Publications

liz1p, a novel fission yeast membrane protein, is required for normal cell division when ribonucleotide reductase is inhibited.	ribonucleotide reductase activity is required for generating deoxyribonucleotides for dna replication. schizosaccharomyces pombe cells lacking ribonucleotide reductase activity arrest during s phase of the cell cycle. in a screen for hydroxyurea-sensitive mutants in s. pombe, we have identified a gene, liz1(+), which when mutated reveals an additional, previously undescribed role for ribonucleotide reductase activity during mitosis. inactivation of ribonucleotide reductase, by either hydroxyurea ...	1999	9950674
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
pseudomonas aeruginosa fur overlaps with a gene encoding a novel outer membrane lipoprotein, omla.	a novel outer membrane lipoprotein in pseudomonas aeruginosa is encoded by the omla gene, which was identified immediately upstream of the fur (ferric uptake regulator) gene. the omla and fur genes were divergently transcribed and had overlapping promoter regions. the proximal fur p2 promoter and the omla promoter shared a 5-bp dna motif for their -10 promoter elements. the distal fur p1 promoter was located within the omla coding sequence, and the omla and fur t1 mrnas overlapped by 154 nucleot ...	1999	9973334
active efflux and diffusion are involved in transport of pseudomonas aeruginosa cell-to-cell signals.	many gram-negative bacteria communicate by n-acyl homoserine lactone signals called autoinducers (ais). in pseudomonas aeruginosa, cell-to-cell signaling controls expression of extracellular virulence factors, the type ii secretion apparatus, a stationary-phase sigma factor (sigmas), and biofilm differentiation. the fact that a similar signal, n-(3-oxohexanoyl) homoserine lactone, freely diffuses through vibrio fischeri and escherichia coli cells has led to the assumption that all ais are freely ...	1999	9973347
conversion of 3-chlorocatechol by various catechol 2,3-dioxygenases and sequence analysis of the chlorocatechol dioxygenase region of pseudomonas putida gj31.	pseudomonas putida gj31 contains an unusual catechol 2,3-dioxygenase that converts 3-chlorocatechol and 3-methylcatechol, which enables the organism to use both chloroaromatics and methylaromatics for growth. a 3.1-kb region of genomic dna of strain gj31 containing the gene for this chlorocatechol 2,3-dioxygenase (cbze) was cloned and sequenced. the cbze gene appeared to be plasmid localized and was found in a region that also harbors genes encoding a transposase, a ferredoxin that was homologou ...	1999	9973359
rapid identification and typing of staphylococcus aureus by pcr-restriction fragment length polymorphism analysis of the aroa gene.	the staphylococcus aureus aroa gene, which encodes 5-enolpyruvylshikimate-3-phosphate synthase, was used as a target for the amplification of a 1,153-bp dna fragment by pcr with a pair of primers of 24 and 19 nucleotides. the pcr products, which were detected by agarose gel electrophoresis, were amplified from all s. aureus strains so far analyzed (reference strains and isolates from cows and sheep with mastitis, as well as 59 isolates from humans involved in four confirmed outbreaks). hybridiza ...	1999	9986814
biodegradation of benzene, toluene, ethylbenzene, and o-xylene by a coculture of pseudomonas putida and pseudomonas fluorescens immobilized in a fibrous-bed bioreactor.	a fibrous-bed bioreactor containing the coculture of pseudomonas putida and p. fluorescens immobilized in a fibrous matrix was developed to degrade benzene (b), toluene (t), ethylbenzene (e), and o-xylene (x) in synthetic waste streams. the kinetics of btex biodegradation by immobilized cells adapted in the fibrous-bed bioreactor and free cells grown in serum bottles were studied. in general, the btex biodegradation rate increased with increasing substrate concentration and then decreased after ...	1999	9990730
altered cytochrome c display precedes apoptotic cell death in drosophila.	drosophila affords a genetically well-defined system to study apoptosis in vivo. it offers a powerful extension to in vitro models that have implicated a requirement for cytochrome c in caspase activation and apoptosis. we found that an overt alteration in cytochrome c anticipates programmed cell death (pcd) in drosophila tissues, occurring at a time that considerably precedes other known indicators of apoptosis. the altered configuration is manifested by display of an otherwise hidden epitope a ...	1999	10037791
3-hydroxylaminophenol mutase from ralstonia eutropha jmp134 catalyzes a bamberger rearrangement.	3-hydroxylaminophenol mutase from ralstonia eutropha jmp134 is involved in the degradative pathway of 3-nitrophenol, in which it catalyzes the conversion of 3-hydroxylaminophenol to aminohydroquinone. to show that the reaction was really catalyzed by a single enzyme without the release of intermediates, the corresponding protein was purified to apparent homogeneity from an extract of cells grown on 3-nitrophenol as the nitrogen source and succinate as the carbon and energy source. 3-hydroxylamin ...	1999	10049374
a novel reduced flavin mononucleotide-dependent methanesulfonate sulfonatase encoded by the sulfur-regulated msu operon of pseudomonas aeruginosa.	when pseudomonas aeruginosa is grown with organosulfur compounds as sulfur sources, it synthesizes a set of proteins whose synthesis is repressed in the presence of sulfate, cysteine, or thiocyanate (so-called sulfate starvation-induced proteins). the gene encoding one of these proteins, pa13, was isolated from a cosmid library of p. aeruginosa pao1 and sequenced. it encoded a 381-amino-acid protein that was related to several reduced flavin mononucleotide (fmnh2)-dependent monooxygenases, and i ...	1999	10049377
complete sequence of a 184-kilobase catabolic plasmid from sphingomonas aromaticivorans f199.	the complete 184,457-bp sequence of the aromatic catabolic plasmid, pnl1, from sphingomonas aromaticivorans f199 has been determined. a total of 186 open reading frames (orfs) are predicted to encode proteins, of which 79 are likely directly associated with catabolism or transport of aromatic compounds. genes that encode enzymes associated with the degradation of biphenyl, naphthalene, m-xylene, and p-cresol are predicted to be distributed among 15 gene clusters. the unusual coclustering of gene ...	1999	10049392
