Publications

distal cleavage of 3-chlorocatechol by an extradiol dioxygenase to 3-chloro-2-hydroxymuconic semialdehyde.	a 2,3-dihydroxybiphenyl 1,2-dioxygenase from the naphthalenesulfonate-degrading bacterium sphingomonas sp. strain bn6 oxidized 3-chlorocatechol to a yellow product with a strongly ph-dependent absorption maximum at 378 nm. a titration curve suggested (de)protonation of an ionizable group with a pka of 4.4. the product was isolated, purified, and converted, by treatment with diazomethane, to a dimethyl derivative and, by incubation with ammonium chloride, to a picolinic acid derivative. mass spec ...	1998	9603871
novel carbazole degradation genes of sphingomonas cb3: sequence analysis, transcription, and molecular ecology.	the degradation of aromatic compounds by bacteria is dependent upon specific catabolic operons. the unique car locus isolated from sphingomonas cb3 encodes the first four enzymes involved in the catabolism of the azaarene carbazole. these include a class ii three-component dioxygenase enzyme system, a dihydrodiol dehydrogenase, an extradiol (meta-cleavage) dioxygenase, and a hydrolase. homology of deduced amino acid sequences is closer to corresponding biphenyl catabolic genes than to previously ...	1998	9636667
enantioselective uptake and degradation of the chiral herbicide dichlorprop [(rs)-2-(2,4-dichlorophenoxy)propanoic acid] by sphingomonas herbicidovorans mh.	sphingomonas herbicidovorans mh was able to completely degrade both enantiomers of the chiral herbicide dichlorprop [(rs)-2-(2,4-dichlorophenoxy)propanoic acid], with preferential degradation of the (s) enantiomer over the (r) enantiomer. these results are in agreement with the recently reported enantioselective degradation of mecoprop [(rs)-2-(4-chloro-2-methylphenoxy)propanoic acid] by this bacterium (c. zipper, k. nickel, w. angst, and h.-p. e. kohler, appl. environ. microbiol. 62:4318-4322, ...	1998	9642189
further characterization of hydrogen peroxide-dependent fatty acid alpha-hydroxylase from sphingomonas paucimobilis.	although fatty acid alpha-hydroxylase (faah) activity has been detected in various species, faah has not been sufficiently characterized. in this report, we describe the properties of faah highly purified from sphingomonas paucimobilis. the faah was purified by about 5,200-fold. blotting analysis with a specific antibody against the faah showed that its apparent molecular mass was approximately 43 kda. faah showed alpha-hydroxylation activity in the presence of h2o2, but little if any activity w ...	1998	9644252
cloning of a sphingomonas paucimobilis syk-6 gene encoding a novel oxygenase that cleaves lignin-related biphenyl and characterization of the enzyme.	sphingomonas paucimobilis syk-6 transforms 2,2'-dihydroxy-3,3'-dimethoxy-5,5'-dicarboxybiphenyl (ddva), a lignin-related biphenyl compound, to 5-carboxyvanillic acid via 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl (oh-ddva) as an intermediate (15). the ring fission of oh-ddva is an essential step in the ddva degradative pathway. a 15-kb ecori fragment isolated from the cosmid library complemented the growth deficiency of a mutant on oh-ddva. subcloning and deletion analysis showed that a ...	1998	9647824
the reductase reda2 of the multi-component dioxin dioxygenase system of sphingomonas sp. rw1 is related to class-i cytochrome p450-type reductases.	the first step in the oxidation of the diaryl ethers dibenzo-p-dioxin and dibenzofuran by the bacterium sphingomonas sp. rw1 is carried out by an atypical multi-component ring hydroxylating dioxygenase. this heteromeric enzyme requires the participation of a flavoprotein, reductase a2, and an iron-sulfur protein, fdx1, to mediate the transfer of electrons from nadh to the dioxygenase for oxygen activation [bünz, p. v. & cook, a. m. (1993) j. bacteriol. 175, 6467-6475]. from the type of ferredoxi ...	1998	9654094
genetic analysis of dioxin dioxygenase of sphingomonas sp. strain rw1: catabolic genes dispersed on the genome.	the dioxin dioxygenase of sphingomonas sp. strain rw1 activates dibenzo-p-dioxin and dibenzofuran for further metabolism by introducing two atoms of oxygen at a pair of vicinal carbon atoms, one of which is involved in one of the bridges between the two aromatic rings, i.e., an angular dioxygenation. the dxna1 and dxna2 cistrons encoding this dioxygenase have been cloned and shown to be located just upstream of a hydrolase gene which specifies an enzyme involved in the subsequent step of the dib ...	1998	9683494
alpha-l-rhamnosidase of sphingomonas sp. r1 producing an unusual exopolysaccharide of sphingan.	a soil bacterium with alpha-l-rhamnosidase was isolated from a cumulative mixed culture containing a polysaccharide of gellan as a carbon source and identified to be sphingomonas paucimobilis, known as a potent producer of gellan. the isolate (designated sphingomonas sp. r1) produced an unusual exopolysaccharide of sphingan (denoted hwr1) distinct from gellan. the rhamnose in gellan was replaced with mannose in hwr1. the bacterium had a peculiar cell surface covered with many complicated plaits. ...	1998	9692187
biochemical and genetic characterization of a gentisate 1, 2-dioxygenase from sphingomonas sp. strain rw5.	a 4,103-bp long dna fragment containing the structural gene of a gentisate 1,2-dioxygenase (ec 1.13.11.4), gtda, from sphingomonas sp. strain rw5 was cloned and sequenced. the gtda gene encodes a 350-amino-acid polypeptide with a predicted size of 38.85 kda. comparison of the gtda gene product with protein sequences in databases, including those of intradiol or extradiol ring-cleaving dioxygenases, revealed no significant homology except for a low similarity (27%) to the 1-hydroxy-2-naphthoate d ...	1998	9696766
amplification of putative chlorocatechol dioxygenase gene fragments from alpha- and beta-proteobacteria.	redundant primers were designed for the pcr amplification of dna from chlorocatechol dioxygenase genes. these primers were used successfully to amplify 270- to 279-bp fragments from a variety of 2,4-dichlorophenoxyacetate- and cholorobenzoate-degrading strains, including species of sphingomonas. three groups of closely related sequences were amplified: one from chlorobenzoate degraders that was 86% similar to the amino acid sequence of the protein coded by the tfdc gene of ralstonia eutropha jmp ...	1998	9699302
microbial communities of printing paper machines.	the microbial content of printing paper machines, running at a temperature of 45-50 degrees c and at ph 4.5-5, was studied. bacteria were prevalent colonizers of the machine wet end and the raw materials. a total of 390 strains of aerobic bacteria were isolated and 86% of these were identified to genus and species by biochemical, chemotaxonomic and phylogenetic methods. the most common bacteria found at the machine wet end were bacillus coagulans and other bacillus species, burkholderia cepacia, ...	1998	9717292
characterization and reclassification of an aromatic- and chloroaromatic-degrading pseudomonas sp., strain hv3, as sphingomonas sp. hv3.	phylogenetic analyses of 16s rrna gene sequences showed that the gram-negative aromatic- and chloroaromatic-degrading pseudomonas sp. strain hv3 carrying the mega-plasmid psky4 belongs to the genus sphingomonas. the 16srrna sequence is most related to sphingomonas chlorophenolica strains atcc 33790(t) (98.5%) and sr3 (98.4%) and sphingomonas sp. ss86 (98.4%). the g+c content was 64 mol%, and the dna-dna hybridization-based relative homology of strain hv3 to the s. chlorophenolica atcc 33790(t) a ...	1998	9734064
