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Abucayon EG, Powell DR, Richter-Addo GB. Carbon-Nitrogen and Nitrogen-Nitrogen Bond Formation from Nucleophilic Attack at Coordinated Nitrosyls in Fe and Ru Heme Models. J Am Chem Soc 2017. [PMID: 28648069 DOI: 10.1021/jacs.7b05209] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The conversion of inorganic NOx species to organo-N compounds is an important component of the global N-cycle. Reaction of a C-based nucleophile, namely the phenyl anion, with the ferric heme nitrosyl [(OEP)Fe(NO)(5-MeIm)]+ generates a mixture of the C-nitroso derivative (OEP)Fe(PhNO)(5-MeIm) and (OEP)Fe(Ph). The related reaction with [(OEP)Ru(NO)(5-MeIm)]+ generates the (OEP)Ru(PhNO)(5-MeIm) product. Reactions with the N-based nucleophile diethylamide results in the formation of free diethylnitrosamine, whereas the reaction with azide results in N2O formation; these products derive from attack of the nucleophiles on the bound NO groups. These results provide the first demonstrations of C-N and N-N bond formation from attack of C-based and N-based nucleophiles on synthetic ferric-NO hemes.
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Affiliation(s)
- Erwin G Abucayon
- Price Family Foundation Institute of Structural Biology and Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Douglas R Powell
- Price Family Foundation Institute of Structural Biology and Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - George B Richter-Addo
- Price Family Foundation Institute of Structural Biology and Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma , Norman, Oklahoma 73019, United States
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Frame CH, Lau E, Nolan EJ, Goepfert TJ, Lehmann MF. Acidification Enhances Hybrid N 2O Production Associated with Aquatic Ammonia-Oxidizing Microorganisms. Front Microbiol 2017; 7:2104. [PMID: 28119667 PMCID: PMC5220105 DOI: 10.3389/fmicb.2016.02104] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 12/13/2016] [Indexed: 02/01/2023] Open
Abstract
Ammonia-oxidizing microorganisms are an important source of the greenhouse gas nitrous oxide (N2O) in aquatic environments. Identifying the impact of pH on N2O production by ammonia oxidizers is key to understanding how aquatic greenhouse gas fluxes will respond to naturally occurring pH changes, as well as acidification driven by anthropogenic CO2. We assessed N2O production rates and formation mechanisms by communities of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in a lake and a marine environment, using incubation-based nitrogen (N) stable isotope tracer methods with 15N-labeled ammonium (15NH4+) and nitrite (15NO2−), and also measurements of the natural abundance N and O isotopic composition of dissolved N2O. N2O production during incubations of water from the shallow hypolimnion of Lake Lugano (Switzerland) was significantly higher when the pH was reduced from 7.54 (untreated pH) to 7.20 (reduced pH), while ammonia oxidation rates were similar between treatments. In all incubations, added NH4+ was the source of most of the N incorporated into N2O, suggesting that the main N2O production pathway involved hydroxylamine (NH2OH) and/or NO2− produced by ammonia oxidation during the incubation period. A small but significant amount of N derived from exogenous/added 15NO2− was also incorporated into N2O, but only during the reduced-pH incubations. Mass spectra of this N2O revealed that NH4+ and 15NO2− each contributed N equally to N2O by a “hybrid-N2O” mechanism consistent with a reaction between NH2OH and NO2−, or compounds derived from these two molecules. Nitrifier denitrification was not an important source of N2O. Isotopomeric N2O analyses in Lake Lugano were consistent with incubation results, as 15N enrichment of the internal N vs. external N atoms produced site preferences (25.0–34.4‰) consistent with NH2OH-dependent hybrid-N2O production. Hybrid-N2O formation was also observed during incubations of seawater from coastal Namibia with 15NH4+ and NO2−. However, the site preference of dissolved N2O here was low (4.9‰), indicating that another mechanism, not captured during the incubations, was important. Multiplex sequencing of 16S rRNA revealed distinct ammonia oxidizer communities: AOB dominated numerically in Lake Lugano, and AOA dominated in the seawater. Potential for hybrid N2O formation exists among both communities, and at least in AOB-dominated environments, acidification may accelerate this mechanism.