the palkbfghjkl promoter is under carbon catabolite repression control in pseudomonas oleovorans but not in escherichia coli alk+ recombinants.	the alk genes are located on the oct plasmid of pseudomonas oleovorans and encode an inducible pathway for the utilization of n-alkanes as carbon and energy sources. we have investigated the influence of alternative carbon sources on the induction of this pathway in p. oleovorans and escherichia coli alk+ recombinants. in doing so, we confirmed earlier reports that induction of alkane hydroxylase activity in pseudomonads is subject to carbon catabolite repression. specifically, synthesis of the ...	1999	10049394
secretion, localization, and antibacterial activity of tasa, a bacillus subtilis spore-associated protein.	the synthesis and subcellular localization of the proteins that comprise the bacillus subtilis spore are under a variety of complex controls. to better understand these controls, we have identified and characterized a 31-kda sporulation protein, called tasa, which is secreted into the culture medium early in sporulation and is also incorporated into the spore. tasa synthesis begins approximately 30 min after the onset of sporulation and requires the sporulation transcription factor genes spo0h a ...	1999	10049401
purification and characterization of gentisate 1,2-dioxygenases from pseudomonas alcaligenes ncib 9867 and pseudomonas putida ncib 9869.	two 3-hydroxybenzoate-inducible gentisate 1,2-dioxygenases were purified to homogeneity from pseudomonas alcaligenes ncib 9867 (p25x) and pseudomonas putida ncib 9869 (p35x), respectively. the estimated molecular mass of the purified p25x gentisate 1, 2-dioxygenase was 154 kda, with a subunit mass of 39 kda. its structure is deduced to be a tetramer. the pi of this enzyme was established to be 4.8 to 5.0. the subunit mass of p35x gentisate 1, 2-dioxygenase was 41 kda, and this enzyme was deduced ...	1999	10049846
molecular characterization of the genes pcag and pcah, encoding protocatechuate 3,4-dioxygenase, which are essential for vanillin catabolism in pseudomonas sp. strain hr199.	pseudomonas sp. strain hr199 is able to utilize eugenol (4-allyl-2-methoxyphenol), vanillin (4-hydroxy-3-methoxybenzaldehyde), or protocatechuate as the sole carbon source for growth. mutants of this strain which were impaired in the catabolism of vanillin but retained the ability to utilize eugenol or protocatechuate were obtained after nitrosoguanidine mutagenesis. one mutant (sk6169) was used as recipient of a pseudomonas sp. strain hr199 genomic library in cosmid pvk100, and phenotypic compl ...	1999	10049847
inhibition of vibrio anguillarum by pseudomonas fluorescens ah2, a possible probiotic treatment of fish.	to study the possible use of probiotics in fish farming, we evaluated the in vitro and in vivo antagonism of antibacterial strain pseudomonas fluorescens strain ah2 against the fish-pathogenic bacterium vibrio anguillarum. as iron is important in virulence and bacterial interactions, the effect of p. fluorescens ah2 was studied under iron-rich and iron-limited conditions. sterile-filtered culture supernatants from iron-limited p. fluorescens ah2 inhibited the growth of v. anguillarum, whereas st ...	1999	10049849
effect of phenylurea herbicides on soil microbial communities estimated by analysis of 16s rrna gene fingerprints and community-level physiological profiles.	the effect of three phenyl urea herbicides (diuron, linuron, and chlorotoluron) on soil microbial communities was studied by using soil samples with a 10-year history of treatment. denaturing gradient gel electrophoresis (dgge) was used for the analysis of 16s rrna genes (16s rdna). the degree of similarity between the 16s rdna profiles of the communities was quantified by numerically analysing the dgge band patterns. similarity dendrograms showed that the microbial community structures of the h ...	1999	10049851
polynucleotide probes that target a hypervariable region of 16s rrna genes to identify bacterial isolates corresponding to bands of community fingerprints.	temperature gradient gel electrophoresis (tgge) is well suited for fingerprinting bacterial communities by separating pcr-amplified fragments of 16s rrna genes (16s ribosomal dna [rdna]). a strategy was developed and was generally applicable for linking 16s rdna from community fingerprints to pure culture isolates from the same habitat. for this, digoxigenin-labeled polynucleotide probes were generated by pcr, using bands excised from tgge community fingerprints as a template, and applied in hyb ...	1999	10049861
degradation of chloronitrobenzenes by a coculture of pseudomonas putida and a rhodococcus sp.	a single microorganism able to mineralize chloronitrobenzenes (cnbs) has not been reported, and degradation of cnbs by coculture of two microbial strains was attempted. pseudomonas putida hs12 was first isolated by analogue enrichment culture using nitrobenzene (nb) as the substrate, and this strain was observed to possess a partial reductive pathway for the degradation of nb. from high-performance liquid chromatography-mass spectrometry and 1h nuclear magnetic resonance analyses, nb-grown cells ...	1999	10049867
enhanced bioaccumulation of heavy metal ions by bacterial cells due to surface display of short metal binding peptides.	metal binding peptides of sequences gly-his-his-pro-his-gly (named hp) and gly-cys-gly-cys-pro-cys-gly-cys-gly (named cp) were genetically engineered into lamb protein and expressed in escherichia coli. the cd2+-to-hp and cd2+-to-cp stoichiometries of peptides were 1:1 and 3:1, respectively. hybrid lamb proteins were found to be properly folded in the outer membrane of e. coli. isolated cell envelopes of e. coli bearing newly added metal binding peptides showed an up to 1.8-fold increase in cd2+ ...	1999	10049868
