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Isono E, Li J, Pulido P, Siao W, Spoel SH, Wang Z, Zhuang X, Trujillo M. Protein degrons and degradation: Exploring substrate recognition and pathway selection in plants. THE PLANT CELL 2024; 36:3074-3098. [PMID: 38701343 PMCID: PMC11371205 DOI: 10.1093/plcell/koae141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/27/2024] [Accepted: 04/07/2024] [Indexed: 05/05/2024]
Abstract
Proteome composition is dynamic and influenced by many internal and external cues, including developmental signals, light availability, or environmental stresses. Protein degradation, in synergy with protein biosynthesis, allows cells to respond to various stimuli and adapt by reshaping the proteome. Protein degradation mediates the final and irreversible disassembly of proteins, which is important for protein quality control and to eliminate misfolded or damaged proteins, as well as entire organelles. Consequently, it contributes to cell resilience by buffering against protein or organellar damage caused by stresses. Moreover, protein degradation plays important roles in cell signaling, as well as transcriptional and translational events. The intricate task of recognizing specific proteins for degradation is achieved by specialized systems that are tailored to the substrate's physicochemical properties and subcellular localization. These systems recognize diverse substrate cues collectively referred to as "degrons," which can assume a range of configurations. They are molecular surfaces recognized by E3 ligases of the ubiquitin-proteasome system but can also be considered as general features recognized by other degradation systems, including autophagy or even organellar proteases. Here we provide an overview of the newest developments in the field, delving into the intricate processes of protein recognition and elucidating the pathways through which they are recruited for degradation.
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Affiliation(s)
- Erika Isono
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Jianming Li
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Pablo Pulido
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain
| | - Wei Siao
- Department of Biology, Aachen RWTH University, Institute of Molecular Plant Physiology, 52074 Aachen, Germany
| | - Steven H Spoel
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Zhishuo Wang
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Xiaohong Zhuang
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Marco Trujillo
- Department of Biology, Aachen RWTH University, Institute of Molecular Plant Physiology, 52074 Aachen, Germany
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2
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Katsuki R, Kanuka M, Ohta R, Yoshida S, Tamura T. Turnover of EDEM1, an ERAD-enhancing factor, is mediated by multiple degradation routes. Genes Cells 2024; 29:486-502. [PMID: 38682256 PMCID: PMC11163939 DOI: 10.1111/gtc.13117] [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: 11/09/2023] [Revised: 03/21/2024] [Accepted: 03/23/2024] [Indexed: 05/01/2024]
Abstract
Quality-based protein production and degradation in the endoplasmic reticulum (ER) are essential for eukaryotic cell survival. During protein maturation in the ER, misfolded or unassembled proteins are destined for disposal through a process known as ER-associated degradation (ERAD). EDEM1 is an ERAD-accelerating factor whose gene expression is upregulated by the accumulation of aberrant proteins in the ER, known as ER stress. Although the role of EDEM1 in ERAD has been studied in detail, the turnover of EDEM1 by intracellular degradation machinery, including the proteasome and autophagy, is not well understood. To clarify EDEM1 regulation in the protein level, degradation mechanism of EDEM1 was examined. Our results indicate that both ERAD and autophagy degrade EDEM1 alike misfolded degradation substrates, although each degradation machinery targets EDEM1 in different folded states of proteins. We also found that ERAD factors, including the SEL1L/Hrd1 complex, YOD1, XTP3B, ERdj3, VIMP, BAG6, and JB12, but not OS9, are involved in EDEM1 degradation in a mannose-trimming-dependent and -independent manner. Our results suggest that the ERAD accelerating factor, EDEM1, is turned over by the ERAD itself, similar to ERAD clients.
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Affiliation(s)
- Riko Katsuki
- Department of Life Science, Graduated School of Engineering ScienceAkita UniversityAkitaJapan
| | - Mai Kanuka
- Department of Life Science, Graduated School of Engineering ScienceAkita UniversityAkitaJapan
| | - Ren Ohta
- Department of Life Science, Graduated School of Engineering ScienceAkita UniversityAkitaJapan
| | - Shusei Yoshida
- Department of Life Science, Faculty of Engineering ScienceAkita UniversityAkitaJapan
| | - Taku Tamura
- Department of Life Science, Graduated School of Engineering ScienceAkita UniversityAkitaJapan
- Department of Life Science, Faculty of Engineering ScienceAkita UniversityAkitaJapan
- Present address:
Biococoon Laboratories Inc.4‐3‐5, UedaMoriokaJapan
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3
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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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4
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Badawi S, Mohamed FE, Varghese DS, Ali BR. Genetic disruption of mammalian endoplasmic reticulum-associated protein degradation: Human phenotypes and animal and cellular disease models. Traffic 2023. [PMID: 37188482 DOI: 10.1111/tra.12902] [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: 03/02/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/17/2023]
Abstract
Endoplasmic reticulum-associated protein degradation (ERAD) is a stringent quality control mechanism through which misfolded, unassembled and some native proteins are targeted for degradation to maintain appropriate cellular and organelle homeostasis. Several in vitro and in vivo ERAD-related studies have provided mechanistic insights into ERAD pathway activation and its consequent events; however, a majority of these have investigated the effect of ERAD substrates and their consequent diseases affecting the degradation process. In this review, we present all reported human single-gene disorders caused by genetic variation in genes that encode ERAD components rather than their substrates. Additionally, after extensive literature survey, we present various genetically manipulated higher cellular and mammalian animal models that lack specific components involved in various stages of the ERAD pathway.
