| assembly of respiratory complexes i, iii, and iv into nadh oxidase supercomplex stabilizes complex i in paracoccus denitrificans. | stable supercomplexes of bacterial respiratory chain complexes iii (ubiquinol:cytochrome c oxidoreductase) and iv (cytochrome c oxidase) have been isolated as early as 1985 (berry, e. a., and trumpower, b. l. (1985) j. biol. chem. 260, 2458-2467). however, these assemblies did not comprise complex i (nadh:ubiquinone oxidoreductase). using the mild detergent digitonin for solubilization of paracoccus denitrificans membranes we could isolate nadh oxidase, assembled from complexes i, iii, and iv in ... | 2004 | 14610094 |
| proton-translocating atp-synthase of paracoccus denitrificans: atp-hydrolytic activity. | tightly coupled membranes of paracoccus denitrificans catalyze oxidative phosphorylation but are incapable of atp hydrolysis. the conditions for observation and registration of the venturicidin-sensitive atpase activity of subbacterial particles derived from this organism are described. the atp hydrolytic activity does not appear after prolonged incubation in the presence of pyruvate kinase and phosphoenol pyruvate (to remove adp), edta (to remove mg2+) and/or inorganic phosphate, whereas the ac ... | 2003 | 14616081 |
| evolution of the bacterial community during granules formation in denitrifying reactors followed by molecular, culture-independent techniques. | the microbial community in two acetate-fed denitrifying reactors, inoculated with methanogenic sludge, was monitored by 16s rdna-based methods (sscp and fish). both reactors converged to similar, stable communities. the predominant organisms belonged to the genera thauera, paracoccus and denitrobacter, detected both by molecular and culture-based methods. | 2003 | 14640202 |
| cytochrome c551 from starkeya novella: characterization, spectroscopic properties, and phylogeny of a diheme protein of the soxax family. | cytochromes from the soxax family have a major role in thiosulfate oxidation via the thiosulfate-oxidizing multi-enzyme system (tomes). previously characterized soxax proteins from rhodovulum sulfidophilum and paracoccus pantotrophus contain three heme c groups, two of which are located on the soxa subunit. in contrast, the soxax protein purified from starkeya novella was found to contain only two heme groups. mass spectrometry showed that a disulfide bond replaced the second heme group found in ... | 2004 | 14645228 |
| sulfur oxidation in paracoccus pantotrophus: interaction of the sulfur-binding protein soxyz with the dimanganese soxb protein. | the central protein of the sulfur-oxidizing enzyme system of paracoccus pantotrophus, soxyz, formed complexes with subunits associated and covalently bound. in denaturing sds-polyacrylamide gel electrophoresis (page) soxy migrated at 12 and soxz at 16kda. sds-page of homogeneous soxyz without reductant separated dimeric complexes of 25, 29, and 32kda identified by the n-terminal amino acid sequences as soxy-y, soxy-z, and soxz-z, and subunit cleavage by reduction suggested their linkage via prot ... | 2003 | 14651972 |
| lucigenin and coelenterazine as superoxide probes in mitochondrial and bacterial membranes. | the chemiluminescent superoxide indicators lucigenin and coelenterazine were compared in rat liver submitochondrial particles and cytoplasmic membranes from paracoccus denitrificans. qualitative monitoring is possible with both probes, but quantitative work with lucigenin is hampered by its dependence on one-electron reduction before the photon-emitting reaction. therefore, calibration of measurements on complex i, capable of efficient lucigenin prereduction with reduced nicotinamide adenine din ... | 2004 | 14654044 |
| identification and distribution of insertion sequences of paracoccus solventivorans. | three novel insertion sequences (iss) (ispso1, ispso2, and ispso3) of the soil bacterium paracoccus solventivorans dsm 11592 were identified by transposition into entrapment vector pmec1. ispso1 (1,400 bp) carries one large open reading frame (orf) encoding a putative basic protein (with a dde motif conserved among transposases [tnps] of elements belonging to the is256 family) with the highest levels of similarity with the hypothetical tnps of rhodospirillum rubrum and sphingopyxis macrogoltabid ... | 2003 | 14660342 |
| fine-tuned regulation by oxygen and nitric oxide of the activity of a semi-synthetic fnr-dependent promoter and expression of denitrification enzymes in paracoccus denitrificans. | in paracoccus denitrificans at least three fumarate and nitrate reductase regulator (fnr)-like proteins [fnrp, nitrite and nitric oxide reductases regulator (nnr) and narr] control the expression of several genes necessary for denitrifying growth. to gain more insight into this regulation, beta-galactosidase activity from a plasmid carrying the lacz gene fused to the escherichia coli melr promoter with the consensus fnr-binding (ff) site was examined. strains defective in the fnrp gene produced ... | 2003 | 14663074 |
| a functional plasmid-borne rrn operon in soil isolates belonging to the genus paracoccus. | plasmid analysis of isolates from a small paracoccus population revealed that all 15 representatives carried at least one endogenous plasmid of 23 or 15 kb in size, in addition to further plasmids of different sizes. it was shown by restriction analysis and hybridization that the 23 and 15 kb plasmids from the different isolates were identical or very similar to each other. by partial sequencing of pol18/23, one of the 23 kb plasmids, a complete rrn operon with the structural genes for 16s, 23s ... | 2003 | 14663090 |
| a superfamily of voltage-gated sodium channels in bacteria. | nachbac, a six-alpha-helical transmembrane-spanning protein cloned from bacillus halodurans, is the first functionally characterized bacterial voltage-gated na(+)-selective channel. as a highly expressing ion channel protein, nachbac is an ideal candidate for high resolution structural determination and structure-function studies. the biological role of nachbac, however, is still unknown. in this report, another 11 structurally related bacterial proteins are described. two of these functionally ... | 2004 | 14665618 |
| 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 inhibit ... | 2003 | 14670598 |
| soluble cua domain of cyanobacterial cytochrome c oxidase. | the genomes of several cyanobacteria show the existence of gene clusters encoding subunits i, ii, and iii of aa(3)-type cytochrome c oxidase. the enzyme occurs on both plasma and thylakoid membranes of these oxygenic phototrophic prokaryotes. here we report the expression and purification of a truncated subunit ii copper a (cu(a)) domain (i.e. the electron entry and donor binding site) of cytochrome c oxidase from the cyanobacterium synechocystis pcc 6803 in high yield. the water-soluble purple ... | 2004 | 14672950 |
| time-resolved resonance raman and time-resolved step-scan ftir studies of nitric oxide reductase from paracoccus denitrificans: comparison of the heme b3-feb site to that of the heme-cub in oxidases. | time-resolved resonance raman (tr(3)) and time-resolved step-scan (trs(2)) ftir spectroscopies have been used to probe the structural dynamics at the heme b(3) proximal and distal sites after carbon monoxide photolysis from fully reduced co-bound nitric oxide reductase. the raman spectra of the transient species exhibit structural differences relative to the equilibrium geometry of heme b(3). the most significant of these is a shift of 8 cm(-1) to higher frequency of the 207 cm(-1) mode, and a s ... | 2003 | 14674760 |
