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PubMed1985

Helix movements and the reconstruction of the haem pocket during the evolution of the cytochrome c family.

Analysis of cytochromes c (tuna), c2 (Rhodospirillum rubrum), c550 (Paracoccus denitrificans) and c551 (Pseudomonas aeruginosa) shows that they contain 48 residues identifiable as homologous from superposition of the structures. The other 34 to 64 residues are in loops that vary greatly in sequence, length and conformation, or in alpha-helices that are found in only some of the structures. Of the 48 homologous residues, 17 are in three segments which pack onto the haem faces. In all four structures, these segments have the same conformations, and the same locations relative to the haem. The other 31 residues are in three alpha-helices which are in contact with each other. These form the back and one side of the haem pocket. In cytochrome c551 the positions of the three alpha-helices have shifted and rotated, in comparison with cytochromes c and c2, by up to 5 A and 25 degrees relative to the haem. These shifts, facilitated by mutations at the helix-helix interfaces, are related to the reconstruction of the propionic acid side of the haem pocket described by Almassy & Dickerson (1978). Together these effects produce alternative structures for the haem pocket. This mechanism of adaptation to mutation contrasts with that observed in the globins. In the globins, mutations also produce changes in helix interfaces and shifts of packed helices, but in the globins these shifts are coupled to conserve the structure of the haem pocket.

Animals↗
PubMed1993

Characterization of a Trypanosoma brucei nuclear gene encoding a protein homologous to a subunit of bovine NADH:ubiquinone oxidoreductase (complex I).

A Trypanosoma brucei gene has been identified that encodes a protein predicted to be a component of the trypanosome homologue of mitochondrial NADH:ubiquinone oxidoreductase (complex I). High homology was found to a 20-kDa component of the iron-sulfur protein fraction of bovine mitochondrial NADH:ubiquinone oxidoreductase and the products of the ndhK locus of Paramecium tetraurelia mitochondria and the NQO6 locus of Paracoccus denitrificans. The homology extends to several other proteins predicted to function as part of electron transport systems, including the psbG/ndhK gene products of chloroplast and cyanobacterial genomes which are thought to be subunits of a NADH:plastoquinone oxidoreductase involved in chlororespiration. The T. brucei ndhK counterpart is nuclearly encoded. An extended amino terminus of the T. brucei ndhK with structural similarity to mitochondrial presequences indicates that its transfer into mitochondria is likely. Stumpy and slender bloodforms and procyclic forms all possess similar levels of ndhK transcripts despite previous reports of stage-regulated expression of complex I-like activity.

Amino Acid Sequence↗
PubMed1984

Denitrification and nitrite reduction: Pseudomonas aeruginosa nitrite-reductase.

Present knowledge of the different enzymatic steps of the denitrification chains in various bacteria, particularly Paracoccus denitrificans and Pseudomonas aeruginosa has been briefly reviewed. The question whether nitric oxide (NO), nitrous oxide (N2O) and other nitrogen derivatives are obligatory intermediates has been discussed. The second part is an extensive review of the structure and the function of a key enzyme in denitrification, cytochrome c551-nitrite-oxidoreductase from P. aeruginosa. Recent results on the stoichiometry of nitrite reduction have been discussed.

Amino Acids↗
PubMed1987

Interposon mutagenesis of soil and water bacteria: a family of DNA fragments designed for in vitro insertional mutagenesis of gram-negative bacteria.

