51
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Hamid SM, Citir M, Terzi EM, Cimen I, Yildirim Z, Dogan AE, Kocaturk B, Onat UI, Arditi M, Weber C, Traynor-Kaplan A, Schultz C, Erbay E. Inositol-requiring enzyme-1 regulates phosphoinositide signaling lipids and macrophage growth. EMBO Rep 2020; 21:e51462. [PMID: 33140520 DOI: 10.15252/embr.202051462] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/19/2020] [Accepted: 09/22/2020] [Indexed: 12/25/2022] Open
Abstract
The ER-bound kinase/endoribonuclease (RNase), inositol-requiring enzyme-1 (IRE1), regulates the phylogenetically most conserved arm of the unfolded protein response (UPR). However, the complex biology and pathology regulated by mammalian IRE1 cannot be fully explained by IRE1's one known, specific RNA target, X box-binding protein-1 (XBP1) or the RNA substrates of IRE1-dependent RNA degradation (RIDD) activity. Investigating other specific substrates of IRE1 kinase and RNase activities may illuminate how it performs these diverse functions in mammalian cells. We report that macrophage IRE1 plays an unprecedented role in regulating phosphatidylinositide-derived signaling lipid metabolites and has profound impact on the downstream signaling mediated by the mammalian target of rapamycin (mTOR). This cross-talk between UPR and mTOR pathways occurs through the unconventional maturation of microRNA (miR) 2137 by IRE1's RNase activity. Furthermore, phosphatidylinositol (3,4,5) phosphate (PI(3,4,5)P3 ) 5-phosphatase-2 (INPPL1) is a direct target of miR-2137, which controls PI(3,4,5)P3 levels in macrophages. The modulation of cellular PI(3,4,5)P3 /PIP2 ratio and anabolic mTOR signaling by the IRE1-induced miR-2137 demonstrates how the ER can provide a critical input into cell growth decisions.
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Affiliation(s)
| | - Mevlut Citir
- The Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Erdem Murat Terzi
- Department of Pathology, Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Ismail Cimen
- Institute for Cardiovascular Prevention, LMU Munich, German Cardiovascular Research Centre, partner site Munich Heart Alliance Munich, Munich, Germany
| | - Zehra Yildirim
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey.,National Nanotechnology Center, Bilkent University, Ankara, Turkey
| | - Asli Ekin Dogan
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey.,National Nanotechnology Center, Bilkent University, Ankara, Turkey
| | - Begum Kocaturk
- Department of Pediatrics and Medicine, Division of Infectious Diseases and Immunology, and Infectious and Immunologic Diseases Research Center, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Umut Inci Onat
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey.,National Nanotechnology Center, Bilkent University, Ankara, Turkey
| | - Moshe Arditi
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Pediatrics and Medicine, Division of Infectious Diseases and Immunology, and Infectious and Immunologic Diseases Research Center, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Christian Weber
- Institute for Cardiovascular Prevention, LMU Munich, German Cardiovascular Research Centre, partner site Munich Heart Alliance Munich, Munich, Germany.,Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Alexis Traynor-Kaplan
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA.,ATK Innovation, Analytics and Discovery, North Bend, WA, USA
| | - Carsten Schultz
- The Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | - Ebru Erbay
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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52
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Pavlović N, Calitz C, Thanapirom K, Mazza G, Rombouts K, Gerwins P, Heindryckx F. Inhibiting IRE1α-endonuclease activity decreases tumor burden in a mouse model for hepatocellular carcinoma. eLife 2020; 9:e55865. [PMID: 33103995 PMCID: PMC7661042 DOI: 10.7554/elife.55865] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 10/26/2020] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a liver tumor that usually arises in patients with cirrhosis. Hepatic stellate cells are key players in the progression of HCC, as they create a fibrotic micro-environment and produce growth factors and cytokines that enhance tumor cell proliferation and migration. We assessed the role of endoplasmic reticulum (ER) stress in the cross-talk between stellate cells and HCC cells. Mice with a fibrotic HCC were treated with the IRE1α-inhibitor 4μ8C, which reduced tumor burden and collagen deposition. By co-culturing HCC-cells with stellate cells, we found that HCC-cells activate IREα in stellate cells, thereby contributing to their activation. Inhibiting IRE1α blocked stellate cell activation, which then decreased proliferation and migration of tumor cells in different in vitro 2D and 3D co-cultures. In addition, we also observed cell-line-specific direct effects of inhibiting IRE1α in tumor cells.
