Publications

monitoring by laser-flow-cytometry of the polycyclic aromatic hydrocarbon-degrading sphingomonas sp. strain 107 during biotreatment of a contaminated soil.	a flow cytometric method (fcm) was used to detect and accurately enumerate a polycyclic aromatic hydrocarbon-degrading bacterial strain, sphingomonas sp. 107, inoculated into a soil sample artificially contaminated with pyrene. to compare the fcm method with colony forming unit (cfu) assays, a rifampicin-resistant sphingomonas sp. 107 was obtained which could be distinguished from the indigenous microflora, since there was no organism resistant to rifampicin in the soil that could transform indo ...	2000	10872079
riboprints as a tool for rapid preliminary identification of sphingomonads.	fourtythree strains of the genus sphingomonas and close relatives were subjected to riboprint analyses generated after digestion of genomic dna with the restriction enzyme ecori and hybridization with e. coli rrnb operon. the majority of strains were characterized by a complex banding pattern in the riboprints. high degrees of similarities in the riboprints were only observed among strains of the same species such as s. yanoikuyae, s. aromaticivorans, s. subarctica and s. chlorophenolica. strain ...	2000	10879985
ability of casamino acids to support gellan production by sphingomonas paucimobilis atcc 31461.	the ability of casamino acids and vitamin-assay casamino acids to support gellan production by sphingomonas paucimobilis atcc 31461 was examined in a medium containing glucose or corn syrup as the carbon source relative to yeast extract supplementation. when glucose or corn syrup served as the carbon source, the presence of yeast extract in the growth medium stimulated gellan production by strain atcc 31461 on casamino acids. using vitamin-assay casamino acids as the nitrogen source, the additio ...	2000	10885499
cloning and expression of genes encoding meta-cleavage enzymes from 4,6-dimethyldibenzothiophene-degrading sphingomonas strain tzs-7.	sphingomonas strain tzs-7 was reported as the first strain to have the ability to degrade 4,6-dimethyldibenzothiophene (4,6-dmdbt) by the ring-destructive pathway. two genes for meta-cleavage dioxygenases were cloned from strain tzs-7. expression of each gene showed that one enzyme was specific for 2,3-dihydroxybiphenyl while another was more specific for catechol. the genes for the two enzymes were named dmdc and cata. the analysis of deduced amino acid sequences indicates that cata falls into ...	2000	10899588
isolation and sequence analysis of repa from the incurable 90 mda plasmid of azospirillum brasilense.	an open reading frame encoding a protein of 312 amino acids was identified in an essential region of the 90 mda plasmid of azospirillum brasilense. the putative protein shows similarity with repa proteins of plasmids of sphingomonas aromacitovorans, rhodotermus marinus, chlorobium limicola and bifidobacterium asteroides and with the repa protein of the broad host range plasmid psa. a putative helix-turn-helix motif was identified in the central part of the a. brasilense repa protein. analysis of ...	2000	10902916
degradation of 2,4-dinitrophenol and selected nitroaromatic compounds by sphingomonas sp. ug30.	sphingomonas strain ug30 mineralizes both p-nitrophenol (pnp) and pentachlorophenol (pcp). our current studies showed that ug30 oxidatively metabolized certain other p-substituted nitrophenols, i.e., p-nitrocatechol, 2,4-dinitrophenol (2,4-dnp), and 4,6-dinitrocresol with liberation of nitrite. 2,6-dnp, o- or m-nitrophenol, picric acid, or the herbicide dinoseb were not metabolized. studies using 14c-labelled 2,4-dnp indicated that in glucose-glutamate broth cultures of ug30, greater than 90% of ...	1999	10907421
molecular identification of oligoalginate lyase of sphingomonas sp. strain a1 as one of the enzymes required for complete depolymerization of alginate.	a bacterium, sphingomonas sp. strain a1, can incorporate alginate into cells through a novel abc (atp-binding cassette) transporter system specific to the macromolecule. the transported alginate is depolymerized to di- and trisaccharides by three kinds of cytoplasmic alginate lyases (a1-i [66 kda], a1-ii [25 kda], and a1-iii [40 kda]) generated from a single precursor through posttranslational autoprocessing. the resultant alginate oligosaccharides were degraded to monosaccharides by cytoplasmic ...	2000	10913091
evaluation of fluorescently labeled lectins for noninvasive localization of extracellular polymeric substances in sphingomonas biofilms.	three strains of sphingomonas were grown as biofilms and tested for binding of five fluorescently labeled lectins (con a-type iv-tritc or -cy5, pha-e-tritc, pna-tritc, uea 1-tritc, and wga-texas red). only cona and wga were significantly bound by the biofilms. binding of the five lectins to artificial biofilms made of the commercially available sphingomonas extracellular polysaccharides was similar to binding to living biofilms. staining of the living and artificial biofilms by cona might be exp ...	2000	10919811
unique heme environment at the putative distal region of hydrogen peroxide-dependent fatty acid alpha-hydroxylase from sphingomonas paucimobilis (peroxygenase p450(spalpha).	fatty acid alpha-hydroxylase from sphingomonas paucimobilis is a hydrogen peroxide-dependent cytochrome p450 (p450) enzyme (p450(spalpha)). in this study, heme-ligand exchange reactions of p450(spalpha) were investigated using the optical spectroscopic method and compared with those of various p450s. alkylamines (c >/= 5) induced changes in the spectrum of ferric p450(spalpha) to one typical of a nitrogenous ligand-bound low-spin form of ferric p450, although their affinities were lower than tho ...	2000	10920253
construction of mutants of sphingomonas paucimobilis defective in terminal mannose in the glycosphingolipid.	mutants of sphingomonaspaucimobilis defective in a part of the carbohydrate moiety of the glycosphingolipid (gsl) were constructed by transposon (tn5)-insertional mutagenesis. defective mutants were selected by elisa using the antibody recognizing the tetrasaccharide-type gsl (gsl-4a) of s. paucimobilis. eight defective mutants were selected from about 8,000 kanamycin-resistant strains, and seven of them were found to lack the terminal mannose of gsl-4a. the chemical structure of the mutant gsl ...	2000	10923808
enhanced attachment of bradyrhizobium japonicum to soybean through reduced root colonization of internally seedborne microorganisms.	internally seedborne microorganisms are those surviving common surface sterilization procedures. such microbes often colonize the radicle surface of a germinating soybean (glycine max) seed, introducing an undefined parameter into studies on attachment and infection by bradyrhizobium japonicum. bacterial isolates from surface-sterilized soybean seed, cv. williams 82 and cv. maverick, used in our studies, were identified as agrobacterium radiobacter, aeromonas sp., bacillus spp., chryseomonas lut ...	2000	10932352
identification of bacteria in water for pharmaceutical use.	different systems for the obtention of water used in biopharmaceutical industry were characterized from the bacteriological point of view. determination of aerobic mesophilic microorganisms was performed; as well as the isolation of contaminant microorganisms for what the techniques of membrane filtration was used. for the identification of the more representative species there were made conventional biochemical tests and quick systems: api. the results show that water serving as tap water for p ...	1998	10932743
