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

An investigation on catalytic nitrite reduction reaction by bioinspired CuII complexes

Catalytic nitrite reductions by Cu^II complexes containing anionic ^Me2Tp, neutral ^Me2Tpm, or neutral ^iPrTIC ligands in the presence of L-ascorbic acid, which served as an electron donor and proton source, were investigated. The results showed that auxiliary ligands are important for copper-mediated catalytic nitrite reduction. Furthermore, the electronic effects of the ligand govern the nitrite reduction efficiency, which should be considered at two control points: one is the susceptibility of the LCu^I-nitrite species to protonation and the other is the susceptibility of LCu^II to reduction giving LCu^I. In addition, an external strong acid leads to the production of nitrous acid, which may suggest that the reactivity of nitrous acid toward the LCu^I species is a third control point.

Influence of δ18 O of water on measurements of δ18 O of nitrite and nitrate

RATIONALE

Oxygen isotope ratio measurements of NO₂ ^- and NO₃ ^- by the azide method and denitrifier method are sensitive to the δ¹⁸ O value of the sample water. However, the influence of δ¹⁸ O_H2O on those measurements has not been quantitatively evaluated and documented so far. Therefore, we investigated the influence of δ¹⁸ O_H2O of a sample on the δ¹⁸ O analysis of NO₂ ^- and NO₃ ^- .

METHODS

We prepared NO₂ ^- and NO₃ ^- standards (with known δ¹⁸ O_NO2- and δ¹⁸ O_NO3- values) dissolved in waters having different δ¹⁸ O_H2O values (δ¹⁸ O_H2O  = -12.6, 25.9, 56.7, and 110.1‰). Nitrite and nitrate were converted into N₂ O using the azide method and the denitrifier method, respectively. The isotope ratios of the generated N₂ O were measured with a Sercon purge-and-trap gas chromatography/isotope ratio mass spectrometry (PT-GC/IRMS) system. The measured δ¹⁸ O values of the produced N₂ O were plotted against known δ¹⁸ O_NO2- and δ¹⁸ O_NO3- values to evaluate the influence of exchange of an oxygen atom with H₂ O during the conversion of NO₂ ^- into N₂ O and NO₃ ^- into N₂ O, respectively.

RESULTS

The degree of oxygen isotope exchange was 10.8 ± 0.3% in the azide method and 5.5 ± 1.0% in the denitrifier method, indicating that the azide method is more susceptible to artifacts arising from differences in the δ¹⁸ O_H2O value of water than the denitrifier method. Thus, the intercept of the standard calibration curve must be corrected to account for differences in δ¹⁸ O_H2O . Abiotic NO₂ -H₂ O equilibrium isotope effect experiments yielded a rate constant of (1.13 ± 007) × 10^-2 (h^-1 ) and an equilibrium isotope effect of 11.9 ± 0.1‰ under the condition of pH = 7.5, 30°C, and 2.5% salinity.

CONCLUSIONS

Oxygen isotope ratio measurements of NO₂ ^- by the azide method are highly sensitive to δ¹⁸ O_H2O as a result of significant oxygen isotope exchange between NO₂ ^- and H₂ O. Therefore, to obtain the most accurate measurements water with the same δ¹⁸ O_H2O value as that of the sample must be used to make the NO₂ ^- and NO₃ ^- standards.

Biochar amendment suppresses N2 O emissions but has no impact on 15 N site preference in an anaerobic soil

RATIONALE

Biochar amendments often decrease N₂ O gas production from soil, but the mechanisms and magnitudes are still not well characterized since N₂ O can be produced via several different microbial pathways. We evaluated the influence of biochar amendment on N₂ O emissions and N₂ O isotopic composition, including ¹⁵ N site preference (SP) under anaerobic conditions.

