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Pereira F, Rettel M, Stein F, Savitski MM, Collinson I, Römisch K. Effect of Sec61 interaction with Mpd1 on endoplasmic reticulum-associated degradation. PLoS One 2019; 14:e0211180. [PMID: 30682149 PMCID: PMC6347170 DOI: 10.1371/journal.pone.0211180] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 01/08/2019] [Indexed: 01/16/2023] Open
Abstract
Proteins that misfold in the endoplasmic reticulum (ER) are transported back to the cytosol for ER-associated degradation (ERAD). The Sec61 channel is one of the candidates for the retrograde transport conduit. Channel opening from the ER lumen must be triggered by ERAD factors and substrates. Here we aimed to identify new lumenal interaction partners of the Sec61 channel by chemical crosslinking and mass spectrometry. In addition to known Sec61 interactors we detected ERAD factors including Cue1, Ubc6, Ubc7, Asi3, and Mpd1. We show that the CPY* ERAD factor Mpd1 binds to the lumenal Sec61 hinge region. Deletion of the Mpd1 binding site reduced the interaction between both proteins and caused an ERAD defect specific for CPY* without affecting protein import into the ER or ERAD of other substrates. Our data suggest that Mpd1 binding to Sec61 is a prerequisite for CPY* ERAD and confirm a role of Sec61 in ERAD of misfolded secretory proteins.
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Affiliation(s)
- Fabio Pereira
- Faculty of Natural Sciences and Technology, Saarland University, Saarbruecken, Germany
| | - Mandy Rettel
- Proteomics Core Facility, EMBL, Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL, Heidelberg, Germany
| | | | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Karin Römisch
- Faculty of Natural Sciences and Technology, Saarland University, Saarbruecken, Germany
- * E-mail:
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52
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Avci D, Lemberg MK. Membrane Protein Dislocation by the Rhomboid Pseudoprotease Dfm1: No Pore Needed? Mol Cell 2018; 69:161-162. [PMID: 29351840 DOI: 10.1016/j.molcel.2017.12.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Defective ER-resident membrane proteins need to be ejected into the cytoplasm in order to be degraded by the proteasome, but the exact mechanism remains unclear. In this issue of Molecular Cell, Neal et al. (2018) reveal that the rhomboid pseudoprotease Dfm1 defines the central ERAD component for membrane protein dislocation.
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Affiliation(s)
- Dönem Avci
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
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53
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Depaoli MR, Hay JC, Graier WF, Malli R. The enigmatic ATP supply of the endoplasmic reticulum. Biol Rev Camb Philos Soc 2018; 94:610-628. [PMID: 30338910 PMCID: PMC6446729 DOI: 10.1111/brv.12469] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 08/20/2018] [Accepted: 08/30/2018] [Indexed: 12/11/2022]
Abstract
The endoplasmic reticulum (ER) is a functionally and morphologically complex cellular organelle largely responsible for a variety of crucial functions, including protein folding, maturation and degradation. Furthermore, the ER plays an essential role in lipid biosynthesis, dynamic Ca2+ storage, and detoxification. Malfunctions in ER‐related processes are responsible for the genesis and progression of many diseases, such as heart failure, cancer, neurodegeneration and metabolic disorders. To fulfill many of its vital functions, the ER relies on a sufficient energy supply in the form of adenosine‐5′‐triphosphate (ATP), the main cellular energy source. Despite landmark discoveries and clarification of the functional principles of ER‐resident proteins and key ER‐related processes, the mechanism underlying ER ATP transport remains somewhat enigmatic. Here we summarize ER‐related ATP‐consuming processes and outline our knowledge about the nature and function of the ER energy supply.
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Affiliation(s)
- Maria R Depaoli
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Jesse C Hay
- Division of Biological Sciences and Center for Structural and Functional Neuroscience, The University of Montana, 32 Campus Drive, HS410, Missoula, MT 59812-4824, U.S.A
| | - Wolfgang F Graier
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria.,BioTechMed Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Roland Malli
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria.,BioTechMed Graz, Mozartgasse 12/II, 8010 Graz, Austria
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54
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Fujii J, Homma T, Kobayashi S, Seo HG. Mutual interaction between oxidative stress and endoplasmic reticulum stress in the pathogenesis of diseases specifically focusing on non-alcoholic fatty liver disease. World J Biol Chem 2018; 9:1-15. [PMID: 30364769 PMCID: PMC6198288 DOI: 10.4331/wjbc.v9.i1.1] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/19/2018] [Accepted: 10/11/2018] [Indexed: 02/05/2023] Open
Abstract
Reactive oxygen species (ROS) are produced during normal physiologic processes with the consumption of oxygen. While ROS play signaling roles, when they are produced in excess beyond normal antioxidative capacity this can cause pathogenic damage to cells. The majority of such oxidation occurs in polyunsaturated fatty acids and sulfhydryl group in proteins, resulting in lipid peroxidation and protein misfolding, respectively. The accumulation of misfolded proteins in the endoplasmic reticulum (ER) is enhanced under conditions of oxidative stress and results in ER stress, which, together, leads to the malfunction of cellular homeostasis. Multiple types of defensive machinery are activated in unfolded protein response under ER stress to resolve this unfavorable situation. ER stress triggers the malfunction of protein secretion and is associated with a variety of pathogenic conditions including defective insulin secretion from pancreatic β-cells and accelerated lipid droplet formation in hepatocytes. Herein we use nonalcoholic fatty liver disease (NAFLD) as an illustration of such pathological liver conditions that result from ER stress in association with oxidative stress. Protecting the ER by eliminating excessive ROS via the administration of antioxidants or by enhancing lipid-metabolizing capacity via the activation of peroxisome proliferator-activated receptors represent promising therapeutics for NAFLD.
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Affiliation(s)
- Junichi Fujii
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, Yamagata 990-9585, Japan
| | - Takujiro Homma
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, Yamagata 990-9585, Japan
| | - Sho Kobayashi
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, Yamagata 990-9585, Japan
| | - Han Geuk Seo
- Sanghuh College of Life Sciences, Konkuk University, Seoul 143-701, South Korea
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55
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Mehrtash AB, Hochstrasser M. Ubiquitin-dependent protein degradation at the endoplasmic reticulum and nuclear envelope. Semin Cell Dev Biol 2018; 93:111-124. [PMID: 30278225 DOI: 10.1016/j.semcdb.2018.09.013] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 01/01/2023]
Abstract
Numerous nascent proteins undergo folding and maturation within the luminal and membrane compartments of the endoplasmic reticulum (ER). Despite the presence of various factors in the ER that promote protein folding, many proteins fail to properly fold and assemble and are subsequently degraded. Regulatory proteins in the ER also undergo degradation in a way that is responsive to stimuli or the changing needs of the cell. As in most cellular compartments, the ubiquitin-proteasome system (UPS) is responsible for the majority of the degradation at the ER-in a process termed ER-associated degradation (ERAD). Autophagic processes utilizing ubiquitin-like protein-conjugating systems also play roles in protein degradation at the ER. The ER is continuous with the nuclear envelope (NE), which consists of the outer nuclear membrane (ONM) and inner nuclear membrane (INM). While ERAD is known also to occur at the NE, only some of the ERAD ubiquitin-ligation pathways function at the INM. Protein degradation machineries in the ER/NE target a wide variety of substrates in multiple cellular compartments, including the cytoplasm, nucleoplasm, ER lumen, ER membrane, and the NE. Here, we review the protein degradation machineries of the ER and NE and the underlying mechanisms dictating recognition and processing of substrates by these machineries.
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Affiliation(s)
- Adrian B Mehrtash
- Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, 06520, CT, USA.
| | - Mark Hochstrasser
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06520, USA; Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, 06520, CT, USA.
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56
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Moon HW, Han HG, Jeon YJ. Protein Quality Control in the Endoplasmic Reticulum and Cancer. Int J Mol Sci 2018; 19:E3020. [PMID: 30282948 PMCID: PMC6213883 DOI: 10.3390/ijms19103020] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 09/22/2018] [Accepted: 10/01/2018] [Indexed: 12/21/2022] Open
Abstract
The endoplasmic reticulum (ER) is an essential compartment of the biosynthesis, folding, assembly, and trafficking of secretory and transmembrane proteins, and consequently, eukaryotic cells possess specialized machineries to ensure that the ER enables the proteins to acquire adequate folding and maturation for maintaining protein homeostasis, a process which is termed proteostasis. However, a large variety of physiological and pathological perturbations lead to the accumulation of misfolded proteins in the ER, which is referred to as ER stress. To resolve ER stress and restore proteostasis, cells have evolutionary conserved protein quality-control machineries of the ER, consisting of the unfolded protein response (UPR) of the ER, ER-associated degradation (ERAD), and autophagy. Furthermore, protein quality-control machineries of the ER play pivotal roles in the control of differentiation, progression of cell cycle, inflammation, immunity, and aging. Therefore, severe and non-resolvable ER stress is closely associated with tumor development, aggressiveness, and response to therapies for cancer. In this review, we highlight current knowledge in the molecular understanding and physiological relevance of protein quality control of the ER and discuss new insights into how protein quality control of the ER is implicated in the pathogenesis of cancer, which could contribute to therapeutic intervention in cancer.
