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Ma Y, Wang J, Liu Y, Wang X, Zhang B, Zhang W, Chen T, Liu G, Xue L, Cui X. Nocardioides: "Specialists" for Hard-to-Degrade Pollutants in the Environment. Molecules 2023; 28:7433. [PMID: 37959852 PMCID: PMC10649934 DOI: 10.3390/molecules28217433] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/24/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
Nocardioides, a genus belonging to Actinomycetes, can endure various low-nutrient conditions. It can degrade pollutants using multiple organic materials such as carbon and nitrogen sources. The characteristics and applications of Nocardioides are described in detail in this review, with emphasis on the degradation of several hard-to-degrade pollutants by using Nocardioides, including aromatic compounds, hydrocarbons, haloalkanes, nitrogen heterocycles, and polymeric polyesters. Nocardioides has unique advantages when it comes to hard-to-degrade pollutants. Compared to other strains, Nocardioides has a significantly higher degradation rate and requires less time to break down substances. This review can be a theoretical basis for developing Nocardioides as a microbial agent with significant commercial and application potential.
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Affiliation(s)
- Yecheng Ma
- College of Biotechnology and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Jinxiu Wang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Yang Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Xinyue Wang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Binglin Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Tuo Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Lingui Xue
- College of Biotechnology and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Xiaowen Cui
- College of Geography and Environment Science, Northwest Normal University, Lanzhou 730070, China
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Tian J, Liu J, Knapp M, Donnan PH, Boggs DG, Bridwell-Rabb J. Custom tuning of Rieske oxygenase reactivity. Nat Commun 2023; 14:5858. [PMID: 37730711 PMCID: PMC10511449 DOI: 10.1038/s41467-023-41428-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 08/27/2023] [Indexed: 09/22/2023] Open
Abstract
Rieske oxygenases use a Rieske-type [2Fe-2S] cluster and a mononuclear iron center to initiate a range of chemical transformations. However, few details exist regarding how this catalytic scaffold can be predictively tuned to catalyze divergent reactions. Therefore, in this work, using a combination of structural analyses, as well as substrate and rational protein-based engineering campaigns, we elucidate the architectural trends that govern catalytic outcome in the Rieske monooxygenase TsaM. We identify structural features that permit a substrate to be functionalized by TsaM and pinpoint active-site residues that can be targeted to manipulate reactivity. Exploiting these findings allowed for custom tuning of TsaM reactivity: substrates are identified that support divergent TsaM-catalyzed reactions and variants are created that exclusively catalyze dioxygenation or sequential monooxygenation chemistry. Importantly, we further leverage these trends to tune the reactivity of additional monooxygenase and dioxygenase enzymes, and thereby provide strategies to custom tune Rieske oxygenase reaction outcomes.
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Affiliation(s)
- Jiayi Tian
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jianxin Liu
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Madison Knapp
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Patrick H Donnan
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - David G Boggs
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
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Dinh MTN, Nguyen VT, Nguyen LTH. The potential application of carbazole-degrading bacteria for dioxin bioremediation. BIORESOUR BIOPROCESS 2023; 10:56. [PMID: 38647625 PMCID: PMC10992316 DOI: 10.1186/s40643-023-00680-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/17/2023] [Indexed: 04/25/2024] Open
Abstract
Extensive research has been conducted over the years on the bacterial degradation of dioxins and their related compounds including carbazole, because these chemicals are highly toxic and has been widely distributed in the environment. There is a pressing need to explore and develop more bacterial strains with unique catabolic features to effectively remediate dioxin-polluted sites. Carbazole has a chemical structure similar to dioxins, and the degradation pathways of these two chemicals are highly homologous. Some carbazole-degrading bacterial strains have been demonstrated to have the ability to degrade dioxins, such as Pseudomonas sp. strain CA10 và Sphingomonas sp. KA1. The introduction of strain KA1 into dioxin-contaminated model soil resulted in the degradation of 96% and 70% of 2-chlorodibenzo-p-dioxin (2-CDD) and 2,3-dichlorodibenzo-p-dioxin (2,3-DCDD), respectively, after 7-day incubation period. These degradation rates were similar to those achieved with strain CA10, which removed 96% of 2-CDD and 80% of 2,3-DCDD from the same model soil. Therefore, carbazole-degrading bacteria hold significant promise as potential candidates for dioxin bioremediation. This paper overviews the connection between the bacterial degradation of dioxins and carbazole, highlighting the potential for dioxin biodegradation by carbazole-degrading bacterial strains.
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Affiliation(s)
- Mai Thi Ngoc Dinh
- Faculty of Biotechnology, Chemistry and Environmental Engineering, Phenikaa University, A9 Building, Nguyen Van Trac Street, Ha Dong District, Hanoi, Vietnam.
- Bioresource Research Center, Phenikaa University, Hanoi, Vietnam.
| | - Van Thi Nguyen
- VNU Institute of Microbiology and Biotechnology, Vietnam National University, E2 Building, 144 Xuan Thuy Street, Cau Giay District, Hanoi, Vietnam
| | - Ly Thi Huong Nguyen
- Department of Physiology, College of Korean Medicine, Dongguk University, Gyeongju, Republic of Korea
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4
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Vasileiadis S, Perruchon C, Scheer B, Adrian L, Steinbach N, Trevisan M, Plaza-Bolaños P, Agüera A, Chatzinotas A, Karpouzas DG. Nutritional inter-dependencies and a carbazole-dioxygenase are key elements of a bacterial consortium relying on a Sphingomonas for the degradation of the fungicide thiabendazole. Environ Microbiol 2022; 24:5105-5122. [PMID: 35799498 DOI: 10.1111/1462-2920.16116] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/28/2022]
Abstract
Thiabendazole (TBZ), is a persistent fungicide/anthelminthic and a serious environmental threat. We previously enriched a TBZ-degrading bacterial consortium and provided first evidence for a Sphingomonas involvement in TBZ transformation. Here, using a multi-omic approach combined with DNA-stable isotope probing (SIP) we verified the key degrading role of Sphingomonas and identify potential microbial interactions governing consortium functioning. SIP and amplicon sequencing analysis of the heavy and light DNA fraction of cultures grown on 13 C-labelled versus 12 C-TBZ showed that 66% of the 13 C-labelled TBZ was assimilated by Sphingomonas. Metagenomic analysis retrieved 18 metagenome-assembled genomes with the dominant belonging to Sphingomonas, Sinobacteriaceae, Bradyrhizobium, Filimonas and Hydrogenophaga. Meta-transcriptomics/-proteomics and non-target mass spectrometry suggested TBZ transformation by Sphingomonas via initial cleavage by a carbazole dioxygenase (car) to thiazole-4-carboxamidine (terminal compound) and catechol or a cleaved benzyl ring derivative, further transformed through an ortho-cleavage (cat) pathway. Microbial co-occurrence and gene expression networks suggested strong interactions between Sphingomonas and a Hydrogenophaga. The latter activated its cobalamin biosynthetic pathway and Sphingomonas its cobalamin salvage pathway to satisfy its B12 auxotrophy. Our findings indicate microbial interactions aligning with the 'black queen hypothesis' where Sphingomonas (detoxifier, B12 recipient) and Hydrogenophaga (B12 producer, enjoying detoxification) act as both helpers and beneficiaries.
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Affiliation(s)
- Sotirios Vasileiadis
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Viopolis, Greece
| | - Chiara Perruchon
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Viopolis, Greece
| | - Benjamin Scheer
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Lorenz Adrian
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Chair of Geobiotechnology, Technische Universität Berlin, Berlin, Germany
| | - Nicole Steinbach
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Marco Trevisan
- Department of Sustainable Food Process, Universitá Cattolica del Sacro Cuore, Piacenza, Italy
| | - Patricia Plaza-Bolaños
- Solar Energy Research Centre (CIESOL), Joint Center University of Almería-CIEMAT, Almeria, Spain
| | - Ana Agüera
- Solar Energy Research Centre (CIESOL), Joint Center University of Almería-CIEMAT, Almeria, Spain
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Institute of Biology, Leipzig University, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Dimitrios G Karpouzas
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Viopolis, Greece
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Chen Z, Hu H, Xu P, Tang H. Soil bioremediation by Pseudomonas brassicacearum MPDS and its enzyme involved in degrading PAHs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:152522. [PMID: 34953839 DOI: 10.1016/j.scitotenv.2021.152522] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/14/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) commonly coexist in contaminated sites, posing a significant threat to ecosystem. Strains that degrade a wide range of substrates play important roles in bioremediation of contaminated environment. In this study, we reveal that Pseudomonas brassicacearum MPDS was able to remove 31.1% naphthalene of 500 mg/kg from soil within 2 d, while its relative abundance decreased significantly on Day 20, indicating its applicable potential in soil remediation. In addition to naphthalene, dibenzofuran, dibenzothiophene, and fluorene as reported previously, strain MPDS is able to degrade carbazole, phenanthrene, pyrene, and 2-bromonaphthalene. Moreover, NahA from strain MPDS has multi-substrate catalytic capacities on naphthalene, dibenzofuran, dibenzothiophene, phenanthrene, and 2-bromonaphthalene into dihydrodiols, while converts fluorene and carbazole into monohydroxy compounds according to GC-MS analysis. This study provides further insights into the exploration of soil remediation by strain MPDS and the mining of enzymes involved in the degradation of PAHs.
