1
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Garapati K, Budhraja R, Saraswat M, Kim J, Joshi N, Sachdeva GS, Jain A, Ligezka AN, Radenkovic S, Ramarajan MG, Udainiya S, Raymond K, He M, Lam C, Larson A, Edmondson AC, Sarafoglou K, Larson NB, Freeze HH, Schultz MJ, Kozicz T, Morava E, Pandey A. A complement C4-derived glycopeptide is a biomarker for PMM2-CDG. JCI Insight 2024; 9:e172509. [PMID: 38587076 PMCID: PMC7615924 DOI: 10.1172/jci.insight.172509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 02/15/2024] [Indexed: 04/09/2024] Open
Abstract
BACKGROUNDDiagnosis of PMM2-CDG, the most common congenital disorder of glycosylation (CDG), relies on measuring carbohydrate-deficient transferrin (CDT) and genetic testing. CDT tests have false negatives and may normalize with age. Site-specific changes in protein N-glycosylation have not been reported in sera in PMM2-CDG.METHODSUsing multistep mass spectrometry-based N-glycoproteomics, we analyzed sera from 72 individuals to discover and validate glycopeptide alterations. We performed comprehensive tandem mass tag-based discovery experiments in well-characterized patients and controls. Next, we developed a method for rapid profiling of additional samples. Finally, targeted mass spectrometry was used for validation in an independent set of samples in a blinded fashion.RESULTSOf the 3,342 N-glycopeptides identified, patients exhibited decrease in complex-type N-glycans and increase in truncated, mannose-rich, and hybrid species. We identified a glycopeptide from complement C4 carrying the glycan Man5GlcNAc2, which was not detected in controls, in 5 patients with normal CDT results, including 1 after liver transplant and 2 with a known genetic variant associated with mild disease, indicating greater sensitivity than CDT. It was detected by targeted analysis in 2 individuals with variants of uncertain significance in PMM2.CONCLUSIONComplement C4-derived Man5GlcNAc2 glycopeptide could be a biomarker for accurate diagnosis and therapeutic monitoring of patients with PMM2-CDG and other CDGs.FUNDINGU54NS115198 (Frontiers in Congenital Disorders of Glycosylation: NINDS; NCATS; Eunice Kennedy Shriver NICHD; Rare Disorders Consortium Disease Network); K08NS118119 (NINDS); Minnesota Partnership for Biotechnology and Medical Genomics; Rocket Fund; R01DK099551 (NIDDK); Mayo Clinic DERIVE Office; Mayo Clinic Center for Biomedical Discovery; IA/CRC/20/1/600002 (Center for Rare Disease Diagnosis, Research and Training; DBT/Wellcome Trust India Alliance).
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Affiliation(s)
- Kishore Garapati
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Rohit Budhraja
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Mayank Saraswat
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jinyong Kim
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Neha Joshi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Gunveen S. Sachdeva
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Anu Jain
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | - Madan Gopal Ramarajan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Savita Udainiya
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Kimiyo Raymond
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Miao He
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Christina Lam
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, Washington, USA
- Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | | | - Andrew C. Edmondson
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kyriakie Sarafoglou
- Division of Pediatric Endocrinology, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, Minnesota, USA
- Department of Experimental and Clinical Pharmacology, University of Minnesota School of Pharmacy, Minneapolis, Minnesota, USA
| | - Nicholas B. Larson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Hudson H. Freeze
- Sanford Children’s Health Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Matthew J. Schultz
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Tamas Kozicz
- Department of Clinical Genomics and
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Anatomy, University of Pécs Medical School, Pécs, Hungary
- Department of Genomics and Genetic Sciences, Icahn School of Medicine at Mount Sinai Hospital, New York, New York, USA
| | - Eva Morava
- Department of Clinical Genomics and
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Anatomy, University of Pécs Medical School, Pécs, Hungary
- Department of Genomics and Genetic Sciences, Icahn School of Medicine at Mount Sinai Hospital, New York, New York, USA
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
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2
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Li C, Wang M, Cheng A, Wu Y, Tian B, Yang Q, Gao Q, Sun D, Zhang S, Ou X, He Y, Huang J, Zhao X, Chen S, Zhu D, Liu M, Jia R. N-Linked Glycosylation and Expression of Duck Plague Virus pUL10 Promoted by pUL49.5. Microbiol Spectr 2023; 11:e0162523. [PMID: 37378543 PMCID: PMC10434065 DOI: 10.1128/spectrum.01625-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Duck plague virus (DPV) is a member of the alphaherpesvirus subfamily, and its genome encodes a conserved envelope protein, protein UL10 (pUL10). pUL10 plays complex roles in viral fusion, assembly, cell-to-cell spread, and immune evasion, which are closely related to its protein characteristics and partners. Few studies have been conducted on DPV pUL10. In this study, we identified the characteristics of pUL10, such as the type of glycosylation modification and subcellular localization. The characteristic differences in pUL10 in transfection and infection suggest that there are other viral proteins that participate in pUL10 modification and localization. Therefore, pUL49.5, the interaction partner of pUL10, was explored. We found that pUL10 interacts with pUL49.5 during transfection and infection. Their interaction entailed multiple interaction sites, including noncovalent forces in the pUL49.5 N-terminal domains and C-terminal domains and a covalent disulfide bond between two conserved cysteines. pUL49.5 promoted pUL10 expression and mature N-linked glycosylation modification. Moreover, deletion of UL49.5 in DPV caused the molecular mass of pUL10 to decrease by approximately3 to 10 kDa, which suggested that pUL49.5 was the main factor affecting the N-linked glycosylation of DPV pUL10 during infection. This study provides a basis for future exploration of the effect of pUL10 glycosylation on virus proliferation. IMPORTANCE Duck plague is a disease with high morbidity and mortality rates, and it causes great losses for the duck breeding industry. Duck plague virus (DPV) is the causative agent of duck plague, and DPV UL10 protein (pUL10) is a homolog of glycoprotein M (gM), which is conserved in herpesviruses. pUL10 plays complex roles in viral fusion, assembly, cell-to-cell spread, and immune evasion, which are closely related to its protein characteristics and partners. In this study, we systematically explored whether pUL49.5 (a partner of pUL10) plays roles in the localization, modification, and expression of pUL10.
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Affiliation(s)
- Chunmei Li
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu City, Sichuan, China
| | - Mingshu Wang
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu City, Sichuan, China
| | - Anchun Cheng
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu City, Sichuan, China
| | - Ying Wu
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu City, Sichuan, China
| | - Bin Tian
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu City, Sichuan, China
| | - Qiao Yang
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu City, Sichuan, China
| | - Qun Gao
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu City, Sichuan, China
| | - Di Sun
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu City, Sichuan, China
| | - Shaqiu Zhang
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu City, Sichuan, China
| | - Xumin Ou
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu City, Sichuan, China
| | - Yu He
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu City, Sichuan, China
| | - Juan Huang
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu City, Sichuan, China
| | - Xinxin Zhao
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu City, Sichuan, China
| | - Shun Chen
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu City, Sichuan, China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu City, Sichuan, China
| | - Mafeng Liu
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu City, Sichuan, China
| | - Renyong Jia
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu City, Sichuan, China
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3
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Newby ML, Fogarty CA, Allen JD, Butler J, Fadda E, Crispin M. Variations within the Glycan Shield of SARS-CoV-2 Impact Viral Spike Dynamics. J Mol Biol 2023; 435:167928. [PMID: 36565991 PMCID: PMC9769069 DOI: 10.1016/j.jmb.2022.167928] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/25/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
The emergence of SARS-CoV-2 variants alters the efficacy of existing immunity, whether arisen naturally or through vaccination. Understanding the structure of the viral spike assists in determining the impact of mutations on the antigenic surface. One class of mutation impacts glycosylation attachment sites, which have the capacity to influence the antigenic structure beyond the immediate site of attachment. Here, we compare the site-specific glycosylation of recombinant viral spike mimetics of B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta), B.1.1.529 (Omicron). The P.1 strain exhibits two additional N-linked glycan sites compared to the other variants analyzed and we investigate the impact of these glycans by molecular dynamics. The acquired N188 site is shown to exhibit very limited glycan maturation, consistent with limited enzyme accessibility. Structural modeling and molecular dynamics reveal that N188 is located within a cavity by the receptor binding domain, which influences the dynamics of these attachment domains. These observations suggest a mechanism whereby mutations affecting viral glycosylation sites have a structural impact across the protein surface.
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Affiliation(s)
- Maddy L Newby
- School of Biological Sciences, University of Southampton, Southampton, UK. https://twitter.com/Maddy_Newby
| | - Carl A Fogarty
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Kildare, Ireland. https://twitter.com/2016Carl
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK. https://twitter.com/JoelDalllen
| | - John Butler
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Elisa Fadda
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Kildare, Ireland.
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK.
