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Pan M, Li C, Wei X, Liu G, Ang EH, Pan B. Pioneering Piezoelectric-Driven Atomic Hydrogen for Efficient Dehalogenation of Halogenated Organic Pollutants. Environ Sci Technol 2024; 58:4008-4018. [PMID: 38347702 DOI: 10.1021/acs.est.3c09579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
The electrocatalytic hydrodehalogenation (EHDH) process mediated by atomic hydrogen (H*) is recognized as an efficient method for degrading halogenated organic pollutants (HOPs). However, a significant challenge is the excessive energy consumption resulting from the recombination of H* to H2 production in the EHDH process. In this study, a promising strategy was proposed to generate piezo-induced atomic H*, without external energy input or chemical consumption, for the degradation and dehalogenation of HOPs. Specifically, sub-5 nm Ni nanoparticles were subtly dotted on an N-doped carbon layer coating on BaTiO3 cube, and the resulted hybrid nanocomposite (Ni-NC@BTO) can effectively break C-X (X = Cl and F) bonds under ultrasonic vibration or mechanical stirring, demonstrating high piezoelectric driven dehalogenation efficiencies toward various HOPs. Mechanistic studies revealed that the dotted Ni nanoparticles can efficiently capture H* to form Ni-H* (Habs) and drive the dehalogenation process to lower the toxicity of intermediates. COMSOL simulations confirmed a "chimney effect" on the interface of Ni nanoparticle, which facilitated the accumulation of H+ and enhanced electron transfer for H* formation by improving the surface charge of the piezocatalyst and strengthening the interfacial electric field. Our work introduces an environmentally friendly dehalogenation method for HOPs using the piezoelectric process independent of the external energy input and chemical consumption.
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Affiliation(s)
- Meilan Pan
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Cong Li
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Xiuzhen Wei
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Guanyu Liu
- School of Materials Science and Engineering, Tongji University, Shanghai 201804, China
| | - Edison Huixiang Ang
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, Singapore 637616, Singapore
| | - Bingjun Pan
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
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2
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Tang K, Brown MR, Risko C, Gish MK, Rumbles G, Pham PH, Luca OR, Barlow S, Marder SR. Beyond n-dopants for organic semiconductors: use of bibenzo[ d]imidazoles in UV-promoted dehalogenation reactions of organic halides. Beilstein J Org Chem 2023; 19:1912-1922. [PMID: 38116245 PMCID: PMC10729154 DOI: 10.3762/bjoc.19.142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023] Open
Abstract
2,2'-Bis(4-dimethylaminophenyl)- and 2,2'-dicyclohexyl-1,1',3,3'-tetramethyl-2,2',3,3'-tetrahydro-2,2'-bibenzo[d]imidazole ((N-DMBI)2 and (Cyc-DMBI)2) are quite strong reductants with effective potentials of ca. -2 V vs ferrocenium/ferrocene, yet are relatively stable to air due to the coupling of redox and bond-breaking processes. Here, we examine their use in accomplishing electron transfer-induced bond-cleavage reactions, specifically dehalogenations. The dimers reduce halides that have reduction potentials less cathodic than ca. -2 V vs ferrocenium/ferrocene, especially under UV photoexcitation (using a 365 nm LED). In the case of benzyl halides, the products are bibenzyl derivatives, whereas aryl halides are reduced to the corresponding arenes. The potentials of the halides that can be reduced in this way, quantum-chemical calculations, and steady-state and transient absorption spectroscopy suggest that UV irradiation accelerates the reactions via cleavage of the dimers to the corresponding radical monomers.
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Affiliation(s)
- Kan Tang
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Megan R Brown
- Department of Chemistry & Center for Applied Energy Research (CAER), University of Kentucky, Lexington, Kentucky, 40506, United States
| | - Chad Risko
- Department of Chemistry & Center for Applied Energy Research (CAER), University of Kentucky, Lexington, Kentucky, 40506, United States
| | - Melissa K Gish
- National Renewable Energy Laboratory, Chemistry and Nanoscience Center, Golden, Colorado, 80401, United States
| | - Garry Rumbles
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80309, United States
- National Renewable Energy Laboratory, Chemistry and Nanoscience Center, Golden, Colorado, 80401, United States
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States,
| | - Phuc H Pham
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Oana R Luca
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Stephen Barlow
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80309, United States
- National Renewable Energy Laboratory, Chemistry and Nanoscience Center, Golden, Colorado, 80401, United States
| | - Seth R Marder
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado 80309, United States
- National Renewable Energy Laboratory, Chemistry and Nanoscience Center, Golden, Colorado, 80401, United States
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States,
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
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Li Z, Guo Z, Wu X, Jiang X, Li H, Xu J, Yang K, Lin D. Few-Atomic Zero-Valent Palladium Ensembles for Efficient Reductive Dehydrogenation and Dehalogenation Catalysis. ACS Nano 2023; 17:22859-22871. [PMID: 37930274 DOI: 10.1021/acsnano.3c07724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Single-atom catalysts (SACs) offer immense potential in heterogeneous catalysis due to their maximized atomic utilization and high selectivity but suffer the problem of low reactivity in catalytic reductive reactions due to their high-valent state. Here, we demonstrate that supported palladium (Pd) ensembles consisting of a few zero-valent Pd atoms (Pd1+c-red/CN) exhibit exceptional reactivity in formic acid (FA) dehydrogenation and 4-chlorophenol (4-CP) dechlorination. The initial FA dehydrogenation and 4-CP dechlorination rates of Pd1+c-red/CN are 42-104 and 16-210 times higher than that of supported Pd SACs (Pd1-ox/CN), respectively. Experimental results and density functional theory (DFT) calculations reveal that optimal adsorption sites of Pd1+c-red/CN stimulate the formation of H*, which is indispensable for 4-CP dechlorination. Moreover, direct electron transfer from Pd atoms to FA with a high electron density on Pd1+c-red/CN also contributes to the rapid 4-CP dechlorination. The superior dehalogenation capability of Pd1+c-red/CN for organohalides of great environmental and health concerns suggested its immense application potential in environmental remediation. This work highlights the pivotal roles of the structure and valence state of Pd ensembles in catalytic reductive reactions and provides a strategy to broaden the application of Pd-based catalysts for dehydrogenation and dehalogenation.
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Affiliation(s)
- Zhenjie Li
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Zhongyuan Guo
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Xinyue Wu
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Xunheng Jiang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Hao Li
- Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Sendai 980-8577, Japan
| | - Jiang Xu
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Kun Yang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Daohui Lin
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- Zhejiang Ecological Civilization Academy, Anji 313300, China
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4
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Song G, Wu H, Jing J, Zhang X, Wang X, Li S, Zhou M. Insights into Electrochemical Dehalogenation by Non-Noble Metal Single-Atom Cobalt with High Efficiency and Low Energy Consumption. Environ Sci Technol 2023; 57:14482-14492. [PMID: 37699122 DOI: 10.1021/acs.est.3c06021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
It is critical to discover a non-noble metal catalyst with high catalytic activity capable of replacing palladium in electrochemical reduction. In this work, a highly efficient single-atom Co-N/C catalyst was synthesized with metal-organic frameworks (MOFs) as a precursor for electrochemical dehalogenation. X-ray absorption spectroscopy (XAS) revealed that Co-N/C exhibited a Co-N4 configuration, which had more active sites and a faster charge-transfer rate and thus enabled the efficient removal of florfenicol (FLO) at a wide pH, achieving a rate constant 3.5 and 2.1 times that of N/C and commercial Pd/C, respectively. The defluorination and dechlorination efficiencies were 67.6 and 95.6%, respectively, with extremely low Co leaching (6 μg L-1), low energy consumption (22.7 kWh kg-1), and high turnover frequency (TOF) (0.0350 min-1), demonstrating excellent dehalogenation performance. Spiking experiments and density functional theory (DFT) verified that Co-N4 was the active site and had the lowest energy barrier for forming atomic hydrogen (H*) (ΔGH*). Capture experiments, electron paramagnetic resonance (EPR), electrochemical tests, and in situ Fourier transform infrared (FTIR) proved that H* and direct electron transfer were responsible for dehalogenation. Toxicity assessment indicated that FLO toxicity decreased significantly after dehalogenation. This work develops a non-noble metal catalyst with broad application prospects in electrocatalytic dehalogenation.
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Affiliation(s)
- Ge Song
- Key Laboratory of Pollution Process and Environmental Criteria, Ministry of Education, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Advanced Water Treatment Technology International Joint Research Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Huizhong Wu
- Key Laboratory of Pollution Process and Environmental Criteria, Ministry of Education, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Advanced Water Treatment Technology International Joint Research Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Jiana Jing
- Key Laboratory of Pollution Process and Environmental Criteria, Ministry of Education, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Advanced Water Treatment Technology International Joint Research Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Xuyang Zhang
- Key Laboratory of Pollution Process and Environmental Criteria, Ministry of Education, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Advanced Water Treatment Technology International Joint Research Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Xuechun Wang
- Key Laboratory of Pollution Process and Environmental Criteria, Ministry of Education, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Advanced Water Treatment Technology International Joint Research Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Shuaishuai Li
- Key Laboratory of Pollution Process and Environmental Criteria, Ministry of Education, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Advanced Water Treatment Technology International Joint Research Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Minghua Zhou
- Key Laboratory of Pollution Process and Environmental Criteria, Ministry of Education, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Tianjin Advanced Water Treatment Technology International Joint Research Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
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5
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Lokesh S, Lard ML, Cook RL, Yang Y. Critical Role of Semiquinones in Reductive Dehalogenation. Environ Sci Technol 2023; 57:14218-14225. [PMID: 37668505 DOI: 10.1021/acs.est.3c03981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Quinones and products of their redox reactions (hydroquinones and semiquinones) have been suggested as important players in the reductive dehalogenation of organohalogens mediated by natural and pyrogenic organic matter, although based on limited direct evidence. This study focused on the reductive dehalogenation of a model organohalogen (triclosan) by 1,4-benzohydroquinone (H2Q). In the presence of H2Q only, degradation of triclosan does not occur within the experimental period (up to 288 h); however, it takes place in the presence of H2Q and FeCl3 under anoxic conditions at pH 5 and 7 (above the pKa of SQ = 4.1) only to be halted in the presence of dissolved oxygen. Kinetic simulation and thermodynamic calculations indicated that benzosemiquinone (SQ-) is responsible for the reductive degradation of triclosan, with the fitted rate constant for the reaction between SQ- and triclosan being 317 M-2 h-1. The critical role of semiquinones in reductive dehalogenation can be relevant to a wide range of quinones in natural and engineering systems based on the reported oxidation-reduction potentials of quinones/semiquinones and semiquinones/hydroquinones and supported by experiments with additional model hydroquinones.
