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PubMed2005

Improvement of NaNO2-oxidizing activity in Nitrobacter vulgaris by coentrapment in polyacrylamide containing polydimethylsiloxane copolymer and DEAE-sephadex.

Removal of nitrite and nitrate from drinking water has attracted great attention in recent years because of the human health risk induced by the exposure to contaminated groundwater and surface water. We have therefore tested a model nitrite oxidation system by coentrapping the NaNO2 oxidizer Nitrobacter vulgaris with polydimethylsiloxane (PDMS) copolymer and DEAE-Sephadex in a polyacrylamide gel. The copolymer and the anion exchanger facilitate the diffusion of oxygen and NaNO2, respectively, into the gel matrix. To test the nitrite-oxidizing activity, the entrapped cells were coupled to a thermal sensor. Coentrapment of 5% (wt/vol) DEAE-Sephadex with Nitrobacter vulgaris increased the nitrite-oxidizing activity by a factor of 3.7 compared to entrapped cells alone, and by the addition of 0.86% (wt/vol) artificial oxygen carrier PDMS copolymer increased the activity further to 4.3 times higher. Operational and storage stability of the coentrapped N.vulgaris also improved. This suggests that this enhanced immobilized cell system can also be used for nitrite oxidation to nitrate in drinking water as an on-line thermally monitored bioreactor.

Acrylic Resins↗
PubMed1970

Effects of pesticides on nitrite oxidation by Nitrobacter agilis.

The influence of pesticides on the growth of Nitrobacter agilis in aerated cultures and on the respiration of N. agilis cell suspensions and cell-free extracts was studied. Two pesticides, aldrin and simazine, were not inhibitory to growth of Nitrobacter, but five compounds [isopropyl N-(3-chlorophenyl) carbamate (CIPC), chlordane, 1,1-dichloro-2,2-bis (p-chlorophenyl) ethane (DDD), heptachlor, and lindane] prevented growth when added to the medium at a concentration of 10 mug/ml. Whereas CIPC and eptam prevented nitrite oxidation by cell suspensions, the addition of DDD and lindane resulted in only partial inhibition of the oxidation. Heptachlor and chlordane also caused only partial inhibition of oxidation, but were more toxic with cell-free extract nitrite oxidase. None of the pesticides inhibited the nitrate reductase activity of cell-free extracts, but most caused some repression of cytochrome c oxidase activity. Heptachlor was the most deleterious compound.

Bacterial Proteins↗
PubMed1979

Deoxyribonucleic acid in Nitrobacter carboxysomes.

Carboxysomes were isolated from Nitrobacter winogradskyi and Nitrobacter agilis. The icosahedral particles contained double-stranded deoxyribonucleic acid (DNA). In the presence of ethidium bromide and cesium chloride, the particle-bound DNA had a buoyant density of rho 25 = 1.701 g/cm3. Electron microscopy revealed the DNA to be a 14-micron circular molecule.

Centrifugation, Density Gradient↗
PubMed1986

Inhibitor Evaluation with Immobilized Nitrobacter agilis Cells.

Nitrobacter agilis was entrapped in calcium alginate beads and used as a floating bed supplied with a continuous flow of nitrite medium. Complete nitrite oxidation was achieved within 30 h, and the system could be maintained for at least 210 h. The immobilized Nitrobacter system was subjected to sulfur oxyanions, acidity, and metal ions. Thiosulfate and tetrathionate (up to 20 mM each) did not inhibit the nitrite oxidation activity. A low pH of 4.2 resulted in the complete cessation of nitrite oxidation, and the activity was not restored upon increasing the pH to 7. Nitrite oxidation by N. agilis was sensitive to 10 mM each Ni and Al but insensitive to 10 mM MoO(4).

Journal Article↗
PubMed1965

Carbon and Energy Sources for the Nitrifying Autotroph Nitrobacter.

