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
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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。
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( Ds FPPS1 and Ds FPPS2) were obtained in this research. Subsequential protein physicochemical property,architectural feature,function and phylogeny relationship analysis of Ds FPPSs were also predicted and analyzed. The results showed that Ds FPPS1 and Ds FPPS2 sequences contained an ORF span of 1 029 bp and 969 bp respectively,encoding 342( Ds FPPS1) and 322( Ds FPPS2) amino acids respectively. The analysis of amino acid composition showed that the dominant components of Ds FPPS1 and Ds FPPS2 were both nonpolar amino acids. The molecular weight of Ds FPPS1 and Ds FPPS2 were 39.68 k D and 36.76 k D,respectively. Isoelectric point were 5.11 and 5.65 for Ds FPPS1 and Ds FPPS2,respectively. Besides,Ds FPPS1 protein was predicted to be a stable protein,but Ds FPPS2 protein was predicted to be an unstable protein. The amino acid sequence analysis showed that Ds FPPS1 and Ds FPPS2 had no signal peptide and transmembrane region. The possible localization of Ds FPPS1 and Ds FPPS2 was both in mitochondria. Ds FPPS1 and Ds FPPS2 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 Ds FPPS1 had higher homology with Chenopodium quinoa,Spinacia oleracea and Beta vulgaris than Ds FPPS2. In addition,the secondary structure of Ds FPPS proteins mainly consisted of α-helixes,which resulted in a bundle of 8 α-helices in tertiary structure. However,tertiary structure analysis showed that Ds FPPS2 protein missed an α-helix compared to Ds FPPS1 protein. The result of phylogenetic analysis indicates that phylogenetic relationships of Ds FPPS1 protein are close to Chenopodiaceae plants consistent with sequence alignment results,while Ds FPPS2 protein is clustered alone in phylogenetic tree. In general,these results provides a certain reference for an insight to molecular function of Ds FPPS and the synthetic biology of sesquiterpenes in D. schraderiana.
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( Ds FPPS1 and Ds FPPS2) were obtained in this research. Subsequential protein physicochemical property,architectural feature,function and phylogeny relationship analysis of Ds FPPSs were also predicted and analyzed. The results showed that Ds FPPS1 and Ds FPPS2 sequences contained an ORF span of 1 029 bp and 969 bp respectively,encoding 342( Ds FPPS1) and 322( Ds FPPS2) amino acids respectively. The analysis of amino acid composition showed that the dominant components of Ds FPPS1 and Ds FPPS2 were both nonpolar amino acids. The molecular weight of Ds FPPS1 and Ds FPPS2 were 39.68 k D and 36.76 k D,respectively. Isoelectric point were 5.11 and 5.65 for Ds FPPS1 and Ds FPPS2,respectively. Besides,Ds FPPS1 protein was predicted to be a stable protein,but Ds FPPS2 protein was predicted to be an unstable protein. The amino acid sequence analysis showed that Ds FPPS1 and Ds FPPS2 had no signal peptide and transmembrane region. The possible localization of Ds FPPS1 and Ds FPPS2 was both in mitochondria. Ds FPPS1 and Ds FPPS2 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 Ds FPPS1 had higher homology with Chenopodium quinoa,Spinacia oleracea and Beta vulgaris than Ds FPPS2. In addition,the secondary structure of Ds FPPS proteins mainly consisted of α-helixes,which resulted in a bundle of 8 α-helices in tertiary structure. However,tertiary structure analysis showed that Ds FPPS2 protein missed an α-helix compared to Ds FPPS1 protein. The result of phylogenetic analysis indicates that phylogenetic relationships of Ds FPPS1 protein are close to Chenopodiaceae plants consistent with sequence alignment results,while Ds FPPS2 protein is clustered alone in phylogenetic tree. In general,these results provides a certain reference for an insight to molecular function of Ds FPPS and the synthetic biology of sesquiterpenes in D. schraderiana.
引文
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CHEN A,KROON PA,POULTER CD,1994.Isoprenyl diphosphate synthases:Protein sequence comparisons,a phylogenetic tree,and predictions of secondary structure[J].Protein Sci,3(4):600-607.
