Publications

modulation of gene expression through chromosomal positioning in escherichia coli.	variations in expression of the nah genes of the nah7 (naphthalene biodegradation) plasmid of pseudomonas putida when placed in different chromosomal locations in escherichia coli have been studied by employing a collection of hybrid mini-t5 transposons bearing lacz fusions to the psal promoter, along with the cognate regulatory gene nahr. insertions of psal-lacz reporters in the proximity of the chromosomal origin of replication, oric, increased accumulation of beta-galactosidase in vivo. posit ...	1997	9202482
construction of a contiguous 874-kb sequence of the escherichia coli -k12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features.	the contiguous 874.423 base pair sequence corresponding to the 50.0-68.8 min region on the genetic map of the escherichia coli k-12 (w3110) was constructed by the determination of dna sequences in the 50.0-57.9 min region (360 kb) and two large (100 kb in all) and five short gaps in the 57.9-68.8 min region whose sequences had been registered in the dna databases. we analyzed its sequence features and found that this region contained at least 894 potential open reading frames (orfs), of which 34 ...	1997	9205837
phospholipid biosynthesis and solvent tolerance in pseudomonas putida strains.	the role of the cell envelope in the solvent tolerance mechanisms of pseudomonas putida was investigated. the responses of a solvent-tolerant strain, p. putida idaho, and a solvent-sensitive strain, p. putida mw1200, were examined in terms of phospholipid content and composition and of phospholipid biosynthetic rate following exposure to a nonmetabolizable solvent, o-xylene. following o-xylene exposure, p. putida mw1200 exhibited a decrease in total phospholipid content. in contrast, p. putida i ...	1997	9209036
bacterial dl-2-haloacid dehalogenase from pseudomonas sp. strain 113: gene cloning and structural comparison with d- and l-2-haloacid dehalogenases.	dl-2-haloacid dehalogenase from pseudomonas sp. strain 113 (dl-dex) catalyzes the hydrolytic dehalogenation of both d- and l-2-haloalkanoic acids to produce the corresponding l- and d-2-hydroxyalkanoic acids, respectively, with inversion of the c2 configuration. dl-dex is a unique enzyme: it acts on the chiral carbon of the substrate and uses both enantiomers as equivalent substrates. we have isolated and sequenced the gene encoding dl-dex. the open reading frame consists of 921 bp corresponding ...	1997	9209038
tolerance to mercury chloride in scenedesmus strains.	mercury chloride toxicity was investigated in two strains of chlorella and in a strain of scenedesmus isolated from polluted areas in tuscany (italy). no hg resistance was found in the autotrophic microorganisms isolated, but scenedesmus sp. strain ar-2489, isolated from the arno river, was able to grow at concentrations of up to 5 micrograms ml-1 of hg. this concentration was twice that which inhibited growth of the two chlorella strains and scenedesmus acutus 8m, the reference strain from a cu ...	1997	9210291
fiber-optic-based biomonitoring of benzene derivatives by recombinant e. coli bearing luciferase gene-fused tol-plasmid immobilized on the fiber-optic end.	tol plasmid in pseudomonas putida mt-2 has a series of genes for the degradation of xylene, toluene, and their derivatives to pyruvate and acetaldehyde (or propionaldehyde). two operons, i.e., upper operon and meta operon, play indispensable roles for the digestion of xylene derivatives: when xyir protein recognizes xylene derivatives, another controlling gene, xyis, is activated, which results in the activation of meta operon. therefore, we have constructed a fusion gene between tol plasmid and ...	1997	9212714
microbial contamination of antiseptic-soaked cotton balls.	we investigated microbial contamination of in-use antiseptics at a hospital. no microbial contamination was observed in 70 samples of 0.02% benzalkonium chloride solution (500-ml volume), 70 samples of 1% titratable i2 povidone-iodine solution (250-ml volume), or 15 samples of 0.1% ethacridine lactate solution (500-ml volume) during use in reduced amounts. nor was any microbial contamination observed in 70 samples of cotton balls soaked in 1% titratable i2 povidone-iodine solution in canisters o ...	1997	9212987
detection and molecular analysis of plant- and insect-associated bacteria harboring aconitate isomerase involved in biosynthesis of trans-aconitic acid as antifeedant in brown planthoppers.	the activity of aconitate isomerase, which is involved in the biosynthesis of trans-aconitic acid as antifeedant in brown planthoppers, was detected in pseudomonas fluorescens lrb3w1 and pseudomonas putida maff301685 but not in pseudomonas putida maff301684. the enzyme activity was induced in the presence of trans-aconitate, and therefore bacteria showing the enzyme activity were easily detected by their ability to grow on the minimal medium containing trans-aconitate as the sole carbon source ( ...	1997	9216883
dnase i footprinting, dna bending and in vitro transcription analyses of clcr and catr interactions with the clcabd promoter: evidence of a conserved transcriptional activation mechanism.	in pseudomonas putida, benzoate and 3-chlorobenzoate are converted to catechol and 3-chlorocatechol, respectively, which are then catabolized to tricarboxylic acid cycle intermediates via the catbca and clcabd pathways. the catbca and clcabd operons are regulated by homologous transcriptional activators catr and clcr. previous studies have demonstrated that in addition to sequence similarities, catr and clcr share functional similarities which allow catr to complement clcr. in this study, we dem ...	1997	9220004
cloning and analysis of the dnag gene encoding pseudomonas putida dna primase.	the dnag gene coding for primase, a key enzyme in dna replication, has been isolated from chromosomal dna of the soil bacterium pseudomonas putida. it maps within the putative mms operon, between the rpsu and rpod genes. comparison of the deduced amino acid sequence of p. putida dnag with sequences of other known bacterial primases reveals the presence of a possible regulatory region which would be unique to pseudomonads. the analysis of nucleotide sequence suggests that stable folding of the dn ...	1997	9224947
microbial degradation of chloroaromatics: use of the meta-cleavage pathway for mineralization of chlorobenzene.	pseudomonas putida gj31 is able to simultaneously grow on toluene and chlorobenzene. when cultures of this strain were inhibited with 3-fluorocatechol while growing on toluene or chlorobenzene, 3-methylcatechol or 3-chlorocatechol, respectively, accumulated in the medium. to establish the catabolic routes for these catechols, activities of enzymes of the (modified) ortho- and meta-cleavage pathways were measured in crude extracts of cells of p. putida gj31 grown on various aromatic substrates, i ...	1997	9226262
pseudomonas monteilii sp. nov., isolated from clinical specimens.	we propose the name pseudomonas monteilii for a new species of gram-negative, rod-shaped, motile bacteria that were nonhemolytic on blood agar and were isolated from clinical sources. the 10 strains of p. monteilii were incapable of liquefing gelatin. they grew at 10 degrees c but not at 41 degrees c, produced fluorescent pigments, catalase, and cytochrome oxidase, and possessed the arginine dihydrolase system. they were capable of respiratory but not fermentative metabolism. they did not hydrol ...	1997	9226917
