1
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Niu Y, Wang N, Xu Q. Development of an Endoplasmic Reticulum Stress-Related Diagnostic Signature in Polycystic Ovary Syndrome. Reprod Sci 2024:10.1007/s43032-024-01619-3. [PMID: 38955938 DOI: 10.1007/s43032-024-01619-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 06/03/2024] [Indexed: 07/04/2024]
Abstract
Polycystic ovary syndrome (PCOS) is a prevalent endocrine and metabolic disorder in premenopausal women. This investigation was to elucidate the underlying mechanism of endoplasmic reticulum stress (ERS) activation in granulosa cells, which has been implicated in the etiology of PCOS. Differentially expressed genes (DEGs) between PCOS and control groups were integrated with ERS gene lists from databases to identify DE-ERS genes, and functional analyses were performed. Univariate regression analysis and the LASSO method were used to select diagnostic factors, followed by establishing a DE-ERS gene-based diagnostic model. A nomogram model was further generated to predict the risk of PCOS. The correlation between ERS gene expression and immune cell proportion was assessed. A total of 14 DE-ERS genes associated with "protein processing in endoplasmic reticulum", "ferroptosis", and "glycerophospholipid metabolism" were selected as PCOS-related factors. An eight-DE-ERS genes-based diagnostic model was developed and displayed satisfactory performance in the training (Area under curve (AUC) = 0.983) and validation datasets (AUC = 0.802). High risk of PCOS can be accurately predicted, which might contribute to clinical decision-making. Moreover, EDEM1 expression was significantly positively correlated with naive B cell infiltration, while PDIA6 was negatively correlated with neutrophil proportion (P < 0.001). We identified eight novel molecules and developed an ERS gene-based diagnostic model in PCOS, which might provide novel insight for finding biomarkers and treatment methods.
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Affiliation(s)
- Yanxin Niu
- Department of Obstetrics and Gynaecology, Jinhua People's Hospital, No.267, Danxi East Road, Jinhua, 321000, Zhejiang, P.R. China
| | - Nan Wang
- Department of Obstetrics and Gynaecology, Jinhua People's Hospital, No.267, Danxi East Road, Jinhua, 321000, Zhejiang, P.R. China
| | - Qiulian Xu
- Department of Obstetrics and Gynaecology, Jinhua People's Hospital, No.267, Danxi East Road, Jinhua, 321000, Zhejiang, P.R. China.
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2
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Fasana E, Fregno I, Galli C, Soldà T, Molinari M. ER-to-lysosome-associated degradation acts as failsafe mechanism upon ERAD dysfunction. EMBO Rep 2024; 25:2773-2785. [PMID: 38773321 PMCID: PMC11169228 DOI: 10.1038/s44319-024-00165-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/25/2024] [Accepted: 04/30/2024] [Indexed: 05/23/2024] Open
Abstract
The endoplasmic reticulum (ER) produces proteins destined to organelles of the endocytic and secretory pathways, the plasma membrane, and the extracellular space. While native proteins are transported to their intra- or extracellular site of activity, folding-defective polypeptides are retro-translocated across the ER membrane into the cytoplasm, poly-ubiquitylated and degraded by 26 S proteasomes in a process called ER-associated degradation (ERAD). Large misfolded polypeptides, such as polymers of alpha1 antitrypsin Z (ATZ) or mutant procollagens, fail to be dislocated across the ER membrane and instead enter ER-to-lysosome-associated degradation (ERLAD) pathways. Here, we show that pharmacological or genetic inhibition of ERAD components, such as the α1,2-mannosidase EDEM1 or the OS9 ERAD lectins triggers the delivery of the canonical ERAD clients Null Hong Kong (NHK) and BACE457Δ to degradative endolysosomes under control of the ER-phagy receptor FAM134B and the LC3 lipidation machinery. Our results reveal that ERAD dysfunction is compensated by the activation of FAM134B-driven ERLAD pathways that ensure efficient lysosomal clearance of orphan ERAD clients.
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Affiliation(s)
- Elisa Fasana
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland
| | - Ilaria Fregno
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland
| | - Carmela Galli
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland
| | - Tatiana Soldà
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland
| | - Maurizio Molinari
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland.
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland.
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3
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Chen SF, Wu CH, Lee YM, Tam K, Liou JY, Shyue SK. Surf4 collaborates with derlin-2 and derlin-1 to mediate cyclooxygenase-2 translocation to the cytosol for degradation. J Cell Sci 2023; 136:jcs260995. [PMID: 37676109 DOI: 10.1242/jcs.260995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 08/09/2023] [Indexed: 09/08/2023] Open
Abstract
Derlin family members participate in the retrotranslocation of endoplasmic reticulum (ER) lumen proteins to the cytosol for ER-associated degradation (ERAD); however, the proteins facilitating this retrotranslocation remain to be explored. Using CRISPR library screening, we have found that derlin-2 and surfeit locus protein 4 (Surf4) are candidates to facilitate degradation of cyclooxygenase-2 (COX-2, also known as PTGS2). Our results show that derlin-2 acts upstream of derlin-1 and that Surf4 acts downstream of derlin-2 and derlin-1 to facilitate COX-2 degradation. Knockdown of derlin-2 or Surf4 impedes the ubiquitylation of COX-2 and the interaction of COX-2 with caveolin-1 (Cav-1) and p97 (also known as VCP) in the cytosol. Additionally, COX-2 degradation is N-glycosylation dependent. Although derlin-2 facilitates degradation of N-glycosylated COX-2, the interaction between derlin-2 and COX-2 is independent of COX-2 N-glycosylation. Derlin-1, Surf4 and p97 preferentially interact with non-glycosylated COX-2, whereas Cav-1 preferentially interacts with N-glycosylated COX-2, regardless of the N-glycosylation pattern. Collectively, our results reveal that Surf4 collaborates with derlin-2 and derlin-1 to mediate COX-2 translocation from the ER lumen to the cytosol. The derlin-2-derlin-1-Surf4-Cav-1 machinery might represent a unique pathway to accelerate COX-2 degradation in ERAD.
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Affiliation(s)
- Shu-Fen Chen
- Cardiovascular Division, Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Chun-Hu Wu
- Cardiovascular Division, Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Yen-Ming Lee
- Cardiovascular Division, Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Kabik Tam
- Cardiovascular Division, Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Jun-Yang Liou
- Institute of Cellular and System Medicine, National Health Research Institutes, Zhunan 35053, Taiwan
| | - Song-Kun Shyue
- Cardiovascular Division, Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
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4
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Durin Z, Houdou M, Legrand D, Foulquier F. Metalloglycobiology: The power of metals in regulating glycosylation. Biochim Biophys Acta Gen Subj 2023; 1867:130412. [PMID: 37348823 DOI: 10.1016/j.bbagen.2023.130412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023]
Abstract
The remarkable structural diversity of glycans that is exposed at the cell surface and generated along the secretory pathway is tightly regulated by several factors. The recent identification of human glycosylation diseases related to metal transporter defects opened a completely new field of investigation, referred to herein as "metalloglycobiology", on how metal changes can affect the glycosylation and hence the glycan structures that are produced. Although this field is in its infancy, this review aims to go through the different glycosylation steps/pathways that are metal dependent and that could be impacted by metal homeostasis dysregulations.
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Affiliation(s)
- Zoé Durin
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F- 59000 Lille, France
| | - Marine Houdou
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F- 59000 Lille, France
| | - Dominique Legrand
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F- 59000 Lille, France
| | - François Foulquier
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F- 59000 Lille, France.
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5
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Miura K, Katsuki R, Yoshida S, Ohta R, Tamura T. Identification of EGF Receptor and Thrombospondin-1 as Endogenous Targets of ER-Associated Degradation Enhancer EDEM1 in HeLa Cells. Int J Mol Sci 2023; 24:12171. [PMID: 37569550 PMCID: PMC10418772 DOI: 10.3390/ijms241512171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Secretory and membrane proteins are vital for cell activities, including intra- and intercellular communication. Therefore, protein quality control in the endoplasmic reticulum (ER) is an essential and crucial process for eukaryotic cells. Endoplasmic reticulum-associated degradation (ERAD) targets misfolded proteins during the protein maturation process in the ER and leads to their disposal. This process maintains the ER productive function and prevents misfolded protein stress (i.e., ER stress). The ERAD-stimulating factor ER degradation-enhancing α mannosidase-like 1 protein (EDEM1) acts on misfolded proteins to accelerate ERAD, thereby maintaining the productivity of the ER. However, the detail mechanism underlying the function of EDEM1 in ERAD is not completely understood due to a lack of established physiological substrate proteins. In this study, we attempted to identify substrate proteins for EDEM1 using siRNA. The matrix component thrombospondin-1 (TSP1) and epidermal growth factor receptor (EGFR) were identified as candidate targets of EDEM1. Their protein maturation status and cellular localization were markedly affected by knockdown of EDEM1. We also showed that EDEM1 physically associates with EGFR and enhances EGFR degradation via ERAD. Our data highlight the physiological role of EDEM1 in maintaining specific target proteins and provide a potential approach to the regulation of expression of clinically important proteins.
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Affiliation(s)
- Kohta Miura
- Department of Life Science, Graduate School of Engineering Science, Akita University, Akita 010-8502, Japan
| | - Riko Katsuki
- Department of Life Science, Graduate School of Engineering Science, Akita University, Akita 010-8502, Japan
| | - Shusei Yoshida
- Department of Life Science, Faculty of Engineering Science, Akita University, Akita 010-8502, Japan
| | - Ren Ohta
- Department of Life Science, Graduate School of Engineering Science, Akita University, Akita 010-8502, Japan
| | - Taku Tamura
- Department of Life Science, Graduate School of Engineering Science, Akita University, Akita 010-8502, Japan
- Department of Life Science, Faculty of Engineering Science, Akita University, Akita 010-8502, Japan
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6
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Zhu B, Jin P, Zhang Y, Shen Y, Wang W, Li S. Genomic and transcriptomic analyses support a silk gland origin of spider venom glands. BMC Biol 2023; 21:82. [PMID: 37055766 PMCID: PMC10099834 DOI: 10.1186/s12915-023-01581-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/29/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND Spiders comprise a hyperdiverse lineage of predators with venom systems, yet the origin of functionally novel spider venom glands remains unclear. Previous studies have hypothesized that spider venom glands originated from salivary glands or evolved from silk-producing glands present in early chelicerates. However, there is insufficient molecular evidence to indicate similarity among them. Here, we provide comparative analyses of genome and transcriptome data from various lineages of spiders and other arthropods to advance our understanding of spider venom gland evolution. RESULTS We generated a chromosome-level genome assembly of a model spider species, the common house spider (Parasteatoda tepidariorum). Module preservation, GO semantic similarity, and differentially upregulated gene similarity analyses demonstrated a lower similarity in gene expressions between the venom glands and salivary glands compared to the silk glands, which questions the validity of the salivary gland origin hypothesis but unexpectedly prefers to support the ancestral silk gland origin hypothesis. The conserved core network in the venom and silk glands was mainly correlated with transcription regulation, protein modification, transport, and signal transduction pathways. At the genetic level, we found that many genes in the venom gland-specific transcription modules show positive selection and upregulated expressions, suggesting that genetic variation plays an important role in the evolution of venom glands. CONCLUSIONS This research implies the unique origin and evolutionary path of spider venom glands and provides a basis for understanding the diverse molecular characteristics of venom systems.
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Affiliation(s)
- Bingyue Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Pengyu Jin
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yiming Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Yunxiao Shen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Wei Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Ecology and Environmental Protection of Rare and Endangered Animals and Plants, Ministry of Education, Guangxi Normal University, Guilin, 541004, China
| | - Shuqiang Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
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7
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Kato M. Identify MicroRNA Targets Using AGO2-CLASH (Cross-linking, Ligation, and Sequencing of Hybrids) and AGO2-CLIP (Cross-Linking and Immuno-Precipitation) in Cells with or Without the MicroRNA of Interest Depleted. Methods Mol Biol 2023; 2666:137-147. [PMID: 37166662 DOI: 10.1007/978-1-0716-3191-1_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
MicroRNAs (miRNAs) are short noncoding RNAs and important players in the regulation of gene expression through post-transcriptional mechanisms. MicroRNAs regulate many cellular processes and are involved in disease progression. Identification of novel miRNA-to-target RNA connections can fill the gaps in the signaling pathways and suggest new therapeutic targets. MiRNA targets are often predicted by base-complementarity of their seed and flanking sequences with target sequences. Direct targets can also be identified by the physical interaction between the miRNA and the target RNA using immunoprecipitation of the Argonaute (AGO) protein, a component of the RNA-induced silencing complex, followed by ligation of AGO-associated miRNA and target RNA and next generation sequencing (CLASH). Databases describing these miRNA-RNA interactions have been generated from cells commonly studied or used. However, because the regulation by miRNAs varies among organs, tissues, cell types and species, identifying relevant targets in specific cells under conditions of interest may not be available. Here, the author describes simplified methods of AGO2-CLASH and AGO2-CLIP to identify miRNA targets by comparing primary cells derived from wild-type mice and those from specific miRNA knockout mice.
