Proton translocation during denitrification by a nitrifying-denitrifying Alcaligenes sp.

A heterotrophic nitrifying Alcaligenes sp. from soil was grown as a denitrifier on nitrate and subjected to oxidant pulse experiments to ascertain the apparent effeciencies of proton translocations during O₂ and nitrogen-oxide respirations. With endogenous substrate as the reducing agent the H⁺/2e^– ratios, extrapolated to zero amount of oxidant per pulse, were 9.4, 3.7, 4.3 and 3.5 for O₂, nitrate, nitrite and N₂O, respectively. The value for O₂ and those for the N-oxides are, respectively, somewhat larger and smaller than corresponding values for Paracoccus denitrificans. None of the three permeant ions employed with the Alcaligenes sp. (valinomycin-K⁺, thiocyanate and triphenylmethylphosphonium) was ideal for all purposes. Thiocyanate provided highest ratios for O₂ but abolished the oxidant pulse response for nitrate and N₂O. Valinomycin was slow to penetrate to the cytoplasmic membrane and relatively high concentrations were required for optimal performance. Triphenylmethylphosphonium enhanced passive proton permeability and diminished proton translocation at concentrations required to realize the maximal oxidant pulse response.     

Study on the chemical evolution of low molecular weight compounds in a highly oxidized atmosphere using electric discharges

The molecular basis for the chemical evolution of low molecular compounds was studied using electric discharges on a higly oxidized atmosphere comprised of CO₂, N₂ and H₂O. In the gas phase, O₂ and CO were formed by the decomposition of CO₂ and their yields were enhanced by the addition of N₂ to the gas mixture. It was demonstrated that H₂O suppressed the reduction of CO₂ while H₂O also had a role in producing organic compounds such as formic acid and formaldehyde. Infrared analysis of the water soluble products and the inner surface of the reaction vessel indicated the production of compounds more complex than formic acid and formaldehyde. These compounds contained the chemical bonds which were identified to be OH, CO, CN and/or CC.     

Additive effects and potential inhibitory mechanism of some common aromatic pollutants on in vitro mitochondrial respiration

The in vitro toxicity of multiple hydrophobic compounds was the focus of this study. A mitochondrial respiratory assay, sensitive to perturbations caused by hydrophobic chemicals, was utilized to measure the effects of individual aromatic hydrocarbon pollutants and their mixtures on mitochondrial respiratory function. Benzene, naphthalene, acenaphthene, and 1-chloronaphthalene, common industrial solvents shown to interact additively in vivo, were evaluated using this in vitro assay system. Mitochondrial respiration was inhibited 50% (EC₅₀) by 525 ppm (6.7 mM) benzene, 15 ppm (117 μM) naphthalene, 3.9 ppm (25.5 μM) acenaphthene, or 3.8 ppm (23.4 μM) 1-chloronaphthalene. NADH:O₂ oxidoreductase (NADH → O₂), NADH: ubiquinone oxidoreductase, and ubiquinol:O₂ oxidoreductase activities were inhibited by all four compounds, whereas succinate:O₂ oxidoreductase, cytochrome c oxidase, and duroquinol: O₂ oxidoreductase activities were not inhibited. Inhibition of mitochondrial respiration occurred at the level of ubiquinone (coenzyme Q₁₀) for all four aromatic hydrocarbons. The ultraviolet absorbance spectrum of isolated Q₁₀ was also altered by naphthalene, acenaphthene, or 1-chloronaphthalene, suggesting a specific interaction between that component of the respiratory chain and these aromatic hydrocarbons. Inhibition by a mixture of 2, 3, or 4 of the compounds tested was additive, reflecting a summation effect of each compound present in the mixture. This additive nature is consistent with previously reported effects of these compounds in vivo and with compounds having similar modes of action. The similar mode of action in vitro is a specific interaction with coenzyme Q₁₀, not a generalized membrane perturbation as speculated to occur in vivo, and is the likely mechanism for the observed additive toxicity.     

