201
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Phase Separation in Membrane Biology: The Interplay between Membrane-Bound Organelles and Membraneless Condensates. Dev Cell 2020; 55:30-44. [PMID: 32726575 DOI: 10.1016/j.devcel.2020.06.033] [Citation(s) in RCA: 196] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/14/2020] [Accepted: 06/26/2020] [Indexed: 12/13/2022]
Abstract
In eukaryotic cells, various membrane-bound organelles compartmentalize diverse cellular activities in a spatially and temporally controlled manner. Numerous membraneless organelles assembled via liquid-liquid phase separation (LLPS), known as condensates, also facilitate compartmentalization of cellular functions. Emerging evidence shows that these two organelle types interact in many biological processes. Membranes modulate the biogenesis and dynamics of phase-separated condensates by serving as assembly platforms or by forming direct contacts. Phase separation of membrane-associated proteins participates in various trafficking events, such as clustering of vesicles for temporally controlled fusion and storage, and transport of membraneless condensates on membrane-bound organelles. Phase separation also acts in cargo trafficking pathways by sorting and docking cargos for translocon-mediated transport across membranes, by shuttling cargos through the nuclear pore complex, and by triggering the formation of surrounding autophagosomes for delivery to lysosomes. The coordinated actions of membrane-bound and membraneless organelles ensure spatiotemporal control of various cellular functions.
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202
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Cinque L, De Leonibus C, Iavazzo M, Krahmer N, Intartaglia D, Salierno FG, De Cegli R, Di Malta C, Svelto M, Lanzara C, Maddaluno M, Wanderlingh LG, Huebner AK, Cesana M, Bonn F, Polishchuk E, Hübner CA, Conte I, Dikic I, Mann M, Ballabio A, Sacco F, Grumati P, Settembre C. MiT/TFE factors control ER-phagy via transcriptional regulation of FAM134B. EMBO J 2020; 39:e105696. [PMID: 32716134 PMCID: PMC7459426 DOI: 10.15252/embj.2020105696] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/11/2020] [Accepted: 06/18/2020] [Indexed: 01/08/2023] Open
Abstract
Lysosomal degradation of the endoplasmic reticulum (ER) via autophagy (ER-phagy) is emerging as a critical regulator of cell homeostasis and function. The recent identification of ER-phagy receptors has shed light on the molecular mechanisms underlining this process. However, the signaling pathways regulating ER-phagy in response to cellular needs are still largely unknown. We found that the nutrient responsive transcription factors TFEB and TFE3-master regulators of lysosomal biogenesis and autophagy-control ER-phagy by inducing the expression of the ER-phagy receptor FAM134B. The TFEB/TFE3-FAM134B axis promotes ER-phagy activation upon prolonged starvation. In addition, this pathway is activated in chondrocytes by FGF signaling, a critical regulator of skeletal growth. FGF signaling induces JNK-dependent proteasomal degradation of the insulin receptor substrate 1 (IRS1), which in turn inhibits the PI3K-PKB/Akt-mTORC1 pathway and promotes TFEB/TFE3 nuclear translocation and enhances FAM134B transcription. Notably, FAM134B is required for protein secretion in chondrocytes, and cartilage growth and bone mineralization in medaka fish. This study identifies a new signaling pathway that allows ER-phagy to respond to both metabolic and developmental cues.
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Affiliation(s)
- Laura Cinque
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | | | - Maria Iavazzo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Natalie Krahmer
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Munich-Neuherberg, Germany.,Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | | | - Rossella De Cegli
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Chiara Di Malta
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Maria Svelto
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Carmela Lanzara
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | | | | | - Antje K Huebner
- Institute of Human Genetics, Jena University Hospital, Friedrich-Schiller-University Jena, Jena, Germany
| | - Marcella Cesana
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.,Department of Advanced Biomedical Sciences, University of Naples "Federico II", Naples, Italy
| | - Florian Bonn
- Institute of Biochemistry II, Goethe University Frankfurt - Medical Faculty, University Hospital, Frankfurt am Main, Germany
| | - Elena Polishchuk
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Christian A Hübner
- Institute of Human Genetics, Jena University Hospital, Friedrich-Schiller-University Jena, Jena, Germany
| | - Ivan Conte
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.,Department of Biology, University of Naples "Federico II", Naples, Italy
| | - Ivan Dikic
- Institute of Human Genetics, Jena University Hospital, Friedrich-Schiller-University Jena, Jena, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Frankfurt am Main, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.,Faculty of Health Sciences, NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.,Department of Translational Medicine, Federico II University, Naples, Italy.,Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Francesca Sacco
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Paolo Grumati
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Carmine Settembre
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.,Department of Translational Medicine, Federico II University, Naples, Italy
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203
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Sharma P, Dando I, Strippoli R, Kumar S, Somoza A, Cordani M, Tafani M. Nanomaterials for Autophagy-Related miRNA-34a Delivery in Cancer Treatment. Front Pharmacol 2020; 11:1141. [PMID: 32792960 PMCID: PMC7393066 DOI: 10.3389/fphar.2020.01141] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 07/13/2020] [Indexed: 01/03/2023] Open
Abstract
Autophagy is an evolutionary conserved physiological process with a fundamental role during development, differentiation, and survival of eukaryotic cells. On the other hand, autophagy dysregulation is observed in many pathological conditions, including cancer. In particular, tumor growth and progression are accompanied and promoted by increased autophagy that allows cancer cells to escape apoptosis and to proliferate also in harsh microenvironments. It is, therefore, clear that the impairment of the autophagic process may represent a valid strategy to inhibit or reduce cancer growth and progression. Among the plethora of molecular players controlling cancer growth, a group of small endogenous noncoding RNAs called microRNAs (miRNAs) has recently emerged. In fact, miRNAs can act as either oncogenes or oncosuppressors depending on their target genes. Moreover, among miRNAs, miRNA-34a has been connected with both tumor repression and autophagy regulation, and its expression is frequently lost in many cancers. Therefore, enforced expression of miRNA-34a in cancer cells may represent a valid strategy to reduce cancer growth. However, such strategy is limited by the fast biodegradation and short half-life of miRNA-34a and by the lack of an efficient intracellular delivery system. The following review describes the autophagic process and its role in cancer as well as the role of miRNAs in general and miRNA-34a in particular in regulating tumor growth by modulating autophagy. Finally, we describe the use of nanoparticles as a promising strategy to selectively deliver miRNA-34a to tumor cells for therapeutic and diagnostic purposes.
