Article

Purinyl-cobamide is a native prosthetic group of reductive dehalogenases

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Abstract

Cobamides such as vitamin B12 are structurally conserved, cobalt-containing tetrapyrrole biomolecules that have essential biochemical functions in all domains of life. In organohalide respiration, a vital biological process for the global cycling of natural and anthropogenic organohalogens, cobamides are the requisite prosthetic groups for carbon–halogen bond-cleaving reductive dehalogenases. This study reports the biosynthesis of a new cobamide with unsubstituted purine as the lower base and assigns unsubstituted purine a biological function by demonstrating that Coα-purinyl-cobamide (purinyl-Cba) is the native prosthetic group in catalytically active tetrachloroethene reductive dehalogenases of Desulfitobacterium hafniense. Cobamides featuring different lower bases are not functionally equivalent, and purinyl-Cba elicits different physiological responses in corrinoid-auxotrophic, organohalide-respiring bacteria. Given that cobamide-dependent enzymes catalyze key steps in essential metabolic pathways, the discovery of a novel cobamide structure and the realization that lower bases can effectively modulate enzyme activities generate opportunities to manipulate functionalities of microbiomes.

  • Compound

    Purinyl-cobamide

  • Compound

    Norpseudo-vitamin B12

  • Compound

    Benzimidazolyl-cobamide

  • Compound

    5-Methoxybenzimidazolyl-cobamide

  • Compound

    p-Cresolyl-cobamide

  • Compound

    5-Hydroxybenzimidazolyl-cobamide

  • Compound

    5-Methylbenzimidazolyl-cobamide

  • Compound

    Vitamin B12

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Acknowledgements

We thank J. Maillard, École Polytechnique Fédérale de Lausanne, France, for providing Dehalobacter restrictus strain PER-K23. We also thank R. Flick from the BioZone Mass Spectrometry facility, Toronto, for LC/MS assistance. This research was supported by a grant from the Superfund Research Program under the National Institute of Environmental Health Sciences (R01ES024294) to F.E.L., with additional support provided by the Strategic Environmental Research and Development Program (SERDP project ER-2312) to F.E.L. and by the Natural Science and Engineering Research Council of Canada (NSERC) Industrial Biocatalysis Network to E.A.E. Y. Yin acknowledges the financial support from the China-UT One-Hundred Scholars Program by the China Scholarship Council and the University of Tennessee.

Author information

Affiliations

  1. Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA.

    • Jun Yan
    • , Meng Bi
    • , Yongchao Yin
    •  & Frank E Löffler
  2. Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, P.R. China.

    • Jun Yan
  3. Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA.

    • Jun Yan
    • , Nannan Jiang
    • , Yi Yang
    • , Burcu Şimşir
    •  & Frank E Löffler
  4. Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.

    • Jun Yan
    • , Nannan Jiang
    •  & Frank E Löffler
  5. Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.

    • Jun Yan
    • , Nannan Jiang
    •  & Frank E Löffler
  6. Department of Chemistry, University of Tennessee, Knoxville, Tennessee, USA.

    • Allen K Bourdon
    • , Abigail T Farmer
    •  & Shawn R Campagna
  7. Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.

    • Po-Hsiang Wang
    • , Olivia Molenda
    • , Andrew T Quaile
    •  & Elizabeth A Edwards
  8. Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA.

    • Nannan Jiang
    •  & Frank E Löffler
  9. Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA.

    • Yi Yang
    • , Burcu Şimşir
    •  & Frank E Löffler
  10. Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee, USA..

    • Frank E Löffler

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Contributions

F.E.L., J.Y., and S.R.C. conceptualized the research and designed experiments. J.Y., M.B., B.S., Y. Yang, and Y. Yin performed cultivation work, corrinoid extraction and purification, and phylogenetic analyses. A.K.B. and A.T.F. performed LC–MS and structural analyses. P.W., O.M. and A.T.Q. performed BN–PAGE, enzyme assays, and proteomic analysis. N.J. generated cobT expression clones. All authors contributed to data analysis and interpretation, and J.Y., S.R.C., E.A.E., and F.E.L. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Jun Yan or Frank E Löffler.

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    Supplementary Results, Supplementary Tables 1–5, Supplementary Figures 1–9

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