| 引用本文: | 周雅,高贝,张道远.齿肋赤藓早期光诱导蛋白ELIPs的生物信息学分析[J].生物信息学,2014,12(4):. |
| ZHOU Ya,GAO Bei,ZHANG Daoyuan.Bioinformatics analysis of early light-induced protein(ELIPs) in Syntrichia caninervis[J].Chinese Journal of Bioinformatics,2014,12(4):. |
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| 摘要: |
| 从齿肋赤藓转录组数据库出发,共得到39条注释的早期光诱导蛋白ScELIPs unigene,其中2条( ScELIP1与ScELIP2)具有完整ORF。利用多种生物信息学分析工具,对这2条ScELIPs序列的同源性、理化性质、保守域、信号肽、疏水性、亚细胞定位、二级结构、跨膜结构、三维结构、活性位点等方面进行分析。结果表明：2条ScELIPs 序列的ORF全长分别为711 bp和624 bp,分别编码236和207个氨基酸,二者都具有完整的Chloroa_b-bind功能域,定位于叶绿体类囊体膜,含有3个跨膜α螺旋,第1、3螺旋通过Glu和Arg残基形成双重对称结构,且具有至少4个叶绿素结合活性位点。通过对得到的2条ScELIPs进行氨基酸序列比对及基因树分析,得出ScELIP1与小立碗藓、山墙藓及盐生杜氏藻聚为一支,而ScELIP2与高等植物聚为一支,表现出ELIP从低等到高等植物的进化特征。本研究为ScELIPs基因后续的克隆和功能研究奠定了基础。 |
| 关键词: 早期光诱导蛋白 生物信息学 齿肋赤藓 |
| DOI：10.3969/j.issn.1672-5565.2014-04.20140401 |
| 分类号: |
| 基金项目:国家重点基础研究发展计划(973计划)(No.2014CB954203)资助。 |
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| Bioinformatics analysis of early light-induced protein(ELIPs) in Syntrichia caninervis |
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ZHOU Ya1, GAO Bei2, ZHANG Daoyuan1
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1.Xinjiang Institute of Ecology and Geography, Chinese Academy of Science, Key Laboratory of Biogeography and Bioresource in Arid Land, Urumqi 830011, China;2.University of Chinese Academy of Sciences,Beijing 100049, China
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| Abstract: |
| Thirty nine ScELIPs unigenes were obtained based on the transcriptome data of Syntrichia caninervis, an extremely desiccation tolerance moss. ScELIP1 and ScELIP2 have complete ORF. Several bioinformatics methods were utilized to analyze and verify the characteristics of ScELIPs such as homologous relationships, physicochemical properties, conserved domain, signal peptide, hydrophobicity, subcellular localization, secondary structure, transmembrane structure, functional domain, three dimensional structure, active sites and so on. The results showed that ORF of ScELIP1 and ScELIP2 are 711 bp and 624 bp and encode 236 and 207 amino acids, respectively. Both of them contain a complete Chloroa_b-bind-functional domain. Subcellular location prediction revealed that the two ScELIPs are both located at the thylakoid membrane of chloroplast. Secondary structure prediction demonstrated that they both have three transmembrane helixes, among which the first and the third one form a double symmetric structure through the Glu and Arg residues. The ScELIPs has at least four active chlorophyll a binding sites. Finally, protein sequence alignment and phylogenetic analysis revealed that ScELIP1 has the closest relationship with moss physcomitrella patens and Tortula ruralis, while ScELIP2 is closer to higher vascular plants, showing the evolutionary trend clue from moss to vascular plants. This study laid a solid foundation for the subsequently cloning and functional research of ELIPs. |
| Key words: Early light-induced protein Bioinformatics Syntrichia caninervis |
