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Martinelli F, Thiele I. Microbial metabolism marvels: a comprehensive review of microbial drug transformation capabilities. Gut Microbes 2024; 16:2387400. [PMID: 39150897 PMCID: PMC11332652 DOI: 10.1080/19490976.2024.2387400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 07/22/2024] [Accepted: 07/25/2024] [Indexed: 08/18/2024] Open
Abstract
This comprehensive review elucidates the pivotal role of microbes in drug metabolism, synthesizing insights from an exhaustive analysis of over two hundred papers. Employing a structural classification system grounded in drug atom involvement, the review categorizes the microbiome-mediated drug-metabolizing capabilities of over 80 drugs. Additionally, it compiles pharmacodynamic and enzymatic details related to these reactions, striving to include information on encoding genes and specific involved microorganisms. Bridging biochemistry, pharmacology, genetics, and microbiology, this review not only serves to consolidate diverse research fields but also highlights the potential impact of microbial drug metabolism on future drug design and in silico studies. With a visionary outlook, it also lays the groundwork for personalized medicine interventions, emphasizing the importance of interdisciplinary collaboration for advancing drug development and enhancing therapeutic strategies.
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Affiliation(s)
- Filippo Martinelli
- School of Medicine, University of Galway, Galway, Ireland
- Digital Metabolic Twin Centre, University of Galway, Galway, Ireland
- The Ryan Institute, University of Galway, Galway, Ireland
| | - Ines Thiele
- School of Medicine, University of Galway, Galway, Ireland
- Digital Metabolic Twin Centre, University of Galway, Galway, Ireland
- The Ryan Institute, University of Galway, Galway, Ireland
- School of Microbiology, University of Galway, Galway, Ireland
- APC Microbiome Ireland, Cork, Ireland
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Klenk JM, Ertl J, Rapp L, Fischer MP, Hauer B. Expression and characterization of the benzoic acid hydroxylase CYP199A25 from Arthrobacter sp. MOLECULAR CATALYSIS 2020. [DOI: 10.1016/j.mcat.2019.110739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Klenk JM, Fischer MP, Dubiel P, Sharma M, Rowlinson B, Grogan G, Hauer B. Identification and characterization of cytochrome P450 1232A24 and 1232F1 from Arthrobacter sp. and their role in the metabolic pathway of papaverine. J Biochem 2019; 166:51-66. [DOI: 10.1093/jb/mvz010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 02/12/2019] [Indexed: 11/13/2022] Open
Abstract
AbstractCytochrome P450 monooxygenases (P450s) play crucial roles in the cell metabolism and provide an unsurpassed diversity of catalysed reactions. Here, we report the identification and biochemical characterization of two P450s from Arthrobacter sp., a Gram-positive organism known to degrade the opium alkaloid papaverine. Combining phylogenetic and genomic analysis suggested physiological roles for P450s in metabolism and revealed potential gene clusters with redox partners facilitating the reconstitution of the P450 activities in vitro. CYP1232F1 catalyses the para demethylation of 3,4-dimethoxyphenylacetic acid to homovanillic acid while CYP1232A24 continues demethylation to 3,4-dihydroxyphenylacetic acid. Interestingly, the latter enzyme is also able to perform both demethylation steps with preference for the meta position. The crystal structure of CYP1232A24, which shares only 29% identity to previous published structures of P450s helped to rationalize the preferred demethylation specificity for the meta position and also the broader substrate specificity profile. In addition to the detailed characterization of the two P450s using their physiological redox partners, we report the construction of a highly active whole-cell Escherichia coli biocatalyst expressing CYP1232A24, which formed up to 1.77 g l−1 3,4-dihydroxyphenylacetic acid. Our results revealed the P450s’ role in the metabolic pathway of papaverine enabling further investigation and application of these biocatalysts.