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4
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Lyu Z, Sycks MM, Espinoza MF, Nguyen KK, Montoya MR, Galapate CM, Mei L, Genereux JC. Monitoring Protein Import into the Endoplasmic Reticulum in Living Cells with Proximity Labeling. ACS Chem Biol 2022; 17:1963-1977. [PMID: 35675579 DOI: 10.1021/acschembio.2c00405] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The proper trafficking of eukaryotic proteins is essential to cellular function. Genetic, environmental, and other stresses can induce protein mistargeting and, in turn, threaten cellular protein homeostasis. Current methods for measuring protein mistargeting are difficult to translate to living cells, and thus the role of cellular signaling networks in stress-dependent protein mistargeting processes, such as ER pre-emptive quality control (ER pQC), is difficult to parse. Herein, we use genetically encoded peroxidases to characterize protein import into the endoplasmic reticulum (ER). We show that the ERHRP/cytAPEX pair provides good selectivity and sensitivity for both multiplexed protein labeling and for identifying protein mistargeting, using the known ER pQC substrate transthyretin (TTR). Although ERHRP labeling induces formation of detergent-resistant TTR aggregates, this is minimized by using low ERHRP expression, without loss of labeling efficiency. cytAPEX labeling recovers TTR that is mistargeted as a consequence of Sec61 inhibition or ER stress-induced ER pQC. Furthermore, we discover that stress-free activation of the ER stress-associated transcription factor ATF6 recapitulates the TTR import deficiency of ER pQC. Hence, proximity labeling is an effective strategy for characterizing factors that influence ER protein import in living cells.
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Affiliation(s)
- Ziqi Lyu
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Melody M Sycks
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Mateo F Espinoza
- Graduate Program of Microbiology, University of California, Riverside, California 92521, United States
| | - Khanh K Nguyen
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Maureen R Montoya
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Cheska M Galapate
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Liangyong Mei
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Joseph C Genereux
- Department of Chemistry, University of California, Riverside, California 92521, United States.,Graduate Program of Microbiology, University of California, Riverside, California 92521, United States
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5
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van Lith M, Pringle MA, Fleming B, Gaeta G, Im J, Gilmore R, Bulleid NJ. A cytosolic reductase pathway is required for efficient N-glycosylation of an STT3B-dependent acceptor site. J Cell Sci 2021; 134:273533. [PMID: 34734627 PMCID: PMC8645230 DOI: 10.1242/jcs.259340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/27/2021] [Indexed: 11/20/2022] Open
Abstract
N-linked glycosylation of proteins entering the secretory pathway is an essential modification required for protein stability and function. Previously, it has been shown that there is a temporal relationship between protein folding and glycosylation, which influences the occupancy of specific glycosylation sites. Here, we used an in vitro translation system that reproduces the initial stages of secretory protein translocation, folding and glycosylation under defined redox conditions. We found that the efficiency of glycosylation of hemopexin was dependent upon a robust NADPH-dependent cytosolic reductive pathway, which could be mimicked by the addition of a membrane-impermeable reducing agent. We identified a hypoglycosylated acceptor site that is adjacent to a cysteine involved in a short-range disulfide. We show that efficient glycosylation at this site is influenced by the cytosolic reductive pathway acting on both STT3A- and STT3B-dependent glycosylation. Our results provide further insight into the important role of the endoplasmic reticulum redox conditions in glycosylation site occupancy and demonstrate a link between redox conditions in the cytosol and glycosylation efficiency.
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Affiliation(s)
- Marcel van Lith
- Institute of Molecular, Cell and Systems Biology, College of Medical Veterinary and Life Sciences, Davidson Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Marie Anne Pringle
- Institute of Molecular, Cell and Systems Biology, College of Medical Veterinary and Life Sciences, Davidson Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Bethany Fleming
- Institute of Molecular, Cell and Systems Biology, College of Medical Veterinary and Life Sciences, Davidson Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Giorgia Gaeta
- Institute of Molecular, Cell and Systems Biology, College of Medical Veterinary and Life Sciences, Davidson Building, University of Glasgow, Glasgow, G12 8QQ, UK.,Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, Headington, Oxford OX3 7LD, UK
| | - Jisu Im
- Institute of Molecular, Cell and Systems Biology, College of Medical Veterinary and Life Sciences, Davidson Building, University of Glasgow, Glasgow, G12 8QQ, UK.,Cellular Protein Chemistry, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Reid Gilmore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Neil J Bulleid
- Institute of Molecular, Cell and Systems Biology, College of Medical Veterinary and Life Sciences, Davidson Building, University of Glasgow, Glasgow, G12 8QQ, UK
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6
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Derking R, Allen JD, Cottrell CA, Sliepen K, Seabright GE, Lee WH, Aldon Y, Rantalainen K, Antanasijevic A, Copps J, Yasmeen A, Cupo A, Cruz Portillo VM, Poniman M, Bol N, van der Woude P, de Taeye SW, van den Kerkhof TLGM, Klasse PJ, Ozorowski G, van Gils MJ, Moore JP, Ward AB, Crispin M, Sanders RW. Enhancing glycan occupancy of soluble HIV-1 envelope trimers to mimic the native viral spike. Cell Rep 2021; 35:108933. [PMID: 33826885 PMCID: PMC8804554 DOI: 10.1016/j.celrep.2021.108933] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/10/2020] [Accepted: 03/11/2021] [Indexed: 12/31/2022] Open
Abstract
Artificial glycan holes on recombinant Env-based vaccines occur when a potential N-linked glycosylation site (PNGS) is under-occupied, but not on their viral counterparts. Native-like SOSIP trimers, including clinical candidates, contain such holes in the glycan shield that induce strain-specific neutralizing antibodies (NAbs) or non-NAbs. To eliminate glycan holes and mimic the glycosylation of native BG505 Env, we replace all 12 NxS sequons on BG505 SOSIP with NxT. All PNGS, except N133 and N160, are nearly fully occupied. Occupancy of the N133 site is increased by changing N133 to NxS, whereas occupancy of the N160 site is restored by reverting the nearby N156 sequon to NxS. Hence, PNGS in close proximity, such as in the N133-N137 and N156-N160 pairs, affect each other's occupancy. We further apply this approach to improve the occupancy of several Env strains. Increasing glycan occupancy should reduce off-target immune responses to vaccine antigens.
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Affiliation(s)
- Ronald Derking
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Christopher A Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kwinten Sliepen
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Gemma E Seabright
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yoann Aldon
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Kimmo Rantalainen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Anila Yasmeen
- Department of Microbiology and Immunology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Albert Cupo
- Department of Microbiology and Immunology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Victor M Cruz Portillo
- Department of Microbiology and Immunology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Meliawati Poniman
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Niki Bol
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Patricia van der Woude
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Steven W de Taeye
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Tom L G M van den Kerkhof
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - P J Klasse
- Department of Microbiology and Immunology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Development, IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - John P Moore
- Department of Microbiology and Immunology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Development, IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands; Department of Microbiology and Immunology, Weill Cornell Medical College, Cornell University, New York, NY, USA.
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7
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Margolin E, Crispin M, Meyers A, Chapman R, Rybicki EP. A Roadmap for the Molecular Farming of Viral Glycoprotein Vaccines: Engineering Glycosylation and Glycosylation-Directed Folding. FRONTIERS IN PLANT SCIENCE 2020; 11:609207. [PMID: 33343609 PMCID: PMC7744475 DOI: 10.3389/fpls.2020.609207] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/09/2020] [Indexed: 05/03/2023]
Abstract
Immunization with recombinant glycoprotein-based vaccines is a promising approach to induce protective immunity against viruses. However, the complex biosynthetic maturation requirements of these glycoproteins typically necessitate their production in mammalian cells to support their folding and post-translational modification. Despite these clear advantages, the incumbent costs and infrastructure requirements with this approach can be prohibitive in developing countries, and the production scales and timelines may prove limiting when applying these production systems to the control of pandemic viral outbreaks. Plant molecular farming of viral glycoproteins has been suggested as a cheap and rapidly scalable alternative production system, with the potential to perform post-translational modifications that are comparable to mammalian cells. Consequently, plant-produced glycoprotein vaccines for seasonal and pandemic influenza have shown promise in clinical trials, and vaccine candidates against the newly emergent severe acute respiratory syndrome coronavirus-2 have entered into late stage preclinical and clinical testing. However, many other viral glycoproteins accumulate poorly in plants, and are not appropriately processed along the secretory pathway due to differences in the host cellular machinery. Furthermore, plant-derived glycoproteins often contain glycoforms that are antigenically distinct from those present on the native virus, and may also be under-glycosylated in some instances. Recent advances in the field have increased the complexity and yields of biologics that can be produced in plants, and have now enabled the expression of many viral glycoproteins which could not previously be produced in plant systems. In contrast to the empirical optimization that predominated during the early years of molecular farming, the next generation of plant-made products are being produced by developing rational, tailor-made approaches to support their production. This has involved the elimination of plant-specific glycoforms and the introduction into plants of elements of the biosynthetic machinery from different expression hosts. These approaches have resulted in the production of mammalian N-linked glycans and the formation of O-glycan moieties in planta. More recently, plant molecular engineering approaches have also been applied to improve the glycan occupancy of proteins which are not appropriately glycosylated, and to support the folding and processing of viral glycoproteins where the cellular machinery differs from the usual expression host of the protein. Here we highlight recent achievements and remaining challenges in glycoengineering and the engineering of glycosylation-directed folding pathways in plants, and discuss how these can be applied to produce recombinant viral glycoproteins vaccines.