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Affiliation(s)
- Srinidhi Lokesh
- Department of Civil and Environmental Engineering, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | - Myron L Lard
- Department of Chemistry, Louisiana State University, 307 Choppin Hall, Baton Rouge, Louisiana 70803, United States
| | - Robert L Cook
- Department of Chemistry, Louisiana State University, 307 Choppin Hall, Baton Rouge, Louisiana 70803, United States
| | - Yu Yang
- Department of Civil and Environmental Engineering, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557, United States
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6
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Kamenická B, Švec P, Weidlich T. Separation of Anionic Chlorinated Dyes from Polluted Aqueous Streams Using Ionic Liquids and Their Subsequent Recycling. Int J Mol Sci 2023; 24:12235. [PMID: 37569613 PMCID: PMC10418802 DOI: 10.3390/ijms241512235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
The effect of ionic liquids on the separation of chlorinated anionic dyes such as Mordant Blue 9 (MB9) or Acid Yellow 17 (AY17) via ion exchange has been investigated in model aqueous solutions that simulate wastewater from the textile dyeing industry. The effect of ionic liquids chemical nature on the separation efficiency of mentioned dyes has been compared. It was found that especially ionic liquid based on quaternary ammonium salts comprising two or three long alkyl chains bound to the quaternary ammonium nitrogen (typically benzalkonium chloride or Aliquat 336) are very effective for the separation of both studied MB9 and AY17 from aqueous solution. In addition, the innovative technique has been developed for the reactivation of spent ionic liquids which is based on the chemical reduction of the formed ion pairs using NaBH4/NiSO4, NaBH4/Na2S2O5 or Raney Al-Ni alloy/NaOH. Thus, only NaBH4/NiSO4 in co-action with Al-Ni alloy enables both effective reduction of the azo bond and subsequent hydrodechlorination of emerging chlorinated aromatic amines. The efficiency of tested dyes separation or regeneration of ion pairs was evaluated by determination of the absorbance at wavelength of the maximum absorbance, of the Chemical Oxidation Demand (COD), and of the Adsorbables Organically bound Halogens (AOX). The formation of ion pairs or products of reduction and hydrodechlorination of these ion pairs has been studied using the 1H NMR and LC-MS techniques.
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Affiliation(s)
- Barbora Kamenická
- Chemical Technology Group, Institute of Environmental and Chemical Engineering, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10 Pardubice, Czech Republic;
| | - Petr Švec
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10 Pardubice, Czech Republic;
| | - Tomáš Weidlich
- Chemical Technology Group, Institute of Environmental and Chemical Engineering, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10 Pardubice, Czech Republic;
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7
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Łomża P, Krucoń T, Tabernacka A. Potential of Microbial Communities to Perform Dehalogenation Processes in Natural and Anthropogenically Modified Environments-A Metagenomic Study. Microorganisms 2023; 11:1702. [PMID: 37512875 PMCID: PMC10385969 DOI: 10.3390/microorganisms11071702] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/15/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Halogenated organic compounds (HOCs) pose a serious problem for the environment. Many are highly toxic and accumulate both in soil and in organisms. Their biological transformation takes place by dehalogenation, in which the halogen substituents are detached from the carbon in the organic compound by enzymes produced by microorganisms. This increases the compounds' water solubility and bioavailability, reduces toxicity, and allows the resulting compound to become more susceptible to biodegradation. The microbial halogen cycle in soil is an important part of global dehalogenation processes. The aim of the study was to examine the potential of microbial communities inhabiting natural and anthropogenically modified environments to carry out the dehalogenation process. The potential of microorganisms was assessed by analyzing the metagenomes from a natural environment (forest soils) and from environments subjected to anthropopression (agricultural soil and sludge from wastewater treatment plants). Thirteen genes encoding enzymes with dehalogenase activity were identified in the metagenomes of both environments, among which, 2-haloacid dehalogenase and catechol 2,3-dioxygenase were the most abundant genes. Comparative analysis, based on comparing taxonomy, identified genes, total halogens content and content of DDT derivatives, demonstrated the ability of microorganisms to transform HOCs in both environments, indicating the presence of these compounds in the environment for a long period of time and the adaptive need to develop mechanisms for their detoxification. Metagenome analyses and comparative analyses indicate the genetic potential of microorganisms of both environments to carry out dehalogenation processes, including dehalogenation of anthropogenic HOCs.
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Affiliation(s)
- Pola Łomża
- Department of Biology, Faculty of Building Services, Hydro and Environmental Engineering, Warsaw University of Technology, 20 Nowowiejska Street, 00-653 Warsaw, Poland
| | - Tomasz Krucoń
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology, University of Warsaw, 1 Miecznikowa Street, 02-089 Warsaw, Poland
| | - Agnieszka Tabernacka
- Department of Biology, Faculty of Building Services, Hydro and Environmental Engineering, Warsaw University of Technology, 20 Nowowiejska Street, 00-653 Warsaw, Poland
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Mohana Rangan S, Rao S, Robles A, Mouti A, LaPat-Polasko L, Lowry GV, Krajmalnik-Brown R, Delgado AG. Decoupling Fe 0 Application and Bioaugmentation in Space and Time Enables Microbial Reductive Dechlorination of Trichloroethene to Ethene: Evidence from Soil Columns. Environ Sci Technol 2023; 57:4167-4179. [PMID: 36866930 PMCID: PMC10018760 DOI: 10.1021/acs.est.2c06433] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/28/2022] [Accepted: 02/14/2023] [Indexed: 06/06/2023]
Abstract
Fe0 is a powerful chemical reductant with applications for remediation of chlorinated solvents, including tetrachloroethene and trichloroethene. Its utilization efficiency at contaminated sites is limited because most of the electrons from Fe0 are channeled to the reduction of water to H2 rather than to the reduction of the contaminants. Coupling Fe0 with H2-utilizing organohalide-respiring bacteria (i.e., Dehalococcoides mccartyi) could enhance trichloroethene conversion to ethene while maximizing Fe0 utilization efficiency. Columns packed with aquifer materials have been used to assess the efficacy of a treatment combining in space and time Fe0 and aD. mccartyi-containing culture (bioaugmentation). To date, most column studies documented only partial conversion of the solvents to chlorinated byproducts, calling into question the feasibility of Fe0 to promote complete microbial reductive dechlorination. In this study, we decoupled the application of Fe0 in space and time from the addition of organic substrates andD. mccartyi-containing cultures. We used a column containing soil and Fe0 (at 15 g L-1 in porewater) and fed it with groundwater as a proxy for an upstream Fe0 injection zone dominated by abiotic reactions and biostimulated/bioaugmented soil columns (Bio-columns) as proxies for downstream microbiological zones. Results showed that Bio-columns receiving reduced groundwater from the Fe0-column supported microbial reductive dechlorination, yielding up to 98% trichloroethene conversion to ethene. The microbial community in the Bio-columns established with Fe0-reduced groundwater also sustained trichloroethene reduction to ethene (up to 100%) when challenged with aerobic groundwater. This study supports a conceptual model where decoupling the application of Fe0 and biostimulation/bioaugmentation in space and/or time could augment microbial trichloroethene reductive dechlorination, particularly under oxic conditions.
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Affiliation(s)
- Srivatsan Mohana Rangan
- School
of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona 85281, United States
- Biodesign
Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona 85287, United States
- Center
for Bio-Mediated and Bio-Inspired Geotechnics (CBBG), Arizona State University, Tempe, Arizona 85281, United States
- Biodesign
Center for Health Through Microbiomes, Arizona
State University, Tempe, Arizona 85287, United States
| | - Shefali Rao
- School
of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona 85281, United States
- Biodesign
Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona 85287, United States
- Center
for Bio-Mediated and Bio-Inspired Geotechnics (CBBG), Arizona State University, Tempe, Arizona 85281, United States
| | - Aide Robles
- School
of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona 85281, United States
- Biodesign
Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona 85287, United States
- Center
for Bio-Mediated and Bio-Inspired Geotechnics (CBBG), Arizona State University, Tempe, Arizona 85281, United States
| | - Aatikah Mouti
- Biodesign
Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona 85287, United States
| | | | - Gregory V. Lowry
- Center
for Environmental Implications of Nanotechnology (CEINT), Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Department
of Civil & Environmental Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Rosa Krajmalnik-Brown
- School
of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona 85281, United States
- Biodesign
Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona 85287, United States
- Center
for Bio-Mediated and Bio-Inspired Geotechnics (CBBG), Arizona State University, Tempe, Arizona 85281, United States
- Biodesign
Center for Health Through Microbiomes, Arizona
State University, Tempe, Arizona 85287, United States
| | - Anca G. Delgado
- School
of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona 85281, United States
- Biodesign
Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona 85287, United States
- Center
for Bio-Mediated and Bio-Inspired Geotechnics (CBBG), Arizona State University, Tempe, Arizona 85281, United States
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9
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Horna-Gray I, Lopez NA, Ahn Y, Saks B, Girer N, Hentschel U, McCarthy PJ, Kerkhof LJ, Häggblom MM. Desulfoluna spp. form a cosmopolitan group of anaerobic dehalogenating bacteria widely distributed in marine sponges. FEMS Microbiol Ecol 2022; 98:6596282. [PMID: 35641184 DOI: 10.1093/femsec/fiac063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 05/18/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
Host-specific microbial communities thrive within sponge tissues and this association between sponge and associated microbiota may be driven by the organohalogen chemistry of the sponge animal. Several sponge species produce diverse organobromine secondary metabolites (e.g. brominated phenolics, indoles, and pyrroles) that may function as a chemical defense against microbial fouling, infection or predation. In this study, anaerobic cultures prepared from marine sponges were amended with 2,6-dibromophenol as the electron acceptor and short chain organic acids as electron donors. We observed reductive dehalogenation from diverse sponge species collected at disparate temperate and tropical waters suggesting that biogenic organohalides appear to enrich for populations of dehalogenating microorganisms in the sponge animal. Further enrichment by successive transfers with 2,6-dibromophenol as the sole electron acceptor demonstrated the presence of dehalogenating bacteria in over 20 sponge species collected from temperate and tropical ecoregions in the Atlantic and Pacific Oceans and the Mediterranean Sea. The enriched dehalogenating strains were closely related to Desulfoluna spongiiphila and Desulfoluna butyratoxydans, suggesting a cosmopolitan association between Desulfoluna spp. and various marine sponges. In vivo reductive dehalogenation in intact sponges was also demonstrated. Organobromide-rich sponges may thus provide a specialized habitat for organohalide-respiring microbes and D. spongiiphila and/or its close relatives are responsible for reductive dehalogenation in geographically widely distributed sponge species.
