151
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D'Eletto M, Oliverio S, Di Sano F. Reticulon Homology Domain-Containing Proteins and ER-Phagy. Front Cell Dev Biol 2020; 8:90. [PMID: 32154249 PMCID: PMC7047209 DOI: 10.3389/fcell.2020.00090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/04/2020] [Indexed: 12/17/2022] Open
Abstract
The endoplasmic reticulum (ER) is a dynamic membrane system comprising different and interconnected subdomains. The ER structure changes in response to different stress conditions through the activation of a selective autophagic pathway called ER-phagy. This represents a quality control mechanism for ER turnover and component recycling. Several ER-resident proteins have been indicated as receptors for ER-phagy; among these, there are proteins characterized by the presence of a reticulon homology domain (RHD). RHD-containing proteins promote ER fragmentation by a mechanism that involves LC3 binding and lysosome delivery. Moreover, the presence of a correct RHD structure is closely related to their capability to regulate ER shape and morphology by curvature induction and membrane remodeling. Deregulation of the ER-selective autophagic pathway due to defects in proteins with RHD has been implicated in several human diseases, infectious and neurodegenerative diseases in particular, as well as in cancer development. While the molecular mechanisms and the physiological role of ER-phagy are not yet fully understood, it is quite clear that this process is involved in different cellular signaling pathways and has an impact in several human pathologies.
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Affiliation(s)
- Manuela D'Eletto
- Department of Biology, University of Rome "Tor Vergata," Rome, Italy
| | - Serafina Oliverio
- Department of Biology, University of Rome "Tor Vergata," Rome, Italy
| | - Federica Di Sano
- Department of Biology, University of Rome "Tor Vergata," Rome, Italy
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152
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Abdrakhmanov A, Gogvadze V, Zhivotovsky B. To Eat or to Die: Deciphering Selective Forms of Autophagy. Trends Biochem Sci 2020; 45:347-364. [PMID: 32044127 DOI: 10.1016/j.tibs.2019.11.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 11/09/2019] [Accepted: 11/18/2019] [Indexed: 12/23/2022]
Abstract
Autophagy is an evolutionarily conserved process whereby damaged and redundant components of the cell are degraded in structures called autophagolysosomes. Currently, three main types of autophagy are recognized: macroautophagy, microautophagy, and chaperone-mediated autophagy (CMA). However, we still know little about some specific types of autophagy that are linked to various intracellular compartments and their roles in the physiology of the whole organism and connections to various diseases. Here, we aim to shed light on the latest insights on and mechanisms of several selective forms of autophagy.
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Affiliation(s)
- Alibek Abdrakhmanov
- Faculty of Medicine, MV Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vladimir Gogvadze
- Faculty of Medicine, MV Lomonosov Moscow State University, 119991 Moscow, Russia; Division of Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 210, 17177 Stockholm, Sweden
| | - Boris Zhivotovsky
- Faculty of Medicine, MV Lomonosov Moscow State University, 119991 Moscow, Russia; Division of Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 210, 17177 Stockholm, Sweden.
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153
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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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154
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Stefely JA, Zhang Y, Freiberger EC, Kwiecien NW, Thomas HE, Davis AM, Lowry ND, Vincent CE, Shishkova E, Clark NA, Medvedovic M, Coon JJ, Pagliarini DJ, Mercer CA. Mass spectrometry proteomics reveals a function for mammalian CALCOCO1 in MTOR-regulated selective autophagy. Autophagy 2020; 16:2219-2237. [PMID: 31971854 DOI: 10.1080/15548627.2020.1719746] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Macroautophagy/autophagy is suppressed by MTOR (mechanistic target of rapamycin kinase) and is an anticancer target under active investigation. Yet, MTOR-regulated autophagy remains incompletely mapped. We used proteomic profiling to identify proteins in the MTOR-autophagy axis. Wild-type (WT) mouse cell lines and cell lines lacking individual autophagy genes (Atg5 or Ulk1/Ulk2) were treated with an MTOR inhibitor to induce autophagy and cultured in media with either glucose or galactose. Mass spectrometry proteome profiling revealed an elevation of known autophagy proteins and candidates for new autophagy components, including CALCOCO1 (calcium binding and coiled-coil domain protein 1). We show that CALCOCO1 physically interacts with MAP1LC3C, a key protein in the machinery of autophagy. Genetic deletion of CALCOCO1 disrupted autophagy of the endoplasmic reticulum (reticulophagy). Together, these results reveal a role for CALCOCO1 in MTOR-regulated selective autophagy. More generally, the resource generated by this work provides a foundation for establishing links between the MTOR-autophagy axis and proteins not previously linked to this pathway. Abbreviations: ATG: autophagy-related; CALCOCO1: calcium binding and coiled-coil domain protein 1; CALCOCO2/NDP52: calcium binding and coiled-coil domain protein 2; CLIR: MAP1LC3C-interacting region; CQ: chloroquine; KO: knockout; LIR: MAP1LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MEF: mouse embryonic fibroblast; MLN: MLN0128 ATP-competitive MTOR kinase inhibitor; MTOR: mechanistic target of rapamycin kinase; reticulophagy: selective autophagy of the endoplasmic reticulum; TAX1BP1/CALCOCO3: TAX1 binding protein 1; ULK: unc 51-like autophagy activating kinase; WT: wild-type.
