Single-cell RNA-seq based elucidation of the antidepressant hyperforin biosynthesisde novoin St. John’s wort

Summary Hyperforin is the compound responsible for the effectiveness of St. John’s wort ( Hypericum perforatum ) as an antidepressant, but its biosynthesis remains unknown. Gene discovery based on co-expression analysis of bulk RNA-sequencing data or genome mining failed to discover the missing steps in hyperforin biosynthesis. Here we sequenced the tetraploid H. perforatum genome. By single-cell RNA-seq, we identified a distinct type of cells, Hyper cells, wherein hyperforin biosynthesis de novo takes place. Through pathway reconstitution in yeast and tobacco, we identify and characterize four transmembrane prenyltransferases to resolve hyperforin biosynthesis. The hyperforin polycyclic scaffold is created by a reaction cascade involving an irregular isoprenoid coupling and a tandem cyclization. Our findings reveal how and where hyperforin is biosynthesized that enables synthetic-biology reconstitution of the complete pathway. These results deepen our comprehension of specialized metabolism at the cellular level, and we anticipate acceleration of pathway elucidation in plant metabolism.