prolyl endopeptidase from sphingomonas capsulata: isolation and characterization of the enzyme and nucleotide sequence of the gene.	prolyl endopeptidase (prolyl oligopeptidase, ec 3.4.21.26) was purified from sphingomonas capsulata ifo 12533, and its gene was cloned and expressed in escherichia coli. the recombinant enzyme was markedly inhibited by diisopropyl phosphofluoridate and hardly affected by sh reagents or metal chelators, similar to the native enzyme purified from s. capsulata. nucleotide sequencing analysis revealed an open reading frame of 2169 bp, coding for a protein of 723 amino acids with a predicted molecula ...	1998	9750174
quantitative detection of sphingomonas chlorophenolica in soil via competitive polymerase chain reaction.	the 16s ribosomal rna gene sequence of the pentachlorophenol degrader sphingomonas chlorophenolica strain ra2 was used to generate specific polymerase chain reaction (pcr) primers for the detection of this strain in soil, whereas a region internal to the two primers was used to provide an s. chlorophenolica strain ra2-specific oligonucleotide probe. the pcr detection system resulted in a 727 bp product detectable via gel electrophoresis and hybridization. it was specific for strain ra2 and its c ...	1998	9750277
emergence of cu(++)-tolerant mutants defective in gellan synthesis in cu(++)-stressed cultures of sphingomonas paucimobilis.	cells defective in gellan synthesis appeared during cultivation of the gellan gum-producing strain sphingomonas paucimobilis r40 with inhibitory concentrations of copper, supplied as cucl2. the percentage of less mucoid colonial variants dramatically increased with the increase in cu++ supplementation, reaching 85% of total viable cells at the maximal concentration for growth. results reported in this work indicate that emergence of colonial variants defective in gellan synthesis results from cu ...	1997	9765805
gene sequences of the pcpb gene of pentachlorophenol-degrading sphingomonas chlorophenolica found in nondegrading bacteria.	bacteria isolated from a pentachlorophenol (pcp) contaminated site grew in the presence of 50 micrograms pcp/ml but were not able to degrade it in either liquid medium or the presence of 1% sterile potting soil as a solid support. probes developed using the gene sequence of pcp-4-monooxygenase (pcpb) from sphingomonas chlorophenolica sp.nov hybridized to two separate isolates. identification based on fatty acid methyl ester profiles (sherlock), substrate utilization (biolog), and 16s rrna showed ...	1998	9783427
implications of rrna operon copy number and ribosome content in the marine oligotrophic ultramicrobacterium sphingomonas sp. strain rb2256.	sphingomonas sp. strain rb2256 is a representative of the dominant class of ultramicrobacteria that are present in marine oligotrophic waters. in this study we examined the rrna copy number and ribosome content of rb2256 to identify factors that may be associated with the relatively low rate of growth exhibited by the organism. it was found that rb2256 contains a single copy of the rrna operon, in contrast to vibrio spp., which contain more than eight copies. the maximum number of ribosomes per ...	1998	9797303
biodegradation pathway of 2-chlorodibenzo-p-dioxin and 2-chlorodibenzofuran in the biphenyl-utilising strain jb1.	the biphenyl-utilising burkholderia (previously alcaligenes) strain jb1 is also able to degrade a number of chlorinated dibenzo-p-dioxins and dibenzofurans. in this study, 4-chlorocatechol and a chlorotrihydroxydiphenyl ether were identified as metabolites of 2-chlorodibenzo-p-dioxin. 5-chlorosalicylic acid and a chlorotrihydroxybiphenyl were metabolites of 2-chlorodibenzofuran. these results show that degradation of these compounds follows pathways in which the initial reaction is angular dioxy ...	1998	9828319
characteristics of phenanthrene-degrading bacteria isolated from soils contaminated with polycyclic aromatic hydrocarbons.	ten bacterial strains were isolated from seven contaminated soils by enrichment with phenanthrene as the sole carbon source. these isolates and another phenanthrene-degrading strain were examined for various characteristics related to phenanthrene degradation and their ability to metabolize 12 other polycyclic aromatic hydrocarbons (pah), ranging in size from two to five rings, after growth in the presence of phenanthrene. fatty acid methyl ester analysis indicated that at least five genera (agr ...	1998	9830104
[bacteremia caused by sphingomonas (pseudomonas) paucimobilis].		1998	9835164
genetic and biochemical characterization of a 2-pyrone-4, 6-dicarboxylic acid hydrolase involved in the protocatechuate 4, 5-cleavage pathway of sphingomonas paucimobilis syk-6.	sphingomonas paucimobilis syk-6 is able to grow on a wide variety of dimeric lignin compounds with guaiacyl moieties, which are converted into protocatechuate by the actions of lignin degradation enzymes in this strain. protocatechuate is a key metabolite in the syk-6 degradation of lignin compounds with guaiacyl moieties, and it is thought that it degrades to pyruvate and oxaloacetate via the protocatechuate 4,5-cleavage pathway. in a 10.5-kb ecori fragment carrying the protocatechuate 4,5-diox ...	1999	9864312
chlorine inactivation of sphingomonas cells attached to goethite particles in drinking water.	bacteria in drinking water, attached or not attached to goethite particles, were disinfected with chlorine. no additional protection was provided to the bacteria by their attachment to particles, and the limited efficiency of inactivation by chlorine was attributed to the presence of bacterial aggregates in both types of suspension.	1999	9872809
isolation of a bacterial strain able to degrade branched nonylphenol.	conventional enrichment of microorganisms on branched nonylphenol (np) as only carbon and energy source yielded mixed cultures able to grow on the organic compound. however, plating yielded no single colonies capable, alone or in combination with other isolates, of degrading the np in liquid culture. therefore, a special approach was used, referred to as "serial dilution-plate resuspension," to reduce culture complexity. in this way, one isolate, ttnp3, tentatively identified as a sphingomonas s ...	1999	9925611
complement activation by bacterial surface glycolipids: a study with planar bilayer membranes.	planar asymmetric glycolipid/phospholipid bilayer membranes were used as a reconstitution model of the lipid matrix of the outer membrane of gram-negative bacteria to study complement (c) activation by various bacterial surface glycolipids with the aim of defining the c activation pathway. as glycolipids the lipopolysaccharides of salmonella enterica serovar minnesota r mutant strains r595 (re lps) and r4 (rd2 lps), pentaacyl lipid a from the lps of the escherichia coli re mutant f515, and glyco ...	1999	9929374
phytanic acid alpha-hydroxylation by bacterial cytochrome p450.	fatty acid alpha-hydroxylase, a cytochrome p450 enzyme, from sphingomonas paucimobilis, utilizes various straight-chain fatty acids as substrates. we investigated whether a recombinant fatty acid alpha-hydroxylase is able to metabolize phytanic acid, a methyl-branched fatty acid. when phytanic acid was incubated with the recombinant enzyme in the presence of h2o2, a reaction product was detected by gas chromatography, whereas a reaction product was not detected in the absence of h2o2. when a hea ...	1998	9930407
rhodanobacter lindaniclasticus gen. nov., sp. nov., a lindane-degrading bacterium.	lindane-degrading activity under aerobic conditions has been observed in two bacterial strains: ut26, phenotypically identified as sphingomonas paucimobilis, and a new single unidentified isolate named rp5557t. the rrs (16s rdna) sequences for both strains and the phenotypic characteristics for the unidentified isolate rp5557t were determined. rp5557t does not have high identity (less than 90% in all cases) with any sequence in the genbank or rdp databases. a phylogenetic analysis based on rrs s ...	1999	10028243