biocatalytic preparation of a chiral synthon for a vasopeptidase inhibitor: enzymatic conversion of n(2)-	[4s-(4i,7i,10aj)]1-octahydro-5-oxo-4-[phenylmethoxy)carbonyl]amino]-7h-pyrido-[2,1-b] [1,3]thiazepine-7-carboxylic acid methyl ester (bms-199541-01) is a key chiral intermediate for the synthesis of omapatrilat (bms-186716), a new vasopeptidease inhibitor under development. by using a selective enrichment culture technique we have isolated a strain of sphingomonas paucimobilis sc 16113, which contains a novel l-lysine epsilon-aminotransferase. this enzyme catalyzed the oxidation of the epsilon-a ...	2000	10938417
polyphasic assignment of an aromatic-degrading pseudomonas sp., strain dj77, in the genus sphingomonas as sphingomonas chungbukensis sp. nov.	pseudomonas sp. strain dj77, which was described as an aromatic-degrading bacterium, was investigated to clarify its taxonomic position. phylogenetic analysis based on 16s rdna sequences indicated that the strain belonged to the genus sphingomonas and formed a monophyletic clade with the type strains of sphingomonas chlorophenolica, sphingomonas herbicidovorans and sphingomonas yanoikuyae with sequence similarity values of 98.1, 96.1 and 95.6%, respectively. genomic relatedness based on dna-dna ...	2000	10939671
distribution of alkb genes within n-alkane-degrading bacteria.	fifty-four bacterial strains belonging to 37 species were tested for their ability to assimilate short chain and/or medium chain liquid n-alkanes. a gene probe derived from the alkb gene of pseudomonas oleovorans atcc 29347 was utilized in hybridization experiments. results of southern hybridization of pcr-amplificates were compared with those of colony hybridization and dot blot hybridization. strongest signals were received only from gram-negative bacteria growing solely with short n-alkanes ( ...	2000	10971768
[osteomyelitis caused by sphingomonas paucimobilis].		2000	10974775
proposal of sphingomonadaceae fam. nov., consisting of sphingomonas yabuuchi et al. 1990, erythrobacter shiba and shimidu 1982, erythromicrobium yurkov et al. 1994, porphyrobacter fuerst et al. 1993, zymomonas kluyver and van niel 1936, and sandaracinobacter yurkov et al. 1997, with the type genus sphingomonas yabuuchi et al. 1990.	based on the results of phylogenetic analysis of the 16s rdna sequences and the presence of n-2'-hydroxymyristoyl dihydrosphingosine 1-glucuronic acid (sgl-1) and 2-hydroxymyristic acid (non-hydroxymyristic acid in zymomonas) in cellular lipids, a new family, sphingomonadaceae, for group 4 of the alpha-subclass of the class proteobacteria is herein proposed and a description of the family is given. the family consists of six genera, sphingomonas, erythrobacter, erythromicrobium, porphyrobacter, ...	2000	10981829
identification of a serine hydrolase which cleaves the alicyclic ring of tetralin.	a gene designated thnd, which is required for biodegradation of the organic solvent tetralin by sphingomonas macrogoltabidus strain tfa, has been identified. sequence comparison analysis indicated that thnd codes for a carbon-carbon bond serine hydrolase showing highest similarity to hydrolases involved in biodegradation of biphenyl. an insertion mutant defective in thnd accumulates the ring fission product which results from the extradiol cleavage of the aromatic ring of dihydroxytetralin. the ...	2000	10986248
regioselectivity and enantioselectivity of naphthalene dioxygenase during arene cis-dihydroxylation: control by phenylalanine 352 in the alpha subunit.	the naphthalene dioxygenase (ndo) system catalyzes the first step in the degradation of naphthalene by pseudomonas sp. strain ncib 9816-4. the enzyme has a broad substrate range and catalyzes several types of reactions including cis-dihydroxylation, monooxygenation, and desaturation. substitution of valine or leucine at phe-352 near the active site iron in the alpha subunit of ndo altered the stereochemistry of naphthalene cis-dihydrodiol formed from naphthalene and also changed the region of ox ...	2000	10986254
identification of novel metabolites in the degradation of phenanthrene by sphingomonas sp. strain p2.	sphingomonas sp. strain p2, which is capable of utilizing phenanthrene as a sole carbon and energy source, was isolated from petroleum-contaminated soil in thailand. gas chromatography-mass spectrometry and (1)h and (13)c nuclear magnetic resonance analyses revealed two novel metabolites from the phenanthrene degradation pathway. one was identified as 5,6-benzocoumarin, which was derived by dioxygenation at the 1- and 2-positions of phenanthrene, and the other was determined to be 1,5-dihydroxy- ...	2000	11004408
enhanced degradation of hexachlorocyclohexane isomers by sphingomonas paucimobilis.	hexachlorocyclohexane (hch) has been banned for use in technologically advanced countries; however, it is still in use in tropical countries like india. earlier we reported the degradation of hch isomers by sphingomonas paucimobilis within 12 days of incubation. here we report the role of different factors that could enhance the degradation rate of hch isomers. we found that an increase in the cell number from 10(2) to 10(8) cells/ml resulted in an increased degradation rate of hch isomers viz. ...	2000	11014865
alginate lyase: review of major sources and enzyme characteristics, structure-function analysis, biological roles, and applications.	alginate lyases, characterized as either mannuronate (ec 4.2.2.3) or guluronate lyases (ec 4.2.2.11), catalyze the degradation of alginate, a complex copolymer of alpha-l-guluronate and its c5 epimer beta-d-mannuronate. lyases have been isolated from a wide range of organisms, including algae, marine invertebrates, and marine and terrestrial microorganisms. this review catalogs the major characteristics of these lyases, the methods for analyzing these enzymes, as well as their biological roles. ...	2000	11018131
gellan gum.	for decades microbial exopolysaccharides have been invaluable ingredients in the food industry, as well as having many attractive pharmaceutical and chemical applications. gellan gum is a comparatively new gum elaborated by the gram-negative bacterium sphingomonas paucimobilis. although its physico-chemical properties have been well characterized, the ecology and physiology of sphingomonas, and the factors influencing the fermentation process for production of this gum have received much less at ...	2000	11039329
microbial degradation of phenanthrene by addition of a sophorolipid mixture.	the influence of sophorolipids on microbial degradation of poorly soluble phenanthrene in liquid and soil suspension culture was evaluated in the work presented. experiments were carried out in two parts. in the first part, important basic physico-chemical characteristics of the biosurfactant and the pollutant used were determined. the critical micelle concentration (cmc) and the solubilization ratio of the biosurfactant were found to be in a good range compared with synthetic surfactants. also, ...	2000	11051416
characterization of sphingomonas isolates from finnish and swedish drinking water distribution systems.	sphingomonas species were commonly isolated from biofilms in drinking water distribution systems in finland (three water meters) and sweden (five water taps in different buildings). the sphingomonas isolates (n = 38) were characterized by chemotaxonomic, physiological and phylogenetic methods. fifteen isolates were designated to species sphingomonas aromaticivorans, seven isolates to s. subterranea, two isolates to s. xenophaga and one isolate to s. stygia. thirteen isolates represented one or m ...	2000	11054174
