Publications

molecular analysis of shower curtain biofilm microbes.	households provide environments that encourage the formation of microbial communities, often as biofilms. such biofilms constitute potential reservoirs for pathogens, particularly for immune-compromised individuals. one household environment that potentially accumulates microbial biofilms is that provided by vinyl shower curtains. over time, vinyl shower curtains accumulate films, commonly referred to as "soap scum," which microscopy reveals are constituted of lush microbial biofilms. to determi ...	2004	15240300
comparative biochemical analysis of three bacterial prolyl endopeptidases: implications for coeliac sprue.	prolyl endopeptidases have potential for treating coeliac sprue, a disease of the intestine caused by proteolytically resistant peptides from proline-rich prolamins of wheat, barley and rye. we compared the properties of three similar bacterial prolyl endopeptidases, including the known enzymes from flavobacterium meningosepticum (fm) and sphingomonas capsulate (sc) and a novel enzyme from myxococcus xanthus (mx). these enzymes were interrogated with reference chromogenic substrates, as well as ...	2004	15245330
are some putative glycogen accumulating organisms (gao) in anaerobic : aerobic activated sludge systems members of the alpha-proteobacteria?	activated sludge plants designed to remove phosphorus microbiologically often perform unreliably. one suggestion is that the polyphosphate-accumulating organisms (pao) are out-competed for substrates by another group of bacteria, the glycogen-accumulating organisms (gao) in the anaerobic zones of these processes. this study used fluorescence in situ hybridization (fish) and denaturing gradient gel electrophoresis (dgge) to analyse the communities from laboratory-scale anaerobic : aerobic sequenc ...	2004	15256569
mtbe biodegradation in a gravity flow, high-biomass retaining bioreactor.	the aerobic biodegradation of methyl tert-butyl ether (mtbe), a widely used fuel oxygenate, was investigated using a pilot-scale biomass-retaining bioreactor called a biomass concentrator reactor (bcr). the reactor was operated for a year at a flow rate of 2500 l/d on cincinnati dechlorinated tap water and an influent mtbe concentration of 5 mg/l. treatment efficiency of mtbe in the reactor during stable operations exceeded 99.9%. the upper 95% confidence levels of effluent mtbe concentrations a ...	2004	15260347
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
monitoring the coral disease, plague type ii, on coral reefs in st. john, u.s. virgin islands.	in july 1997, conspicuous white patches of necrotic tissue and bare skeleton began to appear on scleractinian corals in several bays around st. john, us virgin islands. analysis of diseased coral tissue from five different species confirmed the presence of a sphingomonas-like bacterium, the pathogen for plague type ii. to date, 14 species of hard corals have been affected by plague type ii around st. john. this disease was monitored at haulover and tektite reefs at depths of 7-12 meters. the stu ...	2003	15264553
divergent structures of carbazole degradative car operons isolated from gram-negative bacteria.	southern hybridization analysis of the genomes from the newly-isolated 10 carbazole (car)-utilizing bacteria revealed that 8 of the isolates carried gene clusters homologous to the car-catabolic car operon of pseudomonas resinovorans strain ca10. sequencing analysis showed that two car operons and the neighboring regions of pseudomonas sp. strain k23 are nearly identical to that of strain ca10. in contrast to strains ca10 and k23, caref genes did not exist downstream of the car gene cluster of j ...	2004	15277751
microbiological influences in 'blue water' copper corrosion.	to investigate the influence of micro-organisms associated with copper corrosion on 'blue water' corrosion in drinking water.	2004	15281940
a 19f nmr study of fluorobenzoate biodegradation by sphingomonas sp. hb-1.	while several microorganisms readily degrade 2- and 4-fluorobenzoates, only a very small number appear to catabolise the 3-fluoro isomer, owing to the accumulation of toxic intermediates. here we describe the isolation of a bacterium capable of using 3-fluorobenzoate as a sole source of carbon and energy, and the experiments conducted to define the steps involved in the biodegradation of this compound. the organism was identified as a strain belonging to the genus sphingomonas by sequence analys ...	2004	15321683
comparison of n-eicosane and phenanthrene removal by pure and mixed cultures of two marine bacteria.	the biotransformation activities of two hydrocarbonoclastic marine bacteria, corynebacterium sp. and sphingomonas sp. 2mpii, on n-eicosane and phenanthrene were investigated. during a 56-day experiment, in pure and mixed cultures, corynebacterium sp. and sphingomonas sp. 2mpii removed about 70% of the initial n-eicosane and phenanthrene concentrations (1 and 0.4 g l(-1), respectively). in pure cultures, culturable cell abundances increased over time, from 0.8 to 8.6 x 10(-11) cfu l(-1) (coryneba ...	2004	15325883
molecular identification and characterization of an alginate-binding protein on the cell surface of sphingomonas sp. a1.	cells of sphingomonas sp. a1 (strain a1) directly incorporate a macromolecule, alginate, into cytoplasm through a biosystem, or "super-channel," consisting of a pit on the cell surface, alginate-binding proteins in periplasm, and an abc transporter in the inner membrane. the pit functions as a concentrator for extracellular alginate. through differential display analysis, a protein (p8) with a molecular mass of 20kda and a pi of 7.4 was found to be inducibly expressed in the outer membrane of al ...	2004	15336522
regulation of tetralin biodegradation and identification of genes essential for expression of thn operons.	the tetralin biodegradation genes of sphingomonas macrogolitabida strain tfa are clustered in two closely linked and divergent operons. to analyze expression of both operons under different growth conditions, transcriptional and translational gene fusions of the first genes of each operon to lacz have been constructed in plasmids unable to replicate in sphingomonas and integrated by recombination into the genome of strain tfa. expression analysis indicated that the transcription of both genes is ...	2004	15342579