complete sequence of a 184-kilobase catabolic plasmid from sphingomonas aromaticivorans f199.	the complete 184,457-bp sequence of the aromatic catabolic plasmid, pnl1, from sphingomonas aromaticivorans f199 has been determined. a total of 186 open reading frames (orfs) are predicted to encode proteins, of which 79 are likely directly associated with catabolism or transport of aromatic compounds. genes that encode enzymes associated with the degradation of biphenyl, naphthalene, m-xylene, and p-cresol are predicted to be distributed among 15 gene clusters. the unusual coclustering of gene ...	1999	10049392
contrasting effects of a nonionic surfactant on the biotransformation of polycyclic aromatic hydrocarbons to cis-dihydrodiols by soil bacteria.	the biotransformation of the polycyclic aromatic hydrocarbons (pahs) naphthalene and phenanthrene was investigated by using two dioxygenase-expressing bacteria, pseudomonas sp. strain 9816/11 and sphingomonas yanoikuyae b8/36, under conditions which facilitate mass-transfer limited substrate oxidation. both of these strains are mutants that accumulate cis-dihydrodiol metabolites under the reaction conditions used. the effects of the nonpolar solvent 2,2,4, 4,6,8,8-heptamethylnonane (hmn) and the ...	1999	10049904
identification of the catalytic triad in the haloalkane dehalogenase from sphingomonas paucimobilis ut26.	the haloalkane dehalogenase from sphingomonas paucimobilis ut26 (linb) is the enzyme involved in the gamma-hexachlorocyclohexane degradation. this enzyme hydrolyses a broad range of halogenated aliphatic compounds via an alkyl-enzyme intermediate. linb is believed to belong to the family of alpha/beta-hydrolases which employ a catalytic triad, i.e. nucleophile-histidine-acid, during the catalytic reaction. the position of the catalytic triad within the sequence of linb was probed by a site-direc ...	1999	10100638
genetic analysis of biodegradation of tetralin by a sphingomonas strain.	a strain designated tfa which very efficiently utilizes tetralin has been isolated from the rhine river. the strain has been identified as sphingomonas macrogoltabidus, based on 16s rdna sequence similarity. genetic analysis of tetralin biodegradation has been performed by insertion mutagenesis and by physical analysis and analysis of complementation between the mutants. the genes involved in tetralin utilization are clustered in a region of 9 kb, comprising at least five genes grouped in two di ...	1999	10103288
physiological and phylogenetic diversity of bacteria growing on resin acids.	resin acids are tricyclic diterpenes which are synthesized by trees and are a major cause of toxicity of pulp mill effluents. bacterial strains isolated from three different sources and which grow on resin acids were physiologically characterized. eleven strains, representating distinct groups, were further characterized physiologically and phylogenetically. the isolates had distinct specificities for use, as growth substrates, of the different resin acids tested. the isolates also used fatty ac ...	1999	10188280
effect of calcium on the surfactant tolerance of a fluoranthene degrading bacterium.	surfactants are known to increase the apparent aqueous solubility of polycyclic aromatic hydrocarbons (pahs) and may thus be used to enhance the bioavailability and thereby to stimulate the biodegradation of these hydrophobic compounds. however, surfactants may in some cases reduce or inhibit biodegradation because of toxicity to the bacteria. in this study, toxicity of surfactants on sphingomonas paucimobilis strain epa505 and the effect on fluoranthene mineralization were investigated using tr ...	1998	10192897
in-vitro study of interaction between photooxidation and biodegradation of 2-methylphenanthrene by sphingomonas sp. 2mpii.	this work reports a study of interactions between reactions of photooxidation and reactions of bacterial degradation of an alkylated polyaromatic hydrocarbon (2-methylphenanthrene). bacterial growth was carried out using artificial sunlight as light source. among the various products detected, the major product was identified as the 2-methylphenanthrene aldehyde. sunlight allows accelerated elimination of the substrate. this enhancement of the biodegradation rate of 2 methylphenanthrene is due t ...	1999	10204235
dust-borne bacteria in animal sheds, schools and children's day care centres.	a total of 316 bacterial strains, including psychrophiles, mesophiles and thermophiles, were isolated and identified from indoor dusts in schools, children's day care centres and animal sheds. several species which had not previously been reported from indoor environments were found: sphingomonas, brevibacterium, nocardiopsis, deinococcus and rhodococcus/gordona. a new psychrophilic actinomycete genus was also found in animal sheds, representing a new undescribed peptidoglycan type and an unusua ...	1999	10212408
the role of the sphingomonas species ug30 pentachlorophenol-4-monooxygenase in p-nitrophenol degradation.	pentachlorophenol-4-monooxygenase is an aromatic flavoprotein monooxygenase which hydroxylates pentachlorophenol and a wide range of polyhalogenated phenols at their para position. the pcp-degrading sphingomonas species ug30 was recently shown to mineralize p-nitrophenol. in this study, the ug30 pcpb gene encoding the pentachlorophenol-4-monooxygenase gene was cloned for use to study its potential role in p-nitrophenol degradation. the ug30 pcpb gene consists of 1614 bp with a predicted translat ...	1999	10220902
detection of polycyclic aromatic hydrocarbon degradation genes in different soil bacteria by polymerase chain reaction and dna hybridization.	twenty different strains of pseudomonas, mycobacterium, gordona, sphingomonas, rhodococcus and xanthomonas which degrade polycyclic aromatic hydrocarbons (pah) were characterized in respect to genes encoding degradation enzymes for pah. genomic dna from these strains was hybridized with a fragment of ndob, coding for the large iron sulfur protein (isp alpha) of the naphthalene dioxygenase from pseudomonas putida paw736 (ncib 9816). a group of seven naphthalene-degrading pseudomonas strains showe ...	1999	10220903
removal of dibenzofuran, dibenzo-p-dioxin, and 2-chlorodibenzo-p-dioxin from soils inoculated with sphingomonas sp. strain rw1.	removal of dibenzofuran, dibenzo-p-dioxin, and 2-chlorodibenzo-p-dioxin (2-cdd) (10 ppm each) from soil microcosms to final concentrations in the parts-per-billion range was affected by the addition of sphingomonas sp. strain rw1. rates and extents of removal were influenced by the density of rw1 organisms. for 2-cdd, the rate of removal was dependent on the content of soil organic matter (som), with half-life values ranging from 5.8 h (0% som) to 26.3 h (5.5% som).	1999	10224029
comparison of the fuel oil biodegradation potential of hydrocarbon-assimilating microorganisms isolated from a temperate agricultural soil.	strains of hydrocarbon-degrading microorganisms (bacteria and fungi) were isolated from an agricultural soil in france. in a field, a portion was treated with oily cuttings resulting from the drilling of an onshore well. the cuttings which were spread at the rate of 600 g hc m-2 contained 10% of fuel oil hydrocarbons (hc). another part of the field was left untreated. three months after hc spreading, hc adapted bacteria and fungi were isolated at different soil depths in the two plots and identi ...	1999	10231986
crystallization and preliminary x-ray diffraction analysis of haloalkane dehalogenase linb from sphingomonas paucimobilis ut26.	haloalkane hydrolytic dehalogenase linb from sphingomonas paucimobilis ut26, an enzyme which releases chloride or bromide anion from n-halogenated alkanes and has a broad range of substrate specificity, was crystallized using the hanging-drop vapour-diffusion method at 278 k. the best crystals were obtained by microseeding with a precipitant containing 18-20%(w/v) peg 6000, 0.2 m calcium acetate and 0.1 m tris-hcl ph 8.9. the crystals diffract to at least 1.60 a using synchrotron x-ray under cry ...	1999	10329794