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Affiliation(s)
- Caitlin H Frame
- Department of Environmental Sciences, University of Basel Basel, Switzerland
| | - Evan Lau
- Department of Natural Sciences and Mathematics, West Liberty University West Liberty, WV, USA
| | - E Joseph Nolan
- Department of Natural Sciences and Mathematics, West Liberty University West Liberty, WV, USA
| | | | - Moritz F Lehmann
- Department of Environmental Sciences, University of Basel Basel, Switzerland
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Esclapez J, Zafrilla B, Martínez-Espinosa RM, Bonete MJ. Cu-NirK from Haloferax mediterranei as an example of metalloprotein maturation and exportation via Tat system. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1003-9. [PMID: 23499847 DOI: 10.1016/j.bbapap.2013.03.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 02/28/2013] [Accepted: 03/04/2013] [Indexed: 10/27/2022]
Abstract
The green Cu-NirK from Haloferax mediterranei (Cu-NirK) has been expressed, refolded and retrieved as a trimeric enzyme using an expression method developed for halophilic Archaea. This method utilizes Haloferax volcanii as a halophilic host and an expression vector with a constitutive and strong promoter. The enzymatic activity of recombinant Cu-NirK was detected in both cellular fractions (cytoplasmic fraction and membranes) and in the culture media. The characterization of the enzyme isolated from the cytoplasmic fraction as well as the culture media revealed important differences in the primary structure of both forms indicating that Hfx. mediterranei could carry out a maturation and exportation process within the cell before the protein is exported to the S-layer. Several conserved signals found in Cu-NirK from Hfx. mediterranei sequence indicate that these processes are closely related to the Tat system. Furthermore, the N-terminal sequence of the two Cu-NirK subunits constituting different isoforms revealed that translation of this protein could begin at two different points, identifying two possible start codons. The hypothesis proposed in this work for halophilic Cu-NirK processing and exportation via the Tat system represents the first approximation of this mechanism in the Halobacteriaceae family and in Prokarya in general.
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Affiliation(s)
- J Esclapez
- Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
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Kool DM, Wrage N, Oenema O, Harris D, Van Groenigen JW. The 18O signature of biogenic nitrous oxide is determined by O exchange with water. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:104-108. [PMID: 19061209 DOI: 10.1002/rcm.3859] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
To effectively mitigate emissions of the greenhouse gas nitrous oxide (N(2)O) it is essential to understand the biochemical pathways by which it is produced. The (18)O signature of N(2)O is increasingly used to characterize these processes. However, assumptions on the origin of the O atom and resultant isotopic composition of N(2)O that are based on reaction stoichiometry may be questioned. In particular, our deficient knowledge on O exchange between H(2)O and nitrogen oxides during N(2)O production complicates the interpretation of the (18)O signature of N(2)O.Here we studied O exchange during N(2)O formation in soil, using a novel combination of (18)O and (15)N tracing. Twelve soils were studied, covering soil and land-use variability across Europe. All soils demonstrated the significant presence of O exchange, as incorporation of O from (18)O-enriched H(2)O into N(2)O exceeded their maxima achievable through reaction stoichiometry. Based on the retention of the enrichment ratio of (18)O and (15)N of NO(3)(-) into N(2)O, we quantified O exchange during denitrification. Up to 97% (median 85%) of the N(2)O-O originated from H(2)O instead of from the denitrification substrate NO(3)(-).We conclude that in soil, the main source of atmospheric N(2)O, the (18)O signature of N(2)O is mainly determined by H(2)O due to O exchange between nitrogen oxides and H(2)O. This also challenges the assumption that the O of N(2)O originates from O(2) and NO(3)(-), in ratios reflecting reaction stoichiometry.
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Affiliation(s)
- D M Kool
- Alterra, Wageningen University and Research Centre, Wageningen, The Netherlands.
