Publications

variation in flagellin genes and proteins of burkholderia cepacia.	the majority of isolates of burkholderia cepacia, an important opportunistic pathogen associated with cystic fibrosis, can be classified into two types on the basis of flagellin protein size. electron microscopic analysis indicates that the flagella of strains with the larger flagellin type (type i) are wider in diameter. flagellin genes representative of both types were cloned and sequenced to design oligonucleotide primers for pcr amplification of the central variable domain of b. cepacia flag ...	1998	9495748
enzyme specificity of 2-nitrotoluene 2,3-dioxygenase from pseudomonas sp. strain js42 is determined by the c-terminal region of the alpha subunit of the oxygenase component.	biotransformations with recombinant escherichia coli expressing the genes encoding 2-nitrotoluene 2,3-dioxygenase (2ntdo) from pseudomonas sp. strain js42 demonstrated that 2ntdo catalyzes the dihydroxylation and/or monohydroxylation of a wide range of aromatic compounds. extremely high nucleotide and deduced amino acid sequence identity exists between the components from 2ntdo and the corresponding components from 2,4-dinitrotoluene dioxygenase (2,4-dntdo) from burkholderia sp. strain dnt (form ...	1998	9495758
cloning and sequencing of the sphingomonas (pseudomonas) paucimobilis gene essential for the o demethylation of vanillate and syringate.	sphingomonas (pseudomonas) paucimobilis syk-6 is able to grow on 5,5'-dehydrodivanillic acid (ddva), syringate, vanillate, and other dimeric model compounds of lignin as a sole carbon source. nitrosoguanidine mutagenesis of s. paucimobilis syk-6 was performed, and two mutants with altered ddva degradation pathways were isolated. the mutant strain nt-1 could not degrade ddva, but could degrade syringate, vanillate, and 2,2',3'-trihydroxy-3-methoxy-5,5'-dicarboxybiphenyl (oh-ddva). strain dc-49 co ...	1998	9501423
biochemical and genetic characterization of an extracellular protease from pseudomonas fluorescens cy091.	pseudomonas fluorescens cy091 cultures produce an extracellular protease with an estimated molecular mass of 50 kda. production of this enzyme (designated aprx) was observed in media containing cacl2 or srcl2 but not in media containing zncl2, mgcl2, or mncl2. the requirement of ca2+ (or sr2+) for enzyme production was concentration dependent, and the optimal concentration for production was determined to be 0.35 mm. following ammonium sulfate precipitation and ion-exchange chromatography, the a ...	1998	9501431
bacterial community dynamics during start-up of a trickle-bed bioreactor degrading aromatic compounds.	this study was performed with a laboratory-scale fixed-bed bioreactor degrading a mixture of aromatic compounds (solvesso100). the starter culture for the bioreactor was prepared in a fermentor with a wastewater sample of a care painting facility as the inoculum and solvesso100 as the sole carbon source. the bacterial community dynamics in the fermentor and the bioreactor were examined by a conventional isolation procedure and in situ hybridization with fluorescently labeled rrna-targeted oligon ...	1998	9501433
development and testing of a bacterial biosensor for toluene-based environmental contaminants.	a bacterial biosensor for benzene, toluene, and similar compounds has been constructed, characterized, and field tested on contaminated water and soil. the biosensor is based on a plasmid incorporating the transcriptional activator xylr from the tol plasmid of pseudomonas putida mt-2. the xylr protein binds a subset of toluene-like compounds and activates transcription at its promoter, pu. a reporter plasmid was constructed by placing the luc gene for firefly luciferase under the control of xylr ...	1998	9501440
identification of a chemotaxis gene region from pseudomonas putida.	pseudomonas putida is chemotactic to a range of organic compounds, including several aromatic compounds. genes involved in this behavioral response were identified by tn5 mutagenesis of p. putida prs2000, resulting in a strain that was nonchemotactic to all chemoattractants tested. cloning and sequencing of the dna at the dna at the tn5 insertion site revealed a 13-kb region that contained 12 open reading frames, 9 of which are homologous to chemotaxis, flagellar and motility genes in other bact ...	1998	9503621
species-specific and ubiquitous-dna-based assays for rapid identification of staphylococcus aureus.	staphylococcus aureus is the cause of serious infections in humans, including endocarditis, deep-seated abscesses, and bacteremia, which lead to toxic and septic shock syndromes. rapid and direct identification of this bacterium specifically and ubiquitously directly from clinical specimens would be useful in improving the diagnosis of s. aureus infections in the clinical microbiology laboratory. a wide variety of kits based on biochemical characteristics efficiently identify s. aureus, but the ...	1998	9508283
evaluation of pcr for diagnosis of bordetella pertussis and bordetella parapertussis infections.	pcr, using primers plp1 and plp2, was evaluated for the detection of dna from bordetella pertussis in bacterial strains and in nasopharyngeal samples from patients with a cough lasting at least 7 days. the assay could detect dna from 6 cfu of b. pertussis/10 microl of sample. results of the pcr assay were compared with those of cultures, a determination of serum antibodies against pertussis toxin and filamentous hemagglutinin, and a clinical evaluation of 2,442 coughing episodes. the overall sen ...	1998	9508295
a protein-induced dna bend increases the specificity of a prokaryotic enhancer-binding protein.	control of transcription in prokaryotes often involves direct contact of regulatory proteins with rna polymerase from binding sites located adjacent to the target promoter. alternatively, in the case of genes transcribed by escherichia coli rna polymerase holoenzyme containing the alternate sigma factor sigma54, regulatory proteins bound at more distally located enhancer sites can activate transcription via dna looping by taking advantage of the increasing flexibility of dna over longer distance ...	1998	9512522
cloning and sequencing of a 2,5-dichlorohydroquinone reductive dehalogenase gene whose product is involved in degradation of gamma-hexachlorocyclohexane by sphingomonas paucimobilis.	sphingomonas (formerly pseudomonas) paucimobilis ut26 utilizes gamma-hexachlorocyclohexane (gamma-hch), a halogenated organic insecticide, as a sole carbon and energy source. in a previous study, we showed that gamma-hch is degraded to 2,5-dichlorohydroquinone (2,5-dchq) (y. nagata, r. ohtomo, k. miyauchi, m. fukuda, k. yano, and m. takagi, j. bacteriol. 176:3117-3125, 1994). in the present study, we cloned and characterized a gene, designated lind, directly involved in the degradation of 2,5-dc ...	1998	9515900