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Affiliation(s)
- Mitsuo Kato
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA.
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8
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Radhakrishnan A, Chellapandian H, Ramasamy P, Jeyachandran S. Back2Basics: animal lectins: an insight into a highly versatile recognition protein. JOURNAL OF PROTEINS AND PROTEOMICS 2023; 14:43-59. [PMID: 36597476 PMCID: PMC9799708 DOI: 10.1007/s42485-022-00102-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/15/2022] [Accepted: 12/08/2022] [Indexed: 12/31/2022]
Abstract
The rapid advancement of molecular research has contributed to the discovery of 'Lectin', a carbohydrate-binding protein which specifically interacts with receptors on surface glycan moieties that regulate various critical cellular activities. The first animal lectin reported was 'the asialoglycoprotein receptor' in mammalian cells which helped analyze how animal lectins differ in glycoconjugate binding. Animal lectins are classified into several families, depending on their diverse cellular localization, and the binding specificities of their Carbohydrate-Recognition Domain (CRD) modules. Earlier characterization of animal lectins classified them into two structural families, the C-type (Ca2+-dependent binding) and S-type galectins (sulfhydryl-dependent binding) lectins. The C-type lectin includes the most significant animal lectins, such as endocytic receptors, mannose receptors, selectins, and collectins. The recent developments in research based on the complexity of the carbohydrate ligands, the metabolic processes they perform, their expression levels, and their reliance on divalent cations have identified more than 100 animal lectins and classified them into around 13 different families, such as Calnexin, F-lectin, Intelectin, Chitinase-like lectin, F-box lectin, etc. Understanding their structure and expression patterns have aided in defining their significant functions including cell adhesion, antimicrobial activity, innate immunity, disease diagnostic biomarkers, and drug delivery through specific carbohydrate-protein interactions. Such extensive potential roles of animal lectins made it equally important to plant lectins among researchers. Hence, the review focuses on providing an overview of animal lectins, their taxonomy, structural characteristics, and functions in diverse aspects interconnected to their specific carbohydrate and glycoconjugate binding. Graphical abstract
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Affiliation(s)
- Akshaya Radhakrishnan
- PG & Research Department of Biotechnology & Microbiology, National College, Tiruchirappalli, Tamil Nadu 620001 India
| | - Hethesh Chellapandian
- PG & Research Department of Biotechnology & Microbiology, National College, Tiruchirappalli, Tamil Nadu 620001 India
| | - Pasiyappazham Ramasamy
- Department of Physiology, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu 600077 India
| | - Sivakamavalli Jeyachandran
- PG & Research Department of Biotechnology & Microbiology, National College, Tiruchirappalli, Tamil Nadu 620001 India
- Centre for Biotechnology & Biosignal Transduction, Department of Orthodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu 600077 India
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9
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Viruses Hijack ERAD to Regulate Their Replication and Propagation. Int J Mol Sci 2022; 23:ijms23169398. [PMID: 36012666 PMCID: PMC9408921 DOI: 10.3390/ijms23169398] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 11/25/2022] Open
Abstract
Endoplasmic reticulum-associated degradation (ERAD) is highly conserved in yeast. Recent studies have shown that ERAD is also ubiquitous and highly conserved in eukaryotic cells, where it plays an essential role in maintaining endoplasmic reticulum (ER) homeostasis. Misfolded or unfolded proteins undergo ERAD. They are recognized in the ER, retrotranslocated into the cytoplasm, and degraded by proteasomes after polyubiquitin. This may consist of several main steps: recognition of ERAD substrates, retrotranslocation, and proteasome degradation. Replication and transmission of the virus in the host is a process of a “game” with the host. It can be assumed that the virus has evolved various mechanisms to use the host’s functions for its replication and transmission, including ERAD. However, until now, it is still unclear how the host uses ERAD to deal with virus infection and how the viruses hijack the function of ERAD to obtain a favorable niche or evade the immune clearance of the host. Recent studies have shown that viruses have also evolved mechanisms to use various processes of ERAD to promote their transmission. This review describes the occurrence of ERAD and how the viruses hijack the function of ERAD to spread by affecting the homeostasis and immune response of the host, and we will focus on the role of E3 ubiquitin ligase.
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10
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Scott E, Garnham R, Cheung K, Duxfield A, Elliott DJ, Munkley J. Pro-Survival Factor EDEM3 Confers Therapy Resistance in Prostate Cancer. Int J Mol Sci 2022; 23:ijms23158184. [PMID: 35897761 PMCID: PMC9332126 DOI: 10.3390/ijms23158184] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 02/04/2023] Open
Abstract
Prostate cancer is the most common cancer in men, and it is primarily driven by androgen steroid hormones. The glycosylation enzyme EDEM3 is controlled by androgen signalling and is important for prostate cancer viability. EDEM3 is a mannosidase that trims mannose from mis-folded glycoproteins, tagging them for degradation through endoplasmic reticulum-associated degradation. Here, we find that EDEM3 is upregulated in prostate cancer, and this is linked to poorer disease-free survival. Depletion of EDEM3 from prostate cancer cells induces an ER stress transcriptomic signature, and EDEM3 overexpression is cyto-protective against ER stressors. EDEM3 expression also positively correlates with genes involved in the unfolded protein response in prostate cancer patients, and its expression can be induced through exposure to radiation. Importantly, the overexpression of EDEM3 promotes radio-resistance in prostate cancer cells and radio-resistance can be reduced through depletion of EDEM3. Our data thus implicate increased levels of EDEM3 with a role in prostate cancer pathology and reveal a new therapeutic opportunity to sensitise prostate tumours to radiotherapy.
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Affiliation(s)
- Emma Scott
- Centre for Cancer, Biosciences Institute, Newcastle University, Newcastle-Upon-Tyne NE1 3BZ, UK; (R.G.); (A.D.); (D.J.E.)
- Correspondence: (E.S.); (J.M.)
| | - Rebecca Garnham
- Centre for Cancer, Biosciences Institute, Newcastle University, Newcastle-Upon-Tyne NE1 3BZ, UK; (R.G.); (A.D.); (D.J.E.)
| | - Kathleen Cheung
- Bioinformatic Support Unit, Newcastle University, Newcastle-Upon-Tyne NE1 3BZ, UK;
| | - Adam Duxfield
- Centre for Cancer, Biosciences Institute, Newcastle University, Newcastle-Upon-Tyne NE1 3BZ, UK; (R.G.); (A.D.); (D.J.E.)
| | - David J. Elliott
- Centre for Cancer, Biosciences Institute, Newcastle University, Newcastle-Upon-Tyne NE1 3BZ, UK; (R.G.); (A.D.); (D.J.E.)
| | - Jennifer Munkley
- Centre for Cancer, Biosciences Institute, Newcastle University, Newcastle-Upon-Tyne NE1 3BZ, UK; (R.G.); (A.D.); (D.J.E.)
- Correspondence: (E.S.); (J.M.)
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Zhang J, Xia Y, Wang D, Du Y, Chen Y, Zhang C, Mao J, Wang M, She YM, Peng X, Liu L, Voglmeir J, He Z, Liu L, Li J. A Predominant Role of AtEDEM1 in Catalyzing a Rate-Limiting Demannosylation Step of an Arabidopsis Endoplasmic Reticulum-Associated Degradation Process. FRONTIERS IN PLANT SCIENCE 2022; 13:952246. [PMID: 35874007 PMCID: PMC9302962 DOI: 10.3389/fpls.2022.952246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Endoplasmic reticulum-associated degradation (ERAD) is a key cellular process for degrading misfolded proteins. It was well known that an asparagine (N)-linked glycan containing a free α1,6-mannose residue is a critical ERAD signal created by Homologous to α-mannosidase 1 (Htm1) in yeast and ER-Degradation Enhancing α-Mannosidase-like proteins (EDEMs) in mammals. An earlier study suggested that two Arabidopsis homologs of Htm1/EDEMs function redundantly in generating such a conserved N-glycan signal. Here we report that the Arabidopsis irb1 (reversal of bri1) mutants accumulate brassinosteroid-insensitive 1-5 (bri1-5), an ER-retained mutant variant of the brassinosteroid receptor BRI1 and are defective in one of the Arabidopsis Htm1/EDEM homologs, AtEDEM1. We show that the wild-type AtEDEM1, but not its catalytically inactive mutant, rescues irb1-1. Importantly, an insertional mutation of the Arabidopsis Asparagine-Linked Glycosylation 3 (ALG3), which causes N-linked glycosylation with truncated glycans carrying a different free α1,6-mannose residue, completely nullifies the inhibitory effect of irb1-1 on bri1-5 ERAD. Interestingly, an insertional mutation in AtEDEM2, the other Htm1/EDEM homolog, has no detectable effect on bri1-5 ERAD; however, it enhances the inhibitory effect of irb1-1 on bri1-5 degradation. Moreover, AtEDEM2 transgenes rescued the irb1-1 mutation with lower efficacy than AtEDEM1. Simultaneous elimination of AtEDEM1 and AtEDEM2 completely blocks generation of α1,6-mannose-exposed N-glycans on bri1-5, while overexpression of either AtEDEM1 or AtEDEM2 stimulates bri1-5 ERAD and enhances the bri1-5 dwarfism. We concluded that, despite its functional redundancy with AtEDEM2, AtEDEM1 plays a predominant role in promoting bri1-5 degradation.
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Affiliation(s)
- Jianjun Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Yang Xia
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Dinghe Wang
- University of Chinese Academy of Sciences, Beijing, China
- The Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yamin Du
- Glycomics and Glycan Bioengineering Research Center, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yongwu Chen
- University of Chinese Academy of Sciences, Beijing, China
- The Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Congcong Zhang
- University of Chinese Academy of Sciences, Beijing, China
- The Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Juan Mao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Muyang Wang
- The Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yi-Min She
- The Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xinxiang Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Li Liu
- Glycomics and Glycan Bioengineering Research Center, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zuhua He
- The Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Linchuan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Jianming Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
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12
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Ghenea S, Chiritoiu M, Tacutu R, Miranda-Vizuete A, Petrescu SM. Targeting EDEM protects against ER stress and improves development and survival in C. elegans. PLoS Genet 2022; 18:e1010069. [PMID: 35192599 PMCID: PMC8912907 DOI: 10.1371/journal.pgen.1010069] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 03/10/2022] [Accepted: 02/02/2022] [Indexed: 02/07/2023] Open
Abstract
EDEM-1, EDEM-2 and EDEM-3 are key players for the quality control of newly synthesized proteins in the endoplasmic reticulum (ER) by accelerating disposal and degradation of misfolded proteins through ER Associated Degradation (ERAD). Although many previous studies reported the role of individual ERAD components especially in cell-based systems, still little is known about the consequences of ERAD dysfunction under physiological and ER stress conditions in the context of a multicellular organism. Here we report the first individual and combined characterization and functional interplay of EDEM proteins in Caenorhabditis elegans using single, double, and triple mutant combinations. We found that EDEM-2 has a major role in the clearance of misfolded proteins from ER under physiological conditions, whereas EDEM-1 and EDEM-3 roles become prominent under acute ER stress. In contrast to SEL-1 loss, the loss of EDEMs in an intact organism induces only a modest ER stress under physiological conditions. In addition, chronic impairment of EDEM functioning attenuated both XBP-1 activation and up-regulation of the stress chaperone GRP78/BiP, in response to acute ER stress. We also show that pre-conditioning to EDEM loss in acute ER stress restores ER homeostasis and promotes survival by activating ER hormesis. We propose a novel role for EDEM in fine-tuning the ER stress responsiveness that affects ER homeostasis and survival. ER stress and UPRER malfunctions have been implicated in the pathogenesis of neurodegeneration, metabolic and inflammatory diseases as well as tumor progression and diabetes, whereby disturbed ER homeostasis negatively influences the pathology of the disease. Under ER stress conditions, the cells either activate UPRER-dependent cytoprotective mechanisms when ER stress is at subtoxic levels or, in case of an excessive ER stress, the cytotoxic response stimulates cell death. Here, we used Caenorhabditis elegans to study the cellular responses to ER stress at organismal level. We show that EDEMs respond differently to ER stress stimuli, and moreover, EDEMs deficiencies activate an XBP-1 independent adaptive program to promote organism survival under acute ER stress. Corroborated with the fact that loss of EDEM-2 and EDEM-3 induces resistance to acute ER stress in an intact organism, our data implicate EDEM proteins in a broader response to ER stress than previously established, which opens a new avenue for understanding the regulation of ER stress with implications for clinical and therapeutic investigations.
