLP), autophagosome-independent LD uptake into the vacuole (the yeast lysosome). Here, we show that dithiothreitol- or tunicamycin-induced ER stress also induces µLP and identify an unexpected role for vacuolar membrane dynamics in this process. All stressors studied induce vacuolar fragmentation prior to µLP. Moreover, during µLP, fragmented vacuoles fuse to form cup-shaped structures that encapsulate and ultimately take up LDs. Our studies also indicate that proteins of the endosome sorting complexes required for transport (ESCRT) are upregulated, required for µLP, and recruited to LDs, vacuolar membranes, and sites of vacuolar membrane scission during µLP. We identify possible target proteins for LD-mediated ER proteostasis. Our live-cell imaging studies reveal that one potential target (Nup159) localizes to punctate structures that colocalizes with LDs 1) during movement from ER membranes to the cytosol, 2) during microautophagic uptake into vacuoles, and 3) within the vacuolar lumen. Finally, we find that mutations that inhibit LD biogenesis, homotypic vacuolar membrane fusion or ESCRT function inhibit stress-induced autophagy of Nup159 and other ER proteins. Thus, we have obtained the first direct evidence that LDs and µLP can mediate ER stress-induced ER proteostasis, and identified direct roles for ESCRT and vacuolar membrane fusion in that process.
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Affiliation(s)
- Enrique J Garcia
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Pin-Chao Liao
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Gary Tan
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Jason D Vevea
- HHMI and Department of Neuroscience, University of Wisconsin, Madison, Wisconsin, USA
| | - Cierra N Sing
- Institute of Human Nutrition, Columbia University, New York, NY, USA
| | - Catherine A Tsang
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - J Michael McCaffery
- Integrated Imaging Center, Department of Biology, The Johns Hopkins University, Baltimore, MD, USA
| | - Istvan R Boldogh
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Liza A Pon
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
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21
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Morshed S, Tasnin MN, Ushimaru T. ESCRT machinery plays a role in microautophagy in yeast. BMC Mol Cell Biol 2020; 21:70. [PMID: 33028189 PMCID: PMC7542719 DOI: 10.1186/s12860-020-00314-w] [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: 03/26/2020] [Accepted: 10/01/2020] [Indexed: 02/06/2023] Open
Abstract
Background Microautophagy, which degrades cargos by direct lysosomal/vacuolar engulfment of cytoplasmic cargos, is promoted after nutrient starvation and the inactivation of target of rapamycin complex 1 (TORC1) protein kinase. In budding yeast, microautophagy has been commonly assessed using processing assays with green fluorescent protein (GFP)-tagged vacuolar membrane proteins, such as Vph1 and Pho8. The endosomal sorting complex required for transport (ESCRT) system is proposed to be required for microautophagy, because degradation of vacuolar membrane protein Vph1 was compromised in ESCRT-defective mutants. However, ESCRT is also critical for the vacuolar sorting of most vacuolar proteins, and hence reexamination of the involvement of ESCRT in microautophagic processes is required. Results Here, we show that the Vph1-GFP processing assay is unsuitable for estimating the involvement of ESCRT in microautophagy, because Vph1-GFP accumulated highly in the prevacuolar class E compartment in ESCRT mutants. In contrast, GFP-Pho8 and Sna4-GFP destined for vacuolar membranes via an alternative adaptor protein-3 (AP-3) pathway, were properly localized on vacuolar membranes in ESCRT-deficient cells. Nevertheless, microautophagic degradation of GFP-Pho8 and Sna4-GFP after TORC1 inactivation was hindered in ESCRT mutants, indicating that ESCRT is indeed required for microautophagy after nutrient starvation and TORC1 inactivation. Conclusions These findings provide evidence for the direct role of ESCRT in microautophagy induction.
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Affiliation(s)
- Shamsul Morshed
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan
| | - Most Naoshia Tasnin
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan
| | - Takashi Ushimaru
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan. .,Department of Science, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, 422-8021, Japan.
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22
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Deng S, Liu J, Wu X, Lu W. Golgi Apparatus: A Potential Therapeutic Target for Autophagy-Associated Neurological Diseases. Front Cell Dev Biol 2020; 8:564975. [PMID: 33015059 PMCID: PMC7509445 DOI: 10.3389/fcell.2020.564975] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 08/17/2020] [Indexed: 12/13/2022] Open
Abstract
Autophagy has dual effects in human diseases: appropriate autophagy may protect cells from stress, while excessive autophagy may cause cell death. Additionally, close interactions exist between autophagy and the Golgi. This review outlines recent advances regarding the role of the Golgi apparatus in autophagy. The signaling processes of autophagy are dependent on the normal function of the Golgi. Specifically, (i) autophagy-related protein 9 is mainly located in the Golgi and forms new autophagosomes in response to stressors; (ii) Golgi fragmentation is induced by Golgi-related proteins and accompanied with autophagy induction; and (iii) the endoplasmic reticulum-Golgi intermediate compartment and the reticular trans-Golgi network play essential roles in autophagosome formation to provide a template for lipidation of microtubule-associated protein 1A/1B-light chain 3 and induce further ubiquitination. Golgi-related proteins regulate formation of autophagosomes, and disrupted formation of autophagy can influence Golgi function. Notably, aberrant autophagy has been demonstrated to be implicated in neurological diseases. Thus, targeted therapies aimed at protecting the Golgi or regulating Golgi proteins might prevent or ameliorate autophagy-related neurological diseases. Further studies are needed to investigate the potential application of Golgi therapy in autophagy-based neurological diseases.
