Hyssopus officinalis: MicroRNA-mediated regulation of terpenoid biosynthesis and defense metabolites

This study provides an experimental identification of miRNAs in Hyssop and a prediction of mRNA targets with an eye toward miRNA-mediated regulation of terpenoid biosynthesis. This can help to design future metabolic engineering attempts to improve the yield and quality of source species and unravel its therapeutic potential. MicroRNAs (miRNAs) are important post-transcriptional regulators of plant and animal gene expression. They bind to ARGONAUTE (AGO) proteins to form RNA induced silencing complexes (RISCs) and use base pairing to guide RISC to complementary mRNA for repression. The Lamiaceae family is a rich resource of terpenoids with important commercial and pharmaceutical uses, but little is known about miRNA-mediated control of terpenoid biosynthesis in these species. Here, we applied Trans-kingdom, rapid, affordable purification of RISCs coupled to small RNA sequencing (TraPR-seq) to identify AGO-bound small RNAs in Hyssop (Hyssopus officinalis L.), an important medicinal herb. We identify 15 conserved and 42 novel miRNA families, of which 8 were predicted to be of potential relevance to terpenoid biosynthesis. We also uncover several plausible miRNA targets encoding innate immunity regulators and identify one miRNA as a possible master regulator of defense with targets not only in terpenoid biosynthesis, but also including typical defense regulators such as receptor-like kinases and WRKY transcription factors, and its role in defense responses was boosted by its identification as a confident trigger of phasiRNA production. Our study provides the basis for future exploitation of miRNA regulatory networks for production of valuable terpenoids in Hyssop and gives insight into how miRNAs may coordinately control the expression of defense regulators and defense metabolite production.