Publications

cloning and characterization of a novel cis-naphthalene dihydrodiol dehydrogenase gene (narb) from rhodococcus sp. ncimb12038.	rhodococcus sp. ncimb112038 can utilize naphthalene as its sole carbon and energy source. the gene encoding cis-naphthalene dihydrodiol dehydrogenase (narb) of this strain has been cloned and sequenced. expression of ncimb12038 cis-naphthalene dihydrodiol dehydrogenase was demonstrated in escherichia coli cells. narb encodes a putative protein of 271 amino acids and shares 39% amino acid identity with the cis-naphthalene dihydrodiol dehydrogenase from pseudomonas putida g7. comparison of narb wi ...	2000	10620687
identification of nah-1 genes of the pseudomonas putida naphthalene-degrading npl-41 plasmid operon.	pseudomonas putida bs202 degrades naphthalene via a plasmid-encoded catabolic pathway. the nucleotide sequence of the nahc gene encoding one of this pathway enzymes, 1,2-dihydroxynaphthalene dioxygenase, has been determined. analysis of nucleotide sequence of its flanking regions identified partially the nahf and putative nahq genes. comparison of these three genes with corresponding ones in the nah7 plasmid and dox operon showed a high degree of homology.	1999	10621937
bacteria are not what they eat: that is why they are so diverse.		2000	10629168
biochemical and molecular characterization of phenylacetate-coenzyme a ligase, an enzyme catalyzing the first step in aerobic metabolism of phenylacetic acid in azoarcus evansii.	phenylacetate-coenzyme a ligase (pa-coa ligase; amp forming, ec 6.2. 1.30), the enzyme catalyzing the first step in the aerobic degradation of phenylacetate (pa) in azoarcus evansii, has been purified and characterized. the gene (paak) coding for this enzyme was cloned and sequenced. the enzyme catalyzes the reaction of pa with coa and mgatp to yield phenylacetyl-coa (pacoa) plus amp plus ppi. the enzyme was specifically induced after aerobic growth in a chemically defined medium containing pa o ...	2000	10629172
the pspa protein of escherichia coli is a negative regulator of sigma(54)-dependent transcription.	in eubacteria, expression of genes transcribed by an rna polymerase holoenzyme containing the alternate sigma factor sigma(54) is positively regulated by proteins belonging to the family of enhancer-binding proteins (ebps). these proteins bind to upstream activation sequences and are required for the initiation of transcription at the sigma(54)-dependent promoters. they are typically inactive until modified in their n-terminal regulatory domain either by specific phosphorylation or by the bindin ...	2000	10629175
early cephamycin biosynthetic genes are expressed from a polycistronic transcript in streptomyces clavuligerus.	a polycistronic transcript that is initiated at the lat promoter has been implicated in the expression of the genes involved in early steps of cephamycin c biosynthesis in streptomyces clavuligerus. pcbc is also expressed as a monocistronic transcript from its own promoter. however, an alternative interpretation involving expression via three separate yet interdependent transcripts has also been proposed. to distinguish between these possibilities, mutants lacking the lat promoter and containing ...	2000	10629179
flen, a gene that regulates flagellar number in pseudomonas aeruginosa.	the single polar flagellum of pseudomonas aeruginosa plays an important role in the pathogenesis of infection by this organism. however, regulation of the assembly of this organelle has not been delineated. in analyzing the sequence available at the pseudomonas genome database, an open reading frame (orf), flanked by flagellar genes flhf and flia, that coded for a protein (280 amino acids) with an atp-binding motif at its n terminus was found. the orf was inactivated by inserting a gentamicin ca ...	2000	10629180
hbpr, a new member of the xylr/dmpr subclass within the ntrc family of bacterial transcriptional activators, regulates expression of 2-hydroxybiphenyl metabolism in pseudomonas azelaica hbp1.	the regulation of 2-hydroxybiphenyl and 2,2'-dihydroxybiphenyl degradation in pseudomonas azelaica is mediated by the regulatory gene, hbpr. the hbpr gene encodes a 63-kda protein belonging to the ntrc family of prokaryotic transcriptional activators and having the highest homology to members of the xylr/dmpr subclass. disruption of the hbpr gene in p. azelaica and complementation in trans showed that the hbpr protein was the key regulator for 2-hydroxybiphenyl metabolism. induction experiments ...	2000	10629187
the global carbon metabolism regulator crc is a component of a signal transduction pathway required for biofilm development by pseudomonas aeruginosa.	the transition from a planktonic (free-swimming) existence to growth attached to a surface in a biofilm occurs in response to environmental factors, including the availability of nutrients. we show that the catabolite repression control (crc) protein, which plays a role in the regulation of carbon metabolism, is necessary for biofilm formation in pseudomonas aeruginosa. using phase-contrast microscopy, we found that a crc mutant only makes a dispersed monolayer of cells on a plastic surface but ...	2000	10629189
identification and characterization of the nitrobenzene catabolic plasmids pnb1 and pnb2 in pseudomonas putida hs12.	pseudomonas putida hs12, which is able to grow on nitrobenzene, was found to carry two plasmids, pnb1 and pnb2. the activity assay experiments of wild-type hs12(pnb1 and pnb2), a spontaneous mutant hs121(pnb2), and a cured derivative hs124(pnb1) demonstrated that the catabolic genes coding for the nitrobenzene-degrading enzymes, designated nbz, are located on two plasmids, pnb1 and pnb2. the genes nbza, nbzc, nbzd, and nbze, encoding nitrobenzene nitroreductase, 2-aminophenol 1,6-dioxygenase, 2- ...	2000	10633088
transcription from fusion promoters generated during transposition of transposon tn4652 is positively affected by integration host factor in pseudomonas putida.	we have previously shown that both ends of the tn3 family transposon tn4652 contain integration host factor (ihf) binding sites and that ihf positively regulates expression of the tn4652 transposase gene tnpa in pseudomonas putida (r. hõrak, and m. kivisaar, j. bacteriol. 180:2822-2829, 1998). tn4652 can activate silent genes by creating fusion promoters during the transposition. the promoters are created as fusions between the -35 hexamer provided by the terminal inverted repeats of tn4652 and ...	2000	10633090
functional analysis of the small component of the 4-hydroxyphenylacetate 3-monooxygenase of escherichia coli w: a prototype of a new flavin:nad(p)h reductase subfamily.	escherichia coli w uses the aromatic compound 4-hydroxyphenylacetate (4-hpa) as a sole source of carbon and energy for growth. the monooxygenase which converts 4-hpa into 3,4-dihydroxyphenylacetate, the first intermediate of the pathway, consists of two components, hpab (58.7 kda) and hpac (18.6 kda), encoded by the hpab and hpac genes, respectively, that form a single transcription unit. overproduction of the small hpac component in e. coli k-12 cells has facilitated the purification of the pro ...	2000	10633095
purification and characterization of an iron superoxide dismutase and a catalase from the sulfate-reducing bacterium desulfovibrio gigas.	the iron-containing superoxide dismutase (fesod; ec 1.15.1.1) and catalase (ec 1.11.1.6) enzymes constitutively expressed by the strictly anaerobic bacterium desulfovibrio gigas were purified and characterized. the fesod, isolated as a homodimer of 22-kda subunits, has a specific activity of 1,900 u/mg and exhibits an electron paramagnetic resonance (epr) spectrum characteristic of high-spin ferric iron in a rhombically distorted ligand field. like other fesods from different organisms, d. gigas ...	2000	10633116
