Fluoranthene degradation and binding mechanism study based on the active-site structure of ring-hydroxylating dioxygenase in Microbacterium paraoxydans JPM1

Abstract

In this study, a gram-positive fluoranthene-degrading bacterial strain was isolated from crude oil in Dagang Oilfield and identified as Microbacterium paraoxydans JPM1 by the analysis of 16S rDNA sequence. After 25 days of incubation, the strain JPM1 could degrade 91.78 % of the initial amount of fluoranthene. Moreover, four metabolites 9-fluorenone-1-carboxylic acid, 9-fluorenone, phthalic acid, and benzoic acid were detected in the culture solution. The gene sequence encoding the aromatic-ring-hydroxylating dioxygenase was amplified in the strain JPM1 by PCR. Based on the translated protein sequence, a homology modeling method was applied to build the crystal structure of dioxygenase. Subsequently, the interaction mechanism between fluoranthene and the active site of dioxygenase was simulated and analyzed by molecular docking. Consequently, a feasible degrading pathway of fluoranthene in the strain JPM1 was proposed based on the metabolites and the interaction analyses. Additionally, the thermodynamic analysis showed that the strain JPM1 had high tolerance for fluoranthene, and the influence of fluoranthene for the bacterial growth activity was negligible under 100 to 400 mg L concentrations. Taken together, this study indicates that the strain JPM1 has high potential for further study in bioremediation of polycyclic aromatic hydrocarbon (PAH)-contaminated sites.

Soil Microbiome Structure and Function in Ecopiles Used to Remediate Petroleum-Contaminated Soil

“…Specifically, Microbacterium is one of the genera present in the metagenome with more aromatic hydrocarbon-degrading genes. The degradation of different PAHs by Microbacterium members has been reported (Salam et al, 2014;Jin et al, 2017). The presence of these genes within the soil microbiome suggests that the indigenous soil microflora have significant potential for degrading the petroleum-derived contaminants.…”

Identification of A Ring-Hydroxylating Dioxygenases Capable of Anthracene and Benz[a]anthracene Oxidization from <b><i>Rhodococcus</i></b> sp. P14

“…The gene baaA is induced by various PAHs, which indicates it might be a potential biomarker in the PAH-contaminated environment. A ring-hydroxylating dioxygenase is important for fluoranthene degradation in Microbacterium paraoxydans JPM1 [Jin et al, 2017]. In addition, a ring-hydroxylating dioxygenase was identified in Mycobacterium sp.…”

Draft Genome Sequence of Microbacterium sp. Strain LEMMJ01, Isolated from Antarctic Ornithogenic Soil

“…It is found in different habitats, having been described in sponges, deep-sea sediments, humans, and polar environments ( 3 – 6 ). Microbacterium species have biotechnological importance, such as in biosurfactant production, bioremediation ( 7 ), and the application of their natural pigments, such as carotenoids, in the food, cosmetics, textiles, and pharmaceutical industries ( 8 , 9 ).…”