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Affiliation(s)
- Nataša Pavlović
- Department of Medical Cell Biology, Uppsala UniversityUppsalaSweden
| | - Carlemi Calitz
- Department of Medical Cell Biology, Uppsala UniversityUppsalaSweden
| | - Kess Thanapirom
- Regenerative Medicine & Fibrosis Group, Institute for Liver and Digestive Health, University College LondonLondonUnited Kingdom
| | - Guiseppe Mazza
- Regenerative Medicine & Fibrosis Group, Institute for Liver and Digestive Health, University College LondonLondonUnited Kingdom
| | - Krista Rombouts
- Regenerative Medicine & Fibrosis Group, Institute for Liver and Digestive Health, University College LondonLondonUnited Kingdom
| | - Pär Gerwins
- Department of Medical Cell Biology, Uppsala UniversityUppsalaSweden
- Department of Radiology, Uppsala University HospitalUppsalaSweden
| | - Femke Heindryckx
- Department of Medical Cell Biology, Uppsala UniversityUppsalaSweden
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53
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When Endoplasmic Reticulum Proteostasis Meets the DNA Damage Response. Trends Cell Biol 2020; 30:881-891. [PMID: 33036871 DOI: 10.1016/j.tcb.2020.09.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/31/2020] [Accepted: 09/07/2020] [Indexed: 02/06/2023]
Abstract
Sustaining both proteome and genome integrity (GI) requires the integration of a wide range of mechanisms and signaling pathways. These comprise, in particular, the unfolded protein response (UPR) and the DNA damage response (DDR). These adaptive mechanisms take place respectively in the endoplasmic reticulum (ER) and in the nucleus. UPR and DDR alterations are associated with aging and with pathologies such as degenerative diseases, metabolic and inflammatory disorders, and cancer. We discuss the emerging signaling crosstalk between UPR stress sensors and the DDR, as well as their involvement in cancer biology.
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54
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Urra H, Pihán P, Hetz C. The UPRosome - decoding novel biological outputs of IRE1α function. J Cell Sci 2020; 133:133/15/jcs218107. [PMID: 32788208 DOI: 10.1242/jcs.218107] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Different perturbations alter the function of the endoplasmic reticulum (ER), resulting in the accumulation of misfolded proteins in its lumen, a condition termed ER stress. To restore ER proteostasis, a highly conserved pathway is engaged, known as the unfolded protein response (UPR), triggering adaptive programs or apoptosis of terminally damaged cells. IRE1α (also known as ERN1), the most conserved UPR sensor, mediates the activation of responses to determine cell fate under ER stress. The complexity of IRE1α regulation and its signaling outputs is mediated in part by the assembly of a dynamic multi-protein complex, named the UPRosome, that regulates IRE1α activity and the crosstalk with other pathways. We discuss several studies identifying components of the UPRosome that have illuminated novel functions in cell death, autophagy, DNA damage, energy metabolism and cytoskeleton dynamics. Here, we provide a theoretical analysis to assess the biological significance of the UPRosome and present the results of a systematic bioinformatics analysis of the available IRE1α interactome data sets followed by functional enrichment clustering. This in silico approach decoded that IRE1α also interacts with proteins involved in the cell cycle, transport, differentiation, response to viral infection and immune response. Thus, defining the spectrum of IRE1α-binding partners will reveal novel signaling outputs and the relevance of the pathway to human diseases.