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Affiliation(s)
- Hye Won Moon
- Department of Biochemistry, Chungnam National University College of Medicine, Daejeon 35015, Korea.
- Department of Medical Science, Chungnam National University College of Medicine, Daejeon 35015, Korea.
| | - Hye Gyeong Han
- Department of Biochemistry, Chungnam National University College of Medicine, Daejeon 35015, Korea.
- Department of Medical Science, Chungnam National University College of Medicine, Daejeon 35015, Korea.
| | - Young Joo Jeon
- Department of Biochemistry, Chungnam National University College of Medicine, Daejeon 35015, Korea.
- Department of Medical Science, Chungnam National University College of Medicine, Daejeon 35015, Korea.
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57
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Vigneron N, Ferrari V, Van den Eynde BJ, Cresswell P, Leonhardt RM. Cytosolic Processing Governs TAP-Independent Presentation of a Critical Melanoma Antigen. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2018; 201:1875-1888. [PMID: 30135181 PMCID: PMC6457910 DOI: 10.4049/jimmunol.1701479] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 07/26/2018] [Indexed: 12/30/2022]
Abstract
Cancer immunotherapy has been flourishing in recent years with remarkable clinical success. But as more patients are treated, a shadow is emerging that has haunted other cancer therapies: tumors develop resistance. Resistance is often caused by defects in the MHC class I Ag presentation pathway critical for CD8 T cell-mediated tumor clearance. TAP and tapasin, both key players in the pathway, are frequently downregulated in human cancers, correlating with poor patient survival. Reduced dependence on these factors may promote vaccine efficiency by limiting immune evasion. In this study, we demonstrate that PMEL209-217, a promising phase 3 trial-tested antimelanoma vaccine candidate, is robustly presented by various TAP- and/or tapasin-deficient cell lines. This striking characteristic may underlie its potency as a vaccine. Surprisingly, cytosolic proteasomes generate the peptide even for TAP-independent presentation, whereas tripeptidyl peptidase 2 (TPP2) efficiently degrades the epitope. Consequently, inhibiting TPP2 substantially boosts PMEL209-217 presentation, suggesting a possible strategy to improve the therapeutic efficacy of the vaccine.
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Affiliation(s)
- Nathalie Vigneron
- Ludwig Institute for Cancer Research, Brussels B-1200, Belgium
- de Duve Institute, University of Louvain, Brussels B-1200, Belgium
- Walloon Excellence in Life Sciences and Biotechnology, Brussels B-1200, Belgium
| | - Violette Ferrari
- Ludwig Institute for Cancer Research, Brussels B-1200, Belgium
- de Duve Institute, University of Louvain, Brussels B-1200, Belgium
- Walloon Excellence in Life Sciences and Biotechnology, Brussels B-1200, Belgium
| | - Benoît J Van den Eynde
- Ludwig Institute for Cancer Research, Brussels B-1200, Belgium;
- de Duve Institute, University of Louvain, Brussels B-1200, Belgium
- Walloon Excellence in Life Sciences and Biotechnology, Brussels B-1200, Belgium
| | - Peter Cresswell
- Department of Immunobiology, Yale University, New Haven, CT 06519; and
- Department of Cell Biology, Yale University, New Haven, CT 06519
| | - Ralf M Leonhardt
- Department of Immunobiology, Yale University, New Haven, CT 06519; and
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58
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The Rhomboid Superfamily: Structural Mechanisms and Chemical Biology Opportunities. Trends Biochem Sci 2018; 43:726-739. [DOI: 10.1016/j.tibs.2018.06.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 06/08/2018] [Accepted: 06/30/2018] [Indexed: 12/27/2022]
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59
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Epithelial sodium channel biogenesis and quality control in the early secretory pathway. Curr Opin Nephrol Hypertens 2018; 27:364-372. [DOI: 10.1097/mnh.0000000000000438] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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60
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Ravindran MS. Molecular chaperones: from proteostasis to pathogenesis. FEBS J 2018; 285:3353-3361. [PMID: 29890022 PMCID: PMC7164077 DOI: 10.1111/febs.14576] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/12/2018] [Accepted: 06/07/2018] [Indexed: 12/13/2022]
Abstract
Maintaining protein homeostasis (proteostasis) is essential for a functional proteome. A wide range of extrinsic and intrinsic factors perturb proteostasis, causing protein misfolding, misassembly, and aggregation. This compromises cellular integrity and leads to aging and disease, including neurodegeneration and cancer. At the cellular level, protein aggregation is counteracted by powerful mechanisms comprising of a cascade of enzymes and chaperones that operate in a coordinated multistep manner to sense, prevent, and/or dispose of aberrant proteins. Although these processes are well understood for soluble proteins, there is a major gap in our understanding of how cells handle misfolded or aggregated membrane proteins. This article provides an overview of cellular proteostasis with emphasis on membrane protein substrates and suggests host-virus interaction as a tool to clarify outstanding questions in proteostasis.
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Affiliation(s)
- Madhu Sudhan Ravindran
- Department of Cell and Developmental BiologyUniversity of Michigan Medical SchoolAnn ArborMIUSA
- Present address:
Biocon Bristol‐Myers Squibb R&D CenterBiocon Park, Bommasandra Jigani Link RdBengaluruKarnataka560099India
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61
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Hwang J, Qi L. Quality Control in the Endoplasmic Reticulum: Crosstalk between ERAD and UPR pathways. Trends Biochem Sci 2018; 43:593-605. [PMID: 30056836 PMCID: PMC6327314 DOI: 10.1016/j.tibs.2018.06.005] [Citation(s) in RCA: 343] [Impact Index Per Article: 57.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 05/30/2018] [Accepted: 06/11/2018] [Indexed: 01/14/2023]
Abstract
Endoplasmic reticulum (ER)-associated degradation (ERAD) and the unfolded protein response (UPR) are two key quality-control machineries in the cell. ERAD is responsible for the clearance of misfolded proteins in the ER for cytosolic proteasomal degradation, while UPR is activated in response to the accumulation of misfolded proteins. It has long been thought that ERAD is an integral part of UPR because expression of many ERAD genes is controlled by UPR; however, recent studies have suggested that ERAD has a direct role in controlling the protein turnover and abundance of IRE1α, the most conserved UPR sensor. Here, we review recent advances in our understanding of IRE1α activation and propose that UPR and ERAD engage in an intimate crosstalk to define folding capacity and maintain homeostasis in the ER.
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Affiliation(s)
- Jiwon Hwang
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48105, USA.
| | - Ling Qi
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48105, USA; Division of Metabolism, Endocrinology & Diabetes, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48105, USA.
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62
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Kadowaki H, Nishitoh H. Endoplasmic reticulum quality control by garbage disposal. FEBS J 2018; 286:232-240. [PMID: 29923316 DOI: 10.1111/febs.14589] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/12/2018] [Accepted: 06/18/2018] [Indexed: 11/30/2022]
Abstract
Various types of intracellular and extracellular stresses disturb homeostasis in the endoplasmic reticulum (ER) and, thus, trigger the ER stress response. Unavoidable and/or prolonged ER stress causes cell toxicity and occasionally cell death. The malfunction or death of irreplaceable cells leads to conformational diseases, including diabetes mellitus, ischemic diseases, metabolic diseases, and neurodegenerative diseases. In the past several decades, many studies have revealed the molecular mechanisms of the ER quality control system. Cells resolve ER stress by promptly and accurately reducing the amount of malfolded proteins. Recent reports have revealed that cells possess several types of ER-related disposal systems, including mRNA decay, proteasomal degradation, and autophagy. The removal of dispensable RNAs, proteins, and organelle parts may enable the effective maintenance of a functional ER. Here, we provide a comprehensive understanding of the ER quality control system by focusing on ER-related garbage disposal systems.
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Affiliation(s)
- Hisae Kadowaki
- Laboratory of Biochemistry and Molecular Biology, Department of Medical Sciences, University of Miyazaki, Japan
| | - Hideki Nishitoh
- Laboratory of Biochemistry and Molecular Biology, Department of Medical Sciences, University of Miyazaki, Japan
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63
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Wu X, Rapoport TA. Mechanistic insights into ER-associated protein degradation. Curr Opin Cell Biol 2018; 53:22-28. [PMID: 29719269 DOI: 10.1016/j.ceb.2018.04.004] [Citation(s) in RCA: 239] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 04/11/2018] [Accepted: 04/11/2018] [Indexed: 12/16/2022]
Abstract
Misfolded proteins of the endoplasmic reticulum (ER) are discarded by a conserved process, called ER-associated protein degradation (ERAD). ERAD substrates are retro-translocated into the cytosol, polyubiquitinated, extracted from the ER membrane, and ultimately degraded by the proteasome. Recent in vitro experiments with purified components have given insight into the mechanism of ERAD. ERAD substrates with misfolded luminal or intramembrane domains are moved across the ER membrane through a channel formed by the multispanning ubiquitin ligase Hrd1. Following polyubiquitination, substrates are extracted from the membrane by the Cdc48/p97 ATPase complex and transferred to the proteasome. We discuss the molecular mechanism of these processes and point out remaining open questions.
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Affiliation(s)
- Xudong Wu
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, United States
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, United States.
