Oscillations of nitric oxide concentration in the perturbed denitrification pathway of Paracoccus denitrificans

Modeling the effect of copper availability on bacterial denitrification

When denitrifying bacteria such as Paracoccus denitrificans respire anaerobically they convert nitrate to dinitrogen gas via a pathway which includes the potent greenhouse gas, nitrous oxide (N₂O). The copper-dependent enzyme Nitrous Oxide reductase (Nos) catalyzes the reduction of N₂O to dinitrogen. In low-copper conditions, recent experiments in chemostats have demonstrated that Nos efficiency decreases resulting in significant N₂O emissions. For the first time, a chemostat-based mathematical model is developed that describes the anaerobic denitrification pathway based on Michaelis–Menten kinetics and published kinetic parameters. The model predicts steady-state enzyme levels from experimental data. For low copper concentrations, the predicted Nos level is significantly reduced, whereas the levels for the non copper-dependent reductases in the pathway remain relatively unaffected. The model provides time courses for the pathway metabolites that accurately reflect previously published experimental data. In the absence of experimental data purely predictive analyses can also be readily performed by calculating the relative Nos level directly from the copper concentration. Here, the model quantitatively estimates the increasing level of emitted N₂O as the copper level decreases.

Aerobic denitrification in soils and sediments: From fallacies to factx

Denitrification is the key step of the nitrogen cycle in which gaseous end products are released from the nitrate of terrestrial and aquatic environments. Although this process has always been regarded as an anaerobic one, recent research indicates that aerobic denitrification can be demonstrated with laboratory cultures and suggests that it may be widespread environmentally. Thus, denitrifying bacteria are both taxonomically and physiologically diverse, and may be predominantly aerobic. Simultaneous use of O(2) and NO(3)(-) as alternative terminal oxidants is not precluded in many bacteria, although the use of NO(3)(-) when O(2) is available is of no known advantage.

Mechanisms of transient nitric oxide and nitrous oxide production in a complex biofilm

Nitric oxide (NO) and nitrous oxide (N(2)O) are formed during N-cycling in complex microbial communities in response to fluctuating molecular oxygen (O(2)) and nitrite (NO(2)(-)) concentrations. Until now, the formation of NO and N(2)O in microbial communities has been measured with low spatial and temporal resolution, which hampered elucidation of the turnover pathways and their regulation. In this study, we combined microsensor measurements with metabolic modeling to investigate the functional response of a complex biofilm with nitrifying and denitrifying activity to variations in O(2) and NO(2)(-). In steady state, NO and N(2)O formation was detected if ammonium (NH(4)(+)) was present under oxic conditions and if NO(2)(-) was present under anoxic conditions. Thus, NO and N(2)O are produced by ammonia-oxidizing bacteria (AOB) under oxic conditions and by heterotrophic denitrifiers under anoxic conditions. NO and N(2)O formation by AOB occurred at fully oxic conditions if NO(2)(-) concentrations were high. Modeling showed that steady-state NO concentrations are controlled by the affinity of NO-consuming processes to NO. Transient accumulation of NO and N(2)O occurred upon O(2) removal from, or NO(2)(-) addition to, the medium only if NH(4)(+) was present under oxic conditions or if NO(2)(-) was already present under anoxic conditions. This showed that AOB and heterotrophic denitrifiers need to be metabolically active to respond with instantaneous NO and N(2)O production upon perturbations. Transiently accumulated NO and N(2)O decreased rapidly after their formation, indicating a direct effect of NO on the metabolism. By fitting model results to measurements, the kinetic relationships in the model were extended with dynamic parameters to predict transient NO release from perturbed ecosystems.

Differences in nitric oxide steady states between arginine, hypoxanthine, uracil auxotrophs (AHU) and non-AHU strains of Neisseria gonorrhoeae during anaerobic respiration in the presence of nitrite

Neisseria gonorrhoeae can grow by anaerobic respiration using nitrite as an alternative electron acceptor. Under these growth conditions, N. gonorrhoeae produces and degrades nitric oxide (NO), an important host defense molecule. Laboratory strain F62 has been shown to establish and maintain a NO steady-state level that is a function of the nitrite reductase/NO reductase ratio and is independent of cell number. The nitrite reductase activities (122-197 nmol NO2 reduced x min(-1) x OD600(-1)) and NO reductase activities (88-155 nmol NO reduced x min(-1) x OD600(-1)) in a variety of gonococcal clinical isolates were similar to the specific activities seen in F62 (241 nmol NO2 reduced x min(-1) x OD600(-1) and 88 nmol NO reduced x min(-1) x OD600(-1), respectively). In seven gonococcal strains, the NO steady-state levels established in the presence of nitrite were similar to that of F62 (801-2121 nmol x L-1 NO), while six of the strains, identified as arginine, hypoxanthine, and uracil auxotrophs (AHU), that cause asymptomatic infection in men had either two- to threefold (373-579 nmol x L-1 NO) or about 100-fold (13-24 nmol x L-1 NO) lower NO steady-state concentrations. All tested strains in the presence of a NO donor, 2,2'-(hydroxynitrosohydrazono)bis-ethanimine/NO, quickly lowered and maintained NO levels in the noninflammatory range of NO (<300 nmol x L-1). The generation of a NO steady-state concentration was directly affected by alterations in respiratory control in both F62 and an AHU strain, although differences in membrane function are suspected to be responsible for NO steady-state level differences in AHU strains.

