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PubMed2001

Effect of zinc and benzalkonium chloride on Nitrosomonas communis and potential nitrification in soil.

A bacterial contact assay is described which uses a chemoautotrophic microorganism, Nitrosomonas communis (strain Nm2) to evaluate the biological effect of contaminated soils. The effects of two toxicants on the ammonium oxidation activity of the autochthonous microbial population in the soil are compared with inhibition of the same biological response in the new monospecies bioassay. Experiments were performed using soil samples dosed with organic and inorganic contaminants (benzalkonium chloride and zinc) to demonstrate the mode of operation and the sensitivity of the bioassay. The EC50 values of zinc and benzalkonium chloride were calculated to be 171 and 221 mg kg-1 soil, respectively. The toxic response provided by the bioassay can thus predict the effect of soil pollutants on the autochthonous nitrifying bacteria.

Biological Assay↗
PubMed1995

Interaction with membranes of cytochrome c554 from Nitrosomonas europaea.

Two c-cytochromes extrinsically bound to the membranes of Nitrosomonas europaea have been identified. One is the tetraheme cytochrome c554, a protein previously described as soluble and periplasmic. Depending on the concentration of Fe and Cu in the growth medium, from 50 to 100% of the total cellular cytochrome c554 is membrane-associated. The cytochromes c554 found in the soluble or membrane fractions are identical in the spectroscopic, chromatographic, or primary structural properties examined. The interaction of cytochrome c554 with membranes is ionic in nature; it is disrupted by high concentrations of salt. Both membrane-derived and periplasmic forms of cytochrome c554 rebind tightly to membranes which have been washed free of the cytochrome. Cytochrome c554 binds to phospholipid vesicles, suggesting that phospholipids may play a role in the interaction of this cytochrome with the membrane. During the oxidation of NH2OH, the ability of the soluble hydroxylamine oxidoreductase (HAO) to transfer electrons to its natural electron acceptor, cytochrome c554, is substantially impaired when the latter is bound to phospholipid vesicles. The second c-cytochrome associated with membranes in N. europaea is identified as HAO based on its catalytic activity and the presence of a 464-nm ferrous absorption band. A small fraction of HAO is found to be membrane-bound and only in cells grown under low Fe/low Cu. This subpopulation of HAO can be released from the membranes without detergents.

Binding, Competitive↗
PubMedDate not supplied

Crystallization and preliminary crystallographic analysis of cytochrome c553 peroxidase from Nitrosomonas europaea.

The di-heme peroxidase (cytochrome c553 peroxidase) from Nitrosomonas europaea has been crystallized in a form suitable for high-resolution X-ray structure determination. A complete data set was obtained to 2.5A and the data were indexed in space group P2(1) with a = 88.79 A, b = 55.93 A, c = 144.37 A, beta = 103.87 degrees. The self-rotation function indicates one homodimer per asymmetric unit.

Amino Acid Sequence↗
PubMed1995

The amino acid sequence of Nitrosomonas europaea cytochrome c-552.

The complete amino acid sequence of cytochrome c-552 derived from the chemoautotrophic ammonia-oxidizing bacterium Nitrosomonas europaea was determined. The cytochrome consisted of 81 amino acid residues, and its molecular weight was calculated to be 9098 including heme c. Although the sequence of cytochrome c-552 was highly homologous to those of cytochromes c-551, which were known as the electron-donating components to dissimilatory nitrite reductase in pseudomonads, cytochrome c-552 differed from cytochrome c-551 in two points: (1) the sequence of cytochrome c-552 was shorter by two amino acid residues than that of cytochrome c-551 at the N-terminus and (2) one amino acid insertion was present in cytochrome c-552.

Amino Acid Sequence↗
PubMed1977

Polyhedral inclusion bodies in cells of Nitrosomonas spec.

Polyhedral inclusion bodies were observed in cells of a Nitrosomonas species. They were present in growing cells as well as in resting cells. In thin sections their size was about 130 nm in growing cells and about 185 nm in diameter in resting cells. The bodies were commonly located in the nucleoplasm. They appeared to be bounded by a nonunit membrane and had a granular substructure. In thin sections about 70% of the exponentially grown cells and about 20% of the resting cells of the investigated strain showed 1-7 respectively 1-3 inclusion bodies.

Cell Division↗
PubMed1976

Energy coupling and respiration in Nitrosomonas europaea.

Intact cells of Nitrosomonas europaea grown in an ammonium salts medium will oxidise ammonium ions, hydroxylamine and ascorbate-TMPD; there is no oxidation of carbon monoxide, methane or methanol. The Km value for ammonia oxidation is highly pH dependent with a minimum value of 0.5 mM above pH 8.0. This suggests that free ammonia is the species crossing the cytoplasmic membrane(s). The measurement of respiration driven proton translocation indicates that there is probably only one proton translocating loop (loop 3) association with hydroxylamine oxidation. The oxidation of "endogenous" substrates is sometimes associated with more than one proton-translocating loop. These results indicate that during growth hydroxylamine oxidation is probably associated with a maximum P/O ratio of 1.

