| cell-cell signaling and the agrobacterium tumefaciens ti plasmid copy number fluctuations. | the agrobacterium tumefaciens oncogenic ti plasmids replicate and segregate to daughter cells via repabc cassettes, in which repa and repb are plasmid partitioning genes and repc encodes the replication initiator protein. repabc cassettes are encountered in a growing number of plasmids and chromosomes of the alpha-proteobacteria, and findings from particular representatives of agrobacteria, rhizobia and paracoccus have began to shed light on their structure and functions. amongst repabc replicon ... | 2008 | 18664372 |
| an exceptionally dmso-tolerant alcohol dehydrogenase for the stereoselective reduction of ketones. | a novel short-chain alcohol dehydrogenase from paracoccus pantotrophus dsm 11072, which is applicable for hydrogen transfer, has been identified, cloned, and overexpressed in e. coli. the enzyme stereoselectively reduces several ketones in a sustainable substrate-coupled approach using 2-propanol (5% v/v) as hydrogen donor. the enzyme maintained its activity in organic co-solvents in biphasic as well as monophasic systems and was even active in micro-aqueous media (1% v/v aqueous buffer). in gen ... | 2008 | 18702138 |
| characterization of the quinone reductase activity of the ferric reductase b protein from paracoccus denitrificans. | the ferric reductase b (ferb) protein of paracoccus denitrificans exhibits activity of an nad(p)h: fe(iii) chelate, chromate and quinone oxidoreductase. sequence analysis places ferb in a family of soluble flavin-containing quinone reductases. the enzyme reduces a range of quinone substrates, including derivatives of 1,4-benzoquinone and 1,2- and 1,4-naphthoquinone, via a ping-pong kinetic mechanism. dicoumarol and cibacron blue 3ga are competitive inhibitors of nadh oxidation. in the case of be ... | 2009 | 19138657 |
| characterizations of denitrifying polyphosphate-accumulating bacterium paracoccus sp. strain ykp-9. | a denitrifying polyphosphate-accumulating bacterium (ykp-9) was isolated from activated sludge of a 5-stage biological nutrient removal process with step feed system. this organism was a gram-negative, coccus-shaped, facultative aerobic chemoorganotroph. it had a respiratory type of metabolism with oxygen, nitrate, and nitrite as terminal electron acceptors. the 16s rrna gene sequence of strain ykp-9 was most similar to the 16s rrna gene sequence of paracoccus sp. ol18 (ay312056) (similarity lev ... | 2008 | 19131700 |
| coherent raman detected electron spin resonance spectroscopy of metalloproteins: linking electron spin resonance and magnetic circular dichroism. | the simultaneous excitation of paramagnetic molecules with optical (laser) and microwave radiation in the presence of a magnetic field can cause an amplitude, or phase, modulation of the transmitted light at the microwave frequency. the detection of this modulation indicates the presence of coupled optical and esr transitions. the phenomenon can be viewed as a coherent raman effect or, in most cases, as a microwave frequency modulation of the magnetic circular dichroism by the precessing magneti ... | 2008 | 19021521 |
| identification of a mosaic transposable element of paracoccus marcusii composed of insertion sequence ispmar4 (isas1 family) and an is1247a-driven transposable module (tmo). | a sacb-based trap plasmid was used to clone a mosaic transposable element (te) in the carotenoid producer paracoccus marcusii os22. this element is composed of an insertion sequence (is) ispmar4 (isas1 family), which contains an inserted functional transposable module (tmo) generated by a copy of is1247a (of the is1380 family). besides is1247a sequences, the tmo also contains the 3'-end region of a putative alpha/beta hydrolase gene, whose expression might be activated from the p(2) promoter of ... | 2009 | 19187199 |
| effect of temperature on the life history of the mealybug paracoccus marginatus (hemiptera: pseudococcidae). | effect of temperature on the life history of the mealybug paracoccus marginatus williams & granara de willink (hemiptera: pseudococcidae) was investigated in the laboratory. p. marginatus was able to develop and complete its life cycle at 18, 20, 25, and 30 +/- 1 degrees c. at 15, 34, and 35 degrees c, the eggs hatched after 27.5, 5.9, and 5.5 d of incubation, respectively, but further development of the first-instar nymphs was arrested. no eggs hatched at 37 degrees c. the developmental time fo ... | 2008 | 19133459 |
| different biochemical mechanisms ensure network-wide balancing of reducing equivalents in microbial metabolism. | to sustain growth, the catabolic formation of the redox equivalent nadph must be balanced with the anabolic demand. the mechanisms that ensure such network-wide balancing, however, are presently not understood. based on 13c-detected intracellular fluxes, metabolite concentrations, and cofactor specificities for all relevant central metabolic enzymes, we have quantified catabolic nadph production in agrobacterium tumefaciens, bacillus subtilis, escherichia coli, paracoccus versutus, pseudomonas f ... | 2009 | 19181802 |
| kinetic mechanism for the initial steps in maug-dependent tryptophan tryptophylquinone biosynthesis. | the diheme enzyme maug catalyzes the biosynthesis of tryptophan tryptophylquinone (ttq), the protein-derived cofactor of methylamine dehydrogenase (madh). this process requires the six-electron oxidation of a 119 kda madh precursor protein with incompletely synthesized ttq (premadh). the kinetic mechanism of the initial two-electron oxidation of this natural substrate by maug was characterized. the relative reactivity of free maug toward h(2)o(2) and the o(2) analogue co was essentially the same ... | 2009 | 19196017 |
| characterization of diverse heterocyclic amine-degrading denitrifying bacteria from various environments. | although, there have been many published bacterial strains aerobically degrading the heterocyclic amine compounds, only one strain to date has been reported to degrade pyrrolidine under denitrifying conditions. in this study, denitrifying bacteria degrading pyrrolidine and piperidine were isolated from diverse geological and ecological origins through selective enrichment procedures. based on the comparative sequence results of 16s rrna genes, 30 heterocyclic amine-degrading isolates were groupe ... | 2009 | 19183960 |
| pathway engineering of brassica napus seeds using multiple key enzyme genes involved in ketocarotenoid formation. | brassica napus (canola) plants were genetically manipulated to increase the amount and composition of carotenoids in seeds by using seven key enzyme genes involved in ketocarotenoid formation, which originated from a soil bacterium pantoea ananatis (formerly called erwinia uredovora 20d3), and marine bacteria brevundimonas sp. strain sd212 and paracoccus sp. strain n81106 (formerly called agrobacterium aurantiacum). the seven key gene cassettes, in which each gene was surrounded by an appropriat ... | 2009 | 19204032 |
| simultaneous biodegradation of pyridine and quinoline by two mixed bacterial strains. | experiments were conducted to provide data on the effectiveness of bioaugmentation in the removal of pyridine and quinoline from different wastewaters. a pyridine-degrading bacterial strain (paracoccus sp. bw001) and a quinoline-degrading strain (pseudomonas sp. bw003) were isolated from the activated sludge of a coking wastewater treatment plant. in this study, a consortium of these two bacterial strains was used as inoculum to simultaneously degrade pyridine and quinoline in three types of was ... | 2009 | 19221733 |
