Publications
| Title | Abstract | Year(sorted ascending) Filter | PMID Filter |
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| psychrobacter proteolyticus sp. nov., a psychrotrophic, halotolerant bacterium isolated from the antarctic krill euphausia superba dana, excreting a cold-adapted metalloprotease. | an antarctic marine bacterium (strain 116) excreting an extracellular cold-adapted metalloprotease was subjected to a detailed polyphasic taxonomic investigation. strain 116 was previously isolated from the stomach of a specimen of the antarctic krill euphasia superba dana and tentatively characterized as sphingomonas paucimobilis 116. the 16s rdna sequence analysis showed that the strain is in fact related to species of the genus psychrobacter, next to psychrobacter glacincola (97.4% similarity ... | 2001 | 11403398 |
| microbial reduction of alpha-chloroketone to alpha-chlorohydrin. | microbial reduction of alpha-chloroketone to alpha-chlorohydrin was studied as one of the approaches for construction of the chiral center of the corresponding epoxide. about 100 microorganisms covering many species of candida, pichia, hansenula, geotrichum, rhodococcus and aureobasidium were screened to reduce the alpha-chloroketone stereospecifically. many strains provided the r-alpha-chlorohydrin with 100% enantiomeric excess (ee), e.g., candida sonorensis sc 16117, geotrichum candidum sc 546 ... | 2001 | 11494099 |
| biochemical characterization of the beta-1,4-glucuronosyltransferase gelk in the gellan gum-producing strain sphingomonas paucimobilis a.t.c.c. 31461. | biosynthesis of bacterial polysaccharide-repeat units proceeds by sequential transfer of sugars, from the appropriate sugar donor to an activated lipid carrier, by committed glycosyltransferases (gts). few studies on the mechanism of action for this type of gt are available. sphingomonas paucimobilis a.t.c.c. 31461 produces the industrially important polysaccharide gellan gum. we have cloned the gelk gene from s. paucimobilis a.t.c.c. 31461. gelk belongs to family 1 of the gt classification [cam ... | 2001 | 11513745 |
| convergent and divergent points in catabolic pathways involved in utilization of fluoranthene, naphthalene, anthracene, and phenanthrene by sphingomonas paucimobilis var. epa505. | catabolic pathways for utilization of naphthalene (nap), anthracene (ant), phenanthrene (phe), and fluoranthene (fla) by sphingomonas paucimobilis epa505 were identified. accumulation of catabolic intermediates was investigated with three classes of tn5 mutants with the following polycyclic aromatic hydrocarbon (pah)-negative phenotypes; (class i nap(-) phe(-) fla(-), class ii nap(-) phe(-), and class iii fla(-)). class i mutant 200pbha had a tn5 insertion within a meta ring fission dioxygenase ... | 2001 | 11571621 |
| colorimetric assay for lindane dechlorination by bacteria. | a colorimetric microtitre plate-based assay that detects haloalkane dehalogenase activity was modified to detect dechlorination of gamma-hexachlorocyclohexane (lindane). dechlorination is indicated by the colour change of phenol red from red to yellow, in a weakly buffered solution, as the solution becomes acidic due to hcl formed during dechlorination. enzyme activity can be monitored by reading the absorbance of each well at 540 nm. positive controls for the assay were the known lindane-degrad ... | 2001 | 11576682 |
| identification of protein fold and catalytic residues of gamma-hexachlorocyclohexane dehydrochlorinase lina. | gamma-hexachlorocyclohexane dehydrochlorinase (lina) is a unique dehydrochlorinase that has no homologous sequence at the amino acid-sequence level and for which the evolutionary origin is unknown. we here propose that lina is a member of a novel structural superfamily of proteins containing scytalone dehydratase, 3-oxo-delta(5)-steroid isomerase, nuclear transport factor 2, and the beta-subunit of naphthalene dioxygenase-all known structures with different functions. the catalytic and the activ ... | 2001 | 11746694 |
| structure-specificity relationships for haloalkane dehalogenases. | a structural analysis of the substrate specificity of hydrolytic dehalogenases originating from three different bacterial isolates has been performed using the multiple computer-automated structure evaluation methodology. this methodology identifies structural fragments in substrate molecules that either activate or deactivate biological processes. the analysis presented in this contribution is based on newly measured dehalogenation data combined with data from the literature (91 substrates). th ... | 2001 | 11764149 |
| streptomyces aureofaciens sporulation-specific sigma factor sigma(rpoz) directs expression of a gene encoding protein similar to hydrolases involved in degradation of the lignin-related biphenyl compounds. | a previously established method for the identification of promoters recognized by a heterologous rna polymerase holoenzyme containing a particular sigma factor was used to identify promoters dependent upon a sporulation specific sigma factor, sigma(rpoz), of streptomyces aureofaciens. three new positive dna fragments were identified, and these putative rpoz-dependent promoters, p(ren24), p(ren57), and p(ren71), contained sequences similar to the consensus sequence of flagellar and chemotaxis pro ... | 2001 | 11766963 |
| microflora investigation experiment. | many microorganisms were isolated from condensed water, wiping and scratching of cabin wall and air sampler in russian space station mir by russian astronauts lazutkin et al. in february 1997 as part of nasda "first mir utilization space experiment (jmir)". for example, there were about 2 x 10(6) cells/ml in condensed water sample no. 1 isolated from the transfer-docking compartment of crystal module. we tried the colony isolation, pure culturing and identification from these sampled microorgani ... | 2001 | 11799257 |
| enzymatic reaction of hydrogen peroxide-dependent peroxygenase cytochrome p450s: kinetic deuterium isotope effects and analyses by resonance raman spectroscopy. | cytochromes p450sp(alpha) (cyp152b1) and p450bs(beta) (cyp152a1), which are isolated from sphingomonas paucimobilis and bacillus subtilis, respectively, belong to the p450 superfamily, but catalyze hydroxylation reactions, in which an oxygen atom from h2o2 is efficiently introduced into fatty acids (e.g., myristic acid). p450sp(alpha) produces the alpha-hydroxylated (alpha-oh) products at 100%, while p450bs(beta) produces alpha- and beta-hydroxylated (beta-oh) products at 33 and 67%, respectivel ... | 2002 | 11827534 |
| employment of the human estrogen receptor beta ligand-binding domain and co-activator src1 nuclear receptor-binding domain for the construction of a yeast two-hybrid detection system for endocrine disrupters. | to screen a wide variety of chemicals for endocrine disrupters, and to develop an effective microbial degradation system for them, a good system is needed for the rapid and accurate evaluation of the endocrine-disrupting activities of suspected chemicals and their degradation products. we constructed two-hybrid systems that co-express the gal4p dna binding domain/ligand-binding domain of human estrogen receptor (her) alpha or beta and the gal4p transactivation domain/nuclear receptor-binding dom ... | 2002 | 11872169 |
| recurrent sphingomonas paucimobilis -bacteraemia associated with a multi-bacterial water-borne epidemic among neutropenic patients. | a cluster of septicaemias due to several water-related species occurred in a haematological unit of a university hospital. in recurrent septicaemias of a leukaemic patient caused by sphingomonas paucimobilis, genotyping of the blood isolates by use of random amplified polymorphic dna-analysis verified the presence of two distinct s. paucimobilis strains during two of the separate episodes. a strain of s. paucimobilis identical to one of the patient's was isolated from tap water collected in the ... | 2002 | 11886195 |