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64
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Abstract
The endoplasmic reticulum (ER) is the site of maturation for roughly one-third of all cellular proteins. ER-resident molecular chaperones and folding catalysts promote folding and assembly in a diverse set of newly synthesized proteins. Because these processes are error-prone, all eukaryotic cells have a quality-control system in place that constantly monitors the proteins and decides their fate. Proteins with potentially harmful nonnative conformations are subjected to assisted folding or degraded. Persistent folding-defective proteins are distinguished from folding intermediates and targeted for degradation by a specific process involving clearance from the ER. Although the basic principles of these processes appear conserved from yeast to animals and plants, there are distinct differences in the ER-associated degradation of misfolded glycoproteins. The general importance of ER quality-control events is underscored by their involvement in the biogenesis of diverse cell surface receptors and their crucial maintenance of protein homeostasis under diverse stress conditions.
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Affiliation(s)
- Richard Strasser
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria;
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65
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Alasiri G, Fan LYN, Zona S, Goldsbrough IG, Ke HL, Auner HW, Lam EWF. ER stress and cancer: The FOXO forkhead transcription factor link. Mol Cell Endocrinol 2018; 462:67-81. [PMID: 28572047 DOI: 10.1016/j.mce.2017.05.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/17/2017] [Accepted: 05/24/2017] [Indexed: 12/20/2022]
Abstract
The endoplasmic reticulum (ER) is a cellular organelle with central roles in maintaining proteostasis due to its involvement in protein synthesis, folding, quality control, distribution and degradation. The accumulation of misfolded proteins in the ER lumen causes 'ER stress' and threatens overall cellular proteostasis. To restore ER homeostasis, cells evoke an evolutionarily conserved adaptive signalling and gene expression network collectively called the 'unfolded protein response (UPR)', a complex biological process which aims to restore proteostasis. When ER stress is overwhelming and beyond rectification, the normally pro-survival UPR can shift to induce cell termination. Emerging evidence from mammalian, fly and nematode worm systems reveals that the FOXO Forkhead proteins integrate upstream ER stress and UPR signals with the transcriptional machinery to decrease translation, promote cell survival/termination and increase the levels of ER-resident chaperones and of ER-associated degradation (ERAD) components to restore ER homeostasis. The high rates of protein synthesis/translation associated with cancer cell proliferation and metabolism, as well as mutations resulting in aberrant proteins, also induce ER stress and the UPR. While the pro-survival side of the UPR underlies its ability to sustain and promote cancers, its apoptotic functions can be exploited for cancer therapies by offering the chance to 'flick the proteostatic switch'. To this end, further studies are required to fully reevaluate the roles and regulation of these UPR signalling molecules, including FOXO proteins and their targets, in cancer initiation and progression as well as the effects on inhibiting their functions in cancer cells. This information will help to establish these UPR signalling molecules as possible therapeutic targets and putative biomarkers in cancers.
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Affiliation(s)
- Glowi Alasiri
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Lavender Yuen-Nam Fan
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Stefania Zona
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | | | - Hui-Ling Ke
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Holger Werner Auner
- Department of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK.
| | - Eric Wing-Fai Lam
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK.
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66
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Berner N, Reutter KR, Wolf DH. Protein Quality Control of the Endoplasmic Reticulum and Ubiquitin-Proteasome-Triggered Degradation of Aberrant Proteins: Yeast Pioneers the Path. Annu Rev Biochem 2018; 87:751-782. [PMID: 29394096 DOI: 10.1146/annurev-biochem-062917-012749] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cells must constantly monitor the integrity of their macromolecular constituents. Proteins are the most versatile class of macromolecules but are sensitive to structural alterations. Misfolded or otherwise aberrant protein structures lead to dysfunction and finally aggregation. Their presence is linked to aging and a plethora of severe human diseases. Thus, misfolded proteins have to be rapidly eliminated. Secretory proteins constitute more than one-third of the eukaryotic proteome. They are imported into the endoplasmic reticulum (ER), where they are folded and modified. A highly elaborated machinery controls their folding, recognizes aberrant folding states, and retrotranslocates permanently misfolded proteins from the ER back to the cytosol. In the cytosol, they are degraded by the highly selective ubiquitin-proteasome system. This process of protein quality control followed by proteasomal elimination of the misfolded protein is termed ER-associated degradation (ERAD), and it depends on an intricate interplay between the ER and the cytosol.
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Affiliation(s)
- Nicole Berner
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany; , ,
| | - Karl-Richard Reutter
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany; , ,
| | - Dieter H Wolf
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany; , ,
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67
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Yoo YS, Han HG, Jeon YJ. Unfolded Protein Response of the Endoplasmic Reticulum in Tumor Progression and Immunogenicity. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:2969271. [PMID: 29430279 PMCID: PMC5752989 DOI: 10.1155/2017/2969271] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/29/2017] [Indexed: 12/11/2022]
Abstract
The endoplasmic reticulum (ER) is a pivotal regulator of folding, quality control, trafficking, and targeting of secreted and transmembrane proteins, and accordingly, eukaryotic cells have evolved specialized machinery to ensure that the ER enables these proteins to acquire adequate folding and maturation in the presence of intrinsic and extrinsic insults. This adaptive capacity of the ER to intrinsic and extrinsic perturbations is important for maintaining protein homeostasis, which is termed proteostasis. Failure in adaptation to these perturbations leads to accumulation of misfolded or unassembled proteins in the ER, which is termed ER stress, resulting in the activation of unfolded protein response (UPR) of the ER and the execution of ER-associated degradation (ERAD) to restore homeostasis. Furthermore, both of the two axes play key roles in the control of tumor progression, inflammation, immunity, and aging. Therefore, understanding UPR of the ER and subsequent ERAD will provide new insights into the pathogenesis of many human diseases and contribute to therapeutic intervention in these diseases.
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Affiliation(s)
- Yoon Seon Yoo
- Department of Biochemistry, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
- Department of Medical Science, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
| | - Hye Gyeong Han
- Department of Biochemistry, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
- Department of Medical Science, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
| | - Young Joo Jeon
- Department of Biochemistry, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
- Department of Medical Science, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea
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68
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Tang Y, Zheng M, An R, Chen L, Gong L, Cai H, Liu K, Yu L, Shen J, Du J. Proteasomal degradation of T. gondii ROP18 requires Derlin2. Acta Trop 2017; 174:106-113. [PMID: 28669563 DOI: 10.1016/j.actatropica.2017.06.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 05/28/2017] [Accepted: 06/28/2017] [Indexed: 01/12/2023]
Abstract
T. gondii is an obligate intracellular parasite, belonging to the Phylum Apicomplexa, infecting all warm-blooded animals including humans. During host cell invasion, specialized cytoskeletal and secretory organelles play a pivotal role. ROP18, as a member of the ROP2 family, has been identified as a key virulence factor mediating pathogenesis in T. gondii. Here, we identify an ER-resident protein, Derlin2, a factor implicated in the removal of misfolded proteins from the ER for cytosolic degradation, as a component of the machinery required for ER-associated protein degradation (ERAD). We identified Derlin2 interacting with ROP18 by yeast two-hybrid screening system. The interaction between ROP18 and Derlin2 was further confirmed through in vitro GST pull-down and in vivo immunoprecipitation assays. By immunofluorescence assay, we found that ROP18 co-localized with Derlin2 in the endoplasmic reticulum. Using overexpression and knockdown approaches, we demonstrated that Derlin2 was required for T. gondii ROP18 degradation. Consistently, cycloheximide chase experiments showed that the degradation of ROP18 relied on the Derlin2, but not Derlin1. These results indicate that interaction between Derlin2 and ROP18 is functionally relevant and leads ultimately to degradation of ROP18. The finding provides the basis for future studies on Derlin2-dependent ERAD of T. gondii ROP18 and subsequent antigen generation.
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69
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Schulz J, Avci D, Queisser MA, Gutschmidt A, Dreher LS, Fenech EJ, Volkmar N, Hayashi Y, Hoppe T, Christianson JC. Conserved cytoplasmic domains promote Hrd1 ubiquitin ligase complex formation for ER-associated degradation (ERAD). J Cell Sci 2017; 130:3322-3335. [PMID: 28827405 DOI: 10.1242/jcs.206847] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 08/16/2017] [Indexed: 12/20/2022] Open
Abstract
The mammalian ubiquitin ligase Hrd1 is the central component of a complex facilitating degradation of misfolded proteins during the ubiquitin-proteasome-dependent process of ER-associated degradation (ERAD). Hrd1 associates with cofactors to execute ERAD, but their roles and how they assemble with Hrd1 are not well understood. Here, we identify crucial cofactor interaction domains within Hrd1 and report a previously unrecognised evolutionarily conserved segment within the intrinsically disordered cytoplasmic domain of Hrd1 (termed the HAF-H domain), which engages complementary segments in the cofactors FAM8A1 and Herp (also known as HERPUD1). This domain is required by Hrd1 to interact with both FAM8A1 and Herp, as well as to assemble higher-order Hrd1 complexes. FAM8A1 enhances binding of Herp to Hrd1, an interaction that is required for ERAD. Our findings support a model of Hrd1 complex formation, where the Hrd1 cytoplasmic domain and FAM8A1 have a central role in the assembly and activity of this ERAD machinery.
