1
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Bagdonaite I, Abdurahman S, Mirandola M, Pasqual D, Frank M, Narimatsu Y, Joshi HJ, Vakhrushev SY, Salata C, Mirazimi A, Wandall HH. Targeting host O-linked glycan biosynthesis affects Ebola virus replication efficiency and reveals differential GalNAc-T acceptor site preferences on the Ebola virus glycoprotein. J Virol 2024:e0052424. [PMID: 38757972 DOI: 10.1128/jvi.00524-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Ebola virus glycoprotein (EBOV GP) is one of the most heavily O-glycosylated viral glycoproteins, yet we still lack a fundamental understanding of the structure of its large O-glycosylated mucin-like domain and to what degree the host O-glycosylation capacity influences EBOV replication. Using tandem mass spectrometry, we identified 47 O-glycosites on EBOV GP and found similar glycosylation signatures on virus-like particle- and cell lysate-derived GP. Furthermore, we performed quantitative differential O-glycoproteomics on proteins produced in wild-type HEK293 cells and cell lines ablated for the three key initiators of O-linked glycosylation, GalNAc-T1, -T2, and -T3. The data show that 12 out of the 47 O-glycosylated sites were regulated, predominantly by GalNAc-T1. Using the glycoengineered cell lines for authentic EBOV propagation, we demonstrate the importance of O-linked glycan initiation and elongation for the production of viral particles and the titers of progeny virus. The mapped O-glycan positions and structures allowed to generate molecular dynamics simulations probing the largely unknown spatial arrangements of the mucin-like domain. The data highlight targeting GALNT1 or C1GALT1C1 as a possible way to modulate O-glycan density on EBOV GP for novel vaccine designs and tailored intervention approaches.IMPORTANCEEbola virus glycoprotein acquires its extensive glycan shield in the host cell, where it is decorated with N-linked glycans and mucin-type O-linked glycans. The latter is initiated by a family of polypeptide GalNAc-transferases that have different preferences for optimal peptide substrates resulting in a spectrum of both very selective and redundant substrates for each isoform. In this work, we map the exact locations of O-glycans on Ebola virus glycoprotein and identify subsets of sites preferentially initiated by one of the three key isoforms of GalNAc-Ts, demonstrating that each enzyme contributes to the glycan shield integrity. We further show that altering host O-glycosylation capacity has detrimental effects on Ebola virus replication, with both isoform-specific initiation and elongation playing a role. The combined structural and functional data highlight glycoengineered cell lines as useful tools for investigating molecular mechanisms imposed by specific glycans and for steering the immune responses in future vaccine designs.
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Affiliation(s)
- Ieva Bagdonaite
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | | | - Mattia Mirandola
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Denis Pasqual
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | | | - Yoshiki Narimatsu
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | - Hiren J Joshi
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | - Cristiano Salata
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Ali Mirazimi
- Public Health Agency of Sweden, Solna, Sweden
- Department of Laboratory Medicine (LABMED), Karolinska Institute, Stockholm, Sweden
- National Veterinary Institute, Uppsala, Sweden
| | - Hans H Wandall
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
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2
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Larsen ISB, Povolo L, Zhou L, Tian W, Mygind KJ, Hintze J, Jiang C, Hartill V, Prescott K, Johnson CA, Mullegama SV, McConkie-Rosell A, McDonald M, Hansen L, Vakhrushev SY, Schjoldager KT, Clausen H, Worzfeld T, Joshi HJ, Halim A. The SHDRA syndrome-associated gene TMEM260 encodes a protein-specific O-mannosyltransferase. Proc Natl Acad Sci U S A 2023; 120:e2302584120. [PMID: 37186866 PMCID: PMC10214176 DOI: 10.1073/pnas.2302584120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/21/2023] [Indexed: 05/17/2023] Open
Abstract
Mutations in the TMEM260 gene cause structural heart defects and renal anomalies syndrome, but the function of the encoded protein remains unknown. We previously reported wide occurrence of O-mannose glycans on extracellular immunoglobulin, plexin, transcription factor (IPT) domains found in the hepatocyte growth factor receptor (cMET), macrophage-stimulating protein receptor (RON), and plexin receptors, and further demonstrated that two known protein O-mannosylation systems orchestrated by the POMT1/2 and transmembrane and tetratricopeptide repeat-containing proteins 1-4 gene families were not required for glycosylation of these IPT domains. Here, we report that the TMEM260 gene encodes an ER-located protein O-mannosyltransferase that selectively glycosylates IPT domains. We demonstrate that disease-causing TMEM260 mutations impair O-mannosylation of IPT domains and that TMEM260 knockout in cells results in receptor maturation defects and abnormal growth of 3D cell models. Thus, our study identifies the third protein-specific O-mannosylation pathway in mammals and demonstrates that O-mannosylation of IPT domains serves critical functions during epithelial morphogenesis. Our findings add a new glycosylation pathway and gene to a growing group of congenital disorders of glycosylation.
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Affiliation(s)
- Ida Signe Bohse Larsen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Lorenzo Povolo
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Luping Zhou
- Faculty of Medicine, Institute of Pharmacology, University of Marburg, 35043Marburg, Germany
| | - Weihua Tian
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Kasper Johansen Mygind
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - John Hintze
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Chen Jiang
- Faculty of Medicine, Institute of Pharmacology, University of Marburg, 35043Marburg, Germany
| | - Verity Hartill
- Leeds Institute of Medical Research, University of Leeds, St James’ University Hospital, LeedsLS2 9JT, United Kingdom
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, LeedsLS7 4SA, United Kingdom
| | - Katrina Prescott
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, LeedsLS7 4SA, United Kingdom
| | - Colin A. Johnson
- Leeds Institute of Medical Research, University of Leeds, St James’ University Hospital, LeedsLS2 9JT, United Kingdom
| | | | - Allyn McConkie-Rosell
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC27710
| | - Marie McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC27710
| | - Lars Hansen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Sergey Y. Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Katrine T. Schjoldager
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Thomas Worzfeld
- Faculty of Medicine, Institute of Pharmacology, University of Marburg, 35043Marburg, Germany
- Max-Planck-Institute for Heart and Lung Research, 61231Bad Nauheim, Germany
| | - Hiren J. Joshi
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Adnan Halim
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
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3
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Nason R, Büll C, Konstantinidi A, Sun L, Ye Z, Halim A, Du W, Sørensen DM, Durbesson F, Furukawa S, Mandel U, Joshi HJ, Dworkin LA, Hansen L, David L, Iverson TM, Bensing BA, Sullam PM, Varki A, Vries ED, de Haan CAM, Vincentelli R, Henrissat B, Vakhrushev SY, Clausen H, Narimatsu Y. Display of the human mucinome with defined O-glycans by gene engineered cells. Nat Commun 2021; 12:4070. [PMID: 34210959 PMCID: PMC8249670 DOI: 10.1038/s41467-021-24366-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 06/08/2021] [Indexed: 02/08/2023] Open
Abstract
Mucins are a large family of heavily O-glycosylated proteins that cover all mucosal surfaces and constitute the major macromolecules in most body fluids. Mucins are primarily defined by their variable tandem repeat (TR) domains that are densely decorated with different O-glycan structures in distinct patterns, and these arguably convey much of the informational content of mucins. Here, we develop a cell-based platform for the display and production of human TR O-glycodomains (~200 amino acids) with tunable structures and patterns of O-glycans using membrane-bound and secreted reporters expressed in glycoengineered HEK293 cells. Availability of defined mucin TR O-glycodomains advances experimental studies into the versatile role of mucins at the interface with pathogenic microorganisms and the microbiome, and sparks new strategies for molecular dissection of specific roles of adhesins, glycoside hydrolases, glycopeptidases, viruses and other interactions with mucin TRs as highlighted by examples.
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Affiliation(s)
- Rebecca Nason
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Büll
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andriana Konstantinidi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lingbo Sun
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zilu Ye
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Adnan Halim
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Wenjuan Du
- Section Virology, Division of Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, CL, Utrecht, the Netherlands
| | - Daniel M Sørensen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fabien Durbesson
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
| | - Sanae Furukawa
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ulla Mandel
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hiren J Joshi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leo Alexander Dworkin
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars Hansen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leonor David
- Institute of Molecular Pathology and Immunology of the University of Porto/I3S, Porto, Portugal.,Medical Faculty of the University of Porto, Porto, Portugal
| | - Tina M Iverson
- Departments of Pharmacology and Biochemistry, Vanderbilt University, Nashville, TN, USA
| | - Barbara A Bensing
- Department of Medicine, The San Francisco Veterans Affairs Medical Center, and the University of California, San Francisco, CA, USA
| | - Paul M Sullam
- Department of Medicine, The San Francisco Veterans Affairs Medical Center, and the University of California, San Francisco, CA, USA
| | - Ajit Varki
- The Glycobiology Research and Training Center, and the Department of Cellular and Molecular Medicine, University of California, San Diego, CA, USA
| | - Erik de Vries
- Section Virology, Division of Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, CL, Utrecht, the Netherlands
| | - Cornelis A M de Haan
- Section Virology, Division of Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, CL, Utrecht, the Netherlands
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
| | - Bernard Henrissat
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark. .,GlycoDisplay ApS, Copenhagen, Denmark.
