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Jin J, Shi Y, Zhang B, Wan D, Zhang Q. An integrated method for studying the biodegradation of benzo[a]pyrene by Citrobacter sp. HJS-1 and interaction mechanism based on the structural model of the initial dioxygenase. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:85558-85568. [PMID: 37389752 DOI: 10.1007/s11356-023-28505-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/26/2023] [Indexed: 07/01/2023]
Abstract
A bacterial strain Citrobacter sp. HJS-1 was discovered from the sludge in a drainage canal of a coal mine. Firstly, its biodegradation capacity for benzo[a]pyrene (BaP) was detected under different concentrations. The results proved that the strain possessed excellent biodegradation capacity for BaP with high-efficiency degradation rates ranging from 78.9 to 86.8%. The highest degradation rate was observed in the low-concentration sample, and the high-concentration BaP had a slight influence on the biodegradation capacity due to the potential toxicity of BaP and its oxygen-containing derivatives. Meanwhile, the degradation test for the other five aromatic hydrocarbons (2- to 4-ring) proved that the strain had a comprehensive degradation potential. To clarify the biodegradation mechanism of BaP, a dioxygenase structure was constructed by homology modeling. Then, the interactions between dioxygenase and BaP were researched by molecular simulation. Combined with the identification of the vital BaP-cis-7,8-dihydrodiol intermediate and the interaction analysis, the initial oxidation mode and the binding site of BaP were revealed in the dioxygenase. Taken together, this study has offered a way to understand the biodegradation process of BaP and its interaction mechanism based on experimental and theoretical analysis.
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Affiliation(s)
- Jingnan Jin
- School of Environmental Engineering, Henan University of Technology, Zhengzhou, No. 100 Lianhua Street, High-tech Industrial Development District, Zhengzhou, 450001, Henan, China.
| | - Yahui Shi
- School of Environmental Engineering, Henan University of Technology, Zhengzhou, No. 100 Lianhua Street, High-tech Industrial Development District, Zhengzhou, 450001, Henan, China
| | - Baozhong Zhang
- School of Environmental Engineering, Henan University of Technology, Zhengzhou, No. 100 Lianhua Street, High-tech Industrial Development District, Zhengzhou, 450001, Henan, China
| | - Dongjin Wan
- School of Environmental Engineering, Henan University of Technology, Zhengzhou, No. 100 Lianhua Street, High-tech Industrial Development District, Zhengzhou, 450001, Henan, China
| | - Qingye Zhang
- College of informatics, Huazhong Agricultural University, Wuhan, 430070, China
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Jin J, Shi Y, Zhang B, Wan D, Zhang Q, Li Y. Biotransformation of benzo[ a]pyrene by Pannonibacter sp. JPA3 and the degradation mechanism through the initially oxidized benzo[ a]pyrene-4,5-dihydrodiol to downstream metabolites. RSC Adv 2023; 13:18878-18887. [PMID: 37350855 PMCID: PMC10282733 DOI: 10.1039/d3ra01453c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 06/07/2023] [Indexed: 06/24/2023] Open
Abstract
Owing to its adverse effects on the environment and human health, benzo[a]pyrene (BaP) has attracted considerable attention and has been used as a model compound in ecotoxicology. In this study, Pannonibacter sp. JPA3 as a BaP-degrading strain was isolated from the production water of an oil well. The strain could remove 80% of BaP at an initial concentration of 100 mg L-1 after 35 d culture. The BaP-4,5-dihydrodiol, BaP-4,5-epoxide, 5-hydroxychrysene, and 2-hydroxy-1-naphthoic acid metabolites were identified in the biodegradation process. Simultaneously, the gene sequence coding for dioxygenase in the strain was amplified and a dioxygenase model was built by homology modeling. Combined with the identification of the metabolites, the interaction mechanism of BaP with dioxygenase was investigated using molecular docking. It was assumed that BaP was initially oxidized at the C4-C5 positions in the active cavity of dioxygenase. Moreover, a hypothesis for the progressive degradation mechanism of BaP by this strain was proposed via the identification of the downstream metabolites. In conclusion, our study provided an efficient BaP degrader and a comprehensive reference for the study of the degradation mechanism in terms of the degrading metabolites and theoretical research at the molecular level.