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Sam KA, Strampraad MJ, de Vries S, Ferguson SJ. Very Early Reaction Intermediates Detected by Microsecond Time Scale Kinetics of Cytochrome cd1-catalyzed Reduction of Nitrite. J Biol Chem 2008; 283:27403-27409. [DOI: 10.1074/jbc.m804493200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Morozkina EV, Kurakov AV. Dissimilatory nitrate reduction in fungi under conditions of hypoxia and anoxia: A review. APPL BIOCHEM MICRO+ 2007. [DOI: 10.1134/s0003683807050079] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Roncaroli F, Videla M, Slep LD, Olabe JA. New features in the redox coordination chemistry of metal nitrosyls {M–NO+; M–NO; M–NO−(HNO)}. Coord Chem Rev 2007. [DOI: 10.1016/j.ccr.2007.04.012] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Kool DM, Wrage N, Oenema O, Dolfing J, Van Groenigen JW. Oxygen exchange between (de)nitrification intermediates and H2O and its implications for source determination of NO3- and N2O: a review. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:3569-3578. [PMID: 17935120 DOI: 10.1002/rcm.3249] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Stable isotope analysis of oxygen (O) is increasingly used to determine the origin of nitrate (NO(3)-) and nitrous oxide (N(2)O) in the environment. The assumption underlying these studies is that the (18)O signature of NO(3)- and N(2)O provides information on the different O sources (O(2) and H(2)O) during the production of these compounds by various biochemical pathways. However, exchange of O atoms between H(2)O and intermediates of the (de)nitrification pathways may change the isotopic signal and thereby bias its interpretation for source determination. Chemical exchange of O between H(2)O and various nitrogenous oxides has been reported, but the probability and extent of its occurrence in terrestrial ecosystems remain unclear. Biochemical O exchange between H(2)O and nitrogenous oxides, NO(2)- in particular, has been reported for monocultures of many nitrifiers and denitrifiers that are abundant in nature, with exchange rates of up to 100%. Therefore, biochemical O exchange is likely to be important in most soil ecosystems, and should be taken into account in source determination studies. Failing to do so might lead to (i) an overestimation of nitrification as NO(3)- source, and (ii) an overestimation of nitrifier denitrification and nitrification-coupled denitrification as N(2)O production pathways. A method to quantify the rate and controls of biochemical O exchange in ecosystems is needed, and we argue this can only be done reliably with artificially enriched (18)O compounds. We conclude that in N source determination studies, the O isotopic signature of especially N(2)O should only be used with extreme caution.
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Affiliation(s)
- D M Kool
- Alterra, Wageningen University and Research Centre, Wageningen, The Netherlands.
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Noda H, Ohya H, Kamada H. Efficient Formation of a Nitrosyl(protoporphyrinato)iron(II) Complex on Magnesium Oxide Powder. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2004. [DOI: 10.1246/bcsj.77.1635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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OLABE JOSÉA. REDOX REACTIVITY OF COORDINATED LIGANDS IN PENTACYANO(L)FERRATE COMPLEXES. ADVANCES IN INORGANIC CHEMISTRY 2004. [DOI: 10.1016/s0898-8838(03)55002-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Chevalier AA, Gentil LA, Amorebieta VT, Gutiérrez MM, Olabe JA. The Catalytic Reduction of Nitrite. Metal Coordination and Reaction of Nitrosyl with Hydrazine: Two-Electron Oxidants Can Also Lead to Ammonia. J Am Chem Soc 2000. [DOI: 10.1021/ja0020052] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alberto A. Chevalier
- Departamento de Química Facultad de Ciencias Exactas Universidad Nacional de Mar del Plata B7602AYL Mar del Plata, República Argentina Departamento de Química Inorgánica Analítica y Química Física, Inquimae Universidad de Buenos Aires Pabellón 2, Ciudad Universitaria C1428EHA Buenos Aires, República Argentina
| | - Luis A. Gentil
- Departamento de Química Facultad de Ciencias Exactas Universidad Nacional de Mar del Plata B7602AYL Mar del Plata, República Argentina Departamento de Química Inorgánica Analítica y Química Física, Inquimae Universidad de Buenos Aires Pabellón 2, Ciudad Universitaria C1428EHA Buenos Aires, República Argentina
| | - Valentín T. Amorebieta