requirement of a relatively high threshold level of mg(2+) for cell growth of a rhizoplane bacterium, sphingomonas yanoikuyae ec-s001.	mg(2+) is one of the essential elements for bacterial cell growth. the presence of the magnesium cation (mg(2+)) in various concentrations often affects cell growth restoration in plant-associating bacteria. this study attempted to determine whether mg(2+) levels in sphingomonas yanoikuyae ec-s001 affected cell growth restoration in the host plant and what the threshold level is. s. yanoikuyae ec-s001, isolated from the rhizoplane of spinach seedlings grown from surface-sterilized seeds under as ...	2004	15345402
genetic and phenotypic diversity of (r/s)-mecoprop [2-(2-methyl-4-chlorophenoxy)propionic acid]-degrading bacteria isolated from soils.	twelve mecoprop-degrading bacteria were isolated from soil samples, and their genetic and phenotypic characteristics were investigated. analysis of 16s rdna sequences indicated that the isolates were related to members of the genus sphingomonas. ten different chromosomal dna patterns were obtained by polymerase-chain-reaction (pcr) amplification of repetitive extragenic palindromic (rep) sequences from the 12 isolates. the isolates were found to be able to utilize the chiral herbicide mecoprop a ...	2004	15357300
isolation and characterization of genes encoding polycyclic aromatic hydrocarbon dioxygenase from acenaphthene and acenaphthylene degrading sphingomonas sp. strain a4.	sphingomonas sp. strain a4 is capable of utilizing acenaphthene and acenaphthylene as sole carbon and energy sources, but it is unable to grow on other polycyclic aromatic hydrocarbons (pahs). the genes encoding terminal oxygenase components of ring-hydroxylating dioxygenase (arha1 and arha2) were isolated from this strain by means of the ability to oxidize indole to indigo of the escherichia coli clone containing electron transport proteins from phenanthrene-degrading sphingobium sp. strain p2. ...	2004	15358414
a sphingomonas bacterium interacting with epithelial cells.	bacteria of the genus sphingomonas are environmental organisms that have recently been implicated in a variety of community-acquired and nosocomial infections. during studies on bacteria-cell interactions, we incurred a microorganism contaminating our hela cell culture, possibly from water utilized for reagent preparation; this bacterium appeared to tightly adhere to cell monolayers and to survive, with only limited growth rate, which did not seem to alter cells as far as shape, growth rate or s ...	2004	15380551
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
green fluorescent protein as a marker for monitoring a pentachlorophenol degrader sphingomonas chlorophenolica atcc39723.	sphingomonas chlorophenolica atcc39723 was successfully labeled with the gfp (green fluorescent protein) gene inserted into the pcpb gene by homologous recombination. as the gfp recombinant was easily distinguished from other indigenous organisms, the population of gfp recombinant was monitored after being released into the soil microcosms. their population density dropped from 10(8) to 10(6) (cfu/ml) in the non-sterilized soil microcosms during the first 6 days. moreover, the gfp recombinant wa ...	2004	15459656
electrokinetic transport of pah-degrading bacteria in model aquifers and soil.	an investigation of the mobility, viability, and activity of polycyclic aromatic hydrocarbon (pah) degrading bacteria in an electric field is presented. bench-scale model aquifers were used to test electrophoresis and electroosmosis as potential mechanisms for bacterial dispersion in contaminated sites. glass beads, alluvial sand from lake geneva, and historically polluted clayey soil were used as packing materials. the green-fluorescent protein labeled pah-degrading bacteria sphingomonas sp. l1 ...	2004	15461168
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
genetic analysis of phenoxyalkanoic acid degradation in sphingomonas herbicidovorans mh.	phenoxyalkanoic acid degradation is well studied in beta- and gammaproteobacteria, but the genetic background has not been elucidated so far in alphaproteobacteria. we report the isolation of several genes involved in dichlor- and mecoprop degradation from the alphaproteobacterium sphingomonas herbicidovorans mh and propose that the degradation proceeds analogously to that previously reported for 2,4-dichlorophenoxyacetic acid (2,4-d). two genes for alpha-ketoglutarate-dependent dioxygenases, sd ...	2004	15466552
enzymatic hydrolysis of alpha- and beta-oligo(l-aspartic acid)s by poly(aspartic acid) hydrolases-1 and 2 from sphingomonas sp. kt-1.	the enzymatic hydrolysis of alpha- and beta-oligo(l-aspartic acid)s by paa hydrolase-1 and paa hydrolase-2 (purified from sphingomonas sp. kt-1) was performed to elucidate the mechanism of the microbial degradation by sphingomonas sp. kt-1 of the thermally synthesized alpha,beta-poly(d,l-aspartic acid) (tpaa). gpc analysis of the hydrolyzed products of alpha- and beta-tetra(l-aspartic acid)s by paa hydrolase-1 has showed that paa hydrolase-1 is capable of hydrolyzing only the specific amide bond ...	2004	15468224
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
streptomycin as a selective agent to facilitate recovery and isolation of introduced and indigenous sphingomonas from environmental samples.	sphingomonas is an organism of major interest for the degradation of organic contaminants in soils and other environments. a medium based on the aminoglycoside antibiotic streptomycin (sm) was developed, which, together with the yellow pigmentation of sphingomonas, facilitated the detection, recovery and quantification of culturable sphingomonas from soils. all 29 previously described bacterial strains belonging to 17 different sphingomonas species were able to grow on mineral media containing 2 ...	2004	15479246
