1
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Hollow silica microspheres as robust immobilization carriers. Bioorg Chem 2019; 93:102813. [DOI: 10.1016/j.bioorg.2019.02.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/15/2019] [Accepted: 02/18/2019] [Indexed: 11/17/2022]
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2
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Küppers J, Rabus R, Wilkes H, Christoffers J. Optically Active 1-Deuterio-1-phenylethane - Preparation and Proof of Enantiopurity. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900121] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Julian Küppers
- Institut für Chemie; Carl von Ossietzky Universität Oldenburg; 26111 Oldenburg Germany
| | - Ralf Rabus
- Institut für Chemie und Biologie des Meeres (ICBM); Carl von Ossietzky Universität Oldenburg; 26111 Oldenburg Germany
| | - Heinz Wilkes
- Institut für Chemie und Biologie des Meeres (ICBM); Carl von Ossietzky Universität Oldenburg; 26111 Oldenburg Germany
| | - Jens Christoffers
- Institut für Chemie; Carl von Ossietzky Universität Oldenburg; 26111 Oldenburg Germany
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3
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Jarling R, Kühner S, Basílio Janke E, Gruner A, Drozdowska M, Golding BT, Rabus R, Wilkes H. Versatile transformations of hydrocarbons in anaerobic bacteria: substrate ranges and regio- and stereo-chemistry of activation reactions. Front Microbiol 2015; 6:880. [PMID: 26441848 PMCID: PMC4561516 DOI: 10.3389/fmicb.2015.00880] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 08/10/2015] [Indexed: 12/31/2022] Open
Abstract
Anaerobic metabolism of hydrocarbons proceeds either via addition to fumarate or by hydroxylation in various microorganisms, e.g., sulfate-reducing or denitrifying bacteria, which are specialized in utilizing n-alkanes or alkylbenzenes as growth substrates. General pathways for carbon assimilation and energy gain have been elucidated for a limited number of possible substrates. In this work the metabolic activity of 11 bacterial strains during anaerobic growth with crude oil was investigated and compared with the metabolite patterns appearing during anaerobic growth with more than 40 different hydrocarbons supplied as binary mixtures. We show that the range of co-metabolically formed alkyl- and arylalkyl-succinates is much broader in n-alkane than in alkylbenzene utilizers. The structures and stereochemistry of these products are resolved. Furthermore, we demonstrate that anaerobic hydroxylation of alkylbenzenes does not only occur in denitrifiers but also in sulfate reducers. We propose that these processes play a role in detoxification under conditions of solvent stress. The thermophilic sulfate-reducing strain TD3 is shown to produce n-alkylsuccinates, which are suggested not to derive from terminal activation of n-alkanes, but rather to represent intermediates of a metabolic pathway short-cutting fumarate regeneration by reverse action of succinate synthase. The outcomes of this study provide a basis for geochemically tracing such processes in natural habitats and contribute to an improved understanding of microbial activity in hydrocarbon-rich anoxic environments.
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Affiliation(s)
- René Jarling
- Organic Geochemistry, Chemistry of the Earth, Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences Potsdam, Germany
| | - Simon Kühner
- Department of Microbiology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Eline Basílio Janke
- Organic Geochemistry, Chemistry of the Earth, Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences Potsdam, Germany
| | - Andrea Gruner
- Organic Geochemistry, Chemistry of the Earth, Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences Potsdam, Germany
| | - Marta Drozdowska
- School of Chemistry, Newcastle University Newcastle upon Tyne, UK
| | | | - Ralf Rabus
- Department of Microbiology, Max Planck Institute for Marine Microbiology Bremen, Germany ; General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University Oldenburg, Germany
| | - Heinz Wilkes
- Organic Geochemistry, Chemistry of the Earth, Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences Potsdam, Germany ; Organic Geochemistry, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University Oldenburg, Germany
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4
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Muhr E, Schühle K, Clermont L, Sünwoldt K, Kleinsorge D, Seyhan D, Kahnt J, Schall I, Cordero PR, Schmitt G, Heider J. Enzymes of anaerobic ethylbenzene and p-ethylphenol catabolism in 'Aromatoleum aromaticum': differentiation and differential induction. Arch Microbiol 2015; 197:1051-62. [PMID: 26275558 DOI: 10.1007/s00203-015-1142-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 07/24/2015] [Accepted: 08/06/2015] [Indexed: 01/18/2023]
Abstract
The denitrifying bacterium 'Aromatoleum aromaticum' strain EbN1 is one of the best characterized bacteria regarding anaerobic ethylbenzene degradation. EbN1 also degrades various other aromatic and phenolic compounds in the absence of oxygen, one of them being p-ethylphenol. Despite having similar chemical structures, ethylbenzene and p-ethylphenol have been proposed to be metabolized by completely separate pathways. In this study, we established and applied biochemical and molecular biological methods to show the (almost) exclusive presence and specificity of enzymes involved in the respective degradation pathways by recording enzyme activities, complemented by heme staining, immuno- and biotin-blotting analyses. These combined results substantiated the predicted p-ethylphenol degradation pathway. The identified enzymes include a heme c-containing p-ethylphenol-hydroxylase, both an (R)- and an (S)-specific alcohol dehydrogenase as well as a novel biotin-dependent carboxylase. We also establish an activity assay for benzoylacetate-CoA ligases likely being involved in both metabolic pathways.
