Publications

the pseudomonas aeruginosa devb/sol homolog, pgl, is a member of the hex regulon and encodes 6-phosphogluconolactonase.	a cyclic version of the entner-doudoroff pathway is used by pseudomonas aeruginosa to metabolize carbohydrates. genes encoding the enzymes that catabolize intracellular glucose to pyruvate and glyceraldehyde 3-phosphate are coordinately regulated, clustered at 39 min on the chromosome, and collectively form the hex regulon. within the hex cluster is an open reading frame (orf) with homology to the devb/sol family of unidentified proteins. this orf encodes a protein of either 243 or 238 amino aci ...	2000	10869070
influence of deletions within domain ii of exotoxin a on its extracellular secretion from pseudomonas aeruginosa.	pseudomonas aeruginosa is a gram-negative bacterium that secretes many proteins into the extracellular medium via the xcp machinery. this pathway, conserved in gram-negative bacteria, is called the type ii pathway. the exoproteins contain information in their amino acid sequence to allow targeting to their secretion machinery. this information may be present within a conformational motif. the nature of this signal has been examined for p. aeruginosa exotoxin a (pe). previous studies failed to id ...	2000	10869085
expansion of the clavulanic acid gene cluster: identification and in vivo functional analysis of three new genes required for biosynthesis of clavulanic acid by streptomyces clavuligerus.	clavulanic acid is a potent inhibitor of beta-lactamase enzymes and is of demonstrated value in the treatment of infections by beta-lactam-resistant bacteria. previously, it was thought that eight contiguous genes within the genome of the producing strain streptomyces clavuligerus were sufficient for clavulanic acid biosynthesis, because they allowed production of the antibiotic in a heterologous host (k. a. aidoo, a. s. paradkar, d. c. alexander, and s. e. jensen, p. 219-236, in v. p. gullo et ...	2000	10869089
genes expressed in pseudomonas putida during colonization of a plant-pathogenic fungus.	in vivo expression technology (ivet) was employed to study colonization of phytophthora parasitica by a biological control bacterium, pseudomonas putida 06909, based on a new selection marker. the pyrb gene, which encodes aspartate transcarbamoylase, an enzyme used for pyrimidine biosynthesis, was cloned from p. putida 06909. a pyrb-disrupted mutant did not grow in pyrimidine-deficient media unless it was complemented with pyrbc' behind an active promoter. thirty clones obtained from p. putida 0 ...	2000	10877766
biocontrol of the sugarcane borer eldana saccharina by expression of the bacillus thuringiensis cry1ac7 and serratia marcescens chia genes in sugarcane-associated bacteria.	the cry1ac7 gene of bacillus thuringiensis strain 234, showing activity against the sugarcane borer eldana saccharina, was cloned under the control of the tac promoter. the fusion was introduced into the broad-host-range plasmid pkt240 and the integration vector pjff350 and without the tac promoter into the broad-host-range plasmids pml122 and pkmm0. these plasmids were introduced into a pseudomonas fluorescens strain isolated from the phylloplane of sugarcane and the endophytic bacterium herbas ...	2000	10877771
molecular diversity of plasmids bearing genes that encode toluene and xylene metabolism in pseudomonas strains isolated from different contaminated sites in belarus.	twenty different pseudomonas strains utilizing m-toluate were isolated from oil-contaminated soil samples near minsk, belarus. seventeen of these isolates carried plasmids ranging in size from 78 to about 200 kb (assigned psvs plasmids) and encoding the meta cleavage pathway for toluene metabolism. most plasmids were conjugative but of unknown incompatibility groups, except for one, which belonged to the incp9 group. the organization of the genes for toluene catabolism was determined by restrict ...	2000	10877777
isolation and characterization of 2,3-dichloro-1-propanol-degrading rhizobia.	2,3-dichloro-1-propanol is more chemically stable than its isomer, 1, 3-dichloro-2-propanol, and is therefore more difficult to degrade. the isolation of bacteria capable of complete mineralization of 2, 3-dichloro-1-propanol was successful only from enrichments at high ph. the bacteria thus isolated were found to be members of the alpha division of the proteobacteria in the rhizobium subdivision, most likely agrobacterium sp. they could utilize both dihaloalcohol substrates and 2-chloropropioni ...	2000	10877782