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Affiliation(s)
- Priyanka Sharma
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, NM, United States
| | - Ilaria Dando
- Section of Biochemistry, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Raffaele Strippoli
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy.,Gene Expression Laboratory, National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS, Rome, Italy
| | - Suresh Kumar
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, United States
| | | | | | - Marco Tafani
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
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204
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Sun H, Wang J, Xing Y, Pan YH, Mao X. Gut transcriptomic changes during hibernation in the greater horseshoe bat ( Rhinolophus ferrumequinum). Front Zool 2020; 17:21. [PMID: 32690984 PMCID: PMC7366455 DOI: 10.1186/s12983-020-00366-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 07/10/2020] [Indexed: 11/10/2022] Open
Abstract
Background The gut is the major organ for nutrient absorption and immune response in the body of animals. Although effects of fasting on the gut functions have been extensively studied in model animals (e.g. mice), little is known about the response of the gut to fasting in a natural condition (e.g. hibernation). During hibernation, animals endure the long term of fasting and hypothermia. Results Here we generated the first gut transcriptome in a wild hibernating bat (Rhinolophus ferrumequinum). We identified 1614 differentially expressed genes (DEGs) during four physiological states (Torpor, Arousal, Winter Active and Summer Active). Gene co-expression network analysis assigns 926 DEGs into six modules associated with Torpor and Arousal. Our results reveal that in response to the stress of luminal nutrient deficiency during hibernation, the gut helps to reduce food intake by overexpressing genes (e.g. CCK and GPR17) that regulate the sensitivity to insulin and leptin. At the same time, the gut contributes energy supply by overexpressing genes that increase capacity for ketogenesis (HMGCS2) and selective autophagy (TEX264). Furthermore, we identified separate sets of multiple DEGs upregulated in Torpor and Arousal whose functions are involved in innate immunity. Conclusion This is the first gut transcriptome of a hibernating mammal. Our study identified candidate genes associated with regulation of food intake and enhance of innate immunity in the gut during hibernation. By comparing with previous studies, we found that two DEGs (CPE and HSPA8) were also significantly elevated during torpor in liver and brain of R. ferrumequinum and several DEGs (e.g. TXNIP and PDK1/4) were commonly upregulated during torpor in multiple tissues of different mammals. Our results support that shared expression changes may underlie the hibernation phenotype by most mammals.
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Affiliation(s)
- Haijian Sun
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200062 China
| | - Jiaying Wang
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062 China
| | - Yutong Xing
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062 China
| | - Yi-Hsuan Pan
- Key Laboratory of Brain Functional Genomics of Ministry of Education, School of Life Science, East China Normal University, Shanghai, 200062 China
| | - Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200062 China.,Institute of Eco-Chongming (IEC), East China Normal University, Shanghai, 200062 China
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205
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Mochida K, Yamasaki A, Matoba K, Kirisako H, Noda NN, Nakatogawa H. Super-assembly of ER-phagy receptor Atg40 induces local ER remodeling at contacts with forming autophagosomal membranes. Nat Commun 2020; 11:3306. [PMID: 32620754 PMCID: PMC7335187 DOI: 10.1038/s41467-020-17163-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 06/11/2020] [Indexed: 12/15/2022] Open
Abstract
The endoplasmic reticulum (ER) is selectively degraded by autophagy (ER-phagy) through proteins called ER-phagy receptors. In Saccharomyces cerevisiae, Atg40 acts as an ER-phagy receptor to sequester ER fragments into autophagosomes by binding Atg8 on forming autophagosomal membranes. During ER-phagy, parts of the ER are morphologically rearranged, fragmented, and loaded into autophagosomes, but the mechanism remains poorly understood. Here we find that Atg40 molecules assemble in the ER membrane concurrently with autophagosome formation via multivalent interaction with Atg8. Atg8-mediated super-assembly of Atg40 generates highly-curved ER regions, depending on its reticulon-like domain, and supports packing of these regions into autophagosomes. Moreover, tight binding of Atg40 to Atg8 is achieved by a short helix C-terminal to the Atg8-family interacting motif, and this feature is also observed for mammalian ER-phagy receptors. Thus, this study significantly advances our understanding of the mechanisms of ER-phagy and also provides insights into organelle fragmentation in selective autophagy of other organelles.
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Affiliation(s)
- Keisuke Mochida
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Akinori Yamasaki
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Kazuaki Matoba
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
| | - Hiromi Kirisako
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan.
| | - Hitoshi Nakatogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.
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206
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Mookherjee D, Das S, Mukherjee R, Bera M, Jana SC, Chakrabarti S, Chakrabarti O. RETREG1/FAM134B mediated autophagosomal degradation of AMFR/GP78 and OPA1 -a dual organellar turnover mechanism. Autophagy 2020; 17:1729-1752. [PMID: 32559118 DOI: 10.1080/15548627.2020.1783118] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Turnover of cellular organelles, including endoplasmic reticulum (ER) and mitochondria, is orchestrated by an efficient cellular surveillance system. We have identified a mechanism for dual regulation of ER and mitochondria under stress. It is known that AMFR, an ER E3 ligase and ER-associated degradation (ERAD) regulator, degrades outer mitochondrial membrane (OMM) proteins, MFNs (mitofusins), via the proteasome and triggers mitophagy. We show that destabilized mitochondria are almost devoid of the OMM and generate "mitoplasts". This brings the inner mitochondrial membrane (IMM) in the proximity of the ER. When AMFR levels are high and the mitochondria are stressed, the reticulophagy regulatory protein RETREG1 participates in the formation of the mitophagophore by interacting with OPA1. Interestingly, OPA1 and other IMM proteins exhibit similar RETREG1-dependent autophagosomal degradation as AMFR, unlike most of the OMM proteins. The "mitoplasts" generated are degraded by reticulo-mito-phagy - simultaneously affecting dual organelle turnover.Abbreviations: AMFR/GP78: autocrine motility factor receptor; BAPTA: 1,2-bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid; BFP: blue fluorescent protein; CCCP: carbonyl cyanide m-chlorophenyl hydrazone; CNBr: cyanogen bromide; ER: endoplasmic reticulum; ERAD: endoplasmic-reticulum-associated protein degradation; FL: fluorescence, GFP: green fluorescent protein; HA: hemagglutinin; HEPES: 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid; IMM: inner mitochondrial membrane; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MFN: mitofusin, MGRN1: mahogunin ring finger 1; NA: numerical aperature; OMM: outer mitochondrial membrane; OPA1: OPA1 mitochondrial dynamin like GTPase; PRNP/PrP: prion protein; RER: rough endoplasmic reticulum; RETREG1/FAM134B: reticulophagy regulator 1; RFP: red fluorescent protein; RING: really interesting new gene; ROI: region of interest; RTN: reticulon; SEM: standard error of the mean; SER: smooth endoplasmic reticulum; SIM: structured illumination microscopy; SQSTM1/p62: sequestosome 1; STED: stimulated emission depletion; STOML2: stomatin like 2; TOMM20: translocase of outer mitochondrial membrane 20; UPR: unfolded protein response.
