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Ferro-Novick S, Reggiori F, Brodsky JL. ER-Phagy, ER Homeostasis, and ER Quality Control: Implications for Disease. Trends Biochem Sci 2021; 46:630-639. [PMID: 33509650 DOI: 10.1016/j.tibs.2020.12.013] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/14/2020] [Accepted: 12/22/2020] [Indexed: 12/15/2022]
Abstract
Lysosomal degradation of endoplasmic reticulum (ER) fragments by autophagy, termed ER-phagy or reticulophagy, occurs under normal as well as stress conditions. The recent discovery of multiple ER-phagy receptors has stimulated studies on the roles of ER-phagy. We discuss how the ER-phagy receptors and the cellular components that work with these receptors mediate two important functions: ER homeostasis and ER quality control. We highlight that ER-phagy plays an important role in alleviating ER expansion induced by ER stress, and acts as an alternative disposal pathway for misfolded proteins. We suggest that the latter function explains the emerging connection between ER-phagy and disease. Additional ER-phagy-associated functions and important unanswered questions are also discussed.
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Affiliation(s)
- Susan Ferro-Novick
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093-0668, USA.
| | - Fulvio Reggiori
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, The Netherlands.
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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52
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Loi M, Marazza A, Molinari M. Endoplasmic Reticulum (ER) and ER-Phagy. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2021; 59:99-114. [PMID: 34050863 DOI: 10.1007/978-3-030-67696-4_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The endoplasmic reticulum (ER) is a biosynthetic organelle in eukaryotic cells. Its capacity to produce proteins, lipids and oligosaccharides responds to physiologic and pathologic demand. The transcriptional and translational unfolded protein response (UPR) programs increase ER size and activity. In contrast, ER-phagy programs in all their flavors select ER subdomains for lysosomal clearance. These programs are activated by nutrient deprivation, accumulation of excess ER (recov-ER-phagy), production of misfolded proteins that cannot be degraded by ER-associated degradation and that are removed from cells by the so-called ER-to-lysosome-associated degradation (ERLAD). Selection of ER subdomains to be cleared from cells relies on ER-phagy receptors, a class of membrane-bound proteins displaying cytosolic domains that engage the cytosolic ubiquitin-like protein LC3. Mechanistically, ER clearance proceeds via macro-ER-phagy, micro-ER-phagy and LC3-regulated vesicular delivery.
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Affiliation(s)
- Marisa Loi
- Università della Svizzera italiana, Lugano, Switzerland
- Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - Alessandro Marazza
- Università della Svizzera italiana, Lugano, Switzerland
- Institute for Research in Biomedicine, Bellinzona, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Maurizio Molinari
- Università della Svizzera italiana, Lugano, Switzerland.
- Institute for Research in Biomedicine, Bellinzona, Switzerland.
- Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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53
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Characterization of constitutive ER-phagy of excess membrane proteins. PLoS Genet 2020; 16:e1009255. [PMID: 33275594 PMCID: PMC7744050 DOI: 10.1371/journal.pgen.1009255] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 12/16/2020] [Accepted: 11/05/2020] [Indexed: 11/19/2022] Open
Abstract
Thirty percent of all cellular proteins are inserted into the endoplasmic reticulum (ER), which spans throughout the cytoplasm. Two well-established stress-induced pathways ensure quality control (QC) at the ER: ER-phagy and ER-associated degradation (ERAD), which shuttle cargo for degradation to the lysosome and proteasome, respectively. In contrast, not much is known about constitutive ER-phagy. We have previously reported that excess of integral-membrane proteins is delivered from the ER to the lysosome via autophagy during normal growth of yeast cells. Whereas endogenously expressed ER resident proteins serve as cargos at a basal level, this level can be induced by overexpression of membrane proteins that are not ER residents. Here, we characterize this pathway as constitutive ER-phagy. Constitutive and stress-induced ER-phagy share the basic macro-autophagy machinery including the conserved Atgs and Ypt1 GTPase. However, induction of stress-induced autophagy is not needed for constitutive ER-phagy to occur. Moreover, the selective receptors needed for starvation-induced ER-phagy, Atg39 and Atg40, are not required for constitutive ER-phagy and neither these receptors nor their cargos are delivered through it to the vacuole. As for ERAD, while constitutive ER-phagy recognizes cargo different from that recognized by ERAD, these two ER-QC pathways can partially substitute for each other. Because accumulation of membrane proteins is associated with disease, and constitutive ER-phagy players are conserved from yeast to mammalian cells, this process could be critical for human health.