METHODS

An agricultural soil was incubated with differing levels of biochar. Incubations were conducted under anaerobic conditions for 10 days with and without acetylene, which inhibits N₂ O reduction to N₂ . The N₂ O concentrations were measured every 2 days, the SPs were determined after 5 days of incubation, and the inorganic nitrogen concentrations were measured after the incubation.

RESULTS

The SP values with acetylene were consistent with N₂ O production by bacterial denitrification and those without acetylene were consistent with bacterial denitrification that included N₂ O reduction to N₂ . There was no effect of biochar on N₂ O production in the presence of acetylene between day 3 and day 10. However, in the absence of acetylene, soils incubated with 4% biochar produced less N₂ O than soils with no biochar addition. Different amounts of biochar amendment did not change the SP values.

CONCLUSIONS

Our study used N₂ O emission rates and SP values to understand biochar amendment mechanisms and demonstrated that biochar amendment reduces N₂ O emissions by stimulating the last step of denitrification. It also suggested a possible shift in N₂ O-reducing microbial taxa in 4% biochar samples.

Nitric oxide-release study of a bio-inspired copper(i)-nitrito complex under chemical and biological conditions

The selective and efficient nitrite reduction process is ubiquitous in biological systems. To understand copper-mediated nitrite reduction, we developed a bio-inspired model system to investigate the mechanism of copper-containing nitrite reductase. A well-characterized copper(i)-nitrate complex with amino functionalized 2-(diphenylphosphino)aniline ligands, [(Ph₂PC₆H₄(o-NH₂))₂Cu(ONO)], demonstrated the aniline protonation will cause NO release in an acidic environment. To further understand NO releasing ability, we also performed pH-dependency experiments and confocal imaging to release NO under physiological buffer conditions. According to titration and spectroscopic studies on the protonation reaction of complex [(Ph₂PC₆H₄(o-NH₂))₂Cu(ONO)], we proposed a mechanistic pathway for proton transfer and NO release. Furthermore, DFT calculations predicted that the release of NO takes place via aniline in both organic and aqueous media. These results highlight the importance of the proton-rich microenvironment around the copper(i)-nitrite core to induce nitrate reduction in a chemical and biological environment.

Structure and nitrite reduction reactivity study of bio-inspired copper(i)-nitro complexes in steric and electronic considerations of tridentate nitrogen ligands

Two copper(i)-nitro complexes [Tpm3-tBuCu(NO2)] (1) and [(Ph3P)2N][Tp3-tBuCu(NO2)] (2), containing steric bulky neutral tris(3-tert-butylpyrazolyl)methane and anionic hydrotris(3-tert-butylpyrazolyl)borate ligands, have been synthesized and characterized. Complex 2 adopts a unique κ2-binding mode of Tp3-tBu around the copper(i)-nitro environment in the solid state and shows a four-coordinated tetrahedral geometry surrounded by a nitro and three pz3-tBu groups in solution. Both complexes 1 and 2 allow for the stoichiometric reduction of NO2- to NO with H+ addition. The results of this effort show that increasing steric bulk and electron donation properties on the nitrogen ancillary ligand will improve the nitrite reduction ability of the copper(i)-nitro model complexes.

Isotopocule analysis of biologically produced nitrous oxide in various environments

Natural abundance ratios of isotopocules, molecules that have the same chemical constitution and configuration, but that only differ in isotope substitution, retain a record of a compound's origin and reactions. A method to measure isotopocule ratios of nitrous oxide (N₂ O) has been established by using mass analysis of molecular ions and fragment ions. The method has been applied widely to environmental samples from the atmosphere, ocean, fresh water, soils, and laboratory-simulation experiments. Results show that isotopocule ratios, particularly the ¹⁵ N-site preference (difference between isotopocule ratios ¹⁴ N¹⁵ N¹⁶ O/¹⁴ N¹⁴ N¹⁶ O and ¹⁵ N¹⁴ N¹⁶ O/¹⁴ N¹⁴ N¹⁶ O), have a wide range that depends on their production and consumption processes. Observational and laboratory studies of N₂ O related to biological processes are reviewed and discussed to elucidate complex material cycles of this trace gas, which causes global warming and stratospheric ozone depletion. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:135-160, 2017.