| investigation of protonatable residues in rhodothermus marinus caa3 haem-copper oxygen reductase: comparison with paracoccus denitrificans aa3 haem-copper oxygen reductase. | the rhodothermus marinus caa(3 )haem-copper oxygen reductase contains all the residues of the so-called d- and k-proton channels, with the notable exception of the helix vi glutamate residue (glu278(i) in paracoccus denitrificans aa(3)), being nevertheless a true oxygen reductase reducing o(2) to water, and an efficient proton pump. instead, in the same helix, but one turn below, it has a tyrosine residue (tyr256(i), r. marinus caa(3) numbering), whose hydroxyl group occupies the same spatial po ... | 2004 | 14691678 |
| use of stable-isotope probing, full-cycle rrna analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community. | a denitrifying microbial consortium was enriched in an anoxically operated, methanol-fed sequencing batch reactor (sbr) fed with a mineral salts medium containing methanol as the sole carbon source and nitrate as the electron acceptor. the sbr was inoculated with sludge from a biological nutrient removal activated sludge plant exhibiting good denitrification. the sbr denitrification rate improved from less than 0.02 mg of no(3)(-)-n mg of mixed-liquor volatile suspended solids (mlvss)(-1) h(-1) ... | 2004 | 14711691 |
| energy-dependent transformation of f0.f1-atpase in paracoccus denitrificans plasma membranes. | f(0).f(1)-atp synthase in tightly coupled inside-out vesicles derived from paracoccus denitrificans catalyzes rapid respiration-supported atp synthesis, whereas their atpase activity is very low. in the present study, the conditions required to reveal the deltamu(h+)-generating atp hydrolase activity of the bacterial enzyme have been elucidated. energization of the membranes by respiration results in strong activation of the venturicidin-sensitive atp hydrolysis, which is coupled with generation ... | 2004 | 14722115 |
| isolation and biochemical characterization of two soluble iron(iii) reductases from paracoccus denitrificans. | two soluble enzymes (fera and ferb) catalyzing the reduction of a number of iron(iii) complexes by nadh, were purified to near homogeneity from the aerobically grown iron-limited culture of paracoccus denitrificans using a combination of anion-exchange chromatography (sepharose q), chromatofocusing (mono p), and gel permeation chromatography (superose 12). fera is a monomer with a molecular mass of 19 kda, whereas ferb exhibited a molecular mass of about 55 kda and consists of probably two ident ... | 2004 | 14728682 |
| crystallization and preliminary x-ray diffraction analysis of a dihaem cytochrome c peroxidase from paracoccus denitrificans. | cytochrome c peroxidase was isolated from paracoccus denitrificans and purified to homogeneity in three steps prior to crystallization. two different diffraction-quality crystal forms were obtained by the hanging-drop vapour-diffusion method using a number of screening conditions. the best (needle-shaped) crystal form is suitable for structural studies and was grown from solutions containing 20% peg 8000, 0.1 m tris ph 8.5 and 0.2 m mgcl(2). crystals grew to a maximum length of approximately 0.7 ... | 2004 | 14747715 |
| 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 ... | 2003 | 14753557 |
| redox-dependent open and closed forms of the active site of the bacterial respiratory nitric-oxide reductase revealed by cyanide binding studies. | the bacterial respiratory nitric-oxide reductase (nor) catalyzes the respiratory detoxification of nitric oxide in bacteria and archaea. it is a member of the well known super-family of heme-copper oxidases but has a [heme fe-non-heme fe] active site rather than the [heme fe-cu(b)] active site normally associated with oxygen reduction. paracoccus denitrificans nor is spectrally characterized by a ligand-to-metal charge transfer absorption band at 595 nm, which arises from the high spin ferric he ... | 2004 | 14766741 |
| examination of membrane protein expression in paracoccus denitrificans by two-dimensional gel electrophoresis. | the well-known metabolic versatility of the soil bacterium paracoccus denitrificans poses a challenge for modern proteomic approaches. we describe here improved preparation conditions that allow good separation and quantitative analyses of hundreds of membrane or periplasmic proteins. to illustrate this optimized procedure, the results of a screening for membrane proteins associated predominantly with aerobic or anaerobic (denitrifying) modes of growth are presented. | 2004 | 14768023 |
| microbial community structure of membrane fouling film in an intermittently and continuously aerated submerged membrane bioreactor treating domestic wastewater. | there was an observable difference in microbial community structure between suspended microorganisms and membrane biofouling film in intermittently and continuously aerated smbrs. the dominant quinone type of membrane biofouling film in an intermittently aerated smbr was ubiquinone (uqs)-8, -10 followed by menaquinone (mks)-8(h4) and -8(h2). but that of the continuously aerated smbr was uqs-10, -8 followed by mks-6 and -8(h4). the experimental results also showed that the conditions of an interm ... | 2004 | 14982188 |
| proton uptake upon anaerobic reduction of the paracoccus denitrificans cytochrome c oxidase: a kinetic investigation of the k354m and d124n mutants. | the kinetics and stoichiometry of the redox-linked protonation of the soluble paracoccus denitrificans cytochrome c oxidase were investigated at ph = 7.2-7.5 by multiwavelength stopped-flow spectroscopy, using the ph indicator phenol red. we compared the wild-type enzyme with the k354m and the d124n subunit i mutants, in which the k- and d-proton-conducting pathways are impaired, respectively. upon anaerobic reduction by ru-ii hexamine, the wild-type enzyme binds 3.3 +/- 0.6 h(+)/aa(3), i.e., ap ... | 2004 | 15005632 |
| subunit proximity in the h+-translocating nadh-quinone oxidoreductase probed by zero-length cross-linking. | the proton-translocating nadh-quinone oxidoreductase (ndh-1) of paracoccus denitrificans is composed of 14 different subunits (designated nqo1-14), seven of which are located in the membrane domain and the other seven in the peripheral domain. it has been previously reported that membrane domain subunit nqo7 (nd3) directly interacts with peripheral subunit nqo6 (psst) by using a cross-linker, m-maleimidobenzoyl-n-hydrosuccinimide ester, and heterologous expression [di bernardo, s., and yagi, t. ... | 2004 | 15035646 |
| dynamic water networks in cytochrome c oxidase from paracoccus denitrificans investigated by molecular dynamics simulations. | we present a molecular dynamics study of cytochrome c oxidase from paracoccus denitrificans in the fully oxidized state, embedded in a fully hydrated dimyristoylphosphatidylcholine lipid bilayer membrane. parallel simulations with different levels of protein hydration, 1.125 ns each in length, were carried out under conditions of constant temperature and pressure using three-dimensional periodic boundary conditions and full electrostatics to investigate the distribution and dynamics of water mol ... | 2004 | 15041635 |