We have constructed a series of derivatives of the omega interposon [Prentki and Krisch, Gene 29 (1984) 303-313] that can be used for in vitro insertional mutagenesis. Each of these DNA fragments carries a different antibiotic or Hg2+ resistance gene (ApR, CmR, TcR, KmR or HgR) which is flanked, in inverted orientation, by transcription and translation termination signals and by synthetic polylinkers. The DNA of these interposons can be easily purified and then inserted, by in vitro ligation, into a plasmid linearized either at random by DNase I or at specific sites by restriction enzymes. Plasmid molecules which contain an interposon insertion can be identified by expression of its drug resistance. The position of the interposon can be precisely mapped by the restriction sites in the flanking polylinker. To verify their properties we have used these omega derivatives to mutagenize a broad host range plasmid which contains the entire meta-cleavage pathway of the toluene degradation plasmid pWW0 of Pseudomonas putida. Insertion of these interposons in the plasmid between the promoter and the catechol 2,3-dioxygenase (C23O) gene dramatically reduced the expression of this enzyme in Escherichia coli. We also show that when a plasmid containing an omega interposon is transferred by conjugal mobilization from E. coli to P. putida, Agrobacterium tumefaciens, Erwinia chrysanthemi, Paracoccus denitrificans or Rhizobium leguminosarum, the appropriate interposon drug resistance is usually expressed and, compared to the non-mutated plasmid, much reduced levels of C23O activity are detected. Thus, the selection and/or characterization of omega insertional mutations can be carried out in these bacterial species.

DNA Restriction Enzymes↗
PubMed1988

A bacteriophage T4 expression cassette that functions efficiently in a wide range of gram-negative bacteria.

We have constructed a derivative of the broad-host-range vector RSF1010. This plasmid, p alpha omega, contains an expression cassette derived from bacteriophage T4 gene 32, into which we have inserted the coding sequence for the xylE enzyme (C2,3O) of the TOL plasmid pWWO. The composite plasmid, p alpha xylE omega, was transferred by conjugal mobilisation into a variety of Gram-negative bacteria (Agrobacter, Paracoccus, Erwinia, Pseudomonas, Rhizobium and Xanthomonas). High levels of C2,3O activity were found in almost all of the extracts. Polyacrylamide gel electrophoresis of these extracts revealed a prominent protein band at 35 kDa whose identity as the C2,3O gene product was confirmed by immunoblotting. We have mapped the 5' ends of the gene 32/xylE hybrid transcripts. In all of the Gram-negative bacteria, the proximal P2 promoter is the most efficient promoter in the cassette. In most of the strains a weaker and more distal promoter activity (Pl) was also detected. In both uninfected and phage-infected Escherichia coli cells, the transcript produced from this promoter is processed at a specific site upstream from the gene 32 start codon. The same processing occurred in all the bacterial species examined. The decay of the hybrid xylE transcript has been analyzed in E. coli and Erwinia, and in both strains this mRNA was among the most stable.

Cloning, Molecular↗
PubMed1989

Omegon-Km: a transposable element designed for in vivo insertional mutagenesis and cloning of genes in gram-negative bacteria.

To combine the features of the omega interposons with the advantages of in vivo transposition mutagenesis, we have constructed an artificial transposon, called Omegon-Km. The Omegon-Km transposon is carried on the plasmid pJFF350 which can be conjugally mobilized into a broad range of Gram-negative bacteria. Omegon-Km is flanked, in inverted orientation, by synthetic 28-bp repeats derived from the ends of IS1. In addition, each end of Omegon-Km has the very efficient transcription and translation terminators of the omega interposon. Internally, Omegon-Km carries the selectable kanamycin (Km)-neomycin resistance gene (alph A) which is expressed well in many Gram-negative bacteria. The IS1 transposition functions are located on the donor plasmid but external to Omegon-Km. Thus, insertions of Omegon-Km are very stable because they lack the capacity for further transposition. Omegon-Km mutagenesis is performed by conjugal transfer of pJFF350 from Escherichia coli into any Gram-negative recipient strain in which this plasmid is unable to replicate. Those cells which have had a transposition event are selected by their resistance to Km. Very high frequencies of Omegon-Km transposition were observed in Pseudomonas putida. Preliminary experiments with other Gram-negative soil and water bacteria (Rhizobium leguminosarum, Paracoccus denitrificans) yielded mutants at reasonable levels. The presence of an E. coli-specific origin of replication (ori) within Omegon-Km allows the rapid and easy cloning, in E. coli, of the nucleotide sequences flanking the site of the transposition event.