bioaugmentation of activated sludge by an indigenous 3-chloroaniline-degrading comamonas testosteroni strain, i2gfp.	a strain identified as comamonas testosteroni i2 was isolated from activated sludge and found to be able to mineralize 3-chloroaniline (3-ca). during the mineralization, a yellow intermediate accumulated temporarily, due to the distal meta-cleavage of chlorocatechol. this strain was tested for its ability to clean wastewater containing 3-ca upon inoculation into activated sludge. to monitor its survival, the strain was chromosomally marked with the gfp gene and designated i2gfp. after inoculatio ...	2000	10877785
influence of chlorine substituents on rates of oxidation of chlorinated biphenyls by the biphenyl dioxygenase of burkholderia sp. strain lb400.	biphenyl dioxygenase from burkholderia (pseudomonas) sp. strain lb400 catalyzes the first reaction of a pathway for the degradation of biphenyl and a broad range of chlorinated biphenyls (cbs). the effect of chlorine substituents on catalysis was determined by measuring the specific activity of the enzyme with biphenyl and 18 congeners. the catalytic oxygenase component was purified and incubated with individual cbs in the presence of electron transport proteins and cofactors that were required ...	2000	10877788
molecular analysis of surfactant-driven microbial population shifts in hydrocarbon-contaminated soil.	we analyzed the impact of surfactant addition on hydrocarbon mineralization kinetics and the associated population shifts of hydrocarbon-degrading microorganisms in soil. a mixture of radiolabeled hexadecane and phenanthrene was added to batch soil vessels. witconol sn70 (a nonionic, alcohol ethoxylate) was added in concentrations that bracketed the critical micelle concentration (cmc) in soil (cmc') (determined to be 13 mg g(-1)). addition of the surfactant at a concentration below the cmc' (2 ...	2000	10877792
sequence analysis and initial characterization of two isozymes of hydroxylaminobenzene mutase from pseudomonas pseudoalcaligenes js45.	pseudomonas pseudoalcaligenes js45 grows on nitrobenzene by a partially reductive pathway in which the intermediate hydroxylaminobenzene is enzymatically rearranged to 2-aminophenol by hydroxylaminobenzene mutase (hab mutase). the properties of the enzyme, the reaction mechanism, and the evolutionary origin of the gene(s) encoding the enzyme are unknown. in this study, two open reading frames (haba and habb), each encoding an hab mutase enzyme, were cloned from a p. pseudoalcaligenes js45 genomi ...	2000	10877793
cloning of the malic enzyme gene from corynebacterium glutamicum and role of the enzyme in lactate metabolism.	malic enzyme is one of at least five enzymes, known to be present in corynebacterium glutamicum, capable of carboxylation and decarboxylation reactions coupling glycolysis and the tricarboxylic acid cycle. to date, no information is available concerning the physiological role of the malic enzyme in this bacterium. the male gene from c. glutamicum has been cloned and sequenced. the protein encoded by this gene has been purified to homogeneity, and the biochemical properties have been established. ...	2000	10877795
reactions involved in the lower pathway for degradation of 4-nitrotoluene by mycobacterium strain hl 4-nt-1.	in spite of the variety of initial reactions, the aerobic biodegradation of aromatic compounds generally yields dihydroxy intermediates for ring cleavage. recent investigation of the degradation of nitroaromatic compounds revealed that some nitroaromatic compounds are initially converted to 2-aminophenol rather than dihydroxy intermediates by a number of microorganisms. the complete pathway for the metabolism of 2-aminophenol during the degradation of nitrobenzene by pseudomonas pseudoalcaligene ...	2000	10877799
a new klebsiella planticola strain (cd-1) grows anaerobically at high cadmium concentrations and precipitates cadmium sulfide.	heavy metal resistance by bacteria is a topic of much importance to the bioremediation of contaminated soils and sediments. we report here the isolation of a highly cadmium-resistant klebsiella planticola strain, cd-1, from reducing salt marsh sediments. the strain grows in up to 15 mm cdcl(2) under a wide range of nacl concentrations and at acidic or neutral ph. in growth medium amended with thiosulfate, it precipitated significant amounts of cadmium sulfide (cds), as confirmed by x-absorption ...	2000	10877810