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Affiliation(s)
- Sally Badawi
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Feda E Mohamed
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Divya Saro Varghese
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain, United Arab Emirates
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Li J, Zhang J, Wang Y. Analysis of mannosidase I activity in interphase and mitotic cells by lectin staining and endoglycosidase H treatment. STAR Protoc 2023; 4:102283. [PMID: 37148248 PMCID: PMC10193293 DOI: 10.1016/j.xpro.2023.102283] [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: 01/25/2023] [Revised: 03/03/2023] [Accepted: 04/10/2023] [Indexed: 05/08/2023] Open
Abstract
N-Glycosylation is a common protein modification catalyzed by a series of glycosylation enzymes in the endoplasmic reticulum and Golgi apparatus. Here, based on a previously established Golgi α-mannosidase-I-deficient cell line, we present a protocol to investigate the enzymatic activity of exogenously expressed Golgi α-mannosidase IA in interphase and mitotic cells. We describe steps for cell surface lectin staining and subsequent live cell imaging. We also detail PNGase F and Endo H cleavage assays to analyze protein glycosylation. For complete details on the use and execution of this protocol, please refer to Huang et al.1.
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Affiliation(s)
- Jie Li
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 1105 North University Avenue, Ann Arbor, MI 48109, USA
| | - Jianchao Zhang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 1105 North University Avenue, Ann Arbor, MI 48109, USA
| | - Yanzhuang Wang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 1105 North University Avenue, Ann Arbor, MI 48109, USA; Department of Neurology, University of Michigan School of Medicine, Ann Arbor, MI, USA.
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Kaur U, Kihn KC, Ke H, Kuo W, Gierasch LM, Hebert DN, Wintrode PL, Deredge D, Gershenson A. The conformational landscape of a serpin N-terminal subdomain facilitates folding and in-cell quality control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.537978. [PMID: 37163105 PMCID: PMC10168285 DOI: 10.1101/2023.04.24.537978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Many multi-domain proteins including the serpin family of serine protease inhibitors contain non-sequential domains composed of regions that are far apart in sequence. Because proteins are translated vectorially from N- to C-terminus, such domains pose a particular challenge: how to balance the conformational lability necessary to form productive interactions between early and late translated regions while avoiding aggregation. This balance is mediated by the protein sequence properties and the interactions of the folding protein with the cellular quality control machinery. For serpins, particularly α 1 -antitrypsin (AAT), mutations often lead to polymer accumulation in cells and consequent disease suggesting that the lability/aggregation balance is especially precarious. Therefore, we investigated the properties of progressively longer AAT N-terminal fragments in solution and in cells. The N-terminal subdomain, residues 1-190 (AAT190), is monomeric in solution and efficiently degraded in cells. More β -rich fragments, 1-290 and 1-323, form small oligomers in solution, but are still efficiently degraded, and even the polymerization promoting Siiyama (S53F) mutation did not significantly affect fragment degradation. In vitro, the AAT190 region is among the last regions incorporated into the final structure. Hydrogen-deuterium exchange mass spectrometry and enhanced sampling molecular dynamics simulations show that AAT190 has a broad, dynamic conformational ensemble that helps protect one particularly aggregation prone β -strand from solvent. These AAT190 dynamics result in transient exposure of sequences that are buried in folded, full-length AAT, which may provide important recognition sites for the cellular quality control machinery and facilitate degradation and, under favorable conditions, reduce the likelihood of polymerization.
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Affiliation(s)
- Upneet Kaur
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
| | - Kyle C. Kihn
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Haiping Ke
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
| | - Weiwei Kuo
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
| | - Lila M. Gierasch
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003
| | - Daniel N. Hebert
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003
| | - Patrick L. Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Anne Gershenson
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003
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Erzurumlu Y, Catakli D, Dogan HK. Circadian Oscillation Pattern of Endoplasmic Reticulum Quality Control (ERQC) Components in Human Embryonic Kidney HEK293 Cells. J Circadian Rhythms 2023; 21:1. [PMID: 37033333 PMCID: PMC10077977 DOI: 10.5334/jcr.219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 03/14/2023] [Indexed: 04/05/2023] Open
Abstract
The circadian clock regulates the “push-pull” of the molecular signaling mechanisms that arrange the rhythmic organization of the physiology to maintain cellular homeostasis. In mammals, molecular clock genes tightly arrange cellular rhythmicity. It has been shown that this circadian clock optimizes various biological processes, including the cell cycle and autophagy. Hence, we explored the dynamic crosstalks between the circadian rhythm and endoplasmic reticulum (ER)-quality control (ERQC) mechanisms. ER-associated degradation (ERAD) is one of the most important parts of the ERQC system and is an elaborate surveillance system that eliminates misfolded proteins. It regulates the steady-state levels of several physiologically crucial proteins, such as 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) and the metastasis suppressor KAI1/CD82. However, the circadian oscillation of ERQC members and their roles in cellular rhythmicity requires further investigation. In the present study, we provided a thorough investigation of the circadian rhythmicity of the fifteen crucial ERQC members, including gp78, Hrd1, p97/VCP, SVIP, Derlin1, Ufd1, Npl4, EDEM1, OS9, XTP3B, Sel1L, Ufd2, YOD1, VCIP135 and FAM8A1 in HEK293 cells. We found that mRNA and protein accumulation of the ubiquitin conjugation, binding and processing factors, retrotranslocation-dislocation, substrate recognition and targeting components of ERQC exhibit oscillation under the control of the circadian clock. Moreover, we found that Hrd1 and gp78 have a possible regulatory function on Bmal1 turnover. The findings of the current study indicated that the expression level of ERQC components is fine-tuned by the circadian clock and major ERAD E3 ligases, Hrd1 and gp78, may influence the regulation of circadian oscillation by modulation of Bmal1 stability.
