Publications

importance of biofilm formation for corrosion inhibition of sae 1018 steel by axenic aerobic biofilms.	to investigate if corrosion inhibition by aerobic biofilms is a general phenomenon, carbon steel (sae 1018) coupons were exposed to a complex liquid medium (luria-bertani) and seawater-mimicking medium (vnss) containing fifteen different pure-culture bacterial suspensions representing seven genera. compared to sterile controls, the mass loss in the presence of these bacteria (which are capable of developing a biofilm to various degrees) decreased by 2- to 15-fold. the extent of corrosion inhibit ...	1997	9248069
physiological stress in batch cultures of pseudomonas putida 54g during toluene degradation.	physiological stress associated with toluene exposure in batch cultures of pseudomonas putida 54g was investigated. p. putida 54g cells were grown using a continuous vapor phase feed stream containing 150 ppmv or 750 ppmv toluene as the sole carbon and energy source. cells were enumerated on non-selective (r2a agar plates) and a selective minimal medium incubated in the presence of vapor phase toluene (hcmm2). differential recovery on the two media was used to evaluate bacterial stress, culturab ...	1997	9248070
characteristics of escherichia coli hb101 and pseudomonas putida ppy101 harboring a recombinant plasmid with tandem insertion of the mercury resistance operon.	we constructed the plasmid psupmer2 by inserting tandem copies of the mercury resistance (mer) operon into a broad host range-vector, and introduced it into escherichia coli hb101 and pseudomonas putida ppy101 to increase their mercury resistance. strains harboring plasmid psupmer2 had higher mercury resistance and mercuric reductase activity than those strains harboring the plasmid psupmer which had one copy of the mer operon. mercury resistance of p. putida ppy101 was significantly increased b ...	1997	9255983
polymerase c1 levels and poly(r-3-hydroxyalkanoate) synthesis in wild-type and recombinant pseudomonas strains.	a functional antibody highly specific for polymerase c1 of pseudomonas oleovorans gpo1 was raised and used to determine polymerase c1 levels in in vivo experiments. the polymerase c1 antibodies did not show a cross-reaction with polymerase c2 of p. oleovorans. in wild-type p. oleovorans gpo1 and pseudomonas putida kt2442, amounts of 0.075 and 0.06% polymerase relative to total protein, respectively, were found. p. oleovorans gpo1(pgec405), which contained additional copies of the polymerase c1-e ...	1997	9260937
transcriptional control of the multiple catabolic pathways encoded on the tol plasmid pww53 of pseudomonas putida mt53.	the tol plasmid pww53 encodes a catabolic pathway for the metabolism of toluene. it bears an upper-pathway operon for the oxidation of toluene to benzoate and a copy of the gene that encodes regulatory protein xylr. for metabolism of the aromatic carboxylic acid, it bears two functional homologous meta-pathway operons, together with two functional copies of the xyls regulatory gene (xyls1 and xyls3). in cells growing in the absence of pathway substrates, no mrna from upper- and meta-pathway oper ...	1997	9260942
pcak, a high-affinity permease for the aromatic compounds 4-hydroxybenzoate and protocatechuate from pseudomonas putida.	pcak is a transporter and chemoreceptor protein from pseudomonas putida that is encoded as part of the beta-ketoadipate pathway regulon for aromatic acid degradation. when expressed in escherichia coli, pcak was localized to the membrane and catalyzed the accumulation of two aromatic substrates, 4-hydroxybenzoate and protocatechuate, against a concentration gradient. benzoate inhibited 4-hydroxybenzoate uptake but was not a substrate for pcak-catalyzed transport. a p. putida pcak mutant was defe ...	1997	9260946
cloning and mutational analysis of the gene for the stationary-phase inducible catalase (catc) from pseudomonas putida.	pseudomonas putida, a bacterium that colonizes plant roots and enhances plant growth, produces three isozymes of catalase (a, b, and c) in stationary-phase cells. a catalase probe, generated by pcr analysis of p. putida genomic dna with oligomers based on typical catalase sequences, hybridized to a genomic clone that expressed catalase c in escherichia coli. the catc gene from this clone had a 2,133-bp open reading frame with a high level of identity to the stationary-phase-specific e. coli kate ...	1997	9260972
group ii intron from pseudomonas alcaligenes ncib 9867 (p25x): entrapment in plasmid rp4 and sequence analysis.	pseudomonas alcaligenes ncib 9867 (strain p25x), which grows on 2,5-xylenol and harbours the plasmid rp4, was mated with a plasmid-free derivative of pseudomonas putida ncib 9869, strain ra713, which cannot grow on 2,5-xylenol. some ra713 transconjugants, initially selected on 2,5-xylenol, were found to carry rp4 plasmids that had acquired additional fragments (designated xin) which ranged in size from 2 kb to approximately 26 kb instability of dna inserts in rp4::xin hybrid plasmids was observe ...	1997	9274037
characterization and optimization of a two-phase partitioning bioreactor for the biodegradation of phenol.	a two-phase partitioning bioreactor containing pseudomonas putida atcc 11172 was used to degrade high concentrations of phenol in batch and fed-batch mode. the 2-1 (nominal volume) partitioning bioreactor employs a 1-1 cell-containing aqueous phase, and a 500-ml immiscible and biocompatible second organic phase (2-undecanone), which partitions the toxic substrate into the aqueous phase at a rate based on the metabolic activity of the microorganisms. using this reactor configuration, operated in ...	1997	9274043
crystallization and preliminary x-ray diffraction studies of expressed pseudomonas putida catechol 2,3-dioxygenase.	crystals of recombinant pseudomonas putida catechol 2,3-dioxygenase, metapyrocate-chase, composed of four identical subunits, each with a molecular mass of 35 kda and one nonheme ferrous iron, have been grown by the vapor diffusion method using sodium citrate as the precipitant. repeated macroseeding and the addition of ethanol to protein solutions were together effective for obtaining crystals suitable for further crystallographic characterization. the crystals belong to the tetragonal space gr ...	1997	9276689
microbulbifer hydrolyticus gen. nov., sp. nov., and marinobacterium georgiense gen. nov., sp. nov., two marine bacteria from a lignin-rich pulp mill waste enrichment community.	two numerically important bacteria in marine pulp mill effluent enrichment cultures were isolated. these organisms were gram-negative, rod-shaped, strictly aerobic bacteria. isolate ire-31t (t = type strain) produced hydrolytic enzymes for the breakdown of cellulose, xylan, chitin, gelatin, and tween 80. it also utilized a variety of monosaccharides, disaccharides, amino acids, and volatile fatty acids for growth. isolate kw-40t did not utilize natural polymers, but it could grow on a variety of ...	1997	9103623
description of a novel plasmid replicative origin from a genetically distinct family of conjugative plasmids associated with phytosphere microflora.	a novel replicative origin (oriv) from a conjugative, mercury resistance plasmid (pqbr11, 304 kbp) has been cloned and sequenced. homology to the pqbr11 oriv-containing 3.55 kbp bamhi fragment (pcv1200) was restricted to one of five genetically distinct classes (group i) of narrow host range, mega-plasmids that persist as a genetic component of the pseudomonad community indigenous to the microflora of sugar beet. the oriv of pqbr11 was located within a unique sequence of 300 bp which initiated t ...	1997	9103984