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Affiliation(s)
- Debdatto Mookherjee
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Subhrangshu Das
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Rukmini Mukherjee
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India.,Buchmann Institute for Molecular Life Sciences, Frankfurt Am Main, Germany
| | - Manindra Bera
- Laboratory of Cell Biology, the Rockefeller University, New York, USA
| | | | - Saikat Chakrabarti
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Oishee Chakrabarti
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India.,Homi Bhabha National Institute, Mumbai, India
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207
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An H, Ordureau A, Körner M, Paulo JA, Harper JW. Systematic quantitative analysis of ribosome inventory during nutrient stress. Nature 2020; 583:303-309. [PMID: 32612236 PMCID: PMC7351614 DOI: 10.1038/s41586-020-2446-y] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 05/07/2020] [Indexed: 12/14/2022]
Abstract
Mammalian cells reorganize their proteomes in response to nutrient stress through translational suppression and degradative mechanisms using the proteasome and autophagy systems1,2. Ribosomes are central targets of this response, as they are responsible for translation and subject to lysosomal turnover during nutrient stress3-5. The abundance of ribosomal (r)-proteins (around 6% of the proteome; 107 copies per cell)6,7 and their high arginine and lysine content has led to the hypothesis that they are selectively used as a source of basic amino acids during nutrient stress through autophagy4,7. However, the relative contributions of translational and degradative mechanisms to the control of r-protein abundance during acute stress responses is poorly understood, as is the extent to which r-proteins are used to generate amino acids when specific building blocks are limited7. Here, we integrate quantitative global translatome and degradome proteomics8 with genetically encoded Ribo-Keima5 and Ribo-Halo reporters to interrogate r-protein homeostasis with and without active autophagy. In conditions of acute nutrient stress, cells strongly suppress the translation of r-proteins, but, notably, r-protein degradation occurs largely through non-autophagic pathways. Simultaneously, the decrease in r-protein abundance is compensated for by a reduced dilution of pre-existing ribosomes and a reduction in cell volume, thereby maintaining the density of ribosomes within single cells. Withdrawal of basic or hydrophobic amino acids induces translational repression without differential induction of ribophagy, indicating that ribophagy is not used to selectively produce basic amino acids during acute nutrient stress. We present a quantitative framework that describes the contributions of biosynthetic and degradative mechanisms to r-protein abundance and proteome remodelling in conditions of nutrient stress.
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Affiliation(s)
- Heeseon An
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Alban Ordureau
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Maria Körner
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Biochemistry, University of Würzburg, Würzburg, Germany
| | - Joao A Paulo
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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208
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Sora V, Kumar M, Maiani E, Lambrughi M, Tiberti M, Papaleo E. Structure and Dynamics in the ATG8 Family From Experimental to Computational Techniques. Front Cell Dev Biol 2020; 8:420. [PMID: 32587856 PMCID: PMC7297954 DOI: 10.3389/fcell.2020.00420] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/06/2020] [Indexed: 12/31/2022] Open
Abstract
Autophagy is a conserved and essential intracellular mechanism for the removal of damaged components. Since autophagy deregulation is linked to different kinds of pathologies, it is fundamental to gain knowledge on the fine molecular and structural details related to the core proteins of the autophagy machinery. Among these, the family of human ATG8 proteins plays a central role in recruiting other proteins to the different membrane structures involved in the autophagic pathway. Several experimental structures are available for the members of the ATG8 family alone or in complex with their different biological partners, including disordered regions of proteins containing a short linear motif called LC3 interacting motif. Recently, the first structural details of the interaction of ATG8 proteins with biological membranes came into light. The availability of structural data for human ATG8 proteins has been paving the way for studies on their structure-function-dynamic relationship using biomolecular simulations. Experimental and computational structural biology can help to address several outstanding questions on the mechanism of human ATG8 proteins, including their specificity toward different interactors, their association with membranes, the heterogeneity of their conformational ensemble, and their regulation by post-translational modifications. We here summarize the main results collected so far and discuss the future perspectives within the field and the knowledge gaps. Our review can serve as a roadmap for future structural and dynamics studies of the ATG8 family members in health and disease.
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Affiliation(s)
- Valentina Sora
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Mukesh Kumar
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Emiliano Maiani
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Matteo Lambrughi
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Matteo Tiberti
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Elena Papaleo
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
- Translational Disease System Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
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209
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210
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Chiritoiu M, Chiritoiu GN, Munteanu CVA, Pastrama F, Ivessa NE, Petrescu SM. EDEM1 Drives Misfolded Protein Degradation via ERAD and Exploits ER-Phagy as Back-Up Mechanism When ERAD Is Impaired. Int J Mol Sci 2020; 21:ijms21103468. [PMID: 32423001 PMCID: PMC7279049 DOI: 10.3390/ijms21103468] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/30/2020] [Accepted: 05/07/2020] [Indexed: 01/20/2023] Open
Abstract
Endoplasmic reticulum (ER)-associated degradation (ERAD) is the main mechanism of targeting ER proteins for degradation to maintain homeostasis, and perturbations of ERAD lead to pathological conditions. ER-degradation enhancing α-mannosidase-like (EDEM1) was proposed to extract terminally misfolded proteins from the calnexin folding cycle and target them for degradation by ERAD. Here, using mass-spectrometry and biochemical methods, we show that EDEM1 is found in auto-regulatory complexes with ERAD components. Moreover, the N-terminal disordered region of EDEM1 mediates protein–protein interaction with misfolded proteins, whilst the absence of this domain significantly impairs their degradation. We also determined that overexpression of EDEM1 can induce degradation, even when proteasomal activity is severely impaired, by promoting the formation of aggregates, which can be further degraded by autophagy. Therefore, we propose that EDEM1 maintains ER homeostasis and mediates ERAD client degradation via autophagy when either dislocation or proteasomal degradation are impaired.
