Publications

a super-channel in bacteria: macromolecule uptake and depolymerization systems of sphingomonas sp. a1 with a special cell surface structure.		2002	12520874
genetic analysis and characterization of poly(aspartic acid) hydrolase-1 from sphingomonas sp. kt-1.	sphingomonas sp. kt-1 hydrolyzes poly(aspartic acid) (paa) containing alpha- and beta-amide units and has at least two different types of paa hydrolases. the paa hydrolase-1 hydrolyzes selectively beta-beta amide units in paa. molecular cloning of paa hydrolase-1 from sphingomonas sp. kt-1 has been carried out to characterize its gene products. genetic analysis shows that the deduced amino acid sequence of paa hydrolase-1 has a similarity with those of the catalytic domain of poly(3-hydroxybutyr ...	2003	12523851
degradation of polyvinyl alcohol by sphingomonas sp. sa3 and its symbiote.	a total of 800 samples was taken from taegu province, korea, where many textile factories provide a source of polyvinyl alcohol (pva) waste. these samples were screened for pva-degrading bacteria. a new strain, sa3, was discovered which formed yellow colonies and used pva as the sole carbon and energy source. strain sa3 was identified as a sphingomonas sp., based on the partial nucleotide sequence analysis of 16s ribosomal rna, the presence of 2-hydroxymyristic acid (14:o 2-oh) and sphingolipids ...	2003	12545389
in-field spatial variability in the degradation of the phenyl-urea herbicide isoproturon is the result of interactions between degradative sphingomonas spp. and soil ph.	substantial spatial variability in the degradation rate of the phenyl-urea herbicide isoproturon (ipu) [3-(4-isopropylphenyl)-1,1-dimethylurea] has been shown to occur within agricultural fields, with implications for the longevity of the compound in the soil, and its movement to ground- and surface water. the microbial mechanisms underlying such spatial variability in degradation rate were investigated at deep slade field in warwickshire, united kingdom. most-probable-number analysis showed tha ...	2003	12571001
diversity of 746 heterotrophic bacteria isolated from microbial mats from ten antarctic lakes.	microbial mats, growing in antarctic lakes constitute unique and very diverse habitats. in these mats microorganisms are confronted with extreme life conditions. we isolated 746 bacterial strains from mats collected from ten lakes in the dry valleys (lakes hoare and fryxell), the vestfold hills (lakes ace, druzhby, grace, highway, pendant, organic and watts) and the larsemann hills (lake reid), using heterotrophic growth conditions. these strains were investigated by fatty acid analysis, and by ...	2002	12583721
saccharin as a sole source of carbon and energy for sphingomonas xenophaga skn.	a bacterium, strain skn, that was able to utilize saccharin as the sole source of carbon and energy for aerobic growth, was enriched and isolated from communal sewage. the isolate was identified as a strain of sphingomonas xenophaga. saccharin was quantitatively converted to cell material, sulfate, ammonium and, presumably, co(2). the specific rate of saccharin-dependent oxygen uptake during growth reached a maximum before the culture entered the stationary phase and then fell to undetectable le ...	2003	12610724
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
identification and functional characterization of sphingomonas macrogolitabida strain tfa genes involved in the first two steps of the tetralin catabolic pathway.	five genes involved in the two initial steps of the tetralin biodegradation pathway of sphingomonas macrogolitabida strain tfa have been characterized. thna1a2 and thna3a4, components of the ring-hydroxylating dioxygenase, were encoded in divergently transcribed operons. thna1, thna2, and thna3 were essential for tetralin ring-hydroxylating dioxygenase activity. thnb was identified as a dehydrogenase required for tetralin biodegradation.	2003	12618469
life under nutrient limitation in oligotrophic marine environments: an eco/physiological perspective of sphingopyxis alaskensis (formerly sphingomonas alaskensis).	the oceans of the world are nutrient-limited environments that support a dynamic diversity of microbial life. heterotrophic prokaryotes proliferate in oligotrophic regions and affect nutrient transformation and remineralization thereby impacting directly on the all marine biota. an important challenge in studying the microbial ecology of oligotrophic environments has been the isolation of ecologically important species. this goal has been recognized not only for its relevance in defining the dyn ...	2003	12632213
fluctuation of bacteria isolated from elm tissues during different seasons and from different plant organs.	in this work we isolated a culturable endophytic aerobic heterotrophic bacterial community from the stem and root tissues of elm trees (ulmus spp.) and analyzed its fluctuations. a total of 724 bacterial isolates were collected at different times (april, june, september and december) from two elm trees, one infected with elm yellows phytoplasmas, and one which was healthy-looking. the isolates were grouped into 82 haplotypes, identified by means of amplified ribosomal dna restriction analysis (a ...	2003	12648725
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
shifts in diversity and microscale distribution of the adapted bacterial phenotypes due to hg(ii) spiking in soil.	in a previous experiment [ranjard et al. (2000) fems microbiol ecol 31:107-115], the spatial heterogeneity of a mercury impact on soil bacterial community was revealed by an increase of mercury-resistant (hgr) bacterial numbers in the outer fraction and the sand fractions when compared to those in the silt fractions. the objectives of the present study were (i) to investigate whether mercury exposure affects the diversity and the distribution within the various fractions of the hgr populations a ...	2003	12658524
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
