Merging genome mining with ancient three-way species co-evolution may open a novel gate for informative natural products discovery

Finger millet is an ancient African cereal crop, resistant to many pathogens. It was domesticated 7000 years ago in Ethiopia, reaching India by 3000 BC. Unlike other cereals, finger millet is resistant to the toxigenic fungal pathogen Fusarium graminearum. As this fungus is also ancient to Africa, we hypothesized that the crop may host microbes (endophytes) that co-evolved to combat Fusarium. Here we describe the first ever discovery of endophytes from finger millet. We report a diverse array of anti-Fusarium secondary metabolites isolated from the fungal endophytes. A bacterial endophyte (strain M6) showed potent broad-spectrum antifungal activity including against F.graminearum, and was subsequently shown to be a novel Enterobacter species. Confocal microscopy showed that GFP-tagged M6 colonized different cereal tissues. Mechanistically, M6 caused cleavage of F.graminearum hyphae at septa. At the molecular level, Tn5 mutagenesis aided by whole genome sequencing and gene annotation uncovered 10 operons responsible for the anti-fungal trait, including at least two phenazine biosynthetic ORFs. Real time PCR revealed that most of the candidate genes are inducible by F.graminearum. Knockouts of the genes caused loss of cereal resistance to F.graminearum. Biochemically, three new phenazine derivatives were discovered for the first time. We conclude, informative search for bioactive compounds opens a new revolutionary era for natural products discovery.