1
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Lycus P, Einsle O, Zhang L. Structural biology of proteins involved in nitrogen cycling. Curr Opin Chem Biol 2023; 74:102278. [PMID: 36889028 DOI: 10.1016/j.cbpa.2023.102278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 03/08/2023]
Abstract
Microbial metabolic processes drive the global nitrogen cycle through sophisticated and often unique metalloenzymes that facilitate difficult redox reactions at ambient temperature and pressure. Understanding the intricacies of these biological nitrogen transformations requires a detailed knowledge that arises from the combination of a multitude of powerful analytical techniques and functional assays. Recent developments in spectroscopy and structural biology have provided new, powerful tools for addressing existing and emerging questions, which have gained urgency due to the global environmental implications of these fundamental reactions. The present review focuses on the recent contributions of the wider area of structural biology to understanding nitrogen metabolism, opening new avenues for biotechnological applications to better manage and balance the challenges of the global nitrogen cycle.
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Affiliation(s)
- Pawel Lycus
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany; Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany.
| | - Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany.
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2
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Habib U. Insight in the methylene C-H bond cleavage of ethylbenzene during ethylbenzene hydroxylation using EBDH as a catalyst, a DFT studies. CAN J CHEM 2022. [DOI: 10.1139/cjc-2022-0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hydroxylation of ethylbenzene to (S)-1-phenylethanol with the help of Ethylbenzene dehydrogenase (EBDH) is a stereospecific catalytic reaction. This hydroxylation process involves the C-H bond cleavage of methylene part of ethylbenzene and transfer of its hydrogen to the oxygen atom attached with the metal at the active site of EBDH as a first step which leads to the formation of an intermediate. The second step involves the transfer of OH from the active site metal back to the carbon of intermediate resulting in the formation of (S)-1-phenylethanol. This C-H bond cleavage could be homolytic or heterolytic and directly affect the reaction mechanism of ethylbenzene hydroxylation. In this article, Density Functional Theory (DFT) studies were performed on the ethylbenzene bound EBDH active site model complexes to investigate the impact of C-H bond cleavage of methylene part of ethylbenzene on the reaction mechanism of ethylbenzene hydroxylation. For this, different protonation states and participation of amino acid residues near the Mo center of EBDH were considered. Models with protonation of His192, Lys450, Asp223, and model without protonation were investigated for comparison. Computed relative energies indicate that the overall lowest energy barrier pathway results when ionic (heterolytic) and radical (homolytic) pathways are combined.
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Affiliation(s)
- Uzma Habib
- National University of Sciences and Technology, 66959, SINES, Islamabad, Pakistan
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3
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Le CC, Bae M, Kiamehr S, Balskus EP. Emerging Chemical Diversity and Potential Applications of Enzymes in the DMSO Reductase Superfamily. Annu Rev Biochem 2022; 91:475-504. [PMID: 35320685 DOI: 10.1146/annurev-biochem-032620-110804] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Molybdenum- and tungsten-dependent proteins catalyze essential processes in living organisms and biogeochemical cycles. Among these enzymes, members of the dimethyl sulfoxide (DMSO) reductase superfamily are considered the most diverse, facilitating a wide range of chemical transformations that can be categorized as oxygen atom installation, removal, and transfer. Importantly, DMSO reductase enzymes provide high efficiency and excellent selectivity while operating under mild conditions without conventional oxidants such as oxygen or peroxides. Despite the potential utility of these enzymes as biocatalysts, such applications have not been fully explored. In addition, the vast majority of DMSO reductase enzymes still remain uncharacterized. In this review, we describe the reactivities, proposed mechanisms, and potential synthetic applications of selected enzymes in the DMSO reductase superfamily. We also highlight emerging opportunities to discover new chemical activity and current challenges in studying and engineering proteins in the DMSO reductase superfamily. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Chi Chip Le
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA;
| | - Minwoo Bae
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA;
| | - Sina Kiamehr
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA;
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA;
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4
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Cabral L, Giovanella P, Pellizzer EP, Teramoto EH, Kiang CH, Sette LD. Microbial communities in petroleum-contaminated sites: Structure and metabolisms. CHEMOSPHERE 2022; 286:131752. [PMID: 34426136 DOI: 10.1016/j.chemosphere.2021.131752] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/24/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Over recent decades, hydrocarbon concentrations have been augmented in soil and water, mainly derived from accidents or operations that input crude oil and petroleum into the environment. Different techniques for remediation have been proposed and used to mitigate oil contamination. Among the available environmental recovery approaches, bioremediation stands out since these hydrocarbon compounds can be used as growth substrates for microorganisms. In turn, microorganisms can play an important role with significant contributions to the stabilization of impacted areas. In this review, we present the current knowledge about responses from natural microbial communities (using DNA barcoding, multiomics, and functional gene markers) and bioremediation experiments (microcosm and mesocosm) conducted in the presence of petroleum and chemical dispersants in different samples, including soil, sediment, and water. Additionally, we present metabolic mechanisms for aerobic/anaerobic hydrocarbon degradation and alternative pathways, as well as a summary of studies showing functional genes and other mechanisms involved in petroleum biodegradation processes.
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Affiliation(s)
- Lucélia Cabral
- Laboratório de Micologia Ambiental e Industrial (LAMAI), Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Patricia Giovanella
- Laboratório de Micologia Ambiental e Industrial (LAMAI), Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil; Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Elisa Pais Pellizzer
- Laboratório de Micologia Ambiental e Industrial (LAMAI), Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Elias Hideo Teramoto
- Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil; Laboratório de Estudos de Bacias (LEBAC), Departamento de Geologia Aplicada, Instituto de Geociências e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Chang Hung Kiang
- Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil; Laboratório de Estudos de Bacias (LEBAC), Departamento de Geologia Aplicada, Instituto de Geociências e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Lara Durães Sette
- Laboratório de Micologia Ambiental e Industrial (LAMAI), Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil; Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil.
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5
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Hagel C, Blaum B, Friedrich T, Heider J. Characterisation of the redox centers of ethylbenzene dehydrogenase. J Biol Inorg Chem 2021; 27:143-154. [PMID: 34843002 PMCID: PMC8840923 DOI: 10.1007/s00775-021-01917-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/29/2021] [Indexed: 01/18/2023]
Abstract
Ethylbenzene dehydrogenase (EbDH), the initial enzyme of anaerobic ethylbenzene degradation from the beta-proteobacterium Aromatoleum aromaticum, is a soluble periplasmic molybdenum enzyme consisting of three subunits. It contains a Mo-bis-molybdopterin guanine dinucleotide (Mo-bis-MGD) cofactor and an 4Fe-4S cluster (FS0) in the α-subunit, three 4Fe-4S clusters (FS1 to FS3) and a 3Fe-4S cluster (FS4) in the β-subunit and a heme b cofactor in the γ-subunit. Ethylbenzene is hydroxylated by a water molecule in an oxygen-independent manner at the Mo-bis-MGD cofactor, which is reduced from the MoVI to the MoIV state in two subsequent one-electron steps. The electrons are then transferred via the Fe-S clusters to the heme b cofactor. In this report, we determine the midpoint redox potentials of the Mo-bis-MGD cofactor and FS1-FS4 by EPR spectroscopy, and that of the heme b cofactor by electrochemically induced redox difference spectroscopy. We obtained relatively high values of > 250 mV both for the MoVI-MoV redox couple and the heme b cofactor, whereas FS2 is only reduced at a very low redox potential, causing magnetic coupling with the neighboring FS1 and FS3. We compare the results with the data on related enzymes and interpret their significance for the function of EbDH.
