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Dash DM, Osborne WJ. A systematic review on the implementation of advanced and evolutionary biotechnological tools for efficient bioremediation of organophosphorus pesticides. CHEMOSPHERE 2023; 313:137506. [PMID: 36526134 DOI: 10.1016/j.chemosphere.2022.137506] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 11/11/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Ever since the concept of bioremediation was introduced, microorganisms, microbial enzymes and plants have been used as principal elements for Organophosphate pesticide (OPP) bioremediation. The enzyme systems and genetic profile of these microbes have been studied deeply in past years. Plant growth promoting rhizobacteria (PGPR) are considered as one of the potential candidates for OPP bioremediation and has been widely used to stimulate the phytoremediation potential of plants. Constructed wetlands (CWs) in OPP biodegradation have brought new prospects to microcosm and mesocosm based remediation strategies. Application of synthetic biology has provided a new dimension to the field of OPP bioremediation by introducing concepts like, gene manipulation andediting, expression and regulation of catabolic enzymes, implementation of whole-cell based and enzyme based biosensor systems for the detection and monitoring of OPP pollution in both terrestrial and aquatic environment. System biology and bioinformatics tools have rendered significant knowledge regarding the genetic, enzymatic and biochemical aspects of microbes and plants thereby, helping researchers to analyze the mechanism of OPP biodegradation. Structural biology has provided significant conceptual information regarding OPP biodegradation pathways, structural and functional characterization of metabolites and enzymes, enzyme-pollutant interactions, etc. Therefore, this review discussed the prospects and challenges of most advanced and high throughput strategies implemented for OPP biodegradation. The review also established a comparative analysis of various bioremediation techniques and highlighted the interdependency among them. The review highly suggested the simultaneous implementation of more than one remediation strategy or a combinational approach creating an advantageous hybrid technique for OPP bioremediation.
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Affiliation(s)
- Dipti Mayee Dash
- Department of Bioscience School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India
| | - W Jabez Osborne
- Department of Bioscience School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India.
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Haque MA, Hossain MS, Ahmad I, Akbor MA, Rahman A, Manir MS, Patel HM, Cho KM. Unveiling chlorpyrifos mineralizing and tomato plant-growth activities of Enterobacter sp. strain HSTU-ASh6 using biochemical tests, field experiments, genomics, and in silico analyses. Front Microbiol 2022; 13:1060554. [PMID: 36523825 PMCID: PMC9745158 DOI: 10.3389/fmicb.2022.1060554] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/07/2022] [Indexed: 07/29/2023] Open
Abstract
The chlorpyrifos-mineralizing rice root endophyte Enterobacter sp. HSTU-ASh6 strain was identified, which enormously enhanced the growth of tomato plant under epiphytic conditions. The strain solubilizes phosphate and grew in nitrogen-free Jensen's medium. It secreted indole acetic acid (IAA; 4.8 mg/mL) and ACC deaminase (0.0076 μg/mL/h) and hydrolyzed chlorpyrifos phosphodiester bonds into 3,5,6-trichloro-2-pyridinol and diethyl methyl-monophosphate, which was confirmed by Gas Chromatography - Tandem Mass Spectrometry (GC-MS/MS) analysis. In vitro and in silico (ANI, DDH, housekeeping genes and whole genome phylogenetic tree, and genome comparison) analyses confirmed that the strain belonged to a new species of Enterobacter. The annotated genome of strain HSTU-ASh6 revealed a sets of nitrogen-fixing, siderophore, acdS, and IAA producing, stress tolerance, phosphate metabolizing, and pesticide-degrading genes. The 3D structure of 28 potential model proteins that can degrade pesticides was validated, and virtual screening using 105 different pesticides revealed that the proteins exhibit strong catalytic interaction with organophosphorus pesticides. Selected docked complexes such as α/β hydrolase-crotoxyphos, carboxylesterase-coumaphos, α/β hydrolase-cypermethrin, α/β hydrolase-diazinon, and amidohydrolase-chlorpyrifos meet their catalytic triads in visualization, which showed stability in molecular dynamics simulation up to 100 ns. The foliar application of Enterobacter sp. strain HSTU-ASh6 on tomato plants significantly improved their growth and development at vegetative and reproductive stages in fields, resulting in fresh weight and dry weight was 1.8-2.0-fold and 1.3-1.6-fold higher in where urea application was cut by 70%, respectively. Therefore, the newly discovered chlorpyrifos-degrading species Enterobacter sp. HSTU-ASh6 could be used as a smart biofertilizer component for sustainable tomato cultivation.
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Affiliation(s)
- Md. Azizul Haque
- Department of Biochemistry and Molecular Biology, Hajee Mohammad Danesh Science & Technology University, Dinajpur, Bangladesh
| | - Md. Shohorab Hossain
- Department of Biochemistry and Molecular Biology, Hajee Mohammad Danesh Science & Technology University, Dinajpur, Bangladesh
| | - Iqrar Ahmad
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Md. Ahedul Akbor
- Institute of National Analytical Research and Services, Bangladesh Council of Scientific and Industrial Research, Dhaka, Bangladesh
| | - Aminur Rahman
- Department of Biomedical Sciences, College of Clinical Pharmacy, King Faisal University, Al Hofuf, Saudi Arabia
| | - Md. Serajum Manir
- Institute of Radiation and Polymer Technology, Bangladesh Atomic Energy Research Establishment, Dhaka, Bangladesh
| | - Harun M. Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Kye Man Cho
- Department of GreenBio Science and Agri-Food Bio Convergence Institute, Gyeongsang National University, Jinju, South Korea
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Bhatt P, Zhou X, Huang Y, Zhang W, Chen S. Characterization of the role of esterases in the biodegradation of organophosphate, carbamate, and pyrethroid pesticides. JOURNAL OF HAZARDOUS MATERIALS 2021; 411:125026. [PMID: 33461010 DOI: 10.1016/j.jhazmat.2020.125026] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/08/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
Ester-containing organophosphate, carbamate, and pyrethroid (OCP) pesticides are used worldwide to minimize the impact of pests and increase agricultural production. The toxicity of these chemicals to humans and other organisms has been widely reported. Chemically, these pesticides share an ester bond in their parent structures. A particular group of hydrolases, known as esterases, can catalyze the first step in ester-bond hydrolysis, and this initial regulatory metabolic reaction accelerates the degradation of OCP pesticides. Esterases can be naturally found in plants, animals, and microorganisms. Previous research on the esterase enzyme mechanisms revealed that the active sites of esterases contain serine residues that catalyze reactions via a nucleophilic attack on the substrates. In this review, we have compiled the previous research on esterases from different sources to determine and summarize the current knowledge of their properties, classifications, structures, mechanisms, and their applications in the removal of pesticides from the environment. This review will enhance the understanding of the scientific community when studying esterases and their applications for the degradation of broad-spectrum ester-containing pesticides.
