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Vigil W, Nguyen D, Niks D, Hille R. Rapid-reaction kinetics of the butyryl-CoA dehydrogenase component of the electron-bifurcating crotonyl-CoA-dependent NADH:ferredoxin oxidoreductase from Megasphaera elsdenii. J Biol Chem 2023:104853. [PMID: 37220854 PMCID: PMC10320503 DOI: 10.1016/j.jbc.2023.104853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/25/2023] Open
Abstract
We have investigated the equilibrium properties and rapid-reaction kinetics of the isolated butyryl-CoA dehydrogenase (bcd) component of the electron-bifurcating crotonyl-CoA-dependent NADH:ferredoxin oxidoreductase (EtfAB:bcd) from Megasphaera elsdenii. We find that a neutral FADH• semiquinone accumulates transiently during both reduction with sodium dithionite and with NADH in the presence of catalytic concentrations of EtfAB. In both cases full reduction of bcd to the hydroquinone is eventually observed, but the accumulation of FADH• indicates that a substantial portion of reduction occurs in sequential one-electron processes rather than a single two-electron event. In rapid-reaction experiments following the reaction of reduced bcd with crotonyl-CoA and oxidized bcd with butyryl-CoA, long-wavelength-absorbing intermediates are observed that are assigned to bcdred:crotonyl-CoA and bcdox:butyryl-CoA charge-transfer complexes, demonstrating their kinetic competence in the course of the reaction. In the presence of crotonyl-CoA there is an accumulation of semiquinone that is unequivocally the anionic FAD•- rather than the neutral FADH• seen in the absence of substrate, indicating that binding of substrate/product results in ionization of the bcd semiquinone. In addition to fully characterizing the rapid-reaction kinetics of both the oxidative and reductive half-reactions, our results demonstrate that one-electron processes play an important role in the reduction of bcd in EtfAB:bcd.
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Affiliation(s)
- Wayne Vigil
- Department of Biochemistry, University of California, Riverside, Riverside CA 92521.
| | - Derek Nguyen
- Department of Biochemistry, University of California, Riverside, Riverside CA 92521
| | - Dimitri Niks
- Department of Biochemistry, University of California, Riverside, Riverside CA 92521
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, Riverside CA 92521
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2
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QM/MM study of the [4Fe-4S]-dependent (R)-2-hydroxyisocaproyl-CoA dehydratase: Dehydration via a redox pathway with an α-carbonyl radical intermediate. J Catal 2023. [DOI: 10.1016/j.jcat.2023.01.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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3
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Owatari Y, Iseki S, Ogata D, Yuasa J. Catalytic electron drives host-guest recognition. Chem Sci 2022; 13:5261-5267. [PMID: 35655551 PMCID: PMC9093170 DOI: 10.1039/d2sc01342h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/03/2022] [Indexed: 01/17/2023] Open
Abstract
Electron injection is demonstrated to trigger electrocatalytic chain reactions capable of releasing a solvent molecule and forming a redox active guest molecule. One-electron reduction of a hydroxy anthrone derivative (AQH-CH2CN) results in the formation of an anthraquinone radical anion (AQ˙-) and acetonitrile (CH3CN). The resulting fragment of AQ˙- exhibits high stability under mild reducing conditions, and it has enough reducing power to reduce the reactant of AQH-CH2CN. Hence, subsequent electron transfer from AQ˙- to AQH-CH2CN yields the secondary AQ˙- and CH3CN, while the initial AQ˙- is subsequently oxidized to AQ. Overall, the reactants of AQH-CH2CN are completely converted into AQ and CH3CN in sustainable electrocatalytic chain reactions. These electrocatalytic chain reactions are mild and sustainable, successfully achieving catalytic electron-triggered charge-transfer (CT) complex formation. Reactant AQH-CH2CN is non-planar, making it unsuitable for CT interaction with an electron donor host compound (UHAnt2) bearing parallel anthracene tweezers. However, conversion of AQH-CH2CN to planar electron acceptor AQ by the electrocatalytic chain reactions turns on CT interaction, generating a host CT complex with UHAnt2 (AQ ⊂ UHAnt2). Therefore, sustainable electrocatalytic chain reactions can control CT interactions using only a catalytic amount of electrons, ultimately affording a one-electron switch associated with catalytic electron-triggered turn-on molecular recognition.
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Affiliation(s)
- Yoshihiro Owatari
- Department of Applied Chemistry, Tokyo University of Science 1-3 Kagurazaka, Shinjuku Tokyo 162-8601 Japan +81-3-72-6179
| | - Shuta Iseki
- Department of Applied Chemistry, Tokyo University of Science 1-3 Kagurazaka, Shinjuku Tokyo 162-8601 Japan +81-3-72-6179
| | - Daiji Ogata
- Department of Applied Chemistry, Tokyo University of Science 1-3 Kagurazaka, Shinjuku Tokyo 162-8601 Japan +81-3-72-6179
| | - Junpei Yuasa
- Department of Applied Chemistry, Tokyo University of Science 1-3 Kagurazaka, Shinjuku Tokyo 162-8601 Japan +81-3-72-6179
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4
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Lee H, Hong A, Kwak J, Lee S. Synthesis of UV/blue light-emitting aluminum hydroxide with oxygen vacancy and their application to electrically driven light-emitting diodes. RSC Adv 2022; 12:4322-4328. [PMID: 35425415 PMCID: PMC8981236 DOI: 10.1039/d1ra07942e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/26/2022] [Indexed: 12/22/2022] Open
Abstract
Aluminum hydroxide nanoparticles, one of the essential luminescent materials for display technology, bio-imaging, and sensors due to their non-toxicity, affordable pricing, and rare-earth-free phosphors, are synthesized via a simple method at a reaction time of 10 min at a low temperature of 200 °C. By controlling the precursor's ratio of aluminum acetylacetonate to oleic acid, UV or blue light-emitting aluminum hydroxides with oxygen defects and carbonyl radicals can be synthesized. As a result, aluminum hydroxide (Al(OH)3−x) nanoparticles overwhelmingly emit UVA light (390 nm) because of the oxygen defects in nanoparticles, and carbon-related radicals on the nanoparticles are responsible for the blue-light emission at 465 nm. Electrically driven light-emitting devices are applied using luminescent aluminum hydroxide as an emissive layer, that consists of a cost-efficient inverted bottom-emission structure as [ITO (cathode)/ZnO/emissive layers/2,2′-bis(4-(carbazol-9-yl)phenyl)-biphenyl (BCBP)/MoO3/Al (anode)]. The device with aluminum hydroxide as an emissive layer shows a maximum luminance of 215.48 cd m−2 and external quantum efficiency (EQE) of 0.12%. The new method for synthesizing UV–blue emitting aluminum hydroxides and their application to LEDs will contribute to developing the field of non-toxic optoelectronic material or UV–blue emitting devices. Ultraviolet/blue light-emitting aluminum hydroxide nanoparticles are prepared using a simple method and applied to the electrically driven light-emitting diode as an emissive layer.![]()
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Affiliation(s)
- Heejae Lee
- School of Chemistry, Seoul National University Seoul 08826 Republic of Korea
| | - Ahyoung Hong
- School of Electrical and Computer Engineering, Inter-University Semiconductor Research Center, Seoul National University Seoul 08826 Republic of Korea
| | - Jeonghun Kwak
- School of Electrical and Computer Engineering, Inter-University Semiconductor Research Center, Seoul National University Seoul 08826 Republic of Korea
| | - Seonghoon Lee
- School of Chemistry, Seoul National University Seoul 08826 Republic of Korea
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5
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Buckel W. Energy Conservation in Fermentations of Anaerobic Bacteria. Front Microbiol 2021; 12:703525. [PMID: 34589068 PMCID: PMC8473912 DOI: 10.3389/fmicb.2021.703525] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/30/2021] [Indexed: 02/04/2023] Open
Abstract
Anaerobic bacteria ferment carbohydrates and amino acids to obtain energy for growth. Due to the absence of oxygen and other inorganic electron acceptors, the substrate of a fermentation has to serve as electron donor as well as acceptor, which results in low free energies as compared to that of aerobic oxidations. Until about 10 years ago, anaerobes were thought to exclusively use substrate level phosphorylation (SLP), by which only part of the available energy could be conserved. Therefore, anaerobes were regarded as unproductive and inefficient energy conservers. The discovery of electrochemical Na+ gradients generated by biotin-dependent decarboxylations or by reduction of NAD+ with ferredoxin changed this view. Reduced ferredoxin is provided by oxidative decarboxylation of 2-oxoacids and the recently discovered flavin based electron bifurcation (FBEB). In this review, the two different fermentation pathways of glutamate to ammonia, CO2, acetate, butyrate and H2 via 3-methylaspartate or via 2-hydroxyglutarate by members of the Firmicutes are discussed as prototypical examples in which all processes characteristic for fermentations occur. Though the fermentations proceed on two entirely different pathways, the maximum theoretical amount of ATP is conserved in each pathway. The occurrence of the 3-methylaspartate pathway in clostridia from soil and the 2-hydroxyglutarate pathway in the human microbiome of the large intestine is traced back to the oxygen-sensitivity of the radical enzymes. The coenzyme B12-dependent glutamate mutase in the 3-methylaspartate pathway tolerates oxygen, whereas 2-hydroxyglutaryl-CoA dehydratase is extremely oxygen-sensitive and can only survive in the gut, where the combustion of butyrate produced by the microbiome consumes the oxygen and provides a strict anaerobic environment. Examples of coenzyme B12-dependent eliminases are given, which in the gut are replaced by simpler extremely oxygen sensitive glycyl radical enzymes.