| investigations into the uptake of copper, iron and selenium by a highly sulphated bacterial exopolysaccharide isolated from microbial mats. | a bacterium isolated from microbial mats located on a polynesian atoll produced a high molecular weight (3,000 kda) and highly sulphated exopolysaccharide. previous studies showed that the chemical structure of this eps consisted of neutral sugars, uronic acids, and high proportions of acetate and sulphate groups. the copper- and iron-binding ability of the purified pre-treated native eps was investigated. results showed that this eps had a very high affinity for both copper (9.84 mmol g(-1) eps ... | 2009 | 19198908 |
| thiosulfate oxidation and mixotrophic growth of methylobacterium goesingense and methylobacterium fujisawaense. | the mixotrophic growth with methanol plus thiosulfate was examined in nutrient-limited mixotrophic condition for methylobacterium goesingense cbmb5 and methylobacterium fujisawaense cbmb37. thiosulfate oxidation increased the growth and protein yield in mixotrophic medium that contained 150 mm methanol and 20 mm sodium thiosulfate, at 144 h. respirometric study revealed that thiosulfate was the most preferable reduced inorganic sulfur source, followed by sulfite and sulfur. m. goesingense cbmb5 ... | 2009 | 19190404 |
| new insights into the biodegradation of thiodiglycol, the hydrolysis product of yperite (sulfur mustard gas). | to isolate thiodiglycol (tdg)-degrading bacteria, the mustard gas hydrolysis product, and to characterize the metabolites formed and the enzymes involved in the degradation. | 2009 | 19191966 |
| association of cytochrome c with membrane-bound cytochrome c oxidase proceeds parallel to the membrane rather than in bulk solution. | electron transfer between the water-soluble cytochrome c and the integral membrane protein cytochrome c oxidase (cox) is the terminal reaction in the respiratory chain. the first step in this reaction is the diffusional association of cytochrome c toward cox, and it is still not completely clear whether cytochrome c diffuses in the bulk solution while encountering cox, or whether it prefers to diffuse laterally on the membrane surface. this is a rather crucial question, since in the latter case ... | 2009 | 19254533 |
| the structure of the periplasmic thiol-disulfide oxidoreductase soxs from paracoccus pantotrophus indicates a triple trx/grx/dsbc functionality in chemotrophic sulfur oxidation. | the periplasmic thiol-disulfide oxidoreductase soxs is beneficial for the sulfur-oxidizing (sox) phenotype of the facultative chemotrophic bacterium paracoccus pantotrophus and is not part of the sox enzyme system. soxs combines features of thioredoxins, glutaredoxins and the thiol-disulfide oxidoreductases of the dsb family in structure, target specificity and reaction. the structure of soxs was solved in oxidized and reduced forms at 2.1 and 1.9 a resolution, respectively. soxs revealed high s ... | 2009 | 19237745 |
| electron transfer and energy transduction in the terminal part of the respiratory chain - lessons from bacterial model systems. | this review focuses on the terminal part of the respiratory chain where, macroscopically speaking, electron transfer (et) switches from the two-electron donor, ubiquinol, to the single-electron carrier, cytochrome c, to finally reduce the four-electron acceptor dioxygen. with 3-d structures of prominent representatives of such multi-subunit membrane complexes known for some time, this section of the et chain still leaves a number of key questions unanswered. the two relevant enzymes, ubiquinol:c ... | 2009 | 19268423 |
| the silent form of quinohemoprotein amine dehydrogenase from paracoccus denitrificans. | quinohemoprotein amine dehydrogenase (qh-amdh) from paracoccus denitrificans is an alphabetagamma heterotrimeric enzyme catalyzing oxidative deamination of amines with large substitutes, such as butylamine and benzylamine. the smallest gamma subunit has cross-linking cysteine tryptophylquinone (ctq) as a catalytic center. a hemoprotein similar to qh-amdh in molecular mass, subunit structure, and uv-vis spectral property, but having no enzymatic activity, was isolated. the enzymatically silent fo ... | 2009 | 19270386 |
| the bacterial respiratory nitric oxide reductase. | the two-subunit cytochrome bc complex (norbc) isolated from membranes of the model denitrifying soil bacterium paracoccus denitrificans is the best-characterized example of the bacterial respiratory nitric oxide reductases. these are members of the super-family of haem-copper oxidases and are characterized by the elemental composition of their active site, which contains non-haem iron rather than copper, at which the reductive coupling of two molecules of nitric oxide to form nitrous oxide is ca ... | 2009 | 19290869 |
| ferric reductase a is essential for effective iron acquisition in paracoccus denitrificans. | based on n-terminal sequences obtained from the purified cytoplasmic ferric reductases fera and ferb, their corresponding genes were identified in the published genome sequence of paracoccus denitrificans pd1222. the fera and ferb genes were cloned and individually inactivated by insertion of a kanamycin resistance marker, and then returned to p. denitrificans for exchange with their wild-type copies. the resulting fera and ferb mutant strains showed normal growth in brain heart infusion broth. ... | 2009 | 19332830 |
| paracoccus aestuarii sp. nov., isolated from tidal flat sediment. | a gram-negative micro-organism, designated strain b7(t), was isolated from tidal flat sediment and subjected to a polyphasic taxonomic study involving morphological, physiological, biochemical and 16s rrna gene sequence analyses. a phylogenetic analysis based on the 16s rrna gene sequence indicated that strain b7(t) belonged to the genus paracoccus and was closely related phylogenetically to paracoccus marcusii mh1(t) (97.5 % sequence similarity), paracoccus marinus kkl-a5(t) (97.5 %), paracoccu ... | 2009 | 19329608 |
| interaction between sox proteins of two physiologically distinct bacteria and a new protein involved in thiosulfate oxidation. | organisms using the thiosulfate-oxidizing sox enzyme system fall into two groups: group 1 forms sulfur globules as intermediates (allochromatium vinosum), group 2 does not (paracoccus pantotrophus). while several components of their sox systems are quite similar, i.e. the proteins soxxa, soxyz and soxb, they differ by sox(cd)(2) which is absent in sulfur globule-forming organisms. still, the respective enzymes are partly exchangeable in vitro: p. pantotrophus sox enzymes work productively with a ... | 2009 | 19303410 |
| chaperones of f1-atpase. | mitochondrial f(1)-atpase contains a hexamer of alternating alpha and beta subunits. the assembly of this structure requires two specialized chaperones, atp11p and atp12p, that bind transiently to beta and alpha. in the absence of atp11p and atp12p, the hexamer is not formed, and alpha and beta precipitate as large insoluble aggregates. an early model for the mechanism of chaperone-mediated f(1) assembly (wang, z. g., sheluho, d., gatti, d. l., and ackerman, s. h. (2000) embo j. 19, 1486-1493) h ... | 2009 | 19383603 |
| high resolution crystal structure of paracoccus denitrificans cytochrome c oxidase: new insights into the active site and the proton transfer pathways. | the structure of the two-subunit cytochrome c oxidase from paracoccus denitrificans has been refined using x-ray cryodata to 2.25 a resolution in order to gain further insights into its mechanism of action. the refined structural model shows a number of new features including many additional solvent and detergent molecules. the electron density bridging the heme a(3) iron and cu(b) of the active site is fitted best by a peroxo-group or a chloride ion. two waters or oh(-) groups do not fit, one w ... | 2009 | 19374884 |