Atmospheric emission of nitric oxide and processes involved in its biogeochemical transformation in terrestrial environment

Nitric oxide (NO) is an intra- and intercellular gaseous signaling molecule with a broad spectrum of regulatory functions in biological system. Its emissions are produced by both natural and anthropogenic sources; however, soils are among the most important sources of NO. Nitric oxide plays a decisive role in environmental-atmospheric chemistry by controlling the tropospheric photochemical production of ozone and regulates formation of various oxidizing agents such as hydroxyl radical (OH), which contributes to the formation of acid of precipitates. Consequently, for developing strategies to overcome the deleterious impact of NO on terrestrial ecosystem, it is mandatory to have reliable information about the exact emission mechanism and processes involved in its transformation in soil-atmospheric system. Although the formation process of NO is a complex phenomenon and depends on many physicochemical characteristics, such as organic matter, soil pH, soil moisture, soil temperature, etc., this review provides comprehensive updates about the emission characteristics and biogeochemical transformation mechanism of NO. Moreover, this article will also be helpful to understand the processes involved in the consumption of NO in soils. Further studies describing the functions of NO in biological system are also discussed.

Effect of ligand denticity on the nitric oxide reactivity of cobalt(ii) complexes

NO reactivity of three Co(ii) complexes, 1, 2 and 3 have been studied in degassed methanol solution. The complexes differ from each other in terms of denticity and flexibility of the ligand fameworks. Complex 1 undergoes reductive nitrosylation of the metal ion; 2 results in corresponding [Co^III(NO⁻)] complex; whereas 3 does not react with NO.

Rainwater, soil water, and soil nitrate effects on oxygen isotope ratios of nitrous oxide produced in a green tea (Camellia sinensis) field in Japan

RATIONALE

The oxygen exchange fraction between soil H(2)O and N(2)O precursors differs in soils depending on the responsible N(2)O-producing process: nitrification or denitrification. This study investigated the O-exchange between soil H(2)O and N(2)O precursors in a green tea field with high N(2)O emissions.

METHODS

The rainwater δ(18)O value was measured using cavity ring-down spectrometry (CRDS) and compared with that of soil water collected under the tea plant canopy and between tea plant rows. The intramolecular (15)N site preference in (β) N(α) NO (SP = δ(15)N(α) - δ(15)N(β)) was determined after measuring the δ(15)N(α) and δ(15)N(bulk) values using gas chromatography/isotope ratio mass spectrometry (GC/IRMS), and the δ(18) O values of N(2)O and NO(3)(-) were also measured using GC/IRMS.

RESULTS

The range of δ(18)O values of rainwater (-11.15‰ to -4.91‰) was wider than that of soil water (-7.94‰ to -5.64‰). The δ(18)O value of soil water at 50 cm depth was not immediately affected by rainwater. At 10 cm and 20 cm depths of soil between tea plant rows, linear regression analyses of δ(18)O-N(2)O (relative to δ(18)O-NO(3)(-)) versus δ(18) O-H(2)O (relative to δ(18)O-NO(3)(-)) yielded slopes of 0.76-0.80 and intercepts of 31-35‰.

CONCLUSIONS

In soil between tea plant rows, the fraction of O-exchange between H(2)O and N(2)O precursors was approximately 80%. Assuming that denitrification dominated N(2)O production, the net (18)O-isotope effect for denitrification (NO(3)(-) reduction to N(2)O) was approximately 31-35‰, reflecting the upland condition of the tea field.

Dual isotope and isotopomer signatures of nitrous oxide from fungal denitrification--a pure culture study

RATIONALE

The contribution of fungal denitrification to the emission of the greenhouse gas nitrous oxide (N2O) from soil has not yet been sufficiently investigated. The intramolecular (15)N site preference (SP) of N2O could provide a tool to distinguish between N2O produced by bacteria or fungi, since in previous studies fungi exhibited much higher SP values than bacteria.

