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PubMed1993

Inhibitory effects of tannins on NADH dehydrogenases of various organisms.

We examined the effects of purified tannins and related compounds (33 species) on NADH-ubiquinone-1 oxidoreductase activity in four kinds of organism (Paracoccus denitrificans, Bacillus subtilis, Photobacterium phosphoreum, and Thermus thermophilus HB-8) and rat liver mitochondria. In addition to pentagalloylglucose, which was reported as a potent inhibitor of NADH dehydrogenases (NDH), sanguiin H-11, oolonghomobisflavan A, and polymerized procyanidin are potent inhibitors for both types of NDH (NDH-1 and NDH-2). We found that some other tannins contained in tea are also inhibitors of NDH from all organisms.

Animals↗

PubMed2004

A Brownian dynamics study: the effect of a membrane environment on an electron transfer system.

During the past few years, three-dimensional crystal structures of many of the important integral membrane proteins responsible for the bioenergetic processes of photosynthesis and respiration have been determined. Moreover, a few crystal structures of protein-protein complexes have become available that characterize the interaction between those membrane proteins and the electron carrier protein cytochrome c. Here, we address the association kinetics for binding of cytochrome c to cytochrome c oxidase (COX) from Paracoccus denitrificans by Brownian dynamics simulations. The effects of ionic strength and protein mutations were studied for two different cytochrome c species: the positively charged, dipolar horse heart cytochrome c and the negatively charged physiological electron transfer partner cytochrome c(552). We studied association toward "naked" COX and toward membrane-embedded COX where the membrane is represented as an uncharged DPPC bilayer modeled in atomistic detail. For the nonnatural association toward "naked" COX, the association rates are >100 times larger for horse heart cytochrome c than for cytochrome c(552). Interestingly, the presence of the lipid bilayer leads to a dramatic decrease of the association rate of horse heart cytochrome c, but slightly enhances association of cytochrome c(552), leading to very similar association rates of both proteins to membrane-embedded COX. This finding from computational modeling studies may reflect the optimization of surface patches and of the total net charge on electron transfer pairs in nature.

Animals↗

PubMedDate not supplied

[Microbial decomposition of 3,4-dichloroaniline, adsorbed by activated charcoal].

The accessibility of 3,4-dichloroaniline (DCA) sorbed by activated carbon to degradative microorganisms was studied. A Paracoccus denitrificans strain capable of growing on medium with DCA as the only source of energy, carbon, and nitrogen was used in the experiment. The high sorption capacity of all the carbons studied (powdered RS and SKT-6A and granular AG-3) in relation to DCA (350 to 360, 480 to 520, and 540 to 580 mg/g, respectively) was demonstrated. The sorption capacity correlated positively with the specific surface area and the total volume of the sorbent micropores. The bulk of the DCA was reversibly sorbed and amenable to microbial decomposition; however, the decomposition rates significantly differed. When RS, SKT, and Agrosorb preliminarily saturated with DCA were incubated in a culture of P. denitrificans, the bulk of the reversibly sorbed DCA was decomposed (in the absence of the other carbon sources) in 2, 5, and 10 weeks, respectively, after which the process slowed down. At the end of the experiment (29 weeks), 81 to 87% of the DCA underwent full mineralization, which was accompanied by the release of chlorine ions; a small fraction of the xenobiotic (0.8 to 1.9%) remained a reversibly sorbed fraction (extractable with acetone), and 12 to 17% of the initial DCA seemed to have been chemically transformed and bound by carbon. The studied carbons may be used in biological decontamination of chloroaniline-polluted soils to decrease the toxic effect of chloroanilines on microorganisms.

Adsorption↗

PubMed2000

Mitochondria recycle nitrite back to the bioregulator nitric monoxide.