investigation of an outbreak of pseudomonas putida using antimicrobial susceptibility patterns, pulsed-field gel electrophoresis of genomic dna and restriction fragment length polymorphism of pcr-amplified rrna operons.	seventeen pseudomonas putida isolates were investigated which were collected from the urine specimens of 14 patients and one reflectrometer by comparing antimicrobial susceptibility patterns, pulsed-field gel electrophoresis (pfge) of genomic dna, and restriction fragment length polymorphism (rflp) of pcr-amplified rrna operons. three susceptibility patterns were defined by testing 22 antimicrobial agents, with 14 isolates resistant to all agents. pfge of xbai-genomic dna fragments divided the 1 ...	1999	10637717
multiple antibiotic resistance in stenotrophomonas maltophilia: involvement of a multidrug efflux system.	clinical strains of stenotrophomonas maltophilia are often highly resistant to multiple antibiotics, although the mechanisms of resistance are generally poorly understood. multidrug resistant (mdr) strains were readily selected by plating a sensitive reference strain of the organism individually onto a variety of antibiotics, including tetracycline, chloramphenicol, ciprofloxacin, and norfloxacin. tetracycline-selected mdr strains typically showed cross-resistance to erythromycin and fluoroquino ...	2000	10639352
mechanistic studies of morphine dehydrogenase and stabilization against covalent inactivation.	morphine dehydrogenase (mdh) of pseudomonas putida m10 catalyses the nadp(+)-dependent oxidation of morphine and codeine to morphinone and codeinone. this enzyme forms the basis of a sensitive detection and assay method for heroin metabolites and a biotransformation process for production of hydromorphone and hydrocodone. to improve these processes we have undertaken a thorough examination of the kinetic mechanism of mdh. sequence comparisons indicated that mdh belongs within the aldose reductas ...	2000	10642529
a set of genes encoding a second toluene efflux system in pseudomonas putida dot-t1e is linked to the tod genes for toluene metabolism.	sequence analysis in pseudomonas putida dot-t1e revealed a second toluene efflux system for toluene metabolism encoded by the ttgdef genes, which are adjacent to the tod genes. the ttgdef genes were expressed in response to the presence of aromatic hydrocarbons such as toluene and styrene in the culture medium. to characterize the contribution of the ttgdef system to toluene tolerance in p. putida, site-directed mutagenesis was used to knock out the gene in the wild-type dot-t1e strain and in a ...	2000	10648517
genetic evidence of distinct physiological regulation mechanisms in the sigma(54) pu promoter of pseudomonas putida.	the activity of the toluene-responsive sigma(54) pu promoter of the pww0 tol plasmid of pseudomonas putida is down-regulated in vivo during exponential growth in rich medium and also by the presence of glucose in the culture. although the pu promoter already performs poorly during log growth in minimal medium when amended with casamino acids, the addition of glucose further decreased by two- to threefold the accumulation of beta-galactosidase in a pu-lacz reporter p. putida strain. since pu was ...	2000	10648520
arginine catabolism in the cyanobacterium synechocystis sp. strain pcc 6803 involves the urea cycle and arginase pathway.	cells of the unicellular cyanobacterium synechocystis sp. strain pcc 6803 supplemented with micromolar concentrations of l-[(14)c]arginine took up, concentrated, and catabolized this amino acid. metabolism of l-[(14)c]arginine generated a set of labeled amino acids that included argininosuccinate, citrulline, glutamate, glutamine, ornithine, and proline. production of [(14)c]ornithine preceded that of [(14)c]citrulline, and the patterns of labeled amino acids were similar in cells incubated with ...	2000	10648527
functional domains of the tol plasmid transcription factor xyls.	the alkylbenzoate degradation genes of pseudomonas putida tol plasmid are positively regulated by xyls, an arac family protein, in a benzoate-dependent manner. in this study, we used deletion mutants and hybrid proteins to identify which parts of xyls are responsible for the dna binding, transcriptional activation, and benzoate inducibility. we found that a 112-residue c-terminal fragment of xyls binds specifically to the pm operator in vitro, protects this sequence from dnase i digestion identi ...	2000	10648539
crc is involved in catabolite repression control of the bkd operons of pseudomonas putida and pseudomonas aeruginosa.	crc (catabolite repression control) protein of pseudomonas aeruginosa has shown to be involved in carbon regulation of several pathways. in this study, the role of crc in catabolite repression control has been studied in pseudomonas putida. the bkd operons of p. putida and p. aeruginosa encode the inducible multienzyme complex branched-chain keto acid dehydrogenase, which is regulated in both species by catabolite repression. we report here that this effect is mediated in both species by crc. a ...	2000	10648542
catabolite repression control by crc in 2xyt medium is mediated by posttranscriptional regulation of bkdr expression in pseudomonas putida.	the effect of growth in 2xyt medium on catabolite repression control in pseudomonas putida has been investigated using the bkd operon, encoding branched-chain keto acid dehydrogenase. crc (catabolite repression control protein) was shown to be responsible for repression of bkd operon transcription in 2xyt. bkdr levels were elevated in a p. putida crc mutant, but bkdr transcript levels were the same in both wild type and crc mutant. this suggests that the mechanism of catabolite repression contro ...	2000	10648543
expression and stereochemical and isotope effect studies of active 4-oxalocrotonate decarboxylase.	4-oxalocrotonate decarboxylase (4-od) and vinylpyruvate hydratase (vph) from pseudomonas putida mt-2 form a complex that converts 2-oxo-3-hexenedioate to 2-oxo-4-hydroxypentanoate in the catechol meta fission pathway. to facilitate mechanistic and structural studies of the complex, the two enzymes have been coexpressed and the complex has been purified to homogeneity. in addition, glu-106, a potential catalytic residue in vph, has been changed to glutamine, and the resulting e106qvph mutant has ...	2000	10651637
asp-99 donates a hydrogen bond not to tyr-14 but to the steroid directly in the catalytic mechanism of delta 5-3-ketosteroid isomerase from pseudomonas putida biotype b.	delta 5-3-ketosteroid isomerase (ksi) catalyzes the allylic isomerization of delta 5-3-ketosteroids at a rate approaching the diffusion limit by an intramolecular transfer of a proton. despite the extensive studies on the catalytic mechanism, it still remains controversial whether the catalytic residue asp-99 donates a hydrogen bond to the steroid or to tyr-14. to clarify the role of asp-99 in the catalysis, two single mutants of d99e and d99l and three double mutants of y14f/d99e, y14f/d99n, an ...	2000	10653633
bacterial primary colonization and early succession on surfaces in marine waters as determined by amplified rrna gene restriction analysis and sequence analysis of 16s rrna genes.	the nearly universal colonization of surfaces in marine waters by bacteria and the formation of biofilms and biofouling communities have important implications for ecological function and industrial processes. however, the dynamics of surface attachment and colonization in situ, particularly during the early stages of biofilm establishment, are not well understood. experimental surfaces that differed in their degrees of hydrophilicity or hydrophobicity were incubated in a salt marsh estuary tida ...	2000	10653705