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Affiliation(s)
- Enrico Muhr
- Laboratory of Microbial Biochemistry, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Karola Schühle
- Laboratory of Microbial Biochemistry, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Lina Clermont
- Laboratory of Microbial Biochemistry, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Katharina Sünwoldt
- Laboratory of Microbial Biochemistry, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Daniel Kleinsorge
- Laboratory of Microbial Biochemistry, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Deniz Seyhan
- Laboratory of Microbial Biochemistry, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Jörg Kahnt
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Iris Schall
- Laboratory of Microbial Biochemistry, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Paul R Cordero
- Laboratory of Microbial Biochemistry, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Georg Schmitt
- Laboratory of Microbial Biochemistry, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Johann Heider
- Laboratory of Microbial Biochemistry, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany. .,LOEWE-Center for Synthetic Microbiology, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany.
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5
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Dorer C, Vogt C, Kleinsteuber S, Stams AJM, Richnow HH. Compound-specific isotope analysis as a tool to characterize biodegradation of ethylbenzene. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:9122-32. [PMID: 24971724 DOI: 10.1021/es500282t] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
This study applied one- and two-dimensional compound-specific isotope analysis (CSIA) for the elements carbon and hydrogen to assess different means of microbial ethylbenzene activation. Cultures incubated under nitrate-reducing conditions showed significant carbon and highly pronounced hydrogen isotope fractionation of comparable magnitudes, leading to nearly identical slopes in dual-isotope plots. The results imply that Georgfuchsia toluolica G5G6 and an enrichment culture dominated by an Azoarcus species activate ethylbenzene by anaerobic hydroxylation catalyzed by ethylbenzene dehydrogenase, similar to Aromatoleum aromaticum EbN1. The isotope enrichment pattern in dual plots from two strictly anaerobic enrichment cultures differed considerably from those for benzylic hydroxylation, indicating an alternative anaerobic activation step, most likely fumarate addition. Large hydrogen fractionation was quantified using a recently developed Rayleigh-based approach considering hydrogen atoms at reactive sites. Data from nine investigated microbial cultures clearly suggest that two-dimensional CSIA in combination with the magnitude of hydrogen isotope fractionation is a valuable tool to distinguish ethylbenzene degradation and may be of practical use for monitoring natural or technological remediation processes at field sites.
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Affiliation(s)
- Conrad Dorer
- Department of Isotope Biogeochemistry and §Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research , Permoserstrasse 15, D-04318 Leipzig, Germany
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6
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Rethinking biological activation of methane and conversion to liquid fuels. Nat Chem Biol 2014; 10:331-9. [PMID: 24743257 DOI: 10.1038/nchembio.1509] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 03/25/2014] [Indexed: 11/08/2022]
Abstract
If methane, the main component of natural gas, can be efficiently converted to liquid fuels, world reserves of methane could satisfy the demand for transportation fuels in addition to use in other sectors. However, the direct activation of strong C-H bonds in methane and conversion to desired products remains a difficult technological challenge. This perspective reveals an opportunity to rethink the logic of biological methane activation and conversion to liquid fuels. We formulate a vision for a new foundation for methane bioconversion and suggest paths to develop technologies for the production of liquid transportation fuels from methane at high carbon yield and high energy efficiency and with low CO2 emissions. These technologies could support natural gas bioconversion facilities with a low capital cost and at small scales, which in turn could monetize the use of natural gas resources that are frequently flared, vented or emitted.
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Zhang T, Tremblay PL, Chaurasia AK, Smith JA, Bain TS, Lovley DR. Identification of genes specifically required for the anaerobic metabolism of benzene in Geobacter metallireducens. Front Microbiol 2014; 5:245. [PMID: 24904558 PMCID: PMC4033198 DOI: 10.3389/fmicb.2014.00245] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 05/05/2014] [Indexed: 11/13/2022] Open
Abstract
Although the biochemical pathways for the anaerobic degradation of many of the hydrocarbon constituents in petroleum reservoirs have been elucidated, the mechanisms for anaerobic activation of benzene, a very stable molecule, are not known. Previous studies have demonstrated that Geobacter metallireducens can anaerobically oxidize benzene to carbon dioxide with Fe(III) as the sole electron acceptor and that phenol is an intermediate in benzene oxidation. In an attempt to identify enzymes that might be involved in the conversion of benzene to phenol, whole-genome gene transcript abundance was compared in cells metabolizing benzene and cells metabolizing phenol. Eleven genes had significantly higher transcript abundance in benzene-metabolizing cells. Five of these genes had annotations suggesting that they did not encode proteins that could be involved in benzene metabolism and were not further studied. Strains were constructed in which one of the remaining six genes was deleted. The strain in which the monocistronic gene Gmet 0232 was deleted metabolized phenol, but not benzene. Transcript abundance of the adjacent monocistronic gene, Gmet 0231, predicted to encode a zinc-containing oxidoreductase, was elevated in cells metabolizing benzene, although not at a statistically significant level. However, deleting Gmet 0231 also yielded a strain that could metabolize phenol, but not benzene. Although homologs of Gmet 0231 and Gmet 0232 are found in microorganisms not known to anaerobically metabolize benzene, the adjacent localization of these genes is unique to G. metallireducens. The discovery of genes that are specifically required for the metabolism of benzene, but not phenol in G. metallireducens is an important step in potentially identifying the mechanisms for anaerobic benzene activation.