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Affiliation(s)
- Shuwen Deng
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jia Liu
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiaomei Wu
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Wei Lu
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, China
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23
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Garcia EJ, Liao PC, Tan G, Vevea JD, Sing CN, Tsang CA, McCaffery JM, Boldogh IR, Pon LA. Membrane dynamics and protein targets of lipid droplet microautophagy during ER stress-induced proteostasis in the budding yeast, Saccharomyces cerevisiae. Autophagy 2020; 17:2363-2383. [PMID: 33021864 PMCID: PMC8496710 DOI: 10.1080/15548627.2020.1826691] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Our previous studies reveal a mechanism for lipid droplet (LD)-mediated proteostasis in the endoplasmic reticulum (ER) whereby unfolded proteins that accumulate in the ER in response to lipid imbalance-induced ER stress are removed by LDs and degraded by microlipophagy (µLP), autophagosome-independent LD uptake into the vacuole (the yeast lysosome). Here, we show that dithiothreitol- or tunicamycin-induced ER stress also induces µLP and identify an unexpected role for vacuolar membrane dynamics in this process. All stressors studied induce vacuolar fragmentation prior to µLP. Moreover, during µLP, fragmented vacuoles fuse to form cup-shaped structures that encapsulate and ultimately take up LDs. Our studies also indicate that proteins of the endosome sorting complexes required for transport (ESCRT) are upregulated, required for µLP, and recruited to LDs, vacuolar membranes, and sites of vacuolar membrane scission during µLP. We identify possible target proteins for LD-mediated ER proteostasis. Our live-cell imaging studies reveal that one potential target (Nup159) localizes to punctate structures that colocalizes with LDs 1) during movement from ER membranes to the cytosol, 2) during microautophagic uptake into vacuoles, and 3) within the vacuolar lumen. Finally, we find that mutations that inhibit LD biogenesis, homotypic vacuolar membrane fusion or ESCRT function inhibit stress-induced autophagy of Nup159 and other ER proteins. Thus, we have obtained the first direct evidence that LDs and µLP can mediate ER stress-induced ER proteostasis, and identified direct roles for ESCRT and vacuolar membrane fusion in that process.
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Affiliation(s)
- Enrique J Garcia
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Pin-Chao Liao
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Gary Tan
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Jason D Vevea
- HHMI and Department of Neuroscience, University of Wisconsin, Madison, Wisconsin, USA
| | - Cierra N Sing
- Institute of Human Nutrition, Columbia University, New York, NY, USA
| | - Catherine A Tsang
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - J Michael McCaffery
- Integrated Imaging Center, Department of Biology, The Johns Hopkins University, Baltimore, MD, USA
| | - Istvan R Boldogh
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Liza A Pon
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
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24
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Schuck S. Microautophagy - distinct molecular mechanisms handle cargoes of many sizes. J Cell Sci 2020; 133:133/17/jcs246322. [PMID: 32907930 DOI: 10.1242/jcs.246322] [Citation(s) in RCA: 186] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Autophagy is fundamental for cell and organismal health. Two types of autophagy are conserved in eukaryotes: macroautophagy and microautophagy. During macroautophagy, autophagosomes deliver cytoplasmic constituents to endosomes or lysosomes, whereas during microautophagy lytic organelles take up cytoplasm directly. While macroautophagy has been investigated extensively, microautophagy has received much less attention. Nonetheless, it has become clear that microautophagy has a broad range of functions in biosynthetic transport, metabolic adaptation, organelle remodeling and quality control. This Review discusses the selective and non-selective microautophagic processes known in yeast, plants and animals. Based on the molecular mechanisms for the uptake of microautophagic cargo into lytic organelles, I propose to distinguish between fission-type microautophagy, which depends on ESCRT proteins, and fusion-type microautophagy, which requires the core autophagy machinery and SNARE proteins. Many questions remain to be explored, but the functional versatility and mechanistic diversity of microautophagy are beginning to emerge.
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Affiliation(s)
- Sebastian Schuck
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
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25
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Kurokawa Y, Konishi R, Yoshida A, Tomioku K, Tanabe K, Fujita A. Microautophagy in the yeast vacuole depends on the activities of phosphatidylinositol 4-kinases, Stt4p and Pik1p. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183416. [PMID: 32726584 DOI: 10.1016/j.bbamem.2020.183416] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/10/2020] [Accepted: 07/12/2020] [Indexed: 12/30/2022]
Abstract
Morphologically, the lipophagy in yeast cell mimics microautophagy, which includes a direct amendment of the vacuolar membrane that engulfs lipid droplets (LDs). The molecular mechanism of the membrane modifications that elicits microautophagy still remains elusive. In this study, an analysis of membrane lipid distribution at a nanoscale level showed that PtdIns(4)P is localized in the cytoplasmic leaflet of microautophagic vesicles, which are derived when the vacuole's membrane domains engulfed LDs both in the stationary phase and in acute nitrogen starvation. Furthermore, the PtdIns(4)P-positive raft-like domains engulf LDs through a microautophagic mechanism. When single temperature-conditional mutants of STT4 or PIK1 PtdIns 4-kinases were used, in the vacuole of STT4 and PIK1 mutant cells, microautophagic vesicles drastically decreased at restrictive temperatures, and the labeling density of PtdIns(4)P on the microautophagic vesicles and the sizes of the mutants' microautophagic vesicles also decreased. These results suggest that both Stt4p and Pik1p have important roles in the microautophagy of the vacuole in the stationary phase and under nitrogen starvation conditions.
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Affiliation(s)
- Yuna Kurokawa
- Department of Molecular and Cell Biology and Biochemistry, Basic Veterinary Science, Faculty of Veterinary Medicine, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-0065, Japan
| | - Rikako Konishi
- Department of Molecular and Cell Biology and Biochemistry, Basic Veterinary Science, Faculty of Veterinary Medicine, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-0065, Japan
| | - Akane Yoshida
- Department of Molecular and Cell Biology and Biochemistry, Basic Veterinary Science, Faculty of Veterinary Medicine, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-0065, Japan
| | - Kanna Tomioku
- Department of Molecular and Cell Biology and Biochemistry, Basic Veterinary Science, Faculty of Veterinary Medicine, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-0065, Japan
| | - Kenji Tanabe
- Medical Research Institute, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Akikazu Fujita
- Department of Molecular and Cell Biology and Biochemistry, Basic Veterinary Science, Faculty of Veterinary Medicine, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-0065, Japan.