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Affiliation(s)
- Isabel Horna-Gray
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
| | - Nora A Lopez
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA.,Department of Marine and Coastal Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
| | - Youngbeom Ahn
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA.,Division of Microbiology , National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Brandon Saks
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
| | - Nathaniel Girer
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
| | - Ute Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Peter J McCarthy
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Boca Raton, FL, USA
| | - Lee J Kerkhof
- Department of Marine and Coastal Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
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10
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Abstract
Thousands of heavily fluorinated chemicals are found in the environment, impact human and ecosystem health, and are relatively resistant to biological and chemical degradation. Their persistence in the environment is due to the inability of most microorganisms to biodegrade them. Only a very few examples of polyfluorinated compound biodegradation are known, and the reported rates are very low. This has been mostly attributed to the low chemical reactivity of the C-F bond. This Perspective goes beyond that explanation to highlight microbiological reasons why polyfluorinated compounds resist metabolism. The evolutionary and physiological impediments must be appreciated to better find, study, and harness microbes that degrade polyfluorinated compounds.
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11
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Eisenreich F, Kuster THR, van Krimpen D, Palmans ARA. Photoredox-Catalyzed Reduction of Halogenated Arenes in Water by Amphiphilic Polymeric Nanoparticles. Molecules 2021; 26:5882. [PMID: 34641426 PMCID: PMC8512223 DOI: 10.3390/molecules26195882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 01/16/2023] Open
Abstract
The use of organic photoredox catalysts provides new ways to perform metal-free reactions controlled by light. While these reactions are usually performed in organic media, the application of these catalysts at ambient temperatures in aqueous media is of considerable interest. We here compare the activity of two established organic photoredox catalysts, one based on 10-phenylphenothiazine (PTH) and one based on an acridinium dye (ACR), in the light-activated dehalogenation of aromatic halides in pure water. Both PTH and ACR were covalently attached to amphiphilic polymers that are designed to form polymeric nanoparticles with hydrodynamic diameter DH ranging between 5 and 11 nm in aqueous solution. Due to the hydrophobic side groups that furnish the interior of these nanoparticles after hydrophobic collapse, water-insoluble reagents can gather within the nanoparticles at high local catalyst and substrate concentrations. We evaluated six different amphiphilic polymeric nanoparticles to assess the effect of polymer length, catalyst loading and nature of the catalyst (PTH or ACR) in the dechlorination of a range of aromatic chlorides. In addition, we investigate the selectivity of both catalysts for reducing different types of aryl-halogen bonds present in one molecule, as well as the activity of the catalysts for C-C cross-coupling reactions. We find that all polymer-based catalysts show high activity for the reduction of electron-poor aromatic compounds. For electron-rich compounds, the ACR-based catalyst is more effective than PTH. In the selective dehalogenation reactions, the order of bond stability is C-Cl > C-Br > C-I irrespective of the catalyst applied. All in all, both water-compatible systems show good activity in water, with ACR-based catalysts being slightly more efficient for more resilient substrates.
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Affiliation(s)
| | | | | | - Anja R. A. Palmans
- Laboratory of Macromolecular and Organic Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands; (F.E.); (T.H.R.K.); (D.v.K.)
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12
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Abstract
Cytochrome P450 enzymes, or P450s, are haem monooxygenases renowned for their ability to insert one atom from molecular oxygen into an exceptionally broad range of substrates while reducing the other atom to water. However, some substrates including many organohalide and nitro compounds present little or no opportunity for oxidation. Under hypoxic conditions P450s can perform reductive reactions, contributing electrons to drive reductive elimination reactions. P450s can catalyse dehalogenation and denitration of a range of environmentally persistent pollutants including halogenated hydrocarbons and nitroamine explosives. P450-mediated reductive dehalogenations were first discovered in the context of human pharmacology but have since been observed in a variety of organisms. Additionally, P450-mediated reductive denitration of synthetic explosives has been discovered in bacteria that inhabit contaminated soils. This review will examine the distribution of P450-mediated reductive dehalogenations and denitrations in nature and discuss synthetic biology approaches to developing P450-based reagents for bioremediation.
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Affiliation(s)
- James B. Y. H. Behrendorff
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Synthetic Biology Future Science Platform, Canberra, ACT, Australia
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13
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Williams CK, Lashgari A, Devi N, Ang M, Chaturvedi A, Dhungana P, Jiang JJ. Hydrodechlorination of Dichloromethane by a Metal-Free Triazole-Porphyrin Electrocatalyst: Demonstration of Main-Group Element Electrocatalysis*. Chemistry 2021; 27:6240-6246. [PMID: 33476410 DOI: 10.1002/chem.202005012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Indexed: 01/17/2023]
Abstract
In this work, the electrocatalytic reduction of dichloromethane (CH2 Cl2 ) into hydrocarbons involving a main group element-based molecular triazole-porphyrin electrocatalyst H2PorT8 is reported. This catalyst converted CH2 Cl2 in acetonitrile to various hydrocarbons (methane, ethane, and ethylene) with a Faradaic efficiency of 70 % and current density of -13 mA cm-2 at a potential of -2.2 V vs. Fc/Fc+ using water as a proton source. The findings of this study and its mechanistic interpretations demonstrated that H2PorT8 was an efficient and stable catalyst for the hydrodechlorination of CH2 Cl2 and that main group catalysts could be potentially used for exploring new catalytic reaction mechanisms.
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Affiliation(s)
- Caroline K Williams
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio, 45221-0172, United States
| | - Amir Lashgari
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio, 45221-0172, United States
| | - Nilakshi Devi
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio, 45221-0172, United States
| | - Marcus Ang
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio, 45221-0172, United States
| | - Ashwin Chaturvedi
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio, 45221-0172, United States
| | - Pranita Dhungana
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio, 45221-0172, United States
| | - Jianbing Jimmy Jiang
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, Ohio, 45221-0172, United States
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14
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Maucourt B, Vuilleumier S, Bringel F. Transcriptional regulation of organohalide pollutant utilisation in bacteria. FEMS Microbiol Rev 2020; 44:189-207. [PMID: 32011697 DOI: 10.1093/femsre/fuaa002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 01/31/2020] [Indexed: 12/13/2022] Open
Abstract
Organohalides are organic molecules formed biotically and abiotically, both naturally and through industrial production. They are usually toxic and represent a health risk for living organisms, including humans. Bacteria capable of degrading organohalides for growth express dehalogenase genes encoding enzymes that cleave carbon-halogen bonds. Such bacteria are of potential high interest for bioremediation of contaminated sites. Dehalogenase genes are often part of gene clusters that may include regulators, accessory genes and genes for transporters and other enzymes of organohalide degradation pathways. Organohalides and their degradation products affect the activity of regulatory factors, and extensive genome-wide modulation of gene expression helps dehalogenating bacteria to cope with stresses associated with dehalogenation, such as intracellular increase of halides, dehalogenase-dependent acid production, organohalide toxicity and misrouting and bottlenecks in metabolic fluxes. This review focuses on transcriptional regulation of gene clusters for dehalogenation in bacteria, as studied in laboratory experiments and in situ. The diversity in gene content, organization and regulation of such gene clusters is highlighted for representative organohalide-degrading bacteria. Selected examples illustrate a key, overlooked role of regulatory processes, often strain-specific, for efficient dehalogenation and productive growth in presence of organohalides.
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Affiliation(s)
- Bruno Maucourt
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Stéphane Vuilleumier
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Françoise Bringel
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
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15
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Hayoun K, Geersens E, Laczny CC, Halder R, Lázaro Sánchez C, Manna A, Bringel F, Ryckelynck M, Wilmes P, Muller EEL, Alpha-Bazin B, Armengaud J, Vuilleumier S. Dichloromethane Degradation Pathway from Unsequenced Hyphomicrobium sp. MC8b Rapidly Explored by Pan-Proteomics. Microorganisms 2020; 8:E1876. [PMID: 33260855 DOI: 10.3390/microorganisms8121876] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 12/23/2022] Open
Abstract
Several bacteria are able to degrade the major industrial solvent dichloromethane (DCM) by using the conserved dehalogenase DcmA, the only system for DCM degradation characterised at the sequence level so far. Using differential proteomics, we rapidly identified key determinants of DCM degradation for Hyphomicrobium sp. MC8b, an unsequenced facultative methylotrophic DCM-degrading strain. For this, we designed a pan-proteomics database comprising the annotated genome sequences of 13 distinct Hyphomicrobium strains. Compared to growth with methanol, growth with DCM induces drastic changes in the proteome of strain MC8b. Dichloromethane dehalogenase DcmA was detected by differential pan-proteomics, but only with poor sequence coverage, suggesting atypical characteristics of the DCM dehalogenation system in this strain. More peptides were assigned to DcmA by error-tolerant search, warranting subsequent sequencing of the genome of strain MC8b, which revealed a highly divergent set of dcm genes in this strain. This suggests that the dcm enzymatic system is less strongly conserved than previously believed, and that substantial molecular evolution of dcm genes has occurred beyond their horizontal transfer in the bacterial domain. Our study showed the power of pan-proteomics for quick characterization of new strains belonging to branches of the Tree of Life that are densely genome-sequenced.
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16
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Stolz S, Di Giovannantonio M, Urgel JI, Sun Q, Kinikar A, Borin Barin G, Bommert M, Fasel R, Widmer R. Reversible Dehalogenation in On-Surface Aryl-Aryl Coupling. Angew Chem Int Ed Engl 2020; 59:14106-14110. [PMID: 32338418 DOI: 10.1002/anie.202005443] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Indexed: 11/05/2022]
Abstract
In the emerging field of on-surface synthesis, dehalogenative aryl-aryl coupling is unarguably the most prominent tool for the fabrication of covalently bonded carbon-based nanomaterials. Despite its importance, the reaction kinetics are still poorly understood. Here we present a comprehensive temperature-programmed x-ray photoelectron spectroscopy investigation of reaction kinetics and energetics in the prototypical on-surface dehalogenative polymerization of 4,4''-dibromo-p-terphenyl into poly(para-phenylene) on two coinage metal surfaces, Cu(111) and Au(111). We find clear evidence for reversible dehalogenation on Au(111), which is inhibited on Cu(111) owing to the formation of organometallic intermediates. The incorporation of reversible dehalogenation in the reaction rate equations leads to excellent agreement with experimental data and allows extracting the relevant energy barriers. Our findings deepen the mechanistic understanding and call for its reassessment for surface-confined aryl-aryl coupling on the most frequently used metal substrates.