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Affiliation(s)
- Wolfgang Buckel
- Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität Marburg, Marburg, Germany
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6
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Walton JC. Dissociations of free radicals to generate protons, electrophiles or nucleophiles: role in DNA strand breaks. Chem Soc Rev 2021; 50:7496-7512. [PMID: 34019058 DOI: 10.1039/d1cs00193k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The concept behind the research described in this article was that of marrying the 'soft' methods of radical generation with the effectiveness and flexibility of nucleophile/electrophile synthetic procedures. Classic studies with pulse radiolysis and laser flash photolysis had shown that free radicals could be more acidic than their closed shell counterparts. QM computations harmonised with this and helped to define which radical centres and which structural types were most effective. Radicals based on the sulfonic acid moiety and on the Meldrum's acid moiety (2,2-dimethyl-1,3-dioxane-4,6-dione) were found to be extreme examples in the superacid class. The ethyne unit could be used as a very effective spacer between the radical centre and the site of proton donation. The key factor in promoting acidity was understood to be the thermodynamic stabilisation of the conjugate anion-radicals released on deprotonation. Solvation played a key part in promoting this and theoretical microhydration studies provided notable support. A corollary was that heterolytic dissociations of free radicals to yield either electrophiles or nucleophiles were also enhanced relative to non-radical models. The most effective radical types for spontaneous releases of both these types of reagents were identified. Ethyne units were again effective as spacers. The enhancement of release of phosphate anions by adjacent radical centres was an important special case. Reactive oxygen species and also diradicals from endiyne antibiotics generate C4'-deoxyribose radicals from nucleotides. Radicals of these types spontaneously release phosphate and triphosphate and this is a contributor to DNA and RNA strand breaks.
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Affiliation(s)
- John C Walton
- EaStCHEM School of Chemistry, University of St. Andrews, St. Andrews, Fife KY16 9ST, UK.
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7
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Diverse Energy-Conserving Pathways in Clostridium difficile: Growth in the Absence of Amino Acid Stickland Acceptors and the Role of the Wood-Ljungdahl Pathway. J Bacteriol 2020; 202:JB.00233-20. [PMID: 32967909 DOI: 10.1128/jb.00233-20] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/23/2020] [Indexed: 12/21/2022] Open
Abstract
Clostridium difficile is the leading cause of hospital-acquired antibiotic-associated diarrhea and is the only widespread human pathogen that contains a complete set of genes encoding the Wood-Ljungdahl pathway (WLP). In acetogenic bacteria, synthesis of acetate from 2 CO2 molecules by the WLP functions as a terminal electron accepting pathway; however, C. difficile contains various other reductive pathways, including a heavy reliance on Stickland reactions, which questions the role of the WLP in this bacterium. In rich medium containing high levels of electron acceptor substrates, only trace levels of key WLP enzymes were found; therefore, conditions were developed to adapt C. difficile to grow in the absence of amino acid Stickland acceptors. Growth conditions were identified that produce the highest levels of WLP activity, determined by Western blot analyses of the central component acetyl coenzyme A synthase (AcsB) and assays of other WLP enzymes. Fermentation substrate and product analyses, enzyme assays of cell extracts, and characterization of a ΔacsB mutant demonstrated that the WLP functions to dispose of metabolically generated reducing equivalents. While WLP activity in C. difficile does not reach the levels seen in classical acetogens, coupling of the WLP to butyrate formation provides a highly efficient system for regeneration of NAD+ "acetobutyrogenesis," requiring only low flux through the pathways to support efficient ATP production from glucose oxidation. Additional insights redefine the amino acid requirements in C. difficile, explore the relationship of the WLP to toxin production, and provide a rationale for colocalization of genes involved in glycine synthesis and cleavage within the WLP operon.IMPORTANCE Clostridium difficile is an anaerobic, multidrug-resistant, toxin-producing pathogen with major health impacts worldwide. It is the only widespread pathogen harboring a complete set of Wood-Ljungdahl pathway (WLP) genes; however, the role of the WLP in C. difficile is poorly understood. In other anaerobic bacteria and archaea, the WLP can operate in one direction to convert CO2 to acetic acid for biosynthesis or in either direction for energy conservation. Here, conditions are defined in which WLP levels in C. difficile increase markedly, functioning to support metabolism of carbohydrates. Amino acid nutritional requirements were better defined, with new insight into how the WLP and butyrate pathways act in concert, contributing significantly to energy metabolism by a mechanism that may have broad physiological significance within the group of nonclassical acetogens.
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8
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Jeoung JH, Martins BM, Dobbek H. Double-Cubane [8Fe9S] Clusters: A Novel Nitrogenase-Related Cofactor in Biology. Chembiochem 2020; 21:1710-1716. [PMID: 32187824 PMCID: PMC7317905 DOI: 10.1002/cbic.202000016] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/14/2020] [Indexed: 12/20/2022]
Abstract
Three different types of electron-transferring metallo-ATPases are able to couple ATP hydrolysis to the reduction of low-potential metal sites, thereby energizing an electron. Besides the Fe-protein known from nitrogenase and homologous enzymes, two other kinds of ATPase with different scaffolds and cofactors are used to achieve a unidirectional, energetic, uphill electron transfer to either reduce inactive Co-corrinoid-containing proteins (RACE-type activators) or a second iron-sulfur cluster-containing enzyme of a unique radical enzymes family (archerases). We have found a new cofactor in the latter enzyme family, that is, a double-cubane cluster with two [4Fe4S] subclusters bridged by a sulfido ligand. An enzyme containing this cofactor catalyzes the ATP-dependent reduction of small molecules, including acetylene. Thus, enzymes containing the double-cubane cofactor are analogous in function and share some structural features with nitrogenases.
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Affiliation(s)
- Jae-Hun Jeoung
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| | - Berta M Martins
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
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9
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Affiliation(s)
- John C. Walton
- EaStCHEM School of Chemistry, University of St. Andrews, St. Andrews, Fife KY16 9ST, United Kingdom
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10
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Buckel W. Enzymatic Reactions Involving Ketyls: From a Chemical Curiosity to a General Biochemical Mechanism. Biochemistry 2019; 58:5221-5233. [PMID: 30995029 DOI: 10.1021/acs.biochem.9b00171] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Ketyls are radical anions with nucleophilic properties. Ketyls obtained by enzymatic one-electron reduction of thioesters were proposed as intermediates for the dehydration of (R)-2-hydroxyacyl-CoA to (E)-2-enoyl-CoA. This concept was extended to the Birch-like reduction of benzoyl-CoA to 1,5-cyclohexadienecarboxyl-CoA. Nature uses two methods to achieve the therefore required low reduction potentials of less than -600 mV, either by an ATP-driven electron transfer similar to that catalyzed by the iron protein of nitrogenase or by electron bifurcation. Ketyls formed by thiyl radical-initiated oxidation of alcohols followed by deprotonation are involved in coenzyme B12-independent diol dehydratases, other glycyl radical enzymes mediating key reactions in the degradations of choline, taurine, and 4-hydroxyproline, and all three classes of ribonucleotide reductases. A special case is the dehydration of 4-hydroxybutyryl-CoA to crotonyl-CoA, which most likely proceeds via an oxidation to an allylic ketyl but requires neither a strong reductant nor an external radical generator.