rapid purification of an active recombinant his-tagged 2,3-dihydroxybiphenyl 1,2-dioxygenase from pseudomonas putida ou83.	2,3-dihydroxybiphenyl 1,2-dioxygenase (2,3-dbpd) is an extradiol-type dioxygenase that catalyzes the aromatic ring fission of 2,3-dihydroxybiphenyl, the third step in the biphenyl degradation pathway. the nucleotide sequence of the pseudomonas putida ou83 gene bphc, which encodes 2,3-dbpd, was cloned into a plasmid pqe31. the his-tagged 2,3-dbpd produced by a recombinant escherichia coli strain, sg13009(prep4)(pakc1), and purified with a ni-nitrilotriacetic acid resin affinity column using the h ...	1997	9228766
haloalkanoate dehalogenase ii (dehe) of a rhizobium sp.--molecular analysis of the gene and formation of carbon monoxide from trihaloacetate by the enzyme.	a 3-kb ecori fragment of genomic dna from a rhizobium sp. cloned into puc19 endowed escherichia coli k-12 with the ability to grow, albeit slowly, with 2-chloropropionic acid as substrate. the construct expressed weakly a gene that encoded a non-stereospecific 2-chloropropionic acid dehalogenase (dehalogenase ii; dehe). the dehe gene was not closely linked to the organism's other two dehalogenase genes, dehd and dehl. the derived amino acid sequence of dehe showed little identity with dehd or de ...	1997	9461303
the dimerization of pseudomonas putida cytochrome p450cam: practical consequences and engineering of a monomeric enzyme.	cytochrome p450cam dimerizes via the formation of an intermolecular disulfide bond, complicating the storage and handling of the enzyme, particularly at higher concentrations. the dimeric enzyme is 14% less active than the monomer and forms at a slow but significant rate even at 4 degrees c [k = 1.09 x 10(-3) mm(-1) h(-1)]. to eliminate any ambiguity introduced by dimer formation and to simplify handling and storage of the enzyme, site-directed mutagenesis was used to identify c334 as the single ...	1997	9542996
isolation of a soil psychrotrophic toluene-degrading pseudomonas strain: influence of temperature on the growth characteristics on different substrates.	two psychrotrophic toluene-degrading pseudomonas putida strains were isolated at low temperature from a toluene-polluted soil, thereby demonstrating that toluene degradation at low temperature occurred in nature, a finding of possible interest for soil bioremediation procedures. in one of these strains, two aromatic compounds (toluene and benzoate) were degraded, most likely through different pathways. to study the effect of the growth temperature on the metabolism of these substrates, we studie ...	1997	9765796
production of substituted naphthalene dihydrodiols by engineered escherichia coli containing the cloned naphthalene 1,2-dioxygenase gene from pseudomonas fluorescens n3.	naphthalene dioxygenase, a key enzyme in the dihydroxylation of naphthalene, is encoded by the plasmid pn3, responsible for naphthalene metabolism in pseudomonas fluorescens n3. the naphthalene dioxygenase, including all the sequences for its expression and the regulatory region, has been localized on the 4.3-kb hindiii-clai fragment and on the 3.5-kb hindiii fragment of the plasmid pn3, by southern analysis using as probes naha and nahr genes, the homologous genes of the plasmid nah7 from pseud ...	1997	9765814
evolution of enzymatic activities in the enolase superfamily: partitioning of reactive intermediates by (d)-glucarate dehydratase from pseudomonas putida.	glucarate dehydratase (glucd) from pseudomonas putida catalyzes the dehydration of both (d)-glucarate and (l)-idarate to 3-deoxy-(l)-threo-2-hexulosarate as well as their epimerization. (d)-[6-13c]glucarate and (l)-[6-13c]idarate have been synthesized for use in continuous assay of the reactions catalyzed by glucd by both 13c and 1h nmr spectroscopies, thereby allowing the simultaneous measure of both the dehydration and epimerization reactions. substrate and solvent isotope effects for the dehy ...	1998	9772160
evolution of enzymatic activities in the enolase superfamily: crystal structure of (d)-glucarate dehydratase from pseudomonas putida.	the structure of (d)-glucarate dehydratase from pseudomonas putida (glucd) has been solved at 2.3 a resolution by multiple isomorphous replacement and refined to a final r-factor of 19.0%. the protein crystallizes in the space group i222 with one subunit in the asymmetric unit. the unit cell dimensions are a = 69.6 a, b = 108.8 a, and c = 122.6 a. the crystals were grown using the batch method where the primary precipitant was poly(ethylene glycol) 1000. the structure reveals that glucd is a tet ...	1998	9772161
use of the bact/alert blood culture system for culture of sterile body fluids other than blood.	studies have demonstrated that large-volume culture methods for sterile body fluids other than blood increase recovery compared to traditional plated-medium methods. bact/alert is a fully automated blood culture system for detecting bacteremia and fungemia. in this study, we compared culture in bact/alert standard aerobic and anaerobic bottles, bact/alert fan aerobic and fan anaerobic bottles, and culture on routine media for six specimen types, i.e., continuous ambulatory peritoneal dialysate ( ...	1998	9774578
differential scanning calorimetric study of poly(3-hydroxyoctanoate) inclusions in bacterial cells.	medium chain length polyhydroxyalkanoates, mcl-phas, produced by bacteria as inclusion bodies or granules were analyzed in situ by differential scanning calorimetry (dsc) without isolation from the cells. the kinetic dsc study of pha granules, which contained mostly 3-hydroxyoctanoate units (pho), in pseudomonas putida bm01 cells showed that the polymer within the granules existed in an amorphous state, but it crystallized after dehydration of the cells under freeze-drying condition (below -50 d ...	1998	9777703
maintenance of a pseudomonas fluorescens plasmid in heterologous hosts: metabolic burden as a more reliable variable to predict plasmid instability.	the stability of a large, multiresistance plasmid, pscl of p. fluorescens cas102 was studied in pseudomonas putida and e. coli under various non-stress conditions. both the strains lost the plasmid within 25 days when repeatedly subcultured in lb broth without any antibiotic. the transformants survived in sterile soil and water without any marked reduction in the viability. in sterile soil, p. putida lost 93% and e. coli, 98% of their plasmid containing population in 30 days, while in sterile wa ...	1998	9782786
cloning of the nocardia corallina polyhydroxyalkanoate synthase gene and production of poly-(3-hydroxybutyrate-co-3-hydroxyhexanoate) and poly-(3-hydroxyvalerate-co-3-hydroxyheptanoate).	the polyhydroxyalkanoate (pha) synthase gene (phacnc) from nocardia corallina was identified in a lambda library on a 6-kb bamhi fragment. a 2.8-kb xhoii subfragment was found to contain the intact pha synthase. this 2.8-kb fragment was subjected to dna sequencing and was found to contain the coding region for the pha synthase and a small downstream open reading frame of unknown function. on the basis of dna sequence, phacnc is closest in homology to the pha synthases (phacpai and phacpaii) of p ...	1998	9783428
high expression, purification, and properties of recombinant homocysteine alpha, gamma-lyase.	homocysteine alpha,gamma-lyase from the anaerobic protozoan parasite trichomonas vaginalis has been cloned from genomic dna using pcr methods and expressed in escherichia coli with a vector containing the t7 promoter. the recombinant homocysteine alpha,gamma-lyase (rhcyase) is expressed as the major protein in the host e. coli cells. the enzyme was purified to approximately 90% purity using heat treatment at 50 degreesc, precipitation steps with polyethyleneimine, polyethylene glycol 8000, and h ...	1998	9790890
