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In silico identification of novel selenoproteins in the Drosophila melanogaster genome
Author(s) -
Castellano Sergi,
Morozova Nadya,
Morey Marta,
Berry Marla J,
Serras Florenci,
Corominas Montserrat,
Guigó Roderic
Publication year - 2001
Publication title -
embo reports
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 4.584
H-Index - 184
eISSN - 1469-3178
pISSN - 1469-221X
DOI - 10.1093/embo-reports/kve151
Subject(s) - selenoprotein , selenocysteine , genetics , open reading frame , biology , drosophila melanogaster , codon usage bias , stop codon , gene , genome , computational biology , in silico , untranslated region , messenger rna , peptide sequence , glutathione , biochemistry , glutathione peroxidase , cysteine , enzyme
In selenoproteins, incorporation of the amino acid selenocysteine is specified by the UGA codon, usually a stop signal. The alternative decoding of UGA is conferred by an mRNA structure, the SECIS element, located in the 3′‐untranslated region of the selenoprotein mRNA. Because of the non‐standard use of the UGA codon, current computational gene prediction methods are unable to identify selenoproteins in the sequence of the eukaryotic genomes. Here we describe a method to predict selenoproteins in genomic sequences, which relies on the prediction of SECIS elements in coordination with the prediction of genes in which the strong codon bias characteristic of protein coding regions extends beyond a TGA codon interrupting the open reading frame. We applied the method to the Drosophila melanogaster genome, and predicted four potential selenoprotein genes. One of them belongs to a known family of selenoproteins, and we have tested experimentally two other predictions with positive results. Finally, we have characterized the expression pattern of these two novel selenoprotein genes.