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Affiliation(s)
- Jingnan Jin
- School of Environmental Engineering, Henan University of Technology No. 100 Lianhua Street, High-Tech Industrial Development District Zhengzhou Henan 450001 China +86-371-67756982 +86-371-67756982
| | - Yahui Shi
- School of Environmental Engineering, Henan University of Technology No. 100 Lianhua Street, High-Tech Industrial Development District Zhengzhou Henan 450001 China +86-371-67756982 +86-371-67756982
| | - Baozhong Zhang
- School of Environmental Engineering, Henan University of Technology No. 100 Lianhua Street, High-Tech Industrial Development District Zhengzhou Henan 450001 China +86-371-67756982 +86-371-67756982
| | - Dongjin Wan
- School of Environmental Engineering, Henan University of Technology No. 100 Lianhua Street, High-Tech Industrial Development District Zhengzhou Henan 450001 China +86-371-67756982 +86-371-67756982
| | - Qingye Zhang
- College of Informatics, Huazhong Agricultural University Wuhan 430070 China
| | - Ying Li
- School of Environmental Engineering, Henan University of Technology No. 100 Lianhua Street, High-Tech Industrial Development District Zhengzhou Henan 450001 China +86-371-67756982 +86-371-67756982
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Xue SW, Tian YX, Pan JC, Liu YN, Ma YL. Binding interaction of a ring-hydroxylating dioxygenase with fluoranthene in Pseudomonas aeruginosa DN1. Sci Rep 2021; 11:21317. [PMID: 34716364 PMCID: PMC8556375 DOI: 10.1038/s41598-021-00783-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/18/2021] [Indexed: 11/11/2022] Open
Abstract
Pseudomonas aeruginosa DN1 can efficiently utilize fluoranthene as its sole carbon source, and the initial reaction in the biodegradation process is catalyzed by a ring-hydroxylating dioxygenase (RHD). To clarify the binding interaction of RHD with fluoranthene in the strain DN1, the genes encoding alpha subunit (RS30940) and beta subunit (RS05115) of RHD were functionally characterized through multi-technique combination such as gene knockout and homology modeling as well as molecular docking analysis. The results showed that the mutants lacking the characteristic alpha subunit and/or beta subunit failed to degrade fluoranthene effectively. Based on the translated protein sequence and Ramachandran plot, 96.5% of the primary amino-acid sequences of the alpha subunit in the modeled structure of the RHD were in the permitted region, 2.3% in the allowed region, but 1.2% in the disallowed area. The catalytic mechanism mediated by key residues was proposed by the simulations of molecular docking, wherein the active site of alpha subunit constituted a triangle structure of the mononuclear iron atom and the two oxygen atoms coupled with the predicted catalytic ternary of His217-His222-Asp372 for the dihydroxylation reaction with fluoranthene. Those amino acid residues adjacent to fluoranthene were nonpolar groups, and the C7-C8 positions on the fluoranthene ring were estimated to be the best oxidation sites. The distance of C7-O and C8-O was 3.77 Å and 3.04 Å respectively, and both of them were parallel. The results of synchronous fluorescence and site-directed mutagenesis confirmed the roles of the predicted residues during catalysis. This binding interaction could enhance our understanding of the catalytic mechanism of RHDs and provide a solid foundation for further enzymatic modification.