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Affiliation(s)
- Samuel Stolz
- Empa, Swiss Federal Laboratories for Materials Science and Technology, nanotech@surfaces Laboratory, 8600, Dübendorf, Switzerland.,Institute of Physics, École Polytechnique Fédérale de Lausanne, Laboratory of Nanostructures at Surfaces, 1015, Lausanne, Switzerland
| | - Marco Di Giovannantonio
- Empa, Swiss Federal Laboratories for Materials Science and Technology, nanotech@surfaces Laboratory, 8600, Dübendorf, Switzerland
| | - José I Urgel
- Empa, Swiss Federal Laboratories for Materials Science and Technology, nanotech@surfaces Laboratory, 8600, Dübendorf, Switzerland
| | - Qiang Sun
- Empa, Swiss Federal Laboratories for Materials Science and Technology, nanotech@surfaces Laboratory, 8600, Dübendorf, Switzerland
| | - Amogh Kinikar
- Empa, Swiss Federal Laboratories for Materials Science and Technology, nanotech@surfaces Laboratory, 8600, Dübendorf, Switzerland
| | - Gabriela Borin Barin
- Empa, Swiss Federal Laboratories for Materials Science and Technology, nanotech@surfaces Laboratory, 8600, Dübendorf, Switzerland
| | - Max Bommert
- Empa, Swiss Federal Laboratories for Materials Science and Technology, nanotech@surfaces Laboratory, 8600, Dübendorf, Switzerland
| | - Roman Fasel
- Empa, Swiss Federal Laboratories for Materials Science and Technology, nanotech@surfaces Laboratory, 8600, Dübendorf, Switzerland.,Department of Chemistry and Biochemistry, University of Bern, 3012, Bern, Switzerland
| | - Roland Widmer
- Empa, Swiss Federal Laboratories for Materials Science and Technology, nanotech@surfaces Laboratory, 8600, Dübendorf, Switzerland
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17
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Liu J, Adrian L, Häggblom MM. Transcriptomic and Proteomic Responses of the Organohalide-Respiring Bacterium Desulfoluna spongiiphila to Growth with 2,6-Dibromophenol as the Electron Acceptor. Appl Environ Microbiol 2020; 86:e02146-19. [PMID: 31836581 PMCID: PMC7028966 DOI: 10.1128/aem.02146-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/10/2019] [Indexed: 01/31/2023] Open
Abstract
Organohalide respiration is an important process in the global halogen cycle and for bioremediation. In this study, we compared the global transcriptomic and proteomic analyses of Desulfoluna spongiiphila strain AA1, an organohalide-respiring member of the Desulfobacterota isolated from a marine sponge, with 2,6-dibromophenol or with sulfate as an electron acceptor. The most significant difference of the transcriptomic analysis was the expression of one reductive dehalogenase gene cluster (rdh16), which was significantly upregulated with the addition of 2,6-dibromophenol. The corresponding protein, reductive dehalogenase RdhA16032, was detected in the proteome under treatment with 2,6-dibromophenol but not with sulfate only. There was no significant difference in corrinoid biosynthesis gene expression levels between the two treatments, indicating that the production of corrinoid in D. spongiiphila is constitutive or not specific for organohalide versus sulfate respiration. Electron-transporting proteins or mediators unique for reductive dehalogenation were not revealed in our analysis, and we hypothesize that reductive dehalogenation may share an electron-transporting system with sulfate reduction. The metabolism of D. spongiiphila, predicted from transcriptomic and proteomic results, demonstrates high metabolic versatility and provides insights into the survival strategies of a marine sponge symbiont in an environment rich in organohalide compounds and other secondary metabolites.IMPORTANCE Respiratory reductive dehalogenation is an important process in the overall cycling of both anthropogenic and natural organohalide compounds. Marine sponges produce a vast array of bioactive compounds as secondary metabolites, including diverse halogenated compounds that may enrich for dehalogenating bacteria. Desulfoluna spongiiphila strain AA1 was originally enriched and isolated from the marine sponge Aplysina aerophoba and can grow with both brominated compounds and sulfate as electron acceptors for respiration. An understanding of the overall gene expression and the protein production profile in response to organohalides is needed to identify the full complement of genes or enzymes involved in organohalide respiration. Elucidating the metabolic capacity of this sponge-associated bacterium lays the foundation for understanding how dehalogenating bacteria may control the fate of organohalide compounds in sponges and their role in a symbiotic organobromine cycle.
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Affiliation(s)
- Jie Liu
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Lorenz Adrian
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- Fachgebiet Geobiotechnologie, Technische Universität Berlin, Berlin, Germany
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, USA
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18
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Ito K, Takagi K, Kataoka R, Kiyota H, Iwasaki A. Dissipation, dehalogenation, and denitration of chloroaromatic compounds by Nocardioides sp. strain PD653: Characterization of the substrate specificity. J Pestic Sci 2019; 44:171-176. [PMID: 31530974 PMCID: PMC6718357 DOI: 10.1584/jpestics.d19-024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 05/21/2019] [Indexed: 06/01/2023]
Abstract
The substrate range of Nocardioides sp. strain PD653, capable of mineralizing hexachlorobenzene, was investigated based on the dissipation of substrates and the liberation of halogen ions. Strain PD653 dehalogenated 10 out of 18 halophenol congeners; however, it could dehalogenate only hexachlorobenzene out of seven halobenzene congeners tested. Moreover, dehalogenation activities were shown for chloronitrobenzenes, along with an increase in the number of substituted chlorine atoms except for 2,3,4,5-tetrachloro-1-nitrobenzene. These results suggested that this strain might be applicable to remediate soil contaminated with these persistent chloroaromatic compounds.
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Affiliation(s)
- Koji Ito
- Hazardous Chemical Division, Institute for Agro-Environmental Sciences, NARO, Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Kazuhiro Takagi
- Hazardous Chemical Division, Institute for Agro-Environmental Sciences, NARO, Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Ryota Kataoka
- Department of Environmental Sciences, University of Yamanashi, Takeda, Kofu, Yamanashi 400–8510, Japan
| | - Hiromasa Kiyota
- Graduate school of Environmental and Life Science, Okayama university, Tsushima, Okayama, Okayama 700–8530, Japan
| | - Akio Iwasaki
- Juntendo Medical Technology Innovation Center, Juntendo University, Hongo, Bunkyo-ku, Tokyo, 113–8421, Japan
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19
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Abstract
The responses of bacterial communities to halocarbon were examined using a 28-d incubation of bromoform- and methanol-enriched subarctic surface seawater. Significant increases were observed in dibromomethane concentrations and bacterial 16S rRNA gene copy numbers in the treated substrates incubated for 13 d. The accumulated bacterial community was investigated by denaturing gradient gel electrophoresis and amplicon analyses. The dominant genotypes corresponded to the genera Roseobacter, Lentibacter, and Amylibacter; the family Flavobacteriaceae; and the phylum Planctomycetes, including methylotrophs of the genus Methylophaga and the family Methylophilaceae. Therefore, various phylotypes responded along with the dehalogenation processes in subarctic seawater.
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Affiliation(s)
- Takafumi Kataoka
- Faculty of Marine Science and Technology, Fukui Prefectural University
| | - Atsushi Ooki
- Faculty of Fisheries Sciences, Hokkaido University
| | - Daiki Nomura
- Faculty of Fisheries Sciences, Hokkaido University
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20
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Wang Y, Davis I, Shin I, Wherritt DJ, Griffith WP, Dornevil K, Colabroy KL, Liu A. Biocatalytic Carbon-Hydrogen and Carbon-Fluorine Bond Cleavage through Hydroxylation Promoted by a Histidyl-Ligated Heme Enzyme. ACS Catal 2019; 9:4764-4776. [PMID: 31355048 DOI: 10.1021/acscatal.9b00231] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
LmbB2 is a peroxygenase-like enzyme that hydroxylates L-tyrosine to L-3,4-dihydroxyphenylalanine (DOPA) in the presence of hydrogen peroxide. However, its heme cofactor is ligated by a proximal histidine, not cysteine. We show that LmbB2 can oxidize L-tyrosine analogs with ring-deactivated substituents such as 3-nitro-, fluoro-, chloro-, iodo-L-tyrosine. We also found that the 4-hydroxyl group of the substrate is essential for reacting with the heme-based oxidant and activating the aromatic C-H bond. The most interesting observation of this study was obtained with 3-fluoro-L-tyrosine as a substrate and mechanistic probe. The LmbB2-mediated catalytic reaction yielded two hydroxylated products with comparable populations, i.e., oxidative C-H bond cleavage at C5 to generate 3-fluoro-5-hydroxyl-L-tyrosine and oxygenation at C3 concomitant with a carbon-fluorine bond cleavage to yield DOPA and fluoride. An iron protein-mediated hydroxylation on both C-H and C-F bonds with multiple turnovers is unprecedented. Thus, this finding reveals a significant potential of biocatalysis in C-H/C-X bond (X = halogen) cleavage. Further 18O-labeling results suggest that the source of oxygen for hydroxylation is a peroxide, and that a commonly expected oxidation by a high-valent iron intermediate followed by hydrolysis is not supported for the C-F bond cleavage. Instead, the C-F bond cleavage is proposed to be initiated by a nucleophilic aromatic substitution mediated by the iron-hydroperoxo species. Based on the experimental results, two mechanisms are proposed to explain how LmbB2 hydroxylates the substrate and cleaves C-H/C-F bond. This study broadens the understanding of heme enzyme catalysis and sheds light on enzymatic applications in medicinal and environmental fields.
