A complementary bioinformatics approach to identify potential plant cell wall glycosyltransferase-encoding genes

Area of Science:

• Plant Biology
• Biochemistry
• Bioinformatics

Background:

• Plant cell walls (CW) are synthesized by enzymes including glycosyltransferases (GTs).
• The Carbohydrate-Active enZYmes (CAZy) database classifies known GTs, but many CW-synthesizing GTs remain uncharacterized.
• Identifying novel GTs is crucial for understanding plant cell wall biosynthesis.

Purpose of the Study:

• To identify plant cell wall glycosyltransferases (GTs) not currently classified in the CAZy database.
• To develop a bioinformatics approach for discovering novel GTs involved in plant cell wall synthesis.

Main Methods:

• Utilized bioinformatics tools including Transmembrane Hidden Markov Model 2.0, SUPERFAMILY, Three-Dimensional-Position-Specific Scoring Matrix, and mGenTHREADER.
• Screened the Arabidopsis proteome for proteins with transmembrane domains and predicted GT-related superfamilies.
• Filtered results to exclude known CAZy-classified GTs, yielding potential novel candidates.

Main Results:

• Identified 139 potential novel GT sequences after initial screening and filtering.
• Further analysis revealed 27 sequences with similarity to GT-A or GT-B folds, not previously classified in CAZy.
• Proof of concept demonstrated two of these novel GTs function as xylosyltransferases in pectin synthesis.

Conclusions:

• The bioinformatics approach successfully identified novel putative plant cell wall glycosyltransferases.
• These findings expand the known repertoire of GTs involved in plant cell wall biosynthesis.
• The identified GTs represent new targets for studying the synthesis of complex plant cell wall polysaccharides.