| exploring the terminal region of the proton pathway in the bacterial nitric oxide reductase. | the c-type nitric oxide reductase (cnor) from paracoccus (p.) denitrificans is an integral membrane protein that catalyzes no reduction; 2no+2e(-)+2h(+)-->n(2)o+h(2)o. it is also capable of catalyzing the reduction of oxygen to water, albeit more slowly than no reduction. cnors are divergent members of the heme-copper oxidase superfamily (hcuos) which reduce no, do not pump protons, and the reaction they catalyse is non-electrogenic. all known cnors have been shown to have five conserved glutama ... | 2009 | 19332356 |
| time-resolved oh-->eh transition of the aberrant ba3 oxidase from thermus thermophilus. | the kinetics of single-electron injection into the oxidized nonrelaxed state (oh --> eh transition) of the aberrant ba3 cytochrome oxidase from thermus thermophilus, noted for its lowered efficiency of proton pumping, was investigated by time-resolved optical spectroscopy. two main phases of intraprotein electron transfer were resolved. the first component (tau approximately 17 mus) reflects oxidation of cua and reduction of the heme groups (low-spin heme b and high-spin heme a3 in a ratio close ... | 2009 | 19382345 |
| elevated proton leak of the intermediate oh in cytochrome c oxidase. | the kinetics of the formation and relaxation of transmembrane electric potential (deltapsi) during the complete single turnover of cco was studied in the bovine heart mitochondrial and the aa(3)-type paracoccus denitrificans enzymes incorporated into proteoliposome membrane. the real-time deltapsi kinetics was followed by the direct electrometry technique. the prompt oxidation of cco and formation of the activated, oxidized (o(h)) state of the enzyme leaves the enzyme trapped in the open state t ... | 2009 | 19486696 |
| molecular mimicry in innate immunity: crystal structure of a bacterial tir domain. | macrophages detect pathogen infection via the activation of their plasma membrane-bound toll-like receptor proteins (tlrs). the heterotypic interaction between the toll/interleukin-1 receptor (tir) domains of tlrs and adaptor proteins, like myeloid differentiation primary response gene 88 (myd88), is the first intracellular step in the signaling pathway of the mammalian innate immune response. the hetero-oligomerization of the tirs of the receptor and adaptor brings about the activation of the t ... | 2009 | 19535337 |
| effect of periplasmic nitrate reductase on diauxic lag of paracoccus pantotrophus. | paracoccus pantotrophus expresses two nitrate reductases-membrane bound nitrate reductase (nar) and periplasmic nitrate reductase (nap). in growth experiments with two denitrifying species (paracoccus pantotrophus and alcaligenes eutrophus) that have both nap and nar and two species (pseudomonas denitrificans and pseudomonas fluorescens) with nar only, it was found that diauxic lag is shorter for bacteria that express nap. in p. pantotrophus, napedabc encodes the periplasmic nitrate reductase. t ... | 2009 | 19399903 |
| paracoccus yeei: a new unusual opportunistic bacterium in ambulatory peritoneal dialysis. | paracoccus yeei was identified as the etiologic agent of peritonitis in an ambulatory peritoneal dialysis patient. while the old biochemical identification kits are not able to identify this species, the new colorimetric vitek 2 gn card correctly identified this isolate in 7hours. its identity was confirmed by sequencing of the 16s rrna gene. | 2010 | 19556157 |
| time-resolved o(h)-->e(h) transition of the aberrant ba(3) oxidase from thermus thermophilus. | the kinetics of single-electron injection into the oxidized nonrelaxed state (o(h)-->e(h) transition) of the aberrant ba(3) cytochrome oxidase from thermus thermophilus, noted for its lowered efficiency of proton pumping, was investigated by time-resolved optical spectroscopy. two main phases of intraprotein electron transfer were resolved. the first component (t~17 mus) reflects oxidation of cu(a) and reduction of the heme groups (low-spin heme b and high-spin heme a(3) in a ratio close to 50:5 ... | 2009 | 19413948 |
| surf1, associated with leigh syndrome in humans, is a heme-binding protein in bacterial oxidase biogenesis. | biogenesis of mitochondrial cytochrome c oxidase (cox) relies on a large number of assembly factors, among them the transmembrane protein surf1. the loss of human surf1 function is associated with leigh syndrome, a fatal neurodegenerative disorder caused by severe cox deficiency. in the bacterium paracoccus denitrificans, two homologous proteins, surf1c and surf1q, were identified, which we characterize in the present study. when coexpressed in escherichia coli together with enzymes for heme a s ... | 2009 | 19625251 |
| paracoccus chinensis sp. nov., isolated from sediment of a reservoir. | a gram-negative, short ovoid- to coccus-shaped, aerobic, motile, non-spore-forming bacterium (designated strain ks-11(t)) was isolated from sediment of the eutrophic guanting reservoir in beijing, china. colonies grown on r2a agar plates were circular, convex and colourless to orange. the strain grew in the presence of up to 1 % nacl (optimum, 0 % nacl). growth occurred at 25-40 degrees c (optimum, 28-37 degrees c) and at ph 6.0-9.5 (optimum, ph 7.5-9.0). on the basis of 16s rrna gene sequence s ... | 2009 | 19625438 |
| biomineralization of n,n-dimethylformamide by paracoccus sp. strain dmf. | n,n-dimethylformamide (dmf) is a man-made compound that is widely used as a solvent for the synthesis of various organic compounds. in this study, a bacterial strain paracoccus sp. dmf capable of using dmf as the sole carbon, nitrogen and energy source, was isolated from an enrichment culture developed using activated sludge from domestic waste water treatment unit as the source inoculum. the strain dmf was characterized by biochemical tests and 16s rdna sequence analysis, to be belonging to the ... | 2009 | 19592157 |
| capillary zone electrophoresis with field enhanced sample stacking as a tool for targeted metabolome analysis of adenine nucleotides and coenzymes in paracoccus denitrificans. | the main aim of this work was to demonstrate the applicability of capillary zone electrophoresis in combination with field enhanced sample stacking in targeted metabolome analyses of adenine nucleotides--amp, adp, atp, coenzymes nad(+), nadp(+) and their reduced forms in paracoccus denitrificans. sodium carbonate/hydrogencarbonate buffer (100 mm, ph 9.6) with the addition of beta-cd at a concentration of 10 mm was found to be an effective bge for their separation within 20 min. besides this, spe ... | 2009 | 19551744 |
| endophytic bacteria associated with growing shoot tips of banana (musa sp.) cv. grand naine and the affinity of endophytes to the host. | a cultivation-based assessment of endophytic bacteria present in deep-seated shoot tips of banana suckers was made with a view to generate information on the associated organisms, potential endophytic contaminants in tissue-cultured bananas and to assess if the endophytes shared a beneficial relationship with the host. plating the tissue homogenate from the central core of suckers showed colony growth on nutrient agar from just 75% and 42% of the 12 stocks during may and november, respectively ( ... | 2009 | 19633807 |
| biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaea. | lithotrophic sulfur oxidation is an ancient metabolic process. ecologically and taxonomically diverged prokaryotes have differential abilities to utilize different reduced sulfur compounds as lithotrophic substrates. different phototrophic or chemotrophic species use different enzymes, pathways and mechanisms of electron transport and energy conservation for the oxidation of any given substrate. while the mechanisms of sulfur oxidation in obligately chemolithotrophic bacteria, predominantly belo ... | 2009 | 19645821 |
| a variable temperature spectroscopic study on paracoccuspantotrophus pseudoazurin: protein constraints on the blue cu site. | the blue or type 1 (t1) copper site of paracoccuspantotrophus pseudoazurin exhibits significant absorption intensity in both the 450 and 600 nm regions. these are sigma and pi s(cys) to cu(2+) charge transfer (ct) transitions. the temperature dependent absorption, epr, and resonance raman (rr) vibrations enhanced by these bands indicate that a single species is present at all temperatures. this contrasts the temperature dependent behavior of the t1 center in nitrite reductase [s. ghosh, x. xie, ... | 2009 | 19481814 |
| 50 hz magnetic field effect on the morphology of bacteria. | atomic force microscopy was used to distinguish changes in morphology of bacteria induced by 50 hz 10 mt magnetic field exposure. it is known that alternating magnetic field exposure causes decrease of viability of different bacterial strains. previously we found that the viability of rod-like bacteria exposed to magnetic field decreased twice more in comparison with the spherical ones. motivated by this fact we carried out this study with bacterial cells of both shapes. we used escherichia coli ... | 2009 | 19616439 |
| paracoccus saliphilus sp. nov., a halophilic bacterium isolated from a saline soil. | a gram-negative, coccoid to short rod-shaped, non-spore-forming, moderately halophilic bacterium, designated strain yim 90738t, was isolated from a salt lake in xinjiang province, north-west china, and was subjected to a polyphasic taxonomic study. the strain was non-motile and grew at ph 6.0-8.0 (optimal growth at ph 7.0), 10-55 degrees c (optimal growth at 37 degrees c) and salinities of 1-15% nacl (w/v, optimal growth at 8% nacl). ubiquinone 10 was detected as the major respiratory quinone. t ... | 2009 | 19567556 |
| defining the role of the axial ligand of the type 1 copper site in amicyanin by replacement of methionine with leucine. | the effects of replacing the axial methionine ligand of the type 1 copper site with leucine on the structure and function of amicyanin have been characterized. the crystal structures of the oxidized and reduced forms of the protein reveal that the copper site is now tricoordinate with no axial ligand, and that the copper coordination distances for the two ligands provided by histidines are significantly increased. despite these structural changes, the absorption and epr spectra of m98l amicyanin ... | 2009 | 19715303 |
| uncovering novel biochemistry in the mechanism of tryptophan tryptophylquinone cofactor biosynthesis. | catalytic quinone cofactors derived from post-translational modification of amino acid residues within the enzyme polypeptide have roles in a variety of biological processes ranging from metabolism in bacteria to inflammation and connective tissue maturation in humans. in recent years, studies of the biosynthesis of one of these cofactors, tryptophan tryptophylquinone (ttq), have provided examples of novel chemistry that is required for the generation of these protein-derived cofactors. a novel ... | 2009 | 19648051 |
| heterologous expression and molecular characterization of the nad(p)h:acceptor oxidoreductase (ferb) of paracoccus denitrificans. | ferb is a flavoenzyme capable of reducing quinones, ferric complexes and chromate. its expression in escherichia coli as a hexahistidine fusion resulted in a functional product only when the tag was placed on the c-terminus. the molecular mass values estimated by gel permeation chromatography were compatible with the existence of either dimer or trimer, whereas the light scattering data, together with cross-linking experiments that yielded exclusively monomer and dimer bands on dodecyl sulfate-p ... | 2009 | 19651218 |
| inducible-expression plasmid for rhodobacter sphaeroides and paracoccus denitrificans. | we have developed a stable isopropyl-beta-d-thiogalactopyranoside (iptg)-inducible-expression plasmid, pind4, which allows graduated levels of protein expression in the alphaproteobacteria rhodobacter sphaeroides and paracoccus denitrificans. pind4 confers kanamycin resistance and combines the stable replicon of pmg160 with the laci(q) gene from pyanni3 and the lac promoter, p(a1/04/03), from pjba24. | 2009 | 19684165 |
| ecophysiology and the energetic benefit of mixotrophic fe(ii) oxidation by various strains of nitrate-reducing bacteria. | in order to assess the importance of nitrate-dependent fe(ii) oxidation and its impact on the growth physiology of dominant fe oxidizers, we counted these bacteria in freshwater lake sediments and studied their growth physiology. most probable number counts of nitrate-reducing fe(ii)-oxidizing bacteria in the sediment of lake constance, a freshwater lake in southern germany, yielded about 10(5) cells ml(-1) of the total heterotrophic nitrate-reducing bacteria, with about 1% (10(3) cells ml(-1)) ... | 2009 | 19732145 |
| suicide inactivation of maug during reaction with o(2) or h(2)o(2) in the absence of its natural protein substrate. | maug is a diheme protein that catalyzes the six-electron oxidation of a biosynthetic precursor protein of methylamine dehydrogenase (premadh) with partially synthesized tryptophan tryptophylquinone (ttq) to yield the mature protein with the functional protein-derived ttq cofactor. the biosynthetic reaction proceeds via a relatively stable high valent bis-fe(iv) intermediate. oxidizing equivalents ([o]) for this reaction may be provided by either o(2) plus electrons from an external donor or h(2) ... | 2009 | 19788236 |
| multifrequency pulsed electron paramagnetic resonance on metalloproteins. | metalloproteins often contain metal centers that are paramagnetic in some functional state of the protein; hence electron paramagnetic resonance (epr) spectroscopy can be a powerful tool for studying protein structure and function. dipolar spectroscopy allows the determination of the dipole-dipole interactions between metal centers in protein complexes, revealing the structural arrangement of different paramagnetic centers at distances of up to 8 nm. hyperfine spectroscopy can be used to measure ... | 2010 | 19842617 |
| random transposon vectors puttns for the markerless integration of exogenous genes into gram-negative eubacteria chromosomes. | a set of random transposon vectors puttns that facilitates the markerless integration of new functions into the chromosome of gram-negative bacteria has been developed. the vectors, which are derived from mini-tn5 transposons, are located on a r6k-based suicide delivery plasmid that provides the is50(r) transposase tnp gene in cis, but they are external to the mobile element. the vectors' conjugal transfer to recipients is mediated by rp4 mobilization functions in the donor. internal to the mini ... | 2009 | 19778558 |
| corneal graft rejection complicated by paracoccus yeei infection in a patient who had undergone a penetrating keratoplasty. | a 68-year-old man who had undergone two penetrating keratoplasties of his left eye was admitted with early corneal graft failure. culture of the anterior chamber fluid yielded paracoccus yeei, a nonfermentative gram-negative bacillus which thus far had only been implicated in ocular disease by means of pcr and 16s rrna gene sequencing directly on patient material. | 2010 | 19889897 |