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Affiliation(s)
- Simona Ghenea
- Department of Molecular Cell Biology, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
- * E-mail: (SG); (SMP)
| | - Marioara Chiritoiu
- Department of Molecular Cell Biology, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Robi Tacutu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry, Romanian Academy, Bucharest, Romania
| | - Antonio Miranda-Vizuete
- Redox Homeostasis Group, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - Stefana Maria Petrescu
- Department of Molecular Cell Biology, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
- * E-mail: (SG); (SMP)
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13
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Kuribara T, Totani K. Oligomannose-Type Glycan Processing in the Endoplasmic Reticulum and Its Importance in Misfolding Diseases. BIOLOGY 2022; 11:biology11020199. [PMID: 35205066 PMCID: PMC8869290 DOI: 10.3390/biology11020199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/04/2021] [Accepted: 01/24/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Glycans play many roles in biological processes. For instance, they mediate cell–cell interaction, viral infection, and protein folding of glycoproteins. Glycoprotein folding in the endoplasmic reticulum (ER) is closely related to the onset of diseases such as misfolding diseases caused by accumulation of misfolded proteins in the ER. In this review, we focused on oligomannose-type glycan processing in the ER, which has central roles in glycoprotein folding in the ER, and we summarise relationship between oligomannose-type glycan processing and misfolding diseases arising from the disruption of ER homeostasis. Abstract Glycoprotein folding plays a critical role in sorting glycoprotein secretion and degradation in the endoplasmic reticulum (ER). Furthermore, relationships between glycoprotein folding and several diseases, such as type 2 diabetes and various neurodegenerative disorders, are indicated. Patients’ cells with type 2 diabetes, and various neurodegenerative disorders induce ER stress, against which the cells utilize the unfolded protein response for protection. However, in some cases, chronic and/or massive ER stress causes critical damage to cells, leading to the onset of ER stress-related diseases, which are categorized into misfolding diseases. Accumulation of misfolded proteins may be a cause of ER stress, in this respect, perturbation of oligomannose-type glycan processing in the ER may occur. A great number of studies indicate the relationships between ER stress and misfolding diseases, while little evidence has been reported on the connection between oligomannose-type glycan processing and misfolding diseases. In this review, we summarize alteration of oligomannose-type glycan processing in several ER stress-related diseases, especially misfolding diseases and show the possibility of these alteration of oligomannose-type glycan processing as indicators of diseases.
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14
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Gan L, Liu D, Xie D, Bond Lau W, Liu J, Christopher TA, Lopez B, Liu L, Hu H, Yao P, He Y, Gao E, Koch WJ, Zhao J, Ma XL, Cao Y, Wang Y. Ischemic Heart-Derived Small Extracellular Vesicles Impair Adipocyte Function. Circ Res 2022; 130:48-66. [PMID: 34763521 DOI: 10.1161/circresaha.121.320157] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Patients with acute myocardial infarction suffer systemic metabolic dysfunction via incompletely understood mechanisms. Adipocytes play critical role in metabolic homeostasis. The impact of acute myocardial infarction upon adipocyte function is unclear. Small extracellular vesicles (sEVs) critically contribute to organ-organ communication. Whether and how small extracellular vesicle mediate post-MI cardiomyocyte/adipocyte communication remain unknown. METHODS Plasma sEVs were isolated from sham control (Pla-sEVSham) or 3 hours after myocardial ischemia/reperfusion (Pla-sEVMI/R) and incubated with adipocytes for 24 hours. Compared with Pla-sEVSham, Pla-sEVMI/R significantly altered expression of genes known to be important in adipocyte function, including a well-known metabolic regulatory/cardioprotective adipokine, APN (adiponectin). Pla-sEVMI/R activated 2 (PERK-CHOP and ATF6 [transcription factor 6]-EDEM [ER degradation enhancing alpha-mannosidase like protein 1] pathways) of the 3 endoplasmic reticulum (ER) stress pathways in adipocytes. These pathological alterations were also observed in adipocytes treated with sEVs isolated from adult cardiomyocytes subjected to in vivo myocardial ischemia/reperfusion (MI/R) (Myo-sEVMI/R). Bioinformatic/RT-qPCR analysis demonstrates that the members of miR-23-27-24 cluster are significantly increased in Pla-sEVMI/R, Myo-sEVMI/R, and adipose tissue of MI/R animals. Administration of cardiomyocyte-specific miR-23-27-24 sponges abolished adipocyte miR-23-27-24 elevation in MI/R animals, supporting the cardiomyocyte origin of adipocyte miR-23-27-24 cluster. In similar fashion to Myo-sEVMI/R, a miR-27a mimic activated PERK-CHOP and ATF6-EDEM-mediated ER stress. Conversely, a miR-27a inhibitor significantly attenuated Myo-sEVMI/R-induced ER stress and restored APN production. RESULTS An unbiased approach identified EDEM3 (ER degradation enhancing alpha-mannosidase like protein 3) as a novel downstream target of miR-27a. Adipocyte EDEM3 deficiency phenocopied multiple pathological alterations caused by Myo-sEVMI/R, whereas EDEM3 overexpression attenuated Myo-sEVMI/R-resulted ER stress. Finally, administration of GW4869 or cardiomyocyte-specific miR-23-27-24 cluster sponges attenuated adipocyte ER stress, improved adipocyte endocrine function, and restored plasma APN levels in MI/R animals. CONCLUSIONS We demonstrate for the first time that MI/R causes significant adipocyte ER stress and endocrine dysfunction by releasing miR-23-27-24 cluster-enriched small extracellular vesicle. Targeting small extracellular vesicle-mediated cardiomyocyte-adipocyte pathological communication may be of therapeutic potential to prevent metabolic dysfunction after MI/R.
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Affiliation(s)
- Lu Gan
- Laboratory of Emergency Medicine, Department of Emergency Medicine and National Clinical Research Center for Geriatrics, West China Hospital (L.G., L.L., H.H., P.Y., Y.H., Y.C.), Sichuan University, Chengdu, China
- Department of Emergency Medicine, Thomas Jefferson University, Philadelphia, PA (L.G., D.L., D.X., W.B.L., J.L., T.A.C., B.L., P.Y., J.Z., X.-L.M., Y.W.)
| | - Demin Liu
- Department of Emergency Medicine, Thomas Jefferson University, Philadelphia, PA (L.G., D.L., D.X., W.B.L., J.L., T.A.C., B.L., P.Y., J.Z., X.-L.M., Y.W.)
- Department of Cardiology, The Second Hospital of Hebei Medical University, Shijiazhuang, China (D.L.)
| | - Dina Xie
- Department of Emergency Medicine, Thomas Jefferson University, Philadelphia, PA (L.G., D.L., D.X., W.B.L., J.L., T.A.C., B.L., P.Y., J.Z., X.-L.M., Y.W.)
| | - Wayne Bond Lau
- Department of Emergency Medicine, Thomas Jefferson University, Philadelphia, PA (L.G., D.L., D.X., W.B.L., J.L., T.A.C., B.L., P.Y., J.Z., X.-L.M., Y.W.)
| | - Jing Liu
- Department of Emergency Medicine, Thomas Jefferson University, Philadelphia, PA (L.G., D.L., D.X., W.B.L., J.L., T.A.C., B.L., P.Y., J.Z., X.-L.M., Y.W.)
| | - Theodore A Christopher
- Department of Emergency Medicine, Thomas Jefferson University, Philadelphia, PA (L.G., D.L., D.X., W.B.L., J.L., T.A.C., B.L., P.Y., J.Z., X.-L.M., Y.W.)
| | - Bernard Lopez
- Department of Emergency Medicine, Thomas Jefferson University, Philadelphia, PA (L.G., D.L., D.X., W.B.L., J.L., T.A.C., B.L., P.Y., J.Z., X.-L.M., Y.W.)
| | - Lian Liu
- Laboratory of Emergency Medicine, Department of Emergency Medicine and National Clinical Research Center for Geriatrics, West China Hospital (L.G., L.L., H.H., P.Y., Y.H., Y.C.), Sichuan University, Chengdu, China
| | - Hang Hu
- Laboratory of Emergency Medicine, Department of Emergency Medicine and National Clinical Research Center for Geriatrics, West China Hospital (L.G., L.L., H.H., P.Y., Y.H., Y.C.), Sichuan University, Chengdu, China
| | - Peng Yao
- Department of Emergency Medicine, Thomas Jefferson University, Philadelphia, PA (L.G., D.L., D.X., W.B.L., J.L., T.A.C., B.L., P.Y., J.Z., X.-L.M., Y.W.)
| | - Yarong He
- Laboratory of Emergency Medicine, Department of Emergency Medicine and National Clinical Research Center for Geriatrics, West China Hospital (L.G., L.L., H.H., P.Y., Y.H., Y.C.), Sichuan University, Chengdu, China
| | - Erhe Gao
- Laboratory of Emergency Medicine, Department of Emergency Medicine and National Clinical Research Center for Geriatrics, West China Hospital (L.G., L.L., H.H., P.Y., Y.H., Y.C.), Sichuan University, Chengdu, China
- Center for Translational Medicine, Temple University, Philadelphia, PA (E.G., W.J.K.)
| | - Walter J Koch
- Center for Translational Medicine, Temple University, Philadelphia, PA (E.G., W.J.K.)
| | - Jianli Zhao
- Department of Emergency Medicine, Thomas Jefferson University, Philadelphia, PA (L.G., D.L., D.X., W.B.L., J.L., T.A.C., B.L., P.Y., J.Z., X.-L.M., Y.W.)
| | - Xin-Liang Ma
- Department of Emergency Medicine, Thomas Jefferson University, Philadelphia, PA (L.G., D.L., D.X., W.B.L., J.L., T.A.C., B.L., P.Y., J.Z., X.-L.M., Y.W.)
| | - Yu Cao
- Disaster Medical Center (Y.C.), Sichuan University, Chengdu, China
| | - Yajing Wang
- Department of Emergency Medicine, Thomas Jefferson University, Philadelphia, PA (L.G., D.L., D.X., W.B.L., J.L., T.A.C., B.L., P.Y., J.Z., X.-L.M., Y.W.)
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15
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Demaretz S, Seaayfan E, Bakhos-Douaihy D, Frachon N, Kömhoff M, Laghmani K. Golgi Alpha1,2-Mannosidase IA Promotes Efficient Endoplasmic Reticulum-Associated Degradation of NKCC2. Cells 2021; 11:cells11010101. [PMID: 35011665 PMCID: PMC8750359 DOI: 10.3390/cells11010101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 12/18/2022] Open
Abstract
Mutations in the apically located kidney Na-K-2Cl cotransporter NKCC2 cause type I Bartter syndrome, a life-threatening kidney disorder. We previously showed that transport from the ER represents the limiting phase in NKCC2 journey to the cell surface. Yet very little is known about the ER quality control components specific to NKCC2 and its disease-causing mutants. Here, we report the identification of Golgi alpha1, 2-mannosidase IA (ManIA) as a novel binding partner of the immature form of NKCC2. ManIA interaction with NKCC2 takes place mainly at the cis-Golgi network. ManIA coexpression decreased total NKCC2 protein abundance whereas ManIA knock-down produced the opposite effect. Importantly, ManIA coexpression had a more profound effect on NKCC2 folding mutants. Cycloheximide chase assay showed that in cells overexpressing ManIA, NKCC2 stability and maturation are heavily hampered. Deleting the cytoplasmic region of ManIA attenuated its interaction with NKCC2 and inhibited its effect on the maturation of the cotransporter. ManIA-induced reductions in NKCC2 expression were offset by the proteasome inhibitor MG132. Likewise, kifunensine treatment greatly reduced ManIA effect, strongly suggesting that mannose trimming is involved in the enhanced ERAD of the cotransporter. Moreover, depriving ManIA of its catalytic domain fully abolished its effect on NKCC2. In summary, our data demonstrate the presence of a ManIA-mediated ERAD pathway in renal cells promoting retention and degradation of misfolded NKCC2 proteins. They suggest a model whereby Golgi ManIA contributes to ERAD of NKCC2, by promoting the retention, recycling, and ERAD of misfolded proteins that initially escape protein quality control surveillance within the ER.
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Affiliation(s)
- Sylvie Demaretz
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, F-75006 Paris, France; (S.D.); (E.S.); (D.B.-D.); (N.F.)
- CNRS, ERL8228, F-75006 Paris, France
| | - Elie Seaayfan
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, F-75006 Paris, France; (S.D.); (E.S.); (D.B.-D.); (N.F.)
- CNRS, ERL8228, F-75006 Paris, France
| | - Dalal Bakhos-Douaihy
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, F-75006 Paris, France; (S.D.); (E.S.); (D.B.-D.); (N.F.)
- CNRS, ERL8228, F-75006 Paris, France
| | - Nadia Frachon
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, F-75006 Paris, France; (S.D.); (E.S.); (D.B.-D.); (N.F.)
- CNRS, ERL8228, F-75006 Paris, France
| | - Martin Kömhoff
- Division of Pediatric Nephrology and Transplantation, University Children’s Hospital, Philipps-University, 35043 Marburg, Germany;
| | - Kamel Laghmani
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, F-75006 Paris, France; (S.D.); (E.S.); (D.B.-D.); (N.F.)
