In silico identification of novel selenoproteins in the Drosophila melanogaster genome

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 u...

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Bibliographic Details
Published in:EMBO reports 2001-08, Vol.2 (8), p.697-702
Main Authors: Castellano, Sergi, Morozova, Nadya, Morey, Marta, Berry, Marla J, Serras, Florenci, Corominas, Montserrat, Guigó, Roderic
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Amino acids
Animals
Cell Line
Codon, Terminator - genetics
Drosophila melanogaster - embryology
Drosophila melanogaster - genetics
Gene Expression Profiling
Genome
Humans
In Situ Hybridization
Insect Proteins - chemistry
Insect Proteins - genetics
Molecular Sequence Data
Nucleic Acid Conformation
Proteins - chemistry
Proteins - genetics
Regulatory Sequences, Nucleic Acid - genetics
Scientific Report
Scientific Reports
Selenium Radioisotopes - metabolism
Selenocysteine - metabolism
Selenoproteins
Sequence Alignment
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Summary: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.
ISSN:1469-221X
1469-3178
DOI:10.1093/embo-reports/kve151