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A marine viral halogenase that iodinates diverse substrates

Nature Chemistry volume 11, pages 1091–1097 (2019)Cite this article

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Abstract

Oceanic cyanobacteria are the most abundant oxygen-generating phototrophs on our planet and are therefore important to life. These organisms are infected by viruses called cyanophages, which have recently shown to encode metabolic genes that modulate host photosynthesis, phosphorus cycling and nucleotide metabolism. Herein we report the characterization of a wild-type flavin-dependent viral halogenase (VirX1) from a cyanophage. Notably, halogenases have been previously associated with secondary metabolism, tailoring natural products. Exploration of this viral halogenase reveals it capable of regioselective halogenation of a diverse range of substrates with a preference for forming aryl iodide species; this has potential implications for the metabolism of the infected host. Until recently, a flavin-dependent halogenase that is capable of iodination in vitro had not been reported. VirX1 is interesting from a biocatalytic perspective as it shows strikingly broad substrate flexibility and a clear preference for iodination, as illustrated by kinetic analysis. These factors together render it an attractive tool for synthesis.

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Fig. 1: A protein-based branching analysis of VirX1 against known FDHs and other non-FDH flavoenzymes that reveals the functional relationship, known substrate utilization and branching order between protein clusters.
Fig. 2: The diverse substrate scope of VirX1.
Fig. 3: Crystal structure and homotrimer assembly of VirX1.
Fig. 4: Structural comparison of VirX1 to the flavin-dependent halogenases PrnA (2AQJ) and BrvH (6FRL).

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Data availability

The data that support the findings of this study are available in this Article and its Supplementary Information, or are available from the corresponding author on reasonable request. The structural factors and coordinates of the VirX1 have been deposited in the PDB (PDB ID: 6QGM).

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Acknowledgements

We thank the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007–2013/ERC grant agreement no. 614779 GenoChemetics to R.J.M.G.), Syngenta and Wellcome ISSF (grant no. 204821/Z/16/Z to D.S.G.) for generous financial support. We thank G. Harris and M. Weckener (Harwell) for size-excluion chromatography multiangle light scattering and analytical ultracentrifugation analysis. We thank all of our colleagues, in particular, T. Smith and co-workers in the School of Chemistry and the Biomedical Sciences Research Complex at the University of St Andrews for all of the help that they have afforded us in the aftermath of the BMS fire. We thank I. M. Wilson for assistance with graphics.

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Author notes

  1. These authors contributed equally: Hannes Ludewig and Sunil V. Sharma.

Authors and Affiliations

  1. School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, UK

    Danai S. Gkotsi, Hannes Ludewig, Sunil V. Sharma, Jack A. Connolly, Jagwinder Dhaliwal, Yunpeng Wang & Rebecca J. M. Goss

  2. Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, UK

    Danai S. Gkotsi, Hannes Ludewig, Sunil V. Sharma, Jack A. Connolly, Jagwinder Dhaliwal, Yunpeng Wang & Rebecca J. M. Goss

  3. Department of Chemistry, University of York, Heslington, York, UK

    William P. Unsworth & Richard J. K. Taylor

  4. Syngenta, Jealott’s Hill International Research Centre, Bracknell, Berkshire, UK

    Matthew M. W. McLachlan & Stephen Shanahan

  5. QEDDI, The University of Queensland, Brisbane, Queensland, Australia

    Matthew M. W. McLachlan

  6. Division of Structural Biology, Wellcome Trust Centre of Human Genomics, Oxford, UK

    James H. Naismith

  7. Research Complex at Harwell, Rutherford Laboratory, Didcot, UK

    James H. Naismith

  8. The Rosalind Franklin Institute, Didcot, UK

    James H. Naismith

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  1. Danai S. Gkotsi
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Contributions

D.S.G. and R.J.M.G. conceived and designed the experiments, and the full programme was carried out under the guidance and direction of R.J.M.G. D.S.G. identified VirX1 bioinformatically, established its protein production and purification, determined the iodinase activity and carried out its biochemical investigation and substrate screening. D.S.G. and H.L. carried out the structural analysis of the enzyme under the guidance of J.H.N. D.S.G. and S.V.S. explored the differential reactivity of the substrates with hypoiodous acid, characterized the products of the iodinase and synthesized standards for comparison to products. W.P.U. and R.J.K.T. synthesized a series of spiroindolic compounds and their derivatives, which were utilized as substrates by the enzyme. M.M.W.M. and S.S. contributed to the selection of compounds for the assaying of the iodinase. H.L., J.A.C. and J.H.N. carried out substrate docking to the iodinase. D.S.G. and J.D. assayed PrnA. D.S.G., H.L., J.A.C., J.D. and Y.W. assisted with cloning and protein production. R.J.M.G., S.V.S., D.S.G., H.L. and J.A.C. wrote the paper with contributions from all authors.

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Correspondence to Rebecca J. M. Goss.

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Gkotsi, D.S., Ludewig, H., Sharma, S.V. et al. A marine viral halogenase that iodinates diverse substrates. Nat. Chem. 11, 1091–1097 (2019). https://doi.org/10.1038/s41557-019-0349-z

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