Publications

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
construction and use of an ipb dna module to generate pseudomonas strains with constitutive trichloroethene and isopropylbenzene oxidation activity.	pseudomonas sp. strain jr1 exhibits trichloroethene (tce) oxidation activity with isopropylbenzene (ipb) as the inducer substrate. we previously reported the genes encoding the first three enzymes of the ipb-degradative pathway (ipba1, ipba2, ipba3, ipba4, ipbb, and ipbc) and identified the initial ipb dioxygenase (ipba1 a2a3a4) as responsible for tce cooxidation (u. pflugmacher, b. averhoff, and g. gottschalk, appl. environ. microbiol. 62:3967-3977, 1996). primer extension analyses revealed mul ...	1998	9647815
small-scale dna sample preparation method for field pcr detection of microbial cells and spores in soil.	efficient, nonselective methods to obtain dna from the environment are needed for rapid and thorough analysis of introduced microorganisms in environmental samples and for analysis of microbial community diversity in soil. a small-scale procedure to rapidly extract and purify dna from soils was developed for in-the-field use. amounts of dna released from bacterial vegetative cells, bacterial endospores, and fungal conidia were compared by using hot-detergent treatment, freeze-thaw cycles, and be ...	1998	9647816
molecular cloning, nucleotide sequence, and expression in escherichia coli of a hemolytic toxin (aerolysin) gene from aeromonas trota.	aeromonas trota ak2, which was derived from atcc 49659 and produces the extracellular pore-forming hemolytic toxin aerolysin, was mutagenized with the transposon mini-tn5km1 to generate a hemolysin-deficient mutant, designated strain ak253. southern blotting data indicated that an 8.7-kb noti fragment of the genomic dna of strain ak253 contained the kanamycin resistance gene of mini-tn5km1. the 8.7-kb noti dna fragment was cloned into the vector pgem5zf(-) by selecting for kanamycin resistance, ...	1998	9647817
a two-component monooxygenase catalyzes both the hydroxylation of p-nitrophenol and the oxidative release of nitrite from 4-nitrocatechol in bacillus sphaericus js905.	bacteria that metabolize p-nitrophenol (pnp) oxidize the substrate to 3-ketoadipic acid via either hydroquinone or 1,2,4-trihydroxybenzene (thb); however, initial steps in the pathway for pnp biodegradation via thb are unclear. the product of initial hydroxylation of pnp could be either 4-nitrocatechol or 4-nitroresorcinol. here we describe the complete pathway for aerobic pnp degradation by bacillus sphaericus js905 that was isolated by selective enrichment from an agricultural soil in india. w ...	1998	9647818
cloning of a sphingomonas paucimobilis syk-6 gene encoding a novel oxygenase that cleaves lignin-related biphenyl and characterization of the enzyme.	sphingomonas paucimobilis syk-6 transforms 2,2'-dihydroxy-3,3'-dimethoxy-5,5'-dicarboxybiphenyl (ddva), a lignin-related biphenyl compound, to 5-carboxyvanillic acid via 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl (oh-ddva) as an intermediate (15). the ring fission of oh-ddva is an essential step in the ddva degradative pathway. a 15-kb ecori fragment isolated from the cosmid library complemented the growth deficiency of a mutant on oh-ddva. subcloning and deletion analysis showed that a ...	1998	9647824
a highly selective pcr protocol for detecting 16s rrna genes of the genus pseudomonas (sensu stricto) in environmental samples.	pseudomonas species are plant, animal, and human pathogens; exhibit plant pathogen-suppressing properties useful in biological control; or express metabolic versatilities valued in biotechnology and bioremediation. specific detection of pseudomonas species in the environment may help us gain a more complete understanding of the ecological significance of these microorganisms. the objective of this study was to develop a pcr protocol for selective detection of pseudomonas (sensu stricto) in envir ...	1998	9647828
spatial and temporal variation of phenanthrene-degrading bacteria in intertidal sediments.	phenanthrene-degrading bacteria were isolated from a 1-m2 intertidal sediment site in boston harbor. samples were taken six times over 2 years. a total of 432 bacteria were isolated and characterized by biochemical testing. when clustered on the basis of phenotypic characteristics, the isolates could be separated into 68 groups at a similarity level of approximately 70%. several groups (a total of 200 isolates) corresponded to well-characterized species belonging the genera vibrio and pseudomona ...	1998	9647830
aerobic mineralization of 2,6-dichlorophenol by ralstonia sp. strain rk1.	a new aerobic bacterium was isolated from the sediment of a freshwater pond close to a contaminated site at amponville (france). it was enriched in a fixed-bed reactor fed with 2,6-dichlorophenol (2,6-dcp)as the sole carbon and energy source at ph 7.5 and room temperature. the degradation of 2,6-dcp followed monod kinetics at low initial concentrations. at concentrations above 300 microm (50 mg.liter-1), 2,6-dcp increasingly inhibited its own degradation. the base sequence of the 16s ribosomal d ...	1998	9647831
effect of insertion site and metabolic load on the environmental fitness of a genetically modified pseudomonas fluorescens isolate.	an isolate of pseudomonas fluorescens (sbw25) was modified with different marker genes (laczy, aph-1, and xyle). these marker genes were inserted singly or in combination into two separate (1 mbp apart) and presumably nonessential sites (-6- and ee) on the chromosome of sbw25. this allowed the production of a range of genetically modified sbw25 variants that differed with respect to insertion site of the marker genes and metabolic burden. the environmental fitness of the different sbw25 variants ...	1998	9647841
intergeneric transfer of conjugative and mobilizable plasmids harbored by escherichia coli in the gut of the soil microarthropod folsomia candida (collembola).	the gut of the soil microarthropod folsomia candida provides a habitat for a high density of bacterial cells (t. thimm, a. hoffmann, h. borkott, j. c. munch, and c. c. tebbe, appl. environ. microbiol. 64:2660-2669, 1998). we investigated whether these gut bacteria act as recipients for plasmids from escherichia coli. filter mating with e. coli donor cells and collected feces of f. candida revealed that the broad-host-range conjugative plasmid prp4-luc (prp4 with a luciferase marker gene) transfe ...	1998	9647844
