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Li C, Cui C, Zhang J, Shen J, He B, Long Y, Ye J. Biodegradation of petroleum hydrocarbons based pollutants in contaminated soil by exogenous effective microorganisms and indigenous microbiome. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 253:114673. [PMID: 36827898 DOI: 10.1016/j.ecoenv.2023.114673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 01/19/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Microbial remediation is an eco-friendly and promising approach for the restoration of sites contaminated by petroleum hydrocarbons (PHCs). The degradation of total petroleum hydrocarbons (TPHs), semi volatile organic compounds (SVOCs) and volatile organic compounds (VOCs) of the soil samples collected from a petrochemical site by indigenous microbiome and exogenous microbes (Saccharomyces cerevisiae ATCC 204508/S288c, Candida utilis AS2.281, Rhodotorula benthica CBS9124, Lactobacillus plantarum S1L6, Bacillus thuringiensis GDMCC1.817) was evaluated. Community structure and function of soil microbiome and the mechanism involved in degradation were also revealed. After bioremediation for two weeks, the concentration of TPHs in soil samples was reduced from 17,800 to 13,100 mg/kg. The biodegradation efficiencies of naphthalene, benzo[a]anthracene, benzo[b]fluoranthene, benzo[a]pyrene, indeno[1,2,3-cd]pyrene, dibenzo[a,h]anthracene, 1,2,3-trichloropropane, 1,2-dichloropropane, ethylbenzene and benzene in soil samples with the addition of S. cerevisiae were 38.0%, 35.7%, 36.2%, 40.4%, 33.6%, 36.2%, 12.0%, 43.9%, 43.3% and 43.0%, respectively. The microbial diversity and community structure were improved during the biodegradation process. S. cerevisiae supplemented soil samples exhibited the highest relative abundance of the genus Acinetobacter for bacteria and Saccharomyces for yeast. The findings offer insight into the correlation between microbes and the degradation of PHC-based pollutants during the bioremediation process.
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Affiliation(s)
- Chongshu Li
- School of Environment, Jinan University, Guangzhou 510632, China
| | - Changzheng Cui
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jie Zhang
- Guangzhou Institute of Chemistry, Chinese Academy of Sciences, Guangzhou 510650, China; CAS Testing Technical Services (Guangzhou) Co., Ltd., Guangzhou 510650, China
| | - Jing Shen
- School of Environment, Jinan University, Guangzhou 510632, China
| | - Baoyan He
- School of Environment, Jinan University, Guangzhou 510632, China
| | - Yan Long
- School of Environment, Jinan University, Guangzhou 510632, China
| | - Jinshao Ye
- School of Environment, Jinan University, Guangzhou 510632, China.
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Structure Elucidation and Biochemical Characterization of Environmentally Relevant Novel Extradiol Dioxygenases Discovered by a Functional Metagenomics Approach. mSystems 2019; 4:4/6/e00316-19. [PMID: 31771973 PMCID: PMC6880040 DOI: 10.1128/msystems.00316-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The release of synthetic chemical pollutants in the environment is posing serious health risks. Enzymes, including oxygenases, play a crucial role in xenobiotic degradation. In the present study, we employed a functional metagenomics approach to overcome the limitation of cultivability of microbes under standard laboratory conditions in order to isolate novel dioxygenases capable of degrading recalcitrant pollutants. Fosmid clones possessing dioxygenase activity were further sequenced, and their genes were identified using bioinformatics tools. Two positive fosmid clones, SD3 and RW1, suggested the presence of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC-SD3) and catechol 2,3-dioxygenase (C23O-RW1), respectively. Recombinant versions of these enzymes were purified to examine their pollutant-degrading abilities. The crystal structure of BphC-SD3 was determined at 2.6-Å resolution, revealing a two-domain architecture, i.e., N-terminal and C-terminal domains, with the sequential arrangement of βαβββ in each domain, characteristic of Fe-dependent class II type I extradiol dioxygenases. The structure also reveals the presence of conserved amino acids lining the catalytic pocket and Fe3+ metal ion in the large funnel-shaped active site in the C-terminal domain. Further studies suggest that Fe3+ bound in the BphC-SD3 active site probably imparts aerobic stability. We further demonstrate the potential application of BphC-SD3 in biosensing of catecholic compounds. The halotolerant and oxygen-resistant properties of these enzymes reported in this study make them potential candidates for bioremediation and biosensing applications.IMPORTANCE The disposal and degradation of xenobiotic compounds have been serious issues due to their recalcitrant properties. Microbial oxygenases are the fundamental enzymes involved in biodegradation that oxidize the substrate by transferring oxygen from molecular oxygen. Among oxygenases, catechol dioxygenases are more versatile in biodegradation and are well studied among the bacterial world. The use of catechol dioxygenases in the field is currently not practical due to their aerobically unstable nature. The significance of our research lies in the discovery of aerobically stable and halotolerant catechol dioxygenases that are efficient in degrading the targeted environmental pollutants and, hence, could be used as cost-effective alternatives for the treatment of hypersaline industrial effluents. Moreover, the structural determination of novel catechol dioxygenases would greatly enhance our knowledge of the function of these enzymes and facilitate directed evolution to further enhance or engineer desired properties.
