In Silico Analysis of Golgi Glycosyltransferases: A Case Study on the LARGE-Like Protein Family

Glycosylation is one of the major post-translational modification processes essential for expression and function of many proteins. It has been estimated that 1% of the open reading frames of a genome is dedicated to glycosylation. Many different enzymes are involved in glycosylation, such as glycosyltransferases and glycosidases. Traditionally, glycosyltransferases are classified based on their enzymatic activities by Enzyme Commission (http://www.chem.qmul.ac.uk/iubmb/enzyme/). Based on the activated donor type, glycosyltransferases are named, for example glucosyltransferase, mannosyltransferase and N-acetylglucosaminyltransferases. However, classification of glycosyltransferases based on the biochemical evidence is a difficult task since most of the enzymes are membrane proteins. Reconstruction of enzymatic assay for the membrane proteins are intrinsically more difficult than soluble proteins. Thus the purification of membrane-bound glycosyltransferase is a difficult task. On the other hand, with the recent advancement of genome projects, DNA sequences of an organism are readily available. Furthermore, bioinformatics annotation tools are now commonly used by life science researchers to identify the putative function of a gene. Hence, new approaches based on in silico analysis for classifying glycosyltransferase have been used successfully. The best known database for classification of glycosyltransferase by in silico approach is the CAZy (CarbohydrateActive enZymes) database (http://afmb.cnrs-mrs.fr/CAZy/) (Cantarel et al., 2009). Glycosyltransferases are enzymes involved in synthesizing sugar moieties by transferring activated saccharide donors into various macro-molecules such as DNA, proteins, lipids and glycans. More than 100 glycosyltransferases are localized in the endoplasmic reticulum (ER) and Golgi apparatus and are involved in the glycan synthesis (Narimatsu, H., 2006). The structural studies on the ER and golgi glycosyltransferases has revealed several common domains and motifs present between them. The glycosyltransferases are grouped into functional subfamilies based on similarities of sequence, their enzyme characteristics, donor specificity, acceptor specificity and the specific donor and acceptor linkages (Ishida et al., 2005). The glycosyltransferase sequences comprise of 330-560 amino acids long and share the same type II transmembrane protein structure with four functional domains: a short