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Affiliation(s)
- Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xiaofan Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yaohua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Wenping Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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Hu Y, Zheng L, Zhang J, Shen Y, Zhang X, Lin L. LncRNA-MALAT1 is a promising biomarker for prognostic evaluation of tongue squamous cell carcinoma. Eur Arch Otorhinolaryngol 2020; 277:3155-3160. [PMID: 32383096 DOI: 10.1007/s00405-020-06023-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/27/2020] [Indexed: 01/04/2023]
Abstract
PURPOSE MALAT1 is recognized as an oncogenic lncRNA in various malignancies. Here, the authors aim to explore the association of MALAT1 expression and prognostic implication in tongue squamous cell carcinoma (SCC). METHODS The tongue tissues of 128 tongue SCC cases satisfying strict follow-up criteria and 28 normal cases were subjected to qRT-PCR assay for monitoring MALAT1 expression. Chi-square test was applied to explore the correlation between MALAT1 expression and clinicopathological features of tongue SCC. Kaplan-Meier analysis was used to calculate survival rates. Cox proportional hazard analysis was adopted to analyze the relationship between prognostic factors and patient survival. RESULTS The expression of MALAT1 was upregulated in tongue SCC, compared to normal tongue tissues. The expression level of MALAT1 was correlated to differentiation and stage of tongue SCC, and high MALAT1 expression was associated with low disease-free survival and overall survival rates. Moreover, advanced tongue SCC patients with high MALAT1 level had lower disease-free survival and decreased overall survival rate than patients with low MALAT1 level. These results revealed that MALAT1 overexpression can be considered as a significant prognostic factor to independently predict the disease-free survival and overall survival rate of tongue SCC. CONCLUSIONS The expression level of MALAT1 is closely related with progression of tongue SCC. Furthermore, MALAT1 can serve as an independent biomarker for prognostic evaluation of tongue SCC.
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Affiliation(s)
- Yuqian Hu
- Institute of Molecular Medicine, Medical College of Eastern Liaoning University, Dandong, 118000, China
| | - Linlin Zheng
- Institute of Molecular Medicine, Medical College of Eastern Liaoning University, Dandong, 118000, China
| | - Jinhui Zhang
- Institute of Molecular Medicine, Medical College of Eastern Liaoning University, Dandong, 118000, China
| | - Yue Shen
- Institute of Molecular Medicine, Medical College of Eastern Liaoning University, Dandong, 118000, China
| | - Xiaoyan Zhang
- Department of Pathology, Fifth People's Hospital of Shenyang City, Shenyang Tumor Hospital, Shenyang, 110023, China.
| | - Lijuan Lin
- Institute of Molecular Medicine, Medical College of Eastern Liaoning University, Dandong, 118000, China.
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Allahyari H, Karami A, Tebyanian H, Nouri HR, Khodi S, Farnoosh G, Arab SS, Latifi AM. Applying<i> In Silico</i> Approaches for Designing a Chimeric InaV/N-DFPase Protein and Evaluating its Binding with Diisopropyl-Fluorophosphate. INTERNATIONAL LETTERS OF NATURAL SCIENCES 2019. [DOI: 10.18052/www.scipress.com/ilns.75.41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The N-terminal domain of the ice-nucleation protein InaV (InaV-N) ofPseudomonas syringaewas applied to display the DFPase on the cell surface.In silicotechniques were used to generate a model in order to examine the possibility of DFPase exhibition on the cell surface. The secondary and tertiary structures of a chimeric protein were determined and then, the predicted model was subjected to several repeated cycles of stereochemical evaluation and energy minimization. The homology-modeled structure of the InaV/N-DFPase protein was docked to DFP. The optimizedinaV/N-dfpasegene was translated to 519 amino acids. The minimum free energy of the best-predicted secondary structures was formed by RNA molecules (-215.45 kcal/mol). SOPMA analysis results showed that the main helix peak corresponded to the anchor fragment. Validation of the 3D model indicated that 86.1% of amino acid residues were incorporated into the favored regions. The moldock score was 360.22 for DFP. Results of this study indicated that according toin silicoanalysis, all of these findings were effective in targeting DFPase.
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Affiliation(s)
- Hossein Allahyari
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Karami
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | | | - Hamid Reza Nouri
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Samaneh Khodi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | | | | | - Ali Mohammad Latifi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Meng D, Jiang W, Li J, Huang L, Zhai L, Zhang L, Guan Z, Cai Y, Liao X. An alkaline phosphatase from Bacillus amyloliquefaciens YP6 of new application in biodegradation of five broad-spectrum organophosphorus pesticides. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2019; 54:336-343. [PMID: 30822193 DOI: 10.1080/03601234.2019.1571363] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In recent decades, biodegradation has been considered a promising and eco-friendly way to eliminate organophosphorus pesticides (OPs) from the environment. To enrich current biodegrading-enzyme resources, an alkaline phosphatase (AP3) from Bacillus amyloliquefaciens YP6 was characterized and utilized to test the potential for new applications in the biodegradation of five broad-spectrum OPs. Characterization of AP3 demonstrated that activity was optimal at 40 °C and pH 10.3. The activity of AP3 was enhanced by Mg2+, Ca2+, and Cu2+, and strongly inhibited by Mn2+, EDTA, and L-Cys. Compared to disodium phenyl phosphate, p-nitrophenyl phosphate (pNPP) was more suitable to AP3, and the Vm, Km, kcat, kcat/Km values of AP3 for pNPP were 4,033 U mg-1, 12.2 mmol L-1, 3.3 × 106 s-1, and 2.7 × 108 s-1mol-1L, respectively. Degradation of the five OPs, which included chlorpyrifos, dichlorvos, dipterex, phoxim, and triazophos, was 18.7%, 53.0%, 5.5%, 68.3%, and 96.3%, respectively, after treatment with AP3 for 1 h. After treatment of the OP for 8 h, AP3 activities remained more than 80%, with the exception of phoxim. It can be postulated that AP3 may have a broad OP-degradation ability and could possibly provide excellent potential for biodegradation and bioremediation in polluted ecosystems.