characterization and phylogenetic analysis of a phenanthrene-degrading strain isolated from oil-contaminated soil.	bacterium strain eva17 was isolated from an oil-contaminated soil, and identified as sphingomonas sp. based on analysis of 16s rdna sequence, cellular fatty acid composition and physiological-chemical tests. the salicylate hydroxylase and catechol 2, 3-dioxygenase (c230) were detected in cell-free lysates, suggesting a pathway for phenanthrene catabolism via salicylate and catechol. alignment showed that both of the c230 and gst genes of the strain eva17 had high similarity with homologues of st ...	2004	15495962
microbial degradation of a single branched isomer of nonylphenol by sphingomonas ttnp3.	the endocrine disrupting chemical nonylphenol (np) is a technical product which consists of a complex mixture of nonylphenols with different alkyl side-chain isomers. since the bio-degradation of each np isomer may lead to its own range of metabolites, the isolation and identification of transformation products is very difficult. in order to overcome this difficulty, the nonylphenol isomer 4(3',5'-dimethyl-3'-heptyl)-phenol (p353np) was synthesized, and its degradation by an axenic culture of sp ...	2004	15497847
bioavailability of a nonylphenol isomer in dependence on the association to dissolved humic substances.	humic substances are important environmental components since they represent a very large part of organic compounds on earth. according to many reports, dissolved humic substances are a determinant parameter for the bioavailability of xenobiotic compounds. for the present bioavailability studies, two kinds of dissolved humic substances, a commercially available humic acid and fulvic acids isolated from peat were used. as the relevant xenobiotic, a defined branched nonylphenol isomer, 4(3',5'-dim ...	2004	15497858
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
identification and functional analysis of two aromatic-ring-hydroxylating dioxygenases from a sphingomonas strain that degrades various polycyclic aromatic hydrocarbons.	in 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 ...	2004	15528538
degradation of a nonylphenol single isomer by sphingomonas sp. strain ttnp3 leads to a hydroxylation-induced migration product.	sphingomonas sp. strain ttnp3 degrades 4(3',5'-dimethyl-3'-heptyl)-phenol and unidentified metabolites that were described previously. the chromatographic analyses of the synthesized reference compound and the metabolites led to their identification as 2(3',5'-dimethyl-3'-heptyl)-1,4-benzenediol. this finding indicates that the nonylphenol metabolism of this bacterium involves unconventional degradation pathways where an nih shift mechanism occurs.	2004	15528560
sphingomonas phyllosphaerae sp. nov., from the phyllosphere of acacia caven in argentina.	two bacterial strains (fa1 and fa2(t)) were isolated from the phyllosphere of a leguminous tree, acacia caven, in central argentina. the strains were gram-negative, strictly aerobic, rod-shaped, motile and formed yellow-pigmented colonies on nutrient agar. the two-primer rapd patterns of the two strains were identical, suggesting that they belong to the same species. the complete 16s rrna gene sequences of the two strains were obtained and comparisons demonstrated that they cluster phylogenetica ...	2004	15545449
sphingomonas oligophenolica sp. nov., a halo- and organo-sensitive oligotrophic bacterium from paddy soil that degrades phenolic acids at low concentrations.	the taxonomic position of a halo- and organo-sensitive, oligotrophic soil bacterium, strain s213(t), was investigated. cells were gram-negative, non-motile, strictly aerobic, yellow-pigmented rods of short to medium length on diluted nutrient broth. when 0.1-0.4 % (w/v) nacl was added to diluted media composed of peptone and meat extract, growth was inhibited with increasing nacl concentration and the cells became long aberrant forms. when 6 mm cacl(2) was added, the cells grew quite normally an ...	2004	15545456
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 ...	2005	15549289
influence of the carbon/nitrogen/phosphorus ratio on polycyclic aromatic hydrocarbon degradation by mycobacterium and sphingomonas in soil.	biodegradation of polycyclic aromatic hydrocarbons (pahs) in the environment is often limited due to unfavorable nutrient conditions for the bacteria that use these pahs as sole source of carbon and energy. mycobacterium and sphingomonas are 2 pah-degrading specialists commonly present in pah-polluted soil, but not much is known about their specific nutrient requirements. by adding different inorganic supplements of nitrogen (n) and phosphorus (p), affecting the overall carbon/nitrogen/phosphoru ...	2005	15549290
plant-assisted degradation of phenanthrene as assessed by solid-phase microextraction (spme).	the soil bacterium sphingomonas yanoikuyae was isolated from a petroleum-contaminated soil and grown on mineral salts agar overlaid with the polycyclic aromatic hydrocarbon phenanthrene. the effect of white mustard, sinapis alba, on phenanthrene degradation by s. yanoikuyae in artificially contaminated redi-earth-sand was examined. solid-phase-microextraction (spme) gas chromatography-flame ionization detection (gc-fid) was used to quantify the concentration of phenanthrene in the gas phase of m ...	2004	15554477
bacterial diversity of a soil sample from schirmacher oasis, antarctica.	the bacterial diversity of a soil sample collected in the vicinity of lake zub, schirmacher oasis, antarctica, was determined both by establishing pure colonies of culturable bacteria and by cloning the total 16s rdna of the soil and establishing the phylogeny of the clones. analysis of the 16s rrna gene clones indicated that the bacteria belonged to the classes alpha-proteobacteria, beta-proteobacteria, gamma-proteobacteria, gemmatimonas, bacteriodetes, actinobacteria, chloroflexi and chlamydia ...	2004	15559969
a previously unexposed forest soil microbial community degrades high levels of the pollutant 2,4,6-trichlorophenol.	2,4,6-trichlorophenol (2,4,6-tcp) is a hazardous pollutant that is efficiently degraded by some aerobic soil bacterial isolates under laboratory conditions. the degradation of this pollutant in soils and its effect on the soil microbial community are poorly understood. we report here the ability of a previously unexposed forest soil microbiota to degrade high levels of 2,4,6-tcp and describe the changes in the soil microbial community found by terminal restriction fragment length polymorphism (t ...	2004	15574963