- CNRS, ERL8228, F-75006 Paris, France
- Correspondence:
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16
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Li H, Sun S. Protein Aggregation in the ER: Calm behind the Storm. Cells 2021; 10:cells10123337. [PMID: 34943844 PMCID: PMC8699410 DOI: 10.3390/cells10123337] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 02/06/2023] Open
Abstract
As one of the largest organelles in eukaryotic cells, the endoplasmic reticulum (ER) plays a vital role in the synthesis, folding, and assembly of secretory and membrane proteins. To maintain its homeostasis, the ER is equipped with an elaborate network of protein folding chaperones and multiple quality control pathways whose cooperative actions safeguard the fidelity of protein biogenesis. However, due to genetic abnormalities, the error-prone nature of protein folding and assembly, and/or defects or limited capacities of the protein quality control systems, nascent proteins may become misfolded and fail to exit the ER. If not cleared efficiently, the progressive accumulation of misfolded proteins within the ER may result in the formation of toxic protein aggregates, leading to the so-called “ER storage diseases”. In this review, we first summarize our current understanding of the protein folding and quality control networks in the ER, including chaperones, unfolded protein response (UPR), ER-associated protein degradation (ERAD), and ER-selective autophagy (ER-phagy). We then survey recent research progress on a few ER storage diseases, with a focus on the role of ER quality control in the disease etiology, followed by a discussion on outstanding questions and emerging concepts in the field.
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Affiliation(s)
- Haisen Li
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA;
| | - Shengyi Sun
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA;
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Correspondence:
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17
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Munteanu CVA, Chirițoiu GN, Chirițoiu M, Ghenea S, Petrescu AJ, Petrescu ȘM. Affinity proteomics and deglycoproteomics uncover novel EDEM2 endogenous substrates and an integrative ERAD network. Mol Cell Proteomics 2021; 20:100125. [PMID: 34332121 PMCID: PMC8455867 DOI: 10.1016/j.mcpro.2021.100125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 07/09/2021] [Accepted: 07/25/2021] [Indexed: 02/08/2023] Open
Abstract
Various pathologies result from disruptions to or stress of endoplasmic reticulum (ER) homeostasis, such as Parkinson's disease and most neurodegenerative illnesses, diabetes, pulmonary fibrosis, viral infections and cancers. A critical process in maintaining ER homeostasis is the selection of misfolded proteins by the ER quality-control system (ERQC) for destruction via ER-associated degradation (ERAD). One key protein proposed to act during the first steps of misfolded glycoprotein degradation is the ER degradation-enhancing α-mannosidase-like protein 2 (EDEM2). Therefore, characterization of the EDEM2 associated proteome is of great interest. We took advantage of using melanoma cells overexpressing EDEM2 as a cancer model system, to start documenting at the deglycoproteome level (N-glycosites identification) the emerging link between ER homeostasis and cancer progression. The dataset created for identifying the EDEM2 glyco-clients carrying high mannose/hybrid N-glycans provides a comprehensive N-glycosites analysis mapping over 1000 N-glycosites on more than 600 melanoma glycoproteins. To identify EDEM2-associated proteins we used affinity-proteomics and proteome-wide analysis of sucrose density fractionation in an integrative workflow. Using intensity and spectral count-based quantification, we identify seven new EDEM2 partners, all of which are involved in ERQC and ERAD. Moreover, we defined novel endogenous candidates for EDEM2-dependent ERAD by combining deglycoproteomics, SILAC-based proteomics, and biochemical methods. These included tumor antigens and several ER-transiting endogenous melanoma proteins, including ITGA1 and PCDH2, the expression of which was negatively correlated with that of EDEM2. Tumor antigens are key in the antigen presentation process, whilst ITGA1 and PCDH2 are involved in melanoma metastasis and invasion. EDEM2 could therefore have a regulatory role in melanoma through the modulation of these glycoproteins degradation and trafficking. The data presented herein suggest that EDEM2 is involved in ER homeostasis to a greater extent than previously suggested.
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Affiliation(s)
- Cristian V A Munteanu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry, Splaiul Independenței 296, 060031, Bucharest, Romania
| | - Gabriela N Chirițoiu
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independenței 296, 060031, Bucharest, Romania
| | - Marioara Chirițoiu
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independenței 296, 060031, Bucharest, Romania
| | - Simona Ghenea
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independenței 296, 060031, Bucharest, Romania
| | - Andrei-Jose Petrescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry, Splaiul Independenței 296, 060031, Bucharest, Romania
| | - Ștefana M Petrescu
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independenței 296, 060031, Bucharest, Romania.
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18
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Polla DL, Edmondson AC, Duvet S, March ME, Sousa AB, Lehman A, Niyazov D, van Dijk F, Demirdas S, van Slegtenhorst MA, Kievit AJA, Schulz C, Armstrong L, Bi X, Rader DJ, Izumi K, Zackai EH, de Franco E, Jorge P, Huffels SC, Hommersom M, Ellard S, Lefeber DJ, Santani A, Hand NJ, van Bokhoven H, He M, de Brouwer APM. Bi-allelic variants in the ER quality-control mannosidase gene EDEM3 cause a congenital disorder of glycosylation. Am J Hum Genet 2021; 108:1342-1349. [PMID: 34143952 PMCID: PMC8322938 DOI: 10.1016/j.ajhg.2021.05.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 05/19/2021] [Indexed: 01/10/2023] Open
Abstract
EDEM3 encodes a protein that converts Man8GlcNAc2 isomer B to Man7-5GlcNAc2. It is involved in the endoplasmic reticulum-associated degradation pathway, responsible for the recognition of misfolded proteins that will be targeted and translocated to the cytosol and degraded by the proteasome. In this study, through a combination of exome sequencing and gene matching, we have identified seven independent families with 11 individuals with bi-allelic protein-truncating variants and one individual with a compound heterozygous missense variant in EDEM3. The affected individuals present with an inherited congenital disorder of glycosylation (CDG) consisting of neurodevelopmental delay and variable facial dysmorphisms. Experiments in human fibroblast cell lines, human plasma, and mouse plasma and brain tissue demonstrated decreased trimming of Man8GlcNAc2 isomer B to Man7GlcNAc2, consistent with loss of EDEM3 enzymatic activity. In human cells, Man5GlcNAc2 to Man4GlcNAc2 conversion is also diminished with an increase of Glc1Man5GlcNAc2. Furthermore, analysis of the unfolded protein response showed a reduced increase in EIF2AK3 (PERK) expression upon stimulation with tunicamycin as compared to controls, suggesting an impaired unfolded protein response. The aberrant plasma N-glycan profile provides a quick, clinically available test for validating variants of uncertain significance that may be identified by molecular genetic testing. We propose to call this deficiency EDEM3-CDG.
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Affiliation(s)
- Daniel L Polla
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands; CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | - Andrew C Edmondson
- Department of Pediatrics, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sandrine Duvet
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Michael E March
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ana Berta Sousa
- Serviço de Genética Médica, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, 649-035 Lisboa, Portugal; Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Dmitriy Niyazov
- Tulane School of Medicine, University of Queensland, 1315 Jefferson Highway, New Orleans, LA 70121, USA
| | - Fleur van Dijk
- North West Thames Regional Genetics Service, London North West University Healthcare NHS Trust, Watford Road, Harrow, HA1 3UJ London, UK
| | - Serwet Demirdas
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 Rotterdam, the Netherlands
| | | | - Anneke J A Kievit
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 Rotterdam, the Netherlands
| | - Celine Schulz
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Linlea Armstrong
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Xin Bi
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel J Rader
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kosuke Izumi
- Department of Pediatrics, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Elaine H Zackai
- Department of Pediatrics, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Elisa de Franco
- Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, EX2 5DW Exeter, UK
| | - Paula Jorge
- Centro de Genética Médica Jacinto de Magalhães, Centro Hospitalar do Porto, CHP, E.P.E., 4099-028 Porto, Portugal; Unit for Multidisciplinary Research in Biomedicine, Abel Salazar Institute of Biomedical Sciences, University of Porto, 4099-028 Porto, Portugal
| | - Sophie C Huffels
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Marina Hommersom
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Sian Ellard
- Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, EX2 5DW Exeter, UK; College of Medicine and Health, University of Exeter, Barrack Road, EX2 5DW Exeter, UK
| | - Dirk J Lefeber
- Department of Neurology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Avni Santani
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicholas J Hand
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hans van Bokhoven
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Miao He
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Arjan P M de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands.
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Ninagawa S. N-glycan Dependent Protein Quality Control System in the Endoplasmic Reticulum. TRENDS GLYCOSCI GLYC 2021. [DOI: 10.4052/tigg.2108.2e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Satoshi Ninagawa
- Department of Biophysics, Graduate School of Science, Kyoto University
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20
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Ninagawa S. N-glycan Dependent Protein Quality Control System in the Endoplasmic Reticulum. TRENDS GLYCOSCI GLYC 2021. [DOI: 10.4052/tigg.2108.2j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Satoshi Ninagawa
- Department of Biophysics, Graduate School of Science, Kyoto University
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21
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Nitta K, Kuribara T, Totani K. Synthetic trisaccharides reveal discrimination of endo-glycosidic linkages by exo-acting α-1,2-mannosidases in the endoplasmic reticulum. Org Biomol Chem 2021; 19:4137-4145. [PMID: 33876795 DOI: 10.1039/d1ob00428j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A tri-antennary Man9GlcNAc2 glycan on the surface of endoplasmic reticulum (ER) glycoproteins functions as a glycoprotein secretion or degradation signal after regioselective cleavage of the terminal α-1,2-mannose residue of each branch. Four α-1,2-mannosidases-ER mannosidase I, ER degradation-enhancing α-mannosidase-like protein 1 (EDEM1), EDEM2, and EDEM3-are involved in the production of these signal glycans. Although selective production of signal glycans is important in determining the fate of glycoproteins, the branch-discrimination abilities of the α-1,2-mannosidases are not well understood. A structural feature of the Man9GlcNAc2 glycan is that all terminal glycosidic linkages of the three branches are of the α-1,2 type, while the adjacent inner glycosidic linkages are different. In this study, we examined whether the α-1,2-mannosidases showed branch specificity by discriminating between different inner glycosides. Four trisaccharides with different glycosidic linkages [Manα1-2Manα1-2Man (natural A-branch), Manα1-2Manα1-3Man (natural B-branch), Manα1-2Manα1-6Man (natural C-branch), and Manα1-2Manα1-4Man (unnatural D-branch)] were synthesized and used to evaluate the hypothesis. When synthesizing these oligosaccharides, highly stereoselective glycosylation was achieved with a high yield in each case by adding a weak base or tuning the polarity of the mixed solvent. Enzymatic hydrolysis of the synthetic trisaccharides by a mouse liver ER fraction containing the target enzymes showed that the ER α-1,2-mannosidases had clear specificity for the trisaccharides in the order of A-branch > B-branch > C-branch ≈ D-branch. Various competitive experiments have revealed for the first time that α-1,2-mannosidase with inner glycoside specificity is present in the ER. Our findings suggest that exo-acting ER α-1,2-mannosidases can discriminate between endo-glycosidic linkages.
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Affiliation(s)
- Kyohei Nitta
- Department of Materials and Life Science, Seikei University, Musashino-shi, Tokyo, 180-8633, Japan.
| | - Taiki Kuribara
- Department of Materials and Life Science, Seikei University, Musashino-shi, Tokyo, 180-8633, Japan.
| | - Kiichiro Totani
- Department of Materials and Life Science, Seikei University, Musashino-shi, Tokyo, 180-8633, Japan.
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22
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Zhang J, Zheng B, Zhou X, Zheng T, Wang H, Wang Y, Zhang W. Increased BST-2 expression by HBV infection promotes HBV-associated HCC tumorigenesis. J Gastrointest Oncol 2021; 12:694-710. [PMID: 34012659 DOI: 10.21037/jgo-20-356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background The majority of hepatocellular carcinoma (HCC) is closely associated with hepatitis B virus (HBV) infection, while the mechanism of HCC induced by HBV is debatable. Bone marrow stromal cell antigen 2 (BST-2), an N-glycoprotein, has been characterized as an oncogenic factor in several types of cancer. However, whether BST-2 plays an important role in HCC tumorigenesis remains unknown. Methods A total of 182 HCC tumorous and adjacent nontumor liver tissues were collected. HepG2, Huh7, L02, HepAD38, and HEK293T cell lines were adopted in this study. Tumor proliferation was detected by CCK8, transwell, wound healing, colony formation assays in vitro, and in vivo tumorigenesis was measured by mouse xenografts. NF-κB activation was determined by luciferase assay and Western blot. Protein expression was detected by Western blot, ELISA, or qPCR. Immunoprecipitation was used to confirm the interaction between BST-2 and Syk. Results Here, we observed the higher BST-2 expression in HBV-infected HCC than their paired adjacent tissues and HBV-uninfected HCC tissues, particularly more aberrant non-N-glycosylated BST-2 in HBV-infected HCC tumors. We also observed the increased ER degradation-enhancing α-mannosidase-like protein 3 (EDEM3), which is trimming of N-linked glycans by sequential removal of mannose residues, might result in more non-N-glycosylated form of BST-2. Moreover, we demonstrated that BST-2 and non-N-glycosylated BST-2 N65/92A mutant, not only enhanced the tumor characteristics of hepatoma cell lines in vitro, but also enhanced the growth of mouse xenografts in vivo. Mechanically, N65/92A mutant has stronger ability to promote HCC than BST-2 via NF-κB/ERK1/2 but not NF-κB/anti-apoptotic factors pathway. NF-κB inhibitor attenuated BST-2-mediated tumorigenesis of HCC. Conclusions Our findings illuminate the novel function of BST-2 as an oncogene of HBV-associated HCC, and highlight the novel relationship of N-glycosylation of BST-2 in regulating HCC tumorigenesis in vitro.
