1
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Luo H, Jiao Q, Shen C, Shao C, Xie J, Chen Y, Feng X, Zhang X. Unraveling the roles of endoplasmic reticulum-associated degradation in metabolic disorders. Front Endocrinol (Lausanne) 2023; 14:1123769. [PMID: 37455916 PMCID: PMC10339828 DOI: 10.3389/fendo.2023.1123769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/19/2023] [Indexed: 07/18/2023] Open
Abstract
Misfolded proteins retained in the endoplasmic reticulum cause many human diseases. ER-associated degradation (ERAD) is one of the protein quality and quantity control system located at ER, which is responsible for translocating the misfolded proteins or properly folded but excess proteins out of the ER for proteasomal degradation. Recent studies have revealed that mice with ERAD deficiency in specific cell types exhibit impaired metabolism homeostasis and metabolic diseases. Here, we highlight the ERAD physiological functions in metabolic disorders in a substrate-dependent and cell type-specific manner.
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Affiliation(s)
- Hui Luo
- *Correspondence: Hui Luo, ; Xingwei Zhang,
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2
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Boone M, Ramasamy P, Zuallaert J, Bouwmeester R, Van Moer B, Maddelein D, Turan D, Hulstaert N, Eeckhaut H, Vandermarliere E, Martens L, Degroeve S, De Neve W, Vranken W, Callewaert N. Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit. Nat Commun 2021; 12:6414. [PMID: 34741024 PMCID: PMC8571348 DOI: 10.1038/s41467-021-26720-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 10/15/2021] [Indexed: 11/09/2022] Open
Abstract
While transcriptome- and proteome-wide technologies to assess processes in protein biogenesis are now widely available, we still lack global approaches to assay post-ribosomal biogenesis events, in particular those occurring in the eukaryotic secretory system. We here develop a method, SECRiFY, to simultaneously assess the secretability of >105 protein fragments by two yeast species, S. cerevisiae and P. pastoris, using custom fragment libraries, surface display and a sequencing-based readout. Screening human proteome fragments with a median size of 50-100 amino acids, we generate datasets that enable datamining into protein features underlying secretability, revealing a striking role for intrinsic disorder and chain flexibility. The SECRiFY methodology generates sufficient amounts of annotated data for advanced machine learning methods to deduce secretability patterns. The finding that secretability is indeed a learnable feature of protein sequences provides a solid base for application-focused studies.
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Affiliation(s)
- Morgane Boone
- Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium. .,Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium. .,Department of Biochemistry and Biophysics, UCSF, San Francisco, CA, USA.
| | - Pathmanaban Ramasamy
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium ,grid.8767.e0000 0001 2290 8069Structural Biology Brussels, VUB, Brussels, Belgium ,grid.11486.3a0000000104788040Structural Biology Research Center, VIB, Brussels, Belgium ,Interuniversity Institute of Bioinformatics in Brussels (IB)2, ULB-VUB, Brussels, Belgium
| | - Jasper Zuallaert
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium ,grid.510328.dCenter for Biotech Data Science, Ghent University Global Campus, Songdo, Incheon, South Korea ,grid.5342.00000 0001 2069 7798IDLab, ELIS, UGent, Ghent, Belgium
| | - Robbin Bouwmeester
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Berre Van Moer
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Davy Maddelein
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Demet Turan
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Niels Hulstaert
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Hannah Eeckhaut
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Elien Vandermarliere
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Lennart Martens
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Sven Degroeve
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Wesley De Neve
- grid.510328.dCenter for Biotech Data Science, Ghent University Global Campus, Songdo, Incheon, South Korea ,grid.5342.00000 0001 2069 7798IDLab, ELIS, UGent, Ghent, Belgium
| | - Wim Vranken
- grid.8767.e0000 0001 2290 8069Structural Biology Brussels, VUB, Brussels, Belgium ,grid.11486.3a0000000104788040Structural Biology Research Center, VIB, Brussels, Belgium ,Interuniversity Institute of Bioinformatics in Brussels (IB)2, ULB-VUB, Brussels, Belgium
| | - Nico Callewaert
- Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium. .,Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium.