the bacterial cell-division protein zipa and its interaction with an ftsz fragment revealed by x-ray crystallography.	in escherichia coli, ftsz, a homologue of eukaryotic tubulins, and zipa, a membrane-anchored protein that binds to ftsz, are two essential components of the septal ring structure that mediates cell division. recent data indicate that zipa is involved in the assembly of the ring by linking ftsz to the cytoplasmic membrane and that the zipa-ftsz interaction is mediated by their c-terminal domains. we present the x-ray crystal structures of the c-terminal ftsz-binding domain of zipa and a complex b ...	2000	10880432
models for estimating the non-specific toxicity of organic compounds in short-term bioassays.	the solvation parameter model is used to construct equations for the estimation of the non-specific toxicity of neutral organic compounds to five organisms used for short-term toxicity testing. for the bacteria vibrio fischeri (microtox test) and pseudomonas putida, the protozoan tetrahymena pyriformis (tetratox test), the green alga scendesmus quadricauda and the brine shrimp artemia salina, the main factors resulting in increased non-specific toxicity are size (dominantly) and lone-pair electr ...	2000	10885071
biosynthesis of pyridoxine: origin of the nitrogen atom of pyridoxine in microorganisms.	the amide nitrogen atom of glutamine was incorporated into pyridoxine in four eukaryotes, emericella nidulans, mucor racemosus, neurospora crassa and saccharomyces cerevisiae, and two prokaryotes, staphylococcus aureus and bacillus subtilis, but not in the following prokaryotes, pseudomonas putida, enterobacter aerogenes and escherichia coli. on the other hand, the nitrogen atom of glutamate was incorporated into pyridoxine in p. putida, e. aerogenes and e. coli, but not in s. aureus and b. subt ...	2000	10885790
indigo production by naphthalene-degrading bacteria.	a wild-type naphthalene-degrading strain pseudomonas putida rkj1 and two recombinant strains each of ps. putida and escherichia coli carrying the genes for naphthalene degradation on a recombinant plasmid prkj3, produced indigo and indirubin pigments from indole. naphthalene, salicylate and iptg induced cells of naphthalene-degrading recombinant bacteria produced up to two times higher indigo compared with the uninduced cells. the maximum rates of indigo formation by ps. putida rkj1, ps. putida ...	2000	10886605
structure-activity analysis of buforin ii, a histone h2a-derived antimicrobial peptide: the proline hinge is responsible for the cell-penetrating ability of buforin ii.	buforin ii is a 21-aa potent antimicrobial peptide that forms, in a hydrophobic medium, an amphipathic structure consisting of an n-terminal random coil region (residues 1-4), an extended helical region (residues 5-10), a hinge (residue 11), and a c-terminal regular alpha-helical region (residues 12-21). to elucidate the structural features of buforin ii that are required for its potent antimicrobial activity, we synthesized a series of n- and c-terminally truncated or amino acid-substituted syn ...	2000	10890923
structure of acinetobacter strain adp1 protocatechuate 3, 4-dioxygenase at 2.2 a resolution: implications for the mechanism of an intradiol dioxygenase.	the crystal structures of protocatechuate 3,4-dioxygenase from the soil bacteria acinetobacterstrain adp1 (ac 3,4-pcd) have been determined in space group i23 at ph 8.5 and 5.75. in addition, the structures of ac 3,4-pcd complexed with its substrate 3, 4-dihydroxybenzoic acid (pca), the inhibitor 4-nitrocatechol (4-nc), or cyanide (cn(-)) have been solved using native phases. the overall tertiary and quaternary structures of ac 3,4-pcd are similar to those of the same enzyme from pseudomonas put ...	2000	10891075
characterization of a second tfd gene cluster for chlorophenol and chlorocatechol metabolism on plasmid pjp4 in ralstonia eutropha jmp134(pjp4).	within the 5.9-kb dna region between the tfdr and tfdk genes on the 2,4-dichlorophenoxyacetic acid (2,4-d) catabolic plasmid pjp4 from ralstonia eutropha jmp134, we identified five open reading frames (orfs) with significant homology to the genes for chlorocatechol and chlorophenol metabolism (tfdcdef and tfdb) already present elsewhere on pjp4. the five orfs were organized and assigned as follows: tfdd(ii)c(ii)e(ii)f(ii) and tfdb(ii) (in short, the tfd(ii) cluster), by analogy to tfdcdef and tf ...	2000	10894723