| genetic organization of the basic replicon of plasmid pmth4 of a facultatively methylotrophic bacterium paracoccus methylutens dm12. | two functional regions within the basic replicon of plasmid pmth4 of paracoccus methylutens dm12 have been distinguished that are responsible for the replication of the plasmid (rep) and its stabilization (sta). in the rep region, a gene encoding the putative replication initiation protein repa has been identified, with the highest similarity to the replication protein of plasmid palc1 (paracoccus alcaliphilus). the potential origin of replication (oriv), consisting of five long repeated sequenc ... | 2004 | 15057455 |
| enzymes and genes of taurine and isethionate dissimilation in paracoccus denitrificans. | growth of the alpha-proteobacterium paracoccus denitrificans nknis with taurine or isethionate as sole source of carbon involves sulfoacetaldehyde acetyltransferase (xsc), which is presumably encoded by an xsc gene in subgroup 3, none of whose gene products has been characterized. the genome of the alpha-proteobacterium rhodobacter sphaeroides 2.4.1 was interpreted to contain a nine-gene cluster encoding the inducible dissimilation of taurine, and this deduced pathway included a regulator, a tri ... | 2004 | 15073291 |
| interaction of cytochrome c with cytochrome oxidase: two different docking scenarios. | cytochrome c is the specific and efficient electron transfer mediator between the two last redox complexes of the mitochondrial respiratory chain. its interaction with both partner proteins, namely cytochrome c(1) (of complex iii) and the hydrophilic cu(a) domain (of subunit ii of oxidase), is transient, and known to be guided mainly by electrostatic interactions, with a set of acidic residues on the presumed docking site on the cu(a) domain surface and a complementary region of opposite charges ... | 2004 | 15100042 |
| tryptophan or tyrosine? on the nature of the amino acid radical formed following hydrogen peroxide treatment of cytochrome c oxidase. | it has been reported that different amino acid radicals are formed following the addition of hydrogen peroxide to cytochrome c oxidase (cco) from bovine heart or from paracoccus denitrificans. a broad unresolved signal in the electron paramagnetic resonance (epr) spectra of bovine cco has been assigned to a tryptophan radical, probably trp126 [rigby et al. biochemistry 2000, 39, 5921-5928]. in the p. denitrificans enzyme, a similarly broad signal but with a well-resolved hyperfine structure was ... | 2004 | 15100053 |
| biotinylated polypyrrole films: an easy electrochemical approach for the reagentless immobilization of bacteria on electrode surfaces. | biotinylated bacteria were immobilized onto biotin/avidin modified electrode surfaces. firstly, an electrospotting deposition method, followed by fluorescence microscopy, showed that bacteria were specifically grafted onto a gold surface. fluorescence intensity versus the quantity of bacteria deposited on the surface was correlated, allowing determination of the microbial saturation point. secondly, biotinylated bacteria were immobilized onto a glassy carbon macro-electrode in order to assess im ... | 2004 | 15110291 |
| further insights into quinone cofactor biogenesis: probing the role of maug in methylamine dehydrogenase tryptophan tryptophylquinone formation. | paracoccus denitrificans methylamine dehydrogenase (madh) is an enzyme containing a quinone cofactor tryptophan tryptophylquinone (ttq) derived from two tryptophan residues (betatrp(57) and betatrp(108)) within the polypeptide chain. during cofactor formation, the two tryptophan residues become covalently linked, and two carbonyl oxygens are added to the indole ring of betatrp(57). expression of active madh from p. denitrificans requires four other genes in addition to those that encode the poly ... | 2004 | 15122915 |
| isolation and characterization of novel bacteria degrading polycyclic aromatic hydrocarbons from polluted greek soils. | three bacterial strains, designated as wphe1, sphe1, and ophe1, were isolated from greek soils contaminated with polycyclic aromatic hydrocarbon (pah)-containing waste from the wood processing, steel, and oil refinery industries. wphe1, sphe1, and ophe1 were characterized and identified as species of pseudomonas, microbacterium, and paracoccus, respectively, based on gram staining, biochemical tests, phospholipid analysis, fame analysis, g+c content and 16s rrna gene sequence analysis. the resul ... | 2004 | 15133642 |
| paracoccus pantotrophus napc can reductively activate cytochrome cd1 nitrite reductase. | the oxidized "as isolated" form of paracoccus pantotrophus cytochrome cd1 nitrite reductase has a bis-histidinyl coordinated c heme and a histidine/tyrosine coordinated d1 heme. this form of the enzyme has previously been shown to be kinetically incompetent. upon reduction, the coordination of both hemes changes and the enzyme is kinetically activated. here, we show that p. pantotrophus napc, a tetraheme c-type cytochrome belonging to a large family of such proteins, is capable of reducing, and ... | 2004 | 15135051 |
| investigation of the thermal stability of porin from paracoccus denitrificans by site-directed mutagenesis and fourier transform infrared spectroscopy. | the folding of membrane proteins was addressed using outer membrane protein porin from the soil bacterium paracoccus denitrificans (p. den.). ir spectroscopy and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (sds-page) analysis were used to probe the effect of mutagenesis on the thermal stability of the protein. secondary structure analysis by amide i ir spectroscopy showed that the wild-type protein was predominantly composed of beta-sheet, which supports the x-ray crystal structure ... | 2004 | 15137100 |
| denitrification with epsilon-caprolactam by acclimated mixed culture and by pure culture of bacteria isolated from polyacrylonitrile fibre manufactured wastewater treatment system. | the aim of this study is to isolate denitrifying bacteria utilizing epsilon-caprolactam as the substrate, from a polyacrylonitrile fibre manufactured wastewater treatment system. the aim is also to compare the performance of pan (polyacrylonitrile) mixed bacteria cultures acclimated to epsilon-caprolactam and isolated pure strain for treating different initial epsilon-caprolactam concentrations from synthetic wastewater under anoxic conditions. the result showed that the pan mixed bacteria cultu ... | 2004 | 15137443 |
| catellibacterium nectariphilum gen. nov., sp. nov., which requires a diffusible compound from a strain related to the genus sphingomonas for vigorous growth. | a bacterial strain, designated ast4(t), was isolated from activated sludge. the bacterium did not show significant growth on nutrient broth, but growth was clearly stimulated by addition of supernatant from other bacterial cultures. culture filtrate of a strain related to the genus sphingomonas in particular increased the cell yield and growth rate of strain ast4(t). phylogenetic analysis based on the 16s rrna gene sequences showed that strain ast4(t) is located within the 'rhodobacter group' in ... | 2004 | 15143049 |