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Affiliation(s)
- Corina Hagel
- Labor für Mikrobielle Biochemie and Synmikro Zentrum für Synthetische Mikrobiologie, Philipps Universität Marburg, 35043, Marburg, Germany
| | - Bärbel Blaum
- Institut für Biochemie, Albert-Ludwigs Universität, Albertstr. 21, 79104, Freiburg im Breisgau, Germany
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs Universität, Albertstr. 21, 79104, Freiburg im Breisgau, Germany.
| | - Johann Heider
- Labor für Mikrobielle Biochemie and Synmikro Zentrum für Synthetische Mikrobiologie, Philipps Universität Marburg, 35043, Marburg, Germany.
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6
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Borowiecki P, Telatycka N, Tataruch M, Żądło‐Dobrowolska A, Reiter T, Schühle K, Heider J, Szaleniec M, Kroutil W. Biocatalytic Asymmetric Reduction of γ‐Keto Esters to Access Optically Active γ‐Aryl‐γ‐butyrolactones. Adv Synth Catal 2020. [DOI: 10.1002/adsc.201901483] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Paweł Borowiecki
- Warsaw University of TechnologyFaculty of ChemistryDepartment of Drugs Technology and Biotechnology Koszykowa 3 00-664 Warsaw Poland
| | - Natalia Telatycka
- Warsaw University of TechnologyFaculty of ChemistryDepartment of Drugs Technology and Biotechnology Koszykowa 3 00-664 Warsaw Poland
| | - Mateusz Tataruch
- Jerzy Haber Institute of Catalysis and Surface Chemistry, PAS Niezapominajek 8 30-239 Krakow Poland
| | - Anna Żądło‐Dobrowolska
- Institute of Organic Chemistry Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland
| | - Tamara Reiter
- Institute of ChemistryUniversity of Graz NAWI Graz, BioTechMed Graz, Heinrichstrasse 28 8010 Graz Austria
| | - Karola Schühle
- Laboratory of MicrobiologyLOEWE Center for Synthetic MicrobiologyPhilipps University of Marburg Marburg
| | - Johann Heider
- Laboratory of MicrobiologyLOEWE Center for Synthetic MicrobiologyPhilipps University of Marburg Marburg
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry, PAS Niezapominajek 8 30-239 Krakow Poland
| | - Wolfgang Kroutil
- Institute of ChemistryUniversity of Graz NAWI Graz, BioTechMed Graz, Heinrichstrasse 28 8010 Graz Austria
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7
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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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8
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Rabus R, Wöhlbrand L, Thies D, Meyer M, Reinhold-Hurek B, Kämpfer P. Aromatoleum gen. nov., a novel genus accommodating the phylogenetic lineage including Azoarcus evansii and related species, and proposal of Aromatoleum aromaticum sp. nov., Aromatoleum petrolei sp. nov., Aromatoleum bremense sp. nov., Aromatoleum toluolicum sp. nov. and Aromatoleum diolicum sp. nov. Int J Syst Evol Microbiol 2019; 69:982-997. [DOI: 10.1099/ijsem.0.003244] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Comparative 16S rRNA gene sequence analysis and major physiological differences indicate two distinct sublineages within the genus
Azoarcus
: the
Azoarcus evansii
lineage, comprising
Azoarcus
evansii
(type strain KB740T=DSM 6898T=CIP 109473T=NBRC 107771T),
Azoarcus
buckelii
(type strain U120T=DSM 14744T=LMG 26916T),
Azoarcus
anaerobius
(type strain LuFRes1T=DSM 12081T=LMG 30943T),
Azoarcus
tolulyticus
(type strain Tol-4T=ATCC 51758T=CIP 109470T),
Azoarcus
toluvorans
(type strain Td21T=ATCC 700604T=DSM 15124T) and
Azoarcus
toluclasticus
(type strain MF63T=ATCC 700605T), and the
Azoarcus indigens
lineage, comprising
Azoarcus
indigens
(type strain VB32T=ATCC 51398T=LMG 9092T),
Azoarcus communis
(type strain SWub3T=ATCC 51397T=LMG 9095T) and
Azoarcus
olearius
(type strain DQS-4T=BCRC 80407T=KCTC 23918T=LMG 26893T).
Az. evansii
lineage members have remarkable anaerobic degradation capacities encompassing a multitude of alkylbenzenes, aromatic compounds and monoterpenes, often involving novel biochemical reactions. In contrast,
Az. indigens
lineage members are diazotrophic endophytes lacking these catabolic capacities. It is proposed that species of the
Az. evansii
lineage should be classified in a novel genus, Aromatoleum gen. nov. Finally, based on the literature and new growth, DNA–DNA hybridization and proteomic data, the following five new species are proposed: Aromatoleum aromaticum sp. nov. (type strain EbN1T=DSM 19018T=LMG 30748T and strain pCyN1=DSM 19016=LMG 31004), Aromatoleum petrolei sp. nov. (type strain ToN1T=DSM 19019T=LMG 30746T), Aromatoleumbremense sp. nov. (type strain PbN1T=DSM 19017T=LMG 31005T), Aromatoleum toluolicum sp. nov. (type strain TT=DSM 19020T=LMG 30751T) and Aromatoleum diolicum sp. nov. (type strain 22LinT=DSM 15408T=LMG 30750T).
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Affiliation(s)
- Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky Str. 9-11, D-26111 Oldenburg, Germany
| | - Lars Wöhlbrand
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky Str. 9-11, D-26111 Oldenburg, Germany
| | - Daniela Thies
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, D-28359 Bremen, Germany
| | - Markus Meyer
- Bruker Daltonik GmbH, Fahrenheitstr. 4, D-28359 Bremen, Germany
| | - Barbara Reinhold-Hurek
- Laboratory for General Microbiology, University Bremen, PO Box 330440, D-28334 Bremen, Germany
| | - Peter Kämpfer
- Department for Applied Microbiology, Justus Liebig University, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
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9
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Four Molybdenum-Dependent Steroid C-25 Hydroxylases: Heterologous Overproduction, Role in Steroid Degradation, and Application for 25-Hydroxyvitamin D 3 Synthesis. mBio 2018; 9:mBio.00694-18. [PMID: 29921665 PMCID: PMC6016249 DOI: 10.1128/mbio.00694-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Side chain-containing steroids are ubiquitous constituents of biological membranes that are persistent to biodegradation. Aerobic, steroid-degrading bacteria employ oxygenases for isoprenoid side chain and tetracyclic steran ring cleavage. In contrast, a Mo-containing steroid C-25 dehydrogenase (S25DH) of the dimethyl sulfoxide (DMSO) reductase family catalyzes the oxygen-independent hydroxylation of tertiary C-25 in the anaerobic, cholesterol-degrading bacterium Sterolibacterium denitrificans Its genome contains eight paralogous genes encoding active site α-subunits of putative S25DH-like proteins. The difficult enrichment of labile, oxygen-sensitive S25DH from the wild-type bacteria and the inability of its active heterologous production have largely hampered the study of S25DH-like gene products. Here we established a heterologous expression platform for the three structural genes of S25DH subunits together with an essential chaperone in the denitrifying betaproteobacterium Thauera aromatica K172. Using this system, S25DH1 and three isoenzymes (S25DH2, S25DH3, and S25DH4) were overproduced in a soluble, active form allowing a straightforward purification of nontagged αβγ complexes. All S25DHs contained molybdenum, four [4Fe-4S] clusters, one [3Fe-4S] cluster, and heme B and catalyzed the specific, water-dependent C-25 hydroxylations of various 4-en-3-one forms of phytosterols and zoosterols. Crude extracts from T. aromatica expressing genes encoding S25DH1 catalyzed the hydroxylation of vitamin D3 (VD3) to the clinically relevant 25-OH-VD3 with >95% yield at a rate 6.5-fold higher than that of wild-type bacterial extracts; the specific activity of recombinant S25DH1 was twofold higher than that of wild-type enzyme. These results demonstrate the potential application of the established expression platform for 25-OH-VD3 synthesis and pave the way for the characterization of previously genetically inaccessible S25DH-like Mo enzymes of the DMSO reductase family.IMPORTANCE Steroids are ubiquitous bioactive compounds, some of which are considered an emerging class of micropollutants. Their degradation by microorganisms is the major process of steroid elimination from the environment. While oxygenase-dependent steroid degradation in aerobes has been studied for more than 40 years, initial insights into the anoxic steroid degradation have only recently been obtained. Molybdenum-dependent steroid C25 dehydrogenases (S25DHs) have been proposed to catalyze oxygen-independent side chain hydroxylations of globally abundant zoo-, phyto-, and mycosterols; however, so far, their lability has allowed only the initial characterization of a single S25DH. Here we report on a heterologous gene expression platform that allowed for easy isolation and characterization of four highly active S25DH isoenzymes. The results obtained demonstrate the key role of S25DHs during anoxic degradation of various steroids. Moreover, the platform is valuable for the efficient enzymatic hydroxylation of vitamin D3 to its clinically relevant C-25-OH form.
