| artefacts induced on c-type haem proteins by electrode surfaces. | in this work it is demonstrated that the characterization of c-type haem containing proteins by electrochemical techniques needs to be cautiously performed when using pyrolytic graphite electrodes. an altered form of the cytochromes, which has a redox potential 300 mv lower than that of the native state and displays peroxidatic activity, can be induced by interaction with the pyrolytic graphite electrode. proper control experiments need to be performed, as altered conformations of the enzymes co ... | 2010 | 20963615 |
| bacteria involved in sulfur amendment oxidation and acidification processes of alkaline 'alperujo' compost. | eight strains of sulfur oxidizing bacteria were isolated from alkaline 'alperujo' compost, seven being identified as paracoccus thiocyanatus and one as halothiobacillus neapolitanus. this was the first time that p. thiocyanatus was isolated from mature compost. acidification capability of isolated strains was compared with type strains h. neapolitanus cip104769, thiobacillus denitrificans cip104767 and thiomonas intermedia cip104401. indigenous p. thiocyanatus strains were as much as or more eff ... | 2010 | 20970324 |
| pulse radiolysis studies of temperature dependent electron transfers among redox centers in ba(3)-cytochrome c oxidase from thermus thermophilus: comparison of a- and b-type enzymes. | the functioning of cytochrome c oxidases involves orchestration of long-range electron transfer (et) events among the four redox active metal centers. we report the temperature dependence of electron transfer from the cu(a)(r) site to the low-spin heme-(a)b(o) site, i.e., cu(a)(r) + heme-a(b)(o) → cu(a)(o) + heme-a(b)(r) in three structurally characterized enzymes: a-type aa(3) from paracoccus denitrificans (pdb code 3hb3 ) and bovine heart tissue (pdb code 2zxw ), and the b-type ba(3) from t. t ... | 2010 | 21028883 |
| biotechnological production of astaxanthin with phaffia rhodozyma/xanthophyllomyces dendrorhous. | the oxygenated β-carotene derivative astaxanthin exhibits outstanding colouring, antioxidative and health-promoting properties and is mainly found in the marine environment. to satisfy the growing demand for this ketocarotenoid in the feed, food and cosmetics industries, there are strong efforts to develop economically viable bioprocesses alternative to the current chemical synthesis. however, up to now, natural astaxanthin from haematococcus pluvialis, phaffia rhodozyma or paracoccus carotinifa ... | 2010 | 21046372 |
| [research on search of the carotenoid-producing microorganisms in marine area and the improvement of production ratio]. | carotenoids are liposoluble pigments widely distributed in nature. more than 750 carotenoids are isolated from natural sources, but only a few kinds are used industrially. the production of carotenoid by microorganisms is to be expected, but few carotenoids originate from living things on land. and there is little knowledge about carotenoid-producing microorganisms in the oceans. the possibility still exists of discovering new carotenoid-producing microorganisms. sunlight is very strong in subtr ... | 2010 | 21048402 |
| nirf is a periplasmic protein that binds d₁ heme as part of its essential role in d₁ heme biogenesis. | the cytochrome cd₁ nitrite reductase from paracoccus pantotrophus catalyses the one electron reduction of nitrite to nitric oxide using two heme cofactors. the site of nitrite reduction is the d₁ heme, which is synthesized under anaerobic conditions by using nirecfd-lghjn gene products. in vivo studies with an unmarked deletion strain, δnirf, showed that this gene is essential for cd₁ assembly and consequently for denitrification, which was restored when the δnirf strain was complemented with wi ... | 2010 | 21054787 |
| the antianxiety-like effect of astaxanthin extracted from paracoccus carotinifaciens. | astaxanthin is a red carotenoid pigment and is widely found in living organisms. astaxanthin has a potent antioxidative ability and has been reported as having various biological effects on the central nerve system, such as a protective effect against ischemia/reperfusion injury and improvement in cognitive function. in this study, to investigate the effects of astaxanthin on anxiety and depression, we performed some behavioral trials including the elevated plus maze test, hole-board test, force ... | 2010 | 21072786 |
| a modified culture-based study of bacterial community composition in a tannery wastewater treatment plant. | though culture-independent methods have been used in preference to traditional isolation techniques for characterization of microbial community of wastewater treatment plants, it is difficult to widely apply this approach in resource-poor countries. the present study aimed to develop a test to identify the culturable portion of bacterial community in a high-strength wastewater. wastewater samples were collected from nitrification-denitrification and settling tanks of the treatment plant of elmo ... | 2010 | 21099040 |
| a combined fluorescence spectroscopic and electrochemical approach for the study of thioredoxins. | a new way to study the electrochemical properties of proteins by coupling front-face fluorescence spectroscopy with an optically transparent thin-layer electrochemical cell is presented. first, the approach was examined on the basis of the redox-dependent conformational changes in tryptophans in cytochrome c, and its redox potential was successfully determined. second, an electrochemically induced fluorescence analysis of periplasmic thiol-disulfide oxidoreductases soxs and soxw was performed. s ... | 2010 | 21110519 |