| phylogenetically diverse new sulfur chemolithotrophs of alpha-proteobacteria isolated from indian soils. | five facultative sulfur chemolithotrophs were isolated from soils to study the diversity of sulfur lithotrophy. phenotypic characteristics, including sulfur lithotrophic properties and chemotaxonomic features of the isolates, were similar to those of the members of the colorless sulfur bacteria. 16s rdna sequence analyses rendered placing the isolates to three distinct phylogenetic clusters of alpha-proteobacteria. three isolates, as001, as002, and kct002, were identified as members of the genus ... | 2004 | 15170243 |
| functional roles of four conserved charged residues in the membrane domain subunit nuoa of the proton-translocating nadh-quinone oxidoreductase from escherichia coli. | the h(+)(na(+))-translocating nadh-quinone (q) oxidoreductase (ndh-1) of escherichia coli is composed of 13 different subunits (nuoa-n). subunit nuoa (nd3, nqo7) is one of the seven membrane domain subunits that are considered to be involved in h(+)(na(+)) translocation. we demonstrated that in the paracoccus denitrificans ndh-1 subunit, nqo7 (nd3) directly interacts with peripheral subunits nqo6 (psst) and nqo4 (49 kda) by using cross-linkers (di bernardo, s., and yagi, t. (2001) febs lett. 508 ... | 2004 | 15175326 |
| use of sinorhizobium meliloti as an indicator for specific detection of long-chain n-acyl homoserine lactones. | population-density-dependent gene expression in gram-negative bacteria involves the production of signal molecules characterized as n-acyl homoserine lactones (ahls). the synthesis of ahls by numerous microorganisms has been identified by using biosensor strains based on the agrobacterium tumefaciens and chromobacterium violaceum quorum-sensing systems. the symbiotic nitrogen-fixing bacterium sinorhizobium meliloti is rapidly becoming a model organism for the study of quorum sensing. this organi ... | 2004 | 15184178 |
| 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 ... | 2004 | 15240445 |
| first comprehensively documented case of paracoccus yeei infection in a human. | paracoccus yeei was isolated in pure culture from an aerobic blood culture and bulla fluid from a 67-year-old male. the biochemical identification scheme for this recently described species is outlined. because of its reaction pattern it is not unlikely that p. yeei is underdiagnosed. | 2004 | 15243119 |
| characterisation of [cu4s], the catalytic site in nitrous oxide reductase, by epr spectroscopy. | the enzyme nitrous oxide reductase (n(2)or) has a unique tetranuclear copper centre [cu(4)s], called cu(z), at the catalytic site for the two-electron reduction of n(2)o to n(2). the x- and q-band epr spectra have been recorded from two forms of the catalytic site of the enzyme n(2)or from paracoccus pantotrophus, namely, a form prepared anaerobically, cu(z), that undergoes a one-electron redox cycle and cu(z)*, prepared aerobically, which cannot be redox cycled. the spectra of both species are ... | 2004 | 15252678 |
| structural studies of two mutants of amicyanin from paracoccus denitrificans that stabilize the reduced state of the copper. | mutation of pro94 to phenylalanine or alanine significantly alters the redox properties of the type i copper center of amicyanin. each mutation increases the redox midpoint potential (e(m)) value by at least 140 mv and shifts the pk(a) for the ph dependence of the e(m) value to a more acidic value. atomic resolution (0.99-1.1 a) structures of both the p94f and p94a amicyanin have been determined in the oxidized and reduced states. in each amicyanin mutant, an electron-withdrawing hydrogen bond t ... | 2004 | 15260480 |
| crystallographic and nmr investigation of cobalt-substituted amicyanin. | cobalt(ii) amicyanin was prepared by replacing the copper of the type i copper protein amicyanin from paracoccus denitrificans with cobalt. the structure of the protein and the metal center have been characterized by x-ray crystallography and paramagnetic nmr spectroscopy. the crystal structure indicates that met98, which provides an axial sulfur ligand in native amicyanin, is no longer bound to the metal in cobalt(ii) amicyanin and that a water molecule is recruited from solvent to form the fou ... | 2004 | 15260481 |
| metabolic engineering of ketocarotenoid formation in higher plants. | although higher plants synthesize carotenoids, they do not possess the ability to form ketocarotenoids. in order to generate higher plants capable of synthesizing combinations of ketolated and hydroxylated carotenoids the genes responsible for the carotene 4,4' oxygenase and 3,3' hydroxylase have been transformed into tomato and tobacco. the gene products were produced as a polyprotein. subsequent cleavage of the polyprotein, targeting of the two enzymes to the plastid and enzyme activities have ... | 2004 | 15272869 |
| x-ray structure of the cupredoxin amicyanin, from paracoccus denitrificans, refined at 1.31 a resolution. | high-resolution x-ray diffraction data to d(min) = 1.31 a were collected on a xuong-hamlin area detector from crystals of the blue-copper protein amicyanin, isolated from p. denitrificans. with coordinates from the earlier 2.0 a structure determination as a starting point, simulated annealing and restrained positional and temperature factor refinements using the program x-plor resulted in a final r factor of 15.5%, based on 21 131 unique reflections in the range 8.0-1.3 a. comparison of the 1.31 ... | 1996 | 15299631 |
| nitric oxide oscillations in paracoccus denitrificans: the effects of environmental factors and of segregating nitrite reductase and nitric oxide reductase into separate cells. | nitric oxide is a denitrification intermediate which is produced from nitrite and then further converted via nitrous oxide to nitrogen. here, the effect of low concentrations of the protonophore carbonylcyanide m-chlorophenylhydrazone on the time courses for dissolved gases was examined. while no was found to oscillate, n(2)o only increased gradually as the reduction of nitrite progressed. the frequency and shape of protonophore-induced no oscillations were influenced by temperature and the conc ... | 2004 | 15313228 |
| characterization and expression of genes from the rubisco gene cluster of the chemoautotrophic symbiont of solemya velum: cbblsqo. | chemoautotrophic endosymbionts residing in solemya velum gills provide this shallow water clam with most of its nutritional requirements. the cbb gene cluster of the s. velum symbiont, including cbbl and cbbs, which encode the large and small subunits of the carbon-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco), was cloned and expressed in escherichia coli. the recombinant rubisco had a high specific activity, approximately 3 micromol min(-1) mg protein (-1), and a kco2 ... | 2004 | 15316720 |
| direct immobilization of native yeast iso-1 cytochrome c on bare gold: fast electron relay to redox enzymes and zeptomole protein-film voltammetry. | cyclic voltammetry shows that yeast iso-1-cytochrome c (ycc), chemisorbed on a bare gold electrode via cys102, exhibits fast, reversible interfacial electron transfer (k(0) = 1.8 x 10(3) s(-1)) and retains its native functionality. vectorially immobilized ycc relays electrons to yeast cytochrome c peroxidase, and to both cytochrome cd(1) nitrite reductase (nir) and nitric oxide reductase from paracoccus denitrificans, thereby revealing the mechanistic properties of these enzymes. on a microelect ... | 2004 | 15339197 |
