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Pereyra-Camacho MA, Balderas-Hernández VE, Barba-de la Rosa AP, De Leon-Rodriguez A. Whole-cell biocatalysis for phthalate esters biodegradation in wastewater by a saline soil bacteria SSB-consortium. CHEMOSPHERE 2024; 364:143243. [PMID: 39233295 DOI: 10.1016/j.chemosphere.2024.143243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 08/22/2024] [Accepted: 08/31/2024] [Indexed: 09/06/2024]
Abstract
Phthalic acid esters (PAE) are widely used as plasticizers and have been classified as ubiquitous environmental contaminants of primary concern. PAE have accumulated intensively in surface water, groundwater, and wastewaters; thus, PAE degradation is essential. In the present study, the ability of a saline soil bacteria (SSB)-consortium to degrade synthetic wastewater-phthalates with alkyl chains of different lengths, such as diethyl phthalate (DEP), di-n-butyl phthalate (DBP), benzyl butyl phthalate (BBP), and di (2-ethylhexyl) phthalate (DEHP) was characterized. A central composite design-response surface methodology was applied to optimize the degradation of each phthalate, where the independent variables were temperature (21-41 °C), pH (5.3-8.6) and PAE concentration (79.5-920.4 mg L-1), and Gas Chromatography-Mass Spectrometry was used to identify the metabolites generated during phthalate degradation. Optimal conditions were 31 °C, pH 7.0, and an initial PAE concentration of 500 mg L-1, where the SSB-consortium removed 84.9%, 98.47%, 99.09% and 98.25% of initial DEP, DBP, BBP, and DEHP, respectively, in 168h. A first-order kinetic model explained - the biodegradation progression, while the half-life of PAE degradation ranged from 12.8 to 29.8 h. Genera distribution of the SSB-consortium was determined by bacterial meta-taxonomic analysis. Serratia, Methylobacillus, Acrhomobacter, and Pseudomonas were the predominant genera; however, the type of phthalate directly affected their distribution. Scanning electron microscopy analysis showed that high concentrations (1000 mg L-1) of phthalates induced morphological alterations in the bacterial SSB-consortium. The metabolite profiling showed that DEP, DBP, BBP, and DEHP could be fully metabolized through the de-esterification and β-oxidation pathways. Therefore, the SSB-consortium can be considered a potential candidate for bioremediation of complex phthalate-contaminated water resources.
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Affiliation(s)
- Marco A Pereyra-Camacho
- IPICyT, Instituto Potosino de Investigación Científica y Tecnológica A.C. Camino a la Presa San José No. 2055, Lomas 4a sección, San Luis Potosí, San Luis Potosí, 78216 Mexico
| | - Victor E Balderas-Hernández
- IPICyT, Instituto Potosino de Investigación Científica y Tecnológica A.C. Camino a la Presa San José No. 2055, Lomas 4a sección, San Luis Potosí, San Luis Potosí, 78216 Mexico
| | - Ana P Barba-de la Rosa
- IPICyT, Instituto Potosino de Investigación Científica y Tecnológica A.C. Camino a la Presa San José No. 2055, Lomas 4a sección, San Luis Potosí, San Luis Potosí, 78216 Mexico
| | - Antonio De Leon-Rodriguez
- IPICyT, Instituto Potosino de Investigación Científica y Tecnológica A.C. Camino a la Presa San José No. 2055, Lomas 4a sección, San Luis Potosí, San Luis Potosí, 78216 Mexico.
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Zhao H, Wang L, Bai Y, Li Y, Tang T, Liang H, Gao D. Immobilized enzyme with sustainable chestnut biochar to remediate polycyclic aromatic hydrocarbons contaminated soils. ENVIRONMENTAL TECHNOLOGY 2024; 45:2034-2044. [PMID: 36579925 DOI: 10.1080/09593330.2022.2164221] [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: 08/27/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) contaminated soil severely and are difficult to remediate. In this study, acid-modified chestnut inner shell biochar with abundant pore channels was used as the main raw materials for the immobilization of white-rot fungal crude enzyme. The maximum immobilization rate of crude enzymes (97.25%±6.20%) could be achieved under the optimal conditions of 24 h immobilization of 10 U/mL crude enzymes by 1 g biochar at 25℃ and pH = 5. Meanwhile, immobilization improved the stability of the crude enzyme. The relative activity of the immobilized crude enzyme increased by 59.32% and 49.73% (compared to the free crude enzymes) after 5 weeks of storage at 4°C and 25°C, respectively. It has been verified that chestnut-based immobilized crude enzyme can degrade 37% of benzo[a]pyrene in 10 days for PAHs-contaminated soils. An efficient, feasible, and low-cost remediation method for PAHs-contaminated soils was explored, which provides technical support for the application of crude enzymes in organic contaminated soils.
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Affiliation(s)
- Huan Zhao
- Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
- Collaborative Innovation Center of Energy Conservation & Emission Reduction and Sustainable Urban-Rural Development in Beijing, Beijing, People's Republic of China
| | - Litao Wang
- Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
- Collaborative Innovation Center of Energy Conservation & Emission Reduction and Sustainable Urban-Rural Development in Beijing, Beijing, People's Republic of China
| | - Yuhong Bai
- Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
- Collaborative Innovation Center of Energy Conservation & Emission Reduction and Sustainable Urban-Rural Development in Beijing, Beijing, People's Republic of China
| | - Ying Li
- Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
- Collaborative Innovation Center of Energy Conservation & Emission Reduction and Sustainable Urban-Rural Development in Beijing, Beijing, People's Republic of China
| | - Teng Tang
- Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
- Collaborative Innovation Center of Energy Conservation & Emission Reduction and Sustainable Urban-Rural Development in Beijing, Beijing, People's Republic of China
| | - Hong Liang
- Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
- Collaborative Innovation Center of Energy Conservation & Emission Reduction and Sustainable Urban-Rural Development in Beijing, Beijing, People's Republic of China
| | - Dawen Gao
- Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
- Collaborative Innovation Center of Energy Conservation & Emission Reduction and Sustainable Urban-Rural Development in Beijing, Beijing, People's Republic of China
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Xiong JX, Du LS, Li NN, Wu XT, Xiang Y, Li S, Zou L, Liu D, Huang D, Xie ZF, Wang Y, Li J, Dai J, Yan D, Chao HJ. Pigmentiphaga kullae CHJ604 improved the growth of tobacco by degrading allelochemicals and xenobiotics in continuous cropping obstacles. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133466. [PMID: 38219583 DOI: 10.1016/j.jhazmat.2024.133466] [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: 10/25/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/16/2024]
Abstract
Plant autotoxicity is considered to be one of the important causes of continuous cropping obstacles in modern agriculture, which accumulates a lot of allelochemicals and xenobiotics and is difficult to solve effectively. To overcome tobacco continuous obstacles, a strain Pigmentiphaga kullae CHJ604 isolated from the environment can effectively degrade these compounds in this study. CHJ604 strain can degrade 11 types of autotoxicity allelochemicals and xenobiotics (1646.22 μg/kg) accumulated in the soil of ten-years continuous cropping of tobacco. The 11 allelochemicals and xenobiotics significantly reduced Germination Percentage (GP), Germination Index (GI), and Mean Germination Time (MGT) of tobacco seeds, and inhibited the development of leaves, stems, and roots. These negative disturbances can be eliminated by CHJ604 strain. The degradation pathways of 11 allelochemicals and xenobiotics were obtained by whole genome sequence and annotation of CHJ604 strain. The heterologous expression of a terephthalate 1,2-dioxygenase can catalyze 4-hydroxybenzoic acid, 4-hydroxy-3-methoxybenzoic acid, 4-hydroxybenzaldehyde, and 4-hydroxy-3-methoxy-benzaldehyde, respectively. The phthalate 4,5-dioxygenase can catalyze phthalic acid, diisobutyl phthalate, and dibutyl phthalate. These two enzymes are conducive to the simultaneous degradation of multiple allelochemicals and xenobiotics by strain CHJ604. This study provides new insights into the biodegradation of autotoxicity allelochemicals and xenobiotics as it is the first to describe a degrading bacterium of 11 types of allelochemicals and xenobiotics and their great potential in improving tobacco continuous obstacles.
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Affiliation(s)
- Jia-Xi Xiong
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Ling-Shan Du
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Na-Na Li
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Xiu-Ting Wu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Yang Xiang
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Sha Li
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Lei Zou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Dongqi Liu
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, PR China
| | - Duo Huang
- Hubei Accurate Inspection & Testing Co., Ltd., Wuhan 430223, PR China
| | - Ze Feng Xie
- Hubei Accurate Inspection & Testing Co., Ltd., Wuhan 430223, PR China
| | - Ying Wang
- Hubei Accurate Inspection & Testing Co., Ltd., Wuhan 430223, PR China
| | - Jinhua Li
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Jingcheng Dai
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Dazhong Yan
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Hong-Jun Chao
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, PR China.
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Cárdenas-Moreno Y, González-Bacerio J, García Arellano H, Del Monte-Martínez A. Oxidoreductase enzymes: Characteristics, applications, and challenges as a biocatalyst. Biotechnol Appl Biochem 2023; 70:2108-2135. [PMID: 37753743 DOI: 10.1002/bab.2513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 09/03/2023] [Indexed: 09/28/2023]
Abstract
Oxidoreductases are enzymes with distinctive characteristics that favor their use in different areas, such as agriculture, environmental management, medicine, and analytical chemistry. Among these enzymes, oxidases, dehydrogenases, peroxidases, and oxygenases are very interesting. Because their substrate diversity, they can be used in different biocatalytic processes by homogeneous and heterogeneous catalysis. Immobilization of these enzymes has favored their use in the solution of different biotechnological problems, with a notable increase in the study and optimization of this technology in the last years. In this review, the main structural and catalytical features of oxidoreductases, their substrate specificity, immobilization, and usage in biocatalytic processes, such as bioconversion, bioremediation, and biosensors obtainment, are presented.
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Affiliation(s)
- Yosberto Cárdenas-Moreno
- Laboratory for Enzyme Technology, Centre for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
| | - Jorge González-Bacerio
- Laboratory for Enzyme Technology, Centre for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
- Department of Biochemistry, Faculty of Biology, University of Havana, Havana, Cuba
| | - Humberto García Arellano
- Department of Environmental Sciences, Division of Health and Biological Sciences, Metropolitan Autonomous University, Lerma, Mexico, Mexico
| | - Alberto Del Monte-Martínez
- Laboratory for Enzyme Technology, Centre for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
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Runda ME, de Kok NAW, Schmidt S. Rieske Oxygenases and Other Ferredoxin-Dependent Enzymes: Electron Transfer Principles and Catalytic Capabilities. Chembiochem 2023; 24:e202300078. [PMID: 36964978 DOI: 10.1002/cbic.202300078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 03/27/2023]
Abstract
Enzymes that depend on sophisticated electron transfer via ferredoxins (Fds) exhibit outstanding catalytic capabilities, but despite decades of research, many of them are still not well understood or exploited for synthetic applications. This review aims to provide a general overview of the most important Fd-dependent enzymes and the electron transfer processes involved. While several examples are discussed, we focus in particular on the family of Rieske non-heme iron-dependent oxygenases (ROs). In addition to illustrating their electron transfer principles and catalytic potential, the current state of knowledge on structure-function relationships and the mode of interaction between the redox partner proteins is reviewed. Moreover, we highlight several key catalyzed transformations, but also take a deeper dive into their engineerability for biocatalytic applications. The overall findings from these case studies highlight the catalytic capabilities of these biocatalysts and could stimulate future interest in developing additional Fd-dependent enzyme classes for synthetic applications.