Transcription and activities of NOx reductases in Agrobacterium tumefaciens: the influence of nitrate, nitrite and oxygen availability

The ability of Agrobacetrium tumefaciens to perform balanced transitions from aerobic to anaerobic respiration was studied by monitoring oxygen depletion, transcription of nirK and norB, and the concentrations of nitrite, nitric oxide (NO) and nitrous oxide in stirred batch cultures with different initial oxygen, nitrate or nitrite concentrations. Nitrate concentrations (0.2-2 mM) did not affect oxygen depletion, nor the oxygen concentration at which denitrification was initiated (1-2 microM). Nitrite (0.2-2 mM), on the other hand, retarded the oxygen depletion as it reached approximately 20 microM, and caused initiation of active denitrification as oxygen concentrations reached 10-17 microM. Unbalanced transitions occurred in treatments with high cell densities (i.e. with rapid transition from oxic to anoxic conditions), seen as NO accumulation to muM concentrations and impeded nitrous oxide production. This phenomenon was most severe in nitrite treatments, and reduced the cells' ability to respire oxygen during subsequent oxic conditions. Transcripts of norB were only detectable during the period with active denitrification. In contrast, nirK transcripts were detected at low levels both before and after this period. The results demonstrate that the transition from aerobic to anaerobic metabolism is a regulatory challenge, with implications for survival and emission of trace gases from denitrifying bacteria.

Nitric oxide oscillations in Paracoccus denitrificans: the effects of environmental factors and of segregating nitrite reductase and nitric oxide reductase into separate cells

Nitric oxide is a denitrification intermediate which is produced from nitrite and then further converted via nitrous oxide to nitrogen. Here, the effect of low concentrations of the protonophore carbonylcyanide m-chlorophenylhydrazone on the time courses for dissolved gases was examined. While NO was found to oscillate, N(2)O only increased gradually as the reduction of nitrite progressed. The frequency and shape of protonophore-induced NO oscillations were influenced by temperature and the concentration of electron donor N,N,N',N'-tetramethyl-p-phenylene diamine (TMPD) in a manner compatible with the observed differential effects on the two involved enzyme activities. We demonstrated the existence of a pH interval, where [NO] oscillates even without uncoupler addition. Occurrence of nitric oxide oscillations in mixtures of a nitrite reductase mutant with a nitric oxide reductase mutant suggests that they cannot be due to a competition of the enzymes for redox equivalents from one common respiratory chain.

Fine-tuned regulation by oxygen and nitric oxide of the activity of a semi-synthetic FNR-dependent promoter and expression of denitrification enzymes in Paracoccus denitrificans

In Paracoccus denitrificans at least three fumarate and nitrate reductase regulator (FNR)-like proteins [FnrP, nitrite and nitric oxide reductases regulator (NNR) and NarR] control the expression of several genes necessary for denitrifying growth. To gain more insight into this regulation, beta-galactosidase activity from a plasmid carrying the lacZ gene fused to the Escherichia coli melR promoter with the consensus FNR-binding (FF) site was examined. Strains defective in the fnrP gene produced only very low levels of beta-galactosidase, indicating that FnrP is the principal activator of the FF promoter. Anoxic beta-galactosidase levels were much higher relative to those under oxic growth and were strongly dependent on the nitrogen electron acceptor used, maximal activity being promoted by N(2)O. Additions of nitrate or nitroprusside lowered beta-galactosidase expression resulting from an oxic to micro-oxic switch. These results suggest that the activity of FnrP is influenced not only by oxygen, but also by other factors, most notably by NO concentration. Observations of nitric oxide reductase (NOR) activity in a nitrite-reductase-deficient strain and in cells treated with haemoglobin provided evidence for dual regulation of the synthesis of this enzyme, partly independent of NO. Both regulatory modes were operative in the FnrP-deficient strain, but not in the NNR-deficient strain, suggesting involvement of the NNR protein. This conclusion was further substantiated by comparing the respective NOR promoter activities.