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Affiliation(s)
- Emmanuel Margolin
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Wellcome Trust Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town, South Africa
- Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Ann Meyers
- Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Ros Chapman
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Edward P. Rybicki
- Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
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8
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Schorcht A, van den Kerkhof TLGM, Cottrell CA, Allen JD, Torres JL, Behrens AJ, Schermer EE, Burger JA, de Taeye SW, Torrents de la Peña A, Bontjer I, Gumbs S, Ozorowski G, LaBranche CC, de Val N, Yasmeen A, Klasse PJ, Montefiori DC, Moore JP, Schuitemaker H, Crispin M, van Gils MJ, Ward AB, Sanders RW. Neutralizing Antibody Responses Induced by HIV-1 Envelope Glycoprotein SOSIP Trimers Derived from Elite Neutralizers. J Virol 2020; 94:e01214-20. [PMID: 32999024 PMCID: PMC7925178 DOI: 10.1128/jvi.01214-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022] Open
Abstract
The induction of broadly neutralizing antibodies (bNAbs) is a major goal in vaccine research. HIV-1-infected individuals that develop exceptionally strong bNAb responses, termed elite neutralizers, can inform vaccine design by providing blueprints for the induction of similar bNAb responses. We describe a new recombinant native-like envelope glycoprotein (Env) SOSIP trimer, termed AMC009, based on the viral founder sequences of an elite neutralizer. The subtype B AMC009 SOSIP protein formed stable native-like trimers that displayed multiple bNAb epitopes. Overall, its structure at 4.3-Å resolution was similar to that of BG505 SOSIP.664. The AMC009 trimer resembled one from a second elite neutralizer, AMC011, in having a dense and complete glycan shield. When tested as immunogens in rabbits, the AMC009 trimers did not induce autologous neutralizing antibody (NAb) responses efficiently while the AMC011 trimers did so very weakly, outcomes that may reflect the completeness of their glycan shields. The AMC011 trimer induced antibodies that occasionally cross-neutralized heterologous tier 2 viruses, sometimes at high titer. Cross-neutralizing antibodies were more frequently elicited by a trivalent combination of AMC008, AMC009, and AMC011 trimers, all derived from subtype B viruses. Each of these three individual trimers could deplete the NAb activity from the rabbit sera. Mapping the polyclonal sera by electron microscopy revealed that antibodies of multiple specificities could bind to sites on both autologous and heterologous trimers. These results advance our understanding of how to use Env trimers in multivalent vaccination regimens and the immunogenicity of trimers derived from elite neutralizers.IMPORTANCE Elite neutralizers, i.e., individuals who developed unusually broad and potent neutralizing antibody responses, might serve as blueprints for HIV-1 vaccine design. Here, we studied the immunogenicity of native-like recombinant envelope glycoprotein (Env) trimers based on viral sequences from elite neutralizers. While immunization with single trimers from elite neutralization did not recapitulate the breadth and potency of neutralization observed in these infected individuals, a combination of three subtype B Env trimers from elite neutralizers resulted in some neutralization breadth within subtype B viruses. These results should guide future efforts to design vaccines to induce broadly neutralizing antibodies.
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Affiliation(s)
- Anna Schorcht
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Tom L G M van den Kerkhof
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Experimental Immunology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Christopher A Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Joel D Allen
- School of Biological Science, University of Southampton, Southampton, United Kingdom
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Anna-Janina Behrens
- School of Biological Science, University of Southampton, Southampton, United Kingdom
| | - Edith E Schermer
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Judith A Burger
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Steven W de Taeye
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Alba Torrents de la Peña
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Ilja Bontjer
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Stephanie Gumbs
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Celia C LaBranche
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Natalia de Val
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick National Laboratory, Leidos Biomedical Research Inc., Frederick, Maryland, USA
| | - Anila Yasmeen
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, USA
| | - Per Johan Klasse
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, USA
| | - David C Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, USA
| | | | - Max Crispin
- School of Biological Science, University of Southampton, Southampton, United Kingdom
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, USA
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9
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Harada Y, Nakajima K, Suzuki T, Fukushige T, Kondo K, Seino J, Ohkawa Y, Suzuki T, Inoue H, Kanekura T, Dohmae N, Taniguchi N, Maruyama I. Glycometabolic Regulation of the Biogenesis of Small Extracellular Vesicles. Cell Rep 2020; 33:108261. [DOI: 10.1016/j.celrep.2020.108261] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 08/20/2020] [Accepted: 09/21/2020] [Indexed: 12/13/2022] Open
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10
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Structural Insight into the Mechanism of N-Linked Glycosylation by Oligosaccharyltransferase. Biomolecules 2020; 10:biom10040624. [PMID: 32316603 PMCID: PMC7226087 DOI: 10.3390/biom10040624] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/06/2020] [Accepted: 04/10/2020] [Indexed: 02/06/2023] Open
Abstract
Asparagine-linked glycosylation, also known as N-linked glycosylation is an essential and highly conserved post-translational protein modification that occurs in all three domains of life. This modification is essential for specific molecular recognition, protein folding, sorting in the endoplasmic reticulum, cell-cell communication, and stability. Defects in N-linked glycosylation results in a class of inherited diseases known as congenital disorders of glycosylation (CDG). N-linked glycosylation occurs in the endoplasmic reticulum (ER) lumen by a membrane associated enzyme complex called the oligosaccharyltransferase (OST). In the central step of this reaction, an oligosaccharide group is transferred from a lipid-linked dolichol pyrophosphate donor to the acceptor substrate, the side chain of a specific asparagine residue of a newly synthesized protein. The prokaryotic OST enzyme consists of a single polypeptide chain, also known as single subunit OST or ssOST. In contrast, the eukaryotic OST is a complex of multiple non-identical subunits. In this review, we will discuss the biochemical and structural characterization of the prokaryotic, yeast, and mammalian OST enzymes. This review explains the most recent high-resolution structures of OST determined thus far and the mechanistic implication of N-linked glycosylation throughout all domains of life. It has been shown that the ssOST enzyme, AglB protein of the archaeon Archaeoglobus fulgidus, and the PglB protein of the bacterium Campylobactor lari are structurally and functionally similar to the catalytic Stt3 subunit of the eukaryotic OST enzyme complex. Yeast OST enzyme complex contains a single Stt3 subunit, whereas the human OST complex is formed with either STT3A or STT3B, two paralogues of Stt3. Both human OST complexes, OST-A (with STT3A) and OST-B (containing STT3B), are involved in the N-linked glycosylation of proteins in the ER. The cryo-EM structures of both human OST-A and OST-B complexes were reported recently. An acceptor peptide and a donor substrate (dolichylphosphate) were observed to be bound to the OST-B complex whereas only dolichylphosphate was bound to the OST-A complex suggesting disparate affinities of two OST complexes for the acceptor substrates. However, we still lack an understanding of the independent role of each eukaryotic OST subunit in N-linked glycosylation or in the stabilization of the enzyme complex. Discerning the role of each subunit through structure and function studies will potentially reveal the mechanistic details of N-linked glycosylation in higher organisms. Thus, getting an insight into the requirement of multiple non-identical subunits in the N-linked glycosylation process in eukaryotes poses an important future goal.
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11
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Ramesh B, Abnouf S, Mali S, Moree WJ, Patil U, Bark SJ, Varadarajan N. Engineered ChymotrypsiN for Mass Spectrometry-Based Detection of Protein Glycosylation. ACS Chem Biol 2019; 14:2616-2628. [PMID: 31710461 DOI: 10.1021/acschembio.9b00506] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We have engineered the substrate specificity of chymotrypsin to cleave after Asn by high-throughput screening of large libraries created by comprehensive remodeling of the substrate binding pocket. The engineered variant (chymotrypsiN, ChyB-Asn) demonstrated an altered substrate specificity with an expanded preference for Asn-containing substrates. We confirmed that protein engineering did not compromise the stability of the enzyme by biophysical characterization. Comparison of wild-type ChyB and ChyB-Asn in profiling lysates of HEK293 cells demonstrated both qualitative and quantitative differences in the nature of the peptides and proteins identified by liquid chromatography and tandem mass spectrometry. ChyB-Asn enabled the identification of partially glycosylated Asn sites within a model glycoprotein and in the extracellular proteome of Jurkat T cells. ChymotrypsiN is a valuable addition to the toolkit of proteases to aid the mapping of N-linked glycosylation sites within proteins and proteomes.
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Affiliation(s)
- Balakrishnan Ramesh
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204-4004, United States
| | - Shaza Abnouf
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204-4004, United States
| | - Sujina Mali
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77004, United States
| | - Wilna J. Moree
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77004, United States
| | - Ujwal Patil
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77004, United States
| | - Steven J. Bark
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77004, United States
| | - Navin Varadarajan
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204-4004, United States
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12
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Ramírez AS, Kowal J, Locher KP. Cryo–electron microscopy structures of human oligosaccharyltransferase complexes OST-A and OST-B. Science 2019; 366:1372-1375. [DOI: 10.1126/science.aaz3505] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/13/2019] [Indexed: 12/22/2022]
Abstract
Oligosaccharyltransferase (OST) catalyzes the transfer of a high-mannose glycan onto secretory proteins in the endoplasmic reticulum. Mammals express two distinct OST complexes that act in a cotranslational (OST-A) or posttranslocational (OST-B) manner. Here, we present high-resolution cryo–electron microscopy structures of human OST-A and OST-B. Although they have similar overall architectures, structural differences in the catalytic subunits STT3A and STT3B facilitate contacts to distinct OST subunits, DC2 in OST-A and MAGT1 in OST-B. In OST-A, interactions with TMEM258 and STT3A allow ribophorin-I to form a four-helix bundle that can bind to a translating ribosome, whereas the equivalent region is disordered in OST-B. We observed an acceptor peptide and dolichylphosphate bound to STT3B, but only dolichylphosphate in STT3A, suggesting distinct affinities of the two OST complexes for protein substrates.
