The metabolic redox regime ofPseudomonas putidatunes its evolvability towards novel xenobiotic substrates

Abstract

ABSTRACTDuring evolution of biodegradation pathways for xenobiotic compounds, the transition towards novel substrates of Rieske non-heme iron oxygenases borne by environmental bacteria is frequently associated with faulty reactions. Such reactions release reactive oxygen species (ROS), endowed with high mutagenic potential. The present work studies how the operation of a given metabolic network by a bacterial host may either foster or curtail the still-evolving biochemical pathway for catabolism of 2,4-dinitrotoluene (2,4-DNT). To this end, the genetically tractable strainPseudomonas putidaEM173 was chromosomally implanted with a Tn7 construct carrying the whole genetic complement (recruited from the environmental isolateBurkholderiasp. R34) necessary for complete biodegradation of 2,4-DNT. By using reporter technology and direct measurements of ROS formation, we observed that the engineeredP. putidastrain experienced oxidative stress when catabolizing the nitroaromatic substrate. However, ROS was neither translated into significant activation of the SOS response to DNA damage nor resulted in a mutagenic regime (unlikeBurkholderiasp. R34, the original host of the pathway). To inspect whether the tolerance ofP. putidato oxidative insults could be traced to its characteristic reductive redox regime, we artificially lowered the pool of NAD(P)H by conditional expression of a water forming, NADH-specific oxidase. Under the resulting low-NAD(P)H status, 2,4-DNT triggered a conspicuous mutagenic and genomic diversification scenario. These results indicate that the background biochemical network of environmental bacteria ultimately determines the evolvability of metabolic pathways. Moreover, the data explains the efficacy of some bacteria such as Pseudomonads to host and evolve new catabolic routes.IMPORTANCESome environmental bacteria evolve new capacities for aerobic biodegradation of chemical pollutants by adapting pre-existing redox reactions to recently faced compounds. The process typically starts by co-option of enzymes of an available route to act on the chemical structure of the substrates-to-be. The critical bottleneck is generally the first biochemical step and most of the selective pressure operates on reshaping the initial reaction. In Rieske non-heme iron oxygenases, the interim uncoupling of the novel substrate to the old enzymes results in production of highly mutagenic ROS. In this work, we demonstrate that the background metabolic regime of the bacterium that hosts an evolving catabolic pathway (e.g. biodegradation of the xenobiotic 2,4-DNT) determines whether the cells would either adopt a genetic diversification regime or a robust ROS-tolerant state. These results expose new perspectives to contemporary attempts for rational assembly of whole-cell biocatalysts, as pursued by present-day metabolic engineering.