genetic evidence of separate repressor and activator activities of the xylr regulator of the tol plasmid, pww0, of pseudomonas putida.	the xylr protein encoded by pww0, the tol (toluene biodegradation) plasmid of pseudomonas putida, activates at a distance the transcription of pu and ps, which are the two sigma(54)-dependent promoters of the plasmid, but it also downregulates its own sigma(70)-promoter, pr, which divergently overlaps the upstream activating sites of ps. all regulatory elements that control pr activity have been faithfully reproduced in escherichia coli, and the basis of the autoregulation of xylr transcription ...	1997	9106213
bipolar localization of a chromosome partition protein in bacillus subtilis.	we have determined the subcellular localization of the chromosome partition protein spo0j of bacillus subtilis by immunofluorescence microscopy and visualizing fluorescence of a spo0j-gfp fusion protein. spo0j was associated with a region of the nucleoid proximal to the cell pole, both in growing cells dividing symmetrically and in sporulating cells dividing asymmetrically. additional experiments indicated that spo0j was bound to sites in the origin-proximal third of the chromosome. these result ...	1997	9114058
comparative study of five polycyclic aromatic hydrocarbon degrading bacterial strains isolated from contaminated soils.	five polycyclic aromatic hydrocarbon (pah) degrading bacterial strains, pseudomonas putida 34, pseudomonas fluorescens 62, pseudomonas aeruginosa 57, sphingomonas sp. strain 107, and the unidentified strain pl1, were isolated from two contaminated soils and characterized for specific features regarding pah degradation. degradation efficiency was determined by the rapidity to form clearing zones around colonies when sprayed with different pah solutions and the growth in liquid medium with differe ...	1997	9115093
cloning and expression in pseudomonas putida of two of the histidine utilization genes from rhizobium fredii.	two of the genes encoding histidine utilization (hut) in rhizobium fredii strain hh303 have been cloned in pseudomonas putida and partially characterized. molecular cloning of the genes was achieved by mobilizing an r. fredii cosmid library into a mutant strain of p. putida containing a tn5 element in its histidase (huth) gene. a number of overlapping clones were identified, all of which contain a 7.1-kbp hindiii fragment. the origin of this 7.1-kbp fragment from the chromosome of r. fredii was ...	1997	8939803
choline monooxygenase, an unusual iron-sulfur enzyme catalyzing the first step of glycine betaine synthesis in plants: prosthetic group characterization and cdna cloning.	plants synthesize the osmoprotectant glycine betaine via the route choline --> betaine aldehyde --> glycine betaine. in spinach, the first step is catalyzed by choline monooxygenase (cmo), a ferredoxin-dependent stromal enzyme that has been hypothesized to be an oligomer of identical subunits and to be an fe-s protein. analysis by hplc and matrix-assisted laser desorption ionization ms confirmed that native cmo contains only one type of subunit (mr 42,864). determination of acid-labile sulfur an ...	1997	9096415
modulation of the function of the signal receptor domain of xylr, a member of a family of prokaryotic enhancer-like positive regulators.	the xylr protein controls expression from the pseudomonas putida tol plasmid upper pathway operon promoter (pu) in response to aromatic effectors. xylr-dependent stimulation of transcription from a pu::lacz fusion shows different induction kinetics with different effectors. with toluene, activation followed a hyperbolic curve with an apparent k of 0.95 mm and a maximum beta-galactosidase activity of 2,550 miller units. with o-nitrotoluene, in contrast, activation followed a sigmoidal curve with ...	1998	9457863
expression and characterization of (r)-specific enoyl coenzyme a hydratase involved in polyhydroxyalkanoate biosynthesis by aeromonas caviae.	complementation analysis of a polyhydroxyalkanoate (pha)-negative mutant of aeromonas caviae proved that orf3 in the pha locus (a 402-bp gene located downstream of the pha synthase gene) participates in pha biosynthesis on alkanoic acids, and the orf3 gene is here referred to as phaj(ac). escherichia coli bl21(de3) carrying phaj(ac). under the control of the t7 promoter overexpressed enoyl coenzyme a (enoyl-coa) hydratase, which was purified by one-step anion-exchange chromatography. the n-termi ...	1998	9457873
cloning, sequencing, and expression in escherichia coli of d-hydantoinase gene from pseudomonas putida.		1998	9928097
[antigenic mapping of cytochrome p450 101 (p450cam)].	eighteen linear antigenic sites were found in cytochrome p450 101 (p450cam) from pseudomonas putida by the peptide scanning method. these sites accounted for about 30% of the protein sequence. we found no sequences that completely coincided with the antigenic sites of p450cam in cytochromes p450 from other sources. the linear b-epitopes of p540cam were mainly localized on the boundaries separating the elements of the secondary structure. seventeen of eighteen antigenic sites were found to be on ...	1998	9929735
short-run tests for determining harmful effects of pcb-containing engine oils on cells.	our main objective was to set up reproducible methods for a rapid determination of harmful effects of pcb-containing engine oils on cells. we used a plate method and scenedesmus quadricauda, saccharomyces cerevisiae, rhodotorula glutinis and pseudomonas putida as test organisms.	1998	9867477
isolation and characterization of toluene-sensitive mutants from pseudomonas putida ih-2000.	two toluene-sensitive mutants were generated from pseudomonas putida ih-2000, the first known toluene-tolerant isolate, by tn5 transposon mutagenesis. these mutants were unable to grow in the presence of toluene (log p(ow) 2.8) but they could grow in medium overlaid with organic solvents having a log p(ow) value higher than that of toluene such as p-xylene (log p(ow) 3.1), cyclohexane (log p(ow) 3.4) and n-hexane (log p(ow) 3.9). the tn5 transposable element knocked out a cyob-like gene in one m ...	1998	9868765
rational engineering of the tol meta-cleavage pathway	the meta-cleavage pathway of pseudomonas putida mt-2 was simulated using a biochemical systems simulation developed by regan (1996). a non-competitive inhibition term for catechol-2,3-dioxygenase (c23o) by 2-oh-pent-2,4-dienoate (ki = 150 μm) was incorporated into the model. the simulation predicted steady state accumulation levels in the μm range for metabolites pre-meta-cleavage, and in the mm range for metabolites post-meta-cleavage. the logarithmic gains l[v-i, xj] and l[x-i, xj] clearly ind ...	1998	10191395
lithocholic acid side-chain cleavage to produce 17-keto or 22-aldehyde steroids by pseudomonas putida strain st-491 grown in the presence of an organic solvent, diphenyl ether.	we devised a method to screen for microorganisms capable of growing on bile acids in the presence of organic solvents and producing organic solvent-soluble derivatives. pseudomonas putida biovar a strain st-491 isolated in this study produced decarboxylated derivatives from the bile acids. strain st-491 grown on 0.5% lithocholic acid catabolized approximately 30% of the substrate as a carbon source, and transiently accumulated in the medium androsta-1,4-diene-3,17-dione in an amount of correspon ...	1998	9972239
effect of oxidative stress on the biosynthesis of 2-c-methyl-d-erythritol-2,4-cyclopyrophosphate and isoprenoids by several bacterial strains.	in this study, the gram-negative bacteria xanthomonas campestris, xanthomonas maltophilia, and pseudomonas putida, facultative parasites of plants and animals, were shown to accumulate 2-c-methyl-d-erythritol-2,4-cyclopyrophosphate (mec) in response to benzyl-viologen-induced oxidative stress. corynebacterium ammoniagenes mutants capable of accumulating mec in the absence of an exogenous oxidative stress inducer were obtained. isoprenoid synthesis and mec synthesis in these and other bacteria we ...	1998	9871022