- Departamento de Química Facultad de Ciencias Exactas Universidad Nacional de Mar del Plata B7602AYL Mar del Plata, República Argentina Departamento de Química Inorgánica Analítica y Química Física, Inquimae Universidad de Buenos Aires Pabellón 2, Ciudad Universitaria C1428EHA Buenos Aires, República Argentina
| | - María M. Gutiérrez
- Departamento de Química Facultad de Ciencias Exactas Universidad Nacional de Mar del Plata B7602AYL Mar del Plata, República Argentina Departamento de Química Inorgánica Analítica y Química Física, Inquimae Universidad de Buenos Aires Pabellón 2, Ciudad Universitaria C1428EHA Buenos Aires, República Argentina
| | - José A. Olabe
- Departamento de Química Facultad de Ciencias Exactas Universidad Nacional de Mar del Plata B7602AYL Mar del Plata, República Argentina Departamento de Química Inorgánica Analítica y Química Física, Inquimae Universidad de Buenos Aires Pabellón 2, Ciudad Universitaria C1428EHA Buenos Aires, República Argentina
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George SJ, Allen JW, Ferguson SJ, Thorneley RN. Time-resolved infrared spectroscopy reveals a stable ferric heme-NO intermediate in the reaction of Paracoccus pantotrophus cytochrome cd1 nitrite reductase with nitrite. J Biol Chem 2000; 275:33231-7. [PMID: 10922371 DOI: 10.1074/jbc.m005033200] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytochrome cd(1) is a respiratory enzyme that catalyzes the physiological one-electron reduction of nitrite to nitric oxide. The enzyme is a dimer, each monomer containing one c-type cytochrome center and one active site d(1) heme. We present stopped-flow Fourier transform infrared data showing the formation of a stable ferric heme d(1)-NO complex (formally d(1)Fe(II)-NO(+)) as a product of the reaction between fully reduced Paracoccus pantotrophus cytochrome cd(1) and nitrite, in the absence of excess reductant. The Fe-(14)NO nu(NO) stretching mode is observed at 1913 cm(-1) with the corresponding Fe-(15)NO band at 1876 cm(-1). This d(1) heme-NO complex is still readily observed after 15 min. EPR and visible absorption spectroscopic data show that within 4 ms of the initiation of the reaction, nitrite is reduced at the d(1) heme, and a cFe(III) d(1)Fe(II)-NO complex is formed. Over the next 100 ms there is an electron redistribution within the enzyme to give a mixed species, 55% cFe(III) d(1)Fe(II)-NO and 45% cFe(II) d(1)Fe(II)-NO(+). No kinetically competent release of NO could be detected, indicating that at least one additional factor is required for product release by the enzyme. Implications for the mechanism of P. pantotrophus cytochrome cd(1) are discussed.
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Affiliation(s)
- S J George
- Biological Chemistry Department, John Innes Centre, Colney Lane, Norwich, NR4 7UH and Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
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Abstract
Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.
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Affiliation(s)
- W G Zumft
- Lehrstuhl für Mikrobiologie, Universität Fridericiana, Karlsruhe, Germany
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Murphy ME, Turley S, Adman ET. Structure of nitrite bound to copper-containing nitrite reductase from Alcaligenes faecalis. Mechanistic implications. J Biol Chem 1997; 272:28455-60. [PMID: 9353305 DOI: 10.1074/jbc.272.45.28455] [Citation(s) in RCA: 181] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The structures of oxidized, reduced, nitrite-soaked oxidized and nitrite-soaked reduced nitrite reductase from Alcaligenes faecalis have been determined at 1.8-2.0 A resolution using data collected at -160 degrees C. The active site at cryogenic temperature, as at room temperature, contains a tetrahedral type II copper site liganded by three histidines and a water molecule. The solvent site is empty when crystals are reduced with ascorbate. A fully occupied oxygen-coordinate nitrite occupies the solvent site in crystals soaked in nitrite. Ascorbate-reduced crystals soaked in a glycerol-methanol solution and nitrite at -40 degrees C remain colorless at -160 degrees C but turn amber-brown when warmed, suggesting that NO is released. Nitrite is found at one-half occupancy. Five new solvent sites in the oxidized nitrite bound form exhibit defined but different occupancies in the other three forms. These results support a previously proposed mechanism by which nitrite is bound primarily by a single oxygen atom that is protonable, and after reduction and cleavage of that N-O bond, NO is released leaving the oxygen atom bound to the Cu site as hydroxide or water.