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Li S, Hu S, Shi S, Ren L, Yan W, Zhao H. Microbial diversity and metaproteomic analysis of activated sludge responses to naphthalene and anthracene exposure. RSC Adv 2019; 9:22841-22852. [PMID: 35702527 PMCID: PMC9116109 DOI: 10.1039/c9ra04674g] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 07/18/2019] [Indexed: 11/21/2022] Open
Abstract
The activated sludge process can effectively remove polycyclic aromatic hydrocarbons (PAHs) from wastewater via biodegradation. However, the degradable microorganisms and functional enzymes involved in this process remain unclear. In this study, we successfully employed a laboratory-scale sequential batch reactor to investigate variations in microbial community and protein expression in response to the addition of different PAHs and process time. The analysis of bacterial community structure by 454 pyrosequencing of the 16S rRNA gene indicated that bacteria from Burkholderiales order were dominant in PAHs treated sludge. Mass spectrometry performed with 2D protein profiles of all sludge samples demonstrated that most proteins exhibiting differential expression profiles during the process were derived from Burkholderiales populations; these proteins are involved in DNA replication, fatty acid and glucose metabolism, stress response, protein synthesis, and aromatic hydrocarbon metabolism. Nevertheless, the protein expression profiles indicated that naphthalene, but not anthracene, can induce the expression of PAH-degrading proteins and accelerate its elimination from sludge. Though only naphthalene and anthracene were added into our experimental groups, the differentially expressed enzymes involved in other PAHs (especially biphenyl) metabolism were also detected. This study provides apparent evidence linking the metabolic activities of Burkholderiales populations with the degradation of PAHs in activated sludge processes. Overall, our findings highlighted the successful application of metaproteomics integrated with microbial diversity analysis by high-throughput sequencing technique on the analysis of environmental samples, which could provide a convenience to monitor the changes in proteins expression profiles and their correlation with microbial diversity.
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Affiliation(s)
- Shanshan Li
- Department of Environmental Science & Engineering, Xi'an Jiaotong University Xi'an 710049 China
| | - Shaoda Hu
- Tianjin Key Laboratory for Biomarkers of Occupational and Environmental Hazard, Logistics University of Chinese People's Armed Police Forces Tianjin 300309 China
| | - Sanyuan Shi
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, College of Biotechnology, Tianjin University of Science & Technology Tianjin 300457 China +86-22-80235816
| | - Lu Ren
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, College of Biotechnology, Tianjin University of Science & Technology Tianjin 300457 China +86-22-80235816
| | - Wei Yan
- Department of Environmental Science & Engineering, Xi'an Jiaotong University Xi'an 710049 China
| | - Huabing Zhao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, College of Biotechnology, Tianjin University of Science & Technology Tianjin 300457 China +86-22-80235816
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Zhao Q, Bilal M, Yue S, Hu H, Wang W, Zhang X. Identification of biphenyl 2, 3-dioxygenase and its catabolic role for phenazine degradation in Sphingobium yanoikuyae B1. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2017; 204:494-501. [PMID: 28930694 DOI: 10.1016/j.jenvman.2017.09.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/06/2017] [Accepted: 09/08/2017] [Indexed: 06/07/2023]
Abstract
Phenazines are important nitrogen-containing secondary metabolites that display a range of biological functionalities. However, these compounds have shown lethal effects on humans and, the fate of phenazine in the ecosystem remains uncertain. In this study, we investigated that Sphingobium yanoikuyae B1 could utilize phenazine as a sole carbon source for growth. Intermediate produced during phenazine degradation was purified and identified as 1, 2-dihydrogen 1, 2-dihydroxy phenazine. Biphenyl 2, 3-dioxygenase was determined to be the initial dioxygenase for phenazine degradation through gene cloning and whole cell transformation techniques. Phenazine was converted to 1, 2-dihydrogen 1, 2-dihydroxy phenazine through hydrogenation and hydroxylation, which then transformed to 2-hydroxy phenazine through spontaneous dehydration. ThebphA1fA2f, were evidenced to be the only genes encoding the initial dioxygenase for phenazine degradation. BphB (dihydrodiol dehydrogenase) and BphC (2,3-dihydroxybiphenyl 1,2-dioxygenase) did not exhibit any 1, 2-dihydrogen 1, 2-dihydroxy phenazine and 1, 2-dihydroxy phenazine degradation capability, suggesting no contribution in phenazine degradation. Phylogenetic analysis of the dioxygenases demonstrated enormous biodegradation potential in strain B1. In conclusion, this study opens up new possibilities in better understanding the phenazine degradation in the environment.
