Systems Biology Approaches Used in the Biodegradation of Environmental Priority Pollutant, Polycyclic Aromatic Hydrocarbons
Carl E. Cerniglia, Seong-Jae Kim, Ohgew Kweon
Division of Microbiology, National Center for Toxicological Research/US Food and Drug Administration, Jefferson, AR, USA
Polycyclic aromatic hydrocarbons (PAHs) are one of the ubiquitous priority pollutants, which are known to pose environmental and human health concerns. Systems biology approaches using a PAH-degrading model microorganism, Mycobacterium vanbaalenii PYR-1, have provided a comprehensive genome-level understanding of the structure, behavior, and evolution of the microbial biodegradation mechanism of PAHs. Genome sequencing has provided genome-level genetic background for understanding metabolic capability and biodegradation versatility of the bacterium. Functional genomics based on genomic data, such as metabolomics and proteomics, has also provided system-wide insights into the structure and functional behavior of PAH metabolism at the level of network. In silico structural studies on the catabolic enzymes and comparative functional pan-genomic analysis have provided pleiotropic and epistatic insights into the functional complexity of PAH-degrading enzymes and the relationship between genomic dynamics and phenotypic evolution in the PAH metabolism in the genus Mycobacterium. Systemic analysis of different types but interdependent ‘omics' data is essential to quantify, predict, and enhance metabolic abilities within particular organisms or microbial consortia, which have implications for determining the fate of current and future environmental pollutants.