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Affiliation(s)
- Marioara Chiritoiu
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (M.C.); (G.N.C.)
| | - Gabriela N. Chiritoiu
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (M.C.); (G.N.C.)
| | - Cristian V. A. Munteanu
- Department of Bioinformatics & Structural Biochemistry, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (C.V.A.M.); (F.P.)
| | - Florin Pastrama
- Department of Bioinformatics & Structural Biochemistry, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (C.V.A.M.); (F.P.)
| | - N. Erwin Ivessa
- Center for Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, A-1030 Vienna, Austria;
| | - Stefana M. Petrescu
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (M.C.); (G.N.C.)
- Correspondence: ; Tel.: +40-2-1223-9069
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211
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Shiozaki Y, Miyazaki-Anzai S, Okamura K, Keenan AL, Masuda M, Miyazaki M. GPAT4-Generated Saturated LPAs Induce Lipotoxicity through Inhibition of Autophagy by Abnormal Formation of Omegasomes. iScience 2020; 23:101105. [PMID: 32408172 PMCID: PMC7225743 DOI: 10.1016/j.isci.2020.101105] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/16/2019] [Accepted: 04/22/2020] [Indexed: 12/26/2022] Open
Abstract
Excessive levels of saturated fatty acids are toxic to vascular smooth muscle cells (VSMCs). We previously reported that mice lacking VSMC-stearoyl-CoA desaturase (SCD), a major enzyme catalyzing the detoxification of saturated fatty acids, develop severe vascular calcification from the massive accumulation of lipid metabolites containing saturated fatty acids. However, the mechanism by which SCD deficiency causes vascular calcification is not completely understood. Here, we demonstrate that saturated fatty acids significantly inhibit autophagic flux in VSMCs, contributing to vascular calcification and apoptosis. Mechanistically, saturated fatty acids are accumulated as saturated lysophosphatidic acids (LPAs) (i.e. 1-stearoyl-LPA) possibly synthesized through the reaction of GPAT4 at the contact site between omegasomes and the MAM. The accumulation of saturated LPAs at the contact site causes abnormal formation of omegasomes, resulting in accumulation of autophagosomal precursor isolation membranes, leading to inhibition of autophagic flux. Thus, saturated LPAs are major metabolites mediating autophagy inhibition and vascular calcification.
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Affiliation(s)
- Yuji Shiozaki
- Division of Renal Diseases and Hypertension, University of Colorado-Denver, Aurora, CO, USA
| | - Shinobu Miyazaki-Anzai
- Division of Renal Diseases and Hypertension, University of Colorado-Denver, Aurora, CO, USA
| | - Kayo Okamura
- Division of Renal Diseases and Hypertension, University of Colorado-Denver, Aurora, CO, USA
| | - Audrey L Keenan
- Division of Renal Diseases and Hypertension, University of Colorado-Denver, Aurora, CO, USA
| | - Masashi Masuda
- Division of Renal Diseases and Hypertension, University of Colorado-Denver, Aurora, CO, USA
| | - Makoto Miyazaki
- Division of Renal Diseases and Hypertension, University of Colorado-Denver, Aurora, CO, USA.
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212
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Li Z, Huang W, Wang W. Multifaceted roles of COPII subunits in autophagy. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118627. [DOI: 10.1016/j.bbamcr.2019.118627] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 12/09/2019] [Accepted: 12/14/2019] [Indexed: 01/06/2023]
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213
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Popelka H. Dancing while self-eating: Protein intrinsic disorder in autophagy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:263-305. [PMID: 32828468 DOI: 10.1016/bs.pmbts.2020.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Autophagy is a major catabolic pathway that must be tightly regulated to maintain cellular homeostasis. Protein intrinsic disorder provides a very suitable conformation for regulation; accordingly, the molecular machinery of autophagy is significantly enriched in intrinsically disordered proteins and protein regions (IDPs/IDPRs). Despite experimental challenges that the characterization of IDPRs encounters, remarkable progress has been made in recent years in revealing various roles of IDPs/IDPRs in autophagy. This chapter describes the autophagy pathway from a specific point of view, that of IDPRs. It focuses in detail on structural and mechanistic functions in autophagy that are executed by disordered regions. Via a description of autophagosome biogenesis, linking the cargo to the autophagy machinery, as well as a discussion of certain post-translational regulations, this review reveals many indispensable roles of IDPRs in the functional autophagy pathway. Devastating pathologies such as neurodegeneration, cancer, or diabetes have been linked to a malfunction in IDPs/IDPRs. The same pathologies are associated with dysfunctional autophagy, indicating that autophagic IDPRs may be a paramount causative factor. Several disease-related mechanisms of the autophagy pathway involving protein intrinsic disorder are reported in this chapter, to illustrate a wide-ranging potential of IDPRs in the therapeutic modulation of autophagy.
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Affiliation(s)
- Hana Popelka
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States.
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214
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Cui Y, Parashar S, Zahoor M, Needham PG, Mari M, Zhu M, Chen S, Ho HC, Reggiori F, Farhan H, Brodsky JL, Ferro-Novick S. A COPII subunit acts with an autophagy receptor to target endoplasmic reticulum for degradation. Science 2020; 365:53-60. [PMID: 31273116 DOI: 10.1126/science.aau9263] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 04/13/2019] [Accepted: 06/12/2019] [Indexed: 12/21/2022]
Abstract
The COPII-cargo adaptor complex Lst1-Sec23 selectively sorts proteins into vesicles that bud from the endoplasmic reticulum (ER) and traffic to the Golgi. Improperly folded proteins are prevented from exiting the ER and are degraded. ER-phagy is an autophagic degradation pathway that uses ER-resident receptors. Working in yeast, we found an unexpected role for Lst1-Sec23 in ER-phagy that was independent from its function in secretion. Up-regulation of the stress-inducible ER-phagy receptor Atg40 induced the association of Lst1-Sec23 with Atg40 at distinct ER domains to package ER into autophagosomes. Lst1-mediated ER-phagy played a vital role in maintaining cellular homeostasis by preventing the accumulation of an aggregation-prone protein in the ER. Lst1 function appears to be conserved because its mammalian homolog, SEC24C, was also required for ER-phagy.
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Affiliation(s)
- Yixian Cui
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Smriti Parashar
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Muhammad Zahoor
- Institute of Basic Medical Sciences, Department of Molecular Medicine, University of Oslo, Sognsvannsveien 9, 0372 Oslo, Norway
| | - Patrick G Needham
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Muriel Mari
- Department of Biomedical Sciences of Cells and Systems, University of Groningen Medical Center, Groningen, Netherlands
| | - Ming Zhu
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Shuliang Chen
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Hsuan-Chung Ho
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Fulvio Reggiori
- Department of Biomedical Sciences of Cells and Systems, University of Groningen Medical Center, Groningen, Netherlands
| | - Hesso Farhan
- Institute of Basic Medical Sciences, Department of Molecular Medicine, University of Oslo, Sognsvannsveien 9, 0372 Oslo, Norway
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Susan Ferro-Novick
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA.