[occurrence of gram-negative non-fermenting rods in hemocultures and their sensitivity to antimicrobial agents].	in the period from january 1993 to june 1996 were at the department of microbiology of the university hospital in olomouc 122 strains of gram-negative nonfermentative rod-shaped bacteria isolated from haemocultures. the majority represented the group of 51 strains of the genus acinetobacter (41.8%), complex a. calcoaceticus-baumannii (acb complex). the second largest group were 21 strains (17.2%) of pseudomonas aeruginosa. these were followed by 17 strains (13.9%) of stenotrophomonas maltophilia ...	1998	9919762
mobilization of broad host range plasmid from pseudomonas putida to established biofilm of bacillus azotoformans. i. experiments.	a strain of pseudomonas putida harboring plasmids rk2 and pdlb101 was exposed to a pure culture biofilm of bacillus azotoformans grown in a rotating annular reactor under three different concentrations of the limiting nutrient, succinate. experimental results demonstrated that the broad host range rsf1010 derivative pdlb101 was transferred to and expressed by b. azotoformans. at the lower concentrations, donor mediated plasmid transfer increased with increasing nutrient levels, but the highest n ...	1998	10099203
mobilization of broad host range plasmid from pseudomonas putida to established biofilm of bacillus azotoformans. ii. modeling.	a strain of pseudomonas putida that harbors plasmids rk2 and pdlb101 was exposed to a pure culture biofilm of bacillus azotoformans grown in a rotating annular reactor. transfer of the rk2 mobilizable pdlb101 plasmid to b. azotoformans was monitored over a 4-day period. experimental results demonstrated that the broad host range, rsf1010 derivative pdlb101 was transferred to and expressed by b. azotoformans. in the companion article to this work, the rate of plasmid transfer was quantified as a ...	1998	10099204
two-phase bioconversion product recovery by microfiltration i. steady state studies.	recovery of an aqueous bioconversion product from complex, two-phase pseudomonas putida broths containing 20% (v/v) soybean oil presents a significant challenge for downstream processing. although not used before in multiple-phase separation for complex biotech products, crossflow filtration employing ceramic filters is one of the most attractive options which allow the design of integrated, continuous bioconversion processes. as a first attempt, we studied multichannel, monolithic ceramic membr ...	1998	10099243
growth kinetics of pseudomonas putida g7 on naphthalene and occurrence of naphthalene toxicity during nutrient deprivation.	the objectives of this work were (1) to demonstrate how the chemostat approach could be modified to allow determination of kinetic parameters for a sparingly soluble, volatile substrate such as naphthalene and (2) to examine the influence of the interactions of various nutrients on possible growth-inhibitory effects of naphthalene. pseudomonas putida g7 was used as a model naphthalene-degrading microorganism. naphthalene was found to be toxic to p. putida g7 in the absence of a nitrogen source o ...	1998	10099376
local macromolecule diffusion coefficients in structurally non-uniform bacterial biofilms using fluorescence recovery after photobleaching (frap).	pure culture pseudomonas putida biofilms were cultivated under controlled conditions to a desired overall biofilm thickness, then employed within classical half-cell diffusion chambers to estimate, from transient solute concentrations, the effective diffusion coefficient for several macromolecules of increasing molecular weight and molecular complexity. results of traditional half-cell studies were found to be erroneous due to the existence of microscopic water channels or crevasses that perfora ...	1998	10099452
double inhibition model for degradation of phenol by pseudomonas putida q5.	a semiempirical model, based on the presence of an inhibitory intermediate metabolite excreted to the broth, was developed to better predict the dynamic responses to shock loadings of pseudomonas putida q5 degrading phenol. compared to the haldane equation, the new model exhibited better prediction capabilities for a broad range of inlet concentration and dilution rate step changes. the experiments were performed at 10 degrees and 25 degrees c and ranged from stable responses to washouts. the ti ...	1998	10099464
expression and export of pseudomonas putida ntu-8 creatinase by escherichia coli using the chitinase signal sequence of aeromonas hydrophila.	the gene for the creatinase from pseudomonas putida ntu-8 was sequenced and revealed an open reading frame (orf) of 1209 base pairs encoding a polypeptide of 403 amino acids with a calculated molecular weight (m(r)) of 45,691. the deduced amino acid sequence is very similar to that of the creatinase of pseudomonas putida and flavobacterium sp. an overproduction system for the chitinase signal peptide--creatinase hybrid gene was constructed by using the pqe-51 expression vector in e. coli jm109. ...	1998	10230521
a novel -2fe-2s- ferredoxin from pseudomonas putida mt2 promotes the reductive reactivation of catechol 2,3-dioxygenase.	catechol 2,3-dioxygenase (xyle) is a component of the tol plasmid-encoded pathway for the degradation of toluene and xylenes and catalyzes the dioxygenolytic cleavage of the aromatic ring. purified xyle is oxygen-sensitive and unstable in vitro, particularly in the presence of substituted catechol substrates, but it is stabilized in vivo by another protein, xylt, encoded by the xylt gene located just upstream of xyle. in this study, we have purified to homogeneity the xylt product from a recombi ...	1998	9545294
alkane hydroxylase from acinetobacter sp. strain adp1 is encoded by alkm and belongs to a new family of bacterial integral-membrane hydrocarbon hydroxylases.	degradation of long-chain alkanes by acinetobacter sp. strain adp1 involves rubredoxin and rubredoxin reductase. we complemented a mutant deficient in alkane utilization and sequenced four open reading frames (orfs) on the complementing dna. each of these orfs was disrupted by insertional mutagenesis on the chromosome. as determined from sequence comparisons, orf1 and orf4 seem to encode a rotamase of the ppic type and an acyl coenzyme a dehydrogenase, respectively. disruption of these orfs does ...	1998	9546151
effects of bacterial host and dichloromethane dehalogenase on the competitiveness of methylotrophic bacteria growing with dichloromethane.	methylobacterium sp. strain dm4 and methylophilus sp. strain dm11 can grow with dichloromethane (dcm) as the sole source of carbon and energy by virtue of homologous glutathione-dependent dcm dehalogenases with markedly different kinetic properties (the kcat values of the enzymes of these strains are 0.6 and 3.3 s-1, respectively, and the km values are 9 and 59 microm, respectively). these strains, as well as transconjugant bacteria expressing the dcm dehalogenase gene (dcma) from dm11 or dm4 on ...	1998	9546153
population dynamics of phenol-degrading bacteria in activated sludge determined by gyrb-targeted quantitative pcr.	a method for quantifying bacterial populations introduced into an activated-sludge microbial community is described. the method involves extraction of dna from activated sludge, appropriate dilution of the extracted dna with dna extracted from nonintroduced activated sludge, pcr amplification of a gyrb gene fragment from the introduced strain with a set of strain-specific primers, and quantification of the electrophoresed pcr product by densitometry. the adequacy of the method was examined by an ...	1998	9546154