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26
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O'Hara DM, Pawar G, Kalia SK, Kalia LV. LRRK2 and α-Synuclein: Distinct or Synergistic Players in Parkinson's Disease? Front Neurosci 2020; 14:577. [PMID: 32625052 PMCID: PMC7311858 DOI: 10.3389/fnins.2020.00577] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 05/12/2020] [Indexed: 12/19/2022] Open
Abstract
Parkinson's disease (PD) is the most common neurodegenerative movement disorder, characterized by prominent degeneration of dopaminergic neurons in the substantia nigra and aggregation of the protein α-synuclein within intraneuronal inclusions known as Lewy bodies. Ninety percent of PD cases are idiopathic while the remaining 10% are associated with gene mutations that affect cellular functions ranging from kinase activity to mitochondrial quality control, hinting at a multifactorial disease process. Mutations in LRRK2 and SNCA (the gene coding for α-synuclein) cause monogenic forms of autosomal dominant PD, and polymorphisms in either gene are also associated with increased risk of idiopathic PD. Although Lewy bodies are a defining neuropathological feature of PD, an appreciable subset of patients with LRRK2 mutations present with a clinical phenotype indistinguishable from idiopathic PD but lack Lewy pathology at autopsy, suggesting that LRRK2-mediated PD may occur independently of α-synuclein aggregation. Here, we examine whether LRRK2 and α-synuclein, as mediators of neurodegeneration in PD, exist in common or distinct pathways. Specifically, we review evidence from preclinical models and human neuropathological studies examining interactions between the two proteins. Elucidating the degree of interplay between LRRK2 and α-synuclein will be necessary for treatment stratification once effective targeted disease-modifying therapies are developed.
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Affiliation(s)
- Darren M O'Hara
- Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Grishma Pawar
- Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Suneil K Kalia
- Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Lorraine V Kalia
- Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Division of Neurology, Department of Medicine, University of Toronto, Toronto, ON, Canada.,Edmond J. Safra Program in Parkinson's Disease and the Morton and Gloria Shulman Movement Disorders Clinic, Division of Neurology, Department of Medicine, Toronto Western Hospital, University Health Network, Toronto, ON, Canada.,Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
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27
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Kohler V, Aufschnaiter A, Büttner S. Closing the Gap: Membrane Contact Sites in the Regulation of Autophagy. Cells 2020; 9:E1184. [PMID: 32397538 PMCID: PMC7290522 DOI: 10.3390/cells9051184] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 04/29/2020] [Accepted: 05/07/2020] [Indexed: 12/14/2022] Open
Abstract
In all eukaryotic cells, intracellular organization and spatial separation of incompatible biochemical processes is established by individual cellular subcompartments in form of membrane-bound organelles. Virtually all of these organelles are physically connected via membrane contact sites (MCS), allowing interorganellar communication and a functional integration of cellular processes. These MCS coordinate the exchange of diverse metabolites and serve as hubs for lipid synthesis and trafficking. While this of course indirectly impacts on a plethora of biological functions, including autophagy, accumulating evidence shows that MCS can also directly regulate autophagic processes. Here, we focus on the nexus between interorganellar contacts and autophagy in yeast and mammalian cells, highlighting similarities and differences. We discuss MCS connecting the ER to mitochondria or the plasma membrane, crucial for early steps of both selective and non-selective autophagy, the yeast-specific nuclear-vacuolar tethering system and its role in microautophagy, the emerging function of distinct autophagy-related proteins in organellar tethering as well as novel MCS transiently emanating from the growing phagophore and mature autophagosome.
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Affiliation(s)
- Verena Kohler
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden;
| | - Andreas Aufschnaiter
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden;
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden;
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
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28
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Sieńko K, Poormassalehgoo A, Yamada K, Goto-Yamada S. Microautophagy in Plants: Consideration of Its Molecular Mechanism. Cells 2020; 9:cells9040887. [PMID: 32260410 PMCID: PMC7226842 DOI: 10.3390/cells9040887] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 02/06/2023] Open
Abstract
Microautophagy is a type of autophagy. It is characterized by direct enclosing with the vacuolar/lysosomal membrane, which completes the isolation and uptake of cell components in the vacuole. Several publications present evidence that plants exhibit microautophagy. Plant microautophagy is involved in anthocyanin accumulation in the vacuole, eliminating damaged chloroplasts and degrading cellular components during starvation. However, information on the molecular mechanism of microautophagy is less available than that on the general macroautophagy, because the research focusing on microautophagy has not been widely reported. In yeast and animals, it is suggested that microautophagy can be classified into several types depending on morphology and the requirements of autophagy-related (ATG) genes. This review summarizes the studies on plant microautophagy and discusses possible techniques for a future study in this field while taking into account the information on microautophagy obtained from yeast and animals.
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29
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Sharmin T, Morshed S, Ushimaru T. PP2A promotes ESCRT-0 complex formation on vacuolar membranes and microautophagy induction after TORC1 inactivation. Biochem Biophys Res Commun 2020; 524:614-620. [DOI: 10.1016/j.bbrc.2020.01.129] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 11/29/2022]
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30
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Protein Kinase C Isozymes and Autophagy during Neurodegenerative Disease Progression. Cells 2020; 9:cells9030553. [PMID: 32120776 PMCID: PMC7140419 DOI: 10.3390/cells9030553] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/27/2020] [Accepted: 02/04/2020] [Indexed: 12/16/2022] Open
Abstract
Protein kinase C (PKC) isozymes are members of the Serine/Threonine kinase family regulating cellular events following activation of membrane bound phospholipids. The breakdown of the downstream signaling pathways of PKC relates to several disease pathogeneses particularly neurodegeneration. PKC isozymes play a critical role in cell death and survival mechanisms, as well as autophagy. Numerous studies have reported that neurodegenerative disease formation is caused by failure of the autophagy mechanism. This review outlines PKC signaling in autophagy and neurodegenerative disease development and introduces some polyphenols as effectors of PKC isozymes for disease therapy.
