Mechanism-Based Inactivation of Ammonia Monooxygenase in Nitrosomonas europaea by Allylsulfide

Allylsulfide caused an irreversible inactivation of ammonia monooxygenase (AMO) activity (ammonia-dependent O₂ uptake) in Nitrosomonas europaea. The hydroxylamine oxidoreductase activity (hydrazine-dependent O₂ uptake) of cells was unaffected by allylsulfide. Anaerobic conditions or the presence of allylthiourea, a reversible noncompetitive AMO inhibitor, protected AMO from inactivation by allylsulfide. Ammonia did not protect AMO from inactivation by allylsulfide but instead increased the rate of inactivation. The inactivation of AMO followed pseudo-first-order kinetics, but the observed rates did not saturate with increasing allylsulfide concentrations. The time course of recovery of AMO-dependent nitrite production after complete inactivation by allylsulfide required de novo protein synthesis. Incubation of cells with allylsulfide prevented the ¹⁴C label from ¹⁴C₂H₂ (a suicide mechanism-based inactivator of AMO) from being incorporated into the 27-kDa polypeptide of AMO. Some compounds structurally related to allylsulfide were unable to inactivate AMO. We conclude that allylsulfide is a specific, mechanism-based inactivator of AMO in N. europaea.     

Inhibition of Ammonia Oxidation in Nitrosomonas europaea by Sulfur Compounds: Thioethers Are Oxidized to Sulfoxides by Ammonia Monooxygenase

Organic sulfur compounds are well-known nitrification inhibitors. The inhibitory effects of dimethylsulfide, dimethyldisulfide, and ethanethiol on ammonia oxidation by Nitrosomonas europaea were examined. Both dimethylsulfide and dimethyldisulfide were weak inhibitors of ammonia oxidation and exhibited inhibitory characteristics typical of substrates for ammonia monooxygenase (AMO). Depletion of dimethylsulfide required O(2) and was prevented with either acetylene or allylthiourea, two inhibitors of AMO. The inhibition of ammonia oxidation by dimethylsulfide was examined in detail. Cell suspensions incubated in the presence of ammonia oxidized dimethylsulfide to dimethyl sulfoxide. Depletion of six other thioethers was also prevented by treating cell suspensions with either allylthiourea or acetylene. The oxidative products of three thioethers were identified as the corresponding sulfoxides. The amount of sulfoxide formed accounted for a majority of the amount of sulfide depleted. By using gas chromatography coupled with mass spectrometry, allylmethylsulfide was shown to be oxidized to allylmethylsulfoxide by N. europaea with the incorporation of a single atom of O derived from O(2) into the sulfide. This result supported our conclusion that a monooxygenase was involved in the oxidation of allylmethylsulfide. The thioethers are concluded to be a new class of substrates for AMO. This is the first report of the oxidation of the sulfur atom by AMO in whole cells of N. europaea. The ability of N. europaea to oxidize dimethylsulfide is not unique among the ammonia-oxidizing bacteria. Nitrosococcus oceanus, a marine nitrifier, was also demonstrated to oxidize dimethylsulfide to dimethyl sulfoxide.     

Interaction of Ammonia Monooxygenase from Nitrosomonas europaea with Alkanes, Alkenes, and Alkynes

Ammonia monooxygenase of Nitrosomonas europaea catalyzes the oxidation of alkanes (up to C₈) to alcohols and alkenes (up to C₅) to epoxides and alcohols in the presence of ammonium ions. Straight-chain, N-terminal alkynes (up to C₁₀) all exhibited a time-dependent inhibition of ammonia oxidation without effects on hydrazine oxidation.     

Ammonium Limitation Results in the Loss of Ammonia-Oxidizing Activity in Nitrosomonas europaea

The effects of limiting concentrations of ammonium on the metabolic activity of Nitrosomonas europaea, an obligate ammonia-oxidizing soil bacterium, were investigated. Cells were harvested during late logarithmic growth and were incubated for 24 h in growth medium containing 0, 15, or 50 mM ammonium. The changes in nitrite production and the rates of ammonia- and hydroxylamine-dependent oxygen consumption were monitored. In incubations without ammonium, there was little change in the ammonia oxidation activity after 24 h. With 15 mM ammonium, an amount that was completely consumed, there was an 85% loss of the ammonia oxidation activity after 24 h. In contrast, there was only a 35% loss of the ammonia oxidation activity after 24 h in the presence of 50 mM ammonium, an amount that was not consumed to completion. There was little effect on the hydroxylamine oxidation activity in any of the incubations. The loss of ammonia oxidation activity was not due to differences in steady-state levels of ammonia monooxygenase (AMO) mRNA (amoA) or to degradation of the active site-containing subunit of AMO protein. The incubations were also conducted at a range of pH values to determine whether the loss of ammonia oxidation activity was correlated to the residual ammonium concentration. The loss of ammonia oxidation activity after 24 h was less at lower pH values (where the unoxidized ammonium concentration was higher). When added in conjunction with limiting ammonium, short-chain alkanes, which are alternative substrates for AMO, prevented the loss of ammonia oxidation activity at levels corresponding to their binding affinity for AMO. These results suggest that substrates of AMO can preserve the ammonia-oxidizing activity of N. europaea in batch incubations by protecting either AMO itself or other molecules associated with ammonia oxidation.     