Delwiche, C. C. (University of California, Davis), and M. S. Finstein. Carbon and energy sources for the nitrifying autotroph Nitrobacter. J. Bacteriol. 90:102-107. 1965.-The effect of various organic compounds on the growth and metabolism of the obligatively autotrophic nitrifying organism Nitrobacter was studied. A slight stimulation of both nitrification and growth was obtainable with a number of organic amendments, including yeast extract, Vitamin Free Casamino Acids, and some amino acids. Depending upon culture conditions, a strong stimulation of growth was obtained with acetate as an amendment to the culture solution. Several compounds, including valine, hydroxyproline, and threonine, were inhibitory at concentrations of 10(-3)m. The incorporation of carbon from isotopically labeled organic compounds was demonstrated. Acetate and glycine were particularly strong contributors to cell carbons. These could not substitute for carbon dioxide as a sole carbon source for growth, however, nor could any other of the carbon compounds that were tried.

Journal Article↗
PubMed1965

Permeability of Nitrobacter agilis to Organic Compounds.

Ida, S. (Cornell University, Ithaca, N.Y.), and M. Alexander. Permeability of Nitrobacter agilis to organic compounds. J. Bacteriol. 90:151-156. 1965.-None of a variety of inorganic ions or organic compounds served as a sole energy source for the growth of Nitrobacter agilis, and the test substrates were not oxidized by either intact cells or extracts of the obligate chemoautotroph. The organic substances did not serve as sole carbon sources for the bacterium in a synthetic medium, and they failed to enhance the rate of nitrite oxidation. The organism was permeable to acetate and a number of other simple carbon compounds, however, and exogenously supplied acetate was converted to a number of products. On the basis of these findings, possible reasons are examined for the inability of the chemoautotroph to use exogenous organic compounds as energy or carbon sources.

Journal Article↗
PubMed1965

Stimulation of Nitrobacter agilis by Biotin.

Krulwich, Terry A. (Goucher College, Baltimore, Md.), and Helen B. Funk. Stimulation of Nitrobacter agilis by biotin. J. Bacteriol. 90:729-733. 1965.-Addition of biotin to nitrite-mineral medium greatly stimulated the autotrophic growth of four strains of Nitrobacter agilis. Comparisons of cultures of the organisms grown in parallel at 30 C in nitrite medium and in the medium supplemented with 150 mmug of biotin per ml showed that the vitamin promoted: (i) 2- to 4-fold greater rates of utilization of nitrite, and (ii) 100- to 1,000-fold greater populations of cells per milliliter. Avidin specifically inhibited the biotin stimulation of nitrite utilization at an avidin-biotin ratio of 133:1. Incubation of the four strains of N. agilis at 37 C imposed a requirement for biotin that could be met by daily addition of 150 mmug of the vitamin per ml of medium. The stimulatory effects of the vitamin at 30 C suggest that in N. agilis the synthesis of biotin is rate-limiting for growth.

Journal Article↗
PubMed1993

Close genetic relationship between Nitrobacter hamburgensis nitrite oxidoreductase and Escherichia coli nitrate reductases.

The nitrite oxidoreductase (NOR) from the facultative nitrite-oxidizing bacterium Nitrobacter hamburgensis X14 was investigated genetically. In order to develop a probe for the gene norB, the N-terminal amino acid sequence of the NOR beta-subunit (NorB) was determined. Based on that amino acid sequence, an oligonucleotide was derived that was used for the identification and cloning of gene norB. Sequence analysis of DNA fragments revealed three adjacent open reading frames in the order norA, norX, norB. The DNA sequences of norX and norB represented complete genes while the open reading frame of norA was truncated by the cloning site. The deduced amino acid sequence of protein NorB contained four cysteine clusters with striking homology to those of iron-sulfur centers of bacterial ferredoxins. NorB shares significant sequence similarity to the beta-subunits (NarH, NarY) of the two dissimilatory nitrate reductases (NRA, NRZ) of Escherichia coli. Additionally, the derived amino acid sequence of the truncated open reading frame of norA showed striking resemblance to the alpha-subunits (NarG, NarZ) of the E. coli nitrate reductases.

