1
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Phintha A, Chaiyen P. Unifying and versatile features of flavin-dependent monooxygenases: Diverse catalysis by a common C4a-(hydro)peroxyflavin. J Biol Chem 2023; 299:105413. [PMID: 37918809 PMCID: PMC10696468 DOI: 10.1016/j.jbc.2023.105413] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/18/2023] [Accepted: 10/22/2023] [Indexed: 11/04/2023] Open
Abstract
Flavin-dependent monooxygenases (FDMOs) are known for their remarkable versatility and for their crucial roles in various biological processes and applications. Extensive research has been conducted to explore the structural and functional relationships of FDMOs. The majority of reported FDMOs utilize C4a-(hydro)peroxyflavin as a reactive intermediate to incorporate an oxygen atom into a wide range of compounds. This review discusses and analyzes recent advancements in our understanding of the structural and mechanistic features governing the enzyme functions. State-of-the-art discoveries related to common and distinct structural properties governing the catalytic versatility of the C4a-(hydro)peroxyflavin intermediate in selected FDMOs are discussed. Specifically, mechanisms of hydroxylation, dehalogenation, halogenation, and light-emitting reactions by FDMOs are highlighted. We also provide new analysis based on the structural and mechanistic features of these enzymes to gain insights into how the same intermediate can be harnessed to perform a wide variety of reactions. Challenging questions to obtain further breakthroughs in the understanding of FDMOs are also proposed.
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Affiliation(s)
- Aisaraphon Phintha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, Thailand.
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2
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Jiang H, Zang C, Guo L, Gao X. Carbon vacancies enriched carbon nitride nanotubes for Pd coordination environment optimization: Highly efficient photocatalytic hydrodechlorination and CO 2 cycloaddition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155920. [PMID: 35588820 DOI: 10.1016/j.scitotenv.2022.155920] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/05/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
The use of easily available solar energy to achieve pollutants efficient degradation and waste carbon resource CO2 utilization under mild conditions is highly desired. Herein, novel carbon vacancies enriched nanotubes graphitic carbon nitride (SCNT-500) has been successfully fabricated via melamine (MA) supramolecular hydrogen-bonded self-assembly in the presence of H2SO4. Pd NPs loaded carbon vacancies enriched carbon nitride nanotubes (Pd/SCNT-500) were used for photocatalytic chlorophenols hydrodechlorination and CO2 cycloaddition with styrene oxide. Up to 6.93 s-1 4-chlorophenol hydrodechlorination TOF and obviously improved CO2 cycloaddition efficiency could be realized with Pd/SCNT-500. The improved photocatalytic efficiency should be related to the morphology and carbon vacancies based Pd coordination environment optimization. Such as, the surface area increased nanotubes structure promoted light harvesting along with photoelectrons and holes generation; the carbon vacancies improved excited electrons capture, photoinduced carriers recombination inhibition along with substrates adsorption with electron rich Pd NPs. Mechanism studies not only demonstrated the important role of atomic hydrogen and Pd coordination environment optimization in the chlorophenols hydrodechlorination, but also confirmed the promotion ability of photogenerated electrons on CO2 cycloaddition.
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Affiliation(s)
- Heyan Jiang
- College of Environment and Resources, Chongqing Technology and Business University, Chongqing 400067, PR China; Chongqing Key Laboratory of Catalysis and New Environmental Materials, Chongqing 400067, PR China; Engineering Research Center for Waste Oil Recovery Technology and Equipment, Ministry of Education, Chongqing Technology and Business University, Chongqing 400067, PR China.