METHODS

To further constrain isotopic evidence of fungal denitrification, we incubated six soil fungal strains under denitrifying conditions, with either NO3(-) or NO2(-) as the electron acceptor, and measured the isotopic signature (δ(18)O, δ(15)Nbulk and SP values) of the N2O produced. The nitrogen isotopic fractionation was calculated and the oxygen isotope exchange associated with particular fungal enzymes was estimated.

RESULTS

Five fungi of the order Hypocreales produced N2O with a SP of 35.1 ± 1.7 ‰ after 7 days of anaerobic incubation independent of the electron acceptor, whereas one Sordariales species produced N2O from NO2(-) only, with a SP value of 21.9 ± 1.4 ‰. Smaller isotope effects of (15)Nbulk were associated with larger N2O production. The δ(18)O values were influenced by oxygen exchange between water and denitrification intermediates, which occurred primarily at the nitrite reduction step.

CONCLUSIONS

Our results confirm that SP of N2O is a promising tool to differentiate between fungal and bacterial N2O from denitrification. Modelling of oxygen isotope fractionation processes indicated that the contribution of the NO2(-) and NO reduction steps to the total oxygen exchange differed among the various fungal species studied. However, more information is needed about different biological orders of fungi as they may differ in denitrification enzymes and consequently in the SP and δ(18)O values of the N2O produced.

Fungal oxygen exchange between denitrification intermediates and water

RATIONALE

Fungi can contribute greatly to N2O production from denitrification. Therefore, it is important to quantify the isotopic signature of fungal N2O. The isotopic composition of N2O can be used to identify and analyze the processes of N2O production and N2O reduction. In contrast to bacteria, information about the oxygen exchange between denitrification intermediates and water during fungal denitrification is lacking, impeding the explanatory power of stable isotope methods.

METHODS

Six fungal species were anaerobically incubated with the electron acceptors nitrate or nitrite and (18)O-labeled water to determine the oxygen exchange between denitrification intermediates and water. After seven days of incubation, gas samples were analyzed for N2O isotopologues by isotope ratio mass spectrometry.

RESULTS

All the fungal species produced N2O. N2O production was greater when nitrite was the sole electron acceptor (129 to 6558 nmol N2O g dw(-1)  h(-1)) than when nitrate was the electron acceptor (6 to 47 nmol N2O g dw(-1)  h(-1)). Oxygen exchange was complete with nitrate as electron acceptor in one of five fungi and with nitrite in two of six fungi. Oxygen exchange of the other fungi varied (41 to 89% with nitrite and 11 to 61% with nitrate).

CONCLUSIONS

This is the first report on oxygen exchange with water during fungal denitrification. The exchange appears to be within the range previously reported for bacterial denitrification. This adds to the difficulty of differentiating N2O producing processes based on the origin of N2O-O. However, the large oxygen exchange repeatedly observed for bacteria and now also fungi could lead to less variability in the δ(18)O values of N2O from soils, which could facilitate the assessment of the extent of N2O reduction.

Ammonia oxidation pathways and nitrifier denitrification are significant sources of N2O and NO under low oxygen availability