self-transmissible mercury resistance plasmids with gene-mobilizing capacity in soil bacterial populations: influence of wheat roots and mercury addition.	a set of mercury resistance plasmids was obtained from wheat rhizosphere soil amended or not amended with mercuric chloride via exogenous plasmid isolation by using pseudomonas fluorescens r2f, pseudomonas putida uwc1, and enterobacter cloacae be1 as recipient strains. the isolation frequencies were highest from soil amended with high levels of mercury, and the isolation frequencies from unamended soil were low. with p. putida uwc1 as the recipient, the isolation frequency was significantly enha ...	1998	9546155
19f nuclear magnetic resonance as a tool to investigate microbial degradation of fluorophenols to fluorocatechols and fluoromuconates.	a method was developed to study the biodegradation and oxidative biodehalogenation of fluorinated phenols by 19f nuclear magnetic resonance (nmr). characterization of the 19f nmr spectra of metabolite profiles of a series of fluorophenols, converted by purified phenol hydroxylase, catechol 1,2-dioxygenase, and/or by the yeast-like fungus exophiala jeanselmei, provided possibilities for identification of the 19f nmr chemical shift values of fluorinated catechol and muconate metabolites. as an exa ...	1998	9546160
grazing of tetrahymena sp. on adhered bacteria in percolated columns monitored by in situ hybridization with fluorescent oligonucleotide probes.	predation of attached pseudomonas putida mt2 by the small ciliate tetrahymena sp. was investigated with a percolated column system. grazing rates were examined under static and dynamic conditions and were compared to grazing rates in batch systems containing suspended prey. the prey densities were 2 x 10(8) bacteria per ml of pore space and 2 x 10(8) bacteria per ml of suspension, respectively. postingestion in situ hybridization of bacteria with fluorescent oligonucleotide probes was used to qu ...	1998	9546161
biodegradation of metal-edta complexes by an enriched microbial population.	a mixed culture utilizing edta as the sole carbon source was isolated from a mixed inoculum of water from the river mersey (united kingdom) and sludge from an industrial effluent treatment plant. fourteen component organisms were isolated from the culture, including representatives of the genera methylobacterium, variovorax, enterobacter, aureobacterium, and bacillus. the mixed culture biodegraded metal-edta complexes slowly; the biodegradability was in the order fe > cu > co > ni > cd. by incor ...	1998	9546167
development of a direct in situ pcr method for detection of specific bacteria in natural environments.	we applied hnpp (2-hydroxy-3-naphthoic acid-2'-phenylanilide phosphate) to direct in situ pcr for the routine detection of specific bacterial cells at the single-cell level. pcr was performed on glass slides with digoxigenin-labeled dutp. the digoxigenin-labeled pcr products were detected with alkaline phosphatase-labeled antidigoxigenin antibody and hnpp which was combined with fast red tr. a bright red fluorescent signal was produced from conversion to hnp (dephosphorylated form) by alkaline p ...	1998	9546190
ntn genes determining the early steps in the divergent catabolism of 4-nitrotoluene and toluene in pseudomonas sp. strain tw3.	pseudomonas sp. strain tw3 is able to oxidatively metabolize 4-nitrotoluene and toluene via a route analogous to the upper pathway of the tol plasmids. we report the sequence and organization of five genes, ntnwcmab*, which are very similar to and in the same order as the xyl operon of tol plasmid pww0 and present evidence that they encode enzymes which are expressed during growth on both 4-nitrotoluene and toluene and are responsible for their oxidation to 4-nitrobenzoate and benzoate, respecti ...	1998	9555884
availability of o2 as a substrate in the cytoplasm of bacteria under aerobic and microaerobic conditions.	the growth rates of pseudomonas putida kt2442 and mt-2 on benzoate, 4-hydroxybenzoate, or 4-methylbenzoate showed an exponential decrease with decreasing oxygen tensions (partial o2 tension [po2] values). the oxygen tensions resulting in half-maximal growth rates were in the range of 7 to 8 mbar of o2 (corresponding to 7 to 8 microm o2) (1 bar = 10(5) pa) for aromatic compounds, compared to 1 to 2 mbar for nonaromatic compounds like glucose or succinate. the decrease in the growth rates coincide ...	1998	9555896
the tfdk gene product facilitates uptake of 2,4-dichlorophenoxyacetate by ralstonia eutropha jmp134(pjp4).	uptake of 2,4-dichlorophenoxyacetate (2,4-d) by ralstonia eutropha jmp134(pjp4) was studied and shown to be an energy-dependent process. the uptake system was inducible with 2,4-d and followed saturation kinetics in a concentration range of up to 60 microm, implying the involvement of a protein in the transport process. we identified an open reading frame on plasmid pjp4, which was designated tfdk, whose translation product tfdk was highly hydrophobic and showed resemblance to transport proteins ...	1998	9555911
overexpression, purification, and characterization of the cloned metallo-beta-lactamase l1 from stenotrophomonas maltophilia.	the metallo-beta-lactamase l1 from stenotrophomonas maltophilia was cloned, overexpressed, and characterized by spectrometric and biochemical techniques. results of metal analyses were consistent with the cloned enzyme having 2 mol of tightly bound zn(ii) per monomer. gel filtration chromatography demonstrated that the cloned enzyme exists as a tightly held tetramer with a molecular mass of ca. 115 kda, and matrix-assisted laser desorption ionization and time-of-flight mass spectrometry indicate ...	1998	9559809
alginate lyase promotes diffusion of aminoglycosides through the extracellular polysaccharide of mucoid pseudomonas aeruginosa.	we demonstrated that a 2% suspension of pseudomonas aeruginosa alginate completely blocked the diffusion of gentamicin and tobramycin, but not that of carbenicillin, illustrating how alginate production can help protect p. aeruginosa growing within alginate microcolonies in patients with cystic fibrosis (cf) from the effects of aminoglycosides. this aminoglycoside diffusion barrier was degraded with a semipurified preparation of p. aeruginosa alginate lyase, suggesting that this enzyme deserves ...	1998	9559826
a novel phenol hydroxylase and catechol 2,3-dioxygenase from the thermophilic bacillus thermoleovorans strain a2: nucleotide sequence and analysis of the genes.	the new thermophilic bacillus thermoleovorans strain a2 degrades phenol and cresols via the meta cleavage pathway. the first two enzymes involved in this process, the phenol hydroxylase and catechol 2,3-dioxygenase, encoded by the phea and pheb genes respectively, were cloned and sequenced. the deduced amino acid sequence of phea contains 524 amino acids with a theoretical m(r) of 59,602 da and displays less than 10% amino acid identity to known phenol hydroxylases. the greatest amino acid ident ...	1998	9561730
is1491 from pseudomonas alcaligenes ncib 9867: characterization and distribution among pseudomonas species.	a new insertion sequence, is1491, has been cloned and sequenced. the 2489-bp is1491 was isolated from a pseudomonas alcaligenes ncib 9867 (strain p25x) 4.8-kb psti chromosomal fragment. is1491 is flanked by an imperfect inverted repeat of 23 bp and carries two overlapping open reading frames, orf1 and orf2. both orf1 and orf2 displayed homology to the ista-like and istb-like transposases encoded by the is21 family of insertion sequences, which include two is elements previously isolated from p. ...	1998	9571135
