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      Exploring the glycosylation of mucins by use of O-glycodomain reporters recombinantly expressed in glycoengineered HEK293 cells

      research-article
      1 , 1 , 1 , 1 , 1 , 1 , 1 , 2 , 1 , 3 , 1 , , 1 ,
      The Journal of Biological Chemistry
      American Society for Biochemistry and Molecular Biology
      mucins, O-glycodomains, glycomucinases, cell-based glycan array, glycoengineering, glycosylation, glycosyltransferases, intact mass, ACN, acetonitrile, AOSM, asialo-OSM, FA, formic acid, GALNT, GalNAc transferase, HEK293, human embryonic kidney 293 cell line, KI, knockin, KO, knock out, MS, mass spectrometry, OSM, ovine submaxillary mucin, PSGL-1, P-selectin-glycoprotein ligand 1, SDC3, syndecan-3, TR, tandem repeat, VVA, villosa agglutinin

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          Abstract

          Mucins and glycoproteins with mucin-like regions contain densely O-glycosylated domains often found in tandem repeat (TR) sequences. These O-glycodomains have traditionally been difficult to characterize because of their resistance to proteolytic digestion, and knowledge of the precise positions of O-glycans is particularly limited for these regions. Here, we took advantage of a recently developed glycoengineered cell-based platform for the display and production of mucin TR reporters with custom-designed O-glycosylation to characterize O-glycodomains derived from mucins and mucin-like glycoproteins. We combined intact mass and bottom–up site-specific analysis for mapping O-glycosites in the mucins, MUC2, MUC20, MUC21, protein P-selectin-glycoprotein ligand 1, and proteoglycan syndecan-3. We found that all the potential Ser/Thr positions in these O-glycodomains were O-glycosylated when expressed in human embryonic kidney 293 SimpleCells (Tn-glycoform). Interestingly, we found that all potential Ser/Thr O-glycosites in TRs derived from secreted mucins and most glycosites from transmembrane mucins were almost fully occupied, whereas TRs from a subset of transmembrane mucins were less efficiently processed. We further used the mucin TR reporters to characterize cleavage sites of glycoproteases StcE (secreted protease of C1 esterase inhibitor from EHEC) and BT4244, revealing more restricted substrate specificities than previously reported. Finally, we conducted a bottom–up analysis of isolated ovine submaxillary mucin, which supported our findings that mucin TRs in general are efficiently O-glycosylated at all potential glycosites. This study provides insight into O-glycosylation of mucins and mucin-like domains, and the strategies developed open the field for wider analysis of native mucins.

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          The PRIDE database and related tools and resources in 2019: improving support for quantification data

          Abstract The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world’s largest data repository of mass spectrometry-based proteomics data, and is one of the founding members of the global ProteomeXchange (PX) consortium. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2016. In the last 3 years, public data sharing through PRIDE (as part of PX) has definitely become the norm in the field. In parallel, data re-use of public proteomics data has increased enormously, with multiple applications. We first describe the new architecture of PRIDE Archive, the archival component of PRIDE. PRIDE Archive and the related data submission framework have been further developed to support the increase in submitted data volumes and additional data types. A new scalable and fault tolerant storage backend, Application Programming Interface and web interface have been implemented, as a part of an ongoing process. Additionally, we emphasize the improved support for quantitative proteomics data through the mzTab format. At last, we outline key statistics on the current data contents and volume of downloads, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas.
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            Mucins in cancer: protection and control of the cell surface.

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              Global view of human protein glycosylation pathways and functions

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                Author and article information

                Contributors
                Journal
                J Biol Chem
                J Biol Chem
                The Journal of Biological Chemistry
                American Society for Biochemistry and Molecular Biology
                0021-9258
                1083-351X
                02 March 2022
                April 2022
                02 March 2022
                : 298
                : 4
                : 101784
                Affiliations
                [1 ]Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
                [2 ]Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
                [3 ]GlycoDisplay ApS, Copenhagen, Denmark
                Author notes
                []For correspondence: Henrik Clausen; Sergey Y. Vakhrushev seva@ 123456sund.ku.dk hclau@ 123456sund.ku.dk
                Article
                S0021-9258(22)00224-1 101784
                10.1016/j.jbc.2022.101784
                8980628
                35247390
                c267f5dc-aad8-476c-b477-eb29f0824c42
                © 2022 The Authors

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

                History
                : 3 January 2022
                : 25 February 2022
                Categories
                Research Article

                Biochemistry
                mucins,o-glycodomains,glycomucinases,cell-based glycan array,glycoengineering,glycosylation,glycosyltransferases,intact mass,acn, acetonitrile,aosm, asialo-osm,fa, formic acid,galnt, galnac transferase,hek293, human embryonic kidney 293 cell line,ki, knockin,ko, knock out,ms, mass spectrometry,osm, ovine submaxillary mucin,psgl-1, p-selectin-glycoprotein ligand 1,sdc3, syndecan-3,tr, tandem repeat,vva, villosa agglutinin

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