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Affiliation(s)
- Jonathan A Stefely
- Morgridge Institute for Research , Madison, WI, USA.,Medical Scientist Training Program, School of Medicine and Public Health, University of Wisconsin-Madison , Madison, WI, USA.,Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Yu Zhang
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Elyse C Freiberger
- Department of Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Department of Biomolecular Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Genome Center of Wisconsin , Madison, WI, USA.,Department of Biochemistry, University ofWisconsin-Madison , Madison, Madison, WI, USA
| | - Nicholas W Kwiecien
- Department of Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Department of Biomolecular Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Genome Center of Wisconsin , Madison, WI, USA.,Department of Biochemistry, University ofWisconsin-Madison , Madison, Madison, WI, USA
| | - Hala Elnakat Thomas
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Alexander M Davis
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Nathaniel D Lowry
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Catherine E Vincent
- Genome Center of Wisconsin , Madison, WI, USA.,Department of Chemistry, Hartwick College , Oneonta, NY, USA
| | | | - Nicholas A Clark
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati , Cincinnati, OH, USA
| | - Mario Medvedovic
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati , Cincinnati, OH, USA
| | - Joshua J Coon
- Morgridge Institute for Research , Madison, WI, USA.,Department of Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Department of Biomolecular Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Genome Center of Wisconsin , Madison, WI, USA
| | - David J Pagliarini
- Morgridge Institute for Research , Madison, WI, USA.,Department of Biochemistry, University ofWisconsin-Madison , Madison, Madison, WI, USA
| | - Carol A Mercer
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
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155
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Öztürk Z, O’Kane CJ, Pérez-Moreno JJ. Axonal Endoplasmic Reticulum Dynamics and Its Roles in Neurodegeneration. Front Neurosci 2020; 14:48. [PMID: 32116502 PMCID: PMC7025499 DOI: 10.3389/fnins.2020.00048] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 01/13/2020] [Indexed: 12/13/2022] Open
Abstract
The physical continuity of axons over long cellular distances poses challenges for their maintenance. One organelle that faces this challenge is endoplasmic reticulum (ER); unlike other intracellular organelles, this forms a physically continuous network throughout the cell, with a single membrane and a single lumen. In axons, ER is mainly smooth, forming a tubular network with occasional sheets or cisternae and low amounts of rough ER. It has many potential roles: lipid biosynthesis, glucose homeostasis, a Ca2+ store, protein export, and contacting and regulating other organelles. This tubular network structure is determined by ER-shaping proteins, mutations in some of which are causative for neurodegenerative disorders such as hereditary spastic paraplegia (HSP). While axonal ER shares many features with the tubular ER network in other contexts, these features must be adapted to the long and narrow dimensions of axons. ER appears to be physically continuous throughout axons, over distances that are enormous on a subcellular scale. It is therefore a potential channel for long-distance or regional communication within neurons, independent of action potentials or physical transport of cargos, but involving its physiological roles such as Ca2+ or organelle homeostasis. Despite its apparent stability, axonal ER is highly dynamic, showing features like anterograde and retrograde transport, potentially reflecting continuous fusion and breakage of the network. Here we discuss the transport processes that must contribute to this dynamic behavior of ER. We also discuss the model that these processes underpin a homeostatic process that ensures both enough ER to maintain continuity of the network and repair breaks in it, but not too much ER that might disrupt local cellular physiology. Finally, we discuss how failure of ER organization in axons could lead to axon degenerative diseases, and how a requirement for ER continuity could make distal axons most susceptible to degeneration in conditions that disrupt ER continuity.
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Affiliation(s)
| | - Cahir J. O’Kane
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
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156
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Beese CJ, Brynjólfsdóttir SH, Frankel LB. Selective Autophagy of the Protein Homeostasis Machinery: Ribophagy, Proteaphagy and ER-Phagy. Front Cell Dev Biol 2020; 7:373. [PMID: 32039200 PMCID: PMC6985035 DOI: 10.3389/fcell.2019.00373] [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: 11/11/2019] [Accepted: 12/16/2019] [Indexed: 01/06/2023] Open
Abstract
The eukaryotic cell has developed intricate machineries that monitor and maintain proteome homeostasis in order to ensure cellular functionality. This involves the carefully coordinated balance between protein synthesis and degradation pathways, which are dynamically regulated in order to meet the constantly changing demands of the cell. Ribosomes, together with the endoplasmic reticulum (ER), are the key drivers of protein synthesis, folding, maturation and sorting, while the proteasome plays a pivotal role in terminating the existence of thousands of proteins that are misfolded, damaged or otherwise obsolete. The synthesis, structure and function of these dedicated machines has been studied for decades, however, much less is understood about the mechanisms that control and execute their own turnover. Autophagy, an evolutionarily conserved catabolic pathway, mediates degradation of a large variety of cytosolic substrates, ranging from single proteins to entire organelles or multi-subunit macromolecular complexes. In this review, we focus on selective autophagy of three key components of the protein homeostasis machinery: ribosomes, ER and proteasomes, through the selective autophagy pathways of ribophagy, ER-phagy, and proteaphagy. We discuss newly discovered mechanisms for the selective clearance of these substrates, which are often stress-dependent and involve specialized signals for cargo recognition by a growing number of receptors. We further discuss the interplay between these pathways and their biological impact on key aspects of proteome homeostasis and cellular function in health and disease.