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4
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Macías-León J, Bermejo IA, Asín A, García-García A, Compañón I, Jiménez-Moreno E, Coelho H, Mangini V, Albuquerque IS, Marcelo F, Asensio JL, Bernardes GJL, Joshi HJ, Fiammengo R, Blixt O, Hurtado-Guerrero R, Corzana F. Structural characterization of an unprecedented lectin-like antitumoral anti-MUC1 antibody. Chem Commun (Camb) 2021; 56:15137-15140. [PMID: 33211039 DOI: 10.1039/d0cc06349e] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The molecular basis of antibody 5E5, which recognizes the entire GalNAc unit as a primary epitope is disclosed. The antibody's contacts with the peptide are mostly limited to two residues, allowing it to show some degree of promiscuity. These findings open the door to the chemical design of peptide-mimetics for developing efficient anti-cancer vaccines and diagnostic tools.
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Affiliation(s)
- Javier Macías-León
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain.
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5
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Madsen TD, Hansen LH, Hintze J, Ye Z, Jebari S, Andersen DB, Joshi HJ, Ju T, Goetze JP, Martin C, Rosenkilde MM, Holst JJ, Kuhre RE, Goth CK, Vakhrushev SY, Schjoldager KT. An atlas of O-linked glycosylation on peptide hormones reveals diverse biological roles. Nat Commun 2020; 11:4033. [PMID: 32820167 PMCID: PMC7441158 DOI: 10.1038/s41467-020-17473-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 07/02/2020] [Indexed: 12/17/2022] Open
Abstract
Peptide hormones and neuropeptides encompass a large class of bioactive peptides that regulate physiological processes like anxiety, blood glucose, appetite, inflammation and blood pressure. Here, we execute a focused discovery strategy to provide an extensive map of O-glycans on peptide hormones. We find that almost one third of the 279 classified peptide hormones carry O-glycans. Many of the identified O-glycosites are conserved and are predicted to serve roles in proprotein processing, receptor interaction, biodistribution and biostability. We demonstrate that O-glycans positioned within the receptor binding motifs of members of the neuropeptide Y and glucagon families modulate receptor activation properties and substantially extend peptide half-lives. Our study highlights the importance of O-glycosylation in the biology of peptide hormones, and our map of O-glycosites in this large class of biomolecules serves as a discovery platform for an important class of molecules with potential opportunities for drug designs.
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Affiliation(s)
- Thomas D Madsen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Lasse H Hansen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark.,Department of Clinical Biochemistry, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, DK-2100, Copenhagen O, Denmark
| | - John Hintze
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Zilu Ye
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Shifa Jebari
- Biofisika Institute (UPV/EHU, CSIC), Departamento de Bioquímica, Universidad del País Vasco, Bilbao, 48080, Spain
| | - Daniel B Andersen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Hiren J Joshi
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Tongzhong Ju
- Office of Biotechnology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Jens P Goetze
- Department of Clinical Biochemistry, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, DK-2100, Copenhagen O, Denmark.,Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Cesar Martin
- Office of Biotechnology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Mette M Rosenkilde
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Jens J Holst
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Rune E Kuhre
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Christoffer K Goth
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Katrine T Schjoldager
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark.
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6
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Bagdonaite I, Pallesen EM, Ye Z, Vakhrushev SY, Marinova IN, Nielsen MI, Kramer SH, Pedersen SF, Joshi HJ, Bennett EP, Dabelsteen S, Wandall HH. O-glycan initiation directs distinct biological pathways and controls epithelial differentiation. EMBO Rep 2020; 21:e48885. [PMID: 32329196 PMCID: PMC7271655 DOI: 10.15252/embr.201948885] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 03/03/2020] [Accepted: 03/16/2020] [Indexed: 12/17/2022] Open
Abstract
Post-translational modifications (PTMs) greatly expand the function and potential for regulation of protein activity, and O-glycosylation is among the most abundant and diverse PTMs. Initiation of O-GalNAc glycosylation is regulated by 20 distinct GalNAc-transferases (GalNAc-Ts), and deficiencies in individual GalNAc-Ts are associated with human disease, causing subtle but distinct phenotypes in model organisms. Here, we generate a set of isogenic keratinocyte cell lines lacking either of the three dominant and differentially expressed GalNAc-Ts. Through the ability of keratinocytes to form epithelia, we investigate the phenotypic consequences of the loss of individual GalNAc-Ts. Moreover, we probe the cellular responses through global transcriptomic, differential glycoproteomic, and differential phosphoproteomic analyses. We demonstrate that loss of individual GalNAc-T isoforms causes distinct epithelial phenotypes through their effect on specific biological pathways; GalNAc-T1 targets are associated with components of the endomembrane system, GalNAc-T2 targets with cell-ECM adhesion, and GalNAc-T3 targets with epithelial differentiation. Thus, GalNAc-T isoforms serve specific roles during human epithelial tissue formation.
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Affiliation(s)
- Ieva Bagdonaite
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Emil Mh Pallesen
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Zilu Ye
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Irina N Marinova
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mathias I Nielsen
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Signe H Kramer
- Cell Biology and Physiology, Department of Science, University of Copenhagen, Copenhagen, Denmark
| | - Stine F Pedersen
- Cell Biology and Physiology, Department of Science, University of Copenhagen, Copenhagen, Denmark
| | - Hiren J Joshi
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Eric P Bennett
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.,School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Sally Dabelsteen
- School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Hans H Wandall
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
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7
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Narimatsu Y, Joshi HJ, Schjoldager KT, Hintze J, Halim A, Steentoft C, Nason R, Mandel U, Bennett EP, Clausen H, Vakhrushev SY. Exploring Regulation of Protein O-Glycosylation in Isogenic Human HEK293 Cells by Differential O-Glycoproteomics. Mol Cell Proteomics 2019; 18:1396-1409. [PMID: 31040225 PMCID: PMC6601209 DOI: 10.1074/mcp.ra118.001121] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 03/26/2019] [Indexed: 02/04/2023] Open
Abstract
Most proteins trafficking the secretory pathway of metazoan cells will acquire GalNAc-type O-glycosylation. GalNAc-type O-glycosylation is differentially regulated in cells by the expression of a repertoire of up to twenty genes encoding polypeptide GalNAc-transferase isoforms (GalNAc-Ts) that initiate O-glycosylation. These GalNAc-Ts orchestrate the positions and patterns of O-glycans on proteins in coordinated, but poorly understood ways - guided partly by the kinetic properties and substrate specificities of their catalytic domains, as well as by modulatory effects of their unique GalNAc-binding lectin domains. Here, we provide the hereto most comprehensive characterization of nonredundant contributions of individual GalNAc-T isoforms to the O-glycoproteome of the human HEK293 cell using quantitative differential O-glycoproteomics on a panel of isogenic HEK293 cells with knockout of GalNAc-T genes (GALNT1, T2, T3, T7, T10, or T11). We confirm that a major part of the O-glycoproteome is covered by redundancy, whereas distinct O-glycosite subsets are covered by nonredundant GalNAc-T isoform-specific functions. We demonstrate that the GalNAc-T7 and T10 isoforms function in follow-up of high-density O-glycosylated regions, and that GalNAc-T11 has highly restricted functions and essentially only serves the low-density lipoprotein-related receptors in linker regions (C6XXXTC1) between the ligand-binding repeats.
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Affiliation(s)
- Yoshiki Narimatsu
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.
| | - Hiren J Joshi
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Katrine T Schjoldager
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - John Hintze
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Adnan Halim
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Catharina Steentoft
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Rebecca Nason
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Ulla Mandel
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Eric P Bennett
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Henrik Clausen
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.
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8
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Narimatsu Y, Joshi HJ, Nason R, Van Coillie J, Karlsson R, Sun L, Ye Z, Chen YH, Schjoldager KT, Steentoft C, Furukawa S, Bensing BA, Sullam PM, Thompson AJ, Paulson JC, Büll C, Adema GJ, Mandel U, Hansen L, Bennett EP, Varki A, Vakhrushev SY, Yang Z, Clausen H. An Atlas of Human Glycosylation Pathways Enables Display of the Human Glycome by Gene Engineered Cells. Mol Cell 2019; 75:394-407.e5. [PMID: 31227230 DOI: 10.1016/j.molcel.2019.05.017] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 02/08/2019] [Accepted: 05/10/2019] [Indexed: 11/29/2022]
Abstract
The structural diversity of glycans on cells-the glycome-is vast and complex to decipher. Glycan arrays display oligosaccharides and are used to report glycan hapten binding epitopes. Glycan arrays are limited resources and present saccharides without the context of other glycans and glycoconjugates. We used maps of glycosylation pathways to generate a library of isogenic HEK293 cells with combinatorially engineered glycosylation capacities designed to display and dissect the genetic, biosynthetic, and structural basis for glycan binding in a natural context. The cell-based glycan array is self-renewable and reports glycosyltransferase genes required (or blocking) for interactions through logical sequential biosynthetic steps, which is predictive of structural glycan features involved and provides instructions for synthesis, recombinant production, and genetic dissection strategies. Broad utility of the cell-based glycan array is demonstrated, and we uncover higher order binding of microbial adhesins to clustered patches of O-glycans organized by their presentation on proteins.