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54
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Wang X, Xu Z, Cai Y, Zeng S, Peng B, Ren X, Yan Y, Gong Z. Rheostatic Balance of Circadian Rhythm and Autophagy in Metabolism and Disease. Front Cell Dev Biol 2020; 8:616434. [PMID: 33330516 PMCID: PMC7732583 DOI: 10.3389/fcell.2020.616434] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/04/2020] [Indexed: 02/05/2023] Open
Abstract
Circadian rhythms are physical, behavioral and environmental cycles that respond primarily to light and dark, with a period of time of approximately 24 h. The most essential physiological functions of mammals are manifested in circadian rhythm patterns, including the sleep-wake cycle and nutrient and energy metabolism. Autophagy is a conserved biological process contributing to nutrient and cellular homeostasis. The factors affecting autophagy are numerous, such as diet, drugs, and aging. Recent studies have indicated that autophagy is activated rhythmically in a clock-dependent manner whether the organism is healthy or has certain diseases. In addition, autophagy can affect circadian rhythm by degrading circadian proteins. This review discusses the interaction and mechanisms between autophagy and circadian rhythm. Moreover, we introduce the molecules influencing both autophagy and circadian rhythm. We then discuss the drugs affecting the circadian rhythm of autophagy. Finally, we present the role of rhythmic autophagy in nutrient and energy metabolism and its significance in physiology and metabolic disease.
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Affiliation(s)
- Xiang Wang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Yuan Cai
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Shuangshuang Zeng
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Bi Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Xinxin Ren
- Key Laboratory of Molecular Radiation Oncology of Hunan Province, Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Zhicheng Gong
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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55
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Abstract
Endosomal microautophagy (eMI) is a type of autophagy that allows for the selective uptake and degradation of cytosolic proteins in late endosome/multi-vesicular bodies (LE/MVB). This process starts with the recognition of a pentapeptide amino acid KFERQ-like targeting motif in the substrate protein by the hsc70 chaperone, which then enables binding and subsequent uptake of the protein into the LE/MVB compartment. The recognition of a KFERQ-like motif by hsc70 is the same initial step in chaperone-mediated autophagy (CMA), a form of selective autophagy that degrades the hsc70-targeted proteins in lysosomes in a LAMP-2A dependent manner. The shared step of substrate recognition by hsc70, originally identified for CMA, makes it now necessary to differentiate between the two pathways. Here, we detail biochemical and imaging-based methods to track eMI activity in vitro with isolated LE/MVBs and in cells in culture using fluorescent reporters and highlight approaches to distinguish whether a protein is a substrate of eMI or CMA.
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Affiliation(s)
- Gregory J Krause
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, New York, NY, United States; Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY, United States
| | - Ana Maria Cuervo
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, New York, NY, United States; Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY, United States.
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56
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Omari S, Makareeva E, Gorrell L, Jarnik M, Lippincott-Schwartz J, Leikin S. Mechanisms of procollagen and HSP47 sorting during ER-to-Golgi trafficking. Matrix Biol 2020; 93:79-94. [DOI: 10.1016/j.matbio.2020.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 12/27/2022]
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57
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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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58
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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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59
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COPII mitigates ER stress by promoting formation of ER whorls. Cell Res 2020; 31:141-156. [PMID: 32989223 PMCID: PMC8026990 DOI: 10.1038/s41422-020-00416-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/28/2020] [Indexed: 12/19/2022] Open
Abstract
Cells mitigate ER stress through the unfolded protein response (UPR). Here, we report formation of ER whorls as an effector mechanism of the ER stress response. We found that strong ER stress induces formation of ER whorls, which contain ER-resident proteins such as the Sec61 complex and PKR-like ER kinase (PERK). ER whorl formation is dependent on PERK kinase activity and is mediated by COPII machinery, which facilitates ER membrane budding to form tubular-vesicular ER whorl precursors. ER whorl precursors then go through Sec22b-mediated fusion to form ER whorls. We further show that ER whorls contribute to ER stress-induced translational inhibition by possibly modulating PERK activity and by sequestering translocons in a ribosome-free environment. We propose that formation of ER whorls reflects a new type of ER stress response that controls inhibition of protein translation.
