小立碗藓WRKY基因家族生物信息学分析

Bioinformatics analysis of WRKY gene family in Physcomitrella patens

关键词:  小立碗藓, WRKY转录因子, 基因家族分析, 生物信息

Key words:  Physcomitrella patens, WRKY transcription factor, gene family analysis, bioinformatics

摘要:

WRKY作为最先在植物中发现的转录因子,在植物生长发育等过程中发挥重要作用。为了更好地研究小立碗藓WRKY蛋白的结构与功能,该文以Pfam数据库中WRKY基因家族数据(登录号为PF03106)为材料,分析了小立碗藓(Physcomitrella patens)WRKY基因家族成员的理化性质、蛋白质的二级结构预测、染色体定位、内外显子分布及系统进化关系。结果表明:(1)小立碗藓WRKY基因家族成员共有38个基因,根据WRKY保守结构域个数和锌指结构类型分成Ⅰ、Ⅱ两大类,不含第Ⅲ类(锌指结构为C2HC型),其中部分基因WRKY保守结构域发生变异。(2)WRKY蛋白氨基酸长度在216～775 aa之间、相对分子质量在 24.5～82.8 kDa之间,亚细胞定位显示WRKY家族成员蛋白质定位于细胞核中。(3)WRKY蛋白的二级结构以α-螺旋、延伸链、β-转角、无规卷曲四种构成元件构成,除PpWRKY11(α-螺旋为主)外,其余无规卷曲占比高达70%。(4)与拟南芥的系统进化关系表明,植物在进化过程中WRKY家族成员的数目与进化方式发生改变,WRKY基因家族成员外显子的个数为3～7个。(5)小立碗藓WRKY基因家族成员无规则分散于21条染色体上,并未形成基因簇。该研究通过分析WRKY基因家族的基本结构与性质,能为后续深入研究WRKY转录因子的功能奠定基础。

Abstract:

As a transcription factor first found in plants, WRKY plays an important role in plant growth and development. However, it has not been studied in Physcomitrella patens. By using the WRKY gene family data(accession number is PF03106)in Pfam database, this paper studied the basic information of WRKY in P. patens, which included physicochemical properties, protein secondary structure prediction, chromosome localization, exon and intron distribution and phylogenetic relationship. The results were as follows:(1)The WRKY gene family in P. patens consisted of 38 members which were divided into two major categories ─Ⅰ and Ⅱ, and the conserved domains of some WRKY genes had mutated.(2)The amino acid length of WRKY protein was 216-775 aa and the relative molecular mass was 24.5-82.8 kDa; Subcellular location showed that the proteins of WRKY gene family were distributed in the nucleus.(3)The secondary structure of WRKY protein was composed of four constituent elements: α-helix, extended strand, β-turn, and random coil; Except for PpWRKY11(α-helix dominated), the proportion of random coil was up to 70%.(4)The phylogenetic relationship with Arabidopsis showed that the number of the WRKY family members and the way of their revolution had changed in the process of plants' evolution, the number of exons of WRKY gene family members were 3-7.(5)The members of WRKY gene were randomly dispersed on 21 chromosomes without forming a gene cluster. This study analyzed the basic structure and properties of the WRKY gene family, and it was found that the WRKY gene family of Physcomitrella patens has evolutionary diversity and unique variability in conserved domains, laying the foundation for subsequent research.