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Affiliation(s)
- Zhengshi Chen
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Haiyang Hu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.
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Aghbolagh ZS, Khorrami MRK, Rahmatyan MS. Sum of ranking differences in studies on high performance of catalytic oxidative denitrogenation and desulfurization of model fuel using efficient organic–inorganic hybrid nanocatalyst. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2021. [DOI: 10.1007/s13738-021-02304-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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7
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Wang W, Li Q, Zhang L, Cui J, Yu H, Wang X, Ouyang X, Tao F, Xu P, Tang H. Genetic mapping of highly versatile and solvent-tolerant Pseudomonas putida B6-2 (ATCC BAA-2545) as a 'superstar' for mineralization of PAHs and dioxin-like compounds. Environ Microbiol 2021; 23:4309-4325. [PMID: 34056829 DOI: 10.1111/1462-2920.15613] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 11/25/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) and dioxin-like compounds, including sulfur, nitrogen and oxygen heterocycles, are widespread and toxic environmental pollutants. A wide variety of microorganisms capable of growing with aromatic polycyclic compounds are essential for bioremediation of the contaminated sites and the Earth's carbon cycle. Here, cells of Pseudomonas putida B6-2 (ATCC BAA-2545) grown in the presence of biphenyl (BP) are able to simultaneously degrade PAHs and their derivatives, even when they are present as mixtures, and tolerate high concentrations of extremely toxic solvents. Genetic analysis of the 6.37 Mb genome of strain B6-2 reveals coexistence of gene clusters responsible for central catabolic systems of aromatic compounds and for solvent tolerance. We used functional transcriptomics and proteomics to identify the candidate genes associated with catabolism of BP and a mixture of BP, dibenzofuran, dibenzothiophene and carbazole. Moreover, we observed dynamic changes in transcriptional levels with BP, including in metabolic pathways of aromatic compounds, chemotaxis, efflux pumps and transporters potentially involved in adaptation to PAHs. This study on the highly versatile activities of strain B6-2 suggests it to be a potentially useful model for bioremediation of polluted sites and for investigation of biochemical, genetic and evolutionary aspects of Pseudomonas.
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Affiliation(s)
- Weiwei Wang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qinggang Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Lige Zhang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jie Cui
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hao Yu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaoyu Wang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xingyu Ouyang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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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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Aliphatic Hydrocarbon Profile of Crude-oil Degraded by Bacteria Isolates from Bitumen-polluted Surface Water from Agbabu, Ondo State. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.2.23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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10
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Salam LB, Ishaq A. Biostimulation potentials of corn steep liquor in enhanced hydrocarbon degradation in chronically polluted soil. 3 Biotech 2019; 9:46. [PMID: 30729070 DOI: 10.1007/s13205-019-1580-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 01/17/2019] [Indexed: 12/16/2022] Open
Abstract
The effects of corn steep liquor (CSL) on hydrocarbon degradation and microbial community structure and function was evaluated in field-moist soil microcosms. Chronically polluted soil treated with CSL (AB4) and an untreated control (3S) was compared over a period of 6 weeks. Gas chromatographic fingerprints of residual hydrocarbons revealed removal of 95.95% and 94.60% aliphatic and aromatic hydrocarbon fractions in AB4 system with complete disappearance of nC1-nC8, nC10, nC15, nC20-nC23 aliphatics and aromatics such as naphthalene, acenaphthylene, fluorene, phenanthrene, pyrene, benzo(a)anthracene, and indeno(123-cd)pyrene in 42 days. In 3S system, there is removal of 61.27% and 66.58% aliphatic and aromatic fractions with complete disappearance of nC2 and nC21 aliphatics and naphthalene, acenaphthylene, fluorene, phenanthrene, pyrene, and benzo(a)anthracene aromatics in 42 days. Illumina shotgun sequencing of the DNA extracted from the two systems showed the preponderance of Actinobacteria (31.46%) and Proteobacteria (38.95%) phyla in 3S and AB4 with the dominance of Verticillium (22.88%) and Microbacterium (8.16%) in 3S, and Laceyella (24.23%), Methylosinus (8.93%) and Pedobacter (7.73%) in AB4. Functional characterization of the metagenomic reads revealed diverse metabolic potentials and adaptive traits of the microbial communities in the two systems to various environmental stressors. It also revealed the exclusive detection of catabolic enzymes in AB4 system belonging to the aldehyde dehydrogenase superfamily. The results obtained in this study showed that CSL is a potential resource for bioremediation of hydrocarbon-polluted soils.
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Affiliation(s)
- Lateef B Salam
- Department of Biological Sciences, Microbiology Unit Al-Hikmah University, Ilorin, Kwara Nigeria
| | - Aisha Ishaq
- Department of Biological Sciences, Microbiology Unit Al-Hikmah University, Ilorin, Kwara Nigeria
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Ferraro DJ, Okerlund A, Brown E, Ramaswamy S. One enzyme, many reactions: structural basis for the various reactions catalyzed by naphthalene 1,2-dioxygenase. IUCRJ 2017; 4:648-656. [PMID: 28989720 PMCID: PMC5619856 DOI: 10.1107/s2052252517008223] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/02/2017] [Indexed: 06/07/2023]
Abstract
Rieske nonheme iron oxygenases (ROs) are a well studied class of enzymes. Naphthalene 1,2-dioxygenase (NDO) is used as a model to study ROs. Previous work has shown how side-on binding of oxygen to the mononuclear iron provides this enzyme with the ability to catalyze stereospecific and regiospecific cis-dihydroxylation reactions. It has been well documented that ROs catalyze a variety of other reactions, including mono-oxygenation, desaturation, O- and N-dealkylation, sulfoxidation etc. NDO itself catalyzes a variety of these reactions. Structures of NDO in complex with a number of different substrates show that the orientation of the substrate in the active site controls not only the regiospecificity and stereospecificity, but also the type of reaction catalyzed. It is proposed that the mononuclear iron-activated dioxygen attacks the atoms of the substrate that are most proximal to it. The promiscuity of delivering two products (apparently by two different reactions) from the same substrate can be explained by the possible binding of the substrate in slightly different orientations aided by the observed flexibility of residues in the binding pocket.
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Affiliation(s)
- Daniel J. Ferraro
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Adam Okerlund
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Eric Brown
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - S. Ramaswamy
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- TAS, Institute for Stem Cell Biology and Regenerative Medicine, GKVK POST, Bangalore 560 065, India
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12
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Salam LB, Ilori MO, Amund OO. Properties, environmental fate and biodegradation of carbazole. 3 Biotech 2017; 7:111. [PMID: 28567624 PMCID: PMC5451359 DOI: 10.1007/s13205-017-0743-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 02/13/2017] [Indexed: 01/28/2023] Open
Abstract
The last two decades had witnessed extensive investigation on bacterial degradation of carbazole, an N-heterocyclic aromatic hydrocarbon. Specifically, previous studies have reported the primary importance of angular dioxygenation, a novel type of oxygenation reaction, which facilitates mineralization of carbazole to intermediates of the TCA cycle. Proteobacteria and Actinobacteria are the predominant bacterial phyla implicated in this novel mode of dioxygenation, while anthranilic acid and catechol are the signature metabolites. Several studies have elucidated the degradative genes involved, the diversity of the car gene clusters and the unique organization of the car gene clusters in marine carbazole degraders. However, there is paucity of information regarding the environmental fate as well as industrial and medical importance of carbazole and its derivatives. In this review, attempt is made to harness this information to present a comprehensive outlook that not only focuses on carbazole biodegradation pathways, but also on its environmental fate as well as medical and industrial importance of carbazole and its derivatives.
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Affiliation(s)
- Lateef B Salam
- Department of Microbiology, University of Lagos, Akoka, Lagos, Nigeria.