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Affiliation(s)
- Jasmin Schulz
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Dönem Avci
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Markus A Queisser
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Aljona Gutschmidt
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Lena-Sophie Dreher
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Emma J Fenech
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Norbert Volkmar
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Yuki Hayashi
- Department of Pharmaceutical Sciences, University of Tokyo, Tokyo 113-0033, Japan
| | - Thorsten Hoppe
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - John C Christianson
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
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70
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Schoebel S, Mi W, Stein A, Ovchinnikov S, Pavlovicz R, DiMaio F, Baker D, Chambers MG, Su H, Li D, Rapoport TA, Liao M. Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3. Nature 2017; 548:352-355. [PMID: 28682307 PMCID: PMC5736104 DOI: 10.1038/nature23314] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 06/30/2017] [Indexed: 12/16/2022]
Abstract
Misfolded endoplasmic reticulum (ER) proteins are retro-translocated through the membrane into the cytosol, where they are poly-ubiquitinated, extracted from the ER membrane, and degraded by the proteasome 1–4, a pathway termed ER-associated protein degradation (ERAD). Proteins with misfolded domains in the ER lumen or membrane are discarded through the ERAD-L and –M pathways, respectively. In S. cerevisiae, both pathways require the ubiquitin ligase Hrd1, a multi-spanning membrane protein with a cytosolic RING finger domain 5,6. Hrd1 is the crucial membrane component for retro-translocation 7,8, but whether it forms a protein-conducting channel is unclear. Here, we report a cryo-electron microscopy (cryo-EM) structure of S. cerevisiae Hrd1 in complex with its ER luminal binding partner Hrd3. Hrd1 forms a dimer within the membrane with one or two Hrd3 molecules associated at its luminal side. Each Hrd1 molecule has eight trans-membrane segments, five of which form an aqueous cavity extending from the cytosol almost to the ER lumen, while a segment of the neighboring Hrd1 molecule forms a lateral seal. The aqueous cavity and lateral gate are reminiscent of features in protein-conducting conduits that facilitate polypeptide movement in the opposite direction, i.e. from the cytosol into or across membranes 9–11. Our results suggest that Hrd1 forms a retro-translocation channel for the movement of misfolded polypeptides through the ER membrane.
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Affiliation(s)
- Stefan Schoebel
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
| | - Wei Mi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
| | - Alexander Stein
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Sergey Ovchinnikov
- Institute for Protein Design, University of Washington, Seattle, Washington, USA
| | - Ryan Pavlovicz
- Institute for Protein Design, University of Washington, Seattle, Washington, USA
| | - Frank DiMaio
- Institute for Protein Design, University of Washington, Seattle, Washington, USA
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, Washington, USA
| | - Melissa G Chambers
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
| | - Huayou Su
- National Lab for Parallel and Distributed Processing (PDL), School of Computer Science, National University of Defense Technology, Changsha, China
| | - Dongsheng Li
- National Lab for Parallel and Distributed Processing (PDL), School of Computer Science, National University of Defense Technology, Changsha, China
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
| | - Maofu Liao
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
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71
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The evolving role of ubiquitin modification in endoplasmic reticulum-associated degradation. Biochem J 2017; 474:445-469. [PMID: 28159894 DOI: 10.1042/bcj20160582] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/12/2016] [Accepted: 12/14/2016] [Indexed: 12/13/2022]
Abstract
The endoplasmic reticulum (ER) serves as a warehouse for factors that augment and control the biogenesis of nascent proteins entering the secretory pathway. In turn, this compartment also harbors the machinery that responds to the presence of misfolded proteins by targeting them for proteolysis via a process known as ER-associated degradation (ERAD). During ERAD, substrates are selected, modified with ubiquitin, removed from the ER, and then degraded by the cytoplasmic 26S proteasome. While integral membrane proteins can directly access the ubiquitination machinery that resides in the cytoplasm or on the cytoplasmic face of the ER membrane, soluble ERAD substrates within the lumen must be retrotranslocated from this compartment. In either case, nearly all ERAD substrates are tagged with a polyubiquitin chain, a modification that represents a commitment step to degrade aberrant proteins. However, increasing evidence indicates that the polyubiquitin chain on ERAD substrates can be further modified, serves to recruit ERAD-requiring factors, and may regulate the ERAD machinery. Amino acid side chains other than lysine on ERAD substrates can also be modified with ubiquitin, and post-translational modifications that affect substrate ubiquitination have been observed. Here, we summarize these data and provide an overview of questions driving this field of research.
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72
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Guerriero CJ, Reutter KR, Augustine AA, Preston GM, Weiberth KF, Mackie TD, Cleveland-Rubeor HC, Bethel NP, Callenberg KM, Nakatsukasa K, Grabe M, Brodsky JL. Transmembrane helix hydrophobicity is an energetic barrier during the retrotranslocation of integral membrane ERAD substrates. Mol Biol Cell 2017; 28:2076-2090. [PMID: 28539401 PMCID: PMC5509421 DOI: 10.1091/mbc.e17-03-0184] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/12/2017] [Accepted: 05/16/2017] [Indexed: 12/25/2022] Open
Abstract
Integral membrane proteins fold inefficiently and are susceptible to turnover via the endoplasmic reticulum-associated degradation (ERAD) pathway. During ERAD, misfolded proteins are recognized by molecular chaperones, polyubiquitinated, and retrotranslocated to the cytoplasm for proteasomal degradation. Although many aspects of this pathway are defined, how transmembrane helices (TMHs) are removed from the membrane and into the cytoplasm before degradation is poorly understood. In this study, we asked whether the hydrophobic character of a TMH acts as an energetic barrier to retrotranslocation. To this end, we designed a dual-pass model ERAD substrate, Chimera A*, which contains the cytoplasmic misfolded domain from a characterized ERAD substrate, Sterile 6* (Ste6p*). We found that the degradation requirements for Chimera A* and Ste6p* are similar, but Chimera A* was retrotranslocated more efficiently than Ste6p* in an in vitro assay in which retrotranslocation can be quantified. We then constructed a series of Chimera A* variants containing synthetic TMHs with a range of ΔG values for membrane insertion. TMH hydrophobicity correlated inversely with retrotranslocation efficiency, and in all cases, retrotranslocation remained Cdc48p dependent. These findings provide insight into the energetic restrictions on the retrotranslocation reaction, as well as a new computational approach to predict retrotranslocation efficiency.
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Affiliation(s)
| | - Karl-Richard Reutter
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Andrew A Augustine
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - G Michael Preston
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Kurt F Weiberth
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Timothy D Mackie
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | | | - Neville P Bethel
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158
| | - Keith M Callenberg
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Kunio Nakatsukasa
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260.,Division of Biological Science, Graduate School of Natural Sciences, Nagoya City University, Nagoya, Aichi 467-8501, Japan
| | - Michael Grabe
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
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73
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Cruz FM, Colbert JD, Merino E, Kriegsman BA, Rock KL. The Biology and Underlying Mechanisms of Cross-Presentation of Exogenous Antigens on MHC-I Molecules. Annu Rev Immunol 2017; 35:149-176. [PMID: 28125356 PMCID: PMC5508990 DOI: 10.1146/annurev-immunol-041015-055254] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
To monitor the health of cells, the immune system tasks antigen-presenting cells with gathering antigens from other cells and bringing them to CD8 T cells in the form of peptides bound to MHC-I molecules. Most cells would be unable to perform this function because they use their MHC-I molecules to exclusively present peptides derived from the cell's own proteins. However, the immune system evolved mechanisms for dendritic cells and some other phagocytes to sample and present antigens from the extracellular milieu on MHC-I through a process called cross-presentation. How this important task is accomplished, its role in health and disease, and its potential for exploitation are the subject of this review.
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Affiliation(s)
- Freidrich M Cruz
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts 01655; , , , ,
| | - Jeff D Colbert
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts 01655; , , , ,
| | - Elena Merino
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts 01655; , , , ,
| | - Barry A Kriegsman
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts 01655; , , , ,
| | - Kenneth L Rock
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts 01655; , , , ,
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74
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Harsman A, Schneider A. Mitochondrial protein import in trypanosomes: Expect the unexpected. Traffic 2017; 18:96-109. [PMID: 27976830 DOI: 10.1111/tra.12463] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 12/01/2016] [Accepted: 12/06/2016] [Indexed: 12/11/2022]
Abstract
Mitochondria have many different functions, the most important one of which is oxidative phosphorylation. They originated from an endosymbiotic event between a bacterium and an archaeal host cell. It was the evolution of a protein import system that marked the boundary between the endosymbiotic ancestor of the mitochondrion and a true organelle that is under the control of the nucleus. In present day mitochondria more than 95% of all proteins are imported from the cytosol in a proces mediated by hetero-oligomeric protein complexes in the outer and inner mitochondrial membranes. In this review we compare mitochondrial protein import in the best studied model system yeast and the parasitic protozoan Trypanosoma brucei. The 2 organisms are phylogenetically only remotely related. Despite the fact that mitochondrial protein import has the same function in both species, only very few subunits of their import machineries are conserved. Moreover, while yeast has 2 inner membrane protein translocases, one specialized for presequence-containing and one for mitochondrial carrier proteins, T. brucei has a single inner membrane translocase only, that mediates import of both types of substrates. The evolutionary implications of these findings are discussed.