The continuous increase of nitrous oxide (N2O) abundance in the atmosphere is a global concern. Multiple pathways of N2O production occur in soil, but their significance and dependence on oxygen (O2) availability and nitrogen (N) fertilizer source are poorly understood. We examined N2O and nitric oxide (NO) production under 21%, 3%, 1%, 0.5%, and 0% (vol/vol) O2 concentrations following urea or ammonium sulfate [(NH4)2SO4] additions in loam, clay loam, and sandy loam soils that also contained ample nitrate. The contribution of the ammonia (NH3) oxidation pathways (nitrifier nitrification, nitrifier denitrification, and nitrification-coupled denitrification) and heterotrophic denitrification (HD) to N2O production was determined in 36-h incubations in microcosms by (15)N-(18)O isotope and NH3 oxidation inhibition (by 0.01% acetylene) methods. Nitrous oxide and NO production via NH3 oxidation pathways increased as O2 concentrations decreased from 21% to 0.5%. At low (0.5% and 3%) O2 concentrations, nitrifier denitrification contributed between 34% and 66%, and HD between 34% and 50% of total N2O production. Heterotrophic denitrification was responsible for all N2O production at 0% O2. Nitrifier denitrification was the main source of N2O production from ammonical fertilizer under low O2 concentrations with urea producing more N2O than (NH4)2SO4 additions. These findings challenge established thought attributing N2O emissions from soils with high water content to HD due to presumably low O2 availability. Our results imply that management practices that increase soil aeration, e.g., reducing compaction and enhancing soil structure, together with careful selection of fertilizer sources and/or nitrification inhibitors, could decrease N2O production in agricultural soils.

Effect of different carbon substrates on nitrate stable isotope fractionation during microbial denitrification

In batch experiments, we studied the isotope fractionation in N and O of dissolved nitrate during dentrification. Denitrifying strains Thauera aromatica and "Aromatoleum aromaticum strain EbN1" were grown under strictly anaerobic conditions with acetate, benzoate, and toluene as carbon sources. (18)O-labeled water and (18)O-labeled nitrite were added to the microcosm experiments to study the effect of putative backward reactions of nitrite to nitrate on the stable isotope fractionation. We found no evidence for a reverse reaction. Significant variations of the stable isotope enrichment factor ε were observed depending on the type of carbon source used. For toluene (ε(15)N, -18.1 ± 0.6‰ to -7.3 ± 1.4‰; ε(18)O, -16.5 ± 0.6‰ to -16.1 ± 1.5‰) and benzoate (ε(15)N, -18.9 ± 1.3‰; ε(18)O, -15.9 ± 1.1‰) less negative isotope enrichment factors were calculated compared to those derived from acetate (ε(15)N, -23.5 ± 1.9‰ to -22.1 ± 0.8‰; ε(18)O, -23.7 ± 1.8‰ to -19.9 ± 0.8‰). The observed isotope effects did not depend on the growth kinetics which were similar for the three types of electron donors. We suggest that different carbon sources change the observed isotope enrichment factors by changing the relative kinetics of nitrate transport across the cell wall compared to the kinetics of the intracellular nitrate reduction step of microbial denitrification.

Nitric oxide reactivity of copper(II) complexes of bidentate amine ligands: effect of substitution on ligand nitrosation

Three copper(ii) complexes with bidentate ligands L(1), L(2) and L(3) [L(1), N,N(/)-dimethylethylenediamine; L(2), N,N(/)-diethylethylenediamine and L(3), N,N(/)-diisobutylethylenediamine], respectively, were synthesized as their perchlorate salts. The single crystal structures for all the complexes were determined. The nitric oxide reactivity of the complexes was studied in acetonitrile solvent. The formation of thermally unstable [Cu(II)-NO] intermediate on reaction of the complexes with nitric oxide in acetonitrile solution was observed prior to the reduction of copper(II) centres to copper(I). The reduction was found to result with a simultaneous mono- and di-nitrosation at the secondary amine sites of the ligand. All the nitrosation products were isolated and characterized. The ratio of the yield of mono- and di-nitrosation product was found to be dependent on the N-substitution present in the ligand framework.

Oxygen exchange between (de)nitrification intermediates and H2O and its implications for source determination of NO3- and N2O: a review

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.