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Li D, Guo M, Lv Z, Shao Y, Liang W, Li C. METTL3 activates PERK-eIF2α dependent coelomocyte apoptosis by targeting the endoplasmic reticulum degradation-related protein SEL1L in echinoderms. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194927. [PMID: 36933883 DOI: 10.1016/j.bbagrm.2023.194927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023]
Abstract
N6-methyladenosine (m6A) plays an important role in regulating many physiological and disease processes in vertebrates, in which methyltransferase-like 3 (METTL3) is the best-known m6A methyltransferase. However, the functional roles of invertebrate METTL3 have not yet been highlighted. In this study, we found that METTL3 from Apostichopus japonicus (AjMETTL3) was significantly induced in coelomocytes accompanied by higher levels of m6A modification in response to Vibrio splendidus challenge. Overexpression or silencing of AjMETTL3 in coelomocytes increased or decreased the m6A levels and promoted or inhibited V. splendidus-induced coelomocyte apoptosis, respectively. To further explore the molecular mechanism of AjMETTL3-mediated coelomic immunity, m6A-seq analysis revealed that the endoplasmic reticulum-related degradation (ERAD) pathway was significantly enriched, in which suppressor/enhancer of Lin-12-like (AjSEL1L) was suggested to be a target of AjMETTL3 in a negative regulatory manner. Functional analysis revealed that the increased AjMETTL3 reduced the stability of AjSEL1L mRNA by targeting the m6A modification site of 2004 bp-GGACA-2008 bp. The decreased AjSEL1L was further confirmed to be involved in AjMETTL3-mediated coelomocyte apoptosis. Mechanistically, the inhibited AjSEL1L increased the transcription of AjOS9 and Ajp97 in the EARD pathway to promote ubiquitin protein accumulation and ER stress, which further activated AjPERK-AjeIF2α pathway dependent coelomocyte apoptosis, but not the AjIRE1 or AjATF6 pathway. Taken together, our results supported invertebrate METTL3-mediated coelomocyte apoptosis by regulating the PERK-eIF2α pathway.
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Affiliation(s)
- Dongdong Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Ningbo University, PR China
| | - Ming Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Ningbo University, PR China
| | - Zhimeng Lv
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Ningbo University, PR China
| | - Yina Shao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Ningbo University, PR China
| | - Weikang Liang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Ningbo University, PR China
| | - Chenghua Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Ningbo University, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China.
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Harada Y, Ohkawa Y, Maeda K, Taniguchi N. Glycan quality control in and out of the endoplasmic reticulum of mammalian cells. FEBS J 2022; 289:7147-7162. [PMID: 34492158 DOI: 10.1111/febs.16185] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/23/2021] [Accepted: 09/06/2021] [Indexed: 01/13/2023]
Abstract
The endoplasmic reticulum (ER) is equipped with multiple quality control systems (QCS) that are necessary for shaping the glycoproteome of eukaryotic cells. These systems facilitate the productive folding of glycoproteins, eliminate defective products, and function as effectors to evoke cellular signaling in response to various cellular stresses. These ER functions largely depend on glycans, which contain sugar-based codes that, when needed, function to recruit carbohydrate-binding proteins that determine the fate of glycoproteins. To ensure their functionality, the biosynthesis of such glycans is therefore strictly monitored by a system that selectively degrades structurally defective glycans before adding them to proteins. This system, which is referred to as the glycan QCS, serves as a mechanism to reduce the risk of abnormal glycosylation under conditions where glycan biosynthesis is genetically or metabolically stalled. On the other hand, glycan QCS increases the risk of global hypoglycosylation by limiting glycan availability, which can lead to protein misfolding and the activation of unfolded protein response to maintaining cell viability or to initiate cell death programs. This review summarizes the current state of our knowledge of the mechanisms underlying glycan QCS in mammals and its physiological and pathological roles in embryogenesis, tumor progression, and congenital disorders associated with abnormal glycosylation.
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Affiliation(s)
- Yoichiro Harada
- Department of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, Osaka, Japan
| | - Yuki Ohkawa
- Department of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, Osaka, Japan
| | - Kento Maeda
- Department of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, Osaka, Japan
| | - Naoyuki Taniguchi
- Department of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, Osaka, Japan
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Huang S, Haga Y, Li J, Zhang J, Kweon HK, Seino J, Hirayama H, Fujita M, Moremen KW, Andrews P, Suzuki T, Wang Y. Mitotic phosphorylation inhibits the Golgi mannosidase MAN1A1. Cell Rep 2022; 41:111679. [DOI: 10.1016/j.celrep.2022.111679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 08/16/2022] [Accepted: 10/25/2022] [Indexed: 11/23/2022] Open
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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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Gansemer ER, Rutkowski DT. Pathways Linking Nicotinamide Adenine Dinucleotide Phosphate Production to Endoplasmic Reticulum Protein Oxidation and Stress. Front Mol Biosci 2022; 9:858142. [PMID: 35601828 PMCID: PMC9114485 DOI: 10.3389/fmolb.2022.858142] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
The endoplasmic reticulum (ER) lumen is highly oxidizing compared to other subcellular compartments, and maintaining the appropriate levels of oxidizing and reducing equivalents is essential to ER function. Both protein oxidation itself and other essential ER processes, such as the degradation of misfolded proteins and the sequestration of cellular calcium, are tuned to the ER redox state. Simultaneously, nutrients are oxidized in the cytosol and mitochondria to power ATP generation, reductive biosynthesis, and defense against reactive oxygen species. These parallel needs for protein oxidation in the ER and nutrient oxidation in the cytosol and mitochondria raise the possibility that the two processes compete for electron acceptors, even though they occur in separate cellular compartments. A key molecule central to both processes is NADPH, which is produced by reduction of NADP+ during nutrient catabolism and which in turn drives the reduction of components such as glutathione and thioredoxin that influence the redox potential in the ER lumen. For this reason, NADPH might serve as a mediator linking metabolic activity to ER homeostasis and stress, and represent a novel form of mitochondria-to-ER communication. In this review, we discuss oxidative protein folding in the ER, NADPH generation by the major pathways that mediate it, and ER-localized systems that can link the two processes to connect ER function to metabolic activity.