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Affiliation(s)
- Di Meng
- a Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Jiangsu , China
| | - Wei Jiang
- a Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Jiangsu , China
| | - Jing Li
- a Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Jiangsu , China
| | - Lin Huang
- a Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Jiangsu , China
| | - Lixin Zhai
- a Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Jiangsu , China
| | - Liyuan Zhang
- a Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Jiangsu , China
| | - Zhengbing Guan
- a Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Jiangsu , China
| | - Yujie Cai
- a Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Jiangsu , China
| | - Xiangru Liao
- a Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Jiangsu , China
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Olsen AJ, Halvorsen LA, Yang CY, Barak Ventura R, Yin L, Renfrew PD, Bonneau R, Montclare JK. Impact of phenylalanines outside the dimer interface on phosphotriesterase stability and function. MOLECULAR BIOSYSTEMS 2018; 13:2092-2106. [PMID: 28817149 DOI: 10.1039/c7mb00196g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We explore the significance of phenylalanine outside of the phosphotriesterase (PTE) dimer interface through mutagenesis studies and computational modeling. Previous studies have demonstrated that the residue-specific incorporation of para-fluorophenylalanine (pFF) into PTE improves stability, suggesting the importance of phenylalanines in stabilization of the dimer. However, this comes at a cost of decreased solubility due to pFF incorporation into other parts of the protein. Motivated by this, eight single solvent-exposed phenylalanine mutants are evaluated viarosetta and good correspondence between experiments and these predictions is observed. Three residues, F304, F327, and F335, appear to be important for PTE activity and stability, even though they do not reside in the dimer interface region or active site. While the remaining mutants do not significantly affect structure or activity, one variant, F306L, reveals improved activity at ambient and elevated temperatures. These studies provide further insight into role of these residues on PTE function and stability.
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Affiliation(s)
- Andrew J Olsen
- Department of Chemical and Biomolecular Engineering, New York University, Tandon School of Engineering, New York 11201, USA
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8
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Fan S, Li K, Yan Y, Wang J, Wang J, Qiao C, Yang T, Jia Y, Zhao B. A novel chlorpyrifos hydrolase CPD from Paracoccus sp. TRP: Molecular cloning, characterization and catalytic mechanism. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2017.10.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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9
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Effect of culture conditions on the whole cell activity of recombinant Escherichia coli expressing periplasmic organophosphorus hydrolase and cytosolic GroEL/ES chaperone. BIOTECHNOL BIOPROC E 2016. [DOI: 10.1007/s12257-016-0342-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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10
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Jacquet P, Daudé D, Bzdrenga J, Masson P, Elias M, Chabrière E. Current and emerging strategies for organophosphate decontamination: special focus on hyperstable enzymes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:8200-18. [PMID: 26832878 DOI: 10.1007/s11356-016-6143-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 01/20/2016] [Indexed: 06/05/2023]
Abstract
Organophosphorus chemicals are highly toxic molecules mainly used as pesticides. Some of them are banned warfare nerve agents. These compounds are covalent inhibitors of acetylcholinesterase, a key enzyme in central and peripheral nervous systems. Numerous approaches, including chemical, physical, and biological decontamination, have been considered for developing decontamination methods against organophosphates (OPs). This work is an overview of both validated and emerging strategies for the protection against OP pollution with special attention to the use of decontaminating enzymes. Considerable efforts have been dedicated during the past decades to the development of efficient OP degrading biocatalysts. Among these, the promising biocatalyst SsoPox isolated from the archaeon Sulfolobus solfataricus is emphasized in the light of recently published results. This hyperthermostable enzyme appears to be particularly attractive for external decontamination purposes with regard to both its catalytic and stability properties.
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Affiliation(s)
- Pauline Jacquet
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - David Daudé
- Gene&GreenTK, Faculté de Médecine, 27 boulevard Jean Moulin, Cedex 5, Marseille, 13385, France
| | - Janek Bzdrenga
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Patrick Masson
- Neuropharmacology Laboratory, Kazan Federal University, Kazan, 420008, Russia
| | - Mikael Elias
- Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA
| | - Eric Chabrière
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France.
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Kang DG, Seo JH, Jo BH, Kim CS, Choi SS, Cha HJ. Versatile signal peptide ofFlavobacterium-originated organophosphorus hydrolase for efficient periplasmic translocation of heterologous proteins inEscherichia coli. Biotechnol Prog 2016; 32:848-54. [DOI: 10.1002/btpr.2274] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 04/04/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Dong Gyun Kang
- Dept. of Chemical Engineering; Pohang University of Science and Technology; Pohang 790-784 Korea
| | - Jeong Hyun Seo
- School of Chemical Engineering; Yeungnam University; Gyeongsan 712-749 Korea
| | - Byung Hoon Jo
- Dept. of Chemical Engineering; Pohang University of Science and Technology; Pohang 790-784 Korea
| | - Chang Sup Kim
- School of Biotechnolgy and Graduate School of Biochemistry; Yeungnam University; Gyeongsan 712-749 Korea
| | - Suk Soon Choi
- Dept. of Biological and Environmental Engineering; Semyung University; Jecheon 390-711 Korea
| | - Hyung Joon Cha
- Dept. of Chemical Engineering; Pohang University of Science and Technology; Pohang 790-784 Korea
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Nakayama K, Ohmori T, Ishikawa S, Iwata N, Seto Y, Kawahara K. Expression of recombinant organophosphorus hydrolase in the original producer of the enzyme, Sphingobium fuliginis ATCC 27551. Biosci Biotechnol Biochem 2016; 80:1024-6. [PMID: 26784883 DOI: 10.1080/09168451.2015.1123606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The plasmid encoding His-tagged organophosphorus hydrolase (OPH) cloned from Sphingobium fuliginis was modified to be transferred back to this bacterium. The replication function of S. amiense plasmid was inserted at downstream of OPH gene, and S. fuliginis was transformed with this plasmid. The transformant produced larger amount of active OPH with His-tag than E. coli.
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Affiliation(s)
- Kosuke Nakayama
- a Department of Biosciences, College of Science and Engineering , Kanto Gakuin University , Yokohama , Japan
| | - Takeshi Ohmori
- b Third Department of Forensic Science , National Research Institute of Police Science , Kashiwa , Japan
| | - Satoshi Ishikawa
- a Department of Biosciences, College of Science and Engineering , Kanto Gakuin University , Yokohama , Japan
| | - Natsumi Iwata
- a Department of Biosciences, College of Science and Engineering , Kanto Gakuin University , Yokohama , Japan
| | - Yasuo Seto
- b Third Department of Forensic Science , National Research Institute of Police Science , Kashiwa , Japan
| | - Kazuyoshi Kawahara
- b Third Department of Forensic Science , National Research Institute of Police Science , Kashiwa , Japan
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13
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Simultaneous degradation of organophosphorus and organochlorine pesticides by bacterial consortium. J Taiwan Inst Chem Eng 2014. [DOI: 10.1016/j.jtice.2014.06.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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Nakayama K, Ishikawa S, Kawahara K, Ohmori T, Seto Y. Improvement of organophosphorus hydrolase activity toward nerve agents by amino acid substitutions. Forensic Toxicol 2014. [DOI: 10.1007/s11419-013-0223-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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15
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Biodegradation of chlorpyrifos and its hydrolyzing metabolite 3,5,6-trichloro-2-pyridinol by Sphingobacterium sp. JAS3. Process Biochem 2013. [DOI: 10.1016/j.procbio.2013.06.034] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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16
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Kim CS, Choi BH, Seo JH, Lim G, Cha HJ. Mussel adhesive protein-based whole cell array biosensor for detection of organophosphorus compounds. Biosens Bioelectron 2013; 41:199-204. [DOI: 10.1016/j.bios.2012.08.022] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 07/31/2012] [Accepted: 08/08/2012] [Indexed: 02/07/2023]
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17
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Lu P, Li Q, Liu H, Feng Z, Yan X, Hong Q, Li S. Biodegradation of chlorpyrifos and 3,5,6-trichloro-2-pyridinol by Cupriavidus sp. DT-1. BIORESOURCE TECHNOLOGY 2013; 127:337-342. [PMID: 23131657 DOI: 10.1016/j.biortech.2012.09.116] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 08/21/2012] [Accepted: 09/28/2012] [Indexed: 06/01/2023]
Abstract
A bacterial strain, Cupriavidus sp. DT-1, capable of degrading chlorpyrifos and 3,5,6-trichloro-2-pyridinol (TCP) and using these compounds as sole carbon source was isolated and characterized. Investigation of the degradation pathway showed that chlorpyrifos was first hydrolyzed to TCP, successively dechlorinated to 2-pyridinol, and then subjected to the cleavage of the pyridine ring and further degradation. The mpd gene, encoding the enzyme responsible for chlorpyrifos hydrolysis to TCP, was cloned and expressed in Escherichia coli BL21. Inoculation of chlorpyrifos-contaminated soil with strain DT-1 resulted in a degradation rate of chlorpyrifos and TCP of 100% and 94.3%, respectively as compared to a rate of 28.2% and 19.9% in uninoculated soil. This finding suggests that strain DT-1 has potential for use in bioremediation of chlorpyrifos-contaminated environments.