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Affiliation(s)
- Yifan Wang
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
| | - Ian Davis
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
| | - Inchul Shin
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
| | - Daniel J. Wherritt
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
| | - Wendell P. Griffith
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
| | - Kednerlin Dornevil
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
| | - Keri L. Colabroy
- Department of Chemistry, Muhlenberg College, Allentown, Pennsylvania 18104, United States
| | - Aimin Liu
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
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21
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Shehu D, Alias Z. Dechlorination of polychlorobiphenyl degradation metabolites by a recombinant glutathione S-transferase from Acidovorax sp. KKS102. FEBS Open Bio 2019; 9:408-419. [PMID: 30868049 PMCID: PMC6396153 DOI: 10.1002/2211-5463.12405] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 01/25/2018] [Accepted: 02/05/2018] [Indexed: 11/07/2022] Open
Abstract
A glutathione S-transferase (GST) with a potential dehalogenation function against various organochlorine substrates was identified from a polychlorobiphenyl (PCB)-degrading organism, Acidovorax sp. KKS102. A homolog of the gene BphK (biphenyl upper pathway K), named BphK-KKS, was cloned, purified and biochemically characterized. Bioinformatic analysis indicated several conserved amino acids that participated in the catalytic activity of the enzyme, and site-directed mutagenesis of these conserved amino acids revealed their importance in the enzyme's catalytic activity. The wild-type and mutant (C10F, K107T and A180P) recombinant proteins displayed wider substrate specificity. The wild-type recombinant GST reacted towards 1-chloro-2,4-dinitrobenzene (CDNB), ethacrynic acid, hydrogen peroxide and cumene hydroperoxide. The mutated recombinant proteins, however, showed significant variation in specific activities towards the substrates. A combination of a molecular docking study and a chloride ion detection assay showed potential interaction with and a dechlorination function against 2-, 3- and 4-chlorobenzoates (metabolites generated during PCB biodegradation) in addition to some organochlorine pesticides (dichlorodiphenyltrichloroethane, endosulfan and permethrin). It was demonstrated that the behavior of the dechlorinating activities varied among the wild-type and mutant recombinant proteins. Kinetic studies (using CDNB and glutathione) showed that the kinetic parameters K m, V max, K cat and K m/K cat were all affected by the mutations. While C10F and A180P mutants displayed an increase in GST activity and the dechlorination function of the enzyme, the K107T mutant displayed variable results, suggesting a functional role of Lys107 in determining substrate specificity of the enzyme. These results demonstrated that the enzyme should be valuable in the bioremediation of metabolites generated during PCB biodegradation.
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Affiliation(s)
- Dayyabu Shehu
- Institute of Biological Sciences Faculty of Science University of Malaya Kuala Lumpur Malaysia.,Department of Biochemistry College of Health Sciences Bayero University Kano Nigeria
| | - Zazali Alias
- Institute of Biological Sciences Faculty of Science University of Malaya Kuala Lumpur Malaysia
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22
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Tahara K, Pan L, Ono T, Hisaeda Y. Learning from B 12 enzymes: biomimetic and bioinspired catalysts for eco-friendly organic synthesis. Beilstein J Org Chem 2018; 14:2553-2567. [PMID: 30410616 PMCID: PMC6204771 DOI: 10.3762/bjoc.14.232] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 09/13/2018] [Indexed: 01/12/2023] Open
Abstract
Cobalamins (B12) play various important roles in vivo. Most B12-dependent enzymes are divided into three main subfamilies: adenosylcobalamin-dependent isomerases, methylcobalamin-dependent methyltransferases, and dehalogenases. Mimicking these B12 enzyme functions under non-enzymatic conditions offers good understanding of their elaborate reaction mechanisms. Furthermore, bio-inspiration offers a new approach to catalytic design for green and eco-friendly molecular transformations. As part of a study based on vitamin B12 derivatives including heptamethyl cobyrinate perchlorate, we describe biomimetic and bioinspired catalytic reactions with B12 enzyme functions. The reactions are classified according to the corresponding three B12 enzyme subfamilies, with a focus on our recent development on electrochemical and photochemical catalytic systems. Other important reactions are also described, with a focus on radical-involved reactions in terms of organic synthesis.
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Affiliation(s)
- Keishiro Tahara
- Department of Material Science, Graduate School of Material Science, University of Hyogo, 3-2-1, Kouto, Kamigori, Ako 678-1297, Japan
| | - Ling Pan
- Department of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Toshikazu Ono
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Center for Molecular Systems (CMS), Kyushu University, Fukuoka 819-0395, Japan.,PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Yoshio Hisaeda
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Center for Molecular Systems (CMS), Kyushu University, Fukuoka 819-0395, Japan
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23
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Jochum LM, Schreiber L, Marshall IPG, Jørgensen BB, Schramm A, Kjeldsen KU. Single-Cell Genomics Reveals a Diverse Metabolic Potential of Uncultivated Desulfatiglans-Related Deltaproteobacteria Widely Distributed in Marine Sediment. Front Microbiol 2018; 9:2038. [PMID: 30233524 PMCID: PMC6129605 DOI: 10.3389/fmicb.2018.02038] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/13/2018] [Indexed: 11/13/2022] Open
Abstract
Desulfatiglans-related organisms comprise one of the most abundant deltaproteobacterial lineages in marine sediments where they occur throughout the sediment column in a gradient of increasing sulfate and organic carbon limitation with depth. Characterized Desulfatiglans isolates are dissimilatory sulfate reducers able to grow by degrading aromatic hydrocarbons. The ecophysiology of environmental Desulfatiglans-populations is poorly understood, however, possibly utilization of aromatic compounds may explain their predominance in marine subsurface sediments. We sequenced and analyzed seven Desulfatiglans-related single-cell genomes (SAGs) from Aarhus Bay sediments to characterize their metabolic potential with regard to aromatic compound degradation and energy metabolism. The average genome assembly size was 1.3 Mbp and completeness estimates ranged between 20 and 50%. Five of the SAGs (group 1) originated from the sulfate-rich surface part of the sediment while two (group 2) originated from sulfate-depleted subsurface sediment. Based on 16S rRNA gene amplicon sequencing group 2 SAGs represent the more frequent types of Desulfatiglans-populations in Aarhus Bay sediments. Genes indicative of aromatic compound degradation could be identified in both groups, but the two groups were metabolically distinct with regard to energy conservation. Group 1 SAGs carry a full set of genes for dissimilatory sulfate reduction, whereas the group 2 SAGs lacked any genetic evidence for sulfate reduction. The latter may be due to incompleteness of the SAGs, but as alternative energy metabolisms group 2 SAGs carry the genetic potential for growth by acetogenesis and fermentation. Group 1 SAGs encoded reductive dehalogenase genes, allowing them to access organohalides and possibly conserve energy by their reduction. Both groups possess sulfatases unlike their cultured relatives allowing them to utilize sulfate esters as source of organic carbon and sulfate. In conclusion, the uncultivated marine Desulfatiglans populations are metabolically diverse, likely reflecting different strategies for coping with energy and sulfate limitation in the subsurface seabed.
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Affiliation(s)
- Lara M Jochum
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Lars Schreiber
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Ian P G Marshall
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Bo B Jørgensen
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kasper U Kjeldsen
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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24
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Yu J, Hong Z, Yang X, Jiang Y, Jiang Z, Su W. Bromide-assisted chemoselective Heck reaction of 3-bromoindazoles under high-speed ball-milling conditions: synthesis of axitinib. Beilstein J Org Chem 2018; 14:786-795. [PMID: 29719575 PMCID: PMC5905281 DOI: 10.3762/bjoc.14.66] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 03/21/2018] [Indexed: 11/25/2022] Open
Abstract
A mechanically-activated chemoselective Heck coupling for the synthesis of 3-vinylindazoles has been developed with the aid of catalytic amounts of TBAB and NaBr as both dehalogenation restrainer and grinding auxiliary. After tuning of the chemical conditions and mechanical parameters, a series of non-activated 3-bromoindazoles and a broad scope of olefins worked well to give the corresponding coupling products in good to excellent yields. A further application of this protocol was performed in a two-step mechanochemical Heck/Migita cross coupling, which provided a highly efficient route for the synthesis of axitinib.
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Affiliation(s)
- Jingbo Yu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Zikun Hong
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Xinjie Yang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Yu Jiang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Zhijiang Jiang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Weike Su
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, PR China
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25
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Puentes Jácome LA, Edwards EA. A switch of chlorinated substrate causes emergence of a previously undetected native Dehalobacter population in an established Dehalococcoides-dominated chloroethene-dechlorinating enrichment culture. FEMS Microbiol Ecol 2018; 93:4569067. [PMID: 29088371 DOI: 10.1093/femsec/fix141] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/26/2017] [Indexed: 01/08/2023] Open
Abstract
Chlorobenzenes are soil and groundwater pollutants of concern that can be reductively dehalogenated by organohalide-respiring bacteria from the genera Dehalococcoides and Dehalobacter. The bioaugmentation culture KB-1® harbours Dehalococcoides mccartyi spp. that reductively dehalogenate trichloroethene to ethene. It contains more than 30 reductive dehalogenase genes; some of them are highly similar to genes found in the chlorobenzene-respiring Dehalococcoides mccartyi strain CBDB1. We explored the chlorobenzene dehalogenation capability of the KB-1 enrichment culture using 1,2,4-trichlorobenzene (1,2,4-TCB). We achieved adaptation of KB-1 to 1,2,4-TCB that is dehalogenated to a mixture of dichlorobenzenes, and subsequently to monochlorobenzene and benzene. Surprisingly, a native Dehalobacter population, and not a Dehalococcoides population, couples the dechlorination of 1,2,4-TCB to growth achieving an average yield of 1.1 ± 0.6 × 1013 cells per mole of Cl- released. Interestingly, the dechlorination of 1,2,4-TCB occurs alongside the complete dechlorination of trichloroethene to ethene in cultures fed both electron acceptors. Dehalobacter was not previously identified as a major player in KB-1, but its ecological niche was favoured by the introduction of 1,2,4-TCB. Based on 16S rRNA phylogeny, Dehalobacter populations seem to cluster into specialised clades, and are likely undergoing substrate specialisation as a strategy to reduce competition for electron acceptors.
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Affiliation(s)
- Luz A Puentes Jácome
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 1A1, Canada
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26
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Dai Y, Kizjakina K, Campbell AC, Korasick DA, Tanner JJ, Sobrado P. Flavin-N5 Covalent Intermediate in a Nonredox Dehalogenation Reaction Catalyzed by an Atypical Flavoenzyme. Chembiochem 2017; 19:53-57. [PMID: 29116682 DOI: 10.1002/cbic.201700594] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Indexed: 11/05/2022]
Abstract
The flavin-dependent enzyme 2-haloacrylate hydratase (2-HAH) catalyzes the conversion of 2-chloroacrylate, a major component in the manufacture of acrylic polymers, to pyruvate. The enzyme was expressed in Escherichia coli, purified, and characterized. 2-HAH was shown to be monomeric in solution and contained a non-covalent, yet tightly bound, flavin adenine dinucleotide (FAD). Although the catalyzed reaction was redox-neutral, 2-HAH was active only in the reduced state. A covalent flavin-substrate intermediate, consistent with the flavin-acrylate iminium ion, was trapped with cyanoborohydride and characterized by mass spectrometry. Small-angle X-ray scattering was consistent with 2-HAH belonging to the succinate dehydrogenase/fumarate reductase family of flavoproteins. These studies establish 2-HAH as a novel noncanonical flavoenzyme.
