A systematic framework to derive N-glycan biosynthesis process and the automated construction of glycosylation networks

Wenpin Hou, Yushan Qiu, Nobuyuki Hashimoto, Wai-Ki Ching, Kiyoko F. Aoki-Kinoshita

Abnormalities in glycan biosynthesis have been conclusively related to various diseases, whereas the complexity of the glycosylation process has impeded the quantitative analysis of biochemical experimental data for the identification of glycoforms contributing to disease. To overcome this limitation, the automatic construction of glycosylation reaction networks in silico is a critical step. In this paper, a framework K2014 is developed to automatically construct N-glycosylation networks in MATLAB with the involvement of the 27 most-known enzyme reaction rules of 22 enzymes, as an extension of previous model KB2005. A toolbox named Glycosylation Network Analysis Toolbox (GNAT) is applied to define network properties systematically, including linkages, stereochemical specificity and reaction conditions of enzymes. Our network shows a strong ability to predict a wider range of glycans produced by the enzymes encountered in the Golgi Apparatus in human cell expression systems. Our results demonstrate a better understanding of the underlying glycosylation process and the potential of systems glycobiology tools for analyzing conventional biochemical or mass spectrometry-based experimental data quantitatively in a more realistic and practical way.