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Affiliation(s)
- Tian Zhang
- Department of Microbiology, University of Massachusetts Amherst, MA, USA ; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark Hørsholm, Denmark
| | - Pier-Luc Tremblay
- Department of Microbiology, University of Massachusetts Amherst, MA, USA ; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark Hørsholm, Denmark
| | | | - Jessica A Smith
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | - Timothy S Bain
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | - Derek R Lovley
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
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8
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Callaghan AV. Enzymes involved in the anaerobic oxidation of n-alkanes: from methane to long-chain paraffins. Front Microbiol 2013; 4:89. [PMID: 23717304 PMCID: PMC3653055 DOI: 10.3389/fmicb.2013.00089] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 03/31/2013] [Indexed: 11/13/2022] Open
Abstract
Anaerobic microorganisms play key roles in the biogeochemical cycling of methane and non-methane alkanes. To date, there appear to be at least three proposed mechanisms of anaerobic methane oxidation (AOM). The first pathway is mediated by consortia of archaeal anaerobic methane oxidizers and sulfate-reducing bacteria (SRB) via “reverse methanogenesis” and is catalyzed by a homolog of methyl-coenzyme M reductase. The second pathway is also mediated by anaerobic methane oxidizers and SRB, wherein the archaeal members catalyze both methane oxidation and sulfate reduction and zero-valent sulfur is a key intermediate. The third AOM mechanism is a nitrite-dependent, “intra-aerobic” pathway described for the denitrifying bacterium, ‘Candidatus Methylomirabilis oxyfera.’ It is hypothesized that AOM proceeds via reduction of nitrite to nitric oxide, followed by the conversion of two nitric oxide molecules to dinitrogen and molecular oxygen. The latter can be used to functionalize the methane via a particulate methane monooxygenase. With respect to non-methane alkanes, there also appear to be novel mechanisms of activation. The most well-described pathway is the addition of non-methane alkanes across the double bond of fumarate to form alkyl-substituted succinates via the putative glycyl radical enzyme, alkylsuccinate synthase (also known as methylalkylsuccinate synthase). Other proposed mechanisms include anaerobic hydroxylation via ethylbenzene dehydrogenase-like enzymes and an “intra-aerobic” denitrification pathway similar to that described for ‘Methylomirabilis oxyfera.’
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Affiliation(s)
- Amy V Callaghan
- Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK, USA
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9
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Knack DH, Marshall JL, Harlow GP, Dudzik A, Szaleniec M, Liu SY, Heider J. BN/CC isosteric compounds as enzyme inhibitors: N- and B-ethyl-1,2-azaborine inhibit ethylbenzene hydroxylation as nonconvertible substrate analogues. Angew Chem Int Ed Engl 2013; 52:2599-601. [PMID: 23355270 PMCID: PMC3748812 DOI: 10.1002/anie.201208351] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 11/27/2012] [Indexed: 11/05/2022]
Abstract
Good substrate gone bad! BN/CC isosterism of ethylbenzene leads to N-ethyl-1,2-azaborine and B-ethyl-1,2-azaborine. In contrast to ethylbenzene, which is the substrate for ethylbenzene dehydrogenase (EbDH), N-ethyl-1,2-azaborine (see scheme; Fc=Ferricenium tetrafluoroborate) and B-ethyl-1,2-azaborine are strong inhibitors of EbDH. Thus, the changes provided by BN/CC isosterism can lead to new biochemical reactivity.
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Affiliation(s)
- Daniel H. Knack
- Laboratory for Microbial Biochemistry, Philipps University of Marburg, 35043 Marburg (Germany)
| | | | - Gregory P. Harlow
- Department of Chemistry, University of Oregon, Eugene, OR, 97403-1253 (USA)
| | - Agnieszka Dudzik
- Jerzy Haber Institute for Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków (Poland)
| | - Maciej Szaleniec
- Jerzy Haber Institute for Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków (Poland)
| | - Shih-Yuan Liu
- Department of Chemistry, University of Oregon, Eugene, OR, 97403-1253 (USA)
| | - Johann Heider
- Laboratory for Microbial Biochemistry, Philipps University of Marburg, 35043 Marburg (Germany)
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10
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Knack DH, Marshall JL, Harlow GP, Dudzik A, Szaleniec M, Liu SY, Heider J. BN/CC-isosterische Verbindungen als Enzyminhibitoren: Hemmung der Hydroxylierung von Ethylbenzol durchN- undB-Ethyl-1,2-azaborin als nichtkonvertierbare Substratanaloga. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208351] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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Philipp B, Schink B. Different strategies in anaerobic biodegradation of aromatic compounds: nitrate reducers versus strict anaerobes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:469-478. [PMID: 23760891 DOI: 10.1111/j.1758-2229.2011.00304.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Mononuclear aromatic compounds are degraded anaerobically through pathways that are basically different from those used in the presence of oxygen. Whereas aerobic degradation destabilizes the aromatic π-electron system by oxidative steps through oxygenase reactions, anaerobic degradation is most often initiated by a reductive attack. The benzoyl-CoA pathway is the most important metabolic route in this context, and a broad variety of mononuclear aromatics, including phenol, cresols, toluene, xylenes and ethylbenzene, are channelled into this pathway through various modification reactions. Multifunctional phenolic compounds are metabolized via the reductive resorcinol pathway, the oxidative resorcinol pathway with hydroxyhydroquinone as key intermediate, and the phloroglucinol pathway. Comparison of the various pathways used for modification and degradation of aromatics in the absence of oxygen indicates that the strategies of breakdown of these compounds are largely determined by the redox potentials of the electron acceptors used, and by the overall reaction energetics. Consequently, nitrate reducers quite often use strategies for primary attack on aromatic compounds that differ from those used by sulfate-reducing, iron-reducing or fermenting bacteria.