- Microbiology Unit, Department of Biological Sciences, Al-Hikmah University, Ilorin, Kwara, Nigeria.
| | - Mathew O Ilori
- Department of Microbiology, University of Lagos, Akoka, Lagos, Nigeria
| | - Olukayode O Amund
- Department of Microbiology, University of Lagos, Akoka, Lagos, Nigeria
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Electron Transport in a Dioxygenase-Ferredoxin Complex: Long Range Charge Coupling between the Rieske and Non-Heme Iron Center. PLoS One 2016; 11:e0162031. [PMID: 27656882 PMCID: PMC5033481 DOI: 10.1371/journal.pone.0162031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Accepted: 08/16/2016] [Indexed: 11/19/2022] Open
Abstract
Dioxygenase (dOx) utilizes stereospecific oxidation on aromatic molecules; consequently, dOx has potential applications in bioremediation and stereospecific oxidation synthesis. The reactive components of dOx comprise a Rieske structure Cys2[2Fe-2S]His2 and a non-heme reactive oxygen center (ROC). Between the Rieske structure and the ROC, a universally conserved Asp residue appears to bridge the two structures forming a Rieske-Asp-ROC triad, where the Asp is known to be essential for electron transfer processes. The Rieske and ROC share hydrogen bonds with Asp through their His ligands; suggesting an ideal network for electron transfer via the carboxyl side chain of Asp. Associated with the dOx is an itinerant charge carrying protein Ferredoxin (Fdx). Depending on the specific cognate, Fdx may also possess either the Rieske structure or a related structure known as 4-Cys-[2Fe-2S] (4-Cys). In this study, we extensively explore, at different levels of theory, the behavior of the individual components (Rieske and ROC) and their interaction together via the Asp using a variety of density function methods, basis sets, and a method known as Generalized Ionic Fragment Approach (GIFA) that permits setting up spin configurations manually. We also report results on the 4-Cys structure for comparison. The individual optimized structures are compared with observed spectroscopic data from the Rieske, 4-Cys and ROC structures (where information is available). The separate pieces are then combined together into a large Rieske-Asp-ROC (donor/bridge/acceptor) complex to estimate the overall coupling between individual components, based on changes to the partial charges. The results suggest that the partial charges are significantly altered when Asp bridges the Rieske and the ROC; hence, long range coupling through hydrogen bonding effects via the intercalated Asp bridge can drastically affect the partial charge distributions compared to the individual isolated structures. The results are consistent with a proton coupled electron transfer mechanism.
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Abstract
Two bacterial strains phylogenetically identified as Pseudomonas aeruginosa strains RM1 and SK1 displayed extensive degradation ability on waste engine oil (SAE 40W) in batch cultures. Spectrophotometric analysis revealed the presence of various heavy metals such as lead, chromium and nickel in the waste engine oil. The rate of degradation of waste engine oil by the isolates, for the first 12 days and the last 9 days were 66.3, 31.6 mg l−1 day−1 and 69.6, 40.0 mg l−1 day−1 for strains RM1 and SK1, respectively. Gas chromatographic (GC) analyses of residual waste engine oil, revealed that 66.58, 89.06 % and 63.40, 90.75 % of the initial concentration of the waste engine oil were degraded by strains RM1 and SK1 within 12 and 21 days. GC fingerprints of the waste engine oil after 12 days of incubation of strains RM1 and SK1 showed total disappearance of C15, C23, C24, C25 and C26 hydrocarbon fractions as well as drastic reductions of C13, C14, C16 and PAHs fractions such as C19-anthracene and C22-pyrene. At the end of 21 days incubation, total disappearance of C17-pristane, C22-pyrene, one of the C19-anthracene and significant reduction of C18-phytane (97.2 %, strain RM1; 95.1 %, strain SK1) fractions were observed. In addition, <10 % of Day 0 values of medium fraction ranges C13, and C16 were discernible after 21 days. This study has established the potentials of P. aeruginosa strains RM1 and SK1 in the degradation of aliphatic, aromatic and branched alkane components of waste engine oils.
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15
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Salam LB, Ilori MO, Amund OO. Carbazole degradation in the soil microcosm by tropical bacterial strains. Braz J Microbiol 2015; 46:1037-44. [PMID: 26691461 PMCID: PMC4704645 DOI: 10.1590/s1517-838246420140610] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 11/16/2014] [Indexed: 11/21/2022] Open
Abstract
In a previous study, three bacterial strains isolated from tropical
hydrocarbon-contaminated soils and phylogenetically identified as
Achromobacter sp. strain SL1, Pseudomonas sp.
strain SL4 and Microbacterium esteraromaticum strain SL6 displayed
angular dioxygenation and mineralization of carbazole in batch cultures. In this
study, the ability of these isolates to survive and enhance carbazole degradation in
soil were tested in field-moist microcosms. Strain SL4 had the highest survival rate
(1.8 x 107 cfu/g) after 30 days of incubation in sterilized soil, while
there was a decrease in population density in native (unsterilized) soil when
compared with the initial population. Gas chromatographic analysis after 30 days of
incubation showed that in sterilized soil amended with carbazole (100 mg/kg), 66.96,
82.15 and 68.54% were degraded by strains SL1, SL4 and SL6, respectively, with rates
of degradation of 0.093, 0.114 and 0.095 mg kg−1 h−1. The
combination of the three isolates as inoculum in sterilized soil degraded 87.13%
carbazole at a rate of 0.121 mg kg−1 h−1. In native soil
amended with carbazole (100 mg/kg), 91.64, 87.29 and 89.13% were degraded by strains
SL1, SL4 and SL6 after 30 days of incubation, with rates of degradation of 0.127,
0.121 and 0.124 mg kg−1 h−1, respectively. This study
successfully established the survivability (> 106 cfu/g detected after
30 days) and carbazole-degrading ability of these bacterial strains in soil, and
highlights the potential of these isolates as seed for the bioremediation of
carbazole-impacted environments.
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Affiliation(s)
- Lateef B Salam
- Department of Microbiology, University of Lagos, Lagos, Nigeria
| | - Matthew O Ilori
- Department of Microbiology, University of Lagos, Lagos, Nigeria
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Li S, Xu J, Fan B, Lu Z, Zeng C, Bian Z, Zhou Y, Wang J. Palladium/Zinc Co-Catalyzedsyn-Stereoselectively Asymmetric Ring-Opening Reaction of Oxabenzonorbornadienes with Phenols. Chemistry 2015; 21:9003-7. [PMID: 25907319 DOI: 10.1002/chem.201500816] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 02/27/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Sifeng Li
- Department of Chemistry, South University of Science and Technology of China, Shenzhen, Guangdong, 518055 (P. R. China)
| | - Jianbin Xu
- YMU-HKBU Joint Laboratory of Traditional Natural Medicine, Yunnan Minzu University, Kunming 650500 (P. R. China)
| | - Baomin Fan
- YMU-HKBU Joint Laboratory of Traditional Natural Medicine, Yunnan Minzu University, Kunming 650500 (P. R. China).
- State Key Laboratory of Elemento-organic Chemistry, Nankai University, Tinajim, 300071 (P. R. China).
| | - Zhiwu Lu
- YMU-HKBU Joint Laboratory of Traditional Natural Medicine, Yunnan Minzu University, Kunming 650500 (P. R. China)
| | - Chaoyuan Zeng
- YMU-HKBU Joint Laboratory of Traditional Natural Medicine, Yunnan Minzu University, Kunming 650500 (P. R. China)
| | - Zhaoxiang Bian
- School of Chinese Medicine, Hong Kong Baptist University
| | - Yongyun Zhou
- YMU-HKBU Joint Laboratory of Traditional Natural Medicine, Yunnan Minzu University, Kunming 650500 (P. R. China)
| | - Jun Wang
- Department of Chemistry, South University of Science and Technology of China, Shenzhen, Guangdong, 518055 (P. R. China).