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Affiliation(s)
- Shu-Wen Xue
- grid.412262.10000 0004 1761 5538Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi’an, 710069 Shaanxi China ,grid.412262.10000 0004 1761 5538College of Life Science, Northwest University, 229 Taibai North Rd, Xi’an, 710069 Shaanxi China
| | - Yue-Xin Tian
- grid.412262.10000 0004 1761 5538Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi’an, 710069 Shaanxi China ,grid.412262.10000 0004 1761 5538College of Life Science, Northwest University, 229 Taibai North Rd, Xi’an, 710069 Shaanxi China
| | - Jin-Cheng Pan
- grid.412262.10000 0004 1761 5538Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi’an, 710069 Shaanxi China ,grid.412262.10000 0004 1761 5538College of Life Science, Northwest University, 229 Taibai North Rd, Xi’an, 710069 Shaanxi China
| | - Ya-Ni Liu
- grid.412262.10000 0004 1761 5538Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi’an, 710069 Shaanxi China ,grid.412262.10000 0004 1761 5538College of Life Science, Northwest University, 229 Taibai North Rd, Xi’an, 710069 Shaanxi China
| | - Yan-Ling Ma
- grid.412262.10000 0004 1761 5538Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi’an, 710069 Shaanxi China ,grid.412262.10000 0004 1761 5538College of Life Science, Northwest University, 229 Taibai North Rd, Xi’an, 710069 Shaanxi China
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Zhao X, Miao R, Guo M, Zhou Y. Effects of Fire Phoenix (a genotype mixture of Fesctuca arundinecea L.) and Mycobacterium sp. on the degradation of PAHs and bacterial community in soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:25692-25700. [PMID: 33462693 DOI: 10.1007/s11356-021-12432-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 01/07/2021] [Indexed: 05/25/2023]
Abstract
Phytomicrobial remediation technology of PAH-contaminated soils has drawn great attention due to its low-cost, eco-friendly, and effective characteristics, but the mechanism underlying the removal of PAHs by rhizosphere in wastewater-irrigated soil is so far not clear. To evaluate the dissipation of PAHs and the shifts of bacterial community structure under plant-microorganism symbiotic system in an agricultural soil, a rhizo-box experiment with Fire Phoenix (a genotype mixture of Fesctuca arundinecea L.) or/and inoculated Mycobacterium sp. was conducted for 60 days. The changes of bacterial community structure and the contents of PAHs were analyzed by denaturing gradient gel electrophoresis (DGGE) and high-performance liquid chromatography (HPLC), respectively. The results showed that the removal rate of PAHs in phytomicrobial combined treatment was 53.7% after 60 days. The PAH-degraders were dominated by Microbacterium sp., Sphingomonas sp., Mycobacterium sp., and Flavobacterium sp. The plant of Fire Phoenix induced the appearance of Pseudomonas sp. and TM7 phylum sp. oral clone. The highest of bacterial diversity index was observed in unrhizosphere soils (MR-), rather than that in rhizosphere soils (MR+). In combination, phytomicrobial combined treatment of Fire Phoenix and Mycobacterium strain enhanced the removal rate of PAHs and changed the structure of bacterial community and bacterial diversity. Bacterial community has great effect on PAH degradation in PAH-contaminated soil from the wastewater-irrigated site. Our study can provide support information for PAH degradation enhancement by the synergetic effect of Fire Phoenix and Mycobacterium sp.
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Affiliation(s)
- Xuyang Zhao
- Institute of Environmental and Analytical Sciences, Henan Joint International Research Laboratory of Environmental Pollution Control Materials, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004, Henan, China
| | - Renhui Miao
- International Joint Research Laboratory for Global Change Ecology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 475004, People's Republic of China
| | - Meixia Guo
- Institute of Environmental and Analytical Sciences, Henan Joint International Research Laboratory of Environmental Pollution Control Materials, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004, Henan, China.