quinolobactin, a new siderophore of pseudomonas fluorescens atcc 17400, the production of which is repressed by the cognate pyoverdine.	transposon mutant strain 3g6 of pseudomonas fluorescens atcc 17400 which was deficient in pyoverdine production, was found to produce another iron-chelating molecule; this molecule was identified as 8-hydroxy-4-methoxy-quinaldic acid (designated quinolobactin). the pyoverdine-deficient mutant produced a supplementary 75-kda iron-repressed outer membrane protein (iromp) in addition to the 85-kda iromp present in the wild type. the mutant was also characterized by substantially increased uptake of ...	2000	10653708
characterization and role of the branched-chain aminotransferase (bcat) isolated from lactococcus lactis subsp. cremoris ncdo 763.	in lactococcus lactis, which is widely used as a starter in the cheese industry, the first step of aromatic and branched-chain amino acid degradation is a transamination which is catalyzed by two major aminotransferases. we have previously purified and characterized biochemically and genetically the aromatic aminotransferase, arat. in the present study, we purified and studied the second enzyme, the branched-chain aminotransferase, bcat. we cloned and sequenced the corresponding gene and used a ...	2000	10653720
development of catechol 2,3-dioxygenase-specific primers for monitoring bioremediation by competitive quantitative pcr.	benzene, toluene, xylenes, phenol, naphthalene, and biphenyl are among a group of compounds that have at least one reported pathway for biodegradation involving catechol 2,3-dioxygenase enzymes. thus, detection of the corresponding catechol 2,3-dioxygenase genes can serve as a basis for identifying and quantifying bacteria that have these catabolic abilities. primers that can successfully amplify a 238-bp catechol 2,3-dioxygenase gene fragment from eight different bacteria are described. the ide ...	2000	10653735
biocatalytic synthesis of vanillin.	the conversions of vanillic acid and o-benzylvanillic acid to vanillin were examined by using whole cells and enzyme preparations of nocardia sp. strain nrrl 5646. with growing cultures, vanillic acid was decarboxylated (69% yield) to guaiacol and reduced (11% yield) to vanillyl alcohol. in resting nocardia cells in buffer, 4-o-benzylvanillic acid was converted to the corresponding alcohol product without decarboxylation. purified nocardia carboxylic acid reductase, an atp and nadph-dependent en ...	2000	10653736
selective removal of nitrogen from quinoline and petroleum by pseudomonas ayucida igtn9m.	enrichment culture experiments employing soil and water samples obtained from petroleum-contaminated environments succeeded in the isolation of a pure culture possessing the ability to utilize quinoline as a sole nitrogen source but did not utilize quinoline as a carbon source. this culture was identified as pseudomonas ayucida based on a partial 16s rrna gene sequence, and the strain was given the designation igtn9m. examination of metabolites using thin-layer chromatography and gas chromatogra ...	2000	10653737
culture-dependent and culture-independent characterization of microbial assemblages associated with high-temperature petroleum reservoirs.	recent investigations of oil reservoirs in a variety of locales have indicated that these habitats may harbor active thermophilic prokaryotic assemblages. in this study, we used both molecular and culture-based methods to characterize prokaryotic consortia associated with high-temperature, sulfur-rich oil reservoirs in california. enrichment cultures designed for anaerobic thermophiles, both autotrophic and heterotrophic, were successful at temperatures ranging from 60 to 90 degrees c. heterotro ...	2000	10653739
a novel genetically engineered pathway for synthesis of poly(hydroxyalkanoic acids) in escherichia coli.	a new pathway to synthesize poly(hydroxyalkanoic acids) (pha) was constructed by simultaneously expressing butyrate kinase (buk) and phosphotransbutyrylase (ptb) genes of clostridium acetobutylicum and the two pha synthase genes (phae and phac) of thiocapsa pfennigii in escherichia coli. the four genes were cloned into the bamhi and ecori sites of pbr322, and the resulting hybrid plasmid, pbpp1, conferred activities of all three enzymes to e. coli jm109. cells of this recombinant strain accumula ...	2000	10653745
bacterial activity in the rhizosphere analyzed at the single-cell level by monitoring ribosome contents and synthesis rates.	the growth activity of pseudomonas putida cells colonizing the rhizosphere of barley seedlings was estimated at the single-cell level by monitoring ribosomal contents and synthesis rates. ribosomal synthesis was monitored by using a system comprising a fusion of the ribosomal escherichia coli rrnbp1 promoter to a gene encoding an unstable variant of the green fluorescent protein (gfp). gfp expression in a p. putida strain carrying this system inserted into the chromosome was strongly dependent o ...	2000	10653754
epidemiology and microbiology of surgical wound infections.	this study included 676 surgery patients with signs and symptoms indicative of wound infections, who presented over the course of 6 years. bacterial pathogens were isolated from 614 individuals. a single etiologic agent was identified in 271 patients, multiple agents were found in 343, and no agent was identified in 62. a high preponderance of aerobic bacteria was observed. among the common pathogens were staphylococcus aureus (191 patients, 28.2%), pseudomonas aeruginosa (170 patients, 25.2%), ...	2000	10655417
critical nucleotides in the interaction of catr with the pheba promoter: conservation of the catr-mediated regulation mechanisms between the pheba and catbca operons.	the promoter of the plasmid-borne pheba genes encoding enzymes for phenol degradation resembles the catbca promoter and is activated by catr, the regulator of the chromosomally encoded catechol-degradative catbca genes in pseudomonas putida. in this study, site-directed mutagenesis of the pheba promoter region was performed. the interrupted inverted repeat sequence of the catr recognition binding site (rbs) of the pheba promoter is highly homologous to that of the catbca promoter. however, the r ...	2000	10658664
autoinduction of 2,4-diacetylphloroglucinol biosynthesis in the biocontrol agent pseudomonas fluorescens cha0 and repression by the bacterial metabolites salicylate and pyoluteorin.	the antimicrobial metabolite 2,4-diacetylphloroglucinol (2,4-dapg) contributes to the capacity of pseudomonas fluorescens strain cha0 to control plant diseases caused by soilborne pathogens. a 2, 4-dapg-negative tn5 insertion mutant of strain cha0 was isolated, and the nucleotide sequence of the 4-kb genomic dna region adjacent to the tn5 insertion site was determined. four open reading frames were identified, two of which were homologous to phla, the first gene of the 2,4-dapg biosynthetic oper ...	2000	10671440
characterization and role of tbux in utilization of toluene by ralstonia pickettii pko1.	the tbu regulon of ralstonia pickettii pko1 encodes enzymes involved in the catabolism of toluene, benzene, and related alkylaromatic hydrocarbons. the first operon in this regulon contains genes that encode the tbu pathway's initial catabolic enzyme, toluene-3-monooxygenase, as well as tbut, the ntrc-like transcriptional activator for the entire regulon. it has been previously shown that the organization of tbut, which is located immediately downstream of tbua1ubva2c, and the associated promote ...	2000	10671442
identification of a chitin-binding protein secreted by pseudomonas aeruginosa.	one of the major proteins secreted by pseudomonas aeruginosa is a 43-kda protein, which is cleaved by elastase into smaller fragments, including a 30-kda and a 23-kda fragment. the n-terminal 23-kda fragment was previously suggested as corresponding to a staphylolytic protease and was designated lasd (s. park and d. r. galloway, mol. microbiol. 16:263-270, 1995). however, the sequence of the gene encoding this 43-kda protein revealed that the n-terminal half of the protein is homologous to the c ...	2000	10671445
