A thermodynamic analysis of trinitrotoluene biodegradation pathways

Abstract

Biodegradation of 2,4,6-trinitrotoluene (TNT) proceeds through several different metabolic pathways. However, the reaction steps which are considered rate-controlling have not been fully determined. Glycolysis and other biological pathways contain biochemical reactions which are acutely rate-limiting due to enzyme control. These rate-limiting steps also have large negative Gibbs free energy changes. Since xenobiotic compounds such as TNT can be used by biological systems as nitrogen, carbon, and energy sources, it is plausible that their degradation pathways also contain acutely rate-limiting steps. Identification of these rate-controlling reactions will enhance and better direct genetic engineering techniques to increase specific enzyme levels. The objective of this research has been to identify possible rate-controlling steps (or sets of steps) in reported TNT biodegradation pathways by estimating the Gibbs free energy change for each step and for the overall pathways. The biological standard Gibbs free energy change of reaction was calculated for each pathway step using a group contribution method specifically tailored for biomolecules. Steps with large negative Gibbs free energy changes are assumed to be potentially rate-controlling. Therefore, the possible rate-controlling steps within TNT biodegradation pathways were identified. The microorganisms which utilize degradation pathways with the largest overall negative Gibbs free energy changes were also determined. Such microorganisms can extract more energy from the starting substrate and are thus assumed to have a competitive advantage over other microorganisms. Results from this modeling-based research are consistent with much experimental work.