Nitrite as a stimulus for ammonia-starved Nitrosomonas europaea

Ammonia-starved cells of Nitrosomonas europaea are able to preserve a high level of ammonia-oxidizing activity in the absence of ammonium. However, when the nitrite-oxidizing cells that form part of the natural nitrifying community do not keep pace with the ammonia-oxidizing cells, nitrite accumulates and may subsequently inhibit ammonia oxidation. The maintenance of a high ammonia-oxidizing capacity during starvation is then nullified. In this study we demonstrated that cells of N. europaea starved for ammonia were not sensitive to nitrite, either when they were starved in the presence of nitrite or when nitrite was supplied simultaneously with fresh ammonium. In the latter case, the initial ammonia-oxidizing activity of starved cells was stimulated at least fivefold.     

Regulation of the Synthesis and Activity of Ammonia Monooxygenase in Nitrosomonas europaea by Altering pH To Affect NH(inf3) Availability

The obligately ammonia-oxidizing bacterium Nitrosomonas europaea was incubated in medium containing 50 mM ammonium. Changes in the concentration of nitrite, the pH, and the NH(inf4)(sup+)- and NH(inf2)OH-dependent O(inf2) uptake activities of the cell suspension were monitored. The NH(inf4)(sup+)-dependent O(inf2) uptake activity doubled over the first 3 h of incubation and then slowly returned to its original level over the following 5 h. The extent of stimulation of NH(inf4)(sup+)-dependent O(inf2) uptake activity was decreased by lowering the initial pH of the medium. Radiolabeling studies demonstrated that the stimulation of NH(inf4)(sup+)-dependent O(inf2) uptake activity involved de novo synthesis of several polypeptides. Under O(inf2)-limited conditions, the stimulated NH(inf4)(sup+)-dependent O(inf2) uptake activity was stabilized. Rapid, controlled, and predictable changes in this activity could be caused by acidification of the medium in the absence of ammonia oxidation. These results indicate that the NH(inf4)(sup+)-dependent O(inf2) uptake activity in N. europaea is strongly regulated in response to NH(inf3) concentration.     

Factors Limiting Aliphatic Chlorocarbon Degradation by Nitrosomonas europaea: Cometabolic Inactivation of Ammonia Monooxygenase and Substrate Specificity

The soil nitrifying bacterium Nitrosomonas europaea is capable of degrading trichloroethylene (TCE) and other halogenated hydrocarbons. TCE cometabolism by N. europaea resulted in an irreversible loss of TCE biodegradative capacity, ammonia-oxidizing activity, and ammonia-dependent O(2) uptake by the cells. Inactivation was not observed in the presence of allylthiourea, a specific inhibitor of the enzyme ammonia monooxygenase, or under anaerobic conditions, indicating that the TCE-mediated inactivation required ammonia monooxygenase activity. When N. europaea cells were incubated with [C]TCE under conditions which allowed turnover of ammonia monooxygenase, a number of cellular proteins were covalently labeled with C. Treatment of cells with allylthiourea or acetylene prior to incubation with [C]TCE prevented incorporation of C into proteins. The ammonia-oxidizing activity of cells inactivated in the presence of TCE could be recovered through a process requiring de novo protein synthesis. In addition to TCE, a series of chlorinated methanes, ethanes, and other ethylenes were screened as substrates for ammonia monooxygenase and for their ability to inactivate the ammonia-oxidizing system of N. europaea. The chlorocarbons could be divided into three classes depending on their biodegradability and inactivating potential: (i) compounds which were not biodegradable by N. europaea and which had no toxic effect on the cells; (ii) compounds which were cooxidized by N. europaea and had little or no toxic effect on the cells; and (iii) compounds which were cooxidized and produced a turnover-dependent inactivation of ammonia oxidation by N. europaea.     

