Publications

visualization of dna-protein intermediates during activation of the pu promoter of the tol plasmid of pseudomonas putida.	the atp-dependent multimerization process undergone by the sigma(54)-dependent activator xylr of the tol plasmid pww0 of pseudomonas putida when bound to the upstream activating sequences (uas) of the cognate pu: promoter was examined by transmission electron microscopy (tem). to this end, supercoiled dna templates were combined with increasing concentrations of the constitutive xylr variant xylrdeltaa, with or without atp or its non-hydrolysable analogue atpgammas, and the resulting complexes w ...	2000	11021930
activation of pseudomonas aeruginosa elastase in pseudomonas putida by triggering dissociation of the propeptide-enzyme complex.	the propeptide of pseudomonas aeruginosa elastase functions both as an intramolecular chaperone required for the folding of the enzyme and as an inhibitor that prevents activity of the enzyme before its secretion into the extracellular medium. since expression of the lasb gene, which encodes elastase, in pseudomonas putida did not result in extracellular elastase activity, it has been suggested that the enzyme is not recognized by the xcp secretion machinery of the heterologous host. here, it is ...	2000	11021931
a battery of toxicity tests as indicators of decontamination in composting oily waste.	heterogeneous oily waste from an old dumping site was composted in three windrows constructed from different proportions of waste, sewage sludge, and bark. the objectives of this pilot study were to examine the usefulness of composting as a treatment method for this particular waste and to study decontamination in the composting process by using a battery of toxicity tests. five samples from the windrow having intermediate oil concentrations were tested with toxicity tests based on microbes (pse ...	2000	11023694
heat shock protein 60 sequence comparisons: duplications, lateral transfer, and mitochondrial evolution.	heat shock proteins 60 (groel) are highly expressed essential proteins in eubacterial genomes and in eukaryotic organelles. these chaperone proteins have been advanced as propitious marker sequences for tracing the evolution of mitochondrial (mt) genomes. similarities among hsp60 sequences based on significant segment pair alignment calculations are used to deduce associations of sequences taking into account groel functional/structural domain differences and to relate hsp60 duplications pervasi ...	2000	11027334
energy taxis is the dominant behavior in azospirillum brasilense.	energy taxis encompasses aerotaxis, phototaxis, redox taxis, taxis to alternative electron acceptors, and chemotaxis to oxidizable substrates. the signal for this type of behavior is originated within the electron transport system. energy taxis was demonstrated, as a part of an overall behavior, in several microbial species, but it did not appear as the dominant determinant in any of them. in this study, we show that most behavioral responses proceed through this mechanism in the alpha-proteobac ...	2000	11029423
characterization of the genes for two protocatechuate 3, 4-dioxygenases from the 4-sulfocatechol-degrading bacterium agrobacterium radiobacter strain s2.	the genes for two different protocatechuate 3,4-dioxygenases (p34os) were cloned from the 4-sulfocatechol-degrading bacterium agrobacterium radiobacter strain s2 (dsmz 5681). the pcah1g1 genes encoded a p34o (p34o-i) which oxidized protocatechuate but not 4-sulfocatechol. these genes were part of a protocatechuate-degradative operon which strongly resembled the isofunctional operon from the protocatechuate-degrading strain agrobacterium tumefaciens a348 described previously by d. parke (fems mic ...	2000	11029433
positive selection for mutations affecting bioconversion of aromatic compounds in agrobacterium tumefaciens: analysis of spontaneous mutations in the protocatechuate 3,4-dioxygenase gene.	a positive selection method for mutations affecting bioconversion of aromatic compounds was applied to a mutant strain of agrobacterium tumefaciens a348. the nucleotide sequence of the a348 pcahgb genes, which encode protocatechuate 3,4-dioxygenase (pcahg) and beta-carboxy-cis,cis-muconate cycloisomerase (pcab) for the first two steps in catabolism of the diphenolic protocatechuate, was determined. an omega element was introduced into the pcab gene of a348, creating strain ado2077. in the presen ...	2000	11029436
characterization of the dna- and metal-binding properties of vibrio anguillarum fur reveals conservation of a structural zn(2+) ion.	the ferric uptake regulator, fur, represses iron uptake and siderophore biosynthetic genes under iron-replete conditions. here we report in vitro solution studies on vibrio anguillarum fur binding to the consensus 19-bp escherichia coli iron box in the presence of several divalent metals. we found that v. anguillarum fur binds the iron box in the presence of mn(2+), co(2+), cd(2+), and to a lesser extent ni(2+) but, unlike e. coli fur, not in the presence of zn(2+). we also found that v. anguill ...	2000	11029454
an escherichia coli reference collection group b2- and uropathogen-associated polymorphism in the rpos-muts region of the e. coli chromosome.	chromosomal dnas of enterohemorrhagic, uropathogenic, and laboratory attenuated escherichia coli strains differ in the rpos-muts region. many uropathogens lack a deletion and an insertion characteristic of enterohemorrhagic strains. at the same chromosomal position, they harbor a 2.1-kb insertion of unknown origin with a base composition suggestive of horizontal gene transfer. unlike virulence determinants associated with urinary tract infection and/or neonatal meningitis (pap or prs, sfa, kps, ...	2000	11029456
phospholipid compositional changes of five pseudomonad archetypes grown with and without toluene.	bacterial physiological responses to toluene exposure were investigated in five reference pseudomonad strains that express different toluene degradation pathways: pseudomonas putida mt-2, pseudomonas putida f1, burkholderia cepacia g4, burkholderia pickettii pko1, and pseudomonas mendocina kr1. the intact phospholipids of these archetypes, grown with and without toluene, were characterized using liquid chromatography/electrospray ionization/mass spectrometry. all strains showed significant chang ...	2000	11030576
evaluation of various carbon substrates for the biosynthesis of polyhydroxyalkanoates bearing functional groups by pseudomonas putida.	the ability of pseudomonas putida to synthesize polyhydroxyalkanoate (pha) from 36 different carboxylic acids containing various functional groups was examined. this bacterium did not utilize short carboxylic acids (c(4)-c(6)) containing bromine, methoxy, ethoxy, cyclohexyl, phenoxy, and olefin groups as the sole carbon substrate. no polymer was isolated from the cells grown with carboxylic acids bearing hydroxyl, amino, para-methoxyphenoxy, and para-ethoxyphenoxy groups regardless of the carbon ...	2000	11033174
involvement of naphthalene dioxygenase in indole-3-acetic acid biosynthesis by pseudomonas putida.	two variants of plant growth-promoting strain pseudomonas putida bs1380 harboring the naphthalene degradative plasmid pbs2 and the recombinant plasmid pnau64 that contains the genes encoding for naphthalene dioxygenase were constructed by conjugation. the ability of this strain to produce phytohormone indole-3-acetic acid from different carbon sources was studied. indole-3-acetic acid synthesis by these transconjugants was 15-30 times as much in contrast to a wild-type strain with glucose as the ...	2000	11034292