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Affiliation(s)
- Yumin Dai
- Department of Biochemistry, Virginia Tech, 360 West Campus Drive, Blacksburg, Virginia, 24061, USA
| | - Karina Kizjakina
- Department of Biochemistry, Virginia Tech, 360 West Campus Drive, Blacksburg, Virginia, 24061, USA
| | - Ashley C Campbell
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, USA
| | - David A Korasick
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, USA
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, USA.,Department of Chemistry, University of Missouri, Columbia, Missouri, 65211, USA
| | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, 360 West Campus Drive, Blacksburg, Virginia, 24061, USA
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27
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Chang Y, Zhang G, Han B, Li H, Hu C, Pang Y, Chang Z, Sun X. Polymer Dehalogenation-Enabled Fast Fabrication of N,S-Codoped Carbon Materials for Superior Supercapacitor and Deionization Applications. ACS Appl Mater Interfaces 2017; 9:29753-29759. [PMID: 28805056 DOI: 10.1021/acsami.7b08181] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Doped carbon materials (DCM) with multiple heteroatoms hold broad interest in electrochemical catalysis and energy storage but require several steps to fabricate, which greatly hinder their practical applications. In this study, a facile strategy is developed to enable the fast fabrication of multiply doped carbon materials via room-temperature dehalogenation of polyvinyl dichloride (PVDC) promoted by KOH with the presence of different organic dopants. A N,S-codoped carbon material (NS-DCM) is demonstratively synthesized using two dopants (dimethylformamide for N doping and dimethyl sulfoxide for S doping). Afterward, the precursive room-temperature NS-DCM with intentionally overdosed KOH is submitted to inert annealing to obtain large specific surface area and high conductivity. Remarkably, NS-DCM annealed at 600 °C (named as 600-NS-DCM), with 3.0 atom % N and 2.4 atom % S, exhibits a very high specific capacitance of 427 F g-1 at 1.0 A g-1 in acidic electrolyte and also keeps ∼60% of capacitance at ultrahigh current density of 100.0 A g-1. Furthermore, capacitive deionization (CDI) measurements reveal that 600-NS-DCM possesses a large desalination capacity of 32.3 mg g-1 (40.0 mg L-1 NaCl) and very good cycling stability. Our strategy of fabricating multiply doped carbon materials can be potentially extended to the synthesis of carbon materials with various combinations of heteroatom doping for broad electrochemical applications.
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Affiliation(s)
- Yingna Chang
- State Key Laboratory of Chemical Resource Engineering, College of Science, Beijing University of Chemical Technology , Beijing 100029, China
| | - Guoxin Zhang
- State Key Laboratory of Chemical Resource Engineering, College of Science, Beijing University of Chemical Technology , Beijing 100029, China
- College of Electrical Engineering and Automation, Shandong University of Science and Technology , Qingdao 266590, China
| | - Biao Han
- State Key Laboratory of Chemical Resource Engineering, College of Science, Beijing University of Chemical Technology , Beijing 100029, China
| | - Haoyuan Li
- State Key Laboratory of Chemical Resource Engineering, College of Science, Beijing University of Chemical Technology , Beijing 100029, China
| | - Cejun Hu
- College of Energy, Beijing University of Chemical Technology , Beijing 100029, China
| | - Yingchun Pang
- State Key Laboratory of Chemical Resource Engineering, College of Science, Beijing University of Chemical Technology , Beijing 100029, China
| | - Zheng Chang
- State Key Laboratory of Chemical Resource Engineering, College of Science, Beijing University of Chemical Technology , Beijing 100029, China
| | - Xiaoming Sun
- State Key Laboratory of Chemical Resource Engineering, College of Science, Beijing University of Chemical Technology , Beijing 100029, China
- College of Energy, Beijing University of Chemical Technology , Beijing 100029, China
- Beijing Advanced Innovation Centre for Soft Matter Science and Engineering, Beijing University of Chemical Technology , Beijing 100029, China
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28
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Chaignaud P, Maucourt B, Weiman M, Alberti A, Kolb S, Cruveiller S, Vuilleumier S, Bringel F. Genomic and Transcriptomic Analysis of Growth-Supporting Dehalogenation of Chlorinated Methanes in Methylobacterium. Front Microbiol 2017; 8:1600. [PMID: 28919881 PMCID: PMC5585157 DOI: 10.3389/fmicb.2017.01600] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 08/07/2017] [Indexed: 11/13/2022] Open
Abstract
Bacterial adaptation to growth with toxic halogenated chemicals was explored in the context of methylotrophic metabolism of Methylobacterium extorquens, by comparing strains CM4 and DM4, which show robust growth with chloromethane and dichloromethane, respectively. Dehalogenation of chlorinated methanes initiates growth-supporting degradation, with intracellular release of protons and chloride ions in both cases. The core, variable and strain-specific genomes of strains CM4 and DM4 were defined by comparison with genomes of non-dechlorinating strains. In terms of gene content, adaptation toward dehalogenation appears limited, strains CM4 and DM4 sharing between 75 and 85% of their genome with other strains of M. extorquens. Transcript abundance in cultures of strain CM4 grown with chloromethane and of strain DM4 grown with dichloromethane was compared to growth with methanol as a reference C1 growth substrate. Previously identified strain-specific dehalogenase-encoding genes were the most transcribed with chlorinated methanes, alongside other genes encoded by genomic islands (GEIs) and plasmids involved in growth with chlorinated compounds as carbon and energy source. None of the 163 genes shared by strains CM4 and DM4 but not by other strains of M. extorquens showed higher transcript abundance in cells grown with chlorinated methanes. Among the several thousand genes of the M. extorquens core genome, 12 genes were only differentially abundant in either strain CM4 or strain DM4. Of these, 2 genes of known function were detected, for the membrane-bound proton translocating pyrophosphatase HppA and the housekeeping molecular chaperone protein DegP. This indicates that the adaptive response common to chloromethane and dichloromethane is limited at the transcriptional level, and involves aspects of the general stress response as well as of a dehalogenation-specific response to intracellular hydrochloric acid production. Core genes only differentially abundant in either strain CM4 or strain DM4 total 13 and 58 CDS, respectively. Taken together, the obtained results suggest different transcriptional responses of chloromethane- and dichloromethane-degrading M. extorquens strains to dehalogenative metabolism, and substrate- and pathway-specific modes of growth optimization with chlorinated methanes.
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Affiliation(s)
- Pauline Chaignaud
- Department of Molecular Genetics, Genomics, and Microbiology, UMR 7156 Université de Strasbourg (UNISTRA)-Centre National de la Recherche ScientifiqueStrasbourg, France.,Department of Ecological Microbiology, University of BayreuthBayreuth, Germany
| | - Bruno Maucourt
- Department of Molecular Genetics, Genomics, and Microbiology, UMR 7156 Université de Strasbourg (UNISTRA)-Centre National de la Recherche ScientifiqueStrasbourg, France
| | - Marion Weiman
- UMR 8030 Centre National de la Recherche Scientifique-CEA, DSV/IG/Genoscope, LABGeMEvry, France
| | - Adriana Alberti
- UMR 8030 Centre National de la Recherche Scientifique-CEA, DSV/IG/Genoscope, LABGeMEvry, France
| | - Steffen Kolb
- Department of Ecological Microbiology, University of BayreuthBayreuth, Germany.,Institute of Landscape Biogeochemistry-Leibniz Centre for Agricultural Landscape Research (ZALF)Müncheberg, Germany
| | - Stéphane Cruveiller
- UMR 8030 Centre National de la Recherche Scientifique-CEA, DSV/IG/Genoscope, LABGeMEvry, France
| | - Stéphane Vuilleumier
- Department of Molecular Genetics, Genomics, and Microbiology, UMR 7156 Université de Strasbourg (UNISTRA)-Centre National de la Recherche ScientifiqueStrasbourg, France
| | - Françoise Bringel
- Department of Molecular Genetics, Genomics, and Microbiology, UMR 7156 Université de Strasbourg (UNISTRA)-Centre National de la Recherche ScientifiqueStrasbourg, France
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29
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de Ruiter G, Carsch KM, Takase MK, Agapie T. Selectivity of C-H versus C-F Bond Oxygenation by Homo- and Heterometallic Fe 4 , Fe 3 Mn, and Mn 4 Clusters. Chemistry 2017; 23:10744-10748. [PMID: 28658508 DOI: 10.1002/chem.201702302] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Indexed: 02/03/2023]
Abstract
A series of tetranuclear [LM3 (HFArPz)3 OM'][OTf]2 (M, M'=Fe or Mn) clusters that displays 3-(2-fluorophenyl)pyrazolate (HFArPz) as bridging ligand is reported. With these complexes, manganese was demonstrated to facilitate C(sp2 )-F bond oxygenation via a putative terminal metal-oxo species. Moreover, the presence of both ortho C(sp2 )-H and C(sp2 )-F bonds in proximity of the apical metal center provided an opportunity to investigate the selectivity of intramolecular C(sp2 )-X bond oxygenation (X=H or F) in these isostructural compounds. With iron as the apical metal center, (M'=Fe) C(sp2 )-F bond oxygenation occur almost exclusively, whereas with manganese (M'=Mn), the opposite reactivity is preferred.
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Affiliation(s)
- Graham de Ruiter
- Department of Chemistry and Chemical Engineering, California Institute of Technology; MC 127-72, Pasadena, California, 91125, USA
| | - Kurtis M Carsch
- Department of Chemistry and Chemical Engineering, California Institute of Technology; MC 127-72, Pasadena, California, 91125, USA
| | - Michael K Takase
- Department of Chemistry and Chemical Engineering, California Institute of Technology; MC 127-72, Pasadena, California, 91125, USA
| | - Theodor Agapie
- Department of Chemistry and Chemical Engineering, California Institute of Technology; MC 127-72, Pasadena, California, 91125, USA
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30
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Hayashi H, Yamaguchi J, Jippo H, Hayashi R, Aratani N, Ohfuchi M, Sato S, Yamada H. Experimental and Theoretical Investigations of Surface-Assisted Graphene Nanoribbon Synthesis Featuring Carbon-Fluorine Bond Cleavage. ACS Nano 2017; 11:6204-6210. [PMID: 28525720 DOI: 10.1021/acsnano.7b02316] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Edge-fluorinated graphene nanoribbons are predicted to exhibit attractive structural and electronic properties, which, however, still need to be demonstrated experimentally. Hence, to provide further experimental insights, an anthracene trimer comprising a partially fluorinated central unit is explored as a precursor molecule, with scanning tunneling microscopy and X-ray photoelectron spectroscopy analyses, indicating the formation of partially edge-fluorinated polyanthrylenes via on-surface reactions after annealing at 350 °C on Au(111) under ultrahigh-vacuum conditions. Further annealing at 400 °C leads to the cyclodehydrogenation of partially edge-fluorinated polyanthrylenes to form graphene nanoribbons, resulting in carbon-fluorine bond cleavage despite its high dissociation energy. Extensive theoretical calculations reveal a defluorination-based reaction mechanism, showing that a critical intermediate structure, obtained as a result of H atom migration to the terminal carbon of a fluorinated anthracene unit in polyanthrylene, plays a crucial role in significantly lowering the activation energy of carbon-fluorine bond dissociation. These results suggest the importance of transient structures in intermediate states for synthesizing edge-fluorinated graphene nanoribbons.
