In silico identification of the sea squirt selenoproteome.
In silico identification of the sea squirt selenoproteome.
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DOI：
10.1186/1471-2164-11-289
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发表时间：
2010-05-10
期刊：
影响因子：
4.4
通讯作者：
Ni J
中科院分区：
文献类型：
--
作者：
Jiang L;Liu Q;Ni J
近年来，用于鉴定硒蛋白的计算方法得到了迅速发展。然而，真核生物硒蛋白基因的开放阅读框架（ORF）的识别仍然是一个难题，因为硒蛋白活性中心的硒代半胱氨酸（Sec）残基的TGA密码子是传统的蛋白质翻译的末端信号。虽然利用生物信息学方法从细菌、单细胞真核生物、昆虫和几种脊椎动物的基因组中鉴定硒蛋白，但关于古老脊索动物硒蛋白的研究报道很少。本研究构建了一个基因组装算法SelGenAmic，用于从真核生物基因组中识别硒蛋白基因。基于该算法建立了一个最佳的含TGA的ORF，然后通过保守序列比对进行蛋白质相似性分析，从这些ORF中筛选出硒蛋白基因。该方法提高了从基因组中检测硒蛋白的灵敏度，这是由于基因组中的所有TGA被研究其作为Sec残基解码的可能性的设计。利用该方法，从玻璃海鞘基因组中鉴定出18个硒蛋白基因，使其硒蛋白组成员达到19个。其中一个硒蛋白W基因在3 ′端非翻译区含有两个SECIS元件。此外，二硫键形成蛋白A（DsbA）是首次在古脊索动物玻璃海鞘、赛维氏玻璃海鞘和花文昌鱼中发现的含硒蛋白，而含硒蛋白DsbA以前只在细菌和绿色藻类中发现。基于SelGenAmic算法的方法能够从基因组中识别真核生物硒蛋白基因。将该方法应用于玻璃海鞘，成功地从大规模真核基因组序列中发现了Sec-解码TGA，填补了我们对古老脊索动物硒蛋白认识的差距。
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. 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. 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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影响因子：
11.4
作者：
Novoselov, SV;Rao, M;Gladyshev, VN
通讯作者：
Gladyshev, VN
影响因子：
7.7
作者：
Castellano, S;Novoselov, SV;Guigó, R
通讯作者：
Guigó, R
影响因子：
4.8
作者：
Kryukov, GV;Kryukov, VM;Gladyshev, VN
通讯作者：
Gladyshev, VN
DOI：
10.1073/pnas.0703448104
发表时间：
2007-08-28
影响因子：
11.1
作者：
Shchedrina, Valentina A.;Novoselov, Sergey V.;Gladyshev, Vadim N.
通讯作者：
Gladyshev, Vadim N.
影响因子：
56.9
作者：
Kryukov, GV;Castellano, S;Gladyshev, VN
通讯作者：
Gladyshev, VN