taxonomic study of aromatic-degrading bacteria from deep-terrestrial-subsurface sediments and description of sphingomonas aromaticivorans sp. nov., sphingomonas subterranea sp. nov., and sphingomonas stygia sp. nov.phylogenetic analyses of 16s rrna gene sequences by distance matrix and parsimony methods indicated that six strains of bacteria isolated from deep saturated atlantic coastal plain sediments were closely related to the genus sphingomonas. five of the strains clustered with, but were distinct from, sphingomonas capsulata, whereas the sixth strain was most closely related to blastobacter natatorius. the five strains that clustered with s. capsulata, all of which could degrade aromatic compounds, w ...19978995822
complete sequence of a 184-kilobase catabolic plasmid from sphingomonas aromaticivorans f199.the complete 184,457-bp sequence of the aromatic catabolic plasmid, pnl1, from sphingomonas aromaticivorans f199 has been determined. a total of 186 open reading frames (orfs) are predicted to encode proteins, of which 79 are likely directly associated with catabolism or transport of aromatic compounds. genes that encode enzymes associated with the degradation of biphenyl, naphthalene, m-xylene, and p-cresol are predicted to be distributed among 15 gene clusters. the unusual coclustering of gene ...199910049392
characterization of the tra2 region of the inchi1 plasmid this study, the dna sequence of one of the transfer regions of the inchi1 plasmid r27 was determined. this region, which corresponds to coordinates 0-40 on the r27 map has been called the tra2 region, and is believed to be involved in mating pair formation. dna sequence analysis of the transfer region identified 11 open reading frames which showed similarities to the transfer genes from other conjugative systems. the r27 transfer genes appear to most closely resemble the genes from the f plas ...199910366528
isrm10: a new insertion sequence of sinorhizobium meliloti: nucleotide sequence and geographic this study the description of a new insertion sequence of sinorhizobium meliloti, isrm10, is reported. isrm10 was found in the intergenic region between nodj and nodq of a natural isolated strain. isrm10 was 1047 bp long and showed the typical features of the iss belonging to the is630-tc1/is3 superfamily. in particular the isrm10 nucleotide sequence showed the highest homology (62%) with a sphingomonas aromaticivorans is. isrm10 was present in 32% of the analyzed s. meliloti strains while it ...199910564804
presence of two trans-o-hydroxybenzylidenepyruvate hydratase-aldolases in naphthalenesulfonate-assimilating sphingomonas paucimobilis ta-2: comparison of some properties.two trans-o-hydroxybenzylidenepyruvate hydratase-aldolases named thbp ha a and thbp ha b were purified from a cell-free extract of naphthalenesulfonate-assimilating sphingomonas paucimobilis (formerly pseudomonas sp.) ta-2 to an electrophoretically homogeneous state by successive column chromatographies on deae-cellulose, deae-toyopearl 650m, sephacryl s-100, hydroxyapatite, and mono q. these enzymes were similar to each other in molecular mass (ca. 37 kda on sds-page, ca. 110 kda on ultracentri ...200010731665
characterization of sphingomonas isolates from finnish and swedish drinking water distribution systems.sphingomonas species were commonly isolated from biofilms in drinking water distribution systems in finland (three water meters) and sweden (five water taps in different buildings). the sphingomonas isolates (n = 38) were characterized by chemotaxonomic, physiological and phylogenetic methods. fifteen isolates were designated to species sphingomonas aromaticivorans, seven isolates to s. subterranea, two isolates to s. xenophaga and one isolate to s. stygia. thirteen isolates represented one or m ...200011054174
evidence for a role of rpoe in stressed and unstressed cells of marine vibrio angustum strain s14.we report the cloning, sequencing, and characterization of the rpoe homolog in vibrio angustum s14. the rpoe gene encodes a protein with a predicted molecular mass of 19.4 kda and has been demonstrated to be present as a single-copy gene by southern blot analysis. the deduced amino acid sequence of rpoe is most similar to that of the rpoe homolog of sphingomonas aromaticivorans, sigma(24), displaying sequence similarity and identity of 63 and 43%, respectively. northern blot analysis demonstrate ...200011092857
detection of sphingomonas spp in soil by pcr and sphingolipid biomarker analysis.sphingomonas spp possess unique abilities to degrade refractory contaminants and are found ubiquitously in the environment. we developed sphingomonas genus-specific pcr primers (spf-190 and spr1-852) which showed specific amplification of a 627-bp 16s rdna fragment from sphingomonas spp. a pcr assay using these sphingomonas specific primers was developed to detect sphingomonas aromaticivorans b0695r in three texturally distinct soil types, showing detection limits between 1.3-2.2 x 10(3) cfu g(- ...199911423941
induction of aromatic catabolic activity in sphingomonas aromaticivorans strain f199.enzyme induction studies with sphingomonas aromaticivorans f199 demonstrated that both toluene and naphthalene induced expression of both naphthalene and toluene catabolic enzymes. however, neither aromatic compound induced expression of all the enzymes required for complete mineralization of either naphthalene or toluene. activity measurements in combination with gene sequence analyses indicate that growth on either aromatic substrate in the absence of the other is, therefore, sub-optimal and i ...199911423947
proposal of the genus sphingomonas sensu stricto and three new genera, sphingobium, novosphingobium and sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses.phylogenetic analyses of 16s rrna gene sequences by distance matrix and parsimony methods indicated that the currently known species of the genus sphingomonas can be divided into four clusters. some chemotaxonomic and phenotypic differences were noted among these clusters. three new genera, sphingobium, novosphingobium and sphingopyxis, are proposed in addition to the genus sphingomonas sensu stricto. the genus sphingobium is proposed to accommodate sphingomonas chlorophenolica, sphingomonas her ...200111491340
