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PubMed1992

Comparison of dentrification by Paracoccus denitrificans, Pseudomonas stutzeri and Pseudomonas aeruginosa.

The course of denitrification of nitrate, nitrite and both compounds together by static cultures of Paracoccus denitrificans, Pseudomonas stutzeri and Pseudomonas aeruginosa was studied. These strains represent three different types of denitrification: 1. reduction of nitrate to gaseous nitrogen without accumulation of nitrite (P. denitrificans); 2. partial accumulation of nitrite in growing cultures during reduction of nitrate to gaseous nitrogen (P. aeruginosa) and 3. two-phase denitrification that includes reduction of nitrates at the very beginning of the process, and then, after depletion of the former, the reduction of nitrates to gaseous nitrogen (P. stutzeri). These observations differ from the results reported in the literature and possible reasons are discussed.

Nitrates↗

PubMed1992

Relationship between cardiolipin content and cytochrome c oxidase activity of cytochrome aa3 in Paracoccus denitrificans.

Using cultivation at different oxygen tensions, the molar ratio of cardiolipin to haem a in cells of Paracoccus denitrificans was varied systematically from 30 to 300. The molecular activity of cytochrome aa3 (with N, N, N', N'-tetramethyl-p-phenylenediamine as substrate) remained unchanged in this interval, this ruling out any regulatory effect of physiological cardiolipin levels on the terminal oxidase. Titration of anaerobically grown cells with cyanide indicated the presence of cytochrome aa3 which accounted for about 1/4 of the total electron flow from TMPD to oxygen.

Aerobiosis↗

PubMed1992

Coordinate expression of the enzymes of nitric oxide metabolism in Paracoccus denitrificans.

Cellular activities of nitric oxide producing nitrite reductase (NiR) and nitric oxide reductase (NOR) in Paracoccus denitrificans increased in parallel upon anaerobic adaptation of aerobically grown cells. In addition, both activities exhibited comparable dependences on oxygen supply into the growing culture. The results suggest that the maintenance of a sufficiently high NOR/NiR activity ratio plays an important role in preventing nitric oxide accumulation and its toxic effects on the cells during denitrification.

Anaerobiosis↗

PubMed1991

Nitric oxide reductase. Purification from Paracoccus denitrificans with use of a single column and some characteristics.

Nitric oxide reductase was purified from Paracoccus denitrificans very nearly to homogeneity by a simple method that involved the use of octyl glucoside to solubilize the enzyme from membranes and required a single hydroxyapatite column. The enzyme had specific activities of about 10 mumol NO reduced x min-1 x mg-1 at pH 6.5 in an amperometric assay system using phenazine methosulfate/ascorbate as the reducing agent and about 22 mumol NO reduced x min-1 x mg-1 at pH 5.0, which is the optimum pH. These values are based on average rates over kinetically complex progress curves and would be about three times greater if based on maximum rate values. The enzyme appeared to be reversibly inhibited by NOaq and to have a Km too low (probably less than or equal to 1 microM) to measure reliably by the amperometric method. The effective second-order rate constant of the enzyme lay within 1 to 2 orders of magnitude of the diffusion controlled limit. The enzyme was composed of a tight complex of two cytochromes: a cytochrome c (Mr = 17,500) and a cytochrome b (Mr = 38,000). The mole ratios of cytochrome c to cytochrome b and Mr 17,500 peptide to Mr 38,000 peptide were both about 1.7, and the heme content was about 3 mol/73,000 g (38,000 + 2(17,500)). Each subunit therefore contained only one heme group. The Mr 38,000 peptide aggregated when heated in the sample buffer used for sodium dodecyl sulfate-polyacrylamide gel electrophoresis. In addition to the ascorbate-based activity, the enzyme showed a little NADH-NO oxidoreductase activity which was not inhibited by antimycin A. The enzyme lost activity with a half-life of about 2 days at 4 degrees C but could be preserved at -20 degrees C and in liquid nitrogen. It seemed not to be inactivated by aerobic solutions. These observations, and the recent ones by Carr and Ferguson (Carr, G.J., and Ferguson, S.J. (1990) Biochem. J. 269, 423-429) with a partially purified preparation of nitric oxide reductase, establish that the enzyme from Pa. denitrificans is a cytochrome bc complex which resembles that from Pseudomonas stutzeri (Heiss, B., Frunzke, K., and Zumft, W.G. (1989) J. Bacteriol. 171, 3288-3297). There would appear to be no functional relationship between nitric oxide reductase and a Mr = 34,000 peptide of Pa. denitrificans membranes reported previously to be present in purified preparations of a nitric oxide reductase (Hoglen, J., and Hollocher, T.C. (1989) J. Biol. Chem. 264, 7556-7563).