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Cao J, Lai Q, Yuan J, Shao Z. Genomic and metabolic analysis of fluoranthene degradation pathway in Celeribacter indicus P73T. Sci Rep 2015; 5:7741. [PMID: 25582347 PMCID: PMC4291564 DOI: 10.1038/srep07741] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 11/20/2014] [Indexed: 01/22/2023] Open
Abstract
Celeribacter indicus P73(T), isolated from deep-sea sediment from the Indian Ocean, is capable of degrading a wide range of polycyclic aromatic hydrocarbons (PAHs) and is the first fluoranthene-degrading bacterium within the family Rhodobacteraceae. Here, the complete genome sequence of strain P73(T) is presented and analyzed. Besides a 4.5-Mb circular chromosome, strain P73(T) carries five plasmids, and encodes 4827 predicted protein-coding sequences. One hundred and thirty-eight genes, including 14 dioxygenase genes, were predicted to be involved in the degradation of aromatic compounds, and most of these genes are clustered in four regions. P73_0346 is the first fluoranthene 7,8-dioxygenase to be discovered and the first fluoranthene dioxygenase within the toluene/biphenyl family. The degradative genes in regions B and D in P73(T) are absent in Celeribacter baekdonensis B30, which cannot degrade PAHs. Four intermediate metabolites [acenaphthylene-1(2H)-one, acenaphthenequinone, 1,2-dihydroxyacenaphthylene, and 1,8-naphthalic anhydride] of fluoranthene degradation by strain P73(T) were detected as the main intermediates, indicating that the degradation of fluoranthene in P73(T) was initiated by dioxygenation at the C-7,8 positions. Based on the genomic and metabolitic results, we propose a C-7,8 dioxygenation pathway in which fluoranthene is mineralized to TCA cycle intermediates.
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Affiliation(s)
- Junwei Cao
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration; Key Laboratory of Marine Genetic Resources of Fujian Province; Collaborative Innovation Center of Deep Sea Biology; Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen 361005, China
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, China
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration; Key Laboratory of Marine Genetic Resources of Fujian Province; Collaborative Innovation Center of Deep Sea Biology; Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen 361005, China
| | - Jun Yuan
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration; Key Laboratory of Marine Genetic Resources of Fujian Province; Collaborative Innovation Center of Deep Sea Biology; Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen 361005, China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration; Key Laboratory of Marine Genetic Resources of Fujian Province; Collaborative Innovation Center of Deep Sea Biology; Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen 361005, China
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18
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Tu YT, Liu JK, Lin WC, Lin JL, Kao CM. Enhanced anaerobic biodegradation of OCDD-contaminated soils by Pseudomonas mendocina NSYSU: microcosm, pilot-scale, and gene studies. JOURNAL OF HAZARDOUS MATERIALS 2014; 278:433-443. [PMID: 24997259 DOI: 10.1016/j.jhazmat.2014.06.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 06/10/2014] [Accepted: 06/11/2014] [Indexed: 06/03/2023]
Abstract
In this study, microcosm and pilot-scale experiments were performed to investigate the capability and effectiveness of Pseudomonas mendocina NSYSU (P. mendocina NSYSU) on the bioremediation of octachlorodibenzo-p-dioxin (OCDD)-contaminated soils. The objectives were to evaluate the (1) characteristics of P. mendocina NSYSU, (2) feasibility of enhancing OCDD biodegradation with the addition of P. mendocina NSYSU and lecithin, and (3) variation in microbial diversity and genes responsible for the dechlorination of OCDD. P. mendocina NSYSU was inhibited when salinity was higher than 7%, and it could biodegrade OCDD under reductive dechlorinating conditions. Lecithin could serve as the solubilization agent causing the enhanced solubilization and dechlorination of OCDD. Up to 71 and 62% of OCDD could be degraded after 65 days of incubation under anaerobic conditions with and without the addition of lecithin, respectively. Decreased OCDD concentrations caused significant increase in microbial diversity. Results from the pilot-scale study show that up to 75% of OCDD could be degraded after a 2.5-month operational period with lecithin addition. Results from the gene analyses show that two genes encoding the extradiol/intradiol ring-cleavage dioxygenase and five genes encoding the hydrolase in P. mendocina NSYSU were identified and played important roles in OCDD degradation.
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Affiliation(s)
- Y T Tu
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | - J K Liu
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - W C Lin
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - J L Lin
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | - C M Kao
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung 804, Taiwan.
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19
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Pleiotropic and epistatic behavior of a ring-hydroxylating oxygenase system in the polycyclic aromatic hydrocarbon metabolic network from Mycobacterium vanbaalenii PYR-1. J Bacteriol 2014; 196:3503-15. [PMID: 25070740 DOI: 10.1128/jb.01945-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite the considerable knowledge of bacterial high-molecular-weight (HMW) polycyclic aromatic hydrocarbon (PAH) metabolism, the key enzyme(s) and its pleiotropic and epistatic behavior(s) responsible for low-molecular-weight (LMW) PAHs in HMW PAH-metabolic networks remain poorly understood. In this study, a phenotype-based strategy, coupled with a spray plate method, selected a Mycobacterium vanbaalenii PYR-1 mutant (6G11) that degrades HMW PAHs but not LMW PAHs. Sequence analysis determined that the mutant was defective in pdoA2, encoding an aromatic ring-hydroxylating oxygenase (RHO). A series of metabolic comparisons using high-performance liquid chromatography (HPLC) analysis revealed that the mutant had a lower rate of degradation of fluorene, anthracene, and pyrene. Unlike the wild type, the mutant did not produce a color change in culture media containing fluorene, phenanthrene, and fluoranthene. An Escherichia coli expression experiment confirmed the ability of the Pdo system to oxidize biphenyl, the LMW PAHs naphthalene, phenanthrene, anthracene, and fluorene, and the HMW PAHs pyrene, fluoranthene, and benzo[a]pyrene, with the highest enzymatic activity directed toward three-ring PAHs. Structure analysis and PAH substrate docking simulations of the Pdo substrate-binding pocket rationalized the experimentally observed metabolic versatility on a molecular scale. Using information obtained in this study and from previous work, we constructed an RHO-centric functional map, allowing pleiotropic and epistatic enzymatic explanation of PAH metabolism. Taking the findings together, the Pdo system is an RHO system with the pleiotropic responsibility of LMW PAH-centric hydroxylation, and its epistatic functional contribution is also crucial for the metabolic quality and quantity of the PAH-MN.
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20
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Oba S, Suzuki T, Maeda R, Omori T, Fuse H. Characterization and genetic analyses of a carbazole-degrading gram-positive marine isolate, Janibacter sp. strain OC11. Biosci Biotechnol Biochem 2014; 78:1094-101. [DOI: 10.1080/09168451.2014.917260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
Strain OC11 was isolated from seawater sampled at the coast of Chiba, Japan, in artificial seawater medium with carbazole (CAR) as the sole carbon source. Its 16S ribosomal RNA gene sequence suggested that strain OC11 belongs to the genus Janibacter. The CAR-degradation genes (car genes) of strain OC11 were PCR amplified, using degenerate primers designed based on the car gene sequences of other CAR-degrading bacteria. Complete nucleotide sequences encoding six complete open reading frames were determined, and the first known ferredoxin reductase gene (carAd) was found from a CAR-degrading bacterium isolated from the marine environment. An experiment using a mutant strain suggested that the car genes of strain OC11 are functional in CAR degradation. Southern hybridization indicated that strain OC11 had one car gene cluster in vivo. RT-PCR revealed that transcription of carOC11 constitutes an operon.
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Affiliation(s)
- Shintaro Oba
- Graduate School of Engineering and Science, Shibaura Institute of Technology, Saitama, Japan
| | - Toshihiro Suzuki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Rintaro Maeda
- Graduate School of Applied Chemistry, Shibaura Institute of Technology, Saitama, Japan
| | - Toshio Omori
- Department of Bioscience and Engineering, Shibaura Institute of Technology, Saitama, Japan
| | - Hiroyuki Fuse
- Department of Bioscience and Engineering, Shibaura Institute of Technology, Saitama, Japan
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21
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3-Ketosteroid 9α-hydroxylase enzymes: Rieske non-heme monooxygenases essential for bacterial steroid degradation. Antonie van Leeuwenhoek 2014; 106:157-72. [PMID: 24846050 PMCID: PMC4064121 DOI: 10.1007/s10482-014-0188-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 04/25/2014] [Indexed: 12/26/2022]
Abstract
Various micro-organisms are able to use sterols/steroids as carbon- and energy sources for growth. 3-Ketosteroid 9α-hydroxylase (KSH), a two component Rieske non-heme monooxygenase comprised of the oxygenase KshA and the reductase KshB, is a key-enzyme in bacterial steroid degradation. It initiates opening of the steroid polycyclic ring structure. The enzyme has industrial relevance in the synthesis of pharmaceutical steroids. Deletion of KSH activity in sterol degrading bacteria results in blockage of steroid ring opening and is used to produce valuable C19-steroids such as 4-androstene-3,17-dione and 1,4-androstadiene-3,17-dione. Interestingly, KSH activity is essential for the pathogenicity of Mycobacterium tuberculosis. Detailed information about KSH thus is of medical relevance, and KSH inhibitory compounds may find application in combatting tuberculosis. In recent years, the 3D structure of the KshA protein of M. tuberculosis H37Rv has been elucidated and various studies report biochemical characteristics and possible physiological roles of KSH. The current knowledge is reviewed here and forms a solid basis for further studies on this highly interesting enzyme. Future work may result in the construction of KSH mutants capable of production of specific bioactive steroids. Furthermore, KSH provides an promising target for drugs against the pathogenic agent M. tuberculosis.