biodegradation of polycyclic aromatic hydrocarbons by sphingomonas strains isolated from the terrestrial subsurface.several strains of sphingomonas isolated from deep atlantic coastal plain aquifers at the us department of energy savannah river site (srs) near aiken, sc were shown to degrade a variety of aromatic hydrocarbons in a liquid culture medium. sphingomonas aromaticivorans strain b0695 was the most versatile of the five strains examined. this strain was able to degrade acenaphthene, anthracene, phenanthrene, 2,3-benzofluorene, 2-methylnaphthalene, 2,3-dimethylnaphthalene, and fluoranthene in the pres ...200111494104
use of a two-phase partitioning bioreactor for degrading polycyclic aromatic hydrocarbons by a sphingomonas sp.a two-phase partitioning bioreactor (tppb) utilizing the bacterium sphingomonas aromaticivorans b0695 was used to degrade four low molecular weight (lmw) polycyclic aromatic hydrocarbons (pahs). the tppb concept is based on the use of a biocompatible, immiscible organic solvent in which high concentrations of recalcitrant substrates are dissolved. these substances partition into the cell-containing aqueous phase at rates determined by the metabolic activity of the cells. experiments showed that ...200212111172
cysteine activation is an inherent in vitro property of prolyl-trna synthetases.aminoacyl-trna synthetases are well known for their remarkable precision in substrate selection during aminoacyl-trna formation. some synthetases enhance the accuracy of this process by editing mechanisms that lead to hydrolysis of incorrectly activated and/or charged amino acids. prolyl-trna synthetases (prorss) can be divided into two structurally divergent groups, archaeal-type and bacterial-type enzymes. a striking difference between these groups is the presence of an insertion domain (appro ...200212130657
the unique aromatic catabolic genes in sphingomonads degrading polycyclic aromatic hydrocarbons (pahs).many members of the sphingomonad genus isolated from different geological areas can degrade a wide variety of polycyclic aromatic hydrocarbons (pahs) and related compounds. these sphingomonads such as sphingobium yanoikuyae strain b1, novosphingobium aromaticivorans strain f199, and sphingobium sp. strain p2 have been found to possess a unique group of genes for aromatic degradation, which are distantly related with those in pseudomonads and other genera reported so far both in sequence homology ...200312682862
characterization and regulation of the genes for a novel anthranilate 1,2-dioxygenase from burkholderia cepacia dbo1.anthranilate (2-aminobenzoate) is an important intermediate in tryptophan metabolism. in order to investigate the degradation of tryptophan through anthranilate by burkholderia cepacia, several plasposon mutations were constructed of strain dbo1 and one mutant with the plasposon insertion in the anthranilate dioxygenase (antdo) genes was chosen for further study. the gene sequence obtained from flanking dna of the plasposon insertion site revealed unexpected information. b. cepacia dbo1 antdo (d ...200313129960
a prokaryotic alternative oxidase present in the bacterium novosphingobium aromaticivorans.the alternative oxidase (aox) is a terminal oxidase present in the respiratory chain of all plants as well as some yeasts and trypanosomes, but has not previously been found in a prokaryote. we have identified an aox homologue in novosphingobium aromaticivorans, the first aox found in a prokaryote. we have cloned the gene for the n. aromaticivorans aox and showed it to have a terminal oxidase activity when heterologously expressed in escherichia coli. we have also shown that this novel aox is ex ...200314527685
patients with primary biliary cirrhosis react against a ubiquitous xenobiotic-metabolizing bacterium.infectious and environmental agents have been proposed as immunologic triggers for primary biliary cirrhosis (pbc). recently, a ubiquitous organism that metabolizes organic compounds and estrogens, novosphingobium aromaticivorans, has been defined. importantly, 2 bacterial proteins have homology with the e2 component of the pyruvate dehydrogenase complex (pdc-e2). sera from 97 patients with pbc, 46 first-degree relatives, 10 spouses, and 195 controls were studied for reactivity against n. aromat ...200314578864
prokaryotic origins for the mitochondrial alternative oxidase and plastid terminal oxidase nuclear genes.the mitochondrial alternative oxidase is a diiron carboxylate quinol oxidase (dox) found in plants and some fungi and protists, but not animals. the plastid terminal oxidase is distantly related to alternative oxidase and is most likely also a dox protein. database searches revealed that the alpha-proteobacterium novosphingobium aromaticivorans and the cyanobacteria nostoc sp. pcc7120, synechococcus sp. wh8102 and prochlorococcus marinus subsp. pastoris ccmp1378 each possess a dox homolog. each ...200314675750
cross-species identification of proteins from proteome profiles of the marine oligotrophic ultramicrobacterium, sphingopyxis alaskensis.sphingopyxis (formerly sphingomonas) alaskensis is a model bacterium for studying adaptation to oligotrophy (nutrient-limitation). it has a unique physiology which is fundamentally different to that of the well studied bacteria such as escherichia coli. to begin to identify the genes involved in its physiological responses to nutrient-limited growth and starvation, we developed high resolution two-dimensional electrophoresis (2-de) methods and determined the identity of 12 proteins from a total ...200415174144