molecular cloning and analysis of a putative siderophore abc transporter from staphylococcus aureus.	from a mass-excised staphylococcus aureus lambdazapii expression library, we cloned an operon encoding a novel abc transporter with significant homology to bacterial siderophore transporter systems. the operon encodes four genes designated ssta, -b, -c, and -d encoding two putative cytoplasmic membrane proteins (ssta and sstb), an atpase (sstc), and a membrane-bound 38-kda lipoprotein (sstd). the sst operon is preceded by two putative fur boxes, which indicated that expression of the sst operon ...	2000	11035736
cloning and characterization of smedef, a novel multidrug efflux pump from stenotrophomonas maltophilia.	stenotrophomonas maltophilia is a nosocomial bacterial pathogen intrinsically resistant to several antibiotics. the mechanisms involved in this intrinsic multiresistance phenotype are poorly understood. a library of chromosomal dna from a spontaneous multidrug-resistant s. maltophilia d457r mutant (a. alonso and j. l. martinez, antimicrob. agents chemother. 41:1140-1142, 1997) was screened for complementation of erythromycin susceptibility on an antibiotic-hypersusceptible escherichia coli delta ...	2000	11036026
role of hydrophobic interactions in binding s-(n-aryl/alkyl-n-hydroxycarbamoyl)glutathiones to the active site of the antitumor target enzyme glyoxalase i.	hydrophobic interactions play an important role in binding s-(n-aryl/alkyl-n-hydroxycarbamoyl)glutathiones to the active sites of human, yeast, and pseudomonas putida glyoxalase i, as the log k(i) values for these mechanism-based competitive inhibitors decrease linearly with increasing values of the hydrophobicity constants (pi) of the n-aryl/alkyl substituents. hydrophobic interactions also help to optimize polar interactions between the enzyme and the glutathione derivatives, given that the k( ...	2000	11052803
benr, a xyls homologue, regulates three different pathways of aromatic acid degradation in pseudomonas putida.	pseudomonas putida converts benzoate to catechol using two enzymes that are encoded on the chromosome and whose expression is induced by benzoate. benzoate also binds to the regulator xyls to induce expression of the tol (toluene degradation) plasmid-encoded meta pathway operon for benzoate and methylbenzoate degradation. finally, benzoate represses the ability of p. putida to transport 4-hydroxybenzoate (4-hba) by preventing transcription of pcak, the gene encoding the 4-hba permease. here we i ...	2000	11053377
the malonate decarboxylase operon of acinetobacter calcoaceticus kccm 40902 is regulated by malonate and the transcriptional repressor mdcy.	a regulatory gene-like open reading frame oriented oppositely to mdcl, coined mdcy, was found upstream from the structural genes of the mdclmacdegbh operon in acinetobacter calcoaceticus kccm 40902. to elucidate the function of this gene, mdcy was expressed in escherichia coli, and the mdcy protein was purified to homogeneity. its dna binding activity and binding site were examined by gel retardation and footprinting assays in vitro and by site-directed mutagenesis of the binding sites in vivo. ...	2000	11053382
novel toluene elimination system in a toluene-tolerant microorganism.	in studies of pseudomonas putida ih-2000, a toluene-tolerant microorganism, membrane vesicles (mvs) were found to be released from the outer membrane when toluene was added to the culture. these mvs were found to be composed of phospholipids, lipopolysaccharides (lps), and very low amounts of outer membrane proteins. the mvs also contained a higher concentration of toluene molecules (0.172 +/- 0. 012 mol/mol of lipid) than that found in the cell membrane. in contrast to the wild-type strain, the ...	2000	11053390
development and dynamics of pseudomonas sp. biofilms.	pseudomonas sp. strain b13 and pseudomonas putida ous82 were genetically tagged with the green fluorescent protein and the discosoma sp. red fluorescent protein, and the development and dynamics occurring in flow chamber-grown two-colored monospecies or mixed-species biofilms were investigated by the use of confocal scanning laser microscopy. separate red or green fluorescent microcolonies were formed initially, suggesting that the initial small microcolonies were formed simply by growth of subs ...	2000	11053394
cloning, sequence and crystallographic structure of recombinant iron superoxide dismutase from pseudomonas ovalis.	the gene encoding the iron-dependent superoxide dismutase from pseudomonas ovalis was cloned from a genomic library and sequenced. the orf differs from the previously published protein sequence, which was used for the original structure determination, at 16 positions. the differences include three additional inserted residues, one deleted residue and 12 point substitutions. the gene was subcloned and the recombinant protein overexpressed, purified and crystallized in a trigonal space group. the ...	2000	11053832
natural antibiotic resistance of bacteria isolated from larvae of the oil fly, helaeomyia petrolei.	helaeomyia petrolei (oil fly) larvae inhabit the asphalt seeps of rancho la brea in los angeles, calif. the culturable microbial gut contents of larvae collected from the viscous oil were recently examined, and the majority (9 of 14) of the strains were identified as providencia spp. subsequently, 12 of the bacterial strains isolated were tested for their resistance or sensitivity to 23 commonly used antibiotics. all nine strains classified as providencia rettgeri exhibited dramatic resistance t ...	2000	11055901
key aromatic-ring-cleaving enzyme, protocatechuate 3,4-dioxygenase, in the ecologically important marine roseobacter lineage.	aromatic compound degradation in six bacteria representing an ecologically important marine taxon of the alpha-proteobacteria was investigated. initial screens suggested that isolates in the roseobacter lineage can degrade aromatic compounds via the beta-ketoadipate pathway, a catabolic route that has been well characterized in soil microbes. six roseobacter isolates were screened for the presence of protocatechuate 3,4-dioxygenase, a key enzyme in the beta-ketoadipate pathway. all six isolates ...	2000	11055908
transformation of 2,4,6-trinitrotoluene by purified xenobiotic reductase b from pseudomonas fluorescens i-c.	the enzymatic transformation of 2,4,6-trinitrotoluene (tnt) by purified xenb, an nadph-dependent flavoprotein oxidoreductase from pseudomonas fluorescens i-c, was evaluated by using natural abundance and [u-(14)c]tnt preparations. xenb catalyzed the reduction of tnt either by hydride addition to the aromatic ring or by nitro group reduction, with the accumulation of various tautomers of the protonated dihydride-meisenheimer complex of tnt, 2-hydroxylamino-4,6-dinitrotoluene, and 4-hydroxylamino- ...	2000	11055918
application of siderotyping for characterization of pseudomonas tolaasii and "pseudomonas reactans" isolates associated with brown blotch disease of cultivated mushrooms.	pyoverdine isoelectric focusing analysis and pyoverdine-mediated iron uptake were used as siderotyping methods to analyze a collection of 57 northern and central european isolates of p. tolaasii and "p. reactans." the bacteria, isolated from cultivated agaricus bisporus or pleurotus ostreatus mushroom sporophores presenting brown blotch disease symptoms, were identified according to the white line test (w. c. wong and t. f. preece, j. appl. bacteriol. 47:401-407, 1979) and their pathogenicity to ...	2000	11055932
exogenous isolation of antibiotic resistance plasmids from piggery manure slurries reveals a high prevalence and diversity of incq-like plasmids.	antibiotic resistance plasmids were exogenously isolated in biparental matings with piggery manure bacteria as plasmid donors in escherichia coli cv601 and pseudomonas putida uwc1 recipients. surprisingly, incq-like plasmids were detected by dot blot hybridization with an incq oriv probe in several p. putida uwc1 transconjugants. the capture of incq-like plasmids in biparental matings indicates not only their high prevalence in manure slurries but also the presence of efficiently mobilizing plas ...	2000	11055935