Electron Transport↗
PubMed2002

Molecular biology and biochemistry of ammonia oxidation by Nitrosomonas europaea.

Nitrosomonas europaea uses only NH(3), CO(2) and mineral salts for growth and as such it is an obligate chemo-lithoautotroph. The oxidation of NH(3) is a two-step process catalyzed by ammonia monooxygenase (AMO) and hydroxylamine oxidoreductase (HAO). AMO catalyzes the oxidation of NH(3) to NH(2)OH and HAO catalyzes the oxidation of NH(2)OH to NO(2)(-). AMO is a membrane-bound enzyme composed of three subunits. HAO is located in the periplasm and is a homotrimer with each subunit containing eight c-type hemes. The electron flow from HAO is channeled through cytochrome c(554) to cytochrome c(m552), where it is partitioned for further utilization. Among the ammonia-oxidizing bacteria, the genes for AMO, these cytochromes, and HAO are present in up to three highly similar copies. Mutants with mutations in the copies of amoCAB and hao in N. europaea have been isolated. All of the amoCAB and hao gene copies are functional. N. europaea was selected by the United States Department of Energy for a whole-genome sequencing project. In this article, we review recent research on the molecular biology and biochemistry of NH(3) oxidation in nitrifiers.

Ammonia↗
PubMed2006

Iron nutrition and physiological responses to iron stress in Nitrosomonas europaea.

Nitrosomonas europaea, as an ammonia-oxidizing bacterium, has a high Fe requirement and has 90 genes dedicated to Fe acquisition. Under Fe-limiting conditions (0.2 microM Fe), N. europaea was able to assimilate up to 70% of the available Fe in the medium even though it is unable to produce siderophores. Addition of exogenous siderophores to Fe-limited medium increased growth (final cell mass). Fe-limited cells had lower heme and cellular Fe contents, reduced membrane layers, and lower NH3- and NH2OH-dependent O2 consumption activities than Fe-replete cells. Fe acquisition-related proteins, such as a number of TonB-dependent Fe-siderophore receptors for ferrichrome and enterobactin and diffusion protein OmpC, were expressed to higher levels under Fe limitation, providing biochemical evidence for adaptation of N. europaea to Fe-limited conditions.

Adaptation, Physiological↗
PubMed1998

High rate of aerobic nitrification and denitrification by Nitrosomonas eutropha grown in a fermentor with complete biomass retention in the presence of gaseous NO2 or NO.

A pure culture of the obligately lithoautotrophic ammonia-oxidizer Nitrosomonas eutropha was grown in a laboratory-scale bioreactor with complete biomass retention. The air supply was supplemented with nitrogen dioxide (NO2; 25 or 50 ppm) or nitric oxide (NO; 25 or 50 ppm). Compared to cultures grown without these nitrogenous oxides, the addition of NO2 or NO to the culture resulted in a significant increase of the nitrification rate, specific activity of ammonia oxidation, growth rate, and maximum cell densities. In contrast, the growth yield slightly decreased in the presence of NO or NO2. Maximum cell densities of about 2 x 10(10) cells ml-1 and a maximum nitrification rate of about 221 mmol NH4+ l-1 day-1 were obtained after 3 weeks in the presence of 50 ppm NO2. Furthermore, in the stationary phase about 50% of the nitrite produced was aerobically denitrified to dinitrogen (N2) and traces of nitrous oxide (N2O). When cells were supplemented with NO, a high rate of aerobic denitrification occurred only during the first days of the exponential growth phase.

Aerobiosis↗
PubMed2001

High-resolution structures of the oxidized and reduced states of cytochrome c554 from Nitrosomonas europaea.

Cytochrome c554 (cyt c554) is a tetra-heme cytochrome involved in the oxidation of NH3 by Nitrosomonas europaea. The X-ray crystal structures of both the oxidized and dithionite-reduced states of cyt c554 in a new, rhombohedral crystal form have been solved by molecular replacement, at 1.6 A and 1.8 A resolution, respectively. Upon reduction, the conformation of the polypeptide chain changes between residues 175 and 179, which are adjacent to hemes III and IV. Cyt c554 displays conserved heme-packing motifs that are present in other heme-containing proteins. Comparisons to hydroxylamine oxidoreductase, the electron donor to cyt c554, and cytochrome c nitrite reductase, an enzyme involved in nitrite ammonification, reveal substantial structural similarity in the polypeptide chain surrounding the heme core environment. The structural determinants of these heme-packing motifs extend to the buried water molecules that hydrogen bond to the histidine ligands to the heme iron. In the original structure determination of a tetragonal crystal form, a cis peptide bond between His129 and Phe130 was identified that appeared to be stabilized by crystal contacts. In the rhombohedral crystal form used in the present high-resolution structure determination, this peptide bond adopts the trans conformation, but with disallowed angles of phi and psi.