substrate range and genetic analysis of acinetobacter vanillate demethylase.	an acinetobacter sp. genetic screen was used to probe structure-function relationships in vanillate demethylase, a two-component monooxygenase. mutants with null, leaky, and heat-sensitive phenotypes were isolated. missense mutations tended to be clustered in specific regions, most of which make known contributions to catalytic activity. the vanillate analogs m-anisate, m-toluate, and 4-hydroxy-3,5-dimethylbenzoate are substrates of the enzyme and weakly inhibit the metabolism of vanillate by wi ...	2000	10671462
cloning and characterisation of the rpos gene from plant growth-promoting pseudomonas putida wcs358: rpos is not involved in siderophore and homoserine lactone production.	the rpos gene which encodes a stationary phase sigma factor has been identified and characterised from the rhizosphere-colonising plant growth-promoting pseudomonas putida strain wcs358. the predicted protein sequence has extensive homologies with the rpos proteins form other bacteria, in particular with the rpos sigma factors of the fluorescent pseudomonads. a genomic transposon insertion in the rpos gene was constructed, these mutants were analysed for their ability to produce siderophore (iro ...	1999	10673044
evaluation of antibacterial activity of asparagus racemosus willd. root.	different concentrations (50, 100, 150 microg/ml) of the methanol extract of the roots of asparagus racemosus willd. showed considerable in vitro antibacterial efficacy against escherichia coli, shigella dysenteriae, shigella sonnei, shigella flexneri, vibrio cholerae, salmonella typhi, salmonella typhimurium, pseudomonas putida, bacillus subtilis and staphylococcus aureus. the effects produced by the methanol extract were compared with chloramphenicol.	2000	10685109
the genes for benzene catabolism in pseudomonas putida ml2 are flanked by two copies of the insertion element is1489, forming a class-i-type catabolic transposon, tn5542.	two directly repeated sequences of the is elements is1489v1 and is1489v2 flank the benzene dioxygenase (bedc1c2ba) and the cis-benzene dihydrodiol dehydrogenase (bedd) genes on the catabolic plasmid phmt112 in pseudomonas putida ml2, forming a class-i-type composite transposon, tn5542. both is1489v1 and is1489v2 contain an identical 1371-bp open reading frame, tnpa, that is preceded by a possible ribosome binding site. the tnpa gene of is1489v1 is bound by a pair of 40-bp imperfect inverted repe ...	2000	10686128
mechanisms of stationary phase mutation: a decade of adaptive mutation.	a decade of research on adaptive mutation has revealed a plethora of mutagenic mechanisms that may be important in evolution. the dna synthesis associated with recombination could be an important source of spontaneous mutation in cells that are not proliferating. the movement of insertion elements can be responsive to environmental conditions. insertion elements not only activate and inactivate genes, they also provide sequence homology that allows large-scale genomic rearrangements. some conjug ...	1999	10690404
functional analysis of pvds, an iron starvation sigma factor of pseudomonas aeruginosa.	in pseudomonas aeruginosa, iron modulates gene expression through a cascade of negative and positive regulatory proteins. the master regulator fur is involved in iron-dependent repression of several genes. one of these genes, pvds, was predicted to encode a putative sigma factor responsible for the transcription of a subset of genes of the fur regulon. pvds appears to belong to a structurally and functionally distinct subgroup of the extracytoplasmic function family of alternative sigma factors. ...	2000	10692351
association of the cytoplasmic membrane protein xpsn with the outer membrane protein xpsd in the type ii protein secretion apparatus of xanthomonas campestris pv. campestris.	an xps gene cluster composed of 11 open reading frames is required for the type ii protein secretion in xanthomonas campestris pv. campestris. immediately upstream of the xpsd gene, which encodes an outer membrane protein that serves as the secretion channel by forming multimers, there exists an open reading frame (previously designated orf2) that could encode a protein of 261 amino acid residues. its n-terminal hydrophobic region is a likely membrane-anchoring sequence. antibody raised against ...	2000	10692359
ssra (tmrna) plays a role in salmonella enterica serovar typhimurium pathogenesis.	escherichia coli ssra encodes a small stable rna molecule, tmrna, that has many diverse functions, including tagging abnormal proteins for degradation, supporting phage growth, and modulating the activity of dna binding proteins. here we show that ssra plays a role in salmonella enterica serovar typhimurium pathogenesis and in the expression of several genes known to be induced during infection. moreover, the phage-like attachment site, attl, encoded within ssra, serves as the site of integratio ...	2000	10692360
substrate specificity of naphthalene dioxygenase: effect of specific amino acids at the active site of the enzyme.	the three-component naphthalene dioxygenase (ndo) enzyme system carries out the first step in the aerobic degradation of naphthalene by pseudomonas sp. strain ncib 9816-4. the three-dimensional structure of ndo revealed that several of the amino acids at the active site of the oxygenase are hydrophobic, which is consistent with the enzyme's preference for aromatic hydrocarbon substrates. although ndo catalyzes cis-dihydroxylation of a wide range of substrates, it is highly regio- and enantiosele ...	2000	10692370
ctxphi infection of vibrio cholerae requires the tolqra gene products.	ctxphi is a lysogenic filamentous bacteriophage that encodes cholera toxin. filamentous phages that infect escherichia coli require both a pilus and the products of tolqra in order to enter host cells. we have previously shown that toxin-coregulated pilus (tcp), a type iv pilus that is an essential vibrio cholerae intestinal colonization factor, serves as a receptor for ctxphi. to test whether ctxphi also depends upon tol gene products to infect v. cholerae, we identified and inactivated the v. ...	2000	10692381
glutathione is involved in environmental stress responses in rhizobium tropici, including acid tolerance.	the isolation of rhizobial strains which exhibit an intrinsic tolerance to acidic conditions has been reported and has facilitated studies on the basic mechanisms underlying acid tolerance. rhizobium tropici strain ciat899 displays a high intrinsic tolerance to acidity and therefore was used in this work to study the molecular basis of bacterial responses to acid conditions and other environmental stresses. we generated a collection of r. tropici ciat899 mutants affected in acid tolerance using ...	2000	10692382
evidence for plasmid-mediated chemotaxis of pseudomonas putida towards naphthalene and salicylate.	a naphthalene (nap) and salicylate (sal) degrading microorganism, pseudomonas putida rkj1, is chemotactic towards these compounds. this strain carries a 83 kb plasmid. a 25 kb ecori fragment of the plasmid contains the genes responsible for nap degradation through sal. rkj5, the plasmid-cured derivative of rkj1, is neither capable of degradation nor is chemotactic towards nap or sal. the recombinant plasmid prkj3, which contained a 25 kb ecori fragment, was transferred back into the plasmid-free ...	2000	10696467
inactivation of isocitrate lyase leads to increased production of medium-chain-length poly(3-hydroxyalkanoates) in pseudomonas putida.	medium-chain-length (mcl) poly(3-hydroxyalkanoates) (phas) are storage polymers that are produced from various substrates and accumulate in pseudomonas strains belonging to rrna homology group i. in experiments aimed at increasing pha production in pseudomonas strains, we generated an mcl pha-overproducing mutant of pseudomonas putida kt2442 by transposon mutagenesis, in which the acea gene was knocked out. this mutation inactivated the glyoxylate shunt and reduced the in vitro activity of isoci ...	2000	10698750
