菊叶香藜转录组数据库中FPPS基因的挖掘与生物信息学分析

Mining and bioinformatic analysis of FPPS gene fromDysphania schraderiana transcriptome database

关键词:  法尼基焦磷酸合酶, 转录组, 菊叶香藜, 基因挖掘, 生物信息学

Key words:  farnesyl pyrophosphate synthase, transcriptome, Dysphania schraderiana, gene mining, bioinformatics

摘要:

为深入了解菊叶香藜法尼基焦磷酸合酶基因,该研究对菊叶香藜转录组数据库进行挖掘,获取了两条FPPS基因序列(DsFPPS1和DsFPPS2),并对DsFPPS1和DsFPPS2编码蛋白的理化性质、结构、功能、系统进化进行了分析。结果表明:DsFPPS1和DsFPPS2基因分别包含1 029 bp和969 bp的开放阅读框,分别编码342个(DsFPPS1)和322个(DsFPPS2)氨基酸。DsFPPS1和DsFPPS2位于线粒体内,未发现信号肽和跨膜结构,DsFPPS1为稳定蛋白,DsFPPS2为不稳定蛋白。氨基酸序列比对发现DsFPPS1和DsFPPS2序列相似性为60.53%,均含有5个保守结构域和2个天冬氨酸富集区域。DsFPPS1和DsFPPS2二级结构主要由α-螺旋构成,三级结构为由8个α-螺旋形成的α-螺旋束,但DsFPPS2的三级结构中缺少一个α-螺旋A。系统进化树中DsFPPS1与藜科植物聚为一枝,与藜科植物遗传距离较近,而DsFPPS2单独聚为一枝。通过对菊叶香藜转录组数据库中FPPS基因的挖掘与生物信息学分析,为菊叶香藜FPPS的功能研究及其倍半萜类化合物的生物合成研究奠定了一定的理论基础。

Abstract:

Dysphania schraderiana, in the Chenopodiaceae family, is widely distributed in Lhasa(Tibet, China)and used as a traditional medicine. The essential oil of Dysphania schraderiana contains abundant sesquiterpenes compounds, appeared to possess potential medicinal value. Farnesyl pyrophosphate synthase(FPPS)is a key branch-point enzyme in biosynthesis of terpene. In order to reveal D. schraderiana FPPS gene, the transcriptome database of D. schraderiana was mined and two gene sequences(DsFPPS1 and DsFPPS2)were obtained in this research. Subsequential protein physicochemical property, architectural feature, function and phylogeny relationship analysis of DsFPPSs were also predicted and analyzed. The results showed that DsFPPS1 and DsFPPS2 sequences contained an ORF span of 1 029 bp and 969 bp respectively, encoding 342(DsFPPS1)and 322(DsFPPS2)amino acids respectively. The analysis of amino acid composition showed that the dominant components of DsFPPS1 and DsFPPS2 were both nonpolar amino acids. The molecular weight of DsFPPS1 and DsFPPS2 were 39.68 kD and 36.76 kD, respectively. Isoelectric point were 5.11 and 5.65 for DsFPPS1 and DsFPPS2, respectively. Besides, DsFPPS1 protein was predicted to be a stable protein, but DsFPPS2 protein was predicted to be an unstable protein. The amino acid sequence analysis showed that DsFPPS1 and DsFPPS2 had no signal peptide and transmembrane region. The possible localization of DsFPPS1 and DsFPPS2 was both in mitochondria. DsFPPS1 and DsFPPS2 protein exhibited 60.53% sequence identity, and possessed five conserved domain(Ⅰ-Ⅴ)and two characteristic Asp-rich motifs(DDXXD). The amino acid sequence of DsFPPS1 had higher homology with Chenopodium quinoa, Spinacia oleracea and Beta vulgaris than DsFPPS2. In addition, the secondary structure of DsFPPS proteins mainly consisted of α-helixes, which resulted in a bundle of 8 α-helices in tertiary structure. However, tertiary structure analysis showed that DsFPPS2 protein missed an α-helix compared to DsFPPS1 protein. The result of phylogenetic analysis indicates that phylogenetic relationships of DsFPPS1 protein are close to Chenopodiaceae plants consistent with sequence alignment results, while DsFPPS2 protein is clustered alone in phylogenetic tree. In general, these results provides a certain reference for an insight to molecular function of DsFPPS and the synthetic biology of sesquiterpenes in D. schraderiana.