Computational prediction of RNA secondary structures directing Selenocysteine incorporation in Archaea

Abstract

The UGA codon is most often translated to a stop codon, serving as a termination/nsignal to the protein synthesis. However, in a few cases this codon can also encodes/nthe 21st amino acid, selenocysteine, which is an analog of cysteine containing/nselenium instead of sulfur. Complex and specific translational machinery is needed to/nrecognize a stem-loop structure named SECIS (SEC Insertion Sequence) element,/npresent in the mRNA of Selenoproteins and essential for selenocysteine insertion./nSelenoproteins are present in the three domains of life: Eukarya, Bacteria and/nArchaea; but not in all their species. However, the SECIS element presents several/ndifferences between these three domains in terms of position in the mRNA/nsequence, stem length, secondary structure and conserved patterns. As UGA is/nnormally a translational stop signal, Selenoproteins are normally misannotated. For/nthis reason, dedicated annotation programs had to be developed. Seblastian (1) is a/ncomputational tool for prediction of Selenoprotein genes, based in the identification/nof eukaryotic SECIS as first step. It allows a quick and accurate detection of/nSelenoproteins in eukaryotic genomes. The annotation and information of SECIS/nelements in archaea species is not much extensive. In this project, I created a/nsecondary structure alignment of Archaea SECIS which serves as a model to identify/nthese elements in genomes. I contributed to the development of a computational tool/nfor prediction of Selenoprotein genes in Archaea, based in the identification of the/nSECIS element as first step. This tool will allow the correction of missannotation of/nSelenoproteins in Archaea domain, and possibly the discovery of novel/nSelenoproteins.