Zhang Xiaodong, Li Caixia, Hao Zhanchao, Liu Yongjiang
Food and Pharmacy College, Xuchang University, Xuchang 461000, China.
Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Xuchang 461000, China.
Gene. 2023 Dec 20;888:147757. doi: 10.1016/j.gene.2023.147757. Epub 2023 Sep 3.
Angelica dahurica roots have a long history of use in traditional Chinese medicine due to their high coumarin content. To address the increasing demand for these roots, a synthetic biology approach has been proposed. Nevertheless, our comprehension of coumarin biosynthesis and its regulation remains limited. In this study, we utilized Hiseq2500 sequencing to analyze the transcriptomes of A. dahurica at different growth stages while concurrently quantifying coumarin content. Differentially expressed gene (DEG) analysis was employed to identify key genes involved in coumarin and terpenoid backbone biosynthesis. Weighted gene co-expression network analysis (WGCNA) was applied to identify gene modules strongly associated with coumarin content, elucidating the regulatory relationships between transcription factors (TFs) and pathway genes. Furthermore, KEGG enrichment analysis was used to explore essential pathways governing coumarin biosynthesis, with the identification of hub genes. Our results indicated that total coumarin content was highest in the roots, followed by leaves and stems, across all three developmental stages. Transcriptome analysis identified a total of 92,478 genes, among which 215 and 30 genes were implicated in coumarin and terpenoid backbone biosynthesis, respectively. Within the 73 identified gene modules by WGCNA, three modules-namely aquamarine1 (comprising two OMTs, one CSE, one AACT, one HDS, two PSs, one 2OGO, four UGTs, and seven CYP450s), darkmagenta (containing one UGT and one HDR), and navajowhite2 (consisting of one HCT, three UGTs, one CYP71A25, one OMT, one CSE, one HDS, and one PT)-were strongly associated with imperatorin, oxypeucedanin, and isoimperatorin content, respectively. KEGG enrichment analysis highlighted significant enrichment of cytochrome P450, transporter, and ubiquitin system pathways. Moreover, TF-gene regulatory analysis unveiled the complexity of coumarin biosynthesis, with 17 TF families regulating 17 genes in the aquamarine1 module, 8 TF families regulating 2 genes in the darkmagenta module, and 8 TF families regulating 7 genes in the navajowhite2 module. These comprehensive findings provide valuable insights into coumarin biosynthesis in A. dahurica, facilitating future research and potential applications in traditional Chinese medicine and synthetic biology strategies.
白芷根因其香豆素含量高，在传统中药中有着悠久的使用历史。为了满足对白芷根日益增长的需求，人们提出了一种合成生物学方法。然而，我们对香豆素生物合成及其调控的理解仍然有限。在本研究中，我们利用Hiseq2500测序技术分析了白芷在不同生长阶段的转录组，同时对香豆素含量进行了定量分析。采用差异表达基因（DEG）分析来鉴定参与香豆素和萜类骨架生物合成的关键基因。应用加权基因共表达网络分析（WGCNA）来鉴定与香豆素含量密切相关的基因模块，阐明转录因子（TFs）与途径基因之间的调控关系。此外，利用KEGG富集分析来探索香豆素生物合成的关键途径，并鉴定枢纽基因。我们的结果表明，在所有三个发育阶段，香豆素总含量在根中最高，其次是叶和茎。转录组分析共鉴定出92478个基因，其中分别有215个和30个基因参与香豆素和萜类骨架生物合成。在WGCNA鉴定出的73个基因模块中，有三个模块——即海蓝宝石1模块（包含两个OMT、一个CSE、一个AACT、一个HDS、两个PS、一个2OGO、四个UGT和七个CYP450）、暗品红色模块（包含一个UGT和一个HDR）和纳瓦霍白2模块（由一个HCT、三个UGT、一个CYP71A25、一个OMT、一个CSE、一个HDS和一个PT组成）——分别与欧前胡素、氧化前胡素和异欧前胡素含量密切相关。KEGG富集分析突出了细胞色素P450、转运体和泛素系统途径的显著富集。此外，TF-基因调控分析揭示了香豆素生物合成的复杂性，其中17个TF家族调控海蓝宝石1模块中的17个基因，8个TF家族调控暗品红色模块中的2个基因，8个TF家族调控纳瓦霍白2模块中的7个基因。这些全面的研究结果为白芷中香豆素的生物合成提供了有价值的见解，有助于未来在传统中药和合成生物学策略方面的研究及潜在应用。