structures and properties of gellan polymers produced by sphingomonas paucimobilis atcc 31461 from lactose compared with those produced from glucose and from cheese whey	the dairy industry produces large quantities of whey as a by-product of cheese production and is increasingly looking for new ways to utilize this waste product. gellan gum is reliably produced by sphingomonas paucimobilis in growth media containing lactose, a significant component of cheese whey, as a carbon source. we studied and compared polysaccharide biosynthesis by s. paucimobilis atcc 31461 in media containing glucose, lactose (5 to 30 g/liter), and sweet cheese whey. we found that alteri ...	1999	10347031
enhancement of solubilization and biodegradation of polyaromatic hydrocarbons by the bioemulsifier alasan.	alasan, a high-molecular-weight bioemulsifier complex of an anionic polysaccharide and proteins that is produced by acinetobacter radioresistens ka53 (s. navon-venezia, z. zosim, a. gottlieb, r. legmann, s. carmeli, e. z. ron, and e. rosenberg, appl. environ. microbiol. 61:3240-3244, 1995), enhanced the aqueous solubility and biodegradation rates of polyaromatic hydrocarbons (pahs). in the presence of 500 microg of alasan ml-1, the apparent aqueous solubilities of phenanthrene, fluoranthene, and ...	1999	10347063
characterization of the meta-cleavage compound hydrolase gene involved in degradation of the lignin-related biphenyl structure by sphingomonas paucimobilis syk-6.	sphingomonas paucimobilis syk-6 has the ability to transform a lignin-related biphenyl compound, 2,2'-dihydroxy-3,3'-dimethoxy-5, 5'-dicarboxybiphenyl (ddva), to 5-carboxyvanillic acid (5cva) via 2, 2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl (oh-ddva). in the 4.9-kb hindiii fragment containing the oh-ddva meta-cleavage dioxygenase gene (ligz), we found a novel hydrolase gene (ligy) responsible for the conversion of the meta-cleavage compound of oh-ddva to 5cva. incorporation of 18o from h ...	1999	10347082
a functional 4-hydroxysalicylate/hydroxyquinol degradative pathway gene cluster is linked to the initial dibenzo-p-dioxin pathway genes in sphingomonas sp. strain rw1.	the bacterium sphingomonas sp. strain rw1 is able to use dibenzo-p-dioxin, dibenzofuran, and several hydroxylated derivatives as sole sources of carbon and energy. we have determined and analyzed the nucleic acid sequence of a 9,997-bp hindiii fragment downstream of cistrons dxna1a2, which encode the dioxygenase component of the initial dioxygenase system of the corresponding catabolic pathways. this fragment contains 10 colinear open reading frames (orfs), apparently organized in one compact op ...	1999	10348858
characterization of the tra2 region of the inchi1 plasmid r27.	in this study, the dna sequence of one of the transfer regions of the inchi1 plasmid r27 was determined. this region, which corresponds to coordinates 0-40 on the r27 map has been called the tra2 region, and is believed to be involved in mating pair formation. dna sequence analysis of the transfer region identified 11 open reading frames which showed similarities to the transfer genes from other conjugative systems. the r27 transfer genes appear to most closely resemble the genes from the f plas ...	1999	10366528
proposal of sphingomonas suberifaciens (van bruggen, jochimsen and brown 1990) comb. nov., sphingomonas natatoria (sly 1985) comb. nov., sphingomonas ursincola (yurkov et al. 1997) comb. nov., and emendation of the genus sphingomonas.	based on the results of a phylogenetic analysis of 16s rrna and the presence of sphingoglycolipid in cellular lipids of the type strains, transfer of "rhizomonas" suberifaciens, blastomonas natatoria and erythromonas ursincola to the genus sphingomonas as sphingomonas suberifaciens (van bruggen et al 1990) comb. nov., sphingomonas natatoria (sly 1985) comb. nov., and sphingomonas ursincola (yurkov et al 1997) comb. nov. are herein proposed together with the emendation of genus sphingomonas. the ...	1999	10385200
evidence that pcpa encodes 2,6-dichlorohydroquinone dioxygenase, the ring cleavage enzyme required for pentachlorophenol degradation in sphingomonas chlorophenolica strain atcc 39723.	an enzyme that catalyzes an fe2+-dependent reaction of 2, 6-dichlorohydroquinone with o2 has been isolated from sphingomonas chlorophenolica sp. strain atcc 39723, a soil microorganism capable of complete mineralization of pentachlorophenol. the product of the reaction is too unstable to allow spectroscopic characterization, but is apparently negatively charged and retains the two chlorine atoms of the substrate. the enzyme was partially sequenced using electrospray lc-ms, and one peptide was us ...	1999	10387005
crystal structure of alginate lyase a1-iii from sphingomonas species a1 at 1.78 a resolution.	the three-dimensional structure of alginate lyase a1-iii (alyiii) from a sphingomonas species a1 was determined by x-ray crystallography. the enzyme was crystallized by the hanging-drop vapour-diffusion method in the presence of 49% ammonium sulfate at 20 degrees c. the crystals are monoclinic and belong to the space group c2 with unit cell dimensions of a=49.18 a, b=93.08 a, c=82.10 a and beta=104.12 degrees. there was one molecule of alginate lyase in the asymmetric unit of the crystal. the di ...	1999	10390348
phylogeny and polyphasic taxonomy of caulobacter species. proposal of maricaulis gen. nov. with maricaulis maris (poindexter) comb. nov. as the type species, and emended description of the genera brevundimonas and caulobacter.	the genus caulobacter is composed of prosthecate bacteria often specialized for oligotrophic environments. the taxonomy of caulobacter has relied primarily upon morphological criteria: a strain that visually appeared to be a member of the caulobacter has generally been called one without challenge. a polyphasic approach, comprising 16s rdna sequencing, profiling restriction fragments of 16s-23s rdna interspacer regions, lipid analysis, immunological profiling and salt tolerance characterizations ...	1999	10425763
reclassification of pseudomonas echinoides heumann 1962, 343al, in the genus sphingomonas as sphingomonas echinoides comb. nov.	[pseudomonas] echinoides dsm 1805t (= attc 14820t, dsm 50409t, icbp 2835t, ncib 9420t) has been reinvestigated to clarify its taxonomic position. 16s rdna sequence comparisons demonstrated that this species clusters phylogenetically with species of the genus sphingomonas. investigation of fatty acid patterns, polar lipid profiles, polyamine patterns and quinone systems supported this delineation. substrate utilization profiles and biochemical characteristics displayed no distinct overall similar ...	1999	10425767
catalytic properties of the 3-chlorocatechol-oxidizing 2, 3-dihydroxybiphenyl 1,2-dioxygenase from sphingomonas sp. strain bn6.	the 2,3-dihydroxybiphenyl dioxygenase from sphingomonas sp. strain bn6 (bphc1-bn6) differs from most other extradiol dioxygenases by its ability to oxidize 3-chlorocatechol to 3-chloro-2-hydroxymuconic semialdehyde by a distal cleavage mechanism. the turnover of different substrates and the effects of various inhibitors on bphc1-bn6 were compared with those of another 2,3-dihydroxybiphenyl dioxygenase from the same strain (bphc2-bn6) as well as with those of the archetypical catechol 2,3-dioxyge ...	1999	10438749