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Affiliation(s)
- Peng Lu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Science, Nanjing Agriculture University, Nanjing 210095, People's Republic of China
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Zhang L, Chen R, Dong Z, Li X. Overexpression, crystallization and preliminary X-ray crystallographic analysis of the phosphotriesterase from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:57-60. [PMID: 23295488 PMCID: PMC3539705 DOI: 10.1107/s1744309112049032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 11/29/2012] [Indexed: 11/07/2023]
Abstract
Organophosphates (OPs) are extremely toxic compounds that are used as insecticides or even as chemical warfare agents. Phosphotriesterases (PHPs) are responsible for the detoxification of OPs by catalysing their degradation. Almost 100 PHP structures have been solved to date, yet the crystal structure of the phosphotriesterase from Mycobacterium tuberculosis (mPHP) remains unavailable. This study reports the first crystallization of mPHP. The crystal belonged to space group C222(1), with unit-cell parameters a = 68.03, b = 149.60, c = 74.23 Å, α = β = γ = 90°. An analytical ultracentrifugation experiment suggested that mPHP exists as a dimer in solution, even though one molecule is calculated to be present in the asymmetric unit according to the structural data.
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Affiliation(s)
- Liang Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, People’s Republic of China
| | - Ruyi Chen
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, People’s Republic of China
| | - Zhe Dong
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, People’s Republic of China
| | - Xin Li
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, People’s Republic of China
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19
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Iyer R, Iken B. Identification of water-borne bacterial isolates for potential remediation of organophosphate contamination. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/abc.2013.31018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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20
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Ohmori T, Kawahara K, Nakayama K, Shioda A, Ishikawa S, Kanamori-Kataoka M, Kishi S, Komano A, Seto Y. Decontamination of nerve agents by immobilized organophosphorus hydrolase. Forensic Toxicol 2012. [DOI: 10.1007/s11419-012-0162-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Estimating the biodegradation of pesticide in soils by monitoring pesticide-degrading gene expression. Biodegradation 2012; 24:203-13. [PMID: 22991035 DOI: 10.1007/s10532-012-9574-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 07/09/2012] [Indexed: 10/28/2022]
Abstract
Assessing in situ microbial abilities of soils to degrade pesticides is of great interest giving insight in soil filtering capability, which is a key ecosystem function limiting pollution of groundwater. Quantification of pesticide-degrading gene expression by reverse transcription quantitative PCR (RT-qPCR) was tested as a suitable indicator to monitor pesticide biodegradation performances in soil. RNA extraction protocol was optimized to enhance the yield and quality of RNA recovered from soil samples to perform RT-qPCR assays. As a model, the activity of atrazine-degrading communities was monitored using RT-qPCRs to estimate the level of expression of atzD in five agricultural soils showing different atrazine mineralization abilities. Interestingly, the relative abundance of atzD mRNA copy numbers was positively correlated to the maximum rate and to the maximal amount of atrazine mineralized. Our findings indicate that the quantification of pesticide-degrading gene expression may be suitable to assess biodegradation performance in soil and monitor natural attenuation of pesticide.
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Kang DG, Kim CS, Seo JH, Kim IG, Choi SS, Ha JH, Nam SW, Lim G, Cha HJ. Coexpression of molecular chaperone enhances activity and export of organophosphorus hydrolase in Escherichia coli. Biotechnol Prog 2012; 28:925-30. [DOI: 10.1002/btpr.1556] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 04/10/2012] [Indexed: 11/06/2022]
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23
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Wales ME, Reeves TE. Organophosphorus hydrolase as an in vivo catalytic nerve agent bioscavenger. Drug Test Anal 2012; 4:271-81. [DOI: 10.1002/dta.381] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 10/03/2011] [Accepted: 10/03/2011] [Indexed: 11/12/2022]
Affiliation(s)
- Melinda E. Wales
- Department of Biochemistry & Biophysics; Texas A&M University; College Station; TX; USA
| | - Tony E. Reeves
- Southwest Research Institute; Microencapsulation and Nanomaterials, Chemistry and Chemical Engineering Division; San Antonio; TX; USA
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24
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Ekkhunnatham A, Jongsareejit B, Yamkunthong W, Wichitwechkarn J. Purification and characterization of methyl parathion hydrolase from Burkholderia cepacia capable of degrading organophosphate insecticides. World J Microbiol Biotechnol 2011; 28:1739-46. [DOI: 10.1007/s11274-011-0985-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 12/16/2011] [Indexed: 12/01/2022]
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25
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Wang S, Zhang C, Yan Y. Biodegradation of methyl parathion and p-nitrophenol by a newly isolated Agrobacterium sp. strain Yw12. Biodegradation 2011; 23:107-16. [PMID: 21744158 DOI: 10.1007/s10532-011-9490-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Accepted: 06/07/2011] [Indexed: 10/18/2022]
Abstract
Strain Yw12, isolated from activated sludge, could completely degrade and utilize methyl parathion as the sole carbon, phosphorus and energy sources for growth in the basic salt media. It could also completely degrade and utilize p-nitrophenol as the sole carbon and energy sources for growth in the minimal salt media. Phenotypic features, physiological and biochemical characteristics, and phylogenetic analysis of 16S rRNA sequence showed that this strain belongs to the genus of Agrobacterium sp. Response surface methodology was used to optimize degradation conditions. Under its optimal degradation conditions, 50 mg l(-1) MP was completely degraded within 2 h by strain Yw12 and the degradation product PNP was also completely degraded within 6 h. Furthermore, strain Yw12 could also degrade phoxim, methamidophos, chlorpyrifos, carbofuran, deltamethrin and atrazine when provided as the sole carbon and energy sources. Enzymatic analysis revealed that the MP degrading enzyme of strain Yw12 is an intracellular enzyme and is expressed constitutively. These results indicated that strain Yw12 might be used as a potential and effective organophosphate pesticides degrader for bioremediation of contaminated sites.