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Affiliation(s)
- Anke Harsman
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - André Schneider
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
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75
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Amyotrophic Lateral Sclerosis Pathogenesis Converges on Defects in Protein Homeostasis Associated with TDP-43 Mislocalization and Proteasome-Mediated Degradation Overload. Curr Top Dev Biol 2017; 121:111-171. [DOI: 10.1016/bs.ctdb.2016.07.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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76
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Harsman A, Oeljeklaus S, Wenger C, Huot JL, Warscheid B, Schneider A. The non-canonical mitochondrial inner membrane presequence translocase of trypanosomatids contains two essential rhomboid-like proteins. Nat Commun 2016; 7:13707. [PMID: 27991487 PMCID: PMC5187411 DOI: 10.1038/ncomms13707] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 10/24/2016] [Indexed: 02/07/2023] Open
Abstract
Mitochondrial protein import is essential for all eukaryotes. Here we show that the early diverging eukaryote Trypanosoma brucei has a non-canonical inner membrane (IM) protein translocation machinery. Besides TbTim17, the single member of the Tim17/22/23 family in trypanosomes, the presequence translocase contains nine subunits that co-purify in reciprocal immunoprecipitations and with a presequence-containing substrate that is trapped in the translocation channel. Two of the newly discovered subunits are rhomboid-like proteins, which are essential for growth and mitochondrial protein import. Rhomboid-like proteins were proposed to form the protein translocation pore of the ER-associated degradation system, suggesting that they may contribute to pore formation in the presequence translocase of T. brucei. Pulldown of import-arrested mitochondrial carrier protein shows that the carrier translocase shares eight subunits with the presequence translocase. This indicates that T. brucei may have a single IM translocase that with compositional variations mediates import of presequence-containing and carrier proteins.
The mitochondrial protein import machinery is crucial for eukaryotes but little is known about its evolutionary origin. Here, the authors characterize the translocase of the inner membrane (TIM) in trypanosomes, showing that it contains two rhomboid-like proteins essential for protein import.
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Affiliation(s)
- Anke Harsman
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern CH-3012, Switzerland
| | - Silke Oeljeklaus
- Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestraße 18, Freiburg 79104, Germany
| | - Christoph Wenger
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern CH-3012, Switzerland
| | - Jonathan L Huot
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern CH-3012, Switzerland
| | - Bettina Warscheid
- Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestraße 18, Freiburg 79104, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, Freiburg 79104, Germany
| | - André Schneider
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern CH-3012, Switzerland
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77
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Römisch K. A Case for Sec61 Channel Involvement in ERAD. Trends Biochem Sci 2016; 42:171-179. [PMID: 27932072 DOI: 10.1016/j.tibs.2016.10.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/19/2016] [Accepted: 10/20/2016] [Indexed: 11/25/2022]
Abstract
Proteins that misfold in the endoplasmic reticulum (ER) need to be transported back to the cytosol for degradation by proteasomes, a process known as ER-associated degradation (ERAD). The first candidate discussed as a retrograde protein transport conduit was the Sec61 channel which is responsible for secretory protein transport into the ER during biogenesis. The Sec61 channel binds the proteasome 19S regulatory particle which can extract an ERAD substrate from the ER. Nevertheless its role as a general export channel has been dismissed, and Hrd1 and Der1 have been proposed as alternatives. The discovery of export-specific sec61 mutants and of mammalian ERAD substrates whose export is dependent on the 19S regulatory particle suggest that dismissal of a role of Sec61 in export may have been premature.
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Affiliation(s)
- Karin Römisch
- Department of Biology, Naturwissenschaftlich-technische Fakultät 8, Saarland University, 66123 Saarbruecken, Germany.
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78
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Hu W, Ma Z, Di S, Jiang S, Li Y, Fan C, Yang Y, Wang D. Snapshot: implications for melatonin in endoplasmic reticulum homeostasis. Br J Pharmacol 2016; 173:3431-3442. [PMID: 27759160 PMCID: PMC5120159 DOI: 10.1111/bph.13651] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 09/27/2016] [Accepted: 10/03/2016] [Indexed: 12/13/2022] Open
Abstract
The endoplasmic reticulum (ER) is an important intracellular membranous organelle. Previous studies have demonstrated that the ER is responsible for protein folding and trafficking, lipid synthesis and the maintenance of calcium homeostasis. Interestingly, the morphology and structure of the ER were recently found to be important. Melatonin is a hormone that anticipates the daily onset of darkness in mammals, and it is well known that melatonin acts as an antioxidant by scavenging free radicals and increasing the activity of antioxidant enzymes in the body. Notably, the existing evidence demonstrates that melatonin is involved in ER homeostasis, particularly in the morphology of the ER, indicating a potential protective role of melatonin. This review discusses the existing knowledge regarding the implications for the involvement of melatonin in ER homeostasis.
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Affiliation(s)
- Wei Hu
- Department of Thoracic and Cardiovascular SurgeryAffiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
- Department of Biomedical EngineeringThe Fourth Military Medical UniversityXi'anChina
| | - Zhiqiang Ma
- Department of Thoracic SurgeryTangdu Hospital, The Fourth Military Medical UniversityXi'anChina
| | - Shouyin Di
- Department of Thoracic SurgeryTangdu Hospital, The Fourth Military Medical UniversityXi'anChina
| | - Shuai Jiang
- Department of Aerospace MedicineThe Fourth Military Medical UniversityXi'anChina
| | - Yue Li
- Department of Biomedical EngineeringThe Fourth Military Medical UniversityXi'anChina
| | - Chongxi Fan
- Department of Thoracic SurgeryTangdu Hospital, The Fourth Military Medical UniversityXi'anChina
| | - Yang Yang
- Department of Thoracic and Cardiovascular SurgeryAffiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
- Department of Biomedical EngineeringThe Fourth Military Medical UniversityXi'anChina
| | - Dongjin Wang
- Department of Thoracic and Cardiovascular SurgeryAffiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
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79
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To M, Peterson CWH, Roberts MA, Counihan JL, Wu TT, Forster MS, Nomura DK, Olzmann JA. Lipid disequilibrium disrupts ER proteostasis by impairing ERAD substrate glycan trimming and dislocation. Mol Biol Cell 2016; 28:270-284. [PMID: 27881664 PMCID: PMC5231896 DOI: 10.1091/mbc.e16-07-0483] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 11/09/2016] [Accepted: 11/15/2016] [Indexed: 12/12/2022] Open
Abstract
The endoplasmic reticulum (ER) mediates the folding, maturation, and deployment of the secretory proteome. Proteins that fail to achieve their native conformation are retained in the ER and targeted for clearance by ER-associated degradation (ERAD), a sophisticated process that mediates the ubiquitin-dependent delivery of substrates to the 26S proteasome for proteolysis. Recent findings indicate that inhibition of long-chain acyl-CoA synthetases with triacsin C, a fatty acid analogue, impairs lipid droplet (LD) biogenesis and ERAD, suggesting a role for LDs in ERAD. However, whether LDs are involved in the ERAD process remains an outstanding question. Using chemical and genetic approaches to disrupt diacylglycerol acyltransferase (DGAT)-dependent LD biogenesis, we provide evidence that LDs are dispensable for ERAD in mammalian cells. Instead, our results suggest that triacsin C causes global alterations in the cellular lipid landscape that disrupt ER proteostasis by interfering with the glycan trimming and dislocation steps of ERAD. Prolonged triacsin C treatment activates both the IRE1 and PERK branches of the unfolded protein response and ultimately leads to IRE1-dependent cell death. These findings identify an intimate relationship between fatty acid metabolism and ER proteostasis that influences cell viability.
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Affiliation(s)
- Milton To
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720
| | - Clark W H Peterson
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720
| | - Melissa A Roberts
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720
| | - Jessica L Counihan
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720.,Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Tiffany T Wu
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720
| | - Mercedes S Forster
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720
| | - Daniel K Nomura
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720.,Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - James A Olzmann
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720
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80
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How Polyomaviruses Exploit the ERAD Machinery to Cause Infection. Viruses 2016; 8:v8090242. [PMID: 27589785 PMCID: PMC5035956 DOI: 10.3390/v8090242] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 08/18/2016] [Accepted: 08/23/2016] [Indexed: 12/18/2022] Open
Abstract
To infect cells, polyomavirus (PyV) traffics from the cell surface to the endoplasmic reticulum (ER) where it hijacks elements of the ER-associated degradation (ERAD) machinery to penetrate the ER membrane and reach the cytosol. From the cytosol, the virus transports to the nucleus, enabling transcription and replication of the viral genome that leads to lytic infection or cellular transformation. How PyV exploits the ERAD machinery to cross the ER membrane and access the cytosol, a decisive infection step, remains enigmatic. However, recent studies have slowly unraveled many aspects of this process. These emerging insights should advance our efforts to develop more effective therapies against PyV-induced human diseases.