| evolution of respiratory complex i: "supernumerary" subunits are present in the alpha-proteobacterial enzyme. | modern α-proteobacteria are thought to be closely related to the ancient symbiont of eukaryotes, an ancestor of mitochondria. respiratory complex i from α-proteobacteria and mitochondria is well conserved at the level of the 14 "core" subunits, consistent with that notion. mitochondrial complex i contains the core subunits, present in all species, and up to 31 "supernumerary" subunits, generally thought to have originated only within eukaryotic lineages. however, the full protein composition of ... | 2010 | 21115482 |
| molecular dynamics in cytochrome c oxidase mössbauer spectra deconvolution. | in this work low temperature molecular dynamics simulations of cytochrome c oxidase are used to predict an experimentally observable, namely mössbauer spectra width. predicted lineshapes are used to model lorentzian doublets, with which published cytochrome c oxidase mössbauer spectra were simulated. molecular dynamics imposed constraints to spectral lineshapes permit to obtain useful information, like the presence of multiple chemical species in the binuclear center of cytochrome c oxidase. mor ... | 2010 | 21138729 |
| design of a functional nitric oxide reductase within a myoglobin scaffold. | | 2010 | 20235108 |
| sulfide and ammonium oxidation, acetate mineralization by denitrification in a multipurpose uasb reactor. | the physiological and kinetic behavior of a denitrifying granular sludge exposed to different sulfide loading rates (55-295 mg/l d) were evaluated in a uasb reactor fed with acetate, ammonium and nitrate. at any sulfide loading rates, the consumption efficiencies of sulfide, acetate and ammonium were above 95%, while nitrate consumption efficiencies were around 62-72%. at the highest sulfide loading rate the ammonium was used as electron donor for n(2) production. the increase of sulfide loading ... | 2010 | 21146980 |
| paracoccus niistensis sp. nov., isolated from forest soil, india. | a gram-negative, non-motile, catalase-positive and oxidase-positive, aerobic bacterium designated as nii-0918(t) was isolated from soil sample in western ghat forest, india. 16s rrna gene sequence analysis showed that strain nii-0918(t) belongs to the subclass α-proteobacteria, being related to the genus paracoccus, and sharing highest sequence similarity with paracoccus chinensis nbrc 104937(t) (99.4%), paracoccus marinus nbrc 100640(t) (97.3%), paracoccus koreensis ch05(t) (97.1%) and paracocc ... | 2010 | 20936429 |
| paracoccus denitrificans proton-translocating atpase: kinetics of oxidative phosphorylation. | the initial rates of atp synthesis catalyzed by tightly coupled paracoccus denitrificans plasma membrane were measured. the reaction rate was hyperbolically dependent on the substrates, adp and inorganic phosphate (p(i)). apparent k(m) values for adp and p(i) were 7-11 and 60-120 µm, respectively, at saturating concentration of the second substrate (ph 8.0, saturating mg²(+)). these values were dependent on coupling efficiency. the substrate binding in the atp synthesis reaction proceeds randoml ... | 2010 | 21166644 |
| sodium influence on energy transduction by complexes i from escherichia coli and paracoccus denitrificans. | the nature of the ions that are translocated by escherichia coli and paracoccus denitrificans complexes i was investigated. we observed that e. coli complex i was capable of proton translocation in the same direction to the established deltapsi, showing that in the tested conditions, the coupling ion is the h(+). furthermore, na(+) transport to the opposite direction was also observed, and, although na(+) was not necessary for the catalytic or proton transport activities, its presence increased ... | 2010 | 21172303 |
| effect of seed sludge on characteristics and microbial community of aerobic granular sludge. | aerobic granular sludge was cultivated by using different kinds of seed sludge in sequencing batch airlift reactor. the influence of seed sludge on physical and chemical properties of granular sludge was studied; the microbial community structure was probed by using scanning electron microscope and polymerase chain reaction-denaturing gradient gel electrophoresis (pcr-dgge). the results showed that seed sludge played an important role on the formation of aerobic granules. seed sludge taken from ... | 2010 | 21174960 |
| phylogenetic diversity of bacterial communities in south china sea mesoscale cyclonic eddy perturbations. | eddy pumping drives a set of biogeochemical processes by lifting deep waters into the euphotic zone. to address the potential effect of such physical processes upon the bacterial community, phylogenetic diversity was determined in two cold-core cyclonic eddies in the south china sea. 16s rdna terminal restriction fragment length polymorphism analysis of the microbial communities through the whole water column showed a wider depth range for the intermediate transition water mass at sites inside t ... | 2010 | 21187147 |
| wastewater treatment by alkali bacteria and dynamics of microbial communities in two bioreactors. | in this study, an alkali bacterial consortium was obtained by enrichment cultivation and was used to treat printing and dyeing wastewater (pdw, ph 11-12). the treatment effects and dynamic changes were evaluated in a biocontact oxidation reactor (bor) and a sequencing batch reactor (sbr). during 3 months of continuous operation, the two bioreactors had similar treatment efficiencies (polyvinyl alcohol, pva, 74.5-81.3%; cod, 73.5-77.4%; 2.15 ph decreases). molecular biological analysis indicated ... | 2010 | 21190847 |
| is coproporphyrin iii a copper-acquisition compound in paracoccus denitrificans? | paracoccus denitrificans is a soil bacterium which can respire aerobically and also denitrify if oxygen is absent. both processes are highly dependent on copper enzymes and copper is therefore likely to be an essential trace element for the bacterium. if copper is not easily available, a copper-acquisition mechanism would be highly beneficial. in this paper, we have addressed the question of whether paracoccus secretes a copper-acquisition compound functionally analogous to that found in some me ... | 2011 | 21216223 |