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Affiliation(s)
- Erica R. Gansemer
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - D. Thomas Rutkowski
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
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13
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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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14
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George G, Ninagawa S, Yagi H, Furukawa JI, Hashii N, Ishii-Watabe A, Deng Y, Matsushita K, Ishikawa T, Mamahit YP, Maki Y, Kajihara Y, Kato K, Okada T, Mori K. Purified EDEM3 or EDEM1 alone produces determinant oligosaccharide structures from M8B in mammalian glycoprotein ERAD. eLife 2021; 10:70357. [PMID: 34698634 PMCID: PMC8570694 DOI: 10.7554/elife.70357] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 10/07/2021] [Indexed: 12/04/2022] Open
Abstract
Sequential mannose trimming of N-glycan, from M9 to M8B and then to oligosaccharides exposing the α1,6-linked mannosyl residue (M7A, M6, and M5), facilitates endoplasmic reticulum-associated degradation of misfolded glycoproteins (gpERAD). We previously showed that EDEM2 stably disulfide-bonded to the thioredoxin domain-containing protein TXNDC11 is responsible for the first step (George et al., 2020). Here, we show that EDEM3 and EDEM1 are responsible for the second step. Incubation of pyridylamine-labeled M8B with purified EDEM3 alone produced M7 (M7A and M7C), M6, and M5. EDEM1 showed a similar tendency, although much lower amounts of M6 and M5 were produced. Thus, EDEM3 is a major α1,2-mannosidase for the second step from M8B. Both EDEM3 and EDEM1 trimmed M8B from a glycoprotein efficiently. Our confirmation of the Golgi localization of MAN1B indicates that no other α1,2-mannosidase is required for gpERAD. Accordingly, we have established the entire route of oligosaccharide processing and the enzymes responsible.
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Affiliation(s)
- Ginto George
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Satoshi Ninagawa
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Jun-Ichi Furukawa
- Department of Advanced Clinical Glycobiology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Noritaka Hashii
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Kawasaki, Japan
| | - Akiko Ishii-Watabe
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Kawasaki, Japan
| | - Ying Deng
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Kazutoshi Matsushita
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Tokiro Ishikawa
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yugoviandi P Mamahit
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Yuta Maki
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Japan.,Project Research Center for Fundamental Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Yasuhiro Kajihara
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Japan.,Project Research Center for Fundamental Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Japan
| | - Tetsuya Okada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Kazutoshi Mori
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
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15
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Ronzoni R, Heyer‐Chauhan N, Fra A, Pearce AC, Rüdiger M, Miranda E, Irving JA, Lomas DA. The molecular species responsible for α 1 -antitrypsin deficiency are suppressed by a small molecule chaperone. FEBS J 2021; 288:2222-2237. [PMID: 33058391 PMCID: PMC8436759 DOI: 10.1111/febs.15597] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/28/2020] [Accepted: 10/12/2020] [Indexed: 12/16/2022]
Abstract
The formation of ordered Z (Glu342Lys) α1 -antitrypsin polymers in hepatocytes is central to liver disease in α1 -antitrypsin deficiency. In vitro experiments have identified an intermediate conformational state (M*) that precedes polymer formation, but this has yet to be identified in vivo. Moreover, the mechanism of polymer formation and their fate in cells have been incompletely characterised. We have used cell models of disease in conjunction with conformation-selective monoclonal antibodies and a small molecule inhibitor of polymerisation to define the dynamics of polymer formation, accumulation and secretion. Pulse-chase experiments demonstrate that Z α1 -antitrypsin accumulates as short-chain polymers that partition with soluble cellular components and are partially secreted by cells. These precede the formation of larger, insoluble polymers with a longer half-life (10.9 ± 1.7 h and 20.9 ± 7.4 h for soluble and insoluble polymers, respectively). The M* intermediate (or a by-product thereof) was identified in the cells by a conformation-specific monoclonal antibody. This was completely abrogated by treatment with the small molecule, which also blocked the formation of intracellular polymers. These data allow us to conclude that the M* conformation is central to polymerisation of Z α1 -antitrypsin in vivo; preventing its accumulation represents a tractable approach for pharmacological treatment of this condition; polymers are partially secreted; and polymers exist as two distinct populations in cells whose different dynamics have likely consequences for the aetiology of the disease.
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Affiliation(s)
| | | | - Annamaria Fra
- Department of Molecular and Translational MedicineUniversity of BresciaItaly
| | | | | | - Elena Miranda
- Department of Biology and Biotechnologies‘Charles Darwin’ and Pasteur Institute – Cenci‐Bolognetti FoundationSapienza University of RomeItaly
| | - James A. Irving
- UCL RespiratoryDivision of MedicineUniversity College LondonUK
| | - David A. Lomas
- UCL RespiratoryDivision of MedicineUniversity College LondonUK
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16
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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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17
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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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18
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Li C, Pan B, Liu X, Qin J, Wang X, He B, Pan Y, Sun H, Xu T, Xu X, Zeng K, Wang S. Long intergenic non-coding RNA LINC00485 exerts tumor-suppressive activity by regulating miR-581/EDEM1 axis in colorectal cancer. Aging (Albany NY) 2021; 13:3866-3885. [PMID: 33461166 PMCID: PMC7906134 DOI: 10.18632/aging.202354] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 10/31/2020] [Indexed: 12/24/2022]
Abstract
Long non-coding RNAs (lncRNA) play a vital role in colorectal cancer (CRC) progression. To investigate the role of long intergenic non-coding RNA LINC00485 in CRC, we performed in vitro functional experiments. LoVo tumor-bearing and liver metastasis mice were used as in vivo models. We found that LINC00485 expression was significantly lower in CRC tissues and cancer cells than in paired normal samples and human normal colonic epithelial cells. Lower expression of LINC00485 predicted poor prognosis in CRC patients. LINC00485 knockdown promoted the proliferation, migration, and invasion of FHC cells, while LINC00485 overexpression weakened these abilities of LoVo cells. MicroRNA miR-581 was the downstream target of LINC00485, which was downregulated in CRC samples and cancer cells compared to normal tissues and normal colonic epithelial cells. MiR-581 overexpression induced proliferation, migration, and invasion of FHC cells, while miR-581 antagomir treatment produced opposite results. MiR-581 directly targeted the 3'UTR of EDEM1 and inhibited its expression and induction of epithelial-mesenchymal transition of CRC. In mouse models, LINC00485 knockdown or down-regulation of miR-581 significantly repressed CRC cell growth and prevented CRC liver metastasis. Overall, LINC00485 suppressed CRC tumorigenesis and progression by targeting the miR-581/EDEM1 axis. LINC00485 may be a potential therapeutic target for CRC.
