The O-GlcNAc Database: Introducing New Features and Tools Developed from Community Feedback

Overview

Journal Anal Bioanal Chem

Specialty Chemistry

Date 2024 Oct 8

PMID 39379619

Authors

Florian Malard

Lilyanna Massman

Sebastien Campagne

Stephanie Olivier-Van Stichelen

Affiliations

Soon will be listed here.

Abstract

O-GlcNAc is a reversible post-translational modification found on serine and threonine residues of nucleocytoplasmic proteins. Four years ago, we released the O-GlcNAc Database ( oglcnac.mcw.edu ), a comprehensive catalog of O-GlcNAcylated proteins that has become one of the most cited resources in the field, with hundreds of unique users per month. We are now presenting an updated O-GlcNAc Database, which includes nearly 20,000 O-GlcNAcylated proteins and 48 species, marking substantial growth in data volume and scope. This paper presents the most noteworthy features implemented over the last year, often originating from feedback from the O-GlcNAc community. Among these features, we provide a brief overview of the database content, introduce our new protein viewer mode, and discuss the implementation of subcellular localization information and its applications in the O-GlcNAc score. We also provide an interface to use CytOVS, a tool designed to evaluate and sort O-GlcNAcome datasets derived from MS experiments. In conclusion, this new and improved O-GlcNAc Database represents a significant advancement in providing a comprehensive and expanded resource for researchers in the field of O-GlcNAc biology.

References

Torres C, Hart G . Topography and polypeptide distribution of terminal N-acetylglucosamine residues on the surfaces of intact lymphocytes. Evidence for O-linked GlcNAc. J Biol Chem. 1984; 259(5):3308-17. View

Wulff-Fuentes E, Berendt R, Massman L, Danner L, Malard F, Vora J . The human O-GlcNAcome database and meta-analysis. Sci Data. 2021; 8(1):25. PMC: 7820439. DOI: 10.1038/s41597-021-00810-4. View

Pravata V, Omelkova M, Stavridis M, Desbiens C, Stephen H, Lefeber D . An intellectual disability syndrome with single-nucleotide variants in O-GlcNAc transferase. Eur J Hum Genet. 2020; 28(6):706-714. PMC: 7253464. DOI: 10.1038/s41431-020-0589-9. View

Du P, Zhang X, Lian X, Holscher C, Xue G . O-GlcNAcylation and Its Roles in Neurodegenerative Diseases. J Alzheimers Dis. 2024; 97(3):1051-1068. DOI: 10.3233/JAD-230955. View

Lee J, Pyo K, Kim H . Role and Function of O-GlcNAcylation in Cancer. Cancers (Basel). 2021; 13(21). PMC: 8582477. DOI: 10.3390/cancers13215365. View

Rose A, Hildebrand P . NGL Viewer: a web application for molecular visualization. Nucleic Acids Res. 2015; 43(W1):W576-9. PMC: 4489237. DOI: 10.1093/nar/gkv402. View

Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O . Highly accurate protein structure prediction with AlphaFold. Nature. 2021; 596(7873):583-589. PMC: 8371605. DOI: 10.1038/s41586-021-03819-2. View

Burt R, Alghusen I, Ephrame S, Villar M, Artigues A, Slawson C . Mapping the O-GlcNAc Modified Proteome: Applications for Health and Disease. Front Mol Biosci. 2022; 9:920727. PMC: 9161079. DOI: 10.3389/fmolb.2022.920727. View

Ogawa M, Furukawa K, Okajima T . Extracellular O-linked β-N-acetylglucosamine: Its biology and relationship to human disease. World J Biol Chem. 2014; 5(2):224-30. PMC: 4050115. DOI: 10.4331/wjbc.v5.i2.224. View

10.

Sakaidani Y, Ichiyanagi N, Saito C, Nomura T, Ito M, Nishio Y . O-linked-N-acetylglucosamine modification of mammalian Notch receptors by an atypical O-GlcNAc transferase Eogt1. Biochem Biophys Res Commun. 2012; 419(1):14-9. DOI: 10.1016/j.bbrc.2012.01.098. View

11.

Doncheva N, Morris J, Holze H, Kirsch R, Nastou K, Cuesta-Astroz Y . Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks. J Proteome Res. 2022; 22(2):637-646. PMC: 9904289. DOI: 10.1021/acs.jproteome.2c00651. View