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31
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Sinha A, Israeli R, Cirigliano A, Gihaz S, Trabelcy B, Braus GH, Gerchman Y, Fishman A, Negri R, Rinaldi T, Pick E. The COP9 signalosome mediates the Spt23 regulated fatty acid desaturation and ergosterol biosynthesis. FASEB J 2020; 34:4870-4889. [PMID: 32077151 DOI: 10.1096/fj.201902487r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/02/2020] [Accepted: 01/14/2020] [Indexed: 02/06/2023]
Abstract
The COP9 signalosome (CSN) is a conserved eukaryotic complex, essential for vitality in all multicellular organisms and critical for the turnover of key cellular proteins through catalytic and non-catalytic activities. Saccharomyces cerevisiae is a powerful model organism for studying fundamental aspects of the CSN complex, since it includes a conserved enzymatic core but lacks non-catalytic activities, probably explaining its non-essentiality for life. A previous transcriptomic analysis of an S. cerevisiae strain deleted in the CSN5/RRI1 gene, encoding to the CSN catalytic subunit, revealed a downregulation of genes involved in lipid metabolism. We now show that the S. cerevisiae CSN holocomplex is essential for cellular lipid homeostasis. Defects in CSN assembly or activity lead to decreased quantities of ergosterol and unsaturated fatty acids (UFA); vacuole defects; diminished lipid droplets (LDs) size; and to accumulation of endoplasmic reticulum (ER) stress. The molecular mechanism behind these findings depends on CSN involvement in upregulating mRNA expression of SPT23. Spt23 is a novel activator of lipid desaturation and ergosterol biosynthesis. Our data reveal for the first time a functional link between the CSN holocomplex and Spt23. Moreover, CSN-dependent upregulation of SPT23 transcription is necessary for the fine-tuning of lipid homeostasis and for cellular health.
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Affiliation(s)
- Abhishek Sinha
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa, Oranim, Israel
| | - Ran Israeli
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa, Oranim, Israel
| | - Angela Cirigliano
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Shalev Gihaz
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Beny Trabelcy
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa, Oranim, Israel
| | - Gerhard H Braus
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany
| | - Yoram Gerchman
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa, Oranim, Israel
| | - Ayelet Fishman
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Rodolfo Negri
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Teresa Rinaldi
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Elah Pick
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa, Oranim, Israel
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32
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Abstract
Autophagy is a major intracellular degradation system that derives its degradative abilities from the lysosome. The most well-studied form of autophagy is macroautophagy, which delivers cytoplasmic material to lysosomes via the double-membraned autophagosome. Other forms of autophagy, namely chaperone-mediated autophagy and microautophagy, occur directly on the lysosome. Besides providing the means for degradation, lysosomes are also involved in autophagy regulation and can become substrates of autophagy when damaged. During autophagy, they exhibit notable changes, including increased acidification, enhanced enzymatic activity, and perinuclear localization. Despite their importance to autophagy, details on autophagy-specific regulation of lysosomes remain relatively scarce. This review aims to provide a summary of current understanding on the behaviour of lysosomes during autophagy and outline unexplored areas of autophagy-specific lysosome research.
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Affiliation(s)
- Willa Wen-You Yim
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, 113-0033 Japan
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33
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Zhang X, Ding X, Marshall RS, Paez-Valencia J, Lacey P, Vierstra RD, Otegui MS. Reticulon proteins modulate autophagy of the endoplasmic reticulum in maize endosperm. eLife 2020; 9:51918. [PMID: 32011236 PMCID: PMC7046470 DOI: 10.7554/elife.51918] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/02/2020] [Indexed: 12/18/2022] Open
Abstract
Reticulon (Rtn) proteins shape tubular domains of the endoplasmic reticulum (ER), and in some cases are autophagy receptors for selective ER turnover. We have found that maize Rtn1 and Rtn2 control ER homeostasis and autophagic flux in endosperm aleurone cells, where the ER accumulates lipid droplets and synthesizes storage protein accretions metabolized during germination. Maize Rtn1 and Rtn2 are expressed in the endosperm, localize to the ER, and re-model ER architecture in a dose-dependent manner. Rtn1 and Rtn2 interact with Atg8a using four Atg8-interacting motifs (AIMs) located at the C-terminus, cytoplasmic loop, and within the transmembrane segments. Binding between Rtn2 and Atg8 is elevated upon ER stress. Maize rtn2 mutants display increased autophagy and up-regulation of an ER stress-responsive chaperone. We propose that maize Rtn1 and Rtn2 act as receptors for autophagy-mediated ER turnover, and thus are critical for ER homeostasis and suppression of ER stress.
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Affiliation(s)
- Xiaoguo Zhang
- Department of Botany, Laboratory of Cell and Molecular Biology, University of Wisconsin, Madison, United States
| | - Xinxin Ding
- Department of Botany, Laboratory of Cell and Molecular Biology, University of Wisconsin, Madison, United States
| | | | - Julio Paez-Valencia
- Department of Botany, Laboratory of Cell and Molecular Biology, University of Wisconsin, Madison, United States
| | - Patrick Lacey
- Department of Botany, Laboratory of Cell and Molecular Biology, University of Wisconsin, Madison, United States
| | | | - Marisa S Otegui
- Department of Botany, Laboratory of Cell and Molecular Biology, University of Wisconsin, Madison, United States.,Department of Genetics, University of Wisconsin, Madison, United States
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34
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Molecular mechanisms of selective autophagy in Drosophila. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2020; 354:63-105. [DOI: 10.1016/bs.ircmb.2019.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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35
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Morshed S, Sharmin T, Ushimaru T. TORC1 regulates ESCRT-0 complex formation on the vacuolar membrane and microautophagy induction in yeast. Biochem Biophys Res Commun 2020; 522:88-94. [DOI: 10.1016/j.bbrc.2019.11.064] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 11/10/2019] [Indexed: 11/26/2022]
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36
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Schäfer JA, Schessner JP, Bircham PW, Tsuji T, Funaya C, Pajonk O, Schaeff K, Ruffini G, Papagiannidis D, Knop M, Fujimoto T, Schuck S. ESCRT machinery mediates selective microautophagy of endoplasmic reticulum in yeast. EMBO J 2019; 39:e102586. [PMID: 31802527 PMCID: PMC6960443 DOI: 10.15252/embj.2019102586] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 10/30/2019] [Accepted: 11/11/2019] [Indexed: 01/14/2023] Open
Abstract
ER‐phagy, the selective autophagy of endoplasmic reticulum (ER), safeguards organelle homeostasis by eliminating misfolded proteins and regulating ER size. ER‐phagy can occur by macroautophagic and microautophagic mechanisms. While dedicated machinery for macro‐ER‐phagy has been discovered, the molecules and mechanisms mediating micro‐ER‐phagy remain unknown. Here, we first show that micro‐ER‐phagy in yeast involves the conversion of stacked cisternal ER into multilamellar ER whorls during microautophagic uptake into lysosomes. Second, we identify the conserved Nem1‐Spo7 phosphatase complex and the ESCRT machinery as key components for micro‐ER‐phagy. Third, we demonstrate that macro‐ and micro‐ER‐phagy are parallel pathways with distinct molecular requirements. Finally, we provide evidence that the ESCRT machinery directly functions in scission of the lysosomal membrane to complete the microautophagic uptake of ER. These findings establish a framework for a mechanistic understanding of micro‐ER‐phagy and, thus, a comprehensive appreciation of the role of autophagy in ER homeostasis.