A novel dual-isotope labelling method for distinguishing between soil sources of N2O

We present a novel 18O-15N-enrichment method for the distinction between nitrous oxide (N2O) from nitrification, nitrifier denitrification and denitrification based on a method with single- and double-15N-labelled ammonium nitrate. We added a new treatment with 18O-labelled water to quantify N2O from nitrifier denitrification. The theory behind this is that ammonia oxidisers use oxygen (O2) from soil air for the oxidation of ammonia (NH3), but use H2O for the oxidation of the resulting hydroxylamine (NH2OH) to nitrite (NO2-). Thus, N2O from nitrification would therefore be expected to reflect the 18O signature of soil O2, whereas the 18O signature of N2O from nitrifier denitrification would reflect that of both soil O2 and H2O. It was assumed that (a) there would be no preferential removal of 18O or 16O during nitrifier denitrification or denitrification, (b) the 18O signature of the applied 18O-labelled water would remain constant over the experimental period, and (c) any O exchange between H(2)18O and NO3- would be negligible under the chosen experimental conditions. These assumptions were tested and validated for a silt loam soil at 50% water-filled pore space (WFPS) following application of 400 mg N kg-1 dry soil. We compared the results of our new method with those of a conventional inhibition method using 0.02% v/v acetylene (C2H2) and 80% v/v O2 in helium. Both the 18O-15N-enrichment and inhibitor methods identified nitrifier denitrification to be a major source of N2O, accounting for 44 and 40%, respectively, of N2O production over 24 h. However, compared to our 18O-15N-method, the inhibitor method overestimated the contribution from nitrification at the expense of denitrification, probably due to incomplete inhibition of nitrifier denitrification and denitrification by large concentrations of O2 and a negative effect of C2H2 on denitrification. We consider our new 18O-15N-enrichment method to be more reliable than the use of inhibitors; it enables the distinction between more soil sources of N2O than was previously possible and has provided the first direct evidence of the significance of nitrifier denitrification as a source of N2O in fertilised arable soil.

The mode of decomposition of Angeli's salt (Na2N2O3) and the effects thereon of oxygen, nitrite, superoxide dismutase, and glutathione

The classical view of the aerobic decomposition of Angeli's salt is that it releases NO(2)(-) + NO(-)/HNO the latter then reacting with O(2) to yield ONOO(-). An alternative that has recently been proposed envisions electron transfer to O(2) followed by decomposition to NO(2)(-) + NO. The classical view is now strongly supported by the observation that the rates of decomposition of Angeli's salt under 20% O(2) or 100% O(2) were equal. Moreover, NO(2)(-), which inhibits this decomposition by favoring the back reaction, was more effective in the absence of agents that scavenge NO(-)/HNO. It is thus clear that Angeli's salt is a useful source of NO(-)/HNO for use in defined aqueous systems. The measurements made in the course of this work allowed approximation of the rate constants for the reactions of NO(-)/HNO with NO(2)(-), O(2), glutathione, or Cu, Zn superoxide dismutase. The likelihood of the formation of NO(-)/HNO in vivo is also discussed.

Are there protective enzymatic pathways to regulate high local nitric oxide (NO) concentrations in cells under stress conditions?

This paper examines, from a chemical perspective, the hypothesis of the existence of protective enzymes whose role would be to regulate the high local nitric oxide (NO) concentrations that are released in NO-generating cells in situations of response to oxidative stress. These enzymes should play the role, with respect to NO, either of a reductase or of a dismutase. The energetics of the intervening transformations is herein presented, along with a review of pertinent literature. An attempt is made in order to describe the physiognomy of such enzymes, in relation with the literature data. Experimental investigation is needed to further evaluate the validity of such a hypothesis.

Cell biology and molecular basis of denitrification

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.

Structural gene (nirS) for the cytochrome cd1 nitrite reductase of Alcaligenes eutrophus H16

Denitrification by Alcaligenes eutrophus H16 is genetically linked to megaplasmid pHG1. Unexpectedly, the gene encoding the nitrite reductase (nirS) was identified on chromosomal DNA. The nirS product showed extensive homology with periplasmic nitrite reductases of the heme cd1-type. Disruption of nirS abolished nitrite-reducing ability, indicating that NirS is the enzyme essential for denitrification in A.eutrophus.