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Affiliation(s)
- Michael E Runda
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Niels A W de Kok
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Sandy Schmidt
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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Rogers MS, Gordon AM, Rappe TM, Goodpaster JD, Lipscomb JD. Contrasting Mechanisms of Aromatic and Aryl-Methyl Substituent Hydroxylation by the Rieske Monooxygenase Salicylate 5-Hydroxylase. Biochemistry 2023; 62:507-523. [PMID: 36583545 PMCID: PMC9854337 DOI: 10.1021/acs.biochem.2c00610] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The hydroxylase component (S5HH) of salicylate-5-hydroxylase catalyzes C5 ring hydroxylation of salicylate but switches to methyl hydroxylation when a C5 methyl substituent is present. The use of 18O2 reveals that both aromatic and aryl-methyl hydroxylations result from monooxygenase chemistry. The functional unit of S5HH comprises a nonheme Fe(II) site located 12 Å across a subunit boundary from a one-electron reduced Rieske-type iron-sulfur cluster. Past studies determined that substrates bind near the Fe(II), followed by O2 binding to the iron to initiate catalysis. Stopped-flow-single-turnover reactions (STOs) demonstrated that the Rieske cluster transfers an electron to the iron site during catalysis. It is shown here that fluorine ring substituents decrease the rate constant for Rieske electron transfer, implying a prior reaction of an Fe(III)-superoxo intermediate with a substrate. We propose that the iron becomes fully oxidized in the resulting Fe(III)-peroxo-substrate-radical intermediate, allowing Rieske electron transfer to occur. STO using 5-CD3-salicylate-d8 occurs with an inverse kinetic isotope effect (KIE). In contrast, STO of a 1:1 mixture of unlabeled and 5-CD3-salicylate-d8 yields a normal product isotope effect. It is proposed that aromatic and aryl-methyl hydroxylation reactions both begin with the Fe(III)-superoxo reaction with a ring carbon, yielding the inverse KIE due to sp2 → sp3 carbon hybridization. After Rieske electron transfer, the resulting Fe(III)-peroxo-salicylate intermediate can continue to aromatic hydroxylation, whereas the equivalent aryl-methyl intermediate formation must be reversible to allow the substrate exchange necessary to yield a normal product isotope effect. The resulting Fe(III)-(hydro)peroxo intermediate may be reactive or evolve through a high-valent iron intermediate to complete the aryl-methyl hydroxylation.
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Affiliation(s)
- Melanie S. Rogers
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Adrian M. Gordon
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Todd M. Rappe
- Minnesota NMR Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jason D. Goodpaster
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Comprehensive Genomic Characterization of Marine Bacteria Thalassospira spp. Provides Insights into Their Ecological Roles in Aromatic Hydrocarbon-Exposed Environments. Microbiol Spectr 2022; 10:e0314922. [PMID: 36190412 PMCID: PMC9604089 DOI: 10.1128/spectrum.03149-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The marine bacterial genus Thalassospira has often been identified as an abundant member of polycyclic aromatic hydrocarbon (PAH)-exposed microbial communities. However, despite their potential usability for biotechnological applications, functional genes that are conserved in their genomes have barely been investigated. Thus, the goal of this study was to comprehensively examine the functional genes that were potentially responsible for aromatic hydrocarbon biodegradation in the Thalassospira genomes available from databases, including a new isolate of Thalassospira, strain GO-4, isolated from a phenanthrene-enriched marine bacterial consortium. Strain GO-4 was used in this study as a model organism to link the genomic data and their metabolic functions. Strain GO-4 growth assays confirmed that it utilized a common phenanthrene biodegradation intermediate 2-carboxybenzaldehyde (CBA) as the sole source of carbon and energy, but did not utilize phenanthrene. Consistently, strain GO-4 was found to possess homologous genes of phdK, pht, and pca that encode enzymes for biodegradation of CBA, phthalic acid, and protocatechuic acid, respectively. Further comprehensive genomic analyses for 33 Thalassospira genomes from databases showed that a gene cluster that consisted of phdK and pht homologs was conserved in 13 of the 33 strains. pca gene homologs were found in all examined genomes; however, homologs of the known PAH-degrading genes, such as the pah, phn, or nah genes, were not found. Possibly Thalassospira spp. co-occupy niches with other PAH-degrading bacteria that provide them with PAH degradation intermediates and facilitated their inhabitation in PAH-exposed microbial ecosystems. IMPORTANCE Comprehensive investigation of multiple genomic data sets from targeted microbial taxa deposited in databases may provide substantial information to predict metabolic capabilities and ecological roles in different environments. This study is the first report that details the functional profiling of Thalassospira spp. that have repeatedly been found in polycyclic aromatic hydrocarbon (PAH)-exposed marine bacterial communities by using genomic data from a new isolate, Thalassospira strain GO-4, and other strains in databases. Through screening of functional genes potentially involved in aromatic hydrocarbon biodegradation across 33 Thalassospira genomes and growth assays for strain GO-4, it was suggested that Thalassospira spp. unexceptionally conserved the ability to metabolize single-ring, PAH biodegradation intermediates, while being incapable of utilizing PAHs. This expanded our understanding of this potentially important contributing member to PAH-degrading microbial ecosystems; such species are considered to be specialized in driving downstream reactions of PAH biodegradation.
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Two-component carnitine monooxygenase from Escherichia coli: Functional characterization, Inhibition and mutagenesis of the molecular interface. Biosci Rep 2022; 42:231753. [PMID: 36066069 PMCID: PMC9508527 DOI: 10.1042/bsr20221102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/16/2022] [Accepted: 09/06/2022] [Indexed: 11/23/2022] Open
Abstract
Gut microbial production of trimethylamine (TMA) from l-carnitine is directly linked to cardiovascular disease. TMA formation is facilitated by carnitine monooxygenase, which was proposed as a target for the development of new cardioprotective compounds. Therefore, the molecular understanding of the two-component Rieske-type enzyme from Escherichia coli was intended. The redox cofactors of the reductase YeaX (FMN, plant-type [2Fe-2S] cluster) and of the oxygenase YeaW (Rieske-type [2Fe-2S] and mononuclear [Fe] center) were identified. Compounds meldonium and the garlic-derived molecule allicin were recently shown to suppress microbiota-dependent TMA formation. Based on two independent carnitine monooxygenase activity assays, enzyme inhibition by meldonium or allicin was demonstrated. Subsequently, the molecular interplay of the reductase YeaX and the oxygenase YeaW was addressed. Chimeric carnitine monooxygenase activity was efficiently reconstituted by combining YeaX (or YeaW) with the orthologous oxygenase CntA (or reductase CntB) from Acinetobacter baumannii. Partial conservation of the reductase/oxygenase docking interface was concluded. A structure guided mutagenesis approach was used to further investigate the interaction and electron transfer between YeaX and YeaW. Based on AlphaFold structure predictions, a total of 28 site-directed variants of YeaX and YeaW were kinetically analyzed. Functional relevance of YeaX residues Arg271, Lys313 and Asp320 was concluded. Concerning YeaW, a docking surface centered around residues Arg83, Lys104 and Lys117 was hypothesized. The presented results might contribute to the development of TMA-lowering strategies that could reduce the risk for cardiovascular disease.
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Yin Y, Wu H, Jiang Z, Jiang J, Lu Z. Degradation of Triclosan in the Water Environment by Microorganisms: A Review. Microorganisms 2022; 10:1713. [PMID: 36144315 PMCID: PMC9505857 DOI: 10.3390/microorganisms10091713] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Triclosan (TCS), a kind of pharmaceuticals and personal care products (PPCPs), is widely used and has had a large production over years. It is an emerging pollutant in the water environment that has attracted global attention due to its toxic effects on organisms and aquatic ecosystems, and its concentrations in the water environment are expected to increase since the COVID-19 pandemic outbreak. Some researchers found that microbial degradation of TCS is an environmentally sustainable technique that results in the mineralization of large amounts of organic pollutants without toxic by-products. In this review, we focus on the fate of TCS in the water environment, the diversity of TCS-degrading microorganisms, biodegradation pathways and molecular mechanisms, in order to provide a reference for the efficient degradation of TCS and other PPCPs by microorganisms.
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Affiliation(s)
- Yiran Yin
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hao Wu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhenghai Jiang
- Zhejiang Haihe Environmental Technology Co., Ltd., Jinhua 321012, China
| | - Jingwei Jiang
- Zhejiang Haihe Environmental Technology Co., Ltd., Jinhua 321012, China
| | - Zhenmei Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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Thévenod F, Schreiber T, Lee WK. Renal hypoxia-HIF-PHD-EPO signaling in transition metal nephrotoxicity: friend or foe? Arch Toxicol 2022; 96:1573-1607. [PMID: 35445830 PMCID: PMC9095554 DOI: 10.1007/s00204-022-03285-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/14/2022] [Indexed: 12/18/2022]
Abstract
The kidney is the main organ that senses changes in systemic oxygen tension, but it is also the key detoxification, transit and excretion site of transition metals (TMs). Pivotal to oxygen sensing are prolyl-hydroxylases (PHDs), which hydroxylate specific residues in hypoxia-inducible factors (HIFs), key transcription factors that orchestrate responses to hypoxia, such as induction of erythropoietin (EPO). The essential TM ion Fe is a key component and regulator of the hypoxia–PHD–HIF–EPO (HPHE) signaling axis, which governs erythropoiesis, angiogenesis, anaerobic metabolism, adaptation, survival and proliferation, and hence cell and body homeostasis. However, inadequate concentrations of essential TMs or entry of non-essential TMs in organisms cause toxicity and disrupt health. Non-essential TMs are toxic because they enter cells and displace essential TMs by ionic and molecular mimicry, e. g. in metalloproteins. Here, we review the molecular mechanisms of HPHE interactions with TMs (Fe, Co, Ni, Cd, Cr, and Pt) as well as their implications in renal physiology, pathophysiology and toxicology. Some TMs, such as Fe and Co, may activate renal HPHE signaling, which may be beneficial under some circumstances, for example, by mitigating renal injuries from other causes, but may also promote pathologies, such as renal cancer development and metastasis. Yet some other TMs appear to disrupt renal HPHE signaling, contributing to the complex picture of TM (nephro-)toxicity. Strikingly, despite a wealth of literature on the topic, current knowledge lacks a deeper molecular understanding of TM interaction with HPHE signaling, in particular in the kidney. This precludes rationale preventive and therapeutic approaches to TM nephrotoxicity, although recently activators of HPHE signaling have become available for therapy.