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Affiliation(s)
- Chenmeng Li
- School of Medicine, Southeast University, Nanjing 210009, Jiangsu, China.,General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Bei Pan
- School of Medicine, Southeast University, Nanjing 210009, Jiangsu, China.,General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Xiangxiang Liu
- School of Medicine, Southeast University, Nanjing 210009, Jiangsu, China.,General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Jian Qin
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Xuhong Wang
- School of Medicine, Southeast University, Nanjing 210009, Jiangsu, China.,General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Bangshun He
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Yuqin Pan
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Huiling Sun
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Tao Xu
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Xueni Xu
- School of Medicine, Southeast University, Nanjing 210009, Jiangsu, China.,General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Kaixuan Zeng
- School of Medicine, Southeast University, Nanjing 210009, Jiangsu, China.,General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Shukui Wang
- School of Medicine, Southeast University, Nanjing 210009, Jiangsu, China.,General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu, China.,Jiangsu Collaborative Innovation Center on Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211100, Jiangsu, China
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19
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Kunkle BW, Schmidt M, Klein HU, Naj AC, Hamilton-Nelson KL, Larson EB, Evans DA, De Jager PL, Crane PK, Buxbaum JD, Ertekin-Taner N, Barnes LL, Fallin MD, Manly JJ, Go RCP, Obisesan TO, Kamboh MI, Bennett DA, Hall KS, Goate AM, Foroud TM, Martin ER, Wang LS, Byrd GS, Farrer LA, Haines JL, Schellenberg GD, Mayeux R, Pericak-Vance MA, Reitz C. Novel Alzheimer Disease Risk Loci and Pathways in African American Individuals Using the African Genome Resources Panel: A Meta-analysis. JAMA Neurol 2021; 78:102-113. [PMID: 33074286 PMCID: PMC7573798 DOI: 10.1001/jamaneurol.2020.3536] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/09/2020] [Indexed: 12/11/2022]
Abstract
Importance Compared with non-Hispanic White individuals, African American individuals from the same community are approximately twice as likely to develop Alzheimer disease. Despite this disparity, the largest Alzheimer disease genome-wide association studies to date have been conducted in non-Hispanic White individuals. In the largest association analyses of Alzheimer disease in African American individuals, ABCA7, TREM2, and an intergenic locus at 5q35 were previously implicated. Objective To identify additional risk loci in African American individuals by increasing the sample size and using the African Genome Resource panel. Design, Setting, and Participants This genome-wide association meta-analysis used case-control and family-based data sets from the Alzheimer Disease Genetics Consortium. There were multiple recruitment sites throughout the United States that included individuals with Alzheimer disease and controls of African American ancestry. Analysis began October 2018 and ended September 2019. Main Outcomes and Measures Diagnosis of Alzheimer disease. Results A total of 2784 individuals with Alzheimer disease (1944 female [69.8%]) and 5222 controls (3743 female [71.7%]) were analyzed (mean [SD] age at last evaluation, 74.2 [13.6] years). Associations with 4 novel common loci centered near the intracellular glycoprotein trafficking gene EDEM1 (3p26; P = 8.9 × 10-7), near the immune response gene ALCAM (3q13; P = 9.3 × 10-7), within GPC6 (13q31; P = 4.1 × 10-7), a gene critical for recruitment of glutamatergic receptors to the neuronal membrane, and within VRK3 (19q13.33; P = 3.5 × 10-7), a gene involved in glutamate neurotoxicity, were identified. In addition, several loci associated with rare variants, including a genome-wide significant intergenic locus near IGF1R at 15q26 (P = 1.7 × 10-9) and 6 additional loci with suggestive significance (P ≤ 5 × 10-7) such as API5 at 11p12 (P = 8.8 × 10-8) and RBFOX1 at 16p13 (P = 5.4 × 10-7) were identified. Gene expression data from brain tissue demonstrate association of ALCAM, ARAP1, GPC6, and RBFOX1 with brain β-amyloid load. Of 25 known loci associated with Alzheimer disease in non-Hispanic White individuals, only APOE, ABCA7, TREM2, BIN1, CD2AP, FERMT2, and WWOX were implicated at a nominal significance level or stronger in African American individuals. Pathway analyses strongly support the notion that immunity, lipid processing, and intracellular trafficking pathways underlying Alzheimer disease in African American individuals overlap with those observed in non-Hispanic White individuals. A new pathway emerging from these analyses is the kidney system, suggesting a novel mechanism for Alzheimer disease that needs further exploration. Conclusions and Relevance While the major pathways involved in Alzheimer disease etiology in African American individuals are similar to those in non-Hispanic White individuals, the disease-associated loci within these pathways differ.