| cloning and characterization of linr, involved in regulation of the downstream pathway for gamma-hexachlorocyclohexane degradation in sphingomonas paucimobilis ut26. | in sphingomonas paucimobilis ut26, lind and line activities, which are responsible for the degradation of gamma-hexachlorocyclohexane, are inducibly expressed in the presence of their substrates, 2,5-dichlorohydroquinone (2,5-dchq) and chlorohydroquinone (chq). the nucleotide sequence of the 1-kb upstream region of the line gene was determined, and an open reading frame (orf) was found in divergent orientation from line. because the putative protein product of the orf showed similarity to the ly ... | 2002 | 11916699 |
| exploring the structure and activity of haloalkane dehalogenase from sphingomonas paucimobilis ut26: evidence for product- and water-mediated inhibition. | the hydrolysis of haloalkanes to their corresponding alcohols and inorganic halides is catalyzed by alpha/beta-hydrolases called haloalkane dehalogenases. the study of haloalkane dehalogenases is vital for the development of these enzymes if they are to be utilized for bioremediation of organohalide-contaminated industrial waste. we report the kinetic and structural analysis of the haloalkane dehalogenase from sphingomonas paucimobilis ut26 (linb) in complex with each of 1,2-dichloroethane and 1 ... | 2002 | 11939779 |
| degradation of polycyclic aromatic hydrocarbons dissolved in tween 80 surfactant solutions by sphingomonas paucimobilis epa 505. | the degradation rates of mixtures of pyrene (pyr), fluoranthene (fla), and phenanthrene (phe) by sphingomonas paucimobilis epa 505 were measured in the presence of the nonionic surfactant tween 80. for strain epa 505, fla and phe are growth substrates, while pyr is not. linear degradation rates ranging from 0.05 to 2.2 mg x l(-1) x h(-1) were observed for fla, pyr, and phe at approximately 10(7) colony-forming units (cfu)/ml. at lower biomass, pyr degradation exhibited lognormal degradation. the ... | 2002 | 11958568 |
| molecular structure of the rhamsan-like exocellular polysaccharide rmdp17 from sphingomonas paucimobilis. | x-ray diffraction analysis of the sodium salt of the polysaccharide rmdp17, a 2-deoxy rhamsan analog, reveals that it adopts a gellan-like, half-staggered, threefold, left handed, double helix of pitch 57.4 a. the side chain of the branched polymer is hydrogen bonded to the main chain. sodium ions, linked to the carboxylate groups, promote the association of helices via water molecules. two helices of opposite polarity occupy a trigonal unit cell of dimensions a=17.6 and c=28.7 a. the packing ar ... | 2002 | 11755911 |
| aerobic degradation of 2,4,6-trichlorophenol by a microbial consortium - selection and characterization of microbial consortium. | a microbial consortium that efficiently degrades 2,4,6-tcp (2,4,6-trichlorophenol), as the sole source of carbon and energy under aerobic conditions was selected from municipal activated sludge. six bacterial strains, designated s(1), s(2), s(3), s(4), s(5) and s(6), were isolated from the selected consortium and five were identified as sphingomonas paucimobilis (s(2), s(3)), burkholderia cepacia(s(4)), chryseomonas luteola (s(5)) and vibrio metschnikovii (s(6)). after prolonged cultivation foll ... | 2002 | 12073141 |
| cadmium biosorption by sphingomonas paucimobilis biomass. | among microorganisms isolated in bangkok, the gram-negative bacterium sphingomonas paucimobilis exhibited the greatest cadmium tolerance. it was able to survive in the medium containing cadmium as high as 200 mg/l. however, concentrations of cadmium at 25-200 mg/l inhibited its growth. the biosorption properties for cadmium of this bacterial biomass and the effects of environmental factors (i.e., biosorbent type, initial ph and biosorbent concentration) on the cadmium biosorption were explored. ... | 2002 | 12146636 |
| cloning, functional expression and biochemical characterization of a stereoselective alcohol dehydrogenase from pseudomonas fluorescens dsm50106. | sequencing of a genomic library prepared from pseudomonas fluorescens dsm 50106 identified an orf showing 29% identity to a c alpha-dehydrogenase of pseudomonas paucimobilis and high homology to several sequences with unknown functions derived from genome projects. the corresponding gene adhf1 encodes a dehydrogenase of 296 amino acids with a calculated molecular mass of 31.997 kda. the gene was functionally expressed in e. coli using a rhamnose inducible expression system. the resulting recombi ... | 2002 | 12172614 |
| characterization of the 5-carboxyvanillate decarboxylase gene and its role in lignin-related biphenyl catabolism in sphingomonas paucimobilis syk-6. | sphingomonas paucimobilis syk-6 degrades a lignin-related biphenyl compound, 5,5'-dehydrodivanillate (ddva), to 5-carboxyvanillate (5cva) by the enzyme reactions catalyzed by the ddva o-demethylase (ligx), the ring cleavage oxygenase (ligz), and the meta-cleavage compound hydrolase (ligy). in this study we examined the degradation step of 5cva. 5cva was transformed to vanillate, o-demethylated, and further degraded via the protocatechuate 4,5-cleavage pathway by this strain. a cosmid clone which ... | 2002 | 12200294 |
| cloning and characterization of the ferulic acid catabolic genes of sphingomonas paucimobilis syk-6. | sphingomonas paucimobilis syk-6 degrades ferulic acid to vanillin, and it is further metabolized through the protocatechuate 4,5-cleavage pathway. we obtained a tn5 mutant of syk-6, fa2, which was able to grow on vanillic acid but not on ferulic acid. a cosmid which complemented the growth deficiency of fa2 on ferulic acid was isolated. the 5.2-kb bamhi-ecori fragment in this cosmid conferred the transformation activity of ferulic acid to vanillin on escherichia coli host cells. a sequencing ana ... | 2002 | 12200295 |
| gellan gum biosynthesis in sphingomonas paucimobilis atcc 31461: genes, enzymes and exopolysaccharide production engineering. | the commercial gelling agent, gellan, is an extracellular polysaccharide (eps) produced by sphingomonas paucimobilis atcc 31461. in recent years, significant progress in understanding the relationship between gellan structure and properties and elucidation of the biosynthesis and engineering of this recent product of biotechnology has been made. this review focuses on recent advances in this field. emphasis is given to identification and characterization of genes and enzymes involved, or predict ... | 2002 | 12355314 |
| emendation of the genus sphingomonas yabuuchi et al. 1990 and junior objective synonymy of the species of three genera, sphingobium, novosphingobium and sphingopyxis, in conjunction with blastomonas ursincola. | the 16s rdna sequence similarities between the type strains of sphingomonas paucimobilis and 32 other sphingomonas species range from 90.2 to 99.6%. it might be possible to divide the genus into several new genera according to a dendrogram drawn from 16s rdna sequence similarity. however, the phenotypic and biochemical information needed to define clusters of strains representing distinct genera within this group of organisms was not previously available. although the cellular lipids of type str ... | 2002 | 12361250 |
| cloning and characterization of lin genes responsible for the degradation of hexachlorocyclohexane isomers by sphingomonas paucimobilis strain b90. | hexachlorocyclohexane (hch) has been used extensively against agricultural pests and in public health programs for the control of mosquitoes. commercial formulations of hch consist of a mixture of four isomers, alpha, beta, gamma, and delta. while all these isomers pose serious environmental problems, beta-hch is more problematic due to its longer persistence in the environment. we have studied the degradation of hch isomers by sphingomonas paucimobilis strain b90 and characterized the lin genes ... | 2002 | 12450824 |