lipid composition and taxonomy of [pseudomonas] echinoides: transfer to the genus sphingomonas.	lipid components of [pseudomonas] echinoides ncimb 9420 have been studied as an aid to taxonomic relocation of the organism. non-polar lipids include the carotenoid nostoxanthin and the ubiquinone q-10. the major fatty acids are cis-vaccenic acid [18:1(11c)], hexadecanoic acid (16:0) and 2-hydroxy-tetradecanoic acid (2-oh-14:0), but 11-methyloctadec-11-enoic acid[11-me-18:1(11)] is a significant minor component. the preponderant phospholipids are phosphatidylethanolamine and phosphatidylglycerol ...	2000	11065379
genetic and biochemical characterization of 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase and its role in the protocatechuate 4,5-cleavage pathway in sphingomonas paucimobilis syk-6.	protocatechuate (pca) is the key intermediate metabolite in the lignin degradation pathway of sphingomonas paucimobilis syk-6 and is metabolized to pyruvate and oxaloacetate via the pca 4,5-cleavage pathway. we characterized the 4-carboxy-2-hydroxymuconate-6-semialdehyde (chms) dehydrogenase gene (ligc). chms is the 4,5-cleavage product of pca and is converted into 2-pyrone-4,6-dicarboxylate (pdc) by ligc. we found that ligc was located 295 bp downstream of ligb, which encodes the large subunit ...	2000	11073908
crystal structure of the haloalkane dehalogenase from sphingomonas paucimobilis ut26.	the haloalkane dehalogenase from sphingomonas paucimobilis ut26 (linb) is the enzyme involved in the degradation of the important environmental pollutant gamma-hexachlorocyclohexane. the enzyme hydrolyzes a broad range of halogenated cyclic and aliphatic compounds. here, we present the 1.58 a crystal structure of linb and the 2.0 a structure of linb with 1,3-propanediol, a product of debromination of 1,3-dibromopropane, in the active site of the enzyme. the enzyme belongs to the alpha/beta hydro ...	2000	11087355
the 4-oxalomesaconate hydratase gene, involved in the protocatechuate 4,5-cleavage pathway, is essential to vanillate and syringate degradation in sphingomonas paucimobilis syk-6.	sphingomonas paucimobilis syk-6 is able to grow on various dimeric lignin compounds, which are converted to vanillate and syringate by the actions of unique lignin degradation enzymes in this strain. vanillate and syringate are degraded by the o-demethylase and converted into protocatechuate (pca) and 3-o-methylgallate (3mga), respectively. pca is further degraded via the pca 4,5-cleavage pathway, while the results suggested that 3mga is degraded through another pathway in which pca 4,5-dioxygen ...	2000	11092855
evidence for a role of rpoe in stressed and unstressed cells of marine vibrio angustum strain s14.	we report the cloning, sequencing, and characterization of the rpoe homolog in vibrio angustum s14. the rpoe gene encodes a protein with a predicted molecular mass of 19.4 kda and has been demonstrated to be present as a single-copy gene by southern blot analysis. the deduced amino acid sequence of rpoe is most similar to that of the rpoe homolog of sphingomonas aromaticivorans, sigma(24), displaying sequence similarity and identity of 63 and 43%, respectively. northern blot analysis demonstrate ...	2000	11092857
apparent contradiction: psychrotolerant bacteria from hydrocarbon-contaminated arctic tundra soils that degrade diterpenoids synthesized by trees.	resin acids are tricyclic terpenoids occurring naturally in trees. we investigated the occurrence of resin acid-degrading bacteria on the arctic tundra near the northern coast of ellesmere island (82 degrees n, 62 degrees w). according to most-probable-number assays, resin acid degraders were abundant (10(3) to 10(4) propagules/g of soil) in hydrocarbon-contaminated soils, but they were undetectable (<3 propagules/g of soil) in pristine soils from the nearby tundra. plate counts indicated that t ...	2000	11097882
profile of a nonylphenol-degrading microflora and its potential for bioremedial applications.	nonylphenol (np) is an important intermediate in the production of various commercial and industrial materials, but is also known as a ubiquitous pollutant in urban aquatic environments. we recently studied the np-degrading activities of microflora in several aquatic environments, and found a notable degrading activity for wastewater from a sewage treatment plant in tokyo. this result led us to isolate np-degrading microbes and identify biodegradation products. using conventional plate culture t ...	2000	11098132
reaction mechanism and stereochemistry of gamma-hexachlorocyclohexane dehydrochlorinase lina.	gamma-hexachlorocyclohexane dehydrochlorinase (lina) catalyzes the initial steps in the biotransformation of the important insecticide gamma-hexachlorocyclohexane (gamma-hch) by the soil bacterium sphingomonas paucimobilis ut26. stereochemical analysis of the reaction products formed during conversion of gamma-hch by lina was investigated by gc-ms, nmr, cd, and molecular modeling. the nmr spectra of 1,3,4,5,6-pentachlorocyclohexene (pcch) produced from gamma-hch using either enzymatic dehydrochl ...	2001	11099497
preparation of (s)-n-substituted 4-hydroxy-pyrrolidin-2-ones by regio- and stereoselective hydroxylation with sphingomonas sp. hxn-200.	[reaction: see text] enantiopure (s)-n-substituted 4-hydroxy-pyrrolidin-2-ones have been prepared for the first time by regio- and stereoselective hydroxylation of the corresponding pyrrolidin-2-ones by use of a biocatalyst. hydroxylation of 6 and 8 with sphingomonas sp. hxn-200 afforded 68% of (s)-7 in >99.9% ee and 46% of (s)-9 in 92% ee, respectively. simple crystallization increased the ee of (s)-9 to 99. 9% in 82% yield.	2000	11101461
isolation of bacteria from toxic dinoflagellate alexandrium minutum and their effects on algae toxicity.	attempts were made to isolate the bacteria from toxic dinoflagellate alexandrium minutum t1 and to study the effect of these bacteria on the growth and toxicity of a. minutum t1. it was found that intracellular bacterial species including pasteurella haemolytica, pseudomonas vesicularis, and sphingomonas sp., and extracellular bacterial species including pasteurolla pneumotropica, morganella wisconsensis, flavobacterium oryzihabitans, pseudomonas pseudomallei, and sphingomonas sp. all of them we ...	2000	11126517
identification of four structural genes and two putative promoters necessary for utilization of naphthalene, phenanthrene, fluoranthene by sphingomonas paucimobilis var. epa505.	sphingomonas paucimobilis var. epa505 utilizes fluoranthene (fla), naphthalene (nap), and phenanthrene (phe) as sole carbon sources for energy and growth. a genetic library of epa505 was constructed using mini-tn5 promoter reporter genes encoding for tetracycline resistance (tc(p-)) or luminescence (luxab(p-)). out of 2250 tn5 mutants, ten were deficient in utilization of fla, nap, and/or phe as sole carbon sources. three classes of tn5 mutants were defined: classi (nap(-)phe(-)fla(-)), classii ...	2000	11137301
alpha- and beta-proteobacteria control the consumption and release of amino acids on lake snow aggregates.	we analyzed the composition of aggregate (lake snow)-associated bacterial communities in lake constance from 1994 until 1996 between a depth of 25 m and the sediment surface at 110 m by fluorescent in situ hybridization with rrna-targeted oligonucleotide probes of various specificity. in addition, we experimentally examined the turnover of dissolved amino acids and carbohydrates together with the microbial colonization of aggregates formed in rolling tanks in the lab. generally, between 40 and m ...	2001	11157226