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Affiliation(s)
- Frank Thévenod
- Institute for Physiology, Pathophysiology and Toxicology, ZBAF, Witten/Herdecke University, Stockumer Strasse 12, 58453, Witten, Germany.
| | - Timm Schreiber
- Institute for Physiology, Pathophysiology and Toxicology, ZBAF, Witten/Herdecke University, Stockumer Strasse 12, 58453, Witten, Germany
| | - Wing-Kee Lee
- Physiology and Pathophysiology of Cells and Membranes, Medical School EWL, Bielefeld University, R.1 B2-13, Morgenbreede 1, 33615 Bielefeld, Germany
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11
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Purification and Characterization of the Isoprene Monooxygenase from Rhodococcus sp. Strain AD45. Appl Environ Microbiol 2022; 88:e0002922. [PMID: 35285709 PMCID: PMC9004368 DOI: 10.1128/aem.00029-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Isoprene (2-methyl-1,3-butadiene) is a climate-active gas released to the atmosphere in large quantities, comparable to methane in magnitude. Several bacteria have been isolated which can grow on isoprene as a sole carbon and energy source, but very little information is available about the degradation of isoprene by these bacteria at the biochemical level. Isoprene utilization is dependent on a multistep pathway, with the first step being the oxidation of isoprene to epoxy-isoprene. This is catalyzed by a four-component soluble diiron monooxygenase, isoprene monooxygenase (IsoMO). IsoMO is a six-protein complex comprising an oxygenase (IsoABE), containing the di-iron active site, a Rieske-type ferredoxin (IsoC), a NADH reductase (IsoF), and a coupling/effector protein (IsoD), homologous to the soluble methane monooxygenase and alkene/aromatic monooxygenases. Here, we describe the purification of the IsoMO components from Rhodococcus sp. AD45 and reconstitution of isoprene-oxidation activity in vitro. Some IsoMO components were expressed and purified from the homologous host Rhodococcus sp. AD45-ID, a Rhodococcus sp. AD45 strain lacking the megaplasmid which contains the isoprene metabolic gene cluster. Others were expressed in Escherichia coli and purified as fusion proteins. We describe the characterization of these purified components and demonstrate their activity when combined with Rhodococcus sp. AD45 cell lysate. Demonstration of IsoMO activity in vitro provides a platform for further biochemical and biophysical characterization of this novel soluble diiron center monooxygenase, facilitating new insights into the enzymatic basis for the bacterial degradation of isoprene. IMPORTANCE Isoprene is a highly abundant climate-active gas and a carbon source for some bacteria. Analyses of the genes encoding isoprene monooxygenase (IsoMO) indicate this enzyme is a soluble diiron center monooxygenase in the same family of oxygenases as soluble methane monooxygenase, alkene monooxygenase, and toluene monooxygenase. We report the initial biochemical characterization of IsoMO from Rhodococcus, the first from any bacterium, describing the challenging purification and reconstitution of in vitro activity of its four components. This study lays the foundation for future detailed mechanistic studies of IsoMO, a key enzyme in the global isoprene cycle.
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Structural insights into dihydroxylation of terephthalate, a product of polyethylene terephthalate degradation. J Bacteriol 2022; 204:e0054321. [PMID: 35007143 DOI: 10.1128/jb.00543-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biodegradation of terephthalate (TPA) is a highly desired catabolic process for the bacterial utilization of this Polyethylene terephthalate (PET) depolymerization product, but to date, the structure of terephthalate dioxygenase (TPDO), a Rieske oxygenase (RO) that catalyzes the dihydroxylation of TPA to a cis-diol is unavailable. In this study, we characterized the steady-state kinetics and first crystal structure of TPDO from Comamonas testosteroni KF1 (TPDOKF1). The TPDOKF1 exhibited the substrate specificity for TPA (kcat/Km = 57 ± 9 mM-1s-1). The TPDOKF1 structure harbors characteristics RO features as well as a unique catalytic domain that rationalizes the enzyme's function. The docking and mutagenesis studies reveal that its substrate specificity to TPA is mediated by Arg309 and Arg390 residues, two residues positioned on opposite faces of the active site. Additionally, residue Gln300 is also proven to be crucial for the activity, its substitution to alanine decreases the activity (kcat) by 80%. Together, this study delineates the structural features that dictate the substrate recognition and specificity of TPDO. Importance The global plastic pollution has become the most pressing environmental issue. Recent studies on enzymes depolymerizing polyethylene terephthalate plastic into terephthalate (TPA) show some potential in tackling this. Microbial utilization of this released product, TPA is an emerging and promising strategy for waste-to-value creation. Research from the last decade has discovered terephthalate dioxygenase (TPDO), as being responsible for initiating the enzymatic degradation of TPA in a few Gram-negative and Gram-positive bacteria. Here, we have determined the crystal structure of TPDO from Comamonas testosteroni KF1 and revealed that it possesses a unique catalytic domain featuring two basic residues in the active site to recognize TPA. Biochemical and mutagenesis studies demonstrated the crucial residues responsible for the substrate specificity of this enzyme.
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Mahto JK, Neetu N, Waghmode B, Kuatsjah E, Sharma M, Sircar D, Sharma AK, Tomar S, Eltis LD, Kumar P. Molecular insights into substrate recognition and catalysis by phthalate dioxygenase from Comamonas testosteroni. J Biol Chem 2021; 297:101416. [PMID: 34800435 PMCID: PMC8649396 DOI: 10.1016/j.jbc.2021.101416] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 11/19/2022] Open
Abstract
Phthalate, a plasticizer, endocrine disruptor, and potential carcinogen, is degraded by a variety of bacteria. This degradation is initiated by phthalate dioxygenase (PDO), a Rieske oxygenase (RO) that catalyzes the dihydroxylation of phthalate to a dihydrodiol. PDO has long served as a model for understanding ROs despite a lack of structural data. Here we purified PDOKF1 from Comamonas testosteroni KF1 and found that it had an apparent kcat/Km for phthalate of 0.58 ± 0.09 μM-1s-1, over 25-fold greater than for terephthalate. The crystal structure of the enzyme at 2.1 Å resolution revealed that it is a hexamer comprising two stacked α3 trimers, a configuration not previously observed in RO crystal structures. We show that within each trimer, the protomers adopt a head-to-tail configuration typical of ROs. The stacking of the trimers is stabilized by two extended helices, which make the catalytic domain of PDOKF1 larger than that of other characterized ROs. Complexes of PDOKF1 with phthalate and terephthalate revealed that Arg207 and Arg244, two residues on one face of the active site, position these substrates for regiospecific hydroxylation. Consistent with their roles as determinants of substrate specificity, substitution of either residue with alanine yielded variants that did not detectably turnover phthalate. Together, these results provide critical insights into a pollutant-degrading enzyme that has served as a paradigm for ROs and facilitate the engineering of this enzyme for bioremediation and biocatalytic applications.
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Affiliation(s)
- Jai Krishna Mahto
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | - Neetu Neetu
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | | | - Eugene Kuatsjah
- Department of Microbiology & Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Monica Sharma
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | - Debabrata Sircar
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | | | - Shailly Tomar
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India
| | - Lindsay D Eltis
- Department of Microbiology & Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India.
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Fujishiro T, Ooi M, Takaoka K. Crystal structure of Escherichia coli class II hybrid cluster protein, HCP, reveals a [4Fe-4S] cluster at the N-terminal protrusion. FEBS J 2021; 288:6752-6768. [PMID: 34101368 DOI: 10.1111/febs.16062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 05/06/2021] [Accepted: 06/07/2021] [Indexed: 01/26/2023]
Abstract
Hybrid cluster protein (HCP) is a unique Fe-S-O-type metallocluster-containing enzyme present in many anaerobic organisms and is categorized into three distinct classes (I, II, and III). The class II HCP uniquely utilizes hybrid cluster protein reductase (HCR), unlike the other classes of HCPs. To gain structural insights into the electron transfer system between the class II HCP and HCR, we elucidated the X-ray crystal structure of Escherichia coli HCP (Ec HCP), representing the first report of a class II HCP structure. Surprisingly, Ec HCP was found to harbor a [4Fe-4S] cluster rather than a [2Fe-2S] cluster at the N-terminal Cys-rich region, similar to class I HCPs. It was also found that the Cys-rich motif forms a unique protrusion and that the surrounding charge distributions on the surface of class II Ec HCP are distinct from those of class I HCPs. The functional significance of the Cys-rich region was investigated using an Ec HCP variant (chimeric HCP) containing a class I HCP Cys-rich motif from Desulfovibrio desulfuricans. The biochemical analyses showed that the chimeric HCP lacks the hybrid cluster and the electron-accepting function from HCR despite the formation of the chimeric HCP-HCR complex. Furthermore, HCP-HCR molecular docking analysis suggested that the protrusion area serves as an HCR-binding region. Therefore, the protrusion of the unique Cys-rich motif and the surrounding area of class II HCP are likely important for maturation of Ec HCP and orienting HCR onto the surface of HCP to facilitate electron transfer in the HCP-HCR complex.
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Affiliation(s)
- Takashi Fujishiro
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Miho Ooi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Kyosei Takaoka
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
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Quareshy M, Shanmugam M, Townsend E, Jameson E, Bugg TDH, Cameron AD, Chen Y. Structural basis of carnitine monooxygenase CntA substrate specificity, inhibition, and intersubunit electron transfer. J Biol Chem 2020; 296:100038. [PMID: 33158989 PMCID: PMC7948474 DOI: 10.1074/jbc.ra120.016019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/27/2020] [Accepted: 11/06/2020] [Indexed: 12/27/2022] Open
Abstract
Microbial metabolism of carnitine to trimethylamine (TMA) in the gut can accelerate atherosclerosis and heart disease, and these TMA-producing enzymes are therefore important drug targets. Here, we report the first structures of the carnitine oxygenase CntA, an enzyme of the Rieske oxygenase family. CntA exists in a head-to-tail α3 trimeric structure. The two functional domains (the Rieske and the catalytic mononuclear iron domains) are located >40 Å apart in the same monomer but adjacent in two neighboring monomers. Structural determination of CntA and subsequent electron paramagnetic resonance measurements uncover the molecular basis of the so-called bridging glutamate (E205) residue in intersubunit electron transfer. The structures of the substrate-bound CntA help to define the substrate pocket. Importantly, a tyrosine residue (Y203) is essential for ligand recognition through a π-cation interaction with the quaternary ammonium group. This interaction between an aromatic residue and quaternary amine substrates allows us to delineate a subgroup of Rieske oxygenases (group V) from the prototype ring-hydroxylating Rieske oxygenases involved in bioremediation of aromatic pollutants in the environment. Furthermore, we report the discovery of the first known CntA inhibitors and solve the structure of CntA in complex with the inhibitor, demonstrating the pivotal role of Y203 through a π-π stacking interaction with the inhibitor. Our study provides the structural and molecular basis for future discovery of drugs targeting this TMA-producing enzyme in human gut.
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Affiliation(s)
- Mussa Quareshy
- School of Life Sciences, University of Warwick, Coventry, UK.
| | - Muralidharan Shanmugam
- Manchester Institute of Biotechnology & Photon Science Institute, The University of Manchester, Manchester, UK
| | | | - Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, UK
| | | | | | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, UK.