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Affiliation(s)
- Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark; GlycoDisplay ApS, Copenhagen, Denmark.
| | - Hiren J Joshi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Rebecca Nason
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Julie Van Coillie
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Richard Karlsson
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Lingbo Sun
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Zilu Ye
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Yen-Hsi Chen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark; GlycoDisplay ApS, Copenhagen, Denmark
| | - Katrine T Schjoldager
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Catharina Steentoft
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Sanae Furukawa
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Barbara A Bensing
- Department of Medicine, The San Francisco Veterans Affairs Medical Center, and the University of California, San Francisco, San Francisco, CA 94121, USA
| | - Paul M Sullam
- Department of Medicine, The San Francisco Veterans Affairs Medical Center, and the University of California, San Francisco, San Francisco, CA 94121, USA
| | - Andrew J Thompson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - James C Paulson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Christian Büll
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark; Radiotherapy and OncoImmunology Laboratory, Department of Radiotherapy, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Gosse J Adema
- Radiotherapy and OncoImmunology Laboratory, Department of Radiotherapy, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ulla Mandel
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Lars Hansen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Eric Paul Bennett
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Ajit Varki
- The Glycobiology Research and Training Center and the Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA 92093, USA
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Zhang Yang
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark; GlycoDisplay ApS, Copenhagen, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark.
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9
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Larsen ISB, Narimatsu Y, Clausen H, Joshi HJ, Halim A. Multiple distinct O-Mannosylation pathways in eukaryotes. Curr Opin Struct Biol 2019; 56:171-178. [PMID: 30999272 DOI: 10.1016/j.sbi.2019.03.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/26/2019] [Accepted: 03/01/2019] [Indexed: 12/29/2022]
Abstract
Protein O-mannosylation (O-Man), originally discovered in yeast five decades ago, is an important post-translational modification (PTM) conserved from bacteria to humans, but not found in plants or nematodes. Until recently, the homologous family of ER-located protein O-mannosyl transferases (PMT1-7 in yeast; POMT1/POMT2 in humans), were the only known enzymes involved in directing O-Man biosynthesis in eukaryotes. However, recent studies demonstrate the existence of multiple distinct O-Man glycosylation pathways indicating that the genetic and biosynthetic regulation of O-Man in eukaryotes is more complex than previously envisioned. Introduction of sensitive glycoproteomics strategies provided an expansion of O-Man glycoproteomes in eukaryotes (yeast and mammalian cell lines) leading to the discovery of O-Man glycosylation on important mammalian cell adhesion (cadherin superfamily) and signaling (plexin family) macromolecules, and to the discovery of unique nucleocytoplasmic O-Man glycosylation in yeast. It is now evident that eukaryotes have multiple distinct O-Man glycosylation pathways including: i) the classical PMT1-7 and POMT1/POMT2 pathway conserved in all eukaryotes apart from plants; ii) a yet uncharacterized nucleocytoplasmic pathway only found in yeast; iii) an ER-located pathway directed by the TMTC1-4 genes found in metazoans and protists and primarily dedicated to the cadherin superfamily; and iv) a yet uncharacterized pathway found in metazoans primarily dedicated to plexins. O-Man glycosylation is thus emerging as a much more widespread and evolutionary diverse PTM with complex genetic and biosynthetic regulation. While deficiencies in the POMT1/POMT2 O-Man pathway underlie muscular dystrophies, the TMTC1-4 pathway appear to be involved in distinct congenital disorders with neurodevelopmental phenotypes. Here, we review and discuss the recent discoveries of the new non-classical O-Man glycosylation pathways, their substrates, functions and roles in disease.
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Affiliation(s)
- Ida Signe Bohse Larsen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Hiren J Joshi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.
| | - Adnan Halim
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.
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10
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Steentoft C, Fuhrmann M, Battisti F, Van Coillie J, Madsen TD, Campos D, Halim A, Vakhrushev SY, Joshi HJ, Schreiber H, Mandel U, Narimatsu Y. A strategy for generating cancer-specific monoclonal antibodies to aberrant O-glycoproteins: identification of a novel dysadherin-Tn antibody. Glycobiology 2019; 29:307-319. [PMID: 30726901 PMCID: PMC6430981 DOI: 10.1093/glycob/cwz004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/18/2019] [Accepted: 01/24/2019] [Indexed: 12/25/2022] Open
Abstract
Successful application of potent antibody-based T-cell engaging immunotherapeutic strategies is currently limited mainly to hematological cancers. One major reason is the lack of well-characterized antigens on solid tumors with sufficient cancer specific expression. Aberrantly O-glycosylated proteins contain promising cancer-specific O-glycopeptide epitopes suitable for immunotherapeutic applications, but currently only few examples of such antibody epitopes have been identified. We previously showed that chimeric antigen receptor T-cells directed towards aberrantly O-glycosylated MUC1 can control malignant growth in a mouse model. Here, we present a discovery platform for the generation of cancer-specific monoclonal antibodies targeting aberrant O-glycoproteins. The strategy is based on cancer cell lines engineered to homogeneously express the truncated Tn O-glycoform, the so-called SimpleCells. We used SimpleCells of different cancer origin to elicit monoclonal antibodies with selectivity for aberrant O-glycoproteins. For validation we selected and characterized one monoclonal antibody (6C5) directed to a Tn-glycopeptide in dysadherin (FXYD5), known to be upregulated in cancer and promote metastasis. While dysadherin is widely expressed also in normal cells, we demonstrated that the 6C5 epitope is specifically expressed in cancer.
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Affiliation(s)
- Catharina Steentoft
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Max Fuhrmann
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Federico Battisti
- Department of Experimental Medicine, “Sapienza” University of Rome, Viale Regina Elena 324 Rome, Italy
| | - Julie Van Coillie
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Thomas D Madsen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Diana Campos
- Instituto de Investigação e Inovação e Saúde, Universidade do Porto, Rua Júlio Amaral de Carvalho 45, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Rua Júlio Amaral de Carvalho 45, Porto, Portugal
| | - Adnan Halim
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Hiren J Joshi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Hans Schreiber
- Department of Pathology, Committee on Immunology, Committee on Cancer Biology, The University of Chicago, 5841 S. Maryland Avenue, Chicago, IL, USA
| | - Ulla Mandel
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
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11
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Hintze J, Ye Z, Narimatsu Y, Madsen TD, Joshi HJ, Goth CK, Linstedt A, Bachert C, Mandel U, Bennett EP, Vakhrushev SY, Schjoldager KT. Probing the contribution of individual polypeptide GalNAc-transferase isoforms to the O-glycoproteome by inducible expression in isogenic cell lines. J Biol Chem 2018; 293:19064-19077. [PMID: 30327431 PMCID: PMC6295722 DOI: 10.1074/jbc.ra118.004516] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/04/2018] [Indexed: 12/25/2022] Open
Abstract
The GalNAc-type O-glycoproteome is orchestrated by a large family of polypeptide GalNAc-transferase isoenzymes (GalNAc-Ts) with partially overlapping contributions to the O-glycoproteome besides distinct nonredundant functions. Increasing evidence indicates that individual GalNAc-Ts co-regulate and fine-tune specific protein functions in health and disease, and deficiencies in individual GALNT genes underlie congenital diseases with distinct phenotypes. Studies of GalNAc-T specificities have mainly been performed with in vitro enzyme assays using short peptide substrates, but recently quantitative differential O-glycoproteomics of isogenic cells with and without GALNT genes has enabled a more unbiased exploration of the nonredundant contributions of individual GalNAc-Ts. Both approaches suggest that fairly small subsets of O-glycosites are nonredundantly regulated by specific GalNAc-Ts, but how these isoenzymes orchestrate regulation among competing redundant substrates is unclear. To explore this, here we developed isogenic cell model systems with Tet-On inducible expression of two GalNAc-T genes, GALNT2 and GALNT11, in a knockout background in HEK293 cells. Using quantitative O-glycoproteomics with tandem-mass-tag (TMT) labeling, we found that isoform-specific glycosites are glycosylated in a dose-dependent manner and that induction of GalNAc-T2 or -T11 produces discrete glycosylation effects without affecting the major part of the O-glycoproteome. These results support previous findings indicating that individual GalNAc-T isoenzymes can serve in fine-tuned regulation of distinct protein functions.
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Affiliation(s)
- John Hintze
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Zilu Ye
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Yoshiki Narimatsu
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Thomas Daugbjerg Madsen
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Hiren J Joshi
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Christoffer K Goth
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Adam Linstedt
- the Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Collin Bachert
- the Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Ulla Mandel
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Eric P Bennett
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Sergey Y Vakhrushev
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Katrine T Schjoldager
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
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12
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Joshi HJ, Hansen L, Narimatsu Y, Freeze HH, Henrissat B, Bennett E, Wandall HH, Clausen H, Schjoldager KT. Glycosyltransferase genes that cause monogenic congenital disorders of glycosylation are distinct from glycosyltransferase genes associated with complex diseases. Glycobiology 2018; 28:284-294. [PMID: 29579191 DOI: 10.1093/glycob/cwy015] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Indexed: 12/12/2022] Open
Abstract
Glycosylation of proteins, lipids and proteoglycans in human cells involves at least 167 identified glycosyltransferases (GTfs), and these orchestrate the biosynthesis of diverse types of glycoconjugates and glycan structures. Mutations in this part of the genome-the GTf-genome-cause more than 58 rare, monogenic congenital disorders of glycosylation (CDGs). They are also statistically associated with a large number of complex phenotypes, diseases or predispositions to complex diseases based on Genome-Wide Association Studies (GWAS). CDGs are extremely rare and often with severe medical consequences. In contrast, GWAS are likely to identify more common genetic variations and generally involve less severe and distinct traits. We recently confirmed that structural defects in GTf genes are extremely rare, which seemed at odds with the large number of GWAS pointing to GTf-genes. To resolve this issue, we surveyed the GTf-genome for reported CDGs and GWAS candidates; we found little overlap between the two groups of genes. Moreover, GTf-genes implicated by CDG or GWAS appear to constitute different classes with respect to their: (i) predicted roles in glycosylation pathways; (ii) potential for partial redundancy by closely homologous genes; and (iii) transcriptional regulation as evaluated by RNAseq data. Our analysis suggest that more complex traits are caused by dysregulation rather than structural deficiency of GTfs, which suggests that some glycosylation reactions may be predicted to be under tight regulation for fine-tuning of important biological functions.