Amino Acid Sequence↗
PubMed1977

Enzymatic studies on autotrophically, mixotrophically and heterotrophically grown Nitrobacter agilis with special reference to nitrite oxidase.

Nitrobacter agilis was grown autotrophically on nitrite, mixotrophically on nitrite together with either acetate or pyruvate and heterotrophically on acetate and casamino acids, pyruvate and casamino acids or pyruvate and nitrate. The enzymatic activities differed most in the key enzymes of lithotrophic metabolism. Nitrite oxidase was repressed 90% in 10 days after transition to heterotrophic growth and was no longer detectable after several transfers. The induction of nitrite oxidase began after a lag of 2 days and reached the autotrophic level after 7 days when pyruvate was the carbon and energy source and after 9 days using acetate.

Acetates↗
PubMed1975

Adenine nucleotide pool variations in intact Nitrobacter winogradskyi cells.

1. The ATP pool in Nitrobacter winogradskyi cells was determined by means of the luciferin-luciferase enzyme system and the ADP and AMP pools were measured after enzymatic conversion into ATP. 2. In the first 10 min after addition of nitrite to endogenously respiring cells, which had stood for 5--16 days after completion of the nitrite oxidation, the ATP pool dropped about 60%. 3. During the log phase the ATP pool was approx. 20--40 pmoles/5 mug cell-N. During growth it increased exponentially by 3--4 times the amount until the nitrite had been used up. Subsquently the ATP pool decreased at first rapidly and then more slowly without sinking to 0 in the first 2 months after nitrification. 4. Nitrite oxidizing cells had an energy charge of 0.37 during the log-phase. After approx. 90% of the substrate had been used up the energy charge had reached 0.57. 5. If the CO2 assimilation was inhibited in growing cultures by increased oxygen partial pressure, nitrite oxidation continued but the ATP pool increased. 6. The ATP pool and the activity of the endogenous respiration decreased by more than 50% during the first hours after the substrate had been used up.

Adenine Nucleotides↗
PubMed1984

A relationship between prokaryote and eukaryote observed in Nitrobacter agilis cytochromes AA3 and C.

Cytochrome aa3 (cytochrome c oxidase) and cytochrome c were purified from Nitrobacter agilis, and some of their properties were compared with those of the respective counterparts of eukaryote from the evolutionary point of view. N. agilis cytochrome aa3 has many functional and structural properties similar to those of eukaryotic cytochrome aa3, although its molecule is composed of only two kinds of subunits unlike the eukaryotic cytochrome which is composed of 7 kinds of subunits. N. agilis cytochrome c is homologous to eukaryotic cytochrome c; 50 amino acid residues of the bacterial cytochrome c are identical with those of horse cytochrome c. It reacts with yeast cytochrome c peroxidase as rapidly as eukaryotic cytochrome c does. So far as based on the molecular features of cytochromes aa3 and c, N. agilis appears to be one of the organisms which may link in evolution prokaryote to eukaryote.

Amino Acid Sequence↗
PubMed1984

Source of the oxygen atoms of nitrate in the oxidation of nitrite by Nitrobacter agilis and evidence against a P-O-N anhydride mechanism in oxidative phosphorylation.

15N, 18O Tracer studies were applied to the aerobic oxidation of nitrite to nitrate by the chemolithotrophic bacterium, Nitrobacter agilis. It was established that, in conversion of nitrite to nitrate, one oxygen atom of nitrate arose from water and none from O2 or inorganic phosphate. This result confirms that of Kumar et al. [(1983) FEBS Lett. 152, 71-74]. Oxygen exchange between water and inorganic phosphate was small and that between water and nitrite or nitrate or any reaction intermediates between these two was not detected. Oxidation of nitrite was, therefore, effectively irreversible under the conditions employed. The uptake of extracellular phosphate was sufficient to allow significant transfer of 18O from phosphate to nitrate if oxidative phosphorylation had occurred by way of a P-O-N anhydride between phosphate (or ADP) and nitrate. The results are, therefore, inconsistent with the occurrence of a reaction of this type during nitrite oxidation.