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Affiliation(s)
- Jan M Klenk
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, Stuttgart, Germany
| | - Max-Philipp Fischer
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, Stuttgart, Germany
| | - Paulina Dubiel
- Department of Chemistry, University of York, Heslington, York, UK
| | - Mahima Sharma
- Department of Chemistry, University of York, Heslington, York, UK
| | | | - Gideon Grogan
- Department of Chemistry, University of York, Heslington, York, UK
| | - Bernhard Hauer
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, Stuttgart, Germany
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Chen X, He S, Liang Z, Li QX, Yan H, Hu J, Liu X. Biodegradation of pyraclostrobin by two microbial communities from Hawaiian soils and metabolic mechanism. JOURNAL OF HAZARDOUS MATERIALS 2018; 354:225-230. [PMID: 29753191 DOI: 10.1016/j.jhazmat.2018.04.067] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 04/08/2018] [Accepted: 04/25/2018] [Indexed: 06/08/2023]
Abstract
Pyraclostrobin has been widely and long-termly applicated to agricultural fields. The removal of pyraclostrobin from ecological environment has received wide attention. In this study, using sequential enrichments with pyraclostrobin as a sole carbon source, two microbial communities (HI2 and HI6) capable of catabolizing pyraclostrobin were obtained from Hawaiian soils. The microfloras analysis indicated that only Proteobacteria and Bacteroides could survive in HI2-soil after acclimatization, whereas the number of Proteobacteria in HI6-soil accounted for more than 99%. The percentages of Pseudomonas in the HI2 and HI6 microfloras were 69.3% and 59.3%, respectively. More than 99% of pyraclostrobin (C0 = 100 mg L-1) was degraded by the HI2 and HI6 microorganisms within five days. A unique metabolite was identified by high performance liquid chromatography tandem quadrupole time-of-flight mass spectrometry (HPLC-QTOF-MS/MS). A metabolic pathway involving carbamate hydrolysis was proposed. The tertiary amine group of pyraclostrobin was hydrolyzed to primary amine group with the decarboxylation, which facilitated pyraclostrobin detoxification because carboxylester was an important functional group. The metabolic mechanism suggested that Pseudomonas expressing carboxylesterase might be able to degrade carbamate chemicals. Therefore, Pseudomonas might be an ideal candidate for expression and cloning of carbamate-degrading gene in genomics studies. The current study would have important implications in detoxification and bioremediation of carbamates through the CN bond cleavage of methyl carbamate.
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Affiliation(s)
- Xiaoxin Chen
- College of Chemistry and Environmental Science, Hebei University, Baoding City, Hebei Province, 071002, PR China.
| | - Sheng He
- College of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China.
| | - Zhibin Liang
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, 96822, USA.
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, 96822, USA.
| | - Hai Yan
- College of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China.
| | - Jiye Hu
- College of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China.
| | - Xiaolu Liu
- College of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China.
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Mineralization of melamine and cyanuric acid as sole nitrogen source by newly isolated Arthrobacter spp. using a soil-charcoal perfusion method. World J Microbiol Biotechnol 2015; 31:785-93. [DOI: 10.1007/s11274-015-1832-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 02/25/2015] [Indexed: 10/23/2022]
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Šimoliūnas E, Kaliniene L, Stasilo M, Truncaitė L, Zajančkauskaitė A, Staniulis J, Nainys J, Kaupinis A, Valius M, Meškys R. Isolation and characterization of vB_ArS-ArV2 - first Arthrobacter sp. infecting bacteriophage with completely sequenced genome. PLoS One 2014; 9:e111230. [PMID: 25333962 PMCID: PMC4205034 DOI: 10.1371/journal.pone.0111230] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 09/26/2014] [Indexed: 02/05/2023] Open
Abstract
This is the first report on a complete genome sequence and biological characterization of the phage that infects Arthrobacter. A novel virus vB_ArS-ArV2 (ArV2) was isolated from soil using Arthrobacter sp. 68b strain for phage propagation. Based on transmission electron microscopy, ArV2 belongs to the family Siphoviridae and has an isometric head (∼63 nm in diameter) with a non-contractile flexible tail (∼194×10 nm) and six short tail fibers. ArV2 possesses a linear, double-stranded DNA genome (37,372 bp) with a G+C content of 62.73%. The genome contains 68 ORFs yet encodes no tRNA genes. A total of 28 ArV2 ORFs have no known functions and lack any reliable database matches. Proteomic analysis led to the experimental identification of 14 virion proteins, including 9 that were predicted by bioinformatics approaches. Comparative phylogenetic analysis, based on the amino acid sequence alignment of conserved proteins, set ArV2 apart from other siphoviruses. The data presented here will help to advance our understanding of Arthrobacter phage population and will extend our knowledge about the interaction between this particular host and its phages.
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Affiliation(s)
- Eugenijus Šimoliūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Laura Kaliniene
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Miroslav Stasilo
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Lidija Truncaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Aurelija Zajančkauskaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Juozas Staniulis
- Laboratory of Plant Viruses, Institute of Botany, Nature Research Centre, Vilnius, Lithuania
| | - Juozas Nainys
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Algirdas Kaupinis
- Proteomics Centre, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Mindaugas Valius
- Proteomics Centre, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
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Bordeleau G, Martel R, Bamba AN, Blais JF, Ampleman G, Thiboutot S. Nitroglycerin degradation mediated by soil organic carbon under aerobic conditions. JOURNAL OF CONTAMINANT HYDROLOGY 2014; 166:52-63. [PMID: 25086776 DOI: 10.1016/j.jconhyd.2014.06.012] [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: 11/25/2013] [Revised: 06/20/2014] [Accepted: 06/27/2014] [Indexed: 06/03/2023]
Abstract
The presence of nitroglycerin (NG) has been reported in shallow soils and pore water of several military training ranges. In this context, NG concentrations can be reduced through various natural attenuation processes, but these have not been thoroughly documented. This study aimed at investigating the role of soil organic matter (SOM) in the natural attenuation of NG, under aerobic conditions typical of shallow soils. The role of SOM in NG degradation has already been documented under anoxic conditions, and was attributed to SOM-mediated electron transfer involving different reducing agents. However, unsaturated soils are usually well-oxygenated, and it was not clear whether SOM could participate in NG degradation under these conditions. Our results from batch- and column-type experiments clearly demonstrate that in presence of dissolved organic matter (DOM) leached from a natural soil, partial NG degradation can be achieved. In presence of particulate organic matter (POM) from the same soil, complete NG degradation was achieved. Furthermore, POM caused rapid sorption of NG, which should result in NG retention in the organic matter-rich shallow horizons of the soil profile, thus promoting degradation. Based on degradation products, the reaction pathway appears to be reductive, in spite of the aerobic conditions. The relatively rapid reaction rates suggest that this process could significantly participate in the natural attenuation of NG, both on military training ranges and in contaminated soil at production facilities.
