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

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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−1 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.

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Acknowledgments

This work is supported in part by grants from the International Joint Key Project from Chinese Ministry of Science and Technology (2010DFB23160), the National Natural Science Foundation of China (41273092, 41430106), and Public Welfare Project of Chinese Ministry of Environmental Protection (201409042, 201509049).

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Authors and Affiliations

  1. School of Energy and Environmental Engineering, University of Science and Technology Beijing, No. 30 Xueyuan Road, Haidian District, Beijing, 100083, China

    Jingnan Jin, Jun Yao, Wenjuan Liu & Jianli Liu

  2. College of Science, Huazhong Agricultural University, Wuhan, 430070, China

    Qingye Zhang

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  1. Jingnan Jin
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  2. Jun Yao
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  3. Wenjuan Liu
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  4. Qingye Zhang
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  5. Jianli Liu
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Correspondence to Jun Yao.

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Responsible editor: Gerald Thouand

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Jin, J., Yao, J., Liu, W. et al. Fluoranthene degradation and binding mechanism study based on the active-site structure of ring-hydroxylating dioxygenase in Microbacterium paraoxydans JPM1. Environ Sci Pollut Res 24, 363–371 (2017). https://doi.org/10.1007/s11356-016-7809-4

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