pcau, a transcriptional activator of genes for protocatechuate utilization in acinetobacter.	the acinetobacter pcaijfbdkchg operon encodes the six enzymes that convert protocatechuate to citric acid cycle intermediates. directly downstream from the operon are qui and pob genes encoding sets of enzymes that convert quinate and p-hydroxybenzoate, respectively, to protocatechuate. prior to this investigation, the only known regulatory gene in the pca-qui-pob cluster was pobr, which encodes a transcriptional activator that responds to p-hydroxybenzoate and activates transcription of poba. t ...	1998	9515921
characterization of the gene cassette required for biosynthesis of the (alpha1-->6)-linked n-acetyl-d-mannosamine-1-phosphate capsule of serogroup a neisseria meningitidis.	the (alpha1-->6)-linked n-acetyl-d-mannosamine-1-phosphate meningococcal capsule of serogroup a neisseria meningitidis is biochemically distinct from the sialic acid-containing capsules produced by other disease-associated meningococcal serogroups (e.g., b, c, y, and w-135). we defined the genetic cassette responsible for expression of the serogroup a capsule. the cassette comprised a 4,701-bp nucleotide sequence located between the outer membrane capsule transporter gene, ctra, and gale, encodi ...	1998	9515923
biodegradation of cyanides, cyanates and thiocyanates to ammonia and carbon dioxide by immobilized cells of pseudomonas putida.	pseudomonas putida utilizes cyanide as the sole source of carbon and nitrogen. agar, alginate, and carrageenan were screened as the encapsulating matrices for p. putida. alginate-immobilized cells of p. putida degraded sodium cyanide (nacn) more efficiently than non-immobilized cells or cells immobilized in agar or carrageenan. the end products of biodegradation of cyanide were identified as ammonia (nh3) and carbon dioxide (co2). these products changed the medium ph. in bioreactors, the rate of ...	1998	9523454
characterization of the cvaa and cvi promoters of the colicin v export system: iron-dependent transcription of cvaa is modulated by downstream sequences.	secretion of the escherichia coli toxin colicin v was previously determined to be iron regulated via the fur (ferric uptake regulator) protein, based on studies in fur mutants. the iron dependence of transcription and expression of cvaa, which encodes a transporter accessory protein, and cvi, encoding the colicin v immunity protein, was assessed under conditions of iron excess or depletion. immunoblots showed that production of both cvi and cvaa is iron dependent. the iron-dependent transcriptio ...	1998	9537361
the rhizobium etli rpon locus: dna sequence analysis and phenotypical characterization of rpon, ptsn, and ptsa mutants.	the rpon region of rhizobium etli was isolated by using the bradyrhizobium japonicum rpon1 gene as a probe. nucleotide sequence analysis of a 5,600-bp dna fragment of this region revealed the presence of four complete open reading frames (orfs), orf258, rpon, orf191, and ptsn, coding for proteins of 258, 520, 191, and 154 amino acids, respectively. the gene product of orf258 is homologous to members of the atp-binding cassette-type permeases. orf191 and ptsn are homologous to conserved orfs foun ...	1998	9537369
cloning and characterization of the pseudomonas aeruginosa zwf gene encoding glucose-6-phosphate dehydrogenase, an enzyme important in resistance to methyl viologen (paraquat).	in this study, we cloned the pseudomonas aeruginosa zwf gene, encoding glucose-6-phosphate dehydrogenase (g6pdh), an enzyme that catalyzes the nad+- or nadp+-dependent conversion of glucose-6-phosphate to 6-phosphogluconate. the predicted zwf gene product is 490 residues, which could form a tetramer with a molecular mass of approximately 220 kda. g6pdh activity and zwf transcription were maximal in early logarithmic phase when inducing substrates such as glycerol, glucose, or gluconate were abun ...	1998	9537370
the atrazine catabolism genes atzabc are widespread and highly conserved.	pseudomonas strain adp metabolizes the herbicide atrazine via three enzymatic steps, encoded by the genes atzabc, to yield cyanuric acid, a nitrogen source for many bacteria. here, we show that five geographically distinct atrazine-degrading bacteria contain genes homologous to atza, -b, and -c. the sequence identities of the atz genes from different atrazine-degrading bacteria were greater than 99% in all pairwise comparisons. this differs from bacterial genes involved in the catabolism of othe ...	1998	9537398
occurrence of homologs of the escherichia coli lytb gene in gram-negative bacterial species.	the escherichia coli lytb protein regulates the activity of guanosine 3',5'-bispyrophosphate synthetase i (rela). a southern blot analysis of chromosomal dna with the e. coli lytb gene as a probe revealed the presence of lytb homologs in all of the gram-negative bacterial species examined but not in gram-positive species. the lytb homologs from enterobacter aerogenes and pseudomonas fluorescens complemented the e. coli lytb44 mutant allele.	1998	9537400
atzc is a new member of the amidohydrolase protein superfamily and is homologous to other atrazine-metabolizing enzymes.	pseudomonas sp. strain adp metabolizes atrazine to cyanuric acid via three plasmid-encoded enzymes, atza, atzb, and atzc. the first enzyme, atza, catalyzes the hydrolytic dechlorination of atrazine, yielding hydroxyatrazine. the second enzyme, atzb, catalyzes hydroxyatrazine deamidation, yielding n-isopropylammelide. in this study, the third gene in the atrazine catabolic pathway, atzc, was cloned from a pseudomonas sp. strain adp cosmid library as a 25-kb ecori dna fragment in escherichia coli. ...	1998	9422605
expression and characterization of a heme oxygenase (hmu o) from corynebacterium diphtheriae. iron acquisition requires oxidative cleavage of the heme macrocycle.	a full-length heme oxygenase gene from the pathogenic bacterium corynebacterium diphtheriae has been subcloned and expressed in escherichia coli. the enzyme is expressed at high levels as a soluble catalytically active protein that results in the accumulation of biliverdin within the e. coli cells. the purified heme oxygenase forms a 1:1 complex with heme (kd = 2.5 +/- 1 microm) and has hemeprotein spectra similar to those previously reported for the purified eukaryotic heme oxygenases. in the p ...	1998	9422739