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Affiliation(s)
- Qiang Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Muhammad Bilal
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shengjie Yue
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China; National Experimental Teaching Center for Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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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: 31] [Impact Index Per Article: 4.4] [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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Aukema KG, Escalante DE, Maltby MM, Bera AK, Aksan A, Wackett LP. In Silico Identification of Bioremediation Potential: Carbamazepine and Other Recalcitrant Personal Care Products. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:880-888. [PMID: 27977154 DOI: 10.1021/acs.est.6b04345] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Emerging contaminants are principally personal care products not readily removed by conventional wastewater treatment and, with an increasing reliance on water recycling, become disseminated in drinking water supplies. Carbamazepine, a widely used neuroactive pharmaceutical, increasingly escapes wastewater treatment and is found in potable water. In this study, a mechanism is proposed by which carbamazepine resists biodegradation, and a previously unknown microbial biodegradation was predicted computationally. The prediction identified biphenyl dioxygenase from Paraburkholderia xenovorans LB400 as the best candidate enzyme for metabolizing carbamazepine. The rate of degradation described here is 40 times greater than the best reported rates. The metabolites cis-10,11-dihydroxy-10,11-dihydrocarbamazepine and cis-2,3-dihydroxy-2,3-dihydrocarbamazepine were demonstrated with the native organism and a recombinant host. The metabolites are considered nonharmful and mitigate the generation of carcinogenic acridine products known to form when advanced oxidation methods are used in water treatment. Other recalcitrant personal care products were subjected to prediction by the Pathway Prediction System and tested experimentally with P. xenovorans LB400. It was shown to biodegrade structurally diverse compounds. Predictions indicated hydrolase or oxygenase enzymes catalyzed the initial reactions. This study highlights the potential for using the growing body of enzyme-structural and genomic information with computational methods to rapidly identify enzymes and microorganisms that biodegrade emerging contaminants.
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Affiliation(s)
- Kelly G Aukema
- Department of Biochemistry, Molecular Biology and Biophysics, ‡BioTechnology Institute, and §Department of Mechanical Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
| | - Diego E Escalante
- Department of Biochemistry, Molecular Biology and Biophysics, ‡BioTechnology Institute, and §Department of Mechanical Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
| | - Meghan M Maltby
- Department of Biochemistry, Molecular Biology and Biophysics, ‡BioTechnology Institute, and §Department of Mechanical Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
| | - Asim K Bera
- Department of Biochemistry, Molecular Biology and Biophysics, ‡BioTechnology Institute, and §Department of Mechanical Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
| | - Alptekin Aksan
- Department of Biochemistry, Molecular Biology and Biophysics, ‡BioTechnology Institute, and §Department of Mechanical Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
| | - Lawrence P Wackett
- Department of Biochemistry, Molecular Biology and Biophysics, ‡BioTechnology Institute, and §Department of Mechanical Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
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Dihydroxylation of four- and five-ring aromatic hydrocarbons by the naphthalene dioxygenase from Sphingomonas CHY-1. Appl Microbiol Biotechnol 2015; 100:1253-1263. [DOI: 10.1007/s00253-015-7050-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/20/2015] [Accepted: 09/29/2015] [Indexed: 12/23/2022]
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Loviso CL, Lozada M, Guibert LM, Musumeci MA, Sarango Cardenas S, Kuin RV, Marcos MS, Dionisi HM. Metagenomics reveals the high polycyclic aromatic hydrocarbon-degradation potential of abundant uncultured bacteria from chronically polluted subantarctic and temperate coastal marine environments. J Appl Microbiol 2015; 119:411-24. [PMID: 25968322 DOI: 10.1111/jam.12843] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/22/2015] [Accepted: 04/30/2015] [Indexed: 01/18/2023]
Abstract
AIMS To investigate the potential to degrade polycyclic aromatic hydrocarbons (PAHs) of yet-to-be-cultured bacterial populations from chronically polluted intertidal sediments. METHODS AND RESULTS A gene variant encoding the alpha subunit of the catalytic component of an aromatic-ring-hydroxylating oxygenase (RHO) was abundant in intertidal sediments from chronically polluted subantarctic and temperate coastal environments, and its abundance increased after PAH amendment. Conversely, this marker gene was not detected in sediments from a nonimpacted site, even after a short-term PAH exposure. A metagenomic fragment carrying this gene variant was identified in a fosmid library of subantarctic sediments. This fragment contained five pairs of alpha and beta subunit genes and a lone alpha subunit gene of oxygenases, classified as belonging to three different RHO functional classes. In silico structural analysis suggested that two of these oxygenases contain large substrate-binding pockets, capable of accepting high molecular weight PAHs. CONCLUSIONS The identified uncultured micro-organism presents the potential to degrade aromatic hydrocarbons with various chemical structures, and could represent an important member of the PAH-degrading community in these polluted coastal environments. SIGNIFICANCE AND IMPACT OF THE STUDY This work provides valuable information for the design of environmental molecular diagnostic tools and for the biotechnological application of RHO enzymes.