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Affiliation(s)
- Wolfgang Buckel
- Fachbereich Biologie , Philipps-Universität , 35032 Marburg , Germany
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11
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Syroeshkin MA, Kuriakose F, Saverina EA, Timofeeva VA, Egorov MP, Alabugin IV. Hochkonversion von Reduktionsmitteln. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201807247] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Mikhail A. Syroeshkin
- N. D. Zelinsky Institute of Organic Chemistry Leninskyprosp. 47 119991 Moskau Russland
| | - Febin Kuriakose
- Department of Chemistry and Biochemistry Florida State University Tallahassee FL USA
| | - Evgeniya A. Saverina
- N. D. Zelinsky Institute of Organic Chemistry Leninskyprosp. 47 119991 Moskau Russland
- UMR CNRS 6226 ISCR University of Rennes 1 Rennes Frankreich
| | | | - Mikhail P. Egorov
- N. D. Zelinsky Institute of Organic Chemistry Leninskyprosp. 47 119991 Moskau Russland
| | - Igor V. Alabugin
- Department of Chemistry and Biochemistry Florida State University Tallahassee FL USA
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12
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Syroeshkin MA, Kuriakose F, Saverina EA, Timofeeva VA, Egorov MP, Alabugin IV. Upconversion of Reductants. Angew Chem Int Ed Engl 2019; 58:5532-5550. [DOI: 10.1002/anie.201807247] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Mikhail A. Syroeshkin
- N. D. Zelinsky Institute of Organic Chemistry Leninsky prosp. 47 119991 Moscow Russia
| | - Febin Kuriakose
- Department of Chemistry and Biochemistry Florida State University Tallahassee FL USA
| | - Evgeniya A. Saverina
- N. D. Zelinsky Institute of Organic Chemistry Leninsky prosp. 47 119991 Moscow Russia
- UMR CNRS 6226 ISCR University of Rennes 1 Rennes France
| | | | - Mikhail P. Egorov
- N. D. Zelinsky Institute of Organic Chemistry Leninsky prosp. 47 119991 Moscow Russia
| | - Igor V. Alabugin
- Department of Chemistry and Biochemistry Florida State University Tallahassee FL USA
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13
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Neumann-Schaal M, Jahn D, Schmidt-Hohagen K. Metabolism the Difficile Way: The Key to the Success of the Pathogen Clostridioides difficile. Front Microbiol 2019; 10:219. [PMID: 30828322 PMCID: PMC6384274 DOI: 10.3389/fmicb.2019.00219] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/28/2019] [Indexed: 12/11/2022] Open
Abstract
Strains of Clostridioides difficile cause detrimental diarrheas with thousands of deaths worldwide. The infection process by the Gram-positive, strictly anaerobic gut bacterium is directly related to its unique metabolism, using multiple Stickland-type amino acid fermentation reactions coupled to Rnf complex-mediated sodium/proton gradient formation for ATP generation. Major pathways utilize phenylalanine, leucine, glycine and proline with the formation of 3-phenylproprionate, isocaproate, butyrate, 5-methylcaproate, valerate and 5-aminovalerate. In parallel a versatile sugar catabolism including pyruvate formate-lyase as a central enzyme and an incomplete tricarboxylic acid cycle to prevent unnecessary NADH formation completes the picture. However, a complex gene regulatory network that carefully mediates the continuous adaptation of this metabolism to changing environmental conditions is only partially elucidated. It involves the pleiotropic regulators CodY and SigH, the known carbon metabolism regulator CcpA, the proline regulator PrdR, the iron regulator Fur, the small regulatory RNA CsrA and potentially the NADH-responsive regulator Rex. Here, we describe the current knowledge of the metabolic principles of energy generation by C. difficile and the underlying gene regulatory scenarios.
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Affiliation(s)
- Meina Neumann-Schaal
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,Integrated Centre of Systems Biology (BRICS), Braunschweig University of Technology, Braunschweig, Germany
| | - Dieter Jahn
- Integrated Centre of Systems Biology (BRICS), Braunschweig University of Technology, Braunschweig, Germany.,Institute of Microbiology, Braunschweig University of Technology, Braunschweig, Germany
| | - Kerstin Schmidt-Hohagen
- Integrated Centre of Systems Biology (BRICS), Braunschweig University of Technology, Braunschweig, Germany.,Department of Bioinformatics and Biochemistry, Braunschweig University of Technology, Braunschweig, Germany
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14
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Walton JC. Reflex Carbocation Release from Covalent Molecules by Endogenous Free Radicals. ACS OMEGA 2018; 3:13290-13297. [PMID: 30411034 PMCID: PMC6217609 DOI: 10.1021/acsomega.8b02307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/02/2018] [Indexed: 06/08/2023]
Abstract
Carbocations are pervasive in contemporary organic synthesis, so new and innocuous methods of making them are always desirable. A theoretical approach revealed that compounds in which radical generation takes place may release carbocations advantageously. The radical types and molecular substructures that promote this effect were identified. The best substructures were found to be 1,3-dicarbonyl compounds, particularly those based on the Meldrum's acid theme. Sulfate esters and dithiane rings could also be employed. Radicals generated on oxygen atoms or ethyne units were particularly effective. For these species, carbocation release could be reflex, that is, concurrent with radical generation. Only small radical enhancements were observed for release of lithium cations because of the ionic character of most of the precursors. Ethyne units could be incorporated as spacers between the radical center and the site of carbocation generation. Moreover, the enhancement was transmitted down polyethyne chains of at least six units.
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Affiliation(s)
- John C. Walton
- EaStCHEM School of Chemistry, University of St. Andrews, St. Andrews, Fife KY16 9ST, United Kingdom
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15
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Affiliation(s)
- Christof M. Jäger
- University of Nottingham; Department of Chemical and Environmental Engineering; NG7 2RD Nottingham United Kingdom
| | - Anna K. Croft
- University of Nottingham; Department of Chemical and Environmental Engineering; NG7 2RD Nottingham United Kingdom
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16
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Parthasarathy A, Cross PJ, Dobson RCJ, Adams LE, Savka MA, Hudson AO. A Three-Ring Circus: Metabolism of the Three Proteogenic Aromatic Amino Acids and Their Role in the Health of Plants and Animals. Front Mol Biosci 2018; 5:29. [PMID: 29682508 PMCID: PMC5897657 DOI: 10.3389/fmolb.2018.00029] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 03/21/2018] [Indexed: 12/19/2022] Open
Abstract
Tyrosine, phenylalanine and tryptophan are the three aromatic amino acids (AAA) involved in protein synthesis. These amino acids and their metabolism are linked to the synthesis of a variety of secondary metabolites, a subset of which are involved in numerous anabolic pathways responsible for the synthesis of pigment compounds, plant hormones and biological polymers, to name a few. In addition, these metabolites derived from the AAA pathways mediate the transmission of nervous signals, quench reactive oxygen species in the brain, and are involved in the vast palette of animal coloration among others pathways. The AAA and metabolites derived from them also have integral roles in the health of both plants and animals. This review delineates the de novo biosynthesis of the AAA by microbes and plants, and the branching out of AAA metabolism into major secondary metabolic pathways in plants such as the phenylpropanoid pathway. Organisms that do not possess the enzymatic machinery for the de novo synthesis of AAA must obtain these primary metabolites from their diet. Therefore, the metabolism of AAA by the host animal and the resident microflora are important for the health of all animals. In addition, the AAA metabolite-mediated host-pathogen interactions in general, as well as potential beneficial and harmful AAA-derived compounds produced by gut bacteria are discussed. Apart from the AAA biosynthetic pathways in plants and microbes such as the shikimate pathway and the tryptophan pathway, this review also deals with AAA catabolism in plants, AAA degradation via the monoamine and kynurenine pathways in animals, and AAA catabolism via the 3-aryllactate and kynurenine pathways in animal-associated microbes. Emphasis will be placed on structural and functional aspects of several key AAA-related enzymes, such as shikimate synthase, chorismate mutase, anthranilate synthase, tryptophan synthase, tyrosine aminotransferase, dopachrome tautomerase, radical dehydratase, and type III CoA-transferase. The past development and current potential for interventions including the development of herbicides and antibiotics that target key enzymes in AAA-related pathways, as well as AAA-linked secondary metabolism leading to antimicrobials are also discussed.
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Affiliation(s)
- Anutthaman Parthasarathy
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Penelope J. Cross
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
| | - Lily E. Adams
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Michael A. Savka
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
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17
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Microhydration and the Enhanced Acidity of Free Radicals. Molecules 2018; 23:molecules23020423. [PMID: 29443952 PMCID: PMC6017598 DOI: 10.3390/molecules23020423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/09/2018] [Accepted: 02/14/2018] [Indexed: 12/02/2022] Open
Abstract
Recent theoretical research employing a continuum solvent model predicted that radical centers would enhance the acidity (RED-shift) of certain proton-donor molecules. Microhydration studies employing a DFT method are reported here with the aim of establishing the effect of the solvent micro-structure on the acidity of radicals with and without RED-shifts. Microhydration cluster structures were obtained for carboxyl, carboxy-ethynyl, carboxy-methyl, and hydroperoxyl radicals. The numbers of water molecules needed to induce spontaneous ionization were determined. The hydration clusters formed primarily round the CO2 units of the carboxylate-containing radicals. Only 4 or 5 water molecules were needed to induce ionization of carboxyl and carboxy-ethynyl radicals, thus corroborating their large RED-shifts.