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Affiliation(s)
- Bodo Philipp
- Department of Biology, University of Konstanz, Universitätsstr. 10, D-78457 Konstanz, Germany
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12
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Substrate and inhibitor spectra of ethylbenzene dehydrogenase: perspectives on application potential and catalytic mechanism. Appl Environ Microbiol 2012; 78:6475-82. [PMID: 22773630 DOI: 10.1128/aem.01551-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ethylbenzene dehydrogenase (EbDH) catalyzes the initial step in anaerobic degradation of ethylbenzene in denitrifying bacteria, namely, the oxygen-independent hydroxylation of ethylbenzene to (S)-1-phenylethanol. In our study we investigate the kinetic properties of 46 substrate analogs acting as substrates or inhibitors of the enzyme. The apparent kinetic parameters of these compounds give important insights into the function of the enzyme and are consistent with the predicted catalytic mechanism based on a quantum chemical calculation model. In particular, the existence of the proposed substrate-derived radical and carbocation intermediates is substantiated by the formation of alternative dehydrogenated and hydroxylated products from some substrates, which can be regarded as mechanistic models. In addition, these results also show the surprisingly high diversity of EbDH in hydroxylating different kinds of alkylaromatic and heterocyclic compounds to the respective alcohols. This may lead to attractive industrial applications of ethylbenzene dehydrogenase for a new process of producing alcohols via hydroxylation of the corresponding aromatic hydrocarbons rather than the customary procedure of reducing the corresponding ketones.
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Abstract
Anaerobic ethylbenzene metabolism in the betaproteobacterium Aromatoleum aromaticum is initiated by anaerobic oxidation to acetophenone via (S)-1-phenylethanol. The subsequent carboxylation of acetophenone to benzoylacetate is catalyzed by an acetophenone-induced enzyme, which has been purified and studied. The same enzyme is involved in acetophenone metabolism in the absence of ethylbenzene. Acetophenone carboxylase consists of five subunits with molecular masses of 70, 15, 87, 75, and 34 kDa, whose genes (apcABCDE) form an apparent operon. The enzyme is synthesized at high levels in cells grown on ethylbenzene or acetophenone, but not in cells grown on benzoate. During purification, acetophenone carboxylase dissociates into inactive subcomplexes consisting of the 70-, 15-, 87-, and 75-kDa subunits (apcABCD gene products) and the 34-kDa subunit (apcE gene product), respectively. Acetophenone carboxylase activity was restored by mixing the purified subcomplexes. The enzyme contains 1 Zn(2+) ion per alphabetagammadelta core complex and is dependent on the presence of Mg(2+) or Mn(2+). In spite of the presence of Zn in the enzyme, it is strongly inhibited by Zn(2+) ions. Carboxylation of acetophenone is dependent on ATP hydrolysis to ADP and P(i), exhibiting a stoichiometry of 2 mol ATP per mol acetophenone carboxylated. The enzyme shows uncoupled ATPase activity with either bicarbonate or acetophenone in the absence of the second substrate. These observations indicate that both substrates may be phosphorylated, which is consistent with isotope exchange activity observed with deuterated acetophenone and inhibition by carbamoylphosphate, a structural analogue of carboxyphosphate. A potential mechanism of ATP-dependent acetophenone carboxylation is suggested.
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Carmona M, Zamarro MT, Blázquez B, Durante-Rodríguez G, Juárez JF, Valderrama JA, Barragán MJL, García JL, Díaz E. Anaerobic catabolism of aromatic compounds: a genetic and genomic view. Microbiol Mol Biol Rev 2009; 73:71-133. [PMID: 19258534 PMCID: PMC2650882 DOI: 10.1128/mmbr.00021-08] [Citation(s) in RCA: 264] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Aromatic compounds belong to one of the most widely distributed classes of organic compounds in nature, and a significant number of xenobiotics belong to this family of compounds. Since many habitats containing large amounts of aromatic compounds are often anoxic, the anaerobic catabolism of aromatic compounds by microorganisms becomes crucial in biogeochemical cycles and in the sustainable development of the biosphere. The mineralization of aromatic compounds by facultative or obligate anaerobic bacteria can be coupled to anaerobic respiration with a variety of electron acceptors as well as to fermentation and anoxygenic photosynthesis. Since the redox potential of the electron-accepting system dictates the degradative strategy, there is wide biochemical diversity among anaerobic aromatic degraders. However, the genetic determinants of all these processes and the mechanisms involved in their regulation are much less studied. This review focuses on the recent findings that standard molecular biology approaches together with new high-throughput technologies (e.g., genome sequencing, transcriptomics, proteomics, and metagenomics) have provided regarding the genetics, regulation, ecophysiology, and evolution of anaerobic aromatic degradation pathways. These studies revealed that the anaerobic catabolism of aromatic compounds is more diverse and widespread than previously thought, and the complex metabolic and stress programs associated with the use of aromatic compounds under anaerobic conditions are starting to be unraveled. Anaerobic biotransformation processes based on unprecedented enzymes and pathways with novel metabolic capabilities, as well as the design of novel regulatory circuits and catabolic networks of great biotechnological potential in synthetic biology, are now feasible to approach.