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Affiliation(s)
- Jun Zhang
- Institute of Virology and AIDS Research, the First Hospital of Jilin University, Changchun, China
| | - Baisong Zheng
- Institute of Virology and AIDS Research, the First Hospital of Jilin University, Changchun, China
| | - Xiaolei Zhou
- Institute of Virology and AIDS Research, the First Hospital of Jilin University, Changchun, China
| | - Tianhang Zheng
- Institute of Virology and AIDS Research, the First Hospital of Jilin University, Changchun, China
| | - Hong Wang
- Institute of Virology and AIDS Research, the First Hospital of Jilin University, Changchun, China
| | - Yingchao Wang
- Hepatobiliary Pancreatic Surgery, the First Hospital of Jilin University, Changchun, China
| | - Wenyan Zhang
- Institute of Virology and AIDS Research, the First Hospital of Jilin University, Changchun, China
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23
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In Vitro Mannosidase Assay of EDEMs: ER Degradation-Enhancing α-Mannosidase-Like Proteins. Methods Mol Biol 2021. [PMID: 32306323 DOI: 10.1007/978-1-0716-0430-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Quality control of newly synthesized glycoproteins is tightly regulated by sugar processing of N-glycans and by recognition of specific glycan structures by lectins in the endoplasmic reticulum (ER). Mannose trimming and its recognition determine the targeting of misfolded glycoproteins for ER-associated degradation. ER degradation-enhancing α-mannosidase-like (EDEM) proteins in mammals and their homologue Htm1p/Mnl1p in Saccharomyces cerevisiae are involved in this process. To analyze the function of EDEM proteins, we expressed and purified recombinant EDEM3 from HEK293 cells and assessed its mannose-trimming activity in vitro.
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24
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Kuribara T, Usui R, Totani K. Glycan structure-based perspectives on the entry and release of glycoproteins in the calnexin/calreticulin cycle. Carbohydr Res 2021; 502:108273. [PMID: 33713911 DOI: 10.1016/j.carres.2021.108273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/16/2021] [Accepted: 02/23/2021] [Indexed: 12/16/2022]
Abstract
N-glycans are attached to newly synthesised polypeptides and are involved in the folding, secretion, and degradation of N-linked glycoproteins. In particular, the calnexin/calreticulin cycle, which is the central mechanism of the entry and release of N-linked glycoproteins depending on the folding sates, has been well studied. In addition to biological studies on the calnexin/calreticulin cycle, several studies have revealed complementary roles of in vitro chemistry-based research in the structure-based understanding of the cycle. In this mini-review, we summarise chemistry-based results and highlight their importance for further understanding of the cycle.
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Affiliation(s)
- Taiki Kuribara
- Department of Materials and Life Science, Faculty of Science and Technology, Seikei University, 3-3-1 Kichijoji-kitamachiMusashino-shi, Tokyo, 180-8633, Japan
| | - Ruchio Usui
- Department of Materials and Life Science, Faculty of Science and Technology, Seikei University, 3-3-1 Kichijoji-kitamachiMusashino-shi, Tokyo, 180-8633, Japan
| | - Kiichiro Totani
- Department of Materials and Life Science, Faculty of Science and Technology, Seikei University, 3-3-1 Kichijoji-kitamachiMusashino-shi, Tokyo, 180-8633, Japan.
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25
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Manica G, Ghenea S, Munteanu CVA, Martin EC, Butnaru C, Surleac M, Chiritoiu GN, Alexandru PR, Petrescu AJ, Petrescu SM. EDEM3 Domains Cooperate to Perform Its Overall Cell Functioning. Int J Mol Sci 2021; 22:2172. [PMID: 33671632 PMCID: PMC7926307 DOI: 10.3390/ijms22042172] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/15/2021] [Accepted: 02/19/2021] [Indexed: 01/20/2023] Open
Abstract
EDEM3 recognizes and directs misfolded proteins to the ER-associated protein degradation (ERAD) process. EDEM3 was predicted to act as lectin or as a mannosidase because of its homology with the GH47 catalytic domain of the Man1B1, but the contribution of the other regions remained unresolved. Here, we dissect the molecular determinants governing EDEM3 function and its cellular interactions. LC/MS analysis indicates very few stable ER interactors, suggesting EDEM3 availability for transient substrate interactions. Sequence analysis reveals that EDEM3 consists of four consecutive modules defined as GH47, intermediate (IMD), protease-associated (PA), and intrinsically disordered (IDD) domain. Using an EDEM3 knock-out cell line, we expressed EDEM3 and domain deletion mutants to address EDEM3 function. We find that the mannosidase domain provides substrate binding even in the absence of mannose trimming and requires the IMD domain for folding. The PA and IDD domains deletions do not impair the trimming, but specifically modulate the turnover of two misfolded proteins, NHK and the soluble tyrosinase mutant. Hence, we demonstrate that EDEM3 provides a unique ERAD timing to misfolded glycoproteins, not only by its mannose trimming activity, but also by the positive and negative feedback modulated by the protease-associated and intrinsically disordered domain, respectively.
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Affiliation(s)
- Georgiana Manica
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (G.M.); (S.G.); (G.N.C.); (P.R.A.)
| | - Simona Ghenea
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (G.M.); (S.G.); (G.N.C.); (P.R.A.)
| | - Cristian V. A. Munteanu
- Department of Bioinformatics and Structural Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (C.V.A.M.); (E.C.M.); (C.B.); (M.S.); (A.-J.P.)
| | - Eliza C. Martin
- Department of Bioinformatics and Structural Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (C.V.A.M.); (E.C.M.); (C.B.); (M.S.); (A.-J.P.)
| | - Cristian Butnaru
- Department of Bioinformatics and Structural Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (C.V.A.M.); (E.C.M.); (C.B.); (M.S.); (A.-J.P.)
| | - Marius Surleac
- Department of Bioinformatics and Structural Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (C.V.A.M.); (E.C.M.); (C.B.); (M.S.); (A.-J.P.)
- Research Institute of the University of Bucharest, 030018 Bucharest 17, Romania
| | - Gabriela N. Chiritoiu
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (G.M.); (S.G.); (G.N.C.); (P.R.A.)
| | - Petruta R. Alexandru
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (G.M.); (S.G.); (G.N.C.); (P.R.A.)
| | - Andrei-Jose Petrescu
- Department of Bioinformatics and Structural Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (C.V.A.M.); (E.C.M.); (C.B.); (M.S.); (A.-J.P.)
| | - Stefana M. Petrescu
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (G.M.); (S.G.); (G.N.C.); (P.R.A.)
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26
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Kang JA, Jeon YJ. How Is the Fidelity of Proteins Ensured in Terms of Both Quality and Quantity at the Endoplasmic Reticulum? Mechanistic Insights into E3 Ubiquitin Ligases. Int J Mol Sci 2021; 22:ijms22042078. [PMID: 33669844 PMCID: PMC7923238 DOI: 10.3390/ijms22042078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/16/2021] [Accepted: 02/16/2021] [Indexed: 02/06/2023] Open
Abstract
The endoplasmic reticulum (ER) is an interconnected organelle that plays fundamental roles in the biosynthesis, folding, stabilization, maturation, and trafficking of secretory and transmembrane proteins. It is the largest organelle and critically modulates nearly all aspects of life. Therefore, in the endoplasmic reticulum, an enormous investment of resources, including chaperones and protein folding facilitators, is dedicated to adequate protein maturation and delivery to final destinations. Unfortunately, the folding and assembly of proteins can be quite error-prone, which leads to the generation of misfolded proteins. Notably, protein homeostasis, referred to as proteostasis, is constantly exposed to danger by flows of misfolded proteins and subsequent protein aggregates. To maintain proteostasis, the ER triages and eliminates terminally misfolded proteins by delivering substrates to the ubiquitin–proteasome system (UPS) or to the lysosome, which is termed ER-associated degradation (ERAD) or ER-phagy, respectively. ERAD not only eliminates misfolded or unassembled proteins via protein quality control but also fine-tunes correctly folded proteins via protein quantity control. Intriguingly, the diversity and distinctive nature of E3 ubiquitin ligases determine efficiency, complexity, and specificity of ubiquitination during ERAD. ER-phagy utilizes the core autophagy machinery and eliminates ERAD-resistant misfolded proteins. Here, we conceptually outline not only ubiquitination machinery but also catalytic mechanisms of E3 ubiquitin ligases. Further, we discuss the mechanistic insights into E3 ubiquitin ligases involved in the two guardian pathways in the ER, ERAD and ER-phagy. Finally, we provide the molecular mechanisms by which ERAD and ER-phagy conduct not only protein quality control but also protein quantity control to ensure proteostasis and subsequent organismal homeostasis.
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Affiliation(s)
- Ji An Kang
- Department of Biochemistry, College of Medicine, Chungnam National University, Daejeon 35015, Korea;
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea
| | - Young Joo Jeon
- Department of Biochemistry, College of Medicine, Chungnam National University, Daejeon 35015, Korea;
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea
- Correspondence:
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Hattori T, Hanafusa K, Wada I, Hosokawa N. SEL1L degradation intermediates stimulate cytosolic aggregation of polyglutamine-expanded protein. FEBS J 2021; 288:4637-4654. [PMID: 33576152 DOI: 10.1111/febs.15761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/21/2021] [Accepted: 02/05/2021] [Indexed: 12/01/2022]
Abstract
Misfolded proteins in the endoplasmic reticulum (ER) are degraded by ER-associated degradation (ERAD). In mammalian cells, the HRD1-SEL1L membrane ubiquitin ligase complex plays a central role in this process. However, SEL1L is inherently unstable, and excess SEL1L is also degraded by ERAD. Accordingly, when proteasome activity is inhibited, multiple degradation intermediates of SEL1L appear in the cytosol. In this study, we searched for factors that inhibit SEL1L degradation and identified OS-9 and XTP3-B, two ER lectins that regulate glycoprotein ERAD. SEL1L degradation was characterized by a ladder of degradation products, and the C-terminal Pro-rich region of SEL1L was responsible for generation of this pattern. In the cytosol, these degradation intermediates stimulated aggregation of polyglutamine-expanded Huntingtin protein (Htt-polyQ-GFP) by interacting with aggregation-prone proteins, including Htt-polyQ-GFP. Collectively, our findings indicate that peptide fragments of ER proteins generated during ERAD may affect protein aggregation in the cytosol, revealing the interconnection of protein homeostasis across subcellular compartments.
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Affiliation(s)
- Tokuya Hattori
- Department of Molecular and Cellular Biology, Institute for Frontier Medical Sciences, Kyoto University, Japan
| | - Ken Hanafusa
- Department of Molecular and Cellular Biology, Institute for Frontier Medical Sciences, Kyoto University, Japan
| | - Ikuo Wada
- Department of Cell Science, Institute of Biomedical Sciences, Fukushima Medical University School of Medicine, Japan
| | - Nobuko Hosokawa
- Department of Molecular and Cellular Biology, Institute for Frontier Medical Sciences, Kyoto University, Japan
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28
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Kato M, Abdollahi M, Tunduguru R, Tsark W, Chen Z, Wu X, Wang J, Chen ZB, Lin FM, Lanting L, Wang M, Huss J, Fueger PT, Chan D, Natarajan R. miR-379 deletion ameliorates features of diabetic kidney disease by enhancing adaptive mitophagy via FIS1. Commun Biol 2021; 4:30. [PMID: 33398021 PMCID: PMC7782535 DOI: 10.1038/s42003-020-01516-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 11/23/2020] [Indexed: 01/29/2023] Open
Abstract
Diabetic kidney disease (DKD) is a major complication of diabetes. Expression of members of the microRNA (miRNA) miR-379 cluster is increased in DKD. miR-379, the most upstream 5'-miRNA in the cluster, functions in endoplasmic reticulum (ER) stress by targeting EDEM3. However, the in vivo functions of miR-379 remain unclear. We created miR-379 knockout (KO) mice using CRISPR-Cas9 nickase and dual guide RNA technique and characterized their phenotype in diabetes. We screened for miR-379 targets in renal mesangial cells from WT vs. miR-379KO mice using AGO2-immunopreciptation and CLASH (cross-linking, ligation, sequencing hybrids) and identified the redox protein thioredoxin and mitochondrial fission-1 protein. miR-379KO mice were protected from features of DKD as well as body weight loss associated with mitochondrial dysfunction, ER- and oxidative stress. These results reveal a role for miR-379 in DKD and metabolic processes via reducing adaptive mitophagy. Strategies targeting miR-379 could offer therapeutic options for DKD.