screening of genes involved in isooctane tolerance in saccharomyces cerevisiae by using mrna differential display.	a saccharomyces cerevisiae strain, kk-211, isolated by the long-term bioprocess of stereoselective reduction in isooctane, showed extremely high tolerance to the solvent, which is toxic to yeast cells, but, in comparison with its wild-type parent, dy-1, showed low tolerance to hydrophilic organic solvents, such as dimethyl sulfoxide and ethanol. in order to detect the isooctane tolerance-associated genes, mrna differential display (dd) was employed using mrnas isolated from strains dy-1 and kk-2 ...	2000	11055939
relationships between colony morphotypes and oil tolerance in rhodococcus rhodochrous.	a mucoidal strain of rhodococcus rhodochrous was resistant to 10% (vol/vol) n-hexadecane, while its rough derivatives were sensitive. when the extracellular polysaccharide (eps) produced by the mucoidal strain was added to cultures of the rough strains, the rough strains gained resistance to n-hexadecane. thus, eps confer tolerance to n-hexadecane in members of the genus rhodococcus.	2000	11055965
growth and survival of phosphate-solubilizing bacteria in calcium alginate.	calcium alginate was superior to conventional charcoal-soil (3:1) carrier for phosphate-solubilizing bacteria (psb). high populations of pseudomonas striata (27) and bacillus polymyxa (h-5) could be maintained in this polymer during storage. incorporation of charcoal-soil (3:1) adversely affected the initial loading of these organisms in alginate gel. alginate alone supported maximum survival of these organisms at elevated storage temperature (40 degrees c).	2000	11061188
how do substrates enter and products exit the buried active site of cytochrome p450cam? 1. random expulsion molecular dynamics investigation of ligand access channels and mechanisms.	cytochrome p450s form a ubiquitous protein family with functions including the synthesis and degradation of many physiologically important compounds and the degradation of xenobiotics. cytochrome p450cam from pseudomonas putida has provided a paradigm for the structural understanding of cytochrome p450s. however, the mechanism by which camphor, the natural substrate of cytochrome p450cam, accesses the buried active site is a long-standing puzzle. while there is recent crystallographic and simula ...	2000	11061976
the role of the interdomain b linker in the activation of the xylr protein of pseudomonas putida.	in the presence of toluene and other structural analogues, the enhancer binding protein xylr activates the sigma54 promoter pu of the tol (toluene degradation) plasmid pww0 of pseudomonas putida. introduction of amino acid changes val-219asp and ala-220pro, which enter a proline kink at the interdomain region (b linker) between the a (signal reception) module and the central portion of xylr, originated a protein with unforeseen properties. these included a minor ability to activate pu in the abs ...	2000	11069665
conversion of 4-hydroxyacetophenone into 4-phenyl acetate by a flavin adenine dinucleotide-containing baeyer-villiger-type monooxygenase.	an arylketone monooxygenase was purified from pseudomonas putida jd1 by ion exchange and affinity chromatography. it had the characteristics of a baeyer-villiger-type monooxygenase and converted its substrate, 4-hydroxyacetophenone, into 4-hydroxyphenyl acetate with the consumption of one molecule of oxygen and oxidation of one molecule of nadph per molecule of substrate. the enzyme was a monomer with an m(r) of about 70,000 and contained one molecule of flavin adenine dinucleotide (fad). the en ...	2000	11073896
genetic and biochemical characterization of 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase and its role in the protocatechuate 4,5-cleavage pathway in sphingomonas paucimobilis syk-6.	protocatechuate (pca) is the key intermediate metabolite in the lignin degradation pathway of sphingomonas paucimobilis syk-6 and is metabolized to pyruvate and oxaloacetate via the pca 4,5-cleavage pathway. we characterized the 4-carboxy-2-hydroxymuconate-6-semialdehyde (chms) dehydrogenase gene (ligc). chms is the 4,5-cleavage product of pca and is converted into 2-pyrone-4,6-dicarboxylate (pdc) by ligc. we found that ligc was located 295 bp downstream of ligb, which encodes the large subunit ...	2000	11073908
effects of combination of different -10 hexamers and downstream sequences on stationary-phase-specific sigma factor sigma(s)-dependent transcription in pseudomonas putida.	the main sigma factor activating gene expression, necessary in stationary phase and under stress conditions, is sigma(s). in contrast to other minor sigma factors, rna polymerase holoenzyme containing sigma(s) (esigma(s)) recognizes a number of promoters which are also recognized by that containing sigma(70) (esigma(70)). we have previously shown that transposon tn4652 can activate silent genes in starving pseudomonas putida cells by creating fusion promoters during transposition. the sequence o ...	2000	11073916
interaction of two arginine residues in lactate oxidase with the enzyme flavin: conversion of fmn to 8-formyl-fmn.	two arginine residues, arg-181 and arg-268, are conserved throughout the known family of fmn-containing enzymes that catalyze the oxidation of alpha-hydroxyacids. in the lactate oxidase from aerococcus viridans, these residues have been changed to lysine in two single mutations and in a double mutant form. in addition, arg-181 has been replaced by methionine to determine the effect of removing the positive charge on the residue. the effects of these replacements on the kinetic and thermodynamic ...	2000	11078532
analysis of the alternative pathways for the beta-oxidation of unsaturated fatty acids using transgenic plants synthesizing polyhydroxyalkanoates in peroxisomes.	degradation of fatty acids having cis-double bonds on even-numbered carbons requires the presence of auxiliary enzymes in addition to the enzymes of the core beta-oxidation cycle. two alternative pathways have been described to degrade these fatty acids. one pathway involves the participation of the enzymes 2, 4-dienoyl-coenzyme a (coa) reductase and delta(3)-delta(2)-enoyl-coa isomerase, whereas the second involves the epimerization of r-3-hydroxyacyl-coa via a 3-hydroxyacyl-coa epimerase or th ...	2000	11080293
chitinase genes responsive to cold encode antifreeze proteins in winter cereals.	antifreeze proteins similar to two different chitinases accumulate during cold acclimation in winter rye (secale cereale). to determine whether these cold-responsive chitinases require post-translational modification to bind to ice, cdnas coding for two different full-length chitinases were isolated from a cdna library produced from cold-acclimated winter rye leaves. cht9 is a 1,193-bp clone that encodes a 31.7-kd class i chitinase and cht46 is a 998-bp clone that codes for a 24.8-kd class ii ch ...	2000	11080301
identification of a siderophore receptor required for ferric ornibactin uptake in burkholderia cepacia.	ornibactins are linear hydroxamate siderophores produced by burkholderia cepacia with peptide structures similar to that of pyoverdines produced by the fluorescent pseudomonads. the gene encoding the outer membrane receptor (orba) was identified, sequenced, and demonstrated to have significant homology with hydroxamate receptors produced by other organisms. the orba precursor was predicted to be a protein with a molecular mass of 81 kda. an orba mutant was constructed and demonstrated to be unab ...	2000	11083764