frequency and biodiversity of 2,4-diacetylphloroglucinol-producing bacteria isolated from the maize rhizosphere at different stages of plant growth.	a pseudomonas 2,4-diacetylphloroglucinol (dapg)-producing population that occurred naturally on the roots, in rhizosphere soil of zea mays and in the nonrhizosphere soil was investigated in order to assess the microbial diversity at five stages of plant growth. a total of 1,716 isolates were obtained, and 188 of these isolates were able to produce dapg. dapg producers were isolated at each stage of plant growth, indicating that the maize rhizosphere is colonized by natural dapg producers through ...	2000	10698757
degradation and mineralization of high-molecular-weight polycyclic aromatic hydrocarbons by defined fungal-bacterial cocultures.	this study investigated the biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons (pahs) in liquid media and soil by bacteria (stenotrophomonas maltophilia vun 10,010 and bacterial consortium vun 10,009) and a fungus (penicillium janthinellum vuo 10, 201) that were isolated from separate creosote- and manufactured-gas plant-contaminated soils. the bacteria could use pyrene as their sole carbon and energy source in a basal salts medium (bsm) and mineralized significant amounts ...	2000	10698765
evaluation of autoscan-w/a and the vitek gni+ automicrobic system for identification of non-glucose-fermenting gram-negative bacilli.	the autoscan-w/a (w/a; dade behring microscan inc., west sacramento, calif.) and vitek automicrobic system (vitek ams; biomérieux vitek systems, inc., hazelwood, mo.) are both fully automated microbiology systems. we evaluated the accuracy of these two systems in identifying nonglucose-fermenting gram-negative bacilli. we used the w/a with conventional-panel neg combo type 12 and vitek gni+ identification systems. a total of 301 isolates from 25 different species were tested. of these, 299 isola ...	2000	10699007
the measurement of toluene dioxygenase activity in biofilm culture of pseudomonas putida f1.	toluene dioxygenase (tod) enzyme activity can be measured by the conversion of indole to indigo. indigo is measured spectrophotometrically at 600 nm. however, this method is inadequate to measure the whole-cell enzyme activity when interference by suspended biomass is present. indoxyl is a highly fluorescent intermediate in the conversion of indole to indigo by tod. a fluorescence-based assay was developed and applied to monitor tod activity in whole cells of pseudomonas putida f1 biofilm from a ...	2000	10699674
use of bioassays for assessment of water-extractable ecotoxic potential of soils.	the characterization of contaminated soils is based on heterogeneous strategies considering chemical analyses or bioassays. in the report bioassays for soils, test methods which are at an advanced state of development and standardization are recommended by the german dechema (german society for chemical apparatus, chemical engineering and biotechnology e.v.). following this report six soil samples contaminated with different organic and inorganic substances are applied to bioassays using the fol ...	2000	10702342
clustering of clinical strains of helicobacter pylori analyzed by two-dimensional gel electrophoresis.	strain variations of helicobacter pylori have been tested by numerous methods and compared among different patient groups. the aim of this study was to investigate whether h. pylori expresses disease-specific proteins that can be detected by two-dimensional polyacrylamide gel electrophoresis (2-d page). h. pylori strains isolated from duodenal ulcer, gastric cancer, and gastritis patients were analyzed. extensive variation in spot patterns was observed between the strains, but a dendrogram analy ...	2000	10702510
biodegradability of some antibiotics, elimination of the genotoxicity and affection of wastewater bacteria in a simple test.	most antibiotics and their metabolites are excreted by humans after administration and therefore reach the municipal sewage with the excretions. only little is known about their biodegradability in aquatic environments. it was recognised that genotoxic substances may represent a health hazard to humans but also may affect organisms in the environment. therefore, the biodegradability of some clinically important antibiotic drugs (ciprofloxacin, ofloxacin, metronidazole) and hereby the elimination ...	2000	10705547
protein engineering of cytochrome p450(cam) (cyp101) for the oxidation of polycyclic aromatic hydrocarbons.	mutations of the active site residues f87 and y96 greatly enhanced the activity of cytochrome p450(cam) (cyp101) from pseudomonas putida for the oxidation of the polycyclic aromatic hydrocarbons phenanthrene, fluoranthene, pyrene and benzo[a]pyrene. wild-type p450(cam) had low (<0.01 min(-1)) activity with these substrates. phenanthrene was oxidized to 1-, 2-, 3- and 4-phenanthrol, while fluoranthene gave mainly 3-fluoranthol. pyrene was oxidized to 1-pyrenol and then to 1,6- and 1,8-pyrenequino ...	2000	10708651
the pseudomonas aeruginosa phag gene product is involved in the synthesis of polyhydroxyalkanoic acid consisting of medium-chain-length constituents from non-related carbon sources.	we recently identified the phag(pp) gene encoding (r)-3-hydroxydecanoyl-acp:coa transacylase in pseudomonas putida, which directly links the fatty acid de novo biosynthesis and polyhydroxyalkanoate (pha) biosynthesis. an open reading frame (orf) of which the deduced amino acid sequence shared about 57% identity with phag from p. putida was identified in the p. aeruginosa genome sequence. its coding region (herein called phag(pa)) was amplified by pcr and cloned into the vector pbbr1mcs-2 under l ...	2000	10713430
flow cytometric detection of specific gene expression in prokaryotic cells using in situ rt-pcr.	prokaryotic in situ rt-pcr was coupled with flow cytometry to detect mrna transcripts of the toluene dioxygenase (todc1) gene in intact cells of the bacterium pseudomonas putida f1. recovery efficiency of fixed cells over the course of the entire in situ detection procedure was approximately 81% for both p. putida f1 and ac10r cells. it appeared that lysozyme treatment and pcr thermal cycling were the steps responsible for most of observed cell loss. bacterial cells expressing the todc1 gene cou ...	2000	10713436
tfdr, the lysr-type transcriptional activator, is responsible for the activation of the tfdcb operon of pseudomonas putida 2, 4-dichlorophenoxyacetic acid degradative plasmid pest4011.	in pseudomonas putida est4021, the tfdcb operon of plasmid pest4011 encodes enzymes involved in 2,4-dichlorophenoxyacetic acid degradation. we have identified a gene, tfdr, important for the regulation of the tfdcb operon. sequence analysis of the tfdr gene revealed an open reading frame with amino acid sequence similar to the lysr family of transcriptional activators. the tfdr gene is located upstream and transcribed divergently from the tfdcb operon. utilizing primer extension analysis, the tr ...	2000	10713456
purification and characterization of a catalase from the facultatively psychrophilic bacterium vibrio rumoiensis s-1(t) exhibiting high catalase activity.	catalase from the facultatively psychrophilic bacterium vibrio rumoiensis s-1(t), which was isolated from an environment exposed to h(2)o(2) and exhibited high catalase activity, was purified and characterized, and its localization in the cell was determined. its molecular mass was 230 kda, and the molecule consisted of four identical subunits. the enzyme, which was not apparently reduced by dithionite, showed a soret peak at 406 nm in a resting state. the catalytic activity was 527,500 u. mg of ...	2000	10714995