| | - Cuicui Zang
- College of Environment and Resources, Chongqing Technology and Business University, Chongqing 400067, PR China; Chongqing Key Laboratory of Catalysis and New Environmental Materials, Chongqing 400067, PR China
| | - Lixia Guo
- College of Environment and Resources, Chongqing Technology and Business University, Chongqing 400067, PR China; Chongqing Key Laboratory of Catalysis and New Environmental Materials, Chongqing 400067, PR China
| | - Xue Gao
- College of Environment and Resources, Chongqing Technology and Business University, Chongqing 400067, PR China; Chongqing Key Laboratory of Catalysis and New Environmental Materials, Chongqing 400067, PR China
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3
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Kundu K, Melsbach A, Heckel B, Schneidemann S, Kanapathi D, Marozava S, Merl-Pham J, Elsner M. Linking Increased Isotope Fractionation at Low Concentrations to Enzyme Activity Regulation: 4-Cl Phenol Degradation by Arthrobacter chlorophenolicus A6. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:3021-3032. [PMID: 35148097 PMCID: PMC8892832 DOI: 10.1021/acs.est.1c04939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 01/23/2022] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Slow microbial degradation of organic trace chemicals ("micropollutants") has been attributed to either downregulation of enzymatic turnover or rate-limiting substrate supply at low concentrations. In previous biodegradation studies, a drastic decrease in isotope fractionation of atrazine revealed a transition from rate-limiting enzyme turnover to membrane permeation as a bottleneck when concentrations fell below the Monod constant of microbial growth. With degradation of the pollutant 4-chlorophenol (4-CP) by Arthrobacter chlorophenolicus A6, this study targeted a bacterium which adapts its enzyme activity to concentrations. Unlike with atrazine degradation, isotope fractionation of 4-CP increased at lower concentrations, from ε(C) = -1.0 ± 0.5‰ in chemostats (D = 0.090 h-1, 88 mg L-1) and ε(C) = -2.1 ± 0.5‰ in batch (c0 = 220 mg L-1) to ε(C) = -4.1 ± 0.2‰ in chemostats at 90 μg L-1. Surprisingly, fatty acid composition indicated increased cell wall permeability at high concentrations, while proteomics revealed that catabolic enzymes (CphCI and CphCII) were differentially expressed at D = 0.090 h-1. These observations support regulation on the enzyme activity level─through either a metabolic shift between catabolic pathways or decreased enzymatic turnover at low concentrations─and, hence, reveal an alternative end-member scenario for bacterial adaptation at low concentrations. Including more degrader strains into this multidisciplinary analytical approach offers the perspective to build a knowledge base on bottlenecks of bioremediation at low concentrations that considers bacterial adaptation.
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Affiliation(s)
- Kankana Kundu
- Institute
of Groundwater Ecology, Helmholtz Zentrum
Munchen, Ingolstadter
Landstraße 1, 85764 Neuherberg, Bavaria, Germany
- Center
for Microbial Ecology and Technology (CMET), Faculty of Bioscience
Engineering, University of Ghent, Coupure Links 653, 9000 Ghent, Belgium
| | - Aileen Melsbach
- Institute
of Groundwater Ecology, Helmholtz Zentrum
Munchen, Ingolstadter
Landstraße 1, 85764 Neuherberg, Bavaria, Germany
- Chair
of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstr. 4, D-85748 Garching, Germany
| | - Benjamin Heckel
- Institute
of Groundwater Ecology, Helmholtz Zentrum
Munchen, Ingolstadter
Landstraße 1, 85764 Neuherberg, Bavaria, Germany
| | - Sarah Schneidemann
- Institute
of Groundwater Ecology, Helmholtz Zentrum
Munchen, Ingolstadter
Landstraße 1, 85764 Neuherberg, Bavaria, Germany
| | - Dheeraj Kanapathi
- Institute
of Groundwater Ecology, Helmholtz Zentrum
Munchen, Ingolstadter
Landstraße 1, 85764 Neuherberg, Bavaria, Germany
| | - Sviatlana Marozava
- Institute
of Groundwater Ecology, Helmholtz Zentrum
Munchen, Ingolstadter
Landstraße 1, 85764 Neuherberg, Bavaria, Germany
| | - Juliane Merl-Pham
- Core
Facility Proteomics, Helmholtz Zentrum München, Heidemannstr. 1, 80939 Munich, Germany
| | - Martin Elsner
- Institute
of Groundwater Ecology, Helmholtz Zentrum
Munchen, Ingolstadter
Landstraße 1, 85764 Neuherberg, Bavaria, Germany
- Chair
of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstr. 4, D-85748 Garching, Germany
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4
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Shi H, Jiang X, Li Y, Chen D, Hou C, Zhang Z, Zhang Q, Shen J. Enhanced bio-photodegradation of p-chlorophenol by CdS/g-C 3N 4 3D semiconductor-microbe interfaces. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:151006. [PMID: 34662615 DOI: 10.1016/j.scitotenv.2021.151006] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/09/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
p-chlorophenol (p-CP), one of the highly toxic chlorinated organic compounds, is recalcitrant in conventional biodegradation process. This study reported a synergistic degradation protocol of 3D semiconductor-microbe interfaces, in which graphite felts (GF) and CdS/g-C3N4 nanocomposites were chosen as the carrier and semiconductor for enhanced p-CP degradation. Based on microstructure, photoelectrochemical and degradation performance analysis, the optimal CdS content in CdS/g-C3N4 nanocomposites was 10 wt%. The efficiencies of p-CP and TOC removal in bio-photodegradation system were as high as 95% and 77% without extra electron acceptors/donors, which were far better than those in traditional photodegradation and biodegradation system. High-throughput sequencing analysis suggested that p-CP degradation related species (Chryseobacterium, Stenotrophomonas and Rhodopseudomonas), electroactive species (Chryseobacterium, Stenotrophomonas, Hydrogenophaga and Cupriavidus) and hydrogen-utilizing species (Hydrogenophaga and Cupriavidus) were enriched at 3D semiconductor-microbe interfaces. The enrichment of functional species played a crucial role for p-CP removal and mineralization at 3D semiconductor-microbe interfaces. Moreover, the mechanism of enhanced p-CP bio-photodegradation at 3D semiconductor-microbe interfaces was investigated by utilizing Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2). The results showed that the genes involved in p-CP biodegradation, hydrogen metabolism and extracellular electron transfer were remarkably enriched. Possible mechanism for enhancement of p-CP degradation in bio-photodegradation system was proposed, in which photocatalytic H2 and photoelectron transfer played an important role for enhancing p-CP mineralization by microbes. 3D semiconductor-microbe interfaces could maintain excellent performance for p-CP degradation after long-term operation, which provide a potential alternative for the enhanced treatment of wastewater containing p-CP.
