Selenium (Se), an essential trace element in vivo, is present mainly as selenocystein (Sec) in various selenoproteins. The Sec residue is translated from an in-frame TGA codon, which traditionally functions as a stop ...Selenium (Se), an essential trace element in vivo, is present mainly as selenocystein (Sec) in various selenoproteins. The Sec residue is translated from an in-frame TGA codon, which traditionally functions as a stop codon. Prediction of selenoprotein genes is difficult due to the lack of an effective method for distinguishing the dual function of the TGA codon in the open reading frame of a selenoprotein gene. In this article a eukaryotic bioinformatic prediction system that we have developed was used to predict selenoprotein genes from the genome of the common bottlenose dolphin, Tursiops truncatus. Sixteen selenoprotein genes were predicted, including selenoprotein P and glutathione peroxidase. In particular, a type II iodothyronine deiodinase was found to have two Sec residues, while the type I iodothyronine deiodinase gene has two alternative splice forms. These results provide important information for the investigation of the relationship between a variety of selenoproteins and the evolution of the marine-living dolphin.展开更多
The genetic codon UGA has a dual function： serving as a terminator and encoding selenocysteine. However, most popular gene annotation programs only take it as a stop signal, resulting in misannotation or completely m...The genetic codon UGA has a dual function： serving as a terminator and encoding selenocysteine. However, most popular gene annotation programs only take it as a stop signal, resulting in misannotation or completely missing selenoprotein genes. We developed a computational method named Asec-Prediction that is specific for the prediction of archaeal selenoprotein genes. To evaluate its effectiveness, we first applied it to 14 archaeal genomes with previously known selenoprotein genes, and Asec-Prediction identified all reported selenoprotein genes without redundant results. When we applied it to 12 archaeal genomes that had not been researched for selenoprotein genes, Asec-Prediction detected a novel selenoprotein gene in Methanosarcina acetivorans. Further evidence was also collected to support that the predicted gene should Asec-Prediction is effective be a real selenoprotein gene. for the prediction of archaeal The result shows that selenoprotein genes.展开更多
基金supported by the National Natural Science Foundation of China (31070731)the Natural Science Foundation of Guangdong Province (10151806001000023)
文摘Selenium (Se), an essential trace element in vivo, is present mainly as selenocystein (Sec) in various selenoproteins. The Sec residue is translated from an in-frame TGA codon, which traditionally functions as a stop codon. Prediction of selenoprotein genes is difficult due to the lack of an effective method for distinguishing the dual function of the TGA codon in the open reading frame of a selenoprotein gene. In this article a eukaryotic bioinformatic prediction system that we have developed was used to predict selenoprotein genes from the genome of the common bottlenose dolphin, Tursiops truncatus. Sixteen selenoprotein genes were predicted, including selenoprotein P and glutathione peroxidase. In particular, a type II iodothyronine deiodinase was found to have two Sec residues, while the type I iodothyronine deiodinase gene has two alternative splice forms. These results provide important information for the investigation of the relationship between a variety of selenoproteins and the evolution of the marine-living dolphin.
基金supported by the National Natu-ral Science Foundation of China under Grant No.30525037the National 863 Program under Grant No. 2004AA231060
文摘The genetic codon UGA has a dual function： serving as a terminator and encoding selenocysteine. However, most popular gene annotation programs only take it as a stop signal, resulting in misannotation or completely missing selenoprotein genes. We developed a computational method named Asec-Prediction that is specific for the prediction of archaeal selenoprotein genes. To evaluate its effectiveness, we first applied it to 14 archaeal genomes with previously known selenoprotein genes, and Asec-Prediction identified all reported selenoprotein genes without redundant results. When we applied it to 12 archaeal genomes that had not been researched for selenoprotein genes, Asec-Prediction detected a novel selenoprotein gene in Methanosarcina acetivorans. Further evidence was also collected to support that the predicted gene should Asec-Prediction is effective be a real selenoprotein gene. for the prediction of archaeal The result shows that selenoprotein genes.