comparison of flagellin genes from clinical and environmental pseudomonas aeruginosa isolates.	pseudomonas aeruginosa, an important opportunistic pathogen, was isolated from environmental samples and compared to clinically derived strains. while p. aeruginosa was isolated readily from an experimental mushroom-growing unit, it was found only rarely in other environmental samples. a flagellin gene pcr-restriction fragment length polymorphism analysis of the isolates revealed that environmental and clinical p. aeruginosa strains are not readily distinguishable. the variation in the central r ...	1999	10049879
identification of a novel group of bacteria in sludge from a deteriorated biological phosphorus removal reactor.	the microbial diversity of a deteriorated biological phosphorus removal reactor was investigated by methods not requiring direct cultivation. the reactor was fed with media containing acetate and high levels of phosphate (p/c weight ratio, 8:100) but failed to completely remove phosphate in the effluent and showed very limited biological phosphorus removal activity. denaturing gradient gel electrophoresis (dgge) of pcr-amplified 16s ribosomal dna was used to investigate the bacterial diversity. ...	1999	10049891
combination of fluorescent in situ hybridization and microautoradiography-a new tool for structure-function analyses in microbial ecology.	a new microscopic method for simultaneously determining in situ the identities, activities, and specific substrate uptake profiles of individual bacterial cells within complex microbial communities was developed by combining fluorescent in situ hybridization (fish) performed with rrna-targeted oligonucleotide probes and microautoradiography. this method was evaluated by using defined artificial mixtures of escherichia coli and herpetosiphon aurantiacus under aerobic incubation conditions with ad ...	1999	10049895
contrasting effects of a nonionic surfactant on the biotransformation of polycyclic aromatic hydrocarbons to cis-dihydrodiols by soil bacteria.	the biotransformation of the polycyclic aromatic hydrocarbons (pahs) naphthalene and phenanthrene was investigated by using two dioxygenase-expressing bacteria, pseudomonas sp. strain 9816/11 and sphingomonas yanoikuyae b8/36, under conditions which facilitate mass-transfer limited substrate oxidation. both of these strains are mutants that accumulate cis-dihydrodiol metabolites under the reaction conditions used. the effects of the nonpolar solvent 2,2,4, 4,6,8,8-heptamethylnonane (hmn) and the ...	1999	10049904
metabolic engineering of poly(3-hydroxyalkanoates): from dna to plastic.	poly(3-hydroxyalkanoates) (phas) are a class of microbially produced polyesters that have potential applications as conventional plastics, specifically thermoplastic elastomers. a wealth of biological diversity in pha formation exists, with at least 100 different pha constituents and at least five different dedicated pha biosynthetic pathways. this diversity, in combination with classical microbial physiology and modern molecular biology, has now opened up this area for genetic and metabolic eng ...	1999	10066830
surface motility of serratia liquefaciens mg1.		1999	10074060
role of the alternative sigma factor sigmas in expression of the alks regulator of the pseudomonas oleovorans alkane degradation pathway.	the alks protein activates transcription from the palkb promoter, allowing the expression of a number of genes required for the assimilation of alkanes in pseudomonas oleovorans. we have identified the promoter from which the alks gene is transcribed, palks, and analyzed its expression under different conditions and genetic backgrounds. transcription from palks was very low during the exponential phase of growth and increased considerably when cells reached the stationary phase. the palks -10 re ...	1999	10074066
aspartate 205 in the catalytic domain of naphthalene dioxygenase is essential for activity.	the naphthalene dioxygenase enzyme system carries out the first step in the aerobic degradation of naphthalene by pseudomonas sp. strain ncib 9816-4. the crystal structure of naphthalene dioxygenase (b. kauppi, k. lee, e. carredano, r. e. parales, d. t. gibson, h. eklund, and s. ramaswamy, structure 6:571-586, 1998) indicates that aspartate 205 may provide the most direct route of electron transfer between the rieske [2fe-2s] center of one alpha subunit and mononuclear iron in the adjacent alpha ...	1999	10074076
human papillomavirus type 18 e1 protein is translated from polycistronic mrna by a discontinuous scanning mechanism.	papillomaviruses are small double-stranded dna viruses that replicate episomally in the nuclei of infected cells. the full-length e1 protein of papillomaviruses is required for the replication of viral dna. the viral mrna from which the human papillomavirus type 18 e1 protein is expressed is not known. we demonstrate that in eukaryotic cells, the e1 protein is expressed from polycistronic mrna containing e6, e7, and e1 open reading frames (orfs). the translation of adjacent e7 and e1 orfs is not ...	1999	10074156
comparison of isolation media for recovery of burkholderia cepacia complex from respiratory secretions of patients with cystic fibrosis.	burkholderia cepacia selective agar (bcsa) has previously been devised for isolation of b. cepacia from respiratory secretions of patients with cystic fibrosis and tested under research laboratory conditions. here we describe a study in which bcsa, oxidation-fermentation polymyxin bacitracin lactose agar (ofpbl), and pseudomonas cepacia agar (pca) were compared in routine culture procedures for the ability to grow b. cepacia and inhibit other organisms. three hundred twenty-eight specimens from ...	1999	10074517
environmental risk assessment for the widely used iodinated x-ray contrast agent iopromide (ultravist).	iodinated x-ray contrast media are diagnostic pharmaceuticals that are applied to enhance the contrast between organs or vessels examined and surrounding tissues during radiography. these substances are applied in doses up to ca. 200 g per person (corresponding to approx 100 g iodine) and are rapidly excreted. in the sewage system they contribute to the burden of adsorbable organic halogens (aox). to assess the potential environmental impact of this release, studies on environmental fate and eff ...	1999	10090816
