Denitrification and nitrite reduction: Pseudomonas aeruginosa nitrite-reductase

Probabilistic Models to Predict the Growth Initiation Time for Pseudomonas spp. in Processed Meats Formulated with NaCl and NaNO2

This study developed probabilistic models to determine the initiation time of growth of Pseudomonas spp. in combinations with NaNO2 and NaCl concentrations during storage at different temperatures. The combination of 8 NaCl concentrations (0, 0.25, 0.5, 0.75, 1, 1.25, 1.5, and 1.75%) and 9 NaNO2 concentrations (0, 15, 30, 45, 60, 75, 90, 105, and 120 ppm) were prepared in a nutrient broth. The medium was placed in the wells of 96-well microtiter plates, followed by inoculation of a five-strain mixture of Pseudomonas in each well. All microtiter plates were incubated at 4, 7, 10, 12, and 15℃ for 528, 504, 504, 360 and 144 h, respectively. Growth (growth initiation; GI) or no growth was then determined by turbidity every 24 h. These growth response data were analyzed by a logistic regression to produce growth/no growth interface of Pseudomonas spp. and to calculate GI time. NaCl and NaNO2 were significantly effective (p<0.05) on inhibiting Pseudomonas spp. growth when stored at 4-12℃. The developed model showed that at lower NaCl concentration, higher NaNO2 level was required to inhibit Pseudomonas growth at 4-12℃. However, at 15℃, there was no significant effect of NaCl and NaNO2. The model overestimated GI times by 58.2±17.5 to 79.4±11%. These results indicate that the probabilistic models developed in this study should be useful in calculating the GI times of Pseudomonas spp. in combination with NaCl and NaNO2 concentrations, considering the over-prediction percentage.

Effects of nitrite on modulating ROS generation following ischemia and reperfusion

It has long been known that the generation of reactive oxygen species (ROS) is a major cause of injury after ischemia/reperfusion. More recently it has emerged that the predominant source of these ROS are the mitochondria, which are specifically damaged during prolonged ischemic episodes. Several strategies have been tested to attenuate mitochondrial damage and reperfusion ROS. Most successful has been ischemic preconditioning, a procedure in which repetitive short periods of ischemia and reperfusion reduce injury from a subsequent prolonged ischemia and reperfusion. Recently, ischemic postconditioning, whereby reperfusion after prolonged ischemia is repetitively interrupted for a short period, has also been shown to equally protect as ischemic preconditioning. Both procedures activate the same down-stream kinase pathways that minimize apoptosis and tissue damage. Endothelial nitric oxide synthase is a target of these kinase pathways and nitric oxide (NO) administration can mimic its protective effect. However, the optimal NO dose is difficult to determine and excess NO levels have been shown to be detrimental. A recently described physiological storage pool of NO, nitrite, has been shown to be a potent mediator of cytoprotection after ischemia/reperfusion that mechanistically reduces mitochondrial ROS generation at reperfusion. Here, we describe the sources, bioactivaton, and mechanisms of action of nitrite and discuss the potential of this simple anion as a therapeutic to protect against ischemia/reperfusion injury.

Gated electron transfers and electron pathways in azurin: a NMR dynamic study at multiple fields and temperatures

Dynamic properties of electron transfer pathways in a small blue copper cupredoxin are explored using an extensive 15N NMR relaxation study of reduced Pseudomonas aeruginosa azurin at four magnetic fields (500-900 MHz) and at two temperatures chosen well below the melting point of the protein. Following a careful model-free analysis, several protein regions with different dynamic regimes are identified. Nanosecond time-scale mobility characterizes various residues of the hydrophobic surface patch believed to mark the natural entry point for electrons, notably the surface-exposed copper-ligand His117. These findings are consistent with a gated electron transfer process according to the "dynamic docking" model. Residues 47-49 along intramolecular pathways of electrons show rigidity that is remarkably conserved when increasing the temperature. Three different conformational exchange processes were observed in the millisecond range, one near the only disulfide bridge in the molecule and two near the copper ion. The latter two processes are consistent with previous data such as crystal structures at various pH values and NMR relaxation dispersion experiments; they may indicate an additional gated electron transfer mechanism at slower time-scales.

Incidence and geographical distribution of sudden infant death syndrome in relation to content of nitrate in drinking water and groundwater levels

BACKGROUND

Previous studies indicate that the enteral bacterial urease is inhibited in victims of sudden infant death syndrome (SIDS). One possible inhibitor of this bacterial activity is nitrate. If ambient pollution by nitrate is involved in the etiology of SIDS only a fraction of the nitrate concentration not infrequently found in drinking water would be enough for this inhibition.