bacteria and human autoimmunity: the case of primary biliary cirrhosis.primary biliary cirrhosis is a chronic inflammatory disease of the intrahepatic bile ducts that eventually leads to liver cirrhosis and organ failure, in which several observations suggest an autoimmune origin. similarly to other autoimmune diseases, microbial mediated molecular mimicry is the most widely studied trigger that may break immunologic tolerance in primary biliary cirrhosis.200415201604
cloning and functional analysis by gene disruption of a novel gene involved in indigo production and fluoranthene metabolism in pseudomonas alcaligenes pa-10.a novel indole dioxygenase (idoa) gene has been cloned from pseudomonas alcaligenes pa-10, based on its ability to convert indole to indigo. the chromosomally encoded idoa gene exhibits no similarity to previously cloned naphthalene dioxygenases or to aromatic oxygenases from other species at the nucleotide level. phylogenetic analysis indicates that the idoa gene product is most similar to an acyl-coa dehydrogenase from novosphingobium aromaticivorans. the enzyme encoded by the idoa gene is ess ...200415476978
identification and functional analysis of two aromatic-ring-hydroxylating dioxygenases from a sphingomonas strain that degrades various polycyclic aromatic this study, the enzymes involved in polycyclic aromatic hydrocarbon (pah) degradation in the chrysene-degrading organism sphingomonas sp. strain chy-1 were investigated. [14c]chrysene mineralization experiments showed that pah-grown bacteria produced high levels of chrysene-catabolic activity. one pah-induced protein displayed similarity with a ring-hydroxylating dioxygenase beta subunit, and a second pah-induced protein displayed similarity with an extradiol dioxygenase. the genes encoding t ...200415528538
phosphonium ionic liquids for degradation of phenol in a two-phase partitioning bioreactor.six ionic liquids (ils), which are organic salts that are liquid at room temperature, were tested for their biocompatibility with three xenobiotic-degrading bacteria, pseudomonas putida, achromobacter xylosoxidans, and sphingomonas aromaticivorans. of the 18 pairings, seven were found to demonstrate biocompatibility, with one il (trihexyl(tetradecyl)phosphonium bis(trifluoromethylsulfonyl) amide) being biocompatible with all three organisms. this il was then used in a two-phase partitioning bior ...200515549289
novosphingobium aromaticivorans: a potential initiator of primary biliary cirrhosis.primary biliary cirrhosis (pbc) is characterized by a t-cell-mediated destruction of bile duct epithelial cells that line the small intrahepatic bile ducts. the targets of activated t-lymphocytes are the dihydrolipoamide acetyltransferase components of the 2 oxo acid dehydrogenases, enzyme complexes that are important in oxidative energy metabolism. pyruvate dehydrogenase is the best known of these. its dihydrolipoamide acetyltransferase component is referred to as pdc-e2. a major question in un ...200415554995
novosphingobium lentum sp. nov., a psychrotolerant bacterium from a polychlorophenol bioremediation process.a polychlorophenol-degrading strain, designated mt1(t), and three mt1-like strains, mt101, mt103 and mt104, were isolated from a cold (4-8 degrees c) fluidized-bed process treating chlorophenol-contaminated groundwater in southern finland. the organisms were gram-negative, rod-shaped, catalase-positive, non-spore-forming and non-motile. phylogenetic analysis based on 16s rrna gene sequences indicated that the strains belonged to the alpha-4 subclass of the proteobacteria and were members of the ...200515774628
phylogenetic and immunological definition of four lipoylated proteins from novosphingobium aromaticivorans, implications for primary biliary cirrhosis.novosphingobium aromaticivorans, a unique ubiquitous bacterium that metabolizes xenobiotics and activates environmental estrogens, has been suggested as a pathogenic factor in the development of primary biliary cirrhosis (pbc). to define the molecular basis of pbc sera reactivity, we investigated the characteristic of the bacterial antigens involved. we cloned and sequenced four genes from n. aromaticivorans coding for immunoreactive proteins, arbitrarily named novo 1 through novo 4. we subseque ...200515848043
novosphingobium taihuense sp. nov., a novel aromatic-compound-degrading bacterium isolated from taihu lake, china.a novel aromatic-compound-degrading bacterium, strain t3-b9(t), was isolated from sediment of taihu lake, jiangsu province, south-east china. this bacterial isolate assimilated several aromatic compounds such as phenol, aniline, nitrobenzene, 4-chloronitrobenzene and phenanthrene. the taxonomy of strain t3-b9(t) was studied by polyphasic methods. the organism showed a range of phenotypic and chemotaxonomic properties consistent with those of the genus novosphingobium. the 16s rrna gene sequence ...200515879260
structural and replicative diversity of large plasmids from sphingomonads that degrade polycyclic aromatic compounds and xenobiotics.the plasmids from 16 sphingomonads which degrade various xenobiotics and polycyclic aromatic compounds were compared with the previously sequenced plasmid pnl1 from sphingomonas aromaticivorans f199. the replicase genes repaaab from plasmid pnl1 were amplified by pcr and used as a gene probe for the identification of plasmids belonging to the same incompatibility group as plasmid pnl1. plasmids were prepared from various sphingomonads and hybridized with the repa gene probe. positive hybridizati ...200515942009
alternative oxidase (aox) genes of african trypanosomes: phylogeny and evolution of aox and plastid terminal oxidase clarify evolution and phylogenetic relationships of trypanosome alternative oxidase (aox) molecules, aox genes (cdnas) of the african trypanosomes, trypanosoma congolense and trypanosoma evansi, were cloned by pcr. both aoxs possess conserved consensus motifs (-e-, -exxh-). the putative amino acid sequence of the aox of t. evansi was exactly the same as that of t. brucei. a protein phylogeny of trypanosome aoxs revealed that three genetically and pathogenically distinct strains of t. congolen ...200516014016