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81
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Lemberg MK, Adrain C. Inactive rhomboid proteins: New mechanisms with implications in health and disease. Semin Cell Dev Biol 2016; 60:29-37. [PMID: 27378062 DOI: 10.1016/j.semcdb.2016.06.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 06/25/2016] [Accepted: 06/30/2016] [Indexed: 12/23/2022]
Abstract
Rhomboids, proteases containing an unusual membrane-integral serine protease active site, were first identified in Drosophila, where they fulfill an essential role in epidermal growth factor receptor signaling, by cleaving membrane-tethered growth factor precursors. It has recently become apparent that eukaryotic genomes harbor conserved catalytically inactive rhomboid protease homologs, including derlins and iRhoms. Here we highlight how loss of proteolytic activity was followed in evolution by impressive functional diversification, enabling these pseudoproteases to fulfill crucial roles within the secretory pathway, including protein degradation, trafficking regulation, and inflammatory signaling. We distil the current understanding of the roles of rhomboid pseudoproteases in development and disease. Finally, we address mechanistically how versatile features of proteolytically active rhomboids have been elaborated to serve the sophisticated functions of their pseudoprotease cousins. By comparing functional and structural clues, we highlight common principles shared by the rhomboid superfamily, and make mechanistic predictions.
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Affiliation(s)
- Marius K Lemberg
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
| | - Colin Adrain
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal.
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82
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Avci D, Lemberg MK. Clipping or Extracting: Two Ways to Membrane Protein Degradation. Trends Cell Biol 2016; 25:611-622. [PMID: 26410407 DOI: 10.1016/j.tcb.2015.07.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/18/2015] [Accepted: 07/17/2015] [Indexed: 12/20/2022]
Abstract
Protein degradation is a fundamentally important process that allows cells to recognize and remove damaged protein species and to regulate protein abundance according to functional need. A fundamental challenge is to understand how membrane proteins are recognized and removed from cellular organelles. While most of our understanding of this mechanism comes from studies on p97/Cdc48-mediated protein dislocation along the endoplasmic reticulum (ER)-associated degradation (ERAD) pathway, recent studies have revealed intramembrane proteolysis to be an additional mechanism that can extract transmembrane segments. Here, we review these two principles in membrane protein degradation and discuss how intramembrane proteolysis, which introduces an irreversible step in protein dislocation, is used to drive regulated protein turnover.
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Affiliation(s)
- Dönem Avci
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Marius K Lemberg
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
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83
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Baldridge RD, Rapoport TA. Autoubiquitination of the Hrd1 Ligase Triggers Protein Retrotranslocation in ERAD. Cell 2016; 166:394-407. [PMID: 27321670 DOI: 10.1016/j.cell.2016.05.048] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/19/2016] [Accepted: 05/13/2016] [Indexed: 12/16/2022]
Abstract
Misfolded proteins of the ER are retrotranslocated to the cytosol, where they are polyubiquitinated, extracted from the membrane, and degraded by the proteasome. To investigate how the ER-associated Degradation (ERAD) machinery can accomplish retrotranslocation of a misfolded luminal protein domain across a lipid bilayer, we have reconstituted retrotranslocation with purified S. cerevisiae proteins, using proteoliposomes containing the multi-spanning ubiquitin ligase Hrd1. Retrotranslocation of the luminal domain of a membrane-spanning substrate is triggered by autoubiquitination of Hrd1. Substrate ubiquitination is a subsequent event, and the Cdc48 ATPase that completes substrate extraction from the membrane is not required for retrotranslocation. Ubiquitination of lysines in Hrd1's RING-finger domain is required for substrate retrotranslocation in vitro and for ERAD in vivo. Our results suggest that Hrd1 forms a ubiquitin-gated protein-conducting channel.
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Affiliation(s)
- Ryan D Baldridge
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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84
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Neumann-Staubitz P, Neumann H. The use of unnatural amino acids to study and engineer protein function. Curr Opin Struct Biol 2016; 38:119-28. [DOI: 10.1016/j.sbi.2016.06.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/02/2016] [Accepted: 06/04/2016] [Indexed: 12/21/2022]
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85
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Abstract
The endoplasmic reticulum is the port of entry for proteins into the secretory pathway and the site of synthesis for several important lipids, including cholesterol, triacylglycerol, and phospholipids. Protein production within the endoplasmic reticulum is tightly regulated by a cohort of resident machinery that coordinates the folding, modification, and deployment of secreted and integral membrane proteins. Proteins failing to attain their native conformation are degraded through the endoplasmic reticulum-associated degradation (ERAD) pathway via a series of tightly coupled steps: substrate recognition, dislocation, and ubiquitin-dependent proteasomal destruction. The same ERAD machinery also controls the flux through various metabolic pathways by coupling the turnover of metabolic enzymes to the levels of key metabolites. We review the current understanding and biological significance of ERAD-mediated regulation of lipid metabolism in mammalian cells.
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Affiliation(s)
- Julian Stevenson
- Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720;
| | - Edmond Y Huang
- Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720;
| | - James A Olzmann
- Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720;
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86
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Abstract
The HRD (HMG-CoA reductase degradation) pathway is a conserved route of endoplasmic reticulum-associated degradation (ERAD), by which misfolded ER proteins are ubiquitinated and degraded. ERAD substrates are ubiquitinated by the action of the Hrd1 RING-H2 E3 ligase. Hrd1 is always present in a stoichiometric complex with the ER membrane protein Hrd3, which is also required for HRD-dependent degradation. Despite its conserved presence, unequivocal study of Hrd3 function has been precluded by its central role in Hrd1 stability. Loss of Hrd3 causes unrestricted self-degradation of Hrd1, resulting in significant loss of the core ligase. Accordingly, the degree to which Hrd3 functions independently of Hrd1 stabilization has remained unresolved. By capitalizing on our studies of Usa1 in Hrd1 degradation, we have devised a new approach to evaluate Hrd3 functions in ERAD. We now show that Hrd3 has a direct and critical role in ERAD in addition to Hrd1 stabilization. This direct component of Hrd3 is phenotypically as important as Hrd1 in the native HRD complex. Hrd3 was required the E3 activity of Hrd1, rather than substrate or E2 recruitment to Hrd1. Although Hrd1 can function in some circumstances independent of Hrd3, these studies show an indispensable role for Hrd3 in living cells.
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87
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Pfeiffer A, Stephanowitz H, Krause E, Volkwein C, Hirsch C, Jarosch E, Sommer T. A Complex of Htm1 and the Oxidoreductase Pdi1 Accelerates Degradation of Misfolded Glycoproteins. J Biol Chem 2016; 291:12195-207. [PMID: 27053108 DOI: 10.1074/jbc.m115.703256] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Indexed: 11/06/2022] Open
Abstract
A quality control system in the endoplasmic reticulum (ER) efficiently discriminates polypeptides that are in the process of productive folding from conformers that are trapped in an aberrant state. Only the latter are transported into the cytoplasm and degraded in a process termed ER-associated protein degradation (ERAD). In the ER, an enzymatic cascade generates a specific N-glycan structure of seven mannosyl and two N-acetylglucosamine residues (Man7GlcNAc2) on misfolded glycoproteins to facilitate their disposal. We show that a complex encompassing the yeast lectin-like protein Htm1 and the oxidoreductase Pdi1 converts Man8GlcNAc2 on glycoproteins into the Man7GlcNAc2 signal. In vitro the Htm1-Pdi1 complex processes both unfolded and native proteins albeit with a preference for the former. In vivo, elevated expression of HTM1 causes glycan trimming on misfolded and folded proteins, but only degradation of the non-native species is accelerated. Thus, modification with a Man7GlcNAc2 structure does not inevitably commit a protein for ER-associated protein degradation. The function of Htm1 in ERAD relies on its association with Pdi1, which appears to regulate the access to substrates. Our data support a model in which the balanced activities of Pdi1 and Htm1 are crucial determinants for the efficient removal of misfolded secretory glycoproteins.
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Affiliation(s)
| | - Heike Stephanowitz
- the Leibniz Institute for Molecular Pharmacology, 13125 Berlin, Germany and
| | - Eberhard Krause
- the Leibniz Institute for Molecular Pharmacology, 13125 Berlin, Germany and
| | | | | | - Ernst Jarosch
- From the Max-Delbrück-Center for Molecular Medicine and
| | - Thomas Sommer
- From the Max-Delbrück-Center for Molecular Medicine and Humboldt University, Faculty of Life Science, Institute of Biology, 10099 Berlin, Germany
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88
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Jeong H, Sim HJ, Song EK, Lee H, Ha SC, Jun Y, Park TJ, Lee C. Crystal structure of SEL1L: Insight into the roles of SLR motifs in ERAD pathway. Sci Rep 2016; 6:20261. [PMID: 27064360 PMCID: PMC4746701 DOI: 10.1038/srep20261] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 12/31/2015] [Indexed: 11/09/2022] Open
Abstract
Terminally misfolded proteins are selectively recognized and cleared by the endoplasmic reticulum-associated degradation (ERAD) pathway. SEL1L, a component of the ERAD machinery, plays an important role in selecting and transporting ERAD substrates for degradation. We have determined the crystal structure of the mouse SEL1L central domain comprising five Sel1-Like Repeats (SLR motifs 5 to 9; hereafter called SEL1Lcent). Strikingly, SEL1Lcent forms a homodimer with two-fold symmetry in a head-to-tail manner. Particularly, the SLR motif 9 plays an important role in dimer formation by adopting a domain-swapped structure and providing an extensive dimeric interface. We identified that the full-length SEL1L forms a self-oligomer through the SEL1Lcent domain in mammalian cells. Furthermore, we discovered that the SLR-C, comprising SLR motifs 10 and 11, of SEL1L directly interacts with the N-terminus luminal loops of HRD1. Therefore, we propose that certain SLR motifs of SEL1L play a unique role in membrane bound ERAD machinery.