Synthesis, Structure, and Reactivity of Model Complexes of Copper Nitrite Reductase

The copper(I) and copper(II) complexes with the nitrogen donor ligands bis[(1-methylbenzimidazol-2-yl)methyl]amine (1-BB), bis[2-(1-methylbenzimidazol-2-yl)ethyl]amine (2-BB), N-acetyl-2-BB (AcBB), and tris[2-(1-methylbenzimidazol-2-yl)ethyl]nitromethane (TB) have been studied as models for copper nitrite reductase. The copper(II) complexes form adducts with nitrite and azide that have been isolated and characterized. The Cu(II)-(1-BB) and Cu(II)-AcBB complexes are basically four-coordinated with weak axial interaction by solvent or counterion molecules, whereas the Cu(II)-(2-BB) and Cu(II)-TB complexes prefer to assume five-coordinate structures. A series of solid state structures of Cu(II)-(1-BB) and -(2-BB) complexes have been determined. [Cu(1-BB)(DMSO-O)(2)](ClO(4))(2): triclinic, P&onemacr; (No. 2), a = 9.400(1) Å, b = 10.494(2) Å, c = 16.760(2) Å, alpha = 96.67(1) degrees, beta = 97.10(1) degrees, gamma = 108.45(1) degrees, V = 1534.8(5) Å(3), Z = 2, number of unique data [I >/= 3sigma(I)] = 4438, number of refined parameters = 388, R = 0.058. [Cu(1-BB)(DMSO-O)(2)](BF(4))(2): triclinic, P&onemacr; (No. 2), a = 9.304(5) Å, b = 10.428(4) Å, c = 16.834(8) Å, alpha = 96.85(3) degrees, beta = 97.25(3) degrees, gamma = 108.21(2) degrees, V = 1517(1) Å(3), Z = 2, number of unique data [I >/= 2sigma(I)] = 3388, number of refined parameters = 397, R = 0.075. [Cu(1-BB)(DMSO-O)(NO(2))](ClO(4)): triclinic, P&onemacr; (No. 2), a = 7.533(2) Å, b = 8.936(1) Å, c = 19.168(2) Å, alpha = 97.66(1) degrees, beta = 98.62(1) degrees, gamma = 101.06(1) degrees, V = 1234.4(7) Å(3), Z = 2, number of unique data [I >/= 2sigma(I)] = 3426, number of refined parameters = 325, R = 0.081. [Cu(2-BB)(MeOH)(ClO(4))](ClO(4)): triclinic, P&onemacr; (No. 2), a = 8.493(3) Å, b = 10.846(7) Å, c = 14.484(5) Å, alpha = 93.71(4) degrees, beta = 103.13(3) degrees, gamma = 100.61(4) degrees, V = 1270(1) Å(3), Z = 2, number of unique data [I>/= 2sigma(I)] = 2612, number of refined parameters = 352, R = 0.073. [Cu(2-BB)(N(3))](ClO(4)): monoclinic, P2(1)/n (No. 14), a = 12.024(3) Å, b = 12.588(5) Å, c = 15.408(2) Å, beta = 101,90(2) degrees, V = 2282(1) Å(3), Z = 4, number of unique data [I >/= 2sigma(I)] = 2620, number of refined parameters = 311, R = 0.075. [Cu(2-BB)(NO(2))](ClO(4))(MeCN): triclinic, P&onemacr; (No. 2), a = 7.402(2) Å, b = 12.500(1) Å, c = 14.660(2) Å, alpha = 68.14(1) degrees, beta = 88.02(2) degrees, gamma = 78.61(1) degrees, V = 1233.0(4) Å(3), Z = 2, number of unique data [I>/= 2sigma(I)] = 2088, number of refined parameters = 319, R = 0.070. In all the complexes the 1-BB or 2-BB ligands coordinate the Cu(II) cations through their three donor atoms. The complexes with 2-BB appear to be more flexible than those with 1-BB. The nitrito ligand is bidentate in [Cu(2-BB)(NO(2))](ClO(4))(MeCN) and essentially monodentate in [Cu(1-BB)(DMSO-O)(NO(2))](ClO(4)). The copper(I) complexes exhibit nitrite reductase activity and react rapidly with NO(2)(-) in the presence of stoichiometric amounts of acid to give NO and the corresponding copper(II) complexes. Under the same conditions the reactions between the copper(I) complexes and NO(+) yield the same amount of NO, indicating that protonation and dehydration of bound nitrite are faster than its reduction. The NO evolved from the solution was detected and quantitated as the [Fe(EDTA)(NO)] complex. The order of reactivity of the Cu(I) complexes in the nitrite reduction process is [Cu(2-BB)](+) > [Cu(1-BB)](+) > [Cu(TB)](+) > [Cu(AcBB)](+).