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Affiliation(s)
- Jasmin A Schäfer
- DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Julia P Schessner
- DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Peter W Bircham
- DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Takuma Tsuji
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Charlotta Funaya
- Electron Microscopy Core Facility, Heidelberg University, Heidelberg, Germany
| | - Oliver Pajonk
- DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Katharina Schaeff
- DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Giulia Ruffini
- DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Dimitrios Papagiannidis
- DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Michael Knop
- DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Toyoshi Fujimoto
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Sebastian Schuck
- DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
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Goto-Yamada S, Oikawa K, Bizan J, Shigenobu S, Yamaguchi K, Mano S, Hayashi M, Ueda H, Hara-Nishimura I, Nishimura M, Yamada K. Sucrose Starvation Induces Microautophagy in Plant Root Cells. FRONTIERS IN PLANT SCIENCE 2019; 10:1604. [PMID: 31850051 PMCID: PMC6901504 DOI: 10.3389/fpls.2019.01604] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 11/14/2019] [Indexed: 05/26/2023]
Abstract
Autophagy is an essential system for degrading and recycling cellular components for survival during starvation conditions. Under sucrose starvation, application of a papain protease inhibitor E-64d to the Arabidopsis root and tobacco BY-2 cells induced the accumulation of vesicles, labeled with a fluorescent membrane marker FM4-64. The E-64d-induced vesicle accumulation was reduced in the mutant defective in autophagy-related genes ATG2, ATG5, and ATG7, suggesting autophagy is involved in the formation of these vesicles. To clarify the formation of these vesicles in detail, we monitored time-dependent changes of tonoplast, and vesicle accumulation in sucrose-starved cells. We found that these vesicles were derived from the tonoplast and produced by microautophagic process. The tonoplast proteins were excluded from the vesicles, suggesting that the vesicles are generated from specific membrane domains. Concanamycin A treatment in GFP-ATG8a transgenic plants showed that not all FM4-64-labeled vesicles, which were derived from the tonoplast, contained the ATG8a-containing structure. These results suggest that ATG8a may not always be necessary for microautophagy.
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Affiliation(s)
- Shino Goto-Yamada
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Kazusato Oikawa
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Jakub Bizan
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Shuji Shigenobu
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Katsushi Yamaguchi
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Japan
| | - Shoji Mano
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Makoto Hayashi
- Department of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Japan
| | - Haruko Ueda
- Faculty of Science and Engineering, Konan University, Kobe, Japan
| | | | - Mikio Nishimura
- Faculty of Science and Engineering, Konan University, Kobe, Japan
| | - Kenji Yamada
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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38
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Ishii A, Kurokawa K, Hotta M, Yoshizaki S, Kurita M, Koyama A, Nakano A, Kimura Y. Role of Atg8 in the regulation of vacuolar membrane invagination. Sci Rep 2019; 9:14828. [PMID: 31616012 PMCID: PMC6794316 DOI: 10.1038/s41598-019-51254-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 09/26/2019] [Indexed: 01/23/2023] Open
Abstract
Cellular heat stress can cause damage, and significant changes, to a variety of cellular structures. When exposed to chronically high temperatures, yeast cells invaginate vacuolar membranes. In this study, we found that the expression of Atg8, an essential autophagy factor, is induced after chronic heat stress. In addition, without Atg8, vacuolar invaginations are induced conspicuously, beginning earlier and invaginating vacuoles more frequently after heat stress. Our results indicate that Atg8's invagination-suppressing functions do not require Atg8 lipidation, in contrast with autophagy, which requires Atg8 lipidation. Genetic analyses of vps24 and vps23 further suggest that full ESCRT machinery is necessary to form vacuolar invaginations irrespective of Atg8. In contrast, through a combined mutation with the vacuole BAR domain protein Ivy1, vacuoles show constitutively enhanced invaginated structures. Finally, we found that the atg8Δivy1Δ mutant is sensitive against agents targeting functions of the vacuole and/or plasma membrane (cell wall). Collectively, our findings revealed that Atg8 maintains vacuolar membrane homeostasis in an autophagy-independent function by coordinating with other cellular factors.
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Affiliation(s)
- Ayane Ishii
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Kazuo Kurokawa
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Wako, Saitama, 351-0198, Japan
| | - Miyuu Hotta
- Department of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Suzuka Yoshizaki
- Department of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Maki Kurita
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Aya Koyama
- Department of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Akihiko Nakano
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Wako, Saitama, 351-0198, Japan
| | - Yoko Kimura
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan. .,Department of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan.
