Comprehensive analysis of the N-glycan biosynthetic pathway using bioinformatics to generate UniCorn: A theoretical N-glycan structure database. (5th August 2016)

• Record Type: Journal Article
• Authors: Akune, Yukie; Lin, Chi-Hung; Abrahams, Jodie L.; Zhang, Jingyu; Packer, Nicolle H.; Aoki-Kinoshita, Kiyoko F.; Campbell, Matthew P.
• Is Part Of: Carbohydrate research. Volume 431(2016)
• Page Start: 56
• Page End: 63
• Publication Date: 2016-08-05
• Subjects: Glycoinformatics -- N-glycan synthetic pathway -- Human glycosyltransferases; Carbohydrates -- Periodicals; Chemistry, Organic -- Periodicals; Biochemistry -- Periodicals; Carbohydrates -- Periodicals; Chimie organique -- Périodiques; Glucides -- Périodiques; Biochemistry; Carbohydrates; Chemistry, Organic; Periodicals; Electronic journals; 507.78
• DOI: 10.1016/j.carres.2016.05.012
• Languages: English
• ISSNs: 0008-6215

Abstract

Abstract: 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. Graphical abstract: Highlights: Constructed a library of 45 human glycosyltransferases related to N -glycans. Generated a computational model to simulate reaction networks based on the library. Calculated 1.1 million theoretical N -glycans available in the UniCorn database. UniCorn assists the biocuration and validation of structure entries. Structures can be used for the interpretation and annotation of experimental data.