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215
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Ishaq M, Ojha R, Sharma AP, Singh SK. Autophagy in cancer: Recent advances and future directions. Semin Cancer Biol 2020; 66:171-181. [PMID: 32201367 DOI: 10.1016/j.semcancer.2020.03.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 02/10/2020] [Accepted: 03/16/2020] [Indexed: 02/06/2023]
Abstract
Autophagy is being explored as a potential therapeutic target for enhancing the cytotoxic effects of chemotherapeutic regimens in various malignancies. Autophagy plays a very important role in cancer pathogenesis. Here, we discuss the updates on the modulation of autophagy via dynamic interactions with different organelles and the exploitation of selective autophagy for exploring therapeutic strategies. We further discuss the role of autophagy inhibitors in cancer preclinical and clinical trials, novel autophagy inhibitors, and challenges likely to be faced by clinicians while inducting autophagy modulators in clinical practice.
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Affiliation(s)
- Mohd Ishaq
- School of Medicine, Department of Pathology, Stanford University, CA, USA.
| | - Rani Ojha
- School of Medicine, Department of Pathology, Stanford University, CA, USA.
| | - Aditya P Sharma
- Department of Urology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
| | - Shrawan K Singh
- Department of Urology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
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216
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Liu J, Kuang F, Kroemer G, Klionsky DJ, Kang R, Tang D. Autophagy-Dependent Ferroptosis: Machinery and Regulation. Cell Chem Biol 2020; 27:420-435. [PMID: 32160513 DOI: 10.1016/j.chembiol.2020.02.005] [Citation(s) in RCA: 555] [Impact Index Per Article: 111.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/19/2020] [Accepted: 02/19/2020] [Indexed: 12/20/2022]
Abstract
Macroautophagy (hereafter referred to as autophagy) is an evolutionarily conserved cellular process capable of degrading various biological molecules (e.g., protein, glycogen, lipids, DNA, and RNA) and organelles (e.g., mitochondria, endoplasmic reticulum [ER] ribosomes, lysosomes, and micronuclei) via the lysosomal pathway. Ferroptosis is a type of oxidative stress-dependent regulated cell death associated with iron accumulation and lipid peroxidation. The recently discovered role of autophagy, especially selective types of autophagy (e.g., ferritinophagy, lipophagy, clockophagy, and chaperone-mediated autophagy), in driving cells toward ferroptotic death motivated us to explore the functional interactions between metabolism, immunity, and cell death. Here, we describe types of selective autophagy and discuss the regulatory mechanisms and signaling pathways of autophagy-dependent ferroptosis. We also summarize chemical modulators that are currently available for triggering or blocking autophagy-dependent ferroptosis and that may be developed for therapeutic interventions in human diseases.
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Affiliation(s)
- Jiao Liu
- The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510600, China
| | - Feimei Kuang
- The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510600, China
| | - Guido Kroemer
- Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France; Equipe 11 Labellisée Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, 75006 Paris, France; Institut National de la Santé et de la Recherche Médicale, U1138, Paris, France; Université Pierre et Marie Curie, 75006 Paris, France; Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, 94800 Villejuif, France; Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France; Department of Women's and Children's Health, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Daniel J Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rui Kang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Daolin Tang
- The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510600, China; Department of Surgery, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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217
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Liang JR, Lingeman E, Luong T, Ahmed S, Muhar M, Nguyen T, Olzmann JA, Corn JE. A Genome-wide ER-phagy Screen Highlights Key Roles of Mitochondrial Metabolism and ER-Resident UFMylation. Cell 2020; 180:1160-1177.e20. [PMID: 32160526 DOI: 10.1016/j.cell.2020.02.017] [Citation(s) in RCA: 196] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 11/04/2019] [Accepted: 02/07/2020] [Indexed: 12/13/2022]
Abstract
Selective autophagy of organelles is critical for cellular differentiation, homeostasis, and organismal health. Autophagy of the ER (ER-phagy) is implicated in human neuropathy but is poorly understood beyond a few autophagosomal receptors and remodelers. By using an ER-phagy reporter and genome-wide CRISPRi screening, we identified 200 high-confidence human ER-phagy factors. Two pathways were unexpectedly required for ER-phagy. First, reduced mitochondrial metabolism represses ER-phagy, which is opposite of general autophagy and is independent of AMPK. Second, ER-localized UFMylation is required for ER-phagy to repress the unfolded protein response via IRE1α. The UFL1 ligase is brought to the ER surface by DDRGK1 to UFMylate RPN1 and RPL26 and preferentially targets ER sheets for degradation, analogous to PINK1-Parkin regulation during mitophagy. Our data provide insight into the cellular logic of ER-phagy, reveal parallels between organelle autophagies, and provide an entry point to the relatively unexplored process of degrading the ER network.
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Affiliation(s)
- Jin Rui Liang
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Emily Lingeman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Thao Luong
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Saba Ahmed
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Matthias Muhar
- Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Truc Nguyen
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - James A Olzmann
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, ETH Zürich, 8093 Zürich, Switzerland.
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218
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Fielden J, Wiseman K, Torrecilla I, Li S, Hume S, Chiang SC, Ruggiano A, Narayan Singh A, Freire R, Hassanieh S, Domingo E, Vendrell I, Fischer R, Kessler BM, Maughan TS, El-Khamisy SF, Ramadan K. TEX264 coordinates p97- and SPRTN-mediated resolution of topoisomerase 1-DNA adducts. Nat Commun 2020; 11:1274. [PMID: 32152270 PMCID: PMC7062751 DOI: 10.1038/s41467-020-15000-w] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/16/2020] [Indexed: 12/03/2022] Open
Abstract
Eukaryotic topoisomerase 1 (TOP1) regulates DNA topology to ensure efficient DNA replication and transcription. TOP1 is also a major driver of endogenous genome instability, particularly when its catalytic intermediate-a covalent TOP1-DNA adduct known as a TOP1 cleavage complex (TOP1cc)-is stabilised. TOP1ccs are highly cytotoxic and a failure to resolve them underlies the pathology of neurological disorders but is also exploited in cancer therapy where TOP1ccs are the target of widely used frontline anti-cancer drugs. A critical enzyme for TOP1cc resolution is the tyrosyl-DNA phosphodiesterase (TDP1), which hydrolyses the bond that links a tyrosine in the active site of TOP1 to a 3' phosphate group on a single-stranded (ss)DNA break. However, TDP1 can only process small peptide fragments from ssDNA ends, raising the question of how the ~90 kDa TOP1 protein is processed upstream of TDP1. Here we find that TEX264 fulfils this role by forming a complex with the p97 ATPase and the SPRTN metalloprotease. We show that TEX264 recognises both unmodified and SUMO1-modifed TOP1 and initiates TOP1cc repair by recruiting p97 and SPRTN. TEX264 localises to the nuclear periphery, associates with DNA replication forks, and counteracts TOP1ccs during DNA replication. Altogether, our study elucidates the existence of a specialised repair complex required for upstream proteolysis of TOP1ccs and their subsequent resolution.