differential detection of key enzymes of polyaromatic-hydrocarbon-degrading bacteria using pcr and gene probes.	bacteria with ability to degrade polyaromatic hydrocarbons (pahs), isolated from wastewater and soil samples, were investigated for their taxonomic, physiological and genetic diversity. eighteen isolates able to metabolize naphthalene or phenanthrene as sole carbon source were taxonomically affiliated to different subclasses of the proteobacteria (sphingomonas spp., acidovorax spp., comamonas spp. and pseudomonas spp.) and to phyla of gram-positive bacteria with low and high dna g + c content (p ...	1999	10439412
stability of mutations in a sphingomonas strain.	sphingomonas sp. strain rw1 is able to mineralise dibenzofuran and dibenzo-p-dioxin. three mutants were constructed that could not use dibenzofuran or dibenzo-p-dioxin as a carbon source but were able to grow with the succeeding metabolites of the pathway. two different mutagenic agents were applied, a chemical treatment with 1-methyl-3-nitro-1-nitrosoguanidine, resulting in mutants rw1-n6 and rw1-n7, and a biological insertion mutagenesis with the mini-tn5 transposon pbsl118, resulting in mutan ...	1999	10446715
conserved and hybrid meta-cleavage operons from pah-degrading burkholderia rp007.	we have compared the sequence and gene order of meta-cleavage pathway operons from alpha- and gamma-subgroups of the proteobacteria with operons from burkholderia sp. strain rp007 which belongs to the beta-subgroup of the proteobacteria. burkholderia rp007 was isolated for its ability to degrade phenanthrene and contains two meta-cleavage operons. one exhibits a comparable gene order to previously characterised gamma-subgroup proteobacterial (pseudomonas) meta operons, whilst the other has disti ...	1999	10448110
an assessment of protein profiles from the marine oligotrophic ultramicrobacterium, sphingomonas sp. strain rb2256.	the protein expression profile of a novel marine oligotrophic ultramicrobacterium, sphingomonas sp. strain rb2256, was investigated by two-dimensional polyacrylamide gel electrophoresis (2-d page). analytical reference maps were generated from mid-log phase batches and steady-state chemostat cultures with ph 4-8 immobilised ph gradients (ipgs) followed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis. the resolved proteins were detected by two different methods: radioactive labeling ...	1999	10451121
two different types of dehalogenases, lina and linb, involved in gamma-hexachlorocyclohexane degradation in sphingomonas paucimobilis ut26 are localized in the periplasmic space without molecular processing.	gamma-hexachlorocyclohexane (gamma-hch) is one of several highly chlorinated insecticides that cause serious environmental problems. the cellular proteins of a gamma-hch-degrading bacterium, sphingomonas paucimobilis ut26, were fractionated into periplasmic, cytosolic, and membrane fractions after osmotic shock. most of two different types of dehalogenase, lina (gamma-hexachlorocyclohexane dehydrochlorinase) and linb (1,3,4,6-tetrachloro-1,4-cyclohexadiene halidohydrolase), that are involved in ...	1999	10464214
crystal structure of an aromatic ring opening dioxygenase ligab, a protocatechuate 4,5-dioxygenase, under aerobic conditions.	sphingomonas paucimobilis syk-6 utilizes an extradiol-type catecholic dioxygenase, the ligab enzyme (a protocatechuate 4,5-dioxygenase), to oxidize protocatechuate (or 3,4-dihydroxybenzoic acid, pca). the enzyme belongs to the family of class iii extradiol-type catecholic dioxygenases catalyzing the ring-opening reaction of protocatechuate and related compounds. the primary structure of ligab suggests that the enzyme has no evolutionary relationship with the family of class ii extradiol-type cat ...	1999	10467151
marine bacterial isolates display diverse responses to uv-b radiation.	the molecular and biological consequences of uv-b radiation were investigated by studying five species of marine bacteria and one enteric bacterium. laboratory cultures were exposed to an artificial uv-b source and subjected to various post-uv irradiation treatments. significant differences in survival subsequent to uv-b radiation were observed among the isolates, as measured by culturable counts. uv-b-induced dna photodamage was investigated by using a highly specific radioimmunoassay to measur ...	1999	10473381
poly(aspartic acid) degradation by a sphingomonas sp. isolated from freshwater.	a poly(aspartic acid) degrading bacterium (strain kt-1 [jcm10459]) was isolated from river water and identified as a member of the genus sphingomonas. the isolate degraded only poly(aspartic acid)s of low molecular masses (<5 kda), while the cell extract hydrolyzed high-molecular-mass poly(aspartic acid)s of 5 to 150 kda to yield aspartic acid monomer.	1999	10473451
sphingomonas sp. strain lep1: an aerobic degrader of 4-methylquinoline.	strain lep1, isolated from a bacterial consortium capable of aerobic degradation of 4-methylquinoline (4-mq), was chosen for further characterization as it was the only member of the consortium able to grow on 4-mq in pure culture. lep1 was identified as a sphingomonas sp. based on phylogenetic analysis of 16s rdna. furthermore, the presence of sphingolipids and 2-hydroxy fatty acids in the membrane, and a 63% g + c ratio supports the placement of lep1 in this genus. additional genetic, physiolo ...	1999	10497791
pcpa, which is involved in the degradation of pentachlorophenol in sphingomonas chlorophenolica atcc39723, is a novel type of ring-cleavage dioxygenase.	the pentachlorophenol (pcp) mineralizing bacterium sphingomonas chlorophenolica atcc39723 degrades pcp via 2,6-dichlorohydroquinone (2,6-dchq). the pathway converting pcp to 2,6-dchq has been established previously; however, the pathway beyond 2,6-dchq is not clear, although it has been suggested that a pcpa plays a role in 2, 6-dchq conversion. in this study, pcpa expressed in escherichia coli was purified to homogeneity and shown to have novel ring-cleavage dioxygenase activity in conjunction ...	1999	10526172
characterization of the ybdt gene product of bacillus subtilis: novel fatty acid beta-hydroxylating cytochrome p450.	we have characterized the gene encoding fatty acid alpha-hydroxylase, a cytochrome p450 (p450) enzyme, from sphingomonas paucimobilis. a database homology search indicated that the deduced amino acid sequence of this gene product was 44% identical to that of the ybdt gene product that is a 48 kda protein of unknown function from bacillus subtilis. in this study, we cloned the ybdt gene and characterized this gene product using a recombinant enzyme to clarify function of the ybdt gene product. th ...	1999	10529095
selective and continuous degradation of carbazole contained in petroleum oil by resting cells of sphingomonas sp. cdh-7.	microbial degradation of carbazole (ca), a model of hard-removal heterocyclic nitrogen compounds contained in petroleum oil, was examined using sphingomonas sp. cdh-7 isolated from a soil sample by screening for ca-assimilating microorganisms. cdh-7 used ca as a sole source of carbon and nitrogen, and metabolized ca to ammonia via anthranilic acid as an intermediate product. when cdh-7 was cultivated in the medium containing ca at the concentration of 500 mg/l (2.99 mm), ca was completely degrad ...	1999	10540744
cloning and sequencing of a novel meta-cleavage dioxygenase gene whose product is involved in degradation of gamma-hexachlorocyclohexane in sphingomonas paucimobilis.	sphingomonas (formerly pseudomonas) paucimobilis ut26 utilizes gamma-hexachlorocyclohexane (gamma-hch), a halogenated organic insecticide, as a sole source of carbon and energy. in a previous study, we showed that gamma-hch is degraded to chlorohydroquinone (chq) and then to hydroquinone (hq), although the rate of reaction from chq to hq was slow (k. miyauchi, s. k. suh, y. nagata, and m. takagi, j. bacteriol. 180:1354-1359, 1998). in this study, we cloned and characterized a gene, designated li ...	1999	10542173