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Affiliation(s)
- Hiren J Joshi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Lars Hansen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Hudson H Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Bernard Henrissat
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.,Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille University, F-13288 Marseille, France
| | - Eric Bennett
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Hans H Wandall
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Katrine T Schjoldager
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
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13
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Bagdonaite I, Vakhrushev SY, Joshi HJ, Wandall HH. Viral glycoproteomes: technologies for characterization and outlook for vaccine design. FEBS Lett 2018; 592:3898-3920. [PMID: 29961944 DOI: 10.1002/1873-3468.13177] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/13/2018] [Accepted: 06/26/2018] [Indexed: 12/27/2022]
Abstract
It has long been known that surface proteins of most enveloped viruses are covered with glycans. It has furthermore been demonstrated that glycosylation is essential for propagation and immune evasion for many viruses. The recent development of high-resolution mass spectrometry techniques has enabled identification not only of the precise structures but also the positions of such post-translational modifications on viruses, revealing substantial differences in extent of glycosylation and glycan maturation for different classes of viruses. In-depth characterization of glycosylation and other post-translational modifications of viral envelope glycoproteins is essential for rational design of vaccines and antivirals. In this Review, we provide an overview of techniques used to address viral glycosylation and summarize information on glycosylation of enveloped viruses representing ongoing public health challenges. Furthermore, we discuss how knowledge on glycosylation can be translated to means to prevent and combat viral infections.
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Affiliation(s)
- Ieva Bagdonaite
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Denmark
| | - Hiren J Joshi
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Denmark
| | - Hans H Wandall
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Denmark
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14
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King SL, Goth CK, Eckhard U, Joshi HJ, Haue AD, Vakhrushev SY, Schjoldager KT, Overall CM, Wandall HH. TAILS N-terminomics and proteomics reveal complex regulation of proteolytic cleavage by O-glycosylation. J Biol Chem 2018; 293:7629-7644. [PMID: 29593093 PMCID: PMC5961060 DOI: 10.1074/jbc.ra118.001978] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/27/2018] [Indexed: 12/31/2022] Open
Abstract
Proteolytic processing is an irreversible post-translational modification functioning as a ubiquitous regulator of cellular activity. Protease activity is tightly regulated via control of gene expression, enzyme and substrate compartmentalization, zymogen activation, enzyme inactivation, and substrate availability. Emerging evidence suggests that proteolysis can also be regulated by substrate glycosylation and that glycosylation of individual sites on a substrate can decrease or, in rare cases, increase its sensitivity to proteolysis. Here, we investigated the relationship between site-specific, mucin-type (or GalNAc-type) O-glycosylation and proteolytic cleavage of extracellular proteins. Using in silico analysis, we found that O-glycosylation and cleavage sites are significantly associated with each other. We then used a positional proteomic strategy, terminal amine isotopic labeling of substrates (TAILS), to map the in vivo cleavage sites in HepG2 SimpleCells with and without one of the key initiating GalNAc transferases, GalNAc-T2, and after treatment with exogenous matrix metalloproteinase 9 (MMP9) or neutrophil elastase. Surprisingly, we found that loss of GalNAc-T2 not only increased cleavage, but also decreased cleavage across a broad range of other substrates, including key regulators of the protease network. We also found altered processing of several central regulators of lipid homeostasis, including apolipoprotein B and the phospholipid transfer protein, providing new clues to the previously reported link between GALNT2 and lipid homeostasis. In summary, we show that loss of GalNAc-T2 O-glycosylation leads to a general decrease in cleavage and that GalNAc-T2 O-glycosylation affects key regulators of the cellular proteolytic network, including multiple members of the serpin family.
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Affiliation(s)
- Sarah L King
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
| | - Christoffer K Goth
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
| | - Ulrich Eckhard
- the Centre for Blood Research, Department of Oral Biological and Medical Sciences, Faculty of Dentistry, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Hiren J Joshi
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
| | - Amalie D Haue
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
| | - Sergey Y Vakhrushev
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
| | - Katrine T Schjoldager
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
| | - Christopher M Overall
- the Centre for Blood Research, Department of Oral Biological and Medical Sciences, Faculty of Dentistry, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Hans H Wandall
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
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15
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Narimatsu Y, Joshi HJ, Yang Z, Gomes C, Chen YH, Lorenzetti FC, Furukawa S, Schjoldager KT, Hansen L, Clausen H, Bennett EP, Wandall HH. A validated gRNA library for CRISPR/Cas9 targeting of the human glycosyltransferase genome. Glycobiology 2018; 28:295-305. [PMID: 29315387 DOI: 10.1093/glycob/cwx101] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 12/07/2017] [Indexed: 12/11/2022] Open
Abstract
Over 200 glycosyltransferases are involved in the orchestration of the biosynthesis of the human glycome, which is comprised of all glycan structures found on different glycoconjugates in cells. The glycome is vast, and despite advancements in analytic strategies it continues to be difficult to decipher biological roles of glycans with respect to specific glycan structures, type of glycoconjugate, particular glycoproteins, and distinct glycosites on proteins. In contrast to this, the number of glycosyltransferase genes involved in the biosynthesis of the human glycome is manageable, and the biosynthetic roles of most of these enzymes are defined or can be predicted with reasonable confidence. Thus, with the availability of the facile CRISPR/Cas9 gene editing tool it now seems easier to approach investigation of the functions of the glycome through genetic dissection of biosynthetic pathways, rather than by direct glycan analysis. However, obstacles still remain with design and validation of efficient gene targeting constructs, as well as with the interpretation of results from gene targeting and the translation of gene function to glycan structures. This is especially true for glycosylation steps covered by isoenzyme gene families. Here, we present a library of validated high-efficiency gRNA designs suitable for individual and combinatorial targeting of the human glycosyltransferase genome together with a global view of the predicted functions of human glycosyltransferases to facilitate and guide gene targeting strategies in studies of the human glycome.
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Affiliation(s)
- Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
- GlycoDisplay Aps, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Hiren J Joshi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Zhang Yang
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
- GlycoDisplay Aps, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Catarina Gomes
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
- Instituto de Investigação e Inovação em Saúde,i3S; Institute of Molecular Pathology and Immunology of University of Porto, Ipatimup, Rua Júlio Amaral de Carvalho, 45, Porto 4200-135, Portugal
| | - Yen-Hsi Chen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Flaminia C Lorenzetti
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Sanae Furukawa
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Katrine T Schjoldager
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Lars Hansen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Eric P Bennett
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Hans H Wandall
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
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16
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Joshi HJ, Narimatsu Y, Schjoldager KT, Tytgat HL, Aebi M, Clausen H, Halim A. SnapShot: O-Glycosylation Pathways across Kingdoms. Cell 2018; 172:632-632.e2. [DOI: 10.1016/j.cell.2018.01.016] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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17
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Joshi HJ, Jørgensen A, Schjoldager KT, Halim A, Dworkin LA, Steentoft C, Wandall HH, Clausen H, Vakhrushev SY. GlycoDomainViewer: a bioinformatics tool for contextual exploration of glycoproteomes. Glycobiology 2017; 28:131-136. [DOI: 10.1093/glycob/cwx104] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/07/2017] [Indexed: 11/13/2022] Open
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18
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Bagdonaite I, Nordén R, Joshi HJ, King SL, Vakhrushev SY, Olofsson S, Wandall HH. Global Mapping of O-Glycosylation of Varicella Zoster Virus, Human Cytomegalovirus, and Epstein-Barr Virus. J Biol Chem 2016; 291:12014-28. [PMID: 27129252 DOI: 10.1074/jbc.m116.721746] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Indexed: 12/27/2022] Open
Abstract
Herpesviruses are among the most complex and widespread viruses, infection and propagation of which depend on envelope proteins. These proteins serve as mediators of cell entry as well as modulators of the immune response and are attractive vaccine targets. Although envelope proteins are known to carry glycans, little is known about the distribution, nature, and functions of these modifications. This is particularly true for O-glycans; thus we have recently developed a "bottom up" mass spectrometry-based technique for mapping O-glycosylation sites on herpes simplex virus type 1. We found wide distribution of O-glycans on herpes simplex virus type 1 glycoproteins and demonstrated that elongated O-glycans were essential for the propagation of the virus. Here, we applied our proteome-wide discovery platform for mapping O-glycosites on representative and clinically significant members of the herpesvirus family: varicella zoster virus, human cytomegalovirus, and Epstein-Barr virus. We identified a large number of O-glycosites distributed on most envelope proteins in all viruses and further demonstrated conserved patterns of O-glycans on distinct homologous proteins. Because glycosylation is highly dependent on the host cell, we tested varicella zoster virus-infected cell lysates and clinically isolated virus and found evidence of consistent O-glycosites. These results present a comprehensive view of herpesvirus O-glycosylation and point to the widespread occurrence of O-glycans in regions of envelope proteins important for virus entry, formation, and recognition by the host immune system. This knowledge enables dissection of specific functional roles of individual glycosites and, moreover, provides a framework for design of glycoprotein vaccines with representative glycosylation.