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39
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Iwama R, Ohsumi Y. Analysis of autophagy activated during changes in carbon source availability in yeast cells. J Biol Chem 2019; 294:5590-5603. [PMID: 30755486 DOI: 10.1074/jbc.ra118.005698] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 02/05/2019] [Indexed: 11/06/2022] Open
Abstract
Autophagy is a conserved intracellular degradation system in eukaryotes. Recent studies have revealed that autophagy can be induced not only by nitrogen starvation but also by many other stimuli. However, questions persist regarding the types of conditions that induce autophagy, as well as the particular kinds of autophagy that are induced under these specific conditions. In experimental studies, abrupt nutrient changes are often used to induce autophagy. In this study, we investigated autophagy induction in batch culture on low-glucose medium, in which growth of yeast (Saccharomyces cerevisiae) cells is clearly reflected exclusively by carbon source state. In this medium, cells pass sequentially through three stages: glucose-utilizing, ethanol-utilizing, and ethanol-depleted phases. Using GFP cleavage assay by immunoblotting methods, fluorescence microscopy, and transmission electron microscopy ultrastructural analysis, we found that bulk autophagy and endoplasmic reticulum-phagy are induced starting at the ethanol-utilizing phase, and bulk autophagy is activated to a greater extent in the ethanol-depleted phase. Furthermore, we found that mitophagy is induced by ethanol depletion. Microautophagy occurred after glucose depletion and involved incorporation of cytosolic components and lipid droplets into the vacuolar lumen. Moreover, we observed that autophagy-deficient cells grow more slowly in the ethanol-utilizing phase and exhibit a delay in growth resumption when they are shifted to fresh medium from the ethanol-depleted phase. Our findings suggest that distinct types of autophagy are induced in yeast cells undergoing gradual changes in carbon source availability.
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Affiliation(s)
- Ryo Iwama
- From the Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259-S2-12 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Yoshinori Ohsumi
- From the Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259-S2-12 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
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40
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Nakamura S, Izumi M. Chlorophagy is ATG gene-dependent microautophagy process. PLANT SIGNALING & BEHAVIOR 2018; 14:1554469. [PMID: 30574829 PMCID: PMC6351093 DOI: 10.1080/15592324.2018.1558679] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 12/10/2018] [Indexed: 05/27/2023]
Abstract
Autophagy delivers cytosolic components to lysosomes and the vacuole for degradation. This pathway prevents starvation through bulk degradation and recycling of cytoplasmic components, and maintains cellular homeostasis through selective elimination of damaged proteins and organelles. Autophagic delivery processes are categorized into three types: macroautophagy, microautophagy, and chaperone-mediated autophagy. During macroautophagy, nascent, double membrane-bound vesicles termed autophagosomes sequester a portion of cytoplasm and deliver it to the vacuole/lysosomes. Molecular genetic studies in budding yeasts have identified a set of AUTOPHAGY (ATG) genes required for autophagosome formation. Although microautophagy involves the direct lysosomal/vacuolar engulfment and incorporation of a target into the lumen rather than the formation of autophagosomes, the membrane dynamics and possible roles of ATGs during microautophagy are under investigation. Our recent study revealed an ATG-dependent microautophagy process in plants, during which chloroplasts damaged by high visible light (HL) are selectively eliminated. Here, we discuss the membrane dynamics of the plant microautophagy that enables the transport of whole chloroplasts into the vacuole.
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Affiliation(s)
- Sakuya Nakamura
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Masanori Izumi
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
- Creative Interdisciplinary Research Division, Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
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41
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The intralumenal fragment pathway mediates ESCRT-independent surface transporter down-regulation. Nat Commun 2018; 9:5358. [PMID: 30560896 PMCID: PMC6299085 DOI: 10.1038/s41467-018-07734-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 11/15/2018] [Indexed: 11/10/2022] Open
Abstract
Surface receptor and transporter protein down-regulation is assumed to be exclusively mediated by the canonical multivesicular body (MVB) pathway and ESCRTs (Endosomal Sorting Complexes Required for Transport). However, few surface proteins are known to require ESCRTs for down-regulation, and reports of ESCRT-independent degradation are emerging, suggesting that alternative pathways exist. Here, using Saccharomyces cerevisiae as a model, we show that the hexose transporter Hxt3 does not require ESCRTs for down-regulation conferring resistance to 2-deoxyglucose. This is consistent with GFP-tagged Hxt3 bypassing ESCRT-mediated entry into intralumenal vesicles at endosomes. Instead, Hxt3-GFP accumulates on vacuolar lysosome membranes and is sorted into an area that, upon fusion, is internalized as an intralumenal fragment (ILF) and degraded. Moreover, heat stress or cycloheximide trigger degradation of Hxt3-GFP and other surface transporter proteins (Itr1, Aqr1) by this ESCRT-independent process. How this ILF pathway compares to the MVB pathway and potentially contributes to physiology is discussed. Cell surface receptors are thought to be internalized via the multivesicular bodies (MVBs) in an ESCRT-dependent pathway. Here, the authors report that in yeast, a hexose transporter is internalized via an ESCRT-independent pathway into intralumenal fragments (ILF).
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42
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Ding X, Zhang X, Otegui MS. Plant autophagy: new flavors on the menu. CURRENT OPINION IN PLANT BIOLOGY 2018; 46:113-121. [PMID: 30267997 DOI: 10.1016/j.pbi.2018.09.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 08/28/2018] [Accepted: 09/04/2018] [Indexed: 06/08/2023]
Abstract
Autophagy mediates the delivery of cytoplasmic content to vacuoles or lysosomes for degradation or storage. The best characterized autophagy route called macroautophagy involves the sequestration of cargo in double-membrane autophagosomes and is conserved in eukaryotes, including plants. Recently, several new receptors, some of them plant-specific, that select cargo for macroautophagy have been identified. Some of these receptors appear to participate in regulation of competing catabolic pathways, for example proteasome-mediated versus autophagic degradation under specific stress conditions. Vacuolar microautophagy, a process by which the vacuole directly engulf cytoplasmic material, also occurs in plants but its underlying molecular mechanisms are yet to be elucidated.
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Affiliation(s)
- Xinxin Ding
- Department of Botany, 430 Lincoln Drive, University of Wisconsin-Madison, WI 53706, United States; Laboratory of Molecular and Cellular Biology, 1525 Linden Drive, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Xiaoguo Zhang
- Department of Botany, 430 Lincoln Drive, University of Wisconsin-Madison, WI 53706, United States; Laboratory of Molecular and Cellular Biology, 1525 Linden Drive, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Marisa S Otegui
- Department of Botany, 430 Lincoln Drive, University of Wisconsin-Madison, WI 53706, United States; Laboratory of Molecular and Cellular Biology, 1525 Linden Drive, University of Wisconsin-Madison, Madison, WI 53706, United States; Department of Genetics, 405 Henry Mall, University of Wisconsin-Madison, Madison, WI 53706, United States.