| | - Yanmei Zhou
- Institute of Environmental and Analytical Sciences, Henan Joint International Research Laboratory of Environmental Pollution Control Materials, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004, Henan, China
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Duncan TR, Werner-Washburne M, Northup DE. DIVERSITY OF SIDEROPHORE-PRODUCING BACTERIAL CULTURES FROM CARLSBAD CAVERNS NATIONAL PARK (CCNP) CAVES, CARLSBAD, NEW MEXICO. JOURNAL OF CAVE AND KARST STUDIES : THE NATIONAL SPELEOLOGICAL SOCIETY BULLETIN 2021; 83:29-43. [PMID: 34556971 PMCID: PMC8455092 DOI: 10.4311/2019es0118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Siderophores are microbially-produced ferric iron chelators. They are essential for microbial survival, but their presence and function for cave microorganisms have not been extensively studied. Cave environments are nutrient-limited and previous evidence suggests siderophore usage in carbonate caves. We hypothesize that siderophores are likely used as a mechanism in caves to obtain critical nutrients such as iron. Cave bacteria were collected from Long-term parent cultures (LT PC) or Short-term parent cultures (ST PC) inoculated with ferromanganese deposits (FMD) and carbonate secondary minerals from Lechuguilla and Spider caves in Carlsbad Caverns National Park (CCNP), NM. LT PC were incubated for 10-11 years to identify potential chemolithoheterotrophic cultures able to survive in nutrient-limited conditions. ST PC were incubated for 1-3 days to identify a broader diversity of cave isolates. A total of 170 LT and ST cultures,18 pure and 152 mixed, were collected and used to classify siderophore production and type and to identify siderophore producers. Siderophore production was slow to develop (>10 days) in LT cultures with a greater number of weak siderophore producers in comparison to the ST cultures that produced siderophores in <10 days, with a majority of strong siderophore producers. Overall, 64% of the total cultures were siderophore producers, which the majority preferred hydroxamate siderophores. Siderophore producers were classified into Proteobacteria (Alpha-, Beta-, or Gamma-), Actinobacteria, Bacteroidetes, and Firmicutes phyla using 16S rRNA gene sequencing. Our study supports our hypothesis that cave bacteria have the capability to produce siderophores in the subsurface to obtain critical ferric iron.
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S, Singh SK, Haritash AK. Evolutionary Relationship of Polycyclic Aromatic Hydrocarbons Degrading Bacteria with Strains Isolated from Petroleum Contaminated Soil Based on 16S rRNA Diversity. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1825003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Sakshi
- Department of Environmental Engineering, Delhi Technological University, Shahbad Daulatpur, Delhi, India
| | - S. K. Singh
- Department of Environmental Engineering, Delhi Technological University, Shahbad Daulatpur, Delhi, India
| | - A. K. Haritash
- Department of Environmental Engineering, Delhi Technological University, Shahbad Daulatpur, Delhi, India
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7
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Wang W, Wang L, Shao Z. Polycyclic Aromatic Hydrocarbon (PAH) Degradation Pathways of the Obligate Marine PAH Degrader Cycloclasticus sp. Strain P1. Appl Environ Microbiol 2018; 84:AEM.01261-18. [PMID: 30171002 PMCID: PMC6193391 DOI: 10.1128/aem.01261-18 10.1016/j.biotechadv.2015.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/19/2018] [Indexed: 06/12/2023] Open
Abstract
Bacteria play an important role in the removal of polycyclic aromatic hydrocarbons (PAHs) from polluted environments. In marine environments, Cycloclasticus is one of the most prevalent PAH-degrading bacterial genera. However, little is known regarding the degradation mechanisms for multiple PAHs by CycloclasticusCycloclasticus sp. strain P1 was isolated from deep-sea sediments and is known to degrade naphthalene, phenanthrene, pyrene, and other aromatic hydrocarbons. Here, six ring-hydroxylating dioxygenases (RHDs) were identified in the complete genome of Cycloclasticus sp. P1 and were confirmed to be involved in PAH degradation by enzymatic assays. Further, five gene clusters in its genome were identified to be responsible for PAH degradation. Degradation pathways for naphthalene, phenanthrene, and pyrene were elucidated in Cycloclasticus sp. P1 based on genomic and transcriptomic analysis and characterization of an interconnected metabolic network. The metabolic pathway overlaps in many steps in the degradation of pyrene, phenanthrene, and naphthalene, which were validated by the detection of metabolic intermediates in cultures. This study describes a pyrene degradation pathway for Cycloclasticus. Moreover, the study represents the integration of a PAH metabolic network that comprises pyrene, phenanthrene, and naphthalene degradation pathways. Taken together, these results provide a comprehensive investigation of PAH metabolism in CycloclasticusIMPORTANCE PAHs are ubiquitous in the environment and are carcinogenic compounds and tend to accumulate in food chains due to their low bioavailability and poor biodegradability. Cycloclasticus is an obligate marine PAH degrader and is widespread in marine environments, while the PAH degradation pathways remain unclear. In this report, the degradation pathways for naphthalene, phenanthrene, and pyrene were revealed, and an integrated PAH metabolic network covering pyrene, phenanthrene, and naphthalene was constructed in Cycloclasticus This overlapping network provides streamlined processing of PAHs to intermediates and ultimately to complete mineralization. Furthermore, these results provide an additional context for the prevalence of Cycloclasticus in oil-polluted marine environments and pelagic settings. In conclusion, these analyses provide a useful framework for understanding the cellular processes involved in PAH metabolism in an ecologically important marine bacterium.
