title: A Knowledge-Based System for Display and Prediction of O-Glycosylation Network Behaviour in Response to Enzyme Knockouts.
abstract: O-linked glycosylation is an important post-translational modification of mucin-type protein, changes to which are important biomarkers of cancer. For this study of the enzymes of O-glycosylation, we developed a shorthand notation for representing GalNAc-linked oligosaccharides, a method for their graphical interpretation, and a pattern-matching algorithm that generates networks of enzyme-catalysed reactions. Software for generating glycans from the enzyme activities is presented, and is also available online. The degree distributions of the resulting enzyme-reaction networks were found to be Poisson in nature. Simple graph-theoretic measures were used to characterise the resulting reaction networks. From a study of in-silico single-enzyme knockouts of each of 25 enzymes known to be involved in mucin O-glycan biosynthesis, six of them, β-1,4-galactosyltransferase (β4Gal-T4), four glycosyltransferases and one sulfotransferase, play the dominant role in determining O-glycan heterogeneity. In the absence of β4Gal-T4, all Lewis X, sialyl-Lewis X, Lewis Y and Sda/Cad glycoforms were eliminated, in contrast to knockouts of the N-acetylglucosaminyltransferases, which did not affect the relative abundances of O-glycans expressing these epitopes. A set of 244 experimentally determined mucin-type O-glycans obtained from the literature was used to validate the method, which was able to predict up to 98% of the most common structures obtained from human and engineered CHO cell glycoforms.
authors.affiliation: School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland.
authors.forename: Andrew G
authors.initials: AG
authors.lastname: McDonald
authors.affiliation: School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland.
authors.forename: Keith F
authors.initials: KF
authors.lastname: Tipton
authors.affiliation: School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland.
authors.forename: Gavin P
authors.initials: GP
authors.lastname: Davey
mesh_terms: D000818:Animals; D016466:CHO Cells; D019295:Computational Biology; D003198:Computer Simulation; D003412:Cricetulus; D055786:Gene Knockout Techniques; D005818:Genetic Engineering; D006031:Glycosylation; D016695:Glycosyltransferases / Q000172:deficiency / Q000235:genetics / Q000378:metabolism; D006801:Humans; D051188:Knowledge Bases; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008954:Models, Biological; D009077:Mucins / Q000737:chemistry / Q000378:metabolism*; D011134:Polysaccharides / Q000737:chemistry / Q000378:metabolism; D011499:Protein Processing, Post-Translational; D009626:Terminology as Topic
chemical_list: D009077:Mucins; D011134:Polysaccharides; D016695:Glycosyltransferases