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Natural product diversity associated with the nematode symbionts Photorhabdus and Xenorhabdus

Nature Microbiology volume 2, pages 1676–1685 (2017)Cite this article

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Abstract

Xenorhabdus and Photorhabdus species dedicate a large amount of resources to the production of specialized metabolites derived from non-ribosomal peptide synthetase (NRPS) or polyketide synthase (PKS). Both bacteria undergo symbiosis with nematodes, which is followed by an insect pathogenic phase. So far, the molecular basis of this tripartite relationship and the exact roles that individual metabolites and metabolic pathways play have not been well understood. To close this gap, we have significantly expanded the database for comparative genomics studies in these bacteria. Clustering the genes encoded in the individual genomes into hierarchical orthologous groups reveals a high-resolution picture of functional evolution in this clade. It identifies groups of genes—many of which are involved in secondary metabolite production—that may account for the niche specificity of these bacteria. Photorhabdus and Xenorhabdus appear very similar at the DNA sequence level, which indicates their close evolutionary relationship. Yet, high-resolution mass spectrometry analyses reveal a huge chemical diversity in the two taxa. Molecular network reconstruction identified a large number of previously unidentified metabolite classes, including the xefoampeptides and tilivalline. Here, we apply genomic and metabolomic methods in a complementary manner to identify and elucidate additional classes of natural products. We also highlight the ability to rapidly and simultaneously identify potentially interesting bioactive products from NRPSs and PKSs, thereby augmenting the contribution of molecular biology techniques to the acceleration of natural product discovery.

The Gammaproteobacteria Xenorhabdus and Photorhabdus have a vast secondary metabolite potential1,2. They live in symbiosis with entomopathogenic nematodes of the genera Steinernema and Heterorhabditis, respectively3,4. The dauer stage of the nematodes, known as infective juveniles (IJs), lives in the soil and carries the symbiotic bacteria within their gut. Upon nematode infection of soil-living insect larvae, these bacteria are released into the insect haemolymph, where they produce factors that assist in killing, degradation of tissues and protection from insect immune responses, as well as protection of the insect cadaver from competing microorganisms. The biomass is then used as an energy source for the nematodes to undergo several reproductive cycles within the cadaver, following which the bacteria are then able to continue the mutualism by recolonizing the resulting nematode progeny5. Maintenance of this symbiosis is heavily dependent on several natural products (NPs), often produced by either polyketide synthases (PKSs) or non-ribosomal peptide synthetases (NRPSs)6. In Xenorhabdus, only rhabduscin has an ascribed function in a host species7, although, based on structural similarity, some other NPs are assumed to have analogous functions to those from the better-studied Photorhabdus 8,9.

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Fig. 1: Evolutionary relationships of Xenorhabdus and Photorhabdus.
Fig. 2: Phyletic distribution of biosynthetic gene clusters in the Xenorhabdus/Photorhabdus family (XPF) clade.
Fig. 3: Network analysis of 30 Xenorhabdus and Photorhabdus strains.
Fig. 4
Fig. 5

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Acknowledgements

Research in the Bode Laboratory was supported by a European research starting grant under grant agreement no. 311477. H.B.B. acknowledges the Deutsche Forschungsgemeinschaft for funding of the Impact II qTof mass spectrometer (INST 161/810-1). N.J.T. and Y.M.S. are supported by a Postdoctoral Research Fellowship from the Alexander von Humboldt Foundation. S.J.P. is supported by an Australian National Health and Medical Research Council (NHMRC) project grant APP1105522. T.P.S. is supported by an Australian NHMRC Career Development Fellowship. I.E. acknowledges financial support by the Deutsche Forschungsgemeinschaft (DFG-FOR 2251, project grant EB 285/2-1).

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Author notes

  1. Nicholas J. Tobias, Hendrik Wolff and Bardya Djahanschiri contributed equally to this work.

Authors and Affiliations

  1. Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany

    Nicholas J. Tobias, Hendrik Wolff, Florian Grundmann, Max Kronenwerth, Yi-Ming Shi, Svenja Simonyi, Peter Grün & Helge B. Bode

  2. Department of Applied Bioinformatics, Institute for Cell Biology and Neuroscience, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany

    Bardya Djahanschiri & Ingo Ebersberger

  3. USDA-ARS, SEA, SE Fruit and Tree Nut Research Unit, 21 Dunbar Road, Byron, GA, 31008, USA

    David Shapiro-Ilan

  4. Department of Microbiology and Immunology, University of Melbourne, at the Doherty Institute for Infection and Immunity, Parkville, Victoria, 3010, Australia

    Sacha J. Pidot & Timothy P. Stinear

  5. Senckenberg Climate and Research Centre (BIK-F), Frankfurt am Main, 60325, Germany

    Ingo Ebersberger

  6. Buchmann Institute for Molecular Life Sciences, Goethe-Universität Frankfurt, Frankfurt am Main, 60438, Germany

    Helge B. Bode

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Contributions

N.J.T., H.W., B.D., I.E. and H.B.B. designed the study. N.J.T., H.W., B.D., F.G., M.K., Y.-M.S., S.S., P.G., D.S.-I, S.J.P., T.P.S., I.E. and H.B.B. contributed to analysis of the data. N.J.T., H.W., B.D., Y.-M.S., S.J.P., T.P.S., I.E. and H.B.B. were involved in preparation of the manuscript.

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Correspondence to Helge B. Bode.

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Supplementary Information

Extra results regarding structure elucidation of compounds described in the text and Supplementary Tables 1 and 8–18, as well as Supplementary Figures 1–54 and Supplementary References.

Life Sciences Reporting Summary

Supplementary Table 2

List of locus tags for all orthologous groups.

Supplementary Table 3

HOG gains at Node A.

Supplementary Table 4

HOG gains at Node B.

Supplementary Table 5

HOG gains at Node C.

Supplementary Table 6

Analysis of gene ontology pathways using the HOGs at a given node compared to the last common ancestor.

Supplementary Table 7

Custom database of known natural products.

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Tobias, N.J., Wolff, H., Djahanschiri, B. et al. Natural product diversity associated with the nematode symbionts Photorhabdus and Xenorhabdus . Nat Microbiol 2, 1676–1685 (2017). https://doi.org/10.1038/s41564-017-0039-9

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