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Affiliation(s)
- Manuel Carmona
- Departamento de Microbiología Molecular, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
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15
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Shibata A, Toyota K, Miyake K, Katayama A. Anaerobic biodegradation of 4-alkylphenols in a paddy soil microcosm supplemented with nitrate. CHEMOSPHERE 2007; 68:2096-103. [PMID: 17408723 DOI: 10.1016/j.chemosphere.2007.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2006] [Revised: 02/02/2007] [Accepted: 02/05/2007] [Indexed: 05/14/2023]
Abstract
Anaerobic degradation of phenol, p-cresol, 4-n-propylphenol (n-PP), 4-i-propylphenol (i-PP), 4-n-butylphenol (n-BP) and 4-sec-butylphenol (sec-BP) was observed in a paddy soil supplemented with nitrate. We detected the metabolites 4'-hydroxypropiophenone (HPP) from n-PP, 4-i-propenylphenol from i-PP, and 4-(1-butenyl)phenol and 4'-hydroxybutyrophenone (HBP) from n-BP. Compared with the original soils, Betaproteobacteria became predominant in the microcosm during the degradation of phenol and p-cresol whereas no remarkable change was observed in the community degrading propylphenols and butylphenols. The microcosm, however, did not degrade 4-t-butylphenol (t-BP), 4-t-octylphenol (t-OP) and 4-n-octylphenol (n-OP). Paddy soil supplemented with sulfate or iron (III) as electron acceptors did not degrade phenol and 4-alkylphenols with the exception of the degradation of p-cresol in sulfate-reducing conditions. It was demonstrated for the first time that anaerobic microbial degradation of alkylphenols, in a paddy soil supplemented with nitrate as an electron acceptor, occurred via oxidation of the alpha carbon in the alkyl chain.
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Affiliation(s)
- Atsushi Shibata
- Department of Geotechnical and Environmental Engineering, Nagoya University, Chikusa, Nagoya 464-8603, Japan
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16
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Shibata A, Katayama A. Anaerobic co-metabolic oxidation of 4-alkylphenols with medium-length or long alkyl chains by Thauera sp., strain R5. Appl Microbiol Biotechnol 2007; 75:1151-61. [PMID: 17387471 DOI: 10.1007/s00253-007-0918-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2006] [Revised: 02/28/2007] [Accepted: 03/01/2007] [Indexed: 11/26/2022]
Abstract
A 4-alkylphenol-degrading facultative anaerobic bacterium, strain R5, was isolated from paddy soil after enrichment with 4-n-propylphenol, 4-n-butylphenol and 4-hydroxybenzoate (4-HBA) under nitrate-reducing conditions. Strain R5 is a Gram-negative rod bacillus grown on phenolic compounds with short alkyl chains (<or=C2), organic acids and ethanol. The sequence of the 16S ribosomal RNA gene revealed that the strain is affiliated with Thauera sp. In the presence of 4-HBA as a carbon source, the strain transformed 4-n-alkylphenols with a medium or long-length alkyl chain (C3-C8) to the corresponding oxidised products as follows: 1-(4-hydroxyphenyl)-1-alkenes, -(4-hydroxyphenyl)-1-alkanones and/or 1-(4-hydroxyphenyl)-1-alcohols. The strain also transformed 4-i-propylphenol and 4-sec-butylphenol to (4-hydroxyphenyl)-i-propene and (4-hydroxyphenyl)-sec-butene but not 4-alkylphenols with tertiary alkyl chains (4-t-butylphenol or 4-t-octylphenol). The biotransformation did not proceed without another carbon source and was coupled with nitrate reduction. Biotransformation activity was high in the presence of p-cresol, 4-ethylphenol, 4'-hydroxyacetophenone and 4-HBA as carbon sources and low in the presence of organic acids and ethanol. We suggest that strain R5 co-metabolically transforms alkylphenols to the corresponding metabolites with oxidised alpha carbon in the alkyl chain during coupling with nitrate reduction.