biochemical characterization of broad-specificity enzymes using multivariate experimental design and a colorimetric microplate assay: characterization of the haloalkane dehalogenase mutants.	the ph indicator dye-based colorimetric method and multivariate experimental design were used for the systematic biochemical characterization of the broad-specificity enzymes haloalkane dehalogenases. halogenated compounds for characterization of the enzymes were selected using principal component analysis. the substrates were characterised by 24 physico-chemical and structural descriptors. thirty-four substrates were selected for testing out of 194 halogenated compounds. relative activities det ...	2001	11165344
new broad-host-range promoter probe vectors based on the plasmid rk2 replicon.	broad-host-range plasmid rk2-based promoter probe vectors with a known nucleotide sequence were constructed. in the absence of an upstream promoter, the expression of two tested reporter genes (luc and lacz) in escherichia coli was virtually zero, while insertion of the ptrc promoter resulted in strong inducer-dependent expression. the lacz-based vectors were mobilized into pseudomonas fluorescens st, pseudomonas putida kt2442, sphingomonas spp. and burkholderia spp. lb400, and expression analys ...	2001	11167001
a simple and easy method for the monitoring of environmental pollutants using oligotrophic bacteria.	sphingomonas paucimobilis kps01, an oligotrophic bacterium isolated from soil, may be a useful tool for monitoring heavy metals. previous methods relying on counting of viable cells require a relatively long time and some skill; we have developed a method based on optical density (o.d.) measurements which is significantly faster and does not require skilled personnel. the results of the o.d. and viable count methods were consistent; both methods detected heavy metals at concentrations ranging fr ...	2001	11169034
formation of the metabolic intermediate 2,4,4-trimethyl-2-pentanol during incubation of a sphingomonas sp. strain with the xeno-estrogenic octylphenol.	degradation of branched octylphenol was studied in a bacterial culture of a sphingomonas sp. strain. octylphenol is considered to be the most stable degradation intermediate formed from the corresponding nonionic octylphenol polyethoxylates surfactants during biological wastewater treatment. since octylphenol can exert estrogenic effects in wildlife, a detailed study of its biodegradation is warranted. the aerobic microbiological transformation of octylphenol was examined with and without the ad ...	2000	11194969
identification of the metabolically active members of a bacterial community in a polychlorinated biphenyl-polluted moorland soil.	the presumptive metabolically active members of a bacterial community in a moorland soil in germany, highly polluted with polychlorinated biphenyls (pcbs), were identified by sequencing of cloned reverse transcription-polymerase chain reaction (rt-pcr) amplification products of 16s rrna generated from total rna extracts. analysis of the 16s rrna clone library revealed a considerable diversity of metabolically active bacteria in the soil, despite the acidic ph and high concentrations of pcbs. clo ...	1999	11207739
sphingomonas alaskensis sp. nov., a dominant bacterium from a marine oligotrophic environment.	seven gram-negative strains, isolated in 1990 from a 10(6)-fold dilution series of seawater from resurrection bay, a deep fjord of the gulf of alaska, were identified in a polyphasic taxonomic study. analysis of 16s rdna sequences and dna-homology studies confirmed the phylogenetic position of all strains in the genus sphingomonas and further indicated that all of the strains constitute a single homogeneous genomic species, distinct from all validly described sphingomonas species. the ability to ...	2001	11211276
preferential occurrence of diazotrophic endophytes, azoarcus spp., in wild rice species and land races of oryza sativa in comparison with modern races.	several diazotrophic species of azoarcus spp. occur as endophytes in the pioneer plant kallar grass. the purpose of this study was to screen asian wild rice and cultivated oryza sativa varieties for natural association with these endophytes. populations of culturable diazotrophs in surface-sterilized roots were characterized by 16s rdna sequence analysis, and azoarcus species were identified by genomic fingerprints. a. indigens and azoarcus sp. group c were detected only rarely, whereas azoarcus ...	2000	11220300
specific growth rate plays a critical role in hydrogen peroxide resistance of the marine oligotrophic ultramicrobacterium sphingomonas alaskensis strain rb2256.	the marine oligotrophic ultramicrobacterium sphingomonas alaskensis rb2256 has a physiology that is distinctly different from that of typical copiotrophic marine bacteria, such as vibrio angustum s14. this includes a high level of inherent stress resistance and the absence of starvation-induced stress resistance to hydrogen peroxide. in addition to periods of starvation in the ocean, slow, nutrient-limited growth is likely to be encountered by oligotrophic bacteria for substantial periods of tim ...	2001	11229924
horizontal transfer of an exopolymer complex from one bacterial species to another.	alasan, the exocellular polymeric emulsifier produced by acinetobacter radioresistens ka53 was shown to bind to the surface of sphingomonas paucimobilis epa505 and acinetobacter calcoaceticus rag-1. the presence of alasan on the surface of s. paucimobilis epa505 and a. calcoaceticus rag-1 caused a decrease in their cell-surface hydrophobicities. binding was proportional to the concentration of recipient cells and input alasan. at the highest concentration of a. calcoaceticus rag-1 (4 x 10(9) ml( ...	2000	11234924
an evaluation of terminal-restriction fragment length polymorphism (t-rflp) analysis for the study of microbial community structure and dynamics.	a systematic evaluation of the value and potential of terminal-restriction fragment length polymorphism (t-rflp) analysis for the study of microbial community structure has been undertaken. the reproducibility and robustness of the method has been assessed using environmental dna samples isolated directly from pcb-polluted or pristine soil, and subsequent polymerase chain reaction (pcr) amplification of total community 16s rdna. an initial investigation to assess the variability both within and ...	2000	11243261
crystal structure of alginate lyase a1-iii complexed with trisaccharide product at 2.0 a resolution.	the structure of a1-iii from a sphingomonas species a1 complexed with a trisaccharide product (4-deoxy-l-erythro-hex-4-enepyranosyluronate-mannuronate-mannuronic acid) was determined by x-ray crystallography at 2.0 a with an r-factor of 0.16. the final model of the complex form comprising 351 amino acid residues, 245 water molecules, one sulfate ion and one trisaccharide product exhibited a c(alpha) r.m.s.d. value of 0.154 a with the reported apo form of the enzyme. the trisaccharide was bound i ...	2001	11243798
altering catalytic properties of 3-chlorocatechol-oxidizing extradiol dioxygenase from sphingomonas xenophaga bn6 by random mutagenesis.	the 2,3-dihydroxybiphenyl 1,2-dioxygenase from sphingomonas xenophaga strain bn6 (bphc1) oxidizes 3-chlorocatechol by a rather unique distal ring cleavage mechanism. in an effort to improve the efficiency of this reaction, bphc1 was randomly mutated by error-prone pcr. mutants which showed increased activities for 3-chlorocatechol were obtained, and the mutant forms of the enzyme were shown to contain two or three amino acid substitutions. variant enzymes containing single substitutions were con ...	2001	11244073