| a novel 11-kda inhibitory subunit in the f1fo atp synthase of paracoccus denitrificans and related alpha-proteobacteria. | the f(1)f(o) and f(1)-atpase complexes of paracoccus denitrificans were isolated for the first time by ion exchange, gel filtration, and density gradient centrifugation into functional native preparations. the liposome-reconstituted holoenzyme preserves its tight coupling between f(1) and f(o) sectors, as evidenced by its high sensitivity to the f(o) inhibitors venturicidin and diciclohexylcarbodiimide. comparison and n-terminal sequencing of the band profile in sds-page of the f(1) and f(1)f(o) ... | 2010 | 19783785 |
| deer distance measurement between a spin label and a native fad semiquinone in electron transfer flavoprotein. | the human mitochondrial electron transfer flavoprotein (etf) accepts electrons from at least 10 different flavoprotein dehydrogenases and transfers electrons to a single electron acceptor in the inner membrane. paracoccus denitrificans etf has the identical function, shares the same three-dimensional structure and functional domains, and exhibits the same conformational mobility. it has been proposed that the mobility of the alphaii domain permits the promiscuous behavior of etf with respect to ... | 2009 | 19886689 |
| d(1) haem biogenesis - assessing the roles of three nir gene products. | the synthesis of the modified tetrapyrrole known as d(1) haem requires several dedicated proteins which are coded for by a set of genes that are often found adjacent to the structural gene, nirs, for cytochrome cd(1) nitrite reductase. nire, the product of the first gene in the nir biogenesis operon, was anticipated to catalyse the conversion of uroporphyrinogen iii into precorrin-2; this was confirmed, but it was shown that this enzyme is less sensitive to product inhibition than similar enzyme ... | 2009 | 19796169 |
| functional consortium for denitrifying sulfide removal process. | denitrifying sulfide removal (dsr) process simultaneously converts sulfide, nitrate, and chemical oxygen demand from industrial wastewaters to elemental sulfur, nitrogen gas, and carbon dioxide, respectively. this investigation utilizes a dilution-to-extinction approach at 10(-2) to 10(-6) dilutions to elucidate the correlation between the composition of the microbial community and the dsr performance. in the original suspension and in 10(-2) dilution, the strains stenotrophomonas sp., thauera s ... | 2010 | 19956940 |
| microbial degradation of pyridine by paracoccus sp. isolated from contaminated soil. | a pyridine-degrading strain was isolated from the contaminated soil near the pesticide plant, identified as paracoccus sp., and designated as strain kt-5, on the basis of its partial 16s rrna gene sequence analysis. the effect of different co-substrates including glucose, ammonium chloride and trace elements on biodegradation of pyridine by paracoccus sp. kt-5 was investigated. the results showed that when the initial concentration of pyridine was about 900 mg l(-1), 100 mg l(-1) of glucose incr ... | 2010 | 19945787 |
| protonation of type-1 cu bound histidines: a quantum chemical study. | the protonation of the solvent-exposed histidine ligands of the type-1 cu sites in five proteins, thiobacillus ferrooxidans rusticyanin, pseudomonas aeruginosa azurin, fern plastocyanin, alcaligenes faecalis pseudoazurin, and paracoccus versutus amicyanin, were studied with quantum chemical methods and conductorlike polarizable continuum model (cpcm). active site model molecules consisting of approximately 140 atoms were extracted from x-ray crystal structures and optimized with the homogeneous ... | 2010 | 20000723 |
| comparing the substrate specificities of cytochrome c biogenesis systems i and ii: bioenergetics. | c-type cytochromes require specific post-translational protein systems, which vary in different organisms, for the characteristic covalent attachment of heme to the cytochrome polypeptide. cytochrome c biogenesis system ii, found in chloroplasts and many bacteria, comprises four subunits, two of which (resb and resc) are the minimal functional unit. the ycf5 gene from helicobacter pylori encodes a fusion of resb and resc. heterologous expression of resbc in escherichia coli lacking its own bioge ... | 2010 | 20050916 |
| modulation of the active site conformation by site-directed mutagenesis in cytochrome c oxidase from paracoccus denitrificans. | the structural and functional properties of active site mutants of cytochrome c oxidase from paracoccus denitrificans (pdcco) were investigated with resonance raman spectroscopy. based on the fe-co stretching modes and low frequency heme modes, two conformers (alpha- and beta-forms) were identified that are in equilibrium in the enzyme. the alpha-conformer, which is the dominant species in the wild-type enzyme, has a shorter heme a(3) iron-cu(b) distance and a more distorted heme, as compared to ... | 2010 | 20056281 |
| direct demonstration of half-of-the-sites reactivity in the dimeric cytochrome bc1 complex: enzyme with one inactive monomer is fully active but unable to activate the second ubiquinol oxidation site in response to ligand binding at the ubiquinone reduction site. | we previously proposed that the dimeric cytochrome bc(1) complex exhibits half-of-the-sites reactivity for ubiquinol oxidation and rapid electron transfer between bc(1) monomers (covian, r., kleinschroth, t., ludwig, b., and trumpower, b. l. (2007) j. biol. chem. 282, 22289-22297). here, we demonstrate the previously proposed half-of-the-sites reactivity and intermonomeric electron transfer by characterizing the kinetics of ubiquinol oxidation in the dimeric bc(1) complex from paracoccus denitri ... | 2010 | 19892700 |
| a plate method for screening of bacteria capable of degrading aliphatic nitriles. | a novel indicator plate method was developed for screening of aliphatic-nitrile-degrading bacteria. isolated bacteria were tested for utilization of acetonitrile as sole source of carbon and nitrogen with the release of ammonia. the released ammonia causes increase of the ph of the medium. phenol red indicator is used for detection of ammonia based on colour change of the indicator dye from red to pink. the liberation of ammonia from aliphatic-nitrile-utilizing bacteria is also studied in plates ... | 2010 | 19921293 |
| vibrational resonances and cub displacement controlled by proton motion in cytochrome c oxidase. | cytochrome c oxidase (cco), found in the inner mitochondrial membranes or in many bacteria, catalyzes the four-electron reduction of molecular oxygen to water. four protons are pumped across the inner mitochondrial membrane through cco. in this study, quantum mechanics/molecular mechanics and molecular dynamics calculations are used to probe the spectroscopic characteristics of the ferryl intermediates in the aa(3) cco/o(2) reaction. these highly elaborate calculations, supported by several calc ... | 2010 | 19961168 |
| cloning and characterization of the zeaxanthin glucosyltransferase gene (crtx) from the astaxanthin-producing marine bacterium, paracoccus haeundaensis. | zeaxanthin glucosyltransferase (crtx) mediates the formation of zeaxanthin to zeaxanthin diglucoside. here, we report cloning of the crtx gene responsible for zeaxanthin diglucoside biosynthesis from paracoccus haeundaensis and the production of the corresponding carotenoids in transformed cells carrying this gene. an expression plasmid containing the crtx gene (pstcrt-x) was constructed, and escherichia coli cells containing this plasmid produced the recombinant protein of approximately 46 kda. ... | 2009 | 20075616 |