Competing peroxidase and oxidase reactions in scopoletin-dependent H2O2-initiated oxidation of NADH by horseradish peroxidase

Addition of NADH inhibited the peroxidative loss of scopoletin in presence of horseradish and H₂O₂ and decreased the ratio of scopoletin (consumed):H₂O₂ (added). Concomitantly NADH was oxidized and oxygen was consumed with a stoichiometry of NADH:O₂ of 2:1. On step-wise addition of a small concentration of H₂O₂ a high rate of NADH oxidation was obtained for a progressively decreasing time period followed by termination of the reaction with NADH:H₂O₂ ratio decreasing from about 40 to 10. The rate of NADH oxidation increased linearly with increase in scopoletin concentration. Other phenolic compounds including p-coumarate also supported this reaction to a variable degree. A 418-nm absorbing compound accumulated during oxidation of NADH. The effectiveness of a small concentration of H₂O₂ in supporting NADH oxidation increased in presence of SOD and decreased in presence of cytochrome c, but the reaction terminated even in their presence. The results indicate that the peroxidase is not continuously generating H₂O₂ during scopoletin-mediated NADH oxidation and that both peroxidase and oxidase reactions occur simultaneously competing for an active form of the enzyme.     

Reactive oxygen species in choline deficiency induced carcinogenesis and nitrone inhibition

Reactive oxygen species and free radical processes have been considered important in cancer development for many years. Much research demonstrates that the choline-deficiency induced hepatocarcinogenesis model prominently involves reactive oxygen species. We present a summary of results obtained in our original studies of this model over the last 4 years. We have shown that -phenyl-tert-butyl nitrone (PBN) and some of its hydroxylated derivatives (the 4- and 3-hydroxylated compounds) prevent hepatocarcinogenesis in this model. Mechanistic studies have demonstrated that isolated mitochondria from the livers of rats fed the choline-deficiency defined amino acid diet produce significantly much more H₂O₂ per NADH reducing equivalents oxidized. Based on these observations, we postulate that H₂O₂ is a primary carcinogenic factor in this model. Based on studies of the action of PBN on isolated mitochondria, we postulate that the inhibiting action of PBN involves suppression of H₂O₂ production of mitochondria and generally decreasing the oxidative stress within the preneoplastic lesions. The net effect of the activity of the nitrone compounds appears to be due to their ability to shift the apoptosis/neoplastic tendency balance toward apoptosis of the cells within the preneoplastic lesions. This is considered to be the primary reason the size of the preneoplastic lesions are significantly decreased and why the nitrones are potent anti-carcinogenic agents in this model.     

Superoxide and hydrogen peroxide production in cyanide resistant Arum maculatum mitochondria

Submitochondrial particles from Arum maculatum containing a powerful cyanide insensitive oxidase were assayed by various methods to determine the end product of its interaction with oxygen. Using cytochrome c peroxidase to assay the production of H₂O₂ it was possible to detect H₂O₂ formation by Arum submitochondrial particles oxidizing NADH but not when oxidizing succinate. The rate of production of H₂O₂, however, was insufficient to account for the rate of oxygen uptake due to the alternate oxidase. The production of superoxide was determined using the luminol and adrenochrome assays. It was found that some superoxide was produced when Arum submitochondrial particles oxidized NADH but not when they oxidized succinate and again at insufficient rates to account for the rate of oxygen uptake by the alternate oxidase. stoichiometric determination of the ratio of NADH oxidized to oxygen taken up in the presence of 1 mM KCN, sufficient to inhibit catalase activity such that added peroxide remains stable, showed H₂O to be the only detectable product.It is suggested that although both H₂O₂ and superoxide are produced by A. maculatum submitochondrial particles this is not due to the alternate oxidase but may be due to another component of the respiratory chain possibly at the level of the NADH dehydrogenase.     