enhanced degradation of a mixture of polycyclic aromatic hydrocarbons by a defined microbial consortium in a two-phase partitioning bioreactor.biological treatment methods are effective at destroying polycyclic aromatic hydrocarbons (pahs), and some of the highest rates of pah degradation have been achieved using two-phase-partitioning bioreactors (tppbs). tppbs consist of a cell-containing aqueous phase and a biocompatible and immiscible organic phase that partitions toxic and/or recalcitrant substrates to the cells based on their metabolic demand and on maintaining the thermodynamic equilibrium of the system. in this study, the degra ...200716758271
identification and functional analysis of the genes for naphthalenesulfonate catabolism by sphingomonas xenophaga bn6.sphingomonas xenophaga bn6 degrades various (substituted) naphthalenesulfonates to the corresponding (substituted) salicylates. a gene cluster was identified on the plasmid pbn6 which coded for several enzymes participating in the degradative pathway for naphthalenesulfonates. a dna fragment of 16 915 bp was sequenced which contained 17 orfs. the genes encoding the 1,2-dihydroxynaphthalene dioxygenase, 2-hydroxychromene-2-carboxylate isomerase, and 2'-hydroxybenzalpyruvate aldolase of the naphth ...200616804169
the sphingomonas plasmid pcar3 is involved in complete mineralization of carbazole.we determined the complete 254,797-bp nucleotide sequence of the plasmid pcar3, a carbazole-degradative plasmid from sphingomonas sp. strain ka1. a region of about 65 kb involved in replication and conjugative transfer showed similarity to a region of plasmid pnl1 isolated from the aromatic-degrading novosphingobium aromaticivorans strain f199. the presence of many insertion sequences, transposons, repeat sequences, and their remnants suggest plasticity of this plasmid in genetic structure. alth ...200717172338
p450 enzymes from the bacterium novosphingobium aromaticivorans.twelve of the fifteen potential p450 enzymes from the bacterium novosphingobium aromaticivorans, which is known to degrade a wide range of aromatic hydrocarbons, have been produced via heterologous expression in escherichia coli. the enzymes were tested for their ability to bind a range of substrates including polyaromatic hydrocarbons. while two of the enzymes were found to bind aromatic compounds (cyp108d1 and cyp203a2), the others show binding with a variety of compounds including linear alka ...200717618912
evolution of enzymatic activities in the enolase superfamily: d-mannonate dehydratase from novosphingobium aromaticivorans.the d-mannonate dehydratase (mand) function was assigned to a group of orthologous proteins in the mechanistically diverse enolase superfamily by screening a library of acid sugars. structures of the wild type mand from novosphingobium aromaticivorans were determined at ph 7.5 in the presence of mg2+ and also in the presence of mg2+ and the 2-keto-3-keto-d-gluconate dehydration product; the structure of the catalytically active k271e mutant was determined at ph 5.5 in the presence of the d-manno ...200717944491
phylogenomics and signature proteins for the alpha proteobacteria and its main groups.alpha proteobacteria are one of the largest and most extensively studied groups within bacteria. however, for these bacteria as a whole and for all of its major subgroups (viz. rhizobiales, rhodobacterales, rhodospirillales, rickettsiales, sphingomonadales and caulobacterales), very few or no distinctive molecular or biochemical characteristics are known.200718045498
invariant natural killer t cells trigger adaptive lymphocytes to churn up innate immune response causes autoimmunity has remained an enigma. in this issue of cell host & microbe, mattner et al. demonstrate that invariant natural killer t cells activated by the mucosal commensal novosphingobium aromaticivorans precipitate chronic t cell-mediated autoimmunity against small bile ducts that mirrors human primary biliary cirrhosis. these findings provide a mechanistic understanding of the role of innate immunity toward a microbe in the development of autoimmunity.200818474352
liver autoimmunity triggered by microbial activation of natural killer t cells.humans with primary biliary cirrhosis (pbc), a disease characterized by the destruction of small bile ducts, exhibit signature autoantibodies against mitochondrial pyruvate dehydrogenase complex e2 (pdc-e2) that crossreact onto the homologous enzyme of novosphingobium aromaticivorans, an ubiquitous alphaproteobacterium. here, we show that infection of mice with n. aromaticivorans induced signature antibodies against microbial pdc-e2 and its mitochondrial counterpart but also triggered chronic t ...200818474357
identification of bacterial carotenoid cleavage dioxygenase homologues that cleave the interphenyl alpha,beta double bond of stilbene derivatives via a monooxygenase reaction.carotenoid cleavage oxygenases (ccos), which are also referred to as carotenoid cleavage dioxygenases (ccds) are a new class of nonheme iron-type enzymes that oxidatively cleave double bonds in the conjugated carbon chain of carotenoids. the oxidative cleavage mechanism of these enzymes is not clear, and both monooxygenase and dioxygenase mechanisms have been proposed for different carotenoid cleavage enzymes. ccos have been described from plants, animals, fungi, and cyanobacteria, but little is ...200818478524
bacteria and primary biliary cirrhosis.infectious agents have been postulated to play a pathogenic role in the loss of immunological tolerance and the induction of primary biliary cirrhosis, an immune-mediated cholestatic liver disease characterized by progressive destruction of the small intrahepatic bile ducts and subsequent cirrhosis and liver failure. this review discusses emerging issues implicating infectious agents such as escherichia coli, mycobacteria, chlamydia, helicobacter species, lactobacilli, novosphingobium aromaticiv ...200918498061
