Integrated proteomic, genomic and metabolomic analyses of Pyrene degradation pathway in Novosphingobium pentaromativorans US6-1

Abstract

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous organic pollutants which have contaminated the environment through improper disposal of materials such as creosote, coal tar, and hydrocarbon fuels. The high molecular weight (HMW) PAHs (four or more fused rings) are of particular environmental concern because of their potential mutagenicity and carcinogenicity in mammalian test organisms and in a number of critical aquatic species. Degradation of Pyrene in Novosphingobium pentaromativorans US6-1 was investigated using a combination of metabolomic, genomic, and proteomic technologies. Total proteins were separated by one- and two-dimensional gel electrophoresis after pyrene exposure, and then identified by liquid chromatography/tandem mass spectrometry (LC-MS/MS). Genome sequence data were obtained and aromatic catabolic genes and TCA cycle genes that are responsible for the complete degradation of PAHs have been particularly focused on. Pyrene metabolites were isolated from the culture medium and analyzed by high-pressure liquid chromatography (HPLC), and nuclear magnetic resonance (NMR) analysis. By integrating genomic annotation information with identified metabolites and proteins, we proposed a pyrene degradation pathway for N. pentaromativorans US6-1. Degradation of pyrene in N. pentaromativorans US6-1 proceeds via multiple metabolic routes initiated by mono-(C-1,2 and C-4,5) and dioxygenation (C-4,5) reactions, further degradation via either o-phthalate pathway or salicylate pathway, both pathways were subsequently entered tricarboxylic acid (TCA) cycle and mineralized to CO2. In monoxygenation reaction, 1-Pyrenylsulfate and 1,6-Dimethoxypyrene were not previously reported as intermediates in the degradation of pyrene by bacterial strains, demonstrate new branches in the pathway. Results in this study establish a basis for the understanding of metabolisms of microbial degradation of high molecular weight PAHs, which is necessary in order to design efficien