the gut of the soil microarthropod folsomia candida (collembola) is a frequently changeable but selective habitat and a vector for microorganisms.	interaction potentials between soil microarthropods and microorganisms were investigated with folsomia candida (insecta, collembola) in microcosm laboratory experiments. microscopic analysis revealed that the volumes of the simple, rod-shaped guts of adult specimens varied with their feeding activity, from 0.7 to 11.2 nl. a dense layer of bacterial cells, associated with the peritrophic membrane, was detected in the midgut by scanning electron microscopy. depending on the molting stage, which oc ...	1998	9647845
in situ detection of high levels of horizontal plasmid transfer in marine bacterial communities.	gene transfer of the conjugative plasmid pbf1 from pseudomonas putida to indigenous bacteria in seawater was investigated with a detection system for gene transfer based on the green fluorescent protein (gfp) (c. dahlberg et al., mol. biol. evol. 15:385-390, 1998). pbf1 was tagged with the gfp gene controlled by a lac promoter which is down regulated in the donor cell by a chromosomal repressor (laciq). the plasmid donor cells (pseudomonas putida kt2442) subsequently do not express gfp. transfer ...	1998	9647846
a chromosomally based tod-luxcdabe whole-cell reporter for benzene, toluene, ethybenzene, and xylene (btex) sensing.	a tod-luxcdabe fusion was constructed and introduced into the chromosome of pseudomonas putida f1, yielding the strain tva8. this strain was used to examine the induction of the tod operon when exposed to benzene, toluene, ethylbenzene, and xylene (btex) compounds and aqueous solutions of jp-4 jet fuel constituents. since this system contained the complete lux cassette (luxcdabe), bacterial bioluminescence in response to putative chemical inducers of the tod operon was measured on-line in whole ...	1998	9647859
evaluation of the vitek 2 system for rapid identification of medically relevant gram-negative rods.	the new vitek 2 system (biomérieux) was evaluated at two independent sites with the identification card for gram-negative bacilli (id-gnb card). of the 845 strains tested, which represented 70 different taxa belonging to either the family enterobacteriaceae or the nonenteric bacilli, 716 (84.7%) were correctly identified at the species level. thirty-two (3.8%) additional strains were identified to the species level after the performance of simple, rapid manual tests (oxidase, hemolysis, indole r ...	1998	9650942
characterization of the maleylacetate reductase maca of rhodococcus opacus 1cp and evidence for the presence of an isofunctional enzyme.	maleylacetate reductases (ec 1.3.1.32) have been shown to contribute not only to the bacterial catabolism of some usual aromatic compounds like quinol or resorcinol but also to the degradation of aromatic compounds carrying unusual substituents, such as halogen atoms or nitro groups. genes coding for maleylacetate reductases so far have been analyzed mainly in chloroaromatic compound-utilizing proteobacteria, in which they were found to belong to specialized gene clusters for the turnover of chl ...	1998	9657989
the apee gene of salmonella typhimurium encodes an outer membrane esterase not present in escherichia coli.	salmonella typhimurium aper mutations lead to overproduction of an outer membrane-associated n-acetyl phenylalanine beta-naphthyl ester-cleaving esterase that is encoded by the apee gene (p. collin-osdoby and c. g. miller, mol. gen. genet. 243:674-680, 1994). this paper reports the cloning and nucleotide sequencing of the s. typhimurium apee gene as well as some properties of the esterase that it encodes. the predicted product of apee is a 69.9-kda protein which is processed to a 67-kda species ...	1998	9657991
evidence of two oxidative reaction steps initiating anaerobic degradation of resorcinol (1,3-dihydroxybenzene) by the denitrifying bacterium azoarcus anaerobius.	the denitrifying bacterium azoarcus anaerobius lufres1 grows anaerobically with resorcinol (1,3-dihydroxybenzene) as the sole source of carbon and energy. the anaerobic degradation of this compound was investigated in cell extracts. resorcinol reductase, the key enzyme for resorcinol catabolism in fermenting bacteria, was not present in this organism. instead, resorcinol was hydroxylated to hydroxyhydroquinone (hhq; 1,2,4-trihydroxybenzene) with nitrate or k3fe(cn)6 as the electron acceptor. hhq ...	1998	9658009
isolation and characterization of toluene-sensitive mutants from the toluene-resistant bacterium pseudomonas putida gm73.	to understand the mechanism underlying toluene resistance of a toluene-tolerant bacterium, pseudomonas putida gm73, we carried out tn5 mutagenesis and isolated eight toluene-sensitive mutants. none of the mutants grew in the presence of 20% (vol/vol) toluene in growth medium but exhibited differential sensitivity to toluene. when wild-type cells were treated with toluene (1% [vol/vol]) for 5 min, about 2% of the cells could form colonies. in the mutants ttg1, ttg2, ttg3, and ttg8, the same treat ...	1998	9658016
the central, surface-exposed region of the flagellar hook protein flge of campylobacter jejuni shows hypervariability among strains.	in a previous study, we observed that monoclonal antibodies raised against the hook protein flge of campylobacter jejuni lio 36, isolate 5226, bound exclusively to this strain. the aim of this study was to elucidate the molecular basis for these binding specificities. the hook protein-encoding gene flge of c. jejuni was cloned in escherichia coli and sequenced. the flge genes of four additional c. jejuni strains were amplified by pcr and also sequenced. comparison of the deduced amino acid seque ...	1998	9658019