Nitrite as a Stimulus for Ammonia-Starved Nitrosomonas europaea

Ammonia-starved cells of Nitrosomonas europaea are able to preserve a high level of ammonia-oxidizing activity in the absence of ammonium. However, when the nitrite-oxidizing cells that form part of the natural nitrifying community do not keep pace with the ammonia-oxidizing cells, nitrite accumulates and may subsequently inhibit ammonia oxidation. The maintenance of a high ammonia-oxidizing capacity during starvation is then nullified. In this study we demonstrated that cells of N. europaea starved for ammonia were not sensitive to nitrite, either when they were starved in the presence of nitrite or when nitrite was supplied simultaneously with fresh ammonium. In the latter case, the initial ammonia-oxidizing activity of starved cells was stimulated at least fivefold.     

Oxidation of Ammonia by Spheroplasts of Nitrosomonas europaea

The ammonia-oxidizing activity of Nitrosomonas europaea spheroplasts was restored by addition of hydroxylamine or by preincubation with Mg(2+).     

Kinetic Studies of Ammonia Monooxygenase Inhibition in Nitrosomonas europaea by Hydrocarbons and Halogenated Hydrocarbons in an Optimized Whole-Cell Assay

The inhibitory effects of 15 hydrocarbons and halogenated hydrocarbons on NH₃ oxidation by ammonia monooxygenase (AMO) in intact cells of the nitrifying bacterium Nitrosomonas europaea were determined. Determination of AMO activity, measured as NO₂^- production, required coupling of hydroxylamine oxidoreductase (HAO) activity with NH₃-dependent NH₂OH production by AMO. Hydrazine, an alternate substrate for HAO, was added to the reaction mixtures as a source of reductant for AMO. Most inhibitors exhibited competitive or noncompetitive inhibition patterns. The competitive character generally decreased (K_iE/K_iES increased) as the molecular size of the inhibitors increased. For example, CH₄ and C₂H₄ were competitive inhibitors of NH₃ oxidation, whereas the remaining alkanes (up to C₄) and monohalogenated (Cl, Br, I) alkanes were noncompetitive. Oxidation of C₂H₅Br (noncompetitive) increased as the NH₄⁺ concentration increased up to 40 mM, whereas oxidations of inhibitors with competitive character (K_iE K_iES) were diminished at 40 mM NH₄⁺. Multichlorinated compounds produced nonlinear Lineweaver-Burk plots. Iodinated alkanes (CH₃I, C₂H₅I) and C₂Cl₄ were potent inhibitors of NH₃ oxidation. Maximum rates of NH₃, C₂H₄, and C₂H₆ oxidations were approximately equivalent, suggesting a common rate-determining step. These data support an active-site model for AMO consisting of an NH₃-binding site and a second site that binds noncompetitive inhibitors, with oxidation occurring at either site.     

Ammonia and O2 uptake in relation to proton translocation in cells of Nitrosomonas europaea

The uptake of ammonia and O₂ by washed cells of Nitrosomonas has been followed simultaneously and continuously using electrode techniques. The stoichiometry of NH ₄ ⁺ oxidation, O₂ uptake and NO ₂ ^- production was 1 : 1.5 : 1.0 and for NH₂OH oxidation a ratio of 1 for O₂ : NO ₂ ^- . A variety of inhibitors of electron transport and metals as well as uncouplers restricted ammonia uptake more markedly than O₂ utilization. There is good evidence for the involvement of copper in the NH ₄ ⁺ uptake process.A quinacrine fluorescence technique has been used to study the proton extrusion by washed cells on adding NH₄Cl and NH₂OH respectively as substrates. The uptake of NH ₄ ⁺ was followed by the extrusion of H⁺ and this process was depressed by those inhibitors which were also effective in the electrode experiments. A requirement for copper is also established for the translocation of protons into the medium, resulting from the uptake of NH ₄ ⁺ by cells.Abbreviations mCCCP carbonyl cyanide m-chlorophenylhydrazone - DBP 2,4 dibromophenol - DCCD N-N-dicyclohexylcarbodimide - DIECA Sodium diethyldithiocarbamate - DNP 2,4 dinitrophenol - HOQNO 2-heptyl-4-hydroxyquinoline-N-oxide - NBD chloride 4-chloro-7-nitrobenzo-2-oxa-1,3-diazole - N-serve 2-chloro-6-trichloromethyl-pyridine - PCP pentachlorophenol - 2-TMP 2-trichloromethyl-pyridine - TPB tetraphenylboron - TTFA 1-[thenoyl-(2)]-3,3,3-trifluoracetone - KSCN Potassium thiocyanate     

Anaerobic metabolism of Nitrosomonas europaea

Nitrosomonas europaea is capable of maintaining an anaerobic metabolism, using pyruvate as an electron donor and nitrite as an electron acceptor; utilization of nitrite depends upon supply of both pyruvate and ammonia. The role of ammonia in this reaction was not determined. N europaea also assimilates CO₂ anaerobically into cell material in the presence of nitrite (0.5–1.0 mM), pyruvate and ammonia. This reaction was partially inhibited by nitrite which apparently competed with CO₂ for reducing power. Anaerobic nitrite respiration is sensitive to ionophores, FCCP being the most effective.Non-standard-abbreviations TCA trichloroacetic acid - FCCP carbonylcyanide-p-trifluoromethoxyphenylhydrazon     