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22
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Salam LB, Ilori MO, Amund OO, Numata M, Horisaki T, Nojiri H. Carbazole angular dioxygenation and mineralization by bacteria isolated from hydrocarbon-contaminated tropical African soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:9311-9324. [PMID: 24728574 DOI: 10.1007/s11356-014-2855-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 03/31/2014] [Indexed: 06/03/2023]
Abstract
Four bacterial strains isolated from hydrocarbon-contaminated soils in Lagos, Nigeria, displayed extensive degradation abilities on carbazole, an N-heterocyclic aromatic hydrocarbon. Physicochemical analyses of the sampling sites (ACPP, MWO, NESU) indicate gross pollution of the soils with a high hydrocarbon content (157,067.9 mg/kg) and presence of heavy metals. Phylogenetic analysis of the four strains indicated that they were identified as Achromobacter sp. strain SL1, Pseudomonas sp. strain SL4, Microbacterium esteraromaticum strain SL6, and Stenotrophomonas maltophilia strain BA. The rates of degradation of carbazole by the four isolates during 30 days of incubation were 0.057, 0.062, 0.036, and 0.050 mg L(-1) h(-1) for strains SL1, SL4, SL6, and BA. Gas chromatographic (GC) analyses of residual carbazole after 30 days of incubation revealed that 81.3, 85, 64.4, and 76 % of 50 mg l(-1) carbazole were degraded by strains SL1, SL4, SL6, and BA, respectively. GC-mass spectrometry and high-performance liquid chromatographic analyses of the extracts from the growing and resting cells of strains SL1, SL4, and SL6 cultured on carbazole showed detection of anthranilic acid and catechol while these metabolites were not detected in strain BA under the same conditions. This study has established for the first time carbazole angular dioxygenation and mineralization by isolates from African environment.
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Affiliation(s)
- L B Salam
- Department of Microbiology, University of Lagos, Akoka, Lagos, Nigeria,
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23
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Structural basis of the divergent oxygenation reactions catalyzed by the rieske nonheme iron oxygenase carbazole 1,9a-dioxygenase. Appl Environ Microbiol 2014; 80:2821-32. [PMID: 24584240 DOI: 10.1128/aem.04000-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Carbazole 1,9a-dioxygenase (CARDO), a Rieske nonheme iron oxygenase (RO), is a three-component system composed of a terminal oxygenase (Oxy), ferredoxin, and a ferredoxin reductase. Oxy has angular dioxygenation activity against carbazole. Previously, site-directed mutagenesis of the Oxy-encoding gene from Janthinobacterium sp. strain J3 generated the I262V, F275W, Q282N, and Q282Y Oxy derivatives, which showed oxygenation capabilities different from those of the wild-type enzyme. To understand the structural features resulting in the different oxidation reactions, we determined the crystal structures of the derivatives, both free and complexed with substrates. The I262V, F275W, and Q282Y derivatives catalyze the lateral dioxygenation of carbazole with higher yields than the wild type. A previous study determined the crystal structure of Oxy complexed with carbazole and revealed that the carbonyl oxygen of Gly178 hydrogen bonds with the imino nitrogen of carbazole. In these derivatives, the carbazole was rotated approximately 15, 25, and 25°, respectively, compared to the wild type, creating space for a water molecule, which hydrogen bonds with the carbonyl oxygen of Gly178 and the imino nitrogen of carbazole. In the crystal structure of the F275W derivative complexed with fluorene, C-9 of fluorene, which corresponds to the imino nitrogen of carbazole, was oriented close to the mutated residue Trp275, which is on the opposite side of the binding pocket from the carbonyl oxygen of Gly178. Our structural analyses demonstrate that the fine-tuning of hydrophobic residues on the surface of the substrate-binding pocket in ROs causes a slight shift in the substrate-binding position that, in turn, favors specific oxygenation reactions toward various substrates.
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25
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Daniele MA, Bandera YP, Sharma D, Rungta P, Roeder R, Sehorn MG, Foulger SH. Substrate-baited nanoparticles: a catch and release strategy for enzyme recognition and harvesting. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2012; 8:2083-90. [PMID: 22532510 PMCID: PMC3516911 DOI: 10.1002/smll.201200013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 02/14/2012] [Indexed: 05/31/2023]
Abstract
The isolation of a single type of protein from a complex mixture is vital for the characterization of the function, structure, and interactions of the protein of interest and is typically the most laborious aspect of the protein purification process. In this work, a model system is utilized to show the efficacy of synthesizing a "baited" nanoparticle to capture and recycle enzymes (proteins that catalyze chemical reactions) from crude cell lysate. Enzyme trapping and recycling is illustrated with the carbazole 1,9a-dioxygenase (CARDO) system, an enzyme important in bioremediation and natural product synthesis. The enzymes are baited with azide-modified carbazolyl moieties attached to poly(propargyl acrylate) nanoparticles through a click transformation. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis indicates the single-step procedure to immobilize the enzymes on the particles is capable of significantly concentrating the protein from raw lysate and sequestering all required components of the protein to maintain bioactivity. These results establish a universal model applicable to concentrating and extracting known substrate-protein pairs, but it can be an invaluable tool in recognizing unknown protein-ligand affinities.
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Affiliation(s)
- Michael A Daniele
- Center for Optical Materials Science and Engineering Technologies, School of Materials Science and Engineering, Department of Bioengineering, Clemson University, Clemson, SC 29634, USA
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26
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Suzuki Y, Nakamura M, Otsuka Y, Suzuki N, Ohyama K, Kawakami T, Sato K, Kajita S, Hishiyama S, Takahashi A, Katayama Y. Development of a highly sensitive assay for enzyme-mediated reductive degradation of polychlorinated dibenzo-p-dioxin. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2012; 31:1072-1075. [PMID: 22447772 DOI: 10.1002/etc.1775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 10/12/2011] [Accepted: 01/02/2012] [Indexed: 05/31/2023]
Abstract
The degradation of 2-chloro-4,5-O-(4'-methyl-7', 8'-diphenyl)ether (CMDPE), an analog of 2,7-dichlorodibenzo-p-dioxin (2,7-DCDD), mediated by Geobacillus sp. UZO 3 cell-free extract was monitored. Ethyl acetate extracts of a complete reaction mixture incubated at 65°C for 18 h were analyzed either by thin layer chromatography (TLC) fractionation coupled with spectrometric detection or by gas chromatography-mass spectrometry (GC-MS). The reaction product 4-methylumbelliferone (4MU) was successfully isolated by TLC and visualized by a transilluminator at 450 nm. The 4MU, 4-chlorophenol, and reaction intermediate 6-chlorophenoxy-4-methylumbelliferone were all successfully detected by GC-MS. The presence of these compounds suggest that Geobacillus sp. UZO 3 cell-free extract also catalyzes the reductive cleavage of the diaryl ether bonds of CMDPE in a similar mechanism previously reported in 2,7-DCDD. In the present study, the authors describe a simple and highly sensitive fluorescent assay for a new dioxin degrading enzyme(s).
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Affiliation(s)
- Yuzo Suzuki
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
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27
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Structural and molecular genetic analyses of the bacterial carbazole degradation system. Biosci Biotechnol Biochem 2012; 76:1-18. [PMID: 22232235 DOI: 10.1271/bbb.110620] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Carbazole degradation by several bacterial strains, including Pseudomonas resinovorans CA10, has been investigated over the last two decades. As the initial reaction in degradation pathways, carbazole is commonly oxygenated at angular (C9a) and adjacent (C1) carbons as two hydroxyl groups in a cis configuration. This type of dioxygenation is termed "angular dioxygenation," and is catalyzed by carbazole 1,9a-dioxygenase (CARDO), consisting of terminal oxygenase, ferredoxin, and ferredoxin reductase components. The crystal structures of all components and the electron transfer complex between terminal oxygenase and ferredoxin indicate substrate recognition mechanisms suitable for angular dioxygenation and specific electron transfer among the three components. In contrast, the carbazole degradative car operon of CA10 is located on IncP-7 conjugative plasmid pCAR1. Together with conventional molecular genetic and biochemical investigations, recent genome sequencing and RNA mapping studies have clarified that transcriptional cross-regulation via nucleoid-associated proteins is established between pCAR1 and the host chromosome.