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Affiliation(s)
- Ana S. Ramírez
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), CH-8093 Zürich, Switzerland
| | - Julia Kowal
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), CH-8093 Zürich, Switzerland
| | - Kaspar P. Locher
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), CH-8093 Zürich, Switzerland
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13
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Harada Y, Ohkawa Y, Kizuka Y, Taniguchi N. Oligosaccharyltransferase: A Gatekeeper of Health and Tumor Progression. Int J Mol Sci 2019; 20:ijms20236074. [PMID: 31810196 PMCID: PMC6929149 DOI: 10.3390/ijms20236074] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 11/28/2019] [Accepted: 11/28/2019] [Indexed: 02/06/2023] Open
Abstract
Oligosaccharyltransferase (OST) is a multi-span membrane protein complex that catalyzes the addition of glycans to selected Asn residues within nascent polypeptides in the lumen of the endoplasmic reticulum. This process, termed N-glycosylation, is a fundamental post-translational protein modification that is involved in the quality control, trafficking of proteins, signal transduction, and cell-to-cell communication. Given these crucial roles, N-glycosylation is essential for homeostasis at the systemic and cellular levels, and a deficiency in genes that encode for OST subunits often results in the development of complex genetic disorders. A growing body of evidence has also demonstrated that the expression of OST subunits is cell context-dependent and is frequently altered in malignant cells, thus contributing to tumor cell survival and proliferation. Importantly, a recently developed inhibitor of OST has revealed this enzyme as a potential target for the treatment of incurable drug-resistant tumors. This review summarizes our current knowledge regarding the functions of OST in the light of health and tumor progression, and discusses perspectives on the clinical relevance of inhibiting OST as a tumor treatment.
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Affiliation(s)
- Yoichiro Harada
- Department of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, 3-1-69 Otemae, Chuo-ku, Osaka 541-8567, Japan; (Y.H.); (Y.O.)
| | - Yuki Ohkawa
- Department of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, 3-1-69 Otemae, Chuo-ku, Osaka 541-8567, Japan; (Y.H.); (Y.O.)
| | - Yasuhiko Kizuka
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Gifu 501-1193, Japan;
| | - Naoyuki Taniguchi
- Department of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, 3-1-69 Otemae, Chuo-ku, Osaka 541-8567, Japan; (Y.H.); (Y.O.)
- Correspondence: ; Tel.: +81-6-6945-1181
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14
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Shrimal S, Cherepanova NA, Mandon EC, Venev SV, Gilmore R. Asparagine-linked glycosylation is not directly coupled to protein translocation across the endoplasmic reticulum in Saccharomyces cerevisiae. Mol Biol Cell 2019; 30:2626-2638. [PMID: 31433728 PMCID: PMC6761772 DOI: 10.1091/mbc.e19-06-0330] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Mammalian cells express two oligosaccharyltransferase complexes, STT3A and STT3B, that have distinct roles in N-linked glycosylation. The STT3A complex interacts directly with the protein translocation channel to mediate glycosylation of proteins using an N-terminal-to-C-terminal scanning mechanism. N-linked glycosylation of proteins in budding yeast has been assumed to be a cotranslational reaction. We have compared glycosylation of several glycoproteins in yeast and mammalian cells. Prosaposin, a cysteine-rich protein that contains STT3A-dependent glycosylation sites, is poorly glycosylated in yeast cells and STT3A-deficient human cells. In contrast, a protein with extreme C-terminal glycosylation sites was efficiently glycosylated in yeast by a posttranslocational mechanism. Posttranslocational glycosylation was also observed for carboxypeptidase Y-derived reporter proteins that contain closely spaced acceptor sites. A comparison of two recent protein structures indicates that the yeast OST is unable to interact with the yeast heptameric Sec complex via an evolutionarily conserved interface due to occupation of the OST binding site by the Sec63 protein. The efficiency of glycosylation in yeast is not enhanced for proteins that are translocated by the Sec61 or Ssh1 translocation channels instead of the Sec complex. We conclude that N-linked glycosylation and protein translocation are not directly coupled in yeast cells.
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Affiliation(s)
- Shiteshu Shrimal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Natalia A Cherepanova
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Elisabet C Mandon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Sergey V Venev
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Reid Gilmore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
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15
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Cherepanova NA, Venev SV, Leszyk JD, Shaffer SA, Gilmore R. Quantitative glycoproteomics reveals new classes of STT3A- and STT3B-dependent N-glycosylation sites. J Cell Biol 2019; 218:2782-2796. [PMID: 31296534 PMCID: PMC6683751 DOI: 10.1083/jcb.201904004] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/13/2019] [Accepted: 06/18/2019] [Indexed: 11/24/2022] Open
Abstract
Cherepanova et al. provide quantitative glycoproteomic analyses of human cells that lack either the STT3A or STT3B oligosaccharyltransferase (OST) complex, revealing new classes of STT3A- and STT3B-dependent glycosylation sites and indicating how cooperation between the OST complexes maximizes acceptor site occupancy in cellular glycoproteins. Human cells express two oligosaccharyltransferase complexes (STT3A and STT3B) with partially overlapping functions. The STT3A complex interacts directly with the protein translocation channel to mediate cotranslational glycosylation, while the STT3B complex can catalyze posttranslocational glycosylation. We used a quantitative glycoproteomics procedure to compare glycosylation of roughly 1,000 acceptor sites in wild type and mutant cells. Analysis of site occupancy data disclosed several new classes of STT3A-dependent acceptor sites including those with suboptimal flanking sequences and sites located within cysteine-rich protein domains. Acceptor sites located in short loops of multi-spanning membrane proteins represent a new class of STT3B-dependent site. Remarkably, the lumenal ER chaperone GRP94 was hyperglycosylated in STT3A-deficient cells, bearing glycans on five silent sites in addition to the normal glycosylation site. GRP94 was also hyperglycosylated in wild-type cells treated with ER stress inducers including thapsigargin, dithiothreitol, and NGI-1.
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Affiliation(s)
- Natalia A Cherepanova
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA
| | - Sergey V Venev
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA
| | - John D Leszyk
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA.,Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, MA
| | - Scott A Shaffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA.,Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, MA
| | - Reid Gilmore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA
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16
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Shrimal S, Gilmore R. Oligosaccharyltransferase structures provide novel insight into the mechanism of asparagine-linked glycosylation in prokaryotic and eukaryotic cells. Glycobiology 2019; 29:288-297. [PMID: 30312397 DOI: 10.1093/glycob/cwy093] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/26/2018] [Accepted: 10/09/2018] [Indexed: 11/12/2022] Open
Abstract
Asparagine-linked (N-linked) glycosylation is one of the most common protein modification reactions in eukaryotic cells, occurring upon the majority of proteins that enter the secretory pathway. X-ray crystal structures of the single subunit OSTs from eubacterial and archaebacterial organisms revealed the location of donor and acceptor substrate binding sites and provided the basis for a catalytic mechanism. Cryoelectron microscopy structures of the octameric yeast OST provided substantial insight into the organization and assembly of the multisubunit oligosaccharyltransferases. Furthermore, the cryoelectron microscopy structure of a complex consisting of a mammalian OST complex, the protein translocation channel and a translating ribosome revealed new insight into the mechanism of cotranslational glycosylation.
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Affiliation(s)
- Shiteshu Shrimal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA, USA
| | - Reid Gilmore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA, USA
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17
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Klaver E, Zhao P, May M, Flanagan-Steet H, Freeze HH, Gilmore R, Wells L, Contessa J, Steet R. Selective inhibition of N-linked glycosylation impairs receptor tyrosine kinase processing. Dis Model Mech 2019; 12:dmm.039602. [PMID: 31101650 PMCID: PMC6602306 DOI: 10.1242/dmm.039602] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/08/2019] [Indexed: 12/14/2022] Open
Abstract
Global inhibition of N-linked glycosylation broadly reduces glycan occupancy on glycoproteins, but identifying how this inhibition functionally impacts specific glycoproteins is challenging. This limits our understanding of pathogenesis in the congenital disorders of glycosylation (CDG). We used selective exo-enzymatic labeling of cells deficient in the two catalytic subunits of oligosaccharyltransferase - STT3A and STT3B - to monitor the presence and glycosylation status of cell surface glycoproteins. We show reduced abundance of two canonical tyrosine receptor kinases - the insulin receptor and insulin-like growth factor 1 receptor (IGF-1R) - at the cell surface in STT3A-null cells, due to decreased N-linked glycan site occupancy and proteolytic processing in combination with increased endoplasmic reticulum localization. Providing cDNA for Golgi-resident proprotein convertase subtilisin/kexin type 5a (PCSK5a) and furin cDNA to wild-type and mutant cells produced under-glycosylated forms of PCSK5a, but not furin, in cells lacking STT3A. Reduced glycosylation of PCSK5a in STT3A-null cells or cells treated with the oligosaccharyltransferase inhibitor NGI-1 corresponded with failure to rescue receptor processing, implying that alterations in the glycosylation of this convertase have functional consequences. Collectively, our findings show that STT3A-dependent inhibition of N-linked glycosylation on receptor tyrosine kinases and their convertases combines to impair receptor processing and surface localization. These results provide new insight into CDG pathogenesis and highlight how the surface abundance of some glycoproteins can be dually impacted by abnormal glycosylation.