molecular organization of the ribosomal rna transcription unit and the phylogenetic study of zymomonas mobilis zm4.	previously we reported that zymomonas mobilis zm4 contains three ribosomal transcription units (rrna to c operons) which are clustered around the 50 min region, paci fragments 13 and 6, on the physical map of z. mobilis zm4 [kang, h. l. and kang, h. s. (1998) gene 206, 223-228]. the physical map reveals that the rrna gene set is located on the 76 kb paci fragment 13. the complete nucleotide sequence of the rrna gene set has been determined. the total number of nucleotides of the rrna gene set is ...	2001	11266123
a water-soluble homodimeric serine palmitoyltransferase from sphingomonas paucimobilis ey2395t strain. purification, characterization, cloning, and overproduction.	serine palmitoyltransferase (spt, ec ) is a key enzyme in sphingolipid biosynthesis and catalyzes the decarboxylative condensation of l-serine and palmitoyl-coenzyme a to 3-ketodihydrosphingosine. we found that the gram-negative obligatory aerobic bacteria sphingomonas paucimobilis ey2395(t) have significant spt activity and purified spt to homogeneity. this enzyme is a water-soluble homodimeric protein unlike eukaryotic enzymes, known as heterodimers composed of tightly membrane-bound subunits, ...	2001	11279212
a rapid method to screen degradation ability in chlorophenoxyalkanoic acid herbicide-degrading bacteria.	an agar medium containing a range of related chlorophenoxyalkanoic acid herbicides, 2,4-dichlorophenoxyacetic acid (2,4-d), 2-methyl-4-chlorophenoxyacetic acid (mcpa), racemic mecoprop, (r)-mecoprop and racemic 2,4-dp (2-(2,4-dichlorophenoxy) propionic acid) was developed to assess the catabolic activity of a range of degradative strains.	2001	11298940
proposal of sphingomonas wittichii sp. nov. for strain rw1t, known as a dibenzo-p-dioxin metabolizer.	a polyphasic taxonomic study was performed on sphingomonas sp. strain rw1t. the organism was isolated from water of the river elbe and has been known as a potent metabolizer of dibenzo-p-dioxin and its relatives. tlc of a mild alkaline hydrolysate of extractable cellular lipids of strain rw1t and type strains of 21 sphingomonas species gave a spot of sphingoglycolipid (sgl)-1 (glucuronosyl ceramide), which is characteristic of sphingomonads. in addition, strain rw1t and type strains of three sph ...	2001	11321072
sphingomonas cloacae sp. nov., a nonylphenol-degrading bacterium isolated from wastewater of a sewage-treatment plant in tokyo.	a nonylphenol-assimilating bacterium isolated at a sewage-treatment plant in tokyo was studied phenotypically, genotypically and phylogenetically. analysis of the 16s rdna sequence, the g+c content of the dna (63 mol%) and the isoprenoid quinone composition, as well as the presence of sphingoglycolipid and the whole-cell fatty acid profile, revealed that the isolate is a member of the genus sphingomonas. however, the sequence similarity of the 16s rdna with that of known sphingomonas spp. was fo ...	2001	11321106
isolation and characterization of the genes encoding a novel oxygenase component of angular dioxygenase from the gram-positive dibenzofuran-degrader terrabacter sp. strain dbf63.	a gram-positive bacterium terrabacter sp. strain dbf63 is able to degrade dibenzofuran (df) via initial dioxygenation by a novel angular dioxygenase. the dbfa1 and dbfa2 genes, which encode the large and small subunits of the dibenzofuran 4,4a-dioxygenase (dfdo), respectively, were isolated by a polymerase chain reaction-based method. dbfa1 and dbfa2 showed moderate homology to the large and small subunits of other ring-hydroxylating dioxygenases (less than 40%), respectively, and some motifs su ...	2001	11322788
enzymatic synthesis of chiral intermediates for omapatrilat, an antihypertensive drug.	biocatalytic processes were used to prepare chiral intermediates required for the synthesis of omapatrilat 1 by three different routes. the synthesis and enzymatic conversion of 2-keto-6-hydroxyhexanoic acid 3 to l-6-hydroxynorleucine 2 was demonstrated by reductive amination using beef liver glutamate dehydrogenase. to avoid the lengthy chemical synthesis of the ketoacid 3, a second route was developed to prepare the ketoacid by treatment of racemic 6-hydroxy norleucine [readily available from ...	2001	11337276
fluoranthene-2,3- and -1,5-diones are novel products from the bacterial transformation of fluoranthene.	fluoranthene is one of the predominant compounds found in soils and sediments contaminated with polycyclic aromatic hydrocarbons (pah). four bacterial strains isolated from pah-contaminated soils transformed fluoranthene to a number of products during growth on phenanthrene, including the novel metabolites fluoranthene-2,3-dione (f23q) and fluoranthene-1,5-dione (f15q). given the known toxicity and mutagenicity of f23q, we focused on characterizing this metabolite with respect to its effects on ...	2001	11351535
molecular detection of marine bacterial populations on beaches contaminated by the nakhodka tanker oil-spill accident.	in january 1997, the tanker nakhodka sank in the japan sea, and more than 5000 tons of heavy oil leaked. the released oil contaminated more than 500 km of the coastline, and some still remained even by june 1999. to investigate the long-term influence of the nakhodka oil spill on marine bacterial populations, sea water and residual oil were sampled from the oil-contaminated zones 10, 18, 22 and 29 months after the accident, and the bacterial populations in these samples were analysed by denaturi ...	2001	11359510
aminopeptidase from sphingomonas capsulata.	a novel aminopeptidase with unique substrate specificity was purified from a culture broth of sphingomonas capsulata. this is the first reported aminopeptidase to demonstrate broad substrate specificity and yet release glycine and alanine with the highest efficacy. on a series of pentapeptide amides with different n-terminal amino acids, this enzyme efficiently releases glycine, alanine, leucine, proline, and glutamate with the lowest turnover value of 370 min(-1) for glutamate. at ph 7.5 (ph op ...	2001	11359790
isolation and characterization of polycyclic aromatic hydrocarbon-degrading bacteria associated with the rhizosphere of salt marsh plants.	polycyclic aromatic hydrocarbon (pah)-degrading bacteria were isolated from contaminated estuarine sediment and salt marsh rhizosphere by enrichment using either naphthalene, phenanthrene, or biphenyl as the sole source of carbon and energy. pasteurization of samples prior to enrichment resulted in isolation of gram-positive, spore-forming bacteria. the isolates were characterized using a variety of phenotypic, morphologic, and molecular properties. identification of the isolates based on their ...	2001	11375181
crystallization and preliminary x-ray analysis of algs, a bacterial atp-binding cassette (abc) protein specific to macromolecule import.	sphingomonas sp. a1 possesses a macromolecule (alginate; average molecular size 25 700 da) uptake system mediated by a novel pit-dependent abc transporter. in this system, algs (363 amino-acid residues; 40 kda) functions as an atpase and provides energy for the translocation of high molecular-weight alginate across the cytoplasmic membrane. hexahistidine-tagged algs of sphingomonas sp. a1 was overexpressed in escherichia coli and crystallized by means of the hanging-drop vapour-diffusion method ...	2001	11375517
time-resolved study of biofilm architecture and transport processes using experimental and simulation techniques: the role of eps.	cellular material and extracellular polymeric substances are the basic structural elements in biofilm systems. the structure and role of eps for biofilm development and metabolic processes have not been precisely determined and, therefore, have not yet been included as a necessary element in modelling and simulation studies. this is due to the difficulty of experimentally detecting the extracellular polymeric substances in situ and differentiating them from cellular material on the one hand, and ...	2001	11381960