int-b13, an unusual site-specific recombinase of the bacteriophage p4 integrase family, is responsible for chromosomal insertion of the 105-kilobase clc element of pseudomonas sp. strain b13.	pseudomonas sp. strain b13 carries the clcrabde genes encoding chlorocatechol-degradative enzymes on the self-transmissible 105-kb clc element. the element integrates site and orientation specifically into the chromosomes of various bacterial recipients, with a glycine trna structural gene (glyv) as the integration site. we report here the localization and nucleotide sequence of the integrase gene and the activity of the integrase gene product in mediating site-specific integration. the integras ...	1998	9791097
identification of chlorobenzene dioxygenase sequence elements involved in dechlorination of 1,2,4,5-tetrachlorobenzene.	the teca chlorobenzene dioxygenase and the todcba toluene dioxygenase exhibit substantial sequence similarity yet have different substrate specificities. escherichia coli cells producing recombinant teca enzyme dioxygenate and simultaneously eliminate a halogen substituent from 1,2,4,5-tetrachlorobenzene but show no activity toward benzene, whereas those producing todcba dioxygenate benzene but not tetrachlorobenzene. a hybrid teca dioxygenase variant containing the large alpha-subunit of the to ...	1998	9791099
molecular genetic analysis of phosphite and hypophosphite oxidation by pseudomonas stutzeri wm88.	the first molecular and genetic characterization of a biochemical pathway for oxidation of the reduced phosphorus (p) compounds phosphite and hypophosphite is reported. the pathway was identified in pseudomonas stutzeri wm88, which was chosen for detailed studies from a group of organisms isolated based on their ability to oxidize hypophosphite (+1 valence) and phosphite (+3 valence) to phosphate (+5 valence). the genes required for oxidation of both compounds by p. stutzeri wm88 were cloned on ...	1998	9791102
molecular characterization and regulation of an operon encoding a system for transport of arginine and ornithine and the argr regulatory protein in pseudomonas aeruginosa.	the complete nucleotide sequence for the aot operon of pseudomonas aeruginosa pao1 was determined. this operon contains six open reading frames. the derived sequences for four of these, aotj, aotq, aotm, and aotp, show high similarity to those of components of the periplasmic binding protein-dependent abc (atp binding cassette) transporters of enteric bacteria. transport studies with deletion derivatives established that these four genes function in arginine-inducible uptake of arginine and orni ...	1998	9791103
a novel mechanism for resistance to the antimetabolite n-phosphonoacetyl-l-aspartate by helicobacter pylori.	the mechanism of resistance to n-phosphonoacetyl-l-aspartate (pala), a potent inhibitor of aspartate carbamoyltransferase (which catalyzes the first committed step of de novo pyrimidine biosynthesis), in helicobacter pylori was investigated. at a 1 mm concentration, pala had no effects on the growth and viability of h. pylori. the inhibitor was taken up by h. pylori cells and the transport was saturable, with a km of 14.8 mm and a vmax of 19.1 nmol min-1 microliters of cell water-1. by 31p nucle ...	1998	9791105
wound-released chemical signals may elicit multiple responses from an agrobacterium tumefaciens strain containing an octopine-type ti plasmid.	the vir regions of octopine-type and nopaline-type ti plasmids direct the transfer of oncogenic t-dna from agrobacterium tumefaciens to the nuclei of host plant cells. previous studies indicate that at least two genetic loci at the left ends of these two vir regions are sufficiently conserved to form heteroduplexes visible in the electron microscope. to initiate an investigation of these genetic loci, we determined the dna sequences of these regions of both ti plasmids and identified both conser ...	1998	9791116
gene organization in the trxa/b-oric region of the streptomyces coelicolor chromosome and comparison with other eubacteria.	the gene organization was determined in the trxa/b-rnpa region of the streptomyces coelocolor chromosome, near to the origin of replication, oric. previously, we showed that the trxa and trxb genes, coding for thioredoxin and thioredoxin reductase, respectively, occur in s. coelicolor as a gene cluster and are contained on a cosmid h24 that carries oric and several genes involved in dna replication. here we show that the trxa/b locus is positioned approx. 9.4kb from oric, present the nucleotide ...	1998	9795152
automated confocal laser scanning microscopy and semiautomated image processing for analysis of biofilms.	the purpose of this study was to develop and apply a quantitative optical method suitable for routine measurements of biofilm structures under in situ conditions. a computer program was designed to perform automated investigations of biofilms by using image acquisition and image analysis techniques. to obtain a representative profile of a growing biofilm, a nondestructive procedure was created to study and quantify undisturbed microbial populations within the physical environment of a glass flow ...	1998	9797255
evolution of a pathway for chlorobenzene metabolism leads to natural attenuation in contaminated groundwater	complete metabolism of chlorinated benzenes is not a feature that is generally found in aerobic bacteria but is thought to be due to a novel recombination of two separate gene clusters. such a recombination could be responsible for adaptation of a natural microbial community in response to contamination with synthetic chemicals. this hypothesis was tested in a chlorobenzene (cb)-contaminated aquifer. cb-degrading bacteria from a contaminated site were characterized for a number of years by exami ...	1998	9797264
ratios of carbon isotopes in microbial lipids as an indicator of substrate usage.	the occurrence and abundance of microbial fatty acids have been used for the identification of microorganisms in microbial communities. however, these fatty acids can also be used as indicators of substrate usage. for this, a systematic investigation of the discrimination of the stable carbon isotopes by different microorganisms is necessary. we grew 11 strains representing major bacterial and fungal species with four different isotopically defined carbon sources and determined the isotope ratio ...	1998	9797266
whole-cell kinetics of trichloroethylene degradation by phenol hydroxylase in a ralstonia eutropha jmp134 derivative	the rate, progress, and limits of trichloroethylene (tce) degradation by ralstonia eutropha aek301/pyk3021 whole cells were examined in the absence of aromatic induction. at tce concentrations up to 800 &mgr;m, degradation rates were sustained until tce was no longer detectable. the ks and vmax for tce degradation by aek301/pyk3021 whole cells were determined to be 630 &mgr;m and 22.6 nmol/min/mg of total protein, respectively. the sustained linear rates of tce degradation by aek301/pyk3021 up t ...	1998	9797289
molecular detection, isolation, and physiological characterization of functionally dominant phenol-degrading bacteria in activated sludge.	dna was isolated from phenol-digesting activated sludge, and partial fragments of the 16s ribosomal dna (rdna) and the gene encoding the largest subunit of multicomponent phenol hydroxylase (lmph) were amplified by pcr. an analysis of the amplified fragments by temperature gradient gel electrophoresis (tgge) demonstrated that two major 16s rdna bands (bands r2 and r3) and two major lmph gene bands (bands p2 and p3) appeared after the activated sludge became acclimated to phenol. the nucleotide s ...	1998	9797297
implications of rrna operon copy number and ribosome content in the marine oligotrophic ultramicrobacterium sphingomonas sp. strain rb2256.	sphingomonas sp. strain rb2256 is a representative of the dominant class of ultramicrobacteria that are present in marine oligotrophic waters. in this study we examined the rrna copy number and ribosome content of rb2256 to identify factors that may be associated with the relatively low rate of growth exhibited by the organism. it was found that rb2256 contains a single copy of the rrna operon, in contrast to vibrio spp., which contain more than eight copies. the maximum number of ribosomes per ...	1998	9797303
