The human  O -GlcNAcome database and meta-analysis

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Abstract

Over the past 35 years, ~1700 articles have characterized protein O-GlcNAcylation. Found in almost all living organisms, this post-translational modification of serine and threonine residues is highly conserved and key to biological processes. With half of the primary research articles using human models, the O-GlcNAcome recently reached a milestone of 5000 human proteins identified. Herein, we provide an extensive inventory of human O-GlcNAcylated proteins, their O-GlcNAc sites, identification methods, and corresponding references ( www.oglcnac.mcw.edu). In the absence of a comprehensive online resource for O-GlcNAcylated proteins, this list serves as the only database of O-GlcNAcylated proteins. Based on the thorough analysis of the amino acid sequence surrounding 7002 O-GlcNAc sites, we progress toward a more robust semi-consensus sequence for O-GlcNAcylation. Moreover, we offer a comprehensive meta-analysis of human O-GlcNAcylated proteins for protein domains, cellular and tissue distribution, and pathways in health and diseases, reinforcing that O-GlcNAcylation is a master regulator of cell signaling, equal to the widely studied phosphorylation.

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Most cited references 66

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Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

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The protein kinase complement of the human genome.

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We have catalogued the protein kinase complement of the human genome (the "kinome") using public and proprietary genomic, complementary DNA, and expressed sequence tag (EST) sequences. This provides a starting point for comprehensive analysis of protein phosphorylation in normal and disease states, as well as a detailed view of the current state of human genome analysis through a focus on one large gene family. We identify 518 putative protein kinase genes, of which 71 have not previously been reported or described as kinases, and we extend or correct the protein sequences of 56 more kinases. New genes include members of well-studied families as well as previously unidentified families, some of which are conserved in model organisms. Classification and comparison with model organism kinomes identified orthologous groups and highlighted expansions specific to human and other lineages. We also identified 106 protein kinase pseudogenes. Chromosomal mapping revealed several small clusters of kinase genes and revealed that 244 kinases map to disease loci or cancer amplicons.

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Topography and polypeptide distribution of terminal N-acetylglucosamine residues on the surfaces of intact lymphocytes. Evidence for O-linked GlcNAc.

C. R. TORRES, G W Hart (1984)

Bovine milk galactosyltransferase has been used, in conjunction with UDP-[3H]galactose, as an impermeant probe for accessible GlcNAc residues on the surfaces of lymphocytes. Galactosylation of living thymic lymphocytes is dependent upon cell number, enzyme concentration, UDP-galactose concentration, and Mn2+ concentration. Kinetics of labeling are biphasic, leveling off at approximately 30 min. The data strongly indicate vectorial surface labeling and covalent attachment of galactose. Thymocytes, T-lymphocytes, and B-lymphocytes have approximately 10(6), 3 X 10(6), and 5 X 10(6) galactosylatable sites on their cell surfaces, respectively. Numerous proteins are exogalactosylated that differ quantitatively among the major functional subsets of lymphocytes. Negligible radioactivity is found in lipid. In thymocytes, 49% of the exogalactosylated oligosaccharides are alkali labile, whereas 80 and 90% of that derived from T-lymphocytes and B-lymphocytes can be beta-eliminated, respectively. Sensitivity of the intact proteins or tryptic peptides to the peptide: N-glycosidase also confirms the relative amounts of cell surface, N-linked and O-linked oligosaccharides which are exogalactosylated. Composition, size, and high performance liquid chromatography on two types of high resolution columns establish that the bulk of the exogalactosylated, beta-eliminated oligosaccharides are Gal beta 1-4GlcNAcitol. These data suggest the presence of O-glycosidically linked GlcNAc monosaccharide on many lymphocyte cell-surface proteins. However, additional experiments indicate that the majority of these moieties appear to be cryptic or inside the cell. Thus, these studies not only describe dramatic differences in the amounts and distribution of terminal GlcNAc residues on phenotypically different lymphocyte populations, but they also describe the presence of a novel protein-saccharide linkage, which is present on numerous lymphocyte proteins.

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Author and article information

Contributors

Stephanie Olivier-Van Stichelen: solivier@mcw.edu

Journal

Journal ID (nlm-ta): Sci Data

Journal ID (iso-abbrev): Sci Data

Title: Scientific Data

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2052-4463

Publication date (Electronic): 21 January 2021

Publication date PMC-release: 21 January 2021

Publication date Collection: 2021

Volume: 8

Electronic Location Identifier: 25

Affiliations

[1 ]GRID grid.30760.32, ISNI 0000 0001 2111 8460, Department of Biochemistry, , Medical College of Wisconsin, ; Milwaukee, USA

[2 ]Department of Biochemistry & Molecular Medicine, The George Washington School of Medicine and Health Sciences, Washington, DC 20052 USA

Author information

Eugenia Wulff-Fuentes http://orcid.org/0000-0002-9995-7130

Logan Massman http://orcid.org/0000-0002-5579-4798

Article

Publisher ID: 810

DOI: 10.1038/s41597-021-00810-4

PMC ID: 7820439

PubMed ID: 33479245

SO-VID: f695d9e3-11f4-409b-a0dd-6cbc922cef8c

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 2 October 2020

Date accepted : 5 January 2021

Funding

Funded by: FundRef https://doi.org/10.13039/100000057, U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS);

Award ID: 1U01GM125267

Award Recipient : Jeet Vora Robel Kahsay

Funded by: U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)

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Keywords: glycoproteins,glycosylation,glycobiology,nutrient signalling

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Keywords: glycoproteins, glycosylation, glycobiology, nutrient signalling

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The human O-GlcNAcome database and meta-analysis

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Core Readings in Statistical Mediation Analysis

Most cited references 66

Cytoscape: a software environment for integrated models of biomolecular interaction networks.

The protein kinase complement of the human genome.

Topography and polypeptide distribution of terminal N-acetylglucosamine residues on the surfaces of intact lymphocytes. Evidence for O-linked GlcNAc.

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Cited by 66

Most referenced authors 1,111