By Hashimoto et. al Presented by Samuel Chapman

1. Comprehensive Analysis of Glycosyltransferases in Eukaryotic Genomes for Structural and Functional Characterization of Glycans By Hashimoto et. al Presented by Samuel Chapman

2. Glycosyltransferases • Enzymes instrumental in the creation of complex glycans. • Structurally, there are only a few well-conserved three-dimensional forms. • However, there are many different amino acid sequences and related families that create these forms. • This paper performs a comprehensive analysis of 3426 GTs across 53 families among 35 eukaryotic genomes.

3. Why bother? • Knowledge of organisms’ GTs can accomplish several things: • They can help predict which glycans an organism may have. • They can give a better picture of the biosynthetic pathways involved in GTs and the glycans they create . • They can shed light on relationships among organisms.

4. Procedure • The sequences studied were those that had similarity to known GT sequences. • A Psi-BLAST was performed on each query sequence and compared to the known sequences. • Checking procedures such as removal of false positives and redundant matches, were performed. • The putative GT sequences were grouped into 53 families and six functional categories. Each family has at least one conserved region, and no primary-sequence motif is conserved in all GTs. • The KEGG functional database and ontology is used for functional characterization.

5. Here’s a summary of the percentage of organisms in each kingdom that have each family of GTs (left-to-right: animal, plant, fungus, protist). Each kingdom has its own color. The darker the color, the higher the percentage that has that family.

6. Source: Paper supplementary information, www.sciencedirect.com

7. Some more results • Some GTs were very common. ALG7 family GTs of the N-glycan precursor functional group were common across all kingdoms. • Others were less common: GALNT-family GTs of the O-glycan/glycolipid group were found only in animals. • Some families, such as those in N-glycan precursors, had few (1-2) paralogs, whereas others had many, such as those of the UGT family in land plants (~100) • Parasitic protists had ~.24% of genes for GTs; the other kingdoms had .5-1.1%.

8. Some more results • There were two subfamily analyses. In one, the sialyltransferase family was divided into eight subfamilies; two were exclusive to plants, the other six to animals. Only vertebrates could have all six animal subfamilies at once. • The number of GTs seems to be fairly constant, except for mammals, which have many.

9. Conserved vs. diverged • There are two main groups of GTs: a group of highly-conserved, universal GTs such as those in the ALG family, and a group of divergent ones, such as those in the GALNT family. • Highly-conserved GTs have fewer paralogs, which goes along with the idea that their structures “need” to be more conserved to preserve function.

10. Structure prediction Each organism has a predicted glycan that it can make. This prediction comes from looking at the GTs it has and recognizing that synthesis proceeds in a stepwise manner. In this example, E. histolytica (ehi) is predicted to have this truncated N-glycan precursor because it lacks certain GTs; this prediction has been validated experimentally elsewhere. Structure

11. More prediction • Even though many of the predicted GTs in this study have not been confirmed or characterized, it is possible to infer their presence. For example, in the protistT. cruzi, a fucosylated oligosaccharide has been detected. Therefore, fucosylase-like GTs are candidates for the organism’s hypothetical fucosylase. • Sialyltransferasehomologs are present in plants, but they are not believed to make sialic acid. These homologs are not perfect with animals’, however, and more study is needed to figure out what they are for.

12. How useful is all this? I would say it’s very useful as a jumping-off point for the individual examination of an organism’s GTs. It gives one a good initial framework in terms of prediction. It’s also good in outlining evolutionary relationships, since it offers another class of genes with which to compare organisms. However, the effectiveness appears to be limited in terms of novel predictive power. Most of the predictions seem to be based on simple and/or obvious comparisons. I think it would be very complicated to predict new structures that haven’t been seen before, especially considering the disconnect between genes, GTs, and glycans.

13. Special thanks • Barack Obama • http://timesonline.typepad.com/photos/uncategorized/2009/02/11/barack_obama_rally.jpg • Sarah Palin • http://2.bp.blogspot.com/_E8BpJEni77I/SjJ2qrp_6zI/AAAAAAAAJdg/wJSbr-G3FcI/s400/SarahPalin_sp_photo_4.jpg