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Affiliation(s)
- C L Loviso
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
| | - M Lozada
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
| | - L M Guibert
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
| | - M A Musumeci
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
| | - S Sarango Cardenas
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
| | - R V Kuin
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
| | - M S Marcos
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
| | - H M Dionisi
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
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Characterization of novel polycyclic aromatic hydrocarbon dioxygenases from the bacterial metagenomic DNA of a contaminated soil. Appl Environ Microbiol 2014; 80:6591-600. [PMID: 25128340 DOI: 10.1128/aem.01883-14] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Ring-hydroxylating dioxygenases (RHDs) play a crucial role in the biodegradation of a range of aromatic hydrocarbons found on polluted sites, including polycyclic aromatic hydrocarbons (PAHs). Current knowledge on RHDs comes essentially from studies on culturable bacterial strains, while compelling evidence indicates that pollutant removal is mostly achieved by uncultured species. In this study, a combination of DNA-SIP labeling and metagenomic sequence analysis was implemented to investigate the metabolic potential of main PAH degraders on a polluted site. Following in situ labeling using [(13)C]phenanthrene, the labeled metagenomic DNA was isolated from soil and subjected to shotgun sequencing. Most annotated sequences were predicted to belong to Betaproteobacteria, especially Rhodocyclaceae and Burkholderiales, which is consistent with previous findings showing that main PAH degraders on this site were affiliated to these taxa. Based on metagenomic data, four RHD gene sets were amplified and cloned from soil DNA. For each set, PCR yielded multiple amplicons with sequences differing by up to 321 nucleotides (17%), reflecting the great genetic diversity prevailing in soil. RHDs were successfully overexpressed in Escherichia coli, but full activity required the coexpression of two electron carrier genes, also cloned from soil DNA. Remarkably, two RHDs exhibited much higher activity when associated with electron carriers from a sphingomonad. The four RHDs showed markedly different preferences for two- and three-ring PAHs but were poorly active on four-ring PAHs. Three RHDs preferentially hydroxylated phenanthrene on the C-1 and C-2 positions rather than on the C-3 and C-4 positions, suggesting that degradation occurred through an alternate pathway.
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Baboshin M, Ivashina T, Chernykh A, Golovleva L. Comparison of the substrate specificity of two ring-hydroxylating dioxygenases from Sphingomonas sp. VKM B-2434 to polycyclic aromatic hydrocarbons. Biodegradation 2014; 25:693-703. [PMID: 24874927 DOI: 10.1007/s10532-014-9692-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 05/09/2014] [Indexed: 11/25/2022]
Abstract
The genes of two ring-hydroxylating dioxygenases (RHDs) of Sphingomonas sp. VKM B-2434 were cloned and expressed in Escherichia coli. The relative values of the RHD specificity constants were estimated for six polycyclic aromatic hydrocarbons (PAHs) based on the kinetics of PAH mixture conversion by the recombinant strains. The substrate specificity profiles of the enzymes were found to be very different. Dioxygenase ArhA was the most specific to acenaphthylene and showed a low specificity to fluoranthene. Dioxygenase PhnA was the most specific to anthracene and phenanthrene and showed a considerable specificity to fluoranthene. Knockout derivatives of Sphingomonas sp. VKM B-2434 lacking ArhA, PhnA, and both dioxygenases were constructed. PAH degradation by the single-knockout mutants was in agreement with the substrate specificity of the RHD remaining intact. Double-knockout mutant lacking both enzymes was unable to oxidize PAHs. A mutant form of dioxygenase ArhA with altered substrate specificity was described.