accumulation of alpha-keto acids as essential components in cyanide assimilation by pseudomonas fluorescens ncimb 11764.	pyruvate (pyr) and alpha-ketoglutarate (alphakg) accumulated when cells of pseudomonas fluorescens ncimb 11764 were cultivated on growth-limiting amounts of ammonia or cyanide and were shown to be responsible for the nonenzymatic removal of cyanide from culture fluids as previously reported (j.-l. chen and d. a. kunz, fems microbiol. lett. 156:61-67, 1997). the accumulation of keto acids in the medium paralleled the increase in cyanide-removing activity, with maximal activity (760 micromol of cy ...	1998	9797306
a small, dilute-cytoplasm, high-affinity, novel bacterium isolated by extinction culture and having kinetic constants compatible with growth at ambient concentrations of dissolved nutrients in seawater.	dilutions of raw seawater produced a bacterial isolate capable of extended growth in unamended seawater. its 2.9-mb genome size and 40-fg dry mass were similar to values for many naturally occurring aquatic organotrophs, but water and dna comprised a large portion of this small chemoheterotroph, as compared to escherichia coli. the isolate used only a few aromatic hydrocarbons and acetate, and glucose and amino acid incorporation were entirely absent, although many membrane and cytoplasmic prote ...	1998	9797308
detection of ralstonia solanacearum, which causes brown rot of potato, by fluorescent in situ hybridization with 23s rrna-targeted probes.	during the past few years, ralstonia (pseudomonas) solanacearum race 3, biovar 2, was repeatedly found in potatoes in western europe. to detect this bacterium in potato tissue samples, we developed a method based on fluorescent in situ hybridization (fish). the nearly complete genes encoding 23s rrna of five r. solanacearum strains and one ralstonia pickettii strain were pcr amplified, sequenced, and analyzed by sequence alignment. this resulted in the construction of an unrooted tree and suppor ...	1998	9797321
genetic characterization of pepp, which encodes an aminopeptidase p whose deficiency does not affect lactococcus lactis growth in milk, unlike deficiency of the x-prolyl dipeptidyl aminopeptidase.	we sequenced the pepp gene of lactococcus lactis, which encodes an aminopeptidase p (pepp), and demonstrated that the x-prolyl dipeptidyl aminopeptidase pepx plays a more important role than pepp in nitrogen nutrition. pepp shares homology with methionine aminopeptidases and could play a role in the maturation of nascent proteins.	1998	9797327
a novel screening method for isolating exopolysaccharide-deficient mutants.	a screening method based on differential staining of the wild type and exopolysaccharide-deficient mutants of rhizobium (sinorhizobium) meliloti by the lipophilic dye sudan black b is described. mutants defective in the production of either succinoglycan or eps ii (galactoglucan) were isolated by using this method, which might also prove useful for isolating exopolysaccharide-defective derivatives of other bacteria.	1998	9797329
quantitative structure/activity relationship for the rate of conversion of c4-substituted catechols by catechol-1,2-dioxygenase from pseudomonas putida (arvilla) c1.	the influence of various c4/c5 substituents in catechol (1,2-dihydroxybenzene) derivatives on the overall rate of conversion by catechol-1,2-dioxygenase from pseudomonas putida (arvilla) c1 was investigated. using catechol, 4-methylcatechol, 4-fluorocatechol, 4-chlorocatechol, 4-bromocatechol, 4,5-difluorocatechol and 4-chloro-5-fluorocatechol, it could be demonstrated that substituents at the c4 and/or c5 position decrease the rate of conversion, from 62% (4-methylcatechol) down to 0.7% (4-chlo ...	1998	9799107
cloning and nucleotide sequence of amidase gene from pseudomonas putida.	amidases are a class of enzymes which convert amides to acids and have potential value in the development of commercial bioprocesses for the production of useful chemicals. a gene encoding an amidase in pseudomonas putida 5b has been cloned, sequenced, and overexpressed in escherichia coli. an additional open reading frame (p38k) encoding a putative protein of 38 kda was found immediately upstream of the amidase gene. this work continues our characterization of a p. putida operon, which now appe ...	1998	9809753
expression of alkane hydroxylase from acinetobacter sp. strain adp1 is induced by a broad range of n-alkanes and requires the transcriptional activator alkr.	in acinetobacter sp. strain adp1, alkane degradation depends on at least five essential genes. rubab and xcpr are constitutively transcribed. here we describe inducible transcription of alkm, which strictly depends on the presence of the transcriptional activator alkr. alkr itself is expressed at a low level, while a chromosomally located alkm::lacz fusion is inducible by middle-chain-length alkanes from heptane to undecane, which do not support growth of adp1, and by long-chain-length alkanes f ...	1998	9811637
involvement of the terminal oxygenase beta subunit in the biphenyl dioxygenase reactivity pattern toward chlorobiphenyls.	biphenyl dioxygenase (bph dox) oxidizes biphenyl on adjacent carbons to generate 2,3-dihydro-2,3-dihydroxybiphenyl in comamonas testosteroni b-356 and in pseudomonas sp. strain lb400. the enzyme comprises a two-subunit (alpha and beta) iron sulfur protein (ispbph), a ferredoxin (ferbph), and a ferredoxin reductase (redbph). b-356 bph dox preferentially catalyzes the oxidation of the double-meta-substituted congener 3,3'-dichlorobiphenyl over the double-para-substituted congener 4,4'-dichlorobiph ...	1998	9811638
targeted mutagenesis of sigma54 activator proteins in myxococcus xanthus.	myxococcus xanthus dna segments related to the highly conserved central sequence of sigma54 activator proteins have been investigated. a genetic technique designed to inactivate a gene that encodes such an activator by inserting a plasmid-borne internal fragment of the putative gene has been tested. when the internal fragment inserted by homologous recombination into the corresponding chromosomal locus, the expected duplication of the gene was observed by southern hybridization. the single restr ...	1998	9811647
physical and genetic map of the pasteurella multocida a:1 chromosome.	a physical and genetic map of the pasteurella multocida a:1 genome was generated by using the restriction enzymes apai, ceui, and noti. the positions of 23 restriction sites and 32 genes, including 5 rrn operons, were localized on the 2.35-mbp single circular chromosome. this report presents the first genetic and physical map for this genus.	1998	9811669
synthesis of medium-chain-length polyhydroxyalkanoates in arabidopsis thaliana using intermediates of peroxisomal fatty acid beta-oxidation.	polyhydroxyalkanoate (pha) is a family of polymers composed primarily of r-3-hydroxyalkanoic acids. these polymers have properties of biodegradable thermoplastics and elastomers. medium-chain-length phas (mcl-phas) are synthesized in bacteria by using intermediates of the beta-oxidation of alkanoic acids. to assess the feasibility of producing mcl-phas in plants, arabidopsis thaliana was transformed with the phac1 synthase from pseudomonas aeruginosa modified for peroxisome targeting by addition ...	1998	9811811