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Affiliation(s)
- Brian W. Kunkle
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida
- Dr. John T. MacDonald Foundation, Department of Human Genetics, University of Miami, Miami, Florida
| | - Michael Schmidt
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida
- Dr. John T. MacDonald Foundation, Department of Human Genetics, University of Miami, Miami, Florida
| | - Hans-Ulrich Klein
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, New York
- Gertrude H. Sergievsky Center, Columbia University, New York, New York
- Department of Neurology, Columbia University, New York, New York
| | - Adam C. Naj
- Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | | | - Eric B. Larson
- Department of Medicine, University of Washington, Seattle
- Group Health Research Institute, Group Health, Seattle, Washington
| | - Denis A. Evans
- Rush Institute for Healthy Aging, Rush University Medical Center, Chicago, Illinois
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois
| | - Phil L. De Jager
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, New York
- Gertrude H. Sergievsky Center, Columbia University, New York, New York
- Department of Neurology, Columbia University, New York, New York
| | - Paul K. Crane
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Joe D. Buxbaum
- Department of Psychiatry, Mount Sinai School of Medicine, New York, New York
- Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, New York
- Department of Neuroscience, Mount Sinai School of Medicine, New York, New York
- Friedman Brain Institute, Mount Sinai School of Medicine, New York, New York
| | - Nilufer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida
- Department of Neurology, Mayo Clinic, Jacksonville, Florida
| | - Lisa L. Barnes
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois
- Department of Behavioral Sciences, Rush University Medical Center, Chicago, Illinois
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois
| | - M. Daniele Fallin
- Department of Epidemiology, Johns Hopkins University School of Public Health, Baltimore, Maryland
| | - Jennifer J. Manly
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, New York
- Gertrude H. Sergievsky Center, Columbia University, New York, New York
- Department of Neurology, Columbia University, New York, New York
| | - Rodney C. P. Go
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham
| | | | - M. Ilyas Kamboh
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania
- Alzheimer’s Disease Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - David A. Bennett
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois
| | - Kathleen S. Hall
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis
| | - Alison M. Goate
- Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, New York
- Department of Neuroscience, Mount Sinai School of Medicine, New York, New York
- Friedman Brain Institute, Mount Sinai School of Medicine, New York, New York
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Tatiana M. Foroud
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis
| | - Eden R. Martin
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida
- Dr. John T. MacDonald Foundation, Department of Human Genetics, University of Miami, Miami, Florida
| | - Li-Sao Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Goldie S. Byrd
- Maya Angelou Center for Health Equity, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
- Department of Ophthalmology, Boston University School of Medicine, Boston, Massachusetts
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts
| | - Jonathan L. Haines
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio
| | - Gerard D. Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, New York
- Gertrude H. Sergievsky Center, Columbia University, New York, New York
- Department of Neurology, Columbia University, New York, New York
- Department of Psychiatry, Columbia University, New York, New York
- Epidemiology, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Margaret A. Pericak-Vance
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida
- Dr. John T. MacDonald Foundation, Department of Human Genetics, University of Miami, Miami, Florida
| | - Christiane Reitz
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, New York
- Gertrude H. Sergievsky Center, Columbia University, New York, New York
- Department of Neurology, Columbia University, New York, New York
- Epidemiology, College of Physicians and Surgeons, Columbia University, New York, New York
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20
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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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21
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Kuribara T, Totani K. Structural insights into N-linked glycan-mediated protein folding from chemical and biological perspectives. Curr Opin Struct Biol 2020; 68:41-47. [PMID: 33296772 DOI: 10.1016/j.sbi.2020.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/26/2020] [Accepted: 11/02/2020] [Indexed: 11/26/2022]
Abstract
About half of all newly synthesized proteins have N-linked glycans. These glycans play pivotal roles in controlling the folding, sorting, and degradation of glycoproteins via several glycan-related proteins. The glycan-mediated protein quality control system is important for cellular homeostasis. In this review, we summarize recent advances in our understanding of the system and discuss structural insights from chemical and biological perspectives. In particular, we focus on the mechanisms by which these mediators respond to several folding states of glycoproteins.
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Affiliation(s)
- Taiki Kuribara
- Seikei University, 3-3-1 Kichijoji-kitamachi, Musashino-shi, Tokyo 180-8633, Japan
| | - Kiichiro Totani
- Seikei University, 3-3-1 Kichijoji-kitamachi, Musashino-shi, Tokyo 180-8633, Japan.
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22
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Jiang L, Hu LG. Serpin peptidase inhibitor clade A member 1-overexpression in gastric cancer promotes tumor progression in vitro and is associated with poor prognosis. Oncol Lett 2020; 20:278. [PMID: 33014156 PMCID: PMC7520747 DOI: 10.3892/ol.2020.12141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/01/2020] [Indexed: 12/14/2022] Open
Abstract
Gastric cancer is the second most common cause of cancer-associated death in Asia. The incidence and mortality rates of gastric cancer have markedly increased in the past few decades. Therefore, the identification of novel gastric cancer biomarkers are needed to determine prognosis. The role of serpin peptidase inhibitor clade A member 1 (SERPINA1) has been studied in several types of cancer; however, little is known about its mechanism in gastric cancer. The present study aimed to evaluate SERPINA1 as a potential prognostic biomarker in gastric cancer and to identify the possible mechanisms underlying its action. The expression levels of SERPINA1 in several gastric cancer datasets were assessed, and it was identified that high expression of SERPINA1 was associated to poor clinical outcomes. Furthermore, using histochemical analysis, western blotting, apoptotic analysis, gap closure and invasion assays in cell lines, it was reported that silencing of SERPINA1 inhibited the formation of cellular pseudopodia and did not affect apoptosis, but promoted cell cycle S-phase entry. In addition, overexpression of SERPINA1 increased the migration and invasion of gastric cancer cells, whereas knockdown of SERPINA1 decreased these functions. Moreover, SERPINA1 overexpression increased the protein levels of SMAD4, which is a key regulator of the transforming growth factor (TGF)-β signaling pathway. Taken together, the present data demonstrated that SERPINA1 promotes gastric cancer progression through TGF-β signaling, and suggested that SERPINA1 may be a novel prognostic biomarker from tumor tissue biopsy in gastric cancer.
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Affiliation(s)
- Longchang Jiang
- Translational Safety and Bioanalytical Sciences, Amgen Research, Amgen Asia Research and Development Center, Shanghai 201210, P.R. China
| | - Liangbiao George Hu
- Translational Safety and Bioanalytical Sciences, Amgen Research, Amgen Asia Research and Development Center, Shanghai 201210, P.R. China
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23
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Patel C, Saad H, Shenkman M, Lederkremer GZ. Oxidoreductases in Glycoprotein Glycosylation, Folding, and ERAD. Cells 2020; 9:cells9092138. [PMID: 32971745 PMCID: PMC7563561 DOI: 10.3390/cells9092138] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/17/2022] Open
Abstract
N-linked glycosylation and sugar chain processing, as well as disulfide bond formation, are among the most common post-translational protein modifications taking place in the endoplasmic reticulum (ER). They are essential modifications that are required for membrane and secretory proteins to achieve their correct folding and native structure. Several oxidoreductases responsible for disulfide bond formation, isomerization, and reduction have been shown to form stable, functional complexes with enzymes and chaperones that are involved in the initial addition of an N-glycan and in folding and quality control of the glycoproteins. Some of these oxidoreductases are selenoproteins. Recent studies also implicate glycan machinery–oxidoreductase complexes in the recognition and processing of misfolded glycoproteins and their reduction and targeting to ER-associated degradation. This review focuses on the intriguing cooperation between the glycoprotein-specific cell machineries and ER oxidoreductases, and highlights open questions regarding the functions of many members of this large family.