modular fluorescent-labeled siderophore analogues.	biomimetic analogues 1 of the microbial siderophore (iron carrier) ferrichrome were labeled via piperazine with various fluorescent markers at a site not interfering with iron binding or receptor recognition (compounds 10-12). these iron carriers were built from a tetrahedral carbon symmetrically extended with three strands, each containing an amino acid (g = glycyl, a = alanyl, l = leucyl and p = phenylalanyl) and terminated by a hydroxamic acid, which together define an octahedral iron-binding ...	1998	9572892
a gene system for glucitol transport and metabolism in clostridium beijerinckii ncimb 8052.	the gutd gene of clostridium beijerinckii ncimb 8052 encoding glucitol 6-phosphate dehydrogenase was cloned on a 5.7-kbp chromosomal dna fragment by complementing an escherichia coli gutd mutant strain and selecting for growth on glucitol. five open reading frames (orfs) in the order guta1 guta2 orfx gutb gutd were identified in a 4.0-kbp region of the cloned dna. the deduced products of four of these orfs were homologous to components of the glucitol phosphotransferase system (pts) and glucitol ...	1998	9572925
two new mycobacterium strains and their role in toluene degradation in a contaminated stream.	two toluene-degrading strains, t103 and t104, were isolated from rock surface biomass in a freshwater stream contaminated with toluene. the strains exhibit different capacities for degradation of toluene and other aromatic compounds and have characteristics of the genus mycobacterium. both are aerobic, rod-shaped, gram-positive, nonmotile, and acid-alcohol fast and produce yellow pigments. they have mainly straight-chain saturated and monounsaturated fatty acids with 10 to 20 carbon atoms and la ...	1998	9572941
a mixed culture recovery method indicates that enteric bacteria do not enter the viable but nonculturable state.	a new method, called the mixed culture recovery (mcr) method, has been developed to determine whether recovery of culturable bacterial cells from a population of largely nonculturable cells is due to resuscitation of the nonculturable cells from a viable but nonculturable state or simply to growth of residual culturable cells. the mcr method addresses this issue in that it involves the mixing of two easily distinguishable strains (e.g., lactose positive and negative) in such a way that large num ...	1998	9572945
use of inducible feedback-resistant n-acetylglutamate synthetase (arga) genes for enhanced arginine biosynthesis by genetically engineered escherichia coli k-12 strains.	the goal of this work was to construct escherichia coli strains capable of enhanced arginine production. the arginine biosynthetic capacity of previously engineered e. coli strains with a derepressed arginine regulon was limited by the availability of endogenous ornithine (m. tuchman, b. s. rajagopal, m. t. mccann, and m. h. malamy, appl. environ. microbiol. 63:33-38, 1997). ornithine biosynthesis is limited due to feedback inhibition by arginine of n-acetylglutamate synthetase (nags), the produ ...	1998	9572954
oxidation of methyl-substituted naphthalenes: pathways in a versatile sphingomonas paucimobilis strain	aromatic compounds with alkyl substituents are abundant in fossil fuels. these compounds become important environmental sources of soluble toxic products, developmental inhibitors, etc. principally through biological activities. to assess the effect of methyl substitution on the completeness of mineralization and accumulation of pathway products, an isolate from a phenanthrene enrichment culture, sphingomonas paucimobilis 2322, was used. washed cell suspensions containing cells grown on 2,6-dime ...	1998	9572967
effect of bacterial distribution and activity on conjugal gene transfer on the phylloplane of the bush bean (phaseolus vulgaris).	conjugal plasmid transfer was examined on the phylloplane of bean (phaseolus vulgaris) and related to the spatial distribution pattern and metabolic activity of the bacteria. the donor (pseudomonas putida kt2442) harbored a derivative of the tol plasmid, which conferred kanamycin resistance and had the gfp gene inserted downstream of a lac promoter. a chromosomal insertion of laciq prevented expression of the gfp gene. the recipient (p. putida kt2440) had a chromosomal tetracycline resistance ma ...	1998	9572970
structures of homologous composite transposons carrying cbaabc genes from europe and north america.	is1071 is a class ii transposable element carrying a tnpa gene related to the transposase genes of the tn3 family. copies of is1071 that are conserved with more than 99% nucleotide sequence identity have been found as direct repeats flanking a remarkable variety of catabolic gene sequences worldwide. the sequences of chlorobenzoate catabolic transposons found on pbrc60 (tn5271) in niagara falls, n.y., and on pcpe3 in bologna, italy, show that these transposons were formed from highly homologous ...	1998	9572977
burkholderia cepacia produces a hemolysin that is capable of inducing apoptosis and degranulation of mammalian phagocytes.	burkholderia cepacia is an opportunistic pathogen that has become a major threat to individuals with cystic fibrosis (cf). in approximately 20% of patients, pulmonary colonization with b. cepacia leads to cepacia syndrome, a fatal fulminating pneumonia sometimes associated with septicemia. it has been reported that culture filtrates of clinically derived strains of b. cepacia are hemolytic. in this study, we have characterized a factor which contributes to this hemolytic activity and is secreted ...	1998	9573086
cloning of genes coding for the three subunits of thiocyanate hydrolase of thiobacillus thioparus thi 115 and their evolutionary relationships to nitrile hydratase.	thiocyanate hydrolase is a newly found enzyme from thiobacillus thioparus thi 115 that converts thiocyanate to carbonyl sulfide and ammonia (y. katayama, y. narahara, y. inoue, f. amano, t. kanagawa, and h. kuraishi, j. biol. chem. 267:9170-9175, 1992). we have cloned and sequenced the scn genes that encode the three subunits of the enzyme. the scnb, scna, and scnc genes, arrayed in this order, contained open reading frames encoding sequences of 157, 126, and 243 amino acid residues, respectivel ...	1998	9573140
regulation of the carnitine pathway in escherichia coli: investigation of the cai-fix divergent promoter region.	the divergent structural operons caitabcde and fixabcx of escherichia coli are required for anaerobic carnitine metabolism. transcriptional monocopy lacz fusion studies showed that both operons are coexpressed during anaerobic growth in the presence of carnitine, respond to common environmental stimuli (like glucose and nitrate), and are modulated positively by the same general regulators, crp and fnr, and negatively by h-ns. overproduction of the caif specific regulatory protein mediating the c ...	1998	9573142
mutational analysis of the phosphate-binding loop of rhizobium meliloti dctd, a sigma54-dependent activator.	the phosphate-binding loop of sigma54-dependent activators is thought to participate in atp binding and/or hydrolysis. alanine substitutions at positions 3, 4, 6, 7, and 8 of this motif in rhizobium meliloti dctd disrupted transcriptional activation and atp hydrolysis. interestingly, substitution of alanine at position 7 also affected dna binding.	1998	9573172