| protein composition of paracoccus denitrificans cells grown on various electron acceptors and in the presence of azide. | two-dimensional gel electrophoresis (2-de) with immobilized ph gradients was carried out on total cell lysates and membrane fractions of paracoccus denitrificans with the aim to characterize differences in protein expression during growth under aerobic and various anaerobic conditions (with nitrate, nitrite or nitrous oxide). comparative image analysis of the protein pattern revealed several subgroups of the total 800 protein spots resolved that were characteristically induced or repressed in re ... | 2004 | 15352241 |
| tyrosine 167: the origin of the radical species observed in the reaction of cytochrome c oxidase with hydrogen peroxide in paracoccus denitrificans. | determination of the three-dimensional structure of cytochrome c oxidase, the terminal enzyme of the respiratory chain, from paracoccus denitrificans offers the possibility of site-directed mutagenesis studies to investigate the relationship between the structure and the catalytic function of the enzyme. the mechanism of electron-coupled proton transfer is still, however, poorly understood. the p(m) intermediate of the catalytic cycle is an oxoferryl state the generation of which requires one ad ... | 2004 | 15362855 |
| paracoccus pantotrophus pseudoazurin is an electron donor to cytochrome c peroxidase. | the gene for pseudoazurin was isolated from paracoccus pantotrophus lmd 52.44 and expressed in a heterologous system with a yield of 54.3 mg of pure protein per liter of culture. the gene and protein were shown to be identical to those from p. pantotrophus lmd 82.5. the extinction coefficient of the protein was re-evaluated and was found to be 3.00 mm(-1) cm(-1) at 590 nm. it was confirmed that the oxidized protein is in a weak monomer/dimer equilibrium that is ionic-strength-dependent. the pseu ... | 2004 | 15366931 |
| a novel exopolymer-producing bacterium, paracoccus zeaxanthinifaciens subsp. payriae, isolated from a "kopara" mat located in rangiroa, an atoll of french polynesia. | an aerobic, mesophilic and heterotrophic marine bacterium designated ra19, able to produce two different exocellular polymers and zeaxanthin, was isolated from a french polynesian bacterial mat (localy named "kopara") situated in the atoll of rangiroa. this microorganism, on the basis of its phenotypical features and the genotypic investigations, can be clearly assigned to the parococcus zeaxanthinifaciens species and the name parococcus zeaxanthinifaciens subsp. payriae is proposed. optimal gro ... | 2004 | 15386095 |
| an oxo-ferryl tryptophan radical catalytic intermediate in cytochrome c and quinol oxidases trapped by microsecond freeze-hyperquenching (mhq). | the pre-steady state reaction kinetics of the reduction of molecular oxygen catalyzed by fully reduced cytochrome oxidase from escherichia coli and paracoccus denitrificans were studied using the newly developed microsecond freeze-hyperquenching mixing-and-sampling technique. reaction samples are prepared 60 and 200 micros after direct mixing of dioxygen with enzyme. analysis of the reaction samples by low temperature uv-vis spectroscopy indicates that both enzymes are trapped in the pm state. e ... | 2004 | 15388346 |
| paracoccus haeundaensis sp. nov., a gram-negative, halophilic, astaxanthin-producing bacterium. | an aerobic, non-motile, gram-negative, orange-pigmented, rod-shaped, astaxanthin-producing marine bacterium was isolated from the haeundae coast, korea. this strain, bc74171t, produced carotenoids, mainly astaxanthin. all the type strains of the genus paracoccus were compared with strain bc74171t using 16s rrna gene sequence analysis, fatty acid patterns and physiological reaction profiles. based on the results of these analyses, it is proposed that strain bc74171t represents a novel species, pa ... | 2004 | 15388731 |
| purification and some properties of isocitrate dehydrogenase from paracoccus denitrificans. | nadp-dependent isocitrate dehydrogenase (icdh) from the bacterium paracoccus denitrificans was purified to homogeneity. the purification procedure involved ammonium sulphate fractionation, ion exchange chromatography, and gel permeation chromatography. the specific activity of purified icdh was 801 nkat/mg, the yield of the enzyme 58%. the purity of the enzyme was checked by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulphate. icdh is a dimer composed of two probably id ... | 2004 | 15461143 |
| optimization of an escherichia coli system for cell-free synthesis of selectively n-labelled proteins for rapid analysis by nmr spectroscopy. | cell-free protein synthesis offers rapid access to proteins that are selectively labelled with [15n]amino acids and suitable for analysis by nmr spectroscopy without chromatographic purification. a system based on an escherichia coli cell extract was optimized with regard to protein yield and minimal usage of 15n-labelled amino acid, and examined for the presence of metabolic by-products which could interfere with the nmr analysis. yields of up to 1.8 mg of human cyclophilin a per ml of reaction ... | 2004 | 15479237 |
| no reductase from bacillus azotoformans is a bifunctional enzyme accepting electrons from menaquinol and a specific endogenous membrane-bound cytochrome c551. | bacillus azotoformans is a gram-positive denitrifying soil bacterium, which is capable of respiring nitrate, nitrite, nitric oxide, and nitrous oxide under anaerobic conditions. it contains a unique menaquinol-dependent nitric oxide reductase (qcu(a)nor) with a cu(a) center in its small subunit. the qcu(a)nor exhibits menaquinol-dependent no reductase activity, whereas reduced horse heart cytochrome c was inactive. here we describe the purification of three membrane-bound c cytochromes from b. a ... | 2004 | 15491156 |
| no binding and dynamics in reduced heme-copper oxidases aa3 from paracoccus denitrificans and ba3 from thermus thermophilus. | cytochrome c oxidase (cco) has a high affinity for nitric oxide (no), a property involved in the regulation of respiration. it has been shown that the recombination kinetics of photolyzed no with reduced cco from paracoccus denitrificans on the picosecond time scale depend strongly on the no/enzyme stoichiometry and inferred that more than one no can be accommodated by the active site, already at mildly suprastoichiometric no concentrations. we have largely extended these studies by monitoring r ... | 2004 | 15518562 |
| atr-ftir spectroscopy and isotope labeling of the pm intermediate of paracoccus denitrificans cytochrome c oxidase. | the structure of the p(m) intermediate of paracoccus denitrificans cytochrome c oxidase was investigated by perfusion-induced attenuated total reflection-fourier transform infrared (atr-ftir) spectroscopy. transitions from the oxidized to p(m) state were initiated by perfusion with co/oxygen buffer, and the extent of conversion was quantitated by simultaneously monitoring visible absorption changes. in prior work, tentative assignments of bands were proposed for heme a(3), a change in the enviro ... | 2004 | 15533041 |
| a copper protein and a cytochrome bind at the same site on bacterial cytochrome c peroxidase. | pseudoazurin binds at a single site on cytochrome c peroxidase from paracoccus pantotrophus with a k(d) of 16.4 microm at 25 degrees c, ph 6.0, in an endothermic reaction that is driven by a large entropy change. sedimentation velocity experiments confirmed the presence of a single site, although results at higher pseudoazurin concentrations are complicated by the dimerization of the protein. microcalorimetry, ultracentrifugation, and (1)h nmr spectroscopy studies in which cytochrome c550, pseud ... | 2004 | 15544327 |