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Affiliation(s)
- M E Murphy
- Department of Biological Structure, School of Medicine, University of Washington, Seattle, Washington 98195-7420, USA
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A�mann B, Ostendorp G, Homborg H. InIII-Phthalocyanine: Darstellung, Eigenschaften und Kristallstruktur von Tetra(n-butyl)ammonium-cis-di(nitrito-O,O?)phthalocyaninato(2-)indat(III). Z Anorg Allg Chem 1995. [DOI: 10.1002/zaac.19956211016] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Komeda N, Nagao H, Kushi Y, Adachi GY, Suzuki M, Uehara A, Tanaka K. Molecular Structure of Nitro- and Nitrito-Copper Complexes as Reaction Intermediates in Electrochemical Reduction of Nitrite to Dinitrogen Oxide. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1995. [DOI: 10.1246/bcsj.68.581] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Averill BA. Neuartige Nitrosylkupfer-Komplexe: Beiträge zum Verständnis der dissimilatorischen, kupferhaltigen Nitrit-Reduktasen. Angew Chem Int Ed Engl 1994. [DOI: 10.1002/ange.19941062008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Kastrau DH, Heiss B, Kroneck PM, Zumft WG. Nitric oxide reductase from Pseudomonas stutzeri, a novel cytochrome bc complex. Phospholipid requirement, electron paramagnetic resonance and redox properties. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 222:293-303. [PMID: 8020468 DOI: 10.1111/j.1432-1033.1994.tb18868.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The nitric oxide reductase (NOR) from Pseudomonas stutzeri is a cytochrome bc complex which shows on SDS/PAGE two subunits with apparent molecular masses of 17 kDa and 38 kDa. Two other species of approximately 45 kDa and 74-78 kDa represent the undissociated enzyme complex and an aggregate of the cytochrome b subunit, respectively. The cytochrome b subunit is highly hydrophobic and results in aberrant electrophoretic mobility. The stability of the enzyme in various detergents and at different pH was investigated. The highest specific activity of 60 mumol NO min-1 mg-1 protein was obtained after electrophoresis in the presence of laurylpropanediol-3-phosphorylcholine ether. Purified NOR contained cardiolipin, phosphatidylglycerol, and phosphatidylethanolamine, the latter as the major component. A phospholipid was required for high catalytic activity with either cardiolipin or phosphatidylglycerol increasing the activity of the enzyme as isolated by a factor of up to 5. Free fatty acids inhibited NOR, with cis-9-octadecenoic acid (oleic acid) showing the most pronounced effect. Certain detergents substituted for the phospholipid requirement of NOR. The enzyme, as isolated, in 0.1% Triton X-100, 20 mM Tris/HCl pH 8.5, exhibited a complex set of EPR resonances at low magnetic field, with a prominent peak at g 6.34 resulting from Fe(III) high-spin cytochrome b. The second prominent feature arose from a low-spin Fe(III) heme center with strong lines at apparent g values of 3.02 and 2.29, and a broad resonance at g approximately 1.5 which we assigned to the cytochrome c component of the enzyme. From spin quantitation and computer simulations of the various EPR signals a ratio close to 1:1 for the low-spin/high-spin heme centers in NOR was estimated. Shifting the pH from 8.5 to 5.0, replacing Triton X-100 by other detergents, or adding soybean phospholipids to the protein, led to pronounced changes of the EPR signals in the g = 6 region. In contrast, the strong inhibitor oleic acid did not cause significant spectral changes. NOR which had been reduced by L-ascorbate/phenazine methosulfate prior to incubation with its substrate NO gave the characteristic Fe(II) nitrosyl triplet centered at g approximately 2.01, with a hyperfine splitting of 1.70 mT. In the absence of dioxygen, NOR was quantitatively reduced by either sodium dithionite, or photochemically with deazaflavin and oxalate; the enzyme was reoxidizable by ferricyanide in a fully reversible reaction. Spectroelectrochemical oxidoreductive titrations gave E'o (versus standard hydrogen electrode) = +322 mV for the cytochrome b and +280 mV for the cytochrome c component.
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Affiliation(s)
- D H Kastrau
- Universität Konstanz, Fakultät für Biologie, Germany
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Ye RW, Averill BA, Tiedje JM. Denitrification: production and consumption of nitric oxide. Appl Environ Microbiol 1994; 60:1053-8. [PMID: 8017903 PMCID: PMC201439 DOI: 10.1128/aem.60.4.1053-1058.1994] [Citation(s) in RCA: 162] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- R W Ye
- Department of Microbiology, Michigan State University, East Lansing 48824
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Ozawa S, Sakamoto E, Watanabe Y, Morishima I. Formation of nitrosyl-iron(II)β-oxoporphyrin π-cation radical complexes. Models for a reaction intermediate of dissimilatory nitrite reductases. ACTA ACUST UNITED AC 1994. [DOI: 10.1039/c39940000935] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Jones AM, Hollocher TC. Nitric oxide reductase of Achromobacter cycloclastes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1993. [DOI: 10.1016/0005-2728(93)90121-u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Komeda N, Nagao H, Adachi GY, Suzuki M, Uehara A, Tanaka K. Molecular Structure of Copper Nitrito Complex as the Reaction Intermediate of Dissimilatory Reduction of NO2−. CHEM LETT 1993. [DOI: 10.1246/cl.1993.1521] [Citation(s) in RCA: 19] [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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Abstract
Nitric oxide (NO.), a potentially toxic molecule, has been implicated in a wide range of biological functions. Details of its biochemistry, however, remain poorly understood. The broader chemistry of nitrogen monoxide (NO) involves a redox array of species with distinctive properties and reactivities: NO+ (nitrosonium), NO., and NO- (nitroxyl anion). The integration of this chemistry with current perspectives of NO biology illuminates many aspects of NO biochemistry, including the enzymatic mechanism of synthesis, the mode of transport and targeting in biological systems, the means by which its toxicity is mitigated, and the function-regulating interaction with target proteins.
