Association of dnt genes of Burkholderia sp. DNT with the substrate-blind regulator DntR draws the evolutionary itinerary of 2,4-dinitrotoluene biodegradation

Abstract

SummaryThe regulation of the DNT pathway for biodegradation of 2,4-dinitrotoluene of Burkholderia sp. DNT has been examined by exporting each of its components to Pseudomonas putida KT2440. The cognate regulator DntR does not respond to the pathway substrate, but to the non-substrate salicylate. In order to examine whether such a response to an unrelated inducer was specific or rather a vestige of a previous evolutionary stage, the complete dnt complement or parts of it were expressed functionally for accumulation of various metabolic intermediates. Their effect on expression of dnt genes was then followed both biochemically and by means of a luminescent reporter engineered in the surrogate host. DntR was not only unresponsive to DNT biodegradation products, but it also failed to influence expression of dnt genes at all. Comparison of the dntR/dntA divergent promoter region with similar ones found in various catabolic systems indicated that the leading segment of the DNT biodegradation pathway evolved from a matching portion of naphthalene biodegradation routes existing in other bacteria. That a useless but still active transcriptional factor occurs along enzymes that have already evolved a new substrate specificity suggests that emergence of novel catalytic abilities precedes their submission to cognate regulatory devices, not vice versa.

Key Enzymes Enabling the Growth of Arthrobacter sp. Strain JBH1 with Nitroglycerin as the Sole Source of Carbon and Nitrogen

“…The observations suggest that a mechanism distinct from those of known glycerol kinases is involved in the regulation of MngP. It should be noted that MngP appears to be constitutive in JBH1, which could enable it to function in a new pathway without the regulatory constraints of the system from which it was recruited (13).…”

Constitutive Expression of a Nag-Like Dioxygenase Gene through an Internal Promoter in the 2-Chloronitrobenzene Catabolism Gene Cluster of Pseudomonas stutzeri ZWLR2-1

“…Because the expression of all reported Nag-like nitroarene dioxygenases was induced by salicylate (5,17,29), whole-cell biotransformation was then carried out to determine whether the expression of cnbAcAd-encoded 2CNB dioxygenase (also a Nag-like member) in strain ZWLR2-1 is induced by its substrate 2CNB or salicylate, a usual inducer for Naglike operons. From the assays, the specific activity of 2CNB dioxygenase, the enzyme catalyzing the initial oxidation during 2CNB degradation, was found to be 0.168 Ϯ 0.019 mol · mg Ϫ1 · h Ϫ1 in a 2CNB-incubated cell.…”

“…JS42 (10,32). Although salicylate is no longer the catabolism intermediate during the degradation of these compounds, it still serves as an inducer for NagR-like transcriptional regulators to activate the transcription of Nag-like dioxygenase genes in these strains (5,29,33). However, in the 2CNB degrader Pseudomonas stutzeri ZWLR2-1, no NagR-like transcriptional regulator was present in the catabolism cluster containing the genes encoding the Nag-like 2CNB dioxygenase (8), and the expression of 2CNB dioxygenase is constitutive rather than inducible in all other Nag-like nitroarene dioxygenases previously reported.…”

“…This places selective pressure on microorganisms to develop their abilities to utilize these chemicals to grow. In general, a bacterium that has evolved pathways to metabolize toxic compounds as its sole source of carbon and energy must surmount three problems: (i) shift the specificities of key enzymes to run a complete pathway producing central intermediate metabolites, (ii) acquire or evolve a regulatory device for expression of the corresponding catabolism genes, and (iii) avoid the stress caused by the substrate itself or by its degradation of intermediates (5,6).…”

Role of Nitrogen Limitation in Transformation of RDX (Hexahydro-1,3,5-Trinitro-1,3,5-Triazine) by Gordonia sp. Strain KTR9

“…In lieu of evolving specific regulators that respond directly to the presence of exogenous xenobiotics, the bacterium has instead evolved regulators that respond to the more common environmental state of nitrogen limitation. Perhaps the current regulation of xplAB in strain KTR9 represents a transition state toward specific regulation of RDX degradation, as the evolution of new catabolic activities can precede their respective regulators (32). The observation that nitrogen limitation induces RDX degradation in some bacteria has important practical implications for in situ RDX bioremediation projects that rely on natural attenuation, bioaug- a Cellular roles: transport (T), nitrogen assimilation (N), urea degradation (U), amino acid, nucleoside, and other ammonia generating catabolic process (A), regulation (R), and RDX degradation (X).…”