Amino Acids↗

PubMed1976

Amino acid sequence of Paracoccus denitrificans cytochrome c550.

The amino acid sequence of Paracoccus (formerly Micrococcus) denitrificans cytochrome c550 has been established by a combination of standard chemical techniques and interpretation of a 2.5 A resolution x-ray electron density map. Peptides derived from a trypsin digest were chemically sequenced, and then ordered by fitting them to the density map. The amino acid compositions of chymotryptic peptides confirmed the x-ray map ordering the tryptic peptides. The amino acid sequence of this respiratory, prokaryotic cytochrome with 134 residues is discussed in relation to those of eukaryotic respiratory cytochrome c (103 to 113 amino acids), and prokaryotic, photosynthetic c2 (103 to 124 amino acids). At the primary structure level, c and c550 differ no more from cytochromes c2 than the various cytochromes c2 do from one another. It is suggested that the respiratory electron transport chain in prokaryotes and eukaryotes is a relatively late evolutionary offshoot of the photosynthetic electron transport chain in purple non-sulfur bacteria.

Amino Acid Sequence↗

PubMed1991

Molecular cloning of the L-phenylalanine transaminase gene from Paracoccus denitrificans in Escherichia coli K-12.

The L-phenylalanine transaminase gene of Paracoccus denitrificans was cloned by a shotgun method using the Escherichia coli K-12 mutant DG30, which lacks three distinct transaminase genes. Plasmid pPAP142 was constructed by inserting a 2.2-kb fragment carrying the transaminase gene into pUC18. Strain E. coli K-12 HB101 cells harboring the plasmid produced 20-fold to 30-fold more transaminase than wild type P. denitrificans cells. The nucleotide sequence of the 2.2-kb fragment was determined, revealing that the deduced amino acid sequence of the transaminase of P. denitrificans is similar to that of other transaminases.

Amino Acid Sequence↗

PubMed1990

COX10 codes for a protein homologous to the ORF1 product of Paracoccus denitrificans and is required for the synthesis of yeast cytochrome oxidase.

Respiratory-defective mutants of Saccharomyces cerevisiae assigned to pet complementation group G19 lack cytochrome oxidase activity and cytochromes a and a3. The enzyme deficiency is caused by recessive mutations in the nuclear gene COX10. Analyses of cytochrome oxidase subunits suggest that the product of COX10 provides an essential function at a posttranslational stage of enzyme assembly. The wild type COX10 gene has been cloned by transformation of a mutant from complementation group G19 with a yeast genomic library. Based on the nucleotide sequence of COX10, the primary translation product has an Mr of 52,000. The amino-terminal 190 residues constitute a hydrophilic domain while the carboxyl-terminal region is hydrophobic and has nine potential membrane-spanning segments. The sequence of the carboxyl-terminal hydrophobic region is homologous to an unidentified protein encoded by a reading frame (ORF1) located in one of the cytochrome oxidase operons of Paracoccus denitrificans. The two proteins share 24% identical residues and exhibit very similar hydrophobicity profiles. The bacterial homolog, however, lacks the hydrophilic amino-terminal region of the yeast protein.

Amino Acid Sequence↗

PubMed1989

Inhibition of bovine heart mitochondrial and Paracoccus denitrificans NADH----ubiquinone reductase by dequalinium chloride and three structurally related quinolinium compounds.

1. Dequalinium chloride (DECA) and three related quinolinium compounds inhibit bovine heart mitochondrial and Paracoccus denitrificans electron transport activity, with inhibition localized between NADH and ubiquinone in both electron transport chains. 2. Structure-activity studies reveal that two quinolinium rings and a long bridging group are necessary for significant inhibition of reduction of artificial electron acceptors and coenzyme Q, whereas only one quinolinium ring and a long hydrocarbon side chain are required for significant inhibition of NADH oxidase activity. 3. Inhibition of coenzyme Q reduction by DECA is not reversed by dialysis. 4. Studies comparing DECA inhibition of rotenone-sensitive with rotenone-insensitive preparations indicate that DECA acts by a different inhibitory mechanism than rotenone on mammalian mitochondrial and P. denitrificans NADH----ubiquinone reductase.

Animals↗

PubMed1989

Purification and some characteristics of nitric oxide reductase-containing vesicles from Paracoccus denitrificans.