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3
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Sparks RP, Arango AS, Jenkins JL, Guida WC, Tajkhorshid E, Sparks CE, Sparks JD, Fratti RA. An Allosteric Binding Site on Sortilin Regulates the Trafficking of VLDL, PCSK9, and LDLR in Hepatocytes. Biochemistry 2020; 59:4321-4335. [PMID: 33153264 DOI: 10.1021/acs.biochem.0c00741] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
ApoB lipoproteins (apo B-Lp) are produced in hepatocytes, and their secretion requires the cargo receptor sortilin. We examined the secretion of apo B-Lp-containing very low-density lipoprotein (VLDL), an LDL progenitor. Sortilin also regulates the trafficking of the subtilase PCSK9, which when secreted binds the LDL receptor (LDLR), resulting in its endocytosis and destruction at the lysosome. We show that the site 2 binding compound (cpd984) has multiple effects in hepatocytes, including (1) enhanced Apo-Lp secretion, (2) increased cellular PCSK9 retention, and (3) augmented levels of LDLR at the plasma membrane. We postulate that cpd984 enhances apo B-Lp secretion in part through binding the lipid phosphatidylinositol 3,4,5-trisphosphate (PIP3), which is present at higher levels on circulating VLDL form fed rats relative to after fasting. We attribute the enhanced VLDL secretion to its increased binding affinity for sortilin site 1 induced by cpd984 binding site 2. This hinders PCSK9 binding and secretion, which would subsequently prevent its binding to LDLR leading to its degradation. This suggests that site 2 is an allosteric regulator of site 1 binding. This effect is not limited to VLDL, as cpd984 augments binding of the neuropeptide neurotensin (NT) to sortilin site 1. Molecular dynamics simulations demonstrate that the C-terminus of NT (Ct-NT) stably binds site 1 through an electrostatic interaction. This was bolstered by the ability of Ct-NT to disrupt lower-affinity interactions between sortilin and the site 1 ligand PIP3. Together, these data show that binding cargo at sortilin site 1 is allosterically regulated through site 2 binding, with important ramifications for cellular lipid homeostasis involving proteins such as PCSK9 and LDLR.
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Affiliation(s)
- Robert P Sparks
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Andres S Arango
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jermaine L Jenkins
- Structural Biology & Biophysics Facility, University of Rochester Medical Center, Rochester, New York 14642, United States
| | - Wayne C Guida
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Emad Tajkhorshid
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science & Technology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Charles E Sparks
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, New York 14642, United States
| | - Janet D Sparks
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, New York 14642, United States
| | - Rutilio A Fratti
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
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4
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Reinhard J, Mattes C, Väth K, Radanović T, Surma MA, Klose C, Ernst R. A Quantitative Analysis of Cellular Lipid Compositions During Acute Proteotoxic ER Stress Reveals Specificity in the Production of Asymmetric Lipids. Front Cell Dev Biol 2020; 8:756. [PMID: 32850859 PMCID: PMC7417482 DOI: 10.3389/fcell.2020.00756] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/20/2020] [Indexed: 12/12/2022] Open
Abstract
The unfolded protein response (UPR) is central to endoplasmic reticulum (ER) homeostasis by controlling its size and protein folding capacity. When activated by unfolded proteins in the ER-lumen or aberrant lipid compositions, the UPR adjusts the expression of hundreds of target genes to counteract ER stress. The proteotoxic drugs dithiothreitol (DTT) and tunicamycin (TM) are commonly used to induce misfolding of proteins in the ER and to study the UPR. However, their potential impact on the cellular lipid composition has never been systematically addressed. Here, we report the quantitative, cellular lipid composition of Saccharomyces cerevisiae during acute, proteotoxic stress in both rich and synthetic media. We show that DTT causes rapid remodeling of the lipidome when used in rich medium at growth-inhibitory concentrations, while TM has only a marginal impact on the lipidome under our conditions of cultivation. We formulate recommendations on how to study UPR activation by proteotoxic stress without interferences from a perturbed lipid metabolism. Furthermore, our data suggest an intricate connection between the cellular growth rate, the abundance of the ER, and the metabolism of fatty acids. We show that Saccharomyces cerevisiae can produce asymmetric lipids with two saturated fatty acyl chains differing substantially in length. These observations indicate that the pairing of saturated fatty acyl chains is tightly controlled and suggest an evolutionary conservation of asymmetric lipids and their biosynthetic machineries.