Anhydrides↗
PubMed1984

Na+ and K+ transport in Nitrosomonas europaea and Nitrobacter agilis.

Potassium-depleted cells of Nitrosomonas europaea and Nitrobacter agilis were prepared by diethanolamine treatment and contained less than 5 mM intracellular K+. The addition of K+ to K+-depleted cells of N. europaea and N. agilis resulted in a depolarization of membrane potential (delta psi) by about 5 and 10 mV, respectively. This depolarization was, however, compensated by an equivalent increase in transmembrane pH gradient (delta pH), so that the total proton-motive force (delta p) remained constant, indicating that K+ transport was electrogenic in both bacteria. Using 22Na+-loaded cells, it is shown that both bacteria lack a respiration-dependent Na+ pump; however, antiporters for Na+/H+, K+/Na+ and K+/H+ were detected. Of these, at least the K+/Na+ antiporter required an electrochemical gradient for its operation. It is also shown that the unprotonated form of NH+4 is transported into these bacteria by a simple diffusion mechanism.

Ammonium Chloride↗
PubMed1982

The complete amino acid sequence of Nitrobacter agilis cytochrome c-550.

The amino acid sequence of cytochrome c-550 from the chemoautotroph, Nitrobacter agilis, was completed by using solid-phase sequencing and conventional procedures. The cytochrome was composed of 109 amino acid residues and its molecular weight was calculated to be 12375 including haem c. The cytochrome was homologous to eukaryotic cytochromes c and some photosynthetic bacterial cytochromes c2. In particular, its primary structure was very similar to that of Rhodopseudomonas viridis cytochrome c2. Some of its properties were compared with those of other cytochromes c on the basis of the primary structure.

Amino Acid Sequence↗
PubMed1988

The nitrite oxidizing system of Nitrobacter winogradskyi.

Cytochrome components which participate in the oxidation of nitrite in Nitrobacter winogradskyi have been highly purified and their properties studied in detail. Cytochrome a1c1 is an iron-sulphur molybdoenzyme which has haems a and c and acts as a nitrite-cytochrome c oxidoreductase. Cytochrome c-550 is homologous to eukaryotic cytochrome c and acts as the electron mediator between cytochrome a1c1 and aa3-type cytochrome c oxidase. The oxidase is composed of two kinds of subunits, has two molecules of haem a and two atoms of copper in the molecule, and oxidizes actively eukaryotic ferrocytochrome c as well as its own ferrocytochrome c-550. Further, a flavoenzyme has been obtained which has transhydrogenase activity and catalyses reduction of NADP+ with benzylviologen radical. This enzyme may be responsible for production of NADPH in N. winogradskyi. The electron transfer against redox potential from NO2- to cytochrome c could be pushed through prompt removal by cytochrome aa3 of H+ formed by the dehydrogenation of NO2- + H2O. As cytochrome c in anaerobically kept cell-free extracts is rapidly reduced on addition of NO2-, a membrane potential does not seem necessary for the reduction of cytochrome c by cytochrome a1c1 with NO2- in vivo.

Amino Acid Sequence↗
PubMed1991

Purification and characterization of ATPase from Nitrobacter winogradskyi.

An ATPase was purified from Nitrobacter winogradskyi, and some of its molecular and enzymatic properties were determined. The enzyme was composed of two subunits of 64 and 59 kDa, respectively. The enzyme had its pH optimum at 9.5 and showed a specific activity of 7 units per mg protein. This activity was about 14% and 18% of that of F1-ATPases obtained from Escherichia coli and Sulfolobus acidocaldarius, respectively. The enzyme was 29% and 6% inhibited by 100 microM dicyclohexylcarbodiimide (DCCD) and 100 microM NaN3, respectively. It was not inhibited by 20 mM NaNO3.