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Affiliation(s)
- Mikhail Baboshin
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Prospekt Nauki 5, Pushchino, Moscow Region, Russia
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Khara P, Roy M, Chakraborty J, Ghosal D, Dutta TK. Functional characterization of diverse ring-hydroxylating oxygenases and induction of complex aromatic catabolic gene clusters in Sphingobium sp. PNB. FEBS Open Bio 2014; 4:290-300. [PMID: 24918041 PMCID: PMC4048848 DOI: 10.1016/j.fob.2014.03.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 03/03/2014] [Accepted: 03/03/2014] [Indexed: 11/27/2022] Open
Abstract
Sphingobium sp. PNB, like other sphingomonads, has multiple ring-hydroxylating oxygenase (RHO) genes. Three different fosmid clones have been sequenced to identify the putative genes responsible for the degradation of various aromatics in this bacterial strain. Comparison of the map of the catabolic genes with that of different sphingomonads revealed a similar arrangement of gene clusters that harbors seven sets of RHO terminal components and a sole set of electron transport (ET) proteins. The presence of distinctly conserved amino acid residues in ferredoxin and in silico molecular docking analyses of ferredoxin with the well characterized terminal oxygenase components indicated the structural uniqueness of the ET component in sphingomonads. The predicted substrate specificities, derived from the phylogenetic relationship of each of the RHOs, were examined based on transformation of putative substrates and their structural homologs by the recombinant strains expressing each of the oxygenases and the sole set of available ET proteins. The RHO AhdA1bA2b was functionally characterized for the first time and was found to be capable of transforming ethylbenzene, propylbenzene, cumene, p-cymene and biphenyl, in addition to a number of polycyclic aromatic hydrocarbons. Overexpression of aromatic catabolic genes in strain PNB, revealed by real-time PCR analyses, is a way forward to understand the complex regulation of degradative genes in sphingomonads.
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Affiliation(s)
| | | | | | | | - Tapan K. Dutta
- Department of Microbiology, Bose Institute, P-1/12 C.I.T. Scheme VII M, Kolkata 700054, India
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Singh D, Kumari A, Ramaswamy S, Ramanathan G. Expression, purification and substrate specificities of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2. Biochem Biophys Res Commun 2014; 445:36-42. [PMID: 24491551 DOI: 10.1016/j.bbrc.2014.01.113] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 01/22/2014] [Indexed: 11/18/2022]
Abstract
3-Nitotoluene dioxygenase (3-NTDO) is the first enzyme in the degradation pathway of 3-nitrotoluene (3-NT) by Diaphorobacter sp. strain DS2. The complete gene sequences of 3-NTDO were PCR amplified from genomic DNA of Diaphorobacter sp., cloned, sequenced and expressed. The 3-NTDO gene revealed a multi component structure having a reductase, a ferredoxin and two oxygenase subunits. Clones expressing the different subunits were constructed in pET21a expression vector system and overexpressed in E. coli BL21(DE3) host. Each subunit was individually purified separately to homogeneity. The active recombinant enzyme was reconstituted in vitro by mixing all three purified subunits. The reconstituted recombinant enzyme could catalyse biotransformations on a variety of organic aromatics.
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Affiliation(s)
- Deepak Singh
- Department of Chemistry, Indian Institute of Technology, Kanpur 208016, India
| | - Archana Kumari
- Department of Chemistry, Indian Institute of Technology, Kanpur 208016, India
| | - S Ramaswamy
- Institute of Stem Cell Biology and Regenerative Medicine, Bangalore, India
| | - Gurunath Ramanathan
- Department of Chemistry, Indian Institute of Technology, Kanpur 208016, India.