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Affiliation(s)
- Atsushi Shibata
- Department of Geotechnical and Environmental Engineering, Nagoya University, Chikusa, Nagoya, 464-8603, Japan
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Kloer DP, Hagel C, Heider J, Schulz GE. Crystal Structure of Ethylbenzene Dehydrogenase from Aromatoleum aromaticum. Structure 2006; 14:1377-88. [PMID: 16962969 DOI: 10.1016/j.str.2006.07.001] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Revised: 06/16/2006] [Accepted: 07/03/2006] [Indexed: 11/19/2022]
Abstract
Anaerobic degradation of hydrocarbons was discovered a decade ago, and ethylbenzene dehydrogenase was one of the first characterized enzymes involved. The structure of the soluble periplasmic 165 kDa enzyme was established at 1.88 A resolution. It is a heterotrimer. The alpha subunit contains the catalytic center with a molybdenum held by two molybdopterin-guanine dinucleotides, one with an open pyran ring, and an iron-sulfur cluster with a histidine ligand. During catalysis, electrons produced by substrate oxidation are transferred to a heme in the gamma subunit and then presumably to a separate cytochrome involved in nitrate respiration. The beta subunit contains four iron-sulfur clusters and is structurally related to ferredoxins. The gamma subunit is the first known protein with a methionine and a lysine as axial heme ligands. The catalytic product was modeled into the active center, showing the reaction geometry. A mechanism consistent with activity and inhibition data of ethylbenzene-related compounds is proposed.
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Affiliation(s)
- Daniel P Kloer
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstr. 21, D-79104 Freiburg im Breisgau, Germany
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18
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Kühner S, Wöhlbrand L, Fritz I, Wruck W, Hultschig C, Hufnagel P, Kube M, Reinhardt R, Rabus R. Substrate-dependent regulation of anaerobic degradation pathways for toluene and ethylbenzene in a denitrifying bacterium, strain EbN1. J Bacteriol 2005; 187:1493-503. [PMID: 15687214 PMCID: PMC545613 DOI: 10.1128/jb.187.4.1493-1503.2005] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anaerobic biodegradation of toluene and ethylbenzene is of environmental concern and biochemical interest due to toxicity and novel reactions, respectively. The denitrifying strain EbN1 is unique in anaerobically degrading both alkylbenzenes via different pathways which converge at benzoyl coenzyme A. The organization of genes involved in both pathways was only recently determined for strain EbN1. In the present study, global expression analysis (DNA microarray and proteomics) indicated involvement of several thus-far-unknown proteins in the degradation of both alkylbenzenes. For example, orf68 and orf57, framing the ebd operon, are implicated in ethylbenzene degradation, and the ebA1932 and ebA1936 genes, located 7.2 kb upstream of the bbs operon, are implicated in toluene degradation. In addition, expression studies were now possible on the level of the complete pathways. Growth experiments demonstrated that degradative capacities for toluene and ethylbenzene could be simultaneously induced, regardless of the substrate used for adaptation. Regulation was studied at the RNA (real-time reverse transcription-PCR and DNA microarray) and protein (two-dimensional-difference gel electrophoresis) level by using cells adapted to anaerobic growth with benzoate, toluene, ethylbenzene, or a mixture of toluene and ethylbenzene. Expression of the two toluene-related operons (bss and bbs) was specifically induced in toluene-adapted cells. In contrast, genes involved in anaerobic ethylbenzene degradation were induced in ethylbenzene- and toluene-adapted cells, suggesting that toluene may act as a gratuitous inducer. In agreement with the predicted sequential regulation of the ethylbenzene pathway, Ebd proteins (encoding subunits of ethylbenzene dehydrogenase) were formed in ethylbenzene- but not in acetophenone-adapted cells, while Apc proteins (subunits of predicted acetophenone carboxylase) were formed under both conditions.
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MESH Headings
- Anaerobiosis
- Bacterial Proteins/analysis
- Benzene Derivatives/metabolism
- Betaproteobacteria/metabolism
- Biodegradation, Environmental
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- Electrophoresis, Gel, Two-Dimensional
- Gene Expression Profiling
- Gene Expression Regulation, Bacterial
- Genes, Bacterial
- Molecular Sequence Data
- Oligonucleotide Array Sequence Analysis
- Operon/physiology
- Oxidoreductases/biosynthesis
- RNA, Bacterial/analysis
- RNA, Messenger/analysis
- Sequence Analysis, DNA
- Toluene/metabolism
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Affiliation(s)
- Simon Kühner
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359 Bremen, Germany
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19
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Abstract
Recent advances in molecular biology have extended our understanding of the metabolic processes related to microbial transformation of petroleum hydrocarbons. The physiological responses of microorganisms to the presence of hydrocarbons, including cell surface alterations and adaptive mechanisms for uptake and efflux of these substrates, have been characterized. New molecular techniques have enhanced our ability to investigate the dynamics of microbial communities in petroleum-impacted ecosystems. By establishing conditions which maximize rates and extents of microbial growth, hydrocarbon access, and transformation, highly accelerated and bioreactor-based petroleum waste degradation processes have been implemented. Biofilters capable of removing and biodegrading volatile petroleum contaminants in air streams with short substrate-microbe contact times (<60 s) are being used effectively. Microbes are being injected into partially spent petroleum reservoirs to enhance oil recovery. However, these microbial processes have not exhibited consistent and effective performance, primarily because of our inability to control conditions in the subsurface environment. Microbes may be exploited to break stable oilfield emulsions to produce pipeline quality oil. There is interest in replacing physical oil desulfurization processes with biodesulfurization methods through promotion of selective sulfur removal without degradation of associated carbon moieties. However, since microbes require an environment containing some water, a two-phase oil-water system must be established to optimize contact between the microbes and the hydrocarbon, and such an emulsion is not easily created with viscous crude oil. This challenge may be circumvented by application of the technology to more refined gasoline and diesel substrates, where aqueous-hydrocarbon emulsions are more easily generated. Molecular approaches are being used to broaden the substrate specificity and increase the rates and extents of desulfurization. Bacterial processes are being commercialized for removal of H(2)S and sulfoxides from petrochemical waste streams. Microbes also have potential for use in removal of nitrogen from crude oil leading to reduced nitric oxide emissions provided that technical problems similar to those experienced in biodesulfurization can be solved. Enzymes are being exploited to produce added-value products from petroleum substrates, and bacterial biosensors are being used to analyze petroleum-contaminated environments.
