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Biosynthesis of selenium-containing small molecules in diverse microorganisms


Selenium is an essential micronutrient in diverse organisms. Two routes are known for its insertion into proteins and nucleic acids, via selenocysteine and 2-selenouridine, respectively1. However, despite its importance, pathways for specific incorporation of selenium into small molecules have remained elusive. Here we use a genome-mining strategy in various microorganisms to uncover a widespread three-gene cluster that encodes a dedicated pathway for producing selenoneine, the selenium analogue of the multifunctional molecule ergothioneine2,3. We elucidate the reactions of all three proteins and uncover two novel selenium–carbon bond-forming enzymes and the biosynthetic pathway for production of a selenosugar, which is an unexpected intermediate en route to the final product. Our findings expand the scope of biological selenium utilization, suggest that the selenometabolome is more diverse than previously thought, and set the stage for the discovery of other selenium-containing natural products.

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Fig. 1: Known and new biological pathways for Se incorporation.
Fig. 2: Production of selenoneine by bacteria that carry the three-gene sen cluster.
Fig. 3: SenB, a novel selenosugar synthase.
Fig. 4: SenA, a novel selenoneine synthase.

Data availability

Experimental data supporting the conclusions of this study are available within the article and its Supplementary information. Sequences were retrieved from the NCBI Conserved Domain Database ( and the NCBI Non-redundant Protein Database ( NCBI accession numbers of analysed proteins from V. paradoxus DSM 30034 are as follows: WP_062361878.1 (SenA), WP_080642484.1 (SenB), WP_062361881.1 (SenC), WP_062366250.1 (EgtD) and WP_062366249.1 (EgtB). Raw experimental data and complete bioinformatic datasets can be made available on reasonable request.


  1. Reich, H. J. & Hondal, R. J. Why nature chose selenium. ACS Chem. Biol. 11, 821–841 (2016).

    Article  CAS  PubMed  Google Scholar 

  2. Yamashita, Y. & Yamashita, M. Identification of a novel selenium-containing compound, selenoneine, as the predominant chemical form of organic selenium in the blood of bluefin tuna. J. Biol. Chem. 285, 18134–18138 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Cheah, I. K. & Halliwell, B. Ergothioneine; antioxidant potential, physiological function and role in disease. Biochim. Biophys. Acta 1822, 784–793 (2012).

    Article  CAS  PubMed  Google Scholar 

  4. Rotruck, J. T. et al. Selenium: biochemical role as a component of glutathione peroxidase. Science 179, 588–590 (1973).

    Article  ADS  CAS  PubMed  Google Scholar 

  5. Zhong, L. & Holmgren, A. Essential role of selenium in the catalytic activities of mammalian thioredoxin reductase revealed by characterization of recombinant enzymes with selenocysteine mutations. J. Biol. Chem. 275, 18121–18128 (2000).

    Article  CAS  PubMed  Google Scholar 

  6. Aachmann, F. L. et al. Insights into function, catalytic mechanism, and fold evolution of selenoprotein methionine sulfoxide reductase B1 through structural analysis. J. Biol. Chem. 285, 33315–33323 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Berry, M. J., Kieffer, J. D., Harney, J. W. & Larsen, P. R. Selenocysteine confers the biochemical properties characteristic of the type I iodothyronine deiodinase. J. Biol. Chem. 266, 14155–14158 (1991).

    Article  CAS  PubMed  Google Scholar 

  8. He, S. H. et al. EPR studies with 77Se-enriched (NiFeSe) hydrogenase of Desulfovibrio baculatus. J. Biol. Chem. 264, 2678–2682 (1989).

    Article  CAS  PubMed  Google Scholar 

  9. Wittwer, A. J., Tsai, L., Ching, W. M. & Stadtman, T. C. Identification and synthesis of a naturally occurring selenonucleoside in bacterial tRNAs: 5-[(methylamino)methyl]-2-selenouridine. Biochemistry 23, 4650–4655 (1984).

    Article  CAS  PubMed  Google Scholar 

  10. Weekley, C. M. & Harris, H. H. Which form is that? The importance of selenium speciation and metabolism in the prevention and treatment of disease. Chem. Soc. Rev. 42, 8870–8894 (2013).