regulation of lactose utilization genes in staphylococcus xylosus.	the lactose utilization genes of staphylococcus xylosus have been isolated and characterized. the system is comprised of two structural genes, lacp and lach, encoding the lactose permease and the beta-galactosidase proteins, respectively, and a regulatory gene, lacr, coding for an activator of the arac/xyls family. the lactose utilization genes are divergently arranged, the lacph genes being opposite to lacr. the lacph genes are cotranscribed from one promoter in front of lacp, whereas lacr is t ...	1998	9573174
metalloadsorption by escherichia coli cells displaying yeast and mammalian metallothioneins anchored to the outer membrane protein lamb.	yeast (cup1) and mammalian (hmt-1a) metallothioneins (mts) have been efficiently expressed in escherichia coli as fusions to the outer membrane protein lamb. a 65-amino-acid sequence from the cup1 protein of saccharomyces cerevisiae (yeast [y] mt) was genetically inserted in permissive site 153 of the lamb sequence, which faces the outer medium. a second lamb fusion at position 153 was created with 66 amino acids recruited from the form of human (h) mt that is predominant in the adipose tissue, ...	1998	9573175
2-ketocyclohexanecarboxyl coenzyme a hydrolase, the ring cleavage enzyme required for anaerobic benzoate degradation by rhodopseudomonas palustris.	2-ketocyclohexanecarboxyl coenzyme a (2-ketochc-coa) hydrolase has been proposed to catalyze an unusual hydrolytic ring cleavage reaction as the last unique step in the pathway of anaerobic benzoate degradation by bacteria. this enzyme was purified from the phototrophic bacterium rhodopseudomonas palustris by sequential q-sepharose, phenyl-sepharose, gel filtration, and hydroxyapatite chromatography. the sequence of the 25 n-terminal amino acids of the purified hydrolase was identical to the ded ...	1998	9573182
substrate specificities of hybrid naphthalene and 2,4-dinitrotoluene dioxygenase enzyme systems.	bacterial three-component dioxygenase systems consist of reductase and ferredoxin components which transfer electrons from nad(p)h to a terminal oxygenase. in most cases, the oxygenase consists of two different subunits (alpha and beta). to assess the contributions of the alpha and beta subunits of the oxygenase to substrate specificity, hybrid dioxygenase enzymes were formed by coexpressing genes from two compatible plasmids in escherichia coli. the activities of hybrid naphthalene and 2,4-dini ...	1998	9573183
transcriptional repression mediated by lysr-type regulator catr bound at multiple binding sites.	the catbca operon of pseudomonas putida encodes enzymes involved in the catabolism of benzoate. transcription of this operon requires the lysr-type transcriptional regulator catr and an inducer molecule, cis,cis-muconate. previous gel shift assays and dnase i footprinting have demonstrated that catr occupies two adjacent sites proximal to the catbca promoter in the presence of the inducer. we report the presence of an additional binding site for catr downstream of the catbca promoter within the ...	1998	9573187
regulation of benzoate degradation in acinetobacter sp. strain adp1 by benm, a lysr-type transcriptional activator.	in acinetobacter sp. strain adp1, benzoate degradation requires the ben genes for converting benzoate to catechol and the cat genes for degrading catechol. here we describe a novel transcriptional activator, benm, that regulates the chromosomal ben and cat genes. benm is homologous to catm, a lysr-type transcriptional activator of the cat genes. unusual regulatory features of this system include the abilities of both benm and catm to recognize the same inducer, cis,cis-muconate, and to regulate ...	1998	9573203
a novel 2-aminomuconate deaminase in the nitrobenzene degradation pathway of pseudomonas pseudoalcaligenes js45.	2-aminomuconate, an intermediate in the metabolism of tryptophan in mammals, is also an intermediate in the biodegradation of nitrobenzene by pseudomonas pseudoalcaligenes js45. strain js45 hydrolyzes 2-aminomuconate to 4-oxalocrotonic acid, with the release of ammonia, which serves as the nitrogen source for growth of the microorganism. as an initial step in studying the novel deamination mechanism, we report here the purification and some properties of 2-aminomuconate deaminase. the purified e ...	1998	9573204
a gene cluster encoding steps in conversion of naphthalene to gentisate in pseudomonas sp. strain u2.	pseudomonas sp. strain u2 was isolated from oil-contaminated soil in venezuela by selective enrichment on naphthalene as the sole carbon source. the genes for naphthalene dioxygenase were cloned from the plasmid dna of strain u2 on an 8.3-kb bamhi fragment. the genes for the naphthalene dioxygenase genes nagaa (for ferredoxin reductase), nagab (for ferredoxin), and nagac and nagad (for the large and small subunits of dioxygenase, respectively) were located by southern hybridizations and by nucle ...	1998	9573207
fluorescent pseudomonad pyoverdines bind and oxidize ferrous ion.	major pyoverdines from pseudomonas fluorescens 2-79 (pf-b), p. aeruginosa atcc 15692 (pa-c), and p. putida atcc 12633 (pp-c) were examined by absorption and fluorescence spectroscopic techniques to investigate the interaction between ferrous ion and the pyoverdine ligand. at physiological ph, ferrous ion quenched the fluorescence of all three pyoverdines much faster than ferric ion did. also, increased absorbance at 460 nm was observed to be much faster for fe2+ -pyoverdine than for fe3+ -pyover ...	1998	9575133
defense activation and enhanced pathogen tolerance induced by h2o2 in transgenic tobacco.	transgenic tobacco deficient in the h2o2-removing enzyme catalase (cat1as) was used as an inducible and noninvasive system to study the role of h2o2 as an activator of pathogenesis-related (pr) proteins in plants. excess h2o2 in cat1as plants was generated by simply increasing light intensities. sustained exposure of cat1as plants to excess h2o2 provoked tissue damage, stimulated salicylic acid and ethylene production, and induced the expression of acidic and basic pr proteins with a timing and ...	1998	9576968
genetics of ferulic acid bioconversion to protocatechuic acid in plant-growth-promoting pseudomonas putida wcs358.	transposon tn5 genomic mutants of plant-growth-promoting pseudomonas putida strain wcs358 have been isolated which no longer utilize ferulic and coumaric acids as sole sources of carbon and energy. genetic studies confirmed previous biochemical data showing that ferulic acid is degraded via vanillic acid, and coumaric acid via hydroxybenzoic acid. the genes involved in these enzymic steps were cloned and characterized. two proteins designated fca (26.5 kda) and vdh (50.3 kda) were identified as ...	1998	9579070
characterization of bradyrhizobium japonicum pcabdc genes involved in 4-hydroxybenzoate degradation.	the pca structural genes encode enzymes that participate in the conversion of protocatechuate to succinate and acetylcoenzyme a. a 3. 05-kb region of the bradyrhizobium japonicum strain usda110 genome has been characterized, which contains the pcab, pcad and pcac genes. the predicted protein sequences of the three genes have extensive homologies with beta-carboxy-cis,cis-muconate cycloisomerase (pcab), beta-ketodiapate enol-lactone hydrolase (pcad), and gamma-carboxymuconolactone decarboxylase ( ...	1998	9582432
h2-m3 restricted presentation of a listeria-derived leader peptide.	protective immunity to infection by many intracellular pathogens requires recognition by cytotoxic t lymphocytes (ctls) of antigens presented on major histocompatibility complex (mhc) class i molecules. to be presented for recognition by pathogen-specific ctls, these antigens must gain access to the host cell class i processing pathway. in the case of intracellular bacterial pathogens, the majority of bacterial proteins are retained within the bacterial membrane and therefore remain inaccessible ...	1998	9584149