spatial and temporal analysis of the microbial community in slow sand filters used for treating horticultural irrigation water.	an experimental slow sand filter (ssf) was constructed to study the spatial and temporal structure of a bacterial community suppressive to an oomycete plant pathogen, phytophthora cryptogea. passage of water through the mature sand column resulted in complete removal of zoospores of the plant pathogen. to monitor global changes in the microbial community, bacterial and fungal numbers were estimated on selective media, direct viable counts of fungal spores were made, and the atp content was measu ...	2003	12676691
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
wide geographic distribution of bacteriophages that lyse the same indigenous freshwater isolate (sphingomonas sp. strain b18).	an indigenous freshwater bacterium (sphingomonas sp. strain b18) from lake plubetasee (schleswig-holstein, germany) was used to isolate 44 phages from 13 very different freshwater and brackish habitats in distant geographic areas. this bacterial strain was very sensitive to a broad spectrum of phages from different aquatic environments. phages isolated from geographically distant aquatic habitats, but also those from the same sample, were diverse with respect to morphology and restriction patter ...	2003	12676728
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
synergistic relationships in algal-bacterial microcosms for the treatment of aromatic pollutants.	the potential of algal-bacterial microcosms was studied for the biodegradation of salicylate, phenol and phenanthrene. the isolation and characterization of aerobic bacterial strains capable of mineralizing each pollutant were first conducted. ralstonia basilensis was isolated for salicylate degradation, acinetobacter haemolyticus for phenol and pseudomonas migulae and sphingomonas yanoikuyae for phenanthrene. the green alga chlorella sorokiniana was then cultivated in the presence of the pollut ...	2003	12688473
elucidation of the metabolic pathway of fluorene and cometabolic pathways of phenanthrene, fluoranthene, anthracene and dibenzothiophene by sphingomonas sp. lb126.	the metabolic pathway of the pah fluorene and the cometabolic pathway of the pahs phenanthrene, fluoranthene, anthracene and dibenzothiophene in sphingomonas sp. lb126 were examined. to our knowledge this is the first study on the cometabolic degradation of the three-ring pahs phenanthrene, anthracene and the four-ring pah fluoranthene by a fluorene-utilizing species. metabolism of fluorene was shown to proceed via the 9-fluorenone pathway to form o-phthalic acid and protocatechuic acid. the com ...	2003	12706509
sphingopyxis chilensis sp. nov., a chlorophenol-degrading bacterium that accumulates polyhydroxyalkanoate, and transfer of sphingomonas alaskensis to sphingopyxis alaskensis comb. nov.	the taxonomic position of a chlorophenol-degrading bacterium, strain s37t, was investigated. the 16s rdna sequence indicated that this strain belongs to the genus sphingopyxis, exhibiting high sequence similarity to the 16s rdna sequences of sphingomonas alaskensis lmg 18877t (98.8%), sphingopyxis macrogoltabida lmg 17324t (98.2%), sphingopyxis terrae ifo 15098t (95%) and sphingomonas adhaesiva gifu 11458t (92%). these strains (except sphingopyxis terrae ifo 15098t, which was not investigated) a ...	2003	12710615
action mechanism of a selective anti-cyanobacterial compound, argimicin a.	argimicin a is a potent anti-cyanobacterial compound produced by one of algae-lysing bacteria, sphingomonas sp. m-17. since the compound seemed to exhibit selective activities against cyanobacteria and such selectivity were considered to be quite rare, the mode of action of argimicin a was investigated. argimicin a showed a unique delayed action, i.e., the cyanobacterial cell division continued until at least 36 hours treatment even though the decrement of oxygen evolution has been observed at 2 ...	2003	12715875
isolation and taxonomic and catabolic characterization of a 3,6-dimethylphenanthrene-utilizing strain of sphingomonas sp.	a bacterial strain capable of utilizing 3,6-dimethylphenanthrene (3,6-dmp) as its sole source of carbon and energy was isolated from a creosote-contaminated soil. the isolate was identified as a strain of sphingomonas sp. and was designated strain js1. utilization of 3,6-dmp was demonstrated by an increase in bacterial biomass concomitant with a decrease in 3,6-dmp in a liquid mineral medium with this compound as its sole source of carbon and energy. strain js1 showed a high specificity in the u ...	2003	12718400
an exotype alginate lyase in sphingomonas sp. a1: overexpression in escherichia coli, purification, and characterization of alginate lyase iv (a1-iv).	sphingomonas sp. a1 (strain a1) cells contain three kinds of endotype alginate lyases [a1-i, a1-ii, and a1-iii], all of which are formed from a common precursor through posttranslational processing. in addition to these lyases, another type of lyase (a1-iv) that acts on oligoalginates exists in the bacterium. a1-iv was overexpressed in escherichia coli cells through control of its gene under the t7 promoter. the expression level of the enzyme in e. coli cells was 8.6u/l-culture, which was about ...	2003	12729723
sediment microbes of deep-sea bioherms on the northwest shelf of australia.	the northwest shelf of australia is a region with known petroleum reserves. recent geological investigations have revealed carbonate knolls postulated to be of biological origin. sediment microbial populations at three sites on the northwest shelf, pee shoal, mermaid reef, and scott reef, were investigated for the presence of hydrocarbon-degrading bacteria. from two sampling trips, 246 bacterial strains were purified, and 182 of these strains displayed preferential growth on hydrocarbon-selectiv ...	2003	12739077
