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S-adenosylhomocysteine as a methyl transfer catalyst in biocatalytic methylation reactions

Nature Catalysis volume 2, pages 696–701 (2019)Cite this article

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Abstract

S-adenosylmethionine-dependent methyltransferases form a large family of enzymes that can catalyse regio-, chemo- and stereospecific methylation of complex natural products. These enzymes could be very useful tools for the chemoenzymatic production and diversification of natural or artificial compounds. Despite this potential, in vitro applications of methyltransferases are limited by their requirement for S-adenosylmethionine as a stoichiometric methyl donor. The chemical complexity, instability, high cost and poor atom economy of this reagent prevent preparative in vitro methylation reactions from becoming routine protocols in natural product research and viable options for process development. In this Article we demonstrate that C-, N- and O-specific methyltransferases can be combined with halide methyltransferases to form enzyme cascades that require only catalytic concentrations of S-adenosylmethionine and use methyl iodide as the stoichiometric methyl donor.

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Fig. 1: Natural and artificial SAM cycles.
Fig. 2: HMT/EgtD methyl transfer cascade.
Fig. 3: Activity of SAH nucleosidase.

Data availability

The primary data that support the plots within this paper and other findings of this study are available from the corresponding author on reasonable request.

References

  1. Bornscheuer, U. T. et al. Engineering the third wave of biocatalysis. Nature 485, 185–194 (2012).

    Article  CAS  Google Scholar 

  2. Dong, J. et al. Biocatalytic oxidation reactions: a chemist’s perspective. Angew. Chem. Int. Ed. 57, 9238–9261 (2018).

    Article  CAS  Google Scholar 

  3. de Souza, R. O. M. A., Miranda, L. S. M. & Bornscheuer, U. T. A retrosynthesis approach for biocatalysis in organic synthesis. Chemistry 23, 12040–12063 (2017).

    Article  Google Scholar 

  4. Hönig, M., Sondermann, P., Turner, N. J. & Carreira, E. M. Enantioselective chemo- and biocatalysis: partners in retrosynthesis. Angew. Chem. Int. Ed. 56, 8942–8973 (2017).

    Article  Google Scholar 

  5. Bennett, M. R., Shepherd, S. A., Cronin, V. A. & Micklefield, J. Recent advances in methyltransferase biocatalysis. Curr. Opin. Chem. Biol. 37, 97–106 (2017).

    Article  CAS  Google Scholar 

  6. Liscombe, D. K., Louie, G. V. & Noel, J. P. Architectures, mechanisms and molecular evolution of natural product methyltransferases. Nat. Prod. Rep. 29, 1238–1250 (2012).

    Article  CAS  Google Scholar 

  7. Clarke, S. G. Protein methylation at the surface and buried deep: thinking outside the histone box. Trends Biochem. Sci. 38, 243–252 (2013).

    Article  CAS  Google Scholar 

  8. Barreiro, E. J., Kummerle, A. E. & Fraga, C. A. M. The methylation effect in medicinal chemistry. Chem. Rev. 111, 5215–5246 (2011).

    Article  CAS  Google Scholar 

  9. Serpier, F. et al. Selective methylation of arenes: a radical C–H functionalization/cross-coupling sequence. Angew. Chem. Int. Ed. 57, 10697–10701 (2018).

    Article  CAS  Google Scholar 

  10. Zhu, N., Zhao, J. & Bao, H. Iron catalyzed methylation and ethylation of vinyl arenes. Chem. Sci. 8, 2081–2085 (2017).

    Article  CAS  Google Scholar 

  11. Gui, J. et al. C–H methylation of heteroarenes inspired by radical SAM methyl transferase. J. Am. Chem. Soc. 136, 4853–4856 (2014).

    Article  CAS  Google Scholar 

  12. Jin, J. & MacMillan, D. W. Alcohols as alkylating agents in heteroarene C–H functionalization. Nature 525, 87–90 (2015).

    Article  CAS  Google Scholar 

  13. Liu, W., Yang, X., Zhou, Z. Z. & Li, C. J. Simple and clean photo-induced methylation of heteroarenes with MeOH. Chem 2, 688–702 (2017).

    Article  CAS  Google Scholar 

  14. Chen, X. Y. & Sorensen, E. J. Pd-catalyzed, ortho C–H methylation and fluorination of benzaldehydes using orthanilic acids as transient directing groups. J. Am. Chem. Soc. 140, 2789–2792 (2018).

    Article  CAS  Google Scholar 

  15. Shang, R., Illies, L. & Nakamura, E. Iron-catalyzed ortho C–H methylation of aromatics bearing a simple carbonyl group with methylaluminum and tridentate phosphine ligand. J. Am. Chem. Soc. 138, 10132–10135 (2016).

    Article  CAS  Google Scholar 

  16. Uemura, T., Yamaguchi, M. & Chatani, N. Phenyltrimethylammonium salts as methylation reagents in the nickel-catalyzed methylation of C–H bonds. Angew. Chem. Int. Ed. 55, 3162–3165 (2016).