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Sakshi, Haritash AK. A comprehensive review of metabolic and genomic aspects of PAH-degradation. Arch Microbiol 2020; 202:2033-2058. [DOI: 10.1007/s00203-020-01929-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/14/2020] [Accepted: 05/26/2020] [Indexed: 01/01/2023]
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Boll M, Geiger R, Junghare M, Schink B. Microbial degradation of phthalates: biochemistry and environmental implications. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:3-15. [PMID: 31364812 DOI: 10.1111/1758-2229.12787] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/23/2019] [Accepted: 07/27/2019] [Indexed: 05/10/2023]
Abstract
The environmentally relevant xenobiotic esters of phthalic acid (PA), isophthalic acid (IPA) and terephthalic acid (TPA) are produced on a million ton scale annually and are predominantly used as plastic polymers or plasticizers. Degradation by microorganisms is considered as the most effective means of their elimination from the environment and proceeds via hydrolysis to the corresponding PA isomers and alcohols under oxic and anoxic conditions. Further degradation of PA, IPA and TPA differs fundamentally between anaerobic and aerobic microorganisms. The latter introduce hydroxyl functionalities by dioxygenases to facilitate subsequent decarboxylation by either aromatizing dehydrogenases or cofactor-free decarboxylases. In contrast, anaerobic bacteria activate the PA isomers to the respective thioesters using CoA ligases or CoA transferases followed by decarboxylation to the central intermediate benzoyl-CoA. Decarboxylases acting on the three PA CoA thioesters belong to the UbiD enzyme family that harbour a prenylated flavin mononucleotide (FMN) cofactor to achieve the mechanistically challenging decarboxylation. Capture of the extremely instable PA-CoA intermediate is accomplished by a massive overproduction of phthaloyl-CoA decarboxylase and a balanced production of PA-CoA forming/decarboxylating enzymes. The strategy of anaerobic phthalate degradation probably represents a snapshot of an ongoing evolution of a xenobiotic degradation pathway via a short-lived reaction intermediate.
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Affiliation(s)
- Matthias Boll
- Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Robin Geiger
- Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Madan Junghare
- Department of Biology and Microbial Ecology, University of Konstanz, Constance, Germany
| | - Bernhard Schink
- Department of Biology and Microbial Ecology, University of Konstanz, Constance, Germany
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Rogers MS, Lipscomb JD. Salicylate 5-Hydroxylase: Intermediates in Aromatic Hydroxylation by a Rieske Monooxygenase. Biochemistry 2019; 58:5305-5319. [PMID: 31066545 PMCID: PMC6856394 DOI: 10.1021/acs.biochem.9b00292] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rieske oxygenases (ROs) catalyze a large range of oxidative chemistry. We have shown that cis-dihydrodiol-forming Rieske dioxygenases first react with their aromatic substrates via an active site nonheme Fe(III)-superoxide; electron transfer from the Rieske cluster then completes the product-forming reaction. Alternatively, two-electron-reduced Fe(III)-peroxo or hydroxo-Fe(V)-oxo activated oxygen intermediates are possible and may be utilized by other ROs to expand the catalytic range. Here, the reaction of a Rieske monooxygenase, salicylate 5-hydroxylase, that does not form a cis-dihydrodiol is examined. Single-turnover kinetic studies show fast binding of salicylate and O2. Transfer of the Rieske electron required to form the gentisate product occurs through bonds over ∼12 Å and must also be very fast. However, the observed rate constant for this reaction is much slower than expected and sensitive to substrate type. This suggests that initial reaction with salicylate occurs using the same Fe(III)-superoxo-level intermediate as Rieske dioxygenases and that this reaction limits the observed rate of electron transfer. A transient intermediate (λmax = 700 nm) with an electron paramagnetic resonance (EPR) at g = 4.3 is observed after the product is formed in the active site. The use of 17O2 (I = 5/2) results in hyperfine broadening of the g = 4.3 signal, showing that gentisate binds to the mononuclear iron via its C5-OH in the intermediate. The chromophore and EPR signal allow study of product release in the catalytic cycle. Comparison of the kinetics of single- and multiple-turnover reactions shows that re-reduction of the metal centers accelerates product release ∼300-fold, providing insight into the regulatory mechanism of ROs.
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Affiliation(s)
- Melanie S. Rogers
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Carrillo-Campos J. Estructura y función de las oxigenasas tipo Rieske/mononuclear. TIP REVISTA ESPECIALIZADA EN CIENCIAS QUÍMICO-BIOLÓGICAS 2019. [DOI: 10.22201/fesz.23958723e.2019.0.196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Las oxigenasas Rieske/mononuclear son un grupo de metaloenzimas que catalizan la oxidación de una variedad de compuestos, destaca su participación en la degradación de compuestos xenobióticos contaminantes; estas enzimas también participan en la biosíntesis de algunos compuestos de interés comercial. Poseen una amplia especificidad por el sustrato, convirtiéndolas en un grupo de enzimas con un alto potencial de aplicación en procesos biotecnológicos que hasta el momento no ha sido explotado. La presente revisión aborda aspectos generales acerca de la función y estructura de este importante grupo de enzimas.
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Boonnorat J, Kanyatrakul A, Prakhongsak A, Honda R, Panichnumsin P, Boonapatcharoen N. Effect of hydraulic retention time on micropollutant biodegradation in activated sludge system augmented with acclimatized sludge treating low-micropollutants wastewater. CHEMOSPHERE 2019; 230:606-615. [PMID: 31128507 DOI: 10.1016/j.chemosphere.2019.05.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 04/28/2019] [Accepted: 05/04/2019] [Indexed: 06/09/2023]
Abstract
This research investigates the effect of hydraulic retention time (HRT) on micropollutant biodegradation of two-stage activated sludge (AS) system augmented with acclimatized sludge treating low-micropollutants wastewater. The experimental wastewater was a mixture of landfill leachate and agriculture wastewater, and HRT was varied between 24, 18, and 12 h. The results showed that, under 24 h HRT, the micropollutant biodegradation efficiencies were 87-93% for bisphenol A (BPA), 2,6-di-tert-butyl-phenol (2,6-DTBP), di-butyl-phthalate (DBP), di-(ethylhexyl)-phthalate (DEHP); 75-81% for carbamazepine (CBZ), diclofenac (DCF); and 88% for N,N-diethylmeta-toluamide (DEET). The degradation efficiencies were similar under 18 h HRT: 87-93% for BPA, 2,6-DTBP, DBP, DEHP; 75-80% for CBZ, DCF; and 80% for DEET. However, the efficiencies substantially declined under 12 h HRT: 71-93%, 55-60%, and 50%, respectively. Importantly, the findings revealed that HRT plays a crucial part in micropollutant biodegradation of bioaugmented AS system. More specifically, too short an HRT (12 h) results in low micropollutant removal efficiency, and too long an HRT (24 h) contributes to low daily throughput and high treatment operation cost. As a result, moderate HRT (18 h) is operationally and economically optimal for bioaugmented AS system treating low-micropollutants wastewater.
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Affiliation(s)
- Jarungwit Boonnorat
- Division of Environmental Engineering, Faculty of Engineering, Rajamangala University of Technology Thanyaburi (RMUTT), Klong 6, Pathum Thani, 12110, Thailand.
| | - Alongkorn Kanyatrakul
- Division of Environmental Engineering, Faculty of Engineering, Rajamangala University of Technology Thanyaburi (RMUTT), Klong 6, Pathum Thani, 12110, Thailand
| | - Apichai Prakhongsak
- Division of Environmental Engineering, Faculty of Engineering, Rajamangala University of Technology Thanyaburi (RMUTT), Klong 6, Pathum Thani, 12110, Thailand
| | - Ryo Honda
- Faculty of Geosciences and Civil Engineering, Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Pornpan Panichnumsin
- Excellent Center of Waste Utilization and Management (ECoWaste), King Mongkut's University of Technology Thonburi (KMUTT), Bangkhuntien, Bangkok, 10150, Thailand; National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Nimaradee Boonapatcharoen
- Excellent Center of Waste Utilization and Management (ECoWaste), King Mongkut's University of Technology Thonburi (KMUTT), Bangkhuntien, Bangkok, 10150, Thailand
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A Novel 3-Phytosterone-9α-Hydroxylase Oxygenation Component and Its Application in Bioconversion of 4-Androstene-3,17-Dione to 9α-Hydroxy-4-Androstene-3,17-Dione Coupling with A NADH Regeneration Formate Dehydrogenase. Molecules 2019; 24:molecules24142534. [PMID: 31336696 PMCID: PMC6680482 DOI: 10.3390/molecules24142534] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/01/2019] [Accepted: 07/09/2019] [Indexed: 11/17/2022] Open
Abstract
9α-Hydroxy-4-androstene-3,17-dione (9-OH-AD) is one of the significant intermediates for the preparation of β-methasone, dexamethasone, and other steroids. In general, the key enzyme that enables the biotransformation of 4-androstene-3,17-dione (AD) to 9-OH-AD is 3-phytosterone-9α-hydroxylase (KSH), which consists of two components: a terminal oxygenase (KshA) and ferredoxin reductase (KshB). The reaction is carried out with the concomitant oxidation of NADH to NAD+. In this study, the more efficient 3-phytosterone-9α-hydroxylase oxygenase (KshC) from the Mycobacterium sp. strain VKM Ac-1817D was confirmed and compared with reported KshA. To evaluate the function of KshC on the bioconversion of AD to 9-OH-AD, the characterization of KshC and the compounded system of KshB, KshC, and NADH was constructed. The optimum ratio of KSH oxygenase to reductase content was 1.5:1. An NADH regeneration system was designed by introducing a formate dehydrogenase, further confirming that a more economical process for biological transformation from AD to 9-OH-AD was established. A total of 7.78 g of 9-OH-AD per liter was achieved through a fed-batch process with a 92.11% conversion rate (mol/mol). This enzyme-mediated hydroxylation method provides an environmentally friendly and economical strategy for the production of 9-OH-AD.
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Characterization of phthalate reductase from Ralstonia eutropha CH34 and in silico study of phthalate dioxygenase and phthalate reductase interaction. J Mol Graph Model 2019; 90:161-170. [DOI: 10.1016/j.jmgm.2019.05.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/03/2019] [Accepted: 05/03/2019] [Indexed: 12/17/2022]
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Retnadhas S, Gummadi SN. Identification and characterization of oxidoreductase component (NdmD) of methylxanthine oxygenase system in Pseudomonas sp. NCIM 5235. Appl Microbiol Biotechnol 2018; 102:7913-7926. [PMID: 30014169 DOI: 10.1007/s00253-018-9224-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 06/24/2018] [Accepted: 07/04/2018] [Indexed: 10/28/2022]
Abstract
Pseudomonas sp. NCIM 5235 is a caffeine-degrading bacterial strain that metabolizes caffeine by sequential demethylation using methylxanthine demethylases. These enzymes belong to the class of two-component Rieske oxygenases and require an oxidoreductase, NdmD, for efficient catalysis. NdmD in Pseudomonas sp. has a unique domain fusion in its N-terminal that is not observed in any other Rieske oxygenase reductases reported so far. In this report, a ~ 1.7 kb ndmD gene from the gDNA of Pseudomonas sp. has been isolated and has been cloned in a pET28a expression vector. Soluble NdmD was over-expressed in Escherichia coli BL21 cells and purified by Ni2+ NTA chromatography. Monomeric molecular mass of the protein was found to be ~ 65 kDa and optimal activity was observed at 35 °C and pH 8.0. It showed broad substrate specificity with highest Kcat/km of 490.8 ± 17.7 towards cytochrome c. To determine the role of N-terminal Rieske domain in its reductase activity, two deletion constructs Δ114NdmD and Δ250NdmD were made. Cytochrome c reductase (ccr) activity of the NdmD constructs and demethylase activity of NdmA in the presence of NdmD constructs showed that there is no significant difference in the catalytic activity of NdmD upon deletion of its N-terminal Rieske domain. However, there might be some functional and evolutionary significance for the fusion of Rieske domain to NdmD and we hypothesize that this domain fusion is an intermediate phase of evolution towards the development of a more efficient enzyme system for xenobiotic degradation.
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Affiliation(s)
- Sreeahila Retnadhas
- Applied and Industrial Microbiology Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Sathyanarayana N Gummadi
- Applied and Industrial Microbiology Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India.
