Evolution of Bacterial Pathways for the Degradation of Synthetic Nitroaromatic Compounds

University Of California-Davis, Davis CA

Investigators

Abstract

Nitroaromatic compounds are problematic environmental contaminants due to their stability and toxicity. Because many nitroaromatic compounds are synthetic and have been recently introduced into the environment, bacteria have had a relatively short time to develop pathways for their degradation. This project investigates the mechanisms by which bacteria adapt to synthetic chemicals and evolve new degradation pathways. Acidovorax sp. strain JS42, which was isolated from a site that was contaminated with nitrobenzene, utilizes 2-nitrotoluene and nitrobenzene as sole carbon, nitrogen and energy sources. In this strain, a single new enzymatic reaction is required to catalyze the conversion of these synthetic nitroarene compounds to easily degraded natural products (catechols). The key reaction is catalyzed by a Rieske-type dioxygenase that oxidizes nitrobenzene and nitrotoluene substrates at the nitro-substituted carbon, which results in the release of nitrite. Acidovorax sp. JS42 has not only developed the ability to grow on these synthetic nitroarenes, but it has also developed a strategy to regulate expression of the dioxygenase genes in response to nitroarene compounds. The current project focuses on identifying the global affects of exposure to nitroarene substrates on the physiology of Acidovorax sp. strain JS42. The goals of the project are to: 1) investigate to what extent the newly evolved nitroarene degradation pathway is integrated into global control mechanisms including catabolite repression and nitrogen control, 2) identify mechanisms of solvent tolerance and general stress responses induced by nitroarene compounds, and 3) identify the complete range of mutations resulting from long- and short-term selection of Acidovorax sp. JS42 for growth on the alternative nitroarene substrates 3-nitrotoluene and 4-nitrotoluene. As part of the study, additional laboratory evolution experiments will be carried out under specific selective conditions in order to generate strains with expanded nitroarene degradation abilities. To achieve these goals, a combination of comparative genomics, transcriptomics, and detailed analyses of the genes, enzymes and regulatory mechanisms will be used. These studies will increase our understanding of how bacteria evolve new biodegradation pathways in response to environmental pressures, and whether control of pathway gene expression is integrated into global carbon and nitrogen control systems. Broader Impacts The proposed research will contribute to the education and training of high school, undergraduate, and graduate students, providing them with valuable hands-on laboratory experience. The PI hosts high school students through the UC Davis Young Scholars Program, and also trains summer undergraduate students through the Summer Undergraduate Research Program, which brings students (many from underrepresented groups) from small universities for 10 weeks of summer research. The PI typically has at least two UC Davis undergraduate researchers in the laboratory throughout the year. The PI will also continue to contribute to an undergraduate course called "Introduction to Research", which exposes undergraduates to current ongoing research in the Department of Microbiology. In addition, freely available user-friendly web-based tools for comparative genomics will be developed in conjunction with this project. These analysis tools will be extremely useful to a wide range of research scientists studying genomes from all three domains of life.