An archaeal NADH oxidase causes damage to both proteins and nucleic acids under oxidative stress

NADH oxidases (NOXs) catalyze the two-electron reduction of oxygen to H₂O₂ or four-electron reduction of oxygen to H₂O. In this report, we show that an NADH oxidase from Thermococcus profundus (NOXtp) displays two forms: a native dimeric protein under physiological conditions and an oxidized hexameric form under oxidative stress. Native NOXtp displays high NADH oxidase activity, and oxidized NOXtp can accelerate the aggregation of partially unfolded proteins. The aggregates formed by NOXtp have characteristics similar to β-amyloid and Lewy bodies in neurodegenerative diseases, including an increase of β-sheet content. Oxidized NOXtp can also bind nucleic acids and cause their degradation by oxidizing NADH to produce H₂O₂. Furthermore, Escherichia coli cells expressing NOXtp are less viable than cells not expressing NOXtp after treatment with H₂O₂. As NOXtp shares similar features with eukaryotic cell death isozymes and life may have originated from hyperthermophiles, we suggest that NOXtp may be an ancestor of cell death proteins.     

Regulation of NADH supply for nitrate reduction in green plants via photosynthesis and mitochondrial respiration.

The oxidation of NADH by mitochondrial respiration is inhibited by increased adenylate charge produced by photophosphorylation and under these conditions the reducing equivalents are used for nitrate reduction in the cytoplasm. Thus nitrate appears to function as an alternative electron acceptor to O₂ for NADH generated by the citric acid cycle dehydrogenases. This mechanism ensures that nitrate assimilation occurs only in light and thus the accumulation of toxic levels of nitrite in the dark is avoided.     

Mechanisms for enzymatic reduction of nitric oxide to nitrous oxide - A comparison between nitric oxide reductase and cytochrome c oxidase

Cytochrome c oxidases (CcO) reduce O₂ to H₂O in the respiratory chain of mitochondria and many aerobic bacteria. In addition, some species of CcO can also reduce NO to N₂O and water while others cannot. Here, the mechanism for NO-reduction in CcO is investigated using quantum mechanical calculations. Comparison is made to the corresponding reaction in a “true” cytochrome c-dependent NO reductase (cNOR). The calculations show that in cNOR, where the reduction potentials are low, the toxic NO molecules are rapidly reduced, while the higher reduction potentials in CcO lead to a slower or even impossible reaction, consistent with experimental observations. In both enzymes the reaction is initiated by addition of two NO molecules to the reduced active site, forming a hyponitrite intermediate. In cNOR, N₂O can then be formed using only the active-site electrons. In contrast, in CcO, one proton-coupled reduction step most likely has to occur before N₂O can be formed, and furthermore, proton transfer is most likely rate-limiting. This can explain why different CcO species with the same heme a₃-Cu active site differ with respect to NO reduction efficiency, since they have a varying number and/or properties of proton channels. Finally, the calculations also indicate that a conserved active site valine plays a role in reducing the rate of NO reduction in CcO.     

Copper (II) complex-catalyzed oxidation of NADH by hydrogen peroxide

Among various metal ions of physiological interest, Cu²⁺ is uniquely capable of catalyzing the oxidation of NADH by H₂O₂. This oxidation is stimulated about fivefold in the presence of imidazole. A similar activating effect is found for some imidazole derivatives (1-methyl imidazole, 2-methyl imidazole, andN-acetyl-L-histidine). Some other imidazole-containing compounds (L-histidine,L-histidine methyl ester, andL-carnosine), however, inhibit the Cu²⁺-catalyzed peroxidation of NADH. Other chelating agents such as EDTA andL-alanine are also inhibitory. Stoichiometry for NADH oxidation per mole of H₂O₂ utilized is 1, which excludes the possibility of a two-step oxidation mechanism with a nucleotide free-radical intermediate. About 92% of the NADH oxidation product can be identified as enzymatically active NAD⁺. D₂O, 2,5-dimethylfuran, and 1,4-diazabicyclo [2.2.2]-octane have no significant effect on the oxidation, thus excluding¹O₂ as a mediator. Similarly, OH· is also not a likely intermediate, since the system is not affected by various scavengers of this radical. The results suggest that a copper-hydrogen peroxide intermediate, when complexed with suitable ligands, can generate still another oxygen species much more reactive than its parent compound, H₂O₂.     