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Affiliation(s)
- Carsten J Beese
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.,Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | - Lisa B Frankel
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.,Danish Cancer Society Research Center, Copenhagen, Denmark
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157
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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 2020; 39:e102586. [PMID: 31802527 PMCID: PMC6960443 DOI: 10.15252/embj.2019102586] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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 ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
| | - Julia P Schessner
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
- Present address:
Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Peter W Bircham
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
- Present address:
Laboratory of Systems BiologyVIB Center for Microbiology/Laboratory of Genetics and GenomicsCMPGKU LeuvenLeuvenBelgium
| | - Takuma Tsuji
- Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan
| | - Charlotta Funaya
- Electron Microscopy Core FacilityHeidelberg UniversityHeidelbergGermany
| | - Oliver Pajonk
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
| | - Katharina Schaeff
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
| | - Giulia Ruffini
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
| | - Dimitrios Papagiannidis
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
| | - Michael Knop
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
| | - Toyoshi Fujimoto
- Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan
| | - Sebastian Schuck
- DKFZ‐ZMBH Alliance and CellNetworks Cluster of ExcellenceCenter for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
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158
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Jiang X, Wang X, Ding X, Du M, Li B, Weng X, Zhang J, Li L, Tian R, Zhu Q, Chen S, Wang L, Liu W, Fang L, Neculai D, Sun Q. FAM134B oligomerization drives endoplasmic reticulum membrane scission for ER-phagy. EMBO J 2020; 39:e102608. [PMID: 31930741 DOI: 10.15252/embj.2019102608] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 11/19/2019] [Accepted: 12/10/2019] [Indexed: 12/30/2022] Open
Abstract
Degradation of endoplasmic reticulum (ER) by selective autophagy (ER-phagy) is crucial for ER homeostasis. However, it remains unclear how ER scission is regulated for subsequent autophagosomal sequestration and lysosomal degradation. Here, we show that oligomerization of ER-phagy receptor FAM134B (also referred to as reticulophagy regulator 1 or RETREG1) through its reticulon-homology domain is required for membrane fragmentation in vitro and ER-phagy in vivo. Under ER-stress conditions, activated CAMK2B phosphorylates the reticulon-homology domain of FAM134B, which enhances FAM134B oligomerization and activity in membrane fragmentation to accommodate high demand for ER-phagy. Unexpectedly, FAM134B G216R, a variant derived from a type II hereditary sensory and autonomic neuropathy (HSAN) patient, exhibits gain-of-function defects, such as hyperactive self-association and membrane scission, which results in excessive ER-phagy and sensory neuron death. Therefore, this study reveals a mechanism of ER membrane fragmentation in ER-phagy, along with a signaling pathway in regulating ER turnover, and suggests a potential implication of excessive selective autophagy in human diseases.
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Affiliation(s)
- Xiao Jiang
- Department of Biochemistry, Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinyi Wang
- Department of Biochemistry, Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xianming Ding
- Department of Biochemistry, Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengjie Du
- Department of Neurology of Second Affiliated Hospital, Institute of Neuroscience, Mental Health Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou, China
| | - Boran Li
- Department of Biochemistry, Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xialian Weng
- Department of Cell Biology, Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jingzi Zhang
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, China
| | - Rui Tian
- Department of Biochemistry, Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qi Zhu
- Department of Biochemistry, Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, China
| | - Liang Wang
- Department of Neurology of Second Affiliated Hospital, Institute of Neuroscience, Mental Health Center, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Liu
- Department of Biochemistry, Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lei Fang
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Dante Neculai
- Department of Cell Biology, Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiming Sun
- Department of Biochemistry, Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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159
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Kirkin V. History of the Selective Autophagy Research: How Did It Begin and Where Does It Stand Today? J Mol Biol 2020; 432:3-27. [PMID: 31082435 PMCID: PMC6971693 DOI: 10.1016/j.jmb.2019.05.010] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 02/07/2023]
Abstract
Autophagy, self-eating, is a pivotal catabolic mechanism that ensures homeostasis and survival of the cell in the face of stressors as different as starvation, infection, or protein misfolding. The importance of the research in this field was recognized by the general public after the Nobel Prize for Physiology or Medicine was awarded in 2016 to Yoshinori Ohsumi for discoveries of the mechanisms of autophagy using yeast as a model organism. One of the seminal findings of Ohsumi was on the role ubiquitin-like proteins (UBLs)-Atg5, Atg12, and Atg8-play in the formation of the double-membrane vesicle autophagosome, which is the functional unit of autophagy. Subsequent work by several groups demonstrated that, like the founding member of the UBL family ubiquitin, these small but versatile protein and lipid modifiers interact with a plethora of proteins, which either directly regulate autophagosome formation, for example, components of the Atg1/ULK1 complex, or are involved in cargo recognition, for example, Atg19 and p62/SQSTM1. By tethering the cargo to the UBLs present on the forming autophagosome, the latter proteins were proposed to effectively act as selective autophagy receptors. The discovery of the selective autophagy receptors brought a breakthrough in the autophagy field, supplying the mechanistic underpinning for the formation of an autophagosome selectively around the cytosolic cargo, that is, a protein aggregate, a mitochondrion, or a cytosolic bacterium. In this historical overview, I highlight key steps that the research into selective autophagy has been taking over the past 20 years. I comment on their significance and discuss current challenges in developing more detailed knowledge of the mechanisms of selective autophagy. I will conclude by introducing the new directions that this dynamic research field is taking into its third decade.