Amino Acid Motifs↗
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↗
PubMed1989

Degradation of trichloroethylene by the ammonia-oxidizing bacterium Nitrosomonas europaea.

Suspensions of Nitrosomonas europaea are shown to cause the complete disappearance of 10 microM trichloroethylene at rates of 1 microM mg protein-1. The reaction continues at nearly this rate for many hours. Fresh cells catalyze the reaction in the absence of added ammonium (presumably utilizing endogenous ammonia or stored reductant). In older cells, trichloroethylene degradation depends on the addition of ammonia. Acetylene, 2-chloro 6-trichloromethylpyridine and alpha alpha'dipyridyl, which inhibit the oxidation of ammonia by cells, inhibit the degradation of trichloroethylene. Thus degradation of trichloroethylene is dependent on- and possibly catalyzed by the ammonia oxidizing enzyme.

Ammonia↗
PubMed1991

P460 of hydroxylamine oxidoreductase of Nitrosomonas europaea: Soret resonance Raman evidence for a novel heme-like structure.

P460, an iron-containing chromophore at the active site of Hydroxylamine Oxidoreductase of the ammonia-oxidizing bacterium Nitrosomonas europaea, is a macrocycle of unknown structure with a Soret-like 460-nm absorption band in the ferrous form. The pigment can also be isolated in a peptide, "P460-Fragment". Resonance Raman spectroscopy (lambda ex = 457.9 nm) suggests that P460 is a new type of heme with symmetry properties lower than those of protophorphyrin IX or chlorins and similar to those of chlorophylls and isobacteriochlorins. Some of the resonance Raman vibrations of P460 are shifted in HAO as compared to those of P460-Fragment.

Binding Sites↗
PubMed1992

Acceleration of the oxygen reaction in CuA-deficient Nitrosomonas europaea cytochrome c oxidase as revealed by the flow-flash measurement.

The oxygen reaction of Nitrosomonas europaea cytochrome c oxidase containing either 2Cu or 1Cu per two heme a molecules was investigated by the flow-flash technique at 20 degrees C. The reaction profiles of the bacterial enzyme were essentially the same as those of bovine heart cytochrome c oxidase, although the rate of the primary oxygen compound formation was much slower. The 1Cu enzyme exhibited higher rates for both primary oxygen compound formation and intramolecular electron transfer than the 2Cu enzyme. This result clearly indicates that CuA is not essential functionally for the oxidation of ferrous heme a moieties, and suggests its structural importance in maintaining the molecular integrity of N. europaea cytochrome oxidase.

Copper↗
PubMed1984

Diheme cytochrome c-554 from Nitrosomonas. Soret resonance Raman indication of an unusual ferric 5-coordinate structure.

The diheme cytochrome c-554 which participates in ammonia oxidation in the chemoautotroph , Nitrosomonas europaea has been studied by Soret excitation resonance Raman spectroscopy. The Raman spectrum of reduced cytochrome c-554 at neutral pH is similar classical 6-coordinate low-spin ferrous mammalian cytochrome c. In contrast, the spectrum of ferric cytochrome c-554 suggests a 5-coordinate state which is unusual for c hemes. The oxidized spectrum closely resemble that of horseradish peroxidase (HRP) or cytochrome c peroxidase (CcP) at pH 6.4. The narrow linewidth of the heme core-size vibrations indicates that both heme irons of c-554 have similar geometries.

Cytochrome c Group↗
PubMed1994

The primary structure of cytochrome P460 of Nitrosomonas europaea: presence of a c-heme binding motif.

Cytochrome P460 and hydroxyamine oxidoreductase of Nitrosomonas europaea both catalyze the oxidation of hydroxylamine and contain a 460 nm-absorbing chromophore. The gene (cyp) encoding cytochrome P460 was cloned and sequenced. The predicted amino acid sequence contains a single c-heme binding motif (CXXCH) near the carboxy-terminus. Cytochrome P460 shows little sequence homology to other c-cytochromes including hydroxyamine oxidoreductase. The presence of a signal peptide and a possible c-heme binding site suggest that the cytochrome P460 of N. europaea is periplasmic.

Amino Acid Sequence↗
PubMed1994

Identification of axial ligands of cytochrome c552 from Nitrosomonas europaea.

Cytochrome c552 from Nitrosomonas europaea was analyzed by visible, EPR and MCD spectroscopies. The visible and MCD data show that histidine and methionine are the axial ligands to the heme iron of the ferric protein. The EPR spectrum of the cytochrome shows an atypical highly axial low spin (HALS) type signal with g-values that make it difficult to identify the axial ligands. These results reinforce the value of near-infrared MCD spectroscopy for assigning ligands in ferric heme systems and point out the difficulties in using only EPR spectroscopy for the same purpose. The description of another c-cytochrome exhibiting a HALS-type EPR signal will eventually be helpful in explaining the physical basis for this unusual signal.

Circular Dichroism↗