role of the haemophilus ducreyi ton system in internalization of heme from hemoglobin.	by cloning into escherichia coli and construction of isogenic mutants of haemophilus ducreyi, we showed that the hemoglobin receptor (hgba) is tonb dependent. an e. coli hema tonb mutant expressing h. ducreyi hgba grew on low levels of hemoglobin as a source of heme only when an intact h. ducreyi ton system plasmid was present. in contrast, growth on heme by the e. coli hema tonb mutant expressing hgba was observed only at high concentrations of heme, was tonb independent, and demonstrated that ...	1998	9423852
complementation analysis of the dichelobacter nodosus fimn, fimo, and fimp genes in pseudomonas aeruginosa and transcriptional analysis of the fimnop gene region.	the causative agent of ovine footrot, the gram-negative anaerobe dichelobacter nodosus, produces polar type iv fimbriae, which are the major protective antigens. the d. nodosus genes fimn, fimo, and fimp are homologs of the pseudomonas aeruginosa fimbrial assembly genes, pilb, pilc, and pild, respectively. both the pild and fimp genes encode prepilin peptidases that are responsible for cleavage of the leader sequence from the immature fimbrial subunit. to investigate the functional similarity of ...	1998	9423871
identification and molecular characterization of an efflux pump involved in pseudomonas putida s12 solvent tolerance.	bacteria able to grow in aqueous:organic two-phase systems have evolved resistance mechanisms to the toxic effects of solvents. one such mechanism is the active efflux of solvents from the cell, preserving the integrity of the cell interior. pseudomonas putida s12 is resistant to a wide variety of normally detrimental solvents due to the action of such an efflux pump. the genes for this solvent efflux pump were cloned from p. putida s12 and their nucleotide sequence determined. the deduced amino ...	1998	9417051
identification of bacteria in water for pharmaceutical use.	different systems for the obtention of water used in biopharmaceutical industry were characterized from the bacteriological point of view. determination of aerobic mesophilic microorganisms was performed; as well as the isolation of contaminant microorganisms for what the techniques of membrane filtration was used. for the identification of the more representative species there were made conventional biochemical tests and quick systems: api. the results show that water serving as tap water for p ...	1998	10932743
cloning of the bacillus firmus of4 cls gene and characterization of its gene product.	the gene that codes for cardiolipin (cl) synthase and an adjacent gene that codes for a meca homolog in the alkaliphilic bacteria bacillus firmus of4 have been cloned and sequenced (genbank accession number u88888). the cls gene contains 1509 nucleotides, corresponding to a polypeptide of 57.9 kda. the predicted amino acid sequence has 129 identities and 100 similarities with the escherichia coli cl synthase. homologies were also noted with polypeptide sequences from putative cls genes from baci ...	1998	9443601
cloning and nucleotide sequence of the dna gyrase gyra gene from serratia marcescens and characterization of mutations in gyra of quinolone-resistant clinical isolates.	the sequence of the dna gyrase gyra gene of serratia marcescens atcc 14756 was determined. an open reading frame of 2,640 nucleotides coding for a polypeptide with a calculated molecular mass of 97,460 was found, and its sequence complemented the sequence of an escherichia coli gyra temperature-sensitive mutation. analysis of the pcr products of the quinolone resistance-determining regions of gyra genes from six quinolone-resistant clinical isolates revealed a single amino acid substitution, ser ...	1998	9449286
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
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
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
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
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
functional analysis of the two-gene lysis system of the pneumococcal phage cp-1 in homologous and heterologous host cells.	the two lysis genes cph1 and cpl1 of the streptococcus pneumoniae bacteriophage cp-1 coding for holin and lysozyme, respectively, have been cloned and expressed in escherichia coli. synthesis of the cph1 holin resulted in bacterial cell death but not lysis. the cph1 gene was able to complement a lambda sam mutation in the nonsuppressing e. coli hb101 strain to produce phage progeny, suggesting that the holins encoded by both phage genes have analogous functions and that the pneumococcal holin in ...	1998	9440507
direct sulfhydrylation for methionine biosynthesis in leptospira meyeri.	a gene library of the leptospira meyeri serovar semaranga strain veldrat s.173 dna has been constructed in a mobilizable cosmid with inserts of up to 40 kb. it was demonstrated that a leptospira dna fragment carrying mety complemented escherichia coli strains carrying mutations in metb. the latter gene encodes cystathionine gamma-synthase, an enzyme which catalyzes the second step of the methionine biosynthetic pathway. the mety gene is 1,304 bp long and encodes a 443-amino-acid protein with a m ...	1998	9440513
degradation of chloroaromatics: purification and characterization of a novel type of chlorocatechol 2,3-dioxygenase of pseudomonas putida gj31.	a purification procedure for a new kind of extradiol dioxygenase, termed chlorocatechol 2,3-dioxygenase, that converts 3-chlorocatechol productively was developed. structural and kinetic properties of the enzyme, which is part of the degradative pathway used for growth of pseudomonas putida gj31 with chlorobenzene, were investigated. the enzyme has a subunit molecular mass of 33.4 kda by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. estimation of the native mr value under nondenatur ...	1998	9440519
detoxification of protoanemonin by dienelactone hydrolase.	protoanemonin is a toxic metabolite which may be formed during the degradation of some chloroaromatic compounds, such as polychlorinated biphenyls, by natural microbial consortia. we show here that protoanemonin can be transformed by dienelactone hydrolase of pseudomonas sp. strain b13 to cis-acetylacrylate. although similar km values were observed for cis-dienelactone and protoanemonin, the turnover rate of protoanemonin was only 1% that of cis-dienelactone. this indicates that at least this pe ...	1998	9440530
