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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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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: 50] [Impact Index Per Article: 8.3] [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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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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Zeng J, Zhu Q, Wu Y, Chen H, Lin X. Characterization of a polycyclic aromatic ring-hydroxylation dioxygenase from Mycobacterium sp. NJS-P. CHEMOSPHERE 2017; 185:67-74. [PMID: 28686888 DOI: 10.1016/j.chemosphere.2017.07.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 06/01/2017] [Accepted: 07/01/2017] [Indexed: 06/07/2023]
Abstract
Ring-hydroxylating dioxygenases (RHDs) play a critical role in the biodegradation of polycyclic aromatic hydrocarbons (PAHs). In this study, genes pdoAB encoding a dioxygenase capable of oxidizing various PAHs with up to five-ring benzo[a]pyrene were cloned from Mycobacterium sp. NJS-P. The α-subunit of the PdoAB showed 99% and 93% identity to that from Mycobacterium sp. S65 and Mycobacterium sp. py136, respectively. An Escherichia coli expression experiment revealed that the enzyme is able to oxidize anthracene, phenanthrene, pyrene and benzo[a]pyrene, but not to fluoranthene and benzo[a]anthracene. Furthermore, the results of in silico analysis showed that PdoAB has a large substrate-binding pocket satisfying for accommodation of HMW PAHs, and suggested that the binding energy of intermolecular interaction may predict the substrate conversion of RHDs towards HMW PAHs, especially those may have steric constraints on the substrate-binding pocket, such as benzo[a]pyrene and benzo[a]anthracene.
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Affiliation(s)
- Jun Zeng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing 210008, PR China; Joint Open Laboratory of Soil and the Environment, Hong Kong University and Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Qinghe Zhu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing 210008, PR China; Joint Open Laboratory of Soil and the Environment, Hong Kong University and Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Yucheng Wu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing 210008, PR China; Joint Open Laboratory of Soil and the Environment, Hong Kong University and Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Hong Chen
- Soil and Environment Analysis Center, Institute of Soil Science, Chinese Academy of Science, PR China
| | - Xiangui Lin
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing 210008, PR China; Joint Open Laboratory of Soil and the Environment, Hong Kong University and Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China.
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