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Review
. 2020 Sep 14;21(18):6727.
doi: 10.3390/ijms21186727.

Databases and Bioinformatic Tools for Glycobiology and Glycoproteomics

Xing Li  1 , Zhijue Xu  1 , Xiaokun Hong  1 , Yan Zhang  1 , Xia Zou  1
Affiliations
Review

Databases and Bioinformatic Tools for Glycobiology and Glycoproteomics

Xing Li et al. Int J Mol Sci. .

Abstract

Glycosylation plays critical roles in various biological processes and is closely related to diseases. Deciphering the glycocode in diverse cells and tissues offers opportunities to develop new disease biomarkers and more effective recombinant therapeutics. In the past few decades, with the development of glycobiology, glycomics, and glycoproteomics technologies, a large amount of glycoscience data has been generated. Subsequently, a number of glycobiology databases covering glycan structure, the glycosylation sites, the protein scaffolds, and related glycogenes have been developed to store, analyze, and integrate these data. However, these databases and tools are not well known or widely used by the public, including clinicians and other researchers who are not in the field of glycobiology, but are interested in glycoproteins. In this study, the representative databases of glycan structure, glycoprotein, glycan-protein interactions, glycogenes, and the newly developed bioinformatic tools and integrated portal for glycoproteomics are reviewed. We hope this overview could assist readers in searching for information on glycoproteins of interest, and promote further clinical application of glycobiology.

Keywords: glycan; glycogene; glycoinformatics; glycoprotein; glycosylation; lectin.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Summary of representative glycoinformatic databases using membrane glycoproteins as example. GBPs, glycan binding proteins.
Figure 2
Figure 2
Search interfaces and integrated results of GlyConnect. (a) The two interfaces available in GlyConnect: Search and Browse. (b) The octopus result of glycan structures and relevant glycosites generated by querying protein UniProt accession (e.g., P00533). (c) The octopus results generated by querying glycan structures (e.g., “core-fucosylated”, “sialylated (any)”, and “bisecting”). The associated proteins with these glycans, and disease related to these glycans were shown. (d) The Browse interface displays the results of glycan structures related to a certain tissue (e.g., “pulmonary mucosa”) or disease (e.g., “carcinoma, hepatocellular”) in lists of items and proposes a global view of the data.
Figure 3
Figure 3
Search interfaces and integrated results of GlyGen. (a) The two interfaces available in GlyCen: Glycan Search and Protein Search. (b) The integrated result interface when searching with glycan accession (e.g., G17689DH) was shown. The detailed results of general information, associated protein, and biosynthetic enzyme were displayed. (c) The integrated result interface when searching with protein accession (e.g., P14210) was shown. The detailed results of glycosylation, mutation, and expression disease were displayed.
Figure 4
Figure 4
Data resources and integrated results in GlyCosmos. (a) An overview of the data resources available in GlyCosmos. Users simply click on the icon for a dataset of interest to access it. (b) The integrated result interface when searching with protein accession (e.g., P05067) was shown. The detailed results of sequence and feature with glycosites, and PDB images were displayed. The result interface of GlycomeAtlas (c) and LM-GlycomeAtlas (d) were shown.
Figure 5
Figure 5
Illustration of integration of various databases to promote functional glycobiology study.
See this image and copyright information in PMC

References

    1. Apweiler R., Hermjakob H., Sharon N. On the frequency of protein glycosylation, as deduced from analysis of the swiss-prot database. Biochim. Biophys. Acta. 1999;1473:4–8. doi: 10.1016/S0304-4165(99)00165-8. - DOI - PubMed
    1. Mereiter S., Balmana M., Campos D., Gomes J., Reis C.A. Glycosylation in the era of cancer-targeted therapy: Where are we heading? Cancer Cell. 2019;36:6–16. doi: 10.1016/j.ccell.2019.06.006. - DOI - PubMed
    1. Dalziel M., Crispin M., Scanlan C.N., Zitzmann N., Dwek R.A. Emerging principles for the therapeutic exploitation of glycosylation. Science. 2014;343:1235681. doi: 10.1126/science.1235681. - DOI - PubMed
    1. Strum J.S., Nwosu C.C., Hua S., Kronewitter S.R., Seipert R.R., Bachelor R.J., An H.J., Lebrilla C.B. Automated assignments of n- and o-site specific glycosylation with extensive glycan heterogeneity of glycoprotein mixtures. Anal. Chem. 2013;85:5666–5675. doi: 10.1021/ac4006556. - DOI - PMC - PubMed
    1. Kailemia M.J., Xu G., Wong M., Li Q., Goonatilleke E., Leon F., Lebrilla C.B. Recent advances in the mass spectrometry methods for glycomics and cancer. Anal. Chem. 2018;90:208–224. doi: 10.1021/acs.analchem.7b04202. - DOI - PMC - PubMed

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