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Affiliation(s)
- Hery Urra
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago 8380453, Chile .,Center for Geroscience, Brain Health and Metabolism (GERO), Santiago 7800003, Chile.,Program of Cellular and Molecular Biology, Institute of Biomedical Sciences (ICBM), University of Chile, Santiago 8380453, Chile
| | - Philippe Pihán
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago 8380453, Chile.,Center for Geroscience, Brain Health and Metabolism (GERO), Santiago 7800003, Chile.,Program of Cellular and Molecular Biology, Institute of Biomedical Sciences (ICBM), University of Chile, Santiago 8380453, Chile
| | - Claudio Hetz
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, University of Chile, Santiago 8380453, Chile .,Center for Geroscience, Brain Health and Metabolism (GERO), Santiago 7800003, Chile.,Program of Cellular and Molecular Biology, Institute of Biomedical Sciences (ICBM), University of Chile, Santiago 8380453, Chile.,The Buck Institute for Research in Aging, Novato, CA 94945, USA
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55
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Hetz C, Zhang K, Kaufman RJ. Mechanisms, regulation and functions of the unfolded protein response. Nat Rev Mol Cell Biol 2020; 21:421-438. [PMID: 32457508 DOI: 10.1038/s41580-020-0250-z] [Citation(s) in RCA: 1175] [Impact Index Per Article: 293.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2020] [Indexed: 12/21/2022]
Abstract
Cellular stress induced by the abnormal accumulation of unfolded or misfolded proteins at the endoplasmic reticulum (ER) is emerging as a possible driver of human diseases, including cancer, diabetes, obesity and neurodegeneration. ER proteostasis surveillance is mediated by the unfolded protein response (UPR), a signal transduction pathway that senses the fidelity of protein folding in the ER lumen. The UPR transmits information about protein folding status to the nucleus and cytosol to adjust the protein folding capacity of the cell or, in the event of chronic damage, induce apoptotic cell death. Recent advances in the understanding of the regulation of UPR signalling and its implications in the pathophysiology of disease might open new therapeutic avenues.
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Affiliation(s)
- Claudio Hetz
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile. .,FONDAP Center for Geroscience Brain Health and Metabolism (GERO), Santiago, Chile. .,Program of Cellular and Molecular Biology, Institute of Biomedical Science, University of Chile, Santiago, Chile. .,Buck Institute for Research on Aging, Novato, CA, USA.
| | - Kezhong Zhang
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA. .,Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI, USA.
| | - Randal J Kaufman
- Degenerative Diseases Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
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56
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The UPR sensor IRE1α and the adenovirus E3-19K glycoprotein sustain persistent and lytic infections. Nat Commun 2020; 11:1997. [PMID: 32332742 PMCID: PMC7181865 DOI: 10.1038/s41467-020-15844-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/30/2020] [Indexed: 12/16/2022] Open
Abstract
Persistent viruses cause chronic disease, and threaten the lives of immunosuppressed individuals. Here, we elucidate a mechanism supporting the persistence of human adenovirus (AdV), a virus that can kill immunosuppressed patients. Cell biological analyses, genetics and chemical interference demonstrate that one of five AdV membrane proteins, the E3-19K glycoprotein specifically triggers the unfolded protein response (UPR) sensor IRE1α in the endoplasmic reticulum (ER), but not other UPR sensors, such as protein kinase R-like ER kinase (PERK) and activating transcription factor 6 (ATF6). The E3-19K lumenal domain activates the IRE1α nuclease, which initiates mRNA splicing of X-box binding protein-1 (XBP1). XBP1s binds to the viral E1A-enhancer/promoter sequence, and boosts E1A transcription, E3-19K levels and lytic infection. Inhibition of IRE1α nuclease interrupts the five components feedforward loop, E1A, E3-19K, IRE1α, XBP1s, E1A enhancer/promoter. This loop sustains persistent infection in the presence of the immune activator interferon, and lytic infection in the absence of interferon. Adenovirus (AdV) can cause persistent infections, but underlying mechanisms are poorly understood. Here, Prasad et al. show that the AdV glycoprotein E3-19K activates the unfolded protein response sensor IRE1α, and that this triggers a feedforward loop that sustains persistent infection in the presence of interferon.