biochemical-genetic characterization and distribution of oxa-22, a chromosomal and inducible class d beta-lactamase from ralstonia (pseudomonas) pickettii.	from genomic dna of ralstonia pickettii isolate pic-1, a beta-lactamase gene was cloned that encodes the oxacillinase oxa-22. it differs from known oxacillinases, being most closely related to oxa-9 (38% amino acid identity). the hydrolytic spectrum of oxa-22 is limited mostly to benzylpenicillin, cloxacillin, and restricted-spectrum cephalosporins. oxa-22-like genes were identified as single chromosomal copies in five other r. pickettii clinical isolates. the expression of oxa-22-like beta-lact ...	2000	10898703
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
interactions of dnaa proteins from distantly related bacteria with the replication origin of the broad host range plasmid rk2.	replication initiation of the broad host range plasmid rk2 requires binding of the host-encoded dnaa protein to specific sequences (dnaa boxes) at its replication origin (oriv). in contrast to a chromosomal replication origin, which functionally interacts only with the native dnaa protein of the organism, the ability of rk2 to replicate in a wide range of gram-negative bacterial hosts requires the interaction of oriv with many different dnaa proteins. in this study we compared the interactions o ...	2000	10749858
development of a new lysis solution for releasing genomic dna from bacterial cells for dna amplification by polymerase chain reaction.	a new lysis solution designated tz, consisting of 2.0% triton x-100 plus 2.5 mg sodium azide/ml in 0.1 m tris-hcl buffer at ph 8.0, yielded higher levels of genomic dna from escherichia coli o157:h7 cells compared with a number of other commonly used cell lysis methods. ethidium bromide stained dna bands resulting from pcr amplification of target dna from 100 cfu of e. coli o157:h7 were readily detected following electrophoresis of agarose gels. in contrast, conventional cell lysis methods faile ...	2000	10756522
cloning and characterization of the gene encoding rna polymerase sigma factor sigma(54) of deep-sea piezophilic shewanella violacea.	we have recently reported that a sigma(54)-like factor recognizes a dna element, designated as region a, upstream of a pressure-regulated operon in piezophilic shewanella violacea strain dss12 (nakasone et al., fems microbiology lett. 176 (1999) 351-356). in this study, we isolated and characterized the rpon gene of this piezophilic bacterium. the rpon gene was found to encode a putative protein consisting of 492 amino acid residues with a predicted molecular mass of 55359 da. significant homolo ...	2000	10760597
genetic analysis of functions involved in adhesion of pseudomonas putida to seeds.	many agricultural uses of bacteria require the establishment of efficient bacterial populations in the rhizosphere, for which colonization of plant seeds often constitutes a critical first step. pseudomonas putida kt2440 is a strain that colonizes the rhizosphere of a number of agronomically important plants at high population densities. to identify the functions involved in initial seed colonization by p. putida kt2440, we subjected this strain to transposon mutagenesis and screened for mutants ...	2000	10762233
a new is4 family insertion sequence, is4bsu1, responsible for genetic instability of poly-gamma-glutamic acid production in bacillus subtilis.	certain bacillus subtilis strains, such as b. subtilis (natto) starter strains for the manufacture of natto (fermented soybeans), produce capsular poly-gamma-glutamate (gammapga). in b. subtilis (natto), gammapga synthesis is controlled by the comp-coma two-component regulatory system and thereby induced at the beginning of the stationary growth phase. we have found a new insertion sequence (is), designated is4bsu1, in the comp gene of a spontaneous gammapga-negative mutant of b. subtilis (natto ...	2000	10762236
insertion mutagenesis and membrane topology model of the pseudomonas aeruginosa outer membrane protein oprm.	pseudomonas aeruginosa oprm is a protein involved in multiple-antibiotic resistance as the outer membrane component for the mexa-mexb-oprm efflux system. planar lipid bilayer experiments showed that oprm had channel-forming activity with an average single-channel conductance of only about 80 ps in 1 m kcl. the gene encoding oprm was subjected to insertion mutagenesis by cloning of a foreign epitope from the circumsporozoite form of the malarial parasite plasmodium falciparum into 11 sites. in es ...	2000	10762238
adp-ribosylation of variants of azotobacter vinelandii dinitrogenase reductase by rhodospirillum rubrum dinitrogenase reductase adp-ribosyltransferase.	in a number of nitrogen-fixing bacteria, nitrogenase is posttranslationally regulated by reversible adp-ribosylation of dinitrogenase reductase. the structure of the dinitrogenase reductase from azotobacter vinelandii is known. in this study, mutant forms of dinitrogenase reductase from a. vinelandii that are affected in various protein activities were tested for their ability to be adp-ribosylated or to form a complex with dinitrogenase reductase adp-ribosyltransferase (drat) from rhodospirillu ...	2000	10762264