Growth response of Nitrosomonas europaea to amino acids

Growth responses of Nitrosomonas europaea to individual amino acids or vitamins was observed in log-phase cultures, as was the incorporation of carbon-14 labeled amino acids. Nitrite formation and protein synthesis were increased by l-glutamic acid, l-aspartic acid, l-serine, and l-glutamine. l-Lysine, l-histidine, l-threonine, l-valine, l-methionine, and l-arginine were inhibitory. The other amino acids had no effect on growth. All of the uniformly labeled amino acids added at low concentrations were taken up by growing cells and distributed into cell fractions. From 1 to 12% of the added radioactivity was present in cells analyzed in late log phase, depending on the amino acid; glycine and l-serine caused accumulation of the label to the greatest extent, whereas l-aspartic and l-glutamic acids were among those incorporated to the least extent. Aspartic acid increased both cell protein and nitrite values, but did not alter the ratio of protein to nitrite from that found in controls.     

Ammonia or Ammonium Ion as Substrate for Oxidation by Nitrosomonas europaea Cells and Extracts

The effect of pH on the K(m) values for ammonia was studied in its oxidation by Nitrosomonas cells and cell-free extracts. The K(m) values decreased markedly with increasing pH, suggesting (NH(3)) rather than (NH(4) (+)) as the actual substrate for oxidation.     

Nitrite reductase of Nitrosomonas europaea is not essential for production of gaseous nitrogen oxides and confers tolerance to nitrite

A gene that encodes a periplasmic copper-type nitrite reductase (NirK) was identified in Nitrosomonas europaea. Disruption of this gene resulted in the disappearance of Nir activity in cell extracts. The nitrite tolerance of NirK-deficient cells was lower than that of wild-type cells. Unexpectedly, NirK-deficient cells still produced nitric oxide (NO) and nitrous oxide (N(2)O), the latter in greater amounts than that of wild-type cells. This demonstrates that NirK is not essential for the production of NO and N(2)O by N. europaea. Inactivation of the putative fnr gene showed that Fnr is not essential for the expression of nirK.     

Cometabolism of trihalomethanes by Nitrosomonas europaea

The ammonia-oxidizing bacterium Nitrosomonas europaea (ATCC 19718) was shown to degrade low concentrations (50 to 800 mug/liter) of the four trihalomethanes (trichloromethane [TCM], or chloroform; bromodichloromethane [BDCM]; dibromochloromethane [DBCM]; and tribromomethane [TBM], or bromoform) commonly found in treated drinking water. Individual trihalomethane (THM) rate constants (k1THM) increased with increasing THM bromine substitution, with TBM > DBCM > BDCM > TCM (0.23, 0.20, 0.15, and 0.10 liters/mg/day, respectively). Degradation kinetics were best described by a reductant model that accounted for two limiting reactants, THMs and ammonia-nitrogen (NH3-N). A decrease in the temperature resulted in a decrease in both ammonia and THM degradation rates with ammonia rates affected to a greater extent than THM degradation rates. Similarly to the THM degradation rates, product toxicity, measured by transformation capacity (Tc), increased with increasing THM bromine substitution. Because both the rate constants and product toxicities increase with increasing THM bromine substitution, a water's THM speciation will be an important consideration for process implementation during drinking water treatment. Even though a given water sample may be kinetically favored based on THM speciation, the resulting THM product toxicity may not allow stable treatment process performance.     

Growth of Nitrosomonas europaea on hydroxylamine

Abstract Hydroxylamine is an intermediate in the oxidation of ammonia to nitrite, but until now it has not been possible to grow Nitrosomonas europaea on hydroxylamine. This study demonstrates that cells of N. europaea are capable of growing mixotrophically on ammonia and hydroxylamine. The molar growth yield on hydroxylamine (4.74 g mol⁻¹ at a growth rate of 0.03 h⁻¹) was higher than expected. Aerobically growing cells of N. europaea oxidized ammonia to nitrite with little loss of inorganic nitrogen, while significant inorganic nitrogen losses occurred when cells were growing mixotrophically on ammonia and hydroxylamine. In the absence of oxygen, hydroxylamine was oxidized with nitrite as electron acceptor, while nitrous oxide was produced. Anaerobic growth of N. europaea on ammonium, hydroxylamine and nitrite could not be observed at growth rates of 0.03 h⁻¹ and 0.01 h⁻¹.