highly enantioselective hydrolysis of alicyclic meso-epoxides with a bacterial epoxide hydrolase from sphingomonas sp. hxn-200: simple syntheses of alicyclic vicinal trans-diols.	hydrolysis of n-benzyloxycarbonyl-3,4-epoxy-pyrrolidine and cyclohexene oxide with the epoxide hydrolase of sphingomonas sp. hxn-200, respectively, gave the corresponding vicinal trans-diols in high ee and yield, representing the first example of enantioselective hydrolysis of a meso-epoxide with a bacterial epoxide hydrolase.	2003	12744319
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 genetic system for the rapid isolation of aromatic-ring-hydroxylating dioxygenase activities.	aromatic-ring-hydroxylating dioxygenases (arhdos) are key enzymes in the aerobic bacterial metabolism of aromatic compounds. they are of biotechnological importance as they function as biocatalysts in the stereospecific synthesis of chiral synthons and the degradation of aromatic pollutants. this report describes the development and validation of a system for the rapid isolation and characterization of specific arhdo activities. the system is based on the identification of arhdo gene segments th ...	2003	12777487
site-directed mutagenesis of an extradiol dioxygenase involved in tetralin biodegradation identifies residues important for activity or substrate specificity.	the sequence of the extradiol dioxygenase thnc, involved in tetralin biodegradation, was aligned with other extradiol dioxygenases involved in biodegradation of polycyclic compounds, and a three-dimensional model of thnc, based on the structure of the previously crystallized 2,3-dihydroxybiphenyl dioxygenase from burkholderia fungorum lb400, was built. in order to assess the functional importance of some non-active-site residues whose relevance could not be established by structural information, ...	2003	12777496
microbial diversity of biofilms in dental unit water systems.	we investigated the microbial diversity of biofilms found in dental unit water systems (duws) by three methods. the first was microscopic examination by scanning electron microscopy (sem), acridine orange staining, and fluorescent in situ hybridization (fish). most bacteria present in the biofilm were viable. fish detected the beta and gamma, but not the alpha, subclasses of proteobacteria: in the second method, 55 cultivated biofilm isolates were identified with the biolog system, fatty acid an ...	2003	12788744
microbial consortia that degrade 2,4-dnt by interspecies metabolism: isolation and characterisation.	two consortia, isolated by selective enrichment from a soil sample of a nitroaromatic-contaminated site, degraded 2,4-dnt as their sole nitrogen source without accumulating one or more detectable intermediates. though originating from the same sample, the optimised consortia had no common members, indicating that selective enrichment resulted in different end points. consortium 1 and consortium 2 contained four and six bacterial species respectively, but both had two members that were able to co ...	2003	12801097
xylene monooxygenase, a membrane-spanning non-heme diiron enzyme that hydroxylates hydrocarbons via a substrate radical intermediate.	the non-heme diiron enzyme xylene monooxygenase (xylm) has been shown to hydroxylate hydrocarbons via a hydrogen abstraction-carbon radical recombination mechanism (oxygen rebound). using the radical clock bicyclo[4.1.0]heptane (norcarane) in a whole-cell assay, and observing the ratio of rearranged 3-(hydroxymethyl)cyclohexene and unrearranged 2-norcaranol products, the lifetime of the substrate radical was determined to be approximately 0.2 ns. the wild-type organism pseudomonas putida mt-2 an ...	2003	12811621
microbial contamination of dialysate and its prevention in haemodialysis units.	at the haemodialysis centres of nine hospitals in japan, microbial contamination of treated water (reverse osmosis method), acid and bicarbonate concentrates, and dialysate was investigated. among these fluids used in haemodialysis, the dialysate was most frequently contaminated and had the highest concentration of bacteria. of 40 dialysate samples analysed, 42.5% showed a bacterial count of more than 2000cfu/ml, which was above the association for the advancement of medical instrumentation (aam ...	2003	12818584
a novel antarctic microbial endolithic community within gypsum crusts.	a novel endolithic microbial habitat is described from a climatically extreme site at two step cliffs, alexander island, antarctic peninsula (71 degrees 54's, 68 degrees 13'w). small endolithic colonies (<3 mm in diameter) are found within the translucent gypsum crust that forms on the surface of sandstone boulders. gypsum crusts are found on ice-free rocks throughout the antarctic and therefore offer potential colonization sites at more inhospitable locations, including sites at higher latitude ...	2003	12823188
rhizoremediation of dioxin-like compounds by a recombinant rhizobium tropici strain expressing carbazole 1,9a-dioxygenase constitutively.	a recombinant rhizobium strain, pbk3-is, that constitutively expressed the oxygenase component of carbazole 1,9a-dioxygenase from sphingomonas sp. strain ka1, was constructed. in the water-cultured siratro rhizospheres inoculated with strain pbk3-is, 48% of the dibenzofuran was removed within 3 days (initial substrate, 25 microg). similar results were obtained in soil-cultured siratro rhizospheres using sterile vermiculite. when non-sterile field soils were used instead of sterile vermiculite, t ...	2003	12834297
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
biodegradation of nonylphenol in a continuous packed-bed bioreactor.	a packed bed bioreactor, with 170 ml glass bead carriers and 130 ml medium, was tested for the removal of the endocrine disrupter, nonylphenol, with a sphingomonas sp. the bioreactor was first continuously fed with medium saturated with nonylphenol in an attempt to simulate groundwater pollution. at best, nonylphenol was degraded by 99.5% at a feeding rate of 69 ml h(-1) and a removal rate of 4.3 mg nonylphenol day(-1), resulting in a 7.5-fold decrease in effluent toxicity according to the micro ...	2003	12889825
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