Detection, with a pH indicator, of bacterial mutants unable to denitrify

In order to facilitate isolation of mutants with alterations in the denitrification pathway, a new screening procedure using phenol red incorporated into agar overlay has been defined. Alkalinization in the neighbourhood of denitrifying colonies respiring nitrate or nitrite gives rise to a red circular halo. Antimycin blocked these colour changes, which suggests their association with the periplasmic reduction of nitrite. Inhibition of nitrous oxide reductase by acetylene had no significant effect on alkalinization elicited by nitrate or nitrite. Several mutants negative by the phenol red staining test were generated by transposon Tn5 mutagenesis of Paracoccus denitrificans. All these mutants were defective in the activities of nitrite and nitric oxide reductases while the other denitrification activities were present at the wild-type level.

From no-confidence to nitric oxide acknowledgement: a story of bacterial nitric-oxide reductase

The review briefly summarizes current knowledge of the bacterial nitric-oxide reductase (NOR). This membrane enzyme consists of two subunits, the smaller one contains haem C and the larger one two haems B and nonhaem iron. The protein sequence and structure of metal centres demonstrate the relationship of NOR to the family of terminal oxidases. The binuclear Fe-Fe reaction centre, consisting of antiferromagnetically coupled haem B and nonhaem iron, is analogous to Fe-Cu centre of terminal oxidases. The data on the structure and function of NOR and terminal oxidases suggest that all these enzymes are closely evolutionally related. The catalytic properties are determined most of all by the relatively high toxicity of nitric oxide as a substrate and the resulting strong need to maintain its concentration at nanomolar levels. A kinetic model of the action of the enzyme comprises substrate inhibition. NOR does not conserve the free energy of nitric oxide reduction because it does not work as a proton pump and, moreover, the protons coming into the reaction are taken from periplasm, i.e. they do not cross the membrane.

Kinetic analysis of substrate inhibition in nitric oxide reductase of Paracoccus denitrificans

The current kinetic model for the nitric oxide reductase reaction (Girsch, P., and de Vries, S. (1997) Biochim. Biophys. Acta 1318, 202-216) does not involve the concentration of an electron donor. Here we introduce this variable and show, both theoretically and experimentally, its role in determining the extent of substrate inhibition by the excess of nitric oxide. NO is found to inhibit competitively with the electron donor, possibly by binding to the oxidized form of the enzyme. The observed partial character of the inhibition is tentatively explained by a slow reduction of the non-productive NO complex.

Production and consumption of nitric oxide by denitrifyingFlexibacter canadensis

Production and consumption of nitric oxide (NO) by Flexibacter canadensis cells under anaerobic conditions was investigated using a chemiluminescence NO analyzer. Net NO production from nitrite in the presence of carbonyl cyanide m-chlorophenylhydrazone (CCCP) was pH dependent, increased in the pH range from 4.5 to 6.5, and sharply decreased at pH >6.5. CCCP inhibited NO consumption but only at pH values ≤6.5. This can explain why CCCP stimulation of NO production depends on the pH. Denitrification of nitrite at high concentrations (≥5 mM) also resulted in net NO accumulation. Diethyldithiocarbamate, a copper chelating agent, prevented not only net production of NO during the reduction of nitrite in the presence of CCCP, but also production of nitrous oxide (N2O) from nitrite in the presence of C2H2. This suggests that F. canadensis may possess a copper-type nitrite reductase. However, cytochrome cd1- and copper-containing nitrite reductase DNA probes from Pseudomonas species did not hybridize with the total DNA of F. canadensis, indicating that the nitrite reductase of F. canadensis may possess unique properties. In addition to diethyldithiocarbamate, sulfide, carbon monoxide, azide, cyanide, hydroxylamine and Triton X-100 prevented net NO production from nitrite in the presence of CCCP, and also inhibited NO consumption. C2H2, an inhibitor of N2O reductase, did not affect NO production or consumption.Key words: nitrite reductase, nitric oxide (NO), carbonyl cyanide m-chlorophenylhydrazone (CCCP), Flexibacter canadensis.

Nitric oxide: a synchronizing chemical messenger

Nitric oxide (NO) has been recognized as a ubiquitous chemical messenger in a large number of different biological systems. Its chemical properties make it less specific and less controllable than practically any other neurotransmitter or hormone. In view of this, its extensive biological role as a chemical messenger seems surprising. It is suggested that the biological function of NO evolved early in the anaerobic stage of evolution. In view of its low molecular weight, limited interaction with water, and its electrical neutrality, which allow it to diffuse rapidly through the cytoplasm and biomembranes, it is suggested that the need for NO has been retained by and maintained in eukaryote cells because of its ability to affect many biochemical functions simultaneously, acting primarily as an intracellular synchronizing chemical messenger.