Nitric oxide reductase of Paracoccus denitrificans was purified, with the use of 3-[(3-cholamidopropyl)dimethylammonio]-2-hydroxy-1-propanesulfonate (CHAPSO) detergent, as membrane vesicles of apparent Mr = 2-3 x 10(6). Fifty percent of the protein was a peptide of Mr = 34,000. Further fractionation with sodium dodecyl sulfate (SDS) resulted in vesicles in which the peptide constituted 90-95% of the protein. This peptide, which is rich in Ala, Gly, Ser, Asx, and Glx, is considered to be the peptide of nitric oxide reductase. The CHAPSO- and SDS-fractionated preparations lost activity at 4 degrees C, pH 7.4, with half-times, respectively, of about 6 days and 4 h. Specific activities at 32 degrees C, pH 7.4, of about 0.33 mumol of NO x min-1 x mg-1 were realized after fractionation with CHAPSO in a phenazine methosulfate/ascorbate-based assay. The Km(NO) was less than or equal to 17 microM at pH 7.4. Rates decreased substantially below pH 5 and above pH 7.6. The preparations were free or almost free of cytochromes, exhibited otherwise no absorption bands in the visible region, contained no redox metals except for very small amounts of iron, were not inhibited by EDTA or some other common inhibitors of redox-metal enzymes, and were not observed to catalyze the reduction of nitrate, nitrite, or N2O. An absorption band at 274 nm in both the CHAPSO- and SDS-fractionated preparations was attributed to the presence of a solvent-soluble chromophore. N-Bromosuccinimide (NBS) inactivated the enzyme and bleached the chromophore both in the enzyme preparation and, after its purification, in 95% ethanol. NBS-inactivated enzyme could be reconstituted with purified chromophore, which alone seemed to have no nitric oxide reductase activity, but not with purified chromophore that had been reacted with NBS. Spectral changes interpretable as due to changes in redox state were not observed when enzyme was exposed to NO or certain reducing agents.

Amino Acids↗

PubMed1989

Some characteristics of a chromophoric lipid associated with nitric oxide reductase from Paracoccus denitrificans.

A lipid with a UV chromophore (lambda max = 274 nm) was purified in small amounts from nitric oxide reductase of Paracoccus denitrificans and determined to have a molecular weight of 686, a most probable formula of C43H78O4N2 and about two phenylhydrazine-reactive carbonyls. On the basis of 1H and 13C-NMR, IR and mass spectrometric studies, the chromophoric lipid was inferred to have something like bilateral symmetry and to contain ketone-like carbonyls, alkene centers and at least three alkyl or olefinic chains. Several likely substructures are discussed and an enaminoketone is considered as a model for the chromophore. Evidence was lacking for phosphate, an aromatic ring, a 1,4-quinone, polyunsaturated fatty acyl groups, isoprenyl/isopranyl chains and simple alkyl acids, esters, amides and ethers. The compound appears to have some novel features. On the basis of reconstitution studies, the chromophoric lipid may be essential for nitric oxide reductase activity.

Chemical Phenomena↗

PubMed1988

Resonance Raman spectroscopy of amicyanin, a blue copper protein from Paracoccus denitrificans.

The copper binding site of amicyanin from Paracoccus denitrificans has been examined by resonance Raman spectroscopy. The pattern of vibrational modes is clearly similar to those of the blue copper proteins azurin and plastocyanin. Intense resonance-enhanced peaks are observed at 377, 392, and 430 cm-1 as well as weaker overtones and combination bands in the high frequency region. Most of the peaks below 500 cm-1 shift 0.5-1.5 cm-1 to lower energy when the protein is exposed to D2O. Based on the pattern of conserved amino acids, the axial type EPR spectrum, and the resonance Raman spectrum, it is proposed that the copper binding site in amicyanin contains a Cu(II) ion in a distorted trigonal planar geometry with one cysteine and two histidine ligands and an axial methionine ligand at a considerably longer distance. Furthermore, the presence of multiple intense Raman peaks in the 400 cm-1 region which are sensitive to deuterium substitution leads to the conclusion that the Cu-S stretch is coupled with internal ligand vibrational modes and that the sulfur of the cysteine ligand is likely to be hydrogen-bonded to the polypeptide backbone.

Azurin↗

PubMed1985

Isolation of ubiquinol oxidase from Paracoccus denitrificans and resolution into cytochrome bc1 and cytochrome c-aa3 complexes.