isolation and characterization of a novel sphingomonad capable of growth with chrysene as sole carbon and energy source.	a bacterial strain able to grow in pure culture with chrysene as sole added carbon and energy source was isolated from pah-contaminated soil after successive enrichment cultures in a biphasic growth medium. initially, growth occurred in the form of a biofilm at the interface between the aqueous and non-aqueous liquid phases. however, after a certain time, a transition occurred in the enrichment cultures, with growth occurring in suspension and a concomitant increase in the rate of chrysene degra ...	2004	15598525
characterization of micro-organisms isolated from dairy industry after cleaning and fogging disinfection with alkyl amine and peracetic acid.	to characterize micro-organisms isolated from norwegian dairy production plants after cleaning and fogging disinfection with alkyl amine/peracetic acid and to indicate reasons for survival.	2005	15610421
rapid screening and dereplication of bacterial isolates from marine sponges of the sula ridge by intact-cell-maldi-tof mass spectrometry (icm-ms).	rapid grouping of bacterial isolates is critical in comprehensive microbial studies of environmental samples or screening programmes e.g. in unknown marine environments where large numbers of strains have to be isolated on different growth media. sets of bacteria have been cultured from the marine sponges isops phlegraei, haliclona sp. 1, phakellia ventilabrum and plakortis sp. growing at a depth of about 300 m on the sula ridge close to the norwegian coast. we employed intact-cell maldi-tof (ic ...	2004	15614563
aerobic degradation of polychlorinated biphenyls.	the microbial degradation of polychlorinated biphenyls (pcbs) has been extensively studied in recent years. the genetic organization of biphenyl catabolic genes has been elucidated in various groups of microorganisms, their structures have been analyzed with respect to their evolutionary relationships, and new information on mobile elements has become available. key enzymes, specifically biphenyl 2,3-dioxygenases, have been intensively characterized, structure/sequence relationships have been de ...	2004	15614564
evolutionarily divergent extradiol dioxygenases possess higher specificities for polychlorinated biphenyl metabolites.	the reactivities of four evolutionarily divergent extradiol dioxygenases towards mono-, di-, and trichlorinated (tricl) 2,3-dihydroxybiphenyls (dhbs) were investigated: 2,3-dihydroxybiphenyl dioxygenase (ec 1.13.11.39) from burkholderia sp. strain lb400 (dhbdlb400), dhbdp6-i and dhbdp6-iii from rhodococcus globerulus p6, and 2,2',3-trihydroxybiphenyl dioxygenase from sphingomonas sp. strain rw1 (thbdrw1). the specificity of each isozyme for particular dhbs differed by up to 3 orders of magnitude ...	2005	15629912
catabolic role of a three-component salicylate oxygenase from sphingomonas yanoikuyae b1 in polycyclic aromatic hydrocarbon degradation.	sphingomonas yanoikuyae b1 possesses several different multicomponent oxygenases involved in metabolizing aromatic compounds. six different pairs of genes encoding large and small subunits of oxygenase iron-sulfur protein components have previously been identified in a gene cluster involved in the degradation of both monocyclic and polycyclic aromatic hydrocarbons. insertional inactivation of one of the oxygenase large subunit genes, bpha1c, results in a mutant strain unable to grow on naphthale ...	2005	15649397
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
stable long-term indigo production by overexpression of dioxygenase genes using a chromosomal integrated cascade expression circuit.	in our laboratory we have analyzed different factors to maximize the yield in heterologous protein expression for long-term cultivation, by combination of an efficient cascade expression system and stable integration in the bacterial chromosome. in this work, we have explored this system for the production of indigo dye as a model for biotechnological production, by expressing in escherichia coli the thna1a2a3a4 genes from sphingomonas macrogolitabida strain tfa, which encode the components of a ...	2004	15664075
bacterial glycolipids and analogs as antigens for cd1d-restricted nkt cells.	the cd1 family of proteins binds self and foreign glycolipids for presentation to cd1-restricted t cells. to identify previously uncharacterized active cd1 ligands, especially those of microbial origin, numerous glycolipids were synthesized and tested for their ability to stimulate mouse and human natural killer t (nkt) cells. they included analogs of the well known nkt cell agonist alpha-galactosyl ceramide (alpha-galcer), bacterial glycolipids, and variations of the self-glycolipid, sulfatide. ...	2005	15665086
a novel metabolic pathway for degradation of 4-nonylphenol environmental contaminants by sphingomonas xenophaga bayram: ipso-hydroxylation and intramolecular rearrangement.	several nonylphenol isomers with alpha-quaternary carbon atoms serve as growth substrates for sphingomonas xenophaga bayram, whereas isomers containing hydrogen atoms at the alpha-carbon do not. three metabolites of 4-(1-methyloctyl)-phenol were isolated in mg quantities from cultures of strain bayram supplemented with the growth substrate isomer 4-(1-ethyl-1,4-dimethyl-pentyl)-phenol. they were unequivocally identified as 4-hydroxy-4-(1-methyl-octyl)-cyclohexa-2,5-dienone, 4-hydroxy-4-(1-methyl ...	2005	15665329
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
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
dual substrate biodegradation of a nonionic surfactant and pentachlorophenol by sphingomonas chlorophenolica ra2.	the simultaneous biodegradation of the nonionic surfactant tween 20 (tw20) and pentachlorophenol (pcp) by sphingomonas chlorophenolica sp. strain ra2 (ra2) was measured. as a sole substrate, tw20 biodegradation was best described by the contois kinetic model. during concurrent biodegradation of tw20 and pcp, the biodegradation rates of tw20 were not significantly affected by 50 or 100 mg/l pcp, but were significantly inhibited by 500 mg/l pcp. decreases in cell yield in the presence of pcp sugge ...	2005	15685600
