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Genome mining- and synthetic biology-enabled production of hypermodified peptides

Nature Chemistry volume 11, pages 931–939 (2019)Cite this article

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Abstract

The polytheonamides are among the most complex and biosynthetically distinctive natural products known to date. These potent peptide cytotoxins are derived from a ribosomal precursor processed by 49 mostly non-canonical posttranslational modifications. As the producer is a ‘microbial dark matter’ bacterium only distantly related to any cultivated organism, >70-step chemical syntheses have been developed to access these unique compounds. Here, we mined prokaryotic diversity to establish a synthetic platform based on the new host Microvirgula aerodenitrificans that produces hypermodified peptides within two days. Using this system, we generated the aeronamides, new polytheonamide-type compounds with near-picomolar cytotoxicity. Aeronamides, as well as the polygeonamides produced from deep-rock biosphere DNA, contain the highest numbers of d-amino acids in known biomolecules. With increasing bacterial genomes being sequenced, similar host mining strategies might become feasible to access further elusive natural products from uncultivated life.

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Fig. 1: Structure and BGC of polytheonamides.
Fig. 2: Epimerization of AerA in E. coli.
Fig. 3: Identifying conditions for the expression of the aer BGC.
Fig. 4: Hypermodified aeronamide peptides from expressions in M. aerodenitrificans.
Fig. 5: Generating aeronamide A and characterizing its ion-transport activity.
Fig. 6: Peptides of non-native cores modified by the M. aerodenitrificans platform.

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Data availability

Data analysed in the current study are available from the corresponding author upon reasonable request.

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Acknowledgements

We thank R. Bernier-Latmani and R. Stepanauskas for discussions and DNA samples that contained the geo and vep cluster, and B. I. Morinaka and R. Ueoka for technical advice. This work was supported by the Swiss National Science Foundation (205320_185077), the Helmut Horten Foundation, the EU (ERC Advanced Grant ‘SynPlex’, BluePharmTrain) and Novartis (17B075) to J.P.

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Authors and Affiliations

  1. Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland

    Agneya Bhushan, Eike E. Peters & Jörn Piel

  2. Kantonsschule Obwalden, Sarnen, Switzerland

    Peter J. Egli

  3. Department of Biochemistry, Molecular Biology, and Biophysics and BioTechnology Institute, University of Minnesota–Twin Cities, St Paul, MN, USA

    Michael F. Freeman

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  1. Agneya Bhushan
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Contributions

A.B. and J.P. designed the research. P.J.E. performed the promoter activity assays, and E.E.P. performed liposome experiments. A.B. performed all the other experiments. A.B., M.F.F. and J.P. analysed the data and wrote the manuscript.

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Correspondence to Jörn Piel.

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Supplementary Information contains: Supplementary Materials and Methods, Supplementary Figs. 1–18 and Supplementary Tables 1–3.

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Bhushan, A., Egli, P.J., Peters, E.E. et al. Genome mining- and synthetic biology-enabled production of hypermodified peptides. Nat. Chem. 11, 931–939 (2019). https://doi.org/10.1038/s41557-019-0323-9

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