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Affiliation(s)
- Geneviève Bordeleau
- Institut National de la Recherche Scientifique, Centre Eau, Terre et Environnement (INRS-ETE), 490 de la Couronne, Quebec City, QC, Canada, G1K 9A9.
| | - Richard Martel
- Institut National de la Recherche Scientifique, Centre Eau, Terre et Environnement (INRS-ETE), 490 de la Couronne, Quebec City, QC, Canada, G1K 9A9.
| | - Abraham N'Valoua Bamba
- Université Laval, Département de Géographie, Faculté de foresterie, de géographie et de géomatique, Pavillon Abitibi-Price, 2405, rue de la Terrasse, Local 3137, Quebec City, QC, Canada, G1V 0A6.
| | - Jean-François Blais
- Institut National de la Recherche Scientifique, Centre Eau, Terre et Environnement (INRS-ETE), 490 de la Couronne, Quebec City, QC, Canada, G1K 9A9.
| | - Guy Ampleman
- Defence Research and Development Canada - Valcartier, 2459 Pie-XI Blvd. North, Quebec City, QC, Canada, G3J 1X5.
| | - Sonia Thiboutot
- Defence Research and Development Canada - Valcartier, 2459 Pie-XI Blvd. North, Quebec City, QC, Canada, G3J 1X5.
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Bordeleau G, Martel R, Drouin M, Ampleman G, Thiboutot S. Biodegradation of nitroglycerin from propellant residues on military training ranges. JOURNAL OF ENVIRONMENTAL QUALITY 2014; 43:441-449. [PMID: 25602645 DOI: 10.2134/jeq2013.06.0241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Nitroglycerin (NG) is often present in soils and sometimes in pore water at antitank firing positions due to incomplete combustion of propellants. Various degradation processes can contribute to the natural attenuation of NG in soils and pore water, thus reducing the risks of groundwater contamination. However, until now these processes have been sparsely documented. This study aimed at evaluating the ability of microorganisms from a legacy firing position to degrade dissolved NG, as well as NG trapped within propellant particles. Results from the shake-flask experiments showed that the isolated culture is capable of degrading dissolved NG but not the nitrocellulose matrix of propellant particles, so that the deeply embedded NG molecules cannot be degraded. Furthermore, the results from column experiments showed that in a nutrient-poor sand, degradation of dissolved NG may not be sufficiently rapid to prevent groundwater contamination. Therefore, the results from this study indicate that, under favorable soil conditions, biodegradation can be an important natural attenuation process for NG dissolving out of fresh propellant residues. In contrast, biodegradation does not contribute to the long-term attenuation of NG within old, weathered propellant residues. Although NG in these old residues no longer poses a threat to groundwater quality, if soil clean-up of a legacy site is required, active remediation approaches should be sought.
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Zhuang L, Gui L, Gillham RW, Landis RC. Laboratory and pilot-scale bioremediation of pentaerythritol tetranitrate (PETN) contaminated soil. JOURNAL OF HAZARDOUS MATERIALS 2014; 264:261-268. [PMID: 24316800 DOI: 10.1016/j.jhazmat.2013.11.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 10/31/2013] [Accepted: 11/14/2013] [Indexed: 06/02/2023]
Abstract
PETN (pentaerythritol tetranitrate), a munitions constituent, is commonly encountered in munitions-contaminated soils, and pose a serious threat to aquatic organisms. This study investigated anaerobic remediation of PETN-contaminated soil at a site near Denver Colorado. Both granular iron and organic carbon amendments were used in both laboratory and pilot-scale tests. The laboratory results showed that, with various organic carbon amendments, PETN at initial concentrations of between 4500 and 5000mg/kg was effectively removed within 84 days. In the field trial, after a test period of 446 days, PETN mass removal of up to 53,071mg/kg of PETN (80%) was achieved with an organic carbon amendment (DARAMEND) of 4% by weight. In previous laboratory studies, granular iron has shown to be highly effective in degrading PETN. However, for both the laboratory and pilot-scale tests, granular iron was proven to be ineffective. This was a consequence of passivation of the iron surfaces caused by the very high concentrations of nitrate in the contaminated soil. This study indicated that low concentration of organic carbon was a key factor limiting bioremediation of PETN in the contaminated soil. Furthermore, the addition of organic carbon amendments such as the DARAMEND materials or brewers grain, proved to be highly effective in stimulating the biodegradation of PETN and could provide the basis for full-scale remediation of PETN-contaminated sites.