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57
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Jaud M, Philippe C, Di Bella D, Tang W, Pyronnet S, Laurell H, Mazzolini L, Rouault-Pierre K, Touriol C. Translational Regulations in Response to Endoplasmic Reticulum Stress in Cancers. Cells 2020; 9:cells9030540. [PMID: 32111004 PMCID: PMC7140484 DOI: 10.3390/cells9030540] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/18/2020] [Accepted: 02/24/2020] [Indexed: 12/20/2022] Open
Abstract
During carcinogenesis, almost all the biological processes are modified in one way or another. Among these biological processes affected, anomalies in protein synthesis are common in cancers. Indeed, cancer cells are subjected to a wide range of stresses, which include physical injuries, hypoxia, nutrient starvation, as well as mitotic, oxidative or genotoxic stresses. All of these stresses will cause the accumulation of unfolded proteins in the Endoplasmic Reticulum (ER), which is a major organelle that is involved in protein synthesis, preservation of cellular homeostasis, and adaptation to unfavourable environment. The accumulation of unfolded proteins in the endoplasmic reticulum causes stress triggering an unfolded protein response in order to promote cell survival or to induce apoptosis in case of chronic stress. Transcription and also translational reprogramming are tightly controlled during the unfolded protein response to ensure selective gene expression. The majority of stresses, including ER stress, induce firstly a decrease in global protein synthesis accompanied by the induction of alternative mechanisms for initiating the translation of mRNA, later followed by a translational recovery. After a presentation of ER stress and the UPR response, we will briefly present the different modes of translation initiation, then address the specific translational regulatory mechanisms acting during reticulum stress in cancers and highlight the importance of translational control by ER stress in tumours.
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Affiliation(s)
- Manon Jaud
- Inserm UMR1037, CRCT (Cancer Research Center of Toulouse), F-31037 Toulouse, France; (M.J.); (S.P.); (L.M.)
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France;
| | - Céline Philippe
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (W.T.); (K.R.-P.)
| | - Doriana Di Bella
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (W.T.); (K.R.-P.)
| | - Weiwei Tang
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (W.T.); (K.R.-P.)
| | - Stéphane Pyronnet
- Inserm UMR1037, CRCT (Cancer Research Center of Toulouse), F-31037 Toulouse, France; (M.J.); (S.P.); (L.M.)
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France;
| | - Henrik Laurell
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France;
- Inserm UMR1048, I2MC (Institut des Maladies Métaboliques et Cardiovasculaires), BP 84225, CEDEX 04, 31 432 Toulouse, France
| | - Laurent Mazzolini
- Inserm UMR1037, CRCT (Cancer Research Center of Toulouse), F-31037 Toulouse, France; (M.J.); (S.P.); (L.M.)
- CNRS ERL5294, CRCT, F-31037 Toulouse, France
| | - Kevin Rouault-Pierre
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (W.T.); (K.R.-P.)
| | - Christian Touriol
- Inserm UMR1037, CRCT (Cancer Research Center of Toulouse), F-31037 Toulouse, France; (M.J.); (S.P.); (L.M.)
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France;
- Correspondence:
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58
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Azoramide protects iPSC-derived dopaminergic neurons with PLA2G6 D331Y mutation through restoring ER function and CREB signaling. Cell Death Dis 2020; 11:130. [PMID: 32071291 PMCID: PMC7028918 DOI: 10.1038/s41419-020-2312-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 12/21/2022]
Abstract
The endoplasmic reticulum (ER)-stress-induced cascade events are implicated in Parkinson’s disease (PD). The discovery of drug candidates to protect dopaminergic (DA) neurons from ER-stress-induced oxidative damage is important to resolve the pathological aspects of PD and modify its progress. In this study, we found that a recently identified unfolded protein response (UPR) modulator, azoramide, showed protective effects on patient induced pluripotent stem cells-derived midbrain DA neurons with the homozygous phospholipase A2 group 6 (PLA2G6) D331Y mutant. A series of PD-related cascade events such as ER stress, abnormal calcium homeostasis, mitochondrial dysfunction, increase of reactive oxygen species, and apoptosis were observed in PLA2G6 D331Y mutant DA neurons, whereas azoramide significantly protected PLA2G6 D331Y mutant DA neurons against these events. The beneficial effects of azoramide were abolished by treatment with a cAMP-response element binding protein (CREB) inhibitor. Our results suggest that azoramide is a potential neuroprotectant against DA neuron damage via restoring ER function and the CREB signaling.