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Affiliation(s)
- Hanbin Jeong
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Hyo Jung Sim
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Eun Kyung Song
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Hakbong Lee
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Sung Chul Ha
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Kyungbuk 37673, Korea
| | - Youngsoo Jun
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Tae Joo Park
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Changwook Lee
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Republic of Korea
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89
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Peters SL, Déry MA, LeBlanc AC. Familial prion protein mutants inhibit Hrd1-mediated retrotranslocation of misfolded proteins by depleting misfolded protein sensor BiP. Hum Mol Genet 2016; 25:976-88. [PMID: 26740554 DOI: 10.1093/hmg/ddv630] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/29/2015] [Indexed: 01/09/2023] Open
Abstract
Similar to many proteins trafficking through the secretory pathway, cellular prion protein (PrP) partly retrotranslocates from the endoplasmic reticulum to the cytosol through the endoplasmic reticulum-associated degradation (ERAD) pathway in an attempt to alleviate accumulation of cellular misfolded PrP. Surprisingly, familial PrP mutants fail to retrotranslocate and simultaneously block normal cellular PrP retrotranslocation. That impairments in retrotranslocation of misfolded proteins could lead to global disruptions in cellular homeostasis prompted further investigations into PrP mutant retrotranslocation defects. A gain- and loss-of-function approach identified human E3 ubiquitin ligase, Hrd1, as a critical regulator of PrP retrotranslocation in mammalian cells. Expression of familial human PrP mutants, V210I(129V) and M232R(129V), not only abolished PrP retrotranslocation, but also that of Hrd1-dependent ERAD substrates, transthyretin TTR(D18G) and α1-anti-trypsin A1AT(NHK). Mutant PrP expression decreased binding immunoglobulin protein (BiP) levels by 50% and attenuated ER stress-induced BiP by increasing BiP turnover 6-fold. Overexpression of BiP with PrP mutants rescued retrotranslocation of PrP, TTR(D18G) and A1AT(NHK). PrP mutants-induced cell death was also rescued by co-expression of BiP. These results show that PrP mutants highjack the Hrd1-dependent ERAD pathway, an action that would result in misfolded protein accumulation especially in terminally differentiated neurons. This could explain the age-dependent neuronal degeneration in familial prion diseases.
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Affiliation(s)
- Sarah L Peters
- Bloomfield Center for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Ch. Cote Ste-Catherine, Montreal, QC H3T 1E2, Canada and Department of Neurology and Neurosurgery, McGill University, 3775 University Street, Montreal, QC H2A 2B4, Canada
| | - Marc-André Déry
- Bloomfield Center for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Ch. Cote Ste-Catherine, Montreal, QC H3T 1E2, Canada and Department of Neurology and Neurosurgery, McGill University, 3775 University Street, Montreal, QC H2A 2B4, Canada
| | - Andrea C LeBlanc
- Bloomfield Center for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Ch. Cote Ste-Catherine, Montreal, QC H3T 1E2, Canada and Department of Neurology and Neurosurgery, McGill University, 3775 University Street, Montreal, QC H2A 2B4, Canada
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90
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The Toxicity of a Novel Antifungal Compound Is Modulated by Endoplasmic Reticulum-Associated Protein Degradation Components. Antimicrob Agents Chemother 2015; 60:1438-49. [PMID: 26666917 DOI: 10.1128/aac.02239-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 12/08/2015] [Indexed: 01/06/2023] Open
Abstract
In a search for new antifungal compounds, we screened a library of 4,454 chemicals for toxicity against the human fungal pathogen Aspergillus fumigatus. We identified sr7575, a molecule that inhibits growth of the evolutionary distant fungi A. fumigatus, Cryptococcus neoformans, Candida albicans, and Saccharomyces cerevisiae but lacks acute toxicity for mammalian cells. To gain insight into the mode of inhibition, sr7575 was screened against 4,885 S. cerevisiae mutants from the systematic collection of haploid deletion strains and 977 barcoded haploid DAmP (decreased abundance by mRNA perturbation) strains in which the function of essential genes was perturbed by the introduction of a drug resistance cassette downstream of the coding sequence region. Comparisons with previously published chemogenomic screens revealed that the set of mutants conferring sensitivity to sr7575 was strikingly narrow, affecting components of the endoplasmic reticulum-associated protein degradation (ERAD) stress response and the ER membrane protein complex (EMC). ERAD-deficient mutants were hypersensitive to sr7575 in both S. cerevisiae and A. fumigatus, indicating a conserved mechanism of growth inhibition between yeast and filamentous fungi. Although the unfolded protein response (UPR) is linked to ERAD regulation, sr7575 did not trigger the UPR in A. fumigatus and UPR mutants showed no enhanced sensitivity to the compound. The data from this chemogenomic analysis demonstrate that sr7575 exerts its antifungal activity by disrupting ER protein quality control in a manner that requires ERAD intervention but bypasses the need for the canonical UPR. ER protein quality control is thus a specific vulnerability of fungal organisms that might be exploited for antifungal drug development.
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91
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Abstract
ER-associated degradation (ERAD) is a protein clearance mechanism by which misfolded, misassembled, or metabolically regulated proteins are specifically dislocated from the ER into the cytosol and degraded by the ubiquitin proteasome system. ERAD very likely evolved to maintain proteostasis and sterol homeostasis in the ER. However, the ironic truth is that membrane-penetrating transportation and protein degradation machineries in ERAD are preferably hijacked by exogenous pathogens such as viruses and toxins for their invasion and evasion from immunological surveillance. In this Review, we provide an overview of our current understanding of the pathogenic hijacking of the host cell ERAD, in which pathogens exploit the complex ERAD machinery in a variety of manners for their own use, suggesting flexibility and plasticity of the molecular machinery of ERAD.
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92
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Kadowaki H, Nagai A, Maruyama T, Takami Y, Satrimafitrah P, Kato H, Honda A, Hatta T, Natsume T, Sato T, Kai H, Ichijo H, Nishitoh H. Pre-emptive Quality Control Protects the ER from Protein Overload via the Proximity of ERAD Components and SRP. Cell Rep 2015; 13:944-56. [DOI: 10.1016/j.celrep.2015.09.047] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 08/05/2015] [Accepted: 09/17/2015] [Indexed: 02/06/2023] Open
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93
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Xu C, Ng DTW. Glycosylation-directed quality control of protein folding. Nat Rev Mol Cell Biol 2015; 16:742-52. [PMID: 26465718 DOI: 10.1038/nrm4073] [Citation(s) in RCA: 255] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Membrane-bound and soluble proteins of the secretory pathway are commonly glycosylated in the endoplasmic reticulum. These adducts have many biological functions, including, notably, their contribution to the maturation of glycoproteins. N-linked glycans are of oligomeric structure, forming configurations that provide blueprints to precisely instruct the folding of protein substrates and the quality control systems that scrutinize it. O-linked mannoses are simpler in structure and were recently found to have distinct functions in protein quality control that do not require the complex structure of N-linked glycans. Together, recent studies reveal the breadth and sophistication of the roles of these glycan-directed modifications in protein biogenesis.
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Affiliation(s)
- Chengchao Xu
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Davis T W Ng
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.,Duke University-National University of Singapore Graduate Medical School, 8 College Road, Singapore 169857
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94
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Abstract
SIGNIFICANCE Selenoproteins employ selenium to supplement the chemistry available through the common 20 amino acids. These powerful enzymes are affiliated with redox biology, often in connection with the detection, management, and signaling of oxidative stress. Among them, membrane-bound selenoproteins play prominent roles in signaling pathways, Ca(2+) regulation, membrane complexes integrity, and biosynthesis of lipophilic molecules. RECENT ADVANCES The number of selenoproteins whose physiological roles, protein partners, expression, evolution, and biosynthesis are characterized is steadily increasing, thus offering a more nuanced view of this specialized family. This review focuses on human membrane selenoproteins, particularly the five least characterized ones: selenoproteins I, K, N, S, and T. CRITICAL ISSUES Membrane-bound selenoproteins are the least understood, as it is challenging to provide the membrane-like environment required for their biochemical and biophysical characterization. Hence, their studies rely mostly on biological rather than structural and biochemical assays. Another aspect that has not received much attention is the particular role that their membrane association plays in their physiological function. FUTURE DIRECTIONS Findings cited in this review show that it is possible to infer the structure and the membrane-binding mode of these lesser-studied selenoproteins and design experiments to examine the role of the rare amino acid selenocysteine.