METHODS

Occurrence of SIDS (n = 636) in Sweden during the period 1990 through 1996 were analysed regarding geographical and seasonal distribution in relation to the nitrate concentration in drinking water and changes in the groundwater level.

RESULTS

Both the birth rate and the incidence of SIDS decreased during the study period. One quarter of the municipalities constituting 11% of the population had no cases, the maximum incidence being 6.5 per 1000 live births. Seasonality: The northernmost parts of the country had its highest incidence when the rest of the country had its lowest incidence, and the occurrence of individual deaths was associated with the recharge of groundwater which increases its nitrate content. The local incidence of SIDS was correlated (rs = 0.34-0.87) to maximally recorded concentrations of nitrate in drinking water.

CONCLUSIONS

The seasonal distribution of SIDS was widely different from the south to the north of the country and seems to be associated with differences in the groundwater level changes subsequent to precipitation, frost penetration, and melting of snow. Use of drinking water with high peak concentrations or great variations in nitrate concentration was correlated to the incidence of SIDS.

Sudden infant death syndrome and nitrogen metabolism: further development of a hypothesis

BACKGROUND

A hypothesis suggesting an inducible inability of the enteric bacteria to metabolize urea in infants, resulting in metabolic alkalosis and subsequent respiratory insufficiency, has been proposed as the cause of sudden infant death syndrome (SIDS).

METHODS

Microbiological cultivation and determination of faecal urease activity and faecal urea content were carried out in 30 cases of unexpected infant deaths out of which 22 were considered to be due to SIDS and eight from other causes. The concentration of nitric oxide (NO) in sealed test tubes was determined after incubation of faeces in normal saline.

RESULTS

The SIDS subjects differed significantly from the control cases in two respects: they had low or no sigmoid faecal urease activity and an unmetabolized sigmoid faecal urea content, whereas the control subjects had normal faecal urease activity and none, or very little, remaining faecal urea. The NO concentration in faeces was correlated with the faecal content of urea in the SIDS cases.

CONCLUSION

The present findings lend support to the hypothesis of an insufficient metabolism of enteric urea in infants with SIDS.

Cell biology and molecular basis of denitrification

Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.

Faecal microflora and urease activity during the first six months of infancy

Gastrointestinal degradation of urea might, according to a new hypothesis, have consequences for the regulation of acid-base balance as well as control of breathing during infancy. Thirteen infants were investigated from their first few days of life to the age of 6 months by collecting faecal samples at the age of 3 days, 2, 3, and 6 months, respectively. The faecal microflora was determined after aerobic and anaerobic cultivation and the faecal urease activity was assessed after 36 h aerobic and anaerobic preincubation. The infants were mostly breast fed and had a faecal microflora containing anaerobic bacteria such as Bifidobacteria, Bacterioides and Lactobacilli but also aerobics such as Escherichia coli, Enterococci and sometimes Klebsiella. The faecal pH increased from approximately 5.30 to 5.90, the pH after anaerobic preincubation being on an average 0.2 pH units lower than after aerobic preincubation. Simultaneously the nitric oxide production of the faecal specimens increased approximately 10-fold and the urease activity decreased by a factor of 3 to 5. We also found an inhibitory action of nitrate, nitrite (in mumolar concentration) and nitric oxide (in parts per million concentration) on the faecal urease activity. Hence, the present results warrant further research in order to determine more precisely the action of different concentrations of various nitrous oxides on individual bacterial species, and furthermore, to assay the faecal urease activity in victims of sudden infant death syndrome as well as in infants dead due to other causes.

Bacterial nitrite-reducing enzymes

The enzymic reduction of nitrite takes place in a wide range of bacteria and is found to occur in denitrifying, assimilatory and dissimilatory pathways. In this review we describe the major molecular characteristics of the various enzymes employed in each of these processes.

Nitrite activates the transcription of the Pseudomonas aeruginosa nitrite reductase and cytochrome c-551 operon under anaerobic conditions

The transcription of the Pseudomonas aeruginosa denAB operon, which consists of the nitrite reductase and cytochrome c-551 genes, is induced under anaerobic conditions. However, under anaerobic non-denitrifying conditions (anaerobic growth on arginine), the promoter activity of the operon was approximately one-fifth of that under anaerobic denitrifying conditions (anaerobic growth in the presence of nitrite or nitrate). This result clearly demonstrates that the presence of nitrite or nitrate activates the transcription of P. aeruginosa denAB operon under anaerobic conditions.

Anaerobically induced expression of the nitrite reductase cytochrome c-551 operon from Pseudomonas aeruginosa

The nitrite reductase gene (denA) and the cytochrome c-551 gene (denB) are located only 50 bp apart from each other in the Pseudomonas aeruginosa chromosome. We report evidence that these two genes are co-transcribed as an operon only under anaerobic (denitrifying) conditions. The nucleotide sequence of the promoter (regulatory) region of the operon is highly AT-rich and contains a sequence closely resembling the consensus FNR binding site in E. coli.

