Fosmidomycin biosynthesis diverges from related phosphonate natural products


Fosmidomycin and related molecules comprise a family of phosphonate natural products with potent antibacterial, antimalarial and herbicidal activities. To understand the biosynthesis of these compounds, we characterized the fosmidomycin producer, Streptomyces lavendulae, using biochemical and genetic approaches. We were unable to elicit production of fosmidomycin, instead observing the unsaturated derivative dehydrofosmidomycin, which we showed potently inhibits 1-deoxy-d-xylulose-5-phosphate reductoisomerase and has bioactivity against a number of bacteria. The genes required for dehydrofosmidomycin biosynthesis were established by heterologous expression experiments. Bioinformatics analyses, characterization of intermediates and in vitro biochemistry show that the biosynthetic pathway involves conversion of a two-carbon phosphonate precursor into the unsaturated three-carbon product via a highly unusual rearrangement reaction, catalyzed by the 2-oxoglutarate dependent dioxygenase DfmD. The required genes and biosynthetic pathway for dehydrofosmidomycin differ substantially from that of the related natural product FR-900098, suggesting that the ability to produce these bioactive molecules arose via convergent evolution.

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Fig. 1: The fosmidomycin family of phosphonate natural products.
Fig. 2: S. lavendulae produces dehydrofosmidomycin.
Fig. 3: Characterization of the dfm gene cluster.
Fig. 4: Feeding studies with 2AEP and l-methionine-(methyl-13C).
Fig. 5: Conversion of trimethyl-2AEP to methyldehydrofosmidomycin by DfmD.
Fig. 6: Proposed biosynthetic pathway for dehydrofosmidomycin.

Data availability

The authors declare that all relevant data supporting the findings of this study are available within the paper and its Supplementary Information.


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We thank M. Goettge and K. Wang for helpful discussions, X. Guan for his assistance with NMR experiments, Z. Li for his assistance with HRMS experiments, the UIUC Core Sequencing Facility for sequencing and P. Hergenrother (Chemistry Department, UIUC) for providing strains. This work was funded by the National Institutes of Health (grant nos. P01 GM077596 and R01GM127659 to W.W.M. and F32GM120999 to E.I.P.). NMR spectra were recorded on an instrument purchased with support from NIH grant no. S10 RR028833.

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E.I.P., A.E. and K.-S.J. optimized growth conditions. E.I.P. performed the chemical syntheses, bioactivity analyses and in vitro characterization of enzymes. A.C.E. made the heterologous expression vector. E.I.P. performed the heterologous expression studies and the deletion mutant studies. E.I.P. and W.W.M. analyzed the data and wrote the manuscript, with assistance of A.E., A.C.E. and K.-S.J.

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Correspondence to William W. Metcalf.

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W.W.M. has financial interest in Microbial Pharmaceuticals.

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Parkinson, E.I., Erb, A., Eliot, A.C. et al. Fosmidomycin biosynthesis diverges from related phosphonate natural products. Nat Chem Biol 15, 1049–1056 (2019).

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