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28
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Daniele MA, Bandera YP, Foulger SH. Manipulation of Förster energy transfer of coupled fluorophores through biotransformation by Pseudomonas resinovorans CA10. Photochem Photobiol 2011; 88:129-34. [PMID: 22044050 DOI: 10.1111/j.1751-1097.2011.01023.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An alkyne-terminated anthracene and azide-terminated carbazole were joined through a copper-catalyzed cycloaddition to form a joined donor/acceptor pair. The photonic pair exhibited energy transfer when excited at the peak absorbance of carbazole and fluoresced with an anthracene spectral response. The fluorescent behavior was confirmed as Förster energy transfer (FRET). The lysate of Pseudomonas resinovorans CA10, a member of a predominant group of soil microorganisms that can metabolize a host of substrates, was employed to degrade the pair and alter the luminance spectral characteristics. The FRET was diminished and the corresponding, individual fluorescence of carbazole and anthracene returned. This general approach may find applications in single-cell metabolic studies and bioactivity assays.
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Affiliation(s)
- Michael A Daniele
- Center for Optical Materials Science and Engineering Technologies, School of Materials Science and Engineering, Clemson University, Clemson, SC, USA
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29
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Suzuki Y, Nakamura M, Otsuka Y, Suzuki N, Ohyama K, Kawakami T, Sato K, Kajita S, Hishiyama S, Fujii T, Takahashi A, Katayama Y. Novel enzymatic activity of cell free extract from thermophilic Geobacillus sp. UZO 3 catalyzes reductive cleavage of diaryl ether bonds of 2,7-dichlorodibenzo-p-dioxin. CHEMOSPHERE 2011; 83:868-872. [PMID: 21435685 DOI: 10.1016/j.chemosphere.2011.02.068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 01/30/2011] [Accepted: 02/27/2011] [Indexed: 05/30/2023]
Abstract
We characterized the ability of the cell free extract from polychlorinated dibenzo-p-dioxins degrading bacterium Geobacillus sp. UZO 3 to reduce even highly chlorinated dibenzo-p-dioxins such as octachlorodibenzo-p-dioxins in incineration fly ash. The degradation of 2,7-dichlorodibenzo-p-dioxin (2,7-DCDD) as a model dioxin catalyzed by the cell free extract from this strain implicates that the ether bonds of 2,7-DCDD molecule undergo reductive cleavage, since 4',5-dichloro-2-hydroxydiphenyl ether and 4-chlorophenol were detected as intermediate products of 2,7-DCDD degradation.
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Affiliation(s)
- Yuzoh Suzuki
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture & Technology, Koganei, Tokyo 184-8588, Japan
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Yao SJ, Wang HY, Zhang L, Guo YL. Study on reactions of long-lived phenoxathiin radical cation with aliphatic alcohols, phenol and phenyl halides in ambient condition by fused-droplet electrospray ionization mass spectrometry. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2011; 17:385-394. [PMID: 22006637 DOI: 10.1255/ejms.1136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
he reactions of phenoxathiin radical cations with diverse organic compounds in ambient conditions were realized by using fused-droplet electrospray ionization mass spectrometry. In the investigation, the phenoxathiin radical cation was prepared by electrospray ionization. The reactants included aliphatic alcohols, phenol and phenyl halides and the reaction studies showed the unique reactivity the of phenoxathiin radical cation towards neutral organic compounds in ambient conditions, which has not been revealed in previous studies.
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Affiliation(s)
- Shen-Jun Yao
- Chinese Academy of Sciences, Shanghai 200032, People's Republic of China
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31
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Maeda R, Ishii T, Ito Y, Zulkharnain AB, Iwata K, Omori T. Isolation and characterization of the gene encoding the chloroplast-type ferredoxin component of carbazole 1,9a-dioxygenase from a putative Kordiimonas sp. Biotechnol Lett 2010; 32:1725-31. [DOI: 10.1007/s10529-010-0358-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Accepted: 07/01/2010] [Indexed: 11/30/2022]
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Substrate specificity and structural characteristics of the novel Rieske nonheme iron aromatic ring-hydroxylating oxygenases NidAB and NidA3B3 from Mycobacterium vanbaalenii PYR-1. mBio 2010; 1. [PMID: 20714442 PMCID: PMC2921158 DOI: 10.1128/mbio.00135-10] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 05/05/2010] [Indexed: 11/20/2022] Open
Abstract
The Rieske nonheme iron aromatic ring-hydroxylating oxygenases (RHOs) NidAB and NidA3B3 from Mycobacterium vanbaalenii PYR-1 have been implicated in the initial oxidation of high-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs), forming cis-dihydrodiols. To clarify how these two RHOs are functionally different with respect to the degradation of HMW PAHs, we investigated their substrate specificities to 13 representative aromatic substrates (toluene, m-xylene, phthalate, biphenyl, naphthalene, phenanthrene, anthracene, fluoranthene, pyrene, benz[a]anthracene, benzo[a]pyrene, carbazole, and dibenzothiophene) by enzyme reconstitution studies of Escherichia coli. Both Nid systems were identified to be compatible with type V electron transport chain (ETC) components, consisting of a [3Fe-4S]-type ferredoxin and a glutathione reductase (GR)-type reductase. Metabolite profiles indicated that the Nid systems oxidize a wide range of aromatic hydrocarbon compounds, producing various isomeric dihydrodiol and phenolic compounds. NidAB and NidA3B3 showed the highest conversion rates for pyrene and fluoranthene, respectively, with high product regiospecificity, whereas other aromatic substrates were converted at relatively low regiospecificity. Structural characteristics of the active sites of the Nid systems were investigated and compared to those of other RHOs. The NidAB and NidA3B3 systems showed the largest substrate-binding pockets in the active sites, which satisfies spatial requirements for accepting HMW PAHs. Spatially conserved aromatic amino acids, Phe-Phe-Phe, in the substrate-binding pockets of the Nid systems appeared to play an important role in keeping aromatic substrates within the reactive distance from the iron atom, which allows each oxygen to attack the neighboring carbons.
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The genes coding for the conversion of carbazole to catechol are flanked by IS6100 elements in Sphingomonas sp. strain XLDN2-5. PLoS One 2010; 5:e10018. [PMID: 20368802 PMCID: PMC2848856 DOI: 10.1371/journal.pone.0010018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 03/15/2010] [Indexed: 11/24/2022] Open
Abstract
Background Carbazole is a recalcitrant compound with a dioxin-like structure and possesses mutagenic and toxic activities. Bacteria respond to a xenobiotic by recruiting exogenous genes to establish a pathway to degrade the xenobiotic, which is necessary for their adaptation and survival. Usually, this process is mediated by mobile genetic elements such as plasmids, transposons, and insertion sequences. Findings The genes encoding the enzymes responsible for the degradation of carbazole to catechol via anthranilate were cloned, sequenced, and characterized from a carbazole-degrading Sphingomonas sp. strain XLDN2-5. The car gene cluster (carRAaBaBbCAc) and fdr gene were accompanied on both sides by two copies of IS6100 elements, and organized as IS6100::ISSsp1-ORF1-carRAaBaBbCAc-ORF8-IS6100-fdr-IS6100. Carbazole was converted by carbazole 1,9a-dioxygenase (CARDO, CarAaAcFdr), meta-cleavage enzyme (CarBaBb), and hydrolase (CarC) to anthranilate and 2-hydroxypenta-2,4-dienoate. The fdr gene encoded a novel ferredoxin reductase whose absence resulted in lower transformation activity of carbazole by CarAa and CarAc. The ant gene cluster (antRAcAdAbAa) which was involved in the conversion of anthranilate to catechol was also sandwiched between two IS6100 elements as IS6100-antRAcAdAbAa-IS6100. Anthranilate 1,2-dioxygenase (ANTDO) was composed of a reductase (AntAa), a ferredoxin (AntAb), and a two-subunit terminal oxygenase (AntAcAd). Reverse transcription-PCR results suggested that carAaBaBbCAc gene cluster, fdr, and antRAcAdAbAa gene cluster were induced when strain XLDN2-5 was exposed to carbazole. Expression of both CARDO and ANTDO in Escherichia coli required the presence of the natural reductases for full enzymatic activity. Conclusions/Significance We predict that IS6100 might play an important role in the establishment of carbazole-degrading pathway, which endows the host to adapt to novel compounds in the environment. The organization of the car and ant genes in strain XLDN2-5 was unique, which showed strong evolutionary trail of gene recruitment mediated by IS6100 and presented a remarkable example of rearrangements and pathway establishments.