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10
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Jimenez-Halla JOC, Nazemi A, Cundari TR. DFT study of substituent effects in the hydroxylation of methane and toluene mediated by an ethylbenzene dehydrogenase active site model. J Organomet Chem 2018. [DOI: 10.1016/j.jorganchem.2018.01.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Tsai CL, Tainer JA. Robust Production, Crystallization, Structure Determination, and Analysis of [Fe-S] Proteins: Uncovering Control of Electron Shuttling and Gating in the Respiratory Metabolism of Molybdopterin Guanine Dinucleotide Enzymes. Methods Enzymol 2017; 599:157-196. [PMID: 29746239 DOI: 10.1016/bs.mie.2017.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
[Fe-S] clusters are essential cofactors in all domains of life. They play many biological roles due to their unique abilities for electron transfer and conformational control. Yet, producing and analyzing Fe-S proteins can be difficult and even misleading if not done anaerobically. Due to unique redox properties of [Fe-S] clusters and their oxygen sensitivity, they pose multiple challenges and can lose enzymatic activity or cause their component proteins to be structurally disordered due to [Fe-S] cluster oxidation and loss in air. Here we highlight tested protocols and strategies enabling efficient and stable [Fe-S] protein production, purification, crystallization, X-ray diffraction data collection, and structure determination. From multiple high-resolution anaerobic crystal structures, we furthermore analyze exemplary data defining [Fe-S] clusters, substrate entry, and product exit for the functional oxidation states of type II molybdo-bis(molybdopterin guanine dinucleotide) (Mo-bisMGD) enzymes. Notably, these enzymes perform electron shuttling between quinone pools and specific substrates to catalyze respiratory metabolism. The identified structure-activity relationships for this enzyme class have broad implications germane to perchlorate environments on Earth and Mars extending to an alternative mechanism underlying metabolic origins for the evolution of the oxygen atmosphere. Integrated structural analyses of type II Mo-bisMGD enzymes unveil novel distinctive shared molecular mechanisms for dynamic control of substrate entry and product release gated by hydrophobic residues. Collective findings support a prototypic model for type II Mo-bisMGD enzymes including insights for a fundamental molecular mechanistic understanding of selectivity and regulation by a conformationally gated channel with general implications for [Fe-S] cluster respiratory enzymes.
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Affiliation(s)
- Chi-Lin Tsai
- The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States
| | - John A Tainer
- The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
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12
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Modeling of the Reaction Mechanism of Enzymatic Radical C-C Coupling by Benzylsuccinate Synthase. Int J Mol Sci 2016; 17:514. [PMID: 27070573 PMCID: PMC4848970 DOI: 10.3390/ijms17040514] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/15/2016] [Accepted: 03/24/2016] [Indexed: 11/16/2022] Open
Abstract
Molecular modeling techniques and density functional theory calculations were performed to study the mechanism of enzymatic radical C–C coupling catalyzed by benzylsuccinate synthase (BSS). BSS has been identified as a glycyl radical enzyme that catalyzes the enantiospecific fumarate addition to toluene initiating its anaerobic metabolism in the denitrifying bacterium Thauera aromatica, and this reaction represents the general mechanism of toluene degradation in all known anaerobic degraders. In this work docking calculations, classical molecular dynamics (MD) simulations, and DFT+D2 cluster modeling was employed to address the following questions: (i) What mechanistic details of the BSS reaction yield the most probable molecular model? (ii) What is the molecular basis of enantiospecificity of BSS? (iii) Is the proposed mechanism consistent with experimental observations, such as an inversion of the stereochemistry of the benzylic protons, syn addition of toluene to fumarate, exclusive production of (R)-benzylsuccinate as a product and a kinetic isotope effect (KIE) ranging between 2 and 4? The quantum mechanics (QM) modeling confirms that the previously proposed hypothetical mechanism is the most probable among several variants considered, although C–H activation and not C–C coupling turns out to be the rate limiting step. The enantiospecificity of the enzyme seems to be enforced by a thermodynamic preference for binding of fumarate in the pro(R) orientation and reverse preference of benzyl radical attack on fumarate in pro(S) pathway which results with prohibitively high energy barrier of the radical quenching. Finally, the proposed mechanism agrees with most of the experimental observations, although the calculated intrinsic KIE from the model (6.5) is still higher than the experimentally observed values (4.0) which suggests that both C–H activation and radical quenching may jointly be involved in the kinetic control of the reaction.
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13
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Musat F, Vogt C, Richnow HH. Carbon and Hydrogen Stable Isotope Fractionation Associated with the Aerobic and Anaerobic Degradation of Saturated and Alkylated Aromatic Hydrocarbons. J Mol Microbiol Biotechnol 2016; 26:211-26. [DOI: 10.1159/000442161] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Saturated hydrocarbons (alkanes) and alkylated aromatic hydrocarbons are abundant environmental compounds. Hydrocarbons are primarily removed from the environment by biodegradation, a process usually associated with moderate carbon and significant hydrogen isotope fractionation allowing monitoring of biodegradation processes in the environment. Here, we review the carbon and hydrogen stable isotope fractionation associated with the cleavage of C-H bonds at alkyl chains of hydrocarbons. Propane, <i>n</i>-butane and ethylbenzene were used as model components for alkyl moieties of aliphatic and aromatic hydrocarbons with emphasis on the cleavage of the C-H bond without the involvement of molecular oxygen. The carbon and hydrogen isotope fractionation factors were further used to explore the diagnostic potential for characterizing the mode of bond cleavage under oxic and anoxic conditions. Λ factors, calculated to correlate carbon and hydrogen fractionation, allowed to distinguish between aerobic and anaerobic biodegradation processes in the environment.