fulminant hepatitis complicated by small intestine infection and massive hemorrhage.	a 34-year-old man diagnosed with fulminant hepatitis, caused by hepatitis b virus, and acute renal failure was referred to our hospital. after admission to the intensive care unit, the liver and renal failure were ameliorated. melena requiring transfusion occurred during the course of his illness. endoscopic examination demonstrated pseudomembranes, erosions, ulcers, and hemorrhage in the duodenum, the upper jejunum, and the terminal ileum, suggesting widespread lesions throughout the small inte ...	1998	9658323
pneumonia caused by pseudomonas putida with a mucoid phenotype.		1998	9659539
the crystal structure of benzoylformate decarboxylase at 1.6 a resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes.	the crystal structure of the thiamin diphosphate (thdp)-dependent enzyme benzoylformate decarboxylase (bfd), the third enzyme in the mandelate pathway of pseudomonas putida, has been solved by multiple isomorphous replacement at 1.6 a resolution and refined to an r-factor of 15.0% (free r = 18.6%). the structure of bfd has been compared to that of other thdp-dependent enzymes, including pyruvate decarboxylase. the overall architecture of bfd resembles that of the other family members, and cofact ...	1998	9665697
active monomeric and dimeric forms of pseudomonas putida glyoxalase i: evidence for 3d domain swapping.	3d domain swapping of proteins involves the interconversion of a monomer containing a single domain-domain interface and a 2-fold symmetrical dimer containing two equivalent intermolecular interfaces. human glyoxalase i has the structure of a domain-swapped dimer [cameron, a. d., olin, b., ridderström, m., mannervik, b., and jones, t. a. (1997) embo j. 16, 3386-3395] but pseudomonas putida glyoxalase i has been reported to be monomeric [rhee, h.-i., murata, k., and kimura, a. (1986) biochem. bio ...	1998	9671502
sensorial and microbial effects of gaseous ozone on fresh scad (trachurus trachurus).	the bactericidal activity of gaseous ozone was investigated using a commercial ozone generator. five species of fish bacteria, pseudomonas putida, shewanella putrefaciens, brochothrix thermosphacta, enterobacter sp. and lactobacillus plantarum, were inoculated on agar surfaces and exposed to different ozonation times in a gas chamber. results showed ozone in relatively low concentrations (< 0.27 x 10(-3) g l-1) was an effective bactericide of vegetative cells of the five fish bacteria. the age o ...	1998	9674134
bacterial poly(3-hydroxyalkanoates) bearing carbon-carbon triple bonds.	production of poly(3-hydroxyalkanoates), phas, by pseudomonas oleovorans (p. oleovorans) and pseudomonas putida (p. putida) grown with mixtures of nonanoic acid, na, and 10-undecynoic acid, 10-und( identical with), were investigated. both microorganisms produced phas containing carbon-carbon triple bonds in fractions from 0 to 100%, depending on the composition of the carbon substrate mixture. the amounts of unsaturated repeating units in phas produced by p. oleovorans were higher than those in ...	1998	9680410
biochemical properties and substrate specificities of a recombinantly produced azotobacter vinelandii alginate lyase.	alginate is a polysaccharide composed of beta-d-mannuronic acid (m) and alpha-l-guluronic acid (g). an azotobacter vinelandii alginate lyase gene, algl, was cloned, sequenced, and expressed in escherichia coli. the deduced molecular mass of the corresponding protein is 41.4 kda, but a signal peptide is cleaved off, leaving a mature protein of 39 kda. sixty-three percent of the amino acids in this mature protein are identical to those in algl from pseudomonas aeruginosa. algl was partially purifi ...	1998	9683471
physical and genetic map of the obligate intracellular bacterium coxiella burnetii.	pulsed-field gel electrophoresis and pcr techniques have been used to construct a noti macrorestriction map of the obligate intracellular bacterium coxiella burnetii nine mile. the size of the chromosome has been determined to be 2,103 kb comprising 29 noti restriction fragments. the average resolution is 72.5 kb, or about 3. 5% of the genome. experimental data support the presence of a linear chromosome. published genes were localized on the physical map by southern hybridization. one gene, rec ...	1998	9683477
genetic analysis of dioxin dioxygenase of sphingomonas sp. strain rw1: catabolic genes dispersed on the genome.	the dioxin dioxygenase of sphingomonas sp. strain rw1 activates dibenzo-p-dioxin and dibenzofuran for further metabolism by introducing two atoms of oxygen at a pair of vicinal carbon atoms, one of which is involved in one of the bridges between the two aromatic rings, i.e., an angular dioxygenation. the dxna1 and dxna2 cistrons encoding this dioxygenase have been cloned and shown to be located just upstream of a hydrolase gene which specifies an enzyme involved in the subsequent step of the dib ...	1998	9683494
rapid detection and evaluation of clinical characteristics of emerging multiple-drug-resistant gram-negative rods carrying the metallo-beta-lactamase gene blaimp.	gram-negative rods (gnr) carrying the transferable carbapenem resistance gene blaimp, including pseudomonas aeruginosa and serratia marcescens, have been isolated from more than 20 hospitals in japan. although the emergence of such multiple-drug-resistant bacteria is of utmost clinical concern, little information in regard to the distribution of blaimp-positive gnr in hospitals and the clinical characteristics of infected patients is available. to address this, a system for the rapid detection o ...	1998	9687398
a glutathione s-transferase with activity towards cis-1, 2-dichloroepoxyethane is involved in isoprene utilization by rhodococcus sp. strain ad45.	rhodococcus sp. strain ad45 was isolated from an enrichment culture on isoprene (2-methyl-1,3-butadiene). isoprene-grown cells of strain ad45 oxidized isoprene to 3,4-epoxy-3-methyl-1-butene, cis-1, 2-dichloroethene to cis-1,2-dichloroepoxyethane, and trans-1, 2-dichloroethene to trans-1,2-dichloroepoxyethane. isoprene-grown cells also degraded cis-1,2-dichloroepoxyethane and trans-1, 2-dichloroepoxyethane. all organic chlorine was liberated as chloride during degradation of cis-1,2-dichloroepox ...	1998	9687433