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Affiliation(s)
- J S Stamler
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
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26
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Ye RW, Averill BA, Tiedje JM. Characterization of Tn5 mutants deficient in dissimilatory nitrite reduction in Pseudomonas sp. strain G-179, which contains a copper nitrite reductase. J Bacteriol 1992; 174:6653-8. [PMID: 1328160 PMCID: PMC207644 DOI: 10.1128/jb.174.20.6653-6658.1992] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Tn5 was used to generate mutants that were deficient in the dissimilatory reduction of nitrite for Pseudomonas sp. strain G-179, which contains a copper nitrite reductase. Three types of mutants were isolated. The first type showed a lack of growth on nitrate, nitrite, and nitrous oxide. The second type grew on nitrate and nitrous oxide but not on nitrite (Nir-). The two mutants of this type accumulated nitrite, showed no nitrite reductase activity, and had no detectable nitrite reductase protein bands in a Western blot (immunoblot). Tn5 insertions in these two mutants were clustered in the same region and were within the structural gene for nitrite reductase. The third type of mutant grew on nitrate but not on nitrite or nitrous oxide (N2O). The mutant of this type accumulated significant amounts of nitrite, NO, and N2O during anaerobic growth on nitrate and showed a slower growth rate than the wild type. Diethyldithiocarbamic acid, which inhibited nitrite reductase activity in the wild type, did not affect NO reductase activity, indicating that nitrite reductase did not participate in NO reduction. NO reductase activity in Nir- mutants was lower than that in the wild type when the strains were grown on nitrate but was the same as that in the wild type when the strains were grown on nitrous oxide. These results suggest that the reduction of NO and N2O was carried out by two distinct processes and that mutations affecting nitrite reduction resulted in reduced NO reductase activity following anaerobic growth with nitrate.
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Affiliation(s)
- R W Ye
- Department of Microbiology and Public Health, Michigan State University, East Lansing 48824
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27
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Tanimoto T, Hatano KI, Kim DH, Uchiyama H, Shoun H. Co-denitrification by the denitrifying system of the fungusFusarium oxysporum. FEMS Microbiol Lett 1992. [DOI: 10.1111/j.1574-6968.1992.tb05086.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Ye RW, Arunakumari A, Averill BA, Tiedje JM. Mutants of Pseudomonas fluorescens deficient in dissimilatory nitrite reduction are also altered in nitric oxide reduction. J Bacteriol 1992; 174:2560-4. [PMID: 1556074 PMCID: PMC205894 DOI: 10.1128/jb.174.8.2560-2564.1992] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Five Tn5 mutants of Pseudomonas fluorescens AK-15 deficient in dissimilatory reduction of nitrite were isolated and characterized. Two insertions occurred inside the nitrite reductase structural gene (nirS) and resulted in no detectable nitrite reductase protein on a Western immunoblot. One mutant had Tn5 inserted inside nirC, the third gene in the same operon, and produced a defective nitrite reductase protein. Two other mutants had insertions outside of this nir operon and also produced defective proteins. All of the Nir- mutants characterized showed not only loss of nitrite reductase activity but also a significant decrease in nitric oxide reductase activity. When cells were incubated with 15NO in H2(18)O, about 25% of the oxygen found in nitrous oxide exchanged with H2O. The extent of exchange remained constant throughout the reaction, indicating the incorporation of 18O from H2(18)O reached equilibrium rapidly. In all nitrite reduction-deficient mutants, less than 4% of the 18O exchange was found, suggesting that the hydration and dehydration step was altered. These results indicate that the factors involved in dissimilatory reduction of nitrite influenced the subsequent NO reduction in this organism.
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Affiliation(s)
- R W Ye
- Department of Microbiology and Public Health, Michigan State University, East Lansing 48824-1325
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29
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H218O isotope exchange studies on the mechanism of reduction of nitric oxide and nitrite to nitrous oxide by denitrifying bacteria. Evidence for an electrophilic nitrosyl during reduction of nitric oxide. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)98771-5] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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30
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Goretski J, Hollocher TC. Catalysis of nitrosyl transfer by denitrifying bacteria is facilitated by nitric oxide. Biochem Biophys Res Commun 1991; 175:901-5. [PMID: 2025262 DOI: 10.1016/0006-291x(91)91650-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Two denitrifying bacteria, Pseudomonas stutzeri and Achromobacter cycloclastes, were incubated with Na15NO2 and NaN3 under conditions that allowed catalysis of nitrosyl transfer from nitrite to azide. This transfer, which is presumed to be mediated by the heme- and copper-containing nitrite reductase of P. stutzeri and A. cycloclastes, respectively, leads to formation of isotopically mixed 14,15N2O, whereas denitrification leads to 15N2O. The conditions that emphasized nitrosyl transfer also partially inhibited the nitric oxide reductase system and led to accumulation of 15NO. Absorption of NO from the gas phase by acidic CrSO4 in a sidewell largely abolished nitrosyl transfer to azide. With these two organisms, which are thought to be representative of denitrifiers generally, catalysis of nitrosyl transfer seemed to depend on NO.