| exploration of the cytochrome c oxidase pathway puzzle and examination of the origin of elusive mutational effects. | gaining detailed understanding of the energetics of the proton-pumping process in cytochrome c oxidase (cco) is a problem of great current interest. despite promising mechanistic proposals, so far, a physically consistent model that would reproduce all the relevant barriers needed to create a working pump has not been presented. in addition, there are major problems in elucidating the origin of key mutational effects and in understanding the nature of the apparent pk(a) values associated with th ... | 2011 | 21232525 |
| observation of fast release of no from ferrous d1 haem allows formulation of a unified reaction mechanism for cytochrome cd1 nitrite reductases. | cytochrome cd1 nitrite reductase is a haem-containing enzyme responsible for the reduction of nitrite into no, a key step in the anaerobic respiratory process of denitrification. the active site of cytochrome cd1 contains the unique d1 haem cofactor, from which no must be released. in general, reduced haems bind no tightly relative to oxidized haems. in the present paper, we present experimental evidence that the reduced d1 haem of cytochrome cd1 from paracoccus pantotrophus releases no rapidly ... | 2011 | 21244362 |
| genome sequence of paracoccus sp. strain trp, a chlorpyrifos biodegrader. | paracoccus sp. strain trp, isolated from activated sludge, could completely biodegrade chlorpyrifos and 3,5,6-trichloro-2-pyridinol. here we report the draft genome sequence of paracoccus sp. strain trp, which could be used to predict genes for xenobiotic biodegradation and metabolism. | 2011 | 21257769 |
| denitrification regulatory phenotype, a new term for the characterization of denitrifying bacteria. | current knowledge of denitrification is based on detailed studies of a limited number of organisms. in most cases the importance of these paradigm species in natural ecosystems is questionable. detailed phenotypic studies of a wider range of prokaryotes, both type strains and dominant denitrifiers isolated from complex systems, will aid the generation of more sophisticated mathematical models for the prediction of no and n2o emission to the environment. however, in order to facilitate the compar ... | 2011 | 21265774 |
| electrocatalytic reduction of nitrate and selenate by napab. | bacterial cellular metabolism is renowned for its metabolic diversity and adaptability. however, certain environments present particular challenges. aerobic metabolism of highly reduced carbon substrates by soil bacteria such as paracoccus pantotrophus presents one such challenge since it may result in excessive electron delivery to the respiratory redox chain when compared with the availability of terminal oxidant, o2. the level of a periplasmic ubiquinol-dependent nitrate reductase, nap, is up ... | 2011 | 21265780 |
| proline 96 of the copper ligand loop of amicyanin regulates electron transfer from methylamine dehydrogenase by positioning other residues at the protein-protein interface. | amicyanin is a type 1 copper protein that serves as an electron acceptor for methylamine dehydrogenase (madh). the site of interaction with madh is a "hydrophobic patch" of amino acid residues including those that comprise a "ligand loop" that provides three of the four copper ligands. three prolines are present in this region. pro94 of the ligand loop was previously shown to strongly influence the redox potential of amicyanin but not affinity for madh or mechanism of electron transfer (et). in ... | 2011 | 21268585 |
| electron transfer to the active site of the bacterial nitric oxide reductase is controlled by ligand binding to heme b3. | the active site of the bacterial nitric oxide reductase from paracoccus denitrificans contains a dinuclear centre comprising heme b3 and non heme iron (fe(b)). these metal centres are shown to be at isopotential with midpoint reduction potentials of e(m) ˜ +80 mv. the midpoint reduction potentials of the other two metal centres in the enzyme, heme c and heme b, are greater than the dinuclear centre suggesting that they act as an electron receiving/storage module. reduction of the low-spin heme b ... | 2011 | 21296048 |
| isolation, characterization and identification of a paracoccus sp. 2-haloacid-degrading bacterium from the marine sponge hymeniacidon perlevis. | a 2-haloacid dehalogenase-producing bacterium, designated deh99, was isolated from the marine sponge hymeniacidon perlevis using a modified enrichment medium and a ph indicator method. deh99 could degrade only half of the racemic mixture 2-chloropropionic acid (2-cpa) in the medium. the dehalogenase of deh99 was further determined to be a (s)-2-haloacid dehalogenase, which can degrade 2-cpa, 2-bromopropionic acid (2-bpa), and iodoacetic acid. the gene encoding the (s)-2-haloacid dehalogenase was ... | 2011 | 21298680 |
| diversity of endophytic bacteria within nodules of the sphaerophysa salsula in different regions of loess plateau in china. | a total of 115 endophytic bacteria were isolated from root nodules of the wild legume sphaerophysa salsula grown in two ecological regions of loess plateau in china. the genetic diversity and phylogeny of the strains were revealed by restriction fragment length polymorphism and sequencing of 16s rrna gene and enterobacterial repetitive intergenic consensus-pcr. their symbiotic capacity was checked by nodulation tests and analysis of nifh gene sequence. this is the first systematic study on endop ... | 2011 | 21303396 |