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60
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Snf1 AMPK positively regulates ER-phagy via expression control of Atg39 autophagy receptor in yeast ER stress response. PLoS Genet 2020; 16:e1009053. [PMID: 32986716 PMCID: PMC7544123 DOI: 10.1371/journal.pgen.1009053] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 10/08/2020] [Accepted: 08/14/2020] [Indexed: 12/13/2022] Open
Abstract
Autophagy is a fundamental process responsible for degradation and recycling of intracellular contents. In the budding yeast, non-selective macroautophagy and microautophagy of the endoplasmic reticulum (ER) are caused by ER stress, the circumstance where aberrant proteins accumulate in the ER. The more recent study showed that protein aggregation in the ER initiates ER-selective macroautophagy, referred to as ER-phagy; however, the mechanisms by which ER stress induces ER-phagy have not been fully elucidated. Here, we show that the expression levels of ATG39, encoding an autophagy receptor specific for ER-phagy, are significantly increased under ER-stressed conditions. ATG39 upregulation in ER stress response is mediated by activation of its promoter, which is positively regulated by Snf1 AMP-activated protein kinase (AMPK) and negatively by Mig1 and Mig2 transcriptional repressors. In response to ER stress, Snf1 promotes nuclear export of Mig1 and Mig2. Our results suggest that during ER stress response, Snf1 mediates activation of the ATG39 promoter and consequently facilitates ER-phagy by negatively regulating Mig1 and Mig2.
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61
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Zhao D, Zou CX, Liu XM, Jiang ZD, Yu ZQ, Suo F, Du TY, Dong MQ, He W, Du LL. A UPR-Induced Soluble ER-Phagy Receptor Acts with VAPs to Confer ER Stress Resistance. Mol Cell 2020; 79:963-977.e3. [PMID: 32735772 DOI: 10.1016/j.molcel.2020.07.019] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/01/2020] [Accepted: 07/20/2020] [Indexed: 01/07/2023]
Abstract
Autophagic degradation of the endoplasmic reticulum (ER-phagy) is triggered by ER stress in diverse organisms. However, molecular mechanisms governing ER stress-induced ER-phagy remain insufficiently understood. Here we report that ER stress-induced ER-phagy in the fission yeast Schizosaccharomyces pombe requires Epr1, a soluble Atg8-interacting ER-phagy receptor. Epr1 localizes to the ER through interacting with integral ER membrane proteins VAPs. Bridging an Atg8-VAP association is the main ER-phagy role of Epr1, as it can be bypassed by an artificial Atg8-VAP tether. VAPs contribute to ER-phagy not only by tethering Atg8 to the ER membrane, but also by maintaining the ER-plasma membrane contact. Epr1 is upregulated during ER stress by the unfolded protein response (UPR) regulator Ire1. Loss of Epr1 reduces survival against ER stress. Conversely, increasing Epr1 expression suppresses the ER-phagy defect and ER stress sensitivity of cells lacking Ire1. Our findings expand and deepen the molecular understanding of ER-phagy.
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Affiliation(s)
- Dan Zhao
- National Institute of Biological Sciences, 102206 Beijing, China
| | - Chen-Xi Zou
- College of Life Sciences, Beijing Normal University, 100875 Beijing, China; National Institute of Biological Sciences, 102206 Beijing, China
| | - Xiao-Man Liu
- National Institute of Biological Sciences, 102206 Beijing, China
| | - Zhao-Di Jiang
- National Institute of Biological Sciences, 102206 Beijing, China
| | - Zhong-Qiu Yu
- National Institute of Biological Sciences, 102206 Beijing, China
| | - Fang Suo
- National Institute of Biological Sciences, 102206 Beijing, China
| | - Tong-Yang Du
- College of Life Sciences, Beijing Normal University, 100875 Beijing, China; National Institute of Biological Sciences, 102206 Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, 102206 Beijing, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 102206 Beijing, China
| | - Wanzhong He
- National Institute of Biological Sciences, 102206 Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, 102206 Beijing, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 102206 Beijing, China.