Purification and characterization of an H<Subscript>2</Subscript>O-forming NADH oxidase from <Emphasis Type="Italic">Clostridium aminovalericum</Emphasis>: existence of an oxygen-detoxifying enzyme in an obligate anaerobic bacteria

Clostridium aminovalericum, an obligate anaerobe, is unable to form colonies on PYD agar plates in the presence of 1% O₂. When grown anaerobically in PYD liquid medium, the strain can continue normal growth after the shift from anoxic (sparged with O₂-free N₂ carrier-gas) to microoxic (sparged with 3% O₂/97% N₂ mixed carrier-gas) growth conditions in the mid exponential phase (OD₆₆₀=1.0). When the strain grew under 3% O₂/97% N₂, the medium remains anoxic. Thirty minutes after beginning aeration with 3% O₂, the activity of NADH oxidase in cell-free extracts increased more than five-fold from the level before aeration. We purified NADH oxidase to determine the characteristics of this enzyme in an obligate anaerobe. The purified NADH oxidase dominated the NADH oxidase activity detected in cell-free extracts. The enzyme is a homotetramer composed of a subunit with a molecular mass of 45 kDa. The enzyme shows a spectrum typical of a flavoprotein, and flavin adenine dinucleotide (FAD) was identified as a cofactor. The final product of NADH oxidation was H₂O, and the estimated K_m for oxygen was 61.9 M. These data demonstrate that an O₂-response enzyme that is capable of detoxifying oxygen to water exists in C. aminovalericum.Abbreviations NRIC NODAI Research Institute-Culture Collection Center, Tokyo University of Agriculture, Tokyo, Japan - SDS-PAGE sodium dodecyl sulfate polyacrylamide gel electrophoresis - PMSF phenylmethylsulfonyl fluoride     

Flavin-dependent halogenases involved in secondary metabolism in bacteria

The understanding of biological halogenation has increased during the last few years. While haloperoxidases were the only halogenating enzymes known until 1997, it is now clear that haloperoxidases are hardly, if at all, involved in biosynthesis of more complex halogenated compounds in microorganisms. A novel type of halogenating enzymes, flavin-dependent halogenases, has been identified as a major player in the introduction of chloride and bromide into activated organic molecules. Flavin-dependent halogenases require the activity of a flavin reductase for the production of reduced flavin, required by the actual halogenase. A number of flavin-dependent tryptophan halogenases have been investigated in some detail, and the first three-dimensional structure of a member of this enzyme subfamily, tryptophan 7-halogenase, has been elucidated. This structure suggests a mechanism involving the formation of hypohalous acid, which is used inside the enzyme for regioselective halogenation of the respective substrate. The introduction of halogen atoms into non-activated alkyl groups is catalysed by non-heme Fe^II α-ketoglutarate- and O₂-dependent halogenases. Examples for the use of flavin-dependent halogenases for the formation of novel halogenated compounds in in vitro and in vivo reactions promise a bright future for the application of biological halogenation reactions.     

Purification and characterization of an NADH oxidase from extremely thermophilic anaerobic bacterium Thermotoga hypogea

Thermotoga hypogea is an extremely thermophilic anaerobic bacterium capable of growing at 90°C. It was found to be able to grow in the presence of micromolar molecular oxygen (O₂). Activity of NADH oxidase was detected in the cell-free extract of T. hypogea, from which an NADH oxidase was purified to homogeneity. The purified enzyme was a homodimeric flavoprotein with a subunit of 50 kDa, revealed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. It catalyzed the reduction of O₂ to hydrogen peroxide (H₂O₂), specifically using NADH as electron donor. Its catalytic properties showed that the NADH oxidase had an apparent V_max value of 37 mol NADH oxidized min^–1 mg^–1 protein. Apparent K_m values for NADH and O₂ were determined to be 7.5 M and 85 M, respectively. The enzyme exhibited a pH optimum of 7.0 and temperature optimum above 85°C. The NADH-dependent peroxidase activity was also present in the cell-free extract, which could reduce H₂O₂ produced by the NADH oxidase to H₂O. It seems possible that O₂ can be reduced to H₂O by the oxidase and peroxidase, but further investigation is required to conclude firmly if the purified NADH oxidase is part of an enzyme system that protects anaerobic T. hypogea from accidental exposure to O₂.     