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59
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Abstract
The endoplasmic reticulum (ER) translocon complex is the main gate into the secretory pathway, facilitating the translocation of nascent peptides into the ER lumen or their integration into the lipid membrane. Protein biogenesis in the ER involves additional processes, many of them occurring co-translationally while the nascent protein resides at the translocon complex, including recruitment of ER-targeted ribosome-nascent-chain complexes, glycosylation, signal peptide cleavage, membrane protein topogenesis and folding. To perform such varied functions on a broad range of substrates, the ER translocon complex has different accessory components that associate with it either stably or transiently. Here, we review recent structural and functional insights into this dynamically constituted central hub in the ER and its components. Recent cryo-electron microscopy (EM) studies have dissected the molecular organization of the co-translational ER translocon complex, comprising the Sec61 protein-conducting channel, the translocon-associated protein complex and the oligosaccharyl transferase complex. Complemented by structural characterization of the post-translational import machinery, key molecular principles emerge that distinguish co- and post-translational protein import and biogenesis. Further cryo-EM structures promise to expand our mechanistic understanding of the various biochemical functions involving protein biogenesis and quality control in the ER.
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Affiliation(s)
- Max Gemmer
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Friedrich Förster
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
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60
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Khan S. Do ribosomal protein alterations affect ER stress response in CVID? Clin Exp Immunol 2020; 200:87-88. [PMID: 31990366 DOI: 10.1111/cei.13418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2020] [Indexed: 11/29/2022] Open
Affiliation(s)
- S Khan
- Consultant Immunologist, Hull University Teaching Hospitals NHS Trust, Castle Hill Hospital, Cottingham, UK
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61
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Lenghel A, Gheorghita AM, Vacaru AM, Vacaru AM. What Is the Sweetest UPR Flavor for the β-cell? That Is the Question. Front Endocrinol (Lausanne) 2020; 11:614123. [PMID: 33613449 PMCID: PMC7891099 DOI: 10.3389/fendo.2020.614123] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/24/2020] [Indexed: 01/01/2023] Open
Abstract
Unfolded protein response (UPR) is a process conserved from yeasts to mammals and, based on the generally accepted dogma, helps the secretory performance of a cell, by improving its capacity to cope with a burden in the endoplasmic reticulum (ER). The ER of β-cells, "professional secretory cells", has to manage tremendous amounts of insulin, which elicits a strong pressure on the ER intrinsic folding capacity. Thus, the constant demand for insulin production results in misfolded proinsulin, triggering a physiological upregulation of UPR to restore homeostasis. Most diabetic disorders are characterized by the loss of functional β-cells, and the pathological side of UPR plays an instrumental role. The transition from a homeostatic to a pathological UPR that ultimately leads to insulin-producing β-cell decay entails complex cellular processes and molecular mechanisms which remain poorly described so far. Here, we summarize important processes that are coupled with or driven by UPR in β-cells, such as proliferation, inflammation and dedifferentiation. We conclude that the UPR comes in different "flavors" and each of them is correlated with a specific outcome for the cell, for survival, differentiation, proliferation as well as cell death. All these greatly depend on the way UPR is triggered, however what exactly is the switch that favors the activation of one UPR as opposed to others is largely unknown. Substantial work needs to be done to progress the knowledge in this important emerging field as this will help in the development of novel and more efficient therapies for diabetes.
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62
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Kopp MC, Larburu N, Durairaj V, Adams CJ, Ali MMU. UPR proteins IRE1 and PERK switch BiP from chaperone to ER stress sensor. Nat Struct Mol Biol 2019; 26:1053-1062. [PMID: 31695187 PMCID: PMC6858872 DOI: 10.1038/s41594-019-0324-9] [Citation(s) in RCA: 202] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/01/2019] [Indexed: 12/24/2022]
Abstract
BiP is a major endoplasmic reticulum (ER) chaperone and is suggested to act as primary sensor in the activation of the unfolded protein response (UPR). How BiP operates as a molecular chaperone and as an ER stress sensor is unknown. Here, by reconstituting components of human UPR, ER stress and BiP chaperone systems, we discover that the interaction of BiP with the luminal domains of UPR proteins IRE1 and PERK switch BiP from its chaperone cycle into an ER stress sensor cycle by preventing the binding of its co-chaperones, with loss of ATPase stimulation. Furthermore, misfolded protein-dependent dissociation of BiP from IRE1 is primed by ATP but not ADP. Our data elucidate a previously unidentified mechanistic cycle of BiP function that explains its ability to act as an Hsp70 chaperone and ER stress sensor.