formation of methyl mercaptan from l-methionine by porphyromonas gingivalis.	methyl mercaptan production by oral bacteria is thought to be one of the main causes of oral malodor. we examined the ability of periodontopathic porphyromonas gingivalis to produce methyl mercaptan from l-methionine and found that the invasive strains w83 and w50 produced large amounts of methyl mercaptan. we cloned and sequenced the mgl gene encoding l-methionine-alpha-deamino-gamma-mercaptomethane-lyase (metase) from p. gingivalis w83. the structural mgl gene consisted of 1,200 bp and encoded ...	2000	11083813
crystal structure of nadh-dependent ferredoxin reductase component in biphenyl dioxygenase.	oxidative biodegradation of aromatic compounds by bacteria usually begins with hydroxylation of the aromatic ring by multi-component dioxygenases like benzene dioxygenase, biphenyl dioxygenase, and others. these enzymes are composed of ferredoxin reductase, ferredoxin, and terminal oxygenase. reducing equivalents that originate from nadh are transferred from ferredoxin reductase to ferredoxin and, in turn, to the terminal oxygenase, thus resulting in the activation of a dioxygen. bpha4 is the fe ...	2000	11090282
automated sample-preparation technologies in genome sequencing projects.	a robotic workstation system (biorobot 96oo, qiagen) and a 96-well uv spectrophotometer (spectramax 250, molecular devices) were integrated in to the process of high-throughput automated sequencing of double-stranded plasmid dna templates. an automated 96-well miniprep kit protocol (qiaprep turbo, qiagen) provided high-quality plasmid dna from shotgun clones. the dna prepared by this procedure was used to generate more than two mega bases of final sequence data for two genomic projects (arabidop ...	2000	11092729
phenotypes of fission yeast defective in ubiquinone production due to disruption of the gene for p-hydroxybenzoate polyprenyl diphosphate transferase.	ubiquinone is an essential component of the electron transfer system in both prokaryotes and eukaryotes and is synthesized from chorismate and polyprenyl diphosphate by eight steps. p-hydroxybenzoate (phb) polyprenyl diphosphate transferase catalyzes the condensation of phb and polyprenyl diphosphate in ubiquinone biosynthesis. we isolated the gene (designated ppt1) encoding phb polyprenyl diphosphate transferase from schizosaccharomyces pombe and constructed a strain with a disrupted ppt1 gene. ...	2000	11092853
transcriptional control of the hydrogen cyanide biosynthetic genes hcnabc by the anaerobic regulator anr and the quorum-sensing regulators lasr and rhlr in pseudomonas aeruginosa.	virulence factors of pseudomonas aeruginosa include hydrogen cyanide (hcn). this secondary metabolite is maximally produced at low oxygen tension and high cell densities during the transition from exponential to stationary growth phase. the hcnabc genes encoding hcn synthase were identified on a genomic fragment complementing an hcn-deficient mutant of p. aeruginosa pao1. the hcna promoter was found to be controlled by the fnr-like anaerobic regulator anr and by the quorum-sensing regulators las ...	2000	11092854
the 4-oxalomesaconate hydratase gene, involved in the protocatechuate 4,5-cleavage pathway, is essential to vanillate and syringate degradation in sphingomonas paucimobilis syk-6.	sphingomonas paucimobilis syk-6 is able to grow on various dimeric lignin compounds, which are converted to vanillate and syringate by the actions of unique lignin degradation enzymes in this strain. vanillate and syringate are degraded by the o-demethylase and converted into protocatechuate (pca) and 3-o-methylgallate (3mga), respectively. pca is further degraded via the pca 4,5-cleavage pathway, while the results suggested that 3mga is degraded through another pathway in which pca 4,5-dioxygen ...	2000	11092855
functional expression and characterization of the two cyclic amidohydrolase enzymes, allantoinase and a novel phenylhydantoinase, from escherichia coli.	a superfamily of cyclic amidohydrolases, including dihydropyrimidinase, allantoinase, hydantoinase, and dihydroorotase, all of which are involved in the metabolism of purine and pyrimidine rings, was recently proposed based on the rigidly conserved structural domains in identical positions of the related enzymes. with these conserved domains, two putative cyclic amidohydrolase genes from escherichia coli, flanked by related genes, were identified and characterized. from the genome sequence of e. ...	2000	11092864
mutations in catb, the gene encoding muconate cycloisomerase, activate transcription of the distal ben genes and contribute to a complex regulatory circuit in acinetobacter sp. strain adp1.	mutants of the bacterium acinetobacter sp. strain adp1 were selected to grow on benzoate without the benm transcriptional activator. in the wild type, benm responds to benzoate and cis,cis-muconate to activate expression of the benabcde operon, which is involved in benzoate catabolism. this operon encodes enzymes that convert benzoate to catechol, a compound subsequently degraded by cat gene-encoded enzymes. in this report, four spontaneous mutants were found to carry catb mutations that enabled ...	2000	11092867
transcription activation by a variety of arac/xyls family activators does not depend on the class ii-specific activation determinant in the n-terminal domain of the rna polymerase alpha subunit.	the n-terminal domain of the rna polymerase alpha subunit (alpha-ntd) was tested for a role in transcription activation by a variety of arac/xyls family members. based on substitutions at residues 162 to 165 and an extensive genetic screen we conclude that alpha-ntd is not an activation target for these activators.	2000	11092872
characterization of gtpase activity of trme, a member of a novel gtpase superfamily, from thermotoga maritima.	a gene encoding a putative gtp-binding protein, a trme homologue that is highly conserved in both prokaryotes and eukaryotes, was cloned from thermotoga maritima, a hyperthermophilic bacterium. t. maritima trme was overexpressed in escherichia coli and purified. trme has a gtpase activity but no atpase activity. the gtpase activity can be competed with gtp, gdp, and dgtp but not with gmp, atp, ctp, or utp. k(m) and k(cat) at 70 degrees c were 833 microm and 9.3 min(-1), respectively. our results ...	2000	11092873
crystallization and preliminary crystallographic characterization of recombinant l-methionine-alpha-deamino-gamma-mercaptomethane lyase (methioninase).	l-methionine-alpha-deamino-gamma-mercaptomethane lyase (rmetase) is involved in the alpha,gamma-elimination of methionine to alpha-ketobutyrate, methanethiol and ammonia. the reaction catalyzed by rmetase reduces the methionine concentration of methionine-dependent tumor cells, arresting their growth. towards the goal of developing rmetase into an effective antitumor therapeutic and also to understand the catalytic mechanism of this enzyme, rmetase from pseudomonas putida has been expressed, pur ...	2000	11092940
an insertion sequence prepares pseudomonas putida s12 for severe solvent stress.	the novel insertion sequence iss12 plays a key role in the tolerance of pseudomonas putida s12 to sudden toluene stress. under normal culturing conditions the p. putida s12 genome contained seven copies of iss12. however, a p. putida s12 population growing to high cell density after sudden addition of a separate phase of toluene carried eight copies. the survival frequency of cells in this variant p. putida s12 population was 1000 times higher than in "normal" p. putida s12 populations. analysis ...	2001	11094055
versatile biosensor vectors for detection and quantification of mercury.	three different whole cell biosensor constructs were made by fusing the mercury inducible promoter, p(mer), and its regulatory gene, merr, from transposon tn21 with reporter genes luxcdabe, laczya, or gfp. in escherichia coli these biosensor constructs responded to low levels of mercury by producing light, beta-galactosidase or green fluorescent protein, respectively. since the responses were quantitative, the constructs were used to quantify bioavailable mercury in different environments. the c ...	2000	11094290