Nitric monoxide (NO) exerts a great variety of physiological functions. L-Arginine supplies amino groups which are transformed to NO in various NO-synthase-active isoenzyme complexes. NO-synthesis is stimulated under various conditions increasing the tissue of stable NO-metabolites. The major oxidation product found is nitrite. Elevated nitrite levels were reported to exist in a variety of diseases including HIV, reperfusion injury and hypovolemic shock. Denitrifying bacteria such as Paracoccus denitrificans have a membrane bound set of cytochromes (cyt cd1, cyt bc) which were shown to be involved in nitrite reduction activities. Mammalian mitochondria have similar cytochromes which form part of the respiratory chain. Like in bacteria quinols are used as reductants of these types of cytochromes. The observation of one-e- divergence from this redox-couple to external dioxygen made us to study whether this site of the respiratory chain may also recycle nitrite back to its bioactive form NO. Thus, the aim of the present study was therefore to confirm the existence of a reductive pathway which reestablishes the existence of the bioregulator NO from its main metabolite NO2-. Our results show that respiring mitochondria readily reduce added nitrite to NO which was made visible by nitrosylation of deoxyhemoglobin. The adduct gives characteristic triplet-ESR-signals. Using inhibitors of the respiratory chain for chemical sequestration of respiratory segments we were able to identify the site where nitrite is reduced. The results confirm the ubiquinone/cyt be1 couple as the reductant site where nitrite is recycled. The high affinity of NO to the heme-iron of cytochrome oxidase will result in an impairment of mitochondrial energy-production. "Nitrite tolerance" of angina pectoris patients using NO-donors may be explained in that way.

Animals↗

PubMed1977

Multiple low spin forms of the cytochrome c ferrihemochrome. EPR spectra of various eukaryotic and prokaryotic cytochromes c.

1. Despite the same methionine-sulfur:heme-iron:imidazole-nitrogen hemochrome structure observed by x-ray crystallography in four of the seven c-type eukaryotic and prokaryotic cytochromes examined, and the occurrence of the characteristic 695 nm absorption band correlated with the presence of a methionine-sulfur:heme-iron axial ligand in all seven proteins, they fall into two distinct classes on the basis of their EPR and optical spectra. The horse, tuna, and bakers' yeast iso-1 cytochromes c have a predominant neutral pH EPR form with g1=3.06, g2=2.26, and g3=1.25, while the bakers' yeast iso-2 and Euglena cytochromes c, the Rhodospirillum rubrum cytochrome c2, and the Paracoccus denitrificans cytochrome c550 all have a predominant neutral pH EPR form with g1=3.2, g2=2.05, and g3=1.39. The ferricytochromes with g1=3.06 have a B-Q splitting that is approximately 150 cm-1 larger than the ferricytochromes with g1=3.2. 2. Each of the cytochromes displays up to four low spin EPR forms that are in pH-dependent equilibrium and can all be observed at near neutral pH. As the pH is raised the predominant neutral pH form is converted into two forms with g1=3.4 and g1=3.6, identified by comparsion with model compounds and other heme proteins as epsilon-amino:heme-iron:imidazole and bis-epsilon-amino:heme-iron ferrihemochromes, respectively. 3. The pK for the conversion of the predominant neutral pH EPR form into the alkaline pH forms is the same as the pK for the disappearance of the 695 nm absorption band for the cytochromes, even though these pK values range over 2 pH units. This confirms that the g1=3.06 and g1=3.2 forms contain the methionine-sulfur:heme-iron axial ligand while the g1=3.4 and the g1=3.6 forms do not. 4. At extremes of pH, the horse and bakers' yeast iso-1 proteins display several high and low spin forms that are identified, showing that a variety of protein-derived ligands will coordinate to the heme iron including methionine and cysteine sulfur, histidine imidazole, and lysine epsilon-amine. 5. The spectrum of horse cytochrome c with added azide, cyanide, hydroxide, or imidazole as axial ligands has also been examined. 6. From a comparison of the EPR and optical spectral characteristics of these groups of cytochromes with model compounds, it is suggested that the difference between them is due to a change in the hydrogen bonding or perhaps even in the protonation of N-1 of the heme iron-bound histidine imidazole.

Animals↗

PubMed2003

Effects of SRT and DO on N2O reductase activity in an anoxic-oxic activated sludge system.