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Affiliation(s)
- Megan C Kopp
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, UK
| | - Natacha Larburu
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, UK
| | - Vinoth Durairaj
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, UK
| | - Christopher J Adams
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, UK
| | - Maruf M U Ali
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, UK.
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63
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Karagöz GE, Aragón T, Acosta-Alvear D. Recent advances in signal integration mechanisms in the unfolded protein response. F1000Res 2019; 8. [PMID: 31723416 PMCID: PMC6833987 DOI: 10.12688/f1000research.19848.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/22/2019] [Indexed: 12/15/2022] Open
Abstract
Since its discovery more than 25 years ago, great progress has been made in our understanding of the unfolded protein response (UPR), a homeostatic mechanism that adjusts endoplasmic reticulum (ER) function to satisfy the physiological demands of the cell. However, if ER homeostasis is unattainable, the UPR switches to drive cell death to remove defective cells in an effort to protect the health of the organism. This functional dichotomy places the UPR at the crossroads of the adaptation versus apoptosis decision. Here, we focus on new developments in UPR signaling mechanisms, in the interconnectivity among the signaling pathways that make up the UPR in higher eukaryotes, and in the coordination between the UPR and other fundamental cellular processes.
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Affiliation(s)
- G Elif Karagöz
- Max Perutz Labs Vienna, Medical University of Vienna, Vienna, Austria
| | - Tomás Aragón
- Department of Gene Therapy and Regulation of Gene Expression, University of Navarra, Pamplona, Spain
| | - Diego Acosta-Alvear
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, Santa Barbara, CA, USA
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64
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Nürenberg-Goloub E, Tampé R. Ribosome recycling in mRNA translation, quality control, and homeostasis. Biol Chem 2019; 401:47-61. [DOI: 10.1515/hsz-2019-0279] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/22/2019] [Indexed: 02/07/2023]
Abstract
Abstract
Protein biosynthesis is a conserved process, essential for life. Ongoing research for four decades has revealed the structural basis and mechanistic details of most protein biosynthesis steps. Numerous pathways and their regulation have recently been added to the translation system describing protein quality control and messenger ribonucleic acid (mRNA) surveillance, ribosome-associated protein folding and post-translational modification as well as human disorders associated with mRNA and ribosome homeostasis. Thus, translation constitutes a key regulatory process placing the ribosome as a central hub at the crossover of numerous cellular pathways. Here, we describe the role of ribosome recycling by ATP-binding cassette sub-family E member 1 (ABCE1) as a crucial regulatory step controlling the biogenesis of functional proteins and the degradation of aberrant nascent chains in quality control processes.
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Affiliation(s)
- Elina Nürenberg-Goloub
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt , Max-von-Laue-Str. 9 , D-60438 Frankfurt/Main , Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt , Max-von-Laue-Str. 9 , D-60438 Frankfurt/Main , Germany
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65
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Karagöz GE, Peschek J, Walter P, Acosta-Alvear D. In vitro RNA Cleavage Assays to Characterize IRE1-dependent RNA Decay. Bio Protoc 2019; 9:e3307. [PMID: 33654817 PMCID: PMC7854161 DOI: 10.21769/bioprotoc.3307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/24/2019] [Accepted: 07/21/2019] [Indexed: 11/24/2022] Open
Abstract
The kinase/RNase IRE1 is a key effector of the cellular response to endoplasmic reticulum stress. The RNase activity of IRE1 can be measured in cells or in the test tube. Here we describe a protocol for the in vitro cleavage and analysis of RNA substrates of IRE1. The method consists of the in vitro transcription, purification and re-folding of IRE1 substrate RNAs followed by their cleavage using recombinant cytosolic kinase/RNase domains of IRE1 and the separation of the resulting fragments by denaturing polyacrylamide gel electrophoresis. This protocol allows the study of the cleavage kinetics of IRE1's RNA substrates in vitro.