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Affiliation(s)
- John Reinhard
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, Homburg, Germany.,PZMS, Center for Molecular Signaling, Medical Faculty, Saarland University, Homburg, Germany
| | - Carsten Mattes
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, Homburg, Germany.,PZMS, Center for Molecular Signaling, Medical Faculty, Saarland University, Homburg, Germany
| | - Kristina Väth
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, Homburg, Germany.,PZMS, Center for Molecular Signaling, Medical Faculty, Saarland University, Homburg, Germany
| | - Toni Radanović
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, Homburg, Germany.,PZMS, Center for Molecular Signaling, Medical Faculty, Saarland University, Homburg, Germany
| | | | | | - Robert Ernst
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, Homburg, Germany.,PZMS, Center for Molecular Signaling, Medical Faculty, Saarland University, Homburg, Germany
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5
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Sun Z, Brodsky JL. The degradation pathway of a model misfolded protein is determined by aggregation propensity. Mol Biol Cell 2018; 29:1422-1434. [PMID: 29688814 PMCID: PMC6014095 DOI: 10.1091/mbc.e18-02-0117] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Protein homeostasis in the secretory pathway is maintained by a hierarchy of quality control checkpoints, including endoplasmic reticulum–associated degradation (ERAD), which leads to the destruction of misfolded proteins in the ER, as well as post-ER proteolysis. Although most aberrant proteins are degraded by ERAD, some misfolded proteins escape the ER and are degraded instead by lysosomal/vacuolar proteases. To date, it remains unclear how misfolded membrane proteins are selected for these different fates. Here we designed a novel model substrate, SZ*, to investigate how substrate selection is mediated in yeast. We discovered that SZ* is degraded by both the proteasome and vacuolar proteases, the latter of which occurs after ER exit and requires the multivesicular body pathway. By interrogating how various conditions affect the fate of SZ*, we also discovered that heat-shock and substrate overexpression increase ERAD targeting. These conditions also increase substrate aggregation. We next found that aggregation of the membrane-free misfolded domain in SZ* is concentration dependent, and fusion of this misfolded domain to a post-ER quality control substrate instead targets the substrate for ERAD. Our data indicate that a misfolded membrane protein with a higher aggregation propensity is preferentially retained in the ER and targeted for ERAD.
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Affiliation(s)
- Zhihao Sun
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
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6
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Smith N, Adle DJ, Zhao M, Qin X, Kim H, Lee J. Endoplasmic Reticulum-associated Degradation of Pca1p, a Polytopic Protein, via Interaction with the Proteasome at the Membrane. J Biol Chem 2016; 291:15082-92. [PMID: 27226596 DOI: 10.1074/jbc.m116.726265] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Indexed: 11/06/2022] Open
Abstract
Endoplasmic reticulum-associated degradation (ERAD) plays a critical role in the destruction of terminally misfolded proteins at the secretory pathway. The system also regulates expression levels of several proteins such as Pca1p, a cadmium exporter in yeast. To gain better insight into the mechanisms underlying ERAD of Pca1p and other polytopic proteins by the proteasome in the cytosol, our study determined the roles for the molecular factors of ERAD in dislodging Pca1p from the endoplasmic reticulum (ER). Inactivation of the 20S proteasome leads to accumulation of ubiquitinated Pca1p in the ER membrane, suggesting a role for the proteasome in extraction of Pca1p from the ER. Pca1p formed a complex with the proteasome at the membrane in a Doa10p E3 ligase-dependent manner. Cdc48p is required for recruiting the proteasome to Pca1p. Although the Ufd2p E4 ubiquitin chain extension enzyme is involved in efficient degradation of Pca1p, Ufd2p-deficient cells did not affect the formation of a complex between Pca1p and the proteasome. Two other polytopic membrane proteins undergoing ERAD, Ste6*p and Hmg2p, also displayed the same outcomes observed for Pca1p. However, poly-ubiquitinated Cpy1*p, a luminal ERAD substrate, was detected in the cytosol independent of proteolytic activities of the proteasome. These results indicate that extraction and degradation of polytopic membrane proteins at the ER is a coupled event. This mechanism would relieve the cost of exposed hydrophobic domains in the cytosol during ERAD.