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Affiliation(s)
- Elsenoor Klaver
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Peng Zhao
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Melanie May
- Research Division, Greenwood Genetic Center, Greenwood, SC 29646, USA
| | | | - Hudson H Freeze
- Sanford Children's Health Research Center, Sanford-Burnham-Prebys Discovery Institute, La Jolla, CA 92037, USA
| | - Reid Gilmore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worchester, MA 01655, USA
| | - Lance Wells
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Joseph Contessa
- Departments of Therapeutic Radiology and Pharmacology, Yale University, New Haven, CT 06520, USA
| | - Richard Steet
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA .,Research Division, Greenwood Genetic Center, Greenwood, SC 29646, USA
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18
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Abstract
Frequent mutation of its major antibody target, the glycoprotein hemagglutinin, ensures that the influenza virus is perennially both a rapidly emerging virus and a major threat to public health. One type of mutation escapes immunity by adding a glycan onto an area of hemagglutinin that many antibodies recognize. This study revealed that these glycan changes follow a simple temporal pattern. Every 5 to 7 years, hemagglutinin adds a new glycan, up to a limit. After this limit is reached, no net additions of glycans occur. Instead, glycans are swapped or lost at longer intervals. Eventually, a pandemic replaces the terminally glycosylated hemagglutinin with a minimally glycosylated one from the animal reservoir, restarting the cycle. This pattern suggests the following: (i) some hemagglutinins are evolved for this decades-long process, which is both defined by and limited by successive glycan addition; and (ii) hemagglutinin's antibody dominance and its capacity for mutations are highly adapted features that allow influenza to outpace our antibody-based immunity. Human antibody-based immunity to influenza A virus is limited by antigenic drift resulting from amino acid substitutions in the hemagglutinin (HA) head domain. Glycan addition can cause large antigenic changes but is limited by fitness costs to viral replication. Here, we report that glycans are added to H1 and H3 HAs at discrete 5-to-7-year intervals, until they reach a functional glycan limit, after which glycans are swapped at approximately 2-fold-longer intervals. Consistent with this pattern, 2009 pandemic H1N1 added a glycan at residue N162 over the 2015–2016 season, an addition that required two epistatic HA head mutations for complete glycosylation. These strains rapidly replaced H1N1 strains globally, by 2017 dominating H3N2 and influenza B virus strains for the season. The pattern of glycan modulation that we outline should aid efforts for tracing the epidemic potential of evolving human IAV strains.
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Ma M, Okuyama M, Tagami T, Kikuchi A, Klahan P, Kimura A. Novel α-1,3/α-1,4-Glucosidase from Aspergillus niger Exhibits Unique Transglucosylation to Generate High Levels of Nigerose and Kojibiose. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:3380-3388. [PMID: 30807133 DOI: 10.1021/acs.jafc.8b07087] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
α-Glucosidase from Aspergillus niger (AgdA; typical α-1,4-glucosidase) is known to industrially produce α-(1→6)-glucooligosaccharides. This fungus also has another α-glucosidase-like protein, AgdB. To learn its function, wild-type AgdB was expressed in Pichia pastoris. However, the enzyme displayed two electrophoretic forms due to heterogeneity of N-glycosylation at Asn354. The deglycosylation mutant N354D shared the same properties with wild-type AgdB. N354D demonstrated hydrolytic specificity toward α-(1→3)- and α-(1→4)-glucosidic linkages, indicating that AgdB is an α-1,3-/α-1,4-glucosidase. N354D-catalyzed transglucosylation from maltose was analyzed in short- and long-term reactions, enabling us to learn the transglucosylation specificity and product accumulation, respectively. A short-term reaction (<15 min) synthesized 3II- O-α-glucosyl-maltose and maltotriose, indicating α-1,3-/α-1,4-transferring specificity. A long-term reaction (<24 h) accumulated kojibiose and nigerose using formed glucose as an acceptor substrate. AgdA and AgdB are distinct α-glucosidases. At a high concentration of glucose added exogenously, AgdB largely generated the rare sugars kojibiose and nigerose (exhibiting beneficial physiological functions) with 19% and 24% yields from maltose, respectively.
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Affiliation(s)
- Min Ma
- Research Faculty of Agriculture , Hokkaido University , Kita-9 Nishi-9 , Kita-ku, Sapporo 060-8589 , Japan
| | - Masayuki Okuyama
- Research Faculty of Agriculture , Hokkaido University , Kita-9 Nishi-9 , Kita-ku, Sapporo 060-8589 , Japan
| | - Takayoshi Tagami
- Research Faculty of Agriculture , Hokkaido University , Kita-9 Nishi-9 , Kita-ku, Sapporo 060-8589 , Japan
| | - Asako Kikuchi
- Research Faculty of Agriculture , Hokkaido University , Kita-9 Nishi-9 , Kita-ku, Sapporo 060-8589 , Japan
| | - Patcharapa Klahan
- Research Faculty of Agriculture , Hokkaido University , Kita-9 Nishi-9 , Kita-ku, Sapporo 060-8589 , Japan
| | - Atsuo Kimura
- Research Faculty of Agriculture , Hokkaido University , Kita-9 Nishi-9 , Kita-ku, Sapporo 060-8589 , Japan
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20
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Bilyk KT, Zhuang X, Murphy KR, Cheng CHC. A tale of two genes: divergent evolutionary fate of haptoglobin and hemopexin in hemoglobinless antarctic icefishes. J Exp Biol 2019; 222:jeb.188573. [DOI: 10.1242/jeb.188573] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 02/06/2019] [Indexed: 12/31/2022]
Abstract
Evolution of Antarctic notothenioid fishes in the isolated freezing Southern Ocean have led to remarkable trait gains and losses. One of the most extraordinary was the loss of the major oxygen carrier hemoglobin (Hb) in the icefishes (family Channichthyidae). While the mechanisms of this loss and the resulting compensatory changes have been well studied, the impact of Hb loss on the network of genes that once supported its recycling and disposal has remained unexplored. Here we report the functional fate and underlying molecular changes of two such key Hb-supporting proteins across the icefish family - haptoglobin (Hp) and hemopexin (Hx), crucial in removing cytotoxic free Hb and heme respectively. Hp plays a critical role in binding free Hb for intracellular recycling and absent its primary client, icefish Hp transcription is now vanishingly little and translation into a functional protein is nearly silenced. Hp genotype degeneration has manifested in separate lineages of the icefish phylogeny with three distinct nonsense mutations and a deletion-frameshift, as well as mutated polyadenylation signal sequences. Thus, Hb loss appears to have diminished selective constraint on Hp maintenance, resulting in its stochastic, co-evolutionary drift towards extinction. Hx binds free heme for iron recycling in hepatocytes. In contrast to Hp, Hx genotype integrity is preserved in the icefishes and transcription occurs at comparable levels to the red-blooded notothenioids. The persistence of Hx likely owes to continued selective pressure for its function from mitochondrial and non-Hb cellular hemoproteins.
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Affiliation(s)
- Kevin T. Bilyk
- Department of Biology, Western Kentucky University, USA
- Department of Animal Biology, University of Illinois, Urbana Champaign, USA
| | - Xuan Zhuang
- Department of Ecology & Evolution, University of Chicago, USA
| | - Katherine R. Murphy
- Department of Animal Biology, University of Illinois, Urbana Champaign, USA
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, USA
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21
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Gupta SK, Shukla P. Glycosylation control technologies for recombinant therapeutic proteins. Appl Microbiol Biotechnol 2018; 102:10457-10468. [DOI: 10.1007/s00253-018-9430-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/02/2018] [Accepted: 10/02/2018] [Indexed: 12/12/2022]
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Editing N-Glycan Site Occupancy with Small-Molecule Oligosaccharyltransferase Inhibitors. Cell Chem Biol 2018; 25:1231-1241.e4. [PMID: 30078634 DOI: 10.1016/j.chembiol.2018.07.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/12/2018] [Accepted: 07/03/2018] [Indexed: 12/22/2022]
Abstract
The oligosaccharyltransferase (OST) is a multisubunit enzyme complex that N-glycosylates proteins in the secretory pathway and is considered to be constitutive and unregulated. However, small-molecule OST inhibitors such as NGI-1 provide a pharmacological approach for regulating N-linked glycosylation. Herein we design cell models with knockout of each OST catalytic subunit (STT3A or STT3B) to screen the activity of NGI-1 and its analogs. We show that NGI-1 targets the function of both STT3A and STT3B and use structure-activity relationships to guide synthesis of catalytic subunit-specific inhibitors. Using this approach, pharmacophores that increase STT3B selectivity are characterized and an STT3B-specific inhibitor is identified. This inhibitor has discrete biological effects on endogenous STT3B target proteins such as COX2 but does not activate the cellular unfolded protein response. Together this work demonstrates that subsets of glycoproteins can be regulated through pharmacologic inhibition of N-linked glycosylation.