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Affiliation(s)
- Jun Liu
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware
| | - Sharon Rozovsky
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware
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95
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Nakatsukasa K, Okumura F, Kamura T. Proteolytic regulation of metabolic enzymes by E3 ubiquitin ligase complexes: lessons from yeast. Crit Rev Biochem Mol Biol 2015; 50:489-502. [PMID: 26362128 DOI: 10.3109/10409238.2015.1081869] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Eukaryotic organisms use diverse mechanisms to control metabolic rates in response to changes in the internal and/or external environment. Fine metabolic control is a highly responsive, energy-saving process that is mediated by allosteric inhibition/activation and/or reversible modification of preexisting metabolic enzymes. In contrast, coarse metabolic control is a relatively long-term and expensive process that involves modulating the level of metabolic enzymes. Coarse metabolic control can be achieved through the degradation of metabolic enzymes by the ubiquitin-proteasome system (UPS), in which substrates are specifically ubiquitinated by an E3 ubiquitin ligase and targeted for proteasomal degradation. Here, we review select multi-protein E3 ligase complexes that directly regulate metabolic enzymes in Saccharomyces cerevisiae. The first part of the review focuses on the endoplasmic reticulum (ER) membrane-associated Hrd1 and Doa10 E3 ligase complexes. In addition to their primary roles in the ER-associated degradation pathway that eliminates misfolded proteins, recent quantitative proteomic analyses identified native substrates of Hrd1 and Doa10 in the sterol synthesis pathway. The second part focuses on the SCF (Skp1-Cul1-F-box protein) complex, an abundant prototypical multi-protein E3 ligase complex. While the best-known roles of the SCF complex are in the regulation of the cell cycle and transcription, accumulating evidence indicates that the SCF complex also modulates carbon metabolism pathways. The increasing number of metabolic enzymes whose stability is directly regulated by the UPS underscores the importance of the proteolytic regulation of metabolic processes for the acclimation of cells to environmental changes.
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Affiliation(s)
- Kunio Nakatsukasa
- a Division of Biological Sciences , Graduate School of Science, Nagoya University , Nagoya , Aichi , Japan
| | - Fumihiko Okumura
- a Division of Biological Sciences , Graduate School of Science, Nagoya University , Nagoya , Aichi , Japan
| | - Takumi Kamura
- a Division of Biological Sciences , Graduate School of Science, Nagoya University , Nagoya , Aichi , Japan
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96
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He K, Ravindran MS, Tsai B. A bacterial toxin and a nonenveloped virus hijack ER-to-cytosol membrane translocation pathways to cause disease. Crit Rev Biochem Mol Biol 2015; 50:477-88. [PMID: 26362261 DOI: 10.3109/10409238.2015.1085826] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A dedicated network of cellular factors ensures that proteins translocated into the endoplasmic reticulum (ER) are folded correctly before they exit this compartment en route to other cellular destinations or for secretion. When proteins misfold, selective ER-resident enzymes and chaperones are recruited to rectify the protein-misfolding problem in order to maintain cellular proteostasis. However, when a protein becomes terminally misfolded, it is ejected into the cytosol and degraded by the proteasome via a pathway called ER-associated degradation (ERAD). Strikingly, toxins and viruses can hijack elements of the ERAD pathway to access the host cytosol and cause infection. This review focuses on emerging data illuminating the molecular mechanisms by which these toxic agents co-opt the ER-to-cytosol translocation process to cause disease.
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Affiliation(s)
- Kaiyu He
- a Department of Cell and Developmental Biology , University of Michigan Medical School , Ann Arbor , MI , USA
| | - Madhu Sudhan Ravindran
- a Department of Cell and Developmental Biology , University of Michigan Medical School , Ann Arbor , MI , USA
| | - Billy Tsai
- a Department of Cell and Developmental Biology , University of Michigan Medical School , Ann Arbor , MI , USA
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97
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Habeck G, Ebner FA, Shimada-Kreft H, Kreft SG. The yeast ERAD-C ubiquitin ligase Doa10 recognizes an intramembrane degron. ACTA ACUST UNITED AC 2015; 209:261-73. [PMID: 25918226 PMCID: PMC4411271 DOI: 10.1083/jcb.201408088] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In Saccharomyces cerevisiae, surprisingly, the transmembrane protein Sbh2, which harbors an intramembrane degron, is a substrate of the ubiquitin-protein ligase Doa10. Aberrant endoplasmic reticulum (ER) proteins are eliminated by ER-associated degradation (ERAD). This process involves protein retrotranslocation into the cytosol, ubiquitylation, and proteasomal degradation. ERAD substrates are classified into three categories based on the location of their degradation signal/degron: ERAD-L (lumen), ERAD-M (membrane), and ERAD-C (cytosol) substrates. In Saccharomyces cerevisiae, the membrane proteins Hrd1 and Doa10 are the predominant ERAD ubiquitin-protein ligases (E3s). The current notion is that ERAD-L and ERAD-M substrates are exclusively handled by Hrd1, whereas ERAD-C substrates are recognized by Doa10. In this paper, we identify the transmembrane (TM) protein Sec61 β-subunit homologue 2 (Sbh2) as a Doa10 substrate. Sbh2 is part of the trimeric Ssh1 complex involved in protein translocation. Unassembled Sbh2 is rapidly degraded in a Doa10-dependent manner. Intriguingly, the degron maps to the Sbh2 TM region. Thus, in contrast to the prevailing view, Doa10 (and presumably its human orthologue) has the capacity for recognizing intramembrane degrons, expanding its spectrum of substrates.
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Affiliation(s)
- Gregor Habeck
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Felix A Ebner
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | | | - Stefan G Kreft
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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98
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Abstract
Many protists with high ecological and medical relevance harbor plastids surrounded by four membranes. Thus, nucleus-encoded proteins of these complex plastids have to traverse these barriers. Here we report on the identification of the protein translocators located in two of the plastid surrounding membranes and present recent findings on the mechanisms of protein import into the plastids of diatoms.
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99
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Lau JB, Stork S, Moog D, Sommer MS, Maier UG. N-terminal lysines are essential for protein translocation via a modified ERAD system in complex plastids. Mol Microbiol 2015; 96:609-20. [PMID: 25644868 DOI: 10.1111/mmi.12959] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2015] [Indexed: 01/01/2023]
Abstract
Nuclear-encoded pre-proteins being imported into complex plastids of red algal origin have to cross up to five membranes. Thereby, transport across the second outermost or periplastidal membrane (PPM) is facilitated by SELMA (symbiont-specific ERAD-like machinery), an endoplasmic reticulum-associated degradation (ERAD)-derived machinery. Core components of SELMA are enzymes involved in ubiquitination (E1-E3), a Cdc48 ATPase complex and Derlin proteins. These components are present in all investigated organisms with four membrane-bound complex plastids of red algal origin, suggesting a ubiquitin-dependent translocation process of substrates mechanistically similar to the process of retro-translocation in ERAD. Even if, according to the current model, translocation via SELMA does not end up in the classical poly-ubiquitination, transient mono-/oligo-ubiquitination of pre-proteins might be required for the mechanism of translocation. We investigated the import mechanism of SELMA and were able to show that protein transport across the PPM depends on lysines in the N-terminal but not in the C-terminal part of pre-proteins. These lysines are predicted to be targets of ubiquitination during the translocation process. As proteins lacking the N-terminal lysines get stuck in the PPM, a 'frozen intermediate' of the translocation process could be envisioned and initially characterized.
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Affiliation(s)
- Julia B Lau
- Laboratory for Cell Biology, Philipps Universität Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany
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100
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Mehnert M, Sommermeyer F, Berger M, Kumar Lakshmipathy S, Gauss R, Aebi M, Jarosch E, Sommer T. The interplay of Hrd3 and the molecular chaperone system ensures efficient degradation of malfolded secretory proteins. Mol Biol Cell 2014; 26:185-94. [PMID: 25428985 PMCID: PMC4294667 DOI: 10.1091/mbc.e14-07-1202] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
A central ubiquitin ligase involved in endoplasmic reticulum (ER)–associated protein degradation is the HRD-ligase. The ER-luminal subunit Hrd3 cooperates with the cochaperone Scj1 in clearing misfolded proteins from the ER. Misfolded proteins of the secretory pathway are extracted from the endoplasmic reticulum (ER), polyubiquitylated by a protein complex termed the Hmg-CoA reductase degradation ligase (HRD-ligase), and degraded by cytosolic 26S proteasomes. This process is termed ER-associated protein degradation (ERAD). We previously showed that the membrane protein Der1, which is a subunit of the HRD-ligase, is involved in the export of aberrant polypeptides from the ER. Unexpectedly, we also uncovered a close spatial proximity of Der1 and the substrate receptor Hrd3 in the ER lumen. We report here on a mutant Hrd3KR that is selectively defective for ERAD of soluble proteins. Hrd3KR displays subtle structural changes that affect its positioning toward Der1. Furthermore, increased quantities of the ER-resident Hsp70-type chaperone Kar2 and the Hsp40-type cochaperone Scj1 bind to Hrd3KR. Of note, deletion of SCJ1 impairs ERAD of model substrates and causes the accumulation of client proteins at Hrd3. Our data imply a function of Scj1 in the removal of malfolded proteins from the receptor Hrd3, which facilitates their delivery to downstream-acting components like Der1.
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Affiliation(s)
- Martin Mehnert
- Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | | | - Maren Berger
- Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | | | - Robert Gauss
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology Zurich, 8093 Zurich, Switzerland
| | - Markus Aebi
- Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology Zurich, 8093 Zurich, Switzerland
| | - Ernst Jarosch
- Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Thomas Sommer
- Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany Institute of Biology, Humboldt Universität zu Berlin, 10115 Berlin, Germany
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