Effect of ionophores on denitrification inFlexibacter canadensis

Denitrification by Flexibacter canadensis was investigated by measuring the production and (or) consumption of nitrite, nitric oxide (NO), and nitrous oxide (N2O) under anaerobic conditions. Carbonyl cyanide m-chlorophenylhydrazone (CCCP), carbonyl cyanide p-trifluoromethoxyphenylhydrazone (FCCP), 2,4-dinitrophenol, and nigericin, but not valinomycin-K+inhibited the production of nitrite and N2O from nitrate by intact cells. However, CCCP, FCCP, 2,4-dinitrophenol, nigericin, and valinomycin-K+did not affect nitrite production from nitrate by cell-free extracts. These results suggest that nitrate transport was dependent on the transmembrane pH gradient but not on the membrane potential. CCCP, FCCP, and nigericin but not 2,4-dinitrophenol and valinomycin-K+caused NO accumulation during the reduction of nitrite, and also inhibited NO consumption and N2O production from nitrite by intact cells. These results preclude an explanation for NO accumulation based on the collapse of the proton motive force by ionophores, and imply that CCCP, FCCP, and nigericin perhaps dissociated a nitrite reductase–nitric oxide reductase complex, and (or) inhibited nitric oxide reductase specifically. 2,4-Dinitrophenol and CCCP did not inhibit the reduction of N2O to dinitrogen. Addition of ≤ 1.16 μM dissolved NO did not affect the production of nitrite from nitrate, or the disappearance of nitrite or N2O. The rate of NO consumption was linear with concentrations of dissolved NO up to 67 nM. Above 67 nM NO, NO consumption was inhibited, suggesting that NO is toxic to nitric oxide reductase.Key words: ionophores, denitrification, nitric oxide, Flexibacter canadensis.

Effect of Chloramphenicol on Denitrification in Flexibacter canadensis and "Pseudomonas denitrificans"

It was recently reported that chloramphenicol inhibits existing denitrification enzyme activity in sediments and carbon-starved cultures of "Pseudomonas denitrificans." Therefore, we studied the effect of chloramphenicol on denitrification by Flexibacter canadensis and "P. denitrificans." Production of N(inf2)O from nitrate by F. canadensis cells decreased as the concentration of chloramphenicol was increased, and 10.0 mM chloramphenicol completely inhibited N(inf2)O production. "P. denitrificans" was less sensitive to chloramphenicol, and production of N(inf2)O from nitrate was inhibited by only about 50% even in the presence of 10.0 mM chloramphenicol. These results suggested that inhibition of denitrification enzyme activity depended on the concentration of chloramphenicol. Increasing the concentration of chloramphenicol decreased the rate of production of nitrite from nitrate by F. canadensis cells, and the concentration of chloramphenicol which resulted in 50% inhibition of production of nitrite from nitrate was 2.5 mM. In contrast, the rates of production of nitrite from nitrate by intact cells and cell extracts of "P. denitrificans" were inhibited by only 58 and 54%, respectively, at a chloramphenicol concentration of 10.0 mM. Chloramphenicol caused accumulation of NO from nitrite but not from nitrate and inhibited NO consumption in F. canadensis; however, it had neither effect in "P. denitrificans." Chloramphenicol did not affect N(inf2)O consumption by these organisms. We concluded that chloramphenicol inhibits denitrification at the level of nitrate reduction and, in F. canadensis, also at the level of NO reduction.

Effects of oxygen, pH and nitrate concentration on denitrification by Pseudomonas species

The production of nitrogen-containing gases by denitrification in three organisms was examined using membrane inlet mass spectrometry. The effects of O2 (during both growth and maintenance) and of pH, nitrate concentration and carbon source were tested in non-proliferating cell suspensions. Two strains of Pseudomonas aeruginosa were capable of co-respiration of NO3- and O2 and, under controlled O2 supply, gave oscillatory denitrification. Variations in culture and assay conditions affected both the rate of denitrification and the ratio of end products (N2O:N2). Higher rates were seen following anaerobic growth. Optimum values of pH and nitrate concentration for denitrification are given. Generally, the optimum pH was 7.0-7.5, approximately that of the growth medium. Optimum nitrate concentration was generally 20 mM.

Modelling and analysis of metabolic pathways

Modelling and analysis of metabolic pathways has received an increasing amount of attention over the past few years. Progress has been made in many aspects such as the identification of rate-controlling steps, applications of optimization principles, and stoichiometric analyses. In addition, the scope of modelling has also expanded. These efforts have led to an improved understanding of metabolic pathways and have facilitated their manipulation.