    Article  CAS  PubMed  Google Scholar 

  11. Ehrenreich, A., Forchammer, K., Tormay, P., Veprek, B. & Böck, A. Selenoprotein synthesis in E. coli. Purification and characterisation of the enzyme catalysing selenium activation. Eur. J. Biochem. 206, 767–773 (1992).

    Article  CAS  PubMed  Google Scholar 

  12. Forchhammer, K. & Böck, A. Selenocysteine synthase from Escherichia coli. Analysis of the reaction sequence. J. Biol. Chem. 266, 6324–6328 (1991).

    Article  CAS  PubMed  Google Scholar 

  13. Wolfe, M. D. et al. Functional diversity of the rhodanese homology domain. J. Biol. Chem. 279, 1801–1809 (2004).

    Article  CAS  PubMed  Google Scholar 

  14. Stone, M. J. & Williams, D. H. On the evolution of functional secondary metabolites (natural products). Mol. Microbiol. 6, 29–34 (1992).

    Article  CAS  PubMed  Google Scholar 

  15. Lin, J. et al. Comparative genomics reveals new candidate genes involved in selenium metabolism in prokaryotes. Genome Biol. Evol. 7, 664–676 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Seebeck, F. P. In vitro reconstitution of mycobacterial ergothioneine biosynthesis. J. Am. Chem. Soc. 132, 6632–6633 (2010).

    Article  CAS  PubMed  Google Scholar 

  17. Yamashita, Y. et al. Selenoneine, total selenium, and total mercury content in the muscle of fishes. Fish. Sci. 77, 679–686 (2011).

    Article  CAS  Google Scholar 

  18. Yamashita, M. & Yamashita, Y. in Springer Handbook of Marine Biotechnology (ed. Kim, S. K.) 1059–1069 (Springer, 2015).

  19. Lim, D., Gründemann, D. & Seebeck, F. P. Total synthesis and functional characterization of selenoneine. Angew. Chem. Int. Ed. 58, 15026–15030 (2019).

    Article  CAS  Google Scholar 

  20. Pluskal, T., Ueno, M. & Yanagida, M. Genetic and metabolomic dissection of the ergothioneine and selenoneine biosynthetic pathway in the fission yeast, S. pombe, and construction of an overproduction system. PLoS ONE 9, e97774 (2014).

    Article  ADS  PubMed  PubMed Central  Google Scholar 

  21. Goncharenko, K. V. et al. Selenocysteine as a substrate, an inhibitor and a mechanistic probe for bacterial and fungal iron‐dependent sulfoxide synthases. Chem. Eur. 26, 1328–1334 (2020).

    Article  CAS  Google Scholar 

  22. Goncharenko, K. V., Vit, A., Blankenfeldt, W. & Seebeck, F. P. Structure of the sulfoxide synthase EgtB from the ergothioneine biosynthetic pathway. Angew. Chem. Int. Ed. 54, 2821–2824 (2015).

    Article  CAS  Google Scholar 

  23. Naowarojna, N. et al. Crystal structure of the ergothioneine sulfoxide synthase from Candidatus Chloracidobacterium thermophilum and structure-guided engineering to modulate its substrate selectivity. ACS Catal. 9, 6955–6961 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Stampfli, A. R. et al. An alternative active site architecture for O2 activation in the ergothioneine biosynthetic EgtB from Chloracidobacterium thermophilum. J. Am. Chem. Soc. 141, 5275–5285 (2019).

    Article  CAS  PubMed  Google Scholar 

  25. Vit, A., Mashabela, G. T., Blankenfeldt, W. & Seebeck, F. P. Structure of the ergothioneine-biosynthesis amidohydrolase EgtC. ChemBioChem 16, 1490–1496 (2015).

    Article  CAS  PubMed  Google Scholar 

  26. Song, H. et al. Mechanistic studies of a novel C-S lyase in ergothioneine biosynthesis: the involvement of a sulfenic acid intermediate. Sci Rep. 5, 11870 (2015).

    Article  ADS  PubMed  PubMed Central  Google Scholar 

  27. Reich, H. J., Renga, J. M. & Reich, I. L. Organoselenium chemistry. Conversion of ketones to enones by selenoxide syn elimination. J. Am. Chem. Soc. 97, 5434–5447 (1975).