implication of two glutathione s-transferases in the optimal metabolism of m-toluate by sphingomonas yanoikuyae b1.	a putative glutathione s-transferase (gst) gene (bphk) was identified in the meta-cleavage operon for the degradation of m-toluate by sphingomonas yanoikuyae b1. disruption of bphk resulted in the loss of gst activity against 1-chloro-2,4-dinitrobenzene and a much increased lag time of the mutant strain mb3 (bphk::km) following subculture into m-toluate medium. in contrast, an increased lag time was not observed when mb3 was grown on biphenyl or m-xylene and mb3 showed normal growth on m-toluate ...	2003	12906359
biodegradation of methyl tertiary butyl ether (mtbe) by a bacterial enrichment consortia and its monoculture isolates.	methyl tertiary butyl ether (mtbe), an important gasoline additive, is a recalcitrant compound posing serious environmental health problems. in this study, mtbe-degrading bacteria were enriched from five environmental samples. enrichments from stewart lake sediments and an mtbe contaminated soil displayed the highest rate of mtbe removal; 29.6 and 27.8% respectively, in 28 days. a total of 12 bacterial monocultures isolated from enrichment cultures were screened for mtbe degradation in liquid cu ...	2003	12906382
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
potential of a new biotreatment: sphingomonas cloacae s-3t degrades nonylphenol in industrial wastewater.	sphingomonas cloacae s-3(t), a nonylphenol (np)-degrading bacterium, was evaluated for its utility in the remediation of np-contaminated wastewater. in flask-scale experiments, s-3(t) cells immobilized on porous polypropylene carriers (beads) efficiently degraded np to concentrations routinely measured in aquatic environments [a few parts per billion (ppb), or micrograms per liter). therefore, we constructed and evaluated a laboratory-scale wastewater treatment system with a 3-l carrier-filled c ...	2003	12915961
mineralization of soil-aged isoproturon and isoproturon metabolites by sphingomonas sp. strain srs2.	the aim of the study was to determine the effect of aging of the herbicide isoproturon and its metabolites monodesmethyl-isoproturon and 4-isopropyl-aniline in agricultural soil on their availability to the degrading bacterium sphingomonas sp. strain srs2. the 14c-ring-labeled isoproturon, monodesmethyl-isoproturon, and 4-isopropyl-aniline were added to sterilized soil and stored for 1, 49, 71, or 131 d before inoculation with strain srs2. the availability of the compounds was estimated from the ...	2003	12931879
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
ice from an ice machine is a potential source of bacterial contamination for hpc products -- implications for cell-processing facilities.		2003	12944241
biodegradation of selected uv-irradiated and non-irradiated polycyclic aromatic hydrocarbons (pahs).	biodegradation of uv-irradiated anthracene, pyrene, benz[a]anthracene, and dibenz[a,h]anthracene was compared to that of the non-irradiated samples, individually and in synthetic mixtures with enrichment cultures. combined treatment was repeated for individual anthracene and for the pah mixture with sphingomonas sp. strain epa 505 and sphingomonas yanoikuyae. enrichment culture studies were performed on the pah mixtures in the presence of the main photoproduct of anthracene, pure 9,10-anthracene ...	2003	12948055
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
biochemical and molecular characterization of poly(aspartic acid) hydrolase-2 from sphingomonas sp. kt-1.	poly(aspartic acid) (paa) hydrolase-2 was purified from crude soluble cellular extracts of sphingomonas sp. kt-1 (jcm10459) and characterized to elucidate the mechanism of alpha,beta-poly(d,l-aspartic acid) (tpaa) biodegradation. the molecular mass of paa hydrolase-2 was 42 kda, and the isoelectric point was 9.6. the optimum values of ph and temperature for the hydrolysis of alpha-di(l-aspartic acid) by paa hydrolase-2 were 7.0 and 55 degrees c, respectively. the effect of inhibitors on the hydr ...	2003	12959596
characterization and regulation of the genes for a novel anthranilate 1,2-dioxygenase from burkholderia cepacia dbo1.	anthranilate (2-aminobenzoate) is an important intermediate in tryptophan metabolism. in order to investigate the degradation of tryptophan through anthranilate by burkholderia cepacia, several plasposon mutations were constructed of strain dbo1 and one mutant with the plasposon insertion in the anthranilate dioxygenase (antdo) genes was chosen for further study. the gene sequence obtained from flanking dna of the plasposon insertion site revealed unexpected information. b. cepacia dbo1 antdo (d ...	2003	13129960
sphingomonas aurantiaca sp. nov., sphingomonas aerolata sp. nov. and sphingomonas faeni sp. nov., air- and dustborne and antarctic, orange-pigmented, psychrotolerant bacteria, and emended description of the genus sphingomonas.	seven psychrotolerant, gram-negative bacterial strains, five dust- and airborne isolates (ma101b(t), ma306a, ma405/90, ma-olki(t) and nw12(t)) and two from the antarctic (ant 20 and m3c203b-b), were subjected to a polyphasic characterization to determine their taxonomic position. high 16s rdna sequences similarities (99.3-100.0 %) demonstrated that they were closely related to each other. phylogenetic evaluation of their 16s rdna sequences revealed that they are members of the genus sphingomonas ...	2003	13130003
argimicins b and c, new anti-cyanobacterial compounds produced by sphingomonas sp. m-17.		2003	14513910
microbial degradation of high and low molecular weight polyaromatic hydrocarbons in a two-phase partitioning bioreactor by two strains of sphingomonas sp.	a mixture of six polyaromatic hydrocarbons (naphthalene, phenanthrene, fluoranthene, pyrene, chyrysene and benzo[a]pyrene), varying in size from 2 to 5 rings, was dissolved in dodecane, and used as the delivery phase of a partitioning bioreactor. two species of sphingomonas were then used individually, and as a consortium, to determine which of the pahs were degraded. only low molecular weight pahs (naphthalene, phenanthrene and fluoranthene) were degraded by the individual strains, but the cons ...	2003	14514047