    Article  CAS  Google Scholar 

  17. Cano, R., Zakarian, A. & McGlacken, G. P. Direct asymmetric alkylation of ketones: still unconquered. Angew. Chem. Int. Ed. 56, 9278–9290 (2017).

    Article  CAS  Google Scholar 

  18. Huber, T. D., Johnson, B. R., Zhang, J. & Thorson, J. S. AdoMet analog synthesis and utilization: current state of the art. Curr. Opin. Biotechnol. 42, 189–197 (2016).

    Article  CAS  Google Scholar 

  19. Deen, J. et al. Methyltransferase-directed labeling of biomolecules and its applications. Angew. Chem. Int. Ed. 56, 5182–5200 (2017).

    Article  CAS  Google Scholar 

  20. Chen, H., Wang, Z., Cai, H. & Zhou, C. Progress in the microbial production of S-adenosyl-l-methionine. World J. Microbiol. Biotechnol. 32, 153 (2016).

    Article  CAS  Google Scholar 

  21. Mordhorst, S., Siegrist, J., Mueller, M., Richter, M. & Andexter, J. N. Catalytic alkylation using a cyclic S-adenosylmethionine regeneration system. Angew. Chem. Int. Ed. 56, 4037–4041 (2017).

    Article  CAS  Google Scholar 

  22. Farnberger, J. E. et al. Biocatalytic methylation and demethylation via a shuttle catalysis concept involving corrinoid proteins. Commun. Chem. 1, 82 (2018).

    Article  Google Scholar 

  23. Wolfenden, R. & Yuan, Y. Monoalkyl sulfates as alkylating agents in water, alkylsulfatase rate enhancements and the ‘energy-rich’ nature of sulfate half-esters. Proc. Natl Acad. Sci. USA 104, 83–86 (2007).

    Article  CAS  Google Scholar 

  24. Lewis, C. A. J. & Wolfenden, R. Sulfonium ion condensation: the burden borne by SAM synthetase. Biochemistry 57, 3549–3551 (2018).

    Article  CAS  Google Scholar 

  25. Wuosmaa, A. M. & Hager, L. P. Methyl chloride transferase: a carbocation route for biosynthesis of halometabolites. Science 249, 160–162 (1990).

    Article  CAS  Google Scholar 

  26. Ni, X. & Hager, L. P. Expression of Batis maritima methyl chloride transferase in Escherichia coli. Proc. Natl Acad. Sci. USA 96, 3611–3615 (1999).

    Article  CAS  Google Scholar 

  27. Schmidberger, J. W., James, A. B., Edwards, R., Naismith, J. H. & O’Hagan, D. Halomethane biosynthesis: structure of a SAM-dependent halide methyltransferase from Arabidopsis thaliana. Angew. Chem. Int. Ed. 49, 3646–3648 (2010).

    Article  CAS  Google Scholar 

  28. Bayer, T. S. et al. Synthesis of methyl halides from biomass using engineered microbes. J. Am. Chem. Soc. 131, 6508–6515 (2009).

    Article  CAS  Google Scholar 

  29. Vit, A., Misson, L. E., Blankenfeldt, W. & Seebeck, F. P. Ergothioneine biosynthetic methyltransferase EgtD reveals the structural basis of aromatic amino acid betaine biosynthesis. Chembiochem 16, 119–125 (2015).

    Article  CAS  Google Scholar 

  30. Misson, L. et al. Inhibition and regulation of the ergothioneine biosynthetic methyltransferase EgtD. ACS Chem. Biol. 13, 1333–1342 (2018).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  32. Askari, A. & Melville, D. B. The reaction sequence in ergothioneine biosynthesis: hercynine as an intermediate. J. Biol. Chem. 237, 1615 (1962).

    CAS  PubMed  Google Scholar 

  33. Burn, R., Misson, L. E., Meury, M. & Seebeck, F. P. Anaerobic origin of ergothioneine. Angew. Chem. Int. Ed. 56, 12508–12511 (2017).

    Article  CAS  Google Scholar 

  34. Iwig, D. F. & Booker, S. J. Insight into the polar reactivity of the onium chalcogen analogues of S-adenosyl-l-methionine. Biochemistry 43, 13496–13509 (2004).

    Article  CAS  Google Scholar 

  35. Baba, T. et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the KEIO collection. Mol. Syst. Biol. 2, 2006.0008 (2006).

    Article  Google Scholar 

  36. Kloor, D. & Osswald, H. S-adenosylhomocysteine hydrolase as a target for intracellular adenosine action. Trends Pharmacol. Sci. 25, 294–297 (2004).

    Article  CAS  Google Scholar 

  37. Parveen, N. & Cornell, K. A. Methylthioadenosine/S-adenosylhomocysteine nucleosidase, a critical enzyme for bacterial metabolism. Mol. Microbiol. 79, 7–20 (2011).