location of o-acetyl groups in s-657 using the reductive-cleavage method.	a two-step procedure is described in this paper to identify the position of o-acetyl groups in s-657 polysaccharide. reductive-cleavage experiments performed on the fully methylated (base-catalyzed) polysaccharide, followed by acetylation of anhydroalditols, identified individual sugar residues and their position of linkage. in a second experiment, the polysaccharide was methylated under neutral conditions leaving native acetate groups intact. reductive cleavage of the neutral methylated polysac ...	2001	11383896
structural studies of s-7, another exocellular polysaccharide containing 2-deoxy-arabino-hexuronic acid.	the exocellular polysaccharide s-7, a heteropolysaccharide from azotobacter indicus var. myxogenes has been studied using methylation analysis, smith degradation, partial acid hydrolysis, nmr spectroscopy and mass spectrometry as the principal methods. it is concluded that the repeating unit has the following structure: [structure: see text] the absolute configuration of the deoxyhexuronic acid was deduced from 1h nmr chemical shifts and is most likely d. approximately two o-acetyl groups per re ...	2001	11383898
influence of the nonionic surfactant brij 35 on the bioavailability of solid and sorbed dibenzofuran.	the effect of the nonionic surfactant brij 35 on the bioavailability of solid and teflon-sorbed dibenzofuran for sphingomonas sp. strain hh19k was studied in simple model systems. growth with dibenzofuran and dibenzofuran-specific oxygen uptake in surfactant-free media and with brij 35 above the critical micelle concentration (cmc) were compared with dissolution and desorption in the absence of bacteria. brij 35 accelerated dissolution and biodegradation of solid dibenzofuran by a factor of 2. i ...	2001	11393985
psychrobacter proteolyticus sp. nov., a psychrotrophic, halotolerant bacterium isolated from the antarctic krill euphausia superba dana, excreting a cold-adapted metalloprotease.	an antarctic marine bacterium (strain 116) excreting an extracellular cold-adapted metalloprotease was subjected to a detailed polyphasic taxonomic investigation. strain 116 was previously isolated from the stomach of a specimen of the antarctic krill euphasia superba dana and tentatively characterized as sphingomonas paucimobilis 116. the 16s rdna sequence analysis showed that the strain is in fact related to species of the genus psychrobacter, next to psychrobacter glacincola (97.4% similarity ...	2001	11403398
sphingomonas pituitosa sp. nov., an exopolysaccharide-producing bacterium that secretes an unusual type of sphingan.	strain edivt, an exopolysaccharide-producing bacterium, was subjected to polyphasic characterization. the bacterium produced copious amounts of an extracellular polysaccharide, forming slimy, viscous, intensely yellow-pigmented colonies on czapek-dox (czd) agar. the culture fluids of the liquid version of czd medium were highly viscous after cultivation for 5 d. cells of strain edivt were gram-negative, catalase-positive, oxidase-negative, nonspore-forming, rod-shaped and motile. comparisons of ...	2001	11411704
structural analysis of a new glycosphingolipid from the lipopolysaccharide-lacking bacterium sphingomonas adhaesiva.	a new glycosphingolipid, gsl-4b, was isolated from sphingomonas adhaesiva and found to share the ceramide moiety with gsl-1 and gsl-3 from sphingomonas capsulata studied earlier [kawahara, k.; moll, h.; knirel, y. a.; seydel, u.; zähringer, u. eur. j. biochem. 2000, 267, 1837-1846]. it is heterogeneous with respect to the long-chain bases erythro-2-amino-1,3-octadecanediol (sphinganine), (13z)-erythro-2-amino-13-eicosene-1,3-diol, and (13z)-erythro-2-amino-13,14-methylene-1,3-eicosanediol which ...	2001	11423114
preface to special issue on sphingomonas.		1999	11423938
chlorophenol and nitrophenol metabolism by sphingomonas sp ug30.	sphingomonas sp ug30 is a pentachlorophenol (pcp)-degrading bacterial strain capable of degrading several nitrophenolic compounds, including p-nitrophenol (pnp), 2,4-dinitrophenol (2,4-dnp), p-nitrocatechol and 4,6-dinitro-o-cresol (dnoc). the ability to degrade both chlorophenolic and nitrophenolic compounds is probably not restricted to ug30, but may also be possessed by other pentachlorophenol-degrading sphingomonas spp. the interesting question arises as to whether there is any point of conv ...	1999	11423939
chemotaxonomic characterisation of sphingomonas.	based on published results and investigations done for this study, chemotaxonomic characteristics of all validly described species of the genus sphingomonas, as well as unnamed strains of this genus and related genera such as rhizomonas and blastomonas, are presented. all representatives of this group, here designated as sphingomonads, contain ubiquinone (q-10). the two different polyamine patterns characterized either by the predominant polyamine sym-homospermidine or spermidine separate the sp ...	1999	11423940
detection of sphingomonas spp in soil by pcr and sphingolipid biomarker analysis.	sphingomonas spp possess unique abilities to degrade refractory contaminants and are found ubiquitously in the environment. we developed sphingomonas genus-specific pcr primers (spf-190 and spr1-852) which showed specific amplification of a 627-bp 16s rdna fragment from sphingomonas spp. a pcr assay using these sphingomonas specific primers was developed to detect sphingomonas aromaticivorans b0695r in three texturally distinct soil types, showing detection limits between 1.3-2.2 x 10(3) cfu g(- ...	1999	11423941
detection of sphingomonads and in situ identification in activated sludge using 16s rrna-targeted oligonucleotide probes.	the increasing significance of members of the genus sphingomonas in biotechnological applications has led to an increased interest in the diversity, abundance and ecophysiological potential of this group of gram-negative bacteria. this general focus provides a challenge to improve means for identification of sphingomonads; eg molecular genetic methods for rapid and specific detection could facilitate screening of new isolates. here, fluorescently labeled oligonucleotide probes targeted against 1 ...	1999	11423942
sphingomonads from marine environments.	sphingomonas species play an important role in the ecology of a range of marine habitats. isolates and 16s-rrna clones have been obtained from corals, natural and artificial sources of marine hydrocarbons and eutrophic and oligotrophic waters, and have been isolated as hosts for marine phages. in addition they are found in oceans spanning temperature ranges from polar to temperate waters. while less is known about marine sphingomonads in comparison to their terrestrial counterparts, their import ...	1999	11423943
ecology, physiology, and phylogeny of deep subsurface sphingomonas sp.	several new species of the genus sphingomonas including s. aromaticivorans, s. stygia, and s. subterranea that have the capacity for degrading a broad range of aromatic compounds including toluene, naphthalene, xylenes, p-cresol, fluorene, biphenyl, and dibenzothiophene, were isolated from deeply-buried (>200 m) sediments of the us atlantic coastal plain (acp). in s. aromaticivorans f199, many of the genes involved in the catabolism of these aromatic compounds are encoded on a 184-kb conjugative ...	1999	11423944