comparison of phenotypic and genotypic techniques for identification of unusual aerobic pathogenic gram-negative bacilli.	rapid and accurate identification of bacterial pathogens is a fundamental goal of clinical microbiology, but one that is difficult or impossible for many slow-growing and fastidious organisms. we used identification systems based on cellular fatty acid profiles (sherlock; midi, inc., newark, del.), carbon source utilization (microlog; biolog, inc., hayward, calif.), and 16s rrna gene sequence (microseq; perkin-elmer applied biosystems division, foster city, calif.) to evaluate 72 unusual aerobic ...	1998	9817894
pseudomonas putida infections of the oyster toadfish (opsanus tau).		1998	9818379
the transposable elements resident on the plasmids of pseudomonas putida strain h, tn5501 and tn5502, are cryptic transposons of the tn3 family.	genes for (methyl)phenol degradation in pseudomonas putida strain h (phl genes) are located on the plasmid ppgh1. adjacent to the phl catabolic operon we identified a cryptic transposon, tn5501, of the tn3 family (class ii transposons). the genes encoding the resolvase and the transposase are transcribed in the same direction, as is common for the tn501 subfamily. the enzymes encoded by tn5501, however, show only the overall homology characteristic for resolvases/integrases and transposases of t ...	1998	9819061
isopropylbenzene catabolic pathway in pseudomonas putida re204: nucleotide sequence analysis of the ipb operon and neighboring dna from pre4.	pseudomonas putida re204 employs a set of plasmid-specified enzymes in the catabolism of isopropylbenzene (cumene) and related alkylbenzenes. a 21,768 bp segment of the plasmid pre4, whose sequence is discussed here, includes the ipb (isopropylbenzene catabolic) operon as well as associated genetic elements. the ipb operon, ipbaaabacadbcegfhd, encodes enzymes catalyzing the conversion of isopropylbenzene to isobutyrate, pyruvate, and acetyl-coenzyme a as well as an outer membrane protein (ipbh) ...	1998	9821257
protein organization on the pha inclusion cytoplasmic boundary.	polyhydroxyalkanoate (pha) cellular inclusions consist of polyesters, phospholipids, and proteins. both the polymerase and the depolymerase enzymes are active components of the structure. recently, proteins associated with these inclusions have been described in a number of bacterial species. in order to further clarify the structure and function of these proteins in relation to polymer inclusions, ultrastructural studies of isolated polymer inclusions were initiated. the surface boundary charac ...	1998	9821672
investigation of the function of proteins associated to polyhydroxyalkanoate inclusions in pseudomonas putida bmo1.	polyhydroxyalkanoate (pha) granule associated proteins from pseudomonas oleovorans were purified and the n-terminal sequences of two major proteins migrating in sodium dodecyl sulfate polyacrylamide gels with a relative molecular mass of 18 and 43 kda (ga1 and ga2, respectively) were analyzed. radiolabeled degenerate probes deduced from these amino acid sequences were used to identify genomic dna fragments from p. oleovorans and pseudomonas putida encoding ga1 and ga2. dna sequence analysis of t ...	1998	9821673
formation of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) by pha synthase from ralstonia eutropha.	the acetoacetyl-coa reductase and the polyhydroxyalkanoate (pha) synthase from ralstonia eutropha (formerly alcaligenes eutrophus) were expressed in escherichia coli, klebsiella aerogenes, and pha-negative mutants of r. eutropha and pseudomonas putida. while expression in e. coli strains resulted in the accumulation of poly(3-hydroxybutyrate) [phb], strains of r. eutropha, p. putida and k. aerogenes accumulated poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) [poly(3hb-co-3hhx)] when even chain fat ...	1998	9821674
the type iv leader peptidase/n-methyltransferase of vibrio vulnificus controls factors required for adherence to hep-2 cells and virulence in iron-overloaded mice.	vibrio vulnificus expresses a number of potential virulence determinants that may contribute to its ability to cause a severe and rapidly disseminating septicemia in susceptible hosts. we have cloned and characterized two genes encoding products related to components of the type iv pilus biogenesis and general secretory (type ii) pathways by complementation of a type iv peptidase/n-methyltransferase (pild) mutant of pseudomonas aeruginosa with a v. vulnificus genomic library. one of the genes (v ...	1998	9826339
complete dna sequence and detailed analysis of the yersinia pestis kim5 plasmid encoding murine toxin and capsular antigen.	yersinia pestis, the causative agent of plague, harbors at least three plasmids necessary for full virulence of the organism, two of which are species specific. one of the y. pestis-specific plasmids, pmt1, is thought to promote deep tissue invasion, resulting in more acute onset of symptoms and death. we determined the entire nucleotide sequence of y. pestis kim5 pmt1 and identified potential open reading frames (orfs) encoded by the 100,990-bp molecule. based on codon usage for known yersinial ...	1998	9826348
isolation and transposon mutagenesis of a pseudomonas putida kt2442 toluene-resistant variant: involvement of an efflux system in solvent resistance.	a toluene-resistant variant of pseudomonas putida kt2442, strain tol, was isolated after liquid cultivation under xylene followed by toluene for 1 month in each condition. almost all the populations of the variant strain formed small but readily visible colonies under toluene within 24 h at 30 degrees c. the toluene-resistant strain also showed an increase in resistance to some unrelated antibiotics. several toluene-sensitive tn5 mutants have been isolated from the toluene-resistant strain and s ...	1998	9827328
mutational analysis of the rhizobium etli reca operator.	based upon our earlier studies (a. tapias, a. r. fernández de henestrosa, and j. barbé, j. bacteriol. 179:1573-1579, 1997) we hypothesized that the regulatory sequence of the rhizobium etli reca gene was ttgn11caa. however, further detailed analysis of the r. etli reca operator described in the present work suggests that it may in fact be gaacn7gtac. this new conclusion is based upon pcr mutagenesis analysis carried out in the r. etli reca operator, which indicates that the gaac and gtac submoti ...	1998	9829943
combined physical and genetic map of the pseudomonas putida kt2440 chromosome.	a combined physical and genetic map of the pseudomonas putida kt2440 genome was constructed from data obtained by pulsed-field gel electrophoresis techniques (pfge) and southern hybridization. circular genome size was estimated at 6.0 mb by adding the sizes of 19 swai, 9 pmei, 6 paci, and 6 i-ceui fragments. a complete physical map was achieved by combining the results of (i) analysis of pfge of the dna fragments resulting from digestion of the whole genome with pmei, swai, i-ceui, and paci as w ...	1998	9829947
neonatal pseudomonas putida infection presenting as staphylococcal scalded skin syndrome.	a case of neonatal pseudomonas putida sepsis presenting as staphylococcal scalded skin syndrome is described. staphylococcal scalded skin syndrome is a clinical term used for a spectrum of primarily neonatal blistering skin disorders caused by the exfoliative toxins of staphylococcus aureus. the disease typically begins with general erythema and fever, followed by the formation of large fluid-filled bullae that coalesce and rupture on slightest pressure to leave extensive areas of denuded skin. ...	1998	9832266
expression of the pseudomonas aeruginosa gentamicin resistance gene aacc3 in escherichia coli.	the pseudomonas aeruginosa aacc3 gene was expressed in escherichia coli after cloning of the single gene behind the strong tac promoter. in the original pseudomonas strain, aacc3 is preceded by cysc; together they form a single transcription unit. the ribosome-binding site and start codon of aacc3 are involved in a putative intercistronic hairpin, the stability of which interfered with the aminoglycoside resistance level. in northern blots, full-length transcripts comprising both cysc and aacc3 ...	1998	9835511