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Affiliation(s)
- Hefei Shi
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Xinbai Jiang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Yang Li
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Dan Chen
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Cheng Hou
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Zhenhua Zhang
- Key Laboratory of Biosafety, Nanjing Institute of Environmental Sciences, Nanjing 210042, China
| | - Qian Zhang
- School of Life and Environmental Science, Guilin University of Electronic Technology, Guilin 541004, China
| | - Jinyou Shen
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Chemical Pollution Control Engineering Research Center of Ministry of Education, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
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5
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Pimviriyakul P, Jaruwat A, Chitnumsub P, Chaiyen P. Structural insights into a flavin-dependent dehalogenase HadA explain catalysis and substrate inhibition via quadruple π-stacking. J Biol Chem 2021; 297:100952. [PMID: 34252455 PMCID: PMC8342789 DOI: 10.1016/j.jbc.2021.100952] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/24/2021] [Accepted: 07/08/2021] [Indexed: 12/20/2022] Open
Abstract
HadA is a flavin-dependent monooxygenase catalyzing hydroxylation plus dehalogenation/denitration, which is useful for biodetoxification and biodetection. In this study, the X-ray structure of wild-type HadA (HadAWT) co-complexed with reduced FAD (FADH-) and 4-nitrophenol (4NP) (HadAWT-FADH--4NP) was solved at 2.3-Å resolution, providing the first full package (with flavin and substrate bound) structure of a monooxygenase of this type. Residues Arg101, Gln158, Arg161, Thr193, Asp254, Arg233, and Arg439 constitute a flavin-binding pocket, whereas the 4NP-binding pocket contains the aromatic side chain of Phe206, which provides π-π stacking and also is a part of the hydrophobic pocket formed by Phe155, Phe286, Thr449, and Leu457. Based on site-directed mutagenesis and stopped-flow experiments, Thr193, Asp254, and His290 are important for C4a-hydroperoxyflavin formation with His290, also serving as a catalytic base for hydroxylation. We also identified a novel structural motif of quadruple π-stacking (π-π-π-π) provided by two 4NP and two Phe441 from two subunits. This motif promotes 4NP binding in a nonproductive dead-end complex, which prevents C4a-hydroperoxy-FAD formation when HadA is premixed with aromatic substrates. We also solved the structure of the HadAPhe441Val-FADH--4NP complex at 2.3-Å resolution. Although 4NP can still bind to this variant, the quadruple π-stacking motif was disrupted. All HadAPhe441 variants lack substrate inhibition behavior, confirming that quadruple π-stacking is a main cause of dead-end complex formation. Moreover, the activities of these HadAPhe441 variants were improved by ⁓20%, suggesting that insights gained from the flavin-dependent monooxygenases illustrated here should be useful for future improvement of HadA's biocatalytic applications.
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Affiliation(s)
- Panu Pimviriyakul
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Aritsara Jaruwat
- National Center for Genetic Engineering and Biotechnology, Pathumthani, Thailand
| | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology, Pathumthani, Thailand.