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Singleton DR, Lee J, Dickey AN, Stroud A, Scholl EH, Wright FA, Aitken MD. Polyphasic characterization of four soil-derived phenanthrene-degrading Acidovorax strains and proposal of Acidovorax carolinensis sp. nov. Syst Appl Microbiol 2018; 41:460-472. [PMID: 29937052 DOI: 10.1016/j.syapm.2018.06.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/30/2018] [Accepted: 06/01/2018] [Indexed: 10/14/2022]
Abstract
Four bacterial strains identified as members of the Acidovorax genus were isolated from two geographically distinct but similarly contaminated soils in North Carolina, USA, characterized, and their genomes sequenced. Their 16S rRNA genes were highly similar to those previously recovered during stable-isotope probing (SIP) of one of the soils with the polycyclic aromatic hydrocarbon (PAH) phenanthrene. Heterotrophic growth of all strains occurred with a number of organic acids, as well as phenanthrene, but no other tested PAHs. Optimal growth occurred aerobically under mesophilic temperature, neutral pH, and low salinity conditions. Predominant fatty acids were C16:1ω7c/C16:1ω6c, C16:0, and C18:1ω7c, and were consistent with the genus. Genomic G+C contents ranged from 63.6 to 64.2%. A combination of whole genome comparisons and physiological analyses indicated that these four strains likely represent a single species within the Acidovorax genus. Chromosomal genes for phenanthrene degradation to phthalate were nearly identical to highly conserved regions in phenanthrene-degrading Delftia, Burkholderia, Alcaligenes, and Massilia species in regions flanked by transposable or extrachromosomal elements. The lower degradation pathway for phenanthrene metabolism was inferred by comparisons to described genes and proteins. The novel species Acidovorax carolinensis sp. nov. is proposed, comprising the four strains described in this study with strain NA3T as the type strain (=LMG 30136, =DSM 105008).
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Affiliation(s)
- David R Singleton
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599-7431, USA.
| | - Janice Lee
- Department of Biology, University of North Carolina,Chapel Hill, NC, 27599-3280, USA
| | - Allison N Dickey
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Aaron Stroud
- Department of Biology, University of North Carolina,Chapel Hill, NC, 27599-3280, USA
| | - Elizabeth H Scholl
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Fred A Wright
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Michael D Aitken
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599-7431, USA
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de Sousa STP, Cabral L, Lacerda Júnior GV, Oliveira VM. Diversity of aromatic hydroxylating dioxygenase genes in mangrove microbiome and their biogeographic patterns across global sites. Microbiologyopen 2017; 6. [PMID: 28544594 PMCID: PMC5552929 DOI: 10.1002/mbo3.490] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/16/2017] [Accepted: 03/23/2017] [Indexed: 01/25/2023] Open
Abstract
Aromatic hydrocarbons (AH), such as polycyclic aromatic hydrocarbons, are compounds largely found in nature. Aromatic‐ring‐hydroxylating dioxygenases (ARHD) are proteins involved in AH degradation pathways. We used ARHD functional genes from an oil‐impacted mangrove area and compared their diversity with other sites around the world to understand the ARHD biogeographic distribution patterns. For this, a comprehensive database was established with 166 operational protein families (OPFs) from 1,758 gene sequences obtained from 15 different sites worldwide, of which twelve are already published studies and three are unpublished. Based on a deduced ARHD peptide sequences consensus phylogeny, we examined trends and divergences in the sequence phylogenetic clustering from the different sites. The taxonomic affiliation of the OPF revealed that Pseudomonas, Streptomyces, Variovorax, Bordetella and Rhodococcus were the five most abundant genera, considering all sites. The functional diversity analysis showed the enzymatic prevalence of benzene 1,2‐dioxygenase, 3‐phenylpropionate dioxygenase and naphthalene 1,2‐dioxygenase, in addition to 10.98% of undefined category ARHDs. The ARHD gene correlation analysis among different sites was essentially important to gain insights on spatial distribution patterns, genetic congruence and ecological coherence of the bacterial groups found. This work revealed the genetic potential from the mangrove sediment for AH biodegradation and a considerable evolutionary proximity among the dioxygenase OPFs found in Antarctica and South America sites, in addition to high level of endemism in each continental region.
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Affiliation(s)
- Sanderson T P de Sousa
- Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Paulínia, São Paulo, Brazil.,Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Lucélia Cabral
- Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Paulínia, São Paulo, Brazil
| | - Gileno Vieira Lacerda Júnior
- Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Paulínia, São Paulo, Brazil.,Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Valéria M Oliveira
- Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Paulínia, São Paulo, Brazil
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Kumar V, Sharma N, Maitra SS. Comparative study on the degradation of dibutyl phthalate by two newly isolated Pseudomonas sp. V21b and Comamonas sp. 51F. ACTA ACUST UNITED AC 2017; 15:1-10. [PMID: 28580302 PMCID: PMC5447571 DOI: 10.1016/j.btre.2017.04.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 04/18/2017] [Accepted: 04/18/2017] [Indexed: 11/20/2022]
Abstract
Comparative degradation of DBP by Pseudomonas sp. V21b and Comamonas sp. 51F. Degradation in MSM and contaminated samples. Kinetics of DBP degradation. Stoichiometry of DBP degradation and biomass formation. Phthalate esters genes identification.
Dibutyl phthalate is (DBP) the top priority toxicant responsible for carcinogenicity, teratogenicity and endocrine disruption. This study demonstrates the DBP degradation capability of the two newly isolated bacteria from municipal solid waste leachate samples. The isolated bacteria were designated as Pseudomonas sp. V21b and Comamonas sp. 51F after scanning electron microscopy, transmission electron microscopy, Gram-staining, antibiotic sensitivity tests, biochemical characterization, 16S-rRNA gene identification and phylogenetic studies. They were able to grow on DBP, benzyl butyl phthalate, monobutyl phthalate, diisodecyl phthalate, dioctyl phthalate, and protocatechuate. It was observed that Pseudomonas sp. V21b was more efficient in DBP degradation when compared with Comamonas sp. 51F. It degraded 57% and 76% of the initial DBP in minimal salt medium and in DBP contaminated samples respectively. Kinetics for the effects of DBP concentration on Pseudomonas sp. V21b and Comamonas sp. 51F growth was also evaluated. Stoichiometry for DBP degradation and biomass formation were compared for both the isolates. Two major metabolites diethyl phthalate and monobutyl phthalates were identified using GC–MS in the extracts. Key genes were amplified from the genomes of Pseudomonas sp. V21b and Comamonas sp. 51F. DBP degradation pathway was also proposed.
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Affiliation(s)
- Vinay Kumar
- School of Biotechnology, Jawaharlal Nehru University, Lab no. 117, New Delhi, 110067, India
| | - Neha Sharma
- Arbro Pharmaceuticals Pvt Ltd., New Delhi, 110015, India
| | - S S Maitra
- School of Biotechnology, Jawaharlal Nehru University, Lab no. 117, New Delhi, 110067, India
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Kumar V, Maitra SS. Biodegradation of endocrine disruptor dibutyl phthalate (DBP) by a newly isolated Methylobacillus sp. V29b and the DBP degradation pathway. 3 Biotech 2016; 6:200. [PMID: 28330272 PMCID: PMC5031561 DOI: 10.1007/s13205-016-0524-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/14/2016] [Indexed: 11/24/2022] Open
Abstract
Bacteria of the genus Methylobacillus are methanotrophs, a metabolic feature that is widespread in the phylum Proteobacteria. The study demonstrates the isolation and characterization of a newly isolated Methylobacillus sp. V29b. which grows on methanol, protocatechuate, monobutyl phthalate, dibutyl phthalate, diethyl phthalate, benzyl butyl phthalate, dioctyl phthalate and diisodecyl phthalate. Methylobacillus sp. V29b was characterized with scanning electron microscopy, transmission electron microscopy, Gram staining, antibiotics sensitivity tests and biochemical characterization. It degrades 70 % of the initial DBP in minimal salt medium and 65 % of the initial DBP in samples contaminated with DBP. DBP biodegradation kinetics was explained by the Monod growth inhibition model. Values for maximum specific growth rate (µmax) and half-velocity constant (Ks) are 0.07 h−1 and 998.2 mg/l, respectively. Stoichiometry for DBP degradation was calculated for Methylobacillus sp. V29b. Four metabolic intermediates, dibutyl phthalate (DBP), monobutyl phthalate, phthalic acid and pyrocatechol, were identified. Based on the metabolic intermediates identified, a chemical pathway for DBP degradation was proposed. Six genes for phthalic acid degradation were identified from the genome of Methylobacillus sp. V29b.
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Affiliation(s)
- Vinay Kumar
- Lab No. 117, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - S S Maitra
- Lab No. 117, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
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Boonnorat J, Techkarnjanaruk S, Honda R, Prachanurak P. Effects of hydraulic retention time and carbon to nitrogen ratio on micro-pollutant biodegradation in membrane bioreactor for leachate treatment. BIORESOURCE TECHNOLOGY 2016; 219:53-63. [PMID: 27475331 DOI: 10.1016/j.biortech.2016.07.094] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 07/20/2016] [Accepted: 07/22/2016] [Indexed: 05/22/2023]
Abstract
This research investigated the biodegradation of the micro-pollutants in leachate by the membrane bioreactor (MBR) system under six treatment conditions, comprising two C/N ratios (6, 10) and three hydraulic retention time (HRT) durations (6, 12, 24h). The experimental results indicated that the C/N 6 environment was more advantageous to the bacterial growth. The bacterial communities residing in the sludge were those of heterotrophic bacteria (HB), heterotrophic nitrifying bacteria (HNB) and ammonia oxidizing bacteria (AOB). It was found that HB and HNB produced phenol hydroxylase (PH), esterase (EST), phthalate dioxygenase (PDO) and laccase (LAC) and also enhanced the biodegradation rate constants (k) in the system. At the same time, AOB promoted the production of HB and HNB. The findings also revealed that the 12h HRT was the optimal condition with regard to the highest growth of the bacteria responsible for the biodegradation of phenols and phthalates. Meanwhile, the longer HRT duration (i.e. 24h) was required to effectively bio-degrade carbamazepine (CBZ), N,N-diethyl-m-toluamide (DEET) and diclofenac (DCF).
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Affiliation(s)
- Jarungwit Boonnorat
- Division of Biology, Faculty of Science and Technology, Rajamangala University of Technology Thanyaburi (RMUTT), Klong 6, Pathum Thani 12110, Thailand.
| | - Somkiet Techkarnjanaruk
- Excellent Center of Waste Utilization and Management (ECoWaste), King Mongkut's University of Technology Thonburi (KMUTT), Bangkhuntien, Bangkok 10150, Thailand; National Center for Genetic Engineering and Biotechnology (BIOTEC), Bangkok 10150, Thailand
| | - Ryo Honda
- Research Center for Sustainable Energy and Technology (RSET), Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Pradthana Prachanurak
- Department of Civil Engineering, Faculty of Engineering, Srinakharinwirot University, Ongkharak, Nakhon Nayok 26120, Thailand
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Boonnorat J, Chiemchaisri C, Chiemchaisri W, Yamamoto K. Kinetics of phenolic and phthalic acid esters biodegradation in membrane bioreactor (MBR) treating municipal landfill leachate. CHEMOSPHERE 2016; 150:639-649. [PMID: 26908045 DOI: 10.1016/j.chemosphere.2016.02.050] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/27/2016] [Accepted: 02/10/2016] [Indexed: 06/05/2023]
Abstract
The kinetic of phenolic and phthalic acid esters (PAEs) biodegradation in membrane bioreactor (MBR) treating municipal landfill leachate was investigated. Laboratory-scale MBR was fed with mixture of fresh and stabilized landfill leachate containing carbon to nitrogen (C/N) ratio of 10, 6, 3 and operated under different solid retention time (SRT) of 90, 15 and 5 d. Batch experiments using MBR sludge obtained from each steady-state operating condition revealed highest biodegradation rate constant (k) of 0.059-0.092 h(-1) of the phenolic and PAEs compounds at C/N of 6. Heterotrophic bacteria were the major group responsible for biodegradation of compounds whereas the presence of ammonia-oxidizing bacteria (AOB) helped accelerating their removals. Heterotrophic nitrifying bacteria found under high ammonia condition had an important role in enhancing the biodegradation of phenols and PAEs by releasing phenol hydroxylase (PH), esterase (EST) and phthalate dioxygenase (PDO) enzymes and the presence of AOB helped improving biodegradation of phenolic and PAEs compounds through their co-metabolism.
