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Polyketide assembly lines of uncultivated sponge symbionts from structure-based gene targeting

Nature Chemical Biology volume 5, pages 494–501 (2009)Cite this article

Abstract

There is increasing evidence that uncultivated bacterial symbionts are the true producers of numerous bioactive compounds isolated from marine sponges. The localization and heterologous expression of biosynthetic genes could clarify this issue and provide sustainable supplies for a wide range of pharmaceuticals. However, identification of genes in the usually highly complex symbiont communities remains a challenging task. For polyketides, one of the most important groups of sponge-derived drug candidates, we have developed a general strategy that allows one to rapidly access biosynthetic gene clusters based on chemical moieties. Using this method, we targeted polyketide synthase genes from two different sponge metagenomes. We have obtained from a sponge-bacterial association a complete pathway for the rare and potent antitumor agent psymberin from Psammocinia aff. bulbosa. The data support the symbiont hypothesis and provide insights into natural product evolution in previously inaccessible bacteria.

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Figure 1: Some sponge-derived complex polyketides that have been shown or proposed to be synthesized by symbionts.
Figure 2: Alignment of KS protein sequences.
Figure 3: Agarose gel analysis of PCR products obtained from positive and negative sponge chemotypes using primers specific for KS amplicons.
Figure 4: The psy genes and model for psymberin biosynthesis.

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Acknowledgements

We thank M. Page for assistance with collecting M. hentscheli of known chemotypes and S. Brady for advice on metagenomic library construction. This work was supported by a collaborative grant from the US National Science Foundation and the German Research Foundation to J.P. (PI 430/6-1) and P.C. (NSF-CHE-0617056), by grants from the German Research Foundation to J.P. (SFB 624 and SPP 1152) and by an Alexander von Humboldt Research Fellowship to S.A.v.d.S.

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Author notes

  1. Katja M Fisch and Cristian Gurgui: These authors contributed equally to this work.

Authors and Affiliations

  1. Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Bonn, Germany

    Katja M Fisch, Cristian Gurgui, Nina Heycke, Sonia A van der Sar & Jörn Piel

  2. National Institute of Water & Atmospheric Research Ltd., Wellington, New Zealand

    Sally A Anderson & Victoria L Webb

  3. Genome Analysis, Leibniz-Institute for Age Research–Fritz Lipmann Institute, Jena, Germany

    Stefan Taudien & Matthias Platzer

  4. Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, California, USA

    Brent K Rubio, Sarah J Robinson & Phillip Crews

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Contributions

J.P. designed the research on PKS targeting and isolation, analyzed data and wrote the manuscript; K.M.F. developed the targeting approach; K.M.F. and C.G. constructed libraries and isolated and analyzed the psy genes; N.H. isolated and analyzed the psy genes; S.A.v.d.S. conducted the PKS work on M. hentscheli; S.T. and M.P. sequenced and analyzed PCR amplicons; P.C., B.K.R. and S.J.R. collected and analyzed specimens of P. aff. bulbosa and C. mycofijiensis; V.L.W. designed research to collect and aquaculture the different chemotypes of M. hentscheli; S.A.A. performed the initial analysis of the microbe population in M. hentscheli chemotypes and selected M. hentscheli for the metagenomic work.

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Correspondence to Jörn Piel.

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Fisch, K., Gurgui, C., Heycke, N. et al. Polyketide assembly lines of uncultivated sponge symbionts from structure-based gene targeting. Nat Chem Biol 5, 494–501 (2009). https://doi.org/10.1038/nchembio.176

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