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Affiliation(s)
- Vladimir Kirkin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK.
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160
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Wilkinson S. Emerging Principles of Selective ER Autophagy. J Mol Biol 2020; 432:185-205. [PMID: 31100386 PMCID: PMC6971691 DOI: 10.1016/j.jmb.2019.05.012] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/07/2019] [Accepted: 05/07/2019] [Indexed: 12/13/2022]
Abstract
The endoplasmic reticulum (ER) is a fundamental organelle in cellular metabolism and signal transduction. It is subject to complex, dynamic sculpting of morphology and composition. Degradation of ER content has an important role to play here. Indeed, a major emerging player in ER turnover is ER-phagy, the degradation of ER fragments by selective autophagy, particularly macroautophagy. This article proposes a number of unifying principles of ER-phagy mechanism and compares these with other selective autophagy pathways. A perspective on the likely roles of ER-phagy in determining cell fate is provided. Emerging related forms of intracellular catabolism of the ER or contents, including ER-phagy by microautophagy and selective ER protein removal via the lysosome, are outlined for comparison. Unresolved questions regarding the mechanism of ER-phagy and its significance in cellular and organismal health are put forward. This review concludes with a perspective on how this fundamental knowledge might inform future clinical developments.
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Affiliation(s)
- Simon Wilkinson
- Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, EH4 2XR, United Kingdom
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161
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Shin D, Mukherjee R, Liu Y, Gonzalez A, Bonn F, Liu Y, Rogov VV, Heinz M, Stolz A, Hummer G, Dötsch V, Luo ZQ, Bhogaraju S, Dikic I. Regulation of Phosphoribosyl-Linked Serine Ubiquitination by Deubiquitinases DupA and DupB. Mol Cell 2020; 77:164-179.e6. [PMID: 31732457 PMCID: PMC6941232 DOI: 10.1016/j.molcel.2019.10.019] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/07/2019] [Accepted: 10/11/2019] [Indexed: 12/21/2022]
Abstract
The family of bacterial SidE enzymes catalyzes non-canonical phosphoribosyl-linked (PR) serine ubiquitination and promotes infectivity of Legionella pneumophila. Here, we describe identification of two bacterial effectors that reverse PR ubiquitination and are thus named deubiquitinases for PR ubiquitination (DUPs; DupA and DupB). Structural analyses revealed that DupA and SidE ubiquitin ligases harbor a highly homologous catalytic phosphodiesterase (PDE) domain. However, unlike SidE ubiquitin ligases, DupA displays increased affinity to PR-ubiquitinated substrates, which allows DupA to cleave PR ubiquitin from substrates. Interfering with DupA-ubiquitin binding switches its activity toward SidE-type ligase. Given the high affinity of DupA to PR-ubiquitinated substrates, we exploited a catalytically inactive DupA mutant to trap and identify more than 180 PR-ubiquitinated host proteins in Legionella-infected cells. Proteins involved in endoplasmic reticulum (ER) fragmentation and membrane recruitment to Legionella-containing vacuoles (LCV) emerged as major SidE targets. The global map of PR-ubiquitinated substrates provides critical insights into host-pathogen interactions during Legionella infection.
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Affiliation(s)
- Donghyuk Shin
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Rukmini Mukherjee
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Yaobin Liu
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Alexis Gonzalez
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Florian Bonn
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Yan Liu
- Purdue Institute of Immunology, Inflammation, and Infectious Diseases and Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Vladimir V Rogov
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance and Cluster of Excellence Macromolecular Complexes (CEF), Goethe University, Frankfurt, Germany
| | - Marcel Heinz
- Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany; Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Alexandra Stolz
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany; Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance and Cluster of Excellence Macromolecular Complexes (CEF), Goethe University, Frankfurt, Germany
| | - Zhao-Qing Luo
- Purdue Institute of Immunology, Inflammation, and Infectious Diseases and Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Sagar Bhogaraju
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany.
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162
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NAKATOGAWA H. Autophagic degradation of the endoplasmic reticulum. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2020; 96:1-9. [PMID: 31932525 PMCID: PMC6974406 DOI: 10.2183/pjab.96.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 10/11/2019] [Indexed: 06/10/2023]
Abstract
Autophagy is an intracellular degradation system that is present in most eukaryotes. In the process of autophagy, double membrane vesicles called autophagosomes sequester a wide variety of cellular constituents and deliver them to lytic organelles: lysosomes in mammals and vacuoles in yeast and plants. Although autophagy used to be considered a non-selective process in its target sequestration into autophagosomes, recent studies have revealed that autophagosomes can also selectively sequester certain proteins and organelles that have become unnecessary or harmful for the cell. We recently discovered that the endoplasmic reticulum (ER) is degraded by autophagy in a selective manner in the budding yeast Saccharomyces cerevisiae, and identified "receptor proteins" that play pivotal roles in this "ER-phagy" pathway. Moreover, several ER-phagy receptors in mammalian cells have also been reported. This report provides an overview of our current knowledge on ER-phagy and discuss their mechanisms, physiological roles, and possible links to human diseases.