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
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6
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Zhang J, Lei C, Chen W, Xie Q, Guo Q, Huang B. Electrochemical-driven nanoparticulate catalysis for highly efficient dechlorination of chlorinated environmental pollutant. J Catal 2021. [DOI: 10.1016/j.jcat.2021.01.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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7
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Lim Y, Yu J, Park S, Kim M, Chen S, Bakri NAB, Sabri NIABM, Bae S, Kim HS. Development of biocatalysts immobilized on coal ash-derived Ni-zeolite for facilitating 4-chlorophenol degradation. BIORESOURCE TECHNOLOGY 2020; 307:123201. [PMID: 32220822 DOI: 10.1016/j.biortech.2020.123201] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/12/2020] [Accepted: 03/14/2020] [Indexed: 06/10/2023]
Abstract
A new type of biocatalyst was developed to facilitate the biochemical decomposition of 4-chlorophenol (4-CP) in this study. Oxydoreductases that catalyze the initial steps of 4-CP biodegradation were immobilized on a synthetic inorganic enzyme support. Type-X zeolite, a high-surface area support, was synthesized from coal fly ash, on which nickel ions were plated by impregnation (Ni-zeolite), followed by the effective immobilization (77.5% immobilization yield) of recombinant monooxygenase (CphC-I), dioxygenase (CphA-I), and flavin reductase (Fre) isolated from Pseudarthrobacter chlorophenolicus A6 and Escherichia coli K-12, respectively. The retained catalytic activity of the enzymes immobilized on Ni-zeolite was as high as 64% of the value for the corresponding free enzymes. The Michaelis-Menten kinetic parameters vmax and KM of the immobilized enzymes were determined to be 0.20 mM·min-1 and 0.44 mM, respectively. These results are expected to provide useful information with respect to the development of novel enzymatic treatments for phenolic hydrocarbon contaminants.
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Affiliation(s)
- Yejee Lim
- Civil and Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Jimin Yu
- Civil and Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Sungyoon Park
- Civil and Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Minsoo Kim
- Civil and Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Siyu Chen
- Civil and Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Nurul Aziemah Binti Bakri
- Civil and Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | | | - Sungjun Bae
- Civil and Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Han S Kim
- Civil and Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
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8
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Cordero JA, He K, Okuta E, Echigo S, Itoh S. Effect of biodegradation on haloacetic acid formation potentials of anthropogenic compounds during chlorination. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:18117-18128. [PMID: 32172417 DOI: 10.1007/s11356-020-08125-4] [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: 11/05/2019] [Accepted: 02/17/2020] [Indexed: 06/10/2023]
Abstract
During drinking water treatment processes, anthropogenic compounds act as important precursors of disinfection by-products such as haloacetic acids (HAAs). Several transformations in these precursors occur prior to the disinfection stage, such as partial biodegradation. We hypothesized that this partial biodegradation of anthropogenic compounds potentially affects their HAA formation potentials (HAAFPs). In this study, the HAAFPs of 51 anthropogenic compounds after short-term contact (less than 1 h) and long-term contact (24 h) with activated sludge were compared. Considerable changes were observed particularly in trichloroacetic acid (TCAA) formation potentials (FPs) of phenols, demonstrating that biodegradation should be considered in investigations of potential precursors of HAAs. Phenols with low HAAFPs, such as hydroquinone, show higher HAAFPs after biodegradation, but HAAFPs of most phenols and anilines decreased after biodegradation. Thus, biodegradation will most likely have a positive impact on water quality from the standpoint of HAAFP reduction. For most aliphatic compounds, changes in HAAFP were negligible, but the dichloroacetic acid (DCAA) FP of acrylic acid largely increased. This study illustrates that biodegradation may have a large effect on the HAAFPs of anthropogenic compounds.
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Affiliation(s)
- José Andrés Cordero
- Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, Nishikyo, Kyoto, 615-8540, Japan
| | - Kai He
- Research Center for Environmental Quality Management, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan.
| | - Erika Okuta
- Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, Nishikyo, Kyoto, 615-8540, Japan
| | - Shinya Echigo
- Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, Nishikyo, Kyoto, 615-8540, Japan
- Department of Environmental Health, National Institute of Public Health, Wako, Saitama, 351-0197, Japan
| | - Sadahiko Itoh
- Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, Nishikyo, Kyoto, 615-8540, Japan
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9
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Fang L, Qin H, Shi T, Wu X, Li QX, Hua R. Ortho and para oxydehalogenation of dihalophenols catalyzed by the monooxygenase TcpA and NAD(P)H:FAD reductase Fre. JOURNAL OF HAZARDOUS MATERIALS 2020; 388:121787. [PMID: 31818658 DOI: 10.1016/j.jhazmat.2019.121787] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/19/2019] [Accepted: 11/28/2019] [Indexed: 06/10/2023]
Abstract
Dihalophenols such as dichlorophenols (DCPs) are important industrial chemical intermediates, but also persistent pollutants in the environment. Oxidative dehalogenation by microbes is an efficient biological method to degrade halophenols, but the mechanism is unclear yet. Cupriavidus nantongensis X1T was a type strain of genus Cupriavidus, and could degrade 2,4-dichlorophenol of 50 mg/L within 12 h. The degradation rate constant was approximately 84 fold greater than that by Bacillus endophyticus CP1R43, a well-studied 2,4-DCP-degrading bacterial strain. The genes encoding 2,4,6-trichlorophenol monooxygenase (TcpA) and NAD(P)H:FAD reductase (Fre) from strain X1T were cloned and expressed. The expressed TcpA Fre were purified. The molecular docking of TcpA with DCPs and point mutation experiments showed that the degradation activity of TcpA was associated with the length of the hydrogen bond between the substrates and the amino acids in the active pocket. DCPs were degraded via a stepwise oxidative dechlorination in a positive relationship between the oxidation ability and the electron-withdrawing potential of the p-position group. In addition, TcpA has dual dehalogenation and denitration functions. The results demonstrate that either strain X1T or TcpA and Fre can effectively dehalogenate dihalophenols, which can be useful for the treatment of dihalophenols in wastewaters and remediation of DCP-contaminated environments.