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Affiliation(s)
- Jonathan D Van Hamme
- Department of Biological Sciences, The University College of the Cariboo, Kamloops, British Columbia V2C 5N3
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20
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Kniemeyer O, Fischer T, Wilkes H, Glöckner FO, Widdel F. Anaerobic degradation of ethylbenzene by a new type of marine sulfate-reducing bacterium. Appl Environ Microbiol 2003; 69:760-8. [PMID: 12570993 PMCID: PMC143655 DOI: 10.1128/aem.69.2.760-768.2003] [Citation(s) in RCA: 150] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2002] [Accepted: 11/11/2002] [Indexed: 11/20/2022] Open
Abstract
Anaerobic degradation of the aromatic hydrocarbon ethylbenzene was studied with sulfate as the electron acceptor. Enrichment cultures prepared with marine sediment samples from different locations showed ethylbenzene-dependent reduction of sulfate to sulfide and always contained a characteristic cell type that formed gas vesicles towards the end of growth. A pure culture of this cell type, strain EbS7, was isolated from sediment from Guaymas Basin (Gulf of California). Complete mineralization of ethylbenzene coupled to sulfate reduction was demonstrated in growth experiments with strain EbS7. Sequence analysis of the 16S rRNA gene revealed a close relationship between strain EbS7 and the previously described marine sulfate-reducing strains NaphS2 and mXyS1 (similarity values, 97.6 and 96.2%, respectively), which grow anaerobically with naphthalene and m-xylene, respectively. However, strain EbS7 did not oxidize naphthalene, m-xylene, or toluene. Other compounds utilized by strain EbS7 were phenylacetate, 3-phenylpropionate, formate, n-hexanoate, lactate, and pyruvate. 1-Phenylethanol and acetophenone, the characteristic intermediates in anaerobic ethylbenzene degradation by denitrifying bacteria, neither served as growth substrates nor were detectable as metabolites by gas chromatography-mass spectrometry in ethylbenzene-grown cultures of strain EbS7. Rather, (1-phenylethyl)succinate and 4-phenylpentanoate were detected as specific metabolites in such cultures. Formation of these intermediates can be explained by a reaction sequence involving addition of the benzyl carbon atom of ethylbenzene to fumarate, carbon skeleton rearrangement of the succinate moiety (as a thioester), and loss of one carboxyl group. Such reactions are analogous to those suggested for anaerobic n-alkane degradation and thus differ from the initial reactions in anaerobic ethylbenzene degradation by denitrifying bacteria which employ dehydrogenations.
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Affiliation(s)
- Olaf Kniemeyer
- Max-Planck-Institut für Marine Mikrobiologie, D-28359 Bremen, Germany
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21
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Abstract
A vast array of structurally diverse aromatic compounds is continually released into the environment due to the decomposition of green plants and as a consequence of human industrial activities. Increasing numbers of bacteria that utilize aromatic compounds in the absence of oxygen have been brought into pure culture in recent years. These include most major metabolic types of anaerobic heterotrophs and acetogenic bacteria. Diverse microbes utilize aromatic compounds for diverse purposes. Chlorinated aromatic compounds can serve as electron acceptors in dehalorespiration. Humic substances serve as electron shuttles to enable the use of inorganic electron acceptors, such as insoluble iron oxides, that are not always easily reduced by microbes. Substituents that are attached to aromatic rings may serve as carbon or energy sources for microbes. Examples include acyl side chains and methyl groups. Finally, aromatic compounds can be completely degraded to serve as carbon and energy sources. Routes by which various types of aromatic compounds, including toluene, ethylbenzene, phenol, benzoate, and dihydroxylated compounds, are degraded have been elucidated in recent years. Biochemical strategies employed by microbes to destabilize the aromatic ring in preparation for degradation have become apparent from this work.