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Affiliation(s)
- Hironobu Hayashi
- Graduate School of Materials Science, Nara Institute of Science and Technology , 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Junichi Yamaguchi
- Fujitsu Laboratories Ltd and Fujitsu Limited , 10-1 Morinosato-Wakamiya, Atsugi, Kanagawa 243-0197, Japan
| | - Hideyuki Jippo
- Fujitsu Laboratories Ltd and Fujitsu Limited , 10-1 Morinosato-Wakamiya, Atsugi, Kanagawa 243-0197, Japan
| | - Ryunosuke Hayashi
- Graduate School of Materials Science, Nara Institute of Science and Technology , 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Naoki Aratani
- Graduate School of Materials Science, Nara Institute of Science and Technology , 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Mari Ohfuchi
- Fujitsu Laboratories Ltd and Fujitsu Limited , 10-1 Morinosato-Wakamiya, Atsugi, Kanagawa 243-0197, Japan
| | - Shintaro Sato
- Fujitsu Laboratories Ltd and Fujitsu Limited , 10-1 Morinosato-Wakamiya, Atsugi, Kanagawa 243-0197, Japan
| | - Hiroko Yamada
- Graduate School of Materials Science, Nara Institute of Science and Technology , 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
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31
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Vatsal AA, Zinjarde SS, RaviKumar A. Phenol Is the Initial Product Formed during Growth and Degradation of Bromobenzene by Tropical Marine Yeast, Yarrowia lipolytica NCIM 3589 via an Early Dehalogenation Step. Front Microbiol 2017; 8:1165. [PMID: 28690604 PMCID: PMC5481318 DOI: 10.3389/fmicb.2017.01165] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 06/07/2017] [Indexed: 11/13/2022] Open
Abstract
Bromobenzene (BrB), a hydrophobic, recalcitrant organic compound, is listed by the environmental protection agencies as an environmental and marine pollutant having hepatotoxic, mutagenic, teratogenic, and carcinogenic effects. The tropical marine yeast Yarrowia lipolytica 3589 was seen to grow aerobically on BrB and displayed a maximum growth rate (μmax) of 0.04 h-1. Furthermore, we also observed an increase in cell size and sedimentation velocity for the cells grown on BrB as compared to the glucose grown cells. The cells attached to the hydrophobic bromobenzene droplets through its hydrophobic and acid–base interactions. The BrB (0.5%, 47.6 mM) was utilized by the cells with the release of a corresponding amount of bromide (12.87 mM) and yielded a cell mass of 1.86 g/L after showing 34% degradation in 96 h. Maximum dehalogenase activity of 16.16 U/mL was seen in the cell free supernatant after 24 h of growth. Identification of metabolites formed as a result of BrB degradation, namely, phenol, catechol, cis, cis muconic acid, and carbon dioxide were determined by LC–MS and GC–MS. The initial attack on bromobenzene by Y. lipolytica cells lead to the transient accumulation of phenol as an early intermediate which is being reported for the first time. Degradation of phenol led to catechol which was degraded by the ortho- cleavage pathway forming cis, cis muconic acid and then to Krebs cycle intermediates eventually leading to CO2 production. The study shows that dehalogenation via an extracellular dehalogenase occurs prior to ring cleavage with phenol as the preliminary degradative compound being produced. The yeast was also able to grow on the degradative products, i.e., phenol and catechol, to varying degrees which would be of potential relevance in the degradation and remediation of xenobiotic environmental bromoaromatic pollutants such as bromobenzene.
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Affiliation(s)
- Aakanksha A Vatsal
- Biochemistry Research Laboratory, Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune UniversityPune, India
| | - Smita S Zinjarde
- Biochemistry Research Laboratory, Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune UniversityPune, India
| | - Ameeta RaviKumar
- Biochemistry Research Laboratory, Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune UniversityPune, India
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Goswami A, Rathi AK, Aparicio C, Tomanec O, Petr M, Pocklanova R, Gawande MB, Varma RS, Zboril R. In Situ Generation of Pd-Pt Core-Shell Nanoparticles on Reduced Graphene Oxide (Pd@Pt/rGO) Using Microwaves: Applications in Dehalogenation Reactions and Reduction of Olefins. ACS Appl Mater Interfaces 2017; 9:2815-2824. [PMID: 28035800 DOI: 10.1021/acsami.6b13138] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Core-shell nanocatalysts are a distinctive class of nanomaterials with varied potential applications in view of their unique structure, composition-dependent physicochemical properties, and promising synergism among the individual components. A one-pot microwave (MW)-assisted approach is described to prepare the reduced graphene oxide (rGO)-supported Pd-Pt core-shell nanoparticles, (Pd@Pt/rGO); spherical core-shell nanomaterials (∼95 nm) with Pd core (∼80 nm) and 15 nm Pt shell were nicely distributed on the rGO matrix in view of the choice of reductant and reaction conditions. The well-characterized composite nanomaterials, endowed with synergism among its components and rGO support, served as catalysts in aromatic dehalogenation reactions and for the reduction of olefins with high yield (>98%), excellent selectivity (>98%) and recyclability (up to 5 times); both Pt/rGO and Pd/rGO and even their physical mixtures showed considerably lower conversions (20 and 57%) in dehalogenation of 3-bromoaniline. Similarly, in the reduction of styrene to ethylbenzene, Pd@Pt core-shell nanoparticles (without rGO support) possess considerably lower conversion (60%) compared to Pd@Pt/rGO. The mechanism of dehalogenation reactions with Pd@Pt/rGO catalyst is discussed with the explicit premise that rGO matrix facilitates the adsorption of the reducing agent, thus enhancing its local concentration and expediting the hydrazine decomposition rate. The versatility of the catalyst has been validated via diverse substrate scope for both reduction and dehalogenation reactions.
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Affiliation(s)
- Anandarup Goswami
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Anuj K Rathi
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Claudia Aparicio
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Ondrej Tomanec
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Martin Petr
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Radka Pocklanova
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Manoj B Gawande
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Rajender S Varma
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Radek Zboril
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , Šlechtitelů 27, 783 71 Olomouc, Czech Republic
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Mazur M, Skrobiszewski A, Gładkowski W, Podkowik M, Bania J, Nawrot J, Klejdysz T, Wawrzeńczyk C. Lactones 46. Synthesis, antifeedant and antibacterial activity of γ-lactones with a p-methoxyphenyl substituent. Pest Manag Sci 2016; 72:489-496. [PMID: 25809724 DOI: 10.1002/ps.4012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 03/09/2015] [Accepted: 03/23/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND Lactones are well known for their biological activity. Grosheimin and repin are potent deterrents against storage pests. The unsaturated lactones have exhibited a wide spectrum of antibacterial activity. In our study we focused on the synthesis and evaluation of the biological activity of anisaldehyde derivatives containing lactone function. RESULTS Four new lactones were synthesized in one-step reductive dehalogenation or dehydrohalogenation reactions. These compounds, together with halolactones synthesized earlier, were tested for their antifeedant activity towards Sitophilus granaries, Trogoderma granarium and Tribolium confusum. The results of the tests showed that the highest activity, comparable with that of azadirachtin, towards all tested pests (total coefficient of deterrence 143.3-183.9) was observed for lactone with a vinyl substituent. The antibacterial activity of these compounds was also evaluated. The most potent lactone was active towards gram-positive bacteria strains. CONCLUSIONS The results of biological tests showed that halogen atom removal significantly increased the antifeedant properties of γ-lactones with a p-methoxyphenyl substituent. Unsaturated lactones are most promising in the context of their possible industrial application as crop protection agents. Further structural modifications of lactones with aromatic rings are needed to find important structural factors increasing the antibacterial activity.
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Affiliation(s)
- Marcelina Mazur
- Department of Chemistry, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Andrzej Skrobiszewski
- Department of Chemistry, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Witold Gładkowski
- Department of Chemistry, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Magdalena Podkowik
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Jacek Bania
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Jan Nawrot
- Institute of Plant Protection - National Reasearch Institute, Poznań, Poland
| | - Tomasz Klejdysz
- Institute of Plant Protection - National Reasearch Institute, Poznań, Poland
| | - Czesław Wawrzeńczyk
- Department of Chemistry, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
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Abstract
Iodothyronine deiodinases are a family of enzymes that remove specific iodine atoms from one of the two aromatic rings in thyroid hormones (THs). They thereby fine-tune local TH concentrations and cellular TH signaling. Deiodinases catalyze a remarkable biochemical reaction, i.e., the reductive elimination of a halogenide from an aromatic ring. In metazoans, deiodinases depend on the rare amino acid selenocysteine. The recent solution of the first experimental structure of a deiodinase catalytic domain allowed for a reappraisal of the many mechanistic and mutagenesis data that had been accumulated over more than 30 years. Hence, the structure generates new impetus for research directed at understanding catalytic mechanism, substrate specificity, and regulation of deiodinases. This review will focus on structural and mechanistic aspects of iodothyronine deiodinases and briefly compare these enzymes with dehalogenases, which catalyze related reactions. A general mechanism for the selenium-dependent deiodinase reaction will be described, which integrates the mouse deiodinase 3 crystal structure and biochemical studies. We will summarize further, sometimes isoform-specific molecular features of deiodinase catalysis and regulation, and we will then discuss available compounds for modulating deiodinase activity for therapeutic purposes.