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14
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von Netzer F, Kuntze K, Vogt C, Richnow HH, Boll M, Lueders T. Functional Gene Markers for Fumarate-Adding and Dearomatizing Key Enzymes in Anaerobic Aromatic Hydrocarbon Degradation in Terrestrial Environments. J Mol Microbiol Biotechnol 2016; 26:180-94. [PMID: 26959523 DOI: 10.1159/000441946] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Anaerobic degradation is a key process in many environments either naturally or anthropogenically exposed to petroleum hydrocarbons. Considerable advances into the biochemistry and physiology of selected anaerobic degraders have been achieved over the last decades, especially for the degradation of aromatic hydrocarbons. However, researchers have only recently begun to explore the ecology of complex anaerobic hydrocarbon degrader communities directly in their natural habitats, as well as in complex laboratory systems using tools of molecular biology. These approaches have mainly been facilitated by the establishment of a suite of targeted marker gene assays, allowing for rapid and directed insights into the diversity as well as the identity of intrinsic degrader populations and degradation potentials established at hydrocarbon-impacted sites. These are based on genes encoding either peripheral or central key enzymes in aromatic compound breakdown, such as fumarate-adding benzylsuccinate synthases or dearomatizing aryl-coenzyme A reductases, or on aromatic ring-cleaving hydrolases. Here, we review recent advances in this field, explain the different detection methodologies applied, and discuss how the detection of site-specific catabolic gene markers has improved the understanding of processes at contaminated sites. Functional marker gene-based strategies may be vital for the development of a more elaborate population-based assessment and prediction of aromatic degradation potentials in hydrocarbon-impacted environments.
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Affiliation(s)
- Frederick von Netzer
- Helmholtz Zentrum Mx00FC;nchen - German Research Center for Environmental Health, Institute of Groundwater Ecology, Neuherberg, Germany
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15
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Heider J, Szaleniec M, Sünwoldt K, Boll M. Ethylbenzene Dehydrogenase and Related Molybdenum Enzymes Involved in Oxygen-Independent Alkyl Chain Hydroxylation. J Mol Microbiol Biotechnol 2016; 26:45-62. [PMID: 26960184 DOI: 10.1159/000441357] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Ethylbenzene dehydrogenase initiates the anaerobic bacterial degradation of ethylbenzene and propylbenzene. Although the enzyme is currently only known from a few closely related denitrifying bacterial strains affiliated to the Rhodocyclaceae, it clearly marks a universally occurring mechanism used for attacking recalcitrant substrates in the absence of oxygen. Ethylbenzene dehydrogenase belongs to subfamily 2 of the DMSO reductase-type molybdenum enzymes together with paralogous enzymes involved in the oxygen-independent hydroxylation of p-cymene, the isoprenoid side chains of sterols and even possibly n-alkanes; the subfamily also extends to dimethylsulfide dehydrogenases, selenite, chlorate and perchlorate reductases and, most significantly, dissimilatory nitrate reductases. The biochemical, spectroscopic and structural properties of the oxygen-independent hydroxylases among these enzymes are summarized and compared. All of them consist of three subunits, contain a molybdenum-bis-molybdopterin guanine dinucleotide cofactor, five Fe-S clusters and a heme b cofactor of unusual ligation, and are localized in the periplasmic space as soluble enzymes. In the case of ethylbenzene dehydrogenase, it has been determined that the heme b cofactor has a rather high redox potential, which may also be inferred for the paralogous hydroxylases. The known structure of ethylbenzene dehydrogenase allowed the calculation of detailed models of the reaction mechanism based on the density function theory as well as QM-MM (quantum mechanics - molecular mechanics) methods, which yield predictions of mechanistic properties such as kinetic isotope effects that appeared consistent with experimental data.
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Affiliation(s)
- Johann Heider
- Laboratory of Microbial Biochemistry, LOEWE Center for Synthetic Microbiology, Philipps University of Marburg, Marburg, Germany
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16
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Muhr E, Leicht O, González Sierra S, Thanbichler M, Heider J. A Fluorescent Bioreporter for Acetophenone and 1-Phenylethanol derived from a Specifically Induced Catabolic Operon. Front Microbiol 2016; 6:1561. [PMID: 26858693 PMCID: PMC4729919 DOI: 10.3389/fmicb.2015.01561] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 12/23/2015] [Indexed: 01/18/2023] Open
Abstract
The β-proteobacterium Aromatoleum aromaticum degrades the aromatic ketone acetophenone, a key intermediate of anaerobic ethylbenzene metabolism, either aerobically or anaerobically via a complex ATP-dependent acetophenone carboxylase and a benzoylacetate-CoA ligase. The genes coding for these enzymes (apcABCDE and bal) are organized in an apparent operon and are expressed in the presence of the substrate acetophenone. To study the conditions under which this operon is expressed in more detail, we constructed a reporter strain by inserting a gene fusion of apcA, the first gene of the apc-bal operon, with the gene for the fluorescent protein mCherry into the chromosome of A. aromaticum. The fusion protein indeed accumulated consistently with the expression pattern of the acetophenone-metabolic enzymes under various growth conditions. After evaluating and quantifying the data by fluorescence microscopy, fluorescence-based flow cytometry and immunoblot analysis, mCherry production was found to be proportional to the applied acetophenone concentrations. The reporter strain allowed quantification of acetophenone within a concentration range of 50 μM (detection limit) to 250 μM after 12 and 24 h. Moreover, production of the Apc-mCherry fusion protein in the reporter strain was highly specific and responded to acetophenone and both enantiomers of 1-phenylethanol, which are easily converted to acetophenone. Other analogous substrates showed either a significantly weaker response or none at all. Therefore, the reporter strain provides a basis for the development of a specific bioreporter system for acetophenone with an application potential reaching from environmental monitoring to petroleum prospecting.
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Affiliation(s)
- Enrico Muhr
- Laboratory of Microbial Biochemistry, Department of Microbiology, Philipps-Universität Marburg Marburg, Germany
| | - Oliver Leicht
- Laboratory of Cellular Microbiology, Department of Microbiology, Philipps-Universität Marburg Marburg, Germany
| | - Silvia González Sierra
- LOEWE Center for Synthetic MicrobiologyMarburg, Germany; Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
| | - Martin Thanbichler
- Laboratory of Cellular Microbiology, Department of Microbiology, Philipps-Universität MarburgMarburg, Germany; LOEWE Center for Synthetic MicrobiologyMarburg, Germany; Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
| | - Johann Heider
- Laboratory of Microbial Biochemistry, Department of Microbiology, Philipps-Universität MarburgMarburg, Germany; LOEWE Center for Synthetic MicrobiologyMarburg, Germany
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17
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Ladino-Orjuela G, Gomes E, da Silva R, Salt C, Parsons JR. Metabolic Pathways for Degradation of Aromatic Hydrocarbons by Bacteria. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2016; 237:105-121. [PMID: 26613990 DOI: 10.1007/978-3-319-23573-8_5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The aim of this review was to build an updated collection of information focused on the mechanisms and elements involved in metabolic pathways of aromatic hydrocarbons by bacteria. Enzymes as an expression of the genetic load and the type of electron acceptor available, as an environmental factor, were highlighted. In general, the review showed that both aerobic routes and anaerobic routes for the degradation of aromatic hydrocarbons are divided into two pathways. The first, named the upper pathways, entails the route from the original compound to central intermediate compounds still containing the aromatic ring but with the benzene nucleus chemically destabilized. The second, named the lower pathway, begins with ring de-aromatization and subsequent cleavage, resulting in metabolites that can be used by bacteria in the production of biomass. Under anaerobic conditions the five mechanisms of activation of the benzene ring described show the diversity of chemical reactions that can take place. Obtaining carbon and energy from an aromatic hydrocarbon molecule is a process that exhibits the high complexity level of the metabolic apparatus of anaerobic microorganisms. The ability of these bacteria to express enzymes that catalyze reactions, known only in non-biological conditions, using final electron acceptors with a low redox potential, is a most interesting topic. The discovery of phylogenetic and functional characteristics of cultivable and noncultivable hydrocarbon degrading bacteria has been made possible by improvements in molecular research techniques such as SIP (stable isotope probing) tracing the incorporation of (13)C, (15)N and (18)O into nucleic acids and proteins. Since many metabolic pathways in which enzyme and metabolite participants are still unknown, much new research is required. Therefore, it will surely allow enhancing the known and future applications in practice.