Spectroscopic and kinetic studies on reaction of cytochrome P450nor with nitric oxide. Implication for its nitric oxide reduction mechanism

Cytochrome P450 purified from Fusarium oxysporum (P450nor) is a unique heme enzyme that catalyzes the reduction of nitric oxide to nitrous oxide with electrons directly transferred from NADH (2NO + NADH + H+--> N2O + H2O + NAD+). We studied the reaction of P450nor with NO and NADH using stopped-flow rapid scan and low temperature spectroscopic methods. The NO ligand can bind to the ferric enzyme to form the stable NO bound complex, P450nor(Fe3+NO). Reduction of P450nor(Fe3+NO) with NADH yielded an intermediate, which transiently formed (tau = approximately 100 ms) and spontaneously decomposed to the Fe3+ state. The optical absorption spectrum of the intermediate was different from that of P450nor(Fe2+NO), which was formed by either a one-electron reduction of P450nor(Fe3+NO) with Na2S2O4 or NO binding to P450nor(Fe2+). On the basis of these observations, we suggested that the intermediate is presumably a two-electron reduced product of P450nor(Fe3+NO) by NADH, formally the (Fe3+NO)2-complex. We determined the rate constants of these reactions at 10 degrees C for the NO binding to P450nor(Fe3+) (2.6 x 10(7) M-1 s-1), the NADH reduction of P450nor(Fe3+NO) (0.9 x 10(6) M-1 s-1), and the spontaneous decomposition of the intermediate (0.027 s-1). In these kinetic measurements, it was found that the former two processes are fast enough, while the latter is extremely slow, compared with the fast turnover of the catalytic reaction (1200 s-1 at 10 degrees C), which we measured by monitoring the NADH consumption. Therefore, we suggested that in the catalytic cycle, decomposition of the intermediate is fairly accelerated by free NO, resulting in such a fast turnover. On the basis of several lines of the spectroscopic and the kinetic evidence, we proposed a possible mechanism of the NO reduction by P450nor.

A cytochrome cd1-type nitrite reductase mediates the first step of denitrification in Alcaligenes eutrophus

Respiratory nitrite reductase (NIR) has been purified from the soluble extract of denitrifying cells of Alcaligenes eutrophus strain H16 to apparent electrophoretic homogeneity. The enzyme was induced under anoxic conditions in the presence of nitrite. Purified NIR showed typical features of a cytochrome cd1-type nitrite reductase. It appeared to be a dimer of kDa subunits, its activity was only weakly inhibited by the copper chelator diethyldithiocarbamate, and spectral analysis revealed absorption maxima which were characteristic for the presence of heme c and heme d1. The isoelectric point of 8.6 was considerably higher than the pI determined for cd1 nitrite reductases from pseudomonads. Eighteen amino acids at the N-terminus of the A. eutrophus NIR, obtained by protein sequencing, showed no significant homology to the N-terminal region of nitrite reductases from Pseudomonas stutzeri and Pseudomonas aeruginosa.