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Novel, highly specific N-demethylases enable bacteria to live on caffeine and related purine alkaloids. J Bacteriol 2012; 194:2041-9. [PMID: 22328667 DOI: 10.1128/jb.06637-11] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The molecular basis for the ability of bacteria to live on caffeine as a sole carbon and nitrogen source is unknown. Pseudomonas putida CBB5, which grows on several purine alkaloids, metabolizes caffeine and related methylxanthines via sequential N-demethylation to xanthine. Metabolism of caffeine by CBB5 was previously attributed to one broad-specificity methylxanthine N-demethylase composed of two subunits, NdmA and NdmB. Here, we report that NdmA and NdmB are actually two independent Rieske nonheme iron monooxygenases with N(1)- and N(3)-specific N-demethylation activity, respectively. Activity for both enzymes is dependent on electron transfer from NADH via a redox-center-dense Rieske reductase, NdmD. NdmD itself is a novel protein with one Rieske [2Fe-2S] cluster, one plant-type [2Fe-2S] cluster, and one flavin mononucleotide (FMN) per enzyme. All ndm genes are located in a 13.2-kb genomic DNA fragment which also contained a formaldehyde dehydrogenase. ndmA, ndmB, and ndmD were cloned as His(6) fusion genes, expressed in Escherichia coli, and purified using a Ni-NTA column. NdmA-His(6) plus His(6)-NdmD catalyzed N(1)-demethylation of caffeine, theophylline, paraxanthine, and 1-methylxanthine to theobromine, 3-methylxanthine, 7-methylxanthine, and xanthine, respectively. NdmB-His(6) plus His(6)-NdmD catalyzed N(3)-demethylation of theobromine, 3-methylxanthine, caffeine, and theophylline to 7-methylxanthine, xanthine, paraxanthine, and 1-methylxanthine, respectively. One formaldehyde was produced from each methyl group removed. Activity of an N(7)-specific N-demethylase, NdmC, has been confirmed biochemically. This is the first report of bacterial N-demethylase genes that enable bacteria to live on caffeine. These genes represent a new class of Rieske oxygenases and have the potential to produce biofuels, animal feed, and pharmaceuticals from coffee and tea waste.
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Structural insight into the expanded PCB-degrading abilities of a biphenyl dioxygenase obtained by directed evolution. J Mol Biol 2010; 405:531-47. [PMID: 21073881 DOI: 10.1016/j.jmb.2010.11.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 11/01/2010] [Accepted: 11/02/2010] [Indexed: 11/23/2022]
Abstract
The biphenyl dioxygenase of Burkholderia xenovorans LB400 is a multicomponent Rieske-type oxygenase that catalyzes the dihydroxylation of biphenyl and many polychlorinated biphenyls (PCBs). The structural bases for the substrate specificity of the enzyme's oxygenase component (BphAE(LB400)) are largely unknown. BphAE(p4), a variant previously obtained through directed evolution, transforms several chlorobiphenyls, including 2,6-dichlorobiphenyl, more efficiently than BphAE(LB400), yet differs from the parent oxygenase at only two positions: T335A/F336M. Here, we compare the structures of BphAE(LB400) and BphAE(p4) and examine the biochemical properties of two BphAE(LB400) variants with single substitutions, T335A or F336M. Our data show that residue 336 contacts the biphenyl and influences the regiospecificity of the reaction, but does not enhance the enzyme's reactivity toward 2,6-dichlorobiphenyl. By contrast, residue 335 does not contact biphenyl but contributes significantly to expansion of the enzyme's substrate range. Crystal structures indicate that Thr335 imposes constraints through hydrogen bonds and nonbonded contacts to the segment from Val320 to Gln322. These contacts are lost when Thr is replaced by Ala, relieving intramolecular constraints and allowing for significant movement of this segment during binding of 2,6-dichlorobiphenyl, which increases the space available to accommodate the doubly ortho-chlorinated congener 2,6-dichlorobiphenyl. This study provides important insight about how Rieske-type oxygenases can expand substrate range through mutations that increase the plasticity and/or mobility of protein segments lining the catalytic cavity.
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Summers RM, Louie TM, Yu CL, Subramanian M. Characterization of a broad-specificity non-haem iron N-demethylase from Pseudomonas putida CBB5 capable of utilizing several purine alkaloids as sole carbon and nitrogen source. MICROBIOLOGY-SGM 2010; 157:583-592. [PMID: 20966097 DOI: 10.1099/mic.0.043612-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
N-Demethylation of many xenobiotics and naturally occurring purine alkaloids such as caffeine and theobromine is primarily catalysed in higher organisms, ranging from fungi to mammals, by the well-studied membrane-associated cytochrome P450s. In contrast, there is no well-characterized enzyme for N-demethylation of purine alkaloids from bacteria, despite several reports on their utilization as sole source of carbon and nitrogen. Here, we provide what we believe to be the first detailed characterization of a purified N-demethylase from Pseudomonas putida CBB5. The soluble N-demethylase holoenzyme is composed of two components, a reductase component with cytochrome c reductase activity (Ccr) and a two-subunit N-demethylase component (Ndm). Ndm, with a native molecular mass of 240 kDa, is composed of NdmA (40 kDa) and NdmB (35 kDa). Ccr transfers reducing equivalents from NAD(P)H to Ndm, which catalyses an oxygen-dependent N-demethylation of methylxanthines to xanthine, formaldehyde and water. Paraxanthine and 7-methylxanthine were determined to be the best substrates, with apparent K(m) and k(cat) values of 50.4±6.8 μM and 16.2±0.6 min(-1), and 63.8±7.5 μM and 94.8±3.0 min(-1), respectively. Ndm also displayed activity towards caffeine, theobromine, theophylline and 3-methylxanthine, all of which are growth substrates for this organism. Ndm was deduced to be a Rieske [2Fe-2S]-domain-containing non-haem iron oxygenase based on (i) its distinct absorption spectrum and (ii) significant identity of the N-terminal sequences of NdmA and NdmB with the gene product of an uncharacterized caffeine demethylase in P. putida IF-3 and a hypothetical protein in Janthinobacterium sp. Marseille, both predicted to be Rieske non-haem iron oxygenases.