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Affiliation(s)
- Ieva Bagdonaite
- From the Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark and
| | - Rickard Nordén
- the Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, 413 45 Gothenburg, Sweden
| | - Hiren J Joshi
- From the Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark and
| | - Sarah L King
- From the Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark and
| | - Sergey Y Vakhrushev
- From the Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark and
| | - Sigvard Olofsson
- the Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, 413 45 Gothenburg, Sweden
| | - Hans H Wandall
- From the Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark and
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19
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Neubert P, Halim A, Zauser M, Essig A, Joshi HJ, Zatorska E, Larsen ISB, Loibl M, Castells-Ballester J, Aebi M, Clausen H, Strahl S. Mapping the O-Mannose Glycoproteome in Saccharomyces cerevisiae. Mol Cell Proteomics 2016; 15:1323-37. [PMID: 26764011 PMCID: PMC4824858 DOI: 10.1074/mcp.m115.057505] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Indexed: 11/17/2022] Open
Abstract
O-Mannosylation is a vital protein modification conserved from fungi to humans. Yeast is a perfect model to study this post-translational modification, because in contrast to mammals O-mannosylation is the only type of O-glycosylation. In an essential step toward the full understanding of protein O-mannosylation we mapped the O-mannose glycoproteome in baker's yeast. Taking advantage of an O-glycan elongation deficient yeast strain to simplify sample complexity, we identified over 500 O-glycoproteins from all subcellular compartments for which over 2300 O-mannosylation sites were mapped by electron-transfer dissociation (ETD)-based MS/MS. In this study, we focus on the 293 O-glycoproteins (over 1900 glycosylation sites identified by ETD-MS/MS) that enter the secretory pathway and are targets of ER-localized protein O-mannosyltransferases. We find that O-mannosylation is not only a prominent modification of cell wall and plasma membrane proteins, but also of a large number of proteins from the secretory pathway with crucial functions in protein glycosylation, folding, quality control, and trafficking. The analysis of glycosylation sites revealed that O-mannosylation is favored in unstructured regions and β-strands. Furthermore, O-mannosylation is impeded in the proximity of N-glycosylation sites suggesting the interplay of these types of post-translational modifications. The detailed knowledge of the target proteins and their O-mannosylation sites opens for discovery of new roles of this essential modification in eukaryotes, and for a first glance on the evolution of different types of O-glycosylation from yeast to mammals.
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Affiliation(s)
- Patrick Neubert
- From the ‡Centre for Organismal Studies (COS), Department of Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany
| | - Adnan Halim
- §Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Martin Zauser
- From the ‡Centre for Organismal Studies (COS), Department of Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany
| | - Andreas Essig
- ¶Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Hiren J Joshi
- §Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Ewa Zatorska
- From the ‡Centre for Organismal Studies (COS), Department of Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany
| | - Ida Signe Bohse Larsen
- §Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Martin Loibl
- From the ‡Centre for Organismal Studies (COS), Department of Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany
| | - Joan Castells-Ballester
- From the ‡Centre for Organismal Studies (COS), Department of Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany
| | - Markus Aebi
- ¶Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Henrik Clausen
- §Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Sabine Strahl
- From the ‡Centre for Organismal Studies (COS), Department of Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany;
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20
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Schjoldager KT, Joshi HJ, Kong Y, Goth CK, King SL, Wandall HH, Bennett EP, Vakhrushev SY, Clausen H. Deconstruction of O-glycosylation--GalNAc-T isoforms direct distinct subsets of the O-glycoproteome. EMBO Rep 2015; 16:1713-22. [PMID: 26566661 PMCID: PMC4693523 DOI: 10.15252/embr.201540796] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 10/05/2015] [Accepted: 10/16/2015] [Indexed: 12/20/2022] Open
Abstract
GalNAc-type O-glycosylation is found on most proteins trafficking through the secretory pathway in metazoan cells. The O-glycoproteome is regulated by up to 20 polypeptide GalNAc-Ts and the contributions and biological functions of individual GalNAc-Ts are poorly understood. Here, we used a zinc-finger nuclease (ZFN)-directed knockout strategy to probe the contributions of the major GalNAc-Ts (GalNAc-T1 and GalNAc-T2) in liver cells and explore how the GalNAc-T repertoire quantitatively affects the O-glycoproteome. We demonstrate that the majority of the O-glycoproteome is covered by redundancy, whereas distinct subsets of substrates are modified by non-redundant functions of GalNAc-T1 and GalNAc-T2. The non-redundant O-glycoproteome subsets and specific transcriptional responses for each isoform are related to different cellular processes; for the GalNAc-T2 isoform, these support a role in lipid metabolism. The results demonstrate that GalNAc-Ts have different non-redundant glycosylation functions, which may affect distinct cellular processes. The data serves as a comprehensive resource for unique GalNAc-T substrates. Our study provides a new view of the differential regulation of the O-glycoproteome, suggesting that the plurality of GalNAc-Ts arose to regulate distinct protein functions and cellular processes.
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Affiliation(s)
- Katrine T Schjoldager
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Hiren J Joshi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Yun Kong
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Christoffer K Goth
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Sarah Louise King
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Hans H Wandall
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Eric P Bennett
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Copenhagen N, Denmark
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21
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Bagdonaite I, Nordén R, Joshi HJ, Dabelsteen S, Nyström K, Vakhrushev SY, Olofsson S, Wandall HH. A strategy for O-glycoproteomics of enveloped viruses--the O-glycoproteome of herpes simplex virus type 1. PLoS Pathog 2015; 11:e1004784. [PMID: 25830354 PMCID: PMC4382219 DOI: 10.1371/journal.ppat.1004784] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 03/04/2015] [Indexed: 12/12/2022] Open
Abstract
Glycosylation of viral envelope proteins is important for infectivity and interaction with host immunity, however, our current knowledge of the functions of glycosylation is largely limited to N-glycosylation because it is difficult to predict and identify site-specific O-glycosylation. Here, we present a novel proteome-wide discovery strategy for O-glycosylation sites on viral envelope proteins using herpes simplex virus type 1 (HSV-1) as a model. We identified 74 O-linked glycosylation sites on 8 out of the 12 HSV-1 envelope proteins. Two of the identified glycosites found in glycoprotein B were previously implicated in virus attachment to immune cells. We show that HSV-1 infection distorts the secretory pathway and that infected cells accumulate glycoproteins with truncated O-glycans, nonetheless retaining the ability to elongate most of the surface glycans. With the use of precise gene editing, we further demonstrate that elongated O-glycans are essential for HSV-1 in human HaCaT keratinocytes, where HSV-1 produced markedly lower viral titers in HaCaT with abrogated O-glycans compared to the isogenic counterpart with normal O-glycans. The roles of O-linked glycosylation for viral entry, formation, secretion, and immune recognition are poorly understood, and the O-glycoproteomics strategy presented here now opens for unbiased discovery on all enveloped viruses. Information on site-specific O-glycosylation of viral envelope glycoproteins is generally very limited despite important functions. We present a powerful mass-spectrometry based strategy to globally identify O-glycosylation sites on viral envelope proteins of a given virus in the context of a productive infection. We successfully utilized the strategy to map O-linked glycosylation sites on the complex HSV-1 virus demonstrating that O-glycosylation is widely distributed on most envelope proteins. Moreover, we used genetically engineered keratinocytes lacking O-glycan elongation capacity to demonstrate that O-linked glycans are indeed important for HSV-1 biology as HSV-1 particles produced in these cells had significantly lower titers compared to wild-type keratinocytes. These tools enable wider discovery and detailed analysis of the role of site-specific O-glycosylation in virology.
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Affiliation(s)
- Ieva Bagdonaite
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rickard Nordén
- Department of Clinical Virology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Hiren J. Joshi
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Sally Dabelsteen
- Institute of Odontology, University of Copenhagen, Copenhagen, Denmark
| | - Kristina Nyström
- Department of Clinical Virology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Sergey Y. Vakhrushev
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Sigvard Olofsson
- Department of Clinical Virology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Hans H. Wandall
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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22
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Abstract
This chapter runs through several online predictors enabling prediction of glycosylation sites on protein sequences. Most online methods provide in place documentation and examples, but this chapter provides a general overview and workflow for each method.
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Affiliation(s)
- Hiren J Joshi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Blegdamsvej 3, 2200, Copenhagen N, Denmark
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23
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Kong Y, Joshi HJ, Schjoldager KTBG, Madsen TD, Gerken TA, Vester-Christensen MB, Wandall HH, Bennett EP, Levery SB, Vakhrushev SY, Clausen H. Probing polypeptide GalNAc-transferase isoform substrate specificities by in vitro analysis. Glycobiology 2015; 25:55-65. [PMID: 25155433 PMCID: PMC4245906 DOI: 10.1093/glycob/cwu089] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 08/13/2014] [Accepted: 08/19/2014] [Indexed: 12/16/2022] Open
Abstract
N-acetylgalactosaminyltransferase (GalNAc)-type (mucin-type) O-glycosylation is an abundant and highly diverse modification of proteins. This type of O-glycosylation is initiated in the Golgi by a large family of up to 20 homologous polypeptide GalNAc-T isoenzymes that transfer GalNAc to Ser, Thr and possibly Tyr residues. These GalNAc residues are then further elongated by a large set of glycosyltransferases to build a variety of complex O-glycan structures. What determines O-glycan site occupancy is still poorly understood, although it is clear that the substrate specificities of individual isoenzymes and the repertoire of GalNAc-Ts in cells are key parameters. The GalNAc-T isoenzymes are differentially expressed in cells and tissues in principle allowing cells to produce unique O-glycoproteomes dependent on the specific subset of isoforms present. In vitro analysis of acceptor peptide substrate specificities using recombinant expressed GalNAc-Ts has been the method of choice for probing activities of individual isoforms, but these studies have been hampered by biological validation of actual O-glycosylation sites in proteins and number of substrate testable. Here, we present a systematic analysis of the activity of 10 human GalNAc-T isoenzymes with 195 peptide substrates covering known O-glycosylation sites and provide a comprehensive dataset for evaluating isoform-specific contributions to the O-glycoproteome.
