Department of Biotechnology, Panjab University, BMS Block I, Sector 25, Chandigarh 160014, India.
Department of Biotechnology, Panjab University, BMS Block I, Sector 25, Chandigarh 160014, India.
Plant Sci. 2023 Jun;331:111689. doi: 10.1016/j.plantsci.2023.111689. Epub 2023 Mar 23.
Saussurea lappa (S. lappa) has been known to synthesize medicinally important, costunolide. Due to its immense therapeutic importance, understanding of regulatory mechanism associated with its biosynthesis is crucial. The identification of genes and transcription factors (TFs) in S. lappa, created a clear picture of costunolide biosynthesis pathways. Further to understand the regulation of costunolide biosynthesis by miRNAs, an integrated study of transcriptome, miRNAs, and degradome was performed. Identified candidate miRNAs and associated feed-forward loops (FFLs) illustrates their regulatory role in secondary metabolite biosynthesis. Small RNA and degradome sequencing were performed for leaf and root tissues to determine miRNAs-targets pairs. A total of 711 and 525 such targets were obtained for novel and known miRNAs respectively. This data was used to generate costunolide-specific miRNA-TF-gene interactome to perform systematic analyses through graph theoretical approach. Interestingly, miR171c.1 and sla-miR121 were identified as key regulators to connect and co-regulate both mevalonate and sesquiterpenoid pathways to bio-synthesize costunolide. Tissue-specific FFLs were identified to be involved in costunolide biosynthesis which further suggests the evolutionary co-relation of root-specific networks in synthesis of secondary metabolites in addition to leaf-specific networks. This integrative approach allowed us to determine candidate miRNAs and associated tissue-specific motifs involved in the diversification of secondary metabolites. MiRNAs identified in present study can provide alternatives for bioengineering tool to enhance the synthesis of costunolide and other secondary metabolites in S. lappa.
雪莲已被证明能够合成具有重要药用价值的大根香叶烯醇。由于其巨大的治疗意义，了解与其生物合成相关的调控机制至关重要。雪莲中基因和转录因子（TFs）的鉴定，为大根香叶烯醇生物合成途径提供了清晰的图景。为了进一步了解 miRNA 对大根香叶烯醇生物合成的调控作用，对转录组、miRNA 和降解组进行了综合研究。鉴定出的候选 miRNA 及其相关的前馈环（FFL）说明了它们在次生代谢物生物合成中的调节作用。对叶片和根组织进行了小 RNA 和降解组测序，以确定 miRNA-靶对。分别获得了 711 个和 525 个新型和已知 miRNA 的靶标。这些数据用于生成大根香叶烯醇特异性 miRNA-TF-基因互作组，通过图论方法进行系统分析。有趣的是，miR171c.1 和 sla-miR121 被鉴定为关键调节剂，将甲羟戊酸途径和倍半萜途径连接并共同调节，以生物合成大根香叶烯醇。鉴定出组织特异性的 FFL 参与大根香叶烯醇的生物合成，这进一步表明根特异性网络与叶特异性网络在合成次生代谢物方面的进化相关性。这种综合方法使我们能够确定参与次生代谢物多样化的候选 miRNA 和相关组织特异性基序。本研究中鉴定的 miRNAs 可为增强雪莲中大根香叶烯醇和其他次生代谢物的合成提供生物工程工具的替代方案。