enrichment and molecular characterization of a bacterial culture that degrades methoxy-methyl urea herbicides and their aniline derivatives.	soil treated with linuron for more than 10 years showed high biodegradation activity towards methoxy-methyl urea herbicides. untreated control soil samples taken from the same location did not express any linuron degradation activity, even after 40 days of incubation. hence, the occurrence in the field of a microbiota having the capacity to degrade a specific herbicide was related to the long-term treatment of the soil. the enrichment culture isolated from treated soil showed specific degradatio ...	2000	11097876
cofactor regeneration by a soluble pyridine nucleotide transhydrogenase for biological production of hydromorphone.	we have applied the soluble pyridine nucleotide transhydrogenase of pseudomonas fluorescens to a cell-free system for the regeneration of the nicotinamide cofactors nad and nadp in the biological production of the important semisynthetic opiate drug hydromorphone. the original recombinant whole-cell system suffered from cofactor depletion resulting from the action of an nadp(+)-dependent morphine dehydrogenase and an nadh-dependent morphinone reductase. by applying a soluble pyridine nucleotide ...	2000	11097884
zoospore homing and infection events: effects of the biocontrol bacterium burkholderia cepacia ammdr1 on two oomycete pathogens of pea (pisum sativum l.).	burkholderia cepacia ammdr1 is a biocontrol agent that protects pea and sweet corn seeds from pythium damping-off in field experiments. the goal of this work was to understand the effect of b. cepacia ammdr1 on pythium aphanidermatum and aphanomyces euteiches zoospore homing events and on infection of pea seeds or roots. in vitro, b. cepacia ammdr1 caused zoospore lysis, prevented cyst germination, and inhibited germ tube growth of both oomycetes. b. cepacia ammdr1 also reduced the attractivenes ...	2000	11097889
control of expression of divergent pseudomonas putida put promoters for proline catabolism.	pseudomonas putida kt2440 uses proline as the sole c and n source. utilization of this amino acid involves its uptake, which is mediated by the putp protein, and its conversion into glutamate, mediated by the puta protein. sequence analysis revealed that the puta and putp genes are transcribed divergently. expression from the putp and puta genes was analyzed at the mrna level in different host backgrounds in the absence and presence of proline. expression from the put promoters was induced by pr ...	2000	11097893
relationship between nitrite reduction and active phosphate uptake in the phosphate-accumulating denitrifier pseudomonas sp. strain jr 12.	phosphate uptake by the phosphate-accumulating denitrifier pseudomonas sp. jr12 was examined with different combinations of electron and carbon donors and electron acceptors. phosphate uptake in acetate-supplemented cells took place with either oxygen or nitrate but did not take place when nitrite served as the final electron acceptor. furthermore, nitrite reduction rates by this denitrifier were shown to be significantly reduced in the presence of phosphate. phosphate uptake assays in the prese ...	2000	11097896
composition of soil microbial communities enriched on a mixture of aromatic hydrocarbons.	soil contaminated with c5+, which contained benzene (45%, wt/wt), dicyclopentadiene (dcpd) plus cyclopentadiene (together 20%), toluene (6%), styrene (3%), xylenes (2%), naphthalene (2%), and smaller quantities of other compounds, served as the source for isolation of 55 genomically distinct bacteria (standards). use of benzene as a substrate by these bacteria was most widespread (31 of 44 standards tested), followed by toluene (23 of 44), xylenes (14 of 44), styrene (10 of 44), and naphthalene ...	2000	11097903
fatty acid competition as a mechanism by which enterobacter cloacae suppresses pythium ultimum sporangium germination and damping-off.	interactions between plant-associated microorganisms play important roles in suppressing plant diseases and enhancing plant growth and development. while competition between plant-associated bacteria and plant pathogens has long been thought to be an important means of suppressing plant diseases microbiologically, unequivocal evidence supporting such a mechanism has been lacking. we present evidence here that competition for plant-derived unsaturated long-chain fatty acids between the biological ...	2000	11097912
uptake and active efflux of polycyclic aromatic hydrocarbons by pseudomonas fluorescens lp6a.	the mechanism of transport of polycyclic aromatic hydrocarbons (pahs) by pseudomonas fluorescens lp6a, a pah-degrading bacterium, was studied by inhibiting membrane transport and measuring the resulting change in cellular uptake. three cultures were used: wild-type lp6a which carried a plasmid for pah degradation, a transposon mutant lacking the first enzyme in the pathway for pah degradation, and a cured strain without the plasmid. washed cells were mixed with aqueous solutions of radiolabelled ...	2000	11097918
diversity of l-methionine catabolism pathways in cheese-ripening bacteria.	enzymatic activities that could be involved in methanethiol generation in five cheese-ripening bacteria were assayed, and the major sulfur compounds produced were identified. l-methionine and alpha-keto-gamma-methyl-thio-butyric acid demethiolating activities were detected in whole cells and cell extracts (cfes) of all the bacteria tested. no l-methionine deaminase activity could be detected in any of the ripening bacteria and l-methionine aminotransferase was detected in cfes of brevibacterium ...	2000	11097940
bacterial toxin-antitoxin gene system as containment control in yeast cells.	the potential of a bacterial toxin-antitoxin gene system for use in containment control in eukaryotes was explored. the escherichia coli rele and relb genes were expressed in the yeast saccharomyces cerevisiae. expression of the rele gene was highly toxic to yeast cells. however, expression of the relb gene counteracted the effect of rele to some extent, suggesting that toxin-antitoxin interaction also occurs in s. cerevisiae. thus, bacterial toxin-antitoxin gene systems also have potential appl ...	2000	11097943
isolation and characterisation of ethoprophos-degrading bacteria.	an enrichment culture technique was used to isolate bacteria responsible for the enhanced biodegradation of ethoprophos in a soil from northern greece. restriction fragment length polymorphism patterns of the 16s rrna gene, partial 16s rrna sequence analysis, and sodium dodecylsulfate-polyacrylamide gel electrophoresis total protein profile analysis were used to characterise the isolated bacteria. two of the three ethoprophos-degrading cultures were pure and both isolates were classified as stra ...	2000	11098072
a bioluminescent derivative of pseudomonas putida kt2440 for deliberate release into the environment.	recombinant derivatives of pseudomonas putida strain kt2440 are of potential interest as microbial inoculants to be deliberately released for agricultural applications. to facilitate tracking of this strain and its derivatives after introduction into the environment, a mini-tn5-'luxab transposon was introduced into the chromosome of p. putida kt2440, yielding strain p. putida s1b1. sequencing of the dna region located upstream of the 'luxab genes and similarity search with the p. putida kt2440 g ...	2000	11102686