a 90-kilobase conjugative chromosomal element coding for biphenyl and salicylate catabolism in pseudomonas putida kf715.	the biphenyl and salicylate metabolic pathways in pseudomonas putida kf715 are chromosomally encoded. the bph gene cluster coding for the conversion of biphenyl to benzoic acid and the sal gene cluster coding for the salicylate meta-pathway were obtained from the kf715 genomic cosmid libraries. these two gene clusters were separated by 10-kb dna and were highly prone to deletion when kf715 was grown in nutrient medium. two types of deletions took place at the region including only the bph genes ...	2000	10715002
sal genes determining the catabolism of salicylate esters are part of a supraoperonic cluster of catabolic genes in acinetobacter sp. strain adp1.	a 5-kbp region upstream of the are-ben-cat genes was cloned from acinetobacter sp. strain adp1, extending the supraoperonic cluster of catabolic genes to 30 kbp. four open reading frames, sala, salr, sale, and sald, were identified from the nucleotide sequence. reverse transcription-pcr studies suggested that these open reading frames are organized into two convergent transcription units, salar and salde. the sale gene, encoding a protein of 239 residues, was ligated into expression vector pet5a ...	2000	10715011
mobilization of plasmids and chromosomal dna mediated by the sxt element, a constin found in vibrio cholerae o139.	the vibrio cholerae sxt element encodes resistance to multiple antibiotics and is a conjugative, self-transmissible, and chromosomally integrating element (a constin). excision and self-transfer of the sxt element require an element-encoded integrase. we now report that the sxt element can also mobilize the plasmids rsf1010 and clodf13 in trans as well as chromosomal dna in an hfr-like manner. sxt element-mediated mobilization of plasmids and chromosomal dna, unlike its self-transfer, is not dep ...	2000	10715015
purification and properties of ornithine racemase from clostridium sticklandii.	ornithine racemase has been purified to homogeneity from clostridium sticklandii, as shown by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. this is the first racemase known to be highly specific to ornithine. this plp-dependent enzyme has an m(r) of 92, 000, with a k(m) for l-ornithine of 0.77 +/- 0.05 mm and a k(cat) of 980 +/- 20 s(-1).	2000	10715017
the sulfur-regulated arylsulfatase gene cluster of pseudomonas aeruginosa, a new member of the cys regulon.	a gene cluster upstream of the arylsulfatase gene (atsa) in pseudomonas aeruginosa was characterized and found to encode a putative abc-type transporter, atsrbc. mutants with insertions in the atsr or atsb gene were unable to grow with hexyl-, octyl-, or nitrocatecholsulfate, although they grew normally with other sulfur sources, such as sulfate, methionine, and aliphatic sulfonates. atsrbc therefore constitutes a general sulfate ester transport system, and desulfurization of aromatic and medium ...	2000	10715018
riding the sulfur cycle--metabolism of sulfonates and sulfate esters in gram-negative bacteria.	sulfonates and sulfate esters are widespread in nature, and make up over 95% of the sulfur content of most aerobic soils. many microorganisms can use sulfonates and sulfate esters as a source of sulfur for growth, even when they are unable to metabolize the carbon skeleton of the compounds. in these organisms, expression of sulfatases and sulfonatases is repressed in the presence of sulfate, in a process mediated by the lysr-type regulator protein cysb, and the corresponding genes therefore cons ...	2000	10717312
three types of phenol and p-cresol catabolism in phenol- and p-cresol-degrading bacteria isolated from river water continuously polluted with phenolic compounds.	a total of 39 phenol- and p-cresol-degraders isolated from the river water continuously polluted with phenolic compounds of oil shale leachate were studied. species identification by biolog gn analysis revealed 21 strains of pseudomonas fluorescens (4, 8 and 9 of biotypes a, c and g, respectively), 12 of pseudomonas mendocina, four of pseudomonas putida biotype a1, one of pseudomonas corrugata and one of acinetobacter genospecies 15. computer-assisted analysis of rep-pcr fingerprints clustered t ...	2000	10719200
characterization of vim-2, a carbapenem-hydrolyzing metallo-beta-lactamase and its plasmid- and integron-borne gene from a pseudomonas aeruginosa clinical isolate in france.	pseudomonas aeruginosa col-1 was identified in a blood culture of a 39-year-old-woman treated with imipenem in marseilles, france, in 1996. this strain was resistant to beta-lactams, including ureidopenicillins, ticarcillin-clavulanic acid, cefepime, ceftazidime, imipenem, and meropenem, but remained susceptible to the monobactam aztreonam. the carbapenem-hydrolyzing beta-lactamase gene of p. aeruginosa col-1 was cloned, sequenced, and expressed in escherichia coli dh10b. the deduced 266-amino-a ...	2000	10722487
bordetella pertussis tonb, a bvg-independent virulence determinant.	in gram-negative bacteria, high-affinity iron uptake requires the tonb/exbb/exbd envelope complex to release iron chelates from their specific outer membrane receptors into the periplasm. based on sequence similarities, the bordetella pertussis tonb exbb exbd locus was identified on a cloned dna fragment. the tight organization of the three genes suggests that they are cotranscribed. a putative fur-binding sequence located upstream from tonb was detected in a fur titration assay, indicating that ...	2000	10722583
helicobacter pylori possesses two chey response regulators and a histidine kinase sensor, chea, which are essential for chemotaxis and colonization of the gastric mucosa.	infection of the mucous layer of the human stomach by helicobacter pylori requires the bacterium to be motile and presumably chemotactic. previous studies have shown that fully functional flagella are essential for motility and colonization, but the role of chemotaxis remains unclear. the two-component regulatory system chea/chey has been shown to play a major role in chemotaxis in other enteric bacteria. scrutiny of the 26695 genome sequence suggests that h. pylori has two chey response regulat ...	2000	10722597
presence of two trans-o-hydroxybenzylidenepyruvate hydratase-aldolases in naphthalenesulfonate-assimilating sphingomonas paucimobilis ta-2: comparison of some properties.	two trans-o-hydroxybenzylidenepyruvate hydratase-aldolases named thbp ha a and thbp ha b were purified from a cell-free extract of naphthalenesulfonate-assimilating sphingomonas paucimobilis (formerly pseudomonas sp.) ta-2 to an electrophoretically homogeneous state by successive column chromatographies on deae-cellulose, deae-toyopearl 650m, sephacryl s-100, hydroxyapatite, and mono q. these enzymes were similar to each other in molecular mass (ca. 37 kda on sds-page, ca. 110 kda on ultracentri ...	2000	10731665
the repertoire of dna-binding transcriptional regulators in escherichia coli k-12.	using a combination of several approaches we estimated and characterized a total of 314 regulatory dna-binding proteins in escherichia coli, which might represent its minimal set of transcription factors. the collection is comprised of 35% activators, 43% repressors and 22% dual regulators. within many regulatory protein families, the members are homogeneous in their regulatory roles, physiology of regulated genes, regulatory function, length and genome position, showing that these families have ...	2000	10734204