beijerinckia sp strain b1: a strain by any other name.	beijerinckia sp strain b1 grows with biphenyl as its sole source of carbon and energy. a mutant, strain b8/36, oxidized biphenyl to cis-(2s,3r)-dihydroxy-l-phenylcyclohexa-4,6-diene (cis-biphenyl dihydrodiol). strain b8/36 oxidized anthracene, phenanthrene, benz[a]anthracene and benzo[a]pyrene to cis-dihydrodiols. other substrates oxidized to cis-dihydrodiols were dibenzofuran, dibenzothiophene and dibenzo-p-dioxin. biphenyl dioxygenase activity was observed in cells of beijerinckia b1 and b8/36 ...	1999	11423945
functional analysis of genes involved in biphenyl, naphthalene, phenanthrene, and m-xylene degradation by sphingomonas yanoikuyae b1.	sphingomonas yanoikuyae b1 is able to utilize toluene, m-xylene, p-xylene, biphenyl, naphthalene, phenanthrene, and anthracene as sole sources of carbon and energy for growth. a forty kilobase region of dna containing most of the genes for the degradation of these aromatic compounds was previously cloned and sequenced. insertional inactivation of bphc results in the inability of b1 to grow on both polycyclic and monocyclic compounds. complementation experiments indicate that the metabolic block ...	1999	11423946
induction of aromatic catabolic activity in sphingomonas aromaticivorans strain f199.	enzyme induction studies with sphingomonas aromaticivorans f199 demonstrated that both toluene and naphthalene induced expression of both naphthalene and toluene catabolic enzymes. however, neither aromatic compound induced expression of all the enzymes required for complete mineralization of either naphthalene or toluene. activity measurements in combination with gene sequence analyses indicate that growth on either aromatic substrate in the absence of the other is, therefore, sub-optimal and i ...	1999	11423947
sphingomonas paucimobilis bpsi-3 mutant an2 produces a red catabolite during biphenyl degradation.	the biphenyl degradation pathway of sphingomonas paucimobilis bpsi-3 was investigated using a degradation-deficient mutant generated by 1-methyl-3-nitro-1-nitrosoguanidine (ntg) mutagenesis. the mutant, designated an2, was confirmed as originating from bpsi-3 through the use of eric (enterobacterial repetitive intergenic consensus) pcr and by detection of the diagnostic pigment, nostoxanthin, in cellular methanol extracts. mutant an2 produced a yellow followed by red extracellular substance when ...	1999	11423948
phylogeny of sphingomonas species that degrade pentachlorophenol.	four pentachlorophenol (pcp)-degrading bacteria isolated from geographically diverse areas have been examined in detail as regards their physiology and phylogeny. according to traditional biochemical methods, these strains had been classified as members of the genera arthrobacter, flavobacterium, pseudomonas, and sphingomonas. the pcp degradation pathway has been studied extensively in sphingomonas (flavobacterium) sp strain atcc 39723 and the first three degradation steps catalyzed by a pcp-4-m ...	1999	11423949
colonization of contaminated soil by an introduced bacterium: effects of initial pentachlorophenol levels on the survival of sphingomonas chlorophenolica strain ra2.	the survival of a sphingomonas species that was introduced into pentachlorophenol (pcp)-contaminated soil was monitored with two complementary methods, a respiration-based assay and a most probable number (mpn) technique. sphingomonas chlorophenolicastrain ra2 is a pcp-mineralizing bacterium that was introduced into soil contaminated with a range of pcp concentrations (0-300 &mgr;g pcp g(-1) soil). the population of introduced microorganisms was followed for 170 days using a substrate-induced gr ...	1999	11423950
degradation of the phenoxy acid herbicide diclofop-methyl by sphingomonas paucimobilis isolated from a canadian prairie soil.	sphingomonas paucimobilis, isolated from a soil in manitoba, canada, was able to utilize diclofop-methyl, (r,s)-methyl-2-[4-(2,4-dichlorophenoxy)phenoxy]propionate, as the sole source of carbon and energy. an actively growing aerobic culture completely degraded 1.5 &mgr;g diclofop-methyl ml(-1) to diclofop acid within 54 h, at 25 degrees c. a biphasic growth pattern indicated that this organism was capable of degrading diclofop acid to 4-(2,4-dichlorophenoxy)phenol and 2,4-dichlorophenol and/or ...	1999	11423951
sphingomonas herbicidovorans mh: a versatile phenoxyalkanoic acid herbicide degrader.	sphingomonas herbicidovorans mh was isolated from a dichlorprop-degrading soil column. it is able to grow on phenoxyalkanoic acid herbicides, such as mecoprop, dichlorprop, 2,4-d, mcpa, and 2,4-db. strain mh utilizes both enantiomers of the chiral herbicides mecoprop and dichlorprop as sole carbon and energy sources. enantiomer-specific uptake systems are responsible for transporting the acidic substrates across the cell membrane. catabolism is initiated by two enantiomer-specific alpha-ketoglut ...	1999	11423952
degradation of azo dyes containing aminonaphthol by sphingomonas sp strain 1cx.	sphingomonas sp strain 1cx was isolated from a wastewater treatment plant and is capable of aerobically degrading a suite of azo dyes, using them as a sole source of carbon and nitrogen. all azo dyes known to be decolorized by strain 1cx (orange ii, acid orange 8, acid orange 10, acid red 4, and acid red 88) have in their structure either 1-amino-2-naphthol or 2-amino-1-naphthol. in addition, an analysis of the structures of the dyes degraded suggests that there are certain positions and types o ...	1999	11423953
5-chloropicolinic acid is produced by specific degradation of 4-chlorobenzoic acid by sphingomonas paucimobilis bpsi-3.	we have previously shown that the bacterium sphingomonas paucimobilis bpsi-3, isolated from pcb-contaminated soil, can degrade halogenated biphenyls, naphthalenes, catechols and benzoic acids. however, before such an organism can be used in bioremediation, it is important to characterise the degradation products and determine the degradation pathways to ensure that compounds more toxic or mobile than the original contaminants are not produced. in the degradation of 4-chlorobiphenyl, s. paucimobi ...	1999	11423954
interaction of sphingomonas and pseudomonas strains in the degradation of chlorinated dibenzofurans.	we have studied the concerted degradation of two monochlorodibenzofurans by a bacterial consortium, consisting of the chlorodibenzofurans-cometabolizing and chlorosalicylates-excreting strain sphingomonas sp rw16, and pseudomonas sp rw10, which mineralized the released chlorosalicylates. neither of the organisms was able to grow with chlorodibenzofurans alone. degradation of 2-chloro- and 3-chlorodibenzofuran proceeded to the end products 5-chloro- and 4-chlorosalicylate, respectively, when the ...	1999	11423955
catabolism of 2,7-dichloro- and 2,4,8-trichlorodibenzofuran by sphingomonas sp strain rw1.	due to their physicochemical and toxicological properties, polychlorinated dibenzofurans are regarded as a class of compounds providing reason for serious environmental concern. while the nonhalogenated basic structure dibenzofuran is effectively mineralized by appropriate bacterial strains, its polychlorinated derivatives are not. to elucidate the ability of the strain sphingomonas sp rw1 to metabolize some of these chlorinated derivatives, we performed turnover experiments using 2,7-dichloro- ...	1999	11423956
characterization of sphingomonas paucimobilis syk-6 genes involved in degradation of lignin-related compounds.	sphingomonas paucimobilis syk-6 is able to grow on a wide variety of dimeric lignin compounds. these compounds are degraded via vanillate and syringate by a unique enzymatic system, composed of etherases, o demethylases, ring cleavage oxygenases and side chain cleaving enzymes. these unique and specific lignin modification enzymes are thought to be powerful tools for utilization of the most abundant aromatic biomass, lignin. here, we focus on the genes and enzymes involved in beta-aryl ether cle ...	1999	11423957