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Affiliation(s)
- Nathan Smith
- From the Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska, 68588-0664 and
| | - David J Adle
- From the Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska, 68588-0664 and
| | - Miaoyun Zhao
- From the Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska, 68588-0664 and
| | - Xiaojuan Qin
- From the Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska, 68588-0664 and the College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China 200234
| | - Heejeong Kim
- From the Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska, 68588-0664 and
| | - Jaekwon Lee
- From the Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska, 68588-0664 and
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7
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Buck TM, Plavchak L, Roy A, Donnelly BF, Kashlan OB, Kleyman TR, Subramanya AR, Brodsky JL. The Lhs1/GRP170 chaperones facilitate the endoplasmic reticulum-associated degradation of the epithelial sodium channel. J Biol Chem 2013; 288:18366-80. [PMID: 23645669 DOI: 10.1074/jbc.m113.469882] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The epithelial sodium channel, ENaC, plays a critical role in maintaining salt and water homeostasis, and not surprisingly defects in ENaC function are associated with disease. Like many other membrane-spanning proteins, this trimeric protein complex folds and assembles inefficiently in the endoplasmic reticulum (ER), which results in a substantial percentage of the channel being targeted for ER-associated degradation (ERAD). Because the spectrum of factors that facilitates the degradation of ENaC is incomplete, we developed yeast expression systems for each ENaC subunit. We discovered that a conserved Hsp70-like chaperone, Lhs1, is required for maximal turnover of the ENaC α subunit. By expressing Lhs1 ATP binding mutants, we also found that the nucleotide exchange properties of this chaperone are dispensable for ENaC degradation. Consistent with the precipitation of an Lhs1-αENaC complex, Lhs1 holdase activity was instead most likely required to support the ERAD of αENaC. Moreover, a complex containing the mammalian Lhs1 homolog GRP170 and αENaC co-precipitated, and GRP170 also facilitated ENaC degradation in human, HEK293 cells, and in a Xenopus oocyte expression system. In both yeast and higher cell types, the effect of Lhs1 on the ERAD of αENaC was selective for the unglycosylated form of the protein. These data establish the first evidence that Lhs1/Grp170 chaperones can act as mediators of ERAD substrate selection.
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Affiliation(s)
- Teresa M Buck
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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8
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The yeast ubr1 ubiquitin ligase participates in a prominent pathway that targets cytosolic thermosensitive mutants for degradation. G3-GENES GENOMES GENETICS 2012; 2:619-28. [PMID: 22670231 PMCID: PMC3362944 DOI: 10.1534/g3.111.001933] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2011] [Accepted: 03/16/2012] [Indexed: 12/17/2022]
Abstract
Mutations causing protein misfolding and proteolysis are associated with many genetic diseases. The degradation of these aberrant proteins typically is mediated by protein-quality control pathways that recognize misfolded domains. Several E3 ubiquitin ligases have been shown to target cytosolic misfolded proteins to the proteasome. In this study, we characterized a panel of more than 20 cytosolic thermosensitive mutants from six essential genes in Saccharomyces cerevisiae. These wild-type proteins are stable at restrictive temperature. In contrast, we found that a large portion of the mutants is degraded at nonpermissive temperature in a proteasome-dependent manner. Approximately one-third of the assessed unstable mutants are targeted by the Ubr1 ubiquitin ligase. In two cases, efficient degradation of the thermosensitive mutants is abrogated in the absence of Ubr1 alone, whereas in a third case it is reliant on the dual deletion of Ubr1 and the nuclear E3 ligase San1. We found that the impairment of the degradation of these quality control substrates at the restrictive temperature is associated with the suppression of thermosensitive phenotype. This study confirms that Ubr1 plays an important role in the degradation of cytosolic misfolded proteins and indicates that degradation mediated by protein quality control is a major cause for the conditional lethality of mutated essential genes.