Blotting, Southern↗
PubMed1990

Nucleotide sequence of the Methylobacterium extorquens AM1 moxF and moxJ genes involved in methanol oxidation.

The nucleotide sequence has been determined for two genes involved in methanol oxidation in the facultative methylotroph, Methylobacterium extorquens AM1. The two genes are moxF, encoding the 66-kDa subunit of the methanol dehydrogenase and moxJ, located immediately downstream from moxF, which encodes a 30-kDa protein with unknown function. This information completes the sequence of the 5.86-kb XhoI-SalI fragment containing the moxFJGI region in M. extorquens AM1, and the structure of this gene cluster is presented. Evidence is presented that moxJ is also present in Paracoccus denitrificans. The aa sequence of MoxJ has provided little information concerning its function, but it does appear to contain a signal sequence suggesting a periplasmic location.

Alcohol Oxidoreductases↗
PubMed1991

The gene encoding cytochrome c oxidase subunit II from Rhodobacter sphaeroides; comparison of the deduced amino acid sequence with sequences of corresponding peptides from other species.

The gene (coxII) encoding subunit II of Rhodobacter sphaeroides cytochrome c oxidase (cytochrome aa3) has been isolated by screening a genomic DNA library in phage lambda with a probe derived from coxII of Paracoccus denitrificans. A 2-kb fragment containing coxII DNA was subcloned into the phage M13mp18 and the sequence determined. The 2-kb insert contains the entire coding region for coxII gene, including the ATG start codon and a TGA stop codon. The deduced amino acid (aa) sequence of subunit II of R. sphaeroides shows regions of substantial homology to the corresponding subunit of the bovine mitochondrial oxidase (63% overall) and P. denitrificans oxidase (68% overall). The postulated redox-active copper ion (CuA) binding site involving two Cys and two His residues (as well as an alternative Met residue) is conserved among these species, along with four invariant acidic aa residues (two Asp and two Glu) that may be involved in interactions with cytochrome c, and a region of aromatic residues (Tyr-Gln-Trp-Tyr-Trp-Gly-Tyr-Glu-Tyr) which is postulated to play a role in electron transfer. Hydropathy profile analysis suggests that while the bovine COXII secondary structure contains two transmembrane helices, the R. sphaeroides subunit II has a third such helix that may function as part of a signal sequence, as suggested for P. denitrificans.

Amino Acid Sequence↗
PubMed1995

Identification of five Rhodobacter capsulatus genes encoding the equivalent of ND subunits of the mitochondrial NADH-ubiquinone oxidoreductase.

We previously reported the sequencing of two genes (ndhA and ndhI) encoding two of the subunits of the type-I NADH-ubiquinone oxidoreductase from Rhodobacter capsulatus (Rc). The present paper deals with the cloning and characterization of a chromosomal fragment clustering five new Rc genes which encode subunits of this enzyme. This gene cluster is located immediately downstream from ndhA and ndhI, and also contains two unidentified open reading frames (urf2, urf3). The five genes, nuoJ, nuoK, nuoL, nuoM and nuoN, encode proteins related, respectively, to mitochondrial (mt) subunits ND6, ND4L, ND5, ND4 and ND2. The overall organization of the nuo genes identified in Rc shows similarity to that of the Paracoccus denitrificans (Pd) nqo gene cluster.

Amino Acid Sequence↗
PubMedDate not supplied

Distribution and types of bacteria isolated from an inland saltern.

The physico-chemical characteristics and bacterial populations of an inland saltern were studied. The well water leading into the ponds of the saltern differed from sea water in its total salinity (18% (w/v)) and had lower Mg2+ and SO4(2-) contents and much higher contents of Cl-, Ca2+- and K+. A high proportion of halotolerant microorganisms were isolated, although marine bacteria were not found. Most of the halophilic strains isolated appeared to be typical moderate halophiles, and included six groups: Vibrio (39%), Deleya-Pseudomonas (28%), Acinetobacter (6.5%), Flavobacterium (6.5%), Paracoccus (1.5%), Planococcus (1.5%) and non-classified (17%). All extreme halophiles could be assigned to Halobacterium (31%) and Halococcus (68%).