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Affiliation(s)
- Yun Kong
- Department of Cellular and Molecular Medicine and Odontology, Copenhagen, Center for Glycomics, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Hiren J Joshi
- Department of Cellular and Molecular Medicine and Odontology, Copenhagen, Center for Glycomics, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Katrine Ter-Borch Gram Schjoldager
- Department of Cellular and Molecular Medicine and Odontology, Copenhagen, Center for Glycomics, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Thomas Daugbjerg Madsen
- Department of Cellular and Molecular Medicine and Odontology, Copenhagen, Center for Glycomics, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Thomas A Gerken
- Department of Pediatrics Department of Biochemistry and Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Malene B Vester-Christensen
- Department of Cellular and Molecular Medicine and Odontology, Copenhagen, Center for Glycomics, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Hans H Wandall
- Department of Cellular and Molecular Medicine and Odontology, Copenhagen, Center for Glycomics, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Eric Paul Bennett
- Department of Cellular and Molecular Medicine and Odontology, Copenhagen, Center for Glycomics, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Steven B Levery
- Department of Cellular and Molecular Medicine and Odontology, Copenhagen, Center for Glycomics, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Department of Cellular and Molecular Medicine and Odontology, Copenhagen, Center for Glycomics, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Henrik Clausen
- Department of Cellular and Molecular Medicine and Odontology, Copenhagen, Center for Glycomics, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
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24
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Hansen L, Lind-Thomsen A, Joshi HJ, Pedersen NB, Have CT, Kong Y, Wang S, Sparso T, Grarup N, Vester-Christensen MB, Schjoldager K, Freeze HH, Hansen T, Pedersen O, Henrissat B, Mandel U, Clausen H, Wandall HH, Bennett EP. A glycogene mutation map for discovery of diseases of glycosylation. Glycobiology 2014; 25:211-24. [PMID: 25267602 DOI: 10.1093/glycob/cwu104] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Glycosylation of proteins and lipids involves over 200 known glycosyltransferases (GTs), and deleterious defects in many of the genes encoding these enzymes cause disorders collectively classified as congenital disorders of glycosylation (CDGs). Most known CDGs are caused by defects in glycogenes that affect glycosylation globally. Many GTs are members of homologous isoenzyme families and deficiencies in individual isoenzymes may not affect glycosylation globally. In line with this, there appears to be an underrepresentation of disease-causing glycogenes among these larger isoenzyme homologous families. However, genome-wide association studies have identified such isoenzyme genes as candidates for different diseases, but validation is not straightforward without biomarkers. Large-scale whole-exome sequencing (WES) provides access to mutations in, for example, GT genes in populations, which can be used to predict and/or analyze functional deleterious mutations. Here, we constructed a draft of a functional mutational map of glycogenes, GlyMAP, from WES of a rather homogenous population of 2000 Danes. We cataloged all missense mutations and used prediction algorithms, manual inspection and in case of carbohydrate-active enzymes family GT27 experimental analysis of mutations to map deleterious mutations. GlyMAP (http://glymap.glycomics.ku.dk) provides a first global view of the genetic stability of the glycogenome and should serve as a tool for discovery of novel CDGs.
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Affiliation(s)
- Lars Hansen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, Faculty of Health Sciences
| | - Allan Lind-Thomsen
- Wilhelm Johannsen Center for Genome Research, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen N DK-2200, Denmark
| | - Hiren J Joshi
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, Faculty of Health Sciences
| | - Nis Borbye Pedersen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, Faculty of Health Sciences
| | - Christian Theil Have
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Metabolics Genetics, Universitetsparken, Copenhagen Ø DK-2100, Denmark
| | - Yun Kong
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, Faculty of Health Sciences
| | - Shengjun Wang
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, Faculty of Health Sciences
| | - Thomas Sparso
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Metabolics Genetics, Universitetsparken, Copenhagen Ø DK-2100, Denmark
| | - Niels Grarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Metabolics Genetics, Universitetsparken, Copenhagen Ø DK-2100, Denmark
| | - Malene Bech Vester-Christensen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, Faculty of Health Sciences
| | - Katrine Schjoldager
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, Faculty of Health Sciences
| | - Hudson H Freeze
- Human Genetics Program, Sanford Children's Health Research Center, Sanford Burnham Medical Research Institute, La Jolla, CA 92037, USA
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Metabolics Genetics, Universitetsparken, Copenhagen Ø DK-2100, Denmark
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Metabolics Genetics, Universitetsparken, Copenhagen Ø DK-2100, Denmark
| | - Bernard Henrissat
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, Faculty of Health Sciences Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille 13288, France
| | - Ulla Mandel
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, Faculty of Health Sciences
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, Faculty of Health Sciences
| | - Hans H Wandall
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, Faculty of Health Sciences
| | - Eric P Bennett
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, Faculty of Health Sciences
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Carroll AW, Joshi HJ, Heazlewood JL. Managing the green proteomes for the next decade of plant research. Front Plant Sci 2013; 4:501. [PMID: 24379820 PMCID: PMC3864100 DOI: 10.3389/fpls.2013.00501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 11/22/2013] [Indexed: 05/25/2023]
Affiliation(s)
- Andrew W. Carroll
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of CopenhagenCopenhagen, Denmark
| | - Hiren J. Joshi
- Physical Biosciences Division and Joint BioEnergy Institute, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
| | - Joshua L. Heazlewood
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of CopenhagenCopenhagen, Denmark
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Mann GW, Calley PC, Joshi HJ, Heazlewood JL. MASCP gator: an overview of the Arabidopsis proteomic aggregation portal. Front Plant Sci 2013; 4:411. [PMID: 24167507 PMCID: PMC3806167 DOI: 10.3389/fpls.2013.00411] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 09/27/2013] [Indexed: 05/18/2023]
Abstract
A key challenge in the area of bioinformatics in the coming decades is the ability to manage the wealth of information that is being generated from the variety of high throughput methodologies currently being undertaken in laboratories across the world. While these approaches have made available large volumes of data to the research community, less attention has been given to the problem of how to intuitively present the data to enable greater biological insights. Recently, an attempt was made to tackle this problem in the area of Arabidopsis proteomics. The model plant has been the target of countless proteomics surveys producing an exhaustive array of data and online repositories. The MASCP Gator is an aggregation portal for proteomic data currently being produced by the community and unites a large collection of specialized resources to a single portal (http://gator.masc-proteomics.org/). Here we describe the latest additions, upgrades and features to this resource further expanding its role into protein modifications and genome sequence variations.
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Affiliation(s)
- Gregory W. Mann
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
| | - Paul C. Calley
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
| | - Hiren J. Joshi
- Copenhagen Center for Glycomics, Institute for Cellular and Molecular Medicine, University of CopenhagenCopenhagen, Denmark
| | - Joshua L. Heazlewood
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
- *Correspondence: Joshua L. Heazlewood, Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road MS 978-4466, Berkeley, CA 94720, USA e-mail:
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Steentoft C, Vakhrushev SY, Joshi HJ, Kong Y, Vester-Christensen MB, Schjoldager KTBG, Lavrsen K, Dabelsteen S, Pedersen NB, Marcos-Silva L, Gupta R, Bennett EP, Mandel U, Brunak S, Wandall HH, Levery SB, Clausen H. Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology. EMBO J 2013. [PMID: 23584533 DOI: 10.1038/emboj2013.79] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023] Open
Abstract
Glycosylation is the most abundant and diverse posttranslational modification of proteins. While several types of glycosylation can be predicted by the protein sequence context, and substantial knowledge of these glycoproteomes is available, our knowledge of the GalNAc-type O-glycosylation is highly limited. This type of glycosylation is unique in being regulated by 20 polypeptide GalNAc-transferases attaching the initiating GalNAc monosaccharides to Ser and Thr (and likely some Tyr) residues. We have developed a genetic engineering approach using human cell lines to simplify O-glycosylation (SimpleCells) that enables proteome-wide discovery of O-glycan sites using 'bottom-up' ETD-based mass spectrometric analysis. We implemented this on 12 human cell lines from different organs, and present a first map of the human O-glycoproteome with almost 3000 glycosites in over 600 O-glycoproteins as well as an improved NetOGlyc4.0 model for prediction of O-glycosylation. The finding of unique subsets of O-glycoproteins in each cell line provides evidence that the O-glycoproteome is differentially regulated and dynamic. The greatly expanded view of the O-glycoproteome should facilitate the exploration of how site-specific O-glycosylation regulates protein function.
