Chemically guided single-cell transcriptomics reveals sulfotransferase-mediated scaffold remodeling in securinine biosynthesis

Alkaloids are a structurally diverse group of nitrogen-containing natural products. Unlike other specialized metabolite classes, alkaloids lack a unified biosynthetic pathway or enzyme family. Their scaffold formation and remodeling often use unexpected intermediates and ubiquitous enzymes that have evolved novel, noncanonical functions, making it challenging to elucidate biosynthetic pathways of alkaloids^1–3. To address this, we integrated chemical insights acquired from biomimetic synthesis with single-cell transcriptomics and uncovered key biosynthetic steps of securinega alkaloids in Flueggea suffruticosa. Feeding experiments using stable isotope-labeled candidate intermediates guided us to identify biosynthetic precursors and the corresponding enzyme classes responsible for each transformation. We found that neosecurinanes, (–)-virosine A and (–)-virosine B, are formed through conjugation between 1-piperideine and menisdaurilide. Subsequently, the [2.2.2]-bicyclic neosecurinanes undergo a sulfotransferase-mediated 1,2-amine shift, yielding [3.2.1]-bicyclic securinanes: allosecurinine and securinine. This transformation revealed an unexpected catalytic role of sulfotransferases, not as conventional tailoring enzymes, but as key mediators of scaffold remodeling. We also found a precursor and biosynthetic gene of menisdaurilide. These findings highlight the power of chemically guided single-cell transcriptomics in unravelling complex biosynthetic pathways.