CHRISTIANSON DW,2017.Structural and chemical biology of terpenoid cyclases[J].Chem Rev,117(17):11570.
CLOSA M,VRANOVE,BORTOLOTTI C,et al.,2010.The Arabidopsis thaliana FPP synthase isozymes have overlapping and specific functions in isoprenoid biosynthesis,and complete loss of FPP synthase activity causes early developmental arrest[J].Plant J Cell Mol Biol,63(3):512.
GUO D,LI HL,PENG SQ,2015.Structure conservation and differential expression of farnesyl diphosphate synthase genes in Euphorbiaceous plants[J].Int J Mol Sci,16(9):22402-22414.
KEIM V,MANZANO DA,DAVID,FERNNDEZ FJ,et al.,2012.Characterization of Arabidopsis FPS isozymes and FPSgene expression analysis provide insight into the biosynthesis of isoprenoid precursors in seeds[J].PLoS ONE,7(11):e49109.
LEI M,HE H,ZHANG PF,et al.,2015.Study on the extraction of Chenopodium oetidum essential oil and its inhibition against insect activity[J].J Anhui Agric Sci,43(28):64-66.[雷鸣,何花,张鹏飞,等,2015.菊叶香藜精油的提取及对昆虫活力抑制的研究[J].安徽农业科学,43(28):64-66.]
LI YB,FAN QQ,WANG BL,et al.,2012.Advances in the study of plant farnesyl pyrophosphate synthase(FPPS)gene[J].Chin J Agric Biotechnol,20(3):321-330.[李永波,樊庆琦,王宝莲,等,2012.植物法呢基焦磷酸合酶基因(FPPS)研究进展[J].农业生物技术学报,20(3):321-330.]
LIU ZL,LIU XC,SHI WP,et al.,2015.Essential oil of Dysphania schraderiana in the prevention and control of plant mites:China,104782667A[P].2015-07-22.[刘志龙,刘昕超,石旺鹏,等,2015.菊叶香藜植物挥发油在防治植物螨中的用途.中国,104782667A[P].2015-07-22.]
MU HJ,SUN GP,HWANG YL,et al.,2012.Cedrol enhances extracellular matrix production in dermal fibroblasts in a MAPK-Dependent manner[J].Ann Dermatol,24(1):16-21.
OHARA K,FUKUDA T,ISHIDA Y,et al.,2017.β-Eudesmol,an oxygenized sesquiterpene,stimulates appetite via TRPA1 and the autonomic nervous system[J].Sci Rep,7(1):15785-15081.
PIAO YH,PIAO HS,2012.Research progress in biological activity of sesquiterpene compounds[J].Occup Health,28(18):2291-2293.[朴英花,朴惠顺,2012.倍半萜类化合物生物活性研究进展[J].职业与健康,28(18):2291-2293.]
SUN LC,LI SY,WANG FZ,et al.,2017.Research progresses in the synthetic biology of terpenoids[J].Biotechnol Bull,33(1):64-75.[孙丽超,李淑英,王凤忠,等,2017.萜类化合物的合成生物学研究进展[J].生物技术通报,33(1):64-75.]
TU YY,2011.The discovery of artemisinin(qinghaosu)and gifts from Chinese medicine[J].Nat Med,17(10):1217-1220.
WANG J,YOU S,ZHOU LN,2012.Progress in research of sesquiterpenoids biotransformation[J].J Shenyang Pharm Univ,29(2):76-84.[王佳,游松,周丽娜,2012.倍半萜生物转化的研究进展[J].沈阳药科大学学报,29(2):76-84.]
WU J,FENG Y,HAN C,et al.,2017.Germacrone derivatives:synthesis,biological activity,molecular docking studies and molecular dynamics simulations[J].Oncotarget,8(9):15149-15158.
ZHAO L,PAN CX,PANG KQ,et al.,2018.Gene cloning of PpGL2 transcription factor in peach and its bioinformatics analysis[J].J Southern Agric,49(10):1901-1908.[赵丽,潘彩霞,庞可,等,2018.桃树PpGL2转录因子基因克隆及生物信息学分析[J].南方农业学报,49(10):1901-1908.]
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