putidaredoxin-cytochrome p450cam interaction. spin state of the heme iron modulates putidaredoxin structure.	during the monooxygenase reaction catalyzed by cytochrome p450cam (p450cam), a ternary complex of p450cam, reduced putidaredoxin, and d-camphor is formed as an obligatory reaction intermediate. when ligands such as co, no, and o2 bind to the heme iron of p450cam in the intermediate complex, the epr spectrum of reduced putidaredoxin with a characteristic signal at 346 millitesla at 77 k changed into a spectrum having a new signal at 348 millitesla. the experiment with o2 was carried out by employ ...	1999	10092615
role of bkdr, a transcriptional activator of the sigl-dependent isoleucine and valine degradation pathway in bacillus subtilis.	a new gene, bkdr (formerly called yqir), encoding a regulator with a central (catalytic) domain was found in bacillus subtilis. this gene controls the utilization of isoleucine and valine as sole nitrogen sources. seven genes, previously called yqis, yqit, yqiu, yqiv, bfmbaa, bfmbab, and bfmbb and now referred to as ptb, bcd, buk, lpd, bkda1, bkda2, and bkdb, are located downstream from the bkdr gene in b. subtilis. the products of these genes are similar to phosphate butyryl coenzyme a transfer ...	1999	10094682
binding site recognition by rns, a virulence regulator in the arac family.	the expression of cs1 pili by enterotoxigenic strains of escherichia coli is regulated at the transcriptional level and requires the virulence regulator rns, a member of the arac family of regulatory proteins. rns binds at two separate sites upstream of pcoo (the promoter of cs1 pilin genes), which were identified in vitro with an mbp::rns fusion protein in gel mobility and dnase i footprinting assays. at each site, rns recognizes asymmetric nucleotide sequences in two regions of the major groov ...	1999	10094688
molecular analysis of a novel methanesulfonic acid monooxygenase from the methylotroph methylosulfonomonas methylovora.	methylosulfonomonas methylovora m2 is an unusual gram-negative methylotrophic bacterium that can grow on methanesulfonic acid (msa) as the sole source of carbon and energy. oxidation of msa by this bacterium is carried out by a multicomponent msa monooxygenase (msamo). cloning and sequencing of a 7.5-kbp sphi fragment of chromosomal dna revealed four tightly linked genes encoding this novel monooxygenase. analysis of the deduced msamo polypeptide sequences indicated that the enzyme contains a tw ...	1999	10094704
characterization of mdcr, a regulatory gene of the malonate catabolic system in klebsiella pneumoniae.	the klebsiella pneumoniae mdcr gene, which encodes a lysr-type regulator, was overexpressed in escherichia coli. purified mdcr was found to bind specifically to the control region of either the malonate decarboxylase (mdc) genes or mdcr. we have also demonstrated that mdcr is an activator of the expression of the mdc genes, whereas it represses the transcription of the putative control region of mdcr, pmdcr, indicating a negative autoregulatory control.	1999	10094715
the xyls-dependent pm promoter is transcribed in vivo by rna polymerase with sigma 32 or sigma 38 depending on the growth phase.	the pm promoter of the tol plasmid of pseudomonas putida is expressed at high level along the growth curve. this transcription is dependent on the positive regulator xyls activated by 3-methylbenzoate. the sigma factor sigma 38 is required for expression in early stationary phase and thereafter. to test whether sigma 70 was involved in pm transcription in exponential phase, we have followed mrna synthesis in a rpod thermosensitive strain. no difference in pm transcription was found between the w ...	1999	10096078
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
in vitro antibacterial properties of pexiganan, an analog of magainin.	pexiganan, a 22-amino-acid antimicrobial peptide, is an analog of the magainin peptides isolated from the skin of the african clawed frog. pexiganan exhibited in vitro broad-spectrum antibacterial activity when it was tested against 3,109 clinical isolates of gram-positive and gram-negative, anaerobic and aerobic bacteria. the pexiganan mic at which 90% of isolates are inhibited (mic90) was 32 micrograms/ml or less for staphylococcus spp., streptococcus spp., enterococcus faecium, corynebacteriu ...	1999	10103181
structure of in31, a blaimp-containing pseudomonas aeruginosa integron phyletically related to in5, which carries an unusual array of gene cassettes.	the location and environment of the acquired blaimp gene, which encodes the imp-1 metallo-beta-lactamase, were investigated in a japanese pseudomonas aeruginosa clinical isolate (isolate 101/1477) that produced the enzyme. in this isolate, blaimp was carried on a 36-kb plasmid, and similar to the identical alleles found in serratia marcescens and klebsiella pneumoniae clinical isolates, it was located on a mobile gene cassette inserted into an integron. the entire structure of this integron, nam ...	1999	10103196
biochemical characterization of the pseudomonas aeruginosa 101/1477 metallo-beta-lactamase imp-1 produced by escherichia coli.	the blaimp gene coding for the imp-1 metallo-beta-lactamase produced by a pseudomonas aeruginosa clinical isolate (isolate 101/1477) was overexpressed via a t7 expression system in escherichia coli bl21 (de3), and its product was purified to homogeneity with a final yield of 35 mg/liter of culture. the structural and functional properties of the enzyme purified from e. coli were identical to those of the enzyme produced by p. aeruginosa. the imp-1 metallo-beta-lactamase exhibits a broad-spectrum ...	1999	10103197