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Affiliation(s)
- Jarungwit Boonnorat
- Department of Environmental Engineering, Faculty of Engineering, Kasetsart University, Bangkok, 10900, Thailand
| | - Chart Chiemchaisri
- Department of Environmental Engineering, Faculty of Engineering, Kasetsart University, Bangkok, 10900, Thailand.
| | - Wilai Chiemchaisri
- Department of Environmental Engineering, Faculty of Engineering, Kasetsart University, Bangkok, 10900, Thailand
| | - Kazuo Yamamoto
- Environmental Science Center, University of Tokyo, Tokyo, 113, Japan
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Benjamin S, Pradeep S, Josh MS, Kumar S, Masai E. A monograph on the remediation of hazardous phthalates. JOURNAL OF HAZARDOUS MATERIALS 2015; 298:58-72. [PMID: 26004054 DOI: 10.1016/j.jhazmat.2015.05.004] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 05/02/2015] [Accepted: 05/04/2015] [Indexed: 05/25/2023]
Abstract
Phthalates or phthalic acid esters are a group of xenobiotic and hazardous compounds blended in plastics to enhance their plasticity and versatility. Enormous quantities of phthalates are produced globally for the production of plastic goods, whose disposal and leaching out into the surroundings cause serious concerns to the environment, biota and human health. Though in silico computational, in vitro mechanistic, pre-clinical animal and clinical human studies showed endocrine disruption, hepatotoxic, teratogenic and carcinogenic properties, usage of phthalates continues due to their cuteness, attractive chemical properties, low production cost and lack of suitable alternatives. Studies revealed that microbes isolated from phthalate-contaminated environmental niches efficiently bioremediate various phthalates. Based upon this background, this review addresses the enumeration of major phthalates used in industry, routes of environmental contamination, evidences for health hazards, routes for in situ and ex situ microbial degradation, bacterial pathways involved in the degradation, major enzymes involved in the degradation process, half-lives of phthalates in environments, etc. Briefly, this handy module would enable the readers, environmentalists and policy makers to understand the impact of phthalates on the environment and the biota, coupled with the concerted microbial efforts to alleviate the burden of ever increasing load posed by phthalates.
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Affiliation(s)
- Sailas Benjamin
- Enzyme Technology Laboratory, Biotechnology Division, Department of Botany, University of Calicut, Kerala 673 635, India.
| | - Selvanesan Pradeep
- Enzyme Technology Laboratory, Biotechnology Division, Department of Botany, University of Calicut, Kerala 673 635, India
| | - Moolakkariyil Sarath Josh
- Enzyme Technology Laboratory, Biotechnology Division, Department of Botany, University of Calicut, Kerala 673 635, India
| | - Sunil Kumar
- Solid and Hazardous Waste Management Division, CSIR-NEERI Nehru Marg, Nagpur 440 020, India
| | - Eiji Masai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2137, Japan
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Biochemical Characterization of Inducible ‘Reductase’ Component of Benzoate Dioxygenase and Phthalate Isomer Dioxygenases from Pseudomonas aeruginosa strain PP4. Appl Biochem Biotechnol 2015. [DOI: 10.1007/s12010-015-1744-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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32
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Identification of a gene cluster associated with triclosan catabolism. Biodegradation 2015; 26:235-46. [DOI: 10.1007/s10532-015-9730-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 04/16/2015] [Indexed: 11/26/2022]
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Boonnorat J, Chiemchaisri C, Chiemchaisri W, Yamamoto K. Microbial adaptation to biodegrade toxic organic micro-pollutants in membrane bioreactor using different sludge sources. BIORESOURCE TECHNOLOGY 2014; 165:50-59. [PMID: 24791712 DOI: 10.1016/j.biortech.2014.04.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 04/07/2014] [Accepted: 04/08/2014] [Indexed: 06/03/2023]
Abstract
Biodegradation of toxic organic micro-pollutants in municipal solid waste (MSW) leachate by membrane bioreactor (MBR) was investigated. The MBR systems were seeded with different sludge sources, one was from a pilot-scale MBR system treating MSW leachate and the other was from an activated sludge sewage treatment plant. The biodegradation of BPA, 2,6-DTBP, BHT, DEP, DBP and DEHP, DCP and BBzP, by sludge from both reactors were found improved with time. However, enhanced biodegradation of micro-pollutants was observed in MBR operated under long sludge age condition. Bacterial population analyses determined by PCR-DGGE revealed the development of phenol and phthalate degrading bacteria consortium in MBR sludge during its operation.
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Affiliation(s)
- Jarungwit Boonnorat
- Department of Environmental Engineering, Faculty of Engineering, Kasetsart University, Bangkok 10900, Thailand
| | - Chart Chiemchaisri
- Department of Environmental Engineering, Faculty of Engineering, Kasetsart University, Bangkok 10900, Thailand.
| | - Wilai Chiemchaisri
- Department of Environmental Engineering, Faculty of Engineering, Kasetsart University, Bangkok 10900, Thailand
| | - Kazuo Yamamoto
- Environmental Science Center, University of Tokyo, Tokyo 113, Japan
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Chadha N, Tiwari AK, Kumar V, Milton MD, Mishra AK. In silico thermodynamics stability change analysis involved in BH4 responsive mutations in phenylalanine hydroxylase: QM/MM and MD simulations analysis. J Biomol Struct Dyn 2014; 33:573-83. [PMID: 24628256 DOI: 10.1080/07391102.2014.897258] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The mammalian tetrahydrobiopterin (BH4)-dependent phenylalanine hydroxylases (PAH), involved in important metabolic pathways of phenylalanine, belong to non-heme iron-containing aromatic acid hydroxylases' enzyme (AAH) family. AAHs utilize BH4 as protein co-factor and thus promote hydroxylation reactions of their substrates. Any alterations in BH4 -mediated AAH's pathway or mutations in these enzymes are responsible for various disorders, and thus highlights the importance of mutational analysis to assess the effect on their biosynthetic pathways. Our present studies are aimed at single-site mutations in PAH that lead to thermodynamic stability change upon folding and further validation of designed non-reduced BH2 designed co-factors. We have presented single-site mutational analysis of PAH where single-site mutations have been identified from known literature. Further, in silico studies with the PAH, in silico mutant PAH, and crystallized known mutant A313T forms, involved QM/MM and Molecular Dynamics (MD) simulations analysis. The modified co-factor A showed high affinity with PAH and all mutant PAH with high G-score of -14.851. The best pose high affinity co-factor A subjected to QM/MM optimization which leads to square-pyramidal coordination of non-heme active site. The structural and energetic information obtained from the production phase of 20 ns MD simulation of co-factor-metalloprotein complex results helped to understand the binding mode and involvement of three molecules throughout the reaction pathways' catalysis of PAH. The free energies of binding (dG) of A were found to be -68.181 kcal/mol and -72.249 for 1DMW and 1TDW for A313T mutant. Binding of Co-factor A do not perturb the coordination environment of iron at the active site which resides in 2-Histdine and 1-Glutamate triad, and may enhance the percentage response towards co-factor-mediated therapy.
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Affiliation(s)
- Nidhi Chadha
- a Division of Cyclotron and Radiopharmaceutical Sciences , Institute of Nuclear Medicine and Allied Sciences , Brig. S. K. Mazumdar Road, Delhi 110054 , India
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Bell SG, French L, Rees NH, Cheng SS, Preston G, Wong LL. A phthalate family oxygenase reductase supports terpene alcohol oxidation by CYP238A1 fromPseudomonas putidaKT2440. Biotechnol Appl Biochem 2013; 60:9-17. [DOI: 10.1002/bab.1084] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 12/18/2012] [Indexed: 01/09/2023]
Affiliation(s)
| | - Laura French
- Department of Chemistry; University of Oxford, Inorganic Chemistry Laboratory; Oxford; UK
| | - Nicholas Huw Rees
- Department of Chemistry; University of Oxford, Inorganic Chemistry Laboratory; Oxford; UK
| | - Sophia Shuyi Cheng
- Department of Chemistry; University of Oxford, Inorganic Chemistry Laboratory; Oxford; UK
| | - Gail Preston
- Department of Plant Sciences; University of Oxford; Oxford; UK
| | - Luet-Lok Wong
- Department of Chemistry; University of Oxford, Inorganic Chemistry Laboratory; Oxford; UK
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Fujiu K, Manabe I, Sasaki M, Inoue M, Iwata H, Hasumi E, Komuro I, Katada Y, Taguchi T, Nagai R. Nickel-free stainless steel avoids neointima formation following coronary stent implantation. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2012; 13:064218. [PMID: 27877545 PMCID: PMC5099778 DOI: 10.1088/1468-6996/13/6/064218] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 12/02/2012] [Indexed: 06/06/2023]
Abstract
SUS316L stainless steel and cobalt-chromium and platinum-chromium alloys are widely used platforms for coronary stents. These alloys also contain nickel (Ni), which reportedly induces allergic reactions in some subjects and is known to have various cellular effects. The effects of Ni on neointima formation after stent implantation remain unknown, however. We developed coronary stents made of Ni-free high-nitrogen austenitic stainless steel prepared using a N2-gas pressurized electroslag remelting (P-ESR) process. Neointima formation and inflammatory responses following stent implantation in porcine coronary arteries were then compared between the Ni-free and SUS316L stainless steel stents. We found significantly less neointima formation and inflammation in arteries implanted with Ni-free stents, as compared to SUS316L stents. Notably, Ni2+ was eluted into the medium from SUS316L but not from Ni-free stainless steel. Mechanistically, Ni2+ increased levels of hypoxia inducible factor protein-1α (HIF-1α) and its target genes in cultured smooth muscle cells. HIF-1α and their target gene levels were also increased in the vascular wall at SUS316L stent sites but not at Ni-free stent sites. The Ni-free stainless steel coronary stent reduces neointima formation, in part by avoiding activation of inflammatory processes via the Ni-HIF pathway. The Ni-free-stainless steel stent is a promising new coronary stent platform.