Bacteria↗
PubMed1995

Amperometric detection of histamine at a quinoprotein dehydrogenase enzyme electrode.

Methylamine dehydrogenase, a tryptophan tryptophyl quinone (TTQ) containing quinoprotein, catalyzes the oxidation of a variety of primary aliphatic monomaines and diamines to their respective aldehydes and ammonia. This paper reports the construction and characterization of an enzyme electrode capable of detecting histamine and methylamine at +200 mV versus a saturated calomel reference electrode. The methylamine dehydrogenase isolated from Paracoccus denitrificans was used in conjunction with the insoluble mediator tetracyanoquinodimethane (TCNQ) to construct enzyme electrodes which will potentially provide simple rapid analysis of histamine without the need for the extensive sample pretreatments currently required in HPLC and GLC analysis. The linear response of this amperometric sensor, between 0 and 200 microM, correlates well with elevated histamine levels predominant in patients with chronic myelogenous leukaemia, whilst the observed limit of detection, 4.8 microM, compares favourably with the lower limits of detection reported for a potentiometric histamine sensitive enzyme electrode.

Biosensing Techniques↗
PubMed2003

The mitochondrial and prokaryotic proton-translocating NADH:ubiquinone oxidoreductases: similarities and dissimilarities of the quinone-junction sites.

The catalytic properties of the rotenone-sensitive NADH:ubiquinone reductase (Complex I) in bovine heart submitochondrial particles and in inside-out vesicles derived from Paracoccus denitrificans and Rhodobacter capsulatus were compared. The prokaryotic enzymes catalyze the NADH oxidase and NADH:quinone reductase reactions with similar kinetic parameters as those for the mammalian Complex I, except for lower apparent affinities for the substrates--nucleotides. Unidirectional competitive inhibition of NADH oxidation by ADP-ribose, previously discovered for submitochondrial particles, was also evident for tightly coupled P. denitrificans vesicles, thus suggesting that a second, NAD(+)-specific site is present in the simpler prokaryotic enzyme. The inhibitor sensitivity of the forward and reverse electron transfer reactions was compared. In P. denitrificans and Bos taurus vesicles different sensitivities to rotenone and Triton X-100 for the forward and reverse electron transfer reactions were found. In bovine heart preparations, both reactions showed the same sensitivity to piericidin, and the inhibition was titrated as a straight line. In P. denitrificans, the forward and reverse reactions show different sensitivity to piericidin and the titrations of both activities were curvilinear with apparent I(50) (expressed as mole of inhibitor per mole of enzyme) independent of the enzyme concentration. This behavior is explained by a model involving two different sites rapidly interacting with piericidin within the hydrophobic phase.

Animals↗
PubMed2005

Elucidation of dominant effect on initial bacterial adhesion onto polymer surfaces prepared by radiation-induced graft polymerization.