characterization of an isogenic mutant of streptococcus pyogenes manfredo lacking the ability to make streptococcal acid glycoprotein.	an isogenic mutant of streptococcus pyogenes manfredo that lacks the ability to make streptococcal acid glycoprotein (sagp) has been constructed by inserting a deletion in the sagp gene using the method of allelic exchange. an assay of cell extracts (ce) prepared from the wild-type and mutant manfredo strains for the enzyme arginine deiminase (ad) showed that significant activity was present in wild-type ce but none could be detected in mutant ce. these findings confirm our earlier conclusion th ...	2000	10768929
outer membrane protein a, peptidoglycan-associated lipoprotein, and murein lipoprotein are released by escherichia coli bacteria into serum.	complexes containing lipopolysaccharide (lps) and three outer membrane proteins (omps) are released by gram-negative bacteria incubated in human serum and into the circulation in an experimental model of sepsis. the same omps are bound by immunoglobulin g (igg) in the cross-protective antiserum raised to escherichia coli j5 (anti-j5 igg). this study was performed to identify the three omps. the 35-kda omp was identified as outer membrane protein a (ompa) by immunoblotting studies using ompa-defi ...	2000	10768945
contribution of the hydrogen-bond network involving a tyrosine triad in the active site to the structure and function of a highly proficient ketosteroid isomerase from pseudomonas putida biotype b.	delta(5)-3-ketosteroid isomerase from pseudomonas putida biotype b is one of the most proficient enzymes catalyzing an allylic isomerization reaction at rates comparable to the diffusion limit. the hydrogen-bond network (asp99... wat504...tyr14...tyr55...tyr30) which links the two catalytic residues, tyr14 and asp99, to tyr30, tyr55, and a water molecule in the highly apolar active site has been characterized in an effort to identify its roles in function and stability. the deltag(u)(h2o) determ ...	2000	10769113
survival efficacy of the combination of the methioninase gene and methioninase in a lung cancer orthotopic model.	we have previously demonstrated the antitumor efficacy of recombinant methioninase (rmetase) derived from pseudomonas putida. to enhance the efficacy of rmetase, we have constructed the plgfp-metsn retrovirus encoding the p. putida methioninase (met) gene fused with the green fluorescent protein (gfp) gene. plgfp-metsn or control vector plgfpsn was introduced into the human lung cancer cell line h460. the methionine level of h460-gfp-met cells was reduced to 33% of that of h460-gfp cells. rmetas ...	2000	10770644
identification of the novobiocin biosynthetic gene cluster of streptomyces spheroides ncib 11891.	the novobiocin biosynthetic gene cluster from streptomyces spheroides ncib 11891 was cloned by using homologous deoxynucleoside diphosphate (dndp)-glucose 4,6-dehydratase gene fragments as probes. double-stranded sequencing of 25.6 kb revealed the presence of 23 putative open reading frames (orfs), including the gene for novobiocin resistance, gyrb(r), and at least 11 further orfs to which a possible role in novobiocin biosynthesis could be assigned. an insertional inactivation experiment with a ...	2000	10770754
design of a control system for biotransformation of toxic substrates: toluene hydroxylation by pseudomonas putida uv4.	using the hydroxylation of toluene to toluene cis-glycol by pseudomonas putida uv4 as an example, the design of a feed-back control system for the addition of a toxic, poorly water-soluble substrate to a fed-batch biotransformation is described. in kinetic studies the reaction followed michaelis-menten behavior until toxic toluene concentrations were reached (2.4 mm), above which irreversible denaturation of the biocatalyst was observed. an algorithm, based on a system mass balance, was used to ...	2000	10771056
characterization and expression of the pseudomonas putida bacterioferritin alpha subunit gene.	the root-colonizing pseudomonad pseudomonas putida (pp) appears to produce two subunits, alpha and beta, of the iron-binding protein, bacterioferritin. a gene encoding the alpha-bacterioferritin subunit was located adjacent to the major catalase in pp. the deduced protein sequence of the pp bfralpha gene had a very high identity with other alpha-subunits, possessing conserved amino acids responsible for ferroxidase activity. the gene also lacked a deduced methionine at residue 52, associated wit ...	2000	10773460
