ABSTRACT
Selenium is a micronutrient that supports many cellular functions and it is found within organisms mainly in selenocysteine (Sec) amino acid. This amino acid, also known as the 21st, is encoded by the UGA codon, which usually functions as a Stop codon. This duality makes difficult to predict selenoprotein genes and therefore, there is a need of computational tools to characterize the selenoproteins present in all living being lineages.
The aim of this project was to characterize the selenoproteome in a bony fish: Thunnus orientalis (tuna). The reference specie chosen to base our homology-study was Danio rerio (zebrafish), except for some proteins in which we could not use this specie so that we performed the comparison with Homo sapiens (human).
The methodology used to predict all the selenoproteins in the genome of Thunnus orientalis involved a process of automatization, using different programs of sequence alignment, such as blast; gen prediction, like exonerate; and protein-homology comparison, such as t-coffee; in order to obtain a predicted protein within the tuna genome. We also compared our results with the Selenoprofiles program that served as a reference.
According to the results obtained in our project we have been able to predict 34 selenoproteins. We have also characterized all the 11 related machinery proteins involved in the addition of Sec in the UGA codon. Additionally, we also searched within the tuna genome for the specific tRNA of the 21st amino acid, which they have been successfully found.
This study provides a phylogenetic approach for some selenoproteins families found in Thunnus orientalis genome, as well as it reports different examples of Sec/Cys evolutionary exchange among different taxonomic levels. There have also been found some consistent selenoprotein duplications apparently occurred recently in evolution. Finally, it is interesting to highlight the discovery of a pseudogene among a specific tuna selenoprotein.