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Affiliation(s)
- Li Zhuang
- Guangdong Institute of Eco-environmental and Soil Sciences, Guangzhou 510650, China.
| | - Lai Gui
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada; Pest Management and Regulatory Agency, Health Canada, Ottawa, Ontario K1A 0K9, Canada
| | - Robert W Gillham
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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Halecky M, Spackova R, Paca J, Stiborova M, Kozliak E. Biodegradation of nitroglycerin and ethylene glycol dinitrate by free and immobilized mixed cultures. WATER RESEARCH 2014; 48:529-537. [PMID: 24206758 DOI: 10.1016/j.watres.2013.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 10/01/2013] [Accepted: 10/02/2013] [Indexed: 06/02/2023]
Abstract
Aerobic biodegradation of nitroglycerin (NG) and ethylene glycol dinitrate (EGDN), both as individual substrates and in their mixture, was tested using batch or fed-batch cultivation with free suspended cells enriched from a soil sample subjected to a long-term contamination with explosives. EGDN was degraded only in the presence of glycerol as a co-substrate whereas NG could serve as a sole carbon, energy and nitrogen source for growth, its degradation being only slightly boosted by either glycerol or pyruvate. NG was not sufficient as a co-substrate for microbial growth on EGDN; furthermore, the presence of EGDN inhibited the NG degradation. The growth inhibition by both NG and EGDN was alleviated by the addition of glycerol. At an optimum nitroglycerin concentration of 30 mg/L, a maximum specific degradation rate of 60.9 ± 1.8 mg/gdw/h was observed. The biodegradation of both pollutants occurred with a release of nitrite. A method was developed for growing substantial amounts of NG-degrading biomass in the presence of glycerol for its immobilization on expanded slate in a pot-scale packed-bed reactor. Preliminary reactor tests were conducted in a continuous operation mode yielding a 70-90% NG biodegradation up to a load of 20 mg/L/h, with a removal rate up to 16 mg/L/h.
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Affiliation(s)
- Martin Halecky
- Institute of Chemical Technology, Department of Biotechnology, Prague 16628, Czech Republic.
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Bordeleau G, Savard MM, Martel R, Smirnoff A, Ampleman G, Thiboutot S. Stable isotopes of nitrate reflect natural attenuation of propellant residues on military training ranges. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:8265-8272. [PMID: 23815525 DOI: 10.1021/es4004526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Nitroglycerin (NG) and nitrocellulose (NC) are constituents of double-base propellants used notably for firing antitank ammunitions. Nitroglycerin was detected in soil and water samples from the unsaturated zone (pore water) at an active antitank firing position, where the presence of high nitrate (NO3(-)) concentrations suggests that natural attenuation of NG is occurring. However, concentrations alone cannot assess if NG is the source of NO3(-), nor can they determine which degradation processes are involved. To address this issue, isotopic ratios (δ(15)N, δ(18)O) were measured for NO3(-) produced from NG and NC through various controlled degradation processes and compared with ratios measured in field pore water samples. Results indicate that propellant combustion and degradation mediated by soil organic carbon produced the observed NO3(-) in pore water at this site. Moreover, isotopic results are presented for NO3(-) produced through photolysis of propellant constituents, which could be a dominant process at other sites. The isotopic data presented here constitute novel information regarding a source of NO3(-) that was practically not documented before and a basis to study the contamination by energetic materials in different contexts.
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Affiliation(s)
- Geneviève Bordeleau
- Institut National de la Recherche Scientifique, Centre Eau, Terre et Environnement (INRS-ETE), 490 de la Couronne, Quebec City, QC, G1K 9A9, Canada.
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Husserl J, Hughes JB. Biodegradation of nitroglycerin in porous media and potential for bioaugmentation with Arthrobacter sp. strain JBH1. CHEMOSPHERE 2013; 92:721-724. [PMID: 23664478 DOI: 10.1016/j.chemosphere.2013.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 04/01/2013] [Accepted: 04/02/2013] [Indexed: 06/02/2023]
Abstract
Nitroglycerin (NG) is a toxic explosive found as a contaminant of soil and groundwater. Several microbial strains are capable of partially reducing the NG molecule to dinitro or mononitroesters. Recently, a strain capable of growing on NG as the sole source of carbon and nitrogen (Arthrobacter sp. strain JBH1) was isolated from contaminated soil. Despite the widespread presence of microbial strains capable of transforming NG in contaminated soils and sediments, the extent of NG biodegradation at contaminated sites is still unknown. In this study column experiments were conducted to investigate the extent of microbial degradation of NG in saturated porous media, specifically after bioaugmentation with JBH1. Initial experiments using sterile, low sorptivity sand, showed mineralization of NG after bioaugmentation with JBH1 in the absence of sources of carbon and nitrogen other than NG. Results could be modeled using a first order degradation rate of 0.14d(-1). Further experiments conducted using contaminated soil with high organic carbon content (highly sorptive) resulted in column effluents that did not contain NG although high dinitroester concentrations were observed. Bioaugmentation with JBH1 in sediments containing strains capable of partial transformation of NG resulted in complete mineralization of NG and faster degradation rates.