Nitrous oxide (N2O) is emitted from wastewater treatment processes, and is known to be a green house gas contributing to global warming. It is thus important to develop technology that can suppress N2O emission. The effects of sludge retention time (SRT) and dissolved oxygen (DO) on N2O emission in an anoxic-oxic activated sludge system were estimated. Moreover, the microbial community structure in the sludge, which plays an important role in N2O suppression, was clarified based on nitrous oxide reductase (nosZ) gene analysis by molecular biological techniques. The results showed that under low SRT conditions, nitrification efficiency was reduced and the N2O emission rate in the oxic reactors was increased. It was also observed that N2O emission was enhanced under low DO conditions, where the available oxygen is insufficient for nitrification. Moreover, molecular analysis revealed that the clones identified in this study were closely related to Ralstonia eutropha and Paracoccus denitrificans. The fact that the identified sequences are not closely related to known culturable denitrifier nosZ sequences indicates a substantial in situ diversity of denitrifiers contributing to N2O suppression, which are not reflected in the cultivatable fraction of the population. The further application of these new molecular techniques should serve to enhance our knowledge of the microbial community of denitrifying bacteria contributing to N2O suppression in wastewater treatment systems.

Air Pollution↗

PubMed2004

Comparison of aerobic denitrifying activity among three cultural species with various carbon sources.

Abilities of three aerobic denitrifiers such as Alcaligenes faecalis, Microvirgula aerodenitrificans and Paracoccus pantotrophus were compared from the viewpoints of nitrate removal efficiency and organic matter utilization. First, the effect of carbon source was investigated. Although nitrate reduction was observed in all strains under aerobic conditions, a change of carbon source considerably affected the denitrification ability. In the case of P. pantotrophus, nitrate and nitrite were completely removed in three days under sodium acetate or leucine as a carbon source. In the case of A. faecalis, sufficient nitrate removal was observed only when sodium acetate or ethanol was added. P. pantotrophus and A. faecalis showed a higher ability of nitrate removal than that of M. aerodenitrificans. Therefore, P. pantotrophus was selected in order to investigate the effects of concentration and repetitive addition of carbon. Sodium acetate was used as a sole carbon source. Nitrate was not reduced when the carbon concentration was below 500 mgC/L. However, when carbon source was added repeatedly, nitrate was reduced under 100 mgC/L after the optical density of the bacterium reached above 1.0. This result indicated that a high enough level of bacterial density was necessary to express aerobic denitrification activity.

Aerobiosis↗

PubMedDate not supplied

[Biotransformation of organic substances by an immobilized associative bacterial culture].

Bacterial strains were screened to transform to end-products (carbon monoxide and water) elevated concentrations of acetone, acidic acid, and ethanol in a biocatalyst with an immobilized bacterial association cultivated on solid foam polyvinyl acetate (FPVA). The innocuous association amalgamated Paracoccus denitrificans VKM V-1324, Pseudomonas esterophilus VKM V-1736D and Achromobacter parvulus VKM V-1541D. The biocatalyst was tested with the help of classic methods and equipment for microbes cultivation. Microbial growth was assessed in the optical density units. Comparative evaluation of the biocatalytic activity was performed on gas-chromatographer Pue Unicam-104. Based on test results, specific rates of oxidation of acidic acid, ethanol and acetone per one g of FPVA were 0.75, 0.72, and 0.67 mg/hr, respectively.

Acetic Acid↗

PubMedDate not supplied

[Methanotrophs and methylobacteria are found in woody plant tissues within a winter period].