| sulfide dehydrogenase activity of the monomeric flavoprotein soxf of paracoccus pantotrophus. | flavocytochrome c-sulfide dehydrogenases (fcsds) are complexes of a flavoprotein with a c-type cytochrome performing hydrogen sulfide-dependent cytochrome c reduction in vitro. the amino acid sequence analysis revealed that the phylogenetic relationship of different flavoproteins reflected the relationship of sulfur-oxidizing bacteria. the flavoprotein soxf of paracoccus pantotrophus is 29-67% identical to the flavoprotein subunit of fcsd of phototrophic sulfur-oxidizing bacteria. purification o ... | 2004 | 15544340 |
| a dynamic zinc redox switch. | the crystal structures of glutathione-dependent formaldehyde-activating enzyme (gfa) from paracoccus denitrificans, which catalyzes the formation of s-hydroxymethylglutathione from formaldehyde and glutathione, and its complex with glutathione (gfa-gtt) have been determined. gfa has a new fold with two zinc-sulfur centers, one that is structural (zinc tetracoordinated) and one catalytic (zinc apparently tricoordinated). in gfa-gtt, the catalytic zinc is displaced due to disulfide bond formation ... | 2005 | 15548539 |
| 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 complet ... | 2004 | 15566182 |
| in-situ characterization of microbial community in an a/o submerged membrane bioreactor with nitrogen removal. | the bacterial community involved in removing nitrogen from sewage and their preferred do environment within an anoxic/oxic membrane bioreactor (a/o mbr) was investigated. a continuously operated laboratory-scale a/o mbr was maintained for 360 d. at a sludge age of 150 d and a c/n ratio of 3.5, the system was capable of removing 88% of the influent nitrogen from raw wastewater through typical nitrogen removal transformations (i.e. aerobic ammonia oxidation and anoxic nitrate reduction). character ... | 2004 | 15566185 |
| evidence that the rhizobium regulatory protein rira binds to cis-acting iron-responsive operators (iros) at promoters of some fe-regulated genes. | mutations in rira of rhizobium have been shown to deregulate expression of several genes that are normally repressed by iron. a conserved sequence, the iron-responsive operator (iro), was identified near promoters of vbsc (involved in the synthesis of the siderophore vicibactin), rpoi (specifies an ecf sigma factor needed for vicibactin synthesis) and the two fhua genes (encoding vicibactin receptor). removal of these iro sequences abolished fe-responsive repression. most of these genes were con ... | 2004 | 15583159 |
| [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 c ... | 2004 | 15605736 |
| high nitrate removal from synthetic wastewater with the mixed bacterial culture. | the applicability of the mixed bacterial culture, originated from two-stage anaerobic-aerobic industrial yeasts production wastewater treatment plant for high rate denitrification processes was investigated. after acclimation to nitrate, the dominant strains were pseudomonas and paracoccus sp. complete denitrification with low accumulation of nitrite-n (0.1 mg/l) was found in synthetic wastewater, obeying a zero-order reaction with respect to nitrate and a first-order reaction with respect to bi ... | 2005 | 15627558 |
| probing the access of protons to the k pathway in the paracoccus denitrificans cytochrome c oxidase. | in recent studies on heme-copper oxidases a particular glutamate residue in subunit ii has been suggested to constitute the entry point of the so-called k pathway. in contrast, mutations of this residue (e78(ii)) in the paracoccus denitrificans cytochrome c oxidase do not affect its catalytic activity at all (e78(ii)q) or reduce it to about 50% (e78(ii)a); in the latter case, the mutation causes no drastic decrease in heme a(3) reduction kinetics under anaerobic conditions, when compared to typi ... | 2005 | 15654878 |
| the enigma of paracoccus pantotrophus cytochrome cd(1) activation. | paracoccus pantotrophus cytochrome cd(1) nitrite reductase is isolated under aerobic conditions from anaerobically grown cells in an inactive form. this state requires reductive activation to make it catalytically competent for nitrite reduction. in this work, we discuss the methods of this reductive activation and its consequences for the cell. | 2005 | 15667289 |
| [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 ... | 2004 | 15688941 |
| experimental identification and quantification of glucose metabolism in seven bacterial species. | the structurally conserved and ubiquitous pathways of central carbon metabolism provide building blocks and cofactors for the biosynthesis of cellular macromolecules. the relative uses of pathways and reactions, however, vary widely among species and depend upon conditions, and some are not used at all. here we identify the network topology of glucose metabolism and its in vivo operation by quantification of intracellular carbon fluxes from 13c tracer experiments. specifically, we investigated a ... | 2005 | 15716428 |
| distinct conformation-mediated functions of an active site loop in the catalytic reactions of nad-dependent d-lactate dehydrogenase and formate dehydrogenase. | the three-dimensional structures of nad-dependent d-lactate dehydrogenase (d-ldh) and formate dehydrogenase (fdh), which resemble each other, imply that the two enzymes commonly employ certain main chain atoms, which are located on corresponding loop structures in the active sites of the two enzymes, for their respective catalytic functions. these active site loops adopt different conformations in the two enzymes, a difference likely attributable to hydrogen bonds with asn97 and glu141, which ar ... | 2005 | 15734738 |
| active site aspartate residues are critical for tryptophan tryptophylquinone biogenesis in methylamine dehydrogenase. | the biosynthesis of methylamine dehydrogenase (madh) requires formation of six intrasubunit disulfide bonds, incorporation of two oxygens into residue betatrp57 and covalent cross-linking of betatrp57 to betatrp108 to form the protein-derived cofactor tryptophan tryptophylquinone (ttq). residues betaasp76 and betaasp32 are located in close proximity to the quinone oxygens of ttq in the enzyme active site. these residues are structurally conserved in quinohemoprotein amine dehydrogenase, which po ... | 2005 | 15734739 |
| the effects of ligand exchange and mobility on the peroxidase activity of a bacterial cytochrome c upon unfolding. | the effect on the heme environment upon unfolding paracoccus versutus ferricytochrome c-550 and two site-directed variants, k99e and h118q, has been assessed through a combination of peroxidase activity increase and one-dimensional nmr spectroscopy. at ph 4.5, the data are consistent with a low- to high-spin heme transition, with the k99e mutation resulting in a protein with increased peroxidase activity in the absence of or at low concentrations of denaturant. furthermore, the mobility of the p ... | 2005 | 15744766 |
| evaluation of candidate probiotic strains for gilthead sea bream larvae (sparus aurata) using an in vivo approach. | the aim of this study was to evaluate the effect of six bacterial strains on gilthead sea bream larvae (sparus aurata). | 2005 | 15752217 |
