Discovery of the Phosphonate Flavophos Produced by Burkholderia

Phosphonate natural products have proven value to society as antibiotics and herbicides, and inhibit a range of enzyme targets usually by mimicking the enzyme substrates. In this study, we investigate a family of phosphonate biosynthetic gene clusters (BGCs) found in Burkholderia. Heterologous expression in Escherichia coli resulted in production of an antimicrobial compound. Spectroscopic characterization and chemical synthesis assigned its structure as 2,4-dioxopentylphosphonic acid. One of the biosynthetic enzymes is a member of the domain of unknown function (DUF) 849 family with homology to β-keto acid cleavage enzymes (BKACEs). In vitro characterization shows this enzyme catalyzes chemistry that is divergent from BKACEs. The observed catalytic activity is explained by a series of co-crystal structures with substrates and intermediates. The BGC also contains a gene encoding lumazine synthase (LS), an essential enzyme in flavin biosynthesis. Expression of this gene, or genes encoding LS from a range of organisms, conferred resistance to the new phosphonate, which we therefore call flavophos. Biochemical experiments confirmed inhibition of LS by flavophos.