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
enantioselective trans dihydroxylation of nonactivated c-c double bonds of aliphatic heterocycles with sphingomonas sp. hxn-200.	the bacterial strain sphingomonas sp. hxn-200 was used to catalyze the trans dihydroxylation ofn-substituted 1,2,5,6-tetrahydropyridines 1 and 3-pyrrolines 4 giving the corresponding 3,4-dihydroxypiperidines 3 and 3,4-dihydroxypyrrolidines 6, respectively, with high enantioselectivity and high activity. the trans dihydroxylation was sequentially catalyzed by a monooxygenase and an epoxide hydrolase in the strain with epoxide as intermediate. while both epoxidation and hydrolysis steps contribute ...	2003	14575492
purification and characterization of arylsulfatase from sphingomonas sp. as6330.	arylsulfatase was purified from sphingomonas sp. as6330 through ionic exchange, hydrophobic- and gel-chromatographies. the purity increased 12,800-fold with approximately 19.1% yield against cell homogenate. the enzyme was a monomeric protein with apparent molecular weight of 62 kda as determined by sodium dodecylsulfate-polyacrylamide gel electrophoresis, and 41 kda as determined by gel filtration. the enzyme had optimum reaction conditions for hydrolysis of sulfate ester bonds in agar and p-ni ...	2004	14600791
sphingobium amiense sp. nov., a novel nonylphenol-degrading bacterium isolated from a river sediment.	a nonylphenol-degrading bacterial strain (yt(t)) was isolated previously from a river sediment sample obtained in ami-machi, ibaraki, japan, and identified as a sphingomonas species. in this study, the taxonomic relationship between strain yt(t), a recently described nonylphenol-degrading strain, sphingomonas cloacae, and sphingobium yanoikuyae, which is phylogenetically related, was examined. their phenotypic characteristics were compared and levels of dna-dna relatedness between these strains ...	2003	14657143
identification and distribution of insertion sequences of paracoccus solventivorans.	three novel insertion sequences (iss) (ispso1, ispso2, and ispso3) of the soil bacterium paracoccus solventivorans dsm 11592 were identified by transposition into entrapment vector pmec1. ispso1 (1,400 bp) carries one large open reading frame (orf) encoding a putative basic protein (with a dde motif conserved among transposases [tnps] of elements belonging to the is256 family) with the highest levels of similarity with the hypothetical tnps of rhodospirillum rubrum and sphingopyxis macrogoltabid ...	2003	14660342
efficient degradation of 2,4,6-trichlorophenol requires a set of catabolic genes related to tcp genes from ralstonia eutropha jmp134(pjp4).	2,4,6-trichlorophenol (2,4,6-tcp) is a hazardous pollutant. several aerobic bacteria are known to degrade this compound. one of these, ralstonia eutropha jmp134(pjp4), a well-known, versatile chloroaromatic compound degrader, is able to grow in 2,4,6-tcp by converting it to 2,6-dichlorohydroquinone, 6-chlorohydroxyquinol, 2-chloromaleylacetate, maleylacetate, and beta-ketoadipate. three enzyme activities encoded by tcp genes, 2,4,6-tcp monooxygenase (tcpa), 6-chlorohydroxyquinol 1,2-dioxygenase ...	2003	14660355
detection and sequencing of the microcystin lr-degrading gene, mlra, from new bacteria isolated from japanese lakes.	mlra is the only microcystin-degrading gene detected in sphingomonas sp. mj-pv. the gene has an extremely rare nucleotide sequence and homologous genes have not yet been discovered in the dna database. we discovered the existence of a gene homologous to mlra in new microcystin-degrading bacteria, md-1 and y2. these strains possessed mlra homologues, and the identities of the genes of md-1 and y2 with the corresponding mj-pv exceeded 98% and 84%, respectively. on the other hand, the mlra gene was ...	2003	14680710
combination of microautoradiography and fluorescence in situ hybridization for identification of microorganisms degrading xenobiotic contaminants.	one of the central topics in environmental bioremediation research is to identify microorganisms that are capable of degrading the contaminants of interest. here we report application of combined microautoradiography (mar) and fluorescence in situ hybridization (fish). the method has previously been used in a number of systems; however, here we demonstrate its feasibility in studying the degradation of xenobiotic compounds. with a model system (coculture of pseudomonas putida b2 and sphingomonas ...	2003	14713022
evaluation of bacterial strategies to promote the bioavailability of polycyclic aromatic hydrocarbons.	polycyclic aromatic hydrocarbon (pahs)-degrading bacteria may enhance the bioavailability of pahs by excreting biosurfactants, by production of extracellular polymeric substances, or by forming biofilms. we tested these hypotheses in pure cultures of pahs-degrading bacterial strains. most of the strains did not substantially reduce the surface tension when grown on pahs in liquid shaken cultures. thus, pseudo-solubilization of pahs in biosurfactant micelles seems not to be a general strategy for ...	2004	14716468
bioavailability of pentachlorophenol to acclimatised bacteria under batch and flow-through conditions.	biodegradation of organic contaminants in multi-phase systems, such as soils and aquifers, is often limited by the extent and the rate of contaminant sorption onto the solid matrix. however, information about biodegradation in complex matrices is largely limited to studies of closed systems under batch conditions in which potential bioavailability is characterised by the aqueous-phase concentration of a contaminant. there is little knowledge regarding the influence of flow-through conditions on ...	2004	14716469