| comparison of denitrification at low temperature using encapsulated paracoccus denitrificans, pseudomonas fluorescens and mixed culture. | the aim of this work was to compare denitrification activity of three types of encapsulated biomass containing pure culture of paracoccus denitrificans or pseudomonas fluorescens or mixed culture of psychrophilic denitrifiers cultivated at 5 °c from activated sludge. the experiments were held with synthetic wastewater containing 50 mg l(-1) n-no(3)(-) under the temperature 15, 10, 8 and 5 °c. specific denitrification rates related to the weight of pellets and to the protein content were calculat ... | 2011 | 21306891 |
| electron transfer flavoprotein domain ii orientation monitored using double electron-electron resonance between an enzymatically reduced, native fad cofactor, and spin labels. | human electron transfer flavoprotein (etf) is a soluble mitochondrial heterodimeric flavoprotein that links fatty acid ß-oxidation to the main respiratory chain. the crystal structure of human etf bound to medium chain acyl-coa dehydrogenase indicates that the flavin adenine dinucleotide (fad) domain (aii) is mobile, which permits more rapid electron transfer with donors and acceptors by providing closer access to the flavin and allows etf to accept electrons from at least 10 different flavoprot ... | 2011 | 21308847 |
| paracoccus beibuensis sp. nov., isolated from the south china sea. | a gram-negative, non-motile, short rod-shaped or spherical bacterial strain that accumulates poly-β-hydroxybutyrate (phb) granules was isolated from the beibu gulf in the south china sea. cells have no polar or subpolar flagella, dividing by binary fission. phylogenetic analyses based on 16s rrna gene sequences showed that the strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus paracoccus, family rhodobacteraceae, order rhodobacterales, class ... | 2010 | 20936472 |
| a composite biochemical system for bacterial nitrate and nitrite assimilation as exemplified by paracoccus denitrificans. | the denitrifying bacterium paracoccus denitrificans can grow aerobically or anaerobically using nitrate or nitrite as the sole nitrogen source. the biochemical pathway responsible is expressed from a gene cluster comprising a nitrate/nitrite transporter (nasa), nitrite transporter (nash), nitrite reductase (nasb), ferredoxin (nasg) and nitrate reductase (nasc). nasb and nasg are essential for growth with nitrate or nitrite as the nitrogen source. nadh serves as the electron donor for nitrate and ... | 2011 | 21348864 |
| spectroscopic characterization of the molybdenum cofactor of the sulfane dehydrogenase soxcd from paracoccus pantotrophus. | the bacterial sulfane dehydrogenase soxcd is a distantly related member of the sulfite oxidase (so) enzyme family that is proposed to oxidize protein-bound sulfide (sulfane) of soxy as part of a multienzyme mechanism of thiosulfate metabolism. this study characterized the molybdenum cofactor of soxcd(1), comprising the catalytic molybdopterin subunit soxc and the truncated c-type cytochrome subunit soxd(1). electron paramagnetic resonance spectroscopy of the mo(v) intermediate generated by dithi ... | 2010 | 21142117 |
| interconversions of p and f intermediates of cytochrome c oxidase from paracoccus denitrificans. | cytochrome c oxidase (cco) is the terminal enzyme of the respiratory chain. this redox-driven proton pump catalyzes the four-electron reduction of molecular oxygen to water, one of the most fundamental processes in biology. elucidation of the intermediate structures in the catalytic cycle is crucial for understanding both the mechanism of oxygen reduction and its coupling to proton pumping. using cco from paracoccus denitrificans, we demonstrate that the artificial f state, classically generated ... | 2011 | 21368144 |
| structural basis for the oxidation of protein-bound sulfur by the sulfur cycle molybdohemo-enzyme sulfane dehydrogenase soxcd. | the sulfur cycle enzyme sulfane dehydrogenase soxcd is an essential component of the sulfur oxidation (sox) enzyme system of paracoccus pantotrophus. soxcd catalyzes a six-electron oxidation reaction within the sox cycle. soxcd is an α(2)β(2) heterotetrameric complex of the molybdenum cofactor-containing soxc protein and the diheme c-type cytochrome soxd with the heme domains d(1) and d(2). soxcd(1) misses the heme-2 domain d(2) and is catalytically as active as soxcd. the crystal structure of s ... | 2010 | 21147779 |
| biodegradation of chloroacetamide herbicides by paracoccus sp. fly-8 in vitro. | a butachlor-degrading strain, designated fly-8, was isolated from rice field soil and was identified as paracoccus sp. strain fly-8 could degrade and utilize six chloroacetamide herbicides as carbon sources for growth, and the degradation rates followed the order alachlor > acetochlor > propisochlor > butachlor > pretilachlor > metolachlor. the influence of molecular structure of the chloroacetamide herbicides on the microbial degradation rate was first analyzed; the results indicated that the s ... | 2011 | 21417467 |
| characterization of heme-binding properties of paracoccus denitrificans surf1 proteins. | biogenesis of cytochrome c oxidase (cox) is a highly complex process involving >30 chaperones in eukaryotes; those required for the incorporation of the copper and heme cofactors are also conserved in bacteria. surf1, associated with heme a insertion and with leigh syndrome if defective in humans, is present as two homologs in the soil bacterium paracoccus denitrificans, surf1c and surf1q. in an in vitro interaction assay, the heme a transfer from purified heme a synthase, ctaa, to surf1c was fo ... | 2011 | 21418525 |
| the relationship between redox enzyme activity and electrochemical potential-cellular and mechanistic implications from protein film electrochemistry. | in protein film electrochemistry a redox protein of interest is studied as an electroactive film adsorbed on an electrode surface. for redox enzymes this configuration allows quantification of the relationship between catalytic activity and electrochemical potential. considered as a function of enzyme environment, i.e., ph, substrate concentration etc., the activity-potential relationship provides a fingerprint of activity unique to a given enzyme. here we consider the nature of the activity-pot ... | 2011 | 21423952 |