An enzyme complex with ubiquinol-cytochrome c oxidoreductase, cytochrome c oxidase, and ubiquinol oxidase activities was purified from a detergent extract of the plasma membrane of aerobically grown Paracoccus denitrificans. This ubiquinol oxidase consists of seven polypeptides and contains two b cytochromes, cytochrome c1, cytochrome aa3, and a previously unreported c-type cytochrome. This c-type cytochrome has an apparent Mr of 22,000 and an alpha absorption maximum at 552 nm. Retention of this c cytochrome through purification presumably accounts for the independence of ubiquinol oxidase activity on added cytochrome c. Ubiquinol oxidase can be separated into a 3-subunit bc1 complex, a 3-subunit c-aa3 complex, and a 57-kDa polypeptide. This, together with detection of covalently bound heme and published molecular weights of cytochrome c1 and the subunits of cytochrome c oxidase, allows tentative identification of most of the subunits of ubiquinol oxidase with the prosthetic groups present. Ubiquinol oxidase contains cytochromes corresponding to those of the mitochondrial bc1 complex, cytochrome c oxidase complex, and a bound cytochrome c. Ubiquinol-cytochrome c oxidoreductase activity of the complex is inhibited by inhibitors of the mitochondrial bc1 complex. Thus it seems likely that the pathway of electron transfer through the bc1 complex of ubiquinol oxidase is similar to that through the mitochondrial bc1 complex. The number of polypeptides present is less than half the number in the corresponding mitochondrial complexes. This structural simplicity may make ubiquinol oxidase from P. denitrificans a useful system with which to study the mechanisms of electron transfer and energy transduction in the bc1 and cytochrome c oxidase sections of the respiratory chain.

Cell Membrane↗

PubMed1985

An inducible periplasmic blue copper protein from Paracoccus denitrificans. Purification, properties, and physiological role.

When grown on methylamine as a sole carbon source, Paracoccus denitrificans synthesizes a Type I blue copper protein which mediates electron transfer between methylamine dehydrogenase and cytochrome c. This blue copper protein does not serve as an electron acceptor for methanol dehydrogenase and is not synthesized by cells grown on methanol or succinate. The blue copper protein and methylamine dehydrogenase were localized in the periplasm of P. denitrificans, whereas formate dehydrogenase was cytoplasmic. The copper protein can be purified to high yield in a single step from the periplasmic subcellular fraction prepared from P. denitrificans. The purified protein contains a single 15,000-Da polypeptide chain and one copper atom/molecule and exhibits a pI of 4.8. The oxidized form of the protein absorbs strongly at 595 nm and weakly at 464 nm. The physical and physiological properties of this protein indicate that it is not an azurin, but representative of another class of blue copper proteins.

Bacterial Proteins↗

PubMed1986

Characterization of two inducible periplasmic c-type cytochromes from Paracoccus denitrificans.

When grown on methanol or methylamine, Paracoccus denitrificans synthesized three periplasmic soluble c-type cytochromes, cytochrome c550 and two additional cytochromes which were not present during growth on succinate and have not previously been characterized. These cytochromes have been separated from each other and their physical properties have been determined. The inducible cytochromes, c551i and c553i, exhibit Mr and pI values of 22,000 and 3.5, and 30,000 and 3.8, respectively. Cytochrome c553i binds CO. None of these cytochromes accepted electrons directly from methylamine dehydrogenase, but each accepted electrons from amicyanin, the electron acceptor for methylamine dehydrogenase. Cytochrome c551i was the most efficient electron acceptor for amicyanin, exhibiting a half-time of reaction at least 6 and 15 times faster than those observed for cytochromes c553i and c550, respectively.

Bacterial Proteins↗

PubMed1987

Purification and some characteristics of nitrous oxide reductase from Paracoccus denitrificans.

