Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria

Dimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton and bacteria, is primarily degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: (1) a recent common ancestor of DmdA and GcvT, (2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and (3) an enzymatic adaptation for utilizing DMSP in marine bacteria prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur-rich atmosphere and anoxic ocean, compared to recent Roseobacter eco-orthologs (orthologs performing the same function under different conditions), which should be adapted to lower concentrations of DMSP.

RecBCD possesses strong coupling between DNA and nucleotide binding that may propel a stepping mechanism during translocation

Double strand breaks are the severest genomic damage requiring rapid repair response. In prokaryotes, members of the RecBCD family initiate DNA unwinding essential for double strand break repair mechanism by homologous recombination. RecBCD is a highly processive DNA helicase with an unwinding rate approaching ∼1,600 bp·s-1. The ATPase reaction mechanism enabling RecBCD to achieve this fast unwinding rate and its enzymatic adaptation are not fully understood. Here, we present thermodynamic investigation of DNA and nucleotide binding to RecBCD to reveal the binding linkage and the degree of coupling between its nucleotide cofactor and DNA substrate binding. We find that RecBCD exhibits a weak binding state in the presence of ADP towards double overhang DNA substrate (dohDNA), and the same degree of coupling is observed for RecBCD affinity toward ADP, only in the presence of dohDNA. In the absence of nucleotide cofactor (APO state) or in the presence of AMPpNp, much weaker coupling is observed between the binding of DNA and the nucleotide state towards RecBCD. Other DNA substrates that are not optimally engaged with RecBCD do not exhibit similar degree of coupling. This may be the first evidence for strong and weak binding states that can, in principle, regulate a ‘stepping mechanism’ during processive translocation of RecBCD.

Muscle enzyme activity in humans: role of substrate availability and training

To study the effect of nutrient intake (substrate flux) and training on muscle enzyme activities, 36 untrained healthy men adapted for 7 wk to a fat-rich or a carbohydrate-rich diet. Ten of the 18 subjects on each diet completed an endurance training program, and the remaining 8 served as controls. Maximal oxygen uptake was increased (11%) in the trained groups (P < 0.05). Irrespective of training, beta-hydroxyacyl-CoA-dehydrogenase activity in the vastus lateralis muscle was significantly increased by an average of 25% after adaptation to a fat-rich diet and was unchanged after adaptation to a carbohydrate-rich diet. In contrast, irrespective of diet, muscle citrate synthase activity and hexokinase activity were increased (P < 0.05) after adaptation to training by 17 and 18% in the group fed the carbohydrate, rich diet and by 17 and 12% in the group fed the fat-rich diet, respectively, and were unchanged in the two control groups. We suggest that diet can affect muscle enzymatic adaptation, presumably through an effect on the substrate flux.