| regeneration of amphioxus oral cirri and its skeletal rods: implications for the origin of the vertebrate skeleton. | the oral cirri of amphioxus function as the first filter during feeding by eliminating unwanted large or noxious particulates. in this study, we were able to regenerate cirri following artificial amputation. this is the first firm observation of regeneration in amphioxus. using this regeneration system, we studied skeletogenesis of the cellular skeleton of amphioxus oral cirri. during regeneration, the skeletal cells showed expression of fibrillar collagen and soxe genes. these observations sugg ... | 2011 | 21455946 |
| comparison of denitrification between paracoccus sp. and diaphorobacter sp. | denitrification was compared between paracoccus sp. and diaphorobacter sp. in this study, both of which were isolated from activated sludge of a denitrifying reactor. denitrification of both isolates showed contrasting patterns, where diaphorobacter sp. showed accumulation of nitrite in the medium while paracoccus sp. showed no accumulation. the nitrate reduction rate was 1.5 times more than the nitrite reduction in diaphorobacter sp., as analyzed by the resting state denitrification kinetics. i ... | 2011 | 21509603 |
| the antianxiety-like effect of astaxanthin extracted from paracoccus carotinifaciens. | astaxanthin is a red carotenoid pigment and is widely found in living organisms. astaxanthin has a potent antioxidative ability and has been reported as having various biological effects on the central nerve system, such as a protective effect against ischemia/reperfusion injury and improvement in cognitive function. in this study, to investigate the effects of astaxanthin on anxiety and depression, we performed some behavioral trials including the elevated plus maze test, hole-board test, force ... | 2010 | 21328624 |
| water molecule reorganization in cytochrome c oxidase revealed by ftir spectroscopy. | although internal electron transfer and oxygen reduction chemistry in cytochrome c oxidase are fairly well understood, the associated groups and pathways that couple these processes to gated proton translocation across the membrane remain unclear. several possible pathways have been identified from crystallographic structural models; these involve hydrophilic residues in combination with structured waters that might reorganize to form transient proton transfer pathways during the catalytic cycle ... | 2011 | 21543712 |
| analysis of the activation mechanism of pseudomonas stutzeri cytochrome c peroxidase through an electron transfer chain. | the activation mechanism of pseudomonas stutzeri cytochrome c peroxidase (ccp) was probed through the mediated electrochemical catalysis by its physiological electron donor, p. stutzeri cytochrome c-551. a comparative study was carried out, by performing assays with the enzyme in the resting oxidized state as well as in the mixed-valence activated form, using cyclic voltammetry and a pyrolytic graphite membrane electrode. in the presence of both the enzyme and hydrogen peroxide, the peak-like si ... | 2011 | 21547574 |
| diy series of genetic cassettes useful in construction of versatile vectors specific for alphaproteobacteria. | we have developed a diy (do it yourself) series of genetic cassettes, which facilitate construction of novel versatile vectors for alphaproteobacteria. all the cassettes are based on defined genetic modules derived from three natural plasmids of paracoccus aminophilus jcm 7686. we have constructed over 50 diy cassettes, which differ in structure and specific features. all of them are functional in eight strains representing three orders of alphaproteobacteria: rhodobacterales, rhizobiales and ca ... | 2011 | 21569803 |
| a nitrite sensor based on a highly sensitive nitrite reductase mediator-coupled amperometric detection. | highly sensitive nitrite sensors have been developed for the first time based on mediator-modified electrodes. tetraheme cytochrome c nitrite reductase from sulfurospirillum deleyianum and cytochrome cd(1) nitrite reductase from paracoccus denitrificans are able to accept electrons from artificial electron donors, which simultaneously act as electron mediators between the enzyme and an amperometric electrode. in addition to methyl viologen, redox-active compounds such as phenazines (phenosafrani ... | 1996 | 21619176 |
| allosteric nucleotide-binding site in the mitochondrial nadh:ubiquinone oxidoreductase (respiratory complex i). | the rotenone-insensitive nadh:hexaammineruthenium iii (har) oxidoreductase reactions catalyzed by bovine heart and yarrowia lipolytica submitochondrial particles or purified bovine complex i are stimulated by atp and other purine nucleotides. the soluble fraction of mammalian complex i (fp) and prokaryotic complex i homolog ndh-1 in paracoccus denitrificans plasma membrane lack stimulation of their activities by atp. the stimulation appears as a decrease in apparent k(m) values for nadh and har. ... | 2011 | 21624365 |
| fe/mn superoxide dismutase-encoding gene in paracoccus denitrificans is induced by azide and expressed independently of the fnr-type regulators. | paracoccus denitrificans cells undergo changes in protein composition upon exposure to azide, a known activator of the fumarate-nitrate reduction (fnr)-type transcription factor narr. one of the most prominent protein species inducible by azide is a fe/mn-family superoxide dismutase (sod). azide induces sod at protein, mrna transcript, and enzyme activity levels in the aerobically growing cells. since sod expression remains unaffected in the fnrp-, nnr-, and narr-mutant strains, we postulate a m ... | 2011 | 21399942 |
