Identification of a key peptide cyclase for novel cyclic peptide discovery in Pseudostellaria heterophylla

Orbitides, also known as Caryophyllaceae-type cyclic peptides, from the Traditional Chinese Medicine plant Pseudostellaria heterophylla (Miq.) Pax, exhibit great potential for improving memory and treating diabetes. Orbitides are ribosomally encoded and post-translationally modified peptides; however, the key biosynthetic enzyme mediating this process remains unknown in P. heterophylla. In this study, we investigated the distribution of orbitides in P. heterophylla and mined novel precursor peptide genes and peptide cyclases from multiple omics datasets. The function of PhPCY3, a gene encoding a key tailoring enzyme, was elucidated using transient heterologous expression and virus-induced gene silencing systems. Our findings suggest that PhPCY3 specifically cyclizes linear precursor peptides in planta. Molecular docking and multiple sequence alignment, followed by site-directed mutagenesis, identified N500 and S502 as critical amino acid residues for PhPCY3 function. We identified gene sequences for over 100 precursor peptides and successfully biosynthesized known active orbitides, such as heterophyllin B and pseudostellarin E/F/G. Additionally, four novel orbitides, cyclo-[LDGPPPYF], cyclo-[WGSSTPHT], cyclo-[GLPIGAPWG], and cyclo-[FGDVGPVI], were synthesized using a heterologous expression platform. This study introduces a gene-guided approach for elucidating the biosynthesis pathway and discovering novel orbitides, providing a strategy for mining and biosynthesizing novel orbitides in P. heterophylla and other plants to further investigate their activities.