| dissimilation of cysteate via 3-sulfolactate sulfo-lyase and a sulfate exporter in paracoccus pantotrophus nkncysa. | paracoccus pantotrophus nkncysa utilizes (r)-cysteate (2-amino-3-sulfopropionate) as a sole source of carbon and energy for growth, with either nitrate or molecular oxygen as terminal electron acceptor, and the specific utilization rate of cysteate is about 2 mkat (kg protein)(-1). the initial degradative reaction is catalysed by an (r)-cysteate : 2-oxoglutarate aminotransferase, which yields 3-sulfopyruvate. the latter was reduced to 3-sulfolactate by an nad-linked sulfolactate dehydrogenase [3 ... | 2005 | 15758220 |
| genetic diversity of benzoyl coenzyme a reductase genes detected in denitrifying isolates and estuarine sediment communities. | benzoyl coenzyme a (benzoyl-coa) reductase is a central enzyme in the anaerobic degradation of organic carbon, which utilizes a common intermediate (benzoyl-coa) in the metabolism of many aromatic compounds. the diversity of benzoyl-coa reductase genes in denitrifying bacterial isolates capable of degrading aromatic compounds and in river and estuarine sediment samples from the arthur kill in new jersey and the chesapeake bay in maryland was investigated. degenerate primers were developed from t ... | 2005 | 15812036 |
| effect of the systemic fungicide carboxin on electron transport function in membranes of micrococcus denitrificans. | the systemic fungicide carboxin (5,6-dihydro-2-methyl-1,4-oxathiin-3-carboxanilide) inhibited oxidation of succinate by membranes prepared from micrococcus denitrificans, the k(i) being 16 mum. oxycarboxin (5,6-dihydro-2-methyl-1,4-oxathiin-3-carboxanilide-4,4-dioxide), f831 (5,6-dihydro-2-methyl-1,4-oxathiin-3-carboxanilide-4-oxide), and another succinate oxidase inhibitor, 4,4,4-trifluoro-1-(2-thienyl)-1,3-butanedione (ttb) were less effective inhibitors of succinate oxidation by membranes of ... | 1974 | 15825307 |
| cloning and characterization of a region responsible for the maintenance of megaplasmid ptav3 of paracoccus versutus uw1. | using cointegrate formation, we constructed a basic replicon of the megaplasmid/mini-chromosome ptav3 of paracoccus versutus uw1. it is composed of two adjacent modules, responsible for plasmid replication (rep) and partitioning (par). functional analysis of the par region identified a determinant of incompatibility (inc2), whose presence is crucial for proper partitioning (the partitioning site). database searches revealed that the only known replicon with significant homology to that of ptav3 ... | 2005 | 15848227 |
| a preliminary time-of-flight neutron diffraction study on amicyanin from paracoccus denitrificans. | crystals of the blue copper protein amicyanin suitable for neutron diffraction were grown by the sitting-drop method, followed by repeated macroseeding using solutions prepared with d(2)o. although the crystal sizes were the same, crystals grown using solutions made up in h(2)o in the initial stages of macroseeding and solutions with d(2)o in later stages did not diffract neutrons well. however, when the protein was initially exchanged with buffered d(2)o and then crystallized and also macroseed ... | 2005 | 15858277 |
| development of nitrogen-removal bioreactor using poly(lactic acid) as an energy source. | to control nitrogen such as ammonia in a rearing water of aquatic animals, we developed new bioreactor capable of both nitrification and denitrification. it was consisted of gel-plate immobilized microorganisms and a biodegradable plastic plate composed of three kind of poly(lactic acid) as an energy source of denitrification. when batch treatment experiment by the bioreactor was continuously carried out with an artificial rearing water containing ammonia, nitrogen-removal rate of the bioreactor ... | 2004 | 15858361 |
| thermal stability of outer membrane protein porin from paracoccus denitrificans: ft-ir as a spectroscopic tool to study lipid-protein interaction. | lipid protein interactions play a key role in the stability and function of various membrane proteins. earlier we have reported the extreme thermal stability of porin from paracoccus denitrificans reconstituted into liposomes. here, we used fourier transform infrared spectroscopy for a label free analysis of the global secondary structural changes and local changes in the tyrosine microenvironment. our results show that a mixed lipid system (non-uniform bilayer) optimizes the thermal stability o ... | 2005 | 15862288 |
| sulfur dehydrogenase of paracoccus pantotrophus: the heme-2 domain of the molybdoprotein cytochrome c complex is dispensable for catalytic activity. | sulfur dehydrogenase, sox(cd)(2), is an essential part of the sulfur-oxidizing enzyme system of the chemotrophic bacterium paracoccus pantotrophus. sox(cd)(2) is a alpha(2)beta(2) complex composed of the molybdoprotein soxc (43 442 da) and the hybrid diheme c-type cytochrome soxd (37 637 da). sox(cd)(2) catalyzes the oxidation of protein-bound sulfur to sulfate with a unique six-electron transfer. amino acid sequence analysis identified the heme-1 domain of soxd proteins to be specific for sulfu ... | 2005 | 15865447 |
| soxrs-mediated regulation of chemotrophic sulfur oxidation in paracoccus pantotrophus. | paracoccus pantotrophus gb17 requires thiosulfate for induction of the sulfur-oxidizing (sox) enzyme system. the soxrs genes are divergently oriented to the soxvwxyza-h genes. soxr predicts a transcriptional regulator of the arsr family and soxs a periplasmic thioredoxin. the homogenate mutant gbomegas carrying a disruption of soxs by the omega-kanamycin-resistance-encoding interposon expressed a low thiosulfate-oxidizing activity under heterotrophic and mixotrophic growth conditions. this activ ... | 2005 | 15870478 |
| site-directed mutagenesis of proline 94 to alanine in amicyanin converts a true electron transfer reaction into one that is kinetically coupled. | amicyanin is a type i copper protein that mediates electron transfer (et) from methylamine dehydrogenase (madh) to cytochrome c-551i. pro(94) resides in the "ligand loop" of amicyanin, a sequence of amino acids that contains three of the four copper ligands. et from the reduced o-quinol tryptophan tryptophylquinone of madh to oxidized p94a amicyanin is a true et reaction that exhibits values of electronic coupling (h(ab)) and reorganization energy (lambda) that are the same as for the reaction o ... | 2005 | 15882058 |
| structural insight into soxc and soxd interaction and their role in electron transport process in the novel global sulfur cycle in paracoccus pantotrophus. | microbial oxidation of reduced inorganic sulfur compounds mainly sulfur anions in the environment is one of the major reactions of the global sulfur cycle mediated by phylogenetically diverse prokaryotes. the sulfur oxidizing gene cluster (sox) of alpha-proteobacteria comprises of at least 16 genes, which form two transcriptional units, viz., soxsrt and soxvwxyzabcdefgh. sequence analysis reveals that soxd gene product (soxd) belongs to the di-heme cytochrome c family of electron transport prote ... | 2005 | 15882991 |
| the effect of replacing the axial methionine ligand with a lysine residue in cytochrome c-550 from paracoccus versutus assessed by x-ray crystallography and unfolding. | the structure of cytochrome c-550 from the nonphotosynthetic bacteria paraccocus versutus has been solved by x-ray crystallography to 1.90 a resolution, and reveals a high structural homology to other bacterial cytochromes c(2). the effect of replacing the axial heme-iron methionine ligand with a lysine residue on protein structure and unfolding has been assessed using the m100k variant. from x-ray structures at 1.95 and 1.55 a resolution it became clear that the amino group of the lysine side c ... | 2005 | 15885094 |