construction and characterization of histidine-tagged haloalkane dehalogenase (linb) of a new substrate class from a gamma-hexachlorocyclohexane-degrading bacterium, sphingomonas paucimobilis ut26.	the linb gene product (linb), which is involved in the degradation of gamma-hexachlorocyclohexane in sphingomonas paucimobilis ut26, is a member of haloalkane dehalogenases with a broad range of substrate specificity. elucidation of the factors determining its substrate specificity is of interest. aiming to facilitate purification of recombinant linb protein for site-directed mutagenesis analysis, a 6-histidyl tail was added to the c-terminus of linb. the his-tagged linb was specifically bound w ...	1999	10545279
isrm10: a new insertion sequence of sinorhizobium meliloti: nucleotide sequence and geographic distribution.	in this study the description of a new insertion sequence of sinorhizobium meliloti, isrm10, is reported. isrm10 was found in the intergenic region between nodj and nodq of a natural isolated strain. isrm10 was 1047 bp long and showed the typical features of the iss belonging to the is630-tc1/is3 superfamily. in particular the isrm10 nucleotide sequence showed the highest homology (62%) with a sphingomonas aromaticivorans is. isrm10 was present in 32% of the analyzed s. meliloti strains while it ...	1999	10564804
enhanced biodegradation of phenanthrene by a marine bacterium in presence of a synthetic surfactant.	the biodegradation of phenanthrene by the marine strain sphingomonas sp. 2mpii (dsmz 11572) was enhanced by the solubilizating properties of the nonionic surfactant tween 80. after 197 h of incubation, 85 +/- 4% of the initial amount of phenanthrene (0.4 g l-1) was biodegraded in presence of tween 80 (0.5 g l-1) as opposed to 52 +/- 5% without this synthetic surfactant. these results confirm that the activity of the strain 2mpii is limited by the bioavailability of the polycyclic aromatic hydroc ...	1999	10583752
analysis of the reaction mechanism and substrate specificity of haloalkane dehalogenases by sequential and structural comparisons.	haloalkane dehalogenases catalyse environmentally important dehalogenation reactions. these microbial enzymes represent objects of interest for protein engineering studies, attempting to improve their catalytic efficiency or broaden their substrate specificity towards environmental pollutants. this paper presents the results of a comparative study of haloalkane dehalogenases originating from different organisms. protein sequences and the models of tertiary structures of haloalkane dehalogenases ...	1999	10585505
characterization of 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (pcpa) of sphingomonas chlorophenolica atcc 39723.	pentachlorophenol (pcp) is a general biocide and a major environmental pollutant. the initial steps of pcp degradation by sphingomonas chlorophenolica atcc 39723 have been studied and characterized. two enzymes are responsible for converting pcp to 2, 6-dichloro-p-hydroquinone (2,6-dich) which is a common metabolic intermediate of the biodegradation of polychlorinated phenols. 2, 6-dich is degraded by pcpa from strain atcc 39723, but the reaction end product has been misidentified as 6-chlorohyd ...	1999	10600501
identification of an extradiol dioxygenase involved in tetralin biodegradation: gene sequence analysis and purification and characterization of the gene product.	a genomic region involved in tetralin biodegradation was recently identified in sphingomonas strain tfa. we have cloned and sequenced from this region a gene designated thnc, which codes for an extradiol dioxygenase required for tetralin utilization. comparison to similar sequences allowed us to define a subfamily of 1, 2-dihydroxynaphthalene extradiol dioxygenases, which comprises two clearly different groups, and to show that thnc clusters within group 2 of this subfamily. 1,2-dihydroxy-5,6,7, ...	2000	10633115
analysis of bacterial dna in skin and muscle of the tyrolean iceman offers new insight into the mummification process.	about 80 sequences (16s ribosomal rna gene) of bacterial dna in samples of skin and muscle taken directly from the tyrolean iceman (3350-3100 years b.c.) or recovered during the 1992 archaeological expedition at the alpine site were analyzed to obtain clues to the natural mummification process that allowed the corpse of the neolithic shepherd/hunter to be preserved for more than 5,000 years. the investigation was made more complex by the fact that the surface of the mummy had been swabbed with p ...	2000	10640948
culture-dependent and culture-independent characterization of microbial assemblages associated with high-temperature petroleum reservoirs.	recent investigations of oil reservoirs in a variety of locales have indicated that these habitats may harbor active thermophilic prokaryotic assemblages. in this study, we used both molecular and culture-based methods to characterize prokaryotic consortia associated with high-temperature, sulfur-rich oil reservoirs in california. enrichment cultures designed for anaerobic thermophiles, both autotrophic and heterotrophic, were successful at temperatures ranging from 60 to 90 degrees c. heterotro ...	2000	10653739
crystallization and preliminary x-ray crystallographic analysis of alginate lyase a1-ii from sphingomonas species a1.	alginate lyase a1-ii of sphingomonas species a1 was purified and crystallized using the hanging drop vapor-diffusion method in 0.1 m tris-hcl buffer containing 43% saturated ammonium sulfate, 8% polyethylene glycol 4000 and 0.2 m li(2)so(4) at ph 8.5 and 20 degrees c. the crystals are tetragonal and belong to the space group p4(3)2(1)2 or p4(1)2(1)2 with unit cell dimensions of a=b=144.07 and c=296.38 a. the diffraction data up to 2.8 a were collected by a synchrotron radiation source at spring- ...	2000	10669804
evaluation of autoscan-w/a and the vitek gni+ automicrobic system for identification of non-glucose-fermenting gram-negative bacilli.	the autoscan-w/a (w/a; dade behring microscan inc., west sacramento, calif.) and vitek automicrobic system (vitek ams; biomérieux vitek systems, inc., hazelwood, mo.) are both fully automated microbiology systems. we evaluated the accuracy of these two systems in identifying nonglucose-fermenting gram-negative bacilli. we used the w/a with conventional-panel neg combo type 12 and vitek gni+ identification systems. a total of 301 isolates from 25 different species were tested. of these, 299 isola ...	2000	10699007
structural analysis of two glycosphingolipids from the lipopolysaccharide-lacking bacterium sphingomonas capsulata.	two glycosphingolipids, gsl-1 and gsl-3, were isolated from sphingomonas capsulata and studied by methylation analysis, laser desorption mass spectrometry, and 1h and 13c nmr spectroscopy, including two-dimensional 1h,1h cosy and heteronuclear 13c,1h cosy experiments. gsl-1 and gsl-3 differ in their carbohydrate part, their structures being alpha-d-glcpa-(1-->1)-cer and alpha-d-galp-(1-->6)-alpha-d-glcpn-(1-->4)-alpha-d-glcpa(1-- >1)cer, respectively. variations occur in the ceramide of gsl-1 an ...	2000	10712617
complete nucleotide sequence of a plant tumor-inducing ti plasmid.	crown gall tumor disease in dicot plants is caused by agrobacterium tumefaciens harboring a giant tumor-inducing (ti) plasmid. here, for the first time among agrobacterial plasmids, the nucleotide sequence of a typical nopaline-type ti plasmid (pti-sakura) was determined completely. in total, 195 open reading frames (orfs) were estimated in the 206479 bp long sequence. 20 genes for conjugation, three for replication, 22 for pathogenesis and 37 for genetic colonization of host plants were found w ...	2000	10721727