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9
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Hsu CL, Prasad R, Blackman C, Ng DTW. Endoplasmic reticulum stress regulation of the Kar2p/BiP chaperone alleviates proteotoxicity via dual degradation pathways. Mol Biol Cell 2011; 23:630-41. [PMID: 22190740 PMCID: PMC3279391 DOI: 10.1091/mbc.e11-04-0297] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
ETOC: A procedure to uncouple the highly conserved target gene Kar2/BiP from UPR regulation is used to show that the primary function of its induction is to mediate the disposal of misfolded proteins that would otherwise be toxic. The unfolded protein response (UPR) monitors and maintains protein homeostasis in the endoplasmic reticulum (ER). In budding yeast, the UPR is a transcriptional regulatory pathway that is quiescent under normal conditions. Under conditions of acute ER stress, activation of UPR targets is essential for cell viability. How individual target genes contribute to stress tolerance is unclear. Uncovering these roles is hampered because most targets also play important functions in the absence of stress. To differentiate stress-specific roles from everyday functions, a single target gene was uncoupled from UPR control by eliminating its UPR-specific regulatory element. Through this approach, the UPR remains intact, aside from its inability to induce the designated target. Applying the strategy to the major ER chaperone Kar2p/BiP revealed the physiological function of increasing its cellular concentration. Despite hundreds of target genes under UPR control, we show that activation of KAR2 is indispensable to alleviate some forms of ER stress. Specifically, activation is essential to dispose misfolded proteins that are otherwise toxic. Surprisingly, induced BiP/Kar2p molecules are dedicated to alleviating stress. The inability to induce KAR2 under stress had no effect on its known housekeeping functions.
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Affiliation(s)
- Chia-Ling Hsu
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604
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10
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Olzmann JA, Kopito RR. Lipid droplet formation is dispensable for endoplasmic reticulum-associated degradation. J Biol Chem 2011; 286:27872-4. [PMID: 21693705 DOI: 10.1074/jbc.c111.266452] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteins that fail to fold or assemble in the endoplasmic reticulum (ER) are destroyed by cytoplasmic proteasomes through a process known as ER-associated degradation. Substrates of this pathway are initially sequestered within the ER lumen and must therefore be dislocated across the ER membrane to be degraded. It has been proposed that generation of bicellar structures during lipid droplet formation may provide an "escape hatch" through which misfolded proteins, toxins, and viruses can exit the ER. We have directly tested this hypothesis by exploiting yeast strains defective in lipid droplet formation. Our data demonstrate that lipid droplet formation is dispensable for the dislocation of a plant toxin and the degradation of both soluble and integral membrane glycoproteins.
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Affiliation(s)
- James A Olzmann
- Department of Biology, Stanford University, Stanford, California 94305, USA
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11
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Hebert DN, Molinari M. In and out of the ER: protein folding, quality control, degradation, and related human diseases. Physiol Rev 2007; 87:1377-408. [PMID: 17928587 DOI: 10.1152/physrev.00050.2006] [Citation(s) in RCA: 480] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A substantial fraction of eukaryotic gene products are synthesized by ribosomes attached at the cytosolic face of the endoplasmic reticulum (ER) membrane. These polypeptides enter cotranslationally in the ER lumen, which contains resident molecular chaperones and folding factors that assist their maturation. Native proteins are released from the ER lumen and are transported through the secretory pathway to their final intra- or extracellular destination. Folding-defective polypeptides are exported across the ER membrane into the cytosol and destroyed. Cellular and organismal homeostasis relies on a balanced activity of the ER folding, quality control, and degradation machineries as shown by the dozens of human diseases related to defective maturation or disposal of individual polypeptides generated in the ER.
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Affiliation(s)
- Daniel N Hebert
- Department of Biochemistry and Molecular Biology, Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Massachusetts 01003, USA.