rega, iron, and growth phase regulate expression of the pseudomonas aeruginosa tol-oprl gene cluster.	the tol-oprl region in pseudomonas aeruginosa appears to be involved in pyocin uptake and required for cell viability. the complete nucleotide sequences of the tolqra and oprl genes as well as the incomplete sequences of tolb and orf2 have been previously reported. in addition, the sequence of a p. aeruginosa iron-regulated gene (pig6) has been described and found to share homology with an open reading frame located upstream of the escherichia coli tolqra genes (u. a. ochsner and m. l. vasil, pr ...	2000	10735848
a novel phenanthrene dioxygenase from nocardioides sp. strain kp7: expression in escherichia coli.	nocardioides sp. strain kp7 grows on phenanthrene but not on naphthalene. this organism degrades phenanthrene via 1-hydroxy-2-naphthoate, o-phthalate, and protocatechuate. the genes responsible for the degradation of phenanthrene to o-phthalate (phd) were found by southern hybridization to reside on the chromosome. a 10.6-kb dna fragment containing eight phd genes was cloned and sequenced. the phda, phdb, phdc, and phdd genes, which encode the alpha and beta subunits of the oxygenase component, ...	2000	10735855
multiple interactions between pullulanase secreton components involved in stabilization and cytoplasmic membrane association of pule.	we report attempts to analyze interactions between components of the pullulanase (pul) secreton (type ii secretion machinery) from klebsiella oxytoca encoded by a multiple-copy-number plasmid in escherichia coli. three of the 15 pul proteins (b, h, and n) were found to be dispensable for pullulanase secretion. the following evidence leads us to propose that pule, pull, and pulm form a subcomplex with which pulc and pulg interact. the integral cytoplasmic membrane protein pull prevented proteolys ...	2000	10735856
roles of horizontal gene transfer and gene integration in evolution of 1,3-dichloropropene- and 1,2-dibromoethane-degradative pathways.	the haloalkane-degrading bacteria rhodococcus rhodochrous ncimb13064, pseudomonas pavonaceae 170, and mycobacterium sp. strain gp1 share a highly conserved haloalkane dehalogenase gene (dhaa). here, we describe the extent of the conserved dhaa segments in these three phylogenetically distinct bacteria and an analysis of their flanking sequences. the dhaa gene of the 1-chlorobutane-degrading strain ncimb13064 was found to reside within a 1-chlorobutane catabolic gene cluster, which also encodes a ...	2000	10735862
a second [2fe-2s] ferredoxin from sphingomonas sp. strain rw1 can function as an electron donor for the dioxin dioxygenase.	the first step in the degradation of dibenzofuran and dibenzo-p-dioxin by sphingomonas sp. strain rw1 is carried out by dioxin dioxygenase (dxna1a2), a ring-dihydroxylating enzyme. an open reading frame (fdx3) that could potentially specify a new ferredoxin has been identified downstream of dxna1a2, a two-cistron gene (j. armengaud, b. happe, and k. n. timmis, j. bacteriol. 180:3954-3966, 1998). in the present study, we report a biochemical analysis of fdx3 produced in escherichia coli. this thi ...	2000	10735867
complex function for sica, a salmonella enterica serovar typhimurium type iii secretion-associated chaperone.	salmonella enterica encodes a type iii secretion system within a pathogenicity island located at centisome 63 that is essential for virulence. all type iii secretion systems require the function of a family of low-molecular-weight proteins that aid the secretion process by acting as partitioning factors and/or secretion pilots. one such protein is sica, which is encoded immediately upstream of the type iii secreted proteins sipb and sipc. we found that the absence of sica results in the degradat ...	2000	10735870
construction and characterization of a reca mutant of thiobacillus ferrooxidans by marker exchange mutagenesis.	to construct thiobacillus ferrooxidans mutants by marker exchange mutagenesis, a genetic transfer system is required. the transfer of broad-host-range plasmids belonging to the incompatibility groups incq (pkt240 and pjrd215), incp (pjb3km1), and incw (pufr034) from escherichia coli to two private t. ferrooxidans strains (brgm1 and tf-49) and to two collection strains (atcc 33020 and atcc 19859) by conjugation was analyzed. to knock out the t. ferrooxidans reca gene, a mobilizable suicide plasmi ...	2000	10735871
an algorithm for automated bacterial identification using matrix-assisted laser desorption/ionization mass spectrometry.	an algorithm for bacterial identification using matrix-assisted laser desorption/ionization (maldi) mass spectrometry is being developed. this mass spectral fingerprint comparison algorithm is fully automated and statistically based, providing objective analysis of samples to be identified. based on extraction of reference fingerprint ions from test spectra, this approach should lend itself well to real-world applications where samples are likely to be impure. this algorithm is illustrated using ...	2000	10740862
physiological analysis of the expression of the styrene degradation gene cluster in pseudomonas fluorescens st.	the effects of different carbon sources on expression of the styrene catabolism genes in pseudomonas fluorescens st were analyzed by using a promoter probe vector, ppr9tt, which contains transcription terminators upstream and downstream of the beta-galactosidase reporter system. expression of the promoter of the stysr operon, which codes for the styrene two-component regulatory system, was found to be constitutive and not subject to catabolite repression. this was confirmed by the results of an ...	2000	10742204
properties of engineered poly-3-hydroxyalkanoates produced in recombinant escherichia coli strains.	to prepare medium-chain-length poly-3-hydroxyalkanoates (phas) with altered physical properties, we generated recombinant escherichia coli strains that synthesized phas with altered monomer compositions. experiments with different substrates (fatty acids with different chain lengths) or different e. coli hosts failed to produce phas with altered physical properties. therefore, we engineered a new potential pha synthetic pathway, in which ketoacyl-coenzyme a (coa) intermediates derived from the b ...	2000	10742205
poly(3-hydroxyvalerate) depolymerase of pseudomonas lemoignei.	pseudomonas lemoignei is equipped with at least five polyhydroxyalkanoate (pha) depolymerase structural genes (phaz1 to phaz5) which enable the bacterium to utilize extracellular poly(3-hydroxybutyrate) (phb), poly(3-hydroxyvalerate) (phv), and related polyesters consisting of short-chain-length hxdroxyalkanoates (pha(scl)) as the sole sources of carbon and energy. four genes (phaz1, phaz2, phaz3, and phaz5) encode phb depolymerases c, b, d, and a, respectively. it was speculated that the remain ...	2000	10742216
glutathione-dependent conversion of n-ethylmaleimide to the maleamic acid by escherichia coli: an intracellular detoxification process.	the electrophile n-ethylmaleimide (nem) elicits rapid k(+) efflux from escherichia coli cells consequent upon reaction with cytoplasmic glutathione to form an adduct, n-ethylsuccinimido-s-glutathione (esg) that is a strong activator of the kefb and kefc glutathione-gated k(+) efflux systems. the fate of the esg has not previously been investigated. in this report we demonstrate that nem and n-phenylmaleimide (npm) are rapidly detoxified by e. coli. the detoxification occurs through the formation ...	2000	10742217
isolation of bacteriophages specific to a fish pathogen, pseudomonas plecoglossicida, as a candidate for disease control.	two types of bacteriophage specific to pseudomonas plecoglossicida, the causative agent of bacterial hemorrhagic ascites disease in cultured ayu fish (plecoglossus altivelis), were isolated from diseased ayu and the rearing pond water. one type of phage, which formed small plaques, was tentatively classified as a member of the family myoviridae, and the other type, which formed large plaques, was classified as a member of the family podoviridae. all 27 strains of p. plecoglossicida examined, whi ...	2000	10742221