bioremediation of trace cobalt from simulated spent decontamination solutions of nuclear power reactors using e. coli expressing nicot genes.removal of radioactive cobalt at trace levels (approximately nm) in the presence of large excess (10(6)-fold) of corrosion product ions of complexed fe, cr, and ni in spent chemical decontamination formulations (simulated effluent) of nuclear reactors is currently done by using synthetic organic ion exchangers. a large volume of solid waste is generated due to the nonspecific nature of ion sorption. our earlier work using various fungi and bacteria, with the aim of nuclear waste volume reduction ...200818949474
cloning and characterization of an epoxide hydrolase from novosphingobium aromaticivorans.a gene encoding a putative epoxide hydrolase (ehase) was identified by analyzing an open reading frame of the genome sequence of novosphingobium aromaticivorans, retaining the conserved catalytic residues such as the catalytic triad (asp177, glu328, and his355) and the oxyanion hole. the enantioselective ehase gene (neh) was cloned, and the recombinant ehase could be purified to apparent homogeneity by one step of metal affinity chromatography and further characterized. the purified n. aromatici ...200919083233
characterization of a ring-hydroxylating dioxygenase from phenanthrene-degrading sphingomonas sp. strain lh128 able to oxidize benz[a]anthracene.sphingomonas sp. strain lh128 was isolated from a polycyclic aromatic hydrocarbon (pah)-contaminated soil using phenanthrene as the sole source of carbon and energy. a dioxygenase complex, phna1fa2f, encoding the alpha and beta subunit of a terminal dioxygenase responsible for the initial attack on pahs, was identified and isolated from this strain. phna1f showed 98%, 78%, and 78% identity to the alpha subunit of pah dioxygenase from novosphingobium aromaticivorans strain f199, sphingomonas sp. ...200919172265
purification, crystallization and preliminary x-ray analysis of cytochrome p450 219a1 from novosphingobium aromaticivorans dsm 12444.cytochrome p450 enzymes catalyze a variety of reactions and are widely distributed in living organisms. in recent studies, the first members of five new families of cytochrome p450 enzymes have been identified, including cytochrome p450 219a1 (cyp219a1) from novosphingobium aromaticivorans dsm 12444. it has also been reported that isolongifolen-9-one (c(15)h(22)o), a sesquiterpenoid ketone derivative, is a potential substrate for cyp219a1, inducing a >or=95% shift of the haem spin state to high ...200919342781
a cytochrome p450 class i electron transfer system from novosphingobium aromaticivorans.cytochrome p450 (cyp) enzymes of the cyp101 and cyp111 families from novosphingobium aromaticivorans are heme monooxygenases that catalyze the hydroxylation of a range of terpenoid compounds. cyp101d1 and cyp101d2 oxidized camphor to 5-exo-hydroxycamphor. cyp101b1 and cyp101c1 oxidized beta-ionone to predominantly 3-r-hydroxy-beta-ionone and 4-hydroxy-beta-ionone, respectively. cyp111a2 oxidized linalool to 8-hydroxylinalool. physiologically, these cyp enzymes could receive electrons from arx, a ...201019779713
[predominant strains of polycyclic aromatic hydrocarbon-degrading consortia from deep sea of the middle atlantic ridge].in order to identify the predominant strains of polycyclic aromatic hydrocarbon (pah)-degrading consortia harboring in sea water and surface sediment collected from deep sea of the middle atlantic ridge.200919873754
autoimmune disease triggered by infection with alphaproteobacteria.despite having long been postulated, compelling evidence for the theory that microbial triggers drive autoimmunity has only recently been reported. a specific association between novosphingobium aromaticivorans, an ubiquitous alphaproteobacterium, and primary biliary cirrhosis (pbc) has been uncovered in patients with pbc. notably, the association between novosphingobium infection and pbc has been confirmed in a mouse model in which infection leads to the development of liver lesions resembling ...200920161124
enantioselective hydrolysis of racemic epichlorohydrin using an epoxide hydrolase from novosphingobium aromaticivorans.previously we reported that an epoxide hydrolase (ehase) from novosphingobium aromaticivorans could preferentially hydrolyze (r)-styrene oxide. in this study, we demonstrate that the purified neh could be also effective in chiral resolution of racemic epichlorohydrin (ech). particularly, the purified neh showed excellent hydrolyzing activity toward ech to complete the reaction at a short period of incubation time. enantiopure (s)-ech could be obtained with a high enantiopurity of more than 99.99 ...201020547378
molecular characterization of a class i p450 electron transfer system from novosphingobium aromaticivorans dsm12444.cytochrome p450 (cyp) enzymes of the cyp101 and cyp111 families from the oligotrophic bacterium novosphingobium aromaticivorans dsm12444 are heme monooxygenases that receive electrons from nadh via arx, a [2fe-2s] ferredoxin, and arr, a ferredoxin reductase. these systems show fast nadh turnovers (k(cat) = 39-91 s(-1)) that are efficiently coupled to product formation. the three-dimensional structures of arr, arx, and cyp101d1, which form a physiological class i p450 electron transfer chain, hav ...201020576606
the structure of cyp101d2 unveils a potential path for substrate entry into the active site.the cytochrome p450 cyp101d2 from novosphingobium aromaticivorans dsm12444 is closely related to cyp101d1 from the same bacterium and to p450cam (cyp101a1) from pseudomonas putida. all three are capable of oxidizing camphor stereoselectively to 5-exo-hydroxycamphor. the crystal structure of cyp101d2 revealed that the likely ferredoxin-binding site on the proximal face is largely positively charged, similar to that of cyp101d1. however, both the native and camphor-soaked forms of cyp101d2 had ope ...201020950270
