Biodegradation of p-nitrophenol by Rhodococcus sp. 21391 unveils a two-component p-nitrophenol monooxygenase with broad substrate specificity
Abstract Background Bioremediation relying on highly efficient degrading bacteria constitutes a promising and sustainable avenue for controlling and reducing nitrophenol contamination in the environment. A thorough understanding of the bacterial degradation mechanism of nitrophenol is of paramount i...
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BMC
2025-04-01
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| Series: | Microbial Cell Factories |
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| Online Access: | https://doi.org/10.1186/s12934-025-02712-1 |
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| author | Jian Yang Shanshan Lin Wei Li Xianjie Wang Ru Li |
| author_facet | Jian Yang Shanshan Lin Wei Li Xianjie Wang Ru Li |
| author_sort | Jian Yang |
| collection | DOAJ |
| description | Abstract Background Bioremediation relying on highly efficient degrading bacteria constitutes a promising and sustainable avenue for controlling and reducing nitrophenol contamination in the environment. A thorough understanding of the bacterial degradation mechanism of nitrophenol is of paramount importance for supporting the development of efficient microbial remediation technology. Results In this study, a new bacterium, Rhodococcus sp. 21391, endowed with superior p-nitrophenol (PNP) degradation ability was obtained. Genomic and comparative proteomic analyses revealed that it utilizes the 1,2,4-benzenetriol (BT) pathway for PNP degradation. The catalytic properties of the two-component p-nitrophenol monooxygenase RsNcpAB from the strain were investigated in vitro. The enzyme exhibited a broad substrate selectivity, catalyzing the oxidation of various nitrophenols and halogenated phenols, with significant potential for further research and development. Additionally, the crystal structure of the oxidative component of p-nitrophenol monooxygenase, RsNcpA, was determined. Structural analysis and site-directed mutagenesis revealed that residues Arg100 and His293 in the active site play a crucial role in enzyme catalysis, and a catalytic mechanism model was subsequently proposed. Conclusions This study reports a high-performance nitrophenol-degrading bacterium and enzyme, and reveals their mechanisms at the molecular level. These findings increase the understanding of the bacterial degradation of nitrophenol, thereby providing a crucial foundation for the development of efficient bioremediation technologies. Graphical Abstract |
| format | Article |
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| issn | 1475-2859 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbial Cell Factories |
| spelling | doaj-art-faefafa9aa344292bd83ea149f23c45e2025-08-20T02:27:06ZengBMCMicrobial Cell Factories1475-28592025-04-0124111110.1186/s12934-025-02712-1Biodegradation of p-nitrophenol by Rhodococcus sp. 21391 unveils a two-component p-nitrophenol monooxygenase with broad substrate specificityJian Yang0Shanshan Lin1Wei Li2Xianjie Wang3Ru Li4School of Life and Health Technology, Dongguan University of TechnologyCAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of OceanologyCAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of OceanologyCAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of OceanologyCAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of OceanologyAbstract Background Bioremediation relying on highly efficient degrading bacteria constitutes a promising and sustainable avenue for controlling and reducing nitrophenol contamination in the environment. A thorough understanding of the bacterial degradation mechanism of nitrophenol is of paramount importance for supporting the development of efficient microbial remediation technology. Results In this study, a new bacterium, Rhodococcus sp. 21391, endowed with superior p-nitrophenol (PNP) degradation ability was obtained. Genomic and comparative proteomic analyses revealed that it utilizes the 1,2,4-benzenetriol (BT) pathway for PNP degradation. The catalytic properties of the two-component p-nitrophenol monooxygenase RsNcpAB from the strain were investigated in vitro. The enzyme exhibited a broad substrate selectivity, catalyzing the oxidation of various nitrophenols and halogenated phenols, with significant potential for further research and development. Additionally, the crystal structure of the oxidative component of p-nitrophenol monooxygenase, RsNcpA, was determined. Structural analysis and site-directed mutagenesis revealed that residues Arg100 and His293 in the active site play a crucial role in enzyme catalysis, and a catalytic mechanism model was subsequently proposed. Conclusions This study reports a high-performance nitrophenol-degrading bacterium and enzyme, and reveals their mechanisms at the molecular level. These findings increase the understanding of the bacterial degradation of nitrophenol, thereby providing a crucial foundation for the development of efficient bioremediation technologies. Graphical Abstracthttps://doi.org/10.1186/s12934-025-02712-1Nitrophenol biodegradationComparative proteomep-nitrophenol monooxygenaseSubstrate specificity |
| spellingShingle | Jian Yang Shanshan Lin Wei Li Xianjie Wang Ru Li Biodegradation of p-nitrophenol by Rhodococcus sp. 21391 unveils a two-component p-nitrophenol monooxygenase with broad substrate specificity Microbial Cell Factories Nitrophenol biodegradation Comparative proteome p-nitrophenol monooxygenase Substrate specificity |
| title | Biodegradation of p-nitrophenol by Rhodococcus sp. 21391 unveils a two-component p-nitrophenol monooxygenase with broad substrate specificity |
| title_full | Biodegradation of p-nitrophenol by Rhodococcus sp. 21391 unveils a two-component p-nitrophenol monooxygenase with broad substrate specificity |
| title_fullStr | Biodegradation of p-nitrophenol by Rhodococcus sp. 21391 unveils a two-component p-nitrophenol monooxygenase with broad substrate specificity |
| title_full_unstemmed | Biodegradation of p-nitrophenol by Rhodococcus sp. 21391 unveils a two-component p-nitrophenol monooxygenase with broad substrate specificity |
| title_short | Biodegradation of p-nitrophenol by Rhodococcus sp. 21391 unveils a two-component p-nitrophenol monooxygenase with broad substrate specificity |
| title_sort | biodegradation of p nitrophenol by rhodococcus sp 21391 unveils a two component p nitrophenol monooxygenase with broad substrate specificity |
| topic | Nitrophenol biodegradation Comparative proteome p-nitrophenol monooxygenase Substrate specificity |
| url | https://doi.org/10.1186/s12934-025-02712-1 |
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