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Walton JC. Enhanced Proton Loss from Neutral Free Radicals: Toward Carbon-Centered Superacids. J Phys Chem A 2018; 122:1422-1431. [DOI: 10.1021/acs.jpca.7b11796] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- John C. Walton
- EaStCHEM School of Chemistry, University of St. Andrews, St. Andrews, Fife KY16
9ST, United Kingdom
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19
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van Leest NP, Epping RF, van Vliet KM, Lankelma M, van den Heuvel EJ, Heijtbrink N, Broersen R, de Bruin B. Single-Electron Elementary Steps in Homogeneous Organometallic Catalysis. ADVANCES IN ORGANOMETALLIC CHEMISTRY 2018. [DOI: 10.1016/bs.adomc.2018.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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20
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Kim HJ, Liu YN, McCarty RM, Liu HW. Reaction Catalyzed by GenK, a Cobalamin-Dependent Radical S-Adenosyl-l-methionine Methyltransferase in the Biosynthetic Pathway of Gentamicin, Proceeds with Retention of Configuration. J Am Chem Soc 2017; 139:16084-16087. [PMID: 29091410 DOI: 10.1021/jacs.7b09890] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Many cobalamin (Cbl)-dependent radical S-adenosyl-l-methionine (SAM) methyltransferases have been identified through sequence alignment and/or genetic analysis; however, few have been studied in vitro. GenK is one such enzyme that catalyzes methylation of the 6'-carbon of gentamicin X2 (GenX2) to produce G418 during the biosynthesis of gentamicins. Reported herein, several alternative substrates and fluorinated substrate analogs were prepared to investigate the mechanism of methyl transfer from Cbl to the substrate as well as the substrate specificity of GenK. Experiments with deuterated substrates are also shown here to demonstrate that the 6'-pro-R-hydrogen atom of GenX2 is stereoselectively abstracted by the 5'-dAdo· radical and that methylation occurs with retention of configuration at C6'. Based on these observations, a model of GenK catalysis is proposed wherein free rotation of the radical-bearing carbon is prevented and the radical SAM machinery sits adjacent rather than opposite to the Me-Cbl cofactor with respect to the substrate in the enzyme active site.
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Affiliation(s)
- Hak Joong Kim
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| | - Yung-Nan Liu
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| | - Reid M McCarty
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| | - Hung-Wen Liu
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
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21
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Schmid G, Auerbach H, Pierik AJ, Schünemann V, Boll M. ATP-Dependent Electron Activation Module of Benzoyl-Coenzyme A Reductase from the Hyperthermophilic Archaeon Ferroglobus placidus. Biochemistry 2016; 55:5578-5586. [PMID: 27597116 DOI: 10.1021/acs.biochem.6b00729] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The class I benzoyl-coenzyme A (BzCoA) reductases (BCRs) are key enzymes in the anaerobic degradation of aromatic compounds that catalyze the ATP-dependent dearomatization of their substrate to a cyclic dienoyl-CoA. The phylogenetically distinct Thauera- and Azoarcus-type BCR subclasses are iron-sulfur enzymes and consist of an ATP-hydrolyzing electron activation module and a BzCoA reduction module. More than 20 years after their initial identification, all biochemical information about class I BCRs derives from studies of the wild-type enzyme from the denitrifying bacterium Thauera aromatica (BCRTaro). Here, we describe the first heterologous production and purification of the ATP-hydrolyzing, electron-activating module of an Azoarcus-type BCR from the hyperthermophilic archaeon Ferroglobus placidus, BzdPQFpla. The Fe content, UV/vis spectroscopic, and Mössbauer spectroscopic properties of the 57Fe-enriched enzyme clearly identified a [4Fe-4S]+/2+ cluster with a redox potential (E°') of -376 mV as a cofactor. ATP hydrolysis is required to overcome a redox barrier of ∼250 mV for stoichiometric electron transfer from the [4Fe-4S]+ cluster to the substrate benzene ring (E°'BzCoA/dienoyl-CoA = -622 mV). BzdPQFpla exhibited ATPase activity (15 nmol min-1 mg-1; Km = 270 μM) at 75 °C, which was relatively stable in air in contrast to BCRTaro. The results obtained revealed high levels of functional and molecular similarity between Azoarcus-type BCRs and the homologous ATP-dependent activator components of 2-hydroxyacyl-CoA dehydratases involved in amino acid fermentations. Insights into the diversity and evolution of ATP-dependent electron-activating modules for catalytic or stoichiometric low-potential electron transfer processes are presented.
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Affiliation(s)
- Georg Schmid
- Fakultät für Biologie-Mikrobiologie, Institut für Biologie II, Albert-Ludwigs-Universität Freiburg , D-79104 Freiburg, Germany
| | - Hendrik Auerbach
- Fachbereich Physik, TU Kaiserslautern , 67663 Kaiserslautern, Germany
| | - Antonio J Pierik
- Fachbereich Chemie, TU Kaiserslautern , 67663 Kaiserslautern, Germany
| | - Volker Schünemann
- Fachbereich Physik, TU Kaiserslautern , 67663 Kaiserslautern, Germany
| | - Matthias Boll
- Fakultät für Biologie-Mikrobiologie, Institut für Biologie II, Albert-Ludwigs-Universität Freiburg , D-79104 Freiburg, Germany
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22
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Nami F, Gast P, Groenen EJJ. Rapid Freeze-Quench EPR Spectroscopy: Improved Collection of Frozen Particles. APPLIED MAGNETIC RESONANCE 2016; 47:643-653. [PMID: 27340337 PMCID: PMC4875044 DOI: 10.1007/s00723-016-0783-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/18/2016] [Indexed: 05/22/2023]
Abstract
Rapid freeze-quench (RFQ) in combination with electron paramagnetic resonance (EPR) spectroscopy at X-band is a proven technique to trap and characterize paramagnetic intermediates of biochemical reactions. Preparation of suitable samples is still cumbersome, despite many attempts to remedy this problem, and limits the wide applicability of RFQ EPR. We present a method, which improves the collection of freeze-quench particles from isopentane and their packing in an EPR tube. The method is based on sucking the particle suspension into an EPR tube with a filter at the bottom. This procedure results in a significant reduction of the required volume of reactants, which allows the economical use of valuable reactants such as proteins. The approach also enables the successful collection of smaller frozen particles, which are generated at higher flow rates. The method provides for a reproducible, efficient and fast collection of the freeze-quench particles and can be easily adapted to RFQ EPR at higher microwave frequencies than X-band.
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Affiliation(s)
- Faezeh Nami
- Huygens-Kamerlingh Onnes Laboratory, Department of Physics, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands
| | - Peter Gast
- Huygens-Kamerlingh Onnes Laboratory, Department of Physics, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands
| | - Edgar J. J. Groenen
- Huygens-Kamerlingh Onnes Laboratory, Department of Physics, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands
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Chowdhury NP, Klomann K, Seubert A, Buckel W. Reduction of Flavodoxin by Electron Bifurcation and Sodium Ion-dependent Reoxidation by NAD+ Catalyzed by Ferredoxin-NAD+ Reductase (Rnf). J Biol Chem 2016; 291:11993-2002. [PMID: 27048649 DOI: 10.1074/jbc.m116.726299] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Indexed: 12/31/2022] Open
Abstract
Electron-transferring flavoprotein (Etf) and butyryl-CoA dehydrogenase (Bcd) from Acidaminococcus fermentans catalyze the endergonic reduction of ferredoxin by NADH, which is also driven by the concomitant reduction of crotonyl-CoA by NADH, a process called electron bifurcation. Here we show that recombinant flavodoxin from A. fermentans produced in Escherichia coli can replace ferredoxin with almost equal efficiency. After complete reduction of the yellow quinone to the blue semiquinone, a second 1.4 times faster electron transfer affords the colorless hydroquinone. Mediated by a hydrogenase, protons reoxidize the fully reduced flavodoxin or ferredoxin to the semi-reduced species. In this hydrogen-generating system, both electron carriers act catalytically with apparent Km = 0.26 μm ferredoxin or 0.42 μm flavodoxin. Membrane preparations of A. fermentans contain a highly active ferredoxin/flavodoxin-NAD(+) reductase (Rnf) that catalyzes the irreversible reduction of flavodoxin by NADH to the blue semiquinone. Using flavodoxin hydroquinone or reduced ferredoxin obtained by electron bifurcation, Rnf can be measured in the forward direction, whereby one NADH is recycled, resulting in the simple equation: crotonyl-CoA + NADH + H(+) = butyryl-CoA + NAD(+) with Km = 1.4 μm ferredoxin or 2.0 μm flavodoxin. This reaction requires Na(+) (Km = 0.12 mm) or Li(+) (Km = 0.25 mm) for activity, indicating that Rnf acts as a Na(+) pump. The redox potential of the quinone/semiquinone couple of flavodoxin (Fld) is much higher than that of the semiquinone/hydroquinone couple. With free riboflavin, the opposite is the case. Based on this behavior, we refine our previous mechanism of electron bifurcation.