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Metabolism of mono- and dichloro-dibenzo-p-dioxins by Phanerochaete chrysosporium cytochromes P450. Appl Microbiol Biotechnol 2010; 86:773-80. [DOI: 10.1007/s00253-009-2413-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Isolation and Characterization of a car Gene Cluster from the Naphthalene, Phenanthrene, and Carbazole-Degrading Marine Isolate Lysobacter sp. Strain OC7. Curr Microbiol 2009; 59:154-9. [DOI: 10.1007/s00284-009-9414-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2009] [Revised: 03/12/2009] [Accepted: 04/14/2009] [Indexed: 11/27/2022]
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36
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Leneva NA, Kolomytseva MP, Baskunov BP, Golovleva LA. Phenanthrene and anthracene degradation by microorganisms of the genus Rhodococcus. APPL BIOCHEM MICRO+ 2009. [DOI: 10.1134/s0003683809020094] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Maeda R, Nagashima H, Widada J, Iwata K, Omori T. Novel marine carbazole-degrading bacteria. FEMS Microbiol Lett 2009; 292:203-9. [PMID: 19187209 DOI: 10.1111/j.1574-6968.2009.01497.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Eleven carbazole (CAR)-degrading bacterial strains were isolated from seawater collected off the coast of Japan using two different media. Seven isolates were shown to be most closely related to the genera Erythrobacter, Hyphomonas, Sphingosinicella, Caulobacter, and Lysobacter. Meanwhile, strains OC3, OC6S, OC9, and OC11S showed low similarity to known bacteria, the closest relative being Kordiimonas gwangyangensis GW14-5 (90% similarity). Southern hybridization analysis revealed that only five isolates carried car genes similar to those reported in Pseudomonas resinovorans CA10 (car(CA10)) or Sphingomonas sp. strain KA1 (car(KA1)). The isolates were subjected to GC-MS and the results indicated that these strains degrade CAR to anthranilic acid.
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Affiliation(s)
- Rintaro Maeda
- Graduate School of Applied Chemistry, Shibaura Institute of Technology, Tokyo, Japan
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38
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Waldau D, Methling K, Mikolasch A, Schauer F. Characterization of new oxidation products of 9H-carbazole and structure related compounds by biphenyl-utilizing bacteria. Appl Microbiol Biotechnol 2009; 81:1023-31. [DOI: 10.1007/s00253-008-1723-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Revised: 09/12/2008] [Accepted: 09/16/2008] [Indexed: 11/27/2022]
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39
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Gai Z, Yu B, Wang X, Deng Z, Xu P. Microbial transformation of benzothiophenes, with carbazole as the auxiliary substrate, by Sphingomonas sp. strain XLDN2-5. Microbiology (Reading) 2008; 154:3804-3812. [DOI: 10.1099/mic.0.2008/023176-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Zhonghui Gai
- Key Laboratory of Microbial Metabolism, Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Bo Yu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, PR China
| | - Xiaoyu Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Zixin Deng
- Key Laboratory of Microbial Metabolism, Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Ping Xu
- Key Laboratory of Microbial Metabolism, Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
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Guo W, Li D, Tao Y, Gao P, Hu J. Isolation and description of a stable carbazole-degrading microbial consortium consisting of Chryseobacterium sp. NCY and Achromobacter sp. NCW. Curr Microbiol 2008; 57:251-7. [PMID: 18584242 DOI: 10.1007/s00284-008-9185-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2007] [Accepted: 04/17/2008] [Indexed: 11/30/2022]
Abstract
A stable microbial consortium, separated from a refinery wastewater sample, was able to utilize carbazole as the sole source of carbon, nitrogen, and energy, and liberated ammonia from excess nitrogen. Two bacterial strains (NCY and NCW) were isolated from the microbial consortium using a nutrient agar plate. Based on the 16S rDNA sequence analysis, the two bacteria were identified as Chryseobacterium sp. NCY and Achromobacter sp. NCW, respectively. No intermediates of carbazole degradation were detected by high-performance liquid chromatography. The substrate specificity assay showed that the consortium could utilize compounds similar to carbazole, such as phenanthrene, naphthalene, and imidazole. Neither the pure strain NCY nor NCW could degrade carbazole after domestication for several times. It was suggested that the two bacteria formed a microbial consortium capable of metabolizing carbazole.
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Affiliation(s)
- Weiqiang Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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41
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42
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Characterization of a novel angular dioxygenase from fluorene-degrading Sphingomonas sp. strain LB126. Appl Environ Microbiol 2007; 74:1050-7. [PMID: 18156320 DOI: 10.1128/aem.01627-07] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, the genes involved in the initial attack on fluorene by Sphingomonas sp. strain LB126 were investigated. The alpha and beta subunits of a dioxygenase complex (FlnA1-FlnA2), showing 63 and 51% sequence identity, respectively, to the subunits of an angular dioxygenase from the gram-positive dibenzofuran degrader Terrabacter sp. strain DBF63, were identified. When overexpressed in Escherichia coli, FlnA1-FlnA2 was responsible for the angular oxidation of fluorene, 9-hydroxyfluorene, 9-fluorenone, dibenzofuran, and dibenzo-p-dioxin. Moreover, FlnA1-FlnA2 was able to oxidize polycyclic aromatic hydrocarbons and heteroaromatics, some of which were not oxidized by the dioxygenase from Terrabacter sp. strain DBF63. The quantification of resulting oxidation products showed that fluorene and phenanthrene were the preferred substrates of FlnA1-FlnA2.
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Jaiswal PK, Thakur IS. Isolation and characterization of dibenzofuran-degrading Serratia marcescens from alkalophilic bacterial consortium of the chemostat. Curr Microbiol 2007; 55:447-54. [PMID: 17710482 DOI: 10.1007/s00284-007-9013-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2007] [Accepted: 06/08/2007] [Indexed: 10/22/2022]
Abstract
Alkalophilic bacterial consortium developed by continuous enrichment in the chemostat in presence of 4-chlorosalicylic acid as sole source of carbon and energy contained six bacterial strains, Micrococcus luteus (csa101), Deinococcus radiothilus (csa102), csa103 (Burkholderia gladioli), Alloiococcus otilis (csa104), Micrococcus diversus (csa105), Micrococcus luteus (csa106), identified by the Biolog test method. The strains were tested for utilization of organic compounds in which one of the strains (csa101) had higher potency to utilize dibenzofuran (DF) as sole carbon and energy source identified as Serratia marcescens on the basis of 16S rDNA. The degradation of DF by bacterial strain proceeded through an oxidative route as indicated by 2,2'3-trihydroxybiphenyl, 2-hydroxy-6-(2-hydroxyphenyl)-6-oxo-2,4-hexadienoic acid, salicylic acid, and catechol, which was identified by gas chromatography-mass spectrometry.
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44
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Gai Z, Yu B, Li L, Wang Y, Ma C, Feng J, Deng Z, Xu P. Cometabolic degradation of dibenzofuran and dibenzothiophene by a newly isolated carbazole-degrading Sphingomonas sp. strain. Appl Environ Microbiol 2007; 73:2832-8. [PMID: 17337542 PMCID: PMC1892858 DOI: 10.1128/aem.02704-06] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Accepted: 02/20/2007] [Indexed: 11/20/2022] Open
Abstract
A carbazole-utilizing bacterium was isolated by enrichment from petroleum-contaminated soil. The isolate, designated Sphingomonas sp. strain XLDN2-5, could utilize carbazole (CA) as the sole source of carbon, nitrogen, and energy. Washed cells of strain XLDN2-5 were shown to be capable of degrading dibenzofuran (DBF) and dibenzothiophene (DBT). Examination of metabolites suggested that XLDN2-5 degraded DBF to 2-hydroxy-6-(2-hydroxyphenyl)-6-oxo-2,4-hexadienic acid and subsequently to salicylic acid through the angular dioxygenation pathway. In contrast to DBF, strain XLDN2-5 could transform DBT through the ring cleavage and sulfoxidation pathways. Sphingomonas sp. strain XLDN2-5 could cometabolically degrade DBF and DBT in the growing system using CA as a substrate. After 40 h of incubation, 90% of DBT was transformed, and CA and DBF were completely removed. These results suggested that strain XLDN2-5 might be useful in the bioremediation of environments contaminated by these compounds.