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Affiliation(s)
- Catharina Steentoft
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
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Steentoft C, Vakhrushev SY, Joshi HJ, Kong Y, Vester-Christensen MB, Schjoldager KTBG, Lavrsen K, Dabelsteen S, Pedersen NB, Marcos-Silva L, Gupta R, Paul Bennett E, Mandel U, Brunak S, Wandall HH, Levery SB, Clausen H. Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology. EMBO J 2013; 32:1478-88. [PMID: 23584533 PMCID: PMC3655468 DOI: 10.1038/emboj.2013.79] [Citation(s) in RCA: 983] [Impact Index Per Article: 89.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 03/18/2013] [Indexed: 12/12/2022] Open
Abstract
Glycosylation is the most abundant and diverse posttranslational modification of proteins. While several types of glycosylation can be predicted by the protein sequence context, and substantial knowledge of these glycoproteomes is available, our knowledge of the GalNAc-type O-glycosylation is highly limited. This type of glycosylation is unique in being regulated by 20 polypeptide GalNAc-transferases attaching the initiating GalNAc monosaccharides to Ser and Thr (and likely some Tyr) residues. We have developed a genetic engineering approach using human cell lines to simplify O-glycosylation (SimpleCells) that enables proteome-wide discovery of O-glycan sites using 'bottom-up' ETD-based mass spectrometric analysis. We implemented this on 12 human cell lines from different organs, and present a first map of the human O-glycoproteome with almost 3000 glycosites in over 600 O-glycoproteins as well as an improved NetOGlyc4.0 model for prediction of O-glycosylation. The finding of unique subsets of O-glycoproteins in each cell line provides evidence that the O-glycoproteome is differentially regulated and dynamic. The greatly expanded view of the O-glycoproteome should facilitate the exploration of how site-specific O-glycosylation regulates protein function.
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Affiliation(s)
- Catharina Steentoft
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
| | - Hiren J Joshi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
- Center for Biological Sequence Analysis, Department of Systems Biology Technical University of Denmark, Lyngby, Denmark
| | - Yun Kong
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
| | - Malene B Vester-Christensen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
| | - Katrine T-B G Schjoldager
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
| | - Kirstine Lavrsen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
| | - Sally Dabelsteen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
| | - Nis B Pedersen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
| | - Lara Marcos-Silva
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Ramneek Gupta
- Center for Biological Sequence Analysis, Department of Systems Biology Technical University of Denmark, Lyngby, Denmark
| | - Eric Paul Bennett
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
| | - Ulla Mandel
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Hans H Wandall
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
| | - Steven B Levery
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen, Copenhagen N, Denmark
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Joshi HJ, Christiansen KM, Fitz J, Cao J, Lipzen A, Martin J, Smith-Moritz AM, Pennacchio LA, Schackwitz WS, Weigel D, Heazlewood JL. 1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis thaliana accessions. ACTA ACUST UNITED AC 2012; 28:1303-6. [PMID: 22451271 DOI: 10.1093/bioinformatics/bts133] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION The sequencing of over a thousand natural strains of the model plant Arabidopsis thaliana is producing unparalleled information at the genetic level for plant researchers. To enable the rapid exploitation of these data for functional proteomics studies, we have created a resource for the visualization of protein information and proteomic datasets for sequenced natural strains of A. thaliana. RESULTS The 1001 Proteomes portal can be used to visualize amino acid substitutions or non-synonymous single-nucleotide polymorphisms in individual proteins of A. thaliana based on the reference genome Col-0. We have used the available processed sequence information to analyze the conservation of known residues subject to protein phosphorylation among these natural strains. The substitution of amino acids in A. thaliana natural strains is heavily constrained and is likely a result of the conservation of functional attributes within proteins. At a practical level, we demonstrate that this information can be used to clarify ambiguously defined phosphorylation sites from phosphoproteomic studies. Protein sets of available natural variants are available for download to enable proteomic studies on these accessions. Together this information can be used to uncover the possible roles of specific amino acids in determining the structure and function of proteins in the model plant A. thaliana. An online portal to enable the community to exploit these data can be accessed at http://1001proteomes.masc-proteomics.org/
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Affiliation(s)
- Hiren J Joshi
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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von der Lieth CW, Freire AA, Blank D, Campbell MP, Ceroni A, Damerell DR, Dell A, Dwek RA, Ernst B, Fogh R, Frank M, Geyer H, Geyer R, Harrison MJ, Henrick K, Herget S, Hull WE, Ionides J, Joshi HJ, Kamerling JP, Leeflang BR, Lütteke T, Lundborg M, Maass K, Merry A, Ranzinger R, Rosen J, Royle L, Rudd PM, Schloissnig S, Stenutz R, Vranken WF, Widmalm G, Haslam SM. EUROCarbDB: An open-access platform for glycoinformatics. Glycobiology 2011; 21:493-502. [PMID: 21106561 PMCID: PMC3055595 DOI: 10.1093/glycob/cwq188] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 11/03/2010] [Accepted: 11/03/2010] [Indexed: 01/03/2023] Open
Abstract
The EUROCarbDB project is a design study for a technical framework, which provides sophisticated, freely accessible, open-source informatics tools and databases to support glycobiology and glycomic research. EUROCarbDB is a relational database containing glycan structures, their biological context and, when available, primary and interpreted analytical data from high-performance liquid chromatography, mass spectrometry and nuclear magnetic resonance experiments. Database content can be accessed via a web-based user interface. The database is complemented by a suite of glycoinformatics tools, specifically designed to assist the elucidation and submission of glycan structure and experimental data when used in conjunction with contemporary carbohydrate research workflows. All software tools and source code are licensed under the terms of the Lesser General Public License, and publicly contributed structures and data are freely accessible. The public test version of the web interface to the EUROCarbDB can be found at http://www.ebi.ac.uk/eurocarb.
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Affiliation(s)
| | - Ana Ardá Freire
- Bijvoet-Center for Biomolecular Research, University of Utrecht, Utrecht, The Netherlands
| | - Dennis Blank
- Institute of Biochemistry, Faculty of Medicine, Justus, Liebig University, Giessen, Germany
| | - Matthew P Campbell
- Dublin-Oxford Glycobiology Laboratory, National Institute for Bioprocessing Research and Training (NIBRT), Conway Institute, University College Dublin, Dublin, Ireland
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, UK
| | - Alessio Ceroni
- Division of Molecular Biosciences, Faculty of Natural Sciences, Biochemistry Building, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - David R Damerell
- Division of Molecular Biosciences, Faculty of Natural Sciences, Biochemistry Building, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Anne Dell
- Division of Molecular Biosciences, Faculty of Natural Sciences, Biochemistry Building, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Raymond A Dwek
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, UK
| | - Beat Ernst
- Department of Pharmaceutical Science, University of Basel, BaselSwitzerland
| | - Rasmus Fogh
- European Bioinformatics Institute, Hinxton, UK
| | - Martin Frank
- Core Facility, Molecular Structure Analysis, German Cancer Research Center, Heidelberg, Germany
| | - Hildegard Geyer
- Institute of Biochemistry, Faculty of Medicine, Justus, Liebig University, Giessen, Germany
| | - Rudolf Geyer
- Institute of Biochemistry, Faculty of Medicine, Justus, Liebig University, Giessen, Germany
| | | | - Kim Henrick
- European Bioinformatics Institute, Hinxton, UK
| | - Stefan Herget
- Core Facility, Molecular Structure Analysis, German Cancer Research Center, Heidelberg, Germany
| | - William E Hull
- Core Facility, Molecular Structure Analysis, German Cancer Research Center, Heidelberg, Germany
| | | | - Hiren J Joshi
- Core Facility, Molecular Structure Analysis, German Cancer Research Center, Heidelberg, Germany
- European Bioinformatics Institute, Hinxton, UK
| | - Johannis P Kamerling
- Bijvoet-Center for Biomolecular Research, University of Utrecht, Utrecht, The Netherlands
| | - Bas R Leeflang
- Bijvoet-Center for Biomolecular Research, University of Utrecht, Utrecht, The Netherlands
| | - Thomas Lütteke
- Bijvoet-Center for Biomolecular Research, University of Utrecht, Utrecht, The Netherlands
| | | | - Kai Maass
- Institute of Biochemistry, Faculty of Medicine, Justus, Liebig University, Giessen, Germany
| | | | - René Ranzinger
- Core Facility, Molecular Structure Analysis, German Cancer Research Center, Heidelberg, Germany
| | - Jimmy Rosen
- Bijvoet-Center for Biomolecular Research, University of Utrecht, Utrecht, The Netherlands
| | - Louise Royle
- Dublin-Oxford Glycobiology Laboratory, National Institute for Bioprocessing Research and Training (NIBRT), Conway Institute, University College Dublin, Dublin, Ireland
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, UK
| | - Pauline M Rudd
- Dublin-Oxford Glycobiology Laboratory, National Institute for Bioprocessing Research and Training (NIBRT), Conway Institute, University College Dublin, Dublin, Ireland
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, UK
| | - Siegfried Schloissnig
- Core Facility, Molecular Structure Analysis, German Cancer Research Center, Heidelberg, Germany
| | - Roland Stenutz
- Organic Chemistry, Stockholm University, Stockholm, Sweden
| | | | - Göran Widmalm
- Organic Chemistry, Stockholm University, Stockholm, Sweden
| | - Stuart M Haslam
- Division of Molecular Biosciences, Faculty of Natural Sciences, Biochemistry Building, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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Joshi HJ, Hirsch-Hoffmann M, Baerenfaller K, Gruissem W, Baginsky S, Schmidt R, Schulze WX, Sun Q, van Wijk KJ, Egelhofer V, Wienkoop S, Weckwerth W, Bruley C, Rolland N, Toyoda T, Nakagami H, Jones AM, Briggs SP, Castleden I, Tanz SK, Millar AH, Heazlewood JL. MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data. Plant Physiol 2011; 155:259-70. [PMID: 21075962 PMCID: PMC3075751 DOI: 10.1104/pp.110.168195] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 11/10/2010] [Indexed: 05/18/2023]