[microbial destruction of cyanide and thiocyanate].	the role played by a bacterial community composed of pseudomonas putida, strain 21, pseudomonas stutzeri, strain 18, and pseudomonas sp., strain 5, and by physical and chemical factors in the degradation of cn- and scn- was studied. it was shown that the degradation of cn- is determined both by the action of bacteria and by abiotic physical and chemical factors (ph, o2, temperature, the medium agitation rate, etc.). the contribution of chemical degradation was found to increase drastically at ph ...	2000	10776620
deletion analysis of the escherichia coli taurine and alkanesulfonate transport systems.	the escherichia coli tauabcd and ssueadcb gene clusters are required for the utilization of taurine and alkanesulfonates as sulfur sources and are expressed only under conditions of sulfate or cysteine starvation. taud and ssud encode an alpha-ketoglutarate-dependent taurine dioxygenase and a reduced flavin mononucleotide-dependent alkanesulfonate monooxygenase, respectively. these enzymes are responsible for the desulfonation of taurine and alkanesulfonates. the amino acid sequences of ssuabc a ...	2000	10781534
haloalkane-utilizing rhodococcus strains isolated from geographically distinct locations possess a highly conserved gene cluster encoding haloalkane catabolism.	the sequences of the 16s rrna and haloalkane dehalogenase (dhaa) genes of five gram-positive haloalkane-utilizing bacteria isolated from contaminated sites in europe, japan, and the united states and of the archetypal haloalkane-degrading bacterium rhodococcus sp. strain ncimb13064 were compared. the 16s rrna gene sequences showed less than 1% sequence divergence, and all haloalkane degraders clearly belonged to the genus rhodococcus. all strains shared a completely conserved dhaa gene, suggesti ...	2000	10781539
the ssu locus plays a key role in organosulfur metabolism in pseudomonas putida s-313.	pseudomonas putida s-313 can utilize a broad range of aromatic sulfonates as sulfur sources for growth in sulfate-free minimal medium. the sulfonates are cleaved monooxygenolytically to yield the corresponding phenols. minitn5 mutants of strain s-313 which were no longer able to desulfurize arylsulfonates were isolated and were found to carry transposon insertions in the ssueadcbf operon, which contained genes for an atp-binding cassette-type transporter (ssuabc), a two-component reduced flavin ...	2000	10781557
fabg, an nadph-dependent 3-ketoacyl reductase of pseudomonas aeruginosa, provides precursors for medium-chain-length poly-3-hydroxyalkanoate biosynthesis in escherichia coli.	escherichia coli hosts expressing fabg of pseudomonas aeruginosa showed 3-ketoacyl coenzyme a (coa) reductase activity toward r-3-hydroxyoctanoyl-coa. furthermore, e. coli recombinants carrying the poly-3-hydroxyalkanoate (pha) polymerase-encoding gene phac in addition to fabg accumulated medium-chain-length phas (mcl-phas) from alkanoates. when e. coli fadb or fada mutants, which are deficient in steps downstream or upstream of the 3-ketoacyl-coa formation step during beta-oxidation, respective ...	2000	10781572
purification to homogeneity and characterization of a novel pseudomonas putida chromate reductase.	cr(vi) (chromate) is a widespread environmental contaminant. bacterial chromate reductases can convert soluble and toxic chromate to the insoluble and less toxic cr(iii). bioremediation can therefore be effective in removing chromate from the environment, especially if the bacterial propensity for such removal is enhanced by genetic and biochemical engineering. to clone the chromate reductase-encoding gene, we purified to homogeneity (>600-fold purification) and characterized a novel soluble chr ...	2000	10788340
quantification of phnac and nahac in contaminated new zealand soils by competitive pcr.	unculturable polycyclic aromatic hydrocarbon (pah)-degrading bacteria are a significant reservoir of the microbial potential to catabolize low-molecular-weight pahs. the population of these bacteria is larger than the population of nah-like bacteria that are the dominant organisms in culture-based studies. we used the recently described phn genes of burkholderia sp. strain rp007, which feature only rarely in culture-based studies, as an alternative genotype for naphthalene and phenanthrene degra ...	2000	10788344