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Affiliation(s)
- G. Elif Karagöz
- Max Perutz Labs Vienna, Medical University of Vienna, Vienna, Austria
| | - Jirka Peschek
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, USA
| | - Peter Walter
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, USA
| | - Diego Acosta-Alvear
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
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66
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Shah O'Brien P, Xi Y, Miller JR, Brownell AL, Zeng Q, Yoo GH, Garshott DM, O'Brien MB, Galinato AE, Cai P, Narula N, Callaghan MU, Kaufman RJ, Fribley AM. Disulfiram (Antabuse) Activates ROS-Dependent ER Stress and Apoptosis in Oral Cavity Squamous Cell Carcinoma. J Clin Med 2019; 8:jcm8050611. [PMID: 31064122 PMCID: PMC6571807 DOI: 10.3390/jcm8050611] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 02/06/2023] Open
Abstract
A paucity of advances in the development of novel therapeutic agents for squamous cell carcinomas of the head and neck, oral cavity (OSCC) and oropharynx, has stagnated disease free survival rates over the past two decades. Although immunotherapies targeted against checkpoint inhibitors such as PD-1 or CTLA-4 are just now entering the clinic for late stage disease with regularity the median improvement in overall survival is only about three months. There is an urgent unmet clinical need to identify new therapies that can be used alone or in combination with current approaches to increase survival by more than a few months. Activation of the apoptotic arm of the unfolded response (UPR) with small molecules and natural products has recently been demonstrated to be a productive approach in pre-clinical models of OSCC and several other cancers. The aim of current study was to perform a high throughput screen (HTS) with a diverse chemical library to identify compounds that could induce CHOP, a component of the apoptotic arm of the UPR. Disulfiram (DSF, also known as Antabuse) the well-known aversion therapy used to treat chronic alcoholism emerged as a hit that could generate reactive oxygen species, activate the UPR and apoptosis and reduce proliferation in OSCC cell cultures and xenografts. A panel of murine embryonic fibroblasts null for key UPR intermediates (e.g., Chop and Atf4) was resistant to DSF suggesting that an intact UPR is a key element of the mechanism regulating the antiproliferative effects of DSF.
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Affiliation(s)
- Priyanka Shah O'Brien
- Department of Otolaryngology⁻Head and Neck Surgery, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Yue Xi
- Carman and Ann Adams Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Justin R Miller
- Carman and Ann Adams Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Amy L Brownell
- Carman and Ann Adams Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Qinghua Zeng
- Division of Hematology/Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - George H Yoo
- Department of Otolaryngology⁻Head and Neck Surgery, Wayne State University School of Medicine, Detroit, MI 48201, USA.
- Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Danielle M Garshott
- Carman and Ann Adams Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Matthew B O'Brien
- Henry Ford Hospital, Diagnostic Radiology Residency, Detroit, MI 48202, USA.
| | - Anthony E Galinato
- Henry Ford Hospital, Diagnostic Radiology Residency, Detroit, MI 48202, USA.
| | - Peter Cai
- Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Neha Narula
- Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Michael U Callaghan
- Carman and Ann Adams Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
- Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Randal J Kaufman
- Degenerative Diseases Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
| | - Andrew M Fribley
- Department of Otolaryngology⁻Head and Neck Surgery, Wayne State University School of Medicine, Detroit, MI 48201, USA.
- Carman and Ann Adams Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
- Division of Hematology/Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
- Wayne State University School of Medicine, Detroit, MI 48201, USA.
- Molecular Therapeutics Program, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA.
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67
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Fun XH, Thibault G. Lipid bilayer stress and proteotoxic stress-induced unfolded protein response deploy divergent transcriptional and non-transcriptional programmes. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1865:158449. [PMID: 31028913 DOI: 10.1016/j.bbalip.2019.04.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/14/2019] [Accepted: 04/22/2019] [Indexed: 12/13/2022]
Abstract
The unfolded protein response (UPR) is activated by endoplasmic reticulum (ER) stress and is designed to restore cellular homeostasis through multiple intracellular signalling pathways. In mammals, the UPR programme regulates the expression of hundreds of genes in response to signalling from ATF6, IRE1, and PERK. These three highly conserved stress sensors are activated by the accumulation of unfolded proteins within the ER. Alternatively, IRE1 and PERK sense generalised lipid bilayer stress (LBS) at the ER while ATF6 is activated by an increase of specific sphingolipids. As a result, the UPR supports cellular robustness as a broad-spectrum compensatory pathway that is achieved by deploying a tailored transcriptional programme adapted to the source of ER stress. This review summarises the current understanding of the three ER stress transducers in sensing proteotoxic stress and LBS. The plasticity of the UPR programme in the context of different sources of ER stress will also be discussed.