Samples of tree seeds, buds, and needles collected within a winter period at ambient temperatures from -11 to -17 degrees C were analyzed for the presence of methylotrophic microflora. Thin sections of blue spruce needles were found to contain bacteria morphologically close to pink-pigmented methylobacteria. The methylobacteria that were isolated in pure cultures from samples of linden seeds and buds, pine and blue spruce needles, as well as of lilac, maple, and apple buds, were classified into the genera Methylobacterium and Paracoccus based on the data of morphological studies, enzyme assay, and DNA-DNA hybridization analysis. The methanotrophs that were isolated in pure cultures from samples of linden buds and blue spruce needles were identified into the genus Methylocystis based on the data of morphological studies, enzyme assay, DNA-DNA hybridization, and the phylogenetic analysis of the particulate methane monooxygenase gene pmoA sequences. The inference is made that aerobic methylotrophic bacteria are permanently associated with plants. At the beginning of the vegetative period in spring, the phyllosphere of coniferous and deciduous trees is colonized by the methylotrophic bacteria that have wintered inside plant tissues.

DNA Primers↗

PubMedDate not supplied

[Removal of harmful admixtures from a surrogate atmospheric condensate of a closed habitat with the help of a cultivated bacterial association].

Tested was an idea to eliminate six harmful admixtures reside in a surrogate of atmospheric condensate of closed habitats by a cultivated bacterial association. The purpose was to select members of the bacterial associations that would assimilate acetone, acetic acid, ethanol, ethyl acetate, methylamine and ammonia as free, so immobilized on insoluble cellular polyvinylformal. The resulted association of three bacterial species showed the ability to transform into end products a six-component surrogate of atmospheric condensate. Methylopila capsulata VKM V-1606 metabolized methylamine, Paracoccus denitrificans VKM V-1324--acetone. Pseudomonas esterophilus VKM V-1736 D was found to act as an ethyl acetate destructor decomposing the admixture to ethanol and acidic acid which were oxidized also by this species to carbon dioxide and water. Each of these bacterial strains in the test association metabolized ammonia as a source of nitric nutrition.

Acetaldehyde↗

PubMed1990

The sequence of the cyo operon indicates substantial structural similarities between the cytochrome o ubiquinol oxidase of Escherichia coli and the aa3-type family of cytochrome c oxidases.

The cytochrome o complex is one of two ubiquinol oxidases in the aerobic respiratory system of Escherichia coli. This enzyme catalyzes the two-electron oxidation of ubiquinol-8 which is located in the cytoplasmic membrane, and the four-electron reduction of molecular oxygen to water. The purified oxidase contains at least four subunits by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis and has been shown to couple electron flux to the generation of a proton motive force across the membrane. In this paper, the DNA sequence of the cyo operon, containing the structural genes for the oxidase, is reported. This operon is shown to encode five open reading frames, cyoABCDE. The gene products of three of these, cyoA, cyoB, and cyoC, are clearly related to subunits II, I, and III, respectively, of the eukaryotic and prokaryotic aa3-type cytochrome c oxidases. This family of cytochrome c oxidases contain heme a and copper as prosthetic groups, whereas the E. coli enzyme contains heme b (protoheme IX) and copper. The most striking sequence similarities relate the large subunits (I) of both the E. coli quinol oxidase and the cytochrome c oxidases. It is likely that the sequence similarities reflect a common molecular architecture of the two heme binding sites and of a copper binding site in these enzymes. In addition, the cyoE open reading frame is closely related to a gene denoted ORF1 from Paracoccus dentrificans which is located in between the genes encoding subunits II and III of the cytochrome c oxidase of this organism. The function of the ORF1 gene product is not known. These sequence relationships define a superfamily of membrane-bound respiratory oxidases which share structural features but which have different functions. The E. coli cytochrome o complex oxidizes ubiquinol but has no ability to catalyze the oxidation of reduced cytochrome c. Nevertheless, it is clear that the E. coli oxidase and the aa3-type cytochrome c oxidases must have very similar structures, at least in the vicinity of the catalytic centers, and they are very likely to have similar mechanisms for bioenergetic coupling (proton pumping).

Amino Acid Sequence↗

PubMed1990

Steady-state nitric oxide concentrations during denitrification.