formation of hydride-meisenheimer complexes of picric acid (2,4, 6-trinitrophenol) and 2,4-dinitrophenol during mineralization of picric acid by nocardioides sp. strain cb 22-2.	there are only a few examples of microbial conversion of picric acid (2,4,6-trinitrophenol). none of the organisms that have been described previously is able to use this compound as a sole source of carbon, nitrogen, and energy at high rates. in this study we isolated and characterized a strain, strain cb 22-2, that was able to use picric acid as a sole source of carbon and energy at concentrations up to 40 mm and at rates of 1.6 mmol. h(-1). g (dry weight) of cells(-1) in continuous cultures a ...	1999	10103224
microbiology of the oil fly, helaeomyia petrolei.	helaeomyia petrolei larvae isolated from the asphalt seeps of rancho la brea in los angeles, calif., were examined for microbial gut contents. standard counts on luria-bertani, macconkey, and blood agar plates indicated ca. 2 x 10(5) heterotrophic bacteria per larva. the culturable bacteria represented 15 to 20% of the total population as determined by acridine orange staining. the gut itself contained large amounts of the oil, had no observable ceca, and maintained a slightly acidic ph of 6.3 t ...	1999	10103240
cloning and nucleotide sequence analysis of gyrb of bacillus cereus, b. thuringiensis, b. mycoides, and b. anthracis and their application to the detection of b. cereus in rice.	as 16s rrna sequence analysis has proven inadequate for the differentiation of bacillus cereus from closely related species, we employed the gyrase b gene (gyrb) as a molecular diagnostic marker. the gyrb genes of b. cereus jcm 2152(t), bacillus thuringiensis iam 12077(t), bacillus mycoides atcc 6462(t), and bacillus anthracis pasteur #2h were cloned and sequenced. oligonucleotide pcr primer sets were designed from within gyrb sequences of the respective bacteria for the specific amplification a ...	1999	10103241
estimation of bacterial cell numbers in humic acid-rich salt marsh sediments with probes directed to 16s ribosomal dna	the feasibility of using probes directed towards ribosomal dnas (rdnas) as a quantitative approach to estimating cell numbers was examined and applied to study the structure of a bacterial community in humic acid-rich salt marsh sediments. hybridizations were performed with membrane-bound nucleic acids by using seven group-specific dna oligonucleotide probes complementary to 16s rrna coding regions. these included a general eubacterial probe and probes encompassing most members of the gram-negat ...	1999	10103245
reduction of cell lysate viscosity during processing of poly(3-hydroxyalkanoates) by chromosomal integration of the staphylococcal nuclease gene in pseudomonas putida.	poly(3-hydroxyalkanoates) (phas) are biodegradable thermoplastics which are accumulated by many bacterial species in the form of intracellular granules and which are thought to serve as reserves of carbon and energy. pseudomonas putida accumulates a polyester, composed of medium-side-chain 3-hydroxyalkanoic acids, which has excellent film-forming properties. industrial processing of pha involves purification of the pha granules from high-cell-density cultures. after the fermentation process, cel ...	1999	10103246
production of poly(3-hydroxybutyric acid-co-4-hydroxybutyric acid) and poly(4-hydroxybutyric acid) without subsequent degradation by hydrogenophaga pseudoflava.	a hydrogenophaga pseudoflava strain was able to synthesize poly(3-hydroxybutyric acid-co-4-hydroxybutyric acid) [p(3hb-co-4hb)] having a high level of 4-hydroxybutyric acid monomer unit (4hb) from gamma-butyrolactone. in a two-step process in which the first step involved production of cells containing a minimum amount of poly(3-hydroxybutyric acid) [p(3hb)] and the second step involved polyester accumulation from the lactone, approximately 5 to 10 mol% of the 3-hydroxybutyric acid (3hb) derived ...	1999	10103252
the alkene monooxygenase from xanthobacter strain py2 is closely related to aromatic monooxygenases and catalyzes aromatic monohydroxylation of benzene, toluene, and phenol.	the genes encoding the six polypeptide components of the alkene monooxygenase from xanthobacter strain py2 (xamo) have been located on a 4.9-kb fragment of chromosomal dna previously cloned in cosmid pny2. sequencing and analysis of the predicted amino acid sequences indicate that the components of xamo are homologous to those of the aromatic monooxygenases, toluene 2-, 3-, and 4-monooxygenase and benzene monooxygenase, and that the gene order is identical. the genes and predicted polypeptides a ...	1999	10103255
selection of clc, cba, and fcb chlorobenzoate-catabolic genotypes from groundwater and surface waters adjacent to the hyde park, niagara falls, chemical landfill.	the frequency of isolation of three nonhomologous chlorobenzoate catabolic genotypes (clc, cba, and fcb) was determined for 464 isolates from freshwater sediments and groundwater in the vicinity of the hyde park industrial landfill site in the niagara watershed. samples were collected from both contaminated and noncontaminated sites during spring, summer, and fall and enriched at 4, 22, or 32 degrees c with micromolar to millimolar concentrations of chlorobenzoates and 3-chlorobiphenyl (m. c. pe ...	1999	10103260
phenotypic expression of pcr-generated random mutations in a pseudomonas putida gene after its introduction into an acinetobacter chromosome by natural transformation.	localized sets of random point mutations generated by pcr amplification can be transferred efficiently to the chromosome of acinetobacter adp1 (also known as strain bd413) by natural transformation. the technique does not require cloning of pcr fragments in plasmids: pcr-amplified dna fragments are internalized by cells and directly incorporated into their genomes by homologous recombination. previously such procedures for random mutagenesis could be applied only to acinetobacter genes affording ...	1999	10103267
relationship between succinate transport and production of extracellular poly(3-hydroxybutyrate) depolymerase in pseudomonas lemoignei.	the relationship between extracellular poly(3-hydroxybutyrate) (phb) depolymerase synthesis and the unusual properties of a succinate uptake system was investigated in pseudomonas lemoignei. growth on and uptake of succinate were highly ph dependent, with optima at ph 5.6. above ph 7, growth on and uptake of succinate were strongly reduced with concomitant derepression of phb depolymerase synthesis. the specific succinate uptake rates were saturable by high concentrations of succinate, and maxim ...	1999	10103271