Cell wall-bound malate dehydrogenase from horseradish

Isolated cell walls from horseradish contain NAD-specific malate dehydrogenase which is not released on treatment with 2 M NaCl. This enzyme catalyses a rapid reduction of oxalacetate. Its physiological role, however, is assumed to be the oxidation of malate, thus providing NADH as electron donor in the formation of H₂O₂, by a wall-bound peroxidase. In the presence of malate, NAD and Mn²⁺ ions, cell walls catalyse the synthesis of H₂O₂ which might be utilized in lignin formation. In analogy to the known malate-oxalacetate shuttles, the possibility is discussed that this cell wall-associated malate dehydrogenase is involved in the transport of cytoplasmic reducing equivalents through the plasmalemma into the cell wall.     

N-acetoxy-N-acetylaminoarenes and nitrosoarenes one-electron non-enzymatic and enzymatic oxidation products of various carcinogenic aromatic acethydroxamic acids

A number of carcinogenic aromatic acethydroxamic acids (e.g.N-hydroxy-N-acetyl derivatives of 2-aminofluorene, 3-aminofluorene, 4-aminostilbene, 1-aminonaphthalene, 2-aminonaphthalene, 2-aminophenanthrene, and 4-aminobiphenyl) are readily oxidized by alkaline Fe(CN)₆³⁻ or Ag₂O. The free nitroxide radicals thus formed dismutate in organic solution according to second order kinetics to yield the corresponding N-acetoxy-N-acetylaminoarenes and nitrosoarenes. The structures of the latter products were established by mass and infrared spectrum analyses. Evicence was obtained for a similar one-electron oxidation of these acethydroxamic acids with horseradish peroxidase and H₂O₂ at pH 7. One-electron oxidation of N-hydroxy-2-acetylaminofluorene was also demonstrated with lactoperoxidase and human myeloperoxidase. The possible relevance of a similar peroxidative attack in vivo to the carcinogenic activities of some aromatic amines and amides is discussed.     

Mechanism of nitrite oxidation and oxidoreductase systems inNitrobacter agilis

Chemiosmotic coupling mechanisms operate in the electron transfer reactions from: nitrite to O₂, NO₂ ^– to NAD⁺, ascorbate to O₂, NADH to O₂, and NADH to NO₃ ^–. The enzyme systems catalyzing these reactions are named NO₂ ^–:O₂ oxidoreductase, ATP-dependent NO₂ ^–:NAD⁺ oxidoreductase, ascorbate:O₂ oxidoreductase, NADH:O₂ oxidoreductase, and NADH:NO₃ ^– oxidoreductase, respectively. All of the oxidoreduction reactions are exergonic with the exception of the ATP-dependent NO₂ ^–:NAD⁺ oxidoreductase system, which involves reversed electron flow against the thermodynamic gradients. The mechanism for nitrite oxidation was found to be quite different from that of ascorbate oxidation; both systems were insensitive, however, to rotenone, amytal, antimycin A, and 2-n-heptyl 4-hydroxyquinolineN-oxide. These compounds, on the other hand, severely inhibited the electron transfer reactions catalyzed by NADH:O₂ oxidoreductase, NADH:NO₃ ^– oxidoreductase, and the ATP-dependent NO₂ ^–:NAD⁺ oxidoreductase, indicating a common pathway of electron transport in these oxidoreductase systems. Cyanide inhibited all systems except the NADH:NO₃ ^– oxidoredctase. The uncoupler carbonyl cyanide-m-chlorophenyl hydrazone strongly inhibited NO₂ ^–:O₂ oxidoreductase and ATP-dependent NO₂ ^–:NAD⁺ oxidoreductase, which indicates the involvement of energy-linked reactions in both systems; the uncoupler caused a marked stimulation of the NADH:O₂ oxidoreductase and NADH:NO₃ ^– oxidoreductase without affecting the ascorbate:O₂ oxidoreductase activities.     