| sphingomonas paucimobilis beta-glucosidase bgl1: a member of a new bacterial subfamily in glycoside hydrolase family 1. | the sphingomonas paucimobilis beta-glucosidase bgl1 is encoded by the bgl1 gene, associated with an 1308 bp open reading frame. the deduced protein has a potential signal peptide of 24 amino acids in the n-terminal region, and experimental evidence is consistent with the processing and export of the bgl1 protein through the inner membrane to the periplasmic space. a his(6)-tagged 44.3 kda protein was over-produced in the cytosol of escherichia coli from a recombinant plasmid, which contained the ... | 2003 | 12444924 |
| characterization of the 4-carboxy-4-hydroxy-2-oxoadipate aldolase gene and operon structure of the protocatechuate 4,5-cleavage pathway genes in sphingomonas paucimobilis syk-6. | the protocatechuate (pca) 4,5-cleavage pathway is the essential metabolic route for degradation of low-molecular-weight products derived from lignin by sphingomonas paucimobilis syk-6. in the 10.5-kb ecori fragment carrying the genes for pca 4,5-dioxygenase (ligab), 2-pyrone-4,6-dicarboxylate hydrolase (ligi), 4-oxalomesaconate hydratase (ligj), and a part of 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase (ligc), we found the ligk gene, which encodes 4-carboxy-4-hydroxy-2-oxoadipate (c ... | 2003 | 12486039 |
| formyltetrahydrofolate synthetase sequences from salt marsh plant roots reveal a diversity of acetogenic bacteria and other bacterial functional groups. | sixty-two partial formyltetrahydrofolate synthetase (fthfs) structural gene sequences were recovered from roots of salt marsh plants, including spartina alterniflora, salicornia virginica, and juncus roemerianus. only s. alterniflora roots yielded sequences grouping with fthfs sequences from known acetogens. most other fthfs or fthfs-like sequences grouped with those from sulfate-reducing bacteria. several sequences that grouped with sphingomonas paucimobilis ligh were also recovered. | 2003 | 12514064 |
| roles of the enantioselective glutathione s-transferases in cleavage of beta-aryl ether. | cleavage of the beta-aryl ether linkage is the most important process in lignin degradation. here we characterize the three tandemly located glutathione s-transferase (gst) genes, ligf, lige, and ligg, from low-molecular-weight lignin-degrading sphingomonas paucimobilis syk-6, and we describe the actual roles of these genes in the beta-aryl ether cleavage. based on the identification of the reaction product by electrospray ionization-mass spectrometry, a model compound of beta-aryl ether, alpha- ... | 2003 | 12618439 |
| characterization of the ugpg gene encoding a udp-glucose pyrophosphorylase from the gellan gum producer sphingomonas paucimobilis atcc 31461. | the ugpggene, which codes for a udp-glucose pyrophosphorylase (ugp) (or glucose-1-phosphate uridylyltransferase; ec 2.7.7.9) in sphingomonas paucimobilis atcc 31461, was cloned and sequenced. this industrial strain produces the exopolysaccharide gellan, a new commercial gelling agent, and the ugpg gene may convert glucose-1-phosphate into udp-glucose in the gellan biosynthetic pathway. the ugpg gene is capable of restoring the capacity of an escherichia coli galu mutant to grow on galactose by f ... | 2003 | 12655408 |
| dimethylphthalate hydrolysis by specific microbial esterase. | two bacterial strains: arthrobacter sp. and sphingomonas paucimobilis were isolated from soil by enrichment cultures using dimethylphthalate (dmp) or monomethylphthalate (mmp) as sole carbon source, respectively. dmp was rapidly transformed by an arthrobacter sp. culture with formation of mmp and phthalic acid (pa) which is further degraded. this strain was unable to hydrolyse mmp. a mechanism of degradation of dmp was proposed with two ways: dmp-->pa and dmp-->mmp. the s. paucimobilis strain hy ... | 2003 | 12668024 |
| reconstruction of mycobacterial dehalogenase rv2579 by cumulative mutagenesis of haloalkane dehalogenase linb. | the homology model of protein rv2579 from mycobacterium tuberculosis h37rv was compared with the crystal structure of haloalkane dehalogenase linb from sphingomonas paucimobilis ut26, and this analysis revealed that 6 of 19 amino acid residues which form an active site and entrance tunnel are different in linb and rv2579. to characterize the effect of replacement of these six amino acid residues, mutations were introduced cumulatively into the six amino acid residues of linb. the sixfold mutant, ... | 2003 | 12676719 |
| 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 ... | 2003 | 12682862 |
| bacterial serine palmitoyltransferase: a water-soluble homodimeric prototype of the eukaryotic enzyme. | serine palmitoyltransferase (spt, ec 2.3.1.50) is a key enzyme in sphingolipid biosynthesis and catalyzes the decarboxylative condensation of l-serine and palmitoyl coenzyme a (coa) to 3-ketodihydrosphingosine (kds). we found that the gram-negative obligatory aerobic bacteria sphingomonas paucimobilis ey2395(t) have significant spt activity, and purified spt to homogeneity. unlike eukaryotic enzymes, this enzyme was a water-soluble homodimeric protein. we isolated the spt gene encoding 420 amino ... | 2003 | 12686119 |
| cloning and sequence analysis of the ces10 gene encoding a sphingomonas paucimobilis esterase. | the ces10 gene of the gellan gum-producing strain sphingomonas paucimobilis atcc 31461 was cloned and sequenced. multi-sequence alignment of the deduced protein indicated that ces10 belongs to the serine hydrolase family with a potential catalytic triad comprising ser(153) (within the g-x-s-x-g consensus sequence), his(75) and asp(125). the mixed block results obtained following pattern search and the low identities detected in a blast analysis indicate that ces10 is significantly different from ... | 2003 | 12764567 |
| a common structure of substrate shared by lignostilbenedioxygenase isozymes from sphingomonas paucimobilis tmy1009. | a common structure of substrates of lignostilbenedioxygenases was investigated using synthesized stilbenes. cell-free extracts of sphingomonas paucimobilis tmy1009 degraded only trans-4-hydroxystilbene and trans-4-hydroxy-3-methoxystilbene. other stilbenes that had no 4-hydroxyl group and had a cis structure were not substrates for lignostilbenedioxygenases. these results indicate that a 4-hydroxyl group and trans-structure is necessary for the common structure for substrates of lignostilbenedio ... | 2003 | 12843670 |
| simultaneous and rapid monitoring of biomass and biopolymer production by sphingomonas paucimobilis using fourier transform-near infrared spectroscopy. | the application of fourier transform near infrared spectroscopy (ft-nirs) to near real-time monitoring of polysaccharide and biomass concentration was investigated using a gellan-producing strain of sphingomonas paucimobilis grown in a stirred tank reactor. successful models for both biomass and gellan were constructed despite the physichochemical complexity of the viscous process fluid. modelling of biomass proved more challenging than for gellan, partly because of the low range of biomass conc ... | 2003 | 12889834 |
| screening of bifidobacterium strains isolated from human faeces for antagonistic activities against potentially bacterial pathogens. | as probiotic bacteria, strains belonging to the genus bifidobacterium colonise the gastro-intestinal tract of humans and animals at the time of birth, and they are found in young as well as in adult individuals in great numbers. moreover, they can interact with the development of enteric infections by the production of antimicrobial metabolites. in this work 281 strains of bifidobacteria were anaerobically isolated from human faecal samples, supplied by volunteers of different ages (youngs, adul ... | 2003 | 12906392 |