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Affiliation(s)
- Hitoshi NAKATOGAWA
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
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163
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Johansen T, Lamark T. Selective Autophagy: ATG8 Family Proteins, LIR Motifs and Cargo Receptors. J Mol Biol 2020; 432:80-103. [DOI: 10.1016/j.jmb.2019.07.016] [Citation(s) in RCA: 203] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/05/2019] [Accepted: 07/05/2019] [Indexed: 12/21/2022]
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164
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Abstract
In consistent with other membrane-bound and secretory proteins, immune checkpoint proteins go through a set of modifications in the endoplasmic reticulum (ER) to acquire their native functional structures before they function at their destinations. There are various ER-resident chaperones and enzymes synergistically regulate and catalyze the glycosylation, folding and transporting of proteins. The whole processing is under the surveillance of ER quality control system which allows the correctly folded proteins to exit from the ER with the help of coat proteinII(COPII) coated vesicles, while retains the rest of terminally misfolded ones in the ER and then eliminates them via ER-associated degradation (ERAD) or ER-to-lysosomes-associated degradation (ERLAD). The dysfunction of the ER causes ER stress which triggers unfolded protein response (UPR) to restore ER proteostasis. Unsolvable prolonged ER stress ultimately results in cell death. This chapter reviews the process that proteins undergo in the ER, and the glycosylation, folding and degradation of immune checkpoint proteins as well as the associated potential immunotherapies to date.
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165
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Stephani M, Dagdas Y. Plant Selective Autophagy—Still an Uncharted Territory With a Lot of Hidden Gems. J Mol Biol 2020; 432:63-79. [DOI: 10.1016/j.jmb.2019.06.028] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/22/2019] [Accepted: 06/24/2019] [Indexed: 11/28/2022]
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166
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Stolz A, Grumati P. The various shades of ER-phagy. FEBS J 2019; 286:4642-4649. [PMID: 31386802 PMCID: PMC6916603 DOI: 10.1111/febs.15031] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/16/2019] [Accepted: 08/02/2019] [Indexed: 12/18/2022]
Abstract
Endoplasmic reticulum (ER) is a large and dynamic cellular organelle. ER morphology consists of sheets, tubules, matrixes, and contact sites shared with other membranous organelles. The capacity of the ER to fulfill its numerous biological functions depends on its continuous remodeling and the quality control of its proteome. Selective turnover of the ER by autophagy, termed ER-phagy, plays an important role in maintaining ER homeostasis. ER network integrity and turnover rely on specific ER-phagy receptors, which influence and coordinate alterations in ER morphology and the degradation of ER contents and membranes via the lysosome, by interacting with the LC3/GABARAP family. In this commentary, we discuss general principles and identify the major players in this recently characterized form of selective autophagy, while simultaneously highlighting open questions in the field.
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Affiliation(s)
- Alexandra Stolz
- Structural Genomics Consortium, BMLSGoethe UniversityFrankfurtGermany
- Institute of Biochemistry 2Goethe University School of MedicineFrankfurtGermany
| | - Paolo Grumati
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
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167
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Loi M, Raimondi A, Morone D, Molinari M. ESCRT-III-driven piecemeal micro-ER-phagy remodels the ER during recovery from ER stress. Nat Commun 2019; 10:5058. [PMID: 31699981 PMCID: PMC6838186 DOI: 10.1038/s41467-019-12991-z] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/10/2019] [Indexed: 12/13/2022] Open
Abstract
The endoplasmic reticulum (ER) produces about 40% of the nucleated cell's proteome. ER size and content in molecular chaperones increase upon physiologic and pathologic stresses on activation of unfolded protein responses (UPR). On stress resolution, the mammalian ER is remodeled to pre-stress, physiologic size and function on activation of the LC3-binding activity of the translocon component SEC62. This elicits recov-ER-phagy, i.e., the delivery of the excess ER generated during the phase of stress to endolysosomes (EL) for clearance. Here, ultrastructural and genetic analyses reveal that recov-ER-phagy entails the LC3 lipidation machinery and proceeds via piecemeal micro-ER-phagy, where RAB7/LAMP1-positive EL directly engulf excess ER in processes that rely on the Endosomal Sorting Complex Required for Transport (ESCRT)-III component CHMP4B and the accessory AAA+ ATPase VPS4A. Thus, ESCRT-III-driven micro-ER-phagy emerges as a key catabolic pathway activated to remodel the mammalian ER on recovery from ER stress.
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Affiliation(s)
- Marisa Loi
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Bellinzona, Switzerland
- Department of Biology, Swiss Federal Institute of Technology, 8093, Zurich, Switzerland
| | - Andrea Raimondi
- Experimental Imaging Center, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Diego Morone
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Maurizio Molinari
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Bellinzona, Switzerland.
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland.
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168
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ER-phagy and human diseases. Cell Death Differ 2019; 27:833-842. [PMID: 31659280 DOI: 10.1038/s41418-019-0444-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/04/2019] [Accepted: 10/11/2019] [Indexed: 12/27/2022] Open
Abstract
Autophagy regulates the degradation of unnecessary or dysfunctional cellular components. This catabolic process requires the formation of a double-membrane vesicle, the autophagosome, that engulfs the cytosolic material and delivers it to the lysosome. Substrate specificity is achieved by autophagy receptors, which are characterized by the presence of at least one LC3-interaction region (LIR) or GABARAP-interaction motif (GIM). Only recently, several receptors that mediate the specific degradation of endoplasmic reticulum (ER) components via autophagy have been identified (the process known as ER-phagy or reticulophagy). Here, we give an update on the current knowledge about the role of ER-phagy receptors in health and disease.