reductive and oxidative half-reactions of morphinone reductase from pseudomonas putida m10: a kinetic and thermodynamic analysis.	the reaction of morphinone reductase (mr) with the physiological reductant nadh and the oxidizing substrate codeinone has been studied by multiple and single wavelength stopped-flow spectroscopy. reduction of the enzyme with nadh proceeds in two kinetically resolvable steps. in the first step, the oxidized enzyme forms a charge-transfer intermediate with nadh. the charge-transfer complex is characterized by an increase in absorbance at long wavelength (540 to 650 nm), and its rate of formation i ...	1998	9585575
hypothermia predisposing to pseudomonas putida sepsis in a child with panhypopituitarism.	a 14-year-old boy presented with a 1-week history of hypothermia and obtundation. his medical history included surgical resection of craniopharyngioma with postoperative visual impairment and panhypopituitarism. the patient's rectal temperature remained persistently lower than 35 degrees c during the first 3 days of hospitalization. his blood pressure was 90/56 mmhg on admission. the peripheral blood leukocyte count was 2.7 x 10(10)/l with 18% neutrophils, 19% band forms, 44% metamyelocytes, 3% ...	1998	9585682
a 7.6kb dna region from streptomyces kasugaensis m338-m1 includes some genes responsible for kasugamycin biosynthesis.	a 7.6kb psti-kpni dna fragment including a sequence highly similar to kasugamycin acetyltransferase gene (kac) was isolated from streptomyces kasugaensis m338-m1 and sequenced. nine open reading frames (orfs), designated as orf a, b, c, d, e, f, g, h and i, were recognized in this region, although orf a was incomplete. orf g runs in the opposite direction to the others. the amino acid sequence deduced from orf h showed 98% similarity to that of the kasugamycin acetyltransferase from s. kasugaens ...	1998	9589071
flow cytometric assessment of the postantibiotic effect of methicillin on staphylococcus aureus.	the postantibiotic effect (pae) following a 2-h exposure of staphylococcus aureus nctc 6571 to methicillin (5x the mic) was investigated with fluorescent probes, 5-cyano-2,3-di-4-tolyl tetrazolium chloride (ctc), an indicator of respiratory activity, and the membrane potential-sensitive compound bis-(1,3-dibutylbarbituric acid) trimethine oxonol [dibac4(3)]. counts of the numbers of cfu on solid agar correlated well with information gained from the ctc and dibac4(3) fluorescence intensity distri ...	1998	9593149
molecular characterization of the phenylacetic acid catabolic pathway in pseudomonas putida u: the phenylacetyl-coa catabolon.	fourteen different genes included in a dna fragment of 18 kb are involved in the aerobic degradation of phenylacetic acid by pseudomonas putida u. this catabolic pathway appears to be organized in three contiguous operons that contain the following functional units: (i) a transport system, (ii) a phenylacetic acid activating enzyme, (iii) a ring-hydroxylation complex, (iv) a ring-opening protein, (v) a beta-oxidation-like system, and (vi) two regulatory genes. this pathway constitutes the common ...	1998	9600981
two nearly identical aromatic compound hydrolase genes in a strong polychlorinated biphenyl degrader, rhodococcus sp. strain rha1.	the two 2-hydroxy-6-oxohepta-2,4-dienoate (hohd) hydrolase genes, etbd1 and etbd2, were cloned from a strong polychlorinated biphenyl (pcb) degrader, rhodococcus sp. strain rha1, and their nucleotide sequences were determined. the etbd2 gene was located in the vicinity of bpha gene homologs and encoded an enzyme whose amino-terminal sequence was very similar to the amino-terminal sequence of the hohd hydrolase which was purified from rha1. using the etbd2 gene fragment as a probe, we cloned the ...	1998	9603807
towards a biocatalyst for (s)-styrene oxide production: characterization of the styrene degradation pathway of pseudomonas sp. strain vlb120.	in order to design a biocatalyst for the production of optically pure styrene oxide, an important building block in organic synthesis, the metabolic pathway and molecular biology of styrene degradation in pseudomonas sp. strain vlb120 was investigated. a 5.7-kb xhoi fragment, which contained on the same strand of dna six genes involved in styrene degradation, was isolated from a gene library of this organism in escherichia coli by screening for indigo formation. t7 rna polymerase expression expe ...	1998	9603811
construction of an efficient biologically contained pseudomonas putida strain and its survival in outdoor assays	active biological containment systems consist of two components, a killing element designed to induce cell death and a control element which modulates the expression of the killing function. we constructed a mini-tn5 transposon bearing a fusion of the plac promoter to the gef killing gene and a fusion of the pm promoter to the laci gene plus the positive regulator of the pm promoter, the xyls gene. this mini-tn5 transposon was transferred to the chromosome of pseudomonas putida cmc4, and in cult ...	1998	9603816
low-frequency horizontal transfer of an element containing the chlorocatechol degradation genes from pseudomonas sp. strain b13 to pseudomonas putida f1 and to indigenous bacteria in laboratory-scale activated-sludge microcosms.	the possibilities for low-frequency horizontal transfer of the self-transmissible chlorocatechol degradative genes (clc) from pseudomonas sp. strain b13 were investigated in activated-sludge microcosms. when the clc genes were transferred into an appropriate recipient bacterium such as pseudomonas putida f1, a new metabolic pathway for chlorobenzene degradation was formed by complementation which could be selected for by the addition of mono- or 1, 4-dichlorobenzene (cb). under optimized conditi ...	1998	9603824
cometabolism of 1,1-dichloro-2,2-bis(4-chlorophenyl)ethylene by pseudomonas acidovorans m3gy grown on biphenyl.	1,1-dichloro-2,2-bis(4-chlorophenyl)ethylene (dde), a toxic breakdown product of 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane (ddt), has traditionally been viewed as a dead-end metabolite: there are no published reports detailing enzymatic ring fission of dde by bacteria in either soil or pure culture. in this study, we investigated the ability of pseudomonas acidovorans m3gy to transform dde and its unchlorinated analog, 1,1-diphenylethylene (dpe). while strain m3gy could grow on dpe, cells gr ...	1998	9603826
new unstable variants of green fluorescent protein for studies of transient gene expression in bacteria.	use of the green fluorescent protein (gfp) from the jellyfish aequorea victoria is a powerful method for nondestructive in situ monitoring, since expression of green fluorescence does not require any substrate addition. to expand the use of gfp as a reporter protein, new variants have been constructed by the addition of short peptide sequences to the c-terminal end of intact gfp. this rendered the gfp susceptible to the action of indigenous housekeeping proteases, resulting in protein variants w ...	1998	9603842
establishment of new genetic traits in a microbial biofilm community.	conjugational transfer of the tol plasmid (pwwo) was analyzed in a flow chamber biofilm community engaged in benzyl alcohol degradation. the community consisted of three species, pseudomonas putida ri, acinetobacter sp. strain c6, and an unidentified isolate, d8. only p. putida ri could act as a recipient for the tol plasmid. cells carrying a chromosomally integrated laciq gene and a lacp-gfp-tagged version of the tol plasmid were introduced as donor strains in the biofilm community after its fo ...	1998	9603843