| effect of bioaugmentation by paracoccus sp. strain hpd-2 on the soil microbial community and removal of polycyclic aromatic hydrocarbons from an aged contaminated soil. | a microcosm study was conducted to test the bioremediation potential of paracoccus sp. strain hpd-2 on an aged pah-contaminated soil. bioaugmented microcosms showed a 23.2% decrease in soil total pah concentrations after 28days, with a decline in average concentration from 9942 to 7638microg kg(-1) dry soil. the percentage degradation of 3-, 4- and 5(+6)-ring pahs was 35.1%, 20.7% and 24.3%, respectively. higher counts of culturable pah-degrading bacteria, microbial biomass and enzyme activities ... | 2010 | 20093016 |
| a complex regulatory network controls aerobic ethanol oxidation in pseudomonas aeruginosa: indication of four levels of sensor kinases and response regulators. | in addition to the known response regulator erbr (former agmr) and the two-component regulatory system erasr (former exade), three additional regulatory proteins have been identified as being involved in controlling transcription of the aerobic ethanol oxidation system in pseudomonas aeruginosa. two putative sensor kinases, ercs and ercs', and a response regulator, erdr, were found, all of which show significant similarity to the two-component flhsr system that controls methanol and formaldehyde ... | 2010 | 20093290 |
| paracoccus fistulariae sp. nov., a lipolytic bacterium isolated from bluespotted cornetfish, fistularia commersonii. | a gram-stain-negative, non-motile, non-spore-forming and short rod- or rod-shaped bacterial strain, designated 22-5(t), was isolated from a bluespotted cornetfish, fistularia commersonii, and subjected to taxonomic study. strain 22-5(t) grew optimally at 30 °c and in the presence of 2-5 % (w/v) nacl. phylogenetic analyses based on 16s rrna gene sequences revealed that strain 22-5(t) belonged to the genus paracoccus and joined the cluster comprising paracoccus homiensis dd-r11(t) and parac ... | 2010 | 20097797 |
| unraveling an fnr based regulatory circuit in paracoccus denitrificans using a proteomics-based approach. | the switch from aerobic to anaerobic respiration in the bacterium paracoccus denitrificans is orchestrated by the action of three fnr-type transcription regulators fnrp, nnr and narr, which are sensors for oxygen, nitric oxide and nitrite, respectively. in this work, we analyzed the protein composition of four strains (wild type, fnrp-, nnr- and narr-mutant strains) grown aerobically, semiaerobically and semiaerobically in the presence of nitrate to discover the global role of fnr-family transcr ... | 2010 | 20116460 |
| plasmid pami2 of paracoccus aminophilus jcm 7686 carries n,n-dimethylformamide degradation-related genes whose expression is activated by a luxr family regulator. | n,n-dimethylformamide (dmf), a toxic solvent used in the chemical industry, is frequently present in industrial wastes. plasmid pami2 (18.6 kb) of paracoccus aminophilus jcm 7686 carries genetic information which is crucial for methylotrophic growth of this bacterium, using dmf as the sole source of carbon and energy. besides a conserved backbone related to pagk84 of agrobacterium radiobacter k84, pami2 carries a three-gene cluster coding for the protein dmfr, which has sequence similarities to ... | 2010 | 20118371 |
| paracoccus denitrificans for the effluent recycling during continuous denitrification of liquid food. | nitrate is an undesirable component of several foods. a typical case of contamination with high nitrate contents is whey concentrate, containing nitrate in concentrations up to 25 l. the microbiological removal of nitrate by paracoccus denitrificans under formation of harmless nitrogen in combination with a cell retention reactor is described here. focus lies on the resource-conserving design of a microbal denitrification process. two methods are compared. the application of polyvinyl alcohol-im ... | 2010 | 20187124 |
| electron transfer in paracoccus denitrificans with the modified fbc operon. | membrane fragments of two mutant strains of paracoccus denitrificans genetically modified in the bc(1) complex have been studied for comparison of enzymic activities of succinate-cytochrome-c reductase and its components, viz. succinate dehydrogenase (complex ii) and ubiquinol-cytochrome-c reductase (complex iii) and their response to changes in concentration of succinate, cytochrome c, ionic strength, ph, temperature and sensitivity to antimycin a. the mutants synthesized and assembled the b an ... | 2010 | 20140712 |
| in crystallo posttranslational modification within a maug/pre-methylamine dehydrogenase complex. | maug is a diheme enzyme responsible for the posttranslational modification of two tryptophan residues to form the tryptophan tryptophylquinone (ttq) cofactor of methylamine dehydrogenase (madh). maug converts premadh, containing monohydroxylated betatrp57, to fully functional madh by catalyzing the insertion of a second oxygen atom into the indole ring and covalently linking betatrp57 to betatrp108. we have solved the x-ray crystal structure of maug complexed with premadh to 2.1 angstroms. the c ... | 2010 | 20223990 |
| biodegradation of pyridine by paracoccus sp. kt-5 immobilized on bamboo-based activated carbon. | the performance of pyridine degradation by paracoccus sp. strain kt-5 immobilized on bamboo-based activated carbon was investigated and compared with that of free cells. the results showed that paracoccus sp. was able to attach well on the surface and pores of bamboo-carbon. compared with freely suspended cells, the pyridine-degrading rate of the immobilized cells was higher when initial pyridine concentration was in the range of 489-1476 mg/l, suggesting that the efficiency of pyridine degradat ... | 2010 | 20226655 |
| antibiofilm activity of the marine bacterium pseudoalteromonas sp. strain 3j6. | biofilm formation results in medical threats or economic losses and is therefore a major concern in a variety of domains. in two-species biofilms of marine bacteria grown under dynamic conditions, pseudoalteromonas sp. strain 3j6 formed mixed biofilms with bacillus sp. strain 4j6 but was largely predominant over paracoccus sp. strain 4m6 and vibrio sp. strain d01. the supernatant of pseudoalteromonas sp. 3j6 liquid culture (sn(3j6)) was devoid of antibacterial activity against free-living paraco ... | 2010 | 20363799 |
| a joint x-ray and neutron study on amicyanin reveals the role of protein dynamics in electron transfer. | the joint x-ray/neutron diffraction model of the type i copper protein, amicyanin from paracoccus denitrificans was determined at 1.8 a resolution. the protein was crystallized using reagents prepared in d(2)o. about 86% of the amide hydrogen atoms are either partially or fully exchanged, which correlates well with the atomic depth of the amide nitrogen atom and the secondary structure type, but with notable exceptions. each of the four residues that provide copper ligands is partially deuterate ... | 2010 | 20351252 |
| design of a functional nitric oxide reductase within a myoglobin scaffold. | | 2010 | 20235108 |
| nutrients determine the spatial architecture of paracoccus sp. biofilm. | bacterial biofilms adapt and shape their structure in response to varied environmental conditions. a statistical methodology was adopted in this study to empirically investigate the influence of nutrients on biofilm structural parameters deduced from confocal scanning laser microscope images of paracoccus sp.w1b, a denitrifying bacterium. high concentrations of succinate, mg(++), ca(++), and mn(++) were shown to enhance biofilm formation whereas higher concentration of iron decreased biofilm for ... | 2010 | 20336558 |
