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Exploiting the mosaic structure of trans-acyltransferase polyketide synthases for natural product discovery and pathway dissection

Nature Biotechnology volume 26, pages 225–233 (2008)Cite this article

Abstract

Modular polyketide synthases (PKSs) are giant bacterial enzymes that synthesize many polyketides of therapeutic value. In contrast to PKSs that provide acyltransferase (AT) activities in cis, trans-AT PKSs lack integrated AT domains and exhibit unusual enzymatic features with poorly understood functions in polyketide assembly. This has retarded insight into the assembly of products such as mupirocin, leinamycin and bryostatin 1. We show that trans-AT PKSs evolved in a fundamentally different fashion from cis-AT systems, through horizontal recruitment and assembly of substrate-specific ketosynthase (KS) domains. The insights obtained from analysis of these KS mosaics will facilitate both the discovery of novel polyketides by genome mining, as we demonstrate for the thailandamides of Burkholderia thailandensis, and the extraction of chemical information from short trans-AT PCR products, as we show using metagenomic DNA of marine sponges. Our data also suggest new strategies for dissecting polyketide biosynthetic pathways and engineering polyketide assembly.

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Figure 1: Reactions taking place during a single round of polyketide elongation in a type I cis-AT PKS module.
Figure 2: Polyketides generated by trans-AT PKSs.
Figure 3: Bayesian cladogram of full-length KS domains from trans-AT PKSs.
Figure 4: KS-based prediction of substrate specificities in two trans-AT PKS pathways.
Figure 5: Analysis of a previously uncharacterized polyketide from B. thailandensis.

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Acknowledgements

We thank Andrea Perner, Heike Heinecke and Franziska Rhein for HRMS and NMR measurements, Daniela Werler for sequencing assistance, Martin Roth and Matthias Steinacker of the BioPilotPlant for assistance in fermentation and extraction, and Shigeki Matsunaga for a specimen of the sponge T. swinhoei. This work was supported by the Deutsche Forschungsgemeinschaft (DFG) (PI 430/1-3 and SFB 624 to J.P. and grants of the priority programs SPP1152: PI 430/5-2, Di 910/1-3 He 3268/2-3 to J.P., E.D. and C.H., respectively).

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  1. TuAnh Nguyen and Keishi Ishida: These authors contributed equally to this work.

Authors and Affiliations

  1. Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Str. 1, Bonn, D-53121, Germany

    TuAnh Nguyen, Cristian Gurgui, Thomas Hochmuth & Jörn Piel

  2. Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, Jena, D-07745, Germany

    Keishi Ishida & Christian Hertweck

  3. Department of Molecular Ecology, Institute of Biology, Humboldt University, Chausseestr. 117, D-10115, Berlin, Germany

    Holger Jenke-Kodama & Elke Dittmann

  4. Genome Analysis, Leibniz-Institute for Age Research–Fritz Lipmann Institute, Beutenbergstr. 11, Beutenberg Campus, Jena, D-07745, Germany

    Stefan Taudien & Matthias Platzer

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Contributions

J.P. designed research, performed alignments and phylogenetic calculations, analyzed data and wrote the manuscript; H.J.-K. and E.D. designed research and performed phylogenetic analysis; T.H. analyzed sequence data; T.N. and C.G. isolated and analyzed the PKS cluster from the sponge metagenome; S.T. and M.P. performed sequencing, C.H. designed research and analyzed data, K.I. isolated and characterized thailandamides.

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Correspondence to Jörn Piel.

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Nguyen, T., Ishida, K., Jenke-Kodama, H. et al. Exploiting the mosaic structure of trans-acyltransferase polyketide synthases for natural product discovery and pathway dissection. Nat Biotechnol 26, 225–233 (2008). https://doi.org/10.1038/nbt1379

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