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Affiliation(s)
- Guillermo Ladino-Orjuela
- Laboratory of Biochemistry and Applied Microbiology, Institute of Biosciences, Letters and Exact Sciences (IBILCE) - São Paulo State University (Unesp), Rua Cristóvão Colombo, 2265, São José do Rio Preto, São Paulo, 15013-000, Brazil.
| | - Eleni Gomes
- Laboratory of Biochemistry and Applied Microbiology, Institute of Biosciences, Letters and Exact Sciences (IBILCE) - São Paulo State University (Unesp), Rua Cristóvão Colombo, 2265, São José do Rio Preto, São Paulo, 15013-000, Brazil.
| | - Roberto da Silva
- Laboratory of Biochemistry and Applied Microbiology, Institute of Biosciences, Letters and Exact Sciences (IBILCE) - São Paulo State University (Unesp), Rua Cristóvão Colombo, 2265, São José do Rio Preto, São Paulo, 15013-000, Brazil.
| | - Christopher Salt
- Institute for Biodiversity and Ecosystem Dynamics (IBED), Universiteit Van Amsterdam, 94248, Amsterdam, 1090 GE, The Netherlands.
| | - John R Parsons
- Institute for Biodiversity and Ecosystem Dynamics (IBED), Universiteit Van Amsterdam, 94248, Amsterdam, 1090 GE, The Netherlands.
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18
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Manzella MP, Holmes DE, Rocheleau JM, Chung A, Reguera G, Kashefi K. The complete genome sequence and emendation of the hyperthermophilic, obligate iron-reducing archaeon "Geoglobus ahangari" strain 234(T). Stand Genomic Sci 2015; 10:77. [PMID: 26457129 PMCID: PMC4600277 DOI: 10.1186/s40793-015-0035-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/07/2015] [Indexed: 11/10/2022] Open
Abstract
“Geoglobus ahangari” strain 234T is an obligate Fe(III)-reducing member of the Archaeoglobales, within the archaeal phylum Euryarchaeota, isolated from the Guaymas Basin hydrothermal system. It grows optimally at 88 °C by coupling the reduction of Fe(III) oxides to the oxidation of a wide range of compounds, including long-chain fatty acids, and also grows autotrophically with hydrogen and Fe(III). It is the first archaeon reported to use a direct contact mechanism for Fe(III) oxide reduction, relying on a single archaellum for locomotion, numerous curled extracellular appendages for attachment, and outer-surface heme-containing proteins for electron transfer to the insoluble Fe(III) oxides. Here we describe the annotation of the genome of “G. ahangari” strain 234T and identify components critical to its versatility in electron donor utilization and obligate Fe(III) respiratory metabolism at high temperatures. The genome comprises a single, circular chromosome of 1,770,093 base pairs containing 2034 protein-coding genes and 52 RNA genes. In addition, emended descriptions of the genus “Geoglobus” and species “G. ahangari” are described.
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Affiliation(s)
- Michael P Manzella
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI USA
| | - Dawn E Holmes
- Department of Physical and Biological Sciences, Western New England University, Springfield, MA USA
| | - Jessica M Rocheleau
- Department of Physical and Biological Sciences, Western New England University, Springfield, MA USA
| | - Amanda Chung
- Department of Physical and Biological Sciences, Western New England University, Springfield, MA USA
| | - Gemma Reguera
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI USA
| | - Kazem Kashefi
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI USA
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19
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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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20
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Kalimuthu P, Heider J, Knack D, Bernhardt PV. Electrocatalytic Hydrocarbon Hydroxylation by Ethylbenzene Dehydrogenase from Aromatoleum aromaticum. J Phys Chem B 2015; 119:3456-63. [DOI: 10.1021/jp512562k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Palraj Kalimuthu
- School of Chemistry
and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia
| | - Johann Heider
- Laboratory for
Microbial Biochemistry and Synmikro Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
| | - Daniel Knack
- Laboratory for
Microbial Biochemistry and Synmikro Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
| | - Paul V. Bernhardt
- School of Chemistry
and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia
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21
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Tataruch M, Heider J, Bryjak J, Nowak P, Knack D, Czerniak A, Liesiene J, Szaleniec M. Suitability of the hydrocarbon-hydroxylating molybdenum-enzyme ethylbenzene dehydrogenase for industrial chiral alcohol production. J Biotechnol 2014; 192 Pt B:400-9. [DOI: 10.1016/j.jbiotec.2014.06.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 05/23/2014] [Accepted: 06/25/2014] [Indexed: 10/25/2022]
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22
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Head IM, Gray ND, Larter SR. Life in the slow lane; biogeochemistry of biodegraded petroleum containing reservoirs and implications for energy recovery and carbon management. Front Microbiol 2014; 5:566. [PMID: 25426105 PMCID: PMC4227522 DOI: 10.3389/fmicb.2014.00566] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 10/08/2014] [Indexed: 11/15/2022] Open
Abstract
Our understanding of the processes underlying the formation of heavy oil has been transformed in the last decade. The process was once thought to be driven by oxygen delivered to deep petroleum reservoirs by meteoric water. This paradigm has been replaced by a view that the process is anaerobic and frequently associated with methanogenic hydrocarbon degradation. The thermal history of a reservoir exerts a fundamental control on the occurrence of biodegraded petroleum, and microbial activity is focused at the base of the oil column in the oil water transition zone, that represents a hotspot in the petroleum reservoir biome. Here we present a synthesis of new and existing microbiological, geochemical, and biogeochemical data that expands our view of the processes that regulate deep life in petroleum reservoir ecosystems and highlights interactions of a range of biotic and abiotic factors that determine whether petroleum is likely to be biodegraded in situ, with important consequences for oil exploration and production. Specifically we propose that the salinity of reservoir formation waters exerts a key control on the occurrence of biodegraded heavy oil reservoirs and introduce the concept of palaeopickling. We also evaluate the interaction between temperature and salinity to explain the occurrence of non-degraded oil in reservoirs where the temperature has not reached the 80-90°C required for palaeopasteurization. In addition we evaluate several hypotheses that might explain the occurrence of organisms conventionally considered to be aerobic, in nominally anoxic petroleum reservoir habitats. Finally we discuss the role of microbial processes for energy recovery as we make the transition from fossil fuel reliance, and how these fit within the broader socioeconomic landscape of energy futures.
