丹参Dirigent基因家族的发现与生物信息学分析

Discovery and Bioinformatics Analysis of Dirigent Multigene Family in Salvia miltiorrhiza

Dirigent(DIR)蛋白基因是植物木质素合成过程中一类重要的基因,几乎存在于所有维管植物中,然而药用植物丹参中的DIR和类DIR蛋白基因(SmDIR)还没有被研究过。本研究通过生物信息学方法,对已在Gen Bank上登录的9个丹参转录组数据库进行整合拼接分析,发现了33个SmDIR基因片段,其中5条为完整序列。通过对5条完整SmDIR基因的序列特征、理化性质、跨膜结构域、信号肽、导肽、疏水性/亲水性、蛋白质二级结构、三级结构及结构域等进行预测分析,并将丹参DIR蛋白序列与其它植物的DIR蛋白进行同源比对,构建了丹参和模式植物拟南芥DIR蛋白家族的系统进化树。结果表明,这5条丹参DIR基因的开放阅读框都在594 bp上下,分子量为21.47 k D左右。除了SmDIR5,其余SmDIR蛋白的理论等电点(p I)均低于7,在5.60~6.50范围内,说明大多数丹参的DIR蛋白略呈酸性。Thr、Val、Gly、Leu和Ser等氨基酸是这些SmDIR蛋白共有的主要氨基酸。研究还发现这些丹参DIR蛋白表现出明显的疏水区和亲水区,均存在分泌途径信号肽,可能存在跨膜结构域。蛋白质二级结构中最主要的结构元件是无规则卷曲。氨基酸同源性比对显示,SmDIR4与Erythranthe guttata的类DIR蛋白同源性较高,SmDIR1、SmDIR2、SmDIR3和SmDIR5与芝麻的类DIR蛋白同源性较高。与拟南芥的进化分析显示,这些丹参DIR蛋白基因被分为两大类,归属DIR-b和DIR-d亚家族。本研究对丹参DIR蛋白序列特征进行了系统分析,可为今后深入研究该蛋白提供有利参考。

Dirigent （DIR） protein genes take an important part in the biosynthesis of plant lignin. They exist in almost every vascular plant .However, the DIR and DIR-like protein gene family in Salvia miltiorrhiza （SmDIR） have not been analyzed in detail yet In this study, we did the integrated analysis of 9 transcription profiles registered in GenBank through bioinformatics methods, and found out 33 DIR-like gene segments, among which five were full-length sequences. Forecasting analysis was carried out to analyze the sequence features, physicochemical characters,transmembrane topological structures, signal peptides, leader peptides, hydrohobicity or hydrophilicity, secondary structures, tertiary structures and functional domains in the five full-length proteins. In order to construct the phylogenetic tree of DIR proteins from S. miltiorrhiza and model plant A rabidopsis thaliana, homology analysis was also applied to SmDIRs with other DIR proteins. The result showed that the open reading frames of the five SmDIRs were about 594 bp and the molecular weight were approximately 21.47 kD. Besides SmDIR5, the theoretical isoelectric points of the rest SmDIRs were all lower than 7, varying between 5.60 and 6.50, illuminating that most SmDIRs were acidic. Thr, Val, Gly, Leu and Ser were the major amino acids in all of these DIR proteins. This study also showed that SmDIRs had apparent hydrophobic region, hydrophilicity region, signal peptides, and might had the transmembrane domain. The main secondary structures of the proteins were random coils. In addition, the homology analysis revealed that the homology of SmDIR4 was high with the DIR-like protein in Erythranthe guttata, while SmDIR1, SmDIR2, SmDIR3 and SmDIR5 were high with the DIR-like protein in Sesamum indicum. Compared with the evolutionary analysis ofA. thaliana, these SmDIRs were classified into two groups of DIR-b and DIR-d subfamilies. In a word, this study provided a systemic analysis of dirigent proteins in S. miltiorrhiza. It would provide useful information for SmDIRs studies in the future.