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Affiliation(s)
- Zhonghui Gai
- State Key Laboratory of Microbial Technology, College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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Zhong Y, Luan T, Wang X, Lan C, Tam NFY. Influence of growth medium on cometabolic degradation of polycyclic aromatic hydrocarbons by Sphingomonas sp. strain PheB4. Appl Microbiol Biotechnol 2007; 75:175-86. [PMID: 17216444 DOI: 10.1007/s00253-006-0789-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2006] [Revised: 12/01/2006] [Accepted: 12/04/2006] [Indexed: 11/30/2022]
Abstract
The influence of growth medium on cometabolic degradation of polycyclic aromatic hydrocarbons (PAHs) was investigated when Sphingomonas sp. strain PheB4 isolated from surface mangrove sediments was grown in either phenanthrene-containing mineral salts medium (PMSM) or nutrient broth (NB). The NB-grown culture exhibited a more rapid cometabolic degradation of single and mixed non-growth substrate PAHs compared to the PMSM-grown culture. The concentrations of PAH metabolites were also lower in NB-grown culture than in PMSM-grown culture, suggesting that NB-grown culture removed metabolites at a faster rate, particularly, for metabolites produced from cometabolic degradation of a binary mixture of PAHs. Cometabolic pathways of single PAH (anthracene, fluorene, or fluoranthene) in NB-grown culture showed similarity to that in PMSM-grown culture. However, cometabolic pathways of mixed PAHs were more diverse in NB-grown culture than that in PMSM-grown culture. These results indicated that nutrient rich medium was effective in enhancing cometabolic degradation of mixed PAHs concomitant with a rapid removal of metabolites, which could be useful for the bioremediation of mixed PAHs contaminated sites using Sphingomonas sp. strain PheB4.
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Affiliation(s)
- Yin Zhong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
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46
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Li L, Li Q, Li F, Shi Q, Yu B, Liu F, Xu P. Degradation of carbazole and its derivatives by a Pseudomonas sp. Appl Microbiol Biotechnol 2006; 73:941-8. [PMID: 16896599 DOI: 10.1007/s00253-006-0530-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2006] [Revised: 05/31/2006] [Accepted: 06/01/2006] [Indexed: 11/24/2022]
Abstract
Carbazole, carbazoles with monomethyl or dimethyls substituted on different positions (C(1)-carbazoles or C(2)-carbazoles), and benzocarbazoles, as toxic and mutagenic components of petroleum and creosote contamination, were biodegradable by an isolated bacterial strain Pseudomonas sp. XLDN4-9. C(1)-carbazoles were degraded in preference to carbazole and C(2)-carbazoles. The biodegradation of C(1)-carbazoles or C(2)-carbazoles was influenced by the positions of methyl substitutions. Among C(1)-carbazole isomers, 1-methyl carbazole was the most susceptible. C(2)-carbazole isomers with substitutions on the same benzo-nucleus were more susceptible at a concentration of less than 3.4 microg g(-1) petroleum, especially when harboring one substitution on position 1. In particular, 1,5-dimethyl carbazole was the most recalcitrant dimethyl isomer.
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Affiliation(s)
- Li Li
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
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47
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Inoue K, Ashikawa Y, Usami Y, Noguchi H, Fujimoto Z, Yamane H, Nojiri H. Crystallization and preliminary X-ray diffraction studies of the terminal oxygenase component of carbazole 1,9a-dioxygenase from Nocardioides aromaticivorans IC177. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:1212-4. [PMID: 17142899 PMCID: PMC2225353 DOI: 10.1107/s1744309106044939] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2006] [Accepted: 10/27/2006] [Indexed: 11/10/2022]
Abstract
Carbazole 1,9a-dioxygenase (CARDO) catalyzes the dihydroxylation of carbazole by angular-position (C9a) carbon bonding to the imino nitrogen and its adjacent C1 carbon. CARDO consists of a terminal oxygenase component and two electron-transfer components: ferredoxin and ferredoxin reductase. The terminal oxygenase component (43.9 kDa) of carbazole 1,9a-dioxygenase from Nocardioides aromaticivorans IC177 was crystallized at 293 K using the hanging-drop vapour-diffusion method with PEG 8000 as the precipitant. The crystals diffract to 2.3 A resolution and belong to space group C2.
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Affiliation(s)
- Kengo Inoue
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yuji Ashikawa
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yusuke Usami
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Haruko Noguchi
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Professional Programme for Agricultural Bioinformatics, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Zui Fujimoto
- Department of Biochemistry, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Hisakazu Yamane
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hideaki Nojiri
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Professional Programme for Agricultural Bioinformatics, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Correspondence e-mail:
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Yu B, Ma C, Zhou W, Zhu S, Wang Y, Qu J, Li F, Xu P. Simultaneous biodetoxification of S, N, and O pollutants by engineering of a carbazole-degrading gene cassette in a recombinant biocatalyst. Appl Environ Microbiol 2006; 72:7373-6. [PMID: 16936043 PMCID: PMC1636170 DOI: 10.1128/aem.01374-06] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Accepted: 08/14/2006] [Indexed: 11/20/2022] Open
Abstract
The gene cassette encoding enzymes responsible for degrading carbazole to anthranilic acid was introduced into a dibenzothiophene degrader. The resultant strain, Rhodococcus erythropolis XPDN, could simultaneously transform the model pollutants dibenzothiophene, carbazole, and dibenzofuran to nontoxic metabolites and may have an application potential for bioremediation.
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Affiliation(s)
- Bo Yu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
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49
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Urata M, Uchimura H, Noguchi H, Sakaguchi T, Takemura T, Eto K, Habe H, Omori T, Yamane H, Nojiri H. Plasmid pCAR3 contains multiple gene sets involved in the conversion of carbazole to anthranilate. Appl Environ Microbiol 2006; 72:3198-205. [PMID: 16672458 PMCID: PMC1472349 DOI: 10.1128/aem.72.5.3198-3205.2006] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The carbazole degradative car-I gene cluster (carAaIBaIBbICIAcI) of Sphingomonas sp. strain KA1 is located on the 254-kb circular plasmid pCAR3. Carbazole conversion to anthranilate is catalyzed by carbazole 1,9a-dioxygenase (CARDO; CarAaIAcI), meta-cleavage enzyme (CarBaIBbI), and hydrolase (CarCI). CARDO is a three-component dioxygenase, and CarAaI and CarAcI are its terminal oxygenase and ferredoxin components. The car-I gene cluster lacks the gene encoding the ferredoxin reductase component of CARDO. In the present study, based on the draft sequence of pCAR3, we found multiple carbazole degradation genes dispersed in four loci on pCAR3, including a second copy of the car gene cluster (carAaIIBaIIBbIICIIAcII) and the ferredoxin/reductase genes fdxI-fdrI and fdrII. Biotransformation experiments showed that FdrI (or FdrII) could drive the electron transfer chain from NAD(P)H to CarAaI (or CarAaII) with the aid of ferredoxin (CarAcI, CarAcII, or FdxI). Because this electron transfer chain showed phylogenetic relatedness to that consisting of putidaredoxin and putidaredoxin reductase of the P450cam monooxygenase system of Pseudomonas putida, CARDO systems of KA1 can be classified in the class IIA Rieske non-heme iron oxygenase system. Reverse transcription-PCR (RT-PCR) and quantitative RT-PCR analyses revealed that two car gene clusters constituted operons, and their expression was induced when KA1 was exposed to carbazole, although the fdxI-fdrI and fdrII genes were expressed constitutively. Both terminal oxygenases of KA1 showed roughly the same substrate specificity as that from the well-characterized carbazole degrader Pseudomonas resinovorans CA10, although slight differences were observed.
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Affiliation(s)
- Masaaki Urata
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Xu P, Yu B, Li FL, Cai XF, Ma CQ. Microbial degradation of sulfur, nitrogen and oxygen heterocycles. Trends Microbiol 2006; 14:398-405. [PMID: 16860985 DOI: 10.1016/j.tim.2006.07.002] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2006] [Revised: 06/12/2006] [Accepted: 07/07/2006] [Indexed: 10/24/2022]
Abstract
Sulfur (S), nitrogen (N) and oxygen (O) heterocycles are among the most potent environmental pollutants. Microbial degradation of these pollutants is attracting more and more attention because such bioprocesses are environmentally friendly. The biotechnological potential of these processes is being investigated, for example, to achieve better sulfur removal by immobilized biocatalysts with magnetite nanoparticles or by solvent-tolerant bacteria, and to obtain valuable intermediates from these heterocycles. Other recent advances have demonstrated the mechanisms of angular dioxygenation of nitrogen heterocycles by microbes. However, these technologies are not yet available for large-scale applications so future research must investigate proper modifications for industrial applications of these processes. This review focuses on recent progress in understanding how microbes degrade S, N and O heterocycles.
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Affiliation(s)
- Ping Xu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China.
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