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Affiliation(s)
- Wanpeng Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Xiamen Key Laboratory of Marine Genetic Resources, State Key Laboratory Breeding Base, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Lin Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Xiamen Key Laboratory of Marine Genetic Resources, State Key Laboratory Breeding Base, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Xiamen Key Laboratory of Marine Genetic Resources, State Key Laboratory Breeding Base, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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8
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Polycyclic Aromatic Hydrocarbon (PAH) Degradation Pathways of the Obligate Marine PAH Degrader Cycloclasticus sp. Strain P1. Appl Environ Microbiol 2018; 84:AEM.01261-18. [PMID: 30171002 DOI: 10.1128/aem.01261-18] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/19/2018] [Indexed: 12/13/2022] Open
Abstract
Bacteria play an important role in the removal of polycyclic aromatic hydrocarbons (PAHs) from polluted environments. In marine environments, Cycloclasticus is one of the most prevalent PAH-degrading bacterial genera. However, little is known regarding the degradation mechanisms for multiple PAHs by Cycloclasticus Cycloclasticus sp. strain P1 was isolated from deep-sea sediments and is known to degrade naphthalene, phenanthrene, pyrene, and other aromatic hydrocarbons. Here, six ring-hydroxylating dioxygenases (RHDs) were identified in the complete genome of Cycloclasticus sp. P1 and were confirmed to be involved in PAH degradation by enzymatic assays. Further, five gene clusters in its genome were identified to be responsible for PAH degradation. Degradation pathways for naphthalene, phenanthrene, and pyrene were elucidated in Cycloclasticus sp. P1 based on genomic and transcriptomic analysis and characterization of an interconnected metabolic network. The metabolic pathway overlaps in many steps in the degradation of pyrene, phenanthrene, and naphthalene, which were validated by the detection of metabolic intermediates in cultures. This study describes a pyrene degradation pathway for Cycloclasticus. Moreover, the study represents the integration of a PAH metabolic network that comprises pyrene, phenanthrene, and naphthalene degradation pathways. Taken together, these results provide a comprehensive investigation of PAH metabolism in Cycloclasticus IMPORTANCE PAHs are ubiquitous in the environment and are carcinogenic compounds and tend to accumulate in food chains due to their low bioavailability and poor biodegradability. Cycloclasticus is an obligate marine PAH degrader and is widespread in marine environments, while the PAH degradation pathways remain unclear. In this report, the degradation pathways for naphthalene, phenanthrene, and pyrene were revealed, and an integrated PAH metabolic network covering pyrene, phenanthrene, and naphthalene was constructed in Cycloclasticus This overlapping network provides streamlined processing of PAHs to intermediates and ultimately to complete mineralization. Furthermore, these results provide an additional context for the prevalence of Cycloclasticus in oil-polluted marine environments and pelagic settings. In conclusion, these analyses provide a useful framework for understanding the cellular processes involved in PAH metabolism in an ecologically important marine bacterium.