    Article  CAS  Google Scholar 

  38. Ogg, R. A. The hydrolysis of methyl iodide. J. Am. Chem. Soc. 60, 2000–2001 (1938).

    Article  CAS  Google Scholar 

  39. Heppolette, R. L. & Robertson, R. E. The neutral hydrolysis of the methyl halides. Proc. R. Soc. Lond. A 252, 273–285 (1959).

    Article  CAS  Google Scholar 

  40. Vernon, D. M. & Bohnert, H. J. A novel methyl transferase induced by osmotic stress in the facultative halophyte Mesembryanthemum crystallinum. EMBO J. 11, 2077–2085 (1992).

    Article  CAS  Google Scholar 

  41. Negishi, O., Mun’im, A. & Negishi, Y. Content of methylated inositols in familiar edible plants. J. Agric. Food Chem. 63, 2683–2688 (2015).

    Article  CAS  Google Scholar 

  42. Sarmah, M. P., Shashidhar, M. S., Sureshan, K. M., Gonnade, R. G. & Bhadbhade, M. M. Sulfonate protecting groups. Synthesis of O- and C-methylated inositols: d- and l-ononitol, d- and l-laminitol, mytilitol and scyllo-inositol methyl ether. Tetrahedron 61, 4437–4446 (2005).

    Article  CAS  Google Scholar 

  43. Duchek, J., Adams, D. R. & Hudlicky, T. Chemoenzymatic synthesis of inositols, conduritols and cyclitol analogues. Chem. Rev. 111, 4223–4258 (2011).

    Article  CAS  Google Scholar 

  44. Ley, S. V., Sternfeld, F. & Taylor, S. Microbial oxidation in synthesis: a six step preparation of (+)-pinitol from benzene. Tetrahedron Lett. 28, 225–226 (1987).

    Article  CAS  Google Scholar 

  45. Biastoff, S., Brandt, W. & Dräger, B. Putrescine N-methyltransferase—the start for alkaloids. Phytochemistry 70, 1708–1718 (2009).

    Article  CAS  Google Scholar 

  46. Sommer-Kamann, C., Fires, A., Mordhorst, S., Andexter, J. N. & Müller, M. Asymmetric C-alkylation by the S-adenosylmethionine-dependent methyltransferase SgvM. Angew. Chem. Int. Ed. 56, 4033–4036 (2017).

    Article  CAS  Google Scholar 

  47. Zou, Y. et al. Stereospecific biosynthesis of β-methyltryptophan from (l)-tryptophan features a stereochemical switch. Angew. Chem. Int. Ed. 52, 12951–12955 (2013).

    Article  CAS  Google Scholar 

  48. Mahlert, C., Kopp, F., Thirlway, J., Micklefield, J. & Marahiel, M. A. Stereospecific enzymatic transformation of alpha-ketoglutarate to (2S,3R)-3-methyl glutamate during acidic lipopeptide biosynthesis. J. Am. Chem. Soc. 129, 12011–12008 (2007).

    Article  CAS  Google Scholar 

  49. Sadler, J. C., Chung, C. H., Mosley, J. E., Burley, G. A. & Humphreys, L. D. Structural and functional basis of C-methylation of coumarin scaffolds by NovO. ACS Chem. Biol. 12, 374–379 (2017).

    Article  CAS  Google Scholar 

  50. Pacholec, M., Tao, J. & Walsh, C. T. CouO and NovO: C-methyltransferases for tailoring the aminocoumarin scaffold in coumermycin and novobiocin antibiotic biosynthesis. Biochemistry 44, 14969–14976 (2005).

    Article  CAS  Google Scholar 

  51. Saiz-Lopez, A. et al. Atmospheric chemistry of iodine. Chem. Rev. 112, 1773–1804 (2012).

    Article  CAS  Google Scholar 

  52. Pace, C. N., Vajdos, F., Fee, L., Grimsley, G. & Gray, T. How to measure and predict the molar absorption coefficient of a protein. Protein Sci. 4, 2411–2423 (1995).

    Article  CAS  Google Scholar 

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Acknowledgements

C.L. was a recipient of an SSSTC and CSC postdoctoral fellowship. F.P.S. is supported by the ‘Professur für Molekulare Bionik’. This project was supported by the European Research Council (ERC-2013-StG 336559) and ‘Innovationsraum Biokatalyse’. The authors thank A. Maurer for ESI-HRMS measurements.

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  1. Department for Chemistry, University of Basel, Basel, Switzerland

    Cangsong Liao & Florian P. Seebeck

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Contributions

C.L. and F.P.S. contributed to this paper as follows: original conception and planning (F.P.S. and C.L.), empirical work (C.L.), data analysis and interpretation (C.L. and F.P.S.) and writing of the manuscript (F.P.S. and C.L.).

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Correspondence to Florian P. Seebeck.

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The authors have submitted a patent application (European patent EP18193563) protecting the methodology described in this manuscript.

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Liao, C., Seebeck, F.P. S-adenosylhomocysteine as a methyl transfer catalyst in biocatalytic methylation reactions. Nat Catal 2, 696–701 (2019). https://doi.org/10.1038/s41929-019-0300-0

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