study of enzymatic reaction by electrophoretically mediated microanalysis in a partially filled capillary with indirect or direct detection.	electrophoretically mediated microanalysis (emma), in combination with a partial filling technique and indirect or direct detection, is described for the study of enzymes reacting with the high mobility inorganic or organic anions as substrates or products. part of the capillary is filled with a buffer optimized for the enzymatic reaction, the rest of the capillary with the background electrolyte being optimal for the separation of substrates and products. with haloalkane dehalogenase, chosen as ...	2004	14743481
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
microbial characterization during the early habitation of the international space station.	an evaluation of the microbiota from air, water, and surface samples provided a baseline of microbial characterization onboard the international space station (iss) to gain insight into bacterial and fungal contamination during the initial stages of construction and habitation. using 16s genetic sequencing and rep-pcr, 63 bacterial strains were isolated for identification and fingerprinted for microbial tracking. of the bacterial strains that were isolated and fingerprinted, 19 displayed similar ...	2004	14749908
organization of genes required for gellan polysaccharide biosynthesis in sphingomonas elodea atcc 31461.	sphingomonas elodea atcc 31461 produces gellan, a capsular polysaccharide that is useful as a gelling agent for food and microbiological media. complementation of nonmucoid s. elodea mutants with a gene library resulted in identification of genes essential for gellan biosynthesis. a cluster of 18 genes spanning 21 kb was isolated. these 18 genes are homologous to genes for synthesis of sphingan polysaccharide s-88 from sphingomonas sp. atcc 31554, with predicted amino acid identities varying fro ...	2004	14767675
biodegradation kinetics of volatile hydrophobic organic compounds in cultures with variable fractional volumes.	an extension of the models developed by guha and jaffé (biotechnol bioeng [1996] 50:693-699) to describe the phenanthrene biodegradation kinetics for the cultures with variable fractional volumes is presented. batch experiments were conducted with a culture capable of degrading the phenanthrene using a single culture vessel from which samples were withdrawn over time to monitor the disappearance of phenanthrene. for accurate measurement of phenanthrene concentrations, a sampling procedure design ...	2004	14966799
degradation of the radioactive and non-labelled branched 4(3',5'-dimethyl 3'-heptyl)-phenol nonylphenol isomer by sphingomonas ttnp3.	the degradation of the 4(3',5'-dimethyl-3'-heptyl)-phenol (p353np) nonylphenol isomer in cultures of sphingomonas ttnp3 supplemented with the technical mixture of nonylphenol was first assessed. then the radioactive and non-labelled form of these diastereomers were both synthesised. the radioactive isomers were synthesised using [ring-u-14c]-labelled phenol and 3,5-dimethyl-3-heptanol by friedel and crafts alkylation. the time-course of degradation was performed with and without 14c-p353np; bala ...	2004	14971853
estimation of kinetic parameter for the biotransformation of three-ring azaarenes by the phenanthrene-degrading strain sphingomonas sp. lh128.	we examined the biotransformation of several azaarenes to get information on their rate of removal from contaminated soil by cometabolic degradation. acridine, 9-methyl-acridine, phenanthridine, benzo[f]quinoline, and benzo[h]quinoline were found to be cometabolized by phenanthrene-degrading sphingomonas sp. strain lh128. the transformation of acridine and benzo[h]quinoline was shown to be inhibited at relatively high concentrations (24.9 mg/l and 58.2 mg/l, respectively). maximum biotransformat ...	2004	14982379
[isolation and characteristics of pahs-degrading strains].	the predominant indigenous microbial population and the strain zl5 pahs-degrading were obtained by selective enrichment culture from liaohe viscous oil-contaminated field. the sequence analysis of 16s rdna showed that strain zl5 belonged to sphingomonas sp. the microbial population and the strain could degrade phenanthrene well. 95.28% and 69.24% of phenanthrene in the medium were degraded in 120 hrs. however, the degradation of pyrene by the microbial population or by the strain was low. the de ...	2003	14986388
biodegradation of phthalate esters by two bacteria strains.	in this study two aerobic phthalic acid ester (pae) degrading bacteria strains, dk4 and o18, were isolated from river sediment and petrochemical sludge, respectively. the two strains were found to rapidly degrade pae with shorter alkyl-chains such diethyl phthalate (dep), dipropyl phthalate (dprp), di-n-butyl phthalate (dbp), benzylbutyl phthalate (bbp) and diphenyl phthalate (dpp) are very easily biodegraded, while pae with longer alkyl-chains such as dicyclohexyl phthalate (dcp) and dihexyl ph ...	2004	15006506
[investigation of the bacteria in the seawater of xisha in the south china sea and their antibiotic sensitivity profile].	to investigate the distribution and antibiotic sensitivity of the bacteria in the seawater of xisha in the south china sea.	2004	15041561
hydrocarbon spills on antarctic soils: effects and management.	antarctic exploration and research have led to some significant although localized impacts on the environment. human impacts occur around current or past scientific research stations, typically located on ice-free areas that are predominantly soils. fuel spills, the most common occurrence, have the potential to cause the greatest environmental impact in the antarctic through accumulation of aliphatic and aromatic compounds. effective management of hydrocarbon spills is dependent on understanding ...	2004	15046325
isolation of a beta-carotene over-producing soil bacterium, sphingomonas sp.	a carotenoid-accumulating bacterium isolated from soil, identified as a sphingomonas sp., grew at 0.18 h(-1) and produced 1.7 mg carotenoids g(-1) dry cell, among which beta-carotene (29% of total carotenoids) and nostoxanthin (36%). a mutant strain, obtained by treatment with ethyl methanesulfonate, accumulated up to 3.5 mg carotenoids g(-1) dry cell. accumulation of beta-carotene by this strain depended on the oxygenation of the growth medium, with maximal accumulation (89%) occurring under li ...	2004	15049373