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Affiliation(s)
- Katsuhito Fujiu
- Department of Cardiovascular Medicine, University of Tokyo, 7–3-1 Hongo, Bunkyo, 113-8655, Tokyo, Japan
- Translational Systems Biology and Medicine Initiative (TSBMI), University of Tokyo, Graduate School of Medicine, Tokyo, Japan
| | - Ichiro Manabe
- Department of Cardiovascular Medicine, University of Tokyo, 7–3-1 Hongo, Bunkyo, 113-8655, Tokyo, Japan
| | - Makoto Sasaki
- Graduate School of Pure and Applied Science, University of Tsukuba, Tsukuba, Japan
- Biomaterials Unit, Nano-Bio Field, International Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science, Tsukuba, Japan
| | - Motoki Inoue
- Biomaterials Unit, Nano-Bio Field, International Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science, Tsukuba, Japan
| | - Hiroshi Iwata
- Department of Cardiovascular Medicine, University of Tokyo, 7–3-1 Hongo, Bunkyo, 113-8655, Tokyo, Japan
| | - Eriko Hasumi
- Department of Cardiovascular Medicine, University of Tokyo, 7–3-1 Hongo, Bunkyo, 113-8655, Tokyo, Japan
| | - Issei Komuro
- Department of Cardiovascular Medicine, University of Tokyo, 7–3-1 Hongo, Bunkyo, 113-8655, Tokyo, Japan
| | - Yasuyuki Katada
- Biomaterials Unit, Nano-Bio Field, International Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science, Tsukuba, Japan
| | - Tetsushi Taguchi
- Graduate School of Pure and Applied Science, University of Tsukuba, Tsukuba, Japan
- Biomaterials Unit, Nano-Bio Field, International Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science, Tsukuba, Japan
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Synthesis of short-chain diols and unsaturated alcohols from secondary alcohol substrates by the Rieske nonheme mononuclear iron oxygenase MdpJ. Appl Environ Microbiol 2012; 78:6280-4. [PMID: 22752178 DOI: 10.1128/aem.01434-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Rieske nonheme mononuclear iron oxygenase MdpJ of the fuel oxygenate-degrading bacterial strain Aquincola tertiaricarbonis L108 has been described to attack short-chain tertiary alcohols via hydroxylation and desaturation reactions. Here, we demonstrate that also short-chain secondary alcohols can be transformed by MdpJ. Wild-type cells of strain L108 converted 2-propanol and 2-butanol to 1,2-propanediol and 3-buten-2-ol, respectively, whereas an mdpJ knockout mutant did not show such activity. In addition, wild-type cells converted 3-methyl-2-butanol and 3-pentanol to the corresponding desaturation products 3-methyl-3-buten-2-ol and 1-penten-3-ol, respectively. The enzymatic hydroxylation of 2-propanol resulted in an enantiomeric excess of about 70% for the (R)-enantiomer, indicating that this reaction was favored. Likewise, desaturation of (R)-2-butanol to 3-buten-2-ol was about 2.3-fold faster than conversion of the (S)-enantiomer. The biotechnological potential of MdpJ for the synthesis of enantiopure short-chain alcohols and diols as building block chemicals is discussed.
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Cloning of a dibutyl phthalate hydrolase gene from Acinetobacter sp. strain M673 and functional analysis of its expression product in Escherichia coli. Appl Microbiol Biotechnol 2012; 97:2483-91. [DOI: 10.1007/s00253-012-4232-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 06/05/2012] [Indexed: 10/28/2022]
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Warman AJ, Robinson JW, Luciakova D, Lawrence AD, Marshall KR, Warren MJ, Cheesman MR, Rigby SEJ, Munro AW, McLean KJ. Characterization of Cupriavidus metallidurans CYP116B1--a thiocarbamate herbicide oxygenating P450-phthalate dioxygenase reductase fusion protein. FEBS J 2012; 279:1675-93. [PMID: 22356105 DOI: 10.1111/j.1742-4658.2012.08543.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The novel cytochrome P450/redox partner fusion enzyme CYP116B1 from Cupriavidus metallidurans was expressed in and purified from Escherichia coli. Isolated CYP116B1 exhibited a characteristic Fe(II)CO complex with Soret maximum at 449 nm. EPR and resonance Raman analyses indicated low-spin, cysteinate-coordinated ferric haem iron at both 10 K and ambient temperature, respectively, for oxidized CYP116B1. The EPR of reduced CYP116B1 demonstrated stoichiometric binding of a 2Fe-2S cluster in the reductase domain. FMN binding in the reductase domain was confirmed by flavin fluorescence studies. Steady-state reduction of cytochrome c and ferricyanide were supported by both NADPH/NADH, with NADPH used more efficiently (K(m[NADPH]) = 0.9 ± 0.5 μM and K(m[NADH]) = 399.1 ± 52.1 μM). Stopped-flow studies of NAD(P)H-dependent electron transfer to the reductase confirmed the preference for NADPH. The reduction potential of the P450 haem iron was -301 ± 7 mV, with retention of haem thiolate ligation in the ferrous enzyme. Redox potentials for the 2Fe-2S and FMN cofactors were more positive than that of the haem iron. Multi-angle laser light scattering demonstrated CYP116B1 to be monomeric. Type I (substrate-like) binding of selected unsaturated fatty acids (myristoleic, palmitoleic and arachidonic acids) was shown, but these substrates were not oxidized by CYP116B1. However, CYP116B1 catalysed hydroxylation (on propyl chains) of the herbicides S-ethyl dipropylthiocarbamate (EPTC) and S-propyl dipropylthiocarbamate (vernolate), and the subsequent N-dealkylation of vernolate. CYP116B1 thus has similar thiocarbamate-oxidizing catalytic properties to Rhodoccocus erythropolis CYP116A1, a P450 involved in the oxidative degradation of EPTC.
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Affiliation(s)
- Ashley J Warman
- Department of Biochemistry, University of Leicester, Leicester, UK
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Izzo V, Leo G, Scognamiglio R, Troncone L, Birolo L, Di Donato A. PHK from phenol hydroxylase of Pseudomonas sp. OX1. Insight into the role of an accessory protein in bacterial multicomponent monooxygenases. Arch Biochem Biophys 2011; 505:48-59. [DOI: 10.1016/j.abb.2010.09.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 09/06/2010] [Accepted: 09/25/2010] [Indexed: 11/30/2022]
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Involvement of a novel ABC transporter and monoalkyl phthalate ester hydrolase in phthalate ester catabolism by Rhodococcus jostii RHA1. Appl Environ Microbiol 2009; 76:1516-23. [PMID: 20038686 DOI: 10.1128/aem.02621-09] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phthalate esters (PEs) are important environmental pollutants. While the biodegradation of the parent compound, phthalate (PTH), is well characterized, the biodegradation of PEs is not well understood. In particular, prior to this study, genes involved in the uptake and hydrolysis of these compounds were not conclusively identified. We found that Rhodococcus jostii RHA1 could grow on a variety of monoalkyl PEs, including methyl, butyl, hexyl, and 2-ethylhexyl PTHs. Strain RHA1 could not grow on most dialkyl PEs, but suspensions of cells grown on PTH transformed dimethyl, diethyl, dipropyl, dibutyl, dihexyl and di-(2-ethylhexyl) PTHs. The major products of these dialkyl PEs were PTH and the corresponding monoalkyl PEs, and minor products resulted from the shortening of the alkyl side chains. RHA1 exhibited an inducible, ATP-dependent uptake system for PTH with a K(m) of 22 microM. The deletion and complementation of the patB gene demonstrated that the ATP-binding cassette (ABC) transporter encoded by patDABC is required for the uptake of PTH and monoalkyl PEs by RHA1. The hydrolase encoded by patE of RHA1 was expressed in Escherichia coli. PatE specifically hydrolyzed monoalkyl PEs to PTH but did not transform dialkyl PEs or other aromatic esters. This investigation of RHA1 elucidates key processes that are consistent with the environmental fate of PEs.
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Characterization of the isophthalate degradation genes of Comamonas sp. strain E6. Appl Environ Microbiol 2009; 76:519-27. [PMID: 19933340 DOI: 10.1128/aem.01270-09] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The isophthalate (IPA) degradation gene cluster (iphACBDR) responsible for the conversion of IPA into protocatechuate (PCA) was isolated from Comamonas sp. strain E6, which utilizes phthalate isomers as sole carbon and energy sources via the PCA 4,5-cleavage pathway. Based on amino acid sequence similarity, the iphA, iphC, iphB, iphD, and iphR genes were predicted to code for an oxygenase component of IPA dioxygenase (IPADO), a periplasmic IPA binding receptor, a 1,2-dihydroxy-3,5-cyclohexadiene-1,5-dicarboxylate (1,5-DCD) dehydrogenase, a reductase component of IPADO, and an IclR-type transcriptional regulator, respectively. The iphACBDR genes constitute a single transcriptional unit, and transcription of the iph catabolic operon was induced during growth of E6 on IPA. The iphA, iphD, and iphB genes were expressed in Escherichia coli. Crude IphA and IphD converted IPA in the presence of NADPH into a product which was transformed to PCA by IphB. These results suggested that IPADO is a two-component dioxygenase that consists of a terminal oxygenase component (IphA) and a reductase component (IphD) and that iphB encodes the 1,5-DCD dehydrogenase. Disruption of iphA and iphB resulted in complete loss of growth of E6 on IPA. Inactivation of iphD significantly affected growth on IPA, and the iphC mutant did not grow on IPA at neutral pH. These results indicated that the iphACBD genes are essential for the catabolism of IPA in E6. Disruption of iphR resulted in faster growth of E6 on IPA, suggesting that iphR encodes a repressor for the iph catabolic operon. Promoter analysis of the operon supported this notion.
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Rhodococcus rhodochrous DSM 43269 3-ketosteroid 9alpha-hydroxylase, a two-component iron-sulfur-containing monooxygenase with subtle steroid substrate specificity. Appl Environ Microbiol 2009; 75:5300-7. [PMID: 19561185 DOI: 10.1128/aem.00066-09] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This paper reports the biochemical characterization of a purified and reconstituted two-component 3-ketosteroid 9alpha-hydroxylase (KSH). KSH of Rhodococcus rhodochrous DSM 43269, consisting of a ferredoxin reductase (KshB) and a terminal oxygenase (KshA), was heterologously expressed in Escherichia coli. E. coli cell cultures, expressing both KshA and KshB, converted 4-androstene-3,17-dione (AD) into 9alpha-hydroxy-4-AD (9OHAD) with a >60% molar yield over 48 h of incubation. Coexpression and copurification were critical to successfully obtain pure and active KSH. Biochemical analysis revealed that the flavoprotein KshB is an NADH-dependent reductase using flavin adenine dinucleotide as a cofactor. Reconstitution experiments confirmed that KshA, KshB, and NADH are essential for KSH activity with steroid substrates. KSH hydroxylation activity was inhibited by several divalent metal ions, especially by zinc. The reconstituted KSH displayed subtle steroid substrate specificity; a range of 3-ketosteroids, i.e., 5alpha-Eta, 5beta-Eta, Delta1, and Delta4 steroids, could act as KSH substrates, provided that they had a short side chain. The formation of 9OHAD from AD by KSH was confirmed by liquid chromatography-mass spectrometry analysis and by the specific enzymatic conversion of 9OHAD into 3-hydroxy-9,10-secoandrost-1,3,5(10)-triene-9,17-dione using 3-ketosteroid Delta1-dehydrogenase. Only a single KSH is encoded in the genome of the human pathogen Mycobacterium tuberculosis H37Rv, shown to be important for survival in macrophages. Since no human KSH homolog exists, the M. tuberculosis enzyme may provide a novel target for treatment of tuberculosis. Detailed knowledge about the biochemical properties of KSH thus is highly relevant in the research fields of biotechnology and medicine.