counting and size classification of active soil bacteria by fluorescence in situ hybridization with an rrna oligonucleotide probe.	a fluorescence in situ hybridization (fish) technique based on binding of a rhodamine-labelled oligonucleotide probe to 16s rrna was used to estimate the numbers of ribosome-rich bacteria in soil samples. such bacteria, which have high cellular rrna contents, were assumed to be active (and growing) in the soil. hybridization to an rrna probe, eub338, for the domain bacteria was performed with a soil slurry, and this was followed by collection of the bacteria by membrane filtration (pore size, 0. ...	1999	10103277
cuma, a gene encoding a multicopper oxidase, is involved in mn2+ oxidation in pseudomonas putida gb-1.	pseudomonas putida gb-1-002 catalyzes the oxidation of mn2+. nucleotide sequence analysis of the transposon insertion site of a nonoxidizing mutant revealed a gene (designated cuma) encoding a protein homologous to multicopper oxidases. addition of cu2+ increased the mn2+-oxidizing activity of the p. putida wild type by a factor of approximately 5. the growth rates of the wild type and the mutant were not affected by added cu2+. a second open reading frame (designated cumb) is located downstream ...	1999	10103278
enhanced degradation of polyvinyl alcohol by pycnoporus cinnabarinus after pretreatment with fenton's reagent.	degradation of polyvinyl alcohol (pva) was investigated by using a combination of chemical treatment with fenton's reagent and biological degradation with the white rot fungus pycnoporus cinnabarinus. inclusion of the chemical pretreatment resulted in greater degradation of pva than the degradation observed when biological degradation alone was used.	1999	10103286
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
factors influencing the potential use of aliquat 336 for the in situ extraction of carboxylic acids from cultures of pseudomonas putida.	the use of extraction techniques to alleviate product inhibition in bioprocesses is one of a number of potential separation methods. however, the intimate contact of an organic phase with the broth implies that the organic components of this phase may be present in the aqueous phase at saturation levels. the quaternary amine aliquat 336 (trioctyl/decylmethylammonium entity), dissolved in octan-1-ol showed no inhibition on the growth of pseudomonas putida, at least with respect to molecular toxic ...	1999	10194856
homogenization and crystallization of histidine ammonia-lyase by exchange of a surface cysteine residue.	histidase (histidine ammonia-lyase, ec 4.3.1.3) from pseudomonas putida was expressed in escherichia coli and purified. in the absence of thiols the tetrameric enzyme gave rise to undefined aggregates and suitable crystals could not be obtained. the solvent accessibility along the chain was predicted from the amino acid sequence. among the seven cysteines, only one was labeled as 'solvent-exposed'. the exchange of this cysteine to alanine abolished all undefined aggregations and yielded readily ...	1999	10195286
nahw, a novel, inducible salicylate hydroxylase involved in mineralization of naphthalene by pseudomonas stutzeri an10.	two genes, nahg and nahw, encoding two independent salicylate 1-hydroxylases have been identified in the naphthalene-degrading strain pseudomonas stutzeri an10. while nahg resides in the same transcriptional unit as the meta-cleavage pathway genes, forming the naphthalene degradation lower pathway, nahw is situated outside but in close proximity to this transcriptional unit. the nahg and nahw genes of p. stutzeri an10 are induced and expressed upon incubation with salicylate, and the enzymes tha ...	1999	10197990
inducing effect of diamines on transcription of the cephamycin c genes from the lat and pcbab promoters in nocardia lactamdurans.	the diamines putrescine, cadaverine, and diaminopropane stimulate cephamycin biosynthesis in nocardia lactamdurans, in shake flasks and fermentors, without altering cell growth. intracellular levels of the p7 protein (a component of the methoxylation system involved in cephamycin biosynthesis) were increased by diaminopropane, as shown by immunoblotting studies. lysine-6-aminotransferase and piperideine-6-carboxylate dehydrogenase activities involved in biosynthesis of the alpha-aminoadipic acid ...	1999	10197999
the argr regulatory protein, a helper to the anaerobic regulator anr during transcriptional activation of the arcd promoter in pseudomonas aeruginosa.	pseudomonas aeruginosa, when deprived of oxygen, generates atp from arginine catabolism by enzymes of the arginine deiminase pathway, encoded by the arcdabc operon. under conditions of low oxygen tension, the transcriptional activator anr binds to a site centered 41.5 bp upstream of the arcd transcriptional start. anr-mediated anaerobic induction was enhanced two- to threefold by extracellular arginine. this arginine effect depended, in trans, on the transcriptional regulator argr and, in cis, o ...	1999	10198009
promoter analysis of the cap8 operon, involved in type 8 capsular polysaccharide production in staphylococcus aureus.	the production of type 8 capsular polysaccharide (cp8) in staphylococcus aureus is regulated in response to a variety of environmental factors. the cap8 genes required for the cp8 production in strain becker are transcribed as a single large transcript by a primary promoter located within a 0.45-kb region upstream of the first gene of the cap8 gene cluster. in this study, we analyzed the primary cap8 promoter region in detail. we determined the transcription initiation site of the primary transc ...	1999	10198014
