Date of Award

8-28-2013

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Applied Science

First Advisor

Carl Cerniglia

Second Advisor

John Bush

Abstract

Polycyclic aromatic hydrocarbons (PAHs) are a group of toxic compounds, which consist of two or more fused benzene rings. Due to their ecotoxic, mutagenic, and in some cases carcinogenic properties, sixteen PAHs are on the U.S. Environmental Protection Agency and European Union lists of priority pollutants to be monitored in the environment. Of particular interest are high molecular weight (HMW) PAHs with four or more benzene rings, due to their human carcinogenicity and persistent in the environment. Microbial metabolic activity represents the primary process of biodegradation and bioremediation of PAHs in the environment and has been evaluated as a promising tool for the ecological recovery of PAH contaminated sites. Mycobacterium vanbaalenii PYR-1, which was isolated in 1986 from oil-contaminated estuarine sediment exposed to petrogenic chemicals in the watershed of Redfish Bay, Texas, is the first bacterium reported to degrade the high-molecular-weight (HMW) PAHs, with four or more fused benzene rings. Initial metabolic studies have proved that M. vanbaalenii PYR-1 is able to degrade or transform many PAHs, including some of the HMW PAHs, such as pyrene, fluoranthene, 1-nitropyrene, benzo[a]pyrene, benz[a]anthracene, and 7,12-dimethylbenz[a]anthracene. Following the initial metabolism studies on the pathways of PAH degradation, research over the last 10 years has continued in the direction of characterizing the mechanism of HMW PAH biodegradation in strain PYR-1. The completion of the 6.4-Mb genome sequence of M. vanbaalenii PYR-1 has provided current insights into molecular background of HMW PAH degradation. However, the primary mechanisms responsible for the tremendous variation in the efficacy of PAH biodegradation remain elusive. This dissertation provides current laboratory studies and Bioinformatics & Computational Biology analyses to reconstruct and investigate a metabolic network (MN) from Mycobacterium vanbaalenii PYR-1 for polycyclic aromatic hydrocarbons (PAHs), from the integrated perspective of structure, behavior and evolution. The structure of PAH-MN, with 183 metabolic compounds and 224 chemical reactions, has a typical scale-free nature. Behavior and evolution of the PAH-MN reveals a hierarchical modularity with funnel effects in structure/function and intimate association with evolutionary modules of the functional modules, which are the ring-cleavage process (RCP), side chain process (SCP) and central aromatic process (CAP). The enhanced functional annotation of ring-hydroxylating oxygenase (RHO) systems into the RCP modules provided practical starting points for interpreting and predicting the dynamics of complex metabolic behavior in the degradation of HMW PAH mixtures at the level of MN. Pan-genomic analysis provides the evolutionary insight into the `PAH-Degrading' phenotype from its origin to the present, by going into the structure, behavior, and evolution, pouring over blueprint for the PAH-MN. The bridge between the genome and a PAH-degrading phenotype at the genus level provides high confidence in the evolutionary history. Thanks to these state-of-the-art experiments, our understanding of a system-wide perspective on the biodegradation of PAHs has advanced the evaluation of the metabolic potential and practical applications of the prototype model organism M. vanbaalenii PYR-1 to clean up PAH contamination in aquatic and terrestrial ecosystems.

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