| y25s variant of paracoccus pantotrophus cytochrome cd1 provides insight into anion binding by d1 heme and a rare example of a critical difference between solution and crystal structures. | tyr25 is a ligand to the active site d1 heme in as isolated, oxidized cytochrome cd1 nitrite reductase from paracoccus pantotrophus. this form of the enzyme requires reductive activation, a process that involves not only displacement of tyr25 from the d1 heme but also switching of the ligands at the c heme from bis-histidinyl to his/met. a y25s variant retains this bis-histidinyl coordination in the crystal of the oxidized state that has sulfate bound to the d1 heme iron. this y25s form of the e ... | 2005 | 15901734 |
| site-directed modifications indicate differences in axial haem c iron ligation between the related nrfh and napc families of multihaem c-type cytochromes. | during the last decade, a number of related bacterial membrane-bound multihaem c-type cytochromes, collectively referred to as the napc/nirt family, were identified. these proteins are generally thought to catalyse electron transport between the quinone/quinol pool and periplasmic oxidoreductases. the best-characterized members, the tetrahaem c-type cytochromes nrfh and napc, mediate electron transport to nrfa and napa respectively. amino acid sequence alignments suggest that the nature and posi ... | 2005 | 15907193 |
| miniaturized kinetic growth inhibition assay with denitrifying bacteria paracoccus denitrificans. | a method to cultivate anaerobic bacteria on standard 96-well microplates with automatic recording of growth curves is presented. the method was used as a kinetic growth inhibition assay with denitrifying bacteria paracoccus denitrificans, and applied to various heavy metal ions and selected agrochemicals. incorporated in a battery of other biotest the assay could take into account effects of toxicants on denitrifying organisms. the results (ec50) revealed that the assay was relatively sensitive. ... | 2005 | 15910901 |
| impact of the bacterial type i cytochrome c maturation system on different biological processes. | in the alpha-, beta- and gamma-proteobacteria, the so-called cytochrome c maturation (ccm) system is known to promote the covalent attachment of the haem to periplasmic apocytochrome c. however, in species of pseudomonas, rhizobium, paracoccus and legionella, mutations in ccm genes result in phenotypes that cannot be readily explained by the simple loss of a c-type cytochrome. these phenotypes include loss of siderophore production and utilization, reduced abilities to grow in low-iron condition ... | 2005 | 15916594 |
| 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, pseudomon ... | 2005 | 15922579 |
| maug-dependent in vitro biosynthesis of tryptophan tryptophylquinone in methylamine dehydrogenase. | tryptophan tryptophylquinone (ttq) is the prosthetic group of methylamine dehydrogenase (madh) and is synthesized through post-translational modification of two endogenous tryptophan residues. this modification involves two oxygenation reactions and one cross-linking reaction. it is clearly shown that the incorporation of the second oxygen into betatrp57 and the covalent cross-linking of betatrp57 to betatrp108 are maug-dependent processes. these reaction steps are severely compromised in vivo w ... | 2005 | 15941239 |
| amperometric detection of the bacterial metabolic regulation with a microbial array chip. | a microbial array chip with collagen gel spots entrapping living bacterial cells has been applied to investigate the metabolic regulation in paracoccus denitrificans. scanning electrochemical microscopy (secm) was used to monitor the ferrocyanide production that reflects the electron flow in the respiratory chain located within the internal membrane of p. denitrificans. the ferrocyanide production from p. denitrificans largely depends on the types of the carbon source (glucose or lactate), sugge ... | 2005 | 15967362 |
| performance of calorimetric methods for the investigation of microbial systems in combination with additional sensors. | calorimetric methods are used in combination with online oxygen measurement (using an amperometric sensor) and determination of the optical density (using a fibre optic sensor) to investigate microbial growth behaviour. the calorimetric curves of different batch experiments show a characteristic and reproducible course. changes in the slope of the deltat-time curves indicate the effects of limiting factors on the microbial activity during the cultivation. a first limitation could be correlated w ... | 2005 | 15983768 |
| characterization of beta-carotene ketolases, crtw, from marine bacteria by complementation analysis in escherichia coli. | a complementation analysis was performed in escherichia coli to evaluate the efficiency of beta-carotene ketolases (crtw) from the marine bacteria brevundimonas sp. sd212, paracoccus sp. pc1 (alcaligenes pc-1), and paracoccus sp. n81106 (agrobacterium aurantiacum), for astaxanthin production. each crtw gene was expressed in escherichia coli synthesizing zeaxanthin due to the presence of plasmid paccar25deltacrtx. carotenoids that accumulated in the resulting e. coli transformants were examined b ... | 2005 | 16007373 |
| paracoccus koreensis sp. nov., isolated from anaerobic granules in an upflow anaerobic sludge blanket (uasb) reactor. | a gram-negative, short rod- to coccus-shaped, non-spore-forming bacterium (ch05(t)) was isolated from granules in an upflow anaerobic sludge blanket (uasb) reactor. on the basis of 16s rrna gene sequence similarity, strain ch05(t) was shown to belong to the subclass alpha-proteobacteria, being related to paracoccus solventivorans (97.5%), paracoccus alkenifer (96.9%) and paracoccus kocurii (96.4%). the phylogenetic distance from paracoccus species with validly published names was always less tha ... | 2005 | 16014497 |
| gating of proton and water transfer in the respiratory enzyme cytochrome c oxidase. | the membrane-bound enzyme cytochrome c oxidase is responsible for cell respiration in aerobic organisms and conserves free energy from o2 reduction into an electrochemical proton gradient by coupling the redox reaction to proton-pumping across the membrane. o2 reduction produces water at the bimetallic heme a3/cub active site next to a hydrophobic cavity deep within the membrane. water molecules in this cavity have been suggested to play an important role in the proton-pumping mechanism. here, w ... | 2005 | 16014708 |
| is a third proton-conducting pathway operative in bacterial cytochrome c oxidase? | despite the existence of several three-dimensional structures of cytochrome c oxidases, a detailed understanding of pathways involved in proton movements through the complex remains largely elusive. next to the two well-established pathways (termed d and k), an additional proton-conducting network ('h-channel') has been proposed for the beef heart enzyme. yet, our recent mutational studies on corresponding residues of the paracoccus denitrificans cytochrome c oxidase provide no clues that such a ... | 2005 | 16042608 |