influence of carbon source on nitrate removal by nitrate-tolerant klebsiella oxytoca cect 4460 in batch and chemostat cultures.	the nitrate-tolerant organism klebsiella oxytoca cect 4460 tolerates nitrate at concentrations up to 1 m and is used to treat wastewater with high nitrate loads in industrial wastewater treatment plants. we studied the influence of the c source (glycerol or sucrose or both) on the growth rate and the efficiency of nitrate removal under laboratory conditions. with sucrose as the sole c source the maximum specific growth rate was 0.3 h-1, whereas with glycerol it was 0.45 h-1. in batch cultures k. ...	1998	9687459
conversion of phenylalanine to benzaldehyde initiated by an aminotransferase in lactobacillus plantarum	the production of benzaldehyde from phenylalanine has been studied in various microorganisms, and several metabolic pathways have been proposed in the literature for the formation of this aromatic flavor compound. in this study, we describe benzaldehyde formation from phenylalanine by using a cell extract of lactobacillus plantarum. phenylalanine was initially converted to phenylpyruvic acid by an aminotransferase in the cell extract, and the keto acid was further transformed to benzaldehyde. ho ...	1998	9687465
oxidation of trichloroethylene, 1,1-dichloroethylene, and chloroform by toluene/o-xylene monooxygenase from pseudomonas stutzeri ox1.	toluene/o-xylene monooxygenase (tomo) from pseudomonas stutzeri ox1, which oxidizes toluene and o-xylene, was examined for its ability to degrade the environmental pollutants trichloroethylene (tce), 1, 1-dichloroethylene (1,1-dce), cis-1,2-dce, trans-1,2-dce, chloroform, dichloromethane, phenol, 2,4-dichlorophenol, 2,4,5-trichlorophenol, 2,4,6-trichlorophenol, 2,3,5,6-tetrachlorophenol, and 2,3,4,5, 6-pentachlorophenol. escherichia coli jm109 that expressed tomo from genes on plasmid pbz1260 un ...	1998	9687467
the requirement of rpon (sigma factor sigma54) in denitrification by pseudomonas stutzeri is indirect and restricted to the reduction of nitrite and nitric oxide.	the rpon region of pseudomonas stutzeri was cloned, and an rpon null mutant was constructed. rpon was not essential for denitrification in this bacterium but affected the expression levels and enzymatic activities of cytochrome cd1 nitrite reductase and nitric oxide reductase, whereas those of respiratory nitrate reductase and nitrous oxide reductase were comparable to wild-type levels. since the transcription of the structural genes nirs and norcb, coding for nitrite reductase and the nitric ox ...	1998	9687481
effect of humic fractions and clay on biodegradation of phenanthrene by a pseudomonas fluorescens strain isolated from soil.	the mineralization of phenanthrene in pure cultures of a pseudomonas fluorescens strain, isolated from soil, was measured in the presence of soil humic fractions and montmorillonite. humic acid and clay, either separately or in combination, shortened the acclimation phase. a higher mineralization rate was measured in treatments with humic acid at 100 microg/ml. humic acid at 10 microg/ml stimulated the transformation only in the presence of 10 g of clay per liter. we suggest that sorption of phe ...	1998	9687489
a silent abc transporter isolated from streptomyces rochei f20 induces multidrug resistance.	in the search for heterologous activators for actinorhodin production in streptomyces lividans, 3.4 kb of dna from streptomyces rochei f20 (a streptothricin producer) were characterized. subcloning experiments showed that the minimal dna fragment required for activation was 0.4 kb in size. the activation is mediated by increasing the levels of transcription of the actii-orf4 gene. sequencing of the minimal activating fragment did not reveal any clues about its mechanism; nevertheless, it was sho ...	1998	9696745
biochemical and genetic characterization of a gentisate 1, 2-dioxygenase from sphingomonas sp. strain rw5.	a 4,103-bp long dna fragment containing the structural gene of a gentisate 1,2-dioxygenase (ec 1.13.11.4), gtda, from sphingomonas sp. strain rw5 was cloned and sequenced. the gtda gene encodes a 350-amino-acid polypeptide with a predicted size of 38.85 kda. comparison of the gtda gene product with protein sequences in databases, including those of intradiol or extradiol ring-cleaving dioxygenases, revealed no significant homology except for a low similarity (27%) to the 1-hydroxy-2-naphthoate d ...	1998	9696766
arginine catabolism and the arginine succinyltransferase pathway in escherichia coli.	arginine catabolism produces ammonia without transferring nitrogen to another compound, yet the only known pathway of arginine catabolism in escherichia coli (through arginine decarboxylase) does not produce ammonia. our aims were to find the ammonia-producing pathway of arginine catabolism in e. coli and to examine its function. we showed that the only previously described pathway of arginine catabolism, which does not produce ammonia, accounted for only 3% of the arginine consumed. a search fo ...	1998	9696779
amplification of putative chlorocatechol dioxygenase gene fragments from alpha- and beta-proteobacteria.	redundant primers were designed for the pcr amplification of dna from chlorocatechol dioxygenase genes. these primers were used successfully to amplify 270- to 279-bp fragments from a variety of 2,4-dichlorophenoxyacetate- and cholorobenzoate-degrading strains, including species of sphingomonas. three groups of closely related sequences were amplified: one from chlorobenzoate degraders that was 86% similar to the amino acid sequence of the protein coded by the tfdc gene of ralstonia eutropha jmp ...	1998	9699302
[features of the production of cryiiia delta-endotoxin from bacillus thuringiensis in a recombinant strain of pseudomonas putida under control of pm and xyls regulatory elements].	the addition of 3-methyl benzoate to the culture of the recombinant strain pseudomonas putida ipm-36 (bearing the cryiiia gene of b. thuringiensis subsp, tenebrionis under the control of the pm promoter and the regulator gene xyls) slowed down the growth rate of the recombinant strain and increased, under non-selective conditions, the number of plasmid-free cells. intense synthesis of the coleoptera-specific delta-endotoxin encoded by the cryiiia gene began 6-8 h after the addition of the induce ...	1998	9702728