microbial biofilms: from ecology to molecular genetics.	biofilms are complex communities of microorganisms attached to surfaces or associated with interfaces. despite the focus of modern microbiology research on pure culture, planktonic (free-swimming) bacteria, it is now widely recognized that most bacteria found in natural, clinical, and industrial settings persist in association with surfaces. furthermore, these microbial communities are often composed of multiple species that interact with each other and their environment. the determination of bi ...	2000	11104821
pseudo-outbreak of pseudomonas putida in a hospital outpatient clinic originating from a contaminated commercial anti-fog solution--vancouver, british columbia.		2000	11107658
mutational analysis of the oprm outer membrane component of the mexa-mexb-oprm multidrug efflux system of pseudomonas aeruginosa.	oprm is the outer membrane component of the mexa-mexb-oprm efflux system of pseudomonas aeruginosa. multiple-sequence alignment of this protein and its homologues identified several regions of high sequence conservation that were targeted for site-directed mutagenesis. of several deletions which were stably expressed, two, spanning residues g199 to a209 and a278 to n286 of the mature protein, were unable to restore antibiotic resistance in oprm-deficient strains of p. aeruginosa. still, mutation ...	2001	11114896
characterization and evolution of anthranilate 1,2-dioxygenase from acinetobacter sp. strain adp1.	the two-component anthranilate 1,2-dioxygenase of the bacterium acinetobacter sp. strain adp1 was expressed in escherichia coli and purified to homogeneity. this enzyme converts anthranilate (2-aminobenzoate) to catechol with insertion of both atoms of o(2) and consumption of one nadh. the terminal oxygenase component formed an alpha(3)beta(3) hexamer of 54- and 19-kda subunits. biochemical analyses demonstrated one rieske-type [2fe-2s] center and one mononuclear nonheme iron center in each larg ...	2001	11114907
control of the ferric citrate transport system of escherichia coli: mutations in region 2.1 of the feci extracytoplasmic-function sigma factor suppress mutations in the fecr transmembrane regulatory protein.	transcription of the ferric citrate transport genes is initiated by binding of ferric citrate to the feca protein in the outer membrane of escherichia coli k-12. bound ferric citrate does not have to be transported but initiates a signal that is transmitted by feca across the outer membrane and by fecr across the cytoplasmic membrane into the cytoplasm, where the feci extracytoplasmic-function (ecf) sigma factor becomes active. in this study, we isolated transcription initiation-negative missens ...	2001	11114913
transcriptional organization and dynamic expression of the hbpcad genes, which encode the first three enzymes for 2-hydroxybiphenyl degradation in pseudomonas azelaica hbp1.	pseudomonas azelaica hbp1 degrades the toxic substance 2-hydroxybiphenyl (2-hbp) by means of three enzymes that are encoded by structural genes hbpc, hbpa, and hbpd. these three genes form a small noncontiguous cluster. their expression is activated by the product of regulatory gene hbpr, which is located directly upstream of the hbpcad genes. the hbpr protein is a transcription activator and belongs to the so-called xylr/dmpr subclass within the ntrc family of transcriptional activators. transc ...	2001	11114926
methionine-to-cysteine recycling in klebsiella aerogenes.	in the enteric bacteria escherichia coli and salmonella enterica, sulfate is reduced to sulfide and assimilated into the amino acid cysteine; in turn, cysteine provides the sulfur atom for other sulfur-bearing molecules in the cell, including methionine. these organisms cannot use methionine as a sole source of sulfur. here we report that this constraint is not shared by many other enteric bacteria, which can use either cysteine or methionine as the sole source of sulfur. the enteric bacterium k ...	2001	11114934
arecba is an operon in acinetobacter sp. strain adp1 and is controlled by arer, a sigma(54)-dependent regulator.	the arecba genes in acinetobacter sp. strain adp1, determining growth on benzyl alkanoates, are shown to be transcribed as a single operon and regulated by arer, which encodes a regulatory protein of the ntrc/xylr family. assays of the are enzymes and of two insertions of lacz as a reporter gene have shown that the operon is induced by benzyl acetate, benzyl alcohol, and benzaldehyde, as well as 2- and 4-hydroxybenzyl acetates and benzyl propionate and butyrate. two adjacent sites of transcripti ...	2001	11114944
espc pathogenicity island of enteropathogenic escherichia coli encodes an enterotoxin.	at least five proteins are secreted extracellularly by enteropathogenic escherichia coli (epec), a leading cause of infant diarrhea in developing countries. however only one, espc, is known to be secreted independently of the type iii secretion apparatus encoded by genes located within the 35.6-kb locus of enterocyte effacement pathogenicity island. espc is a member of the autotransporter family of proteins, and the secreted portion of the molecule is 110 kda. here we determine that the espc gen ...	2001	11119520
genetic diversity of pseudomonas aeruginosa strains isolated from ventilated patients with nosocomial pneumonia, cancer patients with bacteremia, and environmental water.	random amplified polymorphic dna typing was used to study the genetic diversity of pseudomonas aeruginosa strains from (i) ventilated patients with nosocomial pneumonia who were hospitalized in intensive care units, (ii) cases of bacteremia in cancer patients with severe neutropenia, and (iii) rivers and swimming pools. genetic diversity was determined by three phylogenetic methods and by statistical analysis of population genetics. the population studied undergoes epidemic clonality with a high ...	2001	11119558
directed evolution of toluene dioxygenase from pseudomonas putida for improved selectivity toward cis-indandiol during indene bioconversion.	toluene dioxygenase (tdo) from pseudomonas putida f1 converts indene to a mixture of cis-indandiol (racemic), 1-indenol, and 1-indanone. the desired product, cis-(1s,2r)-indandiol, is a potential key intermediate in the chemical synthesis of indinavir sulfate (crixivan), merck's hiv-1 protease inhibitor for the treatment of aids. to reduce the undesirable byproducts 1-indenol and 1-indanone formed during indene bioconversion, the recombinant tdo expressed in escherichia coli was evolved by direc ...	2000	11120645
use of substrate responsive-direct viable counts to visualize naphthalene degrading bacteria in a coal tar-contaminated groundwater microbial community.	a microscopy-based method was developed to distinguish naphthalene-degrading bacteria within the microbial community of a coal tar-contaminated groundwater system. pure cultures of pseudomonas putida ncib 9816-4 were used to develop the substrate responsive-direct viable count (sr-dvc) method. cells were concentrated on membrane filters, placed on agar plates of stanier's minimal basal salts media containing antibiotics (nalidixic acid, piromidic acid, pipemidic acid, and cephalexin), and expose ...	2000	11121606
tmrdb (tmrna database).	the tmrna database (tmrdb) is maintained at the university of texas health science center at tyler, texas, and accessible on the world wide web at the url http://psyche.uthct.edu/dbs/tmrdb/tmrdb.++ +html. mirror sites are located at auburn university, auburn, alabama (http://www.ag.auburn.edu/mirror/tmrdb/) and the institute of biological sciences, aarhus, denmark (http://www.bioinf.au. dk/tmrdb/). the tmrdb provides information and citation links about tmrna, a molecule that combines functions ...	2001	11125081
