Discovering Gavialis gangeticus selenoproteins



The aim of this project is the prediction and notation of the selenoproteins in Gavialis gangeticus genome using a computational approach. Our results are based on the homology and were obtained through comparison of described selenoproteins from genomes closely related to gavial's genome. Together with this, we predicted the SECIS elements, so we could delimit the selenoprotein search.

We have analyzed 22 selenoproteins in Gavialis gangeticus's genome with its corresponding SECIS element. We have also found 11 proteins forming part of the synthesis machinery, and 13 cysteine homologues. The classification of these proteins is in the discussion section.

Gallus gallus is the nearest species to gavial with selenoprotein notation. It has been possible to check that most of the selenoproteins found in chicken's genome are also in the gavial's. Selenoproteins GPx1, GPx2, SelM, SelO and SPS2 were found in gavial while they do not have Sec residue in chicken, so they were compared with their homologues from Homo sapiens's genome, which is the best described. As well, DI3, GPx3, TR1, SelU1, SelO, SelH and Sel15, were compared with human because the notation for Gallus gallus was incomplete.

It is important to comment that our project is based in the comparison between proteins from closely related genomes to gavial's with the problem genome. This is a limitation because possible selenoproteins present in our genome would not be characterized if they are not in the genome compared with. In addition, as mentioned in the results, some of the proteins do not have the start or end regions, so it was not possible to predict the whole alignment. This could be solved with a better assembly of the Gavialis gangeticus genome, and the prediction could be improved with a better notation of chicken's genome, because some of the proteins were incomplete.

All the same, some of the incomplete proteins started the alignment with a valine codon (GUG), and it is known this codon can be a mithocondrial alternative initial codon, so, it would be possible this protein not to be uncompleted but to be part of the mithocondrial proteins or it could have an alternative initial codon.

Finally, even the limitations, this research gives a better characterization of the selenoproteins in gavial's genome, which was not notated before. It represents an step forward in selenoprotein field because it provides new knowledge of non described species to date.