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Affiliation(s)
- Ian M. Head
- School of Civil Engineering and Geosciences, Newcastle UniversityNewcastle upon Tyne, UK
| | - Neil D. Gray
- School of Civil Engineering and Geosciences, Newcastle UniversityNewcastle upon Tyne, UK
| | - Stephen R. Larter
- School of Civil Engineering and Geosciences, Newcastle UniversityNewcastle upon Tyne, UK
- Petroleum Reservoir Group, Department of Geoscience, University of CalgaryCalgary, AB, Canada
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23
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Anaerobic activation of p-cymene in denitrifying betaproteobacteria: methyl group hydroxylation versus addition to fumarate. Appl Environ Microbiol 2014; 80:7592-603. [PMID: 25261521 DOI: 10.1128/aem.02385-14] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The betaproteobacteria "Aromatoleum aromaticum" pCyN1 and "Thauera" sp. strain pCyN2 anaerobically degrade the plant-derived aromatic hydrocarbon p-cymene (4-isopropyltoluene) under nitrate-reducing conditions. Metabolite analysis of p-cymene-adapted "A. aromaticum" pCyN1 cells demonstrated the specific formation of 4-isopropylbenzyl alcohol and 4-isopropylbenzaldehyde, whereas with "Thauera" sp. pCyN2, exclusively 4-isopropylbenzylsuccinate and tentatively identified (4-isopropylphenyl)itaconate were observed. 4-Isopropylbenzoate in contrast was detected with both strains. Proteogenomic investigation of p-cymene- versus succinate-adapted cells of the two strains revealed distinct protein profiles agreeing with the different metabolites formed from p-cymene. "A. aromaticum" pCyN1 specifically produced (i) a putative p-cymene dehydrogenase (CmdABC) expected to hydroxylate the benzylic methyl group of p-cymene, (ii) two dehydrogenases putatively oxidizing 4-isopropylbenzyl alcohol (Iod) and 4-isopropylbenzaldehyde (Iad), and (iii) the putative 4-isopropylbenzoate-coenzyme A (CoA) ligase (Ibl). The p-cymene-specific protein profile of "Thauera" sp. pCyN2, on the other hand, encompassed proteins homologous to subunits of toluene-activating benzylsuccinate synthase (termed [4-isopropylbenzyl]succinate synthase IbsABCDEF; identified subunits, IbsAE) and protein homologs of the benzylsuccinate β-oxidation (Bbs) pathway (termed BisABCDEFGH; all identified except for BisEF). This study reveals that two related denitrifying bacteria employ fundamentally different peripheral degradation routes for one and the same substrate, p-cymene, with the two pathways apparently converging at the level of 4-isopropylbenzoyl-CoA.
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24
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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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25
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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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26
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Szaleniec M, Dudzik A, Kozik B, Borowski T, Heider J, Witko M. Mechanistic basis for the enantioselectivity of the anaerobic hydroxylation of alkylaromatic compounds by ethylbenzene dehydrogenase. J Inorg Biochem 2014; 139:9-20. [PMID: 24950385 DOI: 10.1016/j.jinorgbio.2014.05.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 05/16/2014] [Accepted: 05/18/2014] [Indexed: 11/26/2022]
Abstract
The enantioselectivity of reactions catalyzed by ethylbenzene dehydrogenase, a molybdenum enzyme that catalyzes the oxygen-independent hydroxylation of many alkylaromatic and alkylheterocyclic compounds to secondary alcohols, was studied by chiral chromatography and theoretical modeling. Chromatographic analyses of 22 substrates revealed that this enzyme exhibits remarkably high reaction enantioselectivity toward (S)-secondary alcohols (18 substrates converted with >99% ee). Theoretical QM:MM modeling was used to elucidate the structure of the catalytically active form of the enzyme and to study the reaction mechanism and factors determining its high degree of enantioselectivity. This analysis showed that the enzyme imposes strong stereoselectivity on the reaction by discriminating the hydrogen atom abstracted from the substrate. Activation of the pro(S) hydrogen atom was calculated to be 500 times faster than of the pro(R) hydrogen atom. The actual hydroxylation step (i.e., hydroxyl group rebound reaction to a carbocation intermediate) does not appear to be enantioselective enough to explain the experimental data (the calculated rate ratios were in the range of only 2-50 for pro(S): pro(R)-oriented OH rebound).
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Affiliation(s)
- Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Kraków, Poland.
| | - Agnieszka Dudzik
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Kraków, Poland
| | - Bartłomiej Kozik
- Department of Organic Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Kraków, Poland
| | - Johann Heider
- Laboratory for Microbial Biochemistry, Philipps University of Marburg, Karl-von-Frisch Strasse 8, D-35043 Marburg, Germany
| | - Małgorzata Witko
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Kraków, Poland
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27
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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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28
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Affiliation(s)
- Russ Hille
- Department of Biochemistry, University of California, Riverside, Riverside, California 92521, United States
| | - James Hall
- Department of Biochemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Partha Basu
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
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29
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Primers: Functional Genes for Anaerobic Hydrocarbon Degrading Microbes. SPRINGER PROTOCOLS HANDBOOKS 2014. [DOI: 10.1007/8623_2014_44] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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Boll M, Löffler C, Morris BEL, Kung JW. Anaerobic degradation of homocyclic aromatic compounds via arylcarboxyl-coenzyme A esters: organisms, strategies and key enzymes. Environ Microbiol 2013; 16:612-27. [PMID: 24238333 DOI: 10.1111/1462-2920.12328] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/03/2013] [Indexed: 11/28/2022]
Abstract
Next to carbohydrates, aromatic compounds are the second most abundant class of natural organic molecules in living organic matter but also make up a significant proportion of fossil carbon sources. Only microorganisms are capable of fully mineralizing aromatic compounds. While aerobic microbes use well-studied oxygenases for the activation and cleavage of aromatic rings, anaerobic bacteria follow completely different strategies to initiate catabolism. The key enzymes related to aromatic compound degradation in anaerobic bacteria are comprised of metal- and/or flavin-containing cofactors, of which many use unprecedented radical mechanisms for C-H bond cleavage or dearomatization. Over the past decade, the increasing number of completed genomes has helped to reveal a large variety of anaerobic degradation pathways in Proteobacteria, Gram-positive microbes and in one archaeon. This review aims to update our understanding of the occurrence of aromatic degradation capabilities in anaerobic microorganisms and serves to highlight characteristic enzymatic reactions involved in (i) the anoxic oxidation of alkyl side chains attached to aromatic rings, (ii) the carboxylation of aromatic rings and (iii) the reductive dearomatization of central arylcarboxyl-coenzyme A intermediates. Depending on the redox potential of the electron acceptors used and the metabolic efficiency of the cell, different strategies may be employed for identical overall reactions.
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Affiliation(s)
- Matthias Boll
- Institute for Biology II, University of Freiburg, Freiburg, Germany
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31
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Dudzik A, Kozik B, Tataruch M, Wójcik A, Knack D, Borowski T, Heider J, Witko M, Szaleniec M. The reaction mechanism of chiral hydroxylation of p-OH and p-NH2 substituted compounds by ethylbenzene dehydrogenase. CAN J CHEM 2013. [DOI: 10.1139/cjc-2012-0504] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Ethylbenzene dehydrogenase (EbDH; enzyme commission (EC) number: 1.17.99.2) is a unique biocatalyst that hydroxylates alkylaromatic and alkylheterocyclic compounds to (S)-secondary alcohols under anaerobic conditions. The enzyme exhibits a high promiscuity catalyzing oxidation of over 30 substrates, inter alia, para-substituted alkylphenols and alkylanilines. Secondary alcohols with OH and NH2 substituents in the aromatic ring are highly valuable synthons for many biologically active compounds in the fine chemical industry. EbDH hydroxylates most of the studied compounds highly enantioselectively, except for five substrates that harbour OH and NH2 groups in the para position, which exhibit a significant decrease in the percent enantiomeric excess (% ee). This phenomenon is inconsistent with the previously suggested enzyme mechanism, but it may be linked to a stabilization of the carbocation intermediate by deprotonation of the OH or NH2 substituent in the active site that yields a transient quinone (imine) ethide species. This would initiate an alternative reaction pathway involving the addition of a water molecule to a C=C double bond. This hypothesis was cross-validated by density functional theory (DFT) cluster modelling of the alternative reaction pathway with 4-ethylphenol, as well as by experimental assessment of the pH dependency of enantiomeric excesses. The results reported herein suggest that the alternative reaction pathway may significantly contribute to the overall reaction if the carbocation intermediates are stabilized by deprotonation.
