Annotating the Tb Glycome

Glycome… the fancy and less friendly cousin of the proteome and the genome is an interesting component of any organism. Comprising of the enzymes that add, lengthen, reduce, modify and change sugar residues in a protein or lipid, they actually comprise that “unknown” factor that the scientists often do not dare to look into. Glycans are difficult to study : with 9 sugars able to branch in endless possibilities and form zillions of structures, having no template driven synthesis mechanism and extremely challenging to sequence. But still, glycosylation is the most prevalent post-translational modification, often being responsible for cell-cell interaction, infection development, antigen-antibody mediation and reproductive biology to mention a few and hence cannot be disregarded. However, though their role in infection development is acknowledged, very little experimental research is actually available on it. Prokaryotic glycosylation came into the focus of scientific research only in 2002 when a N-glycosylation equivalent pathway was discovered in Campylobacter jejuni. Research has been ongoing since then to identify these genes in other bacteria.

The GlycoMtb team of the OSDD C2D initiative, focuses on the Mtb glycome, a very poorly characterized sector of the Tb genome. The existing genome annotation showed only 100 known genes for glycosylation in Mtb. But clearly, there has to be more…! In an organism that has the most complicated of the cell wall structure that comprises of glycolipids, an organism that fools the host defence mechanism and develops the deadliest of the diseases in humans definitely has more than 100 odd genes for the glycosylation pathway. Armed with this belief, the GlycoMtb team used a 2 pronged approach. The first phase was to look for homologues of bacterial glycan modifying enzymes in Mycobacterium. This gave an important lead… the answer to the genes responsible for glycosylation lay in the 1500 odd genes annotated as “hypothetical protein/conserved hypothetical protein/conserved membrane protein”. Hence bagan the long journey amidst the amino acid sequences, looking for sequence similarity, pattern matches and secondary structure matches. The team finally emerged 2 months later with a full functional prediction of the unnamed proteins…. Reducing the number of "proteins with unknown function" from 1500 to 270. As of now we have about ~400 genes which may be glycan modifying and maybe another hundred or so which are glycoproteins. This phenomenal task has only been possible due to the “nothing is impossible” belief of the team members , essentially made up of master’s students across the country.

The team is still at work incessantly, trying to make a more comprehensive list of the enzymes and proteins which they feel holds the key to a lot of unanswered questions in Mtb infection and hoping to release the data in the upcoming C2D conference in April 2010.