two unusual chlorocatechol catabolic gene clusters in sphingomonas sp. tfd44.	the genes responsible for the degradation of 2,4-dichlorophenoxyacetate (2,4-d) by alpha-proteobacteria have previously been difficult to detect by using gene probes or polymerase chain reaction (pcr) primers. pcr products of the chlorocatechol 1,2-dioxygenase gene, tfdc, now allowed cloning of two chlorocatechol gene clusters from the sphingomonas sp. strain tfd44. sequence characterization showed that the first cluster, tfdd,rfce, comprises all the genes necessary for the conversion of 3,5-dic ...	2004	15688254
a novel nicotinoprotein aldehyde dehydrogenase involved in polyethylene glycol degradation.	a gene (pegc) encoding aldehyde dehydrogenase (aldh) was located 3.4 kb upstream of a gene encoding polyethylene glycol (peg) dehydrogenase (pega) in sphingomonas macrogoltabidus strain 103. aldh was expressed in escherichia coli and purified on a ni-nitrilotriacetic acid agarose column. the recombinant enzyme was a homotetramer consisting of four 46.1-kda subunits. the alignment of the putative amino acid sequence of the cloned enzyme showed high similarity with a group of nad(p)-dependent aldh ...	2005	15726348
degradation of anthracene and pyrene supplied by microcrystals and non-aqueous-phase liquids.	polycyclic aromatic hydrocarbons (pahs) are worldwide environmental pollutants. their bioavailability is limited by a low aqueous solubility, which causes specific adaptations in degrading bacteria. to compare bacterial degrading behavior, a study was conducted on the mineralization, metabolization and formation of biomass from (14)c-anthracene by sphingomonas sp. ba2 compared with those from (14)c-pyrene by gordonia-like strain bp9 and mycobacterium gilvum vf1. different conditions of pah suppl ...	2005	15729557
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
structural and mechanistic analysis of two prolyl endopeptidases: role of interdomain dynamics in catalysis and specificity.	prolyl endopeptidases (peps) are a unique class of serine proteases with considerable therapeutic potential for the treatment of celiac sprue. the crystal structures of two didomain peps have been solved in alternative configurations, thereby providing insights into the mode of action of these enzymes. the structure of the sphingomonas capsulata pep, solved and refined to 1.8-a resolution, revealed an open configuration of the active site. in contrast, the inhibitor-bound pep from myxococcus xan ...	2005	15738423
the gellan gum biosynthetic genes gelc and gele encode two separate polypeptides homologous to the activator and the kinase domains of tyrosine autokinases.	the high-molecular-weight exopolysaccharide gellan is an important commercial gelling agent produced in high yield by the gram-negative bacterium sphingomonas elodea atcc 31461. the cluster of genes required for gellan biosynthesis contains the genes gelc and gele. these encode for two polypeptides homologous to the activator domain and the kinase domain, respectively, of bacterial autophosphorylating tyrosine kinases involved in polysaccharide chain length determination. the gelc/gele pair is a ...	2004	15741740
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
differential degradation of nonylphenol isomers by sphingomonas xenophaga bayram.	sphingomonas xenophaga bayram, isolated from the activated sludge of a municipal wastewater treatment plant, was able to utilize 4-(1-ethyl-1,4-dimethylpentyl)phenol, one of the main isomers of technical nonylphenol mixtures, as a sole carbon and energy source. the isolate degraded 1 mg of 4-(1-ethyl-1,4-dimethylpentyl)phenol/ml in minimal medium within 1 week. growth experiments with five nonylphenol isomers showed that the three isomers with quaternary benzylic carbon atoms [(1,1,2,4-tetrameth ...	2005	15746308
9,10-phenanthrenequinone photoautocatalyzes its formation from phenanthrene, and inhibits biodegradation of naphthalene.	polycyclic aromatic hydrocarbons (pahs) have earned considerable attention due to their widespread environmental distribution and toxicity. in the environment, pahs decompose by a variety of biotic and abiotic pathways. in both polar and nonpolar environments, phenanthrene (phe, a common, three-ring pah) is converted by sunlight to more polar products such as 9,10-phenanthrenequinone (pheq) and subsequent oxidation products such as the corresponding open-ring dicarboxylic acid product. biodegrad ...	2005	15758098
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
recognition of bacterial glycosphingolipids by natural killer t cells.	natural killer t (nkt) cells constitute a highly conserved t lymphocyte subpopulation that has the potential to regulate many types of immune responses through the rapid secretion of cytokines. nkt cells recognize glycolipids presented by cd1d, a class i-like antigen-presenting molecule. they have an invariant t-cell antigen receptor (tcr) alpha-chain, but whether this invariant tcr recognizes microbial antigens is still controversial. here we show that most mouse and human nkt cells recognize g ...	2005	15791257
exogenous and endogenous glycolipid antigens activate nkt cells during microbial infections.	cd1d-restricted natural killer t (nkt) cells are innate-like lymphocytes that express a conserved t-cell receptor and contribute to host defence against various microbial pathogens. however, their target lipid antigens have remained elusive. here we report evidence for microbial, antigen-specific activation of nkt cells against gram-negative, lipopolysaccharide (lps)-negative alpha-proteobacteria such as ehrlichia muris and sphingomonas capsulata. we have identified glycosylceramides from the ce ...	2005	15791258