controlled comparative evaluation of bact/alert fan and esp 80a aerobic media as means for detecting bacteremia and fungemia.	during a one-year period, a total of 6,305 blood cultures were processed in a tertiary-care teaching hospital; 6 to 12 ml of blood was inoculated into both a bact/alert fan aerobic bottle and an esp 80a aerobic bottle. the fan aerobic bottle contains an antimicrobial-absorbing material; the 80a aerobic bottle does not. bottles were processed on their respective continuous-monitoring blood culture instruments for up to five days of incubation. four hundred thirty-three cultures (6.9%) representin ...	1998	9705414
the tomato cf-9 disease resistance gene functions in tobacco and potato to confer responsiveness to the fungal avirulence gene product avr 9	the cf-9 gene encodes an extracytoplasmic leucine-rich repeat protein that confers resistance in tomato to races of the fungus cladosporium fulvum that express the corresponding avirulence gene avr 9. we investigated whether the genomic cf-9 gene functions in potato and tobacco. transgenic tobacco and potato plants carrying cf-9 exhibit a rapid hypersensitive cell death response (hr) to avr 9 peptide injection. cf 9 tobacco plants were reciprocally crossed to avr 9-producing tobacco. a developme ...	1998	9707527
comparison of sample sequences of the salmonella typhi genome to the sequence of the complete escherichia coli k-12 genome.	raw sequence data representing the majority of a bacterial genome can be obtained at a tiny fraction of the cost of a completed sequence. to demonstrate the utility of such a resource, 870 single-stranded m13 clones were sequenced from a shotgun library of the salmonella typhi ty2 genome. the sequence reads averaged over 400 bases and sampled the genome with an average spacing of once every 5,000 bases. a total of 339,243 bases of unique sequence was generated (approximately 7% representation). ...	1998	9712782
rapid monitoring method to assess efficacy of sanitizers against pseudomonas putida biofilms.	biofilms of luminescent pseudomonas putida were developed on rubber surfaces by incubation in brain heart infusion (bhi) broth. scanning electron microscopy (sem) and epifluorescence microscopy (efm) were used to examine biofilm formation. to test the efficacy of two sanitizers commonly employed in dairy plants for cip (cleaning in place) procedures, a novel bioluminescence method and aerobic plating were used to enumerate cells. immediately after the sanitizer treatments an apparent 5-log reduc ...	1998	9713769
mechanism for biotransformation of nonylphenol polyethoxylates to xenoestrogens in pseudomonas putida.	a strain of pseudomonas putida isolated from activated sewage grew aerobically on the xenoestrogen precursor, nonylphenol polyethoxylate (npeox, where x is the number of ethoxylate units) as sole carbon source. comparative growth yields on npeoav6, npeoav9, and npeoav20 (mixtures with average ethoxylate numbers as indicated) were consistent with utilization of all but two ethoxylate units, and the final accumulating metabolite was identified by gas chromatography-mass spectroscopy as nonylphenol ...	1998	9721266
chromosomal integration, tandem amplification, and deamplification in pseudomonas putida f1 of a 105-kilobase genetic element containing the chlorocatechol degradative genes from pseudomonas sp. strain b13.	analysis of chlorobenzene-degrading transconjugants of pseudomonas putida f1 which had acquired the genes for chlorocatechol degradation (clc) from pseudomonas sp. strain b13 revealed that the clc gene cluster was present on a 105-kb amplifiable genetic element (named the clc element). in one such transconjugant, p. putida rr22, a total of seven or eight chromosomal copies of the entire genetic element were present when the strain was cultivated on chlorobenzene. chromosomal integrations of the ...	1998	9721270
purification and characterization of the coniferyl aldehyde dehydrogenase from pseudomonas sp. strain hr199 and molecular characterization of the gene.	the coniferyl aldehyde dehydrogenase (caldh) of pseudomonas sp. strain hr199 (dsm7063), which catalyzes the nad+-dependent oxidation of coniferyl aldehyde to ferulic acid and which is induced during growth with eugenol as the carbon source, was purified and characterized. the native protein exhibited an apparent molecular mass of 86,000 +/- 5,000 da, and the subunit mass was 49.5 +/- 2.5 kda, indicating an alpha2 structure of the native enzyme. the optimal oxidation of coniferyl aldehyde to feru ...	1998	9721273
similarities between the antabc-encoded anthranilate dioxygenase and the benabc-encoded benzoate dioxygenase of acinetobacter sp. strain adp1.	acinetobacter sp. strain adp1 can use benzoate or anthranilate as a sole carbon source. these structurally similar compounds are independently converted to catechol, allowing further degradation to proceed via the beta-ketoadipate pathway. in this study, the first step in anthranilate catabolism was characterized. a mutant unable to grow on anthranilate, acn26, was selected. the sequence of a wild-type dna fragment that restored growth revealed the antabc genes, encoding 54-, 19-, and 39-kda pro ...	1998	9721284
purification, characterization, and sequence analysis of 2-aminomuconic 6-semialdehyde dehydrogenase from pseudomonas pseudoalcaligenes js45.	2-aminonumconic 6-semialdehyde is an unstable intermediate in the biodegradation of nitrobenzene and 2-aminophenol by pseudomonas pseudoalcaligenes js45. previous work has shown that enzymes in cell extracts convert 2-aminophenol to 2-aminomuconate in the presence of nad+. in the present work, 2-aminomuconic semialdehyde dehydrogenase was purified and characterized. the purified enzyme migrates as a single band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis with a molecular mass of ...	1998	9721300