| haloalkane dehalogenase linb from sphingomonas paucimobilis ut26: x-ray crystallographic studies of dehalogenation of brominated substrates. | the haloalkane dehalogenases are detoxifying enzymes that convert a broad range of halogenated substrates to the corresponding alcohols. complete crystal structures of haloalkane dehalogenase from sphingomonas paucimobilis ut26 (linb), and complexes of linb with 1,2-propanediol/1-bromopropane-2-ol and 2-bromo-2-propene-1-ol, products of debromination of 1,2-dibromopropane and 2,3-dibromopropene, respectively, were determined from 1.8 a resolution x-ray diffraction data. published structures of n ... | 2003 | 12939138 |
| catalytic mechanism of the maloalkane dehalogenase linb from sphingomonas paucimobilis ut26. | haloalkane dehalogenases are bacterial enzymes capable of carbon-halogen bond cleavage in halogenated compounds. to obtain insights into the mechanism of the haloalkane dehalogenase from sphingomonas paucimobilis ut26 (linb), we studied the steady-state and presteady-state kinetics of the conversion of the substrates 1-chlorohexane, chlorocyclohexane, and bromocyclohexane. the results lead to a proposal of a minimal kinetic mechanism consisting of three main steps: (i) substrate binding, (ii) cl ... | 2003 | 12952988 |
| preferential surfactant utilization by a pah-degrading strain: effects on micellar solubilization phenomena. | biodegradable nonionic tween series surfactants were employed to assess the effects of synthetic surfactants on the bioavailability of a target polycyclic aromatic hydrocarbon (pah), phenanthrene, in soil/sediment-free micellar solutions. dosages of surfactants in excess of their respective critical micelle concentrations (cmcs) dramatically enhanced solubilization of phenanthrene, but the micellar-solubilized phenanthrene was neither directly nor readily bioavailable to the pah-degrading strain ... | 2003 | 12953868 |
| modification of activity and specificity of haloalkane dehalogenase from sphingomonas paucimobilis ut26 by engineering of its entrance tunnel. | structural comparison of three different haloalkane dehalogenases suggested that substrate specificity of these bacterial enzymes could be significantly influenced by the size and shape of their entrance tunnels. the surface residue leucine 177 positioned at the tunnel opening of the haloalkane dehalogenase from sphingomonas paucimobilis ut26 was selected for modification based on structural and phylogenetic analysis; the residue partially blocks the entrance tunnel, and it is the most variable ... | 2003 | 14525993 |
| [identification, cloning and sequencing of gst gene of bacterium degrading poly-aromatic hydrocarbons]. | a bacterium (designated strain zx4) able to degrade poly aromatic hydrocarbons was isolated from oil-contaminated soil. based on analysis of the 16s rdna sequence, whole cell fatty acid, and biolog-gn, the strain was identified as sphingomonas paucimobilis. the detection of gst (glutathione s-transferase) indicated that the gst from the strain had the activity of conjugating with cdnb and it maybe relate with degradation of pahs. the pcr product of gst gene from the strain confirmed its presence ... | 2003 | 16276887 |
| characteristics of bacterial strains inhabiting the wood of coniferous trees. | the presented studies embraced samples of wood chips from coniferous trees which contained layers of duramen, alburnum and bark. microbiological analysis involved qualitative and quantitative determination of bacterial flora inhabiting the studied wood material. the wood chips were found to contain primarily species belonging to the genera bacillus and pseudomonas. the presence of the potentially pathogenic species bacillus cereus 1, sphingomonas paucimobilis, aeromonas salmonicida and chryseomo ... | 2004 | 15790079 |
| crystal structure of haloalkane dehalogenase linb from sphingomonas paucimobilis ut26 at 0.95 a resolution: dynamics of catalytic residues. | we present the structure of linb, a 33-kda haloalkane dehalogenase from sphingomonas paucimobilis ut26, at 0.95 a resolution. the data have allowed us to directly observe the anisotropic motions of the catalytic residues. in particular, the side-chain of the catalytic nucleophile, asp108, displays a high degree of disorder. it has been modeled in two conformations, one similar to that observed previously (conformation a) and one strained (conformation b) that approached the catalytic base (his27 ... | 2004 | 14744129 |
| reactions of serine palmitoyltransferase with serine and molecular mechanisms of the actions of serine derivatives as inhibitors. | serine palmitoyltransferase (spt) is a key enzyme in sphingolipid biosynthesis and catalyzes the decarboxylative condensation of l-serine and palmitoyl coenzyme a to 3-ketodihydrosphingosine. we have succeeded in the overproduction of a water-soluble homodimeric spt from sphingomonas paucimobilis ey2395(t) in escherichia coli. the recombinant spt showed the characteristic absorption and circular dichroism spectra derived from its coenzyme pyridoxal 5'-phosphate. on the basis of the spectral chan ... | 2004 | 14744154 |
| purification and characterization of ascorbic acid 2-kinase from flavobacterium devorans atcc 10829. | maximum activity for phosphorylating c(2)-oh of the ascorbic acid was observed at the time of 16 h incubation from the culture of flavobacterium devorans atcc 10829. the enzyme was purified 1.178-fold, via ammonium sulfate fractionation, fast q anion exchange, and phenyl agarose chromatography. gel chromatography and sds-polyacrylamide electrophoresis experiments showed that the enzyme is a tetramer with subunit mw of 29 kda. among available second substrates, pyrophosphate showed the highest ac ... | 2004 | 15016454 |
| organization of lin genes and is6100 among different strains of hexachlorocyclohexane-degrading sphingomonas paucimobilis: evidence for horizontal gene transfer. | the organization of lin genes and is6100 was studied in three strains of sphingomonas paucimobilis (b90a, sp+, and ut26) which degraded hexachlorocyclohexane (hch) isomers but which had been isolated at different geographical locations. dna-dna hybridization data revealed that most of the lin genes in these strains were associated with is6100, an insertion sequence classified in the is6 family and initially found in mycobacterium fortuitum. eleven, six, and five copies of is6100 were detected in ... | 2004 | 15060023 |
| a novel tetrahydrofolate-dependent o-demethylase gene is essential for growth of sphingomonas paucimobilis syk-6 with syringate. | sphingomonas paucimobilis syk-6 degrades syringate to 3-o-methylgallate (3mga), which is finally converted to pyruvate and oxaloacetate via multiple pathways in which protocatechuate 4,5-dioxygenase, 3mga dioxygenase, and gallate dioxygenase are involved. here we isolated the syringate o-demethylase gene (desa), which complemented the growth deficiency on syringate of a tn5 mutant of the syk-6 derivative strain. the desa gene is located 929 bp downstream of fera, encoding feruloyl-coenzyme a syn ... | 2004 | 15090517 |
| electrophoretically mediated microanalysis with partial filling technique and indirect or direct detection as a tool for inhibition studies of enzymatic reaction. | the inhibition of the model enzyme, haloalkane dehalogenase from sphingomonas paucimobilis, was investigated by a combination of electrophoretically mediated microanalysis with a partial filling technique, followed by indirect or direct detection. in this setup, part of the capillary is filled with a buffer suitable for the enzymatic reaction (20 mm glycine buffer, ph 8.6) whereas the rest of the capillary is filled with the background electrolyte optimal for separation of substrates and product ... | 2004 | 15095444 |