role of yersinia intermedia and pseudomonas putida in the development of a fruity off-flavour in pasteurized milk.	analysis by gas chromatography-mass spectrometry of pasteurized milk with a fruity (pineapple like) off odour and a sour, rancid and soapy taste indicated the presence of concentrations at microg/ml levels of ethyl butanoate, ethyl hexanoate, ethyl octanoate, ethyl decanoate, octanoic acid, decanoic acid and dodecanoic acid. the off-odour and taste were attributed to the presence of these compounds in the milk. microbiological examination confirmed that the milk was also contaminated with a seri ...	2000	11131069
genetic transformation and biotechnological application of the yeast arxula adeninivorans.	the relatively unknown, non-pathogenic, dimorphic, haploid, ascomycetous yeast arxula adeninivorans exhibits some unusual properties which are of biotechnological interest. the yeast is able to assimilate and ferment many compounds as sole source of carbon and/or nitrogen, it utilises n-alkanes and degrades starch efficiently. a. adeninivorans features such as thermo- and haloresistance as well as the yeast's uncommon growth and secretion behaviour should be especially emphasised. in media conta ...	2000	11131385
homologous functional expression of cryptic phag from pseudomonas oleovorans establishes the transacylase-mediated polyhydroxyalkanoate biosynthetic pathway.	various pseudomonads are capable of the synthesis of polyhydroxyalkanoate (pha), composed of medium chain length (mcl) 3-hydroxy fatty acids (c6-c14), when grown on simple carbon sources such as, for example, gluconate or acetate. in pseudomonas putida, the fatty acid de novo synthesis and pha synthesis are linked by the transacylase phag. southern hybridization experiments with digoxigenin-labeled phag(pp) from p. putida and genomic dna from various pseudomonads indicate that phag homologues ar ...	2000	11131392
the solvent efflux system of pseudomonas putida s12 is not involved in antibiotic resistance.	the active efflux system contributing to the solvent tolerance of pseudomonas putida s12 was characterized physiologically. the mutant p. putida jk1, which lacks the active efflux system, was compared with the wild-type organism. none of 20 known substrates of common multi-drug-resistant pumps had a stronger growth-inhibiting effect on the mutant than on the wild type. the amount of [14c]toluene accumulating in p. putida s12 increased in the presence of the solvent xylene and in the presence of ...	2000	11131400
enriching vermicompost by nitrogen fixing and phosphate solubilizing bacteria.	the effect of inoculation of vermicompost with nitrogen-fixing azotobacter chroococcum strains, azospirillum lipoferum and the phosphate solubilizing pseudomonas striata on n and p contents of the vermicompost was assessed. inoculation of n2 fixing bacteria into vermicompost increased contents of n and p. enriching vermicompost with rock phosphate improved significantly the available p when inoculated with p. striata. during the incubation period, the inoculated bacterial strains proliferated ra ...	2001	11131802
occurrence of tn4371-related mobile elements and sequences in (chloro)biphenyl-degrading bacteria.	tn4371, a 55-kb transposable element involved in the degradation and biphenyl or 4-chlorobiphenyl identified in ralstonia eutropha a5, displays a modular structure including a phage-like integrase gene (int), a pseudomonas-like (chloro)biphenyl catabolic gene cluster (bph), and rp4- and ti-plasmid-like transfer genes (trb) (c. merlin, d. springael, and a. toussaint, plasmid 41:40-54, 1999). southern blot hybridization was used to examine the presence of different regions of tn4371 in a collectio ...	2001	11133426
direct cloning from enrichment cultures, a reliable strategy for isolation of complete operons and genes from microbial consortia.	enrichment cultures of microbial consortia enable the diverse metabolic and catabolic activities of these populations to be studied on a molecular level and to be explored as potential sources for biotechnology processes. we have used a combined approach of enrichment culture and direct cloning to construct cosmid libraries with large (>30-kb) inserts from microbial consortia. enrichment cultures were inoculated with samples from five environments, and high amounts of avidin were added to the cu ...	2001	11133432
rapid detection, identification, and enumeration of escherichia coli cells in municipal water by chemiluminescent in situ hybridization.	a new chemiluminescent in situ hybridization (cish) method provides simultaneous detection, identification, and enumeration of culturable escherichia coli cells in 100 ml of municipal water within one working day. following filtration and 5 h of growth on tryptic soy agar at 35 degrees c, individual microcolonies of e. coli were detected directly on a 47-mm-diameter membrane filter using soybean peroxidase-labeled peptide nucleic acid (pna) probes targeting a species-specific sequence in e. coli ...	2001	11133438
role of the dmpr-mediated regulatory circuit in bacterial biodegradation properties in methylphenol-amended soils.	pathway substrates and some structural analogues directly activate the regulatory protein dmpr to promote transcription of the dmp operon genes encoding the (methyl)phenol degradative pathway of pseudomonas sp. strain cf600. while a wide range of phenols can activate dmpr, the location and nature of substituents on the basic phenolic ring can limit the level of activation and thus utilization of some compounds as assessed by growth on plates. here we address the role of the aromatic effector res ...	2001	11133441
rapid, quantitative pcr monitoring of growth of clostridium botulinum type e in modified-atmosphere-packaged fish.	a rapid, quantitative pcr assay (taqman assay) which quantifies clostridium botulinum type e by amplifying a 280-bp sequence from the botulinum neurotoxin type e (bont/e) gene is described. with this method, which uses the hydrolysis of an internal fluoregenic probe and monitors in real time the increase in the intensity of fluorescence during pcr by using the abi prism 7700 sequence detection system, it was possible to perform accurate and reproducible quantification of the c. botulinum type e ...	2001	11133447
polyhydroxyalkanoate degradation is associated with nucleotide accumulation and enhances stress resistance and survival of pseudomonas oleovorans in natural water microcosms.	pseudomonas oleovorans gpo1 and its polyhydroxyalkanoic acid (pha) depolymerization-minus mutant, gpo500 phaz, residing in natural water microcosms, were utilized to asses the effect of pha availability on survival and resistance to stress agents. the wild-type strain showed increased survival compared to the pha depolymerase-minus strain. the appearance of a round cellular shape, characteristic of bacteria growing under starvation conditions, was delayed in the wild type in comparison to the mu ...	2001	11133449
pantoea agglomerans strain eh318 produces two antibiotics that inhibit erwinia amylovora in vitro.	pantoea agglomerans (synonym: erwinia herbicola) strain eh318 produces through antibiosis a complex zone of inhibited growth in an overlay seeded with erwinia amylovora, the causal agent of fire blight. this zone is caused by two antibiotics, named pantocin a and b. using a genomic library of eh318, two cosmids, pcpp702 and pcpp704, were identified that conferred on escherichia coli the ability to inhibit growth of e. amylovora. the two cosmids conferred different antibiotic activities on e. col ...	2001	11133457
chloromethane utilization gene cluster from hyphomicrobium chloromethanicum strain cm2(t) and development of functional gene probes to detect halomethane-degrading bacteria.	hyphomicrobium chloromethanicum cm2(t), an aerobic methylotrophic member of the alpha subclass of the class proteobacteria, can grow with chloromethane as the sole carbon and energy source. h. chloromethanicum possesses an inducible enzyme system for utilization of chloromethane, in which two polypeptides (67-kda cmua and 35-kda cmub) are expressed. previously, four genes, cmua, cmub, cmuc, and puru, were shown to be essential for growth of methylobacterium chloromethanicum on chloromethane. the ...	2001	11133460
