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Discovery of the selenium-containing antioxidant ovoselenol derived from convergent evolution

Nature Chemistry (2024)Cite this article

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Abstract

Selenium is an essential micronutrient, but its presence in biology has been limited to protein and nucleic acid biopolymers. The recent identification of a biosynthetic pathway for selenium-containing small molecules suggests that there is a larger family of selenometabolites that remains to be discovered. Here we identify a recently evolved branch of abundant and uncharacterized metalloenzymes that we predict are involved in selenometabolite biosynthesis using a bioinformatic search strategy that relies on the mapping of composite active site motifs. Biochemical studies confirm this prediction and show that these enzymes form an unusual C–Se bond onto histidine, thus giving rise to a distinct selenometabolite and potent antioxidant that we have termed ovoselenol. Aside from providing insights into the evolution of this enzyme class and the structural basis of C–Se bond formation, our work offers a blueprint for charting the microbial selenometabolome in the future.

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Fig. 1: LMW thiols and selenols in biology.
Fig. 2: Identification of divergent NHISS clades with potentially distinct functions.
Fig. 3: Discovery of OVS and its biosynthetic pathway.
Fig. 4: Mutagenesis and X-ray crystal structure analysis of OvsA reveal the basis for C–Se bond regioselectivity.

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Data availability

Protein crystal structure coordinates have been deposited with the PDB (https://www.rcsb.org/) under accession numbers 8U42 (OvsA), 8U41 (Ovs+His) and 8UX5 (OvsA-YNF). Other referenced crystal structures are available in the PDB under accession numbers 8KHQ, 4X8D, 6O6L, 8K5I and 8K5J. Experimental data supporting the conclusions of this study are available within the Article and its Supplementary Information. Source data are provided with this paper and include sequences retrieved from the NCBI Non-redundant Protein Database (https://www.ncbi.nlm.nih.gov/protein/), bioinformatic analyses and raw experimental data from main text figures. Due to large file sizes, additional raw data from Supplementary Information will be made available upon request from the corresponding author.

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Acknowledgements

We thank the Eli Lilly-Edward C. Taylor Fellowship in Chemistry (to C.M.K.), the National Science Foundation (Graduate Research Fellowship Program no. 1937971 to K.A.I. and NSF CAREER award no. 184786 to M.R.S.) and the National Institutes of Health (grant R35 GM147557 to K.M.D. and grant R01 GM140034 to M.R.S.) for financial support. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. This research used resources of the APS and the Center for High-Energy X-ray Sciences (CHEXS). APS is a US Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under contract no. DE-AC02-06CH11357. Use of the LS-CAT Sector 21 was supported by the Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor (grant 085P1000817). GM/CA@APS has been funded by the National Cancer Institute (ACB-12002) and the National Institute of General Medical Sciences (AGM-12006, P30GM138396). The Eiger 16M detector at GM/CA-XSD was funded by NIH grant S10 OD012289. CHEXS is supported by the NSF award DMR-1829070, and the MacCHESS resource is supported by NIGMS award 1-P30-GM124166-01A1 and NYSTAR.

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Author notes

  1. These authors contributed equally: Chase M. Kayrouz, Kendra A. Ireland.

Authors and Affiliations

  1. Department of Chemistry, Princeton University, Princeton, NJ, USA

    Chase M. Kayrouz, Vanessa Y. Ying & Mohammad R. Seyedsayamdost

  2. Department of Chemistry, Emory University, Atlanta, GA, USA

    Kendra A. Ireland & Katherine M. Davis

  3. Department of Molecular Biology, Princeton University, Princeton, NJ, USA

    Mohammad R. Seyedsayamdost

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Contributions

C.M.K. and M.R.S. conceived of the idea for the study. C.M.K. performed all bioinformatic and biochemistry experiments. K.A.I. performed all structural biology experiments. V.Y.Y. synthesized SeGlcNAc and performed electrochemical measurements. C.M.K., K.A.I., V.Y.Y., K.M.D. and M.R.S. analysed data and prepared the manuscript.

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Correspondence to Mohammad R. Seyedsayamdost.

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Supplementary information

Supplementary Information

Supplementary Tables 1–8, Figs. 1–17, additional discussion of OvsA structure, source data of uncropped DNA gel scans, and references.

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Source data

Source Data Fig. 2

Sequences retrieved from NCBI database (accession numbers, composite motifs and classifications).

Source Data Fig. 3

Phylogenetic distribution of ovsA genes, BGC co-occurrence data, extracted ion chromatograms, mass spectra and CV traces.

Source Data Fig. 4

Extracted ion chromatograms and NMR spectra.

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Kayrouz, C.M., Ireland, K.A., Ying, V.Y. et al. Discovery of the selenium-containing antioxidant ovoselenol derived from convergent evolution. Nat. Chem. (2024). https://doi.org/10.1038/s41557-024-01600-2

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