lessons learned from sphingomonas species that degrade abietane triterpenoids.	abietane terpenoid-degrading organisms include sphingomonas spp which inhabit natural environments and biological treatment systems. an isolate from the high arctic indicates that these organisms occur far from trees which synthesize abietanes and suggests that some of these organisms can occupy a niche in hydrocarbon-degrading soil communities. abietane-degrading sphingomonas spp provide additional evidence that the phylogeny of this genus is independent of the catabolic capabilities of its mem ...	1999	11423958
complete analysis of genes and enzymes for gamma-hexachlorocyclohexane degradation in sphingomonas paucimobilis ut26.	gamma-hexachlorocyclohexane (gamma-hch; also called bhc or lindane) is one of the highly chlorinated pesticides which can cause serious environmental problems. sphingomonas paucimobilis ut26 degrades gamma-hch under aerobic conditions. the unique degradation pathway of gamma-hch in ut26 is revealed. in the upstream pathway, gamma-hch is transformed to 2,5-dichlorohydroquinone (2,5-dchq) by two different dehalogenases (lina and linb) and one dehydrogenase (linc) which are expressed constitutively ...	1999	11423959
degradation of substituted naphthalenesulfonic acids by sphingomonas xenophaga bn6.	sphingomonas xenophaga bn6 was isolated from the river elbe as a member of a multispecies bacterial culture which mineralized 6-aminonaphthalene-2-sulfonate. pure cultures of strain bn6 converted a wide range of amino- and hydroxynaphthalene-2-sulfonates via a catabolic pathway similar to that described for the metabolism of naphthalene to salicylate by pseudomonas putida nah7 or pseudomonas sp ncib 9816. in contrast to the naphthalene-degrading pseudomonads, s. xenophaga bn6 only partially degr ...	1999	11423960
chemical structure and function of glycosphingolipids of sphingomonas spp and their distribution among members of the alpha-4 subclass of proteobacteria.	sphingomonas spp are phylogenetically placed in the alpha-4 subclass of proteobacteria. they have glycosphingolipids (gsl) in their membranes instead of lipopolysaccharide (lps) as in other gram-negative bacteria. s. paucimobilis, the type species of the genus, has gsl-1, which contains only glucuronic acid (glca) as a sugar moiety, and gsl-4a, which contains a tetrasaccharide including glca. gsl-1 and gsl-4a form the outer membrane of s. paucimobilis with outer membrane proteins and phospholipi ...	1999	11423962
interaction of peptides and proteins with bacterial surface glycolipids: a comparison of glycosphingolipids and lipopolysaccharides.	the bacterial cell wall of gram-negative bacteria consists, in addition to the cytoplasmic membrane, of another permeability barrier, the outer membrane. the lipid distribution between both sides of this membrane is strictly asymmetric. the outer leaflet is made up of glycolipids, usually lipopolysaccharides. in sphingomonas spp glycosphingolipids were found to substitute for lipopolysaccharides. in this review, it is shown by an electrophysiological approach that glycosphingolipid can replace l ...	1999	11423963
special cell surface structure, and novel macromolecule transport/depolymerization system of sphingomonas sp a1.	a bacterium isolated from soil as an alginate lyase producer shows characteristic morphological and taxonomical properties consistent with being classified in the genus sphingomonas. the bacterium utilizes high molecular weight (hmw)-alginate for growth by depolymerization of the polymer with intracellular alginate lyases, which are generated from a common precursor protein through autoregulated post-translational modifications. electron microscopic observations of the cell surface and of thin s ...	1999	11423964
planktonic/sessile dimorphism of polysaccharide-encapsulated sphingomonads.	sphingomonads have acquired diverse metabolic activities to inhabit a wide range of environments. several strains of sphingomonas display phenotypic dimorphism and can adopt either a planktonic or sessile behavior in liquid media. the sessile state is marked by the presence of a viscous exopolysaccharide capsule. specific types of these capsular polysaccharides are harvested from large-scale fermentations for use as rheology modifiers in many industrial and food applications. sensing of environm ...	1999	11423965
evaluation of rheological properties of the exopolysaccharide of sphingomonas paucimobilis gs-1 for application in oil exploration.	analysis of an exopolysaccharide of sphingomonas paucimobilis gs-1 (eps/gs-1) with respect to its rheological properties, cross-linking ability with chrome alum and performance test at 75 +/- 5 degrees c revealed its strong suspending ability, shear thinning property, and thixotrophic nature which are required to impart desirable rheology to drilling mud. the organism fulfilled all the specified requirements and its properties were superior to those of currently-used xc polymer (a xanthan produc ...	1999	11423966
growth of a bacterial consortium on triclosan.	triclosan is a polychlorinated hydroxy diphenylether that has been widely used as an antimicrobial compound. an enrichment using triclosan as a sole source of carbon and energy yielded a consortium of bacteria capable of growing on this compound. the dichloro ring was partially mineralized, resulting in the conversion of approximately 35% of the [(14)c]triclosan to [(14)c]co(2). use of molecular fingerprinting techniques and 16s rdna cloning and sequencing aided in the identification and eventua ...	2001	11451514
phosphorus-31 nuclear magnetic resonance study of the effect of pentachlorophenol (pcp) on the physiologies of pcp-degrading microorganisms.	free and agarose-encapsulated pentachlorophenol (pcp)-degrading sphingomonas sp. isolates ug25 and ug30 were compared to sphingomonas chlorophenolica atcc 39723 with respect to the ability to degrade pcp. pretreatment of the ug25 and ug30 strains with 50 microg of pcp per ml enabled the cells to subsequently degrade higher levels of this environmental pollutant. similar treatment of atcc 39723 cells had no effect on the level of pcp degraded by this strain. phosphorus-31 nuclear magnetic resonan ...	2001	11472931
proposal of the genus sphingomonas sensu stricto and three new genera, sphingobium, novosphingobium and sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses.	phylogenetic analyses of 16s rrna gene sequences by distance matrix and parsimony methods indicated that the currently known species of the genus sphingomonas can be divided into four clusters. some chemotaxonomic and phenotypic differences were noted among these clusters. three new genera, sphingobium, novosphingobium and sphingopyxis, are proposed in addition to the genus sphingomonas sensu stricto. the genus sphingobium is proposed to accommodate sphingomonas chlorophenolica, sphingomonas her ...	2001	11491340
sphingomonas aquatilis sp. nov., sphingomonas koreensis sp. nov., and sphingomonas taejonensis sp. nov., yellow-pigmented bacteria isolated from natural mineral water.	the taxonomic status of four strains from several mineral water sources in taejon, korea, was examined. the dna base compositions of these strains ranged from 62 to 66 mol %. all of the strains contained sphingolipids and ubiquinone 10 as the main respiratory quinone. the cellular fatty acids of these strains included octadecenoic acid, hexadecanoic acid and 2-hydroxymyristic acid, without 3-hydroxy fatty acids. on the basis of morphological, physiological and chemotaxonomic characteristics, tog ...	2001	11491350