| sphingomonas yabuuchiae sp. nov. and brevundimonas nasdae sp. nov., isolated from the russian space laboratory mir. | on the basis of phenotypic and genotypic characteristics and 16s rrna gene sequence analysis, novel species belonging to the genera sphingomonas and brevundimonas were identified from samples taken from the russian space laboratory mir. strain a1-18(t) was isolated from the air. 16s rdna sequence analysis showed that strain a1-18(t) formed a coherent cluster with sphingomonas sanguinis, sphingomonas parapaucimobilis, sphingomonas paucimobilis and sphingomonas roseiflava with sequence similarity ... | 2004 | 15143030 |
| characterization of the 3-o-methylgallate dioxygenase gene and evidence of multiple 3-o-methylgallate catabolic pathways in sphingomonas paucimobilis syk-6. | sphingomonas paucimobilis syk-6 is able to grow on various lignin-derived biaryls as the sole source of carbon and energy. these compounds are degraded to vanillate and syringate by the unique and specific enzymes in this strain. vanillate and syringate are converted to protocatechuate (pca) and 3-o-methylgallate (3mga), respectively, by the tetrahydrofolate-dependent o-demethylases. previous studies have suggested that these compounds are further degraded via the pca 4,5-cleavage pathway. howev ... | 2004 | 15262932 |
| degradation of aromatic hydrocarbons by sphingomonas paucimobilis strain epa505. | to determine the substrate range capability of sphingomonas paucimobilis strain epa505, a number of aromatic compounds were tested as potential growth substrates. strain epa505 grew on phenanthrene, naphthalene, fluoranthene, toluene, benzoic acid, 2,3- and 3,4-dihydroxybenzoic acids, 1-chloro-2,4-dinitrobenzene, anthracene, 2-hydroxy-3-naphthoic acid and 1-hydroxy- 2-naphthoic acid, salicylic acid, and catechol. strain epa505 was unable to grow on coumarine 3-carboxylic acid, naphthalene dicarb ... | 2004 | 15386141 |
| thermophilic, reversible gamma-resorcylate decarboxylase from rhizobium sp. strain mtp-10005: purification, molecular characterization, and expression. | we found the occurrence of thermophilic reversible gamma-resorcylate decarboxylase (gamma-rdc) in the cell extract of a bacterium isolated from natural water, rhizobium sp. strain mtp-10005, and purified the enzyme to homogeneity. the molecular mass of the enzyme was determined to be about 151 kda by gel filtration, and that of the subunit was 37.5 kda by sodium dodecyl sulfate-polyacrylamide gel electrophoresis; in other words, the enzyme was a homotetramer. the enzyme was induced specifically ... | 2004 | 15466039 |
| reversible and nonoxidative gamma-resorcylic acid decarboxylase: characterization and gene cloning of a novel enzyme catalyzing carboxylation of resorcinol, 1,3-dihydroxybenzene, from rhizobium radiobacter. | we found a gamma-resorcylic acid (gamma-ra, 2,6-dihydroxybenzoic acid) decarboxylase, as a novel enzyme applicable to carboxylation of resorcinol (re, 1,3-dihydroxybenzene) to form gamma-ra, in a bacterial strain rhizobium radiobacter wu-0108 isolated through the screening of gamma-ra degrading microorganisms. the activities for carboxylation of re and decarboxylation of gamma-ra were detected in the cell-free extracts of r. radiobacter wu-0108 grown aerobically with gamma-ra. the enzyme, gamma- ... | 2004 | 15474471 |
| dynamics of multiple lin gene expression in sphingomonas paucimobilis b90a in response to different hexachlorocyclohexane isomers. | sphingomonas paucimobilis b90a is able to degrade the alpha-, beta-, gamma-, and delta-isomers of hexachlorocyclohexane (hch). it contains the genes lina, linb, linc, lind, line, and linr, which have been implicated in hch degradation. in this study, dynamic expression of the lin genes was measured in chemostat-grown s. paucimobilis b90a by rna dot blot hybridization and real-time reverse transcriptase pcr upon exposure to a pulse of different hch isomers. irrespective of the addition of hch, li ... | 2004 | 15528530 |
| three-block bi-focal pls (3bif-pls) and its application in qsar. | when x and y are multivariate, the two-block partial least squares (pls) method is often used. in this paper, we outline an extension addressing a special case of the three-block (x/y/z) problem, where z sits "under" y. we have called this approach three-block bi-focal pls (3bif-pls). it views the x/y relationship as the dominant problem, and seeks to use the additional information in z in order to improve the interpretation of the y-part of the x/y association. two data sets are used to illustr ... | 2004 | 15669704 |
| quantitative analysis of substrate specificity of haloalkane dehalogenase linb from sphingomonas paucimobilis ut26. | haloalkane dehalogenases are microbial enzymes that cleave a carbon-halogen bond in halogenated compounds. the haloalkane dehalogenase linb, isolated from sphingomonas paucimobilis ut26, is a broad-specificity enzyme. fifty-five halogenated aliphatic and cyclic hydrocarbons were tested for dehalogenation with the linb enzyme. the compounds for testing were systematically selected using a statistical experimental design. steady-state kinetic constants k(m) and k(cat) were determined for 25 substr ... | 2005 | 15736949 |
| a tetrahydrofolate-dependent o-demethylase, ligm, is crucial for catabolism of vanillate and syringate in sphingomonas paucimobilis syk-6. | vanillate and syringate are converted into protocatechuate (pca) and 3-o-methylgallate (3mga), respectively, by o-demethylases in sphingomonas paucimobilis syk-6. pca is further degraded via the pca 4,5-cleavage pathway, while 3mga is degraded through multiple pathways in which pca 4,5-dioxygenase (ligab), 3mga 3,4-dioxygenase (desz), and an unidentified 3mga o-demethylase and gallate dioxygenase are participants. for this study, we isolated a 4.7-kb smai fragment that conferred on escherichia c ... | 2005 | 15743951 |
| identification and characterization of genes involved in the downstream degradation pathway of gamma-hexachlorocyclohexane in sphingomonas paucimobilis ut26. | sphingomonas paucimobilis ut26 utilizes gamma-hexachlorocyclohexane (gamma-hch) as a sole source of carbon and energy. in our previous study, we cloned and characterized genes that are involved in the conversion of gamma-hch to maleylacetate (ma) via chlorohydroquinone (chq) in ut26. in this study, we identified and characterized an ma reductase gene, designated linf, that is essential for the utilization of gamma-hch in ut26. a gene named lineb, whose deduced product showed significant identity ... | 2005 | 15659662 |
| identification of insertion sequence from a gamma-hexachlorocyclohexane degrading bacterium, sphingomonas paucimobilis ut26. | tn5-derived mutants of the gamma-hexachlorocyclohexane-degrading bacterium sphingomonas paucimobilis ut26 were genetically characterized, and an endogenous insertion sequence (is) which belongs to the is1380 family was identified. the is, named issp1, existed as multi copies in ut26, and its transposition appeared to be activated during the process of tn5-mutagenesis. it was found that transposon mutagenesis can cause endogenous mutations. | 2005 | 15665490 |
| degradation of beta-hexachlorocyclohexane by haloalkane dehalogenase linb from sphingomonas paucimobilis ut26. | beta-hexachlorocyclohexane (beta-hch) is the most recalcitrant among the alpha-, beta-, gamma-, and delta-isomers of hch and causes serious environmental pollution problems. we demonstrate here that the haloalkane dehalogenase linb, reported earlier to mediate the second step in the degradation of gamma-hch in sphingomonas paucimobilis ut26, metabolizes beta-hch to produce 2,3,4,5,6-pentachlorocyclohexanol. | 2005 | 15812056 |
| osteomyelitis and secondary septic arthritis caused by sphingomonas paucimobilis. | we describe a case of osteomyelitis and secondary septic arthritis caused by sphingomonas paucimobilis in an immunosupressed adolescent which did not present typically, leading to a delay in diagnosis. this case highlights the need to thoroughly investigate musculoskeletal pain in the immunocompromised patient in order to exclude an infection as a cause. | 2005 | 15827879 |