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Affiliation(s)
- Nilanjan Pal Chowdhury
- From the Laboratorium für Mikrobiologie, Fachbereich Biologie and Synmikro and the Max-Plank-Institut für terrestrische Mikrobiologie, 35043 Marburg, Germany
| | - Katharina Klomann
- From the Laboratorium für Mikrobiologie, Fachbereich Biologie and Synmikro and
| | - Andreas Seubert
- the Fachbereich Chemie, Philipps-Universität, 35032 Marburg, and
| | - Wolfgang Buckel
- From the Laboratorium für Mikrobiologie, Fachbereich Biologie and Synmikro and the Max-Plank-Institut für terrestrische Mikrobiologie, 35043 Marburg, Germany
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24
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Weinert T, Huwiler SG, Kung JW, Weidenweber S, Hellwig P, Stärk HJ, Biskup T, Weber S, Cotelesage JJH, George GN, Ermler U, Boll M. Structural basis of enzymatic benzene ring reduction. Nat Chem Biol 2015; 11:586-91. [PMID: 26120796 DOI: 10.1038/nchembio.1849] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/15/2015] [Indexed: 12/19/2022]
Abstract
In chemical synthesis, the widely used Birch reduction of aromatic compounds to cyclic dienes requires alkali metals in ammonia as extremely low-potential electron donors. An analogous reaction is catalyzed by benzoyl-coenzyme A reductases (BCRs) that have a key role in the globally important bacterial degradation of aromatic compounds at anoxic sites. Because of the lack of structural information, the catalytic mechanism of enzymatic benzene ring reduction remained obscure. Here, we present the structural characterization of a dearomatizing BCR containing an unprecedented tungsten cofactor that transfers electrons to the benzene ring in an aprotic cavity. Substrate binding induces proton transfer from the bulk solvent to the active site by expelling a Zn(2+) that is crucial for active site encapsulation. Our results shed light on the structural basis of an electron transfer process at the negative redox potential limit in biology. They open the door for biological or biomimetic alternatives to a basic chemical synthetic tool.
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Affiliation(s)
| | - Simona G Huwiler
- Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Johannes W Kung
- Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, Strasbourg, France
| | - Hans-Joachim Stärk
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research UFZ, Leipzig, Germany
| | - Till Biskup
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
| | - Stefan Weber
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
| | - Julien J H Cotelesage
- 1] Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada. [2] Canadian Light Source, Saskatoon, Saskatchewan, Canada
| | - Graham N George
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ulrich Ermler
- Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Matthias Boll
- Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany
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Substrate-induced radical formation in 4-hydroxybutyryl coenzyme A dehydratase from Clostridium aminobutyricum. Appl Environ Microbiol 2014; 81:1071-84. [PMID: 25452282 DOI: 10.1128/aem.03099-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
4-Hydroxybutyryl-coenzyme A (CoA) dehydratase (4HBD) from Clostridium aminobutyricum catalyzes the reversible dehydration of 4-hydroxybutyryl-CoA to crotonyl-CoA and the irreversible isomerization of vinylacetyl-CoA to crotonyl-CoA. 4HBD is an oxygen-sensitive homotetrameric enzyme with one [4Fe-4S](2+) cluster and one flavin adenine dinucleotide (FAD) in each subunit. Upon the addition of crotonyl-CoA or the analogues butyryl-CoA, acetyl-CoA, and CoA, UV-visible light and electron paramagnetic resonance (EPR) spectroscopy revealed an internal one-electron transfer to FAD and the [4Fe-4S](2+) cluster prior to hydration. We describe an active recombinant 4HBD and variants produced in Escherichia coli. The variants of the cluster ligands (H292C [histidine at position 292 is replaced by cysteine], H292E, C99A, C103A, and C299A) had no measurable dehydratase activity and were composed of monomers, dimers, and tetramers. Variants of other potential catalytic residues were composed only of tetramers and exhibited either no measurable (E257Q, E455Q, and Y296W) hydratase activity or <1% (Y296F and T190V) dehydratase activity. The E455Q variant but not the Y296F or E257Q variant displayed the same spectral changes as the wild-type enzyme after the addition of crotonyl-CoA but at a much lower rate. The results suggest that upon the addition of a substrate, Y296 is deprotonated by E455 and reduces FAD to FADH·, aided by protonation from E257 via T190. In contrast to FADH·, the tyrosyl radical could not be detected by EPR spectroscopy. FADH· appears to initiate the radical dehydration via an allylic ketyl radical that was proposed 19 years ago. The mode of radical generation in 4HBD is without precedent in anaerobic radical chemistry. It differs largely from that in enzymes, which use coenzyme B12, S-adenosylmethionine, ATP-driven electron transfer, or flavin-based electron bifurcation for this purpose.
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Koleva P, Ketabi A, Valcheva R, Gänzle MG, Dieleman LA. Chemically defined diet alters the protective properties of fructo-oligosaccharides and isomalto-oligosaccharides in HLA-B27 transgenic rats. PLoS One 2014; 9:e111717. [PMID: 25369019 PMCID: PMC4219767 DOI: 10.1371/journal.pone.0111717] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 10/07/2014] [Indexed: 01/04/2023] Open
Abstract
Non-digestible oligosaccharides (NDO) were shown to reduce inflammation in experimental colitis, but it remains unclear whether microbiota changes mediate their colitis-modulating effects. This study assessed intestinal microbiota and intestinal inflammation after feeding chemically defined AIN-76A or rat chow diets, with or without supplementation with 8 g/kg body weight of fructo-oligosaccharides (FOS) or isomalto-oligosaccharides (IMO). The study used HLA-B27 transgenic rats, a validated model of inflammatory bowel disease (IBD), in a factorial design with 6 treatment groups. Intestinal inflammation and intestinal microbiota were analysed after 12 weeks of treatment. FOS and IMO reduced colitis in animals fed rat chow, but exhibited no anti-inflammatory effect when added to AIN-76A diets. Both NDO induced specific but divergent microbiota changes. Bifidobacteria and Enterobacteriaceae were stimulated by FOS, whereas copy numbers of Clostridium cluster IV were decreased. In addition, higher concentrations of total short-chain fatty acids (SCFA) were observed in cecal contents of rats on rat chow compared to the chemically defined diet. AIN-76A increased the relative proportions of propionate, iso-butyrate, valerate and iso-valerate irrespective of the oligosaccharide treatment. The SCFA composition, particularly the relative concentration of iso-butyrate, valerate and iso-valerate, was associated (P ≤ 0.004 and r ≥ 0.4) with increased colitis and IL-1 β concentration of the cecal mucosa. This study demonstrated that the protective effects of fibres on colitis development depend on the diet. Although diets modified specific cecal microbiota, our study indicates that these changes were not associated with colitis reduction. Intestinal inflammation was positively correlated to protein fermentation and negatively correlated with carbohydrate fermentation in the large intestine.
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Affiliation(s)
- Petya Koleva
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada
| | - Ali Ketabi
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Rosica Valcheva
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada
| | - Michael G. Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
- School of Food and Pharmaceutical Engineering, Hubei University of Technology, Wuhan, China
| | - Levinus A. Dieleman
- Centre of Excellence for Gastrointestinal Inflammation and Immunity Research, University of Alberta, Edmonton, Canada
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Buckel W, Kung JW, Boll M. The benzoyl-coenzyme a reductase and 2-hydroxyacyl-coenzyme a dehydratase radical enzyme family. Chembiochem 2014; 15:2188-94. [PMID: 25204868 DOI: 10.1002/cbic.201402270] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Wolfgang Buckel
- Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität Marburg, Karl-von-Frisch-Strasse 8, 35043 Marburg (Germany)
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Dark-operative protochlorophyllide oxidoreductase generates substrate radicals by an iron-sulphur cluster in bacteriochlorophyll biosynthesis. Sci Rep 2014; 4:5455. [PMID: 24965831 PMCID: PMC4071322 DOI: 10.1038/srep05455] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 06/09/2014] [Indexed: 11/21/2022] Open
Abstract
Photosynthesis converts solar energy to chemical energy using chlorophylls (Chls). In a late stage of biosynthesis of Chls, dark-operative protochlorophyllide (Pchlide) oxidoreductase (DPOR), a nitrogenase-like enzyme, reduces the C17 = C18 double bond of Pchlide and drastically changes the spectral properties suitable for photosynthesis forming the parental chlorin ring for Chl a. We previously proposed that the spatial arrangement of the proton donors determines the stereospecificity of the Pchlide reduction based on the recently resolved structure of the DPOR catalytic component, NB-protein. However, it was not clear how the two-electron and two-proton transfer events are coordinated in the reaction. In this study, we demonstrate that DPOR initiates a single electron transfer reaction from a [4Fe-4S]-cluster (NB-cluster) to Pchlide, generating Pchlide anion radicals followed by a single proton transfer, and then, further electron/proton transfer steps transform the anion radicals into chlorophyllide (Chlide). Thus, DPOR is a unique iron-sulphur enzyme to form substrate radicals followed by sequential proton- and electron-transfer steps with the protein folding very similar to that of nitrogenase. This novel radical-mediated reaction supports the biosynthesis of Chl in a wide variety of photosynthetic organisms.