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Affiliation(s)
- Xiu Hui Fun
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Guillaume Thibault
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
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68
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Hoffman AM, Chen Q, Zheng T, Nicchitta CV. Heterogeneous translational landscape of the endoplasmic reticulum revealed by ribosome proximity labeling and transcriptome analysis. J Biol Chem 2019; 294:8942-8958. [PMID: 31004035 DOI: 10.1074/jbc.ra119.007996] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/27/2019] [Indexed: 12/21/2022] Open
Abstract
The endoplasmic reticulum (ER) is a nexus for mRNA localization and translation, and recent studies have demonstrated that ER-bound ribosomes also play a transcriptome-wide role in regulating proteome composition. The Sec61 translocon (SEC61) serves as the receptor for ribosomes that translate secretory/integral membrane protein-encoding mRNAs, but whether SEC61 also serves as a translation site for cytosolic protein-encoding mRNAs remains unknown. Here, using a BioID proximity-labeling approach in HEK293T Flp-In cell lines, we examined interactions between ER-resident proteins and ribosomes in vivo Using in vitro analyses, we further focused on bona fide ribosome interactors (i.e. SEC61) and ER proteins (ribophorin I, leucine-rich repeat-containing 59 (LRRC59), and SEC62) previously implicated in associating with ribosomes. We observed labeling of ER-bound ribosomes with the SEC61β and LRRC59 BioID reporters, comparatively modest labeling with the ribophorin I reporter, and no labeling with the SEC62 reporter. A biotin pulse-chase/subcellular fractionation approach to examine ribosome exchange at the SEC61β and LRRC59 sites revealed that, at steady state, ribosomes at these sites comprise both rapid- and slow-exchanging pools. Global translational initiation arrest elicited by the inhibitor harringtonine accelerated SEC61β reporter-labeled ribosome exchange. RNA-Seq analyses of the mRNAs associated with SEC61β- and LRRC59-labeled ribosomes revealed both site-enriched and shared mRNAs and further established that the ER has a transcriptome-wide role in regulating proteome composition. These results provide evidence that ribosomes interact with the ER membrane via multiple modes and suggest regulatory mechanisms that control global proteome composition via ER membrane-bound ribosomes.
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Affiliation(s)
| | - Qiang Chen
- Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Tianli Zheng
- Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Christopher V Nicchitta
- From the Departments of Biochemistry and .,Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710
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69
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Lang S, Nguyen D, Pfeffer S, Förster F, Helms V, Zimmermann R. Functions and Mechanisms of the Human Ribosome-Translocon Complex. Subcell Biochem 2019; 93:83-141. [PMID: 31939150 DOI: 10.1007/978-3-030-28151-9_4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The membrane of the endoplasmic reticulum (ER) in human cells harbors the protein translocon, which facilitates membrane insertion and translocation of almost every newly synthesized polypeptide targeted to organelles of the secretory pathway. The translocon comprises the polypeptide-conducting Sec61 channel and several additional proteins, which are associated with the heterotrimeric Sec61 complex. This ensemble of proteins facilitates ER targeting of precursor polypeptides, Sec61 channel opening and closing, and modification of precursor polypeptides in transit through the Sec61 complex. Recently, cryoelectron tomography of translocons in native ER membranes has given unprecedented insights into the architecture and dynamics of the native, ribosome-associated translocon and the Sec61 channel. These structural data are discussed in light of different Sec61 channel activities including ribosome receptor function, membrane insertion or translocation of newly synthesized polypeptides as well as the possible roles of the Sec61 channel as a passive ER calcium leak channel and regulator of ATP/ADP exchange between cytosol and ER.
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Affiliation(s)
- Sven Lang
- Competence Center for Molecular Medicine, Saarland University Medical School, Building 44, 66421, Homburg, Germany.
| | - Duy Nguyen
- Center for Bioinformatics, Saarland University, 66041, Saarbrücken, Germany
| | - Stefan Pfeffer
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152, Martinsried, Germany
- ZMBH, 69120, Heidelberg, Germany
| | - Friedrich Förster
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152, Martinsried, Germany
- Center for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, 66041, Saarbrücken, Germany
| | - Richard Zimmermann
- Competence Center for Molecular Medicine, Saarland University Medical School, Building 44, 66421, Homburg, Germany
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