investigation of two evolutionarily unrelated halocarboxylic acid dehalogenase gene families.	dehalogenases are key enzymes in the metabolism of halo-organic compounds. this paper describes a systematic approach to the isolation and molecular analysis of two families of bacterial alpha-halocarboxylic acid (alphaha) dehalogenase genes, called group i and group ii deh genes. the two families are evolutionarily unrelated and together represent almost all of the alphaha deh genes described to date. we report the design and evaluation of degenerate pcr primer pairs for the separate amplificat ...	1999	10198020
localization of escherichia coli rpoc mutations that affect rna polymerase assembly and activity at high temperature.	we localized five rpoc (beta') mutations affecting escherichia coli rna polymerase assembly. the ts4, xh56, and r120 mutations changed beta' residues conserved throughout eubacteria; the je10092 mutation occurred in the hypervariable region; rpoc1 (tsx) changed a universally conserved residue and corresponds to yeast rpb1-1. thus, distinct, predominantly conserved beta' residues participate in interactions holding rna polymerase together.	1999	10198039
characterization of two novel type i ribosome-inactivating proteins from the storage roots of the andean crop mirabilis expansa.	two novel type i ribosome-inactivating proteins (rips) were found in the storage roots of mirabilis expansa, an underutilized andean root crop. the two rips, named me1 and me2, were purified to homogeneity by ammonium sulfate precipitation, cation-exchange perfusion chromatography, and c4 reverse-phase chromatography. the two proteins were found to be similar in size (27 and 27.5 kd) by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and their isoelectric points were determined to be ...	1999	10198104
a novel aromatic-ring-hydroxylating dioxygenase from the diterpenoid-degrading bacterium pseudomonas abietaniphila bkme-9.	pseudomonas abietaniphila bkme-9 is able to degrade dehydroabietic acid (dha) via ring hydroxylation by a novel dioxygenase. the dita1, dita2, and dita3 genes, which encode the alpha and beta subunits of the oxygenase and the ferredoxin of the diterpenoid dioxygenase, respectively, were isolated and sequenced. the ferredoxin gene is 9. 2 kb upstream of the oxygenase genes and 872 bp upstream of a putative meta ring cleavage dioxygenase gene, ditc. a tn5 insertion in the alpha subunit gene, dita1 ...	1999	10217753
benzene-induced uncoupling of naphthalene dioxygenase activity and enzyme inactivation by production of hydrogen peroxide.	naphthalene dioxygenase (ndo) is a multicomponent enzyme system that oxidizes naphthalene to (+)-cis-(1r,2s)-1,2-dihydroxy-1, 2-dihydronaphthalene with consumption of o2 and two electrons from nad(p)h. in the presence of benzene, nadh oxidation and o2 utilization were partially uncoupled from substrate oxidation. approximately 40 to 50% of the consumed o2 was detected as hydrogen peroxide. the rate of benzene-dependent o2 consumption decreased with time, but it was partially increased by the add ...	1999	10217759
in vitro transcriptional studies of the bkd operon of pseudomonas putida: l-branched-chain amino acids and d-leucine are the inducers.	bkdr is the transcriptional activator of the bkd operon, which encodes the four proteins of the branched-chain keto acid dehydrogenase multienzyme complex of pseudomonas putida. in this study, hydroxyl radical footprinting revealed that bkdr bound to only one face of dna over the same region identified in dnase i protection assays. deletions of even a few bases in the 5' region of the bkdr-binding site greatly reduced transcription, confirming that the entire protected region is necessary for tr ...	1999	10217783
adenosylcobalamin-mediated methyl transfer by toluate cis-dihydrodiol dehydrogenase of the tol plasmid pww0.	we identified and characterized a methyl transfer activity of the toluate cis-dihydrodiol (4-methyl-3,5-cyclohexadiene-cis-1, 2-diol-1-carboxylic acid) dehydrogenase of the tol plasmid pww0 towards toluene cis-dihydrodiol (3-methyl-4,5-cyclohexadiene-cis-1, 2-diol). when the purified enzyme from the recombinant escherichia coli containing the xyll gene was incubated with toluene cis-dihydrodiol in the presence of nad+, the end products differed depending on the presence of adenosylcobalamin (coe ...	1999	10217792
crystal structure of histidine ammonia-lyase revealing a novel polypeptide modification as the catalytic electrophile.	histidine ammonia-lyase (ec 4.3.1.3) catalyzes the nonoxidative elimination of the alpha-amino group of histidine and is closely related to the important plant enzyme phenylalanine ammonia-lyase. the crystal structure of histidase from pseudomonas putida was determined at 2.1 a resolution revealing a homotetramer with d2 symmetry, the molecular center of which is formed by 20 nearly parallel alpha-helices. the chain fold, but not the sequence, resembles those of fumarase c and related proteins. ...	1999	10220322
microscopic methods for distinguishing among three cell types in tol plasmid-carrying pseudomonas putida cultures.	microscopic methods were developed that enable the sensitive quantification of different cell types that are generated by plasmid instability processes when pseudomonas putida paw164 (x+), which carries a tol plasmid (pww0-164), is grown in chemostat culture. cells that have lost the structural tol genes (x-) or the entire tol plasmid (x0) can be quantified in a background of 6000 x+ cells using catechol agarose miniplates. x0 cells can be quantified in a background of 3500 x+ or x- cells using ...	1999	10220895
detection of polycyclic aromatic hydrocarbon degradation genes in different soil bacteria by polymerase chain reaction and dna hybridization.	twenty different strains of pseudomonas, mycobacterium, gordona, sphingomonas, rhodococcus and xanthomonas which degrade polycyclic aromatic hydrocarbons (pah) were characterized in respect to genes encoding degradation enzymes for pah. genomic dna from these strains was hybridized with a fragment of ndob, coding for the large iron sulfur protein (isp alpha) of the naphthalene dioxygenase from pseudomonas putida paw736 (ncib 9816). a group of seven naphthalene-degrading pseudomonas strains showe ...	1999	10220903