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23
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Kitajima T, Xue W, Liu YS, Wang CD, Liu SS, Fujita M, Gao XD. Construction of green fluorescence protein mutant to monitor STT3B-dependent N-glycosylation. FEBS J 2017; 285:915-928. [PMID: 29282902 DOI: 10.1111/febs.14375] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 11/06/2017] [Accepted: 12/21/2017] [Indexed: 12/21/2022]
Abstract
Oligosaccharyltransferases (OSTs) mediate the en bloc transfer of N-glycan intermediates onto the asparagine residue in glycosylation sequons (N-X-S/T, X≠P). These enzymes are typically heteromeric complexes composed of several membrane-associated subunits, in which STT3 is highly conserved as a catalytic core. Metazoan organisms encode two STT3 genes (STT3A and STT3B) in their genome, resulting in the formation of at least two distinct OST isoforms consisting of shared subunits and complex specific subunits. The STT3A isoform of OST primarily glycosylates substrate polypeptides cotranslationally, whereas the STT3B isoform is involved in cotranslational and post-translocational glycosylation of sequons that are skipped by the STT3A isoform. Here, we describe mutant constructs of monomeric enhanced green fluorescent protein (mEGFP), which are susceptible to STT3B-dependent N-glycosylation. The endoplasmic reticulum-localized mEGFP (ER-mEGFP) mutants contained an N-glycosylation sequon at their C-terminus and exhibited increased fluorescence in response to N-glycosylation. Isoform-specific glycosylation of the constructs was confirmed by using STT3A- or STT3B-knockout cell lines. Among the mutant constructs that we tested, the ER-mEGFP mutant containing the N185 -C186 -T187 sequon was the best substrate for the STT3B isoform in terms of glycosylation efficiency and fluorescence change. Our results suggest that the mutant ER-mEGFP is useful for monitoring STT3B-dependent post-translocational N-glycosylation in cells of interest, such as those from putative patients with a congenital disorder of glycosylation.
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Affiliation(s)
- Toshihiko Kitajima
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Wei Xue
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yi-Shi Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Chun-Di Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Si-Si Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Morihisa Fujita
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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24
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Shrimal S, Cherepanova NA, Gilmore R. DC2 and KCP2 mediate the interaction between the oligosaccharyltransferase and the ER translocon. J Cell Biol 2017; 216:3625-3638. [PMID: 28860277 PMCID: PMC5674889 DOI: 10.1083/jcb.201702159] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/29/2017] [Accepted: 07/27/2017] [Indexed: 12/21/2022] Open
Abstract
The STT3A isoform of the oligosaccharyltransferase is adjacent to the protein translocation channel to catalyze co-translational N-glycosylation of proteins in the endoplasmic reticulum. Shrimal et al. show that the DC2 and KCP2 subunits of the STT3A isoform of the oligosaccharyltransferase are responsible for mediating the interaction between the STT3A complex and the protein translocation channel to allow co-translational N-glycosylation of proteins. In metazoan organisms, the STT3A isoform of the oligosaccharyltransferase is localized adjacent to the protein translocation channel to catalyze co-translational N-linked glycosylation of proteins in the endoplasmic reticulum. The mechanism responsible for the interaction between the STT3A complex and the translocation channel has not been addressed. Using genetically modified human cells that are deficient in DC2 or KCP2 proteins, we show that loss of DC2 causes a defect in co-translational N-glycosylation of proteins that mimics an STT3A−/− phenotype. Biochemical analysis showed that DC2 and KCP2 are responsible for mediating the interaction between the protein translocation channel and the STT3A complex. Importantly, DC2- and KCP2-deficient STT3A complexes are stable and enzymatically active. Deletion mutagenesis revealed that a conserved motif in the C-terminal tail of DC2 is critical for assembly into the STT3A complex, whereas the lumenal loop and the N-terminal cytoplasmic segment are necessary for the functional interaction between the STT3A and Sec61 complexes.
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Affiliation(s)
- Shiteshu Shrimal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA
| | - Natalia A Cherepanova
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA
| | - Reid Gilmore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA
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25
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Diversification in the HIV-1 Envelope Hyper-variable Domains V2, V4, and V5 and Higher Probability of Transmitted/Founder Envelope Glycosylation Favor the Development of Heterologous Neutralization Breadth. PLoS Pathog 2016; 12:e1005989. [PMID: 27851829 PMCID: PMC5112890 DOI: 10.1371/journal.ppat.1005989] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 10/11/2016] [Indexed: 11/19/2022] Open
Abstract
A recent study of plasma neutralization breadth in HIV-1 infected individuals at nine International AIDS Vaccine Initiative (IAVI) sites reported that viral load, HLA-A*03 genotype, and subtype C infection were strongly associated with the development of neutralization breadth. Here, we refine the findings of that study by analyzing the impact of the transmitted/founder (T/F) envelope (Env), early Env diversification, and autologous neutralization on the development of plasma neutralization breadth in 21 participants identified during recent infection at two of those sites: Kigali, Rwanda (n = 9) and Lusaka, Zambia (n = 12). Single-genome analysis of full-length T/F Env sequences revealed that all 21 individuals were infected with a highly homogeneous population of viral variants, which were categorized as subtype C (n = 12), A1 (n = 7), or recombinant AC (n = 2). An extensive amino acid sequence-based analysis of variable loop lengths and glycosylation patterns in the T/F Envs revealed that a lower ratio of NXS to NXT-encoded glycan motifs correlated with neutralization breadth. Further analysis comparing amino acid sequence changes, insertions/deletions, and glycan motif alterations between the T/F Env and autologous early Env variants revealed that extensive diversification focused in the V2, V4, and V5 regions of gp120, accompanied by contemporaneous viral escape, significantly favored the development of breadth. These results suggest that more efficient glycosylation of subtype A and C T/F Envs through fewer NXS-encoded glycan sites is more likely to elicit antibodies that can transition from autologous to heterologous neutralizing activity following exposure to gp120 diversification. This initiates an Env-antibody co-evolution cycle that increases neutralization breadth, and is further augmented over time by additional viral and host factors. These findings suggest that understanding how variation in the efficiency of site-specific glycosylation influences neutralizing antibody elicitation and targeting could advance the design of immunogens aimed at inducing antibodies that can transition from autologous to heterologous neutralizing activity.
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26
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Oligosaccharyltransferase inhibition induces senescence in RTK-driven tumor cells. Nat Chem Biol 2016; 12:1023-1030. [PMID: 27694802 DOI: 10.1038/nchembio.2194] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 07/29/2016] [Indexed: 12/21/2022]
Abstract
Asparagine (N)-linked glycosylation is a protein modification critical for glycoprotein folding, stability, and cellular localization. To identify small molecules that inhibit new targets in this biosynthetic pathway, we initiated a cell-based high-throughput screen and lead-compound-optimization campaign that delivered a cell-permeable inhibitor, NGI-1. NGI-1 targets oligosaccharyltransferase (OST), a hetero-oligomeric enzyme that exists in multiple isoforms and transfers oligosaccharides to recipient proteins. In non-small-cell lung cancer cells, NGI-1 blocks cell-surface localization and signaling of the epidermal growth factor receptor (EGFR) glycoprotein, but selectively arrests proliferation in only those cell lines that are dependent on EGFR (or fibroblast growth factor, FGFR) for survival. In these cell lines, OST inhibition causes cell-cycle arrest accompanied by induction of p21, autofluorescence, and cell morphology changes, all hallmarks of senescence. These results identify OST inhibition as a potential therapeutic approach for treating receptor-tyrosine-kinase-dependent tumors and provides a chemical probe for reversibly regulating N-linked glycosylation in mammalian cells.
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27
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Jerczynski O, Lacroix-Pépin N, Boilard E, Calvo E, Bernet A, Fortier MA, Björkgren I, Sipilä P, Belleannée C. Role of Dicer1-Dependent Factors in the Paracrine Regulation of Epididymal Gene Expression. PLoS One 2016; 11:e0163876. [PMID: 27695046 PMCID: PMC5047620 DOI: 10.1371/journal.pone.0163876] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 09/15/2016] [Indexed: 12/21/2022] Open
Abstract
Dicer1 is an endoribonuclease involved in the biogenesis of functional molecules such as microRNAs (miRNAs) and endogenous small interfering RNAs (endo-siRNAs). These small non-coding RNAs are important regulators of post-transcriptional gene expression and participate in the control of male fertility. With the knowledge that 1) Dicer1-dependent factors are required for proper sperm maturation in the epididymis, and that 2) miRNAs are potent mediators of intercellular communication in most biological systems, we investigated the role of Dicer1-dependent factors produced by the proximal epididymis (initial segment/caput)- including miRNAs- on the regulation of epididymal gene expression in the distal epididymis regions (i.e. corpus and cauda). To this end, we performed comparative microarray and ANOVA analyses on control vs. Defb41iCre/wt;Dicer1fl/fl mice in which functional Dicer1 is absent from the principal cells of the proximal epididymis. We identified 35 and 33 transcripts that displayed significant expression level changes in the corpus and cauda regions (Fold change > 2 or < -2; p < 0.002), respectively. Among these transcripts, Zn-alpha 2-glycoprotein (Azgp1) encodes for a sperm equatorial protein whose expression in the epididymis of Dicer1 cKO mice is significantly increased compared to controls. In addition, 154 miRNAs, including miR-210, miR-672, miR-191 and miR-204, showed significantly impaired biogenesis in the absence of Dicer1 from the principal cells of the proximal epididymis (Fold change > 2 or < -2; p < 0.01). These miRNAs are secreted via extracellular vesicles (EVs) derived from the DC2 epididymal principal cell line, and their expression correlates with target transcripts involved in distinct biological pathways, as evidenced by in silico analysis. Albeit correlative and based on in silico approach, our study proposes that Dicer1-dependent factors trigger- directly or not-significant genes expression changes in distinct regions of this organ. The paracrine control of functions important to post-testicular sperm maturation by Dicer1-dependent factors may open new avenues for the identification of molecular targets important to male fertility control.