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Affiliation(s)
- Johana Husserl
- Department of Civil and Environmental Engineering, Universidad de los Andes, Bogotá, Colombia.
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Bordeleau G, Martel R, Ampleman G, Thiboutot S, Poulin I. The fate and transport of nitroglycerin in the unsaturated zone at active and legacy anti-tank firing positions. JOURNAL OF CONTAMINANT HYDROLOGY 2012; 142-143:11-21. [PMID: 23047138 DOI: 10.1016/j.jconhyd.2012.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 08/21/2012] [Accepted: 09/04/2012] [Indexed: 06/01/2023]
Abstract
The environmental fate of nitroglycerin (NG) in the unsaturated zone was evaluated in the context of double-base propellant residue deposition at anti-tank training ranges. Fresh propellant residues were collected during live anti-tank training. Surface soils, sub-surface soils and water samples from the unsaturated zone were collected at an active anti-tank range, and at a legacy site where NG-based propellants have been used. Results show that the residues are composed of intact propellant particles, as well as small quantities of NG, dinitroglycerin (DNG) and nitrate which are rapidly dissolved by precipitation, resulting in sporadic pulses of those compounds in water from the unsaturated zone after rain/snow melt events. The dissolved NG and DNG can be progressively degraded in the unsaturated zone, releasing nitrate as an end-product. Over a period of several years, small propellant particles located at the soil surface can be carried downward through the soil pore system by infiltration water, which explains the presence of NG in sub-surface soils at the legacy site, more than 35 years after site closure. NG is no longer leached from these old particles, therefore the detection of NG in sub-surface soils does not signify that groundwater is at risk of contamination by NG.
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Affiliation(s)
- Geneviève Bordeleau
- Institut National de la Recherche Scientifique, Centre Eau, Terre et Environnement, 490 de la Couronne, Quebec City, Qc, Canada.
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Zhuang L, Gui L, Gillham RW. Biodegradation of pentaerythritol tetranitrate (PETN) by anaerobic consortia from a contaminated site. CHEMOSPHERE 2012; 89:810-816. [PMID: 22647196 DOI: 10.1016/j.chemosphere.2012.04.062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 04/23/2012] [Accepted: 04/30/2012] [Indexed: 06/01/2023]
Abstract
This study examined the role of denitrifying and sulfate-reducing bacteria in biodegradation of pentaerythritol tetranitrate (PETN). Microbial inocula were obtained from a PETN-contaminated soil. PETN degradation was evaluated using nitrate and/or sulfate as electron acceptors and acetate as a carbon source. Results showed that under different electron acceptor conditions tested, PETN was sequentially reduced to pentaerythritol via the intermediary formation of tri-, di- and mononitrate pentaerythritol (PETriN, PEDN and PEMN). The addition of nitrate enhanced the degradation rate of PETN by stimulating greater microbial activity and growth of nitrite reducing bacteria that were responsible for degrading PETN. However, a high concentration of nitrite (350mgL(-1)) accumulated from nitrate reduction, consequently caused self-inhibition and temporarily delayed PETN biodegradation. In contrast, PETN degraded at very similar rates in the presence and absence of sulfate, while PETN inhibited sulfate reduction. It is apparent that denitrifying bacteria possessing nitrite reductase were capable of using PETN and its intermediates as terminal electron acceptors in a preferential utilization sequence of PETN, PETriN, PEDN and PEMN, while sulfate-reducing bacteria were not involved in PETN biodegradation. This study demonstrated that under anaerobic conditions and with sufficient carbon source, PETN can be effectively biotransformed by indigenous denitrifying bacteria, providing a viable means of treatment for PETN-containing wastewaters and PETN-contaminated soils.
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Affiliation(s)
- Li Zhuang
- Guangdong Institute of Eco-environmental and Soil Sciences, Guangzhou, China.
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Abstract
Explosives are synthesized globally mainly for military munitions. Nitrate esters, such as GTN and PETN, nitroaromatics like TNP and TNT and nitramines with RDX, HMX and CL20, are the main class of explosives used. Their use has resulted in severe contamination of environment and strategies are now being developed to clean these substances in an economical and eco-friendly manner. The incredible versatility inherited in microbes has rendered these explosives as a part of the biogeochemical cycle. Several microbes catalyze mineralization and/or nonspecific transformation of explosive waste either by aerobic or anaerobic processes. It is likely that ongoing genetic adaptation, with the recruitment of silent sequences into functional catabolic routes and evolution of substrate range by mutations in structural genes, will further enhance the catabolic potential of bacteria toward explosives and ultimately contribute to cleansing the environment of these toxic and recalcitrant chemicals. This review summarizes information on the biodegradation and biotransformation pathways of several important explosives. Isolation, characterization, utilization and manipulation of the major detoxifying enzymes and the molecular basis of degradation are also discussed. This may be useful in developing safer and economic microbiological methods for clean up of soil and water contaminated with such compounds. The necessity of further investigations concerning the microbial metabolism of these substances is also discussed.