| crystallization and initial x-ray diffraction studies of the flavoenzyme nad(p)h:(acceptor) oxidoreductase (ferb) from the soil bacterium paracoccus denitrificans. | the flavin-dependent enzyme ferb from paracoccus denitrificans reduces a broad range of compounds, including ferric complexes, chromate and most notably quinones, at the expense of the reduced nicotinamide adenine dinucleotide cofactors nadh or nadph. recombinant unmodified and semet-substituted ferb were crystallized under similar conditions by the hanging-drop vapour-diffusion method with microseeding using peg 4000 as the precipitant. ferb crystallized in several different crystal forms, some ... | 2010 | 20383015 |
| the 1.4 a resolution structure of paracoccus pantotrophus pseudoazurin. | pseudoazurins are small type 1 copper proteins that are involved in the flow of electrons between various electron donors and acceptors in the bacterial periplasm, mostly under denitrifying conditions. the previously determined structure of paracoccus pantotrophus pseudoazurin in the oxidized form was improved to a nominal resolution of 1.4 a, with r and r(free) values of 0.188 and 0.206, respectively. this high-resolution structure makes it possible to analyze the interactions between the monom ... | 2010 | 20516588 |
| cell-free synthesis of cytochrome c oxidase, a multicomponent membrane protein. | cell-free protein synthesis is a useful technique that can site-specifically incorporate isotope-labeled amino acids into proteins. this incorporation is essential for infrared analyses of the electronic state of a specific amino acid residue used to elucidate protein function. although 17 membrane proteins have been synthesized in their active state by cell-free systems, to date no hetero-subunit protein has been synthesized with this technique, suggesting that there are serious technical limit ... | 2010 | 20373004 |
| paracoccus sphaerophysae sp. nov., a siderophore-producing, endophytic bacterium isolated from root nodules of sphaerophysa salsula. | an aerobic, brown-pigmented, non-spore-forming, endophytic bacterium, designated strain zy-3(t), was isolated from root nodules of sphaerophysa salsula, a native leguminous herb belonging to the family leguminosae growing in north-western china. cells of strain zy-3(t) were non-motile, gram-negative rods. strain zy-3(t) produced siderophores and showed antifungal activity. phylogenetic analysis of the 16s rrna gene sequence indicated that the closest relative of this organism was paracoccus halo ... | 2011 | 20400662 |
| substrate control of internal electron transfer in bacterial nitric-oxide reductase. | nitric -oxide reductase (nor) from paracoccus denitrificans catalyzes the reduction of nitric oxide (no) to nitrous oxide (n(2)o) (2no + 2h(+) + 2e(-) -->n(2)o + h(2)o) by a poorly understood mechanism. nor contains two low spin hemes c and b, one high spin heme b(3), and a non-heme iron fe(b). here, we have studied the reaction between fully reduced nor and no using the "flow-flash" technique. fully (four-electron) reduced nor is capable of two turnovers with no. initial binding of no to reduce ... | 2010 | 20547487 |
| formation of palladium(0) nanoparticles at microbial surfaces. | the increasing demand and limited natural resources for industrially important platinum-group metal (pgm) catalysts render the recovery from secondary sources such as industrial waste economically interesting. in the process of palladium (pd) recovery, microorganisms have revealed a strong potential. hitherto, bacteria with the property of dissimilatory metal reduction have been in focus, although the biochemical reactions linking enzymatic pd(ii) reduction and pd(0) deposition have not yet been ... | 2010 | 20506339 |
| similarity of cytochrome c oxidases in different organisms. | most of biological oxygen reduction is catalyzed by the heme-copper oxygen reductases. these enzymes are redox-driven proton pumps that take part in generating the proton gradient in both prokaryotes and mitochondria that drives synthesis of atp. the enzymes have been divided into three evolutionarily-related groups: the a-, b-, and c-families. recent comparative studies suggest that all oxygen reductases perform the same chemistry for oxygen reduction and comprise the same essential elements of ... | 2010 | 20589635 |
| [removal of pyridine using suspended and attached growing bacterium of paracoccus denitrificans w12]. | in this study, a pyridine-degrading bacterium, paracoccus denitrifican w12, was isolated. it was cultivated to grow on the surface of activated bamboo charcoal (abc) particles so that the abc turned into biological activated bamboo charcoal (babc) covered with biofilm of the w12. free cells of the w12 and the babc were separately tested in removing pyridine from aqueous solution. the results showed that 0.31 g x l(-1) suspended growing-w12 completely degraded 48.70-1399 mg x l(-1) of pyridine wi ... | 2010 | 20527191 |
| paracoccus isoporae sp. nov., isolated from the reef-building coral isopora palifera. | a bacterial strain, designated sw-3(t), was isolated from the reef-building coral isopora palifera, from southern taiwan, and was characterized by using a polyphasic taxonomic approach. cells of strain sw-3(t) were gram-reaction-negative, aerobic, rod-shaped and motile by means of monopolar flagella and formed cream-white colonies. phylogenetic analyses based on 16s rrna gene sequences showed that strain sw-3(t) belonged to the genus paracoccus and its most closely related neighbours were p. aes ... | 2011 | 20543151 |
| surface residues dynamically organize water bridges to enhance electron transfer between proteins. | cellular energy production depends on electron transfer (et) between proteins. in this theoretical study, we investigate the impact of structural and conformational variations on the electronic coupling between the redox proteins methylamine dehydrogenase and amicyanin from paracoccus denitrificans. we used molecular dynamics simulations to generate configurations over a duration of 40 ns (sampled at 100-fs intervals) in conjunction with an et pathway analysis to estimate the et coupling strengt ... | 2010 | 20547871 |
| diversity and abundance of oil-degrading bacteria and alkane hydroxylase (alkb) genes in the subtropical seawater of xiamen island. | in this report, the diversity of oil-degrading bacteria and alkb gene was surveyed in the seawater around xiamen island. forty-four isolates unique in 16s rrna sequence were obtained after enrichment with crude oil. most of the obtained isolates exhibited growth with diesel oil and crude oil. alkb genes were positively detected in 16 isolates by degenerate polymerase chain reaction (pcr). and for the first time, alkb genes were found in bacteria of gallaecimonas, castellaniella, paracoccus, and ... | 2010 | 20683589 |
| in vitro antibacterial activity of ibuprofen and acetaminophen. | ibuprofen and acetaminophen are common chemical agents that have anti-inflammatory, antipyretic, and analgesic activity. | 2010 | 20606962 |
| anodic biofilms in microbial fuel cells harbor low numbers of higher-power-producing bacteria than abundant genera. | microbial fuel cell (mfc) anode communities often reveal just a few genera, but it is not known to what extent less abundant bacteria could be important for improving performance. we examined the microbial community in an mfc fed with formic acid for more than 1 year and determined using 16s rrna gene cloning and fluorescent in situ hybridization that members of the paracoccus genus comprised most (approximately 30%) of the anode community. a paracoccus isolate obtained from this biofilm (paraco ... | 2010 | 20632002 |