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Affiliation(s)
- Mitsuo Kato
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA.
| | - Maryam Abdollahi
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Ragadeepthi Tunduguru
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Walter Tsark
- Transgenic Mouse Facility, Center for Comparative Medicine, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Zhuo Chen
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Xiwei Wu
- Integrative Genomics Core, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Jinhui Wang
- Integrative Genomics Core, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Feng-Mao Lin
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Linda Lanting
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Mei Wang
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Janice Huss
- Department of Cellular and Molecular Endocrinology, Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Patrick T Fueger
- Department of Cellular and Molecular Endocrinology, Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
- Comprehensive Metabolic Phenotyping Core, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - David Chan
- Division of Biology and Biological Engineering, Caltech, 1200 East California Boulevard, Pasadena, CA, 91125, USA
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA.
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA.
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Abstract
Folding of proteins is essential so that they can exert their functions. For proteins that transit the secretory pathway, folding occurs in the endoplasmic reticulum (ER) and various chaperone systems assist in acquiring their correct folding/subunit formation. N-glycosylation is one of the most conserved posttranslational modification for proteins, and in eukaryotes it occurs in the ER. Consequently, eukaryotic cells have developed various systems that utilize N-glycans to dictate and assist protein folding, or if they consistently fail to fold properly, to destroy proteins for quality control and the maintenance of homeostasis of proteins in the ER.
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Abstract
N-glycosylation is a highly conserved glycan modification, and more than 7000 proteins are N-glycosylated in humans. N-glycosylation has many biological functions such as protein folding, trafficking, and signal transduction. Thus, glycan modification to proteins is profoundly involved in numerous physiological and pathological processes. The N-glycan precursor is biosynthesized in the endoplasmic reticulum (ER) from dolichol phosphate by sequential enzymatic reactions to generate the dolichol-linked oligosaccharide composed of 14 sugar residues, Glc3Man9GlcNAc2. The oligosaccharide is then en bloc transferred to the consensus sequence N-X-S/T (X represents any amino acid except proline) of nascent proteins. Subsequently, the N-glycosylated nascent proteins enter the folding step, in which N-glycans contribute largely to attaining the correct protein fold by recruiting the lectin-like chaperones, calnexin, and calreticulin. Despite the N-glycan-dependent folding process, some glycoproteins do not fold correctly, and these misfolded glycoproteins are destined to degradation by proteasomes in the cytosol. Properly folded proteins are transported to the Golgi, and N-glycans undergo maturation by the sequential reactions of glycosidases and glycosyltransferases, generating complex-type N-glycans. N-Acetylglucosaminyltransferases (GnT-III, GnT-IV, and GnT-V) produce branched N-glycan structures, affording a higher complexity to N-glycans. In this chapter, we provide an overview of the biosynthetic pathway of N-glycans in the ER and Golgi.
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31
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Ninagawa S, George G, Mori K. Mechanisms of productive folding and endoplasmic reticulum-associated degradation of glycoproteins and non-glycoproteins. Biochim Biophys Acta Gen Subj 2020; 1865:129812. [PMID: 33316349 DOI: 10.1016/j.bbagen.2020.129812] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND The quality of proteins destined for the secretory pathway is ensured by two distinct mechanisms in the endoplasmic reticulum (ER): productive folding of newly synthesized proteins, which is assisted by ER-localized molecular chaperones and in most cases also by disulfide bond formation and transfer of an oligosaccharide unit; and ER-associated degradation (ERAD), in which proteins unfolded or misfolded in the ER are recognized and processed for delivery to the ER membrane complex, retrotranslocated through the complex with simultaneous ubiquitination, extracted by AAA-ATPase to the cytosol, and finally degraded by the proteasome. SCOPE OF REVIEW We describe the mechanisms of productive folding and ERAD, with particular attention to glycoproteins versus non-glycoproteins, and to yeast versus mammalian systems. MAJOR CONCLUSION Molecular mechanisms of the productive folding of glycoproteins and non-glycoproteins mediated by molecular chaperones and protein disulfide isomerases are well conserved from yeast to mammals. Additionally, mammals have gained an oligosaccharide structure-dependent folding cycle for glycoproteins. The molecular mechanisms of ERAD are also well conserved from yeast to mammals, but redundant expression of yeast orthologues in mammals has been encountered, particularly for components involved in recognition and processing of glycoproteins and components of the ER membrane complex involved in retrotranslocation and simultaneous ubiquitination of glycoproteins and non-glycoproteins. This may reflect an evolutionary consequence of increasing quantity or quality needs toward mammals. GENERAL SIGNIFICANCE The introduction of innovative genome editing technology into analysis of the mechanisms of mammalian ERAD, as exemplified here, will provide new insights into the pathogenesis of various diseases.
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Affiliation(s)
- Satoshi Ninagawa
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
| | - Ginto George
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Kazutoshi Mori
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
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Wright MT, Kouba L, Plate L. Thyroglobulin Interactome Profiling Defines Altered Proteostasis Topology Associated With Thyroid Dyshormonogenesis. Mol Cell Proteomics 2020; 20:100008. [PMID: 33581410 PMCID: PMC7950113 DOI: 10.1074/mcp.ra120.002168] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 10/15/2020] [Accepted: 11/18/2020] [Indexed: 12/02/2022] Open
Abstract
Thyroglobulin (Tg) is a secreted iodoglycoprotein serving as the precursor for triiodothyronine and thyroxine hormones. Many characterized Tg gene mutations produce secretion-defective variants resulting in congenital hypothyroidism. Tg processing and secretion is controlled by extensive interactions with chaperone, trafficking, and degradation factors comprising the secretory proteostasis network. While dependencies on individual proteostasis network components are known, the integration of proteostasis pathways mediating Tg protein quality control and the molecular basis of mutant Tg misprocessing remain poorly understood. We employ a multiplexed quantitative affinity purification-mass spectrometry approach to define the Tg proteostasis interactome and changes between WT and several congenital hypothyroidism variants. Mutant Tg processing is associated with common imbalances in proteostasis engagement including increased chaperoning, oxidative folding, and engagement by targeting factors for endoplasmic reticulum-associated degradation. Furthermore, we reveal mutation-specific changes in engagement with N-glycosylation components, suggesting distinct requirements for 1 Tg variant on dual engagement of both oligosaccharyltransferase complex isoforms for degradation. Modulating dysregulated proteostasis components and pathways may serve as a therapeutic strategy to restore Tg secretion and thyroid hormone biosynthesis.
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Affiliation(s)
- Madison T Wright
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Logan Kouba
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Lars Plate
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA; Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA.
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Molecular adaptation to calsequestrin 2 (CASQ2) point mutations leading to catecholaminergic polymorphic ventricular tachycardia (CPVT): comparative analysis of R33Q and D307H mutants. J Muscle Res Cell Motil 2020; 41:251-258. [PMID: 32902830 PMCID: PMC7666291 DOI: 10.1007/s10974-020-09587-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 08/29/2020] [Indexed: 12/16/2022]
Abstract
Homozygous calsequestrin 2 (CASQ2) point mutations leads to catecholaminergic polymorphic ventricular tachycardia: a common pathogenetic feature appears to be the drastic reduction of mutant CASQ2 in spite of normal transcription. Comparative biochemical analysis of R33Q and D307H knock in mutant mice identifies different pathogenetic mechanisms for CASQ2 degradation and different molecular adaptive mechanisms. In particular, each CASQ2 point mutation evokes specific adaptive cellular and molecular processes in each of the four adaptive pathways investigated. Thus, similar clinical phenotypes and identical cellular mechanism for cardiac arrhythmia might imply different molecular adaptive mechanisms.
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Qin X, Denton WD, Huiting LN, Smith KS, Feng H. Unraveling the regulatory role of endoplasmic-reticulum-associated degradation in tumor immunity. Crit Rev Biochem Mol Biol 2020; 55:322-353. [PMID: 32633575 DOI: 10.1080/10409238.2020.1784085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
During malignant transformation and cancer progression, tumor cells face both intrinsic and extrinsic stress, endoplasmic reticulum (ER) stress in particular. To survive and proliferate, tumor cells use multiple stress response pathways to mitigate ER stress, promoting disease aggression and treatment resistance. Among the stress response pathways is ER-associated degradation (ERAD), which consists of multiple components and steps working together to ensure protein quality and quantity. In addition to its established role in stress responses and tumor cell survival, ERAD has recently been shown to regulate tumor immunity. Here we summarize current knowledge on how ERAD promotes protein degradation, regulates immune cell development and function, participates in antigen presentation, exerts paradoxical roles on tumorigenesis and immunity, and thus impacts current cancer therapy. Collectively, ERAD is a critical protein homeostasis pathway intertwined with cancer development and tumor immunity. Of particular importance is the need to further unveil ERAD's enigmatic roles in tumor immunity to develop effective targeted and combination therapy for successful treatment of cancer.
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Affiliation(s)
- Xiaodan Qin
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, Center for Cancer Research, Boston University School of Medicine, Boston, MA, USA
| | - William D Denton
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, Center for Cancer Research, Boston University School of Medicine, Boston, MA, USA
| | - Leah N Huiting
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, Center for Cancer Research, Boston University School of Medicine, Boston, MA, USA
| | - Kaylee S Smith
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, Center for Cancer Research, Boston University School of Medicine, Boston, MA, USA
| | - Hui Feng
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, Center for Cancer Research, Boston University School of Medicine, Boston, MA, USA
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Hepatocyte-specific deletion of peroxisomal protein PEX13 results in disrupted iron homeostasis. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165882. [PMID: 32565019 DOI: 10.1016/j.bbadis.2020.165882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 05/11/2020] [Accepted: 06/16/2020] [Indexed: 12/31/2022]
Abstract
Peroxisomes are organelles, abundant in the liver, involved in a variety of cellular functions, including fatty acid metabolism, plasmalogen synthesis and metabolism of reactive oxygen species. Several inherited disorders are associated with peroxisomal dysfunction; increasingly many are associated with hepatic pathologies. The liver plays a principal role in regulation of iron metabolism. In this study we examined the possibility of a relationship between iron homeostasis and peroxisomal integrity. We examined the effect of deleting Pex13 in mouse liver on systemic iron homeostasis. We also used siRNA-mediated knock-down of PEX13 in a human hepatoma cell line (HepG2/C3A) to elucidate the mechanisms of PEX13-mediated regulation of hepcidin. We demonstrate that transgenic mice lacking hepatocyte Pex13 have defects in systemic iron homeostasis. The ablation of Pex13 expression in hepatocytes leads to a significant reduction in hepatic hepcidin levels. Our results also demonstrate that a deficiency of PEX13 gene expression in HepG2/C3A cells leads to decreased hepcidin expression, which is mediated through an increase in the signalling protein SMAD7, and endoplasmic reticulum (ER) stress. This study identifies a novel role for a protein involved in maintaining peroxisomal integrity and function in iron homeostasis. Loss of Pex13, a protein important for peroxisomal function, in hepatocytes leads to a significant increase in ER stress, which if unresolved, can affect liver function. The results from this study have implications for the management of patients with peroxisomal disorders and the liver-related complications they may develop.
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Xu YX, Peloso GM, Nagai TH, Mizoguchi T, Deik A, Bullock K, Lin H, Musunuru K, Yang Q, Vasan RS, Gerszten RE, Clish CB, Rader D, Kathiresan S. EDEM3 Modulates Plasma Triglyceride Level through Its Regulation of LRP1 Expression. iScience 2020; 23:100973. [PMID: 32213464 PMCID: PMC7093811 DOI: 10.1016/j.isci.2020.100973] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/06/2019] [Accepted: 03/05/2020] [Indexed: 01/10/2023] Open
Abstract
Human genetics studies have uncovered genetic variants that can be used to guide biological research and prioritize molecular targets for therapeutic intervention for complex diseases. We have identified a missense variant (P746S) in EDEM3 associated with lower blood triglyceride (TG) levels in >300,000 individuals. Functional analyses in cell and mouse models show that EDEM3 deficiency strongly increased the uptake of very-low-density lipoprotein and thereby reduced the plasma TG level, as a result of up-regulated expression of LRP1 receptor. We demonstrate that EDEM3 deletion up-regulated the pathways for RNA and endoplasmic reticulum protein processing and transport, and consequently increased the cell surface mannose-containing glycoproteins, including LRP1. Metabolomics analyses reveal a cellular TG accumulation under EDEM3 deficiency, a profile consistent with individuals carrying EDEM3 P746S. Our study identifies EDEM3 as a regulator of blood TG, and targeted inhibition of EDEM3 may provide a complementary approach for lowering elevated blood TG concentrations.