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Affiliation(s)
- Jane Gibson
- Department of Microbiology, 3-432 Bowen Science Building, The University of Iowa, Iowa City 52242, USA
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22
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Johnson HA, Pelletier DA, Spormann AM. Isolation and characterization of anaerobic ethylbenzene dehydrogenase, a novel Mo-Fe-S enzyme. J Bacteriol 2001; 183:4536-42. [PMID: 11443088 PMCID: PMC95348 DOI: 10.1128/jb.183.15.4536-4542.2001] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2001] [Accepted: 04/27/2001] [Indexed: 11/20/2022] Open
Abstract
The first step in anaerobic ethylbenzene mineralization in denitrifying Azoarcus sp. strain EB1 is the oxidation of ethylbenzene to (S)-(-)-1-phenylethanol. Ethylbenzene dehydrogenase, which catalyzes this reaction, is a unique enzyme in that it mediates the stereoselective hydroxylation of an aromatic hydrocarbon in the absence of molecular oxygen. We purified ethylbenzene dehydrogenase to apparent homogeneity and showed that the enzyme is a heterotrimer (alphabetagamma) with subunit masses of 100 kDa (alpha), 35 kDa (beta), and 25 kDa (gamma). Purified ethylbenzene dehydrogenase contains approximately 0.5 mol of molybdenum, 16 mol of iron, and 15 mol of acid-labile sulfur per mol of holoenzyme, as well as a molydopterin cofactor. In addition to ethylbenzene, purified ethylbenzene dehydrogenase was found to oxidize 4-fluoro-ethylbenzene and the nonaromatic hydrocarbons 3-methyl-2-pentene and ethylidenecyclohexane. Sequencing of the encoding genes revealed that ebdA encodes the alpha subunit, a 974-amino-acid polypeptide containing a molybdopterin-binding domain. The ebdB gene encodes the beta subunit, a 352-amino-acid polypeptide with several 4Fe-4S binding domains. The ebdC gene encodes the gamma subunit, a 214-amino-acid polypeptide that is a potential membrane anchor subunit. Sequence analysis and biochemical data suggest that ethylbenzene dehydrogenase is a novel member of the dimethyl sulfoxide reductase family of molybdopterin-containing enzymes.
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Affiliation(s)
- H A Johnson
- Environmental Engineering and Science, Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305-4020, USA
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23
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Kniemeyer O, Heider J. Ethylbenzene dehydrogenase, a novel hydrocarbon-oxidizing molybdenum/iron-sulfur/heme enzyme. J Biol Chem 2001; 276:21381-6. [PMID: 11294876 DOI: 10.1074/jbc.m101679200] [Citation(s) in RCA: 156] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The initial enzyme of ethylbenzene metabolism in denitrifying Azoarcus strain EbN1, ethylbenzene dehydrogenase, was purified and characterized. The soluble periplasmic enzyme is the first known enzyme oxidizing a nonactivated hydrocarbon without molecular oxygen as cosubstrate. It is a novel molybdenum/iron-sulfur/heme protein of 155 kDa, which consists of three subunits (96, 43, and 23 kDa) in an alphabetagamma structure. The N-terminal amino acid sequence of the alpha subunit is similar to that of other molybdenum proteins such as selenate reductase from the related species Thauera selenatis. Ethylbenzene dehydrogenase is unique in that it oxidizes the hydrocarbon ethylbenzene, a compound without functional groups, to (S)-1-phenylethanol. Formation of the product was evident by coupling to an enantiomer-specific (S)-1-phenylethanol dehydrogenase from the same organism. The apparent K(m) of the enzyme for ethylbenzene is very low at <2 microm. Oxygen does not affect ethylbenzene dehydrogenase activity in extracts but inactivates the purified enzyme, if the heme b cofactor is in the reduced state. A variant of ethylbenzene dehydrogenase exhibiting significant activity also with the homolog n-propylbenzene was detected in a related Azoarcus strain (PbN1).
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Affiliation(s)
- O Kniemeyer
- Max-Planck-Institut für marine Mikrobiologie, Celsiusstrasse 1, 28359 Bremen, Germany
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24
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Abstract
Saturated and aromatic hydrocarbons are wide-spread in our environment. These compounds exhibit low chemical reactivity and for many decades were thought to undergo biodegradation only in the presence of free oxygen. During the past decade, however, an increasing number of microorganisms have been detected that degrade hydrocarbons under strictly anoxic conditions.
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Affiliation(s)
- F Widdel
- Max-Planck-Institut für Marine Mikrobiologie, Celsiusstrasse 1, D-28359, Bremen, Germany.
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25
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Elshahed MS, Gieg LM, Mcinerney MJ, Suflita JM. Signature metabolites attesting to the in situ attenuation of alkylbenzenes in anaerobic environments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2001; 35:682-689. [PMID: 11349278 DOI: 10.1021/es001571u] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Accurate assessment of the fate of hydrocarbons spilt in aquifers is essential for gauging associated health and ecological risks. Regulatory pressure to actively remediate such contaminated ecosystems can be substantially diminished if solid evidence for in situ microbial destruction of pollutants is obtained. In laboratory incubations, sediment-associated microorganisms from a gas condensate-contaminated aquifer anaerobically biodegraded toluene, ethylbenzene, xylene, and toluic acid isomers with stoichiometric amounts of sulfate consumed or methane produced. The activation of the alkylated aromatic contaminants involved conversion to their corresponding benzylsuccinic acid derivatives, a reaction known to occur for toluene and m-xylene decay, but one previously unrecognized for ethylbenzene, o- and p-xylene, and m-toluate metabolism. Benzylsuccinates were further biodegraded to toluates, phthalates, and benzoate. In laboratory incubations, these metabolites were transiently produced. Several of the metabolites were also detected in groundwater samples from an aquifer where alkylbenzene concentrations decreased over time, suggesting that anaerobic microbial metabolism of these contaminants also occurs in situ. Our studies confirm the utility of the aforementioned compounds as signature metabolites attesting to the natural attenuation of aromatic hydrocarbons in anaerobic environments.
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Affiliation(s)
- M S Elshahed
- Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019, USA
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