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Affiliation(s)
| | - Clemens Steegborn
- Institut für Biochemie und MolekularbiologieRheinische Friedrich-Wilhelms-Universität Bonn, Nussallee 11, 53115 Bonn, GermanyLehrstuhl BiochemieUniversität Bayreuth, Universitätsstrasse 30, 95445 Bayreuth, Germany
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Kimura R, Sawayama Y, Nakazaki A, Miyamoto K, Uchiyama M, Nishikawa T. Unexpected metal-free transformation of gem-Dibromomethylenes to ketones under acetylation conditions. Chem Asian J 2015; 10:1035-41. [PMID: 25605400 DOI: 10.1002/asia.201403277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Indexed: 11/10/2022]
Abstract
Novel conditions for the transformation of gem-dibromomethylenes to ketones are described. gem-Dibromo compounds were treated with acetic anhydride and triethylamine in dichloromethane/water at room temperature under an air atmosphere to give the corresponding ketones in moderate yields. A radical mechanism is proposed based on experimental results.
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Affiliation(s)
- Rino Kimura
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601 (Japan), Fax: (+81) 52-789-4111
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Kawai M, Futagami T, Toyoda A, Takaki Y, Nishi S, Hori S, Arai W, Tsubouchi T, Morono Y, Uchiyama I, Ito T, Fujiyama A, Inagaki F, Takami H. High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes. Front Microbiol 2014; 5:80. [PMID: 24624126 PMCID: PMC3939436 DOI: 10.3389/fmicb.2014.00080] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 02/13/2014] [Indexed: 02/01/2023] Open
Abstract
Marine subsurface sediments on the Pacific margin harbor diverse microbial communities even at depths of several hundreds meters below the seafloor (mbsf) or more. Previous PCR-based molecular analysis showed the presence of diverse reductive dehalogenase gene (rdhA) homologs in marine subsurface sediment, suggesting that anaerobic respiration of organohalides is one of the possible energy-yielding pathways in the organic-rich sedimentary habitat. However, primer-independent molecular characterization of rdhA has remained to be demonstrated. Here, we studied the diversity and frequency of rdhA homologs by metagenomic analysis of five different depth horizons (0.8, 5.1, 18.6, 48.5, and 107.0 mbsf) at Site C9001 off the Shimokita Peninsula of Japan. From all metagenomic pools, remarkably diverse rdhA-homologous sequences, some of which are affiliated with novel clusters, were observed with high frequency. As a comparison, we also examined frequency of dissimilatory sulfite reductase genes (dsrAB), key functional genes for microbial sulfate reduction. The dsrAB were also widely observed in the metagenomic pools whereas the frequency of dsrAB genes was generally smaller than that of rdhA-homologous genes. The phylogenetic composition of rdhA-homologous genes was similar among the five depth horizons. Our metagenomic data revealed that subseafloor rdhA homologs are more diverse than previously identified from PCR-based molecular studies. Spatial distribution of similar rdhA homologs across wide depositional ages indicates that the heterotrophic metabolic processes mediated by the genes can be ecologically important, functioning in the organic-rich subseafloor sedimentary biosphere.
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Affiliation(s)
- Mikihiko Kawai
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Nankoku, Japan ; Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan
| | - Taiki Futagami
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Nankoku, Japan ; Department of Bioscience and Biotechnology, Kyushu University Fukuoka, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, Center for Information Biology, National Institute of Genetics Mishima, Japan
| | - Yoshihiro Takaki
- Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan
| | - Shinro Nishi
- Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan
| | - Sayaka Hori
- Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan
| | - Wataru Arai
- Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan
| | - Taishi Tsubouchi
- Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan
| | - Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Nankoku, Japan ; Geobio-Engineering and Technology Group, Submarine Resources Research Project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Nankoku, Japan
| | - Ikuo Uchiyama
- National Institute for Basic Biology, National Institutes of Natural Sciences Okazaki, Japan ; Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies Okazaki, Japan
| | - Takehiko Ito
- Department of Biological Sciences, Tokyo Institute of Technology Yokohama, Japan
| | - Asao Fujiyama
- Comparative Genomics Laboratory, Center for Information Biology, National Institute of Genetics Mishima, Japan
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Nankoku, Japan ; Geobio-Engineering and Technology Group, Submarine Resources Research Project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Nankoku, Japan
| | - Hideto Takami
- Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan
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Kang C, Zhou Y, Du Z, Bian Z, Wang J, Qiu X, Gao L, Sun Y. Dehydrogenation and dehalogenation of amines in MALDI-TOF MS investigated by isotopic labeling. J Mass Spectrom 2013; 48:1318-1324. [PMID: 24338887 DOI: 10.1002/jms.3296] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Revised: 10/05/2013] [Accepted: 10/13/2013] [Indexed: 06/03/2023]
Abstract
Secondary and tertiary amines have been reported to form [M-H](+) that correspond to dehydrogenation in matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). In this investigation, we studied the dehydrogenation of amines in MALDI-TOF MS by isotopic labeling. Aliphatic amines were labeled with deuterium on the methylene of an N-benzyl group, which resulted in the formation of [M-D](+) and [M-H](+) ions by dedeuteration and dehydrogenation, respectively. This method revealed the proton that was removed. The spectra of most tertiary amines with an N-benzyl group showed high-intensity [M-D](+) and [M-H](+) ion peaks, whereas those of secondary amines showed low-intensity ion peaks. Ratios between the peak intensities of [M-D](+) and [M-H](+) greater than 1 suggested chemoselective dehydrogenation at the N-benzyl groups. The presence of an electron donor group on the N-benzyl groups enhanced the selectivity. The dehalogenation of amines with an N-(4-halobenzyl) group was also observed alongside dehydrogenation. The amino ions from dehalogenation can undergo second dehydrogenation. These results provide the first direct evidence about the position at which dehydrogenation of an amine occurs and the first example of dehalogenation of haloaromatic compounds in MALDI-TOF MS. These results should be helpful in the structural identification and elucidation of synthetic and natural molecules.
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Affiliation(s)
- Chuanqing Kang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, 130022, China
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Cañete ÁF, Salas CO, Zacconi FC. Efficient indium-mediated dehalogenation of aromatics in ionic liquid media. Molecules 2012; 18:398-407. [PMID: 23275048 PMCID: PMC6270286 DOI: 10.3390/molecules18010398] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 12/10/2012] [Accepted: 12/24/2012] [Indexed: 11/25/2022] Open
Abstract
An efficient indium-mediated dehalogenation reaction of haloaromatics and haloheteroaromatics in ionic liquids has been studied. This method is simple and effective in the presence of [bmim]Br. Furthermore, this methodology is environmentally friendly compared with conventional ones.
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Affiliation(s)
- Álvaro F. Cañete
- Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul 78204336, Región Metropolitana, Santiago, Chile
| | | | - Flavia C. Zacconi
- Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul 78204336, Región Metropolitana, Santiago, Chile
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Maness AD, Bowman KS, Yan J, Rainey FA, Moe WM. Dehalogenimonas spp. can Reductively Dehalogenate High Concentrations of 1,2-Dichloroethane, 1,2-Dichloropropane, and 1,1,2-Trichloroethane. AMB Express 2012; 2:54. [PMID: 23046725 PMCID: PMC3492069 DOI: 10.1186/2191-0855-2-54] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 10/02/2012] [Indexed: 11/30/2022] Open
Abstract
The contaminant concentrations over which type strains of the species Dehalogenimonas alkenigignens and Dehalogenimonas lykanthroporepellens were able to reductively dechlorinate 1,2-dichloroethane (1,2-DCA), 1,2-dichloropropane (1,2-DCP), and 1,1,2-trichloroethane (1,1,2-TCA) were evaluated. Although initially isolated from an environment with much lower halogenated solvent concentrations, D. alkenigignens IP3-3T was found to reductively dehalogenate chlorinated alkanes at concentrations comparable to D. lykanthroporepellens BL-DC-9T. Both species dechlorinated 1,2-DCA, 1,2-DCP, and 1,1,2-TCA present at initial concentrations at least as high as 8.7, 4.0, and 3.5 mM, respectively. The ability of Dehalogenimonas spp. to carry out anaerobic reductive dechlorination even in the presence of high concentrations of chlorinated aliphatic alkanes has important implications for remediation of contaminated soil and groundwater.
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Affiliation(s)
- Andrew D Maness
- Department of Civil and Environmental Engineering, Louisiana State University, 3513B Patrick Taylor Hall, Baton Rouge, LA, 70803, USA
| | - Kimberly S Bowman
- Department of Civil and Environmental Engineering, Louisiana State University, 3513B Patrick Taylor Hall, Baton Rouge, LA, 70803, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Jun Yan
- Department of Civil and Environmental Engineering, Louisiana State University, 3513B Patrick Taylor Hall, Baton Rouge, LA, 70803, USA
- Present address: Jun Yan, Department of Microbiology and Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA
| | - Fred A Rainey
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK, 99508, USA
| | - William M Moe
- Department of Civil and Environmental Engineering, Louisiana State University, 3513B Patrick Taylor Hall, Baton Rouge, LA, 70803, USA
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40
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Kajander T, Lehtiö L, Schlömann M, Goldman A. The structure of Pseudomonas P51 Cl-muconate lactonizing enzyme: co-evolution of structure and dynamics with the dehalogenation function. Protein Sci 2003; 12:1855-64. [PMID: 12930985 PMCID: PMC2323983 DOI: 10.1110/ps.0388503] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Bacterial muconate lactonizing enzymes (MLEs) catalyze the conversion of cis,cis-muconate as a part of the beta-ketoadipate pathway, and some MLEs are also able to dehalogenate chlorinated muconates (Cl-MLEs). The basis for the Cl-MLEs dehalogenating activity is still unclear. To further elucidate the differences between MLEs and Cl-MLEs, we have solved the structure of Pseudomonas P51 Cl-MLE at 1.95 A resolution. Comparison of Pseudomonas MLE and Cl-MLE structures reveals the presence of a large cavity in the Cl-MLEs. The cavity may be related to conformational changes on substrate binding in Cl-MLEs, at Gly52. Site-directed mutagenesis on Pseudomonas MLE core positions to the equivalent Cl-MLE residues showed that the variant Thr52Gly was rather inactive, whereas the Thr52Gly-Phe103Ser variant had regained part of the activity. These residues form a hydrogen bond in the Cl-MLEs. The Cl-MLE structure, as a result of the Thr-to-Gly change, is more flexible than MLE: As a mobile loop closes over the active site, a conformational change at Gly52 is observed in Cl-MLEs. The loose packing and structural motions in Cl-MLE may be required for the rotation of the lactone ring in the active site necessary for the dehalogenating activity of Cl-MLEs. Furthermore, we also suggest that differences in the active site mobile loop sequence between MLEs and Cl-MLEs result in lower active site polarity in Cl-MLEs, possibly affecting catalysis. These changes could result in slower product release from Cl-MLEs and make it a better enzyme for dehalogenation of substrate.
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Affiliation(s)
- Tommi Kajander
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, FIN-00014 Helsinki, Finland
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