Unraveling chloromethane conversion in the acetogen Acetobacterium dehalogenans

Chloromethane (CM) is an abundant environmental pollutant that contributes significantly to ozone depletion [1]. Acetobacterium dehalogenans is one of the few isolated anaerobic bacteria shown to utilize CM as its carbon and energy source [2]. The enzyme system responsible for its CM demethylation/dehalogenation has not been identified so far. We aim to identify and characterize this system and to understand the metabolic changes of A. dehalogenans during growth on CM versus the methoxylated aromatic syringate. We analyzed the growth and substrate conversion of A. dehalogenans grown on CM, syringate and both substrates and used comparative transcriptomics to analyze the gene expression pattern of A. dehalogenans grown under these conditions. We identified a corrinoid-dependent methyltransferase system with three adjacent genes mtcABC which were highly upregulated during growth on CM in comparison to syringate. We heterologously produced and purified the corresponding proteins in E. coli, subsequently performed activity assays to determine their substrate specificity, and conducted X-ray crystallography. We discovered that this Mtc methyltransferase system demethylates methyl halides such as chloromethane and iodomethane. X-ray crystallography of the MtcB methyltransferase revealed a hydrophobic internal channelling system for methyl halides. Phylogenetic analysis showed that homologous proteins are encoded by several other anaerobic bacteria, especially Bacillota. Such organisms may also have the potential to convert methyl halides such as CM. The Mtc system is most closely related to the archaeal Mto system, which converts methoxylated aromatic compounds. In summary, we identified and characterized a novel enzyme system used for methyl halide demethylation in anaerobic microorganisms.

[1] Harper, D. B. (2000). Nat Prod Rep, 17, 337-348.

[2] Traunecker, J., et al. (1991). Arch Microbiol, 156, 416–421.