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Bordeleau G, Martel R, Lévesque R, Ampleman G, Thiboutot S, Marois A. Overestimation of nitrate and nitrite concentrations in water samples due to the presence of nitroglycerin or hexahydro-1,3,5-trinitro-1,3,5-triazine. J Chromatogr A 2012; 1252:130-5. [DOI: 10.1016/j.chroma.2012.06.082] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 06/20/2012] [Accepted: 06/25/2012] [Indexed: 11/29/2022]
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17
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Rocheleau S, Kuperman RG, Dodard SG, Sarrazin M, Savard K, Paquet L, Hawari J, Checkai RT, Thiboutot S, Ampleman G, Sunahara GI. Phytotoxicity and uptake of nitroglycerin in a natural sandy loam soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2011; 409:5284-5291. [PMID: 21975007 DOI: 10.1016/j.scitotenv.2011.08.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 08/26/2011] [Accepted: 08/29/2011] [Indexed: 05/31/2023]
Abstract
Nitroglycerin (NG) is widely used for the production of explosives and solid propellants, and is a soil contaminant of concern at some military training ranges. NG phytotoxicity data reported in the literature cannot be applied directly to development of ecotoxicological benchmarks for plant exposures in soil because they were determined in studies using hydroponic media, cell cultures, and transgenic plants. Toxicities of NG in the present studies were evaluated for alfalfa (Medicago sativa), barnyard grass (Echinochloa crusgalli), and ryegrass (Lolium perenne) exposed to NG in Sassafras sandy loam soil. Uptake and degradation of NG were also evaluated in ryegrass. The median effective concentration values for shoot growth ranged from 40 to 231 mg kg(-1) in studies with NG freshly amended in soil, and from 23 to 185 mg kg(-1) in studies with NG weathered-and-aged in soil. Weathering-and-aging NG in soil did not significantly affect the toxicity based on 95% confidence intervals for either seedling emergence or plant growth endpoints. Uptake studies revealed that NG was not accumulated in ryegrass but was transformed into dinitroglycerin in the soil and roots, and was subsequently translocated into the ryegrass shoots. The highest bioconcentration factors for dinitroglycerin of 685 and 40 were determined for roots and shoots, respectively. Results of these studies will improve our understanding of toxicity and bioconcentration of NG in terrestrial plants and will contribute to ecological risk assessment of NG-contaminated sites.
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Affiliation(s)
- Sylvie Rocheleau
- Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montreal, Quebec, Canada H4P 2R2
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18
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Assessing the effect of oxygen and microbial inhibitors to optimize ferricyanide-mediated BOD assay. Talanta 2011; 85:455-62. [DOI: 10.1016/j.talanta.2011.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 04/01/2011] [Accepted: 04/04/2011] [Indexed: 11/22/2022]
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19
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Podlipná R, Fialová Z, Vaněk T. Degradation of nitroesters by plant tissue cultures. JOURNAL OF HAZARDOUS MATERIALS 2010; 184:591-596. [PMID: 20843601 DOI: 10.1016/j.jhazmat.2010.08.076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 08/09/2010] [Accepted: 08/18/2010] [Indexed: 05/29/2023]
Abstract
Nitrate esters are widely used as effective explosives, important components of explosive ranges, and energetic plasticizers. The environmental problem arising from the production and use of these compounds can be solved using biotechnology. Phytoremediation appears as an efficient technology for this purpose. The uptake and transformation of nitroglycerine (NG) and ethylene glycol dinitrate (EGDN) from wastewater by plants using in vitro regenerants of Juncus inflexus and Phragmites australis were investigated. The plants were exposed to the NG, (600 mg l(-1)), the parent compound disappeared during 20 days and degradation products as dinitroglycerine (DNG) and mononitroglycerine (MNG) were identified in the medium. During 20 days the starting concentration of 100 mg l(-1) EGDN disappeared in the case of J. inflexus or decreased to 5% in the case of P. australis. Ethylene glycol mononitrate as the degradation product was identified. Using this approach directly to the wastewater from production of explosives, the starting concentration of nitroesters mixture (total concentration 270 mg l(-1)) was decreased by in vitro regenerants of reed (P. australis) during 6 weeks to the water contained only MNG (48 mg l(-1)).
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Affiliation(s)
- Radka Podlipná
- Laboratory of Plant Biotechnologies, Joint Laboratory of Institute of Experimental Botany AS CR, v.v.i., and Research Institute of Crop Production, v.v.i., Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Zuzana Fialová
- Laboratory of Plant Biotechnologies, Joint Laboratory of Institute of Experimental Botany AS CR, v.v.i., and Research Institute of Crop Production, v.v.i., Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Tomáš Vaněk
- Laboratory of Plant Biotechnologies, Joint Laboratory of Institute of Experimental Botany AS CR, v.v.i., and Research Institute of Crop Production, v.v.i., Rozvojová 263, 165 02 Prague 6, Czech Republic.