Surface-modified polyethylene (PE) membrane sheets were prepared by the radiation-induced graft polymerization (RIGP) of an epoxy-group-containing monomer, glycidyl methacrylate (GMA). The epoxy ring of GMA was opened by introducing diethylamine (DEA) or sodium sulfite (SS). We examined the properties of these sheets by measuring the amount of grafting polymer, surface roughness and membrane potential, and also investigated the adhesion of five Gram-negative bacteria, Escherichia coli, Pseudomonas aeruginosa, Pseudomonas putida, Pseudomonas fluorescens and Paracoccus denitrificans, onto the prepared sheet surfaces. A linear relationship between the degree of grafting (dg) and surface roughness was observed. Moreover, membrane potential was dependent on the amount of DEA or SS as the ionizable group. These results indicate that RIGP enables the control of the physicochemical properties of such a sheet surface by adjusting dg and the subsequent conversion of functional groups. A batch test on bacterial adhesion onto the sheets clarified that the DEA-containing sheet (DEA sheet) exhibited an adhesion rate constant, k, significantly greater than those of other types of sheet. Clearly, the adhesion rate constant of the DEA sheet increased with dg, indicating that electrostatic interaction is the most decisive factor for bacterial adhesion when it works as an attractive force. Furthermore, the densities of bacteria adhering onto the GMA-containing sheet (GMA sheet) and the SS-containing sheet (SS sheet) were almost the same as that onto a PE sheet, whereas that onto a DEA sheet significantly increased. Thus, the introduction of the GMA- and SS-containing graft chain did not have much influence on bacterial adhesion onto the surfaces, supporting the conclusion that the promotion of bacterial adhesion onto the GMA and SS sheets was due to an increase in surface area resulting from RIGP. Moreover, the scanning electron microscopy images of the sheet surfaces indicate that the conditions and morphologies of initial bacterial adhesion are dependent on surface properties, particularly membrane potential.

Bacterial Adhesion↗
PubMed2006

Electron transfer among the CuA-, heme b- and a3-centers of Thermus thermophilus cytochrome ba3.

The 1-methyl-nicotinamide radical (MNA(*)), produced by pulse radiolysis has previously been shown to reduce the Cu(A)-site of cytochromes aa(3), a process followed by intramolecular electron transfer (ET) to the heme a but not to the heme a(3) [Farver, O., Grell, E., Ludwig, B., Michel, H. and Pecht, I. (2006) Rates and equilibrium of CuA to heme a electron transfer in Paracoccus denitrificans cytochrome c oxidase. Biophys. J. 90, 2131-2137]. Investigating this process in the cytochrome ba(3) of Thermus thermophilus (Tt), we now show that MNA(*) also reduces Cu(A) with a subsequent ET to the heme b and then to heme a(3), with first-order rate constants 11200 s(-1), and 770 s(-1), respectively. The results provide clear evidence for ET among the three spectroscopically distinguishable centers and indicate that the binuclear a(3)-Cu(B) center can be reduced in molecules containing a single reduction equivalent.

Cytochrome b Group↗
PubMed2005

Isolation of PAH-degrading bacteria from mangrove sediments and their biodegradation potential.

Surface sediment samples were collected from seven mangrove swamps in Hong Kong SAR with different degrees of contamination. The total concentrations of 16 PAHs in these sediments ranged from 169.41 to 1058.37 ng g(-1) with the highest concentration found in Ma Wan and the lowest in Kei Ling Ha Lo Wai mangrove swamp. In each swamp, three bacterial consortia were enriched from sediments using phenanthrene (Phe) as the sole carbon and energy source, and individual bacterial colony showing Phe degradation was isolated and identified by 16S rDNA gene sequence. The consortia enriched from Sai Keng and Ho Chung sediments had highest ability to degrade mixed PAHs in liquid medium, with 90% Phe and Fla (fluoranthene) degraded in 7 days. On the other hand, Kei Ling Ha Lo Wai-enriched consortia degraded less than 40% Phe and Fla. Pyrene (Pyr) was hardly degraded by the consortia enriched from sediments. Bacterial isolates, namely Rhodococcus (HCCS), Sphingomonas (MWFG) and Paracoccus (SPNT) were capable to degrade mixed PAHs (Phe + Fla + Pyr). Their degradation percentages could be lower, comparable or even higher than their respective enriched consortia, depending on the consortium and the type of PAH compounds. These results suggest that PAH-degrading bacteria enriched from mangrove sediments, either as a mixed culture or as a single isolate could be used for PAHs bioremediation.

Bacteria↗
PubMed2006

Bacteria associated with orchid roots and microbial production of auxin.