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Ternan NG, Jain S, Graham RLJ, McMullan G. Semiquantitative analysis of clinical heat stress in Clostridium difficile strain 630 using a GeLC/MS workflow with emPAI quantitation. PLoS One 2014; 9:e88960. [PMID: 24586458 PMCID: PMC3933415 DOI: 10.1371/journal.pone.0088960] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 01/16/2014] [Indexed: 12/11/2022] Open
Abstract
Clostridium difficile is considered to be the most frequent cause of infectious bacterial diarrhoea in hospitals worldwide yet its adaptive ability remains relatively uncharacterised. Here, we used GeLC/MS and the exponentially modified protein abundance index (emPAI) calculation to determine proteomic changes in response to a clinically relevant heat stress. Reproducibility between both biological and technical replicates was good, and a 37°C proteome of 224 proteins was complemented by a 41°C proteome of 202 proteins at a 1% false discovery rate. Overall, 236 C. difficile proteins were identified and functionally categorised, of which 178 were available for comparative purposes. A total of 65 proteins (37%) were modulated by 1.5-fold or more at 41°C compared to 37°C and we noted changes in the majority of proteins associated with amino acid metabolism, including upregulation of the reductive branch of the leucine fermentation pathway. Motility was reduced at 41°C as evidenced by a 2.7 fold decrease in the flagellar filament protein, FliC, and a global increase in proteins associated with detoxification and adaptation to atypical conditions was observed, concomitant with decreases in proteins mediating transcriptional elongation and the initiation of protein synthesis. Trigger factor was down regulated by almost 5-fold. We propose that under heat stress, titration of the GroESL and dnaJK/grpE chaperones by misfolded proteins will, in the absence of trigger factor, prevent nascent chains from emerging efficiently from the ribosome causing translational stalling and also an increase in secretion. The current work has thus allowed development of a heat stress model for the key cellular processes of protein folding and export.
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Affiliation(s)
- Nigel G. Ternan
- Northern Ireland Centre for Food and Health (NICHE), School of Biomedical Sciences, University of Ulster, Coleraine, Co. Londonderry, Northern Ireland, United Kingdom
- * E-mail:
| | - Shailesh Jain
- Northern Ireland Centre for Food and Health (NICHE), School of Biomedical Sciences, University of Ulster, Coleraine, Co. Londonderry, Northern Ireland, United Kingdom
| | - Robert L. J. Graham
- School of Medicine, University of Manchester, Manchester, Greater Manchester, United Kingdom
| | - Geoff McMullan
- Northern Ireland Centre for Food and Health (NICHE), School of Biomedical Sciences, University of Ulster, Coleraine, Co. Londonderry, Northern Ireland, United Kingdom
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Parthasarathy A, Kahnt J, Chowdhury NP, Buckel W. Phenylalanine catabolism in Archaeoglobus fulgidus VC-16. Arch Microbiol 2013; 195:781-97. [DOI: 10.1007/s00203-013-0925-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 08/29/2013] [Accepted: 08/31/2013] [Indexed: 01/06/2023]
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31
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Kim HJ, McCarty RM, Ogasawara Y, Liu YN, Mansoorabadi SO, LeVieux J, Liu HW. GenK-catalyzed C-6' methylation in the biosynthesis of gentamicin: isolation and characterization of a cobalamin-dependent radical SAM enzyme. J Am Chem Soc 2013; 135:8093-6. [PMID: 23679096 PMCID: PMC3796153 DOI: 10.1021/ja312641f] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The existence of cobalamin (Cbl)-dependent enzymes that are members of the radical S-adenosyl-l-methionine (SAM) superfamily was previously predicted on the basis of bioinformatic analysis. A number of these are Cbl-dependent methyltransferases, but the details surrounding their reaction mechanisms have remained unclear. In this report we demonstrate the in vitro activity of GenK, a Cbl-dependent radical SAM enzyme that methylates an unactivated sp(3) carbon during the biosynthesis of gentamicin, an aminoglycoside antibiotic. Experiments to investigate the stoichiometry of the GenK reaction revealed that 1 equiv each of 5'-deoxyadenosine and S-adenosyl-homocysteine are produced for each methylation reaction catalyzed by GenK. Furthermore, isotope-labeling experiments demonstrate that the S-methyl group from SAM is transferred to Cbl and the aminoglycoside product during the course of the reaction. On the basis of these results, one mechanistic possibility for the GenK reaction can be ruled out, and further questions regarding the mechanisms of Cbl-dependent radical SAM methyltransferases, in general, are discussed.
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Affiliation(s)
- Hak Joong Kim
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Reid M. McCarty
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Yasushi Ogasawara
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Yung-nan Liu
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Steven O. Mansoorabadi
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jake LeVieux
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hung-wen Liu
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
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32
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Knauer SH, Buckel W, Dobbek H. On the ATP-dependent activation of the radical enzyme (R)-2-hydroxyisocaproyl-CoA dehydratase. Biochemistry 2012; 51:6609-22. [PMID: 22827463 DOI: 10.1021/bi300571z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Members of the 2-hydroxyacyl-CoA dehydratase enzyme family catalyze the β,α-dehydration of various CoA-esters in the fermentation of amino acids by clostridia. Abstraction of the nonacidic β-proton of the 2-hydroxyacyl-CoA compounds is achieved by the reductive generation of ketyl radicals on the substrate, which is initiated by the transfer of an electron at low redox potentials. The highly energetic electron needed on the dehydratase is donated by a [4Fe-4S] cluster containing ATPase, termed activator. We investigated the activator of the 2-hydroxyisocaproyl-CoA dehydratase from Clostridium difficile. The activator is a homodimeric protein structurally related to acetate and sugar kinases, Hsc70 and actin, and has a [4Fe-4S] cluster bound in the dimer interface. The crystal structures of the Mg-ADP, Mg-ADPNP, and nucleotide-free states of the reduced activator have been solved at 1.6-3.0 Å resolution, allowing us to define the position of Mg(2+) and water molecules in the vicinity of the nucleotides and the [4Fe-4S] cluster. The structures reveal redox- and nucleotide dependent changes agreeing with the modulation of the reduction potential of the [4Fe-4S] cluster by conformational changes. We also investigated the propensity of the activator to form a complex with its cognate dehydratase in the presence of Mg-ADP and Mg-ADPNP and together with the structural data present a refined mechanistic scheme for the ATP-dependent electron transfer between activator and dehydratase.
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Affiliation(s)
- Stefan H Knauer
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
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Enzyme catalyzed radical dehydrations of hydroxy acids. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1824:1278-90. [PMID: 22178228 DOI: 10.1016/j.bbapap.2011.11.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2011] [Accepted: 11/28/2011] [Indexed: 11/24/2022]
Abstract
BACKGROUND The steadily increasing field of radical biochemistry is dominated by the large family of S-adenosylmethionine dependent enzymes, the so-called radical SAM enzymes, of which several new members are discovered every year. Here we report on 2- and 4-hydroxyacyl-CoA dehydratases which apply a very different method of radical generation. In these enzymes ketyl radicals are formed by one-electron reduction or oxidation and are recycled after each turnover without further energy input. Earlier reviews on 2-hydroxyacyl-CoA dehydratases were published in 2004 [J. Kim, M. Hetzel, C.D. Boiangiu, W. Buckel, FEMS Microbiol. Rev. 28 (2004) 455-468. W. Buckel, M. Hetzel, J. Kim, Curr. Opin. Chem. Biol. 8 (2004) 462-467.] SCOPE OF REVIEW The review focuses on four types of 2-hydroxyacyl-CoA dehydratases that are involved in the fermentation of amino acids by anaerobic bacteria, especially clostridia. These enzymes require activation by one-electron transfer from an iron-sulfur protein driven by hydrolysis of ATP. The review further describes the proposed mechanism that is highlighted by the identification of the allylic ketyl radical intermediate and the elucidation of the crystal structure of 2-hydroxyisocapryloyl-CoA dehydratase. With 4-hydroxybutyryl-CoA dehydratase the crystal structure, the complete stereochemistry and the function of several conserved residues around the active site could be identified. Finally potential biotechnological applications of the radical dehydratases are presented. GENERAL SIGNIFICANCE The action of the activator as an 'Archerase' shooting electrons into difficultly reducible acceptors becomes an emerging principle in anaerobic metabolism. The dehydratases may provide useful tools in biotechnology. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.