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Affiliation(s)
- Ryan M Summers
- Department of Chemical and Biochemical Engineering and Center for Biocatalysis and Bioprocessing, University of Iowa, Iowa City, IA 52242, USA
| | - Tai Man Louie
- Department of Chemical and Biochemical Engineering and Center for Biocatalysis and Bioprocessing, University of Iowa, Iowa City, IA 52242, USA
| | - Chi Li Yu
- Department of Chemical and Biochemical Engineering and Center for Biocatalysis and Bioprocessing, University of Iowa, Iowa City, IA 52242, USA
| | - Mani Subramanian
- Department of Chemical and Biochemical Engineering and Center for Biocatalysis and Bioprocessing, University of Iowa, Iowa City, IA 52242, USA
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Kanaly RA, Harayama S. Advances in the field of high-molecular-weight polycyclic aromatic hydrocarbon biodegradation by bacteria. Microb Biotechnol 2010; 3:136-64. [PMID: 21255317 PMCID: PMC3836582 DOI: 10.1111/j.1751-7915.2009.00130.x] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 05/22/2009] [Accepted: 05/26/2009] [Indexed: 11/26/2022] Open
Abstract
Interest in understanding prokaryotic biotransformation of high-molecular-weight polycyclic aromatic hydrocarbons (HMW PAHs) has continued to grow and the scientific literature shows that studies in this field are originating from research groups from many different locations throughout the world. In the last 10 years, research in regard to HMW PAH biodegradation by bacteria has been further advanced through the documentation of new isolates that represent diverse bacterial types that have been isolated from different environments and that possess different metabolic capabilities. This has occurred in addition to the continuation of in-depth comprehensive characterizations of previously isolated organisms, such as Mycobacterium vanbaalenii PYR-1. New metabolites derived from prokaryotic biodegradation of four- and five-ring PAHs have been characterized, our knowledge of the enzymes involved in these transformations has been advanced and HMW PAH biodegradation pathways have been further developed, expanded upon and refined. At the same time, investigation of prokaryotic consortia has furthered our understanding of the capabilities of microorganisms functioning as communities during HMW PAH biodegradation.
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Affiliation(s)
- Robert A Kanaly
- Department of Genome Systems, Faculty of Bionanoscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Kanagawa-ken, Yokohama 236-0027, Japan.
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Characterization of a ring-hydroxylating dioxygenase from phenanthrene-degrading Sphingomonas sp. strain LH128 able to oxidize benz[a]anthracene. Appl Microbiol Biotechnol 2009; 83:465-75. [PMID: 19172265 DOI: 10.1007/s00253-009-1858-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2008] [Revised: 01/03/2009] [Accepted: 01/05/2009] [Indexed: 10/21/2022]
Abstract
Sphingomonas sp. strain LH128 was isolated from a polycyclic aromatic hydrocarbon (PAH)-contaminated soil using phenanthrene as the sole source of carbon and energy. A dioxygenase complex, phnA1fA2f, encoding the alpha and beta subunit of a terminal dioxygenase responsible for the initial attack on PAHs, was identified and isolated from this strain. PhnA1f showed 98%, 78%, and 78% identity to the alpha subunit of PAH dioxygenase from Novosphingobium aromaticivorans strain F199, Sphingomonas sp. strain CHY-1, and Sphingobium yanoikuyae strain B1, respectively. When overexpressed in Escherichia coli, PhnA1fA2f was able to oxidize low-molecular-weight PAHs, chlorinated biphenyls, dibenzo-p-dioxin, and the high-molecular-weight PAHs benz[a]anthracene, chrysene, and pyrene. The action of PhnA1fA2f on benz[a]anthracene produced two benz[a]anthracene dihydrodiols.