| isolation and characterization of phenanthrene-degrading sphingomonas paucimobilis strain zx4. | phenanthrene-degrading bacterium strain zx4 was isolated from an oil-contaminated soil, and identified as sphingomonas paucimobilis based on 16s rdna sequence, cellular fatty acid composition, mol% g + c and biolog-gn tests. besides phenanthrene, strain zx4 could also utilize naphthalene, fluorene and other aromatic compounds. the growth on salicylic acid and catechol showed that the strain degraded phenanthrene via salicylate pathway, while the assay of catechol 2,3-dioxygenase revealed catecho ... | 2005 | 15865153 |
| cell wall glycosphingolipids of sphingomonas paucimobilis are cd1d-specific ligands for nkt cells. | the current consensus on characterization of nkt cells is based on their reactivity to the synthetic glycolipid, alpha-galactosylceramide (alpha-galcer) in a cd1d-dependent manner. because of the limited availability of alpha-galcer, there is a constant search for cd1d-presented ligands that activate nkt cells. the alpha-anomericity of the carbohydrate is considered to be an important requisite for the cd1d-specific activation of nkt cells. the gram-negative, lipopolysaccharide-free bacterium sp ... | 2005 | 15915536 |
| cloning, sequence analysis, and expression of the gene encoding sphingomonas paucimobilis fp2001 alpha-l -rhamnosidase. | the gene (rham) encoding the alpha-l-rhamnosidase of sphingomonas paucimobilis fp2001 was cloned, sequenced, and expressed in escherichia coli. the rham consisted of 3,354 nucleotides and had a promoter and shine-dalgarno sequences typical in bacteria. the rham encoding a protein (rham) deducted from the sequence consisted of 1,117 amino acids and had a putative signal peptide of 25 amino acids. rham has no similarity to other known rhamnosidases. rham has a sugar-binding domain of glycoside hyd ... | 2005 | 15991055 |
| ['in vitro' activity of different antimicrobial agents on gram-negative nonfermentative bacilli, excluding pseudomonas aeruginosa and acinetobacter spp]. | gram-negative nonfermentative bacilli (nfb) are widely spread in the environment. besides of difficulties for identification, they often have a marked multiresistance to antimicrobial agents, including those active against pseudomonas aeruginosa. the objective of this study was to evaluate the 'in vitro' activity of different antimicrobial agents on 177 gram-negative nonfermentative bacilli isolates (excluding pseudomonas aeruginosa and acinetobacter spp.) isolated from clinical specimens. minim ... | 2005 | 15991478 |
| molecular characterization of the gallate dioxygenase from pseudomonas putida kt2440. the prototype of a new subgroup of extradiol dioxygenases. | in this work we have characterized the gala gene product from pseudomonas putida kt2440, a ring-cleavage dioxygenase that acts specifically on gallate to produce 4-oxalomesaconate. the protein is a trimer composed by three identical subunits of 47.6 kda (419 amino acids) that uses fe2+ as the main cofactor. the gallate dioxygenase showed maximum activity at ph 7.0, and the km and vmax values for gallate were 144 microm and 53.2 micromol/min/mg of protein, respectively. a phylogenetic study sugge ... | 2005 | 16030014 |
| characterization of the gallate dioxygenase gene: three distinct ring cleavage dioxygenases are involved in syringate degradation by sphingomonas paucimobilis syk-6. | sphingomonas paucimobilis syk-6 converts vanillate and syringate to protocatechuate (pca) and 3-o-methylgallate (3mga) in reactions with the tetrahydrofolate-dependent o-demethylases ligm and desa, respectively. pca is further degraded via the pca 4,5-cleavage pathway, whereas 3mga is metabolized via three distinct pathways in which pca 4,5-dioxygenase (ligab), 3mga 3,4-dioxygenase (desz), and 3mga o-demethylase (ligm) are involved. in the 3mga o-demethylation pathway, ligm converts 3mga to gall ... | 2005 | 16030198 |
| 16s rdna phylogeny and distribution of lin genes in novel hexachlorocyclohexane-degrading sphingomonas strains. | hexachlorocyclohexane (hch) is a highly recalcitrant pesticide that persists in soils. three novel hch-degrading strains (ds2, ds2-2 and ds3-1) were isolated after enrichment from hch-contaminated soil from germany. these strains efficiently degraded the alpha-, gamma- and delta-isomers of hch, while strain ds3-1 also degraded beta-hch. based on 16s rdna analysis, strain ds3-1 was closely related to sphingomonas taejonensis, while strains ds2 and ds2-2 were closely related to sphingomonas flava ... | 2005 | 16104856 |
| a second 5-carboxyvanillate decarboxylase gene, ligw2, is important for lignin-related biphenyl catabolism in sphingomonas paucimobilis syk-6. | a lignin-related biphenyl compound, 5,5'-dehydrodivanillate (ddva), is degraded to 5-carboxyvanillate (5cva) by the enzyme reactions catalyzed by ddva o-demethylase (ligx), meta-cleavage oxygenase (ligz), and meta-cleavage compound hydrolase (ligy) in sphingomonas paucimobilis syk-6. 5cva is then transformed to vanillate by a nonoxidative 5cva decarboxylase and is further degraded through the protocatechuate 4,5-cleavage pathway. a 5cva decarboxylase gene, ligw, was isolated from syk-6 (x. peng, ... | 2005 | 16151081 |
| hexachlorocyclohexane-degrading bacterial strains sphingomonas paucimobilis b90a, ut26 and sp+, having similar lin genes, represent three distinct species, sphingobium indicum sp. nov., sphingobium japonicum sp. nov. and sphingobium francense sp. nov., and reclassification of [sphingomonas] chungbukensis as sphingobium chungbukense comb. nov. | three strains of sphingomonas paucimobilis, b90a, ut26 and sp+, isolated from different geographical locations, were found to degrade hexachlorocyclohexane. phylogenetic analysis based on 16s rrna gene sequences indicated that these strains do not fall in a clade that includes the type strain, sphingomonas paucimobilis atcc 29837(t), but form a coherent cluster with [sphingomonas] chungbukensis imsnu 11152(t) followed by sphingobium chlorophenolicum atcc 33790(t). the three strains showed low dn ... | 2005 | 16166696 |
| [rare bacteria species found in wounds of tsunami patients. predominance of gram-negative rods, increased antibiotic resistance]. | microbiological cultures from 229 patients seeking medical advise in stockholm after the tsunami catastrophe december 2004 were analysed at the clinical microbiology laboratory, karolinska university hospital, stockholm, sweden. gram-negative rods were the most common findings from wound cultures. common human pathogens as escherichia coli, proteus species, klebsiella spp, and pseudomonas aeruginosa were isolated. however, more rare species of gram-negative rods were also isolated, e.g. myroides ... | 2005 | 16416946 |
| non-specific biodegradation of the organophosphorus pesticides, cadusafos and ethoprophos, by two bacterial isolates. | an enrichment culture technique was used for the isolation of microorganisms responsible for the enhanced biodegradation of the nematicide cadusafos in soils from a potato monoculture area in northern greece. mineral salts medium supplemented with nitrogen (msmn), where cadusafos (10 mg l(-1)) was the sole carbon source, and soil extract medium (sem) were used for the isolation of cadusafos-degrading bacteria. two pure bacterial cultures, named cadi and cadii, were isolated and subsequently char ... | 2005 | 16329956 |
