PDF(Pubmed)
Abstract：
Saffron (Crocus sativus L.) is being embraced as the most important medicinal plant and the commercial source of saffron spice. Despite the beneficial economic and medicinal properties of saffron, the regulatory mechanism of the correlation of TFs and genes related to the biosynthesis of the apocarotenoids pathway is less obvious. Realizing these regulatory hierarchies of gene expression networks related to secondary metabolites production events is the main challenge owing to the complex and extensive interactions between the genetic behaviors. Recently, high throughput expression data have been highly feasible for constructing co-regulation networks to reveal the regulated processes and identifying novel candidate hub genes in response to complex processes of the biosynthesis of secondary metabolites. Herein, we performed Weighted Gene Co-expression Network Analysis (WGCNA), a systems biology method, to identify 11 regulated modules and hub TFs related to secondary metabolites. Three specialized modules were found in the apocarotenoids pathway. Several hub TFs were identified in notable modules, including MADS, C2H2, ERF, bZIP, HD-ZIP, and zinc finger protein MYB and HB, which were potentially associated with apocarotenoid biosynthesis. Furthermore, the expression levels of six hub TFs and six co-regulated genes of apocarotenoids were validated with RT-qPCR. The results confirmed that hub TFs specially MADS, C2H2, and ERF had a high correlation (P < 0.05) and a positive effect on genes under their control in apocarotenoid biosynthesis (CCD2, GLT2, and ADH) among different C. sativus ecotypes in which the metabolite contents were assayed. Promoter analysis of the co-expressed genes of the modules involved in apocarotenoids biosynthesis pathway suggested that not only are the genes co-expressed, but also share common regulatory motifs specially related to hub TFs of each module and that they may describe their common regulation. The result can be used to engineer valuable secondary metabolites of C. sativus by manipulating the hub regulatory TFs.
摘要：
藏红花（CrocussativusL.）被认为是最重要的药用植物和藏红花香料的商业来源。尽管藏红花具有有益的经济和药用特性，TFs与载脂蛋白类胡萝卜素途径生物合成相关基因的调控机制不太明显。由于遗传行为之间复杂而广泛的相互作用，实现与次生代谢物生产事件相关的基因表达网络的这些调控层次结构是主要挑战。最近,高通量表达数据对于构建共调网络以揭示调节过程和识别响应次级代谢产物生物合成的复杂过程的新候选hub基因是高度可行的。在这里，我们进行了加权基因共表达网络分析(WGCNA)，系统生物学方法，确定11个与次生代谢物相关的调节模块和集线器TFs。在载脂蛋白类胡萝卜素途径中发现了三个专门的模块。在著名的模块中确定了几个集线器TF，包括MADS,C2H2,ERF,bZIP,HD-ZIP,锌指蛋白MYB和HB,这可能与载脂蛋白类胡萝卜素的生物合成有关。此外，通过RT-qPCR验证了6个中心TFs和6个载脂蛋白类胡萝卜素共调基因的表达水平。结果证实，集线器TFs特别是MADS，C2H2和ERF具有高度相关性（P<0.05），并且在测定代谢物含量的不同C.sativus生态型中，它们控制的基因在载脂蛋白类胡萝卜素生物合成（CCD2，GLT2和ADH）中具有正效应。参与类胡萝卜素生物合成途径的模块共表达基因的启动子分析表明，不仅基因共表达，但也共享与每个模块的集线器TFs特别相关的共同监管主题，并且它们可以描述它们的共同监管。该结果可用于通过操纵中枢调节TF来设计C.sativus的有价值的次级代谢产物。