Three species of denitrifying bacteria, Paracoccus denitrificans, Pseudomonas stutzeri strain JM300, and Achromobacter cycloclastes, were allowed to reduce nitrate or nitrite in anaerobic, closed vials while the equilibration of gases between aqueous and gas phases was facilitated by vigorous stirring. The gas phase was sampled and analyzed for NO with use of a chemiluminescence detector calibrated against bottled NO standards or against NO produced by the nitrite-iodide reaction. [NOaq] was inferred from [NOg] and the solubility of NO. NO was detected only during denitrification in amounts that, once established, did not change with time, were independent of the initial concentration of nitrate or nitrite, and were largely independent of cell concentration, at least when nitrate was the oxidant. The usual level of NO was promptly re-established following the addition of exogenous NO or following the loss of NO by sparging. The aforementioned properties are expected for a steady-state intermediate in denitrification. Steady-state [NOaq] ranged between 1 and 65 nM depending on species and conditions. Similar results were also obtained in a related experiment in which P. stutzeri strain ZoBell respired nitrite under growth conditions. The very low steady-state [NOaq] observed during denitrification imply that the maximum activity of nitric oxide reductase in vivo, if it could be realized, would be large relative to that for nitrite reductase. This circumstance allows NO to be an intermediate without reaching toxic steady-state levels.

Alcaligenes↗

PubMed1985

Denitrification of high concentrations of nitrites and nitrates in synthetic medium with different sources of organic carbon. III. Methanol.

The denitrification of nitrites and nitrates (1000 mg N/l) in medium containing methanol as a source of organic carbon was studied. Continuous cultures of mixed population of autochtonic microflora from bottom sludge of nitrogenous wastewater reservoir were set up in a chemostat-type column and packed bed reactor. The efficiency of denitrification of nitrates in packed bed reactor was 506.7 mg N/l/h whereas denitrification of nitrites was from 8.7 to 16.0 mg N/l/h depending on the granulation of the filing material. In the latter case 83% nitrogen was removed from the medium. One of the factors causing low efficiency of denitrification of nitrites is excessive alkalization of the medium in the bed. The use of a three-step bed with adjusted pH resulted in complete denitrification of nitrites with efficiency 60 mg N/l/h. The bacteria inside the bed were dominated by Paracoccus denitrificans and by Pseudomonas aeruginosa when nitrates were present. The sensitivity of P. denitrificans to high concentrations of nitrites seems to be the second factor contributing to low efficiency of denitrification with methanol as organic substrate.

Culture Media↗

PubMed1988

Evolution of cytochrome c oxidase.

The current view on the regulatory function of nuclear-encoded subunits of cytochrome c oxidase from higher evolved organisms is presented. The activity of monomeric laurylmaltoside-dissolved, but not of reconstituted cytochrome c oxidase, is strongly affected by anions accompanied by a conformational change of the enzyme, as shown by changed visible spectra. Addition of uncoupler to proteoliposomes induces the same anion sensitivity as obtained with the soluble enzyme, suggesting dissociation of the dimeric membrane-bound enzyme by uncoupler. Nucleotides are suggested to regulate cytochrome c oxidase activity at 3 different sites: 1) Interaction of ATP with a cytosolic site (outside) increases the Km for cytochrome c in the enzyme from bovine heart and Paracoccus denitrificans; 2) binding of ADP at a matrix site decreases, and 3) binding of ATP at another matrix site increases the Km for cytochrome c of the mammalian enzyme.

Amino Acid Sequence↗

PubMed1985

On the structure of heme d1. An isobacteriochlorin derivative as the prosthetic group of dissimilatory nitrite reductase?

Timkovich and co-workers have recently proposed a chlorin macrocycle structure for the heme d1 prosthetic group isolated from cytochrome cd1 of Pseudomonas aeruginosa and Paracoccus denitrificans (Timkovich, R., Cork, M. S., and Taylor, P. V. (1984) J. Biol. Chem. 259, 1577-1585; 15089-15093). However, this chlorin structure deduced by them is not entirely consistent with the spectral data. An alternative structure is proposed here based on the available spectral evidence. It is suggested that heme d1 in vivo is not a chlorin, but a dioxo-isobacteriochlorin having two adjacent pyrrole rings saturated.

