Abstract
Plant specialized metabolites are ecologically specialized, mostly lineage-specific molecules whose chemical diversity has been exploited by humans for medical, agriculture, and industrial applications. The mechanisms that gave rise to these phenotypic novelties are unclear, particularly those involving the co-option of recently duplicated genes into functional modules. Here, we show that a LINE retrotransposon (EPCOT3) is responsible for the recruitment of newly duplicated gene CYP82C2 into the WRKY33 regulon and the indole-3-carbonylnitrile (ICN) biosynthetic pathway. WRKY33 is an ancient regulator of plant specialized metabolism, functionally conserved since the gymnosperm-angiosperm split over 300 million years ago. Preferred WRKY33 binding sites are carried by EPCOT3, which inserted upstream of CYP82C2 and underwent chromatin remodeling to become an enhancer that coordinately regulates CYP82C2 gene expression in response to pathogen effectors. The regulatory neofunctionalization of CYP82C2 gave rise to pathogen-inducible expression of species-specific metabolite 4-hydroxy-ICN, which is required for antibacterial defense in Arabidopsis thaliana. Our results suggest that the transposable element EPCOT3 contributed clade/species-specific innovations to a core regulon that functions as an extended regulon in specialized metabolism and plant innate immunity.
Summary Plant secondary or specialized metabolites are essential for plant survival in complex environments and collectively number in the hundreds of thousands. The genetics and epigenetics of chemical diversity in plant specialized metabolism remain unclear. Here, we describe an expansion of the core interactions between an ancient transcription factor and its target biosynthetic genes by mobile genetic elements that disseminate transcription factor binding sites in the genome and undergo chromatin remodeling to become transcriptional enhancers. The extended interactions led to the biosynthesis of a species-specific antimicrobial metabolite important for plant survival. Our findings contribute to a growing understanding of chemical innovation, a critically important but poorly understood process in evolutionary biology.
Author Contributions
B.B. and N.K.C performed pathogen assays and ChIP-PCR experiments. B.B. and Y.K. profiled accessions and species. B.B. performed all other experiments. B.B. and N.K.C. interpreted the results and wrote the paper.