| enantioselective transformation of alpha-hexachlorocyclohexane by the dehydrochlorinases lina1 and lina2 from the soil bacterium sphingomonas paucimobilis b90a. | sphingomonas paucimobilis b90a contains two variants, lina1 and lina2, of a dehydrochlorinase that catalyzes the first and second steps in the metabolism of hexachlorocyclohexanes (r. kumari, s. subudhi, m. suar, g. dhingra, v. raina, c. dogra, s. lal, j. r. van der meer, c. holliger, and r. lal, appl. environ. microbiol. 68:6021-6028, 2002). on the amino acid level, lina1 and lina2 were 88% identical to each other, and lina2 was 100% identical to lina of s. paucimobilis ut26. incubation of chir ... | 2005 | 16332842 |
| [isolation and characterization of a hch degradation sphingomanas sp. stain bhc-a]. | an aerobic bacterium was isolated successfully from a long-term contaminated upland field, which was named bhc-a. the bacterium can utilize hexachlorocycloexane as a sole carbon source and decompose this substance rapidly and completely. according to its physiological & biochemical characters and the homology analysis of its 16s rdna sequence, this strain was identified as sphingomonas sp. stain bhc-a canmineralize not only alpha, gamma and delta-hch rapidly, but also 5 mg/l beta-hch in 12h comp ... | 2005 | 16342765 |
| [screening methods for detection of metallo-beta-lactamase producing gram negative rods]. | modified hodge test and a method using a disk with imipenem plus 1000 mg of edta were used to determine the presence of metallo-beta-lactamase producing gram-negative rods among 166 clinical isolates from hospitals in iaşi and galaţi. of 9 imipenem resistant strains found, only one pseudomonas aeruginosa gave positive results with both tests and other two p. aeruginosa clinical isolates gave negative results with both tests. the rest of the strains (2 p. aeruginosa, 2 acinetobacter baumanii, 1 s ... | 2005 | 16607806 |
| [metabolic pathway, genes, and enzymes for the degradation of chlorinated pesticide, gamma-hexachlorocyclohexane]. | 2005 | 16218450 | |
| gram-negative bacteria from patients seeking medical advice in stockholm after the tsunami catastrophe. | microbiological cultures from 229 patients seeking medical advice in stockholm after the tsunami catastrophe of december 2004 were analysed at the clinical microbiology laboratory, karolinska university hospital, stockholm, sweden. gram-negative bacilli were the most common findings from wound cultures. common human pathogens such as escherichia coli, proteus species, klebsiella spp., and pseudomonas aeruginosa were isolated. more rare species of gram-negative bacilli, e.g. myroides odoratus, sp ... | 2006 | 16798691 |
| improvement in production and quality of gellan gum by sphingomonas paucimobilis under high dissolved oxygen tension levels. | the effect of agitation rate and dissolved oxygen tension (dot) on growth and gellan production by sphingomonas paucimobilis was studied. higher cell growth of 5.4 g l(-1) was obtained at 700 rpm but maximum gellan (15 g l(-1)) was produced at 500 rpm. dot levels above 20% had no effect on cell growth but gellan yield was increased to 23 g l(-1 )with increase in dot level to 100%. higher dot levels improved the viscosity and molecular weight of the polymer with change in acetate and glycerate co ... | 2006 | 16820976 |
| growth inhibition by metabolites of gamma-hexachlorocyclohexane in sphingobium japonicum ut26. | the growth of a gamma-hexachlorocyclohexane (gamma-hch)-degrading bacterium sphingobium japonicum (formerly sphingomonas paucimobilis) ut26 in rich medium was inhibited by gamma-hch. this growth inhibition was not observed in a mutant that lacked the initial or second step enzymatic activity for gamma-hch degradation, suggesting that metabolites of gamma-hch are toxic to ut26. two metabolites of gamma-hch, 2,5-dichlorophenol (2,5-dcp) and 2,5-dichlorohydroquinone (2,5-dchq), showed a direct toxi ... | 2006 | 16636477 |
| modeling for gellan gum production by sphingomonas paucimobilis atcc 31461 in a simplified medium. | gellan gum production was carried out by sphingomonas paucimobilis atcc 31461 in a simplified medium with a short incubation time, and a kinetic model for understanding, controlling, and optimizing the fermentation process was proposed. the results revealed that glucose was the best carbon source and that the optimal concentration was 30 g liter(-1). as for the fermenting parameters, considerably large amounts of gellan gum were yielded by an 8-h-old culture and a 4% inoculum at 200 rpm on a rot ... | 2006 | 16672479 |
| plasmid-encoded gamma-hexachlorocyclohexane degradation genes and insertion sequences in sphingobium francense (ex-sphingomonas paucimobilis sp+). | the lin genes encode the gamma-hexachlorocyclohexane (gamma-hch or lindane) catabolic pathway in lindane-degrading strains. the location and stability of these genes have been explored in the lindane-degrading sphingobium francense strain sp+, and in two non-lindane-degrading mutants (sp1- and sp2-). the lin genes, lina, linb, line and linx were localized by hybridization on three of the six plasmids of the s. francense strain sp+ showing dispersal within the genome. the linc gene was detected b ... | 2006 | 16553860 |
| characterization of the novel hch-degrading strain, microbacterium sp. itrc1. | a gram-positive microbacterium sp. strain, itrc1, that was able to degrade the persistent and toxic hexachlorocyclohexane (hch) isomers was isolated and characterized. the itrc1 strain has the capacity to degrade all four major isomers of hch present in both liquid cultures and aged contaminated soil. dna fragments corresponding to the two initial genes involved in gamma-hch degradative pathway, encoding enzymes for gamma-pentachlorocyclohexene hydrolytic dehalogenase (linb) and a 2,5-dichloro-2 ... | 2006 | 16315057 |
| efficient production of 2-pyrone 4,6-dicarboxylic acid as a novel polymer-based material from protocatechuate by microbial function. | sphingomonas paucimobilis syk-6, which can degrade various low molecular weight compounds derived from plant polyphenols such as lignin, lignan, and tannin, metabolizes these substances via 2-pyrone-4,6-dicarboxylic acid (pdc). we focused on this metabolic intermediate as a potential raw material for novel, bio-based polymers. we cloned the ligab and ligc genes of syk-6, which respectively encode protocatechuate 4,5-dioxygenase and 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase, into a ... | 2006 | 16322989 |
| suspected ventilator-associated pneumonia in cardiac patients admitted to the coronary care unit. | to determine the incidence, risk factors, associated pathogens, and outcome of ventilator-associated pneumonia (vap) in patients admitted to a coronary care unit (ccu). | 2006 | 16438476 |
| surveying biotransformations with à la carte genetic traps: translating dehydrochlorination of lindane (gamma-hexachlorocyclohexane) into lacz-based phenotypes. | the ability of the product of a desired reaction to activate a bacterial transcriptional regulator was exploited to develop genetic traps that render the catalytic activity born by a dna clone into a selectable/scorable phenotype. we established this strategy with a system to expose the activity of dehydrochlorinases acting upon gamma-hexachlorocyclohexane (gamma-hch or lindane). to this end, the effector-binding protein, xylr, was evolved by gene shuffling plus mutagenic polymerase chain reacti ... | 2006 | 16478460 |
| distribution of gamma-hexachlorocyclohexane-degrading genes on three replicons in sphingobium japonicum ut26. | sphingobium japonicum (formerly sphingomonas paucimobilis) ut26 utilizes the important insecticide gamma-hexachlorocyclohexane as a sole source of carbon and energy. in previous studies, we isolated and characterized six structural genes (lina to linf) and one regulatory gene (linr) of ut26 for the degradation of gamma-hexachlorocyclohexane to beta-ketoadipate. our analysis in this study indicated that the ut26 genome consists of three large circular replicons of 3.6 mb, 670 kb, and 185 kb. the ... | 2006 | 16487327 |
