Department of Plant Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
Sci Rep. 2024 Jul 9;14(1):15839. doi: 10.1038/s41598-024-65870-z.
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.
藏红花（Crocus sativus L.）作为最重要的药用植物和藏红花香料的商业来源而备受推崇。尽管藏红花具有有益的经济和药用特性，但与类胡萝卜素途径生物合成相关的 TF 和基因的相关性的调控机制尚不明显。由于遗传行为之间的复杂和广泛的相互作用，实现与次生代谢产物生产事件相关的基因表达网络的这些调控层次是主要挑战。最近，高通量表达数据对于构建共调控网络非常可行，以揭示受调控的过程并识别响应次生代谢物生物合成复杂过程的新型候选枢纽基因。在此，我们进行了加权基因共表达网络分析（WGCNA），这是一种系统生物学方法，以鉴定与次生代谢物相关的 11 个调节模块和枢纽 TF。在类胡萝卜素途径中发现了三个专门的模块。在显著模块中鉴定出几个枢纽 TF，包括 MADS、C2H2、ERF、bZIP、HD-ZIP 和锌指蛋白 MYB 和 HB，它们可能与类胡萝卜素生物合成有关。此外，使用 RT-qPCR 验证了六个枢纽 TF 和六个类胡萝卜素共调控基因的表达水平。结果证实，枢纽 TF 特别是 MADS、C2H2 和 ERF 与不同藏红花生态型中类胡萝卜素生物合成（CCD2、GLT2 和 ADH）受其控制的基因具有高度相关性（P<0.05）和正相关。涉及类胡萝卜素生物合成途径的模块的共表达基因的启动子分析表明，不仅基因共表达，而且还共享共同的调节基序，特别是与每个模块的枢纽 TF 有关，并且它们可能描述了它们的共同调节。该结果可用于通过操纵枢纽调节 TF 来工程化藏红花有价值的次生代谢产物。