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Affiliation(s)
- Chaitanya Patel
- The Shmunis School of Biomedicine and Cancer Research, Cell Biology Division, George Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; (C.P.); (H.S.); (M.S.)
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Haddas Saad
- The Shmunis School of Biomedicine and Cancer Research, Cell Biology Division, George Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; (C.P.); (H.S.); (M.S.)
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Marina Shenkman
- The Shmunis School of Biomedicine and Cancer Research, Cell Biology Division, George Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; (C.P.); (H.S.); (M.S.)
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Gerardo Z. Lederkremer
- The Shmunis School of Biomedicine and Cancer Research, Cell Biology Division, George Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; (C.P.); (H.S.); (M.S.)
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
- Correspondence:
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24
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Kanuka M, Ouchi F, Kato N, Katsuki R, Ito S, Miura K, Hikida M, Tamura T. Endoplasmic Reticulum Associated Degradation of Spinocerebellar Ataxia-Related CD10 Cysteine Mutant. Int J Mol Sci 2020; 21:ijms21124237. [PMID: 32545905 PMCID: PMC7352294 DOI: 10.3390/ijms21124237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/12/2020] [Accepted: 06/12/2020] [Indexed: 12/31/2022] Open
Abstract
Spinocerebellar ataxia (SCA) is one of the most severe neurodegenerative diseases and is often associated with misfolded protein aggregates derived from the genetic mutation of related genes. Recently, mutations in CD10 such as C143Y have been identified as SCA type 43. CD10, also known as neprilysin or neuroendopeptidase, digests functional neuropeptides, such as amyloid beta, in the extracellular region. In this study, we explored the cellular behavior of CD10 C143Y to gain an insight into the functional relationship of the mutation and SCA pathology. We found that wild-type CD10 is expressed on the plasma membrane and exhibits endopeptidase activity in a cultured cell line. CD10 C143Y, however, forms a disulfide bond-mediated oligomer that does not appear by the wild-type CD10. Furthermore, the CD10 C143Y mutant was retained in the endoplasmic reticulum (ER) by the molecular chaperone BiP and was degraded through the ER-associated degradation (ERAD) process, in which representative ERAD factors including EDEM1, SEL1L, and Hrd1 participate in the degradation. Suppression of CD10 C143Y ERAD recovers intracellular transport but not enzymatic activity. Our results indicate that the C143Y mutation in CD10 negatively affects protein maturation and results in ER retention and following ERAD. These findings provide beneficial insight into SCA type 43 pathology.
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Affiliation(s)
- Mai Kanuka
- Department of Life Science, Graduate school of Engineering and Resource, Akita University, Akita 010-8502, Japan; (M.K.); (N.K.); (R.K.); (S.I.); (K.M.); (M.H.)
| | - Fuka Ouchi
- Department of Life Science, Faculty of Engineering Science, Akita University, Akita 010-8502, Japan;
| | - Nagisa Kato
- Department of Life Science, Graduate school of Engineering and Resource, Akita University, Akita 010-8502, Japan; (M.K.); (N.K.); (R.K.); (S.I.); (K.M.); (M.H.)
| | - Riko Katsuki
- Department of Life Science, Graduate school of Engineering and Resource, Akita University, Akita 010-8502, Japan; (M.K.); (N.K.); (R.K.); (S.I.); (K.M.); (M.H.)
| | - Saori Ito
- Department of Life Science, Graduate school of Engineering and Resource, Akita University, Akita 010-8502, Japan; (M.K.); (N.K.); (R.K.); (S.I.); (K.M.); (M.H.)
| | - Kohta Miura
- Department of Life Science, Graduate school of Engineering and Resource, Akita University, Akita 010-8502, Japan; (M.K.); (N.K.); (R.K.); (S.I.); (K.M.); (M.H.)
| | - Masaki Hikida
- Department of Life Science, Graduate school of Engineering and Resource, Akita University, Akita 010-8502, Japan; (M.K.); (N.K.); (R.K.); (S.I.); (K.M.); (M.H.)
- Department of Life Science, Faculty of Engineering Science, Akita University, Akita 010-8502, Japan;
| | - Taku Tamura
- Department of Life Science, Graduate school of Engineering and Resource, Akita University, Akita 010-8502, Japan; (M.K.); (N.K.); (R.K.); (S.I.); (K.M.); (M.H.)
- Department of Life Science, Faculty of Engineering Science, Akita University, Akita 010-8502, Japan;
- Correspondence: ; Tel.: +81-18-889-2377
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25
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Chiritoiu M, Chiritoiu GN, Munteanu CVA, Pastrama F, Ivessa NE, Petrescu SM. EDEM1 Drives Misfolded Protein Degradation via ERAD and Exploits ER-Phagy as Back-Up Mechanism When ERAD Is Impaired. Int J Mol Sci 2020; 21:ijms21103468. [PMID: 32423001 PMCID: PMC7279049 DOI: 10.3390/ijms21103468] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/30/2020] [Accepted: 05/07/2020] [Indexed: 01/20/2023] Open
Abstract
Endoplasmic reticulum (ER)-associated degradation (ERAD) is the main mechanism of targeting ER proteins for degradation to maintain homeostasis, and perturbations of ERAD lead to pathological conditions. ER-degradation enhancing α-mannosidase-like (EDEM1) was proposed to extract terminally misfolded proteins from the calnexin folding cycle and target them for degradation by ERAD. Here, using mass-spectrometry and biochemical methods, we show that EDEM1 is found in auto-regulatory complexes with ERAD components. Moreover, the N-terminal disordered region of EDEM1 mediates protein–protein interaction with misfolded proteins, whilst the absence of this domain significantly impairs their degradation. We also determined that overexpression of EDEM1 can induce degradation, even when proteasomal activity is severely impaired, by promoting the formation of aggregates, which can be further degraded by autophagy. Therefore, we propose that EDEM1 maintains ER homeostasis and mediates ERAD client degradation via autophagy when either dislocation or proteasomal degradation are impaired.