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12
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Abstract
Glycosylation of asparagine residues in Asn-x-Ser/Thr motifs is a common covalent modification of proteins in the lumen of the endoplasmic reticulum (ER). By substantially contributing to the overall hydrophilicity of the polypeptide, pre-assembled core glycans inhibit possible aggregation caused by the inevitable exposure of hydrophobic patches on the as yet unstructured chains. Thereafter, N-glycans are modified by ER-resident enzymes glucosidase I (GI), glucosidase II (GII), UDP-glucose:glycoprotein glucosyltransferase (UGT) and mannosidase(s) and become functional appendices that determine the fate of the associated polypeptide. Recent work has improved our understanding of how the removal of terminal glucose residues from N-glycans allows newly synthesized proteins to access the calnexin chaperone system; how substrate retention in this specialized chaperone system is regulated by de-/re-glucosylation cycles catalyzed by GII and UGT1; and how acceleration of N-glycan dismantling upon induction of EDEM variants promotes ER-associated degradation (ERAD) under conditions of ER stress. In particular, characterization of cells lacking certain ER chaperones has revealed important new information on the mechanisms regulating protein folding and quality control. Tight regulation of N-glycan modifications is crucial to maintain protein quality control, to ensure the synthesis of functional polypeptides and to avoid constipation of the ER with folding-defective polypeptides.
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Affiliation(s)
- Lloyd W Ruddock
- Biocenter Oulu and Department of Biochemistry, University of Oulu, FIN-90014 Oulu, Finland
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13
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Park SH, Bolender N, Eisele F, Kostova Z, Takeuchi J, Coffino P, Wolf DH. The cytoplasmic Hsp70 chaperone machinery subjects misfolded and endoplasmic reticulum import-incompetent proteins to degradation via the ubiquitin-proteasome system. Mol Biol Cell 2007; 18:153-65. [PMID: 17065559 PMCID: PMC1751312 DOI: 10.1091/mbc.e06-04-0338] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Revised: 10/13/2006] [Accepted: 10/17/2006] [Indexed: 11/11/2022] Open
Abstract
The mechanism of protein quality control and elimination of misfolded proteins in the cytoplasm is poorly understood. We studied the involvement of cytoplasmic factors required for degradation of two endoplasmic reticulum (ER)-import-defective mutated derivatives of carboxypeptidase yscY (DeltassCPY* and DeltassCPY*-GFP) and also examined the requirements for degradation of the corresponding wild-type enzyme made ER-import incompetent by removal of its signal sequence (DeltassCPY). All these protein species are rapidly degraded via the ubiquitin-proteasome system. Degradation requires the ubiquitin-conjugating enzymes Ubc4p and Ubc5p, the cytoplasmic Hsp70 Ssa chaperone machinery, and the Hsp70 cochaperone Ydj1p. Neither the Hsp90 chaperones nor Hsp104 or the small heat-shock proteins Hsp26 and Hsp42 are involved in the degradation process. Elimination of a GFP fusion (GFP-cODC), containing the C-terminal 37 amino acids of ornithine decarboxylase (cODC) directing this enzyme to the proteasome, is independent of Ssa1p function. Fusion of DeltassCPY* to GFP-cODC to form DeltassCPY*-GFP-cODC reimposes a dependency on the Ssa1p chaperone for degradation. Evidently, the misfolded protein domain dictates the route of protein elimination. These data and our further results give evidence that the Ssa1p-Ydj1p machinery recognizes misfolded protein domains, keeps misfolded proteins soluble, solubilizes precipitated protein material, and escorts and delivers misfolded proteins in the ubiquitinated state to the proteasome for degradation.
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Affiliation(s)
- Sae-Hun Park
- *Institut fuer Biochemie, Universitaet Stuttgart, 70569 Stuttgart, Germany; and
| | - Natalia Bolender
- *Institut fuer Biochemie, Universitaet Stuttgart, 70569 Stuttgart, Germany; and
| | - Frederik Eisele
- *Institut fuer Biochemie, Universitaet Stuttgart, 70569 Stuttgart, Germany; and
| | - Zlatka Kostova
- *Institut fuer Biochemie, Universitaet Stuttgart, 70569 Stuttgart, Germany; and
| | - Junko Takeuchi
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143
| | - Philip Coffino
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143
| | - Dieter H. Wolf
- *Institut fuer Biochemie, Universitaet Stuttgart, 70569 Stuttgart, Germany; and
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