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Affiliation(s)
- Liancheng Fang
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Han Qin
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Taozhong Shi
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xiangwei Wu
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, 1955 East-West Road, Honolulu, HI 96822, United States.
| | - Rimao Hua
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China.
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10
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Pimviriyakul P, Wongnate T, Tinikul R, Chaiyen P. Microbial degradation of halogenated aromatics: molecular mechanisms and enzymatic reactions. Microb Biotechnol 2020; 13:67-86. [PMID: 31565852 PMCID: PMC6922536 DOI: 10.1111/1751-7915.13488] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 09/01/2019] [Accepted: 09/03/2019] [Indexed: 12/12/2022] Open
Abstract
Halogenated aromatics are used widely in various industrial, agricultural and household applications. However, due to their stability, most of these compounds persist for a long time, leading to accumulation in the environment. Biological degradation of halogenated aromatics provides sustainable, low-cost and environmentally friendly technologies for removing these toxicants from the environment. This minireview discusses the molecular mechanisms of the enzymatic reactions for degrading halogenated aromatics which naturally occur in various microorganisms. In general, the biodegradation process (especially for aerobic degradation) can be divided into three main steps: upper, middle and lower metabolic pathways which successively convert the toxic halogenated aromatics to common metabolites in cells. The most difficult step in the degradation of halogenated aromatics is the dehalogenation step in the middle pathway. Although a variety of enzymes are involved in the degradation of halogenated aromatics, these various pathways all share the common feature of eventually generating metabolites for utilizing in the energy-producing metabolic pathways in cells. An in-depth understanding of how microbes employ various enzymes in biodegradation can lead to the development of new biotechnologies via enzyme/cell/metabolic engineering or synthetic biology for sustainable biodegradation processes.
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Affiliation(s)
- Panu Pimviriyakul
- Department of BiotechnologyFaculty of Engineering and Industrial TechnologySilpakorn UniversityNakhon Pathom73000Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC)Wangchan ValleyRayong21210Thailand
| | - Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme TechnologyFaculty of ScienceMahidol UniversityBangkok10400Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC)Wangchan ValleyRayong21210Thailand
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11
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12
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Yang JW, Cho W, Lim Y, Park S, Lee D, Jang HA, Kim HS. Evaluation of aromatic hydrocarbon decomposition catalyzed by the dioxygenase system and substitution of ferredoxin and ferredoxin reductase. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:34047-34057. [PMID: 30244447 DOI: 10.1007/s11356-018-3200-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/11/2018] [Indexed: 05/25/2023]
Abstract
In this study, the catalytic activity and kinetic characteristics of the aromatic hydrocarbon dioxygenase system and the possibility of substituting its ferredoxin and ferredoxin reductase components were evaluated. The genes encoding toluene dioxygenase and toluene dihydrodiol dehydrogenase were cloned from Pseudomonas putida F1, and the corresponding enzymes were overexpressed and purified to homogeneity. Oxidative hydroxylation of toluene to cis-toluene dihydrodiol was catalyzed by toluene dioxygenase, and its subsequent dehydrogenation to 3-methylcatechol was catalyzed by toluene dihydrodiol dehydrogenase. The specific activity of the dioxygenase was 2.82 U/mg-protein, which is highly remarkable compared with the values obtained in previous researches conducted with crude extracts or insoluble forms of enzymes. Kinetic parameters, as characterized by the Hill equation, were vmax = 497.2 μM/min, KM = 542.4 μM, and nH = 2.2, suggesting that toluene dioxygenase has at least three cooperative binding sites for toluene. In addition, the use of alternative ferredoxins and reductases was examined. Ferredoxin cloned from CYP153 could transfer electrons to the iron sulfur protein component of toluene dioxygenase. The ferredoxin could be reduced by ferredoxin, rubredoxin, and putidaredoxin reductases of CYP153, alkane-1 monooxygenase, and camphor 5-monooxygenase, respectively. The results provide useful information regarding the effective enzymatic biotreatment of hazardous aromatic hydrocarbon contaminants.
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Affiliation(s)
- Jun Won Yang
- Civil and Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, South Korea
| | - Wooyoun Cho
- Civil and Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, South Korea
| | - Yejee Lim
- Civil and Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, South Korea
| | - Sungyoon Park
- Civil and Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, South Korea
| | - Dayoung Lee
- Civil and Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, South Korea
| | - Hyun-A Jang
- Civil and Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, South Korea
| | - Han S Kim
- Civil and Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05029, South Korea.