spatial distribution of respiratory activity in pseudomonas putida 54g biofilms degrading volatile organic compounds (voc).	all over the world, microbial systems are used to clean soils, waters and air streams that have been contaminated with volatile organic compounds (voc). information about the structure and function of the microbes that metabolize these contaminants can be gained by studying these microbial systems. here we describe the spatial patterns of respiratory activity in pseudomonas putida 54g aerobic biofilms degrading two voc, toluene and ethanol. oxygen concentration profiles within the biofilm were m ...	1999	10222587
negative regulation of the pseudomonas aeruginosa outer membrane porin oprd selective for imipenem and basic amino acids.	pseudomonas aeruginosa oprd is a specific porin which facilitates the uptake of basic amino acids and imipenem, a carbapenem antibiotic. resistance to imipenem due to the loss of oprd is an important mechanism for the loss of clinical effectiveness. to investigate the negative regulatory mechanisms influencing oprd expression, a gene upstream of the coregulated mexef-oprn efflux operon, designated mext, was cloned. the predicted 304-amino-acid mature mext protein showed strong homology to lysr-t ...	1999	10223918
activation and inactivation of pseudomonas stutzeri methylbenzene catabolism pathways mediated by a transposable element.	the arrangement of the genes involved in o-xylene, m-xylene, and p-xylene catabolism was investigated in three pseudomonas stutzeri strains: the wild-type strain ox1, which is able to grow on o-xylene but not on the meta and para isomers; the mutant m1, which grows on m-xylene and p-xylene but is unable to utilize the ortho isomer; and the revertant r1, which can utilize all the three isomers of xylene. a 3-kb insertion sequence (is) termed isps1, which inactivates the m-xylene and p-xylene cata ...	1999	10223973
rhodococcus erythropolis dcl14 contains a novel degradation pathway for limonene.	strain dcl14, which is able to grow on limonene as a sole source of carbon and energy, was isolated from a freshwater sediment sample. this organism was identified as a strain of rhodococcus erythropolis by chemotaxonomic and genetic studies. r. erythropolis dcl14 also assimilated the terpenes limonene-1,2-epoxide, limonene-1,2-diol, carveol, carvone, and (-)-menthol, while perillyl alcohol was not utilized as a carbon and energy source. induction tests with cells grown on limonene revealed that ...	1999	10224006
cloning, expression, and nucleotide sequence of the pseudomonas aeruginosa 142 ohb genes coding for oxygenolytic ortho dehalogenation of halobenzoates.	we have cloned and characterized novel oxygenolytic ortho-dehalogenation (ohb) genes from 2-chlorobenzoate (2-cba)- and 2,4-dichlorobenzoate (2,4-dcba)-degrading pseudomonas aeruginosa 142. among 3,700 escherichia coli recombinants, two clones, dh5alphaf'(pod22) and dh5alphaf'(pod33), converted 2-cba to catechol and 2,4-dcba and 2,5-dcba to 4-chlorocatechol. a subclone of pod33, plasmid pe43, containing the 3,687-bp minimized ohb dna region conferred to p. putida pb2440 the ability to grow on 2- ...	1999	10224014
construction and characterization of two recombinant bacteria that grow on ortho- and para-substituted chlorobiphenyls.	cloning and expression of the aromatic ring dehalogenation genes in biphenyl-growing, polychlorinated biphenyl (pcb)-cometabolizing comamonas testosteroni vp44 resulted in recombinant pathways allowing growth on ortho- and para-chlorobiphenyls (cbs) as a sole carbon source. the recombinant variants were constructed by transformation of strain vp44 with plasmids carrying specific genes for dehalogenation of chlorobenzoates (cbas). plasmid pe43 carries the pseudomonas aeruginosa 142 ohb genes codi ...	1999	10224015
removal of dibenzofuran, dibenzo-p-dioxin, and 2-chlorodibenzo-p-dioxin from soils inoculated with sphingomonas sp. strain rw1.	removal of dibenzofuran, dibenzo-p-dioxin, and 2-chlorodibenzo-p-dioxin (2-cdd) (10 ppm each) from soil microcosms to final concentrations in the parts-per-billion range was affected by the addition of sphingomonas sp. strain rw1. rates and extents of removal were influenced by the density of rw1 organisms. for 2-cdd, the rate of removal was dependent on the content of soil organic matter (som), with half-life values ranging from 5.8 h (0% som) to 26.3 h (5.5% som).	1999	10224029
microbial biomass and activity in lead-contaminated soil	microbial community diversity, potential microbial activity, and metal resistance were determined in three soils whose lead contents ranged from 0.00039 to 48 mmol of pb kg of soil-1. biomass levels were directly related to lead content. a molecular analysis of 16s rrnas suggested that each soil contained a complex, diverse microbial community. a statistical analysis of the phospholipid fatty acids indicated that the community in the soil having the highest lead content was not related to the co ...	1999	10224032
microbial degradation of octamethylcyclotetrasiloxane.	the microbial degradation of low-molecular-weight polydimethylsiloxanes was investigated through laboratory experiments. octamethylcyclotetrasiloxane was found to be biodegraded under anaerobic conditions in composted sewage sludge, as monitored by the occurrence of the main polydimethylsiloxane degradation product, dimethylsilanediol, compared to that found in experiments with sterilized control samples.	1999	10224038
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
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
times to detection of bacteria and yeasts in bactec 9240 blood culture bottles.	a 7-day incubation protocol was instituted with the bactec 9240 system for a 1-year period to determine the times to detection of clinically relevant organisms. a total of 23,686 blood and 693 sterile body fluid cultures were received; some cultures were held longer by special request. of 1,609 likely skin contaminants, 42 were recovered on day 5, 34 on day 6, 16 on day 7, and 5 on day 8. of 2,803 usual pathogens, 34 were recovered on day 5, 24 on day 6, 15 on day 7 and 1 on day 8. twenty-one of ...	1999	10325369
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