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169
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Conway O, Akpinar HA, Rogov VV, Kirkin V. Selective Autophagy Receptors in Neuronal Health and Disease. J Mol Biol 2019; 432:2483-2509. [PMID: 31654670 DOI: 10.1016/j.jmb.2019.10.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/27/2019] [Accepted: 10/10/2019] [Indexed: 12/14/2022]
Abstract
Neurons are electrically excitable, postmitotic cells that perform sensory, relaying, and motor functions. Because of their unique morphological and functional specialization, cells of this type are sensitive to the stress caused by accumulation of misfolded proteins or damaged organelles. Autophagy is the fundamental mechanism that ensures sequestration of cytosolic material and its subsequent degradation in lysosomes of eukaryotic cells, thereby providing cell-autonomous nutrients and removing harmful cargos. Strikingly, mice and flies lacking functional autophagy develop early onset progressive neurodegeneration. Like in human neurodegenerative diseases (NDDs)-Alzheimer's disease, Parkinson's disease, frontotemporal dementia, Huntington's disease, and amyotrophic lateral sclerosis-characteristic protein aggregates observed in autophagy-deficient neurons in the animal models are indicators of the ongoing neuronal pathology. A number of selective autophagy receptors (SARs) have been characterized that interact both with the cargo and components of the autophagic machinery, thus providing the molecular basis for selective degradation of sizable cytosolic components. Interference with autophagy in experimental models, but also during the pathological vagaries in neurons, will thus have far-reaching consequences for a range of selective autophagy pathways critical for the normal functioning of the nervous system. Here, we review the key principles behind the selective autophagy and discuss how the SARs may be involved in the pathogenesis of NDDs. Using recently published examples, we also examine the emerging role of less well studied selective autophagy pathways in neuronal health and disease. We conclude by discussing targeting selective autophagy as an emerging therapeutic modality in NDDs.
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Affiliation(s)
- Owen Conway
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK
| | - Hafize Aysin Akpinar
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK
| | - Vladimir V Rogov
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt Am Main, Germany
| | - Vladimir Kirkin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK.
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170
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Kirkin V, Rogov VV. A Diversity of Selective Autophagy Receptors Determines the Specificity of the Autophagy Pathway. Mol Cell 2019; 76:268-285. [PMID: 31585693 DOI: 10.1016/j.molcel.2019.09.005] [Citation(s) in RCA: 296] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/03/2019] [Accepted: 09/06/2019] [Indexed: 12/21/2022]
Abstract
The clearance of surplus, broken, or dangerous components is key for maintaining cellular homeostasis. The failure to remove protein aggregates, damaged organelles, or intracellular pathogens leads to diseases, including neurodegeneration, cancer, and infectious diseases. Autophagy is the evolutionarily conserved pathway that sequesters cytoplasmic components in specialized vesicles, autophagosomes, which transport the cargo to the degradative compartments (vacuoles or lysosomes). Research during the past few decades has elucidated how autophagosomes engulf their substrates selectively. This type of autophagy involves a growing number of selective autophagy receptors (SARs) (e.g., Atg19 in yeasts, p62/SQSTM1 in mammals), which bind to the cargo and simultaneously engage components of the core autophagic machinery via direct interaction with the ubiquitin-like proteins (UBLs) of the Atg8/LC3/GABARAP family and adaptors, Atg11 (in yeasts) or FIP200 (in mammals). In this Review, we critically discuss the biology of the SARs with special emphasis on their interactions with UBLs.
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Affiliation(s)
- Vladimir Kirkin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research London, Sutton SM2 5NG, UK.
| | - Vladimir V Rogov
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Strasse 9, 60438 Frankfurt am Main, Germany.
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171
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Sun Z, Brodsky JL. Protein quality control in the secretory pathway. J Cell Biol 2019; 218:3171-3187. [PMID: 31537714 PMCID: PMC6781448 DOI: 10.1083/jcb.201906047] [Citation(s) in RCA: 228] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/22/2019] [Accepted: 08/29/2019] [Indexed: 12/23/2022] Open
Abstract
Protein folding is inherently error prone, especially in the endoplasmic reticulum (ER). Even with an elaborate network of molecular chaperones and protein folding facilitators, misfolding can occur quite frequently. To maintain protein homeostasis, eukaryotes have evolved a series of protein quality-control checkpoints. When secretory pathway quality-control pathways fail, stress response pathways, such as the unfolded protein response (UPR), are induced. In addition, the ER, which is the initial hub of protein biogenesis in the secretory pathway, triages misfolded proteins by delivering substrates to the proteasome or to the lysosome/vacuole through ER-associated degradation (ERAD) or ER-phagy. Some misfolded proteins escape the ER and are instead selected for Golgi quality control. These substrates are targeted for degradation after retrieval to the ER or delivery to the lysosome/vacuole. Here, we discuss how these guardian pathways function, how their activities intersect upon induction of the UPR, and how decisions are made to dispose of misfolded proteins in the secretory pathway.