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Affiliation(s)
- Shenghui Wang
- Graduate School, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, China
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26
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Ali M, Naqvi TA, Kanwal M, Rasheed F, Hameed A, Ahmed S. Detection of the organophosphate degrading gene opdA in the newly isolated bacterial strain Bacillus pumilus W1. ANN MICROBIOL 2011. [DOI: 10.1007/s13213-011-0251-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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27
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Choi SS, Seo SH, Kang DG, Ha JH, Cha HJ. Removal of neurotoxic ethyl parathion pesticide by two-stage chemical/enzymatic treatment system using Fenton’s reagent and organophosphorous hydrolase. KOREAN J CHEM ENG 2010. [DOI: 10.1007/s11814-010-0115-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Shen YJ, Lu P, Mei H, Yu HJ, Hong Q, Li SP. Isolation of a methyl parathion-degrading strain Stenotrophomonas sp. SMSP-1 and cloning of the ophc2 gene. Biodegradation 2010; 21:785-92. [PMID: 20182770 DOI: 10.1007/s10532-010-9343-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Accepted: 02/11/2010] [Indexed: 11/25/2022]
Abstract
A rod-shaped, gram-negative bacterium Stenotrophomonas sp. SMSP-1 was isolated from the sludge of a wastewater treating system of a pesticide manufacturer. Strain SMSP-1 could hydrolyze methyl parathion to p-nitrophenol (PNP) and dimethyl phosphorothioate but could not degrade PNP further. Strain SMSP-1 was able to hydrolyze other organophosphate pesticides, including fenitrothion, ethyl parathion, fenthion, and phoxim, but not chlorpyrifos. A 4395-bp DNA fragment, including an organophosphorus hydrolase encoding gene ophc2, was cloned from the chromosome of strain SMSP-1 using the shotgun technique. Its sequence analysis showed that ophc2 was associated with a typical mobile element ISPpu12 consisting of tnpA (encoding a transposase), lspA (encoding a lipoprotein signal peptidase), and orf1 (encoding a CDF family heavy metal/H(+) antiporter). The ophc2 gene was effectively expressed in E. coli. This is the second report of cloning the ophc2 gene and the first report of this gene from the genus of Stenotrophomonas.
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Affiliation(s)
- Yu-jia Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
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29
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Organophosphate hydrolase in Brevundimonas diminuta is targeted to the periplasmic face of the inner membrane by the twin arginine translocation pathway. J Bacteriol 2009; 191:6292-9. [PMID: 19700527 DOI: 10.1128/jb.00824-09] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A twin arginine translocation (Tat) motif, involved in transport of folded proteins across the inner membrane, was identified in the signal peptide of the membrane-associated organophosphate hydrolase (OPH) of Brevundimonas diminuta. Expression of the precursor form of OPH carrying a C-terminal His tag in an opd-negative background and subsequent immunoblotting with anti-His antibodies showed that only the mature form of OPH associated with the membrane and that the precursor form of OPH was entirely found in the cytoplasm. When OPH was expressed without the signal peptide, most of it remained in the cytoplasm, where it was apparently correctly folded and showed activity comparable to that of the membrane-associated OPH encoded by the wild-type opd gene. Amino acid substitutions in the invariant arginine residues of the Tat signal peptide affected both the processing and localization of OPH, confirming a critical role for the Tat system in membrane targeting of OPH in B. diminuta. The localization of OPH to the periplasmic face of the inner membrane in B. diminuta was demonstrated by proteinase K treatment of spheroplasts and also by fluorescence-activated cell sorting analysis of cells expressing OPH-green fluorescent protein fusions with and without an SsrA tag that targets cytoplasmic proteins to the ClpXP protease.
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30
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Kolakowski JE, Defrank JJ, Harvey SP, Szafraniec LL, Beaudry WT, Lai K, Wild JR. Enzymatic Hydrolysis of the Chemical Warfare Agent VX and its Neurotoxic Analogues by Organophosphorus Hydrolase. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.3109/10242429709003196] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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31
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Petrikovics I, Wales ME, Jaszberenyi JC, Budai M, Baskin SI, Szilasi M, Logue BA, Chapela P, Wild JR. Enzyme-based intravascular defense against organophosphorus neurotoxins: Synergism of dendritic-enzyme complexes with 2-PAM and atropine. Nanotoxicology 2009. [DOI: 10.1080/17435390500128271] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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32
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Singh S, Kang SH, Mulchandani A, Chen W. Bioremediation: environmental clean-up through pathway engineering. Curr Opin Biotechnol 2008; 19:437-44. [PMID: 18760355 DOI: 10.1016/j.copbio.2008.07.012] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Revised: 07/24/2008] [Accepted: 07/29/2008] [Indexed: 11/25/2022]
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33
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Pei L, McGuinn GD, Petrikovics I, Pu L, Cannon EP, Way JL. Determination of Organophosphorus Acid Anhydrase in Blood. ACTA ACUST UNITED AC 2008. [DOI: 10.3109/15376519309068443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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34
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Kang DG, Li L, Ha JH, Choi SS, Cha HJ. Efficient cell surface display of organophosphorous hydrolase using N-terminal domain of ice nucleation protein in Escherichia coli. KOREAN J CHEM ENG 2008. [DOI: 10.1007/s11814-008-0132-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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35
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Burnworth M, Rowan SJ, Weder C. Fluorescent Sensors for the Detection of Chemical Warfare Agents. Chemistry 2007; 13:7828-36. [PMID: 17705326 DOI: 10.1002/chem.200700720] [Citation(s) in RCA: 176] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Along with biological and nuclear threats, chemical warfare agents are some of the most feared weapons of mass destruction. Compared to nuclear weapons they are relatively easy to access and deploy, which makes them in some aspects a greater threat to national and global security. A particularly hazardous class of chemical warfare agents are the nerve agents. Their rapid and severe effects on human health originate in their ability to block the function of acetylcholinesterase, an enzyme that is vital to the central nervous system. This article outlines recent activities regarding the development of molecular sensors that can visualize the presence of nerve agents (and related pesticides) through changes of their fluorescence properties. Three different sensing principles are discussed: enzyme-based sensors, chemically reactive sensors, and supramolecular sensors. Typical examples are presented for each class and different fluorescent sensors for the detection of chemical warfare agents are summarized and compared.