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Affiliation(s)
- J Goretski
- Department of Biochemistry, Brandeis University, Waltham, MA 02254
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Goretski J, Hollocher TC. The kinetic and isotopic competence of nitric oxide as an intermediate in denitrification. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)40133-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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32
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Suzuki S, Yoshimura T, Kohzuma T, Shidara S, Masuko M, Sakurai T, Iwasaki H. Spectroscopic evidence for a copper-nitrosyl intermediate in nitrite reduction by blue copper-containing nitrite reductase. Biochem Biophys Res Commun 1989; 164:1366-72. [PMID: 2556127 DOI: 10.1016/0006-291x(89)91820-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The reactions of nitrogen monoxide (NO) with the blue copper-containing nitrite reductases from Alcaligenes sp. NCIB 11015 and Achromobacter cycloclastes IAM 1013 were investigated spectroscopically. The electron paramagnetic resonance (EPR) signals of the blue coppers vanished in the presence of NO at 77 K, being fully restored by the removal of NO. The additions of NO to the enzyme solutions resulted in the substantial bleaching of the visible absorption bands at room temperature. The reactions were also completely reversible. These results suggest the formation of a cuprous nitrosyl complex (Cu+-NO+), which is likely the intermediate in the enzymatic nitrite reduction.
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Affiliation(s)
- S Suzuki
- Institute of Chemistry, College of General Education, Osaka University, Japan
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Purification and some characteristics of nitric oxide reductase-containing vesicles from Paracoccus denitrificans. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)83270-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Nitrogen isotopic fractionation and 18O exchange in relation to the mechanism of denitrification of nitrite by Pseudomonas stutzeri. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)37696-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Bonner FT, Hughes MN. The Aqueous Solution Chemistry of Nitrogen in Low Positive Oxidation States. COMMENT INORG CHEM 1988. [DOI: 10.1080/02603598808072309] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Goretski J, Hollocher TC. Trapping of nitric oxide produced during denitrification by extracellular hemoglobin. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)69208-7] [Citation(s) in RCA: 126] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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37
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Abstract
The reaction between hydroxylamine (NH2OH) and human hemoglobin (Hb) at pH 6-8 and the reaction between NH2OH and methemoglobin (Hb+) chiefly at pH 7 were studied under anaerobic conditions at 25 degrees C. In presence of cyanide, which was used to trap Hb+, Hb was oxidized by NH2OH to methemoglobin cyanide with production of about 0.5 mol NH+4/mol of heme oxidized at pH 7. The conversion of Hb to Hb+ was first order in [Hb] (or nearly so) but the pseudo-first-order rate constant was not strictly proportional to [NH2OH]. Thus, the apparent second-order rate constant at pH 7 decreased from about 30 M-1 X s-1 to a limiting value of 11.3 M-1 X s-1 with increasing [NH2OH]. The rate of Hb oxidation was not much affected by cyanide, whereas there was no reaction between NH2OH and carbonmonoxyhemoglobin (HbCO). The pseudo-first-order rate constant for Hb oxidation at 500 microM NH2OH increased from about 0.008 s-1 at pH 6 to 0.02 s-1 at pH 8. The oxidation of Hb by NH2OH terminated prematurely at 75-90% completion at pH 7 and at 30-35% completion at pH 8. Data on the premature termination of reaction fit the titration curve for a group with pK = 7.5-7.7. NH2OH was decomposed by Hb+ to N2, NH+4, and a small amount of N2O in what appears to be a dismutation reaction. Nitrite and hydrazine were not detected, and N2 and NH+4 were produced in nearly equimolar amounts. The dismutation reaction was first order in [Hb+] and [NH2OH] only at low concentrations of reactants and was cleanly inhibited by cyanide. The spectrum of Hb+ remained unchanged during the reaction, except for the gradual formation of some choleglobin-like (green) pigment, whereas in the presence of CO, HbCO was formed. Kinetics are consistent with the view advanced previously by J. S. Colter and J. H. Quastel [1950) Arch. Biochem. 27, 368-389) that the decomposition of NH2OH proceeds by a mechanism involving a Hb/Hb+ cycle (reactions [1] and [2]) in which Hb is oxidized to Hb+ by NH2OH.