Close linkage in Pseudomonas stutzeri of the structural genes for respiratory nitrite reductase and nitrous oxide reductase, and other essential genes for denitrification

The structural gene, nirS, for the respiratory nitrite reductase (cytochrome cd1) from Pseudomonas stutzeri was identified by (i) sequencing of the N-terminus of the purified protein and partial sequencing of the cloned gene, (ii) immunoscreening of clones from a lambda gt11 expression library, (iii) mapping of the transposon Tn5 insertion site in the nirS mutant strain MK202, and (iv) complementation of strain MK202 with a plasmid carrying the insert from an immunopositive lambda clone. A mutation causing overproduction of cytochrome c552 mapped on the same 8.6 kb EcoRI fragment within 1.7 kb of the mutation affecting nirS. Two mutations affecting nirD, which cause the synthesis of an inactive cytochrome cd1 lacking heme d1, mapped 1.1 kb apart within a 10.5 kb EcoRI fragment contiguous with the fragment carrying nirS. Nir- mutants of another type that had low level synthesis of cytochrome cd1, had Tn5 insertions within an 11 kb EcoRI fragment unlinked to the nirS+ and nirD+ fragments. Cosmid mapping provided evidence that nirS and nirD, and the previously identified gene cluster for nitrous oxide respiration are closely linked. The nirS gene and the structural gene for nitrous oxide reductase, nosZ, are transcribed in the same direction and are separated by approximately 14 kb. Several genes for copper processing are located within the intervening region.

Involvement of the hydrophobic patch of azurin in the electron-transfer reactions with cytochrome C551 and nitrite reductase

The electron-transfer reactions of site-specific mutants of the blue copper protein azurin from Pseudomonas aeruginosa with its presumed physiological redox partners cytochrome c551 and nitrite reductase were investigated by temperature-jump and stopped-flow experiments. In the hydrophobic patch of azurin Met44 was replaced by Lys, and in the His35 patch His35 was replaced by Phe, Leu and Gln. Both patches were previously thought to be involved in electron transfer. 1H-NMR spectroscopy revealed only minor changes in the three-dimensional structure of the mutants compared to wild-type azurin. Observed changes in midpoint potentials could be attributed to electrostatic effects. The slow relaxation phase observed in temperature-jump experiments carried out on equilibrium mixtures of wild-type azurin and cytochrome c551 was definitively shown to be due to a conformational relaxation involving His35. Analysis of the kinetic data demonstrated the involvement of the hydrophobic but not the His35 patch of azurin in the electron transfer reactions with both cytochrome c551 and nitrite reductase.

Isolation and sequencing of the Alcaligenes denitrificans azurin-encoding gene: comparison with the genes encoding blue copper proteins from Pseudomonas aeruginosa and Alcaligenes faecalis

The gene (azu) encoding azurin from Alcaligenes denitrificans has been cloned and sequenced. The gene codes for a pre-protein with a 19-aa signal peptide. Comparison with the sequences coding for the blue copper proteins from Pseudomonas aeruginosa and Alcaligenes faecalis reveals the presence of ntrA and fnr boxes in front of all three genes, instead of a regular [-10, -35]-promoter. In P. aeruginosa, the azu gene is terminated by a bidirectional terminator and flanked by open reading frames on the opposite strand.

Cloning and sequencing of the gene encoding cytochrome c-551 from Pseudomonas aeruginosa

The cytochrome c-551 gene from Pseudomonas aeruginosa was cloned by using two oligonucleotide probes, which had been synthesized based on the known primary structure of the protein. The restriction map of the cloned DNA and sequence analysis showed that the cytochrome c-551 gene is located 50 bp downstream of the nitrite reductase gene, which has recently been cloned and sequenced. DNA sequence analysis also indicated that cytochrome c-551 is synthesized in vivo as a precursor having an amino-terminal signal sequence consisting of 22 amino acid residues.

The structural gene for cytochrome c551 from Pseudomonas aeruginosa. The nucleotide sequence shows a location downstream of the nitrite reductase gene

The gene coding for Pseudomonas aeruginosa cytochrome c551 has been cloned and its nucleotide sequence determined. Cytochrome c551 is expressed as a 104 amino acid pre-protein from which a signal peptide of 22 amino acids is cleaved off during the translocation across the cytoplasmic membrane. The gene is located just downstream of the gene coding for nitrite reductase on the Pseudomonas aeruginosa chromosome, suggesting that these genes form an operon.