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Liu Z, Liu Y, Zeng G, Shao B, Chen M, Li Z, Jiang Y, Liu Y, Zhang Y, Zhong H. Application of molecular docking for the degradation of organic pollutants in the environmental remediation: A review. CHEMOSPHERE 2018; 203:139-150. [PMID: 29614407 DOI: 10.1016/j.chemosphere.2018.03.179] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 03/24/2018] [Accepted: 03/26/2018] [Indexed: 05/02/2023]
Affiliation(s)
- Zhifeng Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
| | - Yujie Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
| | - Binbin Shao
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Ming Chen
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Zhigang Li
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Yilin Jiang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Yang Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Yu Zhang
- Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an, Shaanxi 712046, PR China
| | - Hua Zhong
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China; State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, Hubei 430072, PR China
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10
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Fu B, Xu T, Cui Z, Ng HL, Wang K, Li J, Li QX. Mutation of Phenylalanine-223 to Leucine Enhances Transformation of Benzo[a]pyrene by Ring-Hydroxylating Dioxygenase of Sphingobium sp. FB3 by increasing Accessibility of the Catalytic Site. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:1206-1213. [PMID: 29336152 DOI: 10.1021/acs.jafc.7b05018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Burning of agricultural biomass generates polycyclic aromatic hydrocarbons (PAHs) including the carcinogen benzo[a]pyrene, of which the catabolism is primarily initiated by a ring-hydroxylating dioxygenase (RHD). This study explores catalytic site accessibility and its role in preferential catabolism of some PAHs over others. The genes flnA1f, flnA2f, flnA3, and flnA4, encoding the oxygenase α and β subunits, ferredoxin, and ferredoxin reductase, respectively, of the RHD enzyme complex (FlnA) were cloned from Sphingobium sp. FB3 and coexpressed in E. coli BL21. The FlnA effectively transformed fluoranthene but not benzo[a]pyrene. Substitution of the bulky phenylalanine-223 by leucine reduces the steric constraint in the substrate entrance to make the catalytic site of FlnA more accessible to large substrates, as visualized by 3D modeling, and allows the FlnA mutant to efficiently transform benzo[a]pyrene. Accessibility of the catalytic site to PAHs is a mechanism of RHD substrate specificity. The results shed light on why some PAHs are more recalcitrant than others.
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Affiliation(s)
- Bo Fu
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University , 2 Yuanmingyuan West Road, Beijing 100193, China
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa , Honolulu, Hawaii 96822, United States
| | - Ting Xu
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University , 2 Yuanmingyuan West Road, Beijing 100193, China
| | - Zhongli Cui
- Department of Microbiology, College of Life Sciences, Key Laboratory for Microbiological Engineering of Agricultural Environment of Ministry of Agriculture, Nanjing Agricultural University , Nanjing, Jiangsu 201195, China
| | - Ho Leung Ng
- Department of Biochemistry & Molecular Biophysics, Kansas State University , Manhattan, Kansas 66506, United States
| | - Kai Wang
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University , 2 Yuanmingyuan West Road, Beijing 100193, China
| | - Ji Li
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University , 2 Yuanmingyuan West Road, Beijing 100193, China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa , Honolulu, Hawaii 96822, United States
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Draft Genome Sequence of Microbacterium sp. Strain LEMMJ01, Isolated from Antarctic Ornithogenic Soil. GENOME ANNOUNCEMENTS 2017; 5:5/29/e00672-17. [PMID: 28729273 PMCID: PMC5522940 DOI: 10.1128/genomea.00672-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the 3,637,012-bp draft genome sequence of Microbacterium sp. strain LEMMJ01, isolated from ornithogenic soil from King George Island, Antarctica. The total number of genes presented in the draft genome sequence was 3,553, and the total number of coding sequences was 3,497. In addition, genes related to the production of terpene and carotenoids were revealed.
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