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Affiliation(s)
- D A Bazylinski
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02254
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Shapleigh JP, Davies KJ, Payne WJ. Detergent inhibition of nitric-oxide reductase activity. BIOCHIMICA ET BIOPHYSICA ACTA 1987; 911:334-40. [PMID: 3028488 DOI: 10.1016/0167-4838(87)90074-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Gas chromatography revealed that exposure of extracts of the denitrifiers 'Achromobacter cycloclastes', Paracoccus denitrificans, Pseudomonas aeruginosa and Pseudomonas perfectomarina to Triton X-100 inhibited reduction of NO to N2O, and thus concomitantly inhibited reduction of NO2- to N2O. After exposure of extracts to Triton X-100, the ratio of H+ consumed to NO2- added decreased from approx. 2.0 (for untreated extracts) to approx. 1.5, which indicated that NO2- was reduced to NO by the treated extracts. Addition of a CHAPS-soluble extract (devoid of nitrite reductase activity but rich in nitric-oxide reductase activity) to the Triton X-100-treated extract of P. denitrificans restored capacity for reduction of NO2- on to N2O. Exposure to either the NO that accumulated from reduction of NO2- or to enthetic NO transiently inhibited rates of NO2- reduction in Triton X-100-treated extracts. Use of an Oxides of Nitrogen analyzer indicated that only 5-33% of NO2- reduced by untreated extracts appeared in the stripping gas as NO, whereas 80-95% of NO2- reduced by Triton X-100-treated extracts was recovered as NO.
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Abstract
Three strains of Pseudomonas aeruginosa were grown anaerobically on exogenous N2O in a defined medium under conditions that assured the maintenance of highly anaerobic conditions for periods of 1 week or more. The bacteria were observed reproducibly to increase their cell density by factors of 3 to 9, but not more, depending on the initial amount of N2O. Growth on N2O was cleanly blocked by acetylene. Cell yields, CO2 production, and N2O uptake all increased with initial PN2O at PN2O less than or equal to 0.1 atm. Growth curves were atypical in the sense that growth rates decreased with time. This is the first observation of growth of P. aeruginosa on N2O as the sole oxidant. N2O was shown to be an obligatory, freely diffusible intermediate during growth of strains PAO1 and P1 on nitrate. All three strains used this endogenous N2O efficiently for growth. For strains PAO1 and P1, it was confirmed that exogenous N2O had little effect on the cell yields of cultures growing with nitrate; thus, for these strains exogenous N2O neither directly inhibited growth nor was used significantly for growth. On the other hand, strain P2 grew abundantly on exogenous N2O when small and growth-limiting concentrations of nitrate or nitrate (2 to 10 mM) were included in the medium. The dramatic effect of these N-anions was realized in large part even when the exogenous N2O was introduced immediately after the quantitative conversion of anion-nitrogen to N2. No evidence was found for a factor in filter-sterilized spent medium that stimulated fresh inocula to grow abundantly on N2O.(ABSTRACT TRUNCATED AT 250 WORDS)
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Abstract
Respiration of NO resulted in transient proton translocation in anaerobically grown cells of four physiologically diverse denitrifiers. Paracoccus denitrificans, Rhodopseudomonas sphaeroides subsp. denitrificans, "Achromobacter cycloclastes," and Rhizobium japonicum gave, respectively, H+/NO ratios of 3.65, 4.96, 1.94, and 1.12. Antimycin A completely inhibited NO-dependent proton translocation in P. denitrificans and severely restricted translocation in the R. sphaeroides strain. Proton uptake during NO respiration with antimycin A-inhibited cells supplied with an artificial electron source provided evidence for the periplasmic consumption of protons. Values obtained were consistent with the expected ratios of 0.5 mol of H+/mol of NO for reduction of NO to N2O and 1.0 mol of H+/mol of NO for reduction of NO to N2. These data are consistent with the presence of a unique NO reductase found only in anaerobically grown denitrifying cells.
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Shapleigh J, Payne W. Differentiation ofc,d1cytochrome and copper nitrite reductase production in denitrifiers. FEMS Microbiol Lett 1985. [DOI: 10.1111/j.1574-6968.1985.tb01610.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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