Hub genes and their post-transcriptional controllers in Tanacetum parthenium’s MEP and MEV biosynthetic pathways

<h2>Abstract</h2><h3>Background</h3> <i>Tanacetum parthenium</i> L. produces a rich array of specialized metabolites, among which terpenoids constitute a major and structurally diverse class biosynthesized through the methyl-D-erythritol phosphate (MEP) and mevalonate (MEV) pathways. A critical step in understanding and manipulating these biosynthetic networks involves the identification of hub genes, which act as central regulators exerting significant control over metabolic flux. Elucidating these key genetic elements is therefore fundamental for advancing our understanding of terpenoid biosynthesis and for enabling targeted strategies in metabolic engineering. <h3>Results</h3> Protein-protein interaction network (PPI-Net) analysis identified three MEP pathway hub genes (<i>DXS</i>, <i>HDS</i>, and <i>HDR</i>) and two MEV pathway hub genes (<i>HMGS</i> and <i>HMGR</i>), governing terpenoid biosynthesis in <i>T. parthenium</i>. Gene ontology revealed enrichment in cellular metabolic processes and anatomical entities. Twelve conserved motifs (10–29 base pairs) in hub gene promoters were linked to stress responses and transcriptional regulation. Six miRNAs (20–21 nucleotides) targeted DXS via cleavage, indicating post-transcriptional control. <h3>Conclusions</h3> This study establishes <i>DXS</i>, <i>HDS</i>, <i>HDR</i>, <i>HMGS</i>, and <i>HMGR</i> as key regulatory hubs for terpenoid biosynthesis in <i>T. parthenium</i>. Their regulation by transcription factors, miRNAs, and environmental interactions provides targets for pathway engineering and heterologous reconstruction to enhance bioactive terpenoid production.