superoxide dismutase activity in pseudomonas putida affects utilization of sugars and growth on root surfaces.	to investigate the role of superoxide dismutases (sod) in root colonization and oxidative stress, mutants of pseudomonas putida lacking manganese-superoxide dismutase (mnsod) (soda), iron-superoxide dismutase (fesod) (sodb), or both were generated. the soda sodb mutant did not grow on components washed from bean root surfaces or glucose in minimal medium. the sodb and soda sodb mutants were more sensitive than wild type to oxidative stress generated within the cell by paraquat treatment. in sing ...	2000	10742227
characterization of the protocatechuic acid catabolic gene cluster from streptomyces sp. strain 2065.	protocatechuate 3,4-dioxygenase (ec 1.13.11.3) catalyzes the ring cleavage step in the catabolism of aromatic compounds through the protocatechuate branch of the beta-ketoadipate pathway. a protocatechuate 3,4-dioxygenase was purified from streptomyces sp. strain 2065 grown in p-hydroxybenzoate, and the n-terminal sequences of the beta- and alpha-subunits were obtained. pcr amplification was used for the cloning of the corresponding genes, and dna sequencing of the flanking regions showed that t ...	2000	10742233
production of pectate lyases and cellulases by chryseomonas luteola strain mfcl0 depends on the growth temperature and the nature of the culture medium: evidence for two critical temperatures.	several extracellular enzymes that are responsible for plant tissue maceration were detected in culture supernatant of the psychrotrophic bacterium chryseomonas luteola mfcl0. isoelectrofocusing experiments showed that pectate lyase (pl) activity resulted from the cumulative action of three major isoenzymes, designated pli, plii, and pliii. cellulolytic activity was also detected in culture supernatants. these enzymes exhibited different behaviors with respect to growth temperature. plii was not ...	2000	10742239
role of tfdc(i)d(i)e(i)f(i) and tfdd(ii)c(ii)e(ii)f(ii) gene modules in catabolism of 3-chlorobenzoate by ralstonia eutropha jmp134(pjp4).	the enzymes chlorocatechol-1,2-dioxygenase, chloromuconate cycloisomerase, dienelactone hydrolase, and maleylacetate reductase allow ralstonia eutropha jmp134(pjp4) to degrade chlorocatechols formed during growth in 2,4-dichlorophenoxyacetate or 3-chlorobenzoate (3-cb). there are two gene modules located in plasmid pjp4, tfdc(i)d(i)e(i)f(i) (module i) and tfdd(ii)c(ii)e(ii)f(ii) (module ii), putatively encoding these enzymes. to assess the role of both tfd modules in the degradation of chloroaro ...	2000	10742248
nitrile hydratase and amidase from rhodococcus rhodochrous hydrolyze acrylic fibers and granular polyacrylonitriles.	rhodococcus rhodochrous ncimb 11216 produced nitrile hydratase (320 nkat mg of protein(-1)) and amidase activity (38.4 nkat mg of protein(-1)) when grown on a medium containing propionitrile. these enzymes were able to hydrolyze nitrile groups of both granular polyacrylonitriles (pan) and acrylic fibers. nitrile groups of pan40 (molecular mass, 40 kda) and pan190 (molecular mass, 190 kda) were converted into the corresponding carbonic acids to 1.8 and 1.0%, respectively. in contrast, surfacial n ...	2000	10742253
the viable-but-nonculturable state induced by abiotic stress in the biocontrol agent pseudomonas fluorescens cha0 does not promote strain persistence in soil.	the effects of oxygen limitation, low redox potential, and high nacl stress for 7 days in vitro on the rifampin-resistant biocontrol inoculant pseudomonas fluorescens cha0-rif and its subsequent persistence in natural soil for 54 days were investigated. throughout the experiment, the strain was monitored using total cell counts (immunofluorescence microscopy), kogure's direct viable counts, and colony counts (on rifampin-containing plates). under in vitro conditions, viable-but-nonculturable (vb ...	2000	10742257
involvement of two plasmids in fenitrothion degradation by burkholderia sp. strain nf100.	a bacterium capable of utilizing fenitrothion (o,o-dimethyl o-4-nitro-m-tolyl phosphorothioate) as a sole carbon source was isolated from fenitrothion-treated soil. this bacterium was characterized taxonomically as being a member of the genus burkholderia and was designated strain nf100. nf100 first hydrolyzed an organophosphate bond of fenitrothion, forming 3-methyl-4-nitrophenol, which was further metabolized to methylhydroquinone. the ability to degrade fenitrothion was found to be encoded on ...	2000	10742273
xylene monooxygenase catalyzes the multistep oxygenation of toluene and pseudocumene to corresponding alcohols, aldehydes, and acids in escherichia coli jm101.	xylene monooxygenase of pseudomonas putida mt-2 catalyzes the methylgroup hydroxylation of toluene and xylenes. to investigate the potential of xylene monooxygenase to catalyze multistep oxidations of one methyl group, we tested recombinant escherichia coli expressing the monooxygenase genes xylm and xyla under the control of the alk regulatory system of pseudomonas oleovorans gpo1. expression of xylene monooxygenase genes could efficiently be controlled by n-octane and dicyclopropylketone. xyle ...	2000	10744688
a material-balance approach for modeling bacterial chemotaxis to a consumable substrate in the capillary assay.	a mathematical model was developed to simulate the movement of chemotactic bacteria into and within a capillary tube containing a metabolizable chemoattractant. the model was based on a material balance that accounts for the transport of bacteria and chemoattractant as well as consumption of the substrate throughout the capillary assay system. by solving the model with a numerical method, it was possible to predict the concentration of substrate and bacteria at points within the capillary and th ...	2000	10745199
growth kinetics of pseudomonas putida in cometabolism of phenol and 4-chlorophenol in the presence of a conventional carbon source.	growth kinetics of pseudomonas putida (atcc 49451) in cometabolism of phenol and 4-chlorophenol (4-cp) in the presence of sodium glutamate (sg) were studied. in the ternary substrate mixture, phenol and sg are growth substrates while 4-cp is a nongrowth substrate. cell growth on phenol was found to follow andrews kinetics and cells displayed substrate inhibition pattern on sodium glutamate in the range of 0-4 g l(-1) as well. a cell growth model for the ternary substrate system was established b ...	2000	10745212
production of medium-chain-length polyhydroxyalkanoates by high-cell-density cultivation of pseudomonas putida under phosphorus limitation.	high-cell-density fed-batch cultures of pseudomonas putida were carried out for the production of medium-chain-length polyhydroxyalkanoates (phas) using oleic acid as a carbon source. by employing an optimal feeding strategy without the limitation of any nutrient, a high cell concentration of 173 g/l was achieved, but the pha concentration and pha content were only 32.3 g/l and 18.7 wt%, respectively. to increase the pha concentration and content, phosphorus limitation was applied during fed-bat ...	2000	10745215
molecular cloning, sequencing, expression, and site-directed mutagenesis of the 1h-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase gene from arthrobacter spec. rü61a.	the ring cleaving enzyme 1h-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase (hod)) of arthrobacter spec. rü61a is part of the quinaldine degradation pathway. carbon monoxide and n-acetyl-anthranilate are the products formed by dioxygenolytic cleavage of two c-c bonds in the substrate's pyridine ring. the gene coding for hod was cloned and sequenced. an isoelectric point of ph 5.40 and a molecular mass of 31,838 da was deduced from the sequence. hod is shown to be remarkably similar to 1h-3-hydroxy-4-o ...	2000	10746195