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Distal end of 105-125 loop--a putative reductase binding domain of phthalate dioxygenase. Arch Biochem Biophys 2009; 487:10-8. [PMID: 19464996 DOI: 10.1016/j.abb.2009.05.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 05/14/2009] [Accepted: 05/17/2009] [Indexed: 11/21/2022]
Abstract
The phthalate dioxygenase system consists of the dioxygenase, PDO, which contains a Rieske [2Fe-2S] center and a Fe(II)-mononuclear center, and the reductase, PDR. Involvement of the distal end of the 105-125 loop of PDO in its interaction with PDR was tested by substituting charged residues in the loop with alanines and by replacing the conserved tryptophan-94. Compared to wild-type PDO, all variants had lower catalytic activity and the Rieske centers were reduced more slowly by reduced PDR. The rates of oxidation of the Rieske centers by oxygen, which represent electron transfer between the Rieske and mononuclear centers, were essentially unaffected. These results suggest that positively charged residues of the distal end of the 105-125 loop are collectively involved in PDR binding with the PDO. Contrary to expectations, Trp94 variants were not directly involved in electron transfer between PDR and PDO. The tryptophan appears to have mainly a structural role, apparently preserving the hydrophilic environment of the Rieske center.
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Pope SD, Chen LL, Stewart V. Purine utilization by Klebsiella oxytoca M5al: genes for ring-oxidizing and -opening enzymes. J Bacteriol 2009; 191:1006-17. [PMID: 19060149 PMCID: PMC2632102 DOI: 10.1128/jb.01281-08] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Accepted: 11/25/2008] [Indexed: 11/20/2022] Open
Abstract
The enterobacterium Klebsiella oxytoca uses a variety of inorganic and organic nitrogen sources, including purines, nitrogen-rich compounds that are widespread in the biosphere. We have identified a 23-gene cluster that encodes the enzymes for utilizing purines as the sole nitrogen source. Growth and complementation tests with insertion mutants, combined with sequence comparisons, reveal functions for the products of these genes. Here, we report our characterization of 12 genes, one encoding guanine deaminase and the others encoding enzymes for converting (hypo)xanthine to allantoate. Conventionally, xanthine dehydrogenase, a broadly distributed molybdoflavoenzyme, catalyzes sequential hydroxylation reactions to convert hypoxanthine via xanthine to urate. Our results show that these reactions in K. oxytoca are catalyzed by a two-component oxygenase (HpxE-HpxD enzyme) homologous to Rieske nonheme iron aromatic-ring-hydroxylating systems, such as phthalate dioxygenase. Our results also reveal previously undescribed enzymes involved in urate oxidation to allantoin, catalyzed by a flavoprotein monooxygenase (HpxO enzyme), and in allantoin conversion to allantoate, which involves allantoin racemase (HpxA enzyme). The pathway also includes the recently described PuuE allantoinase (HpxB enzyme). The HpxE-HpxD and HpxO enzymes were discovered independently by de la Riva et al. (L. de la Riva, J. Badia, J. Aguilar, R. A. Bender, and L. Baldoma, J. Bacteriol. 190:7892-7903, 2008). Thus, several enzymes in this K. oxytoca purine utilization pathway differ from those in other microorganisms. Isofunctional homologs of these enzymes apparently are encoded by other species, including Acinetobacter, Burkholderia, Pseudomonas, Saccharomyces, and Xanthomonas.
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Affiliation(s)
- Scott D Pope
- Department of Microbiology, University of California, One Shields Ave., Davis, CA 95616-8665, USA
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Vamsee-Krishna C, Phale PS. Carbon source-dependent modulation of NADP-glutamate dehydrogenases in isophthalate-degrading Pseudomonas aeruginosa strain PP4, Pseudomonas strain PPD and Acinetobacter lwoffii strain ISP4. MICROBIOLOGY-SGM 2008; 154:3329-3337. [PMID: 18957586 DOI: 10.1099/mic.0.2008/022087-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Acinetobacter lwoffii strain ISP4 metabolizes isophthalate rapidly compared with Pseudomonas aeruginosa strain PP4 and Pseudomonas strain PPD. Isophthalate has been reported to be a potent competitive inhibitor of glutamate dehydrogenase (GDH). Exogenous supplementation of isophthalate with glutamate or alpha-ketoglutarate at 1 mM concentration caused strains PP4 and PPD to grow faster than in the presence of isophthalate alone; however, no such effect was observed in strain ISP4. When grown on isophthalate, all strains showed activity of NADP-dependent GDH (NADP-GDH), while cells grown on glucose, 2x yeast extract-tryptone broth (2YT) or glutamate showed activities of both NAD-dependent GDH (NAD-GDH) and NADP-GDH. Activity staining, inhibition and thermal stability studies indicated the carbon source-dependent presence of two (GDH(I) and GDH(II)), three (GDH(A), GDH(B) and GDH(C)) and one (GDH(P)) forms of NADP-GDH in strains PP4, PPD and ISP4, respectively. The results demonstrate the carbon source-dependent modulation of different forms of NADP-GDH in these bacterial strains. This modulation may help the efficient utilization of isophthalate as a carbon source by overcoming the inhibitory effect on GDH.
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Affiliation(s)
- C Vamsee-Krishna
- Biotechnology Group, School of Biosciences and Bioengineering, Indian Institute of Technology - Bombay, Powai, Mumbai 400 076, India
| | - Prashant S Phale
- Biotechnology Group, School of Biosciences and Bioengineering, Indian Institute of Technology - Bombay, Powai, Mumbai 400 076, India
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Purification of the NADH reductase component of the steroid 9alpha-hydroxylase fromMycobacterium fortuitum. Arch Pharm Res 2008; 20:590-6. [PMID: 18982265 DOI: 10.1007/bf02975217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/1997] [Indexed: 10/21/2022]
Abstract
The NADH reductase component of the steroid 9alpha-hydroxylase fromMycobacterium fortuitum was purified to homogeneity. Recovery of the enzyme from the 50 approximately 60% ammonium sulfate saturated fraction was 49%, with a purification factor of 100-fold. The NADH reductase has a relative molecular mass of 60 KDa as determined by SDS-PAGE. The absorption maxima at 410 and 450 nm indicate the presence of iron-sulfur group and flavin. These prosthetic groups seemed to function as redox groups that transfer electrons from NADH to the following protein. The K(M) value for NADH as substrate was 68 muM. The NH(2)-terminal amino acid sequence of the reductase was determined as Met-Asp-Ala-Ile-Thr-Asn-Val-Pro-Leu-Pro-Ala-Asn-Glu-Pro-Val-His-Asp-Tyr-Ala-Thr. This sequence does not show a homology with the NH(2)-terminal sequences reported for the reductase component of other monooxygenases, suggesting that the NADH reductase component of the steroid 9alpha-hydroxylase system is novel.
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Vamsee-Krishna C, Phale PS. Bacterial degradation of phthalate isomers and their esters. Indian J Microbiol 2008; 48:19-34. [PMID: 23100697 DOI: 10.1007/s12088-008-0003-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Revised: 10/03/2007] [Accepted: 10/19/2007] [Indexed: 10/22/2022] Open
Abstract
Phthalate isomers and their esters are used heavily in various industries. Excess use and leaching from the product pose them as major pollutants. These chemicals are toxic, teratogenic, mutagenic and carcinogenic in nature. Various aspects like toxicity, diversity in the aerobic bacterial degradation, enzymes and genetic organization of the metabolic pathways from various bacterial strains are reviewed here. Degradation of these esters proceeds by the action of esterases to form phthalate isomers, which are converted to dihydroxylated intermediates by specific and inducible phthalate isomer dioxygenases. Metabolic pathways of phthalate isomers converge at 3,4-dihydroxybenzoic acid, which undergoes either ortho- or meta- ring cleavage and subsequently metabolized to the central carbon pathway intermediates. The genes involved in the degradation are arranged in operons present either on plasmid or chromosome or both, and induced by specific phthalate isomer. Understanding metabolic pathways, diversity and their genetic regulation may help in constructing bacterial strains through genetic engineering approach for effective bioremediation and environmental clean up.
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Affiliation(s)
- C Vamsee-Krishna
- Biotechnology group School of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai, 400 076 India
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Chauhan A, Fazlurrahman, Oakeshott JG, Jain RK. Bacterial metabolism of polycyclic aromatic hydrocarbons: strategies for bioremediation. Indian J Microbiol 2008; 48:95-113. [PMID: 23100704 DOI: 10.1007/s12088-008-0010-9] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Revised: 01/21/2008] [Accepted: 02/04/2008] [Indexed: 10/22/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are compounds of intense public concern due to their persistence in the environment and potentially deleterious effects on human, environmental and ecological health. The clean up of such contaminants using invasive technologies has proven to be expensive and more importantly often damaging to the natural resource properties of the soil, sediment or aquifer. Bioremediation, which exploits the metabolic potential of microbes for the clean-up of recalcitrant xenobiotic compounds, has come up as a promising alternative. Several approaches such as improvement in PAH solubilization and entry into the cell, pathway and enzyme engineering and control of enzyme expression etc. are in development but far from complete. Successful application of the microorganisms for the bioremediation of PAH-contaminated sites therefore requires a deeper understanding of the physiology, biochemistry and molecular genetics of potential catabolic pathways. In this review, we briefly summarize important strategies adopted for PAH bioremediation and discuss the potential for their improvement.
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Affiliation(s)
- Archana Chauhan
- Institute of Microbial Technology, Sector-39A, Chandigarh, India
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50
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Singleton DR, Richardson SD, Aitken MD. Effects of enrichment with phthalate on polycyclic aromatic hydrocarbon biodegradation in contaminated soil. Biodegradation 2007; 19:577-87. [PMID: 17990065 DOI: 10.1007/s10532-007-9163-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2007] [Accepted: 10/29/2007] [Indexed: 11/26/2022]
Abstract
The effect of enrichment with phthalate on the biodegradation of polycyclic aromatic hydrocarbons (PAH) was tested with bioreactor-treated and untreated contaminated soil from a former manufactured gas plant (MGP) site. Soil samples that had been treated in a bioreactor and enriched with phthalate mineralized (14)C-labeled phenanthrene and pyrene to a greater extent than unenriched samples over a 22.5-h incubation, but did not stimulate benzo[a]pyrene mineralization. In contrast to the positive effects on (14)C-labeled phenanthrene and pyrene, no significant differences were found in the extent of biodegradation of native PAH when untreated contaminated soil was incubated with and without phthalate amendment. Denaturing-gradient gel electrophoresis (DGGE) profiles of bacterial 16S rRNA genes from unenriched and phthalate-enriched soil samples were substantially different, and clonal sequences matched to prominent DGGE bands revealed that beta-Proteobacteria related to Ralstonia were most highly enriched by phthalate addition. Quantitative real-time PCR analyses confirmed that, of previously determined PAH-degraders in the bioreactor, only Ralstonia-type organisms increased in response to enrichment, accounting for 89% of the additional bacterial 16S rRNA genes resulting from phthalate enrichment. These findings indicate that phthalate amendment of this particular PAH-contaminated soil did not significantly enrich for organisms associated with high molecular weight PAH degradation or have any significant effect on overall degradation of native PAH in the soil.
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Affiliation(s)
- David R Singleton
- Department of Environmental Sciences and Engineering, School of Public Health, University of North Carolina, Chapel Hill, NC 27599, USA.
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