| the electron transfer complex between nitrous oxide reductase and its electron donors. | identifying redox partners and the interaction surfaces is crucial for fully understanding electron flow in a respiratory chain. in this study, we focused on the interaction of nitrous oxide reductase (n(2)or), which catalyzes the final step in bacterial denitrification, with its physiological electron donor, either a c-type cytochrome or a type 1 copper protein. the comparison between the interaction of n(2)or from three different microorganisms, pseudomonas nautica, paracoccus denitrificans, a ... | 2011 | 21739254 |
| Potential activity of the purine compounds caffeine and aminophylline on bacteria. | Purine compounds are special types of alkaloids. Caffeine and aminophylline are considered the most important members of purines due to their wide use in therapeutics. | 2011 | 21731299 |
| nitrate-dependent degradation of acetone by alicycliphilus and paracoccus strains and comparison of acetone carboxylase enzymes. | a novel acetone-degrading, nitrate-reducing bacterium, strain kn bun08, was isolated from an enrichment culture with butanone and nitrate as the sole sources of carbon and energy. the cells were motile short rods, 0.5 to 1 by 1 to 2 μm in size, which gave gram-positive staining results in the exponential growth phase and gram-negative staining results in the stationary-growth phase. based on 16s rrna gene sequence analysis, the isolate was assigned to the genus alicycliphilus. besides butanone a ... | 2011 | 21841031 |
| proton transfer in ba(3) cytochrome c oxidase from thermus thermophilus. | the respiratory heme-copper oxidases catalyze reduction of o(2) to h(2)o, linking this process to transmembrane proton pumping. these oxidases have been classified according to the architecture, location and number of proton pathways. most structural and functional studies to date have been performed on the a-class oxidases, which includes those that are found in the inner mitochondrial membrane and bacteria such as rhodobacter sphaeroides and paracoccus denitrificans (aa(3)-type oxidases in the ... | 2011 | 22172736 |
| a novel cold-active beta-d-galactosidase from the paracoccus sp. 32d - gene cloning, purification and characterization. | abstract: background: beta-d-galactosidases (ec 3.2.1.23) catalyze the hydrolysis of terminal non-reducing beta-d-galactose residues in beta-d-galactosides. cold-active beta-d-galactosidases have recently become a focus of attention of researchers and dairy product manufactures owing to theirs ability to: (i) eliminate of lactose from refrigerated milk for people afflicted with lactose intolerance, (ii) convert lactose to glucose and galactose which increase the sweetness of milk and decreases ... | 2011 | 22166118 |
| genome of a novel isolate of paracoccus denitrificans capable of degrading n,n-dimethylformamide. | the bacterial genus paracoccus is comprised of metabolically versatile organisms having diverse degradative capabilities and potential industrial and environmental applications for bioremediation in particular. we report a de novo-assembled sequence and annotation of the genome of a novel isolate of paracoccus denitrificans originally sourced from coal mine tailings in india. the isolate was capable of utilizing n,n-dimethylformamide (dmf) as a source of carbon and nitrogen and therefore holds p ... | 2011 | 21914898 |
| expression of nitrous oxide reductase in paracoccus denitrificans is regulated by oxygen and nitric oxide through fnrp and nnr. | the reductases performing the four steps of denitrification are controlled by a network of transcriptional regulators and ancillary factors responding to intra- and extracellular signals amongst which are oxygen and n-oxides (no and no2-). although many components of the regulatory network have been identified, there are gaps in our understanding of their role(s) in controlling the expression of the various reductases, in particular the environmentally important n2o-reductase (n2or). we investig ... | 2011 | 22174385 |
| X-ray structure of the dimeric cytochrome bc(1) complex from the soil bacterium Paracoccus denitrificans at 2.7-Å resolution. | The respiratory cytochrome bc(1) complex is a fundamental enzyme in biological energy conversion. It couples electron transfer from ubiquinol to cytochrome c with generation of proton motive force which fuels ATP synthesis. The complex from the a-proteobacterium Paracoccus denitrificans, a model for the medically relevant mitochondrial complexes, lacked structural characterization. We show by LILBID mass spectrometry that truncation of the organism-specific, acidic N-terminus of cytochrome c(1) ... | 2011 | 21996020 |
| the acidic domain of cytochrome c₁ in paracoccus denitrificans, analogous to the acidic subunits in eukaryotic bc₁ complexes, is not involved in the electron transfer reaction to its native substrate cytochrome c(552). | the cytochrome bc(1) complex is a key component in several respiratory pathways. one of the characteristics of the eukaryotic complex is the presence of a small acidic subunit, which is thought to guide the interaction of the complex with its electron acceptor and facilitate electron transfer. paracoccus denitrificans represents the only example of a prokaryotic organism in which a highly acidic domain is covalently fused to the cytochrome c(1) subunit. in this work, a deletion variant lacking t ... | 2011 | 21856278 |
| Photoinitiated Electron Transfer within the Paracoccus denitrificans Cytochrome bc(1) Complex: Mobility of the Iron-Sulfur Protein Is Modulated by the Occupant of the Q(o) Site. | Domain rotation of the Rieske iron-sulfur protein (ISP) between the cytochrome (cyt) b and cyt c(1) redox centers plays a key role in the mechanism of the cyt bc(1) complex. Electron transfer within the cyt bc(1) complex of Paracoccus denitrificans was studied using a ruthenium dimer to rapidly photo-oxidize cyt c(1) within 1 µs and initiate the reaction. In the absence of any added quinol or inhibitor of the bc(1) complex at pH 8.0, electron transfer from reduced ISP to cyt c(1) was biphasic wi ... | 2011 | 22026826 |
