Publications

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design of a functional nitric oxide reductase within a myoglobin scaffold. 201020235108
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 ...201020226655
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 ...201020383015
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 ...201020589635
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 ...201020632002
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 ...201020683589
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 ...201020709842
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 ...201020935084
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 ...201020351252
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 ...201021172303
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 ...201021187147
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.201019556157
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) ...201019783785
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 ...201019842617
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.201019889897
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 ...201020093016
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 ...201020093290
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 ...201020050916
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 ...201020056281
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 ...201019961168
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 ...201019921293
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 ...201122172736
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 ...201122170791
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 ...201121947860
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 ...201121916462
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 ...201122086549
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 ...201122150877
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 ...201122092764
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 ...201122101784
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 ...201121960015
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 ...201122112564
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 ...201121871433
[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.201122233060
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 ...201121914898
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 ...201122174385
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) ...201121996020
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 ...201121856278
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 ...201122026826
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 ...201121983703
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 ...201121969534
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 ...201120400662
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 ...201121547574
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. ...201121624365
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 ...201121673887
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 ...201121739254
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.201121731299
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 ...201121232525
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 ...201121244362
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 ...201121265774
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 ...201121265780
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 ...201121268585
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 ...201121308847
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 ...201121368144
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 ...201121399942
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 ...201121417467
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 ...201121543712
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 ...201121569803
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 ...201121841031
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 ...201122166118
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 ...201121925501
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 ...201121945856
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 ...201121216223
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.201121257769
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 ...201120854281
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 ...201121418525
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 ...201121423952
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 ...201121455946
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 ...201121509603
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 ...201121518884
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 ...201121348864
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 ...201121355604
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 ...201121296048
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 ...201121298680
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 ...201121303396
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 ...201121306891
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 ...201120543151
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 ...201222133637
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