| microbial contamination of nebulization solution and its measures. | we evaluated the microbial contamination of nebulization solutions in medication cups from a total of 76 ultrasonic nebulizers in use in 10 hospitals. in addition, an interview survey was given to nurses to evaluate the disinfection methods of these ultrasonic nebulizers. of a total of 76 nebulization solution samples, 11 (14.5%) were contaminated with 10-10(2) colony-forming units (cfu)/ml and 9 (11.8%) with 10(3)-10(5) cfu/ml. the major contaminants were glucose non-fermentative bacilli such a ... | 2006 | 16508154 |
| expression of glycosylated haloalkane dehalogenase linb in pichia pastoris. | heterologous expression of the bacterial enzyme haloalkane dehalogenase linb from sphingomonas paucimobilis ut26 in methylotrophic yeast pichia pastoris is reported. the haloalkane dehalogenase gene linb was subcloned into the ppiczalphaa vector and integrated into the genome of p. pastoris. the recombinant linb secreted from the yeast was purified to homogeneity and biochemically characterized. the deglycosylation experiment and mass spectrometry measurements showed that the recombinant linb ex ... | 2006 | 16216524 |
| bacterial decontamination of duwl biofilm using oxygenal 6. | the aim of this study was bacteriological assessment of the dental unit waterlines (duwl) biofilm - concentration and composition of the aerobe and facultative anaerobe bacterial microflora, and evaluation of the influence of a disinfecting product, oxygenal 6, on the biofilm composition. tubing fragments were taken from 25 units twice, before and after disinfection, and bacterial suspension of the biofilm was obtained from the samples. the bacterial flora was determined with the plate culture m ... | 2006 | 16841887 |
| postoperative endophthalmitis caused by sphingomonas paucimobilis. | we present a case in which a new organism, sphingomonas paucimobilis, caused endophthalmitis after phacoemulsification in a 73-year-old woman. the case shows a recurrent acute endophthalmitis with complete resolution only after vitrectomy. this organism has not been described as a cause of endophthalmitis and was resistant to initial medical management. we also describe an interaction between this organism and a co-infective organism that may account for the unusual clinical course. | 2006 | 16857516 |
| effects of a small electric current on sterilization of a dental unit water line. | in the present study, water was circulated in a simulated dental unit water line with electrifying a small current. the morphology of the biofilm developed on inner surface of the water line and the number of heterotrophic bacteria were investigated to elucidate the effect of a low level electric current on the biofilms formation associated with bacteria reproduction. destruction and malconformation of biofilms by electrification was observed using sem, in addition to deformation and hypertrophy ... | 2006 | 16913572 |
| statistical approach to optimization of fermentative production of gellan gum from sphingomonas paucimobilis atcc 31461. | gellan gum, a high-molecular-weight anionic linear polysaccharide produced by pure-culture fermentation from sphingomonas paucimobilis atcc 31461, has elicited industrial interest in recent years as a high-viscosity biogum, a suspending agent, a gelling agent, and an agar substitute in microbial media. in this paper we report on the optimization of gellan gum production using a statistical approach. in the first step, the one factor-at-a-time method was used to investigate the effect of medium c ... | 2006 | 17046526 |
| deproteinization of gellan gum produced by sphingomonas paucimobilis atcc 31461. | deproteinization is a technical bottleneck in the purification of viscous water-soluble polysaccharides. the aim of this work is to provide an appropriate approach to deproteinize crude gellan gum. several methods of deproteinization were investigated, including sevag method, alkaline protease, papain and neutral protease. the results revealed that sevag method had high deproteinization efficiency (87.9%), but it showed dissatisfactory recovery efficiency of gellan gum (28.6%), which made it les ... | 2007 | 17069918 |
| measurement of biodegradability parameters for single unsubstituted and methylated polycyclic aromatic hydrocarbons in liquid bacterial suspensions. | substrate depletion experiments were conducted to characterize aerobic biodegradation of 20 single polycyclic aromatic hydrocarbons (pahs) by induced sphingomonas paucimobilis strain epa505 in liquid suspensions. pahs consisted of low molecular weight, unsubstituted, and methyl-substituted homologs. a material balance equation containing the andrews kinetic model, an extension of the monod model accounting for substrate inhibition, was numerically fitted to batch depletion data to estimate extan ... | 2007 | 17115446 |
| kinetics of biodegradation of binary and ternary mixtures of pahs. | the kinetics of biodegradation of mixtures of polycyclic aromatic hydrocarbons (pahs) by sphingomonas paucimobilis strain epa505 were investigated. the investigation focused on three- and four-ring pahs, specifically 2-methylphenanthrene, fluoranthene, and pyrene. uptake rates in aerobic batch suspended cultivations were measured for the individual pahs and their binary and ternary mixtures. it was observed that kinetics were influenced by the mixture composition and the kinetic properties of th ... | 2007 | 17115447 |
| genetic and biochemical investigations on bacterial catabolic pathways for lignin-derived aromatic compounds. | lignins are the most abundant aromatic compounds in nature, and their decomposition is essential to the terrestrial carbon cycle. white rot fungi secreting phenol oxidases are assumed to be involved in the initial degradation of native lignin, whereas bacteria play a main role in the mineralization of lignin-derived low-molecular-weight compounds in soil. there are a number of reports on the degradation pathways for lignin-derived aromatic compounds, but their catabolism has not been enzymatical ... | 2007 | 17213657 |
| biological pretreatment with two bacterial strains for enzymatic hydrolysis of office paper. | the cellulose-hydrolyzing strains, sphingomonas paucimobilis mk1 and bacillus circulans mk2, were separated from soil and were grown together in a single culture plate. growth b. circulans mk2 in liquid culture required symbiosis with s. paucimobilis mk1. biological pretreatment with the combined strain suspension after the liquid culture improved enzymatic hydrolysis of office paper from municipal wastes. sugar recovery by s. paucimobilis mk1 (51%) was 1.4 times higher than that of the untreate ... | 2007 | 17487532 |
| molecular characterization of membrane-associated soluble serine palmitoyltransferases from sphingobacterium multivorum and bdellovibrio stolpii. | serine palmitoyltransferase (spt) is a key enzyme in sphingolipid biosynthesis and catalyzes the decarboxylative condensation of l-serine and palmitoyl coenzyme a (coa) to form 3-ketodihydrosphingosine (kds). eukaryotic spts comprise tightly membrane-associated heterodimers belonging to the pyridoxal 5'-phosphate (plp)-dependent alpha-oxamine synthase family. sphingomonas paucimobilis, a sphingolipid-containing bacterium, contains an abundant water-soluble homodimeric spt of the same family (h. ... | 2007 | 17557831 |
| the structure of serine palmitoyltransferase; gateway to sphingolipid biosynthesis. | sphingolipid biosynthesis commences with the condensation of l-serine and palmitoyl-coa to produce 3-ketodihydrosphingosine (kds). this reaction is catalysed by the plp-dependent enzyme serine palmitoyltransferase (spt; ec 2.3.1.50), which is a membrane-bound heterodimer (spt1/spt2) in eukaryotes such as humans and yeast and a cytoplasmic homodimer in the gram-negative bacterium sphingomonas paucimobilis. unusually, the outer membrane of s. paucimobilis contains glycosphingolipid (gsl) instead o ... | 2007 | 17559874 |