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

Securinega alkaloids possess a distinctive tetracyclic scaffold and are pharmaceutically relevant, yet their biosynthesis in Flueggea suffruticosa remains unresolved. Here, we combine chemical logic with stable-isotope-labeled feeding experiments and single-cell transcriptomics to elucidate the core biosynthetic pathway. We identify a reductase, FsMS, that reduces premenisdaurilide to menisdaurilide, which then conjugates with 1-piperideine to generate the [2.2.2]-bicyclic neosecurinanes, (–)-virosine A and (–)-virosine B. We also identify two sulfotransferases, FsNSST1 and FsNSST2, that O-sulfate these neosecurinanes; the resulting sulfate esters undergo a spontaneous 1,2-amine shift to yield the [3.2.1]-bicyclic securinanes, allosecurinine and securinine. This transformation reveals an unexpected biosynthetic role of sulfotransferases, not as conventional tailoring enzymes, but as key mediators of scaffold remodeling. The newly identified biosynthetic genes are co-expressed within a specific vasculature-associated cell type, enabling prioritization of additional pathway candidates. These findings highlight the power of chemically guided single-cell transcriptomics in unraveling complex biosynthetic pathways. Securinega alkaloids, comprising a distinctive tetracyclic scaffold, have long been studied, but their biosynthesis has remained largely unknown. Here, the authors employ chemical insights with single-cell transcriptomics to reveal key biosynthetic steps of securinega alkaloids in Flueggea suffruticosa.