repression of phenol catabolism by organic acids in ralstonia eutropha.	during batch growth of ralstonia eutropha (previously named alcaligenes eutrophus) on phenol in the presence of acetate, acetate was found to be the preferred substrate; this organic acid was rapidly metabolized, and the specific rate of phenol consumption was considerably decreased, although phenol consumption was not abolished. this decrease corresponded to a drop in phenol hydroxylase and catechol-2,3-dioxygenase specific activities, and the synthesis of the latter was repressed at the transc ...	1998	9435054
survival in soil of different toluene-degrading pseudomonas strains after solvent shock.	we assayed the tolerance to solvents of three toluene-degrading pseudomonas putida strains and pseudomonas mendocina kr1 in liquid and soil systems. p. putida dot-t1 tolerated concentrations of heptane, propylbenzene, octanol, and toluene of at least 10% (vol/vol), while p. putida f1 and eez15 grew well in the presence of 1% (vol/vol) propylbenzene or 10% (vol/vol) heptane, but not in the presence of similar concentrations of octanol or toluene. p. mendocina kr1 grew only in the presence of hept ...	1998	9435060
rhizoremediation of trichloroethylene by a recombinant, root-colonizing pseudomonas fluorescens strain expressing toluene ortho-monooxygenase constitutively.	trichloroethylene (tce) was removed from soils by using a wheat rhizosphere established by coating seeds with a recombinant, tce-degrading pseudomonas fluorescens strain that expresses the toma+ (toluene o-monooxygenase) genes from burkholderia cepacia pr1(23)(tom23c). a transposon integration vector was used to insert toma+ into the chromosome of p. fluorescens 2-79, producing a stable strain that expressed constitutively the monooxygenase at a level of 1.1 nmol/min.mg of protein (initial tce c ...	1998	9435067
biodegradation of phosphonomycin by rhizobium huakuii pmy1.	the biodegradation by rhizobium huakuii pmy1 of up to 10 mm phosphonomycin as a carbon, energy, and phosphorus source with accompanying p(i) release is described. this biodegradation represents a further mechanism of resistance to this antibiotic and a novel, phosphate-deregulated route for organophosphonate metabolism by rhizobium spp.	1998	9435089
identification of the open reading frame for the pseudomonas putida d-hydantoinase gene and expression of the gene in escherichia coli.	a dna fragment containing the gene for d-hydantoinase was cloned from pseudomonas putida ccrc 12857 into escherichia coli. the cloned gene contained an open reading frame (orf) of 1485 nucleotides encoding a protein of 53.4 kda in which the carboxyl terminal end is longer than that previously deduced from strain dsm 84. this orf was verified by amino acid sequencing of amino and carboxyl termini, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and amino acid sequence comparison. delet ...	1998	9434154
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
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
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
effect of trichloroethylene on the competitive behavior of toluene-degrading bacteria.	the influence of trichloroethylene (tce) on a mixed culture of four different toluene-degrading bacterial strains (pseudomonas putida mt-2, p. putida f1, p. putida gj31, and burkholderia cepacia g4) was studied with a fed-batch culture. the strains were competing for toluene, which was added at a very low rate (31 nmol mg of cells [dry weight] h). all four strains were maintained in the mixed culture at comparable numbers when tce was absent. after the start of the addition of tce, the viabiliti ...	1998	16349481
initial reductive reactions in aerobic microbial metabolism of 2,4,6-trinitrotoluene.	because of its high electron deficiency, initial microbial transformations of 2,4,6-trinitrotoluene (tnt) are characterized by reductive rather than oxidation reactions. the reduction of the nitro groups seems to be the dominating mechanism, whereas hydrogenation of the aromatic ring, as described for picric acid, appears to be of minor importance. thus, two bacterial strains enriched with tnt as a sole source of nitrogen under aerobic conditions, a gram-negative strain called tnt-8 and a gram-p ...	1998	16349484
identification of hydrocarbon-degrading bacteria in soil by reverse sample genome probing.	bacteria with limited genomic cross-hybridization were isolated from soil contaminated with c5+, a mixture of hydrocarbons, and identified by partial 16s rrna sequencing. filters containing denatured genomic dnas were used in a reverse sample genome probe (rsgp) procedure for analysis of the effect of an easily degradable compound (toluene) and a highly recalcitrant compound (dicyclopentadiene [dcpd]) on community composition. hybridization with labeled total-community dna isolated from soil exp ...	1998	16349504
light-mediated nitrite accumulation during denitrification by pseudomonas sp. strain jr12.	the effect of light on the denitrifying characteristics of a nonphotosynthetic denitrifier, pseudomonas sp. strain jr12, was examined. already at low light intensities, nitrite accumulated as a result of light inhibition of nitrite but not of nitrate reduction rates. exposure of this bacterium to light caused a photooxidation of cytochrome c, an intermediate electron carrier in its respiratory pathway. photoinhibition of nitrite reduction was reversible, as nitrite reduction rates returned to pr ...	1998	16349525
long-term reduction of cold hardiness following ingestion of ice-nucleating bacteria in the colorado potato beetle, leptinotarsa decemlineata.	we investigated the effect of ingestion of ice-nucleating bacteria on the supercooling capacity and cold hardiness of the colorado potato beetle (leptinotarsa decemlineata say), a freeze-intolerant species that overwinters as adults in shallow, terrestrial burrows. ingestion of ice-nucleating bacteria (enterobacter agglomerans, pseudomonas fluorescens, pseudomonas putida, pseudomonas syringae), fed on slices of potato tuber, caused an abrupt decrease in supercooling capacity. no change occurred ...	1998	12770317
metabolism of benzene, toluene, and xylene hydrocarbons in soil	enrichment cultures obtained from soil exposed to benzene, toluene, and xylene (btx) mineralized benzene and toluene but cometabolized only xylene isomers, forming polymeric residues. this observation prompted us to investigate the metabolism of 14c-labeled btx hydrocarbons in soil, either individually or as mixtures. btx-supplemented soil was incubated aerobically for up to 4 weeks in a sealed system that automatically replenished any o2 consumed. the decrease in solvent vapors and the producti ...	1998	9835584
