title: 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-1concentrations. Taken together, this study indicates that the strain JPM1 has high potential for further study in bioremediation of polycyclic aromatic hydrocarbon (PAH)-contaminated sites.
authors.affiliation: School of Energy and Environmental Engineering, University of Science and Technology Beijing, No. 30 Xueyuan Road, Haidian District, Beijing, 100083, China.
authors.forename: Jingnan
authors.initials: J
authors.lastname: Jin
authors.affiliation: School of Energy and Environmental Engineering, University of Science and Technology Beijing, No. 30 Xueyuan Road, Haidian District, Beijing, 100083, China. yaojun@ustb.edu.cn.
authors.forename: Jun
authors.initials: J
authors.lastname: Yao
authors.affiliation: School of Energy and Environmental Engineering, University of Science and Technology Beijing, No. 30 Xueyuan Road, Haidian District, Beijing, 100083, China.
authors.forename: Wenjuan
authors.initials: W
authors.lastname: Liu
authors.affiliation: College of Science, Huazhong Agricultural University, Wuhan, 430070, China.
authors.forename: Qingye
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: School of Energy and Environmental Engineering, University of Science and Technology Beijing, No. 30 Xueyuan Road, Haidian District, Beijing, 100083, China.
authors.forename: Jianli
authors.initials: J
authors.lastname: Liu
mesh_terms: D039903:Actinobacteria / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001673:Biodegradation, Environmental; D020134:Catalytic Domain; D004269:DNA, Bacterial / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D049308:Dioxygenases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D005449:Fluorenes / Q000378:metabolism*; D006900:Hydroxylation; D062105:Molecular Docking Simulation; D010578:Petroleum / Q000382:microbiology; D011485:Protein Binding
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D005449:Fluorenes; D010578:Petroleum; C007738:fluoranthene; D049308:Dioxygenases
keywords: 9-fluorenone-1-carboxylic acid; Biodegradation; Fluoranthene; Microbacterium; Microcalorimetry; Molecular docking