detection of groel in activated sludge: a model for detection of system stress.	groel is a ubiquitous constitutively synthesized protein that is also stress inducible. activated sludge, which is a standard biological process used in wastewater treatment systems, is made up of a diverse microbial consortium. the synthesis of groel in activated sludge was significantly induced after heat (42 degrees c) shock. the increased level of groel expression was shown to be due to de novo protein synthesis. we have demonstrated a method which shows that stress proteins can be detected ...	2000	10728556
presence of two trans-o-hydroxybenzylidenepyruvate hydratase-aldolases in naphthalenesulfonate-assimilating sphingomonas paucimobilis ta-2: comparison of some properties.	two trans-o-hydroxybenzylidenepyruvate hydratase-aldolases named thbp ha a and thbp ha b were purified from a cell-free extract of naphthalenesulfonate-assimilating sphingomonas paucimobilis (formerly pseudomonas sp.) ta-2 to an electrophoretically homogeneous state by successive column chromatographies on deae-cellulose, deae-toyopearl 650m, sephacryl s-100, hydroxyapatite, and mono q. these enzymes were similar to each other in molecular mass (ca. 37 kda on sds-page, ca. 110 kda on ultracentri ...	2000	10731665
use of oligotrophic bacteria for the biological monitoring of heavy metals.	oligotrophic bacteria exhibited active growth even in nutritionally deficient medium made with nutrient broth that had been diluted with distilled water, 1 : 10 000. the oligotrophic bacteria, sphingomonas paucimobilis kps01 and burkholderia cepacia kpc01 and kpc02 were found to be highly susceptible to heavy metals and to be potentially useful as sensors for the assessment of toxicity. the susceptibility of the bacteria to metals was measured by incubating the bacteria with metals of varying co ...	2000	10735254
a second [2fe-2s] ferredoxin from sphingomonas sp. strain rw1 can function as an electron donor for the dioxin dioxygenase.	the first step in the degradation of dibenzofuran and dibenzo-p-dioxin by sphingomonas sp. strain rw1 is carried out by dioxin dioxygenase (dxna1a2), a ring-dihydroxylating enzyme. an open reading frame (fdx3) that could potentially specify a new ferredoxin has been identified downstream of dxna1a2, a two-cistron gene (j. armengaud, b. happe, and k. n. timmis, j. bacteriol. 180:3954-3966, 1998). in the present study, we report a biochemical analysis of fdx3 produced in escherichia coli. this thi ...	2000	10735867
phylogenetic analysis of aerobic freshwater and marine enrichment cultures efficient in hydrocarbon degradation: effect of profiling method.	aerobically grown enrichment cultures derived from hydrocarbon-contaminated seawater and freshwater sediments were generated by growth on crude oil as sole carbon source. both cultures displayed a high rate of degradation for a wide range of hydrocarbon compounds. the bacterial species composition of these cultures was investigated by pcr of the 16s rdna gene using multiple primer combinations. near full-length 16s rdna clone libraries were generated and screened by restriction analysis prior to ...	2000	10739339
the function of cytoplasmic flavin reductases in the reduction of azo dyes by bacteria.	a flavin reductase, which is naturally part of the ribonucleotide reductase complex of escherichia coli, acted in cell extracts of recombinant e. coli strains under aerobic and anaerobic conditions as an "azo reductase." the transfer of the recombinant plasmid, which resulted in the constitutive expression of high levels of activity of the flavin reductase, increased the reduction rate for different industrially relevant sulfonated azo dyes in vitro almost 100-fold. the flavin reductase gene (fr ...	2000	10742223
quantitation of the population size and metabolic activity of a resin acid degrading bacterium in activated sludge using slot-blot hybridization to measure the rrna:rdna ratio.	the 16s rrna:rdna ratio is a useful parameter for measuring metabolic activity of a selected member of a complex microbial community, as in pulp effluent activated sludge systems. the rna:dna ratio of sphingomonas sp. dha-33, previously isolated from a sequencing batch reactor treating pulp mill effluent, is positively correlated with its growth rate (µ) under steady-state conditions. dha-33 was grown in a chemostat with growth rates ranging from 0.04 to 0.15 cell divisions per hour. dha-33 was ...	1999	10758181
a novel sphingoglycolipid containing galacturonic acid and 2-hydroxy fatty acid in cellular lipids of sphingomonas yanoikuyae.	a novel sphingoglycolipid was isolated from sphingomonas yanoikuyae, and its structure was identified as a galacturonosyl-beta (1-->1)-ceramide. this was a characteristic sphingoglycolipid present in s. yanoikuyae and certain other species of sphingomonas, such as sphingomonas mali, sphingomonas terrae, and sphingomonas macrogoltabidus, but not in the type species of sphingomonas, sphingomonas paucimobilis.	2000	10762275
isolation of adherent polycyclic aromatic hydrocarbon (pah)-degrading bacteria using pah-sorbing carriers.	two different procedures were compared to isolate polycyclic aromatic hydrocarbon (pah)-utilizing bacteria from pah-contaminated soil and sludge samples, i.e., (i) shaken enrichment cultures in liquid mineral medium in which pahs were supplied as crystals and (ii) a new method in which pah degraders were enriched on and recovered from hydrophobic membranes containing sorbed pahs. both techniques were successful, but selected from the same source different bacterial strains able to grow on pahs a ...	2000	10788347
products from the incomplete metabolism of pyrene by polycyclic aromatic hydrocarbon-degrading bacteria.	pyrene is a regulated pollutant at sites contaminated with polycyclic aromatic hydrocarbons (pah). it is mineralized by some bacteria but is also transformed to nonmineral products by a variety of other pah-degrading bacteria. we examined the formation of such products by four bacterial strains and identified and further characterized the most apparently significant of these metabolites. pseudomonas stutzeri strain p16 and bacillus cereus strain p21 transformed pyrene primarily to cis-4,5-dihydr ...	2000	10788360
physiological responses to starvation in the marine oligotrophic ultramicrobacterium sphingomonas sp. strain rb2256.	sphingomonas sp. strain rb2256 is representative of the ultramicrobacteria that proliferate in oligotrophic marine waters. while this class of bacteria is well adapted for growth with low concentrations of nutrients, their ability to respond to complete nutrient deprivation has not previously been investigated. in this study, we examined two-dimensional protein profiles for logarithmic and stationary-phase cells and found that protein spot intensity was regulated by up to 70-fold. a total of 72 ...	2000	10788378
coexistence of two different o demethylation systems in lignin metabolism by sphingomonas paucimobilis syk-6: cloning and sequencing of the lignin biphenyl-specific o-demethylase (ligx) gene.	sphingomonas paucimobilis syk-6 can grow on several dimeric model compounds of lignin as a carbon and energy source. it has o demethylation systems on three kinds of substrates: 5, 5'-dehydrodivanillic acid (ddva), syringate, and vanillate. we previously reported the cloning of a gene involved in the tetrahydrofolate-dependent o demethylation of syringate and vanillate. in the study reported here, we cloned the gene responsible for ddva o demethylation. using nitrosoguanidine mutagenesis, a muta ...	2000	10788391