The azurin gene from Pseudomonas aeruginosa. Cloning and characterization

We have cloned and sequenced the Pseudomonas aeruginosa azurin structural gene and its flanking regions. The DNA sequence predicts a pre-protein with a signal peptide of 19 amino acids followed by the 128-amino-acid mature azurin protein. Nuclease-S1 mapping and primer elongation experiments indicated two 5' termini of the azurin transcript. The major transcript of the azurin gene is initiated around 35 base pairs upstream from the translational start. The minor transcript, with a promoter region sharing homology with a consensus nif promoter of Klebsiella pneumoniae and also with other Pseudomonas genes, is initiated 145 base pairs upstreams of the azurin initiation codon. Downstream from the azurin structural gene a sequence similar to a transcriptional terminator is found. Northern blot analysis indicated two sizes of the azurin mRNA (0.54 kb and 0.65 kb) confirming the S1 mapping and the predictions from the nucleotide sequence.

A spectrophotometric assay for dissimilatory nitrite reductases

A spectrophotometric assay for dissimilatory nitrite reductases has been developed utilizing mammalian cytochrome c (equine heart) as reductant and spectrophotometric agent. The copper-containing nitrite reductase from Achromobacter cycloclastes has been shown to have apparent Km's for reduced cytochrome c and nitrite of 86 +/- 5 and 5.63 +/- 0.03 microM, respectively. The heme cd-containing enzyme from Pseudomonas stutzeri was shown to have apparent Km's for reduced cytochrome c and nitrite of 260 +/- 60 and 1.8 +/- 0.8 microM, respectively. This assay represents a simple, general method for consistently evaluating the activity of the copper- and heme cd-containing nitrite reductases that are capable of utilizing readily available mammalian cytochrome c as electron donor and should be useful for mechanistic studies of these enzymes.

Defects in cytochrome cd1-dependent nitrite respiration of transposon Tn5-induced mutants from Pseudomonas stutzeri

Mutants with defective respiratory nitrite utilization (Nir- phenotype) were obtained by transposon Tn5 insertion into genomic DNA of the ZoBell strain of Pseudomonas stutzeri. Three representative mutants were characterized with respect to their activities of nitrite and nitric oxide reduction, cytochrome cd1 content, and pattern of soluble c-type cytochromes. Mutant strain MK201 overproduced cytochrome c552 about fourfold by comparison with the wild type, but possessed an in vitro functional cytochrome cd1. Mutant strain MK202 lacked cytochrome cd1 and, simultaneously, had low amounts of cytochrome c552 and the split alpha-peak c-type cytochrome. Strain MK203 synthesized nitrite reductase defective in the heme d1 prosthetic group. Irrespective of these biochemically distinct Nir- phenotypes, all mutants preserved the nitric oxide-reducing capability of the wild type. The mutant characteristics demonstrate that cytochrome cd1 is essential for nitrite respiration of P. stutzeri and establish the presence of a nitric oxide-reducing system distinct from cytochrome cd1. They also indicate the functional or regulatory interdependence of c-type cytochromes.

The azurin gene from Pseudomonas aeruginosa codes for a pre-protein with a signal peptide. Cloning and sequencing of the azurin gene

The azurin gene from Pseudomonas aeruginosa is located on a 1.3 kb long PstI DNA fragment. Its nucleotide sequence has been determined. It appears that the gene codes for a pre-protein with a 19 amino acid long signal sequence which possibly assists in the transport of the azurin over the periplasmic membrane.

Isolation and characterization of a blue copper protein from Thiobacillus versutus

The blue copper protein induced during growth of Thiobacillus versutus on methylamine was purified and characterized. It is an acidic protein (isoelectric point 4.7), contains one Cu2+ ion/enzyme molecule, is a monomeric protein (molecular mass about 14 kDa), has a maximum in its absorption spectrum at 596 nm (molar absorption coefficient 3.9 X 10(3) M-1 cm-1), shows an axial type-I electron paramagnetic resonance spectrum (g parallel = 2.239, g perpendicular = 2.046 and A parallel = 5.6 mT) and has a redox potential (Eo) of + 260 mV. In view of these properties and in view of the fact that the protein is active as an electron carrier between methylamine dehydrogenase and cytochrome c, it is concluded that it is similar to the amicyanins isolated from Methylomonas sp. strain J and Pseudomonas sp. strain AM 1.

Stoichiometry of nitrite reduction catalyzed by Pseudomonas aeruginosa nitrite-reductase

The stoichiometry of the reduction of nitrite catalyzed by Pseudomonas aeruginosa nitrite-reductase (cytochrome cd1) has been shown to yield nitrous oxide as the final product. Gas chromatography experiments demonstrated that nitric oxide is also formed as a free intermediate. A sequential formation of NO and N2O is discussed as opposed to the parallel formation of the two products.