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62
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Bo Otto F, Thumm M. Nucleophagy-Implications for Microautophagy and Health. Int J Mol Sci 2020; 21:ijms21124506. [PMID: 32599961 PMCID: PMC7352367 DOI: 10.3390/ijms21124506] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/18/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
Nucleophagy, the selective subtype of autophagy that targets nuclear material for autophagic degradation, was not only shown to be a model system for the study of selective macroautophagy, but also for elucidating the role of the core autophagic machinery within microautophagy. Nucleophagy also emerged as a system associated with a variety of disease conditions including cancer, neurodegeneration and ageing. Nucleophagic processes are part of natural cell development, but also act as a response to various stress conditions. Upon releasing small portions of nuclear material, micronuclei, the autophagic machinery transfers these micronuclei to the vacuole for subsequent degradation. Despite sharing many cargos and requiring the core autophagic machinery, recent investigations revealed the aspects that set macro- and micronucleophagy apart. Central to the discrepancies found between macro- and micronucleophagy is the nucleus vacuole junction, a large membrane contact site formed between nucleus and vacuole. Exclusion of nuclear pore complexes from the junction and its exclusive degradation by micronucleophagy reveal compositional differences in cargo. Regarding their shared reliance on the core autophagic machinery, micronucleophagy does not involve normal autophagosome biogenesis observed for macronucleophagy, but instead maintains a unique role in overall microautophagy, with the autophagic machinery accumulating at the neck of budding vesicles.
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63
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The Role of Deubiquitinating Enzymes in the Various Forms of Autophagy. Int J Mol Sci 2020; 21:ijms21124196. [PMID: 32545524 PMCID: PMC7352190 DOI: 10.3390/ijms21124196] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 12/20/2022] Open
Abstract
Deubiquitinating enzymes (DUBs) have an essential role in several cell biological processes via removing the various ubiquitin patterns as posttranslational modification forms from the target proteins. These enzymes also contribute to the normal cytoplasmic ubiquitin pool during the recycling of this molecule. Autophagy, a summary name of the lysosome dependent self-degradative processes, is necessary for maintaining normal cellular homeostatic equilibrium. Numerous forms of autophagy are known depending on how the cellular self-material is delivered into the lysosomal lumen. In this review we focus on the colorful role of DUBs in autophagic processes and discuss the mechanistic contribution of these molecules to normal cellular homeostasis via the possible regulation forms of autophagic mechanisms.
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64
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65
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Kaul Z, Mookherjee D, Das S, Chatterjee D, Chakrabarti S, Chakrabarti O. Loss of tumor susceptibility gene 101 (TSG101) perturbs endoplasmic reticulum structure and function. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118741. [PMID: 32422153 DOI: 10.1016/j.bbamcr.2020.118741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 05/02/2020] [Accepted: 05/08/2020] [Indexed: 12/30/2022]
Abstract
Tumor susceptibility gene 101 (TSG101), an ESCRT-I protein, is implicated in multiple cellular processes and its functional depletion can lead to blocked lysosomal degradation, cell cycle arrest, demyelination and neurodegeneration. Here, we show that loss of TSG101 results in endoplasmic reticulum (ER) stress and this causes ER membrane remodelling (EMR). This correlates with an expansion of ER, increased vacuolation, altered relative distribution of the rough and smooth ER and disruption of three-way junctions. Blocked lysosomal degradation due to TSG101 depletion leads to ER stress and Ca2+ leakage from ER stores, causing destabilization of actin cytoskeleton. Inhibiting Ca2+ release from the ER by blocking ryanodine receptors (RYRs) with Dantrolene partially rescues the ER stress phenotypes. Hence, in this study we have identified the involvement of TSG101 in modulating ER stress mediated remodelling by engaging the actin cytoskeleton. This is significant because functional depletion of TSG101 effectuates ER-stress, perturbs the structure, mobility and function of the ER, all aspects closely associated with neurodegenerative diseases. SUMMARY STATEMENT: We show that tumor susceptibility gene (TSG) 101 regulates endoplasmic reticulum (ER) stress and its membrane remodelling. Loss of TSG101 perturbs structure, mobility and function of the ER as a consequence of actin destabilization.
