A High-Quality Genome-Scale Model for Rhodococcus opacus Metabolism.

Rhodococcus opacus is a bacterium that has a high tolerance to aromatic compounds and can produce significant amounts of triacylglycerol (TAG). Here, we present iGR1773, the first genome-scale model (GSM) of R. opacus PD630 metabolism based on its genomic sequence and associated data. The model includes 1773 genes, 3025 reactions, and 1956 metabolites, was developed in a reproducible manner using CarveMe, and was evaluated through Metabolic Model tests (MEMOTE). We combine the model with two Constraint-Based Reconstruction and Analysis (COBRA) methods that use transcriptomics data to predict growth rates and fluxes: E-Flux2 and SPOT (Simplified Pearson Correlation with Transcriptomic data). Growth rates are best predicted by E-Flux2. Flux profiles are more accurately predicted by E-Flux2 than flux balance analysis (FBA) and parsimonious FBA (pFBA), when compared to 44 central carbon fluxes measured by 13C-Metabolic Flux Analysis (13C-MFA). Under glucose-fed conditions, E-Flux2 presents an R2 value of 0.54, while predictions based on pFBA had an inferior R2 of 0.28. We attribute this improved performance to the extra activity information provided by the transcriptomics data. For phenol-fed metabolism, in which the substrate first enters the TCA cycle, E-Flux2's flux predictions display a high R2 of 0.96 while pFBA showed an R2 of 0.93. We also show that glucose metabolism and phenol metabolism function with similar relative ATP maintenance costs. These findings demonstrate that iGR1773 can help the metabolic engineering community predict aromatic substrate utilization patterns and perform computational strain design.

Mechanism and Kinetics of the Reaction of Nitrate Radicals with Carboxylic Acids.

Rate constants for the reaction of nitrate radical (NO3 ⋅) with several carboxylic acids (RCO2 H) were measured in acetonitrile using laser flash photolysis, and found to be on the order of 105 -106  M-1 s-1 . No observable H/D kinetic isotope effect was observed at the carboxyl O-H group, α-C-H bond and (possibly) in the case of formic acid, the formylic C-H bond. This suggests that NO3 ⋅ does not abstract hydrogen from any of these positions despite the fact that all these processes are thermodynamically favorable. Reactivity increases with increased length and/or branching of the alkyl side chain (R), and approaches, but does not quite reach, that of an alkane towards NO3 ⋅. The relative inertness of carboxylic acids towards NO3 ⋅ can be explained by the polar effect.