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13
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Zhao ZQ, Zheng TC, Zhang WJ, Shen XL, Lv L, Li YM. Degradation of 3-fluoroanilne by Rhizobium sp. JF-3. Biodegradation 2019; 30:433-445. [PMID: 31240422 DOI: 10.1007/s10532-019-09885-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 06/19/2019] [Indexed: 01/07/2023]
Abstract
The interest of fluoroanilines in the environment is due to their extensive applications in industry and their low natural biodegradability. A pure bacterial strain capable of degrading 3-fluoroaniline (3-FA) as the sole source of carbon and energy was isolated from a sequencing batch reactor operating for the treatment of 3-FA. The strain (designated as JF-3) was identified by 16S rRNA gene analysis as a member of the genus Rhizobium. When grown in 3-FA medium at concentrations of 100-700 mg/L, strain JF-3 almost completely removed 3-FA within 72 h. However, the obvious cell growth inhibition was observed in cultures treated with 3-FA concentrations greater than 500 mg/L. The degradation kinetics of 3-FA were consistent with Haldane's model with the maximum degradation rate as 67.66 mg/(g dry cell h). The growth kinetics of strain JF-3 followed Andrew's model with the maximum growth rate as 30.87 h-1. Also, strain JF-3 was able to degrade 4-fluoroaniline, aniline, and catechol, but hardly grew on 2-fluoroaniline, 2,4-dfluoroaniline, 2,3,4-trifluoroaniline, 3-fluorocatechol, and 4-fluorocatechol. Additionally, it was able to grow over a wide pH range (pH 6-10), and also showed tolerance to salinity with lower than 1.0%. This result, in combination with the enzyme assays and analysis of metabolite intermediates, indicated an unconventional pathway for 3-fluoroaniline metabolism that involved conversion to 3-aminophenol and resorcinol by monooxygenase, and which was subsequently metabolized via the ortho-cleavage pathway. To our knowledge, this is the first report on the utilization of 3-FA as a growth substrate by Rhizobium sp.
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Affiliation(s)
- Zhi-Qing Zhao
- College of Chemical & Material Engineering, Quzhou University, Quzhou, 324000, People's Republic of China. .,College of Environment & Resource Sciences, Zhejiang University, Hangzhou, People's Republic of China.
| | - Tu-Cai Zheng
- College of Chemical & Material Engineering, Quzhou University, Quzhou, 324000, People's Republic of China
| | - Wen-Jing Zhang
- Institute of Environmental Planning, Ministry of Environmental Protection, Beijing, 100012, People's Republic of China
| | - Xiao-Li Shen
- College of Chemical & Material Engineering, Quzhou University, Quzhou, 324000, People's Republic of China
| | - Liang Lv
- College of Chemical & Material Engineering, Quzhou University, Quzhou, 324000, People's Republic of China
| | - Yan-Mei Li
- Engineering Division, Department of Mine, Metallurgy and Geology Engineering, University of Guanajuato, Guanajuato, Gto, 36000, Mexico
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14
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Liu Y, Ou H, Li S, You Q, Liu H, Liao G, Wang D. One-step preparation of polyimide-inlaid amine-rich porous organic block copolymer for efficient removal of chlorophenols from aqueous solution. J Environ Sci (China) 2019; 78:215-229. [PMID: 30665640 DOI: 10.1016/j.jes.2018.09.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/21/2018] [Accepted: 09/25/2018] [Indexed: 06/09/2023]
Abstract
A novel polyimide-inlaid amine-rich porous organic block copolymer (PI-b-ARPOP) was prepared via one-step polymerization by using different molar ratios of melamine (MA)/terephthalaldehyde (TA)/pyromellitic dianhydride (PMDA), at molar ratios of 4/3/1, 4/2/2 and 4/1/3. The copolymer contained both aminal groups belonging to ARPOP and imide groups belonging to PI, and the bonding styles of the monomers and growth orientations of the polymeric chains were diversiform, forming an excellent porous structure. Notably, MA/TA/PMDA (4/2/2) had a surface area and pore volume of 487.27 m2/g and 1.169 cm3/g, respectively. The adsorption performance of the materials towards 2,4-dichlorophenol (2,4-DCP) in ultra-pure water was systematically studied. The pH value of 7 was optimal in aqueous solution. Na+ and Cl- ions did not negatively affect the adsorption process, while humic acid (HA) slightly decreased the capacity. The equilibrium time was 40 sec, and the maximum adsorption capacity reached 282.49 mg/g at 298 K. The removal process was endothermic and spontaneous, and the copolymer could maintain its porous structure and consistent performance after regeneration by treatment with alkali. Moreover, to further assess the practical applicability of the material, the adsorption performance towards 2,4-DCP in river water was also investigated. This paper demonstrated that the PI-b-ARPOP can be an efficient and practical adsorbent to remove chlorophenols from aqueous solution.