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Affiliation(s)
- Zhihao Sun
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
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172
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Mechanistic Connections between Endoplasmic Reticulum (ER) Redox Control and Mitochondrial Metabolism. Cells 2019; 8:cells8091071. [PMID: 31547228 PMCID: PMC6769559 DOI: 10.3390/cells8091071] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/06/2019] [Accepted: 09/07/2019] [Indexed: 12/21/2022] Open
Abstract
The past decade has seen the emergence of endoplasmic reticulum (ER) chaperones as key determinants of contact formation between mitochondria and the ER on the mitochondria-associated membrane (MAM). Despite the known roles of ER–mitochondria tethering factors like PACS-2 and mitofusin-2, it is not yet entirely clear how they mechanistically interact with the ER environment to determine mitochondrial metabolism. In this article, we review the mechanisms used to communicate ER redox and folding conditions to the mitochondria, presumably with the goal of controlling mitochondrial metabolism at the Krebs cycle and at the electron transport chain, leading to oxidative phosphorylation (OXPHOS). To achieve this goal, redox nanodomains in the ER and the interorganellar cleft influence the activities of ER chaperones and Ca2+-handling proteins to signal to mitochondria. This mechanism, based on ER chaperones like calnexin and ER oxidoreductases like Ero1α, controls reactive oxygen production within the ER, which can chemically modify the proteins controlling ER–mitochondria tethering, or mitochondrial membrane dynamics. It can also lead to the expression of apoptotic or metabolic transcription factors. The link between mitochondrial metabolism and ER homeostasis is evident from the specific functions of mitochondria–ER contact site (MERC)-localized Ire1 and PERK. These functions allow these two transmembrane proteins to act as mitochondria-preserving guardians, a function that is apparently unrelated to their functions in the unfolded protein response (UPR). In scenarios where ER stress cannot be resolved via the activation of mitochondrial OXPHOS, MAM-localized autophagosome formation acts to remove defective portions of the ER. ER chaperones such as calnexin are again critical regulators of this MERC readout.
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173
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De Leonibus C, Cinque L, Settembre C. Emerging lysosomal pathways for quality control at the endoplasmic reticulum. FEBS Lett 2019; 593:2319-2329. [PMID: 31388984 DOI: 10.1002/1873-3468.13571] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 07/30/2019] [Accepted: 08/02/2019] [Indexed: 01/01/2023]
Abstract
Protein misfolding occurring in the endoplasmic reticulum (ER) might eventually lead to aggregation and cellular distress, and is a primary pathogenic mechanism in multiple human disorders. Mammals have developed evolutionary-conserved quality control mechanisms at the level of the ER. The best characterized is the ER-associated degradation (ERAD) pathway, through which misfolded proteins translocate from the ER to the cytosol and are subsequently proteasomally degraded. However, increasing evidence indicates that additional quality control mechanisms apply for misfolded ER clients that are not eligible for ERAD. This review focuses on the alternative, ERAD-independent, mechanisms of clearance of misfolded polypeptides from the ER. These processes, collectively referred to as ER-to-lysosome-associated degradation, involve ER-phagy, microautophagy or vesicular transport. The identification of the underlying molecular mechanisms is particularly important for developing new therapeutic approaches for human diseases associated with protein aggregate formation.
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Affiliation(s)
| | - Laura Cinque
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Carmine Settembre
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.,Department of Medical and Translational Science, University of Naples "Federico II", Italy
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174
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Delorme-Axford E, Popelka H, Klionsky DJ. TEX264 is a major receptor for mammalian reticulophagy. Autophagy 2019; 15:1677-1681. [PMID: 31362563 DOI: 10.1080/15548627.2019.1646540] [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] [Indexed: 12/14/2022] Open
Abstract
The endoplasmic reticulum (ER) is the main site of cellular protein and calcium homeostasis, as well as lipid synthesis in eukaryotic cells. Reticulophagy is the selective clearance and degradation of ER components and membranes by the cellular autophagy machinery. Recently, 2 groups (the laboratories of Noboru Mizushima and Wade Harper) independently identified the previously uncharacterized protein TEX264 (testis expressed gene 264) as a major receptor for selective reticulophagy in mammalian cells. Here we highlight and integrate the major findings of their recent work. Abbreviations: AIM: Atg8-interacting motif; AP-MS: affinity purification-mass spectrometry; ATL3: atlastin GTPase 3; Baf A1: bafilomycin A1; CCPG1: cell cycle progression 1; CRISPR: clustered regularly interspaced short palindromic repeats; GABARAP: gamma-aminobutyric acid receptor associated protein; GFP: green fluorescent protein; GyrI: gyrase inhibitor; IDR: intrinsically disordered region; IP: immunoprecipitation; KO: knockout; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MEF: mouse embryonic fibroblast; MS: mass spectrometry; MTOR: mechanistic target of rapamycin kinase; RB1CC1/FIP200: RB1-inducible coiled-coil 1; RFP: red fluorescent protein; RNAi: RNA interference; RTN3: reticulon 3; RTN3L: long isoform of RTN3; siRNA: small interfering RNA; SARS: selective autophagy receptors; ss: signal sequence; TEM: transmission electron microscopy, TEX264: testis expressed gene 264; TMT: tandem mass tagging.