Adenosine Triphosphatases↗
PubMed1991

Cytochromes c of Nitrobacter winogradskyi and Thiobacillus novellus: structure, function and evolution.

The amino acid sequences of Thiobacillus novellus and Nitrobacter winogradskyi cytochromes c have been compared with those of cytochromes c from several other organisms. The two bacterial cytochromes resemble eukaryotic cytochromes c; 49 amino-acid residues are identical between T. novellus and horse cytochromes c, and 50 residues identical between N. winogradskyi and horse cytochromes c. However, their reactivity with cow cytochrome c oxidase is about 80% lower than the reactivity of eukaryotic cytochromes c with the cow mitochondrial oxidase, while they react with yeast cytochrome c peroxidase as rapidly as eukaryotic cytochromes c. The numbers of identical amino-acid residues between T. novellus and animal cytochromes c are 45-53 and those between N. winogradskyi and animal cytochromes c 47-53, while those between the two bacterial cytochromes and yeast and protozoan cytochromes c are around 40. Thus, N. winogradskyi and T. novellus cytochromes c are more similar to animal cytochromes c than to yeast and protozoan cytochromes c on the basis of the amino-acid sequence.

Amino Acid Sequence↗
PubMed1976

Energy-conserving reactions in phosphorylating electron-transport particles from Nitrobacter winogradskyi. Activation of nitrite oxidation by the electrical component of the protonmotive force.

1. In electron-transport particles (ET particles) prepared from Nitrobacter winogradskyi, the uncoupling agent carbonyl cyanide phenylhydrazone increased the rate of NADH oxidation but decreased the rate of oxidation of NO2-. Its effectiveness in stimulating NADH oxidation closely paralleled its effectiveness in inhibiting NO2- oxidation. 2. In the presence of ADP and phosphate the oxidation of NADH was stimulated, whereas the oxidation of NO2- was inhibited. In the presence of excess of Pi the concentration dependence with respect to ADP was the same for acceleration of NADH oxidation and inhibition of NO2- oxidation. 3. Oligomycin inhibited NADH oxidation and stimulated the oxidation of NO2-. The concentration of oligomycin required to produce half-maximal effect in both systems was the same. 4. The apparent Km for NO2- was not affected by ADP together with Pi, by uncoupling agent or by oligomycin. 5. With NADH as substrate, classical respiratory control was observed. With NO2- as substrate the respiratory-control ratio was less than unity. 6. A reversible uptake of H+ accompanied the oxidation of NO2- by ET particles. 7. In the presence of NH4Cl or cyclohexylamine hydrochloride, H+ uptake was abolished and increased rates of NO2- oxidation were observed. When valinomycin was present in the reaction medium, low concentrations of NH4Cl inhibited NO2- oxidation. 8. Pretreatment of ET particles with oligomycin enhanced the stimulation of NO2- oxidation induced by NH4Cl or by cyclohexylamine hydrochloride. Pretreatment with the uncoupler carbonyl cyanide phenylhydrazone prevented these stimulations. 9. In the presence of dianemycin together with K+, the uptake of H+ was abolished and the rate of NO2- oxidation was increased. In contrast, in the presence of valinomycin together with K+, the uptake of H+ was increased, and the rate of NO2- oxidation decreased. 10. Sodium tetraphenylboron was found to be an inhibitor of NO2- oxidation, but caused a stimulation of NADH oxidation which was dependent on the presence of NH4Cl or cyclohexylamine hydrochloride. 11. It is concluded that the enhanced rate of NO2- oxidation observed in the absence of energy-dissipating processes clearly relates to some state before the involvement of adenine nucleotides, and it is suggested that the oxidation of NO2- generates a protonmotive force, the electrical component of which controls the rate of NO2- oxidation.

Adenosine Diphosphate↗