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43
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Cresto N, Gardier C, Gubinelli F, Gaillard MC, Liot G, West AB, Brouillet E. The unlikely partnership between LRRK2 and α-synuclein in Parkinson's disease. Eur J Neurosci 2018; 49:339-363. [PMID: 30269383 DOI: 10.1111/ejn.14182] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 09/11/2018] [Accepted: 09/17/2018] [Indexed: 12/19/2022]
Abstract
Our understanding of the mechanisms underlying Parkinson's disease, the once archetypical nongenetic neurogenerative disorder, has dramatically increased with the identification of α-synuclein and LRRK2 pathogenic mutations. While α-synuclein protein composes the aggregates that can spread through much of the brain in disease, LRRK2 encodes a multidomain dual-enzyme distinct from any other protein linked to neurodegeneration. In this review, we discuss emergent datasets from multiple model systems that suggest these unlikely partners do interact in important ways in disease, both within cells that express both LRRK2 and α-synuclein as well as through more indirect pathways that might involve neuroinflammation. Although the link between LRRK2 and disease can be understood in part through LRRK2 kinase activity (phosphotransferase activity), α-synuclein toxicity is multilayered and plausibly interacts with LRRK2 kinase activity in several ways. We discuss common protein interactors like 14-3-3s that may regulate α-synuclein and LRRK2 in disease. Finally, we examine cellular pathways and outcomes common to both mutant α-synuclein expression and LRRK2 activity and points of intersection. Understanding the interplay between these two unlikely partners in disease may provide new therapeutic avenues for PD.
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Affiliation(s)
- Noémie Cresto
- Neurodegenerative Diseases Laboratory, UMR9199, CEA, CNRS, Université Paris Sud, Université Paris-Saclay, and MIRCen (Molecular Imaging Research Centre), Institut François Jacob, DRF, CEA, Fontenay-aux-Roses, France
| | - Camille Gardier
- Neurodegenerative Diseases Laboratory, UMR9199, CEA, CNRS, Université Paris Sud, Université Paris-Saclay, and MIRCen (Molecular Imaging Research Centre), Institut François Jacob, DRF, CEA, Fontenay-aux-Roses, France
| | - Francesco Gubinelli
- Neurodegenerative Diseases Laboratory, UMR9199, CEA, CNRS, Université Paris Sud, Université Paris-Saclay, and MIRCen (Molecular Imaging Research Centre), Institut François Jacob, DRF, CEA, Fontenay-aux-Roses, France
| | - Marie-Claude Gaillard
- Neurodegenerative Diseases Laboratory, UMR9199, CEA, CNRS, Université Paris Sud, Université Paris-Saclay, and MIRCen (Molecular Imaging Research Centre), Institut François Jacob, DRF, CEA, Fontenay-aux-Roses, France
| | - Géraldine Liot
- Neurodegenerative Diseases Laboratory, UMR9199, CEA, CNRS, Université Paris Sud, Université Paris-Saclay, and MIRCen (Molecular Imaging Research Centre), Institut François Jacob, DRF, CEA, Fontenay-aux-Roses, France
| | - Andrew B West
- Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Emmanuel Brouillet
- Neurodegenerative Diseases Laboratory, UMR9199, CEA, CNRS, Université Paris Sud, Université Paris-Saclay, and MIRCen (Molecular Imaging Research Centre), Institut François Jacob, DRF, CEA, Fontenay-aux-Roses, France
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44
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Kimura N, Yanagisawa K. Traffic jam hypothesis: Relationship between endocytic dysfunction and Alzheimer's disease. Neurochem Int 2018; 119:35-41. [DOI: 10.1016/j.neuint.2017.07.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 06/30/2017] [Accepted: 07/07/2017] [Indexed: 01/07/2023]
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45
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Rahman MA, Terasawa M, Mostofa MG, Ushimaru T. The TORC1–Nem1/Spo7–Pah1/lipin axis regulates microautophagy induction in budding yeast. Biochem Biophys Res Commun 2018; 504:505-512. [DOI: 10.1016/j.bbrc.2018.09.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 09/02/2018] [Indexed: 01/28/2023]
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Abstract
Protein homeostasis (proteostasis) is an essential pillar for correct cellular function. Impairments in proteostasis are encountered both in aging and in several human disease conditions. Molecular chaperones are important players for proteostasis; in particular, heat shock protein 70 (Hsp70) has an essential role in protein folding, disaggregation, and degradation. We have recently proposed a model for Hsp70 functioning as a “multiple socket”. In the model, Hsp70 provides a physical platform for the binding of client proteins, other chaperones, and cochaperones. The final fate of the client protein is dictated by the set of Hsp70 interactions that occur in a given cellular context. Obtaining structural information of the different Hsp70-based protein complexes will provide valuable knowledge to understand the functional mechanisms behind the master role of Hsp70 in proteostasis. We additionally evaluate some of the challenges for attaining high-resolution structures of such complexes.