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Affiliation(s)
- Mark Burnworth
- Department of Macromolecular Science and Engineering, Case Western Reserve University, 2100 Adelbert Road, Cleveland OH 44106-7202, USA
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36
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Paliwal S, Wales M, Good T, Grimsley J, Wild J, Simonian A. Fluorescence-based sensing of p-nitrophenol and p-nitrophenyl substituent organophosphates. Anal Chim Acta 2007; 596:9-15. [PMID: 17616234 DOI: 10.1016/j.aca.2007.05.034] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2006] [Revised: 05/17/2007] [Accepted: 05/23/2007] [Indexed: 11/20/2022]
Abstract
A novel detection method for organophosphate neurotoxins has been described, based on the fluorescence quenching of a Coumarin derivative. These dyes are similar in structure to some organophosphates (OPs), and they fluoresce in the blue-green region of the spectra. This methodology has been utilized for the detection of organophosphates whose hydrolysis product is p-nitrophenol by using an enzyme, organophosphorus hydrolase (OPH). Coumarin1 in the presence of p-nitrophenol results in a quenching of fluorescence, providing a direct measure of the concentration of p-nitrophenol present in the sample. The decrease in fluorescence intensity is proportional to the paraoxon concentration in the range of 7.0x10(-7)-1.7x10(-4) M. The specificity of this sensing application for p-nitrophenyl substituent OPs has also been demonstrated. OPs are a class of synthetic organic pesticides which generally have a short residual life and can cause numerous acute and chronic health effects. They have been an integral part of the agricultural industry for the past several decades due to their target specificities and selectable toxicities. The toxic nature of these compounds can be attributed to the species-specific inhibition of acetylcholinesterase (AChE), an important enzyme responsible for the regeneration of neural synaptic function. In addition to their wide agricultural and urban usage, they have also been exploited for the development of neurological chemical warfare agents. Currently available technologies for OP detection include sol-gel thin films, screen printed electrodes, acoustic patterning, gas chromatography-mass spectrometry, and various other intricate techniques that have limited field applicabilities. This optically-based approach promises much simpler and more direct detection capabilities.
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Affiliation(s)
- Sheetal Paliwal
- Materials Research and Education Center, Auburn University, United States
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37
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Ramanathan M, Simonian AL. Array biosensor based on enzyme kinetics monitoring by fluorescence spectroscopy: Application for neurotoxins detection. Biosens Bioelectron 2007; 22:3001-7. [PMID: 17270415 DOI: 10.1016/j.bios.2006.12.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2006] [Revised: 12/12/2006] [Accepted: 12/15/2006] [Indexed: 10/23/2022]
Abstract
The aim of the present work is to develop an evanescence wave array biosensor exploiting the "kinetic" approach of enzymatic reaction and further detection of the reaction products via pH sensitive fluorophore reporter. To demonstrate the feasibility of this approach, we have developed a biosensor array with the potential for direct detection of organophosphates using as a biorecognition element, an enzyme organophosphorus hydrolase (OPH), conjugated with a pH-sensitive fluorophore, carboxynaphthofluorescein (CNF). The presence of reference spots allows the discrimination of the enzymatic and non-enzymatic based pH changes; bovine serum albumin (BSA) was used as a non-enzymatic scaffold protein for CNF attachment at the reference spots. An array biosensor unit developed at the Naval Research Laboratories (NRL) was adopted as the detection platform and appropriately modified for enzyme-based measurements. A planar multi-mode waveguide was covered with an optically transparent TiO(2) layer to increase the surface area available for immobilization. The biosensor enabled the detection of 2.5 microM paraoxon, and 10 microM DFP and parathion, respectively. Very short response time of 30s can be achieved with a total analysis time of less than 2 min. When operated at room temperature and stored at 4 degrees C, the waveguide retained reasonable activity for greater than 45 days.
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Affiliation(s)
- M Ramanathan
- Materials Research and Education Center, Samuel Ginn College of Engineering, 274 Wilmore Laboratory, Auburn University, 201 Ross Hall, Auburn, AL-36849, USA
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38
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Pakala SB, Gorla P, Pinjari AB, Krovidi RK, Baru R, Yanamandra M, Merrick M, Siddavattam D. Biodegradation of methyl parathion and p-nitrophenol: evidence for the presence of a p-nitrophenol 2-hydroxylase in a Gram-negative Serratia sp. strain DS001. Appl Microbiol Biotechnol 2006; 73:1452-62. [PMID: 17043828 DOI: 10.1007/s00253-006-0595-z] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2006] [Revised: 07/22/2006] [Accepted: 08/07/2006] [Indexed: 11/30/2022]
Abstract
A soil bacterium capable of utilizing methyl parathion as sole carbon and energy source was isolated by selective enrichment on minimal medium containing methyl parathion. The strain was identified as belonging to the genus Serratia based on a phylogram constructed using the complete sequence of the 16S rRNA. Serratia sp. strain DS001 utilized methyl parathion, p-nitrophenol, 4-nitrocatechol, and 1,2,4-benzenetriol as sole carbon and energy sources but could not grow using hydroquinone as a source of carbon. p-Nitrophenol and dimethylthiophosphoric acid were found to be the major degradation products of methyl parathion. Growth on p-nitrophenol led to release of stoichiometric amounts of nitrite and to the formation of 4-nitrocatechol and benzenetriol. When these catabolic intermediates of p-nitrophenol were added to resting cells of Serratia sp. strain DS001 oxygen consumption was detected whereas no oxygen consumption was apparent when hydroquinone was added to the resting cells suggesting that it is not part of the p-nitrophenol degradation pathway. Key enzymes involved in degradation of methyl parathion and in conversion of p-nitrophenol to 4-nitrocatechol, namely parathion hydrolase and p-nitrophenol hydroxylase component "A" were detected in the proteomes of the methyl parathion and p-nitrophenol grown cultures, respectively. These studies report for the first time the existence of a p-nitrophenol hydroxylase component "A", typically found in Gram-positive bacteria, in a Gram-negative strain of the genus Serratia.
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Affiliation(s)
- Suresh B Pakala
- Department of Animal Sciences, University of Hyderabad, Hyderabad, 500 046, India
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39
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Zhang R, Cui Z, Zhang X, Jiang J, Gu JD, Li S. Cloning of the organophosphorus pesticide hydrolase gene clusters of seven degradative bacteria isolated from a methyl parathion contaminated site and evidence of their horizontal gene transfer. Biodegradation 2006; 17:465-72. [PMID: 16477356 DOI: 10.1007/s10532-005-9018-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2005] [Accepted: 09/02/2005] [Indexed: 10/25/2022]
Abstract
Seven organophosphorus pesticide-degrading bacteria harboring the methyl parathion degrading (mpd) gene were isolated from a methyl parathion contaminated site. In this study, the 4.7 kb mpd gene cluster, conserved in all seven bacteria capable of degrading methyl parathion, was cloned and further analysis revealed that this cluster contained five ORFs and the mpd gene was associated with a mobile element, IS6100. In addition to mpd gene ORF and tnpA ORF, three other ORFs showed high homology to the permease component of ABC-type transport system, the general secretion pathway protein B, and the RNA polymerase sigma 70 factor, respectively. The mpd genes of these 7 strains were subcloned and expressed in E. coli, SDS-PAGE and zymogram analysis showed that two expression products of mpd genes in E. coli were found, but the one without signal peptide showed the hydrolytic activities. Our evidences collectively suggest that mpd gene cluster may be disseminated through horizontal gene transfer based on phylogenetic analysis of the cluster and their host bacterial strains, and comparisons of GC content of the cluster and respective host's chromosome.