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Affiliation(s)
- Yu-Xin Xu
- Center for Genomic Medicine, Massachusetts General Hospital, Simches 5.500, 185 Cambridge St., Boston, MA 02114, USA.
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Taylor H Nagai
- Center for Genomic Medicine, Massachusetts General Hospital, Simches 5.500, 185 Cambridge St., Boston, MA 02114, USA
| | - Taiji Mizoguchi
- Center for Genomic Medicine, Massachusetts General Hospital, Simches 5.500, 185 Cambridge St., Boston, MA 02114, USA
| | - Amy Deik
- The Metabolomics Program, Broad Institute, Cambridge, MA 02142, USA
| | - Kevin Bullock
- The Metabolomics Program, Broad Institute, Cambridge, MA 02142, USA
| | - Honghuang Lin
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Kiran Musunuru
- Cardiovascular Institute, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Ramachandran S Vasan
- Preventive Medicine and Epidemiology, Boston University School of Medicine, Boston, MA 02118, USA; Framingham Heart Study of the NHLBI and Boston University School of Medicine, Framingham, MA 01702, USA
| | - Robert E Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Clary B Clish
- The Metabolomics Program, Broad Institute, Cambridge, MA 02142, USA
| | - Daniel Rader
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sekar Kathiresan
- Center for Genomic Medicine, Massachusetts General Hospital, Simches 5.500, 185 Cambridge St., Boston, MA 02114, USA.
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Zhang J, Wu J, Liu L, Li J. The Crucial Role of Demannosylating Asparagine-Linked Glycans in ERADicating Misfolded Glycoproteins in the Endoplasmic Reticulum. FRONTIERS IN PLANT SCIENCE 2020; 11:625033. [PMID: 33510762 PMCID: PMC7835635 DOI: 10.3389/fpls.2020.625033] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/08/2020] [Indexed: 05/04/2023]
Abstract
Most membrane and secreted proteins are glycosylated on certain asparagine (N) residues in the endoplasmic reticulum (ER), which is crucial for their correct folding and function. Protein folding is a fundamentally inefficient and error-prone process that can be easily interfered by genetic mutations, stochastic cellular events, and environmental stresses. Because misfolded proteins not only lead to functional deficiency but also produce gain-of-function cellular toxicity, eukaryotic organisms have evolved highly conserved ER-mediated protein quality control (ERQC) mechanisms to monitor protein folding, retain and repair incompletely folded or misfolded proteins, or remove terminally misfolded proteins via a unique ER-associated degradation (ERAD) mechanism. A crucial event that terminates futile refolding attempts of a misfolded glycoprotein and diverts it into the ERAD pathway is executed by removal of certain terminal α1,2-mannose (Man) residues of their N-glycans. Earlier studies were centered around an ER-type α1,2-mannosidase that specifically cleaves the terminal α1,2Man residue from the B-branch of the three-branched N-linked Man9GlcNAc2 (GlcNAc for N-acetylglucosamine) glycan, but recent investigations revealed that the signal that marks a terminally misfolded glycoprotein for ERAD is an N-glycan with an exposed α1,6Man residue generated by members of a unique folding-sensitive α1,2-mannosidase family known as ER-degradation enhancing α-mannosidase-like proteins (EDEMs). This review provides a historical recount of major discoveries that led to our current understanding on the role of demannosylating N-glycans in sentencing irreparable misfolded glycoproteins into ERAD. It also discusses conserved and distinct features of the demannosylation processes of the ERAD systems of yeast, mammals, and plants.
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Affiliation(s)
- Jianjun Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Jiarui Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Linchuan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Jianming Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
- *Correspondence: Jianming Li, ;
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Fu Z, Agudelo P, Wells CE. Detoxification-related gene expression accompanies anhydrobiosis in the foliar nematode ( Aphelenchoides fragariae). J Nematol 2020; 52:1-12. [PMID: 32449331 PMCID: PMC7266049 DOI: 10.21307/jofnem-2020-047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Indexed: 12/19/2022] Open
Abstract
The foliar nematode (Aphelenchoides fragariae) is a quarantined pest that infects a broad range of herbaceous and woody plants. Previous work has demonstrated its remarkable ability to survive rapid and extreme desiccation, although the specific molecular mechanisms underlying its anhydrobiotic response have not been characterized. The authors used RNA sequencing and de novo transcriptome assembly to compare patterns of gene expression between hydrated and 24-hr desiccated nematodes. In total, 2,083 and 953 genes were significantly up- and downregulated, respectively, in desiccated nematodes. Of the 100 annotated genes with the largest positive fold-changes, more than one third encoded putative detoxification-related proteins. Genes encoding enzymes of Phase I and Phase II detoxification systems were among the most strongly upregulated in the transcriptome, including 35 cytochrome p450s, 23 short chain dehydrogenase/reductases, 5 glutathione-S-transferases, and 22 UDP-glucuronosyltransferases. Genes encoding heat shock proteins, unfolded protein response enzymes, and intrinsically disordered proteins were also upregulated. Anhydrobiosis in A. fragariae appears to involve both strategies to minimize protein misfolding and aggregation, and wholesale induction of the cellular detoxification machinery. These processes may be controlled in part through the activity of forkhead transcription factors similar to Caenorhabditis elegans’ daf-16, a number of which were differentially expressed under desiccation.
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Affiliation(s)
- Zhen Fu
- School of Agricultural, Forest, and Environmental Sciences , Clemson University , Clemson, SC, 29634 ; Department of Entomology , Washington State University , Pullman, WA, 99164
| | - Paula Agudelo
- School of Agricultural, Forest, and Environmental Sciences , Clemson University , Clemson, SC, 29634
| | - Christina E Wells
- Department of Biological Sciences , Clemson University , Clemson, SC, 29634
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Lefterov I, Wolfe CM, Fitz NF, Nam KN, Letronne F, Biedrzycki RJ, Kofler J, Han X, Wang J, Schug J, Koldamova R. APOE2 orchestrated differences in transcriptomic and lipidomic profiles of postmortem AD brain. Alzheimers Res Ther 2019; 11:113. [PMID: 31888770 PMCID: PMC6937981 DOI: 10.1186/s13195-019-0558-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/19/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND The application of advanced sequencing technologies and improved mass-spectrometry platforms revealed significant changes in gene expression and lipids in Alzheimer's disease (AD) brain. The results so far have prompted further research using "multi-omics" approaches. These approaches become particularly relevant, considering the inheritance of APOEε4 allele as a major genetic risk factor of AD, disease protective effect of APOEε2 allele, and a major role of APOE in brain lipid metabolism. METHODS Postmortem brain samples from inferior parietal lobule genotyped as APOEε2/c (APOEε2/carriers), APOEε3/3, and APOEε4/c (APOEε4/carriers), age- and gender-matched, were used to reveal APOE allele-associated changes in transcriptomes and lipidomes. Differential gene expression and co-expression network analyses were applied to identify up- and downregulated Gene Ontology (GO) terms and pathways for correlation to lipidomics data. RESULTS Significantly affected GO terms and pathways were determined based on the comparisons of APOEε2/c datasets to those of APOEε3/3 and APOEε4/c brain samples. The analysis of lists of genes in highly correlated network modules and of those differentially expressed demonstrated significant enrichment in GO terms associated with genes involved in intracellular proteasomal and lysosomal degradation of proteins, protein aggregates and organelles, ER stress, and response to unfolded protein, as well as mitochondrial function, electron transport, and ATP synthesis. Small nucleolar RNA coding units important for posttranscriptional modification of mRNA and therefore translation and protein synthesis were upregulated in APOEε2/c brain samples compared to both APOEε3/3 and APOEε4/c. The analysis of lipidomics datasets revealed significant changes in ten major lipid classes (exclusively a decrease in APOEε4/c samples), most notably non-bilayer-forming phosphatidylethanolamine and phosphatidic acid, as well as mitochondrial membrane-forming lipids. CONCLUSIONS The results of this study, despite the advanced stage of AD, point to the significant differences in postmortem brain transcriptomes and lipidomes, suggesting APOE allele associated differences in pathogenic mechanisms. Correlations within and between lipidomes and transcriptomes indicate coordinated effects of changes in the proteasomal system and autophagy-canonical and selective, facilitating intracellular degradation, protein entry into ER, response to ER stress, nucleolar modifications of mRNA, and likely myelination in APOEε2/c brains. Additional research and a better knowledge of the molecular mechanisms of proteostasis in the early stages of AD are required to develop more effective diagnostic approaches and eventually efficient therapeutic strategies.
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Affiliation(s)
- Iliya Lefterov
- Department of Environmental and Occupational Health, University of Pittsburgh, 130 De Soto Str., Pittsburgh, PA, 15261, USA.
| | - Cody M Wolfe
- Department of Environmental and Occupational Health, University of Pittsburgh, 130 De Soto Str., Pittsburgh, PA, 15261, USA
| | - Nicholas F Fitz
- Department of Environmental and Occupational Health, University of Pittsburgh, 130 De Soto Str., Pittsburgh, PA, 15261, USA
| | - Kyong Nyon Nam
- Department of Environmental and Occupational Health, University of Pittsburgh, 130 De Soto Str., Pittsburgh, PA, 15261, USA
| | - Florent Letronne
- Department of Environmental and Occupational Health, University of Pittsburgh, 130 De Soto Str., Pittsburgh, PA, 15261, USA
| | - Richard J Biedrzycki
- Department of Environmental and Occupational Health, University of Pittsburgh, 130 De Soto Str., Pittsburgh, PA, 15261, USA
| | - Julia Kofler
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA
| | - Xianlin Han
- Department of Medicine & Biochemistry, Barshop Institute for Longevity and Aging Studies, UT Health-San Antonio, San Antonio, TX, 78229, USA
| | - Jianing Wang
- Department of Medicine & Biochemistry, Barshop Institute for Longevity and Aging Studies, UT Health-San Antonio, San Antonio, TX, 78229, USA
| | - Jonathan Schug
- Department of Genetics, Functional Genomics Core, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Radosveta Koldamova
- Department of Environmental and Occupational Health, University of Pittsburgh, 130 De Soto Str., Pittsburgh, PA, 15261, USA.
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Adams BM, Ke H, Gierasch LM, Gershenson A, Hebert DN. Proper secretion of the serpin antithrombin relies strictly on thiol-dependent quality control. J Biol Chem 2019; 294:18992-19011. [PMID: 31662433 DOI: 10.1074/jbc.ra119.010450] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/24/2019] [Indexed: 01/04/2023] Open
Abstract
The protein quality control machinery of the endoplasmic reticulum (ERQC) ensures that client proteins are properly folded. ERQC substrates may be recognized as nonnative by the presence of exposed hydrophobic surfaces, free thiols, or processed N-glycans. How these features dictate which ERQC pathways engage a given substrate is poorly understood. Here, using metabolic labeling, immunoprecipitations, various biochemical assays, and the human serpin antithrombin III (ATIII) as a model, we explored the role of ERQC systems in mammalian cells. Although ATIII has N-glycans and a hydrophobic core, we found that its quality control depended solely on free thiol content. Mutagenesis of all six Cys residues in ATIII to Ala resulted in its efficient secretion even though the product was not natively folded. ATIII variants with free thiols were retained in the endoplasmic reticulum but not degraded. These results provide insight into the hierarchy of ERQC systems and reveal a fundamental vulnerability of ERQC in a case of reliance on the thiol-dependent quality control pathway.
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Affiliation(s)
- Benjamin M Adams
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003.,Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Massachusetts 01003
| | - Haiping Ke
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003
| | - Lila M Gierasch
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003.,Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Massachusetts 01003.,Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003.,Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Massachusetts 01003
| | - Daniel N Hebert
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003 .,Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Massachusetts 01003
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Hanafusa K, Wada I, Hosokawa N. SDF2-like protein 1 (SDF2L1) regulates the endoplasmic reticulum localization and chaperone activity of ERdj3 protein. J Biol Chem 2019; 294:19335-19348. [PMID: 31624144 DOI: 10.1074/jbc.ra119.009603] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 10/01/2019] [Indexed: 11/06/2022] Open
Abstract
Molecular chaperones facilitate protein folding by associating with nascent polypeptides, thereby preventing protein misfolding and aggregation. Endoplasmic reticulum (ER) chaperone BiP, the sole HSP70 chaperone in the ER, is regulated by HSP40 chaperones, including ER-resident protein ERdj3 (DNAJB11). ERdj3 lacks an ER retrieval signal, is secreted under ER stress conditions, and functions as a chaperone in the extracellular space, but how its secretion is regulated remains unclear. We recently showed that ERdj3 forms a complex with ER-resident stromal cell-derived factor 2 (SDF2) and SDF2L1 (SDF2-like protein 1) and thereby prevents protein aggregation during the BiP chaperone cycle. However, the contribution of the ERdj3-SDF2L1 complex to protein quality control is poorly understood. Here, we analyzed the intracellular localization and chaperone activity of ERdj3 in complex with SDF2L1. We found that ERdj3 was retained in the ER by associating with SDF2/SDF2L1. In vitro analyses revealed that the ERdj3 dimer incorporated two SDF2L1 molecules; otherwise, ERdj3 alone formed a homotetramer. The ERdj3-SDF2L1 complex suppressed ER protein aggregation, and this suppression did not require substrate transfer to BiP. The ERdj3-SDF2L1 complex inhibited aggregation of denatured GSH S-transferase (GST) in vitro and maintained GST in a soluble oligomeric state. Both in cellulo and in vitro, the chaperone activities of the ERdj3-SDF2L1 complex were higher than those of ERdj3 alone. These findings suggest that, under normal conditions, ERdj3 functions as an ER chaperone in complex with SDF2/SDF2L1 but is secreted into the extracellular space when it cannot form this complex.