structural analysis of cyp101c1 from novosphingobium aromaticivorans dsm12444.cyp101c1 from novosphingobium aromaticivorans dsm12444 is a homologue of cyp101d1 and cyp101d2 enzymes from the same bacterium and cyp101a1 from pseudomonas putida. cyp101c1 does not bind camphor but is capable of binding and hydroxylating ionone derivatives including α- and β-ionone and β-damascone. the activity of cyp101c1 was highest with β-damascone (k(cat)=86 s(-1)) but α-ionone oxidation was the most regioselective (98 % at c3). the crystal structures of hexane-2,5-diol- and β-ionone-bound ...201121154803
genetic susceptibility to autoimmune liver disease.autoimmune hepatitis (aih), primary sclerosing cholangitis (psc) and primary biliary cirrhosis (pbc) are considered as putative autoimmune diseases of the liver. whereas strong evidence that bacterial infection may trigger pbc exists, the etiologies for psc and aih remain unknown. although there have been significant discoveries of genetic polymorphisms that may underlie the susceptibility to these liver diseases, their associations with environmental triggers and the subsequent implications hav ...201121307981
identification of cd101 as a susceptibility gene for novosphingobium aromaticivorans-induced liver autoimmunity.environmental and genetic factors define the susceptibility of an individual to autoimmune disease. although common genetic pathways affect general immunological tolerance mechanisms in autoimmunity, the effects of such genes could vary under distinct immune challenges within different tissues. in this study, we demonstrate this by observing that autoimmune type 1 diabetes-protective haplotypes at the insulin-dependent diabetes susceptibility region 10 (idd10) introgressed from chromosome 3 of c ...201121613619
crystallization and preliminary x-ray analysis of cyp153c1 from novosphingobium aromaticivorans dsm12444.cytochrome p450 (cyp) enzymes constitute a large family of haemoproteins that catalyze the monooxygenation of a great variety of endogenous and exogenous organic compounds. in common with other members of the cyp153 family of alkane hydroxylases, cyp153c1 from the oligotrophic bacterium novosphingobium aromaticivorans dsm 12444 can bind linear alkanes such as heptane, octane and nonane. here, the production, purification and crystallization of cyp153c1 and the collection of high-resolution diffr ...201121821906
a group of sequence-related sphingomonad enzymes catalyzes cleavage of β-aryl ether linkages in lignin β-guaiacyl and β-syringyl ether dimers.lignin biosynthesis occurs via radical coupling of guaiacyl and syringyl hydroxycinnamyl alcohol monomers (i.e., "monolignols") through chemical condensation with the growing lignin polymer. with each chain-extension step, monolignols invariably couple at their β-positions, generating chiral centers. here, we report on activities of bacterial glutathione-s-transferase (gst) enzymes that cleave β-aryl ether bonds in lignin dimers that are composed of different monomeric units. our data reveal tha ...201425232892
popular and unpopular infectious agents linked to primary biliary cirrhosis.primary biliary cirrhosis (pbc) is a progressive cholestatic liver disease characterized by the autoimmune destruction of the biliary epithelial cells of the small and medium-size bile ducts. the disease affects middle aged women and usually affects more than one member within a family. the pathognomonic serological hallmark of the disease is the presence of circulating anti-mitochondrial antibodies, and disease-specific anti-nuclear antibodies. susceptibility genes and environmental risk factor ...201226000132
cyp101j2, cyp101j3, and cyp101j4, 1,8-cineole-hydroxylating cytochrome p450 monooxygenases from sphingobium yanoikuyae strain b2.we report the isolation and characterization of three new cytochrome p450 monooxygenases: cyp101j2, cyp101j3, and cyp101j4. these p450s were derived from sphingobium yanoikuyae b2, a strain that was isolated from activated sludge based on its ability to fully mineralize 1,8-cineole. genome sequencing of this strain in combination with purification of native 1,8-cineole-binding proteins enabled identification of 1,8-cineole-binding p450s. the p450 enzymes were cloned, heterologously expressed (n- ...201627590809
engineered deinococcus radiodurans r1 with nicot genes for bioremoval of trace cobalt from spent decontamination solutions of nuclear power reactors.the aim of the present work was to engineer bacteria for the removal of co in contaminated effluents. radioactive cobalt ((60)co) is known as a major contributor for person-sievert budgetary because of its long half-life and high γ-energy values. some bacterial ni/co transporter (nicot) genes were described to have preferential uptake for cobalt. in this study, the nicot genes nxia and nvoa from rhodopseudomonas palustris cga009 (rp) and novosphingobium aromaticivorans f-199 (na), respectively, ...201526112211
"nico buster": engineering e. coli for fast and efficient capture of cobalt and nickel.metal contamination is widespread and results from natural geogenic and constantly increasing anthropogenic sources (mainly mining and extraction activities, electroplating, battery and steel manufacturing or metal finishing). consequently, there is a growing need for methods to detoxify polluted ecosystems. industrial wastewater, surface water and ground water need to be decontaminated to alleviate the contamination of soils and sediments and, ultimately, the human food chain. in nuclear power ...201425104972