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Affiliation(s)
- Agnieszka Dudzik
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences Niezapominajek 8, 30-239 Kraków, Poland
| | - Bartłomiej Kozik
- Department of Organic Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland
| | - Mateusz Tataruch
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences Niezapominajek 8, 30-239 Kraków, Poland
| | - Anna Wójcik
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences Niezapominajek 8, 30-239 Kraków, Poland
| | - Daniel Knack
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences Niezapominajek 8, 30-239 Kraków, Poland
- Laboratory for Microbial Biochemistry, Philipps University of Marburg, Karl-von-Frisch Strasse 8, D-35043 Marburg, Germany
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences Niezapominajek 8, 30-239 Kraków, Poland
| | - Johann Heider
- Laboratory for Microbial Biochemistry, Philipps University of Marburg, Karl-von-Frisch Strasse 8, D-35043 Marburg, Germany
| | - Małgorzata Witko
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences Niezapominajek 8, 30-239 Kraków, Poland
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences Niezapominajek 8, 30-239 Kraków, Poland
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Identification of a possible respiratory arsenate reductase in Denitrovibrio acetiphilus, a member of the phylum Deferribacteres. Arch Microbiol 2013; 195:661-70. [DOI: 10.1007/s00203-013-0915-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 07/09/2013] [Accepted: 07/17/2013] [Indexed: 01/05/2023]
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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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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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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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Kartal B, de Almeida NM, Maalcke WJ, Op den Camp HJM, Jetten MSM, Keltjens JT. How to make a living from anaerobic ammonium oxidation. FEMS Microbiol Rev 2013; 37:428-61. [PMID: 23210799 DOI: 10.1111/1574-6976.12014] [Citation(s) in RCA: 291] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 10/25/2012] [Accepted: 11/21/2012] [Indexed: 11/28/2022] Open
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria primarily grow by the oxidation of ammonium coupled to nitrite reduction, using CO2 as the sole carbon source. Although they were neglected for a long time, anammox bacteria are encountered in an enormous species (micro)diversity in virtually any anoxic environment that contains fixed nitrogen. It has even been estimated that about 50% of all nitrogen gas released into the atmosphere is made by these 'impossible' bacteria. Anammox catabolism most likely resides in a special cell organelle, the anammoxosome, which is surrounded by highly unusual ladder-like (ladderane) lipids. Ammonium oxidation and nitrite reduction proceed in a cyclic electron flow through two intermediates, hydrazine and nitric oxide, resulting in the generation of proton-motive force for ATP synthesis. Reduction reactions associated with CO2 fixation drain electrons from this cycle, and they are replenished by the oxidation of nitrite to nitrate. Besides ammonium or nitrite, anammox bacteria use a broad range of organic and inorganic compounds as electron donors. An analysis of the metabolic opportunities even suggests alternative chemolithotrophic lifestyles that are independent of these compounds. We note that current concepts are still largely hypothetical and put forward the most intriguing questions that need experimental answers.
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Affiliation(s)
- Boran Kartal
- Department of Microbiology, Faculty of Science, Institute of Wetland and Water Research, Radboud University of Nijmegen, Nijmegen, The Netherlands
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Vogt C, Richnow HH. Bioremediation via in situ microbial degradation of organic pollutants. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 142:123-46. [PMID: 24337042 DOI: 10.1007/10_2013_266] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Contamination of soil and natural waters by organic pollutants is a global problem. The major organic pollutants of point sources are mineral oil, fuel components, and chlorinated hydrocarbons. Research from the last two decades discovered that most of these compounds are biodegradable under anoxic conditions. This has led to the rise of bioremediation strategies based on the in situ biodegradation of pollutants. Monitored natural attenuation is a concept by which a contaminated site is remediated by natural biodegradation; to evaluate such processes, a combination of chemical and microbiological methods are usually used. Compound specific stable isotope analysis emerged as a key method for detecting and quantifying in situ biodegradation. Natural attenuation processes can be initiated or accelerated by manipulating the environmental conditions to become favorable for indigenous pollutant degrading microbial communities or by adding externally breeded specific pollutant degrading microorganisms; these techniques are referred to as enhanced natural attenuation. Xenobiotic micropollutants, such as pesticides or pharmaceuticals, contaminate diffusively large areas in low concentrations; the biodegradation pattern of such contaminations are not yet understood.
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Affiliation(s)
- Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany,
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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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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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Yadav S, Yadav R, Yadav K. Stereoselective benzylic hydroxylation of ethylbenzene and propylbenzene using the mycelia of Aspergillus flavus MTCC-1783 and MTCC-1884. CAN J CHEM 2012. [DOI: 10.1139/v2012-034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The aim of this study was to provide syntheses of optically pure (R)-1-phenylethanol and (R)-1-phenylpropanol from ethylbenzene and propylbenzene, respectively, using the fungal mycelia of new fungal species, namely Aspergillus flavus MTCC-1783 and Aspergillus flavus MTCC-1884, as catalysts. The mycelia of A. flavus MTCC- 1783 and A. flavus MTCC-1884 were prepared by growing the fungal strains in liquid culture medium containing ethylmethylketone as the sole carbon source. The mycelia were suspended in potassium phosphate buffer pH 7.0. The suspensions of mycelia were used for the transformations of ethylbenzene and propylbenzene. Ethylbenzene and propylbenzene were converted to (R)-1-phenylethanol and (R)-1-phenylpropanol, in 100% and 99% ee, respectively. The mycelia of A. flavus MTCC-1783 and A. flavus MTCC-1884 can be used for the preparation of (R)-1-phenylethanol and (R)-1-phenylpropanol in 100% and 99% ee, respectively, from ethylbenzene and propylbenzene, respectively. The studies report convenient methods for the syntheses of optically pure isomers, (R)-1-phenylethanol and (R)-1-phenylpropanol, which are important chiral building blocks in the preparations of fine chemicals and pharmaceuticals. The reactions are ecofriendly, occur at 30 °C, and the time required was 24 h.
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Affiliation(s)
- Saroj Yadav
- Department of Chemistry, D.D.U. Gorakhpur University, Gorakhpur-273 009, India
| | - R.S.S. Yadav
- Department of Chemistry, D.D.U. Gorakhpur University, Gorakhpur-273 009, India
| | - K.D.S. Yadav
- Department of Chemistry, D.D.U. Gorakhpur University, Gorakhpur-273 009, India
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Szaleniec M. Prediction of enzyme activity with neural network models based on electronic and geometrical features of substrates. Pharmacol Rep 2012; 64:761-81. [DOI: 10.1016/s1734-1140(12)70873-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 04/16/2012] [Indexed: 11/26/2022]
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Wawrik B, Mendivelso M, Parisi VA, Suflita JM, Davidova IA, Marks CR, Van Nostrand JD, Liang Y, Zhou J, Huizinga BJ, Strąpoć D, Callaghan AV. Field and laboratory studies on the bioconversion of coal to methane in the San Juan Basin. FEMS Microbiol Ecol 2012; 81:26-42. [PMID: 22146015 DOI: 10.1111/j.1574-6941.2011.01272.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 11/18/2011] [Accepted: 11/28/2011] [Indexed: 11/30/2022] Open
Abstract
The bioconversion of coal to methane in the San Juan Basin, New Mexico, was investigated. Production waters were analyzed via enrichment studies, metabolite-profiling, and culture-independent methods. Analysis of 16S rRNA gene sequences indicated the presence of methanogens potentially capable of acetoclastic, hydrogenotrophic, and methylotrophic metabolisms, predominantly belonging to the Methanosarcinales and Methanomicrobiales. Incubations of produced water and coal readily produced methane, but there was no correlation between the thermal maturity and methanogenesis. Coal methanogenesis was greater when samples with a greater richness of Firmicutes were utilized. A greater archaeal diversity was observed in the presence of several aromatic and short-chain fatty acid metabolites. Incubations amended with lactate, hydrogen, formate, and short-chain alcohols produced methane above un-amended controls. Methanogenesis from acetate was not observed. Metabolite profiling showed the widespread occurrence of putative aromatic ring intermediates including benzoate, toluic acids, phthalic acids, and cresols. The detection of saturated and unsaturated alkylsuccinic acids indicated n-alkane and cyclic alkane/alkene metabolism. Microarray analysis complemented observations based on hybridization to functional genes related to the anaerobic metabolism of aromatic and aliphatic substrates. These data suggest that coal methanogenesis is unlikely to be limited by methanogen biomass, but rather the activation and degradation of coal constituents.