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Affiliation(s)
- Ruifu Zhang
- Department of Microbiology, Key Laboratory for Microbiological Engineering of Agricultural Environment of Ministry of Agriculture, Nanjing Agricultural University, 6 Tongwei Road, 210095, Nanjing, Jiangsu, P.R. China
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40
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Wang L, Zhang L, Chen H, Tian Q, Zhu G. Isolation of a triazophos-degrading strain Klebsiella sp. E6 effectively utilizing triazophos as sole nitrogen source. FEMS Microbiol Lett 2005; 253:259-65. [PMID: 16243454 DOI: 10.1016/j.femsle.2005.09.044] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2005] [Revised: 09/26/2005] [Accepted: 09/27/2005] [Indexed: 11/23/2022] Open
Abstract
A triazophos-degrading strain, Klebsiella sp. E6, was isolated by enrichment technology from soil that had been exposed long-term to triazophos. The strain grew well at pH 7.0-8.0 with a broad temperature profile ranging from 32 to 37 degrees C. It could keep good growth on methanol as carbon source and TAP as additional carbon source or nitrogen source. The experiment on the degradation activities of strain E6 showed that it utilized TAP more effectively when TAP was supplied as the sole nitrogen source, as opposed to additional carbon source. The intermediates of triazophos metabolism indicated that degradation occurred through a hydrolysis mechanism, one of the products of which, 1-phenyl-3-hydroxy-1,2,4-triazole, was also mineralized by strain E6.
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Affiliation(s)
- Lihong Wang
- College of Materials Science and Chemical Engineering, Zhejiang University, Hangzhou 310027, PR China
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41
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42
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Grimsley JK, Calamini B, Wild JR, Mesecar AD. Structural and mutational studies of organophosphorus hydrolase reveal a cryptic and functional allosteric-binding site. Arch Biochem Biophys 2005; 442:169-79. [PMID: 16188223 DOI: 10.1016/j.abb.2005.08.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2005] [Revised: 08/04/2005] [Accepted: 08/07/2005] [Indexed: 11/27/2022]
Abstract
Organophosphorus hydrolase detoxifies a broad range of organophosphate pesticides and the chemical warfare agents (CWAs) sarin and VX. Previously, rational genetic engineering produced OPH variants with 30-fold enhancements in the hydrolysis of CWA and their analogs. One interesting variant (H254R) in which the histidine at position 254 was changed to an arginine showed a 4-fold increase in the hydrolysis of demetonS (VX analog), a 14-fold decrease with paraoxon (an insecticide), and a 183-fold decrease with DFP (sarin analog). The three-dimensional structure of this enzyme at 1.9A resolution with the inhibitor, diethyl 4-methylbenzylphosphonate (EBP), revealed that the inhibitor did not bind at the active site, but bound exclusively into a well-defined surface pocket 12 A away from the active site. This structural feature was accompanied by non-competitive inhibition of paraoxon hydrolysis by EBP with H254R, in contrast to the native enzyme, which showed competitive inhibition. These parallel structure-function characteristics identify a functional, allosteric site on the surface of this enzyme.
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Affiliation(s)
- Janet K Grimsley
- Biochemistry and Biophysics Department, Texas A&M University, College Station, TX 77843-2128, USA
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43
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Zhang R, Cui Z, Jiang J, He J, Gu X, Li S. Diversity of organophosphorus pesticide-degrading bacteria in a polluted soil and conservation of their organophosphorus hydrolase genes. Can J Microbiol 2005; 51:337-43. [PMID: 15980896 DOI: 10.1139/w05-010] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Seven methyl parathion-degrading bacteria were isolated from a long-term methyl parathion contaminated soil and were found to belong to the genera Pseudaminobacter, Achromobacter, Brucella, and Ochrobactrum. Southern blot analysis using an mpd gene probe revealed that their hydrolase genes were similar to the mpd gene from Plesiomonas sp. strain M6 and were all located on the chromosome. Gene libraries were constructed from genomic DNA of each of the 7 organophosphorus pesticide-degrading bacteria, and their mpd genes were cloned and sequenced. Sequence analysis revealed that their hydrolase genes were conserved, and that the G+C content of the mpd genes were distinctly different from that of the chromosome-located 16S rRNA gene, suggesting that the mpd gene could be transferred and expressed among a variety of bacterial hosts.Key words: methyl parathion, degrading bacteria, Southern blot, mpd gene.
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Affiliation(s)
- Ruifu Zhang
- Department of Microbiology, MOA Key Lab of Microbiological Engineering of Agricultural Environment, Nanjing Agricultural University, Nanjing, People's Republic of China
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44
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Nanoparticle-based optical biosensors for the direct detection of organophosphate chemical warfare agents and pesticides. Anal Chim Acta 2005. [DOI: 10.1016/j.aca.2004.06.056] [Citation(s) in RCA: 160] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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45
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Cao X, Mabrouki M, Mello SV, Leblanc RM, Rastogi VK, Cheng TC, DeFrank JJ. The interaction between OPH and paraoxon at the air–water interface studied by AFM and epifluorescence microscopies. Colloids Surf B Biointerfaces 2005; 40:75-81. [PMID: 15642457 DOI: 10.1016/j.colsurfb.2004.05.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The paraoxon hydrolysis reaction catalyzed by organophosphorus hydrolase (OPH) monolayer at the air-water interface was studied. OPH-paraoxon interactions, occurring at the two-dimensional interface, by close-packed, highly orientated OPH monolayer, were investigated by several different surface chemistry techniques; e.g. surface pressure area isotherms, atomic force microscopy (AFM), and in situ epifluorescence microscopy. The characterization of OPH Langmuir and Langmuir-Blodgett films prepared in both the presence and absence of paraoxon, demonstrated significantly distinctive feature when compared with one another. Continuous growth of the OPH aggregates is a distinct phenomenon associated with hydrolysis, in addition to the pH changes in the local environment of the enzyme macromolecules.
