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In silico identification of the sea squirt selenoproteome.

Jiang L, Liu Q, Ni J - BMC Genomics (2010)

Bottom Line: Among them a selenoprotein W gene was found to have two SECIS elements in the 3'-untranslated region.The method based on SelGenAmic algorithm is capable of identifying eukaryotic selenoprotein genes from their genomes.Application of this method to Ciona intestinalis proves its successes in finding Sec-decoding TGA from large-scale eukaryotic genome sequences, which fills the gap in our knowledge on the ancient chordate selenoproteins.

View Article: PubMed Central - HTML - PubMed

Affiliation: Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, PR China.

ABSTRACT

Background: Computational methods for identifying selenoproteins have been developed rapidly in recent years. However, it is still difficult to identify the open reading frame (ORF) of eukaryotic selenoprotein gene, because the TGA codon for a selenocysteine (Sec) residue in the active centre of selenoprotein is traditionally a terminal signal of protein translation. Although the identification of selenoproteins from genomes through bioinformatics methods has been conducted in bacteria, unicellular eukaryotes, insects and several vertebrates, only a few results have been reported on the ancient chordate selenoproteins.

Results: A gene assembly algorithm SelGenAmic has been constructed and presented in this study for identifying selenoprotein genes from eukaryotic genomes. A method based on this algorithm was developed to build an optimal TGA-containing-ORF for each TGA in a genome, followed by protein similarity analysis through conserved sequence alignments to screen out selenoprotein genes form these ORFs. This method improved the sensitivity of detecting selenoproteins from a genome due to the design that all TGAs in the genome were investigated for its possibility of decoding as a Sec residue. Using this method, eighteen selenoprotein genes were identified from the genome of Ciona intestinalis, leading to its member of selenoproteome up to 19. Among them a selenoprotein W gene was found to have two SECIS elements in the 3'-untranslated region. Additionally, the disulfide bond formation protein A (DsbA) was firstly identified as a selenoprotein in the ancient chordates of Ciona intestinalis, Ciona savignyi and Branchiostoma floridae, while selenoprotein DsbAs had only been found in bacteria and green algae before.

Conclusion: The method based on SelGenAmic algorithm is capable of identifying eukaryotic selenoprotein genes from their genomes. Application of this method to Ciona intestinalis proves its successes in finding Sec-decoding TGA from large-scale eukaryotic genome sequences, which fills the gap in our knowledge on the ancient chordate selenoproteins.

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Comparison between the gene structures of newly identified DsbA selenoprotein genes and the coding regions of originally misannotated genes. A. Ciona intestinalis DsbA; B. Branchiostoma floridae DsbA. In the misannotated version, the downstream 2 exons and 1 intron are very long that they are indicated by broken line and interrupted rectangles.
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Figure 8: Comparison between the gene structures of newly identified DsbA selenoprotein genes and the coding regions of originally misannotated genes. A. Ciona intestinalis DsbA; B. Branchiostoma floridae DsbA. In the misannotated version, the downstream 2 exons and 1 intron are very long that they are indicated by broken line and interrupted rectangles.

Mentions: Selenoprotein DsbA has only been found in multiple prokaryote species, microbial marine communities, symbiotic bacterium of a gutless worm, and picoeukaryote Micromonas [11,12,19,22-24]. In this paper, DsbA was firstly reported as selenoprotein in a multicellular organism, Ciona intestinalis. The structural information for selenoprotein DsbA gene of Ciona intestinalis is shown in Figure 8A indicated as newly annotated, while the originally released gene is indicated as misannotated, where the upstream part of the first exon, including the Sec-TGA, was misannotated as the UTR of the gene.


In silico identification of the sea squirt selenoproteome.

Jiang L, Liu Q, Ni J - BMC Genomics (2010)

Comparison between the gene structures of newly identified DsbA selenoprotein genes and the coding regions of originally misannotated genes. A. Ciona intestinalis DsbA; B. Branchiostoma floridae DsbA. In the misannotated version, the downstream 2 exons and 1 intron are very long that they are indicated by broken line and interrupted rectangles.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2874816&req=5

Figure 8: Comparison between the gene structures of newly identified DsbA selenoprotein genes and the coding regions of originally misannotated genes. A. Ciona intestinalis DsbA; B. Branchiostoma floridae DsbA. In the misannotated version, the downstream 2 exons and 1 intron are very long that they are indicated by broken line and interrupted rectangles.
Mentions: Selenoprotein DsbA has only been found in multiple prokaryote species, microbial marine communities, symbiotic bacterium of a gutless worm, and picoeukaryote Micromonas [11,12,19,22-24]. In this paper, DsbA was firstly reported as selenoprotein in a multicellular organism, Ciona intestinalis. The structural information for selenoprotein DsbA gene of Ciona intestinalis is shown in Figure 8A indicated as newly annotated, while the originally released gene is indicated as misannotated, where the upstream part of the first exon, including the Sec-TGA, was misannotated as the UTR of the gene.

Bottom Line: Among them a selenoprotein W gene was found to have two SECIS elements in the 3'-untranslated region.The method based on SelGenAmic algorithm is capable of identifying eukaryotic selenoprotein genes from their genomes.Application of this method to Ciona intestinalis proves its successes in finding Sec-decoding TGA from large-scale eukaryotic genome sequences, which fills the gap in our knowledge on the ancient chordate selenoproteins.

View Article: PubMed Central - HTML - PubMed

Affiliation: Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, PR China.

ABSTRACT

Background: Computational methods for identifying selenoproteins have been developed rapidly in recent years. However, it is still difficult to identify the open reading frame (ORF) of eukaryotic selenoprotein gene, because the TGA codon for a selenocysteine (Sec) residue in the active centre of selenoprotein is traditionally a terminal signal of protein translation. Although the identification of selenoproteins from genomes through bioinformatics methods has been conducted in bacteria, unicellular eukaryotes, insects and several vertebrates, only a few results have been reported on the ancient chordate selenoproteins.

Results: A gene assembly algorithm SelGenAmic has been constructed and presented in this study for identifying selenoprotein genes from eukaryotic genomes. A method based on this algorithm was developed to build an optimal TGA-containing-ORF for each TGA in a genome, followed by protein similarity analysis through conserved sequence alignments to screen out selenoprotein genes form these ORFs. This method improved the sensitivity of detecting selenoproteins from a genome due to the design that all TGAs in the genome were investigated for its possibility of decoding as a Sec residue. Using this method, eighteen selenoprotein genes were identified from the genome of Ciona intestinalis, leading to its member of selenoproteome up to 19. Among them a selenoprotein W gene was found to have two SECIS elements in the 3'-untranslated region. Additionally, the disulfide bond formation protein A (DsbA) was firstly identified as a selenoprotein in the ancient chordates of Ciona intestinalis, Ciona savignyi and Branchiostoma floridae, while selenoprotein DsbAs had only been found in bacteria and green algae before.

Conclusion: The method based on SelGenAmic algorithm is capable of identifying eukaryotic selenoprotein genes from their genomes. Application of this method to Ciona intestinalis proves its successes in finding Sec-decoding TGA from large-scale eukaryotic genome sequences, which fills the gap in our knowledge on the ancient chordate selenoproteins.

Show MeSH
Related in: MedlinePlus