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Association of dnt genes of Burkholderia sp. DNT with the substrate-blind regulator DntR draws the evolutionary itinerary of 2,4-dinitrotoluene biodegradation.
Mol Microbiol. 2011 Oct; 82(2):287-99
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07 Oct 2011
New Finding
DOI: 10.3410/f.13335001.14701117
Data presented in this paper support the hypothesis that evolution of the capability to utilize new substrates in bacteria involves innovation of metabolic enzymes, followed by subsequent optimization of gene regulation.
DNT (2,4-dinitrotoluene) is a toxic nitrogen-containing aromatic compound. Non some...Continue reading
DNT (2,4-dinitrotoluene) is a toxic nitrogen-containing aromatic compound. Non some...Continue reading
Data presented in this paper support the hypothesis that evolution of the capability to utilize new substrates in bacteria involves innovation of metabolic enzymes, followed by subsequent optimization of gene regulation.
DNT (2,4-dinitrotoluene) is a toxic nitrogen-containing aromatic compound. Nonetheless, some bacteria have evolved the ability to utilize DNT as the sole source of carbon and energy. Genes encoding enzymes for DNT utilization (dnt) in Burkholderia are similar to those for naphthalene degradation (nah), including a LasR-type regulator preceding the catabolic genes (i.e. DntR for dnt genes and NahR for nah genes). NahR is known to regulate the expression of nah genes via interacting with salicylate, an intermediate of the naphthalene degradation pathway {1, 2}.
To test the predicted regulatory role of DntR in dnt genes expression, the authors performed a serious of carefully designed experiments in the genetic background of Pseudomonas putida KT2440. Their results show that DntR activates dnt gene expression in a salicylate-dependent manner. Surprisingly, DntR-mediated dnt expression is not induced by its own substrate (DNT) or by intermediates of the DNT pathway. The experimental data, supported by in silico analysis, suggested that the DNT utilization pathway has evolved from a pre-existing pathway for naphthalene degradation, most likely via gene duplication.
Together, studies on DNT utilization implicate an evolutionary trajectory of new catabolic pathways for artificial compounds that are released into the environments: degradative enzymes evolve first, followed by the emergence of substrate-specific regulation.
DNT (2,4-dinitrotoluene) is a toxic nitrogen-containing aromatic compound. Nonetheless, some bacteria have evolved the ability to utilize DNT as the sole source of carbon and energy. Genes encoding enzymes for DNT utilization (dnt) in Burkholderia are similar to those for naphthalene degradation (nah), including a LasR-type regulator preceding the catabolic genes (i.e. DntR for dnt genes and NahR for nah genes). NahR is known to regulate the expression of nah genes via interacting with salicylate, an intermediate of the naphthalene degradation pathway {1, 2}.
To test the predicted regulatory role of DntR in dnt genes expression, the authors performed a serious of carefully designed experiments in the genetic background of Pseudomonas putida KT2440. Their results show that DntR activates dnt gene expression in a salicylate-dependent manner. Surprisingly, DntR-mediated dnt expression is not induced by its own substrate (DNT) or by intermediates of the DNT pathway. The experimental data, supported by in silico analysis, suggested that the DNT utilization pathway has evolved from a pre-existing pathway for naphthalene degradation, most likely via gene duplication.
Together, studies on DNT utilization implicate an evolutionary trajectory of new catabolic pathways for artificial compounds that are released into the environments: degradative enzymes evolve first, followed by the emergence of substrate-specific regulation.
References
Disclosures
None declared
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Rainey P and Zhang X: F1000Prime Recommendation of [de Las Heras A et al., Mol Microbiol 2011, 82(2):287-99]. In F1000Prime, 07 Oct 2011; DOI: 10.3410/f.13335001.14701117. F1000Prime.com/13335001#eval14701117
F1000Prime Recommendations, Dissents and Comments for [de Las Heras A et al., Mol Microbiol 2011, 82(2):287-99]. In F1000Prime, 22 May 2013; F1000Prime.com/13335001
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The 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.
© 2011 Blackwell Publishing Ltd.
DOI: 10.1111/j.1365-2958.2011.07825.x
PMID: 21923773
