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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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Primary sequences and secondary structures of the two SECIS elements in the Ciona intestinalis SelW1 gene. Core conserved functional sites are indicated by bold letters in the secondary structures and white letters on a black background in the primary sequences.
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Figure 7: Primary sequences and secondary structures of the two SECIS elements in the Ciona intestinalis SelW1 gene. Core conserved functional sites are indicated by bold letters in the secondary structures and white letters on a black background in the primary sequences.

Mentions: The primary sequences and secondary structures of the two SECIS elements are shown in Figure 7. Both of them belong to the form II SECIS element, which have an additional minihelix in the apical loop [2]. The two SECIS elements were both detected by SECISearch 2.19 under the "default" pattern to limit the conservation and energy cutoff. In addition, SECIS 2 could also be detected under the "strict" pattern. The COVE scores were 24.91 for SECIS 1 and 23.70 for SECIS 2, which are much higher than 15, the recommended COVE score cutoff for SECISearch2.19 [14]. The COVE score was calculated by matching the query sequence with the known SECIS secondary model. If the score exceeds 15, the query sequence is considered as a true SECIS according to the recommendation of SECISearch2.19. Therefore, both SECIS elements could be functionally active. Up to the present, two potential SECIS elements have only been found in SelP and human Sep 15 genes [6,20]. The SelP gene contains more than one Sec-TGAs, and experimental evidence has shown that its two SECIS elements are necessary for the efficient incorporation of multiple Sec residues into SelP. Whereas the Sep 15 gene contains only one Sec residue, and its upstream SECIS has been proved nonfunctional [21]. Interestingly, the predicted Ciona SelW1 gene also contains one Sec residue and two SECIS elements. Only SECIS 2 can be detected by the "strict" pattern of SECISearch 2.19. Those suggested that SECIS 2 has a higher possibility of being functional. From the characteristics of Ciona SelW1 gene structure, it seems that this gene is more analogous to human Sep15 that its SECIS 1 may be nonfunctional while SECIS 2 is used for Sec incorporation. However, conclusion can only be drawn after experimental results on functional analyses of these two SECIS elements.


In silico identification of the sea squirt selenoproteome.

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

Primary sequences and secondary structures of the two SECIS elements in the Ciona intestinalis SelW1 gene. Core conserved functional sites are indicated by bold letters in the secondary structures and white letters on a black background in the primary sequences.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 7: Primary sequences and secondary structures of the two SECIS elements in the Ciona intestinalis SelW1 gene. Core conserved functional sites are indicated by bold letters in the secondary structures and white letters on a black background in the primary sequences.
Mentions: The primary sequences and secondary structures of the two SECIS elements are shown in Figure 7. Both of them belong to the form II SECIS element, which have an additional minihelix in the apical loop [2]. The two SECIS elements were both detected by SECISearch 2.19 under the "default" pattern to limit the conservation and energy cutoff. In addition, SECIS 2 could also be detected under the "strict" pattern. The COVE scores were 24.91 for SECIS 1 and 23.70 for SECIS 2, which are much higher than 15, the recommended COVE score cutoff for SECISearch2.19 [14]. The COVE score was calculated by matching the query sequence with the known SECIS secondary model. If the score exceeds 15, the query sequence is considered as a true SECIS according to the recommendation of SECISearch2.19. Therefore, both SECIS elements could be functionally active. Up to the present, two potential SECIS elements have only been found in SelP and human Sep 15 genes [6,20]. The SelP gene contains more than one Sec-TGAs, and experimental evidence has shown that its two SECIS elements are necessary for the efficient incorporation of multiple Sec residues into SelP. Whereas the Sep 15 gene contains only one Sec residue, and its upstream SECIS has been proved nonfunctional [21]. Interestingly, the predicted Ciona SelW1 gene also contains one Sec residue and two SECIS elements. Only SECIS 2 can be detected by the "strict" pattern of SECISearch 2.19. Those suggested that SECIS 2 has a higher possibility of being functional. From the characteristics of Ciona SelW1 gene structure, it seems that this gene is more analogous to human Sep15 that its SECIS 1 may be nonfunctional while SECIS 2 is used for Sec incorporation. However, conclusion can only be drawn after experimental results on functional analyses of these two SECIS elements.

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