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Affiliation(s)
- Yanyang Liu
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Material Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Haijian Ou
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Material Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Shangqing Li
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Material Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Qingliang You
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, School of Chemical and Environmental Engineering, Jianghan University, Wuhan 430056, China
| | - Huixian Liu
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Material Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Guiying Liao
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Material Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Dongsheng Wang
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Material Science and Chemistry, China University of Geosciences, Wuhan 430074, China; State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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15
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Sánchez-González M, Álvarez-Uribe H, Rivera-Solís R, González-Burgos A, Escalante-Réndiz D, Rojas-Herrera R. Analysis of a phenol-adapted microbial community: degradation capacity, taxonomy and metabolic description. J Appl Microbiol 2019; 126:771-779. [DOI: 10.1111/jam.14166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 11/13/2018] [Accepted: 11/19/2018] [Indexed: 12/24/2022]
Affiliation(s)
- M. Sánchez-González
- Facultad de Ingeniería Química; Universidad Autónoma de Yucatán; Mérida, Yucatán México
| | - H. Álvarez-Uribe
- Facultad de Ingeniería Química; Universidad Autónoma de Yucatán; Mérida, Yucatán México
| | - R. Rivera-Solís
- Facultad de Ingeniería Química; Universidad Autónoma de Yucatán; Mérida, Yucatán México
| | - A. González-Burgos
- Facultad de Ingeniería Química; Universidad Autónoma de Yucatán; Mérida, Yucatán México
| | - D. Escalante-Réndiz
- Facultad de Ingeniería Química; Universidad Autónoma de Yucatán; Mérida, Yucatán México
| | - R. Rojas-Herrera
- Facultad de Ingeniería Química; Universidad Autónoma de Yucatán; Mérida, Yucatán México
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16
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Pimviriyakul P, Surawatanawong P, Chaiyen P. Oxidative dehalogenation and denitration by a flavin-dependent monooxygenase is controlled by substrate deprotonation. Chem Sci 2018; 9:7468-7482. [PMID: 30319747 PMCID: PMC6180312 DOI: 10.1039/c8sc01482e] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 08/08/2018] [Indexed: 12/19/2022] Open
Abstract
Enzymes that are capable of detoxifying halogenated phenols (HPs) and nitrophenols (NPs) are valuable for bioremediation and waste biorefining. HadA monooxygenase was found to perform dual functions of oxidative dehalogenation (hydroxylation plus halide elimination) and denitration (hydroxylation plus nitro elimination). Rate constants associated with individual steps of HadA reactions with phenol, halogenated phenols and nitrophenols were measured using combined transient kinetic approaches of stopped-flow absorbance/fluorescence and rapid-quench flow techniques. Density functional theory was used to calculate the thermodynamic and electronic parameters associated with hydroxylation and group elimination steps. These parameters were correlated with the rate constants of hydroxylation, group elimination, and overall product formation to identify factors controlling individual steps. The results indicated that the hydroxylation rate constant is higher when the pK a of the phenolic group is lower, i.e. it is more easily deprotonated, but not higher when the energy gap between the E LUMO of the C4a-hydroperoxy-FAD intermediate and the E HOMO of the phenolate substrate is lower. These data suggest that the substrate deprotonation has a higher energy barrier than the -OH transfer, and thus controls the hydroxylation step. For the group elimination, the process is controlled by the ability of the C-X bond to break. For the overall product formation (hydroxylation and group elimination combined), this analysis showed that the rate constant of product formation is dependent on the pK a value of the substrate, indicating that the overall reaction is controlled by substrate deprotonation. This step also likely has the highest energy barrier and thus controls the overall process of oxidative dehalogenation and denitration by HadA. This report is the first to identify a key mechanistic factor controlling the enzymatic processes of oxidative dehalogenation and denitration.
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Affiliation(s)
- Panu Pimviriyakul
- School of Biomolecular Science and Engineering , Vidyasirimedhi Institute of Science and Technology (VISTEC) , Wangchan Valley , Rayong , 21210 , Thailand .
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology , Faculty of Science , Mahidol University , Bangkok , 10400 , Thailand
| | - Panida Surawatanawong
- Department of Chemistry and Center of Excellence for Innovation in Chemistry , Faculty of Science , Mahidol University , Bangkok , 10400 , Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering , Vidyasirimedhi Institute of Science and Technology (VISTEC) , Wangchan Valley , Rayong , 21210 , Thailand .