Associative bacteria of terrestrial (Paphiopedilum appletonianum) and epiphytic (Pholidota articulata) tropical orchids were investigated. Microbial community of epiphytic plant differed from that of the terrestrial one. Streptomyces, Bacillus, Pseudomonas, Burkholderia, Erwinia and Nocardia strains populated Paphiopedilum roots, whereas Pseudomonas, Flavobacterium, Stenotrophomonas, Pantoea, Chryseobacterium, Bacillus, Agrobacterium, Erwinia, Burkholderia and Paracoccus strains colonized Pholidota roots. Endophytic bacteria populations were represented with less diversity: Streptomyces, Bacillus, Erwinia and Pseudomonas genera were isolated from P. appletonianum, and Pseudomonas, Bacillus, and Flavobacterium genera were isolated from Ph. articulata. Microorganisms produced indole-3-acetic acid (IAA). Variations in its biosynthesis among the strains of the same genus were also observed. The highest auxin level was detected during the stationary growth phase. Biological activity of microbial IAA was proved by treatment of kidney bean cuttings with bacterial supernatants, revealing considerable stimulation of root formation and growth.

Bacteria↗
PubMed2002

Redox properties of an engineered purple Cu(A) azurin.

Purple Cu(A) centers are a class of binuclear, mixed-valence copper complexes found in cytochrome c oxidase and nitrous oxide reductase. An engineered Cu(A) protein was formed by replacing a portion of the amino acid sequence that contains three of the ligands to the native type I copper center of Pseudomonas aeruginosa azurin with the corresponding portion of sequence from the Cu(A) center of cytochrome c oxidase from Paracoccus denitrificans [Proc. Natl. Acad. Sci. USA 93 (1996) 461]. Oxidation-reduction midpoint potential (E(m)) values of the Cu(A) azurin of +399+/-10 and +380+/-2mV, respectively, were determined by cyclic voltammetry and spectrochemical titration. An n value of one was obtained, indicating that the redox reaction is cycling between the mixed valence and the fully reduced states. Whereas the E(m) value of native azurin is pH dependent, the E(m) value of Cu(A) azurin is not, as expected for the Cu(A) center. Similarities and differences in the redox properties are discussed in terms of the known crystal structures of Cu(A) centers in cytochrome c oxidase and Cu(A) azurin.

Azurin↗
PubMed2003

Characterization of the interaction of Rhodobacter capsulatus cytochrome c peroxidase with charge reversal mutants of cytochrome c(2).

Steady-state kinetics for the reaction of Rhodobacter capsulatus bacterial cytochrome c peroxidase (BCCP) with its substrate cytochrome c(2) were investigated. The Rb. capsulatus BCCP is dependent on calcium for activation as previously shown for the Pseudomonas aeruginosa BCCP and Paracoccus denitrificans enzymes. Furthermore, the activity shows a bell-shaped pH dependence with optimum at pH 7.0. Enzyme activity is greatest at low ionic strength and drops off steeply as ionic strength increases, resulting in an apparent interaction domain charge product of -13. All cytochromes c(2) show an asymmetric distribution of surface charge, with a concentration of 14 positive charges near the exposed heme edge of Rb. capsulatus c(2) which potentially may interact with approximately 6 negative charges, localized near the edge of the high-potential heme of the Rb. capsulatus BCCP. To test this proposal, we constructed charge reversal mutants of the 14 positively charged residues located on the front face of Rb. capsulatus cytochrome c(2) and examined their effect on steady-state kinetics with BCCP. Mutated residues in Rb. capsulatus cytochrome c(2) that showed the greatest effects on binding and enzyme activity are K12E, K14E, K54E, K84E, K93E, and K99E, which is consistent with the site of electron transfer being located at the heme edge. We conclude that a combination of long-range, nonspecific electrostatic interactions as well as localized salt bridges between, e.g., cytochrome c(2) K12, K14, K54, and K99 with BCCP D194, D241, and D6, account for the observed kinetics.

Calcium↗