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Affiliation(s)
- María Rosario Fernández-Fernández
- Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus de la Universidad Autónoma de Madrid, Cantoblanco, E-28049 Madrid, Spain
| | - José María Valpuesta
- Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus de la Universidad Autónoma de Madrid, Cantoblanco, E-28049 Madrid, Spain
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47
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Khan M, Imam H, Siddiqui A. Subversion of cellular autophagy during virus infection: Insights from hepatitis B and hepatitis C viruses. LIVER RESEARCH 2018; 2:146-156. [PMID: 31803515 PMCID: PMC6892584 DOI: 10.1016/j.livres.2018.09.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Autophagy is a self-eating process, in which the damaged or excessed cell organelles and misfolded protein aggregates are removed from the cellular microenvironment. Autophagy is generally thought of as a pro-survival mechanism which is not only important for balancing energy supply at times of nutrient deprivation but also in the removal of various stress stimuli to ensure homeostasis. In addition to the target materials of "self" origin, autophagy can also eliminate intracellular pathogens and acts as a defense mechanism to curb infections. In addition, autophagy is linked to the host cell's innate immune response. However, viruses have evolved various strategies to manipulate and overtake host cell machinery to establish productive replication and maintain infectious process. In fact, replication of many viruses has been found to be autophagy-dependent and suppression of autophagy can potentially affect the viral replication. Thus, autophagy can either serve as an anti-viral defense mechanism or a pro-viral process that supports viral replication. Hepatitis B virus (HBV) and hepatitis C virus (HCV) are known to co-opt cellular autophagy process as a pro-viral tool. Both viruses also induce mitophagy, which contributes to the establishment of chronic hepatitis. This review focuses on the roles of autophagy and mitophagy in the chronic liver disease pathogenesis associated with HBV and HCV infections.
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48
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Jacomin AC, Gul L, Sudhakar P, Korcsmaros T, Nezis IP. What We Learned From Big Data for Autophagy Research. Front Cell Dev Biol 2018; 6:92. [PMID: 30175097 PMCID: PMC6107789 DOI: 10.3389/fcell.2018.00092] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 07/27/2018] [Indexed: 12/13/2022] Open
Abstract
Autophagy is the process by which cytoplasmic components are engulfed in double-membraned vesicles before being delivered to the lysosome to be degraded. Defective autophagy has been linked to a vast array of human pathologies. The molecular mechanism of the autophagic machinery is well-described and has been extensively investigated. However, understanding the global organization of the autophagy system and its integration with other cellular processes remains a challenge. To this end, various bioinformatics and network biology approaches have been developed by researchers in the last few years. Recently, large-scale multi-omics approaches (like genomics, transcriptomics, proteomics, lipidomics, and metabolomics) have been developed and carried out specifically focusing on autophagy, and generating multi-scale data on the related components. In this review, we outline recent applications of in silico investigations and big data analyses of the autophagy process in various biological systems.
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Affiliation(s)
| | - Lejla Gul
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Padhmanand Sudhakar
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
- Gut Microbes and Health Programme, Quadram Institute, Norwich Research Park, Norwich, United Kingdom
| | - Tamas Korcsmaros
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
- Gut Microbes and Health Programme, Quadram Institute, Norwich Research Park, Norwich, United Kingdom
| | - Ioannis P. Nezis
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
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49
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Mostofa MG, Rahman MA, Koike N, Yeasmin AM, Islam N, Waliullah TM, Hosoyamada S, Shimobayashi M, Kobayashi T, Hall MN, Ushimaru T. CLIP and cohibin separate rDNA from nucleolar proteins destined for degradation by nucleophagy. J Cell Biol 2018; 217:2675-2690. [PMID: 29959231 PMCID: PMC6080932 DOI: 10.1083/jcb.201706164] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 02/15/2018] [Accepted: 05/02/2018] [Indexed: 12/16/2022] Open
Abstract
Nutrient starvation or inactivation of TORC1 induces separation of rDNA and nucleolar proteins in yeast. Mostofa et al. report that the rDNA tethering CLIP–cohibin system repositions nucleolar proteins to sites proximal to the nuclear–vacuolar junction (NVJ), where micronucleophagy occurs, whereas rDNA moves to regions distal to the NVJ. Nutrient starvation or inactivation of target of rapamycin complex 1 (TORC1) in budding yeast induces nucleophagy, a selective autophagy process that preferentially degrades nucleolar components. DNA, including ribosomal DNA (rDNA), is not degraded by nucleophagy, even though rDNA is embedded in the nucleolus. Here, we show that TORC1 inactivation promotes relocalization of nucleolar proteins and rDNA to different sites. Nucleolar proteins move to sites proximal to the nuclear–vacuolar junction (NVJ), where micronucleophagy (or piecemeal microautophagy of the nucleus) occurs, whereas rDNA dissociates from nucleolar proteins and moves to sites distal to NVJs. CLIP and cohibin, which tether rDNA to the inner nuclear membrane, were required for repositioning of nucleolar proteins and rDNA, as well as effective nucleophagic degradation of the nucleolar proteins. Furthermore, micronucleophagy itself was necessary for the repositioning of rDNA and nucleolar proteins. However, rDNA escaped from nucleophagic degradation in CLIP- or cohibin-deficient cells. This study reveals that rDNA–nucleolar protein separation is important for the nucleophagic degradation of nucleolar proteins.
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Affiliation(s)
- Md Golam Mostofa
- Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
| | | | - Naoki Koike
- Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Akter Mst Yeasmin
- Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Nafisa Islam
- Course of Biological Science, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | | | - Shun Hosoyamada
- Laboratory of Genome Regeneration, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan
| | | | - Takehiko Kobayashi
- Laboratory of Genome Regeneration, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan
| | | | - Takashi Ushimaru
- Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan .,Course of Biological Science, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
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Oku M, Sakai Y. Three Distinct Types of Microautophagy Based on Membrane Dynamics and Molecular Machineries. Bioessays 2018; 40:e1800008. [PMID: 29708272 DOI: 10.1002/bies.201800008] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/02/2018] [Indexed: 01/13/2023]
Abstract
Microautophagy is originally defined as lysosomal (vacuolar) membrane dynamics to directly enwrap and transport cytosolic components into the lumen of the lytic organelle. Molecular details of microautophagy had remained unknown until genetic studies in yeast identified a set of proteins required for the process. Subsequent studies with other experimental model organisms resulted in a series of discoveries that accompanied an expansion of the definition of microautophagy to also encompass endosomal membrane dynamics. These findings, however, still impose puzzling, non-integrated images as to the molecular mechanism of microautophagy. By reviewing recent studies on microautophagy in various experimental systems, we propose the classification of microautophagy into three types, as the basis for developing a comprehensive view of the process.
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Affiliation(s)
- Masahide Oku
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Yasuyoshi Sakai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.,Research Unit for Physiological Chemistry, The Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, 606-8502, Japan
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