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Affiliation(s)
- John Fielden
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Katherine Wiseman
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Ignacio Torrecilla
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Shudong Li
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Samuel Hume
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Shih-Chieh Chiang
- The University of Sheffield Neuroscience Institute and the Healthy Lifespan Institute, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 2TN, Sheffield, UK
| | - Annamaria Ruggiano
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Abhay Narayan Singh
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Raimundo Freire
- Unidad de Investigación, Hospital Universitario de Canarias, Ofra s/n, La Cuesta, 38320, La Laguna, Tenerife, Spain
- Instituto de Tecnologías Biomédicas, Universidad de La Laguna, 38200, La Laguna, Tenerife, Spain
- Universidad Fernando Pessoa Canarias, 35450, Las Palmas de Gran Canaria, Spain
| | - Sylvana Hassanieh
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Enric Domingo
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Iolanda Vendrell
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Roman Fischer
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Benedikt M Kessler
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Timothy S Maughan
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Sherif F El-Khamisy
- The University of Sheffield Neuroscience Institute and the Healthy Lifespan Institute, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 2TN, Sheffield, UK
| | - Kristijan Ramadan
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK.
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219
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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: 200] [Impact Index Per Article: 40.0] [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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220
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Liu Y, Wang S, Wang Z, Ding M, Li X, Guo J, Han G, Zhao P. Dexmedetomidine Alleviated Endoplasmic Reticulum Stress via Inducing ER-phagy in the Spinal Cord of Neuropathic Pain Model. Front Neurosci 2020; 14:90. [PMID: 32184704 PMCID: PMC7058658 DOI: 10.3389/fnins.2020.00090] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/22/2020] [Indexed: 12/12/2022] Open
Abstract
Studies demonstrated that spinal autophagy was impaired in spinal nerve ligation (SNL) rats. However, the relationship of endoplasmic reticulum (ER) stress and ER-phagy and whether dexmedetomidine (DEX) modulates ER-phagy remain unclear. In this study, male Sprague-Dawley (SD) rats and the SNL animal model were used. 4-Phenylbutyric acid (4-PBA), tunicamycin (TM), rapamycin (RAP), and 3-methyladenine (3-MA) were intrathecally administered, respectively to demonstrate the relationship of ER stress and ER-phagy. Dexmedetomidine (30 μg/kg) was administered as treatment. Mechanical withdrawal threshold (MWT) and thermal withdrawal latency (TWL) tests were performed to evaluate nociceptive hypersensitivity. Protein expressions were examined by Western blot, and the location of glucose-regulated protein 78 (Grp78) was examined by immunofluorescence staining. SNL induced ER stress and ER-phagy impairment. ER stress was altered in rostral ventromedial medulla (RVM); 4-phenylbutyric acid induced analgesic effect via inhibiting ER stress and unfolded protein response (UPR) pathways to induce ER-phagy; tunicamycin led to worsening pain through enhancing ER stress and UPR pathways to further impair ER-phagy. Rapamycin provided analgesic effect through enhancing ER-phagy to relieve SNL-induced ER stress and UPR pathway activation; 3-methyladenine deteriorated pain via further impairing ER-phagy to aggravate ER stress. Dexmedetomidine provided analgesic effect through elevating ER-phagy. In conclusion, ER stress led to ER-phagy impairment in the spinal cord of SNL rats and participated in the nociceptive descending system. ER-phagy impairment was both a trigger and an effector of ER stress via UPR pathways in SNL rats. Dexmedetomidine targeted ER-phagy to provide analgesic effect.
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Affiliation(s)
- Yongda Liu
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China.,Department of Pain Management, Shengjing Hospital of China Medical University, Shenyang, China
| | - Shuang Wang
- Department of Anesthesiology, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Zhibin Wang
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China.,Department of Pain Management, Shengjing Hospital of China Medical University, Shenyang, China
| | - Mengmeng Ding
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China.,Department of Pain Management, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xingyue Li
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China.,Department of Pain Management, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jiao Guo
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China.,Department of Pain Management, Shengjing Hospital of China Medical University, Shenyang, China
| | - Guang Han
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China.,Department of Pain Management, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ping Zhao
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China.,Department of Pain Management, Shengjing Hospital of China Medical University, Shenyang, China
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221
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Houri K, Mori T, Onodera Y, Tsujimoto T, Takehara T, Nakao S, Teramura T, Fukuda K. miR-142 induces accumulation of reactive oxygen species (ROS) by inhibiting pexophagy in aged bone marrow mesenchymal stem cells. Sci Rep 2020; 10:3735. [PMID: 32111926 PMCID: PMC7048811 DOI: 10.1038/s41598-020-60346-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 02/06/2020] [Indexed: 12/26/2022] Open
Abstract
Elevation of the levels of reactive oxygen species (ROS) is a major tissue-degenerative phenomenon involved in aging and aging-related diseases. The detailed mechanisms underlying aging-related ROS generation remain unclear. Presently, the expression of microRNA (miR)-142-5p was significantly upregulated in bone marrow mesenchymal stem cells (BMMSCs) of aged mice. Overexpression of miR-142 and subsequent observation revealed that miR-142 involved ROS accumulation through the disruption of selective autophagy for peroxisomes (pexophagy). Mechanistically, attenuation of acetyltransferase Ep300 triggered the upregulation of miR-142 in aged BMMSCs, and miR-142 targeted endothelial PAS domain protein 1 (Epas1) was identified as a regulatory protein of pexophagy. These findings support a novel molecular mechanism relating aging-associated ROS generation and organelle degradation in BMMSCs, and suggest a potential therapeutic target for aging-associated disorders that are accompanied by stem cell degeneration.