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20
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Halasz A, Thiboutot S, Ampleman G, Hawari J. Microwave-assisted hydrolysis of nitroglycerin (NG) under mild alkaline conditions: new insight into the degradation pathway. CHEMOSPHERE 2010; 79:228-32. [PMID: 20129642 DOI: 10.1016/j.chemosphere.2010.01.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Revised: 01/11/2010] [Accepted: 01/12/2010] [Indexed: 05/17/2023]
Abstract
Nitroglycerin (NG), a nitrate ester, is widely used in the pharmaceutical industry and as an explosive in dynamite and as propellant. Currently NG is considered as a key environmental contaminant due to the discharge of wastewater tainted with the chemical from the military and pharmaceutical industry. The present study describes hydrolytic degradation of NG (200 microM) at pH 9 using either conventional or microwave-assisted heating at 50 degrees C. We found that hydrolytic degradation of NG inside the microwave chamber was much higher than its degradation using conventional heating. Products distributions in both heating systems were closely related and included nitrite, nitrate, formic acid, and the novel intermediates 2-hydroxypropanedial (OCHCH(OH)HCO) and glycolic acid (CH2(OH)COOH). Two other intermediates glycolaldehyde (CH2(OH)CHO) and glyoxylic acid (CHOCOOH) were only detected in the microwave treated samples. The molar ratio of nitrite to nitrate in the presence and absence of microwave heating was 2.5 and 2.8, respectively. In both microwave assisted and conventional heating a nitrogen mass balance of 96% and 98% and a carbon mass balance of 58% and 78%, respectively, were obtained. The lower C mass recovery might be attributed to further unknown reactions, e.g., polymerization of the aldehydes CH2(OH)CHO, CHOCOOH and OCHCH(OH)HCO. A hydrolytic degradation pathway for NG was proposed involving denitration (loss of 2 NO2(-)) from the two primary carbons and the loss of one nitrate from the secondary carbon to produce 2-hydroxypropanedial.
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Affiliation(s)
- Annamaria Halasz
- Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Ave., Montreal, Quebec, Canada H4P2R2
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21
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Growth of Arthrobacter sp. strain JBH1 on nitroglycerin as the sole source of carbon and nitrogen. Appl Environ Microbiol 2010; 76:1689-91. [PMID: 20061454 DOI: 10.1128/aem.02400-09] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Arthrobacter sp. strain JBH1 was isolated from nitroglycerin-contaminated soil by selective enrichment. Detection of transient intermediates and simultaneous adaptation studies with potential intermediates indicated that the degradation pathway involves the conversion of nitroglycerin to glycerol via 1,2-dinitroglycerin and 1-mononitroglycerin, with concomitant release of nitrite. Glycerol then serves as the source of carbon and energy.
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22
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Martel R, Bellavance-Godin A, Lévesque R, Côté S. Determination of Nitroglycerin and Its Degradation Products by Solid-Phase Extraction and LC–UV. Chromatographia 2009. [DOI: 10.1365/s10337-009-1415-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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23
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Getenga Z, Dörfler U, Iwobi A, Schmid M, Schroll R. Atrazine and terbuthylazine mineralization by an Arthrobacter sp. isolated from a sugarcane-cultivated soil in Kenya. CHEMOSPHERE 2009; 77:534-539. [PMID: 19674769 DOI: 10.1016/j.chemosphere.2009.07.031] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Revised: 07/14/2009] [Accepted: 07/16/2009] [Indexed: 05/28/2023]
Abstract
A tropical soil from a Kenyan sugarcane-cultivated field showed a very high capability to mineralize (14)C-ring-labeled atrazine. In laboratory experiments this soil mineralized about 90% of the applied atrazine within 98 d. The atrazine-degrading microbial community was enriched in liquid cultures containing atrazine as the sole N source and 100 mgL(-1) glucose as additional C source. From the enrichment culture a bacterial strain was isolated and identified by comparative sequence analysis of the 16S-rDNA as member of the genus Arthrobacter. The enriched mixed culture as well as the isolated strain, designated as Arthrobacter sp. strain GZK-1, could grow on atrazine and terbuthylazine as sole N-sources; Arthrobacter sp. GZK-1 mineralized (14)C-ring-labeled atrazine up to 88% to (14)CO(2) and (14)C-ring-labeled terbuthylazine up to 65% to (14)CO(2) in a liquid culture within 14 d. The enriched microbial consortium as well as the isolated strain could be a potential solution for the remediation of s-triazine polluted agricultural soils.