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17
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Pimviriyakul P, Chaiyen P. A complete bioconversion cascade for dehalogenation and denitration by bacterial flavin-dependent enzymes. J Biol Chem 2018; 293:18525-18539. [PMID: 30282807 DOI: 10.1074/jbc.ra118.005538] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 09/29/2018] [Indexed: 12/17/2022] Open
Abstract
Halogenated phenol and nitrophenols are toxic compounds that are widely accumulated in the environment. Enzymes in the had operon from the bacterium Ralstonia pickettii DTP0602 have the potential for application as biocatalysts in the degradation of many of these toxic chemicals. HadA monooxygenase previously was identified as a two-component reduced FAD (FADH-)-utilizing monooxygenase with dual activities of dehalogenation and denitration. However, the partner enzymes of HadA, that is, the flavin reductase and quinone reductase that provide the FADH- for HadA and reduce quinone to hydroquinone, remain to be identified. In this report, we overexpressed and purified the flavin reductases, HadB and HadX, to investigate their functional and catalytic properties. Our results indicated that HadB is an FMN-dependent quinone reductase that converts the quinone products from HadA to hydroquinone compounds that are more stable and can be assimilated by downstream enzymes in the pathway. Transient kinetics indicated that HadB prefers NADH and menadione as the electron donor and acceptor, respectively. We found that HadX is an FAD-bound flavin reductase, which can generate FADH- for HadA to catalyze dehalogenation or denitration reactions. Thermodynamic and transient kinetic experiments revealed that HadX prefers to bind FAD over FADH- and that HadX can transfer FADH- from HadX to HadA via free diffusion. Moreover, HadX rapidly catalyzed NADH-mediated reduction of flavin and provided the FADH- for a monooxygenase of a different system. Combination of all three flavin-dependent enzymes, i.e. HadA/HadB/HadX, reconstituted an effective dehalogenation and denitration cascade, which may be useful for future bioremediation applications.
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Affiliation(s)
- Panu Pimviriyakul
- From the School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210 and.,the Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 14000, Thailand
| | - Pimchai Chaiyen
- From the School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210 and
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18
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Kwean OS, Cho SY, Yang JW, Cho W, Park S, Lim Y, Shin MC, Kim HS, Park J, Kim HS. 4-Chlorophenol biodegradation facilitator composed of recombinant multi-biocatalysts immobilized onto montmorillonite. BIORESOURCE TECHNOLOGY 2018; 259:268-275. [PMID: 29571170 DOI: 10.1016/j.biortech.2018.03.066] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/11/2018] [Accepted: 03/12/2018] [Indexed: 06/08/2023]
Abstract
A biodegradation facilitator which catalyzes the initial steps of 4-chlorophenol (4-CP) oxidation was prepared by immobilizing multiple enzymes (monooxygenase, CphC-I and dioxygenase, CphA-I) onto a natural inorganic support. The enzymes were obtained via overexpression and purification after cloning the corresponding genes (cphC-I and cphA-I) from Arthrobacter chlorophenolicus A6. Then, the recombinant CphC-I was immobilized onto fulvic acid-activated montmorillonite. The immobilization yield was 60%, and the high enzyme activity (82.6%) was retained after immobilization. Kinetic analysis indicated that the Michaelis-Menten model parameters for the immobilized CphC-I were similar to those for the free enzyme. The enzyme stability was markedly enhanced after immobilization. The immobilized enzyme exhibited a high level of activity even after repetitive use (84.7%) and powdering (65.8%). 4-CP was sequentially oxidized by a multiple enzyme complex, comprising the immobilized CphC-I and CphA-I, via the hydroquinone pathway: oxidative transformation of 4-CP to hydroxyquinol followed by ring fission of hydroxyquinol.
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Affiliation(s)
- Oh Sung Kwean
- Civil and Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05030, Republic of Korea
| | - Su Yeon Cho
- Civil and Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05030, Republic of Korea
| | - Jun Won Yang
- Civil and Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05030, Republic of Korea
| | - Wooyoun Cho
- Civil and Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05030, Republic of Korea
| | - Sungyoon Park
- Civil and Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05030, Republic of Korea
| | - Yejee Lim
- Civil and Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05030, Republic of Korea
| | - Min Chul Shin
- Environmental Engineering, Chonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju Jeollabuk-do 54896, Republic of Korea; The Soil and R&D Center, H-Plus Eco Ltd., 222 Seokchonhosu-ro, Songpa-gu, Seoul 05610, Republic of Korea
| | - Han-Suk Kim
- The Soil and R&D Center, H-Plus Eco Ltd., 222 Seokchonhosu-ro, Songpa-gu, Seoul 05610, Republic of Korea
| | - Joonhong Park
- Civil and Environmental Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Han S Kim
- Civil and Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05030, Republic of Korea.
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