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Accessing chemical diversity from the uncultivated symbionts of small marine animals

Abstract

Chemistry drives many biological interactions between the microbiota and host animals, yet it is often challenging to identify the chemicals involved. This poses a problem, as such small molecules are excellent sources of potential pharmaceuticals, pretested by nature for animal compatibility. We discovered anti-HIV compounds from small, marine tunicates from the Eastern Fields of Papua New Guinea. Tunicates are a reservoir for new bioactive chemicals, yet their small size often impedes identification or even detection of the chemicals within. We solved this problem by combining chemistry, metagenomics, and synthetic biology to directly identify and synthesize the natural products. We show that these anti-HIV compounds, the divamides, are a novel family of lanthipeptides produced by symbiotic bacteria living in the tunicate. Neighboring animal colonies contain structurally related divamides that differ starkly in their biological properties, suggesting a role for biosynthetic plasticity in a native context wherein biological interactions take place.

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Figure 1: Discovery of anti-HIV lanthipeptides, the divamides.
Figure 2: The semi–in vivo synthesis of divamides A and B involves in vivo, chemical, and enzymatic steps.
Figure 3: Cytoprotection assays reveal two biological activities of divamide A.
Figure 4: Segregation of anti-HIV and cytotoxic properties by flow cytometry.
Figure 5: Cinnamycin and divamide both interact with membranes.

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Acknowledgements

This work was funded by the National Institutes of Health (NIH) through Fogarty International Center Grant ICBG U01TW006671, R01 GM102602, and R01 GM107557, as well as the American Federation for Pharmaceutical Education (AFPE) Pre-Doctoral Fellowship and the American Chemical Society (ACS) Division of Medicinal Chemistry Pre-Doctoral Fellowship. Funding for the Varian INOVA 600 and 500 MHz NMR spectrometers was provided by NIH Grant RR06262. We thank the lab of J.C. Vederas (University of Alberta) for providing us with methyllanthionine GC–MS standards and M.S. Donia for providing suggestions in the preparation of the manuscript.

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T.E.S., E.W.S., C.M.I., and L.R.B. designed the research. T.E.S. and E.W.S. wrote the paper. T.E.S. purified and characterized compounds from both tunicates and E. coli, constructed pDiv-2, pDiv-3, and pRSFDuet-DivMT expression vectors, performed all in vitro synthetic steps in divamide production, and designed Figures. C.D.P. and T.E.S. performed biological assays. E.P. constructed the pDiv expression vector. Z.P.H. aided in the purification of compounds from E. coli. J.K. sequenced and assembled the E11-036 cluster. M.M.Z. assembled the partial E11-037 cluster. M.K.H. collected animal material. T.P.W. and T.E.S. collected 900 MHz NMR spectra and the 500 MHz 13C NMR spectrum for compound 1. T.K.M. obtained permits for tunicate collection. T.S.B. provided access to the University of Wisconsin National Magnetic Resonance Facility at Madison (NMRFAM) facility. L.R.B. and C.M.I. provided technical and conceptual assistance.

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Correspondence to Eric W Schmidt.

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Supplementary Tables 1–9 and Supplementary Figures 1–5 (PDF 3957 kb)

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Supplementary Note 1

Chemical characterization of the divamides (PDF 22622 kb)

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Smith, T., Pond, C., Pierce, E. et al. Accessing chemical diversity from the uncultivated symbionts of small marine animals. Nat Chem Biol 14, 179–185 (2018). https://doi.org/10.1038/nchembio.2537

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