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Affiliation(s)
- Olivia Jerczynski
- Department of Obstetrics, Gynecology and Reproduction, Université Laval, CHU de Québec Research Center (CHUL), Quebec City, Quebec, Canada
| | - Nicolas Lacroix-Pépin
- Department of Obstetrics, Gynecology and Reproduction, Université Laval, CHU de Québec Research Center (CHUL), Quebec City, Quebec, Canada
| | - Eric Boilard
- Department of Immunity and Infectious Diseases, Université Laval, CHU de Québec Research Center (CHUL), Quebec City, Quebec, Canada
| | - Ezequiel Calvo
- Endocrinology unit, CHU de Québec Research Center (CHUL), Quebec City, Quebec, Canada
| | - Agathe Bernet
- Department of Obstetrics, Gynecology and Reproduction, Université Laval, CHU de Québec Research Center (CHUL), Quebec City, Quebec, Canada
| | - Michel A. Fortier
- Department of Obstetrics, Gynecology and Reproduction, Université Laval, CHU de Québec Research Center (CHUL), Quebec City, Quebec, Canada
| | - Ida Björkgren
- Department of Physiology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Petra Sipilä
- Department of Physiology, Institute of Biomedicine, University of Turku, Turku, Finland
- Turku Center for Disease Modeling, University of Turku, Turku, Finland
| | - Clémence Belleannée
- Department of Obstetrics, Gynecology and Reproduction, Université Laval, CHU de Québec Research Center (CHUL), Quebec City, Quebec, Canada
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28
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Effects of N-Glycosylation of the human cation channel TRPA1 on agonist-sensitivity. Biosci Rep 2016; 36:BSR20160149. [PMID: 27582506 PMCID: PMC5052711 DOI: 10.1042/bsr20160149] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/30/2016] [Indexed: 12/30/2022] Open
Abstract
Determining the functional significance of post-translational modifications advances our understanding of many broadly-expressed proteins, and particularly ion channels. The enzymes that catalyze these modifications are often expressed in a cell-type specific manner, resulting in considerable structural diversity among post-translationally modified proteins that are expressed across a variety of cell types. TRP channels exhibit notably variable behavior between cell types in vitro and in vivo , and they are frequently modified with N-glycans that contribute to protein function. TRPA1 possesses two putative N-linked glycosylation sites at N747 and N753 that have not yet been studied in detail. Here, we show that both of these sites can be modified with an N-glycan and that the glycan at position N747 modulates agonist-sensitivity of TRPA1 in vitro Additionally, we found that N-glycosylation also modulates cooperative effects of temperature and the agonist cinnamaldehyde on TRPA1 channel activation. Collectively, these findings suggest a dynamic role played by the N-glycosylation of human TRPA1. They also provide further evidence of the versatility of N-glycans and will assist in efforts to fully understand the complex regulation of TRPA1 activity.
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29
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Cherepanova N, Shrimal S, Gilmore R. N-linked glycosylation and homeostasis of the endoplasmic reticulum. Curr Opin Cell Biol 2016; 41:57-65. [PMID: 27085638 DOI: 10.1016/j.ceb.2016.03.021] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 03/24/2016] [Accepted: 03/30/2016] [Indexed: 01/17/2023]
Abstract
As a major site of protein biosynthesis, homeostasis of the endoplasmic reticulum is critical for cell viability. Asparagine linked glycosylation of newly synthesized proteins by the oligosaccharyltransferase plays a central role in ER homeostasis due to the use of protein-linked oligosaccharides as recognition and timing markers for glycoprotein quality control pathways that discriminate between correctly folded proteins and terminally malfolded proteins destined for ER associated degradation. Recent findings indicate how the oligosaccharyltransferase achieves efficient and accurate glycosylation of the diverse proteins that enter the endoplasmic reticulum. In metazoan organisms two distinct OST complexes cooperate to maximize the glycosylation of nascent proteins. The STT3B complex glycosylates acceptor sites that have been skipped by the translocation channel associated STT3A complex.
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Affiliation(s)
- Natalia Cherepanova
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, United States
| | - Shiteshu Shrimal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, United States
| | - Reid Gilmore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, United States.
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30
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Abstract
Protein glycosylation is an essential co- and post-translational modification of secretory and membrane proteins in all eukaryotes. The initial steps of N-glycosylation and N-glycan processing are highly conserved between plants, mammals and yeast. In contrast, late N-glycan maturation steps in the Golgi differ significantly in plants giving rise to complex N-glycans with β1,2-linked xylose, core α1,3-linked fucose and Lewis A-type structures. While the essential role of N-glycan modifications on distinct mammalian glycoproteins is already well documented, we have only begun to decipher the biological function of this ubiquitous protein modification in different plant species. In this review, I focus on the biosynthesis and function of different protein N-linked glycans in plants. Special emphasis is given on glycan-mediated quality control processes in the ER and on the biological role of characteristic complex N-glycan structures.
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Affiliation(s)
- Richard Strasser
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
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Mammalian cells lacking either the cotranslational or posttranslocational oligosaccharyltransferase complex display substrate-dependent defects in asparagine linked glycosylation. Sci Rep 2016; 6:20946. [PMID: 26864433 PMCID: PMC4750078 DOI: 10.1038/srep20946] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 01/13/2016] [Indexed: 02/01/2023] Open
Abstract
Asparagine linked glycosylation of proteins is an essential protein modification reaction in most eukaryotic organisms. Metazoan organisms express two oligosaccharyltransferase complexes that are composed of a catalytic subunit (STT3A or STT3B) assembled with a shared set of accessory subunits and one to two complex specific subunits. siRNA mediated knockdowns of STT3A and STT3B in HeLa cells have shown that the two OST complexes have partially non-overlapping roles in N-linked glycosylation. However, incomplete siRNA mediated depletion of STT3A or STT3B reduces the impact of OST complex loss, thereby complicating the interpretation of experimental results. Here, we have used the CRISPR/Cas9 gene editing technology to create viable HEK293 derived cells lines that are deficient for a single catalytic subunit (STT3A or STT3B) or two STT3B-specific accessory subunits (MagT1 and TUSC3). Analysis of protein glycosylation in the STT3A, STT3B and MagT1/TUSC3 null cell lines revealed that these cell lines are superior tools for investigating the in vivo role and substrate preferences of the STT3A and STT3B complexes.
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Zacchi LF, Schulz BL. N-glycoprotein macroheterogeneity: biological implications and proteomic characterization. Glycoconj J 2015; 33:359-76. [DOI: 10.1007/s10719-015-9641-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/04/2015] [Accepted: 11/20/2015] [Indexed: 10/22/2022]
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Abstract
INTRODUCTION Glycans are increasingly important in the development of new biopharmaceuticals with optimized efficacy, half-life, and antigenicity. Current expression platforms for recombinant glycoprotein therapeutics typically do not produce homogeneous glycans and frequently display non-human glycans which may cause unwanted side effects. To circumvent these issues, glyco-engineering has been applied to different expression systems including mammalian cells, insect cells, yeast, and plants. AREAS COVERED This review summarizes recent developments in glyco-engineering focusing mainly on in vivo expression systems for recombinant proteins. The highlighted strategies aim at producing glycoproteins with homogeneous N- and O-linked glycans of defined composition. EXPERT OPINION Glyco-engineering of expression platforms is increasingly recognized as an important strategy to improve biopharmaceuticals. A better understanding and control of the factors leading to glycan heterogeneity will allow simplified production of recombinant glycoprotein therapeutics with less variation in terms of glycosylation. Further technological advances will have a major impact on manufacturing processes and may provide a completely new class of glycoprotein therapeutics with customized functions.
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Affiliation(s)
- Martina Dicker
- a 1 University of Natural Resources and Life Sciences , Department of Applied Genetics and Cell Biology , Muthgasse 18, Vienna, Austria
| | - Richard Strasser
- b 2 University of Natural Resources and Life Sciences, Department of Applied Genetics and Cell Biology , Muthgasse 18, Vienna, Austria +43 1 47654 6705 ; +43 1 47654 6392 ;
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Harada Y, Hirayama H, Suzuki T. Generation and degradation of free asparagine-linked glycans. Cell Mol Life Sci 2015; 72:2509-33. [PMID: 25772500 PMCID: PMC11113800 DOI: 10.1007/s00018-015-1881-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 02/19/2015] [Accepted: 03/05/2015] [Indexed: 10/23/2022]
Abstract
Asparagine (N)-linked protein glycosylation, which takes place in the eukaryotic endoplasmic reticulum (ER), is important for protein folding, quality control and the intracellular trafficking of secretory and membrane proteins. It is known that, during N-glycosylation, considerable amounts of lipid-linked oligosaccharides (LLOs), the glycan donor substrates for N-glycosylation, are hydrolyzed to form free N-glycans (FNGs) by unidentified mechanisms. FNGs are also generated in the cytosol by the enzymatic deglycosylation of misfolded glycoproteins during ER-associated degradation. FNGs derived from LLOs and misfolded glycoproteins are eventually merged into one pool in the cytosol and the various glycan structures are processed to a near homogenous glycoform. This article summarizes the current state of our knowledge concerning the formation and catabolism of FNGs.