| molecular determinants for substrate selectivity of ω-transaminases. | ω-transaminase (ω-ta) is an industrially important enzyme for production of chiral amines. about 20 (s)-specific ω-tas known to date show remarkably similar substrate selectivity characterized by stringent steric constraint precluding entry of a substituent larger than an ethyl group in the small binding pocket (s) and dual recognition of an aromatic substituent as well as a carboxylate group in the large pocket (l). the strictly defined substrate selectivity of the available ω-tas remains a lim ... | 2011 | 21983703 |
| Mutagenesis of tryptophan199 suggests that hopping is required for MauG-dependent tryptophan tryptophylquinone biosynthesis. | The diheme enzyme MauG catalyzes the posttranslational modification of the precursor protein of methylamine dehydrogenase (preMADH) to complete biosynthesis of its protein-derived tryptophan tryptophylquinone (TTQ) cofactor. Catalysis proceeds through a high valent bis-Fe(IV) redox state and requires long-range electron transfer (ET), as the distance between the modified residues of preMADH and the nearest heme iron of MauG is 19.4 Å. Trp199 of MauG resides at the MauG-preMADH interface, positio ... | 2011 | 21969534 |
| revised transmembrane orientation of the nadh:quinone oxidoreductase subunit nuoa. | nuoa is a small membrane spanning subunit of respiratory chain nadh:quinone oxidoreductase (complex i). unlike the other complex i core protein subunits, the nuoa protein has no known homologue in other enzyme systems. the transmembrane orientation of nuoa cannot be unambiguously predicted, due to the small size of the polypeptide and the varying distribution of charged amino acid residues in nuoa from different organisms. novel analyses of nuoa from escherichia coli complex i expressed as fusio ... | 2011 | 21925501 |
| Role of Surf1 in heme recruitment for bacterial COX biogenesis. | Biogenesis of the mitochondrial cytochrome c oxidase (COX) is a highly complex process involving subunits encoded both in the nuclear and the organellar genome; in addition, a large number of assembly factors participate in this process. The soil bacterium Paracoccus denitrificans is an interesting alternative model for the study of COX biogenesis events because the number of chaperones involved is restricted to an essential set acting in the metal centre formation of oxidase, and the high degre ... | 2011 | 21945856 |
| protective effects of astaxanthin from paracoccus carotinifaciens on murine gastric ulcer models. | the purpose of this study was to investigate the effect of astaxanthin extracted from paracoccus carotinifaciens on gastric mucosal damage in murine gastric ulcer models. mice were pretreated with astaxanthin for 1 h before ulcer induction. gastric ulcers were induced in mice by oral administration of hydrochloride (hcl)/ethanol or acidified aspirin. the effect of astaxanthin on lipid peroxidation in murine stomach homogenates was also evaluated by measuring the level of thiobarbituric acid reac ... | 2011 | 22170791 |
| effects of stimulation of copper bioleaching on microbial community in vineyard soil and copper mining waste. | long-term copper application in vineyards and copper mining activities cause heavy metal pollution sites. such sites need remediation to protect soil and water quality. bioremediation of contaminated areas through bioleaching can help to remove copper ions from the contaminated soils. thus, the aim of this work was to evaluate the effects of different treatments for copper bioleaching in two diverse copper-contaminated soils (a 40-year-old vineyard and a copper mining waste) and to evaluate the ... | 2011 | 21947860 |
| efficient electron transfer in a protein network lacking specific interactions. | in many biochemical processes, proteins need to bind partners amidst a sea of other molecules. generally, partner selection is achieved by formation of a single-orientation complex with well-defined, short-range interactions. we describe a protein network that functions effectively in a metabolic electron transfer process but lacks such specific interactions. the soil bacterium paracoccus denitrificans oxidizes a variety of compounds by channeling electrons into the main respiratory pathway. upo ... | 2011 | 21916462 |
| catalyzing denitrification of paracoccus versutus by immobilized 1,5-dichloroanthraquinone. | the accelerating effect of non-dissolved redox mediator (1,5-dichloroanthraquinone) on the biological denitrification was investigated in this paper using 1,5-dichloroanthraquinone immobilized by calcium alginate (ca) and a heterotrophic denitrification bacterium of paracoccus versutus (gu111570). the results suggested that the denitrification rate was enhanced 2.1 fold by 25 mmol l(-1) 1,5-dichloroanthraquinone of this study, and a positive correlation was found for the denitrification rate and ... | 2011 | 22086549 |
| sulfoquinovose degraded by pure cultures of bacteria with release of c(3) -organosulfonates: complete degradation in two-member communities. | sulfoquinovose (sq, 6-deoxy-6-sulfoglucose) was synthesized chemically. an hplc-elsd method to separate sq and other chromophore-free sulfonates, e.g. 2,3-dihydroxypropane-1-sulfonate (dhps), was developed. a set of 10 genome-sequenced, sulfonate-utilizing bacteria did not utilize sq, but an isolate, pseudomonas putida sq1, from an enrichment culture did so. the molar growth yield with sq was half of that with glucose, and 1 mol 3-sulfolactate (mol sq)(-1) was formed during growth. the 3-sulfol ... | 2011 | 22150877 |
