Comprehensive analysis of the N-glycan biosynthetic pathway using bioinformatics to generate UniCorn: A theoretical N-glycan structure database.
Glycan structures attached to proteins are comprised of diverse monosaccharide sequences and linkages that are produced from precursor nucleotide-sugars by a series of glycosyltransferases. Databases of these structures are an essential resource for the interpretation of analytical data and the development of bioinformatics tools. However, with no template to predict what structures are possible the human glycan structure databases are incomplete and rely heavily on the curation of published, experimentally determined, glycan structure data. In this work, a library of 45 human glycosyltransferases was used to generate a theoretical database of N-glycan structures comprised of 15 or less monosaccharide residues. Enzyme specificities were sourced from major online databases including Kyoto Encyclopedia of Genes and Genomes (KEGG) Glycan, Consortium for Functional Glycomics (CFG), Carbohydrate-Active enZymes (CAZy), GlycoGene DataBase (GGDB) and BRENDA. Based on the known activities, more than 1.1 million theoretical structures and 4.7 million synthetic reactions were generated and stored in our database called UniCorn. Furthermore, we analyzed the differences between the predicted glycan structures in UniCorn and those contained in UniCarbKB (www.unicarbkb.org), a database which stores experimentally described glycan structures reported in the literature, and demonstrate that UniCorn can be used to aid in the assignment of ambiguous structures whilst also serving as a discovery database.
Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, Balaclava Road, North Ryde, NSW, 2109, Australia; Department of Bioinformatics, Graduate School of Engineering, Soka University, 1-236, Tangi, Hachioji, 192-8577, Tokyo, Japan.
Yukie
Y
Akune
Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, Balaclava Road, North Ryde, NSW, 2109, Australia.
Chi-Hung
CH
Lin
Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, Balaclava Road, North Ryde, NSW, 2109, Australia.
Jodie L
JL
Abrahams
Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, Balaclava Road, North Ryde, NSW, 2109, Australia.
Jingyu
J
Zhang
Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, Balaclava Road, North Ryde, NSW, 2109, Australia.
Nicolle H
NH
Packer
Department of Bioinformatics, Graduate School of Engineering, Soka University, 1-236, Tangi, Hachioji, 192-8577, Tokyo, Japan.
Kiyoko F
KF
Aoki-Kinoshita
Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, Balaclava Road, North Ryde, NSW, 2109, Australia. Electronic address: matthew.campbell@mq.edu.au.
Matthew P
MP
Campbell
D053898:Biosynthetic Pathways; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D016695:Glycosyltransferases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D015394:Molecular Structure; D011134:Polysaccharides / Q000096:biosynthesis / Q000737:chemistry*
D011134:Polysaccharides; D016695:Glycosyltransferases
Glycoinformatics; Human glycosyltransferases; N-glycan synthetic pathway