Cytochrome c Group↗

PubMed1984

Bacterial microflora participating in the removal of nitrogen from industrial wastewaters by nitrification and denitrifaction.

Nitrification and denitrification were used to purify industrial nitrogenous-organic wastewaters containing 1,130 mg N/l (mainly in the form of ammonium and urea) and with mean COD 1,050 mg O2/l. The use of a five-step system consisting of two denitrifying beds and three nitrifying activated sludge reactors gave 99% removal of nitrogen and 54% reduction in COD during total retention time of the wastes of 81 hours. The participation of stage I nitrifying bacteria in the activated sludge was 4.4 to 5.8% and of stage II nitrifying bacteria 21.9 to 53.8%. Denitrifying bacteria in the denitrifying beds accounted for 90% of the isolated population, which was dominated by Alcaligenes faecalis and Paracoccus denitrificans.

Alcaligenes↗

PubMed1984

Proposed structure for the noncovalently associated heme prosthetic group of dissimilatory nitrite reductases. Identification of substituents.

The substituents of the noncovalently associated heme prosthetic group of the bacterial nitrite reductase-cytochrome oxidase (EC 1.9.6.1 or EC 1.9.3.2.) from Pseudomonas aeruginosa (ATCC 19429) and Paracoccus denitrificans (ATCC 13456) have been identified. This was accomplished by 1H NMR, infrared, visible, and mass spectroscopic techniques applied to semi-purified heme and purified methyl ester derivatives of the iron-free porphyrin. The main structural features are as follows. 1) The macrocycle is a reduced porphyrin of the chlorin type, that is, one of the pyrrole rings has been saturated so that the beta-carbons have sp3-hybridization. 2) The chlorin is a tetracarboxylic acid. 3) The substituents of the saturated pyrrole ring are two methyl groups and two hydroxymethyl groups. 4) The substituents of the unsaturated pyrrole rings are: (i) two methyl groups (ii) a propionic acid (iii) an acrylic acid, and (iv) two directly bonded formic acid groups. No firm evidence has been obtained for the relative positions of these unsaturated beta-pyrrolic substituents around the macrocyclic ring, but a proposed structure will be discussed. Several previously inexplicable chemical properties of the heme in extracts or in the intact enzyme can be now interpreted in view of the proposed structure. The trivial name "acrylochlorin" is suggested for the macrocycle.

Heme↗

PubMed1980

First practical assay for soluble nitrous oxide reductase of denitrifying bacteria and a partial kinetic characterization.

Lysis of spheroplasts made from denitrification-adapted Paracoccus denitrificans released a soluble nitrous oxide reductase which was assayed spectrophotometrically under anaerobic conditions by following the oxidation of methyl or benzyl viologen cation radical upon reduction of N2O to N2. Other classes of reductants so far tested, including dithionite, could not substitute for viologen dyes. Viologen dyes, therefore, afford the first practical assay for this previously elusive enzyme of denitrifying bacteria. The assay is specifically an in vitro assay, because the dyes cannot couple with intracellular nitrous oxide reductase. The enzyme exhibited simple saturation kinetics with respect to both N2O and reduced viologen dye. The Km for N2O was about 5 microM at 22 degrees C and pH 7.1 and the apparent Km for reduced benzyl and methyl viologen was 0.9 and 0.5 microM, respectively. Both dyes afforded the same Vmax value. Oxidized viologen dyes were not inhibiting to 1 mM nor was N2 to 1 atm. In fresh lysates, Vmax was about 1.2 mumol of N2O X min-1 x mg of protein-1 or about twice that for intact cells or spheroplasts utilizing yeast extract or lactate. Enzyme activity was observed to be labile in crude preparations under anaerobic conditions. Nitrous oxide reductase was inhibited by acetylene, CO, azide, and cyanide with Ki values of 28, 3.5, 0.35, and 0.045 microM, respectively. All showed noncompetitive inhibition with respect to N2O.

Kinetics↗