regio- and stereospecific conversion of 4-alkylphenols by the covalent flavoprotein vanillyl-alcohol oxidase.	the regio- and stereospecific conversion of prochiral 4-alkylphenols by the covalent flavoprotein vanillyl-alcohol oxidase was investigated. the enzyme was active, with 4-alkylphenols bearing aliphatic side chains of up to seven carbon atoms. optimal catalytic efficiency occurred with 4-ethylphenol and 4-n-propylphenols. these short-chain 4-alkylphenols are stereoselectively hydroxylated to the corresponding (r)-1-(4'-hydroxyphenyl)alcohols (f. p. drijfhout, m. w. fraaije, h. jongejan, w. j. h. ...	1998	9791114
nutrient uptake by microorganisms according to kinetic parameters from theory as related to cytoarchitecture.	the abilities of organisms to sequester substrate are described by the two kinetic constants specific affinity, a degrees, and maximal velocity vmax. specific affinity is derived from the frequency of substrate-molecule collisions with permease sites on the cell surface at subsaturating concentrations of substrates. vmax is derived from the number of permeases and the effective residence time, tau, of the transported molecule on the permease. the results may be analyzed with affinity plots (v/s ...	1998	9729603
electrostatic steering and ionic tethering in enzyme-ligand binding: insights from simulations.	to bind at an enzyme's active site, a ligand must diffuse or be transported to the enzyme's surface, and, if the binding site is buried, the ligand must diffuse through the protein to reach it. although the driving force for ligand binding is often ascribed to the hydrophobic effect, electrostatic interactions also influence the binding process of both charged and nonpolar ligands. first, electrostatic steering of charged substrates into enzyme active sites is discussed. this is of particular re ...	1998	9600896
osmotic stress induces expression of choline monooxygenase in sugar beet and amaranth.	choline monooxygenase (cmo) catalyzes the committing step in the synthesis of glycine betaine, an osmoprotectant accumulated by many plants in response to salinity and drought. to investigate how these stresses affect cmo expression, a spinach (spinacia oleracea l., chenopodiaceae) probe was used to isolate cmo cdnas from sugar beet (beta vulgaris l., chenopodiaceae), a salt- and drought-tolerant crop. the deduced beet cmo amino acid sequence comprised a transit peptide and a 381-residue mature ...	1998	9489025
genotypic and phenotypic responses of a riverine microbial community to polycyclic aromatic hydrocarbon contamination.	the phenotypic and genotypic adaptation of a freshwater sedimentary microbial community to elevated (22 to 217 microgram [dry weight] of sediment-1) levels of polycyclic aromatic hydrocarbons (pahs) was determined by using an integrated biomolecular approach. central to the approach was the use of phospholipid fatty acid (plfa) profiles to characterize the microbial community structure and nucleic acid analysis to quantify the frequency of degradative genes. the study site was the little scioto ...	1998	9726892
characterization of quinohemoprotein amine dehydrogenase from pseudomonas putida.	quinohemoprotein amine dehydrogenase (amdh) was purified and crystallized from the soluble fraction of pseudomonas putida ifo 15366 grown on n-butylamine medium. amdh gave a single component in analytical ultracentrifugation showing an intrinsic sedimentation coefficient of 5.8s. amdh showed a typical absorption spectrum of cytochrome c showing maxima at 554, 522, 420, and 320 nm in the reduced form and one peak at 410 nm, a shoulder at 350 nm, and a broad hill around 530 nm in the oxidized form ...	1998	27315927
a new type of flagellin gene in pseudomonas putida.	previously established pcr amplification and southern hybridization procedures were developed for the isolation of the 0.8-kb flagellin gene in pseudomonas putida. the deduced protein sequence has significant homology to the n- and c-terminal sequences of other bacterial flagellins. we propose that p. putida flagellin genes can be divided at least into three size groups: type i (2.0 kb), type ii (1.4 kb), and type iii (0.8 kb). type i and type ii flagellin genes have been reported. the new 0.8-k ...	1999	12501380
increased flow of fatty acids toward beta-oxidation in developing seeds of arabidopsis deficient in diacylglycerol acyltransferase activity or synthesizing medium-chain-length fatty acids.	synthesis of polyhydroxyalkanoates (phas) from intermediates of fatty acid beta-oxidation was used as a tool to study fatty acid degradation in developing seeds of arabidopsis. transgenic plants expressing a peroxisomal pha synthase under the control of a napin promoter accumulated pha in developing seeds to a final level of 0. 06 mg g(-1) dry weight. in plants co-expressing a plastidial acyl-acyl carrier protein thioesterase from cuphea lanceolata and a peroxisomal pha synthase, approximately 1 ...	1999	10594123
cloning and characterisation of the rpos gene from plant growth-promoting pseudomonas putida wcs358: rpos is not involved in siderophore and homoserine lactone production.	the rpos gene which encodes a stationary phase sigma factor has been identified and characterised from the rhizosphere-colonising plant growth-promoting pseudomonas putida strain wcs358. the predicted protein sequence has extensive homologies with the rpos proteins form other bacteria, in particular with the rpos sigma factors of the fluorescent pseudomonads. a genomic transposon insertion in the rpos gene was constructed, these mutants were analysed for their ability to produce siderophore (iro ...	1999	10673044
degradation of substituted naphthalenesulfonic acids by sphingomonas xenophaga bn6.	sphingomonas xenophaga bn6 was isolated from the river elbe as a member of a multispecies bacterial culture which mineralized 6-aminonaphthalene-2-sulfonate. pure cultures of strain bn6 converted a wide range of amino- and hydroxynaphthalene-2-sulfonates via a catabolic pathway similar to that described for the metabolism of naphthalene to salicylate by pseudomonas putida nah7 or pseudomonas sp ncib 9816. in contrast to the naphthalene-degrading pseudomonads, s. xenophaga bn6 only partially degr ...	1999	11423960
