GlycoForm and Glycologue: two software applications for the rapid construction and display of N-glycans from mammalian sources

Abstract

Background: The display of N-glycan carbohydrate structures is an essential part of glycoinformatics. Several tools exist for building such structures graphically, by selecting from a palette of symbols or sugar names, or else by specifying a structure in one of the chemical naming schemes currently available.

Findings: In the present work we present two tools for displaying N-glycans found in the mammalian CHO (Chinese hamster ovary) cell line, both of which take as input a 9-digit identifier that uniquely defines each structure. The first of these, GlycoForm, is designed to display a single structure automatically from an identifier entered by the user. The display is updated in real time, using symbols for the sugar residues, or in text-only form. Structures can be added to a library, which is recorded in a preference file and loaded automatically at start. Individual structures can be saved in a variety of bitmap image formats. The second program, Glycologue, reads a file containing columnar data of nine-digit codes, which can be displayed on-screen and printed at high resolution.

Conclusion: A key advantage of both programs is the speed and facility with which carbohydrate structures can be drawn. It is anticipated that these programs will be useful to glycobiologists, systems biologists and biotechnologists interested in N-glycosylation systems in mammalian cells.

Figure 1

The N-glycan encoding system of GlycoForm and Glycologue. (a) The trimannosyl core structure, Man3, with the numeric value 300000000. (b) Extension levels of a branch attached to one of the exposed mannose residues of the core structure. The value of "x" is either 6 or 2 when a branch occurs at either of these two positions on the "upper" (α-1,6) mannose; "x" takes the values 4 or 2 at those positions on the "lower" (α-1,3) mannose. The extension level of a branch is encoded as a single digit from 0-6. Extension levels 3 and 6 signify a N-acetylneuraminate (sialic acid) residue α-2,3-linked to galactose.

Figure 2

GlycoForm output, showing the N-glycan structure with code 3 1 0 0 3 3 3 3 3 in CFG symbols. Clicking on any digit in the GlycoForm code reveals the Krambeck and Betenbaugh descriptor for that position (see Table 1). Screenshot of the Mac OS X version.

Figure 3

Sample N-glycan structures depicted using both the CFG and UOXF symbolisms and in text-only form. Oligomannose, hybrid and complex examples are shown. The corresponding identifier is displayed at the bottom of each column.

Figure 4

Sample Glycologue output. Shown are 45 N-glycan structures, with the Krambeck and Betenbaugh code printed beneath each; the structures are based on a study of recombinant human erythropoeitin expressed in Chinese hamster ovary cells [10].