structural basis for heavy metal detoxification by an atm1-type abc exporter.although substantial progress has been achieved in the structural analysis of exporters from the superfamily of adenosine triphosphate (atp)-binding cassette (abc) transporters, much less is known about how they selectively recognize substrates and how substrate binding is coupled to atp hydrolysis. we have addressed these questions through crystallographic analysis of the atm1/abcb7/hmt1/abcb6 ortholog from novosphingobium aromaticivorans dsm 12444, naatm1, at 2.4 angstrom resolution. consisten ...201424604198
escherichia coli infection induces autoimmune cholangitis and anti-mitochondrial antibodies in non-obese diabetic (nod).b6 (idd10/idd18) mice.several epidemiological studies have demonstrated that patients with primary biliary cirrhosis (pbc) have a higher incidence of urinary tract infections (uti) and there is significant homology of the immunodominant mitochondrial autoantigen, the e2 component of the pyruvate dehydrogenase complex (pdc-e2), between mammals and bacteria. previous work has demonstrated that non-obese diabetic (nod).b6 idd10/idd18 infected with novosphingobium aromaticivorans developed liver lesions similar to human ...201424128311
potential roles for infectious agents in the pathophysiology of primary biliary cirrhosis: what's new?primary biliary cirrhosis (pbc) is a progressive cholestatic liver disease serologically characterized by the presence of high-titer antimitochondrial antibodies and, histologically by chronic nonsuppurative cholangitis and granulomata. the aetiology of the disease remains elusive, although genetic, epigenetic, environmental, and infectious factors have been considered important for the induction of the disease in genetically prone individuals. the disease shows a striking female predominance an ...201323188623
structure and mechanism of nov1, a resveratrol-cleaving dioxygenase.stilbenes are diphenyl ethene compounds produced naturally in a wide variety of plant species and some bacteria. stilbenes are also derived from lignin during kraft pulping. stilbene cleavage oxygenases (scos) cleave the central double bond of stilbenes, forming two phenolic aldehydes. here, we report the structure of an sco. the x-ray structure of nov1 from novosphingobium aromaticivorans was determined in complex with its substrate resveratrol (1.89 å), its product vanillin (1.75 å), and witho ...201627911781
description of novosphingobiumflavum sp. nov., isolated from soil.a novel yellow bacterial strain, designated ucm-28t, was isolated from forest soil in gyeonggi-do, south korea. the isolated strain was gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped, and grew at 10-37 °c, ph 5.5-9 and with 0-1 % nacl. it could reduce nitrate to nitrite and hydrolyse aesculin. we determined the taxonomic position of strain ucm-28t; based on the 16s rrna gene sequence, the strain belongs to the genus novosphingobium. the bacterium showed the highest si ...201627306976
substrate distortion and the catalytic reaction mechanism of 5-carboxyvanillate decarboxylase.5-carboxyvanillate decarboxylase (ligw) catalyzes the conversion of 5-carboxyvanillate to vanillate in the biochemical pathway for the degradation of lignin. this enzyme was shown to require mn(2+) for catalytic activity and the kinetic constants for the decarboxylation of 5-carboxyvanillate by the enzymes from sphingomonas paucimobilis syk-6 (kcat = 2.2 s(-1) and kcat/km = 4.0 × 10(4) m(-1) s(-1)) and novosphingobium aromaticivorans (kcat = 27 s(-1) and kcat/km = 1.1 × 10(5) m(-1) s(-1)) were d ...201626714575
[polymorphism of the bpha genes in bacteria destructing biphenyl/chlorinated biphenils].polychlorinated biphenyls (pcbs) are persistent organic pollutants. biphenyl 2,3-dioxygenase (bdo) is a key enzyme that determines the range of pcbs oxidized by a bacterial strain. bdo subunit α (bpha1) plays an essential role in substrate recognition and binding. the genes for dioxygenases that hydroxylate aromatic rings were screened and analyzed phylogenetically. genes found in biphenyl-oxidizing rhodococcus erythropolis strains g12a, b7b, and b106a proved to be similar to the published nucle ...201726299864
proposal of novosphingobium rhizosphaerae sp. nov., isolated from the rhizosphere.a yellow, gram-stain-negative, rod-shaped, non-spore-forming bacterium (strain jm-1(t)) was isolated from the rhizosphere of a field-grown zea mays plant in auburn, al, usa. 16s rrna gene sequence analysis of strain jm-1(t) showed high sequence similarity to the type strains of novosphingobium capsulatum (98.9%), novosphingobium aromaticivorans (97.4%), novosphingobium subterraneum (97.3%) and novosphingobium taihuense (97.1%); sequence similarities to all other type strains of species of the ge ...201525320143
novosphingobium aquiterrae sp. nov., isolated from ground water.a gram-staining-negative, strictly aerobic, non-motile, non-spore-forming, yellow and rod-shaped bacterium, designated e-ii-3(t), was isolated from ground water at daejeon in korea. strain e-ii-3(t) grew between 4 and 45 °c (optimal growth at 28 °c), between ph 6.0 and 9.0 (optimal growth at ph 7.5) and at salinities of 0-2.0 % (w/v) nacl, growing optimally with 0.5 % (w/v) nacl. on the basis of 16s rrna gene sequence analysis, strain e-ii-3(t) was shown to belong to the genus novosphingobium an ...201424994774
novosphingobium kunmingense sp. nov., isolated from a phosphate mine.a yellow-pigmented, gram-stain-negative, strictly aerobic, rod-shaped, round-ended bacterium, designated strain 18-11hk(t), was isolated from a phosphate mine situated in the suburb of kunming in yunnan province in south-western china. the taxonomic status of this strain was evaluated by using a polyphasic approach. on the basis of 16s rrna gene sequence similarity, strain 18-11hk(t) was shown to belong to the genus novosphingobium, showing the highest levels of sequence similarity with respect ...201424737793