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Das D, Eser BE, Sciore A, Marsh ENG, Han J. Oxygen-independent decarbonylation of aldehydes by cyanobacterial aldehyde decarbonylase: a new reaction of diiron enzymes. Angew Chem Int Ed Engl 2011; 50:7148-52. [PMID: 21671322 PMCID: PMC3335439 DOI: 10.1002/anie.201101552] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 05/17/2011] [Indexed: 11/06/2022]
Affiliation(s)
- Debasis Das
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, (U.S.A.)
| | - Bekir E. Eser
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, (U.S.A.)
| | - Aaron Sciore
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, (U.S.A.)
| | - E. Neil G. Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, (U.S.A.)
| | - Jaehong Han
- School of Biological Sciences, Chung-Ang University, Anseong 456-756, (Korea)
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Das D, Eser BE, Han J, Sciore A, Marsh ENG. Oxygen-Independent Decarbonylation of Aldehydes by Cyanobacterial Aldehyde Decarbonylase: A New Reaction of Diiron Enzymes. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101552] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Parthasarathy A, Pierik AJ, Kahnt J, Zelder O, Buckel W. Substrate specificity of 2-hydroxyglutaryl-CoA dehydratase from Clostridium symbiosum: toward a bio-based production of adipic acid. Biochemistry 2011; 50:3540-50. [PMID: 21434666 DOI: 10.1021/bi1020056] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Expression of six genes from two glutamate fermenting clostridia converted Escherichia coli into a producer of glutaconate from 2-oxoglutarate of the general metabolism (Djurdjevic, I. et al. 2010, Appl. Environ. Microbiol.77, 320-322). The present work examines whether this pathway can also be used to reduce 2-oxoadipate to (R)-2-hydroxyadipic acid and dehydrate its CoA thioester to 2-hexenedioic acid, an unsaturated precursor of the biotechnologically valuable adipic acid (hexanedioic acid). 2-Hydroxyglutaryl-CoA dehydratase from Clostridium symbiosum, the key enzyme of this pathway and a potential radical enzyme, catalyzes the reversible dehydration of (R)-2-hydroxyglutaryl-CoA to (E)-glutaconyl-CoA. Using a spectrophotometric assay and mass spectrometry, it was found that (R)-2-hydroxyadipoyl-CoA, oxalocrotonyl-CoA, muconyl-CoA, and butynedioyl-CoA, but not 3-methylglutaconyl-CoA, served as alternative substrates. Hydration of butynedioyl-CoA most likely led to 2-oxosuccinyl-CoA, which spontaneously hydrolyzed to oxaloacetate and CoASH. The dehydratase is not specific for the CoA-moiety because (R)-2-hydroxyglutaryl-thioesters of N-acetylcysteamine and pantetheine served as almost equal substrates. Whereas the related 2-hydroxyisocaproyl-CoA dehydratase generated the stable and inhibitory 2,4-pentadienoyl-CoA radical, the analogous allylic ketyl radical could not be detected with muconyl-CoA and 2-hydroxyglutaryl-CoA dehydratase. With the exception of (R)-2-hydroxyglutaryl-CoA, all mono-CoA-thioesters of dicarboxylates used in this study were synthesized with glutaconate CoA-transferase from Acidaminococcus fermentans. The now possible conversion of (R)-2-hydroxyadipate via (R)-2-hydroxyadipoyl-CoA and 2-hexenedioyl-CoA to 2-hexenedioate paves the road for a bio-based production of adipic acid.
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Knauer SH, Buckel W, Dobbek H. Structural basis for reductive radical formation and electron recycling in (R)-2-hydroxyisocaproyl-CoA dehydratase. J Am Chem Soc 2011; 133:4342-7. [PMID: 21366233 DOI: 10.1021/ja1076537] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The radical enzyme (R)-2-hydroxyisocaproyl-CoA dehydratase catalyzes the dehydration of (R)-2-hydroxyisocaproyl-CoA in the fermentation of l-leucine by the human pathogenic bacterium Clostridium difficile. In contrast to other radical enzymes, such as bacterial class II ribonucleotide reductase or biotin synthase, the Fe/S cluster containing (R)-2-hydroxyisocaproyl-CoA dehydratase requires no special cofactors such as coenzyme B(12) or S-adenosylmethionine for radical generation. Instead it uses a single high-energy electron that is recycled after each turnover. The catalyzed reaction, an atypical α/β-dehydration, depends on the reductive formation of ketyl radicals on the substrate generated by injection of a single electron from the ATP-dependent activator protein. So far, it is unknown how the active electron is recycled and how unwanted side reactions are prevented, allowing for up to 10,000 turnovers. The crystal structure reveals that the heterodimeric protein contains two [4Fe-4S] clusters at a distance of 12 Å, each coordinated by three cysteines and one terminal ligand. The cluster in the α-subunit is part of the active site. In the absence of substrate, a water/hydroxide ion acts as the fourth ligand. The substrate replaces this ligand and coordinates the cluster via the carbonyl-oxygen of the thioester group. The cluster in the β-subunit has a terminal sulfhydryl/sulfido ligand and can act as a reservoir to protect the electron from unwanted side reactions via a recycling mechanism. The crystal structure of (R)-2-hydroxyisocaproyl-CoA dehydratase serves as a model for the reductively radical-generating metalloenzymes of the (R)-2-hydroxyacyl-CoA dehydratase and benzoyl-CoA reductase families.
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Affiliation(s)
- Stefan H Knauer
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
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Fonknechten N, Chaussonnerie S, Tricot S, Lajus A, Andreesen JR, Perchat N, Pelletier E, Gouyvenoux M, Barbe V, Salanoubat M, Le Paslier D, Weissenbach J, Cohen GN, Kreimeyer A. Clostridium sticklandii, a specialist in amino acid degradation:revisiting its metabolism through its genome sequence. BMC Genomics 2010; 11:555. [PMID: 20937090 PMCID: PMC3091704 DOI: 10.1186/1471-2164-11-555] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 10/11/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Clostridium sticklandii belongs to a cluster of non-pathogenic proteolytic clostridia which utilize amino acids as carbon and energy sources. Isolated by T.C. Stadtman in 1954, it has been generally regarded as a "gold mine" for novel biochemical reactions and is used as a model organism for studying metabolic aspects such as the Stickland reaction, coenzyme-B12- and selenium-dependent reactions of amino acids. With the goal of revisiting its carbon, nitrogen, and energy metabolism, and comparing studies with other clostridia, its genome has been sequenced and analyzed. RESULTS C. sticklandii is one of the best biochemically studied proteolytic clostridial species. Useful additional information has been obtained from the sequencing and annotation of its genome, which is presented in this paper. Besides, experimental procedures reveal that C. sticklandii degrades amino acids in a preferential and sequential way. The organism prefers threonine, arginine, serine, cysteine, proline, and glycine, whereas glutamate, aspartate and alanine are excreted. Energy conservation is primarily obtained by substrate-level phosphorylation in fermentative pathways. The reactions catalyzed by different ferredoxin oxidoreductases and the exergonic NADH-dependent reduction of crotonyl-CoA point to a possible chemiosmotic energy conservation via the Rnf complex. C. sticklandii possesses both the F-type and V-type ATPases. The discovery of an as yet unrecognized selenoprotein in the D-proline reductase operon suggests a more detailed mechanism for NADH-dependent D-proline reduction. A rather unusual metabolic feature is the presence of genes for all the enzymes involved in two different CO2-fixation pathways: C. sticklandii harbours both the glycine synthase/glycine reductase and the Wood-Ljungdahl pathways. This unusual pathway combination has retrospectively been observed in only four other sequenced microorganisms. CONCLUSIONS Analysis of the C. sticklandii genome and additional experimental procedures have improved our understanding of anaerobic amino acid degradation. Several specific metabolic features have been detected, some of which are very unusual for anaerobic fermenting bacteria. Comparative genomics has provided the opportunity to study the lifestyle of pathogenic and non-pathogenic clostridial species as well as to elucidate the difference in metabolic features between clostridia and other anaerobes.
