Evolution of Bacterial Pathways for the Degradation of Synthetic Nitroaromatic Compounds

由于其稳定性和毒性，硝基芳香族化合物是一种有问题的环境污染物。由于许多硝基芳香族化合物是人工合成的，最近被引入环境中，细菌有相对较短的时间来开发它们的降解途径。该项目研究细菌适应合成化学品并进化出新的降解途径的机制。嗜酸菌Acidovorax sp.JS42菌株是从一个被硝基苯污染的地方分离出来的，它利用邻硝基甲苯和硝基苯作为唯一的碳、氮和能源。在该菌株中，需要一个新的酶反应来催化这些合成的硝基芳烃化合物转化为容易降解的天然产物(儿茶酚)。关键反应是由Rieske型双加氧酶催化的，该酶在硝基取代碳上氧化硝基苯和硝基甲苯底物，从而导致亚硝酸盐的释放。嗜酸菌Acidovorax sp.JS42不仅开发了在这些合成的硝基芳烃上生长的能力，而且还开发了一种策略来调节双加氧酶基因的表达，以响应硝基芳烃化合物。目前的项目重点是确定暴露在硝基芳烃底物中对Acidovorax sp.生理的全球影响。菌株JS42。该项目的目标是：1)研究新进化的硝基芳烃降解途径在多大程度上整合到全球控制机制中，包括分解代谢抑制和氮素控制；2)确定硝基芳烃化合物诱导的溶剂耐受性和一般胁迫反应的机制；3)确定长期和短期选择Acidovorax sp.所导致的完整的突变范围。JS42用于在可替代的3-硝基甲苯和4-硝基甲苯底物上生长。作为研究的一部分，将在特定的选择条件下进行额外的实验室进化实验，以产生具有扩展的硝基芳烃降解能力的菌株。为了实现这些目标，将结合使用比较基因组学、转录组学和对基因、酶和调节机制的详细分析。这些研究将增加我们对细菌如何进化新的生物降解途径以响应环境压力，以及途径基因表达的控制是否整合到全球碳和氮控制系统中的理解。广泛影响拟议的研究将有助于高中、本科生和研究生的教育和培训，为他们提供宝贵的动手实验室经验。PI通过加州大学戴维斯分校青年学者计划接待高中生，并通过夏季本科生研究计划培训夏季本科生，该计划吸引来自小型大学的学生(许多来自代表性不足的群体)进行为期10周的夏季研究。PI通常全年都有至少两名加州大学戴维斯分校的本科生研究人员在实验室。PI还将继续为一门名为“研究导论”的本科课程做出贡献，这门课程让本科生接触到微生物学系目前正在进行的研究。此外，还将结合这一项目开发免费提供的、方便用户使用的网上比较基因组学工具。这些分析工具将对研究生命所有三个领域的基因组的广泛研究科学家非常有用。

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 ImpactsThe 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.