direct evidence for sphingomonas sp. a1 periplasmic proteins as macromolecule-binding proteins associated with the abc transporter: molecular insights into alginate transport in the periplasm.	a gram-negative bacterium, sphingomonas sp. a1, has a macromolecule (alginate) import system consisting of a pit on the cell surface and an alginate-specific atp-binding cassette importer in the inner membrane. transport of alginate from the pit to the abc importer is probably mediated by two periplasmic binding protein homologues (algq1 and algq2). here we describe characteristics of binding of algq1 and algq2 to alginate and its oligosaccharides through surface plasmon resonance biosensor anal ...	2005	15794643
diversity of carbazole-degrading bacteria having the car gene cluster: isolation of a novel gram-positive carbazole-degrading bacterium.	twenty-seven carbazole-utilizing bacterial strains were isolated from environmental samples, and were classified into 14 groups by amplified ribosomal dna restriction analysis. southern hybridization analyses showed that 3 and 17 isolates possessed the car gene homologs of pseudomonas resinovorans ca10 and sphingomonas sp. strain ka1, respectively. of the 17 isolates, 2 isolates also have the homolog of the caraa gene of sphingomonas sp. strain cb3. while the genome of one isolate, a gram-positi ...	2005	15796992
evaluation of bioremediation effectiveness on crude oil-contaminated sand.	a treatability study was conducted using sea sand spiked with 3% or 6% (w/w) of arabian light crude oil to determine the most effective bioremediation strategies for different levels of contamination. the sea sand used in the study was composed of gravel (0.1%), sand (89.0%), and silt and clay (10.9%). the water content of the sea sand was adjusted to 12.6% (w/w) for the study. different combinations of the following treatments were applied to the sand in biometer flasks: the concentration of oi ...	2004	15811413
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
characterization of sphingomonas aldehyde dehydrogenase catalyzing the conversion of various aromatic aldehydes to their carboxylic acids.	an aldehyde dehydrogenase gene, designated phnn, was isolated from a genome library of the 1,4-dimethylnaphthalene-utilizing soil bacterium, sphingomonas sp. 14dn61. escherichia coli expressing the phnn gene converted 1,4-dihydroxymethylnaphthalene to 1-hydroxymethyl-4-naphthoic acid. the putative amino acid sequence of the phnn gene product had 31-42% identity with those of nad(+)-dependent short-chain aliphatic aldehyde dehydrogenases and a secondary alcohol dehydrogenase. the nad(p)(+)-bindin ...	2005	15812642
biochemical and molecular characterization of a periplasmic hydrolase for oxidized polyvinyl alcohol from sphingomonas sp. strain 113p3.	oxidized polyvinyl alcohol hydrolase (oph) and polyvinyl alcohol dehydrogenase were found to be constitutively present in the periplasm of sphingomonas sp. strain 113p3 (formerly pseudomonas sp. 113p3). the oph was purified to homogeneity with a yield of 40 % and a 5.9-fold increase in specific activity. the enzyme was a homodimer consisting of 35 kda subunits. its activity was inhibited by pmsf, hg(2+) and zn(2+). the enzyme hydrolysed oxidized polyvinyl alcohol (oxidized pva) and p-nitrophenyl ...	2005	15817792
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
[auxin production by bacteria associated with orchid roots].	bacteria associated with the roots of greenhouse tropical orchids were shown to produce indole-3-acetic acid (iaa) and to excrete it into the culture liquid. the presence and activity of iaa were demonstrated colorimetrically, by thin-layer chromatography, and by biotests. the associated bacteria varied in their ability to excrete indole compounds (1-28 microg/ml nutrient broth). addition of tryptophan to the growth medium enhanced phytohormone production. upon addition of 200 microg/ml tryptoph ...	2005	15835779
[cloning, expression of the gene of dehydrochlorination of bhc from enrichment and its degradation experiment].	a high effective enrichment that could degrade four isomers of bhc completely was got from the soil polluted by gamma-bhc, but the pure culture was not obtained yet. the 471 bp sequence of linn was amplified from the total dna of enrichment by polymerase chain reaction (pcr). the nucleotide sequence analysis showed that the linn gene had high homology with reported lina up to 99%. then the amplified fragment linn was cloned in the proper orientation into the site between nde i and hind iii of pe ...	2005	15847161
structure and function of bacterial super-biosystem responsible for import and depolymerization of macromolecules.	generally, when microbes assimilate macromolecules, they incorporate low-molecular-weight products derived from macromolecules through the actions of extracellular degrading enzymes. however, a gram-negative bacterium, sphingomonas sp. a1, has a smart biosystem for the import and depolymerization of macromolecules. the bacterial cells directly incorporate a macromolecule, alginate, into the cytoplasm through a "superchannel", as we named it. the superchannel consists of a pit on the cell surface ...	2005	15849405
[ion beam implantation in breeding efficient degradation bacteria].	sphingomonas sp. an1 was mutagenized and breeded by n+ implantation, mutants capable of degrading anthrancene was obtained. the research review that the degrading rate increased by 29.3% and 36.2% while the mutagenized rate was 80% - 100% and 60% - 80%. in addition, the maximum concentration of enduring anthracene reached 300mg/l and 400mg/l. their heritance stability were examined for fifteen transfers. among these strains, two strains,an815-3 and an315-5s,showed predominant character of surviv ...	2005	15859427
benzo[a]pyrene co-metabolism in the presence of plant root extracts and exudates: implications for phytoremediation.	benzo[a]pyrene, a high molecular weight (hmw) polycyclic aromatic hydrocarbon (pah) was removed from solution by sphingomonas yanoikuyae jar02 while growing on root products as a primary carbon and energy source. plant root extracts of osage orange (maclura pomifera), hybrid willow (salix albaxmatsudana), or kou (cordia subcordata), or plant root exudates of white mulberry (morus alba) supported 15-20% benzo[a]pyrene removal over 24 h that was similar to a succinate grown culture and an unfed ac ...	2005	15862401