molecular screening for alkane hydroxylase genes in gram-negative and gram-positive strains.	we have developed highly degenerate oligonucleotides for polymerase chain reaction (pcr) amplification of genes related to the pseudomonas oleovorans gpo1 and acinetobacter sp. adp1 alkane hydroxylases, based on a number of highly conserved sequence motifs. in all gram-negative and in two out of three gram-positive strains able to grow on medium- (c6-c11) or long-chain n-alkanes (c12-c16), pcr products of the expected size were obtained. the pcr fragments were cloned and sequenced and found to e ...	1999	11207749
13c/12c isotope fractionation of aromatic hydrocarbons during microbial degradation.	the influence of microbial degradation on the 13c/12c isotope composition of aromatic hydrocarbons is presented using toluene as a model compound. four different toluene-degrading bacterial strains grown in batch culture with oxygen, nitrate, ferric iron or sulphate as electron acceptors were studied as representatives of different environmental redox conditions potentially prevailing in contaminated aquifers. the biological degradation induced isotope shifts in the residual, non-degraded toluen ...	1999	11207760
cell envelope mutants of pseudomonas putida: physiological characterization and analysis of their ability to survive in soil.	to generate mutants with altered lipopolysaccharides (lps) of the wild-type pseudomonas putida kt2442, we used the mini-tn5luxab-km transposon. a mutant was found among luminescent colonies and selected as a negative clone in enzyme-linked immunosorbent assay (elisa) with monoclonal antibody (mab) 7.3b, which recognizes the o-antigen of p. putida lps. the dna region of the lps mutant interrupted by the minitransposon insertion was cloned and sequenced. comparison of the deduced amino acid sequen ...	1999	11207769
cloning and characterization of pseudomonas putida genes encoding the phosphate-specific transport system.	the pstscab genes of pseudomonas putida prs2000, encoding the phosphate (pi)-specific transport (pst) system, were cloned. the psts gene of pseudomonas aeruginosa pao1, of which the pstcab genes had been cloned previously, was also cloned (nikata, t. et al., mol. gen. genet., 250, 692-698, 1996). the predicted translation products of the p. putida pstscab genes showed 83, 75, 78 and 88% amino acid identity with their p. aeruginosa counterparts. two well-conserved pho box sequences were found in ...	1999	16232467
continuous production of l-carnitine with nadh regeneration by a nanofiltration membrane reactor with coimmobilized l-carnitine dehydrogenase and glucose dehydrogenase.	l-carnitine dehydrogenase (cdh) was partially purified from pseudomonas putida iam12014 for the stereospecific reduction of 3-dehydrocarnitine to l-carnitine. cdh and glucose dehydrogenase (gdh) were coimmobilized in a nanofiltration membrane bioreactor (nfmbr) for the continuous production of l-carnitine from 3-dehydrocarnitine with nadh regeneration. in the nfmbr, nad was partially immobilized through rejection by the nanofiltration membrane and effectively regenerated by the conjugation react ...	1999	16232482
analysis of a simple biodegradation process for the removal of volatile organic chemicals from wastewater based on a gas stripping principle.	a simple biodegradation system consisting of an air stripping tank and a bioreactor was proposed for the treatment of volatile organic chemicals in wastewater. toluene was used as a model of volatile organic chemicals. an aqueous solution of toluene and a basic mineral medium were placed in the air stripping tank and bioreactor, respectively. toluene was stripped by supplying compressed air into the stripping tank through a sparger, and the stripped toluene was degraded by pseudomonas putida mt- ...	1999	16232508
nucleotide sequences and characterization of genes encoding naphthalene upper pathway of pseudomonas aeruginosa pak1 and pseudomonas putida ous82.	a 12,808-nucleotide containing dna fragment cloned from naphthalene-utilizing (nah+) pseudomonas aeruginosa pak1 was analyzed and compared with the genes (pah(ous)) of a 14,462-nucleotide dna fragment from pseudomonas putida ous82. the dna sequence analyses demonstrated that the naphthalene upper-pathway genes and their deduced enzymes were very similar between the two bacteria: nucleotide similarities, 83-93%; amino acid similarities, 79-95%. these genes were also similar to those of the nah op ...	1999	16232545
construction of recombinants pseudomonas putida bo14 and escherichia coli qefca8 for ferulic acid biotransformation to vanillin.	recombinants pseudomonas putida bo14 and escherichia coli qefca8 capable of ferulic acid biotransformation to vanillin were constructed using homologous recombination and a pcr based cloning strategy, respectively. in the liquid culture of p. putida bo14, 26.81+/-2.30 microg vanillin ml(-1) of culture filtrate was detected. in the case of recombinant e. coli qefca8, 19.37+/-1.95 microg vanillin ml(-1) of culture filtrate was detected. results indicate that the strains could be useful for the bio ...	1999	16232583
differential organization and transcription of the cat2 gene cluster in aniline-assimilating acinetobacter lwoffii k24.	catabc genes encode proteins that are responsible for the first three steps of one branch of the beta-ketoadipate pathway involved in the degradation of various aromatic compound by bacteria. aniline-assimilating acinetobacter lwoffii k24 is known to have the two-catabc gene clusters (cat1 and cat2) on the chromosome (kim et al., j. bacteriol., 179: 5226-5231, 1997). the order of the cat2 gene cluster is catb2a2c2, which has not been found in other bacteria. in this report, we analyzed the trans ...	1999	16232607
pcar-mediated activation and repression of pca genes from pseudomonas putida are propagated by its binding to both the -35 and the -10 promoter elements.	degradation of protocatechuate in pseudomonas putida is accomplished by the products of the pca genes (pcah,g, pcabdc, pcai, j and pcaf ). in p. putida, all these genes (with the exception of pcah,g ) are activated by the regulatory protein pcar, in association with the pathway intermediate beta-ketoadipate. having previously cloned and characterized the pcar locus, we have overexpressed and purified the pcar protein to homogeneity. the purified pcar protein was shown to form a homodimer in solu ...	1999	10231483