    Article  CAS  Google Scholar 

  28. Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-hit: accelerated for clustering the next-generation sequencing data. Bioinformatics. 28, 3150–3152 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).

    Article  CAS  PubMed  Google Scholar 

  30. McCulloch, K. M., Kinsland, C., Begley, T. P. & Ealick, S. E. Structural studies of thiamin monophosphate kinase in complex with substrates and products. Biochemistry 47, 3810–3821 (2008).

    Article  CAS  PubMed  Google Scholar 

  31. Katoh, K. Mafft: a novel method for rapid multiple sequence alignment based on fast fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  32. Tareen, A. & Kinney, J. B. Logomaker: beautiful sequence logos in python. Bioinformatics 36, 2272–2274 (2019).

    Article  PubMed Central  Google Scholar 

  33. Veres, Z., Kim, I. Y., Scholz, T. D. & Stadtman, T. C. Selenophosphate synthetase. Enzyme properties and catalytic reaction. J. Biol. Chem. 269, 10597–10603 (1994).

    Article  CAS  PubMed  Google Scholar 

  34. Kim, I. Y., Veres, Z. & Stadtman, T. C. Escherichia coli mutant SELD enzymes. The cysteine 17 residue is essential for selenophosphate formation from ATP and selenide. J. Biol. Chem. 267, 19650–19654 (1992).

    Article  CAS  PubMed  Google Scholar 

  35. Glass, R. S. et al. Monoselenophosphate: synthesis, characterization, and identity with the prokaryotic biological selenium donor, compound SePX. Biochemistry 32, 12555–12559 (1993).

    Article  CAS  PubMed  Google Scholar 

  36. Vit, A., Misson, L., Blankenfeldt, W. & Seebeck, F. P. Ergothioneine biosynthetic methyltransferase EgtD reveals the structural basis of aromatic amino acid betaine biosynthesis. ChemBioChem 16, 119–125 (2014).

    Article  PubMed  Google Scholar 

  37. Kumar, A. A., Illyes, T. Z., Kover, K. E. & Szilagyi, L. Convenient syntheses of 1,2-trans selenoglycosides using isoselenuronium salts as glycosylselenenyl transfer reagents. Carbohydrate Res. 360, 8–18 (2012).

    Article  CAS  Google Scholar 

  38. Pravdic, N. & Fletcher, H. G. The behavior of 2-acetamido-2-deoxy-d-mannose with isopropenyl acetate in the presence of p-toluenesulfonic acid. I. Isolation and identification of derivatives of 2-amino-d-glucal (2-amino-1,2-dideoxy-d-arabino-hex-1-enopyranose) and of other products. J. Org. Chem. 32, 1806–1810 (1967).

    Article  CAS  PubMed  Google Scholar 

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We thank Andy K. L. Nguy for helpful discussions and the Edward C. Taylor 3rd Year Fellowship in Chemistry (to C.M.K.), the Life Sciences Research Foundation Postdoctoral Fellowship sponsored by the Open Philanthropy Project (to J.H.), the Swiss National Science Foundation Early “Postdoc Mobility” Fellowship (no. P2EZP2_187995 to N.H.), the National Science Foundation CAREER Award (no. 1847932 to M.R.S.), and the US National Institutes of Health (GM129496 to M.R.S.) for financial support.

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Authors and Affiliations



C.M.K. and M.R.S. conceived the idea for the study. C.M.K. designed and performed the bioinformatic search and all experiments described in the paper. J.H. synthesized and purified SeGlcNAc and 2AG. N.H. conceived the selenoxide elimination. C.M.K. and M.R.S. analysed the data and prepared the manuscript.

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Correspondence to Mohammad R. Seyedsayamdost.

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Nature thanks the anonymous reviewers for their contribution to the peer review of this work.

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This file contains Supplementary Tables 1–8; coding DNA sequences and amino acid sequences of recombinant proteins; Supplementary Figs. 1–11 and Supplementary Schemes 1–4.

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Kayrouz, C.M., Huang, J., Hauser, N. et al. Biosynthesis of selenium-containing small molecules in diverse microorganisms. Nature 610, 199–204 (2022).

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