expression of the transposase gene tnpa of tn4652 is positively affected by integration host factor.	tn4652 is a derivative of the toluene degradation transposon tn4651 that belongs to the tn3 family of transposons (m. tsuda and t. iino, mol. gen. genet. 210:270-276, 1987). we have sequenced the transposase gene tnpa of transposon tn4652 and mapped its promoter to the right end of the element. the deduced amino acid sequence of tnpa revealed 96.2% identity with the putative transposase of tn5041. homology with other tn3 family transposases was only moderate (about 20 to 24% identity), suggestin ...	1998	9603867
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
activation and repression of transcription at the double tandem divergent promoters for the xylr and xyls genes of the tol plasmid of pseudomonas putida.	the xylr and xyls genes are divergent and control transcription of the tol plasmid catabolic pathways for toluene metabolism. four promoters are found in the 300-bp intergenic region: pr1 and pr2 are constitutive sigma70-dependent tandem promoters that drive expression of xylr, while expression of the xyls gene is driven from ps2, a constitutive sigma70-dependent promoter, and by the regulatable sigma54 class ps1 promoter. in ps1 the xylr targets (upstream activator sequences [uass]) overlap the ...	1998	9603877
characterization of the hca cluster encoding the dioxygenolytic pathway for initial catabolism of 3-phenylpropionic acid in escherichia coli k-12.	we have identified, cloned, and sequenced the hca cluster encoding the dioxygenolytic pathway for initial catabolism of 3-phenylpropionic acid (pp) in escherichia coli k-12. this cluster maps at min 57.5 of the chromosome and is composed of five catabolic genes arranged as a putative operon (hcaa1a2cbd) and two additional genes transcribed in the opposite direction that encode a potential permease (hcat) and a regulator (hcar). sequence comparisons revealed that while hcaa1a2cd genes encode the ...	1998	9603882
implications of the xylq gene of tol plasmid pww102 for the evolution of aromatic catabolic pathways.	pseudomonas putida strain o2c2 is able to grow on toluene, m-xylene and p-xylene through benzoate and the corresponding methylbenzoates (toluates). the catabolic genes are encoded on a large tol plasmid, pww102, of > 220 kb. the complete catabolic genes were cloned on four large overlapping restriction fragments covering a total of 28 kb of the plasmid, which was carefully mapped by restriction enzyme analysis. the presence of the xyl genes on the cloned dna was confirmed by assay of representat ...	1998	9611813
purification, characterization, and gene analysis of catechol 2,3-dioxygenase from the aniline-assimilating bacterium pseudomonas species aw-2.	catechol 2,3-dioxygenase (c23d; ec 1.13.1.2) was purified to homogeneity from a cell extract of pseudomonas sp. aw-2 grown on aniline, and the purified c23d was characterized. the molecular mass estimated by gel filtration was 110 kda. the enzyme dissociated into four identical subunits each with the molecular mass of 33 kda. the enzyme had high activity for 3-methylcatechol as well as catechol, and differed from the enzyme from pseudomonas putida mt-2, which carries the tol plasmid, in optimal ...	1998	9614705
activity-dependent fluorescent labeling of bacteria that degrade toluene via toluene 2,3-dioxygenase.	alternative substrates for the toluene 2,3-dioxygenase pathway of several pseudomonads served as enzyme-activity-dependent fluorescent probes for the bacteria. phenylacetylene and cinnamonitrile were transformed to fluorescent and brightly colored products by pseudomonas putida f1, pseudomonas fluorescens cfs215, and burkholderia (pseudomonas) strain js150. active bacteria transformed phenylacetylene, producing bright yellow solutions containing the putative product 2-hydroxy-6-oxo-7-octyn-2,4-d ...	1998	9615486
characterization of the hcnabc gene cluster encoding hydrogen cyanide synthase and anaerobic regulation by anr in the strictly aerobic biocontrol agent pseudomonas fluorescens cha0.	the secondary metabolite hydrogen cyanide (hcn) is produced by pseudomonas fluorescens from glycine, essentially under microaerophilic conditions. the genetic basis of hcn synthesis in p. fluorescens cha0 was investigated. the contiguous structural genes hcnabc encoding hcn synthase were expressed from the t7 promoter in escherichia coli, resulting in hcn production in this bacterium. analysis of the nucleotide sequence of the hcnabc genes showed that each hcn synthase subunit was similar to kno ...	1998	9620970
cloning and comparison of flic genes and identification of glycosylation in the flagellin of pseudomonas aeruginosa a-type strains.	pseudomonas aeruginosa a-type strains produce flagellin proteins which vary in molecular weight between strains. to compare the properties of a-type flagellins, the flagellin genes of several pseudomonas aeruginosa a-type strains, as determined by interaction with specific anti-a monoclonal antibody, were cloned and sequenced. pcr amplification of the a-type flagellin gene fragments from five strains each yielded a 1.02-kb product, indicating that the gene size is not likely to be responsible fo ...	1998	9620973
crystal structure and enzyme mechanism of delta 5-3-ketosteroid isomerase from pseudomonas testosteroni.	bacterial delta 5-3-ketosteroid isomerase (ksi) from pseudomonas testosteroni has been intensively studied as a prototype for understanding an enzyme-catalyzed allylic rearrangement involving intramolecular proton transfer. asp38 serves as a general base to abstract the proton from the steroid c4-h, which is a much stronger base than the carboxyl group of this residue. this unfavorable proton transfer requires 11 kcal/mol of energy which has to be provided by favorable interactions between catal ...	1998	9622484
inhibition of human peripheral blood mononuclear cell proliferation by streptococcus pyogenes cell extract is associated with arginine deiminase activity.	streptococcus pyogenes (group a streptococcus) cell extracts (ce) have a remarkably powerful and dose-dependent inhibitory effect on antigen, superantigen, or mitogen-stimulated human peripheral blood mononuclear cell (pbmc) proliferation in vitro. purification of the inhibitory component present in s. pyogenes type m5 (manfredo strain) ce by anion-exchange chromatography followed by gel filtration chromatography showed that the inhibitor had an approximate native molecular mass of 100 kda. sodi ...	1998	9632565
heterogeneity in levels of vacuolating cytotoxin gene (vaca) transcription among helicobacter pylori strains.	broth culture supernatants from tox+ helicobacter pylori strains induce vacuolation of hela cells in vitro and contain vaca in concentrations that are higher than those found in supernatants from tox- h. pylori strains. to investigate the basis for this phenomenon, we analyzed the transcription of the vacuolating cytotoxin gene (vaca) in eight tox+ strains (each with a type s1/m1 vaca genotype) and nine tox- strains (each with a type s2/m2 vaca genotype). most of the tox+ and tox- strains tested ...	1998	9632570
segregational and structural instability of recombinant plasmid carrying genes for naphthalene degrading pathway.	the stability of recombinant plasmid carrying genes for naphthalene mineralization was determined. a strain of pseudomonas putida capable of mineralizing naphthalene (nap+) via salicylate (sal+) was isolated, and all regulatory and structural genes for the whole pathway were found to be encoded on a 25 kb ecori fragment of an approximately 83 kb plasmid present in this strain. the 25 kb ecori fragment was cloned into a tetracycline-resistant (tcr) cloning vector plafr3 and the recombinant plasmi ...	1998	9633091