(s)-mandelate dehydrogenase from pseudomonas putida: mechanistic studies with alternate substrates and ph and kinetic isotope effects.	(s)-mandelate dehydrogenase from pseudomonas putida, a member of the flavin mononucleotide-dependent alpha-hydroxy acid oxidase/dehydrogenase family, oxidizes (s)-mandelate to benzoylformate. the enzyme was purified with a carboxy-terminal histidine tag. steady-state kinetic parameters indicate that it preferentially binds large substrates. a good correlation was obtained between the kcat, the substrate kinetic isotope effect (kie), and the pka of the substrate alpha-proton. the kcat decreased a ...	1999	10231535
rgd inclusion in the hexon monomer provides adenovirus type 5-based vectors with a fiber knob-independent pathway for infection.	hypervariable region 5 (hvr5) is a hydrophilic, serotypically nonconserved loop of the hexon monomer which extrudes from the adenovirus (ad) capsid. we have replaced the hvr5 sequence of ad5 with that of heterologous peptides and studied their effects on virus viability and peptide accessibility. a poliovirus model epitope was first inserted in a series of nine "isogenic" viruses that differed in their flanking spacers. whereas virus productivity was not profoundly altered by any of these modifi ...	1999	10233980
monitoring the conjugal transfer of plasmid rp4 in activated sludge and in situ identification of the transconjugants.	a gfpmut3b-tagged derivative of broad host-range plasmid rp4 was used to monitor the conjugative transfer of the plasmid from a pseudomonas putida donor strain to indigenous bacteria in activated sludge. transfer frequencies were determined to be in the range of 4 x 10(-6) to 1 x 10(-5) transconjugants per recipient. in situ hybridisation with fluorescently labeled, rrna-targeted oligonucleotides was used to phylogenetically affiliate the bacteria that had received the plasmid.	1999	10234817
electron transfer from quinohemoprotein alcohol dehydrogenase to blue copper protein azurin in the alcohol oxidase respiratory chain of pseudomonas putida hk5.	a blue copper protein was purified together with a type ii quinohemoprotein alcohol dehydrogenase (adh iib) from the soluble fraction of pseudomonas putida hk5 grown on n-butanol. the purified blue copper protein was shown to be azurin, on the basis of several properties such as its absorption maximum (623 nm), its low molecular mass (17 500 da), its acidic nature (pi of 4.1), its relatively high redox potential (306 mv), the presence of an intramolecular disulfide bond, and n-terminal amino aci ...	1999	10320337
the a modules of the azotobacter vinelandii mannuronan-c-5-epimerase alge1 are sufficient for both epimerization and binding of ca2+.	the industrially important polysaccharide alginate is composed of the two sugar monomers beta-d-mannuronic acid (m) and its epimer alpha-l-guluronic acid (g). in the bacterium azotobacter vinelandii, the g residues originate from a polymer-level reaction catalyzed by one periplasmic and at least five secreted mannuronan c-5-epimerases. the secreted enzymes are composed of repeats of two protein modules designated a (385 amino acids) and r (153 amino acids). the modular structure of one of the ep ...	1999	10322003
role of quinolinate phosphoribosyl transferase in degradation of phthalate by burkholderia cepacia dbo1.	two distinct regions of dna encode the enzymes needed for phthalate degradation by burkholderia cepacia dbo1. a gene coding for an enzyme (quinolinate phosphoribosyl transferase) involved in the biosynthesis of nad+ was identified between these two regions by sequence analysis and functional assays. southern hybridization experiments indicate that dbo1 and other phthalate-degrading b. cepacia strains have two dissimilar genes for this enzyme, while non-phthalate-degrading b. cepacia strains have ...	1999	10322007
diverse oxygenations catalyzed by carbazole 1,9a-dioxygenase from pseudomonas sp. strain ca10.	carbazole 1,9a-dioxygenase (cardo) from pseudomonas sp. strain ca10 is a multicomponent enzyme that catalyzes the angular dioxygenation of carbazole, dibenzofuran, and dibenzo-p-dioxin. it was revealed by gas chromatography-mass spectrometry and 1h and 13c nuclear magnetic resonance analyses that xanthene and phenoxathiin were converted to 2,2',3-trihydroxydiphenylmethane and 2,2',3-trihydroxydiphenyl sulfide, respectively. thus, for xanthene and phenoxathiin, angular dioxygenation by cardo occu ...	1999	10322011
isolation and characterization of the cis-trans-unsaturated fatty acid isomerase of pseudomonas oleovorans gpo12.	pseudomonas oleovorans contains an isomerase which catalyzes the cis-trans conversion of the abundant unsaturated membrane fatty acids 9-cis-hexadecenoic acid (palmitoleic acid) and 11-cis-octadecenoic acid (vaccenic acid). we purified the isomerase from the periplasmic fraction of pseudomonas oleovorans. the molecular mass of the enzyme was estimated to be 80 kda under denaturing conditions and 70 kda under native conditions, suggesting a monomeric structure of the active enzyme. n-terminal seq ...	1999	10322030
nahy, a catabolic plasmid-encoded receptor required for chemotaxis of pseudomonas putida to the aromatic hydrocarbon naphthalene.	pseudomonas putida g7 exhibits chemotaxis to naphthalene, but the molecular basis for this was not known. a new gene, nahy, was found to be cotranscribed with meta cleavage pathway genes on the nah7 catabolic plasmid for naphthalene degradation. the nahy gene encodes a 538-amino-acid protein with a membrane topology and a c-terminal region that resemble those of chemotaxis transducer proteins. a p. putida g7 nahy mutant grew on naphthalene but was not chemotactic to this aromatic hydrocarbon. th ...	1999	10322041
phylogenetic analysis of ara+ and ara- burkholderia pseudomallei isolates and development of a multiplex pcr procedure for rapid discrimination between the two biotypes.	a burkholderia pseudomallei-like organism has recently been identified among some soil isolates of b. pseudomallei in an area with endemic melioidosis. this organism is almost identical to b. pseudomallei in terms of morphological and biochemical profiles, except that it differs in ability to assimilate l-arabinose. these ara+ isolates are also less virulent than the ara- isolates in animal models. in addition, clinical isolates of b. pseudomallei available to date are almost exclusively ara-. t ...	1999	10325345