genetic and molecular organization of the alkylbenzene catabolism operon in the psychrotrophic strain pseudomonas putida 01g3.	the 11-kb sequence encompassing the alkylbenzene upper pathway in pseudomonas putida 01g3, a psychrotrophic strain able to degrade alkylbenzenes at low temperatures, was characterized. together with a potential regulator (ebdr), six putative enzymes (ebdaaabacadbc) were identified, and they exhibited highly significant similarities with enzymes implicated in the equivalent pathway in p. putida re204. ebd genes appeared to be preferentially induced by ethylbenzene. multiple-alignment data and gro ...	2001	11133479
fimw is a negative regulator affecting type 1 fimbrial expression in salmonella enterica serovar typhimurium.	type 1 fimbriae are proteinaceous surface appendages that carry adhesins specific for mannosylated glycoproteins. these fimbriae are found on most members of the family enterobacteriaceae and are known to facilitate binding to a variety of eukaryotic cells, including those found on the mucosal surfaces of the alimentary tract. we have shown that the regulation of type 1 fimbrial expression in salmonella enterica serovar typhimurium is controlled, in part, by the products of four genes found with ...	2001	11133935
the gdhb gene of pseudomonas aeruginosa encodes an arginine-inducible nad(+)-dependent glutamate dehydrogenase which is subject to allosteric regulation.	the nad(+)-dependent glutamate dehydrogenase (nad-gdh) from pseudomonas aeruginosa pao1 was purified, and its amino-terminal amino acid sequence was determined. this sequence information was used in identifying and cloning the encoding gdhb gene and its flanking regions. the molecular mass predicted from the derived sequence for the encoded nad-gdh was 182.6 kda, in close agreement with that determined from sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the purified enzyme (180 kda ...	2001	11133942
nag genes of ralstonia (formerly pseudomonas) sp. strain u2 encoding enzymes for gentisate catabolism.	ralstonia sp. strain u2 metabolizes naphthalene via gentisate to central metabolites. we have cloned and sequenced a 21.6-kb region spanning the nag genes. upstream of the pathway genes are nagy, homologous to chemotaxis proteins, and nagr, a regulatory gene of the lysr family. divergently transcribed from nagr are the genes for conversion of naphthalene to gentisate (nagaaghabacadbfcqed) (s. l. fuenmayor, m. wild, a. l. boyes, and p. a. williams, j. bacteriol. 180:2522-2530, 1998), which except ...	2001	11133965
initiation of anaerobic degradation of p-cresol by formation of 4-hydroxybenzylsuccinate in desulfobacterium cetonicum.	the anaerobic bacterium desulfobacterium cetonicum oxidized p-cresol completely to co(2) with sulfate as the electron acceptor. during growth, 4-hydroxybenzylsuccinate accumulated in the medium. this finding indicated that the methyl group of p-cresol is activated by addition to fumarate, analogous to anaerobic toluene, m-xylene, and m-cresol degradation. in cell extracts, the formation of 4-hydroxybenzylsuccinate from p-cresol and fumarate was detected at an initial rate of 0.57 nmol min(-1) (m ...	2001	11133971
genetic and physiological characterization of ohr, encoding a protein involved in organic hydroperoxide resistance in pseudomonas aeruginosa.	the ohr (organic hydroperoxide resistance) gene product of pseudomonas aeruginosa was essential for optimal resistance to organic hydroperoxides (ohps) but not to hydrogen peroxide or paraquat. a deltaohr mutant was hypersusceptible to ohps in disk inhibition assays and showed enhanced killing by ohps in liquid culture. the ohr gene product was demonstrated to contribute to the decomposition of ohps. transcription of ohr was induced up to 15-fold upon exposure to ohps, and this induction was ind ...	2001	11133975
copper-modulated gene expression and senescence in the filamentous fungus podospora anserina.	we have previously shown that the control of cellular copper homeostasis by the copper-modulated transcription factor grisea has an important impact on the phenotype and lifespan of podospora anserina. here we demonstrate that copper depletion leads to the induction of an alternative respiratory pathway and to an increase in lifespan. this response compensates mitochondrial dysfunctions via the expression of paaox, a nuclear gene coding for an alternative oxidase. it resembles the retrograde res ...	2001	11134328
analysis of the type iv fimbrial-subunit gene fima of xanthomonas hyacinthi: application in pcr-mediated detection of yellow disease in hyacinths.	a sensitive and specific detection method was developed for xanthomonas hyacinthi; this method was based on amplification of a subsequence of the type iv fimbrial-subunit gene fima from strain s148. the fima gene was amplified by pcr with degenerate dna primers designed by using the n-terminal and c-terminal amino acid sequences of trypsin fragments of fima. the nucleotide sequence of fima was determined and compared with the nucleotide sequences coding for the fimbrial subunits in other type iv ...	2001	11157222
iron-binding compounds from agrobacterium spp.: biological control strain agrobacterium rhizogenes k84 produces a hydroxamate siderophore.	iron-binding compounds were produced in various amounts in response to iron starvation by a collection of agrobacterium strains belonging to the species a. tumefaciens, a. rhizogenes, and a. vitis. the crown gall biocontrol agent a. rhizogenes strain k84 produced a hydroxamate iron chelator in large amounts. production of this compound, and also of a previously described antibiotic-like substance called als84, occurred only in cultures of strain k84 grown in iron-deficient medium. similarly, sen ...	2001	11157228
cloning, sequencing, and characterization of a gene cluster involved in edta degradation from the bacterium bnc1.	edta is a chelating agent, widely used in many industries. because of its ability to mobilize heavy metals and radionuclides, it can be an environmental pollutant. the edta monooxygenases that initiate edta degradation have been purified and characterized in bacterial strains bnc1 and dsm 9103. however, the genes encoding the enzymes have not been reported. the edta monooxygenase gene was cloned by probing a genomic library of strain bnc1 with a probe generated from the n-terminal amino acid seq ...	2001	11157232
purification, stability, and mineralization of 3-hydroxy-2- formylbenzothiophene, a metabolite of dibenzothiophene.	3-hydroxy-2-formylbenzothiophene (hfbt) is a metabolite found in many bacterial cultures that degrade dibenzothiophene (dbt) via the kodama pathway. the fate of hfbt in cultures and in the environment is unknown. in this study, hfbt was produced by a dbt-degrading bacterium and purified by sublimation. when stored in organic solvent or as a crystal, the hfbt slowly decomposed, yielding colored products. two of these were identified as thioindigo and cis-thioindigo. the supernatant of the dbt-deg ...	2001	11157249
the adna transcriptional factor affects persistence and spread of pseudomonas fluorescens under natural field conditions.	a soil plot was inoculated with a mixture of pseudomonas fluorescens pf0-2, the wild type, and pf0-5a, a tn5 insertion mutant in adna, at 7.84 log cfu/g of soil. over a period of 231 days, culturable populations of both strains were measured at selected times below and away from the point of inoculation. pf0-5a did not spread as fast and attained significantly lower populations than pf0-2. at sample depths below the inoculation site, the adna mutant showed a significant decrease in cfu/g of soil ...	2001	11157254