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Affiliation(s)
- Zenia Kaul
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA..
| | - Debdatto Mookherjee
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Subhrangshu Das
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, CN 6, Sector V, Salt Lake, Kolkata 700091, India
| | - Debmita Chatterjee
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Saikat Chakrabarti
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, CN 6, Sector V, Salt Lake, Kolkata 700091, India
| | - Oishee Chakrabarti
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Homi Bhabha National Institute, India.
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66
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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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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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ER-Phagy: Quality Control and Turnover of Endoplasmic Reticulum. Trends Cell Biol 2020; 30:384-398. [PMID: 32302550 DOI: 10.1016/j.tcb.2020.02.001] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/30/2020] [Accepted: 02/03/2020] [Indexed: 12/11/2022]
Abstract
The endoplasmic reticulum (ER) is the largest organelle in cells and has fundamental functions, such as folding, processing, and trafficking of proteins, cellular metabolism, and ion storage. To maintain its function, it is turned over constitutively, and even more actively under certain stress conditions. Quality control of the ER is mediated primarily by two pathways: the ubiquitin-proteasome system and autophagy (termed 'ER-phagy'). The identification of ER-phagy adaptor molecules has shed light on the mechanisms and physiological significance of ER-phagy. Here, we describe recent findings on various types of ER-phagy and present unanswered questions related to their mechanism and regulation.
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Affiliation(s)
- Nava Segev
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail:
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70
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Li J, Hochstrasser M. Microautophagy regulates proteasome homeostasis. Curr Genet 2020; 66:683-687. [PMID: 32077993 DOI: 10.1007/s00294-020-01059-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 01/28/2020] [Accepted: 01/30/2020] [Indexed: 02/06/2023]
Abstract
Proteasomes are highly abundant protein complexes that are responsible for most regulated protein degradation in cells under favorable growth conditions. When yeast cells are under nutritional stress, most proteasomes exit the nucleus and either accumulate in cytoplasmic condensates called proteasome storage granules (PSGs) or are directed to the vacuole by autophagy. Nitrogen starvation does not cause PSG formation but leads to degradation of proteasomes through the classical macroautophagy pathway. By contrast, carbon starvation or extended incubation in stationary phase results in both PSG formation and macroautophagy of proteasomes. Unexpectedly, we found that glucose limitation also causes proteasomes to be taken up directly into vacuoles by a microautophagy mechanism. Macro- and micro-autophagy occur in parallel in glucose-starved cells, and microautophagy appears biased toward aberrant or inactive proteasomes, leaving functional proteasomes to accumulate in PSGs. PSGs dissolve and proteasomes remobilize to the nucleus within minutes after glucose refeeding. We showed that AMP-activated protein kinase (AMPK) and endosomal-sorting-complex-required-for-transport (ESCRT) factors are required for proteasome microautophagy and also impact PSG dissipation and nuclear reimport of proteasomes after glucose refeeding. The insoluble protein deposit (IPOD) compartment provides an alternative means of proteasome homeostasis, including when microautophagy is impaired. Our findings reveal a surprising diversity of mechanisms for proteasome quality and quantity control during starvation. A mechanistic understanding of the AMPK-regulated ESCRT-mediated microautophagy pathway could provide new avenues for manipulating proteasome homeostasis and treating human disease.
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Affiliation(s)
- Jianhui Li
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA. .,Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA.
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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: 52] [Impact Index Per Article: 13.0] [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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Abstract
Changing conditions necessitate cellular adaptation, which frequently entails adjustment of organelle size and shape. The endoplasmic reticulum (ER) is an organelle of exceptional morphological plasticity. In budding yeast, ER stress triggers the de novo formation of ER subdomains called ER whorls. These whorls are selectively degraded by a poorly defined type of microautophagy. We recently showed that ESCRT proteins are essential for microautophagic uptake of ER whorls into lysosomes, likely by mediating the final scission of the lysosomal membrane. Furthermore, ER-selective microautophagy acts in parallel with ER-selective macroautophagy. The molecular machineries for these two types of autophagy are distinct and their contributions to ER turnover vary according to conditions, suggesting that they serve different functions. Our study provides evidence for a direct role of ESCRTs in microautophagy and extends our understanding of how autophagy promotes organelle homeostasis.
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Affiliation(s)
- Jasmin A Schäfer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, Heidelberg, Germany
| | - Sebastian Schuck
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, Heidelberg, Germany
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