Eshaghi Mahsa, Rashidi-Monfared Sajad
Department of Plant Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
Biochem Biophys Rep. 2025 Jul 23;43:102147. doi: 10.1016/j.bbrep.2025.102147. eCollection 2025 Sep.
L. (Opium poppy) is one of the world's most economically valuable medicinal plants, and it is the industrial source of essential compounds such as painkillers and other pharmecutical drugs. Recently, large amounts of opium poppy transcriptome data have become accessible in public databases, consisting of data on the different tissues and ecotypes. Despite the importance of this plant, there is little information about the regulatory mechanisms involved in secondary metabolites, especially in benzylisoquinoline alkaloids (BIAs) biosynthesis at the omics level in opium poppy. Herein, we employed co-expression and co-regulation network analysis using Weighted Gene Co-expression Network Analysis (WGCNA) to infer and reveal gene interactions in opium poppy by using RNA-Seq data. To validate possible hub transcription factors (TFs), partial least squares regression (PLS) and Receiver operating characteristic (ROC) analyses were conducted. We identified nine significant co-regulated modules (comprising1501 genes) and hub TF genes related to the biosynthesis of BIAs, including WRKY3, WRKY32, MYB3R-5, bZIP, APRR2, MYB43, MYB82, bHLH, and WRKY40. The results suggest that these hub genes can play a vital role in co-regulating genes involved in secondary metabolic pathways in opium poppy. Also, we detected common regulatory motifs related to hub TFs (WRKY and MYB) of important co-regulated BIA modules. We implied their common regulatory role in the biosynthesis of secondary metabolites in the opium poppy. The results illustrated that co-expressed genes of the modules share common regulatory motifs, especially related to hub TFs of each module, and that they may define their common regulation. ROC analysis with high diagnostic value (AUC = 1) identified the possible role of the hub TF involved in the BIAs pathways. PLS analysis showed a considerable effect of hub TFs (WRKY and bZIP) on the related genes. Our WGCNA analysis at the omics level, along with identifying hub TFs, highlights the regulatory potential of these genes and the primary molecular mechanisms involved in the BIA biosynthetic pathway in opium poppy. These findings provide valuable insights for the regulon engineering of candidate hub TFs in expression systems.
罂粟是世界上经济价值最高的药用植物之一，是止痛药和其他药品等重要化合物的工业来源。最近，公共数据库中可获取大量罂粟转录组数据，包括不同组织和生态型的数据。尽管这种植物很重要，但关于次生代谢产物，特别是罂粟中苄基异喹啉生物碱（BIA）生物合成的组学水平调控机制的信息却很少。在此，我们使用加权基因共表达网络分析（WGCNA）进行共表达和共调控网络分析，以利用RNA测序数据推断和揭示罂粟中的基因相互作用。为了验证可能的枢纽转录因子（TF），进行了偏最小二乘回归（PLS）和接受者操作特征（ROC）分析。我们鉴定出九个与BIA生物合成相关的显著共调控模块（包含1501个基因）和枢纽TF基因，包括WRKY3、WRKY32、MYB3R-5、bZIP、APRR2、MYB43、MYB82、bHLH和WRKY40。结果表明，这些枢纽基因在共同调控参与罂粟次生代谢途径的基因方面可发挥至关重要的作用。此外，我们检测到与重要共调控BIA模块的枢纽TF（WRKY和MYB）相关的常见调控基序。我们推测它们在罂粟次生代谢产物生物合成中具有共同调控作用。结果表明，模块的共表达基因共享常见调控基序，特别是与每个模块的枢纽TF相关的基序，并且它们可能定义了其共同调控。具有高诊断价值（AUC = 1）的ROC分析确定了参与BIA途径的枢纽TF的可能作用。PLS分析表明枢纽TF（WRKY和bZIP）对相关基因有显著影响。我们在组学水平上的WGCNA分析，连同鉴定枢纽TF，突出了这些基因及其参与罂粟BIA生物合成途径的主要分子机制的调控潜力。这些发现为表达系统中候选枢纽TF的调控子工程提供了有价值的见解。