Nitrous oxide reductase from the denitrifying bacterium Paracoccus denitrificans has been purified very nearly to homogeneity by an anaerobic procedure that results in a product with high specific activity. The enzyme is a dimer of about Mr 144,000 composed of two subunits of apparently equal Mr and contains 4 mol of Cu per mol of subunit. The isoelectric point is 4.3; specific activity at 25 degrees C, pH 7.1, is 122 mumol X min-1 X mg of protein-1; and Km is about 7 microM N2O under the same conditions. The N2O- and O2-oxidized forms of the enzyme had principal absorption bands at 550 and 820 nm; the dithionite-reduced form, at 650 nm. The extinction coefficient at 550 nm for the oxidized enzyme is about 5300 (M subunit)-1 X cm-1. Ferricyanide-oxidized enzyme and enzyme exposed to O2 for a couple of days at 4 degrees C exhibited additional bands at 480, 620, and 780 nm and had very low specific activities. Cu-EPR signals were observed with oxidized and reduced forms of the enzyme with g perpendicular values at 2.042 and 2.055, respectively. The O2-oxidized enzyme had g parallel and A parallel values of about 2.244 and 35 gauss, respectively, based on the observation of four hyperfine lines in the g parallel region. The enzyme may therefore contain at least one Cu atom approximating the "Type 1" class. Spin counts against Cu-EDTA standards suggest that 20-30% of the enzyme-bound Cu is EPR detectable in the O2-oxidized enzyme and 7-15% in the enzyme as prepared and in the reduced enzyme. Much of the Cu thus appears to be EPR silent. Nitrous oxide reductase was observed to undergo turnover-dependent inactivation, and nitrite and fluoride among other anions were found to accelerate this process. In a number of characteristics, the enzyme resembles nitrous oxide reductase recently purified from Pseudomonas perfectomarina and Rhodopseudomonas sphaeroides, particularly the former. Some differences appear related to whether or not purification is carried out entirely under anaerobic conditions.

Amino Acids↗

PubMed1987

EPR characterization of the iron-sulfur clusters in the NADH: ubiquinone oxidoreductase segment of the respiratory chain in Paracoccus denitrificans.

The physicochemical properties of the iron-sulfur clusters present in the NADH:ubiquinone oxidoreductase of Paracoccus denitrificans have been examined in the cytoplasmic membrane particles by redox potentiometry and EPR spectroscopy. Analogous to the iron-sulfur clusters present in the mitochondrial NADH: ubiquinone oxidoreductase, we have found two binuclear and three tetranuclear EPR detectable iron-sulfur clusters, namely, N-1a, N-1b, N-2, N-3, and N-4. In the bacterial system, the two binuclear clusters differ in line shape and in Em values; the cluster with more rhombic symmetry (gx,y,z = 1.918, 1.937, 2.029) has the Em7.0 value of -150 while the almost axial one (gx,y,z = 1.929, 1.941, 2.019) has Em7.0 of -270 mV. The Em of the former cluster is pH dependent (-60 mV/pH) as in the case of mammalian N-1a while the latter is pH independent as is the mammalian cluster N-1b. The pH-dependent P. denitrificans [2Fe-2S] cluster, which we have labeled N-1a, has an Em7.0 as high as that of N-2, in contrast to the mammalian N-1a. Thus N-1a is reducible with a physiological reductant, NADH in this bacterial system. The Em of the cluster N-2 is also pH dependent (Em7.0 = -130 mV) with a pK value near 7.7. The Em values of all other clusters exhibit no pH dependence as in the case of their mammalian counterparts. We have found that the cluster N-1a is the most labile component among the five iron-sulfur clusters and may give rise to variable relative spin concentrations and extremely low Em values due to the facile modifications of the microenvironment of the cluster. The P. denitrificans NADH:ubiquinone oxidoreductase provides a unique and useful site I model system where redox composition is similar to the mitochondrial enzyme but with fewer numbers of polypeptides (Yagi, T. (1986) Arch. Biochem. Biophys. 250, 302-311).

Animals↗

PubMed1987

The respiratory chain and energy conservation in the mitochondrion-like bacterium Paracoccus denitrificans.

Paracoccus denitrificans has a flexible electron transport chain containing various inducible dehydrogenases, oxidases and reductases. The sequence of electron carriers and stoichiometry of energy transduction is well known, with the exception of all functional aspects of the different c-type cytochromes. The mitochondrion-like characteristics of the respiratory chain have stimulated much research at the molecular level, which should help to elucidate the structure-function relationship of the components of the different respiratory complexes isolated.

Adenosine Triphosphate↗

PubMed1988

Complex formation between methylamine dehydrogenase and amicyanin from Paracoccus denitrificans.

Two proteins isolated from Paracoccus denitrificans, the copper-containing electron carrier amicyanin and the pyrroloquinoline quinone-containing enzyme methylamine dehydrogenase, have been shown to form a complex. Complex formation between methylamine dehydrogenase and either oxidized or reduced amicyanin resulted in alterations in the absorbance spectrum of the pyrroloquinoline quinone prosthetic group of methylamine dehydrogenase. Binding of amicyanin to the enzyme exhibited positive cooperativity. Complex formation with methylamine dehydrogenase shifted the oxidation-reduction midpoint potential of amicyanin by 73 mV, from +294 to +221 mV, making electron transfer from amicyanin to cytochrome c551 (Em = +190 mV) thermodynamically possible.

Bacterial Proteins↗