Bioinformatics of selenoproteins

Selenoproteins are widely distributed in prokaryotes and eukaryotes. The catalytic site of selenoproteins is selenocysteine (Sec) encoded by a traditional stop codon UGA. The dual functions of UGA as either a stop signal or encoding a Sec residue result in difficulty in the prediction of selenoproteins via bioinformatics. General programs for gene analysis fail to correctly assign the TGA function, leading to the mis-annotation of selenoproteins in the released genomic sequences. Recently, several methods have been developed for in silico identification of selenoproteins from genomic sequences, including the search for SECIS elements, re-analysis of selenoprotein coding regions, and local sequence alignment for Sec/Cys pairs. Application of those methods has made a great achievement in discovering new selenoproteins and identifying selenoproteomes in a variety of organisms. In addition, it also accelerates other selenoprotein-related researches, such as the analysis of selenoprotein evolution, identification of catalytic cysteine residues, study on dual-functional genetic codes and setup of selenoprotein databases. The fast growing results from the bioinformatics of selenoproteins not only help us to obtain insights into global trends of selenium utilization and distribution in life systems and the environment, but also provide theoretical bases for the discovery and design of new drugs against cancer and other diseases.