| Electrogenic events upon photolysis of CO from fully reduced cytochrome c oxidase. | CO photolysis from fully reduced Paracoccus denitrificans aa(3)-type cytochrome c oxidase in the absence of O(2) was studied by time-resolved potential electrometry. Surprisingly, photo dissociation of the uncharged carbon monoxide results in generation of a small-amplitude electric potential with the same sign as the physiological charge separation during activity. The number of electrogenic events after CO photolysis depends on the state of the enzyme. CO photolysis following immediately after ... | 2012 | 22133637 |
| functional characterization of the type ii pami restriction-modification system derived from plasmid pami7 of paracoccus aminophilus jcm 7686. | plasmid pami7 of the methylotrophic bacterium paracoccus aminophilus jcm 7686 (alphaproteobacteria) encodes a functional type ii restriction-modification (r-m) system designated pami. homologous systems were identified in the genomes of distinct taxonomic groups of bacteria and archaea, which provides evidence that horizontal gene transfer has contributed to the wide dissemination of r-m modules - even between domains. analysis of the cleavage specificity of the r.pami endonuclease revealed that ... | 2011 | 22092764 |
| Cloning and characterization of a novel amidase from Paracoccus sp. M-1, showing aryl acylamidase and acyl transferase activities. | A novel amidase gene, designated pamh, was cloned from Paracoccus sp. M-1. Site-directed mutagenesis and bioinformatic analysis showed that the PamH protein belonged to the amidase signature enzyme family. PamH was expressed in Escherichia coli, purified, and characterized. The molecular mass of PamH was determined to be 52 kDa with an isoelectric point of 5.13. PamH displayed its highest enzymatic activity at 45°C and at pH 8.0 and was stable within a pH range of 5.0-10.0. The PamH enzyme exhib ... | 2011 | 22101784 |
| paracoccus oceanense sp. nov., isolated from the west pacific. | a gram-negative, short ovoid- to coccus-shaped, aerobic, motile, non-spore-forming bacterium (designated strain jlt1679(t)) was isolated from west pacific. cells have subpolar flagella, dividing by binary fission. phylogenetic analyses based on 16s rrna gene sequences showed that the strain belongs to branch of the evolutionary radiation occupied by the genus paracoccus, family rhodobacteraceae, order rhodobacterales, class alphaproteobacteria. the closest neighbours were paracoccus stylophorae ... | 2011 | 21960015 |
| Free energy analysis of ?-transaminase reactions to dissect how the enzyme controls the substrate selectivity. | ?-Transaminase (?-TA) is the only naturally occurring enzyme allowing asymmetric amination of ketones for production of chiral amines. The active site of the enzyme was proposed to consist of two differently sized substrate binding pockets and the stringent steric constraint in the small pocket has presented a significant challenge to production of structurally diverse chiral amines. To provide a mechanistic understanding of how the (S)-specific ?-TA from Paracoccus denitrificans achieves the st ... | 2011 | 22112564 |
| Cytochrome c oxidase: Charge translocation coupled to single-electron partial steps of the catalytic cycle. | The paper presents a survey of time-resolved studies of charge translocation by cytochrome c oxidase coupled to transfer of the 1st, 2nd 3rd and 4th electrons in the catalytic cycle. Single-electron photoreduction experiments carried out with the A-class cytochrome c oxidases of aa(3) type from mitochondria, Rhodobacter sphaeroides and Paracoccus denitrificans as well as with the ba(3)-type oxidase from Thermus thermophilus indicate that the protonmotive mechanisms, although similar, may not be ... | 2011 | 21871433 |
| [screening and identification of two heterotrophic nitrifying bacteria and characterization of their capacity for nitrogen removal]. | two heterotrophic nitrifying bacteria, p2 and p9 isolated from piggery wastewater, were studied for their capacity of nitrification and nitrogen removal. | 2011 | 22233060 |
| microbial growth at hyperaccelerations up to 403,627 x g. | it is well known that prokaryotic life can withstand extremes of temperature, ph, pressure, and radiation. little is known about the proliferation of prokaryotic life under conditions of hyperacceleration attributable to extreme gravity, however. we found that living organisms can be surprisingly proliferative during hyperacceleration. in tests reported here, a variety of microorganisms, including gram-negative escherichia coli, paracoccus denitrificans, and shewanella amazonensis; gram-positive ... | 2011 | 21518884 |
| crystal structures of co and no adducts of maug in complex with pre-methylamine dehydrogenase: implications for the mechanism of dioxygen activation. | maug is a diheme enzyme responsible for the post-translational formation of the catalytic tryptophan tryptophylquinone (ttq) cofactor in methylamine dehydrogenase (madh). maug can utilize hydrogen peroxide, or molecular oxygen and reducing equivalents, to complete this reaction via a catalytic bis-fe(iv) intermediate. crystal structures of diferrous, fe(ii)-co, and fe(ii)-no forms of maug in complex with its premadh substrate have been determined and compared to one another as well as to the str ... | 2011 | 21355604 |
| carotenoid ╬▓-ring hydroxylase and ketolase from marine bacteria-promiscuous enzymes for synthesizing functional xanthophylls. | marine bacteria belonging to genera paracoccus and brevundimonas of the ╬▒-proteobacteria class can produce côéäôéç-type dicyclic carotenoids containing two ╬▓-end groups (╬▓ rings) that are modified with keto and hydroxyl groups. these bacteria produce astaxanthin, adonixanthin, and their derivatives, which are ketolated by carotenoid ╬▓-ring 4(4')-ketolase (4(4')-oxygenase; crtw) and hydroxylated by carotenoid ╬▓-ring 3(3')-hydroxylase (crtz). in addition, the genus brevundimonas possesses a g ... | 2011 | 21673887 |