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Affiliation(s)
| | - Hana Popelka
- Life Sciences Institute, University of Michigan , Ann Arbor , MI , USA
| | - Daniel J Klionsky
- Life Sciences Institute, University of Michigan , Ann Arbor , MI , USA
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175
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Evans CS, Holzbaur ELF. Quality Control in Neurons: Mitophagy and Other Selective Autophagy Mechanisms. J Mol Biol 2019; 432:240-260. [PMID: 31295455 DOI: 10.1016/j.jmb.2019.06.031] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/28/2019] [Accepted: 06/29/2019] [Indexed: 12/19/2022]
Abstract
The cargo-specific removal of organelles via selective autophagy is important to maintain neuronal homeostasis. Genetic studies indicate that deficits in these pathways are implicated in neurodegenerative diseases, including Parkinson's and amyotrophic lateral sclerosis. Here, we review our current understanding of the pathways that regulate mitochondrial quality control, and compare these mechanisms to those regulating turnover of the endoplasmic reticulum and the clearance of protein aggregates. Research suggests that there are multiple mechanisms regulating the degradation of specific cargos, such as dysfunctional organelles and protein aggregates. These mechanisms are critical for neuronal health, as neurons are uniquely vulnerable to impairment in organelle quality control pathways due to their morphology, size, polarity, and postmitotic nature. We highlight the consequences of dysregulation of selective autophagy in neurons and discuss current challenges in correlating noncongruent findings from in vitro and in vivo systems.
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Affiliation(s)
- Chantell S Evans
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6085, USA.
| | - Erika L F Holzbaur
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6085, USA.
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176
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Abstract
Macroautophagy is an intracellular degradation system that delivers diverse cytoplasmic materials to lysosomes via autophagosomes. Recent advances have enabled identification of several selective autophagy substrates and receptors, greatly expanding our understanding of the cellular functions of autophagy. In this review, we describe the diverse cellular functions of macroautophagy, including its essential contribution to metabolic adaptation and cellular homeostasis. We also discuss emerging findings on the mechanisms and functions of various types of selective autophagy.
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Affiliation(s)
- Hideaki Morishita
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; ,
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; ,
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177
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An H, Harper JW. Ribosome Abundance Control Via the Ubiquitin-Proteasome System and Autophagy. J Mol Biol 2019; 432:170-184. [PMID: 31195016 DOI: 10.1016/j.jmb.2019.06.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/03/2019] [Accepted: 06/03/2019] [Indexed: 12/13/2022]
Abstract
Ribosomes are central to the life of a cell, as they translate the genetic code into the amino acid language of proteins. Moreover, ribosomal abundance within the cell is coordinated with protein production required for cell function or processes such as cell division. As such, it is not surprising that these elegant machines are both highly regulated at the level of both their output of newly translated proteins but also at the level of ribosomal protein expression, ribosome assembly, and ribosome turnover. In this review, we focus on mechanisms that regulate ribosome abundance through both the ubiquitin-proteasome system and forms of autophagy referred to as "ribophagy." We discussed mechanisms employed in both yeast and mammalian cells, including the various machineries that are important for recognition and degradation of ribosomal components. In addition, we discussed controversies in the field and how the development of new approaches for examining flux through the proteasomal and autophagic systems in the context of a systematic inventory of ribosomal components is necessary to fully understand how ribosome abundance is controlled under various physiological conditions.
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Affiliation(s)
- Heeseon An
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA.
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178
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Wilkinson S. Picky Eating at the ER-phagy Buffet. Trends Biochem Sci 2019; 44:731-733. [PMID: 31176531 DOI: 10.1016/j.tibs.2019.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 05/17/2019] [Accepted: 05/24/2019] [Indexed: 12/28/2022]
Abstract
The degradation of the endoplasmic reticulum (ER) by autophagy (ER-phagy) regulates proteostasis. Two studies (An et al., Mol. Cell, 2019; Chino et al., Mol. Cell, 2019) have uncovered a new ER-phagy molecule, TEX264, yielding insight into how ER is packaged for degradation, and have illuminated the extent of redundancy between different ER-phagy 'pathways' in remodelling the ER proteome.
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Affiliation(s)
- Simon Wilkinson
- Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, UK.
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179
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Wilkinson S. ER-phagy: shaping up and destressing the endoplasmic reticulum. FEBS J 2019; 286:2645-2663. [PMID: 31116513 PMCID: PMC6772018 DOI: 10.1111/febs.14932] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/09/2019] [Accepted: 05/20/2019] [Indexed: 12/16/2022]
Abstract
The endoplasmic reticulum (ER) network has central roles in metabolism and cellular organization. The ER undergoes dynamic alterations in morphology, molecular composition and functional specification. Remodelling of the network under fluctuating conditions enables the continual performance of ER functions and minimizes stress. Recent data have revealed that selective autophagy‐mediated degradation of ER fragments, or ER‐phagy, fundamentally contributes to this remodelling. This review provides a perspective on established views of selective autophagy, comparing these with emerging mechanisms of ER‐phagy and related processes. The text discusses the impact of ER‐phagy on the function of the ER‐ and the cell, both in normal physiology and when dysregulated within disease settings. Finally, unanswered questions regarding the mechanisms and significance of ER‐phagy are highlighted.
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Affiliation(s)
- Simon Wilkinson
- Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
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