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Affiliation(s)
- Boris Wawrik
- Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA.
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Abstract
Aromatic compounds are both common growth substrates for microorganisms and prominent environmental pollutants. The crucial step in their degradation is overcoming the resonance energy that stabilizes the ring structure. The classical strategy for degradation comprises an attack by oxygenases that hydroxylate and finally cleave the ring with the help of activated molecular oxygen. Here, we describe three alternative strategies used by microorganisms to degrade aromatic compounds. All three of these methods involve the use of CoA thioesters and ring cleavage by hydrolysis. However, these strategies are based on different ring activation mechanisms that consist of either formation of a non-aromatic ring-epoxide under oxic conditions, or reduction of the aromatic ring under anoxic conditions using one of two completely different systems.
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Yadav S, Yadav RS, Yadava S, Yadav KD. Stereoselective hydroxylation of ethylbenzene to (R)-1-phenylethanol using mycelia of Aspergillus niger as catalyst. CATAL COMMUN 2011. [DOI: 10.1016/j.catcom.2011.01.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Thermostable properties of the periplasmic selenate reductase from Thauera selenatis. Biochimie 2010; 92:1268-73. [DOI: 10.1016/j.biochi.2010.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 06/04/2010] [Indexed: 11/18/2022]
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46
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Abstract
Whole-cell biocatalysis utilizes native or recombinant enzymes produced by cellular metabolism to perform synthetically interesting reactions. Besides hydrolases, oxidoreductases represent the most applied enzyme class in industry. Oxidoreductases are attributed a high future potential, especially for applications in the chemical and pharmaceutical industries, as they enable highly interesting chemistry (e.g., the selective oxyfunctionalization of unactivated C-H bonds). Redox reactions are characterized by electron transfer steps that often depend on redox cofactors as additional substrates. Their regeneration typically is accomplished via the metabolism of whole-cell catalysts. Traditionally, studies towards productive redox biocatalysis focused on the biocatalytic enzyme, its activity, selectivity, and specificity, and several successful examples of such processes are running commercially. However, redox cofactor regeneration by host metabolism was hardly considered for the optimization of biocatalytic rate, yield, and/or titer. This article reviews molecular mechanisms of oxidoreductases with synthetic potential and the host redox metabolism that fuels biocatalytic reactions with redox equivalents. The tools discussed in this review for investigating redox metabolism provide the basis for studies aiming at a deeper understanding of the interplay between synthetically active enzymes and metabolic networks. The ultimate goal of rational whole-cell biocatalyst engineering and use for fine chemical production is discussed.
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Lowe EC, Bydder S, Hartshorne RS, Tape HLU, Dridge EJ, Debieux CM, Paszkiewicz K, Singleton I, Lewis RJ, Santini JM, Richardson DJ, Butler CS. Quinol-cytochrome c oxidoreductase and cytochrome c4 mediate electron transfer during selenate respiration in Thauera selenatis. J Biol Chem 2010; 285:18433-42. [PMID: 20388716 PMCID: PMC2881769 DOI: 10.1074/jbc.m110.115873] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 04/01/2010] [Indexed: 11/06/2022] Open
Abstract
Selenate reductase (SER) from Thauera selenatis is a periplasmic enzyme that has been classified as a type II molybdoenzyme. The enzyme comprises three subunits SerABC, where SerC is an unusual b-heme cytochrome. In the present work the spectropotentiometric characterization of the SerC component and the identification of redox partners to SER are reported. The mid-point redox potential of the b-heme was determined by optical titration (E(m) + 234 +/- 10 mV). A profile of periplasmic c-type cytochromes expressed in T. selenatis under selenate respiring conditions was undertaken. Two c-type cytochromes were purified ( approximately 24 and approximately 6 kDa), and the 24-kDa protein (cytc-Ts4) was shown to donate electrons to SerABC in vitro. Protein sequence of cytc-Ts4 was obtained by N-terminal sequencing and liquid chromatography-tandem mass spectrometry analysis, and based upon sequence similarities, was assigned as a member of cytochrome c(4) family. Redox potentiometry, combined with UV-visible spectroscopy, showed that cytc-Ts4 is a diheme cytochrome with a redox potential of +282 +/- 10 mV, and both hemes are predicted to have His-Met ligation. To identify the membrane-bound electron donors to cytc-Ts4, growth of T. selenatis in the presence of respiratory inhibitors was monitored. The specific quinol-cytochrome c oxidoreductase (QCR) inhibitors myxothiazol and antimycin A partially inhibited selenate respiration, demonstrating that some electron flux is via the QCR. Electron transfer via a QCR and a diheme cytochrome c(4) is a novel route for a member of the DMSO reductase family of molybdoenzymes.
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Affiliation(s)
- Elisabeth C. Lowe
- From the School of Biosciences, Centre for Biocatalysis, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - Sarah Bydder
- the Department of Microbiology, La Trobe University, 3086 Victoria, Australia
| | - Robert S. Hartshorne
- the School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Hannah L. U. Tape
- From the School of Biosciences, Centre for Biocatalysis, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - Elizabeth J. Dridge
- From the School of Biosciences, Centre for Biocatalysis, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - Charles M. Debieux
- From the School of Biosciences, Centre for Biocatalysis, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - Konrad Paszkiewicz
- From the School of Biosciences, Centre for Biocatalysis, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - Ian Singleton
- the Institute for Research on Environment and Sustainability, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Richard J. Lewis
- the Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom, and
| | - Joanne M. Santini
- the Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - David J. Richardson
- the School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Clive S. Butler
- From the School of Biosciences, Centre for Biocatalysis, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
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Szaleniec M, Borowski T, Schühle K, Witko M, Heider J. Ab Inito Modeling of Ethylbenzene Dehydrogenase Reaction Mechanism. J Am Chem Soc 2010; 132:6014-24. [DOI: 10.1021/ja907208k] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maciej Szaleniec
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
| | - Tomasz Borowski
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
| | - Karola Schühle
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
| | - Malgorzata Witko
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
| | - Johann Heider
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
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Anaerobic oxidation of fatty acids and alkenes by the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus. Appl Environ Microbiol 2010; 76:3057-60. [PMID: 20305028 DOI: 10.1128/aem.02810-09] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Archaeoglobus fulgidus oxidizes fatty acids (C(4) to C(18)) and n-alk-1-enes (C(12:1) to C(21:1)) in the presence of thiosulfate as a terminal electron acceptor. End products of metabolism were CO(2) and sulfide. Growth on perdeuterated hexadecene yielded C(15)- to C(17)-labeled fatty acids as metabolites, thus confirming the ability of A. fulgidus to oxidize alkyl chains.
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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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