Mechanistic insight into 3‐methylmercaptopropionate metabolism and kinetical regulation of demethylation pathway in marine dimethylsulfoniopropionate‐catabolizing bacteria

Abstract

SummaryThe vast majority of oceanic dimethylsulfoniopropionate (DMSP) is thought to be catabolized by bacteria via the DMSP demethylation pathway. This pathway contains four enzymes termed DmdA, DmdB, DmdC and DmdD/AcuH, which together catabolize DMSP to acetylaldehyde and methanethiol as carbon and sulfur sources respectively. While molecular mechanisms for DmdA and DmdD have been proposed, little is known of the catalytic mechanisms of DmdB and DmdC, which are central to this pathway. Here, we undertake physiological, structural and biochemical analyses to elucidate the catalytic mechanisms of DmdB and DmdC. DmdB, a 3‐methylmercaptopropionate (MMPA)‐coenzyme A (CoA) ligase, undergoes two sequential conformational changes to catalyze the ligation of MMPA and CoA. DmdC, a MMPA‐CoA dehydrogenase, catalyzes the dehydrogenation of MMPA‐CoA to generate MTA‐CoA with Glu435 as the catalytic base. Sequence alignment suggests that the proposed catalytic mechanisms of DmdB and DmdC are likely widely adopted by bacteria using the DMSP demethylation pathway. Analysis of the substrate affinities of involved enzymes indicates that Roseobacters kinetically regulate the DMSP demethylation pathway to ensure DMSP functioning and catabolism in their cells. Altogether, this study sheds novel lights on the catalytic and regulative mechanisms of bacterial DMSP demethylation, leading to a better understanding of bacterial DMSP catabolism.

Metagenomic Insights Into the Cycling of Dimethylsulfoniopropionate and Related Molecules in the Eastern China Marginal Seas

“…These data suggest that AcuH is the major methylthioacryloyl-CoA hydratase responsible for generating MeSH in these environments. The high abundances of dmdB, dmdC, and acuH may be linked to the high plasticity and flexibility of the corresponding enzymes (Reisch et al, 2011a;Bullock et al, 2014;Shao et al, 2019).…”

“…The DMSP demethylation pathway that can result in the generation of MeSH (Reisch et al, 2011a) is initiated by the DmdA enzyme that was identified in Ruegeria pomeroyi (Howard et al, 2006) and is common in many marine alpha-proteobacteria, including SAR11 bacteria (Reisch et al, 2008(Reisch et al, , 2011b. Many diverse bacteria that do not always have the capacity to demethylate DMSP (lacking dmdA in their genomes) contain dmdBCD/acuH, which encode enzymes that degrade the product of DMSP demethylation, methylmercaptopropionate (MMPA), to generate MeSH (Shao et al, 2019). Thus, the presence of dmdBCD is considered an indicator of MMPA degradation rather than of DMSP.…”

Towards a systematic understanding of structure–function relationship of dimethylsulfoniopropionate‐catabolizing enzymes

“…The work presented in this issue by Shao et al () significantly advances our understanding of how MMPA is further catabolized by two enzymes in this pathway: DmdB, an ATP‐dependent CoA ligase, and DmdC, a flavin‐containing CoA dehydrogenase. DmdB shows high similarity to bacterial short‐chain fatty acid CoA ligases – and, remarkably, the two homologous DmdB proteins of Ruegeria pomeroyi DSS‐3 can accept a range of fatty acids as substrates (Bullock et al , ).…”

“…DmdB shows high similarity to bacterial short‐chain fatty acid CoA ligases – and, remarkably, the two homologous DmdB proteins of Ruegeria pomeroyi DSS‐3 can accept a range of fatty acids as substrates (Bullock et al , ). The crystal structure of DmdB was obtained in the presence of ADP, a competitive inhibitor of this enzyme, and the structure of an inactive Lys523Ala mutant was obtained in complex with AMP and MMPA (Shao et al , ). DmdB forms an asymmetric dimer with ADP bound to one chain while leaving the binding pocket of the other chain empty.…”

“…Shao et al () also resolved the structure of the next enzyme in this pathway, DmdC. This enzyme belongs to the CoA dehydrogenase family (Reisch et al , ); members of this family are best known for their role in β‐oxidation of fatty acids.…”