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
biodegradation of bisphenol a by cells and cell lysate from sphingomonas sp. strain ao1.	the capacity and pathway of bisphenol a [bpa; 2,2-bis(4-hydroxyphenyl)propane] degradation in sphingomonas sp. strain ao1, which was isolated from the soil of a vegetable-growing field in japan, were investigated. the bacterial strain was able to grow in a basal mineral salt medium containing bpa as the sole carbon source (bsmb medium), and was able to degrade 115 microg ml(-1) bpa in 6 h in l medium. several bpa metabolites were detected in the culture supernatant by hplc and then identified by ...	2005	15865158
microbial community dynamics in bioaugmented sequencing batch reactors for bromoamine acid removal.	sphingomonas xenophaga qyy with the ability to degrade bromoamine acid (baa) was previously isolated from sludge samples. the enhancement of baa removal by strain qyy in sequencing batch reactors (sbrs) was investigated in this study. the results showed that augmented sbrs exhibited stronger abilities to degrade baa than the non-augmented control one. in order to estimate the relationship between community dynamics and function of augmented sbrs, a combined method based on fingerprints (ribosoma ...	2005	15869973
identification and phenotypic characterization of sphingomonas wittichii strain rw1 by peptide mass fingerprinting using matrix-assisted laser desorption ionization-time of flight mass spectrometry.	mass spectrometry is a potentially attractive means of monitoring the survival and efficacy of bioaugmentation agents, such as the dioxin-mineralizing bacterium sphingomonas wittichii strain rw1. the biotransformation activity of rw1 phenotypes is determined primarily by the presence and concentration of the dioxin dioxygenase, an enzyme initiating the degradation of both dibenzo-p-dioxin and dibenzofuran (df). we explored the possibility of identifying and characterizing putative cultures of rw ...	2005	15870332
architecture of a nascent sphingomonas sp. biofilm under varied hydrodynamic conditions.	the architecture of a sphingomonas biofilm was studied during early phases of its formation, using strain l138, a gfp-tagged derivative of sphingomonas sp. strain lb126, as a model organism and flow cells and confocal laser scanning microscopy as experimental tools. spatial and temporal distribution of cells and exopolymer secretions (eps) within the biofilm, development of microcolonies under flow conditions representing varied reynolds numbers, and changes in diffusion length with reference to ...	2005	15870359
optimizing contaminant desorption and bioavailability in dense slurry systems. 2. pah bioavailability and rates of degradation.	the effects of mechanical mixing on rates of polycyclic aromatic hydrocarbon (pah) biodegradation in dense geosorbent slurry (67% solids content, w/w) systems were evaluated using laboratory-scale intermittently mixed batch bioreactors. a pah-contaminated soil and a phenanthrene-sorbed mineral sorbent (alpha-al2o3) were respectively employed as slurry solids in aerobic and anaerobic biodegradation studies. both slurries exhibited a characteristic behavior of pseudoplastic non-newtonian fluids, a ...	2005	15871264
fluorescent methods to study dna, rna, proteins and cytoplasmic membrane polarization in the pentachlorophenol-mineralizing bacterium sphingomonas sp. ug30 during nutrient starvation in water.	the effect of sodium pentachlorophenolate (napcp) exposure on the nutrient-starved pentachlorophenol (pcp)-mineralizing bacterium sphingomonas sp. ug30 was assessed using fluorescent methods to measure dna, rna, total cellular protein, and cytoplasmic membrane proteins. ug30 cells were inoculated into sterilized speed river (guelph, on, canada) water samples in the presence of 50, 100, and 250 ppm napcp. no marked changes were observed in the total cellular dna, rna or protein levels over 90 d, ...	2005	15883769
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
two kinds of chlorocatechol 1,2-dioxygenase from 2,4-dichlorophenoxyacetate-degrading sphingomonas sp. strain tfd44.	two kinds of chlorocatechol 1,2-dioxygenase (ccd), tfdc and tfdc2 were detected in sphingomonas sp. strain tfd44. these two ccds could be simultaneously synthesized in tfd44 during its growth with 2,4-d as the sole carbon and energy sources. the apparent subunit molecular masses of tfdc and tfdc2 estimated by sds-page analysis were 33.8 and 33.1 kda, respectively. the genes encoding the two ccds were cloned and expressed in escherichia coli. the two purified ccds showed broad substrate specifici ...	2005	15916749
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 ...	2005	15942009
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
isolation of soil bacteria adapted to degrade humic acid-sorbed phenanthrene.	the goal of these studies was to determine how sorption by humic acids affected the bioavailability of polynuclear aromatic hydrocarbons (pahs) to pah-degrading microbes. micellar solutions of humic acid were used as sorbents, and phenanthrene was used as a model pah. enrichments from pah-contaminated soils established with nonsorbed phenanthrene yielded a total of 25 different isolates representing a diversity of bacterial phylotypes. in contrast, only three strains of burkholderia spp. and one ...	2005	16000791
culture independent detection of sphingomonas sp. epa 505 related strains in soils contaminated with polycyclic aromatic hydrocarbons (pahs).	the sphingomonas genus hosts many interesting pollutant-degrading strains. sphingomonas sp. epa505 is the best studied polycyclic aromatic hydrocarbon (pah)-degrading sphingomonas strain. based on 16s rrna gene sequence analysis, sphingomonas sp. strain epa505 forms a separate branch in the sphingomonas phylogenetic tree grouping exclusively pah-degrading isolates. for specific pcr detection and monitoring of sphingomonas sp. epa505 and related strains in pah-contaminated soils, a new 16s rrna g ...	2005	16003481