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Affiliation(s)
- Nuria Fonknechten
- Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, F-91057 Evry, France
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Jain S, Graham RL, McMullan G, Ternan NG. Proteomic analysis of the insoluble subproteome of Clostridium difficile strain 630. FEMS Microbiol Lett 2010; 312:151-9. [DOI: 10.1111/j.1574-6968.2010.02111.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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Kim J, Pierik AJ, Buckel W. A complex of 2-hydroxyisocaproyl-coenzyme A dehydratase and its activator from Clostridium difficile stabilized by aluminium tetrafluoride-adenosine diphosphate. Chemphyschem 2010; 11:1307-12. [PMID: 20146278 DOI: 10.1002/cphc.200900876] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The dehydration of 2-hydroxyisocaproyl-CoA to isocaprenoyl-CoA is the chemically most demanding step in the reduction of leucine to isocaproate by Clostridium difficile, because the beta-hydrogen of the substrate is not acidic (pK(a) ca. 40). A two-component system, composed of a homodimeric activator and an heterodimeric dehydratase, catalyses this unusual alpha,beta-elimination of water. The reduced activator transfers an electron from its [4Fe-4S](+) cluster to that of the dehydratase in an ATP-dependent manner, similar to the iron protein of nitrogenase. Here we show that AlF(4)(-) x ADP traps the interaction of the activator with the dehydratase by forming a stable complex containing 1.0 mol homodimeric activator, 1.0 mol heterodimeric dehydratase and 1.2 mol ADP. The complex (148 kDa) was isolated by size exclusion chromatography, affinity chromatography using the Strep-tag at the activator, or most conveniently by ultrafiltration (100 kDa cut off membrane). Kinetic and EPR-spectroscopic experiments revealed that the complex formation proceeds much slower than the activation but in an almost irreversible manner. The isolated complex is devoid of any activity, because the dehydratase is in the oxidized form whereas the activator remains in the reduced state due to the presence of dithionite.
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Affiliation(s)
- Jihoe Kim
- Fachbereich Biologie, Philipps Universität, 35032 Marburg, Germany
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Parthasarathy A, Buckel W, Smith DM. On the thermodynamic equilibrium between (R)-2-hydroxyacyl-CoA and 2-enoyl-CoA. FEBS J 2010; 277:1738-46. [PMID: 20180803 DOI: 10.1111/j.1742-4658.2010.07597.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A combined experimental and computational approach has been applied to investigate the equilibria between several alpha-hydroxyacyl-CoA compounds and their 2-enoyl-CoA derivatives. In contrast to those of their beta, gamma and delta counterparts, the equilibria for the alpha-compounds are relatively poorly characterized, but qualitatively they appear to be unusually sensitive to substituents. Using a variety of techniques, we have succeeded in measuring the equilibrium constants for the reactions beginning from 2-hydroxyglutaryl-CoA and lactyl-CoA. A complementary computational evaluation of the equilibrium constants shows quantitative agreement with the measured values. By examining the computational results, we arrive at an explanation of the substituent sensitivity and provide a prediction for the, as yet unmeasured, equilibrium involving 2-hydroxyisocaproyl-CoA.
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Abstract
An increasing number of enzymes are being discovered that contain radicals or catalyze reactions via radical intermediates. These radical enzymes are able to open reaction pathways that two-electron steps cannot achieve. Recently, organic chemists started to apply related radical chemistry for synthetic purposes, whereby an electron energized by light is recycled in every turnover. This Minireview compares this new type of reaction with enzymes that use recycling radicals and single electrons as cofactors.
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Affiliation(s)
- Wolfgang Buckel
- Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität, 35032 Marburg, Germany.
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Proteomic and genomic characterization of highly infectious Clostridium difficile 630 spores. J Bacteriol 2009; 191:5377-86. [PMID: 19542279 PMCID: PMC2725610 DOI: 10.1128/jb.00597-09] [Citation(s) in RCA: 173] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Clostridium difficile, a major cause of antibiotic-associated diarrhea, produces highly resistant spores that contaminate hospital environments and facilitate efficient disease transmission. We purified C. difficile spores using a novel method and show that they exhibit significant resistance to harsh physical or chemical treatments and are also highly infectious, with <7 environmental spores per cm(2) reproducibly establishing a persistent infection in exposed mice. Mass spectrometric analysis identified approximately 336 spore-associated polypeptides, with a significant proportion linked to translation, sporulation/germination, and protein stabilization/degradation. In addition, proteins from several distinct metabolic pathways associated with energy production were identified. Comparison of the C. difficile spore proteome to those of other clostridial species defined 88 proteins as the clostridial spore "core" and 29 proteins as C. difficile spore specific, including proteins that could contribute to spore-host interactions. Thus, our results provide the first molecular definition of C. difficile spores, opening up new opportunities for the development of diagnostic and therapeutic approaches.
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Zhang Z. Use of whole cell culture of Aeromonas sp. as enantioselective scavenger: a facile preparation of l-amino acid derivatives in high enantiomeric excess. Bioorg Med Chem Lett 2009; 19:1129-31. [PMID: 19150596 DOI: 10.1016/j.bmcl.2008.12.100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2008] [Revised: 12/23/2008] [Accepted: 12/25/2008] [Indexed: 11/17/2022]
Abstract
The bacterium Aeromonas sp. (CGMCC 2226) can enantioselectively scavenge D-isomer, making L-amino acid derivatives (AADs) in high ee. The enantioselective scavenger (ES) has shown a broad substrate scope. Eleven L-AADs, Phe derivatives substituted with methyl-, mono- and dichloro-, bromo-, and nitro-group, were produced in high ee from corresponding racemates.
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Affiliation(s)
- Zizhang Zhang
- Department of Chemistry, Zhejiang University, 38 Zheda Road, Hangzhou 310027, PR China.
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Takeuchi Y, Fujiwara T, Shimone Y, Miyataka H, Satoh T, Kirk KL, Hori H. Possible involvement of radical intermediates in the inhibition of cysteine proteases by allenyl esters and amides. Bioorg Med Chem Lett 2008; 18:6202-5. [PMID: 18951789 PMCID: PMC2607570 DOI: 10.1016/j.bmcl.2008.10.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Revised: 09/08/2008] [Accepted: 10/01/2008] [Indexed: 11/30/2022]
Abstract
In order to investigate crystallographically the mechanism of inhibition of cysteine protease by alpha-methyl-gamma,gamma-diphenylallenecarboxylic acid ethyl ester 3, a cysteine protease inhibitor having in vivo stability, we synthesized N-(alpha-methyl-gamma,gamma-diphenylallenecarbonyl)-L-phenylalanine ethyl ester 4. Reaction of 4 with thiophenol, the SH group of which has similar pK(a) value to that of cysteine protease, produced oxygen-mediated radical adducts 6 and 7 in ambient air but did not proceed under oxygen-free conditions. Catalytic activities of two thiol enzymes including cathepsin B were also lowered in the absence of oxygen. These results suggest that cysteine protease can act through an oxygen-dependent radical mechanism.
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Affiliation(s)
- Yoshio Takeuchi
- Graduate School of Medicine and Pharmaceutical Sciences for Research, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan.
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Xiao Y, Liu P. IspH Protein of the Deoxyxylulose Phosphate Pathway: Mechanistic Studies with C1-Deuterium-Labeled Substrate and Fluorinated Analogue. Angew Chem Int Ed Engl 2008; 47:9722-5. [DOI: 10.1002/anie.200803452] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Xiao Y, Liu P. IspH Protein of the Deoxyxylulose Phosphate Pathway: Mechanistic Studies with C1-Deuterium-Labeled Substrate and Fluorinated Analogue. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200803452] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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The ether-cleaving methyltransferase system of the strict anaerobe Acetobacterium dehalogenans: analysis and expression of the encoding genes. J Bacteriol 2008; 191:588-99. [PMID: 19011025 DOI: 10.1128/jb.01104-08] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anaerobic O-demethylases are inducible multicomponent enzymes which mediate the cleavage of the ether bond of phenyl methyl ethers and the transfer of the methyl group to tetrahydrofolate. The genes of all components (methyltransferases I and II, CP, and activating enzyme [AE]) of the vanillate- and veratrol-O-demethylases of Acetobacterium dehalogenans were sequenced and analyzed. In A. dehalogenans, the genes for methyltransferase I, CP, and methyltransferase II of both O-demethylases are clustered. The single-copy gene for AE is not included in the O-demethylase gene clusters. It was found that AE grouped with COG3894 proteins, the function of which was unknown so far. Genes encoding COG3894 proteins with 20 to 41% amino acid sequence identity with AE are present in numerous genomes of anaerobic microorganisms. Inspection of the domain structure and genetic context of these orthologs predicts that these are also reductive activases for corrinoid enzymes (RACEs), such as carbon monoxide dehydrogenase/acetyl coenzyme A synthases or anaerobic methyltransferases. The genes encoding the O-demethylase components were heterologously expressed with a C-terminal Strep-tag in Escherichia coli, and the recombinant proteins methyltransferase I, CP, and AE were characterized. Gel shift experiments showed that the AE comigrated with the CP. The formation of other protein complexes with the O-demethylase components was not observed under the conditions used. The results point to a strong interaction of the AE with the CP. This is the first report on the functional heterologous expression of acetogenic phenyl methyl ether-cleaving O-demethylases.
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