active recruitment of sigma54-rna polymerase to the pu promoter of pseudomonas putida: role of ihf and alphactd.	the sequence elements determining the binding of the sigma54-containing rna polymerase (sigma54-rnap) to the pu promoter of pseudomonas putida have been examined. contrary to previous results in related systems, we show that the integration host factor (ihf) binding stimulates the recruitment of the enzyme to the -12/-24 sequence motifs. such a recruitment, which is fully independent of the activator of the system, xylr, requires the interaction of the c-terminal domain of the alpha subunit of r ...	1998	9724648
evolution of an enzyme active site: the structure of a new crystal form of muconate lactonizing enzyme compared with mandelate racemase and enolase.	muconate lactonizing enzyme (mle), a component of the beta-ketoadipate pathway of pseudomonas putida, is a member of a family of related enzymes (the "enolase superfamily") that catalyze the abstraction of the alpha-proton of a carboxylic acid in the context of different overall reactions. new untwinned crystal forms of mle were obtained, one of which diffracts to better than 2.0-a resolution. the packing of the octameric enzyme in this crystal form is unusual, because the asymmetric unit contai ...	1998	9724714
cloning, nucleotide sequence, and expression in escherichia coli of levansucrase genes from the plant pathogens pseudomonas syringae pv. glycinea and p. syringae pv. phaseolicola.	plant-pathogenic bacteria produce various extracellular polysaccharides (epss) which may function as virulence factors in diseases caused by these bacteria. the eps levan is synthesized by the extracellular enzyme levansucrase in pseudomonas syringae, erwinia amylovora, and other bacterial species. the lsc genes encoding levansucrase from p. syringae pv. glycinea pg4180 and p. syringae pv. phaseolicola ncppb 1321 were cloned, and their nucleotide sequences were determined. heterologous expressio ...	1998	9726857
contribution of indole-3-acetic acid production to the epiphytic fitness of erwinia herbicola	erwinia herbicola 299r produces large quantities of indole-3-acetic acid (iaa) in culture media supplemented with l-tryptophan. to assess the contribution of iaa production to epiphytic fitness, the population dynamics of the wild-type strain and an iaa-deficient mutant of this strain on leaves were studied. strain 299xyle, an isogenic iaa-deficient mutant of strain 299r, was constructed by insertional interruption of the indolepyruvate decarboxylase gene of strain 299r with the xyle gene, which ...	1998	9726868
substrate specificity of and product formation by muconate cycloisomerases: an analysis of wild-type enzymes and engineered variants.	muconate cycloisomerases play a crucial role in the bacterial degradation of aromatic compounds by converting cis,cis-muconate, the product of catechol ring cleavage, to (4s)-muconolactone. chloromuconate cycloisomerases catalyze both the corresponding reaction and a dehalogenation reaction in the transformation of chloroaromatic compounds. this study reports the first thorough examination of the substrate specificity of the muconate cycloisomerases from pseudomonas putida prs2000 and acinetobac ...	1998	9726873
conversion of methionine to thiols by lactococci, lactobacilli, and brevibacteria	methanethiol has been strongly associated with desirable cheddar cheese flavor and can be formed from the degradation of methionine (met) via a number of microbial enzymes. methionine gamma-lyase is thought to play a major role in the catabolism of met and generation of methanethiol in several species of bacteria. other enzymes that have been reported to be capable of producing methanethiol from met in lactic acid bacteria include cystathionine beta-lyase and cystathionine gamma-lyase. the objec ...	1998	9726877
purification and characterization of l-methionine gamma-lyase from brevibacterium linens bl2	l-methionine gamma-lyase (ec 4.4.1.11) was purified to homogeneity from brevibacterium linens bl2, a coryneform bacterium which has been used successfully as an adjunct bacterium to improve the flavor of cheddar cheese. the enzyme catalyzes the alpha,gamma elimination of methionine to produce methanethiol, alpha-ketobutyrate, and ammonia. it is a pyridoxal phosphate-dependent enzyme, with a native molecular mass of approximately 170 kda, consisting of four identical subunits of 43 kda each. the ...	1998	9726878
pseudomonas sp. strain 273, an aerobic alpha, omega-dichloroalkanedegrading bacterium.	a gram-negative, aerobic bacterium was isolated from soil; this bacterium grew in 50% (vol/vol) suspensions of 1,10-dichlorodecane (1,10-dcd) as the sole source of carbon and energy. phenotypic and small-subunit ribosomal rna characterizations identified the organism, designated strain 273, as a member of the genus pseudomonas. after induction with 1,10-dcd, pseudomonas sp. strain 273 released stoichiometric amounts of chloride from c5 to c12 alpha, omega-dichloroalkanes in the presence of oxyge ...	1998	9726906
a new metabolic link between fatty acid de novo synthesis and polyhydroxyalkanoic acid synthesis. the phag gene from pseudomonas putida kt2440 encodes a 3-hydroxyacyl-acyl carrier protein-coenzyme a transferase.	to investigate the metabolic link between fatty acid de novo synthesis and polyhydroxyalkanoic acid (pha) synthesis, we isolated mutants of pseudomonas putida kt2440 deficient in this metabolic route. the gene phag was cloned by phenotypic complementation of these mutants; it encoded a protein of 295 amino acids with a molecular mass of 33,876 da, and the amino acid sequence exhibited 44% amino acid identity to the primary structure of the rhla gene product, which is involved in the rhamnolipid ...	1998	9727022
molecular regulation of beta-lactam biosynthesis in filamentous fungi.	the most commonly used beta-lactam antibiotics for the therapy of infectious diseases are penicillin and cephalosporin. penicillin is produced as an end product by some fungi, most notably by aspergillus (emericella) nidulans and penicillium chrysogenum. cephalosporins are synthesized by both bacteria and fungi, e.g., by the fungus acremonium chrysogenum (cephalosporium acremonium). the biosynthetic pathways leading to both secondary metabolites start from the same three amino acid precursors an ...	1998	9729600