identification of the pgmg gene, encoding a bifunctional protein with phosphoglucomutase and phosphomannomutase activities, in the gellan gum-producing strain sphingomonas paucimobilis atcc 31461.	the pgmg gene of sphingomonas paucimobilis atcc 31461, the industrial gellan gum-producing strain, was cloned and sequenced. it encodes a 50,059-da polypeptide that has phosphoglucomutase (pgm) and phosphomannomutase (pmm) activities and is 37 to 59% identical to other bifunctional proteins with pgm and pmm activities from gram-negative species, including pseudomonas aeruginosa algc. purified pgmg protein showed a marked preference for glucose-1-phosphate (g1p); the catalytic efficiency was abou ...	2000	10788412
polyphasic classification of 0.2 microm filterable bacteria from the western mediterranean sea	the 0.2 microm filtration of sea water samples from the mediterranean sea (bay of calvi, corsica), collected from 10 m and 35 m depth led to the isolation of several gram-negative bacterial strains able to grow on full-strength media as well as on diluted media. the analysis of the 16s rrna gene sequences and estimation of the phylogenetic relationships of these facultative oligotrophic bacteria indicated that they grouped into two phylogenetic branches. the strains re10f/2, re10f/5 (10 m depth ...	1999	10794152
multimicrobial sensor using microstructured three-dimensional electrodes based on silicon technology.	two microbial strains with different substrate spectra were immobilized separately within a single biosensor chip featuring four individually addressable platinum electrodes. these were sputtered onto the inner surface of four isolated pyramidal cavities ("containments") micromachined on a silicon wafer. the biosensor chip was integrated into a flow-through system to measure the oxygen consumption of the immobilized microorganisms in the presence of assimilable analytes. as a model system, a yea ...	2000	10815960
comparison of biotin production by recombinant sphingomonas sp. under various agitation conditions.	biotin production by fermentation of recombinant sphingomonas sp./psp304 was investigated. a complex medium containing 60g/l of glycerol and 30g/l of yeast extract was suitable for biotin production. biotin was produced in the late logarithmic or stationary phase after glycerol starvation. the optimum ph value for biotin production was 7.0. when the dissolved oxygen concentration (do) was controlled at a constant level, the biotin concentration produced after 120h was significantly lower than th ...	2000	10817818
recruitment of a double bond isomerase to serve as a reductive dehalogenase during biodegradation of pentachlorophenol.	tetrachlorohydroquinone dehalogenase catalyzes the replacement of chlorine atoms on tetrachlorohydroquinone and trichlorohydroquinone with hydrogen atoms during the biodegradation of pentachlorophenol by sphingomonas chlorophenolica. the sequence of the active site region of tetrachlorohydroquinone dehalogenase is very similar to those of the corresponding regions of maleylacetoacetate isomerases, enzymes that catalyze the glutathione-dependent isomerization of a cis double bond in maleylacetoac ...	2000	10820000
description of sphingomonas xenophaga sp. nov. for strains bn6t and n,n which degrade xenobiotic aromatic compounds.	the taxonomic position of two bacterial strains, bn6t and n,n, with the ability to degrade xenobiotic aromatic compounds (naphthalenesulfonates or n,n-dimethylaniline) was investigated. the 165 rrna gene sequence, the g+c content of the dna (62-63 mol%) and the detection of ubiquinone q-10, 2-hydroxymyristic acid and the sphingoglycolipid present clearly placed the two strains into the genus sphingomonas. both strains are representatives of one species according to the level of dna relatedness ( ...	2000	10826785
aerobic denitrifiers isolated from diverse natural and managed ecosystems.	twenty-eight bacterial strains were isolated from an ecosystem adapted to fluctuating oxic-anoxic conditions. this ecosystem comprised a mixture of different natural and wastewater treatment environments. among the 28 strains isolated, 10 exhibited aerobic denitrifying activity, i.e., co-respiration of oxygen and nitrate and simultaneous production of nitrite by 4 of them and of nitrogen gas by the remaining 6. comparisons between the 16s rdna sequences of the 10 strains showed that 3 of them we ...	2000	10833227
overexpression in escherichia coli, purification, and characterization of sphingomonas sp. a1 alginate lyases.	a bacterium sphingomonas sp. a1 produces three kinds of alginate lyases [a1-i (66 kda), a1-ii (25 kda), and a1-iii (40 kda)] from a single precursor, through posttranslational processing. overexpression systems for these alginate lyases were constructed in escherichia coli cells by controlling of the lyase genes under t7 promoter and terminator. expression levels of a1-i, a1-ii, and a1-iii in e. coli cells were 3.50, 3.04, and 2.13 ku/liter of culture, respectively, and were over 10-fold higher ...	2000	10833394
evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach.	the pathway for degradation of the xenobiotic pesticide pentachlorophenol in sphingomonas chlorophenolica probably evolved in the past few decades by the recruitment of enzymes from two other catabolic pathways. the first and third enzymes in the pathway, pentachlorophenol hydroxylase and 2,6-dichlorohydroquinone dioxygenase, may have originated from enzymes in a pathway for degradation of a naturally occurring chlorinated phenol. the second enzyme, a reductive dehalogenase, may have evolved fro ...	2000	10838562
physiological and genetic comparison of two aromatic hydrocarbon-degrading sphingomonas strains.	sphingomonas yanoikuyae strain b1 is able to degrade a wider range of aromatic hydrocarbons than s. paucimobilis strain tne12 can degrade. various culture techniques were used to corroborate that b1 used m-xylene, biphenyl, toluene, naphthalene, and phenanthrene as sole carbon and energy sources. in contrast, tne12 could not mineralize m-xylene, biphenyl, toluene, or naphthalene. however, fluoranthene served as carbon and energy source for tne12 but not b1. southern blots were performed using th ...	2000	10850662
fatty acid-specific, regiospecific, and stereospecific hydroxylation by cytochrome p450 (cyp152b1) from sphingomonas paucimobilis: substrate structure required for alpha-hydroxylation.	fatty acid alpha-hydroxylase from sphingomonas paucimobilis is an unusual cytochrome p450 enzyme that hydroxylates the alpha-carbon of fatty acids in the presence of h2o2. herein, we describe our investigation concerning the utilization of various substrates and the optical configuration of the alpha-hydroxyl product using a recombinant form of this enzyme. this enzyme can metabolize saturated fatty acids with carbon chain lengths of more than 10. the km value for pentadecanoic acid (c15) was th ...	2000	10858020
carbofuran degradation mediated by three related plasmid systems.	two carbofuran-metabolizing sphingomonas strains, ta and cd, were isolated from soils with differing histories of exposure to carbofuran. these strains were compared with a previously described strain, sphingomonas sp. cfo6, with regard to growth rate, formation of metabolites, and plasmid content and structure. extensive regions of similarity were observed between the three different plasmid systems as evidenced by cross hybridization. in addition, all three systems harbor is1412, an insertion ...	2000	10858578
a novel bacterial atp-binding cassette transporter system that allows uptake of macromolecules.	a gram-negative bacterium, sphingomonas sp. strain a1, isolated as a producer of alginate lyase, has a characteristic cell envelope structure and forms a mouth-like pit on its surface. the pit is produced only when the cells have to incorporate and assimilate alginate. an alginate uptake-deficient mutant was derived from cells of strain a1. one open reading frame, algs (1,089 bp), exhibiting homology to the bacterial atp-binding domain of an abc transporter, was cloned as a fragment complementin ...	2000	10869078