distribution of nevskia ramosa and other rosette-forming neustonic bacteria.	samples from 27 natural and artificial aquatic environments were analyzed for the presence of rosette-forming bacteria by a combined cultivation and molecular biological approach. rosette-forming bacteria developed in 20 enrichment cultures with ammonia-free medium under air. three morphotypes could be distinguished. the most abundant type i resembled nevskia ramosa and formed hydrophobic, flat, and dichotomously branching rosettes. type ii rosettes were three-dimensional and were observed in 10 ...	2004	15054677
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
occurrence and phylogenetic diversity of sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons.	bacterial strains of the genus sphingomonas are often isolated from contaminated soils for their ability to use polycyclic aromatic hydrocarbons (pah) as the sole source of carbon and energy. the direct detection of sphingomonas strains in contaminated soils, either indigenous or inoculated, is, as such, of interest for bioremediation purposes. in this study, a culture-independent pcr-based detection method using specific primers targeting the sphingomonas 16s rrna gene combined with denaturing ...	2004	15066784
root nodule bradyrhizobium spp. harbor tfdaalpha and cada, homologous with genes encoding 2,4-dichlorophenoxyacetic acid-degrading proteins.	the distribution of tfdaalpha and cada, genes encoding 2,4-dichlorophenoxyacetate (2,4-d)-degrading proteins which are characteristic of the 2,4-d-degrading bradyrhizobium sp. isolated from pristine environments, was examined by pcr and southern hybridization in several bradyrhizobium strains including type strains of bradyrhizobium japonicum usda110 and bradyrhizobium elkanii usda94, in phylogenetically closely related agromonas oligotrophica and rhodopseudomonas palustris, and in 2,4-d-degradi ...	2004	15066803
sphingomonas sp. strain sb5 degrades carbofuran to a new metabolite by hydrolysis at the furanyl ring.	microorganisms capable of degrading carbofuran were isolated from soils and examined for the degradation of this pesticide at ring structure. an isolate that could degrade carbofuran and carbofuran-7-phenol was selected for further studies. the 16s rrna analysis results showed that the isolate belongs to the genus of sphingomonas, close to dioxin and dicamba degraders, and is named sphingomonas sp. sb5. sb5 did not show any similarity of 16s rrna to known carbofuran degraders. when time-course d ...	2004	15080638
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
origin and diversity of alginate lyases of families pl-5 and -7 in sphingomonas sp. strain a1.	sphingomonas sp. strain a1 has three endotype alginate lyases (a1-i, a1-ii [family pl-7], and a1-iii [family pl-5]), each of which is encoded by a single gene. in addition to those of these lyases, a gene (the a1-ii' gene) showing significant identity with the a1-ii gene was present in the bacterial genome and coded for an alginate lyase with broad substrate specificity. since no expression of a1-ii' was observed even in bacterial cells grown on alginate, the a1-ii' gene was thought to be a sile ...	2004	15090531
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
bacteriophages and insertion sequences of chromobacterium violaceum atcc 12472.	a fluid genome is a great advantage to prokaryotes, enabling quick adaptation to various types of ecological niches and to diverse environmental selective pressures. a substantial portion of these sudden changes is mediated by lateral gene transfer (lgt), through genetic recombination mechanisms, such as transformation, conjugation and transduction. the recent sequencing of several organisms has offered a new approach to the study of lgt, using comparison and analysis of nucleotide sequences dis ...	2004	15100989
bacterial communities associated with flowering plants of the ni hyperaccumulator thlaspi goesingense.	thlaspi goesingense is able to hyperaccumulate extremely high concentrations of ni when grown in ultramafic soils. recently it has been shown that rhizosphere bacteria may increase the heavy metal concentrations in hyperaccumulator plants significantly, whereas the role of endophytes has not been investigated yet. in this study the rhizosphere and shoot-associated (endophytic) bacteria colonizing t. goesingense were characterized in detail by using both cultivation and cultivation-independent te ...	2004	15128517
microbial characterization of organic carrier colonization during a model biofiltration experiment.	dynamic microbial characterization of the colonization of organic carrier during a model biofiltration experiment using methanol as air pollutant.	2004	15130150
structure and function of a hypothetical pseudomonas aeruginosa protein pa1167 classified into family pl-7: a novel alginate lyase with a beta-sandwich fold.	structural and functional analyses of alginate lyases are important in the clarification of the biofilm-dependent ecosystem in pseudomonas aeruginosa and in the development of therapeutic agents for bacterial disease. most alginate lyases are classified into polysaccharide lyase (pl) family-5 and -7 based on their primary structures. family pl-7 enzymes are still poorly characterized especially in structural properties. among family pl-7, a gene coding for a hypothetical protein (pa1167) homolog ...	2004	15136569
heterologous gene expression in thermus thermophilus: beta-galactosidase, dibenzothiophene monooxygenase, pnb carboxy esterase, 2-aminobiphenyl-2,3-diol dioxygenase, and chloramphenicol acetyl transferase.	enzymes from thermophiles are preferred for industrial applications because they generally show improved tolerance to temperature, pressure, solvents, and ph as compared with enzymes from mesophiles. however, nearly all thermostable enzymes used in industrial applications or available commercially are produced as recombinant enzymes in mesophiles, typically escherichia coli. the development of high-temperature bioprocesses, particularly those involving cofactor-requiring enzymes and/or multi-ste ...	2004	15138843