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Affiliation(s)
- Kei Houri
- Department of Anesthesiology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Tatsufumi Mori
- Kindai University Life Science Research Institute, Kindai University, Osaka, Japan
| | - Yuta Onodera
- Division of Cell Biology for Regenerative Medicine, Institute of Advanced Clinical Medicine, Kindai University Faculty of Medicine, Osaka, Japan
| | - Takatoshi Tsujimoto
- Department of Anesthesiology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Toshiyuki Takehara
- Division of Cell Biology for Regenerative Medicine, Institute of Advanced Clinical Medicine, Kindai University Faculty of Medicine, Osaka, Japan
| | - Shinichi Nakao
- Department of Anesthesiology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Takeshi Teramura
- Division of Cell Biology for Regenerative Medicine, Institute of Advanced Clinical Medicine, Kindai University Faculty of Medicine, Osaka, Japan.
| | - Kanji Fukuda
- Division of Cell Biology for Regenerative Medicine, Institute of Advanced Clinical Medicine, Kindai University Faculty of Medicine, Osaka, Japan
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222
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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: 19] [Impact Index Per Article: 3.8] [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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223
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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: 71] [Impact Index Per Article: 14.2] [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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224
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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: 10.4] [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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225
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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: 80] [Impact Index Per Article: 16.0] [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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226
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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: 51] [Impact Index Per Article: 10.2] [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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227
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Cavalli G, Cenci S. Autophagy and Protein Secretion. J Mol Biol 2020; 432:2525-2545. [PMID: 31972172 DOI: 10.1016/j.jmb.2020.01.015] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/08/2020] [Accepted: 01/12/2020] [Indexed: 12/13/2022]
Abstract
Autophagy - conventional for macroautophagy - is a major recycling strategy that ensures cellular homeostasis through the selective engulfment of cytoplasmic supramolecular cargos in double membrane vesicles and their rapid dispatch to the lysosome for digestion. As autophagy operates in the cytoplasm, its interference with secretory proteins, that is, proteins destined to the plasma membrane or the extracellular space, generally synthesized and routed within the endoplasmic reticulum (ER), has been relatively overlooked in the past. However, mounting evidence reveals that autophagy in fact heavily regulates protein secretion through diverse mechanisms. First, autophagy is closely involved in the unconventional secretion of leaderless proteins, a pool of proteins destined extracellularly, but lacking an ER-targeted leader sequence, and thus manufactured in the cytosol. Autophagy-related (ATG) genes now appear instrumental to the underlying pathways, hence the recently coined concept of secretory autophagy, or better ATG gene-dependent secretion. Indeed, ATG genes regulate unconventional protein secretion at multiple levels, ranging from intracellular inflammatory signaling, for example, through the control of mitochondrial health and inflammasome activity, to trafficking of leaderless proteins. Moreover, perhaps less expectedly, autophagy also participates in the control of conventional secretion, intersecting the secretory apparatus at multiple points, though with surprising differences among professional secretory cell types that disclose remarkable and unpredicted specificity. This review synopsizes the multiple mechanisms whereby autophagy interfaces with conventional and unconventional protein secretory pathways and discusses the relative teleology. Altogether, the diverse controls exerted on protein secretion broaden and deepen the homeostatic significance of autophagy within the cell.
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Affiliation(s)
- Giulio Cavalli
- Unit of Immunology, Rheumatology, Allergy and Rare Diseases, Ospedale San Raffaele, Milano, Italy; Vita-Salute San Raffaele University, Milano, Italy
| | - Simone Cenci
- Vita-Salute San Raffaele University, Milano, Italy; Unit of Age Related Diseases, Division of Genetics and Cell Biology, Ospedale San Raffaele, Milano, Italy.
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228
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Autophagy as a Cellular Stress Response Mechanism in the Nervous System. J Mol Biol 2020; 432:2560-2588. [PMID: 31962122 DOI: 10.1016/j.jmb.2020.01.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/11/2019] [Accepted: 01/10/2020] [Indexed: 12/13/2022]
Abstract
Cells of an organism face with various types of insults during their lifetime. Exposure to toxins, metabolic problems, ischaemia/reperfusion, physical trauma, genetic diseases, neurodegenerative diseases are among the conditions that trigger cellular stress responses. In this context, autophagy is one of the mechanisms that supports cell survival under stressful conditions. Autophagic vesicle engulfs the cargo and transports it to lysosome for degradation and turnover. As such, autophagy eliminates abnormal proteins, clears damaged organelles, limits oxidative stress and helps to improve metabolic balance. Nervous system cells and particularly postmitotic neurons are highly sensitive to a spectrum of insults, and autophagy emerges as one of the key stress response mechanism, ensuring health and survival of these vulnerable cell types. In this review, we will overview mechanisms through which cells cope with stress, and how these stress responses regulate autophagy, with a special focus on the nervous system.
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229
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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: 71] [Impact Index Per Article: 14.2] [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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230
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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: 102] [Impact Index Per Article: 20.4] [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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231
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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: 90] [Impact Index Per Article: 18.0] [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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232
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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: 98] [Impact Index Per Article: 19.6] [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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233
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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: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [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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234
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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: 1.6] [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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235
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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: 452] [Impact Index Per Article: 90.4] [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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236
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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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237
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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: 26] [Impact Index Per Article: 4.3] [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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238
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Guamán-Ortiz LM, Bailon-Moscoso N, Morocho V, Vega-Ojeda D, Gordillo F, Suárez AI. Onoseriolide, from Hedyosmum racemosum, induces cytotoxicity and apoptosis in human colon cancer cells. Nat Prod Res 2019; 35:3151-3155. [PMID: 31736362 DOI: 10.1080/14786419.2019.1690485] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The number of colon cancer patients is increasing, and new alternatives for treatment are important. We focused on the sesquiterpene lactone onoseriolide from Hedyosmum racemosum, which is widely used in traditional medicine. This compound was evaluated to determine its cytotoxic effect and the mechanism of cell death that is induced in the human colon cancer cell line RKO. A dose-dependent decrease in cell viability was observed. p53 expression increased followed by an increase in p21 expression, which is involved in cell cycle arrest in the G2/M phase. Caspase-3 activation and PARP-1 cleavage, which are apoptotic markers, were also monitored. Autophagy markers were also studied, and Beclin 1 was downregulated, while LC-3II increased in a dose-dependent manner. There were no changes in SQSTM1/p62 regulation. Onoseriolide exerts cytotoxic and cytostatic effects, activating the autophagy pathway as a protective mechanism and apoptosis as the cell death pathway.