distribution of a nocardia brasiliensis catalase gene fragment in members of the genera nocardia, gordona, and rhodococcus.	an immunodominant protein from nocardia brasiliensis, p61, was subjected to amino-terminal and internal sequence analysis. three sequences of 22, 17, and 38 residues, respectively, were obtained and compared with the protein database from genbank by using the blast system. the sequences showed homology to some eukaryotic catalases and to a bromoperoxidase-catalase from streptomyces violaceus. its identity as a catalase was confirmed by analysis of its enzymatic activity on h2o2 and by a double-s ...	1999	10325357
toluene metabolism by the solvent-tolerant pseudomonas putida dot-t1 strain, and its role in solvent impermeabilization.	pseudomonas putida dot-t1e is a solvent-tolerant strain able to grow with toluene as the sole c-source. tn5 mutagenesis was carried out and a mutant unable to use toluene as the sole c-source was isolated. dna was sequenced upstream and downstream of the site where the tn5 was inserted. analysis of the dna revealed 13 open reading frames (orfs) homologous to the tod genes for the toluene dioxygenase pathway of p. putida f1, which are organized in two operons: todxfc1c2badegih and todst. the tn5 ...	1999	10333523
allylic or benzylic stabilization is essential for catalysis by bacterial benzyl alcohol dehydrogenases.	benzyl alcohol dehydrogenase from acinetobacter calcoaceticus (ac-badh) and tol plasmid-encoded benzyl alcohol dehydrogenase from pseudomonas putida (tol-badh) have previously been shown to oxidize a variety of aromatic alcohols but not aliphatic substrates. here, we have expressed the genes for ac-badh and tol-badh in escherichia coli, purified the resulting over-expressed enzymes, and shown that each is an effective catalyst of both benzylic and allylic alcohol oxidation, but not of oxidation ...	1999	10334943
the iiantr (ptsn) protein of pseudomonas putida mediates the c source inhibition of the sigma54-dependent pu promoter of the tol plasmid.	the gene cluster adjacent to the sequence of rpon (encoding sigma factor sigma54) of pseudomonas putida has been studied with respect to the c source regulation of the pu promoter of the upper tol (toluene catabolism) operon. the region includes four open reading frames (orfs), two of which (named ptsn and ptso genes) encode proteins similar to components of the phosphoenolpyruvate:sugar phosphotransferase system. each of the four genes was disrupted with a nonpolar insertion, and the effects in ...	1999	10336451
genetic characterization of wild-type and mutant fur genes of bordetella avium.	for most, if not all, organisms, iron (fe) is an essential element. in response to the nutritional requirement for fe, bacteria evolved complex systems to acquire the element from the environment. the genes encoding these systems are often coordinately regulated in response to the fe concentration. recent investigations revealed that bordetella avium, a respiratory pathogen of birds, expressed a number of fe-regulated genes (t. d. connell, a. dickenson, a. j. martone, k. t. militello, m. j. fili ...	1999	10338537
cloning and characterization of mdc genes encoding malonate decarboxylase from pseudomonas putida.	the dna fragment encoding malonate decarboxylase, involved in malonate assimilation, was cloned from pseudomonas putida. the 11-kb dna fragment contained nine open reading frames, which were designated mdcabcdeghlm in the given order. n-terminal protein sequencing established that the mdca, mdcc, mdcd, mdce and mdch genes encoded subunits alpha, delta, beta, gamma and epsilon of the malonate decarboxylase, respectively. malonate decarboxylase was functionally expressed in escherichia coli from p ...	1999	10339824
chemoselective nitro group reduction and reductive dechlorination initiate degradation of 2-chloro-5-nitrophenol by ralstonia eutropha jmp134.	ralstonia eutropha jmp134 utilizes 2-chloro-5-nitrophenol as a sole source of nitrogen, carbon, and energy. the initial steps for degradation of 2-chloro-5-nitrophenol are analogous to those of 3-nitrophenol degradation in r. eutropha jmp134. 2-chloro-5-nitrophenol is initially reduced to 2-chloro-5-hydroxylaminophenol, which is subject to an enzymatic bamberger rearrangement yielding 2-amino-5-chlorohydroquinone. the chlorine of 2-amino-5-chlorohydroquinone is removed by a reductive mechanism, ...	1999	10347008
an alkane-responsive expression system for the production of fine chemicals	membrane-located monooxygenase systems, such as the pseudomonas putida mt-2-derived xylene oxygenase, are attractive for challenging transformations of apolar compounds, including enantiospecific epoxidations, but are difficult to synthesize at levels that are useful for application to biotechnological processes. in order to construct efficient biocatalysis strains, we utilized the alkane-responsive regulatory system of the oct plasmid-located alk genes of pseudomonas oleovorans gpo1, a very att ...	1999	10347009
monooxygenase-mediated 1,2-dichloroethane degradation by pseudomonas sp. strain dca1.	a bacterial strain, designated pseudomonas sp. strain dca1, was isolated from a 1,2-dichloroethane (dca)-degrading biofilm. strain dca1 utilizes dca as the sole carbon and energy source and does not require additional organic nutrients, such as vitamins, for optimal growth. the affinity of strain dca1 for dca is very high, with a km value below the detection limit of 0.5 microm. instead of a hydrolytic dehalogenation, as in other dca utilizers, the first step in dca degradation in strain dca1 is ...	1999	10347028
role of pfka and general carbohydrate catabolism in seed colonization by enterobacter cloacae.	enterobacter cloacae a-11 is a transposon mutant of strain 501r3 that was deficient in cucumber spermosphere colonization and in the utilization of certain carbohydrates (d. p. roberts, c. j. sheets, and j. s. hartung, can. j. microbiol. 38:1128-1134, 1992). in vitro growth of strain a-11 was reduced or deficient on most carbohydrates that supported growth of strain 501r3 but was unaffected on fructose, glycerol, and all amino acids and organic acids tested. colonization by strain a-11 was signi ...	1999	10347036
characterization of a pseudomonas putida allylic alcohol dehydrogenase induced by growth on 2-methyl-3-buten-2-ol.	we have been working to develop an enzymatic assay for the alcohol 2-methyl-3-buten-2-ol (232-mb), which is produced and emitted by certain pines. to this end we have isolated the soil bacterium pseudomonas putida mb-1, which uses 232-mb as a sole carbon source. strain mb-1 contains inducible 3-methyl-2-buten-1-ol (321-mb) and 3-methyl-2-buten-1-al dehydrogenases, suggesting that 232-mb is metabolized by isomerization to 321-mb followed by oxidation. 321-mb dehydrogenase was purified to near-hom ...	1999	10347052