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Affiliation(s)
- Marioara Chiritoiu
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (M.C.); (G.N.C.)
| | - Gabriela N. Chiritoiu
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (M.C.); (G.N.C.)
| | - Cristian V. A. Munteanu
- Department of Bioinformatics & Structural Biochemistry, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (C.V.A.M.); (F.P.)
| | - Florin Pastrama
- Department of Bioinformatics & Structural Biochemistry, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (C.V.A.M.); (F.P.)
| | - N. Erwin Ivessa
- Center for Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, A-1030 Vienna, Austria;
| | - Stefana M. Petrescu
- Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania; (M.C.); (G.N.C.)
- Correspondence: ; Tel.: +40-2-1223-9069
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26
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Arigoni-Affolter I, Scibona E, Lin CW, Brühlmann D, Souquet J, Broly H, Aebi M. Mechanistic reconstruction of glycoprotein secretion through monitoring of intracellular N-glycan processing. SCIENCE ADVANCES 2019; 5:eaax8930. [PMID: 31807707 PMCID: PMC6881162 DOI: 10.1126/sciadv.aax8930] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 09/18/2019] [Indexed: 05/06/2023]
Abstract
N-linked glycosylation plays a fundamental role in determining the thermodynamic stability of proteins and is involved in multiple key biological processes. The mechanistic understanding of the intracellular machinery responsible for the stepwise biosynthesis of N-glycans is still incomplete due to limited understanding of in vivo kinetics of N-glycan processing along the secretory pathway. We present a glycoproteomics approach to monitor the processing of site-specific N-glycans in CHO cells. On the basis of a model-based analysis of structure-specific turnover rates, we provide a kinetic description of intracellular N-glycan processing along the entire secretory pathway. This approach refines and further extends the current knowledge on N-glycans biosynthesis and provides a basis to quantify alterations in the glycoprotein processing machinery.
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Affiliation(s)
| | - Ernesto Scibona
- Institute for Chemical and Bioengineering, Department of Chemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Chia-Wei Lin
- Institute of Microbiology, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - David Brühlmann
- Merck Healthcare, Biotech Process Sciences, Route de Fenil 25, 1804 Corsier-sur-Vevey, Switzerland
| | - Jonathan Souquet
- Merck Healthcare, Biotech Process Sciences, Route de Fenil 25, 1804 Corsier-sur-Vevey, Switzerland
| | - Hervé Broly
- Merck Healthcare, Biotech Process Sciences, Route de Fenil 25, 1804 Corsier-sur-Vevey, Switzerland
| | - Markus Aebi
- Institute of Microbiology, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
- Corresponding author.
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27
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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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28
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Tax G, Lia A, Santino A, Roversi P. Modulation of ERQC and ERAD: A Broad-Spectrum Spanner in the Works of Cancer Cells? JOURNAL OF ONCOLOGY 2019; 2019:8384913. [PMID: 31662755 PMCID: PMC6791201 DOI: 10.1155/2019/8384913] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/27/2019] [Indexed: 12/21/2022]
Abstract
Endoplasmic reticulum glycoprotein folding quality control (ERQC) and ER-associated degradation (ERAD) preside over cellular glycoprotein secretion and maintain steady glycoproteostasis. When cells turn malignant, cancer cell plasticity is affected and supported either by point mutations, preferential isoform selection, altered expression levels, or shifts to conformational equilibria of a secreted glycoprotein. Such changes are crucial in mediating altered extracellular signalling, metabolic behavior, and adhesion properties of cancer cells. It is therefore conceivable that interference with ERQC and/or ERAD can be used to selectively damage cancers. Indeed, inhibitors of the late stages of ERAD are already in the clinic against cancers such as multiple myeloma. Here, we review recent advances in our understanding of the complex relationship between glycoproteostasis and cancer biology and discuss the potential of ERQC and ERAD modulators for the selective targeting of cancer cell plasticity.
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Affiliation(s)
- Gábor Tax
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 7RH, UK
| | - Andrea Lia
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 7RH, UK
- Institute of Sciences of Food Production, C.N.R. Unit of Lecce, via Monteroni, I-73100 Lecce, Italy
| | - Angelo Santino
- Institute of Sciences of Food Production, C.N.R. Unit of Lecce, via Monteroni, I-73100 Lecce, Italy
| | - Pietro Roversi
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 7RH, UK
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29
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Abstract
The site of protein folding and maturation for the majority of proteins that are secreted, localized to the plasma membrane or targeted to endomembrane compartments is the endoplasmic reticulum (ER). It is essential that proteins targeted to the ER are properly folded in order to carry out their function, as well as maintain protein homeostasis, as accumulation of misfolded proteins could lead to the formation of cytotoxic aggregates. Because protein folding is an error-prone process, the ER contains protein quality control networks that act to optimize proper folding and trafficking of client proteins. If a protein is unable to reach its native state, it is targeted for ER retention and subsequent degradation. The protein quality control networks of the ER that oversee this evaluation or interrogation process that decides the fate of maturing nascent chains is comprised of three general types of families: the classical chaperones, the carbohydrate-dependent system, and the thiol-dependent system. The cooperative action of these families promotes protein quality control and protein homeostasis in the ER. This review will describe the families of the ER protein quality control network and discuss the functions of individual members.
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Affiliation(s)
- Benjamin M Adams
- Department of Biochemistry and Molecular Biology, University of Massachusetts, 240 Thatcher Road, Amherst, MA, 01003, USA
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Michela E Oster
- Department of Biochemistry and Molecular Biology, University of Massachusetts, 240 Thatcher Road, Amherst, MA, 01003, USA
| | - Daniel N Hebert
- Department of Biochemistry and Molecular Biology, University of Massachusetts, 240 Thatcher Road, Amherst, MA, 01003, USA.
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, 01003, USA.
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30
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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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31
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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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