growth kinetics of suspended microbial cells: from single-substrate-controlled growth to mixed-substrate kinetics.	growth kinetics, i.e., the relationship between specific growth rate and the concentration of a substrate, is one of the basic tools in microbiology. however, despite more than half a century of research, many fundamental questions about the validity and application of growth kinetics as observed in the laboratory to environmental growth conditions are still unanswered. for pure cultures growing with single substrates, enormous inconsistencies exist in the growth kinetic data reported. the low q ...	1998	9729604
aerobic anoxygenic phototrophic bacteria.	the aerobic anoxygenic phototrophic bacteria are a relatively recently discovered bacterial group. although taxonomically and phylogenetically heterogeneous, these bacteria share the following distinguishing features: the presence of bacteriochlorophyll a incorporated into reaction center and light-harvesting complexes, low levels of the photosynthetic unit in cells, an abundance of carotenoids, a strong inhibition by light of bacteriochlorophyll synthesis, and the inability to grow photosynthet ...	1998	9729607
linkage map of escherichia coli k-12, edition 10: the traditional map.	this map is an update of the edition 9 map by berlyn et al. (m. k. b. berlyn, k. b. low, and k. e. rudd, p. 1715-1902, in f. c. neidhardt et al., ed., escherichia coli and salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). it uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. the latter are included as ...	1998	9729611
physiological and molecular biological characterization of ammonia oxidation of the heterotrophic nitrifier pseudomonas putida.	the heterotrophic nitrifier pseudomonas putida aerobically oxidized ammonia to hydroxylamine, nitrite, and nitrate. product formation was accompanied by a small but significant release of no, whereas n2o evolution could not be detected under the assay conditions employed. the isolate reduced nitrate to nitrite and partially further to no under anaerobic conditions. aerobically grown cells utilized gamma-aminobutyrate as a carbon source and as a n-source by ammonification. the physiological exper ...	1998	9732537
phylogenetic relationships of pseudomonas putida strains deduced from the nucleotide sequences of gyrb, rpod and 16s rrna genes.	phylogenetic analysis of 20 pseudomonas strains (pseudomonas putida, pseudomonas fluorescens and pseudomonas chlororaphis) was conducted by using the nucleotide sequences of the genes for 16s rna, dna gyrase b subunit (gyrb) and rna polymerase delta 70 factor (rpod), which have been determined by the direct sequencing of pcr-amplified fragments. on the basis of gyrb and rpod sequences, these strains were split into two major clusters: one including the type strain of p. putida and all biovar a s ...	1998	9734035
influence of the tonb energy-coupling protein on efflux-mediated multidrug resistance in pseudomonas aeruginosa.	tonb couples the energized state of the cytoplasmic membrane to the operation of outer membrane receptors responsible for fe(iii) siderophore uptake across the outer membrane of gram-negative bacteria. a tonb mutant of pseudomonas aeruginosa deficient in iron siderophore uptake was shown in the present study to be hypersusceptible to a wide variety of antibiotics, reminiscent of the phenotype of mutants defective in the mexab-oprm antibiotic efflux operon. this was not related to influences of a ...	1998	9736539
outbreak of pseudomonas fluorescens bacteremia among oncology patients.	from 7 to 24 march 1997, four patients developed pseudomonas fluorescens bacteremia at the hospital; one on the oncology ward and the other three in the chemotherapy room. these patients all had underlying malignancies and had the port-a-cath (smiths industries medical systems, deltec, inc., st. paul, minn.) implants. three patients had primary bacteremia, and one had port-a-cath-related infection. none of these patients had received a blood transfusion before the episodes of bacteremia. all pat ...	1998	9738043
the rpos gene regulates op2, an operon for the lower pathway of xylene catabolism on the tol plasmid, and the stress response in pseudomonas putida mt-2.	operon op2 on the pseudomonas putida tol plasmid encodes enzymes for m-toluate catabolism; transcription of this operon is activated by xyls in the presence of m-toluate. because transcriptional activation of op2 specifically occurs in the stationary phase of growth both in p. putida and in escherichia coli, we suspected that its transcription is dependent on rpos (sigmas). therefore, we constructed a rpos disruption strain of p. putida mt-2, and assayed op2 expression and other phenotypes. op2 ...	1998	9738882
colicin import into escherichia coli cells.		1998	9748429
mutation analysis of pobr and pcau, closely related transcriptional activators in acinetobacter.	acinetobacter pobr and pcau are transcriptional activators that closely resemble each other in primary structure, dna-binding sites, metabolic modulators, and physiological function. pobr responds to the inducer-metabolite p-hydroxybenzoate and activates transcription of poba, the structural gene for the enzyme that converts p-hydroxybenzoate to protocatechuate. this compound, differing from p-hydroxybenzoate only in that it contains an additional oxygen atom, binds to pcau and thereby specifica ...	1998	9748437
carbon-source-dependent expression of the palkb promoter from the pseudomonas oleovorans alkane degradation pathway.	pseudomonas oleovorans gpo1 can metabolize medium-chain-length alkanes by means of an enzymatic system whose induction is regulated by the alks protein. in the presence of alkanes, alks activates the expression of promoter palkb, from which most of the genes of the pathway are transcribed. in addition, expression of the first enzyme of the pathway, alkane hydroxylase, is known to be influenced by the carbon source present in the growth medium, indicating the existence of an additional overimpose ...	1998	9748457