| structure at 1.5 a resolution of cytochrome c(552) with its flexible linker segment, a membrane-anchored protein from paracoccus denitrificans. | electron transfer (et) between the large membrane-integral redox complexes in the terminal part of the respiratory chain is mediated either by a soluble c-type cytochrome, as in mitochondria, or by a membrane-anchored cytochrome c, as described for the et chain of the bacterium paracoccus denitrificans. here, the structure of cytochrome c(552) from p. denitrificans with the linker segment that attaches the globular domain to the membrane anchor is presented. cytochrome c(552) including the linke ... | 2010 | 20606266 |
| long-term hg pollution-induced structural shifts of bacterial community in the terrestrial isopod (porcellio scaber) gut. | in previous studies we detected lower species richness and lower hg sensitivity of the bacteria present in egested guts of porcellio scaber (crustacea, isopoda) from chronically hg polluted than from unpolluted environment. basis for such results were further investigated by sequencing of 16s rrna genes of mercury-resistant (hgr) isolates and clone libraries. we observed up to 385 times higher numbers of hgr bacteria in guts of animals from polluted than from unpolluted environment. the majority ... | 2010 | 20724045 |
| phaseolus vulgaris seed-borne endophytic community with novel bacterial species such as rhizobium endophyticum sp. nov. | the bacterial endophytic community present in different phaseolus vulgaris (bean) cultivars was analyzed by 16s ribosomal rna gene sequences of cultured isolates derived from surface disinfected roots and immature seeds. isolated endophytes from tissue-macerates belonged to over 50 species in 24 different genera and some isolates from acinetobacter, bacillus, enterococcus, nocardioides, paracoccus, phyllobacterium, and sphingomonas seem to correspond to new lineages. phytate solubilizing bacteri ... | 2010 | 20822874 |
| effects of electrochemical reduction reactions on the biodegradation of recalcitrant organic compounds (rocs) and bacterial community diversity. | five bacterial species, capable of degrading the recalcitrant organic compounds (rocs) diethyleneglycol monomethylether (dgmme), 1-amino-2-propanol (apol), 1-methyl-2- pyrrolidinone (nmp), diethyleneglycol monoethylether (dgmee), tetraethyleneglycol (teg), and tetrahydrothiophene 1,1-dioxide (sulfolane), were isolated from an enrichment culture. cupriavidus sp. catabolized 93.5+/-1.7 mg/l of teg, 99.3+/-1.2 mg/l of dgmme, 96.1+/-1.6mg/l of apol, and 99.5+/-0.5mg/l of nmp in 3 days. acineobacter ... | 2010 | 20798588 |
| denitrification response patterns during the transition to anoxic respiration and posttranscriptional effects of suboptimal ph on nitrous [corrected] oxide reductase in paracoccus denitrificans. | denitrification in soil is a major source of atmospheric n(2)o. soil ph appears to exert a strong control on the n(2)o/n(2) product ratio (high ratios at low ph), but the reasons for this are not well understood. to explore the possible mechanisms involved, we conducted an in-depth investigation of the regulation of denitrification in the model organism paracoccus denitrificans during transition to anoxia both at ph 7 and when challenged with phs ranging from 6 to 7.5. the kinetics of gas transf ... | 2010 | 20709842 |
| chromate reductase activity of the paracoccus denitrificans ferric reductase b (ferb) protein and its physiological relevance. | the homodimeric flavoprotein ferb of paracoccus denitrificans catalyzed the reduction of chromate with nadh as electron donor. when present, oxygen was reduced concomitantly with chromate. the recombinant enzyme had a maximum activity at ph 5.0. the stoichiometric ratio of nadh oxidized to chromate reduced was found to be 1.53 ± 0.09 (o(2) absent) or > 2 (o(2) present), the apparent k (m) value for chromate amounted to 70 ± 10 μm with the maximum rate of 2.9 ± 0.3 μmol nadh s(-1) (mg protein)(-1 ... | 2010 | 20821194 |
| amicyanin transfers electrons from methylamine dehydrogenase to cytochrome c-551i via a ping-pong mechanism, not a ternary complex. | the first crystal structure of a ternary redox protein complex was comprised of the enzyme methylamine dehydrogenase (madh) and two electron transfer proteins, amicyanin and cytochrome c-551i from paracoccus denitrificans [chen et al. science 1994, 264, 86-90]. the arrangement of the proteins suggested possible electron transfer from the active site of madh via the amicyanin copper ion to the cytochrome heme iron, although the distance between the metals is large. we studied the interactions bet ... | 2010 | 20873742 |
| complex prokaryotic genome structure: rapid evolution of chromosome ii. | although many bacteria with two chromosomes have been sequenced, the roles of such complex genome structuring are still unclear. to uncover levels of chromosome i (ci) and chromosome ii (cii) sequence divergence, mauve 2.2.0 was used to align the ci- and cii-specific sequences of bacteria with complex genome structuring in two sets of comparisons: the first set was conducted among the ci and cii of bacterial strains of the same species, while the second set was conducted among the ci and cii of ... | 2010 | 20924417 |
| [study on the function of plasmid in pyridine-degrading bacteria]. | in order to identify the characteristics of the plasmids of degrading bacterial strains and the relationship between the plasmids' function and biodegradation, plasmids were isolated from two bacterial strains (paracoccus sp. bw001 and shinella zoogloeoides bc026) and pulse-field gel electrophoresis was used to identify the distribution of plasmids and their molecular size. two large plasmids with 190-245 kb and one small plasmid with 4.5-5.0 kb were found in the bw001, and at least 3 large plas ... | 2010 | 20825045 |
| paracoccus caeni sp. nov., isolated from sludge. | a gram-negative, non-motile bacterium, designated mj17t, was isolated from sludge at the daejeon sewage disposal plant in south korea and was characterized using a polyphasic taxonomic approach. comparative 16s rrna gene sequence analysis showed that strain mj17t belongs to the genus paracoccus in the family rhodobacteraceae of the class alphaproteobacteria. the 16s rrna gene sequence similarities between strain mj17t and type strains of the genus paracoccus were 94.1-97.4% and highest to paraco ... | 2010 | 20851920 |
| case of paracoccus yeei infection documented in a transplanted heart. | after a successful cardiac transplantation, routine endomyocardial biopsies showed severe infiltrates comparable with myocarditis. polymerase chain reaction analysis of native myocardial samples revealed infection with paracoccus yeei, and the clinical condition of the patient deteriorated. after administration of ciprofloxacin, his clinical condition improved, and further biopsies showed no infiltrates in the cardiac specimens. to our knowledge this is the first documented case of p. yeei infec ... | 2011 | 20854281 |
| paracoccus stylophorae sp. nov., isolated from the reef-building coral stylophora pistillata. | a bacterial strain designated ktw-16(t) was isolated from the reef-building coral stylophora pistillata, collected from southern taiwan and was characterized using a polyphasic taxonomic approach. strain ktw-16(t) was gram-negative, facultatively anaerobic, pale-yellow colored, short rod-shaped, and non-motile. phylogenetic analyses based on 16s rrna gene sequences showed that strain ktw-16(t) belonged to the genus paracoccus in the alphaproteobacteria. sequence similarities to type strains of t ... | 2010 | 20935084 |