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
catellibacterium nectariphilum gen. nov., sp. nov., which requires a diffusible compound from a strain related to the genus sphingomonas for vigorous growth.	a bacterial strain, designated ast4(t), was isolated from activated sludge. the bacterium did not show significant growth on nutrient broth, but growth was clearly stimulated by addition of supernatant from other bacterial cultures. culture filtrate of a strain related to the genus sphingomonas in particular increased the cell yield and growth rate of strain ast4(t). phylogenetic analysis based on the 16s rrna gene sequences showed that strain ast4(t) is located within the 'rhodobacter group' in ...	2004	15143049
isolation of an exopolysaccharide-producing bacterium, sphingomonas sp. cs101, which forms an unusual type of sphingan.	an exopolysaccharide-producing gram negative bacterium was isolated and determined to be a sphingomonas sp. (cs101). a sugar composition analysis of an exopolysaccharide indicated that the sphingomonas sp. cs101 secreted an exopolysaccharide composed of glucose, mannose, fucose, and rhamnose in the ratio of 2.1:1.1:1.0:0.1, suggesting that this exoplysaccharide is an unusual type of sphingan family. the mean molecular weight of the exopolysaccharide was determined to be 4.2x10(5) da by size excl ...	2004	15170124
cross-species identification of proteins from proteome profiles of the marine oligotrophic ultramicrobacterium, sphingopyxis alaskensis.	sphingopyxis (formerly sphingomonas) alaskensis is a model bacterium for studying adaptation to oligotrophy (nutrient-limitation). it has a unique physiology which is fundamentally different to that of the well studied bacteria such as escherichia coli. to begin to identify the genes involved in its physiological responses to nutrient-limited growth and starvation, we developed high resolution two-dimensional electrophoresis (2-de) methods and determined the identity of 12 proteins from a total ...	2004	15174144
detection and characterization of conjugative degradative plasmids in xenobiotic-degrading sphingomonas strains.	a systematic survey for the presence of plasmids in 17 different xenobiotic-degrading sphingomonas strains was performed. in almost all analyzed strains, two to five plasmids with sizes of about 50 to 500 kb were detected by using pulsed-field gel electrophoresis. a comparison of plasmid preparations untreated or treated with s1 nuclease suggested that, in general, sphingomonas plasmids are circular. hybridization experiments with labeled gene probes suggested that large plasmids are involved in ...	2004	15175300
[bacterial systems of sugar transport].		2003	15176119
overexpression, purification, and characterization of atp-nad kinase of sphingomonas sp. a1.	the nad kinase gene (nadk) of sphingomonas sp. a1 was cloned and then overexpressed in escherichia coli, and the gene product (nadk) was purified from the e. coli cells through five steps with a 25% yield of activity. nadk was a homodimer of 32 kda subunits, utilized atp or other nucleoside triphosphates, but not inorganic polyphosphates, as phosphoryl donors for the phosphorylation of nad, most efficiently at ph 8.0 and 50-55 degrees c, and was designated as atp-nad kinase (nadk). nadk showed n ...	2004	15177293
characterization of degradation process of cyanobacterial hepatotoxins by a gram-negative aerobic bacterium.	a bacterium termed 7cy, capable of decomposing cyanobacterial toxins, was isolated from surface water sample of lake suwa and degradation of microcystin-rr and nodularin-har was investigated. the isolated 7cy was a gram-negative, aerobic bacillus, and a member of a genus sphingomonas. the strain degraded microcystin-ly, -lw, and -lf completely as well as microcystin-lr within 4 days after their addition (6 microg/ml) whereas degradation of nodularin-har did not occur at all during experiment. on ...	2004	15207597
treatment of atrazine by integrating photocatalytic and biological processes.	this research examines the degradation of atrazine by photocatalytic oxidation (pco) under different experimental conditions. deisopropylatrazine, deethylatrazine and deethyldeisopropylatrazine were formed as major intermediates based on gas chromatography-mass spectrometry. the reaction mixture was found to be toxic towards two bioassays, i.e. the microtox and amphipods survival tests even when atrazine was completely degraded by pco within 2 h under optimized conditions. the results indicate t ...	2004	15210274
isolation of adda from microcystin-lr by microbial degradation.	the intact adda was isolated from microcystin-lr by a microbial degradation using an isolated sphingomonas strain, b-9. the reaction of microcystin-lr with cell extract of this strain proceeded smoothly to give the final degradation product by way of two intermediates, linearized microcystin-lr and a tetrapeptide. the purified adda that was structurally characterized using various spectral data did not show the toxicity to mice or inhibition to protein phosphatase activity in contrast to the nat ...	2004	15225569
isolation and characterization of polycyclic aromatic hydrocarbons-degrading sphingomonas sp. strain zl5.	a bacterial strain zl5, capable of growing on phenanthrene as a sole carbon and energy source but not naphthalene, was isolated by selective enrichment from crude-oil-contaminated soil of liaohe oil field in china. the isolate was identified as a sphingomonas sp. strain on the basis of 16s ribosomal dna analysis. strain zl5 grown on phenanthrene exhibited catechol 2,3-dioxygenase (c23o) activity but no catechol 1,2-dioxygenase, gentisate 1,2-dioxygenase, protocatechuate 3,4-dioxygenase and proto ...	2004	15228078