黄沙鳖β-防御素基因家族的鉴定及生物信息学分析

Identification and Bioinformatics Analysis of β-Defensin Gene Family in Huangsha Soft-Shelled Turtle

摘要: β-防御素是一种富含半胱氨酸的小分子阳离子抗菌肽，在生物机体天然免疫中发挥重要的作用。本研究基于黄沙鳖转录组数据库和PCR验证鉴定了黄沙鳖β-防御素基因(Hs-BDs)家族，并对其进行蛋白理化性质、蛋白结构和进化关系等生物信息学分析。实验结果表明，共鉴定出18个具有完整蛋白编码区的Hs-BDs家族成员，这些Hs-BDs编码蛋白的氨基酸残基数量在59~94之间，蛋白分子量介于6759.13~10731.32 Da，等电点在8.82~10.45之间。系统进化树分析可将18个Hs-BDs家族成员分为4个亚类(Class I~IV)。随机选择部分Hs-BDs进行蛋白结构分析，这些Hs-BDs前体蛋白二级结构主要由α-螺旋、β-折叠片和无规则卷曲3种结构组成；成熟蛋白三级结构预测结果显示6个保守的半胱氨酸残基分别以Cys1-Cys5、Cys2-Cys4和Cys3-Cys6的方式连接形成3个分子内二硫键。本文结果可为进一步研究黄沙鳖β-防御素基因家族的详细功能以及抗菌肽的研发提供基础数据。

Abstract: β-defensin is a small cationic antimicrobial peptide rich in cysteine, which plays an important role in innate immunity of the living organism. In this study, the β-defensin genes of Huangsha soft- shelled turtle (Hs-BDs) family were identified based on transcriptome database of Huangsha soft- shelled turtle and PCR validation, and the physicochemical properties of protein, protein structure and evolutionary relationship were also analyzed. The results showed that a total of 18 members of Hs-BDs family with complete coding regions were identified. The number of amino acid residues of these Hs-BDs proteins ranged from 59 to 94, the molecular weight ranged from 6759.13 to 10,731.32 Da, and the isoelectric point ranged from 8.82 to 10.45. The 18 members of Hs-BDs family were divided into four subgroups (Class I~IV) according to the phylogenetic tree analysis. Some Hs-BDs were randomly selected for protein structure analysis and the results showed that the secondary structures of Hs-BDs preprotein are mainly composed of α-helix, β-sheet and random coil. Six conserved cysteine residues were linked to form three intramolecular disulfide bonds in the form of Cys1-Cys5, Cys2-Cys4 and Cys3-Cys6, respectively. The results of this study can provide basic data for further research on the detailed functions of β-defensin gene family and the development of antimicrobial peptides.