degradation of polychlorinated biphenyl metabolites by naphthalene-catabolizing enzymes.	the ability of the dehydrogenase and ring cleavage dioxygenase of the naphthalene degradation pathway to transform 3,4-dihydroxylated biphenyl metabolites was investigated. 1,2-dihydro-1, 2-dihydroxynaphthalene dehydrogenase was expressed as a histidine-tagged protein. the purified enzyme transformed 2, 3-dihydro-2,3-dihydroxybiphenyl, 3,4-dihydro-3,4-dihydroxybiphenyl, and 3,4-dihydro-3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl to 2, 3-dihydroxybiphenyl, 3,4-dihydroxybiphenyl (3,4-dhb), and 3, ...	1998	9835542
use of 13c nuclear magnetic resonance and gas chromatography to examine methionine catabolism by lactococci.	formation of methanethiol from methionine is widely believed to play a significant role in development of cheddar cheese flavor. however, the catabolism of methionine by cheese-related microorganisms has not been well characterized. two independent methionine catabolic pathways are believed to be present in lactococci, one initiated by a lyase and the other initiated by an aminotransferase. to differentiate between these two pathways and to determine the possible distribution between the pathway ...	1998	9835547
cloning and characterization of nadp-mannitol dehydrogenase cdna from the button mushroom, agaricus bisporus, and its expression in response to nacl stress.	mannitol, a six-carbon sugar alcohol, is the main storage carbon in the button mushroom, agaricus bisporus. given the physiological importance of mannitol metabolism in growth, fruit body development, and salt tolerance of a. bisporus, the enzyme responsible for mannitol biosynthesis, nadp-dependent mannitol dehydrogenase (mtdh) (ec 1.1.1.138), was purified to homogeneity, and mtdh cdna was cloned, sequenced, and characterized. to our knowledge, this represents the first report on the isolation ...	1998	9835550
isolation of marine polycyclic aromatic hydrocarbon (pah)-degrading cycloclasticus strains from the gulf of mexico and comparison of their pah degradation ability with that of puget sound cycloclasticus strains.	phenanthrene- and naphthalene-degrading bacteria were isolated from four offshore and nearshore locations in the gulf of mexico by using a modified most-probable-number technique. the concentrations of these bacteria ranged from 10(2) to 10(6) cells per ml of wet surficial sediment in mildly contaminated and noncontaminated sediments. a total of 23 strains of polycyclic aromatic hydrocarbon (pah)-degrading bacteria were obtained. based on partial 16s ribosomal dna sequences and phenotypic charac ...	1998	9835552
purification and characterization of gallic acid decarboxylase from pantoea agglomerans t71	oxygen-sensitive gallic acid decarboxylase from pantoea (formerly enterobacter) agglomerans t71 was purified from a cell extract after stabilization by reducing agents. this enzyme has a molecular mass of approximately 320 kda and consists of six identical subunits. it is highly specific for gallic acid. gallic acid decarboxylase is unique among similar decarboxylases in that it requires iron as a cofactor, as shown by plasma emission spectroscopy (which revealed an iron content of 0.8 mol per m ...	1998	9835557
psychrotolerant bacteria isolated from arctic soil that degrade polychlorinated biphenyls at low temperatures	psychrotolerant polychlorinated biphenyl (pcb)-degrading bacteria were isolated at 7 degreesc from pcb-contaminated arctic soil by using biphenyl as the sole organic carbon source. these isolates were distinguished from each other by differences in substrates that supported growth and substrates that were oxidized. 16s ribosomal dna sequences suggest that these isolates are most closely related to the genus pseudomonas. total removal of aroclor 1242, and rates of removal of selected pcb congener ...	1998	9835569
assessment of changes in microbial community structure during operation of an ammonia biofilter with molecular tools.	biofiltration has been used for two decades to remove odors and various volatile organic and inorganic compounds in contaminated off-gas streams. although biofiltration is widely practiced, there have been few studies of the bacteria responsible for the removal of air contaminants in biofilters. in this study, molecular techniques were used to identify bacteria in a laboratory-scale ammonia biofilter. both 16s rrna and ammonia monooxygenase (amoa) genes were used to characterize the heterotrophi ...	1998	9835577
characterization of cell lysis in pseudomonas putida induced upon expression of heterologous killing genes.	active biological containment systems are based on the controlled expression of killing genes. these systems are of interest for the pseudomonadaceae because of the potential applications of these microbes as bioremediation agents and biopesticides. the physiological effects that lead to cell death upon the induction of expression of two different heterologous killing genes in nonpathogenic pseudomonas putida kt2440 derivatives have been analyzed. p. putida cmc4 and cmc12 carry in their chromoso ...	1998	9835581
detection and isolation of novel rhizopine-catabolizing bacteria from the environment	microbial rhizopine-catabolizing (moc) activity was detected in serial dilutions of soil and rhizosphere washes. the activity observed generally ranged between 10(6) and 10(7) catabolic units per g, and the numbers of nonspecific culture-forming units were found to be approximately 10 times higher. a diverse set of 37 isolates was obtained by enrichment on scyllo-inosamine-containing media. however, none of the bacteria that were isolated were found to contain dna sequences homologous to the kno ...	1998	9835587
an immunological strategy to monitor in situ the phosphate starvation state in thiobacillus ferrooxidans	thiobacillus ferrooxidans is one of the chemolithoautotrophic bacteria important in industrial biomining operations. during the process of ore bioleaching, the microorganisms are subjected to several stressing conditions, including the lack of some essential nutrients, which can affect the rates and yields of bioleaching. when t. ferrooxidans is starved for phosphate, the cells respond by inducing the synthesis of several proteins, some of which are outer membrane proteins of high molecular weig ...	1998	9835593
species-specific oligonucleotides for enumeration of pseudomonas putida f1, burkholderia sp. strain js150, and bacillus subtilis atcc 7003 in biodegradation experiments.	species-specific sequences were identified within the v4 variable region of 16s rrna of two bacterial species capable of aromatic hydrocarbon metabolism, pseudomonas putida f1 and burkholderia sp. strain js150, and a third, bacillus subtilis atcc 7003, that can function as a secondary degrader. fluorescent in situ hybridization (fish) with species-specific oligonucleotides was used for direct counting of these species throughout a phenol biodegradation experiment in batch culture. traditional di ...	1998	9835594
recombinant klebsiella oxytoca strains with improved efficiency in removal of high nitrate loads	klebsiella oxytoca cect 4460 removes high nitrate loads from industrial wastewaters without accumulation of nitrite under optimal culture conditions; however, under nonoptimal conditions nitrite accumulates. this situation reflects an in vivo-limited functioning of nitrite reductase in this strain. as a way to overcome this limitation, an increase in the nitrite reductase gene dose in k. oxytoca cect 4460 was considered. to achieve this, we cloned and transferred into this strain the klebsiella ...	1998	9835599