Abstract
Proteomics has become a critical tool in the functional understanding of plant processes at the molecular level. Proteomics-based studies have also contributed to the ever-expanding array of data in modern biology, with many generating Web portals and online resources that contain incrementally expanding and updated information. Many of these resources reflect specialist research areas with significant and novel information that is not currently captured by centralized repositories. The Arabidopsis (Arabidopsis thaliana) community is well served by a number of online proteomics resources that hold an abundance of functional information. These sites can be difficult to locate among a multitude of online resources. Furthermore, they can be difficult to navigate in order to identify specific features of interest without significant technical knowledge. Recently, members of the Arabidopsis proteomics community involved in developing many of these resources decided to develop a summary aggregation portal that is capable of retrieving proteomics data from a series of online resources on the fly. The Web portal is known as the MASCP Gator and can be accessed at the following address: http://gator.masc-proteomics.org/. Significantly, proteomics data displayed at this site retrieve information from the data repositories upon each request. This means that information is always up to date and displays the latest data sets. The site also provides hyperlinks back to the source information hosted at each of the curated databases to facilitate more in-depth analysis of the primary data.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Joshua L. Heazlewood
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (H.J.J., J.L.H.); Department of Biology, Eidgenössisch Technische Hochschule Zurich, CH–8092 Zurich, Switzerland (M.H.-H., K.B., W.G.); Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany (S.B.); Max-Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (R.S., W.X.S.); Department of Plant Biology, Cornell University, Ithaca, New York 14853 (Q.S., K.J.v.W.); Molecular Systems Biology, University of Vienna, 1090 Vienna, Austria (V.E., S.W., W.W.); Institut National de la Santé et de la Recherche Médicale, Laboratoire d’Etude de la Dynamique des Protéomes, U880, F–38000 Grenoble, France (C.B.); Commissariat à l’Énergie Atomique et aux Énergies Alternatives, Direction des Sciences du Vivant, Institut de Recherches en Technologies et Sciences pour le Vivant, F–38000 Grenoble, France (C.B., N.R.); Université Joseph Fourier, F–38000 Grenoble, France (C.B., N.R.); CNRS, Laboratoire de Physiologie Cellulaire Végétale, UMR5168, F–38000 Grenoble, France (N.R.); INRA, UMR1200, F–38000 Grenoble, France (N.R.); RIKEN Plant Science Center and RIKEN Bioinformatics and Systems Engineering Division, Tsurumi-ku, Yokohama 230–0045, Japan (T.T., H.N.); The Sainsbury Laboratory, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom (A.M.J.); Division of Biology, University of California San Diego, La Jolla, California 92093 (S.P.B.); Centre of Excellence for Computational Systems Biology (I.C.) and Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks (I.C., S.K.T., A.H.M.), University of Western Australia, Crawley 6009, Western Australia, Australia
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Oikawa A, Joshi HJ, Rennie EA, Ebert B, Manisseri C, Heazlewood JL, Scheller HV. An integrative approach to the identification of Arabidopsis and rice genes involved in xylan and secondary wall development. PLoS One 2010; 5:e15481. [PMID: 21124849 PMCID: PMC2990762 DOI: 10.1371/journal.pone.0015481] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 09/24/2010] [Indexed: 11/19/2022] Open
Abstract
Xylans constitute the major non-cellulosic component of plant biomass. Xylan biosynthesis is particularly pronounced in cells with secondary walls, implying that the synthesis network consists of a set of highly expressed genes in such cells. To improve the understanding of xylan biosynthesis, we performed a comparative analysis of co-expression networks between Arabidopsis and rice as reference species with different wall types. Many co-expressed genes were represented by orthologs in both species, which implies common biological features, while some gene families were only found in one of the species, and therefore likely to be related to differences in their cell walls. To predict the subcellular location of the identified proteins, we developed a new method, PFANTOM (plant protein family information-based predictor for endomembrane), which was shown to perform better for proteins in the endomembrane system than other available prediction methods. Based on the combined approach of co-expression and predicted cellular localization, we propose a model for Arabidopsis and rice xylan synthesis in the Golgi apparatus and signaling from plasma membrane to nucleus for secondary cell wall differentiation. As an experimental validation of the model, we show that an Arabidopsis mutant in the PGSIP1 gene encoding one of the Golgi localized candidate proteins has a highly decreased content of glucuronic acid in secondary cell walls and substantially reduced xylan glucuronosyltransferase activity.
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Affiliation(s)
- Ai Oikawa
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California, USA
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Abstract
The GlycoViewer (http://www.systemsbiology.org.au/glycoviewer) is a web-based tool that can visualize, summarize and compare sets of glycan structures. Its input is a group of glycan structures; these can be entered as a list in IUPAC format or via a sugar structure builder. Its output is a detailed graphic, which summarizes all salient features of the glycans according to the shapes of the core structures, the nature and length of any chains, and the types of terminal epitopes. The tool can summarize up to hundreds of structures in a single figure. This allows unique, high-level views to be generated of glycans from one protein, from a cell, a tissue or a whole organism. Use of the tool is illustrated in the analysis of normal and disease-associated glycans from the human glycoproteome.
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Affiliation(s)
- Hiren J Joshi
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
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Toukach P, Joshi HJ, Ranzinger R, Knirel Y, von der Lieth CW. Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de. Nucleic Acids Res 2007; 35:D280-6. [PMID: 17202164 PMCID: PMC1899093 DOI: 10.1093/nar/gkl883] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Functional glycomics, the scientific attempt to identify and assign functions to all glycan molecules synthesized by an organism, is an emerging field of science. In recent years, several databases have been started, all aiming to support deciphering the biological function of carbohydrates. However, diverse encoding and storage schemes are in use amongst these databases, significantly hampering the interchange of data. The mutual online access between the Bacterial Carbohydrate Structure DataBase (BCSDB) and the GLYCOSCIENCES.de portal, as a first reported attempt of a structure-based direct interconnection of two glyco-related databases is described. In this approach, users have to learn only one interface, will always have access to the latest data of both services, and will have the results of both searches presented in a consistent way. The establishment of this connection helped to find shortcomings and inconsistencies in the database design and functionality related to underlying data concepts and structural representations. For the maintenance of the databases, duplication of work can be easily avoided, and will hopefully lead to a better worldwide acceptance of both services within the community of glycoscienists. BCSDB is available at and the GLYCOSCIENCES.de portal at
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Affiliation(s)
| | - Hiren J Joshi
- German Cancer Research Center, Spectroscopic Department (B090)Molecular Modeling, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - René Ranzinger
- German Cancer Research Center, Spectroscopic Department (B090)Molecular Modeling, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | | | - Claus-W. von der Lieth
- German Cancer Research Center, Spectroscopic Department (B090)Molecular Modeling, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
- To whom correspondence should be addressed. Tel: +49 6221 424541; Fax: +49 6221 42454;
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Joshi HJ, Harrison MJ, Schulz BL, Cooper CA, Packer NH, Karlsson NG. Development of a mass fingerprinting tool for automated interpretation of oligosaccharide fragmentation data. Proteomics 2004; 4:1650-64. [PMID: 15174134 DOI: 10.1002/pmic.200300784] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The bioinformatic tool GlycosidIQ was developed for computerized interpretation of oligosaccharide mass spectrometric fragmentation based on matching experimental data with theoretically fragmented oligosaccharides generated from the database GlycoSuiteDB. This use of the software for glycofragment mass fingerprinting obviates a large part of the manual, labor intensive, and technically challenging interpretation of oligosaccharide fragmentation. Using 130 negative ion electrospray ionization-tandem mass spectrometry fragment spectra from identified oligosaccharide structures, it was shown that the GlycosidIQ scoring algorithms were able to correctly identify oligosaccharides in the great majority of cases (correct structure top ranked in 78% of the cases and an additional 17% were ranked second highest in the sample set).
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Cooper CA, Joshi HJ, Harrison MJ, Wilkins MR, Packer NH. GlycoSuiteDB: a curated relational database of glycoprotein glycan structures and their biological sources. 2003 update. Nucleic Acids Res 2003; 31:511-3. [PMID: 12520065 PMCID: PMC165546 DOI: 10.1093/nar/gkg099] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
GlycoSuiteDB is an annotated and curated relational database of glycan structures reported in the literature. It contains information on the glycan type, core type, linkages and anomeric configurations, mass, composition and the analytical methods used by the researchers to determine the glycan structure. Native and recombinant sources are detailed, including species, tissue and/or cell type, cell line, strain, life stage, disease, and if known the protein to which the glycan structures are attached. There are links to SWISS-PROT/TrEMBL and PubMed where applicable. Recent developments include the implementation of searching by 2D structure and substructure, disease and reference. The database is updated twice a year, and now contains over 7650 entries. Access to GlycoSuiteDB is available at http://www.glycosuite.com.
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Affiliation(s)
- Catherine A Cooper
- Proteome Systems Limited, 1/35-41 Waterloo Road, North Ryde, Sydney, NSW 2113, Australia.
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