Identification and characterisation of an elusive bacterial enzyme system for chloromethane dehalogenation

Chloromethane, a toxic gas primarily produced naturally, contributes to stratospheric ozone destruction. The anaerobic acetogen Acetobacterium dehalogenans can utilise chloromethane as a carbon and energy source, but the associated dehalogenase/methyltransferase has remained elusive. Through comparative transcriptomics we identify a gene cluster, cdmBCA, which encodes a corrinoid-dependent methyltransferase system distinct from the characterised Cmu system used for chloromethane degradation in aerobic methylotrophs. Biochemical characterisation reveals that the Cdm system reacts with other haloalkanes, but not with methoxylated aromatics, unlike closely related O-demethylases. X-ray structural analysis of the protein CdmB shows a hydrophobic channelling system directing haloalkanes towards cobalamin-dependent activation. Homologous proteins are found in anaerobic prokaryotes, particularly within the phyla Bacillota and Asgardarchaeota, suggesting previously unidentified microbial transformation of chloromethane in the environment. Discovery of the Cdm dehalogenation/methyltransferase system sheds light on the microbial contribution to the global chloromethane cycle.