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Affiliation(s)
| | - Natalia Bailon-Moscoso
- Departamento de Ciencias de la Salud, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Vladimir Morocho
- Departamento de Química y Ciencias Exactas, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Daisy Vega-Ojeda
- Departamento de Ciencias de la Salud, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Fernando Gordillo
- Departamento de Química y Ciencias Exactas, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Alírica I Suárez
- Departamento de Química y Ciencias Exactas, Universidad Técnica Particular de Loja, Loja, Ecuador.,Facultad de Farmacia, Universidad Central de Venezuela, Caracas, Venezuela
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239
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Maejima Y. The critical roles of protein quality control systems in the pathogenesis of heart failure. J Cardiol 2019; 75:219-227. [PMID: 31699567 DOI: 10.1016/j.jjcc.2019.09.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 09/26/2019] [Indexed: 01/30/2023]
Abstract
Heart failure is a refractory disease with a prevalence that has continuously increased around the world. Over the past decade, we have made remarkable progress in the treatment of heart failure, including drug therapies, device therapies, and regeneration therapies. However, as each of these heart failure therapies does not go much beyond symptomatic therapy, there is a compelling need to establish novel therapeutic strategies for heart failure in a fundamental way. As cardiomyocytes are terminally differentiated cells, protein quality control is critical for maintaining cellular homeostasis, optimal performance, and longevity. There are five evolutionarily conserved mechanisms for ensuring protein quality control in cells: the ubiquitin-proteasome system, autophagy, the unfolded protein response, SUMOylation, and NEDDylation. Recent research has clarified the molecular mechanism underlying how these processes degrade misfolded proteins and damaged organelles in cardiomyocytes. In addition, a growing body of evidence suggests that deviation from appropriate levels of protein quality control causes cellular dysfunction and death, which in turn leads to heart failure. We herein review recent advances in understanding the role of protein quality control systems in heart disease and discuss the therapeutic potential of modulating protein quality control systems in the human heart.
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Affiliation(s)
- Yasuhiro Maejima
- Department of Cardiovascular Medicine, Tokyo Medical and Dental University, Tokyo, Japan.
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240
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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: 103] [Impact Index Per Article: 17.2] [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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241
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Jia R, Bonifacino JS. Negative regulation of autophagy by UBA6-BIRC6-mediated ubiquitination of LC3. eLife 2019; 8:e50034. [PMID: 31692446 PMCID: PMC6863627 DOI: 10.7554/elife.50034] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 11/05/2019] [Indexed: 12/14/2022] Open
Abstract
Although the process of autophagy has been extensively studied, the mechanisms that regulate it remain insufficiently understood. To identify novel autophagy regulators, we performed a whole-genome CRISPR/Cas9 knockout screen in H4 human neuroglioma cells expressing endogenous LC3B tagged with a tandem of GFP and mCherry. Using this methodology, we identified the ubiquitin-activating enzyme UBA6 and the hybrid ubiquitin-conjugating enzyme/ubiquitin ligase BIRC6 as autophagy regulators. We found that these enzymes cooperate to monoubiquitinate LC3B, targeting it for proteasomal degradation. Knockout of UBA6 or BIRC6 increased autophagic flux under conditions of nutrient deprivation or protein synthesis inhibition. Moreover, UBA6 or BIRC6 depletion decreased the formation of aggresome-like induced structures in H4 cells, and α-synuclein aggregates in rat hippocampal neurons. These findings demonstrate that UBA6 and BIRC6 negatively regulate autophagy by limiting the availability of LC3B. Inhibition of UBA6/BIRC6 could be used to enhance autophagic clearance of protein aggregates in neurodegenerative disorders.
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Affiliation(s)
- Rui Jia
- Neurosciences and Cellular and Structural Biology DivisionEunice Kennedy Shriver National Institute of Child Health and Human Development National Institutes of HealthBethesdaUnited States
| | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology DivisionEunice Kennedy Shriver National Institute of Child Health and Human Development National Institutes of HealthBethesdaUnited States
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242
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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: 81] [Impact Index Per Article: 13.5] [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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243
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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: 52] [Impact Index Per Article: 8.7] [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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244
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The viral F-box protein P0 induces an ER-derived autophagy degradation pathway for the clearance of membrane-bound AGO1. Proc Natl Acad Sci U S A 2019; 116:22872-22883. [PMID: 31628252 PMCID: PMC6842623 DOI: 10.1073/pnas.1912222116] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The viral suppressor of RNA silencing P0 is known to target plant antiviral ARGONAUTE (AGO) proteins for degradation via an autophagy-related process. Here we utilized P0 to gain insight into the cellular degradation dynamics of AGO1, the major plant effector of RNA silencing. We revealed that P0 targets endoplasmic reticulum (ER)-associated AGO1 by inducing the formation of ER-related bodies that are delivered to the vacuole with both P0 and AGO1 as cargos. This process involves ATG8-interacting proteins 1 and 2 (ATI1 and ATI2) that interact with AGO1 and negatively regulate its transgene-silencing activity. Together, our results reveal a layer of ER-bound AGO1 posttranslational regulation that is manipulated by P0 to subvert plant antiviral defense. RNA silencing is a major antiviral defense mechanism in plants and invertebrates. Plant ARGONAUTE1 (AGO1) is pivotal in RNA silencing, and hence is a major target for counteracting viral suppressors of RNA-silencing proteins (VSRs). P0 from Turnip yellows virus (TuYV) is a VSR that was previously shown to trigger AGO1 degradation via an autophagy-like process. However, the identity of host proteins involved and the cellular site at which AGO1 and P0 interact were unknown. Here we report that P0 and AGO1 associate on the endoplasmic reticulum (ER), resulting in their loading into ER-associated vesicles that are mobilized to the vacuole in an ATG5- and ATG7-dependent manner. We further identified ATG8-Interacting proteins 1 and 2 (ATI1 and ATI2) as proteins that associate with P0 and interact with AGO1 on the ER up to the vacuole. Notably, ATI1 and ATI2 belong to an endogenous degradation pathway of ER-associated AGO1 that is significantly induced following P0 expression. Accordingly, ATI1 and ATI2 deficiency causes a significant increase in posttranscriptional gene silencing (PTGS) activity. Collectively, we identify ATI1 and ATI2 as components of an ER-associated AGO1 turnover and proper PTGS maintenance and further show how the VSR P0 manipulates this pathway.
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245
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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: 368] [Impact Index Per Article: 61.3] [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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246
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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: 262] [Impact Index Per Article: 43.7] [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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247
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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: 98] [Impact Index Per Article: 16.3] [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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248
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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: 6.7] [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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249
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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: 28] [Impact Index Per Article: 4.7] [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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250
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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: 62] [Impact Index Per Article: 10.3] [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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