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Affiliation(s)
- Zachary Getenga
- Department of Physical Sciences-Masinde Muliro University of Science and Technology, PO Box 190, Kakamega 50100, Kenya
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Mongodin EF, Shapir N, Daugherty SC, DeBoy RT, Emerson JB, Shvartzbeyn A, Radune D, Vamathevan J, Riggs F, Grinberg V, Khouri H, Wackett LP, Nelson KE, Sadowsky MJ. Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1. PLoS Genet 2007; 2:e214. [PMID: 17194220 PMCID: PMC1713258 DOI: 10.1371/journal.pgen.0020214] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2006] [Accepted: 11/02/2006] [Indexed: 01/24/2023] Open
Abstract
Arthrobacter sp. strains are among the most frequently isolated, indigenous, aerobic bacterial genera found in soils. Member of the genus are metabolically and ecologically diverse and have the ability to survive in environmentally harsh conditions for extended periods of time. The genome of Arthrobacter aurescens strain TC1, which was originally isolated from soil at an atrazine spill site, is composed of a single 4,597,686 basepair (bp) circular chromosome and two circular plasmids, pTC1 and pTC2, which are 408,237 bp and 300,725 bp, respectively. Over 66% of the 4,702 open reading frames (ORFs) present in the TC1 genome could be assigned a putative function, and 13.2% (623 genes) appear to be unique to this bacterium, suggesting niche specialization. The genome of TC1 is most similar to that of Tropheryma, Leifsonia, Streptomyces, and Corynebacterium glutamicum, and analyses suggest that A. aurescens TC1 has expanded its metabolic abilities by relying on the duplication of catabolic genes and by funneling metabolic intermediates generated by plasmid-borne genes to chromosomally encoded pathways. The data presented here suggest that Arthrobacter's environmental prevalence may be due to its ability to survive under stressful conditions induced by starvation, ionizing radiation, oxygen radicals, and toxic chemicals. Soil systems contain the greatest diversity of microorganisms on earth, with 5,000–10,000 species of microorganism per gram of soil. Arthrobacter sp. strains have a primitive life cycle and are among the most frequently isolated, indigenous soil bacteria, found in common and deep subsurface soils, arctic ice, and environments contaminated with industrial chemicals and radioactive materials. To better understand how these bacteria survive in environmentally harsh conditions, the authors used a structural genomics approach to identify genes involved in soil survival of Arthrobacter aurescens strain TC1, a bacterium originally isolated for its ability to degrade the herbicide atrazine. They found that the genome of this bacterium comprises a single circular chromosome and two plasmids that encode for a large number proteins involved in stress responses due to starvation, desiccation, oxygen radicals, and toxic chemicals. A. aurescens' metabolic versatility is in part due to the presence of duplicated catabolic genes and its ability to funnel plasmid-derived intermediates into chromosomally encoded pathways. Arthrobacter's array of genes that allow for survival in stressful conditions and its ability to produce a temperature-tolerant “cyst”-like resting cell render this soil microorganism able to survive and prosper in a variety of environmental conditions.
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Affiliation(s)
- Emmanuel F Mongodin
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Nir Shapir
- The BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Sean C Daugherty
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Robert T DeBoy
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Joanne B Emerson
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Alla Shvartzbeyn
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Diana Radune
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Jessica Vamathevan
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Florenta Riggs
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Viktoria Grinberg
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Hoda Khouri
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Lawrence P Wackett
- The BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Karen E Nelson
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Michael J Sadowsky
- The BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- * To whom correspondence should be addressed. E-mail:
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25
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Marshall SJ, Krause D, Blencowe DK, White GF. Characterization of glycerol trinitrate reductase (NerA) and the catalytic role of active-site residues. J Bacteriol 2004; 186:1802-10. [PMID: 14996811 PMCID: PMC355970 DOI: 10.1128/jb.186.6.1802-1810.2004] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glycerol trinitrate reductase (NerA) from Agrobacterium radiobacter, a member of the old yellow enzyme (OYE) family of oxidoreductases, was expressed in and purified from Escherichia coli. Denaturation of pure enzyme liberated flavin mononucleotide (FMN), and spectra of NerA during reduction and reoxidation confirmed its catalytic involvement. Binding of FMN to apoenzyme to form the holoenzyme occurred with a dissociation constant of ca. 10(-7) M and with restoration of activity. The NerA-dependent reduction of glycerol trinitrate (GTN; nitroglycerin) by NADH followed ping-pong kinetics. A structural model of NerA based on the known coordinates of OYE showed that His-178, Asn-181, and Tyr-183 were close to FMN in the active site. The NerA mutation H178A produced mutant protein with bound FMN but no activity toward GTN. The N181A mutation produced protein that did not bind FMN and was isolated in partly degraded form. The mutation Y183F produced active protein with the same k(cat) as that of wild-type enzyme but with altered K(m) values for GTN and NADH, indicating a role for this residue in substrate binding. Correlation of the ratio of K(m)(GTN) to K(m)(NAD(P)H), with sequence differences for NerA and several other members of the OYE family of oxidoreductases that reduce GTN, indicated that Asn-181 and a second Asn-238 that lies close to Tyr-183 in the NerA model structure may influence substrate specificity.
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