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Furukawa K, Fujihara H. Microbial degradation of polychlorinated biphenyls: Biochemical and molecular features. J Biosci Bioeng 2008; 105:433-49. [PMID: 18558332 DOI: 10.1263/jbb.105.433] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Accepted: 02/04/2008] [Indexed: 11/17/2022]
Affiliation(s)
- Kensuke Furukawa
- Depatment of Food and Bioscience, Faculty of Food and Nutrition, Beppu University, Beppu, Ohita 874-8501, Japan.
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Ashikawa Y, Uchimura H, Fujimoto Z, Inoue K, Noguchi H, Yamane H, Nojiri H. Crystallization and preliminary X-ray diffraction studies of the ferredoxin reductase component in the Rieske nonhaem iron oxygenase system carbazole 1,9a-dioxygenase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:499-502. [PMID: 17554172 PMCID: PMC2335075 DOI: 10.1107/s174430910702163x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Accepted: 05/02/2007] [Indexed: 11/10/2022]
Abstract
Carbazole 1,9a-dioxygenase (CARDO), which consists of an oxygenase component (CARDO-O) and the electron-transport components ferredoxin (CARDO-F) and ferredoxin reductase (CARDO-R), catalyzes dihydroxylation at the C1 and C9a positions of carbazole. CARDO-R was crystallized at 277 K using the hanging-drop vapour-diffusion method with the precipitant PEG 8000. Two crystal types (types I and II) were obtained. The type I crystal diffracted to a maximum resolution of 2.80 A and belonged to space group P4(2)2(1)2, with unit-cell parameters a = b = 158.7, c = 81.4 A. The type II crystal was obtained in drops from which type I crystals had been removed; it diffracted to 2.60 A resolution and belonged to the same space group, with unit-cell parameters a = b = 161.8, c = 79.5 A.
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Affiliation(s)
- Yuji Ashikawa
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hiromasa Uchimura
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Zui Fujimoto
- Protein Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Kengo Inoue
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Haruko Noguchi
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Professional Programme for Agricultural Bioinformatics, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hisakazu Yamane
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hideaki Nojiri
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Professional Programme for Agricultural Bioinformatics, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Correspondence e-mail:
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Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1. BMC STRUCTURAL BIOLOGY 2007; 7:10. [PMID: 17349044 PMCID: PMC1847435 DOI: 10.1186/1472-6807-7-10] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Accepted: 03/09/2007] [Indexed: 11/10/2022]
Abstract
Background The initial step involved in oxidative hydroxylation of monoaromatic and polyaromatic compounds by the microorganism Sphingobium yanoikuyae strain B1 (B1), previously known as Sphingomonas yanoikuyae strain B1 and Beijerinckia sp. strain B1, is performed by a set of multiple terminal Rieske non-heme iron oxygenases. These enzymes share a single electron donor system consisting of a reductase and a ferredoxin (BPDO-FB1). One of the terminal Rieske oxygenases, biphenyl 2,3-dioxygenase (BPDO-OB1), is responsible for B1's ability to dihydroxylate large aromatic compounds, such as chrysene and benzo[a]pyrene. Results In this study, crystal structures of BPDO-OB1 in both native and biphenyl bound forms are described. Sequence and structural comparisons to other Rieske oxygenases show this enzyme to be most similar, with 43.5 % sequence identity, to naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4. While structurally similar to naphthalene 1,2-dioxygenase, the active site entrance is significantly larger than the entrance for naphthalene 1,2-dioxygenase. Differences in active site residues also allow the binding of large aromatic substrates. There are no major structural changes observed upon binding of the substrate. BPDO-FB1 has large sequence identity to other bacterial Rieske ferredoxins whose structures are known and demonstrates a high structural homology; however, differences in side chain composition and conformation around the Rieske cluster binding site are noted. Conclusion This is the first structure of a Rieske oxygenase that oxidizes substrates with five aromatic rings to be reported. This ability to catalyze the oxidation of larger substrates is a result of both a larger entrance to the active site as well as the ability of the active site to accommodate larger substrates. While the biphenyl ferredoxin is structurally similar to other Rieske ferredoxins, there are distinct changes in the amino acids near the iron-sulfur cluster. Because this ferredoxin is used by multiple oxygenases present in the B1 organism, this ferredoxin-oxygenase system provides the structural platform to dissect the balance between promiscuity and selectivity in protein-protein electron transport systems.
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