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Affiliation(s)
- Xihui Cao
- Department of Chemistry, University of Miami, Coral Gables, FL 33124, USA
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46
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Simonian A, Flounders A, Wild J. FET-Based Biosensors for The Direct Detection of Organophosphate Neurotoxins. ELECTROANAL 2004. [DOI: 10.1002/elan.200403078] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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47
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Fu G, Cui Z, Huang T, Li S. Expression, purification, and characterization of a novel methyl parathion hydrolase. Protein Expr Purif 2004; 36:170-6. [PMID: 15249038 DOI: 10.1016/j.pep.2004.04.019] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2003] [Revised: 04/20/2004] [Indexed: 11/23/2022]
Abstract
The mpd gene coding for a novel methyl parathion hydrolase (MPH) was previously reported and its putative open reading frame was also identified. To further confirm its coding region, the intact region encoding MPH was obtained by PCR and expressed in Escherichia coli as a hexa-His C-terminal fusion protein. The fusion protein was purified to homogeneity by metal-affinity chromatography. The enzyme activity and zymogram assay showed that the fusion protein was functional in degrading methyl parathion. The amino terminal sequencing of the purified recombinant MPH indicated that a signal peptide of the first 35 amino acids was cleaved from its precursor to form active MPH. A rat polyclonal antiserum was raised against the purified mature fusion protein. The results of Western blot and zymogram demonstrated that mature MPH in native Plesiomonas sp. strain M6 was also processed from its precursor by cleavage of a putative signal peptide at the amino terminus. The production of active MPH in E. coli was greatly improved after the coding region for the signal peptide was deleted. HPLC gel filtration of the purified mature recombinant MPH revealed that the MPH was a monomer.
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Affiliation(s)
- Guoping Fu
- Key Lab of Microbiological Engineering of Agricultural Environment of Ministry of Agriculture, Nanjing Agricultural University, 1 Weigang, Nanjing, Jiangsu 210095, People's Republic of China
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48
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Aubert SD, Li Y, Raushel FM. Mechanism for the Hydrolysis of Organophosphates by the Bacterial Phosphotriesterase. Biochemistry 2004; 43:5707-15. [PMID: 15134445 DOI: 10.1021/bi0497805] [Citation(s) in RCA: 224] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phosphotriesterase (PTE) from Pseudomonas diminuta is a zinc metalloenzyme that hydrolyzes a variety of organophosphorus compounds. The kinetic parameters of Zn/Zn PTE, Cd/Cd PTE, and a mixed-metal Zn/Cd hybrid PTE were obtained with a variety of substrates to determine the role of each metal ion in binding and catalysis. pH-rate profiles for the hydrolysis of diethyl p-nitrophenyl phosphate (I) and diethyl p-chlorophenyl phosphate (II) demonstrated that the ionization of a single group in the pH range of 5-10 was critical for substrate turnover. The pK(a) values determined from the kinetic assays were dependent on the identity of the metal ion that occupied the alpha site within the binuclear metal center. These results suggest that the hydrolytic nucleophile is activated as a hydroxide via the ionization of a water molecule attached to the alpha-metal ion. The kinetic constants for the hydrolysis of II and diethyl p-chlorophenyl thiophosphate (IV) were determined for the metal substituted forms of PTE. The kinetic constants for IV were greater than those for II. The inverse thio effect is consistent with the polarization of the phosphoryl oxygen/sulfur bond via a direct ligation to the metal center. The rate enhancement is greater when Cd(2+) occupies the beta-metal-ion position. A series of alanine and asparagine mutations were used to characterize the catalytic roles of Asp233, His254, and Asp301. Mutations to either Asp233 or His254 resulted in an enhanced rate of hydrolysis for the sluggish substrate, diethyl p-chlorophenyl phosphate, and a decrease in the kinetic constants for paraoxon (I). These results are consistent with the existence of a proton relay from Asp301 to His254 to Asp233 that is used to ferry protons away from the active site with substrates that do not require activation of the leaving group phenol. A mechanism for the hydrolysis of organophosphates by the bacterial PTE has been proposed.
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Affiliation(s)
- Sarah D Aubert
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
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Harcourt RL, Horne I, Sutherland TD, Hammock BD, Russell RJ, Oakeshott JG. Development of a simple and sensitive fluorimetric method for isolation of coumaphos-hydrolysing bacteria. Lett Appl Microbiol 2002; 34:263-8. [PMID: 11940156 DOI: 10.1046/j.1472-765x.2002.01078.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS To develop a simple, rapid and sensitive fluorimetric assay to detect, isolate and characterize a soil bacterium capable of degrading the organophosphorus pesticide, coumaphos. METHODS AND RESULTS A high throughput microtitre plate-based method was used to quantify coumaphos hydrolysis by the bacterium. The fluorescent hydrolysis product of coumaphos, chlorferon, was detected at levels as low as 10 nmol l(-1). Incorporation of coumaphos into agar plates allowed the rapid detection of coumaphos-hydrolysing bacteria when exposed to an excitation wavelength of approximately 340 nm. The coumaphos-hydrolysing enzyme could be visualized when bacterial cell extracts were separated on SDS-PAGE, incubated with coumaphos and exposed to an excitation source as above. CONCLUSIONS This method is 100-fold more sensitive than the currently used spectrophotometric method for coumaphos. SIGNIFICANCE AND IMPACT OF THE STUDY This is a unique and versatile tool to screen for bacteria possessing phosphotriesterase activity.
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Affiliation(s)
- R L Harcourt
- Commonwealth Scientific and Industrial Research Organization (CSIRO) Entomology, GPO Box 1700, Canberra, ACT 2601, Australia
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50
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Walker AW, Keasling JD. Metabolic engineering of Pseudomonas putida for the utilization of parathion as a carbon and energy source. Biotechnol Bioeng 2002; 78:715-21. [PMID: 12001163 DOI: 10.1002/bit.10251] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Pseudomonas putida KT2442 was engineered to use the organophosphate pesticide parathion, a compound similar to other organophosphate pesticides and chemical warfare agents, as a source of carbon and energy. The initial step in the engineered degradation pathway was parathion hydrolysis by organophosphate hydrolase (OPH) to p-nitrophenol (PNP) and diethyl thiophosphate, compounds that cannot be metabolized by P. putida KT2442. The gene encoding the native OPH (opd), with and without the secretory leader sequence, was cloned into broad-host-range plasmids under the control of tac and taclac promoters. Expression of opd from the tac promoter resulted in high OPH activity, whereas expression from the taclac promoter resulted in low activity. A plasmid-harboring operons encoding enzymes for p-nitrophenol transformation to beta-ketoadipate was transformed into P. putida allowing the organism to use 0.5 mM PNP as a carbon and energy source. Transformation of P. putida with the plasmids harboring opd and the PNP operons allowed the organism to utilize 0.8 mM parathion as a source of carbon and energy. Degradation studies showed that parathion formed a separate dense, non-aqueous phase liquid phase but was still bioavailable.
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Affiliation(s)
- Andy W Walker
- Department of Chemical Engineering, University of California, Berkeley 94720-1462, USA
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