Peroxo-bridged divanadate as selective bromide oxidant in bromoperoxidation

Diperoxovanadate is effective only in presence of free vanadate in vanadium-dependent bromoperoxidation at physiological pH. Peroxide in the form of bridged divanadate complex (VOOV-type), but not the bidentate form as in diperoxovanadate, is proposed to be the oxidant of bromide. In order to obtain direct evidence, peroxo-divanadate complexes with glycyl-glycine, glycyl-alanine and glycyl-asparagine as heteroligands were synthesized. By elemental analysis and spectral studies they were characterized to be triperoxo-divanadates, [V₂O₂(O₂)₃(peptide)₃].H₂O, with the two vanadium atoms bridged by a peroxide and a heteroligand. The dipeptide seems to stabilize the peroxo-bridge by inter-ligand interaction, possibly hydrogen bonding. This is indicated by rapid degradation of these compounds on dissolving in water with partial loss of peroxide accompanied by release of bubbles of oxygen. The ⁵¹V-NMR spectra of such solutions showed diperoxovanadate and decavanadate (oligomerized from vanadate) as the products. Additional oxygen was released on treating these solutions with catalase as expected of residual diperoxovanadate. The solid compounds when added to the reaction mixtures showed transient, rapid bromoperoxidation reaction, but not oxidation of NADH or inactivation of glucose oxidase, the other two activities shown by a mixture of diperoxovanadate and vanadyl. This demonstration of peroxide-bridged divanadate as a powerful, selective oxidant of bromide, active at physiological pH, should make it a possible candidate of mimic in the action of vanadium in bromoperoxidase proteins.     

Artifacts associated with the use of thiocyanate and valinomycin/K+ as permeant ions in oxidant pulse experiments on denitrifying bacteria

By means of¹⁵N-tracer and oxidant pulse methods and with nitrate-grownParacoccus denitrificans it was found that KSCN completely inhibited reduction of N₂O and nitrate in the 1 to 10 mM range, but had little or no effect on reduction of O₂ or nitrite at 150 mM. These observations confirm a previous report. Potassium thiocyanate was insufficiently permeant across the cytoplasmic membrane ofParacoccus denitrificans andPseudomonas denitrificans even at 150 mM to prevent membrane polarization when oxidant pulses were large. Polarization and inhibition artifacts due to KSCN have created some confusion in the literature. Whereas valinomycin had little direct effect on reduction of nitrite, N₂O, and O₂ individually byPa. denitrificans, it caused a temporary nitrite-dependent inhibition of N₂O reduction. Under nonpolarizing conditions the H⁺/2e^– ratios for O₂, N₂O, and nitrite (8.0, 4.3, and 4.5, respectively) confirmed those reported previously from this laboratory. The present results largely but not entirely agree with data from another laboratory.     

Metabolism of Inorganic N Compounds by Ammonia-Oxidizing Bacteria

ABSTRACT

Ammonia oxidizing bacteria extract energy for growth from the oxidation of ammonia to nitrite. Ammonia monooxygenase, which initiates ammonia oxidation, remains enigmatic given the lack of purified preparations. Genetic and biochemical studies support a model for the enzyme consisting of three subunits and metal centers of copper and iron. Knowledge of hydroxylamine oxidoreductase, which oxidizes hydroxylamine formed by ammonia monooxygenase to nitrite, is informed by a crystal structure and detailed spectroscopic and catalytic studies. Other inorganic nitrogen compounds, including NO, N₂O, NO₂, and N₂ can be consumed and/or produced by ammonia-oxidizing bacteria. NO and N₂O can be produced as byproducts of hydroxylamine oxidation or through nitrite reduction. NO₂ can serve as an alternative oxidant in place of O₂ in some ammonia-oxidizing strains. Our knowledge of the diversity of inorganic N metabolism by ammonia-oxidizing bacteria continues to grow. Nonetheless, many questions remain regarding the enzymes and genes involved in these processes and the role of these pathways in ammonia oxidizers.