isolation and physiological characterization of the pentachlorophenol degrading bacterium sphingomonas chlorophenolica.	many chlorophenols tend to persist in the environment, and they may become public health hazards. among chlorophenols, pentachlorophenol (pcp) is a priority pollutant that has been used widely as a general biocide in commercial wood treatment. owing to the rapid industrial growth, serious soil and water pollutions by chlorophenols has been reported in taiwan. in this study, 10 indigenous pcp-degrading bacterial strains were isolated from a pcp-degrading mixed culture, and the potential of both t ...	2006	16005492
[oligotrophic bacteria and their applications in environmental science].	oligotrophic bacteria are a group of microbes living in oligotrophic environments. their diversity and biomass are dominant in biosphere, and thus, play an important role in biogeochemical cycles. since 1980s, their oligotrophic mechanisms, responses to starvation, and roles in ecosystems have been one of the most advanced subjects in microbial ecological research. much attention has been paid to the theoretical values and applied perspectives of oligotrophic bacteria. this paper reviewed the co ...	2005	16011186
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
isolation and identification of sphingomonas sp. that yields tert-octylphenol monoethoxylate under aerobic conditions.	topsoil samples were collected from eight golf courses in yamaguchi prefecture, japan, and enrichment cultures were carried out with a basal-salt medium containing 0.2% 4-tert-octylphenol polyethoxylate (oppeo) as sole carbon source. oppeo-degrading activity was detected in one of the samples, from which a strain of oppeo-degrading bacterium was isolated. the isolated bacterium grew on a nutritionally enriched medium (ne medium) containing 0.2% oppeo as sole carbon source, and accumulated 4-tert ...	2005	16041123
a mechanistic investigation of the thiol-disulfide exchange step in the reductive dehalogenation catalyzed by tetrachlorohydroquinone dehalogenase.	tetrachlorohydroquinone dehalogenase catalyzes the reductive dehalogenation of tetrachloro- and trichlorohydroquinone to give 2,6-dichlorohydroquinone in the pathway for degradation of pentachlorophenol by sphingobium chlorophenolicum. previous work has suggested that this enzyme may have originated from a glutathione-dependent double bond isomerase such as maleylacetoacetate isomerase or maleylpyruvate isomerase. while some of the elementary steps in these two reactions may be similar, the fina ...	2005	16042413
taking the fungal highway: mobilization of pollutant-degrading bacteria by fungi.	the capacity of fungi to serve as vectors for the dispersion of pollutant-degrading bacteria was analyzed in laboratory model systems mimicking water-saturated (agar surfaces) and unsaturated soil environments (glass-bead-filled columns). two common soil fungi (fusarium oxysporum and rhexocercosporidium sp.) forming hydrophilic and hydrophobic mycelia, respectively, and three polycyclic aromatic hydrocarbon degrading bacteria (achromobacter sp. sk1, mycobacterium frederiksbergense lb501tg, and s ...	2005	16047804
cis-dihydrodiol, arene oxide and phenol metabolites of dictamnine: key intermediates in the biodegradation and biosynthesis of furoquinoline alkaloids.	biotransformation of the parent furoquinoline alkaloid dictamnine and its 4-chlorofuroquinoline precursor, using the b8/36 bacterial mutant strain of sphingomonas yanoikuyae, yielded, via biphenyl dioxygenase-catalysed dihydroxylation, the first isolable alkaloid cis-dihydrodiol metabolites; these metabolites were used in the chemoenzymatic synthesis of postulated arene oxide and phenol intermediates, and a range of derived furoquinoline alkaloids.	2005	16075095
physicochemical properties and biological activities of deae-derivatized sphingomonas gellan.	physicochemical characteristics and biological activities of sphingomonas gellan (s-gellan) were investigated. the s-gellan weight fractions of glc and glcua were 0.45 and 0.25, respectively, and the molar ratio of glc:rha:glcua was approximately 4:2:3. the s-gellan was chemically derivatized with diethylaminoethyl chloride-hcl (deae-hcl), and the resulting modified s-gellan contained both positive and negative charges. the elemental and ir analyses were conducted to confirm the successful incor ...	2005	16076099
a structural basis for depolymerization of alginate by polysaccharide lyase family-7.	alginate lyases depolymerize alginate, a heteropolysaccharide consisting of alpha-l-guluronate and beta-d-mannuronate, through a beta-elimination reaction. their structure/function relationships are expected to provide information valuable to future industrial alginate processing and drug design for pseudomonas aeruginosa alginate biofilm-dependent infection, but much remains unknown. here, we present the crystal structure at 1.0 a resolution and the results of mutational analysis of sphingomona ...	2005	16081095
proteins encoded by sphingomonas elodea atcc 31461 rmla and ugpg genes, involved in gellan gum biosynthesis, exhibit both dtdp- and udp-glucose pyrophosphorylase activities.	the commercial gelling agent gellan is a heteropolysaccharide produced by sphingomonas elodea atcc 31461. in this work, we carried out the biochemical characterization of the enzyme encoded by the first gene (rmla) of the rml 4-gene cluster present in the 18-gene cluster required for gellan biosynthesis (gel cluster). based on sequence homology, the putative rml operon is presumably involved in the biosynthesis of dtdp-rhamnose, the sugar necessary for the incorporation of rhamnose in the gellan ...	2005	16085866
degradation of chlorophenols using pentachlorophenol-degrading bacteria sphingomonas chlorophenolica in a batch reactor.	chlorophenols are common environmental contaminants that have been used as the major component in wide-spectrum biocides in industry and agriculture. many chlorophenols tend to persist in the environment and may become public health hazards. this research studied the ability of the pentachlorophenol (pcp)-degrading bacterium sphingomonas chlorophenolica to degrade and dechlorinate other chlorophenols. in addition, the characteristics of s. chlorophenolica were also investigated. when s. chloroph ...	2005	16086107