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Affiliation(s)
- Ken Hanafusa
- Laboratory of Molecular and Cellular Biology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Ikuo Wada
- Department of Cell Sciences, Institute of Biomedical Sciences, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Nobuko Hosokawa
- Laboratory of Molecular and Cellular Biology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
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Abdoli A, Nakhaie M, Feizi N, Salimi Jeda A, Ramezani A. Harmonized Autophagy Versus Full-Fledged Hepatitis B Virus: Victorious or Defeated. Viral Immunol 2019; 32:322-334. [PMID: 31483214 DOI: 10.1089/vim.2019.0042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Autophagy is a finely tuned process in the regulation of innate immunity to avoid excessive inflammatory responses and inflammasome signaling. In contrast, the results of recent studies have shown that autophagy may disease-dependently contribute to the pathogenesis of liver diseases, such as fibrosis, cirrhosis, and hepatocellular carcinoma (HCC) during hepatitis B virus (HBV) infection. HBV has learned to subvert the cell's autophagic machinery to promote its replication. Given the great impact of the autophagy mechanism on the HBV infection and HCC, recognizing these factors may be offered new hope for human intervention and treatment of chronic HBV. This review focuses on recent findings viewing the dual role of autophagy plays in the pathogenesis of HBV infected hepatocytes.
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Affiliation(s)
- Asghar Abdoli
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Mohsen Nakhaie
- Department of Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Neda Feizi
- Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, Rome, Italy
| | - Ali Salimi Jeda
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Amitis Ramezani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
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Balancing the Photoreceptor Proteome: Proteostasis Network Therapeutics for Inherited Retinal Disease. Genes (Basel) 2019; 10:genes10080557. [PMID: 31344897 PMCID: PMC6722924 DOI: 10.3390/genes10080557] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/09/2019] [Accepted: 07/16/2019] [Indexed: 12/17/2022] Open
Abstract
The light sensing outer segments of photoreceptors (PRs) are renewed every ten days due to their high photoactivity, especially of the cones during daytime vision. This demands a tremendous amount of energy, as well as a high turnover of their main biosynthetic compounds, membranes, and proteins. Therefore, a refined proteostasis network (PN), regulating the protein balance, is crucial for PR viability. In many inherited retinal diseases (IRDs) this balance is disrupted leading to protein accumulation in the inner segment and eventually the death of PRs. Various studies have been focusing on therapeutically targeting the different branches of the PR PN to restore the protein balance and ultimately to treat inherited blindness. This review first describes the different branches of the PN in detail. Subsequently, insights are provided on how therapeutic compounds directed against the different PN branches might slow down or even arrest the appalling, progressive blinding conditions. These insights are supported by findings of PN modulators in other research disciplines.
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Intracellular Transport and Cytotoxicity of the Protein Toxin Ricin. Toxins (Basel) 2019; 11:toxins11060350. [PMID: 31216687 PMCID: PMC6628406 DOI: 10.3390/toxins11060350] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/13/2019] [Accepted: 06/14/2019] [Indexed: 12/17/2022] Open
Abstract
Ricin can be isolated from the seeds of the castor bean plant (Ricinus communis). It belongs to the ribosome-inactivating protein (RIP) family of toxins classified as a bio-threat agent due to its high toxicity, stability and availability. Ricin is a typical A-B toxin consisting of a single enzymatic A subunit (RTA) and a binding B subunit (RTB) joined by a single disulfide bond. RTA possesses an RNA N-glycosidase activity; it cleaves ribosomal RNA leading to the inhibition of protein synthesis. However, the mechanism of ricin-mediated cell death is quite complex, as a growing number of studies demonstrate that the inhibition of protein synthesis is not always correlated with long term ricin toxicity. To exert its cytotoxic effect, ricin A-chain has to be transported to the cytosol of the host cell. This translocation is preceded by endocytic uptake of the toxin and retrograde traffic through the trans-Golgi network (TGN) and the endoplasmic reticulum (ER). In this article, we describe intracellular trafficking of ricin with particular emphasis on host cell factors that facilitate this transport and contribute to ricin cytotoxicity in mammalian and yeast cells. The current understanding of the mechanisms of ricin-mediated cell death is discussed as well. We also comment on recent reports presenting medical applications for ricin and progress associated with the development of vaccines against this toxin.
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45
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Shenkman M, Lederkremer GZ. Compartmentalization and Selective Tagging for Disposal of Misfolded Glycoproteins. Trends Biochem Sci 2019; 44:827-836. [PMID: 31133362 DOI: 10.1016/j.tibs.2019.04.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/18/2019] [Accepted: 04/24/2019] [Indexed: 01/08/2023]
Abstract
The ability of mammalian cells to correctly identify and degrade misfolded secretory proteins, most of them bearing N-glycans, is crucial for their correct function and survival. An inefficient disposal mechanism results in the accumulation of misfolded proteins and consequent endoplasmic reticulum (ER) stress. N-glycan processing creates a code that reveals the folding status of each molecule, enabling continued folding attempts or targeting of the doomed glycoprotein for disposal. We review here the main steps involved in the accurate processing of unfolded glycoproteins. We highlight recent data suggesting that the processing is not stochastic, but that there is selective accelerated glycan trimming on misfolded glycoprotein molecules.
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Affiliation(s)
- Marina Shenkman
- School of Molecular Cell Biology and Biotechnology, George Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Gerardo Z Lederkremer
- School of Molecular Cell Biology and Biotechnology, George Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
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46
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Ushioda R, Nagata K. Redox-Mediated Regulatory Mechanisms of Endoplasmic Reticulum Homeostasis. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a033910. [PMID: 30396882 DOI: 10.1101/cshperspect.a033910] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The endoplasmic reticulum (ER) is a dynamic organelle responsible for many cellular functions in eukaryotic cells. Proper redox conditions in the ER are necessary for the functions of many luminal pathways and the maintenance of homeostasis. The redox environment in the ER is oxidative compared with that of the cytosol, and a network of oxidoreductases centering on the protein disulfide isomerase (PDI)-Ero1α hub complex is constructed for efficient electron transfer. Although these oxidizing environments are advantageous for oxidative folding for protein maturation, electron transfer is strictly controlled by Ero1α structurally and spatially. The ER redox environment shifts to a reductive environment under certain stress conditions. In this review, we focus on the reducing reactions that maintain ER homeostasis and introduce their significance in an oxidative ER environment.
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Affiliation(s)
- Ryo Ushioda
- Laboratory of Molecular and Cellular Biology, Department of Molecular Biosciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan.,Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Kazuhiro Nagata
- Laboratory of Molecular and Cellular Biology, Department of Molecular Biosciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan.,Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto 603-8555, Japan
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47
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Nowakowska-Gołacka J, Sominka H, Sowa-Rogozińska N, Słomińska-Wojewódzka M. Toxins Utilize the Endoplasmic Reticulum-Associated Protein Degradation Pathway in Their Intoxication Process. Int J Mol Sci 2019; 20:E1307. [PMID: 30875878 PMCID: PMC6471375 DOI: 10.3390/ijms20061307] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/08/2019] [Accepted: 03/10/2019] [Indexed: 12/25/2022] Open
Abstract
Several bacterial and plant AB-toxins are delivered by retrograde vesicular transport to the endoplasmic reticulum (ER), where the enzymatically active A subunit is disassembled from the holotoxin and transported to the cytosol. In this process, toxins subvert the ER-associated degradation (ERAD) pathway. ERAD is an important part of cellular regulatory mechanism that targets misfolded proteins to the ER channels, prior to their retrotranslocation to the cytosol, ubiquitination and subsequent degradation by a protein-degrading complex, the proteasome. In this article, we present an overview of current understanding of the ERAD-dependent transport of AB-toxins to the cytosol. We describe important components of ERAD and discuss their significance for toxin transport. Toxin recognition and disassembly in the ER, transport through ER translocons and finally cytosolic events that instead of overall proteasomal degradation provide proper folding and cytotoxic activity of AB-toxins are discussed as well. We also comment on recent reports presenting medical applications for toxin transport through the ER channels.
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Affiliation(s)
- Jowita Nowakowska-Gołacka
- Department of Medical Biology and Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
| | - Hanna Sominka
- Department of Medical Biology and Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
| | - Natalia Sowa-Rogozińska
- Department of Medical Biology and Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
| | - Monika Słomińska-Wojewódzka
- Department of Medical Biology and Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
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48
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Kofanova O, Bellora C, Quesada RA, Bulla A, Panadero-Fajardo S, Keipes M, Shea K, Stone M, Lescuyer P, Betsou F. IL8 and EDEM3 gene expression ratio indicates peripheral blood mononuclear cell (PBMC) quality. J Immunol Methods 2019; 465:13-19. [DOI: 10.1016/j.jim.2018.11.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 11/19/2018] [Accepted: 11/19/2018] [Indexed: 10/27/2022]
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49
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Profiling Optimal Conditions for Capturing EDEM Proteins Complexes in Melanoma Using Mass Spectrometry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:155-167. [PMID: 31347047 DOI: 10.1007/978-3-030-15950-4_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Endoplasmic reticulum (ER) resident and secretory proteins that fail to reach their native conformation are selected for degradation through the ER-Associated Degradation (ERAD) pathway. The ER degradation-enhancing alpha-mannosidase-like proteins (EDEMs) were shown to be involved in this pathway but their precise role is still under investigation. Mass spectrometry analysis has contributed significantly to the characterization of protein complexes in the last years. The recent advancements in instrumentation, especially within resolution and speed can provide unique insights concerning the molecular architecture of protein-protein interactions in systems biology. Previous reports have suggested that several protein complexes in ERAD are sensitive to the extraction conditions. Indeed, whilst EDEM proteins can be recovered in most detergents, some of their partners are not solubilized, which further emphasizes the importance of the experimental setup. Here, we define such dynamic interactions of EDEM proteins by employing offline protein fractionation, nanoLC-MS/MS and describe how mass spectrometry can contribute to the characterization of such complexes, particularly within a disease context like melanoma.
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50
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Shenkman M, Ron E, Yehuda R, Benyair R, Khalaila I, Lederkremer GZ. Mannosidase activity of EDEM1 and EDEM2 depends on an unfolded state of their glycoprotein substrates. Commun Biol 2018; 1:172. [PMID: 30374462 PMCID: PMC6194124 DOI: 10.1038/s42003-018-0174-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 09/21/2018] [Indexed: 12/31/2022] Open
Abstract
Extensive mannose trimming of nascent glycoprotein N-glycans signals their targeting to endoplasmic reticulum-associated degradation (ERAD). ER mannosidase I (ERManI) and the EDEM protein family participate in this process. However, whether the EDEMs are truly mannosidases can be addressed only by measuring mannosidase activity in vitro. Here, we reveal EDEM1 and EDEM2 mannosidase activities in vitro. Whereas ERManI significantly trims free N-glycans, activity of the EDEMs is modest on free oligosaccharides and on glycoproteins. However, mannosidase activity of ERManI and the EDEMs is significantly higher on a denatured glycoprotein. The EDEMs associate with oxidoreductases, protein disulfide isomerase, and especially TXNDC11, enhancing mannosidase activity on glycoproteins but not on free N-glycans. The finding that substrate unfolded status increases mannosidase activity solves an important conundrum, as current models suggest general slow mannose trimming. As we show, misfolded or unfolded glycoproteins are subject to differentially faster trimming (and targeting to ERAD) than well-folded ones.
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Affiliation(s)
- Marina Shenkman
- School of Molecular Cell Biology and Biotechnology, George Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Efrat Ron
- School of Molecular Cell Biology and Biotechnology, George Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Rivka Yehuda
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Ron Benyair
- School of Molecular Cell Biology and Biotechnology, George Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Isam Khalaila
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Gerardo Z Lederkremer
- School of Molecular Cell Biology and Biotechnology, George Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel.
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