structure and function of a novel ld-carboxypeptidase a involved in peptidoglycan recycling.approximately 50% of cell wall peptidoglycan in gram-negative bacteria is recycled with each generation. the primary substrates used for peptidoglycan biosynthesis and recycling in the cytoplasm are glcnac-murnac(anhydro)-tetrapeptide and its degradation product, the free tetrapeptide. this complex process involves ∼15 proteins, among which the cytoplasmic enzyme ld-carboxypeptidase a (ldca) catabolizes the bond between the last two l- and d-amino acid residues in the tetrapeptide to form the tr ...201324123814
the dynamics of camphor in the cytochrome p450 cyp101d2.the recent crystal structures of cyp101d2, a cytochrome p450 protein from the oligotrophic bacterium novosphingobium aromaticivorans dsm12444 revealed that both the native (substrate-free) and camphor-soaked forms have open conformations. furthermore, two other potential camphor-binding sites were also identified from electron densities in the camphor-soaked structure, one being located in the access channel and the other in a cavity on the surface near the f-helix side of the f-g loop termed th ...201323832606
novosphingobium ginsenosidimutans sp. nov., with the ability to convert ginsenoside.a gram-negative, strictly aerobic, non-motile, non-sporeforming, and rod-shaped bacterial strain designated fw-6t was isolated from a freshwater sample and its taxonomic position was investigated by using a polyphasic approach. strain fw-6t grew optimally at 10-42 degrees c and at ph 7.0 on nutrient and r2a agar. strain fw-6t displayed beta- glucosidase activity that was responsible for its ability to transform ginsenoside rb1 (one of the dominant active components of ginseng) to rd. on the basi ...201323568197
top-down characterization of the post-translationally modified intact periplasmic proteome from the bacterium novosphingobium aromaticivorans.the periplasm of gram-negative bacteria is a dynamic and physiologically important subcellular compartment where the constant exposure to potential environmental insults amplifies the need for proper protein folding and modifications. top-down proteomics analysis of the periplasmic fraction at the intact protein level provides unrestricted characterization and annotation of the periplasmic proteome, including the post-translational modifications (ptms) on these proteins. here, we used single-dim ...201323555055
discovery of pinoresinol reductase genes in sphingomonads.bacterial genes for the degradation of major dilignols produced in lignifying xylem are expected to be useful tools for the structural modification of lignin in plants. for this purpose, we isolated pinz involved in the conversion of pinoresinol from sphingobium sp. strain syk-6. pinz showed 43-77% identity at amino acid level with bacterial nmra-like proteins of unknown function, a subgroup of atypical short chain dehydrogenases/reductases, but revealed only 15-21% identity with plant pinoresin ...201323199737
novosphingobium sediminis sp. nov., isolated from the sediment of a eutrophic lake.a gram-negative, rod-shaped, aerobic, non-motile, bacterium (yg-17(t)) was isolated from eutrophic taihu lake sediment. colonies grown on yg agar plates were circular, convex, and yellow-colored. on the basis of 16s rrna gene sequence similarity, strain yg-17(t) was shown to be closely related to novosphingobium aromaticivorum (97.9%), followed by novosphingobium stygium (97.5%), novosphingobium subterranea (96.9%) and novosphingobium taihuense (96.7%). the dna-dna relatedness values of strain y ...201223149680
animal models of primary biliary cirrhosis: materials and methods.primary biliary cirrhosis (pbc) is a female-predominant autoimmune disease of the liver characterized by immune-mediated destruction of the intrahepatic bile ducts and the presence of antimitochondrial antibodies (amas). there have been limited advances in understanding the molecular pathogenesis of the disease because of the difficulty in accessing human tissues and the absence of appropriate animal models. recently, several unique murine models that manifest the serological, biochemical, and h ...201222933075
improving the affinity and activity of cyp101d2 for hydrophobic substrates.cyp101d2 is a cytochrome p450 monooxygenase from novosphingobium aromaticivorans which is closely related to cyp101a1 (p450cam) from pseudomonas putida. both enzymes selectively hydroxylate camphor to 5-exo-hydroxycamphor, and the residues that line the active sites of both enzymes are similar including the pre-eminent tyr96 residue. however, met98 and leu253 in cyp101d2 replace phe98 and val247 in cyp101a1, and camphor binding only results in a maximal change in the spin state to 40 % high-spin ...201322820521
characterization of an apo-carotenoid 13,14-dioxygenase from novosphingobium aromaticivorans that converts β-apo-8'-carotenal to β-apo-13-carotenone.a putative carotenoid oxygenase from novosphingobium aromaticivorans was purified with a specific activity of 0.8 u/mg by his-trap affinity chromatography. the native enzyme was estimated to be a 52 kda monomer. enzyme activity for β-apo-8'-carotenal was maximal at ph 8.0 and 45 °c, with a half life of 15.3 h, k(m) of 21 μm, and k(cat) of 25 l/min. the enzyme exhibited cleavage activity only for carotenoids containing one β-ionone ring and its catalytic efficiency (k(cat)/k(m)) followed the orde ...201222711425
structure and function of cyp108d1 from novosphingobium aromaticivorans dsm12444: an aromatic hydrocarbon-binding p450 enzyme.cyp108d1 from novosphingobium aromaticivorans dsm12444 binds a range of aromatic hydrocarbons such as phenanthrene, biphenyl and phenylcyclohexane. its structure, which is reported here at 2.2 å resolution, is closely related to that of cyp108a1 (p450terp), an α-terpineol-oxidizing enzyme. the compositions and structures of the active sites of these two enzymes are very similar; the most significant changes are the replacement of glu77 and thr103 in cyp108a1 by thr79 and val105 in cyp108d1. othe ...201222349230
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