construction of a bioluminescent reporter strain to detect polychlorinated biphenyls	a bioluminescent reporter strain, ralstonia eutropha env307(putk60), was constructed for the detection of polychlorinated biphenyls by inserting the biphenyl promoter upstream of the bioluminescence genes. in the presence of a nonionic surfactant, which enhances the solubility of chlorinated biphenyls, bioluminescence was induced three- to fourfold over background by biphenyl, monochlorinated biphenyls, and aroclor 1242. the minimum detection limits for these compounds ranged from 0.15 mg/liter ...	1998	9835601
induction of the tod operon by trichloroethylene in pseudomonas putida tva8.	bioluminescence, mrna levels, and toluene degradation rates in pseudomonas putida tva8 were measured as a function of various concentrations of toluene and trichloroethylene (tce). tva8 showed an increasing bioluminescence response to increasing tce and toluene concentrations. compared to uninduced tva8 cultures, todc1 mrna levels increased 11-fold for tce-treated cultures and 13-fold for toluene-treated cultures. compared to uninduced p. putida f1 cultures, todc1 mrna levels increased 4.4-fold ...	1998	9835608
simultaneous degradation of chloro- and methyl-substituted aromatic compounds: competition between pseudomonas strains using the ortho and meta pathway or the ortho pathway exclusively.	pseudomonas sp. d7-4 and pseudomonas sp. b13 fr1(pfrc20p) degraded mixtures of chloro- and methyl-substituted benzoates exclusively via an extended ortho pathway, whereas in pseudomonas putida wr 201 both ortho and meta fission were induced by mixtures of 3-chloro- and 3-methylbenzoate or even by 3-chloro-benzoate alone. the competition behaviour of these strains was compared in batch and in chemostat cultures.. despite misrouting of metabolites, strain wr201 was competitive, in a lot of the com ...	1998	9840960
phosphate starvation-independent 2-aminoethylphosphonic acid biodegradation in a newly isolated strain of pseudomonas putida, ng2.	a strain of pseudomonas putida that utilized the biogenic organophosphonate 2-aminoethylphosphonic acid as sole carbon and energy, nitrogen and phosphorus source contained 2-aminoethylphosphonic acid: pyruvate aminotransferase and phosphonoacetaldehyde hydrolase (phosphonatase) activities which were inducible by the presence of 2-aminoethylphosphonic acid in the culture medium, regardless of the phosphate status of the cells. neither of these activities were induced in their phosphate-free or ph ...	1998	9841125
molecular genetics of the genus paracoccus: metabolically versatile bacteria with bioenergetic flexibility.	paracoccus denitrificans and its near relative paracoccus versutus (formerly known as thiobacilllus versutus) have been attracting increasing attention because the aerobic respiratory system of p. denitrificans has long been regarded as a model for that of the mitochondrion, with which there are many components (e.g., cytochrome aa3 oxidase) in common. members of the genus exhibit a great range of metabolic flexibility, particularly with respect to processes involving respiration. prominent exam ...	1998	9841665
the virulence plasmid of yersinia, an antihost genome.	the 70-kb virulence plasmid enables yersinia spp. (yersinia pestis, y. pseudotuberculosis, and y. enterocolitica) to survive and multiply in the lymphoid tissues of their host. it encodes the yop virulon, an integrated system allowing extracellular bacteria to disarm the cells involved in the immune response, to disrupt their communications, or even to induce their apoptosis by the injection of bacterial effector proteins. this system consists of the yop proteins and their dedicated type iii sec ...	1998	9841674
bacterial iron transport: 1h nmr determination of the three-dimensional structure of the gallium complex of pyoverdin g4r, the peptidic siderophore of pseudomonas putida g4r.	among the fluorescent pseudomonas species, pseudomonas putida is a rare case of a nitrogen-fixing bacterium that transforms nitrogen into ammonia. when grown under iron-deficient conditions, it produces two major pyoverdins: pyoverdin g4r and pyoverdin g4ra. their primary structures have been established using fab-ms and one- and two-dimensional 15n, 13c, and 1h nmr on both the unlabeled and 15n-labeled compounds [salah el din, a. l. m., et al. (1997) tetrahedron 53, 12539-12552]. the two pyover ...	1998	9843403
siderotyping of fluorescent pseudomonads: characterization of pyoverdines of pseudomonas fluorescens and pseudomonas putida strains from antarctica.	five independent fluorescent pseudomonad isolates originating from antarctica were analysed for their pyoverdine systems. a pyoverdine-related siderotyping, which involved pyoverdine-induced growth stimulation, pyoverdine-mediated iron uptake, pyoverdine analysis by electrophoresis and isoelectric focusing, revealed three different pyoverdine-related siderotypes among the five isolates. one siderotype, including pseudomonas fluorescens 1w and p. fluorescens 10cw, was identical to that of p. fluo ...	1998	9846748
malonate decarboxylase of pseudomonas putida is composed of five subunits.	two different forms of malonate decarboxylase were purified from pseudomonas putida. the active form was composed of the five different subunits alpha (60 kda), beta (33 kda), gamma (28 kda), delta (13 kda), and epsilon (30 kda) and the inactive form was composed of the four subunits lacking the epsilon subunit. the former catalyzed the decarboxylation of malonate to acetate, but the latter could not, although it retained both activities of acetyl-coa:malonate coa transferase and malonyl-coa dec ...	1998	9851033
cloning and molecular analysis of the poly(3-hydroxybutyrate) and poly(3-hydroxybutyrate-co-3-hydroxyalkanoate) biosynthesis genes in pseudomonas sp. strain 61-3.	two types of polyhydroxyalkanoate (pha) biosynthesis gene loci (phb and pha) of pseudomonas sp. strain 61-3, which produces a blend of poly(3-hydroxybutyrate) [p(3hb)] homopolymer and a random copolymer (poly(3-hydroxybutyrate-co-3-hydroxyalkanoate) [p(3hb-co-3ha]) consisting of 3ha units of 4 to 12 carbon atoms, were cloned and analyzed at the molecular level. in the phb locus, three open reading frames encoding polyhydroxybutyrate (phb) synthase (phbcps), beta-ketothiolase (phbaps), and nadph- ...	1998	9851987
novel organization of the genes for phthalate degradation from burkholderia cepacia dbo1.	burkholderia cepacia dbo1 is able to utilize phthalate as the sole source of carbon and energy for growth. two overlapping cosmid clones containing the genes for phthalate degradation were isolated from this strain. subcloning and activity analysis localized the genes for phthalate degradation to two separate regions on the cosmid clones. analysis of the nucleotide sequence of these two regions showed that the genes for phthalate degradation are arranged in at least three transcriptional units. ...	1998	9851995
incp plasmids are unusually effective in mediating conjugation of escherichia coli and saccharomyces cerevisiae: involvement of the tra2 mating system.	mobilizable shuttle plasmids containing the origin-of-transfer (orit) region of plasmids f (incfi), colib-p9 (inci1), and rp4/rp1 (incpalpha) were constructed to test the ability of the cognate conjugation system to mediate gene transfer from escherichia coli to saccharomyces cerevisiae. only the palpha system caused detectable mobilization to yeast, giving peak values of 5 x 10(-5) transconjugants per recipient cell in 30 min. transfer of the shuttle plasmid required carriage of orit in cis and ...	1998	9851996