nucleotide sequence and characterization of cdra, a cell division-related gene of helicobacter pylori.	we identified cell division-related gene cdra in helicobacter pylori hpk5. the putative gene product, cdra, is a 367-amino-acid polypeptide that exhibited a high level of homology to conserved hypothetical atp-binding protein hp0066 of h. pylori 26695, except in the n-terminal region, and showed some similarity to the ftsk/spoiiie family proteins. we isolated a cdra-disrupted mutant by allelic exchange mutagenesis. because of the low transformation frequency, the possibility that a suppressing m ...	1998	9748467
growth medium-dependent regulation of myxococcus xanthus fatty acid content is controlled by the esg locus.	we compared the cellular fatty acid profiles of myxococcus xanthus cells grown in either a casitone-based complex medium or a chemically defined medium. the cells grown in the complex medium had a much higher content of the abundant branched-chain fatty acid iso-15:0 and several other branched-chain species. the higher branched-chain fatty acid content of the cells grown in the complex medium was dependent on the esg locus, which encodes the e1alpha and e1beta components of a branched-chain keto ...	1998	9748468
[evaluation of antibacterial activities of various antibiotics against glucose non-fermentative gram-negative rods other than pseudomonas aeruginosa].	mics of piperacillin, sulbactam/cefoperazone, minocycline (mino), gentamicin, amikacin, flomoxef, ceftazidime, cefozopran, cefsulodin and imipenem were determined, against 189 clinical isolated strains of glucose non-fermentative gram-negative rods (nfgnr; acinetobacter baumannii (44), alcaligenes faecalis (5), alcaligenes xylosoxidans (25), burkholderia cepacia (12), chryseobacterium indologenes (23), chryseobacterium meningosepticum (9), pseudomonas fluorescens (8), pseudomonas putida (12), st ...	1998	9755431
crystallization and preliminary x-ray diffraction studies of the oxygenating subunit of 3,6-diketocamphane monooxygenase from pseudomonas putida.	the oxygenating constituent of the 3,6-diketocamphane monooxygenase isozyme from pseudomonas putida ncimb 10007 has been crystallized under two different conditions. crystals were initially grown from polyethylene glycol (peg) 8000 and sodium acetate using the vapour-phase diffusion method. the crystals were of orthorhombic p212121 space group, with cell dimensions a = 55.8, b = 94.5 and c = 163.7 a and diffracted to 2.8 a resolution. more recently, improved crystals, which diffracted beyond 2 a ...	1998	9757131
c-type cytochromes and manganese oxidation in pseudomonas putida mnb1.	pseudomonas putida mnb1 is an isolate from an mn oxide-encrusted pipeline that can oxidize mn(ii) to mn oxides. we used transposon mutagenesis to construct mutants of strain mnb1 that are unable to oxidize manganese, and we characterized some of these mutants. the mutants were divided into three groups: mutants defective in the biogenesis of c-type cytochromes, mutants defective in genes that encode key enzymes of the tricarboxylic acid cycle, and mutants defective in the biosynthesis of tryptop ...	1998	9758766
the cytochrome c maturation operon is involved in manganese oxidation in pseudomonas putida gb-1.	a pseudomonas putida strain, strain gb-1, oxidizes mn2+ to mn oxide in the early stationary growth phase. it also secretes a siderophore (identified as pyoverdine) when it is subjected to iron limitation. after transposon (tn5) mutagenesis several classes of mutants with differences in mn2+ oxidation and/or secretion of the mn2+-oxidizing activity were identified. preliminary analysis of the tn5 insertion site in one of the nonoxidizing mutants suggested that a multicopper oxidase-related enzyme ...	1998	9758767
secondary metabolite- and endochitinase-dependent antagonism toward plant-pathogenic microfungi of pseudomonas fluorescens isolates from sugar beet rhizosphere	forty-seven isolates representing all biovars of pseudomonas fluorescens (biovars i to vi) were collected from the rhizosphere of field-grown sugar beet plants to select candidate strains for biological control of preemergence damping-off disease. the isolates were tested for in vitro antagonism toward the plant-pathogenic microfungi pythium ultimum and rhizoctonia solani in three different plate test media. mechanisms of fungal inhibition were elucidated by tracing secondary-metabolite producti ...	1998	9758768
analysis of the gene cluster encoding toluene/o-xylene monooxygenase from pseudomonas stutzeri ox1.	the toluene/o-xylene monooxygenase cloned from pseudomonas stutzeri ox1 displays a very broad range of substrates and a very peculiar regioselectivity, because it is able to hydroxylate more than one position on the aromatic ring of several hydrocarbons and phenols. the nucleotide sequence of the gene cluster coding for this enzymatic system has been determined. the sequence analysis revealed the presence of six open reading frames (orfs) homologous to other genes clustered in operons coding for ...	1998	9758777
plasmids responsible for horizontal transfer of naphthalene catabolism genes between bacteria at a coal tar-contaminated site are homologous to pdtg1 from pseudomonas putida ncib 9816-4	the presence of a highly conserved nahac allele among phylogenetically diverse bacteria carrying naphthalene-catabolic plasmids provided evidence for in situ horizontal gene transfer at a coal tar-contaminated site (j. b. herrick, k. g. stuart-keil, w. c. ghiorse, and e. l. madsen, appl. environ. microbiol. 63:2330-2337, 1997). the objective of the present study was to identify and characterize the different-sized naphthalene-catabolic plasmids in order to determine the probable mechanism of hor ...	1998	9758778
a plant growth-promoting bacterium that decreases nickel toxicity in seedlings	a plant growth-promoting bacterium, kluyvera ascorbata sud165, that contained high levels of heavy metals was isolated from soil collected near sudbury, ontario, canada. the bacterium was resistant to the toxic effects of ni2+, pb2+, zn2+, and cro4-, produced a siderophore(s), and displayed 1-aminocyclopropane-1-carboxylic acid deaminase activity. canola seeds inoculated with this bacterium and then grown under gnotobiotic conditions in the presence of high concentrations of nickel chloride were ...	1998	9758782