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Affiliation(s)
- Yoichiro Harada
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan
| | - Hiroto Hirayama
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan
| | - Tadashi Suzuki
- Glycometabolome Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan
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Shrimal S, Gilmore R. Reduced expression of the oligosaccharyltransferase exacerbates protein hypoglycosylation in cells lacking the fully assembled oligosaccharide donor. Glycobiology 2015; 25:774-83. [PMID: 25792706 DOI: 10.1093/glycob/cwv018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 03/09/2015] [Indexed: 11/13/2022] Open
Abstract
A defect in the assembly of the oligosaccharide donor (Dol-PP-GlcNAc(2)Man(9)Glc(3)) for N-linked glycosylation causes hypoglycosylation of proteins by the oligosaccharyltransferase (OST). Mammalian cells express two OST complexes that have different catalytic subunits (STT3A or STT3B). We monitored glycosylation of proteins in asparagine-linked glycosylation 6 (ALG6) deficient cell lines that assemble Dol-PP-GlcNAc(2)Man(9) as the largest oligosaccharide donor. Based upon pulse labeling experiments, 30-40% of STT3A-dependent glycosylation sites and 20% of STT3B-dependent sites are skipped in ALG6-congenital disorders of glycosylation fibroblasts supporting previous evidence that the STT3B complex has a relaxed preference for the fully assembled oligosaccharide donor. Glycosylation of STT3B-dependent sites was more severely reduced in the ALG6 deficient MI8-5 cell line. Protein immunoblot analysis and RT-PCR revealed that MI8-5 cells express 2-fold lower levels of STT3B than the parental Chinese hamster ovary cells. The combination of reduced expression of STT3B and the lack of the optimal Dol-PP-GlcNAc(2)Man(9)Glc(3) donor synergize to cause very severe hypoglycosylation of proteins in MI8-5 cells. Thus, differences in OST subunit expression can modify the severity of hypoglycosylation displayed by cells with a primary defect in the dolichol oligosaccharide assembly pathway.
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Affiliation(s)
- Shiteshu Shrimal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Reid Gilmore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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Shrimal S, Cherepanova NA, Gilmore R. Cotranslational and posttranslocational N-glycosylation of proteins in the endoplasmic reticulum. Semin Cell Dev Biol 2014; 41:71-8. [PMID: 25460543 DOI: 10.1016/j.semcdb.2014.11.005] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 11/12/2014] [Accepted: 11/14/2014] [Indexed: 11/19/2022]
Abstract
Asparagine linked glycosylation of proteins is an essential protein modification reaction in most eukaryotic organisms. N-linked oligosaccharides are important for protein folding and stability, biosynthetic quality control, intracellular traffic and the physiological function of many N-glycosylated proteins. In metazoan organisms, the oligosaccharyltransferase is composed of a catalytic subunit (STT3A or STT3B) and a set of accessory subunits. Duplication of the catalytic subunit gene allowed cells to evolve OST complexes that act sequentially to maximize the glycosylation efficiency of the large number of proteins that are glycosylated in metazoan organisms. We will summarize recent progress in understanding the mechanism of (a) cotranslational glycosylation by the translocation channel associated STT3A complex, (b) the role of the STT3B complex in mediating cotranslational or posttranslocational glycosylation of acceptor sites that have been skipped by the STT3A complex, and (c) the role of the oxidoreductase MagT1 in STT3B-dependent glycosylation of cysteine-proximal acceptor sites.
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Affiliation(s)
- Shiteshu Shrimal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, United States
| | - Natalia A Cherepanova
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, United States
| | - Reid Gilmore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, United States.
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Cherepanova NA, Shrimal S, Gilmore R. Oxidoreductase activity is necessary for N-glycosylation of cysteine-proximal acceptor sites in glycoproteins. ACTA ACUST UNITED AC 2014; 206:525-39. [PMID: 25135935 PMCID: PMC4137057 DOI: 10.1083/jcb.201404083] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Stabilization of protein tertiary structure by disulfides can interfere with glycosylation of acceptor sites (NXT/S) in nascent polypeptides. Here, we show that MagT1, an ER-localized thioredoxin homologue, is a subunit of the STT3B isoform of the oligosaccharyltransferase (OST). The lumenally oriented active site CVVC motif in MagT1 is required for glycosylation of STT3B-dependent acceptor sites including those that are closely bracketed by disulfides or contain cysteine as the internal residue (NCT/S). The MagT1- and STT3B-dependent glycosylation of cysteine-proximal acceptor sites can be reduced by eliminating cysteine residues. The predominant form of MagT1 in vivo is oxidized, which is consistent with transient formation of mixed disulfides between MagT1 and a glycoprotein substrate to facilitate access of STT3B to unmodified acceptor sites. Cotranslational N-glycosylation by the STT3A isoform of the OST, which lacks MagT1, allows efficient modification of acceptor sites in cysteine-rich protein domains before disulfide bond formation. Thus, mammalian cells use two mechanisms to achieve N-glycosylation of cysteine proximal acceptor sites.
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Affiliation(s)
- Natalia A Cherepanova
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Shiteshu Shrimal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Reid Gilmore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
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Honarmand Ebrahimi K, West GM, Flefil R. Mass spectrometry approach and ELISA reveal the effect of codon optimization on N-linked glycosylation of HIV-1 gp120. J Proteome Res 2014; 13:5801-11. [PMID: 25285362 PMCID: PMC4261944 DOI: 10.1021/pr500740n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The genes encoding many viral proteins such as HIV-1 envelope glycoprotein gp120 have a tendency for codons that are poorly used by the human genome. Why these codons are frequently present in the HIV genome is not known. The presence of these codons limits expression of HIV-1 gp120 for biochemical studies. The poor codons are replaced by synonymous codons that are frequently present in the highly expressed human genes to overexpress this protein. Whether this codon optimization affects functional properties of gp120 such as its N-linked glycosylation is unknown. We applied a bottom-up mass-spectrometry-based workflow for the direct measurement of deglycosylated and unglycosylated peptides with putative N-linked glycosylation sites, that is, NxS/T motifs. Using this mass-spectrometry approach in combination with ELISA, it is found that codon optimization significantly reduces the frequency with which the dolichol pyrophosphate-linked oligosaccharide is added by the catalytic subunits of oligosaccharide transferase complex to the glycosylation sites. This reduction affects binding of glycan-dependent broadly neutralizing antibodies. These data are essential for biochemical studies of gp120 and successful development of a vaccine against HIV-1. Furthermore, they demonstrate a mass-spectrometry approach for studying the site-specific N-linked glycosylation efficiency of glycoproteins.
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Affiliation(s)
- Kourosh Honarmand Ebrahimi
- Department of Infectious Diseases and ‡Mass Spectrometry and Proteomics, The Scripps Research Institute , Scripps Florida, 130 Scripps Way No. 2A2, Jupiter, Florida 33458, United States
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Malaby HLH, Kobertz WR. The middle X residue influences cotranslational N-glycosylation consensus site skipping. Biochemistry 2014; 53:4884-93. [PMID: 25029371 PMCID: PMC4372077 DOI: 10.1021/bi500681p] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
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Asparagine (N)-linked glycosylation
is essential for efficient
protein folding in the endoplasmic reticulum (ER) and anterograde
trafficking through the secretory pathway. N-Glycans are attached
to nascent polypeptides at consensus sites, N-X-T/S (X ≠ P),
by one of two enzymatic isoforms of the oligosaccharyltransferase
(OST), STT3A or STT3B. Here, we examined the effect of the consensus
site X and hydroxyl residue on the distributions of co- and post-translational
N-glycosylation of a type I transmembrane glycopeptide scaffold. Using
rapid radioactive pulse–chase experiments to resolve co-translational
(STT3A) and post-translational (STT3B) events, we determined that
NXS consensus sites containing large hydrophobic and negatively charged
middle residues are frequently skipped by STT3A during protein translation.
Post-translational modification of the cotranslationally skipped sites
by STT3B was similarly hindered by the middle X residue, resulting
in hypoglycosylation of NXS sites containing large hydrophobic and
negatively charged side chains. In contrast, NXT consensus sites (barring
NWT) were efficiently modified by the cotranslational machinery, reducing
STT3B’s role in modifying consensus sites skipped during protein
translation. A strong correlation between cotranslational N-glycosylation
efficiency and the rate of post-translational N-glycosylation was
determined, showing that the OST STT3A and STT3B isoforms are similarly
influenced by the hydroxyl and middle X consensus site residues. Substituting
various middle X residues into an OST eubacterial homologous structure
revealed that small and polar consensus site X residues fit well in
the peptide binding site whereas large hydrophobic and negatively
charged residues were harder to accommodate, indicating conserved
enzymatic mechanisms for the mammalian OST isoforms.
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Affiliation(s)
- Heidi L H Malaby
- Department of Biochemistry and Molecular Pharmacology and Programs in Neuroscience and Chemical Biology, University of Massachusetts Medical School , 364 Plantation Street, Worcester, Massachusetts 01605-2324, United States
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