Journal of Biological Chemistry
Volume 295, Issue 34, 21 August 2020, Pages 11971-11981
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MtcB, a member of the MttB superfamily from the human gut acetogen Eubacterium limosum, is a cobalamin-dependent carnitine demethylase

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The trimethylamine methyltransferase MttB is the first described member of a superfamily comprising thousands of microbial proteins. Most members of the MttB superfamily are encoded by genes that lack the codon for pyrrolysine characteristic of trimethylamine methyltransferases, raising questions about the activities of these proteins. The superfamily member MtcB is found in the human intestinal isolate Eubacterium limosum ATCC 8486, an acetogen that can grow by demethylation of l-carnitine. Here, we demonstrate that MtcB catalyzes l-carnitine demethylation. When growing on l-carnitine, E. limosum excreted the unusual biological product norcarnitine as well as acetate, butyrate, and caproate. Cellular extracts of E. limosum grown on l-carnitine, but not lactate, methylated cob-(I)alamin or tetrahydrofolate using l-carnitine as methyl donor. MtcB, along with the corrinoid protein MtqC and the methylcorrinoid:tetrahydrofolate methyltransferase MtqA, were much more abundant in E. limosum cells grown on l-carnitine than on lactate. Recombinant MtcB methylates either cob(I)alamin or Co(I)-MtqC in the presence of l-carnitine and, to a much lesser extent, γ-butyrobetaine. Other quaternary amines were not substrates. Recombinant MtcB, MtqC, and MtqA methylated tetrahydrofolate via l-carnitine, forming a key intermediate in the acetogenic Wood–Ljungdahl pathway. To our knowledge, MtcB methylation of cobalamin or Co(I)-MtqC represents the first described mechanism of biological l-carnitine demethylation. The conversion of l-carnitine and its derivative γ-butyrobetaine to trimethylamine by the gut microbiome has been linked to cardiovascular disease. The activities of MtcB and related proteins in E. limosum might demethylate proatherogenic quaternary amines and contribute to the perceived health benefits of this human gut symbiont.

bacterial metabolism
microbiology
energy metabolism
folate
microbiome
enzyme catalysis
cobalamin
one-carbon metabolism
carnitine
acetogenesis

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This article contains supporting information.

Author contributions—D. J. K., L. Z., and J. A. K. data curation; D. J. K., E. J. B., L. Z., and J. A. K. formal analysis; D. J. K., E. J. B., L. Z., and J. A. K. investigation; D. J. K., L. Z., and J. A. K. visualization; D. J. K., E. J. B., L. Z., and J. A. K. methodology; D. J. K. and J. A. K. writing-original draft; D. J. K., E. J. B., L. Z., and J. A. K. writing-review and editing; E. J. B., L. Z., and J. A. K. resources; L. Z. software; L. Z. and J. A. K. funding acquisition; J. A. K. conceptualization; J. A. K. supervision; J. A. K. validation; J. A. K. project administration.

Funding and additional information—This research was supported by National Institutes of Health Grant 1R01DK109345 (to J. A. K.). The Fusion Orbitrap instrument was supported by National Institutes of Health Grant S10 OD018056 (to L. Z.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Conflict of interest—The authors declare that they have no conflicts of interest with the contents of this article.

Present address for Duncan J. Kountz: Dept. of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA.

Abbreviations—The abbreviations used are:

    TMA

    trimethylamine

    TMAO

    trimethylamine N-oxide

    nonPyl

    nonpyrrolysine

    THF

    tetrahydrofolate

    emPAI

    exponentially modified protein abundance index

    PIPE

    polymerase incomplete primer extension

    OD

    optical density

    MFS

    major facilitator family

    CI

    confidence interval.