sequence diversity of the opri gene, coding for major outer membrane lipoprotein i, among rrna group i pseudomonads.	the sequence of opri, the gene coding for the major outer membrane lipoprotein i, was determined by pcr sequencing for representatives of 17 species of rrna group i pseudomonads, with a special emphasis on pseudomonas aeruginosa and pseudomonas fluorescens. within the p. aeruginosa species, opri sequences for 25 independent isolates were found to be identical, except for one silent substitution at position 96. the opri sequences diverged more for the other rrna group i pseudomonads (85 to 91% si ...	1998	9851998
the modified beta-ketoadipate pathway in rhodococcus rhodochrous n75: enzymology of 3-methylmuconolactone metabolism.	rhodococcus rhodochrous n75 is able to metabolize 4-methylcatechol via a modified beta-ketoadipate pathway. this organism has been shown to activate 3-methylmuconolactone by the addition of coenzyme a (coa) prior to hydrolysis of the butenolide ring. a lactone-coa synthetase is induced by growth of r. rhodochrous n75 on p-toluate as a sole source of carbon. the enzyme has been purified 221-fold by ammonium sulfate fractionation, hydrophobic chromatography, gel filtration, and anion-exchange chro ...	1998	9852013
the yvyd gene of bacillus subtilis is under dual control of sigmab and sigmah.	during a search by computer-aided inspection of two-dimensional (2d) protein gels for sigmab-dependent general stress proteins exhibiting atypical induction profiles, a protein initially called hst23 was identified as a product of the yvyd gene of bacillus subtilis. in addition to the typical sigmab-dependent, stress- and starvation-inducible pattern, yvyd is also induced in response to amino acid depletion. by primer extension of rna isolated from the wild-type strain and appropriate mutants ca ...	1998	9852014
active efflux of organic solvents by pseudomonas putida s12 is induced by solvents.	induction of the membrane-associated organic solvent efflux system srpabc of pseudomonas putida s12 was examined by cloning a 312-bp dna fragment, containing the srp promoter, in the broad-host-range reporter vector pkrz-1. compounds that are capable of inducing expression of the srpabc genes include aromatic and aliphatic solvents and alcohols. general stress conditions such as ph, temperature, nacl, or the presence of organic acids did not induce srp transcription. although the solvent efflux ...	1998	9852029
transcriptional activation of the catechol and chlorocatechol operons: variations on a theme.	the ortho-cleavage pathways of catechol and 3-chlorocatechol are central catabolic pathways of pseudomonas putida that convert aromatic and chloroaromatic compounds to tricarboxylic acid (tca)-cycle intermediates. they are encoded by the evolutionarily related catbca and clcabd operons, respectively. expression of the cat and clc operons requires the lysr-type transcriptional activators catr and clcr, and the inducer molecules cis,cis-muconate and 2-chloro-cis,cis-muconate. in addition to sequen ...	1998	9858745
protein binding in vivo to op2 promoter of the pseudomonas putida tol plasmid.	the transcription of op2 encoding enzymes for m-toluate catabolism on the pseudomonas putida tol plasmid is activated by basal-level xyls protein in the presence of m-toluate or by overproduced xyls protein in the absence of m-toluate. in this study, in vivo dimethyl sulfate (dms) footprinting was performed to understand the mechanism of transcriptional regulation of op2 promoter by xyls. in the presence of overproduced xyls without m-toluate, several protected nucleotides were observed, indicat ...	1998	9861447
anticancer efficacy in vivo and in vitro, synergy with 5-fluorouracil, and safety of recombinant methioninase.	the elevated exogenous-methionine dependency of tumors for growth has been observed in all major cancer cell types. we have previously cloned a methioninase (rmetase) from pseudomonas putida to deplete methionine. growth inhibition followed by apoptotic cell death was induced by treatment of tumor cells with rmetase in vitro. a single i.p. injection of 300 units of rmetase can lower the serum methionine level in the mice from 70 microm to less than 1 microm within 2 h and maintain this depleted ...	1998	9635582
efflux pumps involved in toluene tolerance in pseudomonas putida dot-t1e.	the basic mechanisms underlying solvent tolerance in pseudomonas putida dot-t1e are efflux pumps that remove the solvent from bacterial cell membranes. the solvent-tolerant p. putida dot-t1e grows in the presence of high concentrations (e.g., 1% [vol/vol]) of toluene and octanol. growth of p. putida dot-t1e cells in lb in the presence of toluene supplied via the gas phase has a clear effect on cell survival: the sudden addition of 0.3% (vol/vol) toluene to p. putida dot-t1e pregrown with toluene ...	1998	9642183
enantioselective uptake and degradation of the chiral herbicide dichlorprop [(rs)-2-(2,4-dichlorophenoxy)propanoic acid] by sphingomonas herbicidovorans mh.	sphingomonas herbicidovorans mh was able to completely degrade both enantiomers of the chiral herbicide dichlorprop [(rs)-2-(2,4-dichlorophenoxy)propanoic acid], with preferential degradation of the (s) enantiomer over the (r) enantiomer. these results are in agreement with the recently reported enantioselective degradation of mecoprop [(rs)-2-(4-chloro-2-methylphenoxy)propanoic acid] by this bacterium (c. zipper, k. nickel, w. angst, and h.-p. e. kohler, appl. environ. microbiol. 62:4318-4322, ...	1998	9642189
identification of a specific chaperone for sptp, a substrate of the centisome 63 type iii secretion system of salmonella typhimurium.	salmonella typhimurium uses of a type iii protein secretion system encoded at centisome 63 of its chromosome to deliver effector molecule into the host cell. these proteins stimulate host cell responses such as reorganization of the actin cytoskeleton and activation of transcription factors. one of these effector proteins is sptp, a tyrosine phosphatase that causes disruption of the host cell actin cytoskeleton. a characteristic feature of many substrates of type iii secretion systems is their a ...	1998	9642193
cloning, sequencing, and phenotypic characterization of the rpos gene from pseudomonas putida kt2440.	a gene homologous to the rpos gene of escherichia coli was cloned from a pseudomonas putida kt2440 gene bank by complementation of the rpos-deficient strain e. coli zk918. the rpos gene of p. putida complemented the acid sensitivity and catalase deficiency of the rpos mutant of e. coli and stimulated expression of the rpos-controlled promoter, bolap1. the gene was sequenced and found to be highly similar to the rpos genes of other gram-negative bacteria. like in other gram-negative bacteria, a h ...	1998	9642197
rapid method for the detection of genetically engineered microorganisms by polymerase chain reaction from soil and sediments.	a rapid and sensitive method for the detection of genetically engineered microorganisms in soil and sediments has been devised by in vitro amplification of the target dnas by a polymerase chain reaction. a cloned catechol 2,3-dioxygenase gene located on the recombinant plasmid poh101 was transferred to pseudomonas putida mmb2442 by triparental crossing and used as a target organism. for the polymerase chain reaction from soil and sediment samples, the template dna was released from a 100-mg soil ...	1998	9643968
root colonization by agrobacterium tumefaciens is reduced in cel, attb, attd, and attr mutants.	root colonization by agrobacterium tumefaciens was measured by using tomato and arabidopsis thaliana roots dipped in a bacterial suspension and planted in soil. wild-type bacteria showed extensive growth on tomato roots; the number of bacteria increased from 10(3) bacteria/cm of root length at the time of inoculation to more than 10(7) bacteria/cm after 10 days. the numbers of cellulose-minus and nonattaching attb, attd, and attr mutant bacteria were less than 1/10,000th the number of wild-type ...	1998	9647796