Publications

crystal structure of nadh-dependent ferredoxin reductase component in biphenyl dioxygenase.	oxidative biodegradation of aromatic compounds by bacteria usually begins with hydroxylation of the aromatic ring by multi-component dioxygenases like benzene dioxygenase, biphenyl dioxygenase, and others. these enzymes are composed of ferredoxin reductase, ferredoxin, and terminal oxygenase. reducing equivalents that originate from nadh are transferred from ferredoxin reductase to ferredoxin and, in turn, to the terminal oxygenase, thus resulting in the activation of a dioxygen. bpha4 is the fe ...	2000	11090282
automated sample-preparation technologies in genome sequencing projects.	a robotic workstation system (biorobot 96oo, qiagen) and a 96-well uv spectrophotometer (spectramax 250, molecular devices) were integrated in to the process of high-throughput automated sequencing of double-stranded plasmid dna templates. an automated 96-well miniprep kit protocol (qiaprep turbo, qiagen) provided high-quality plasmid dna from shotgun clones. the dna prepared by this procedure was used to generate more than two mega bases of final sequence data for two genomic projects (arabidop ...	2000	11092729
phenotypes of fission yeast defective in ubiquinone production due to disruption of the gene for p-hydroxybenzoate polyprenyl diphosphate transferase.	ubiquinone is an essential component of the electron transfer system in both prokaryotes and eukaryotes and is synthesized from chorismate and polyprenyl diphosphate by eight steps. p-hydroxybenzoate (phb) polyprenyl diphosphate transferase catalyzes the condensation of phb and polyprenyl diphosphate in ubiquinone biosynthesis. we isolated the gene (designated ppt1) encoding phb polyprenyl diphosphate transferase from schizosaccharomyces pombe and constructed a strain with a disrupted ppt1 gene. ...	2000	11092853
transcriptional control of the hydrogen cyanide biosynthetic genes hcnabc by the anaerobic regulator anr and the quorum-sensing regulators lasr and rhlr in pseudomonas aeruginosa.	virulence factors of pseudomonas aeruginosa include hydrogen cyanide (hcn). this secondary metabolite is maximally produced at low oxygen tension and high cell densities during the transition from exponential to stationary growth phase. the hcnabc genes encoding hcn synthase were identified on a genomic fragment complementing an hcn-deficient mutant of p. aeruginosa pao1. the hcna promoter was found to be controlled by the fnr-like anaerobic regulator anr and by the quorum-sensing regulators las ...	2000	11092854
the 4-oxalomesaconate hydratase gene, involved in the protocatechuate 4,5-cleavage pathway, is essential to vanillate and syringate degradation in sphingomonas paucimobilis syk-6.	sphingomonas paucimobilis syk-6 is able to grow on various dimeric lignin compounds, which are converted to vanillate and syringate by the actions of unique lignin degradation enzymes in this strain. vanillate and syringate are degraded by the o-demethylase and converted into protocatechuate (pca) and 3-o-methylgallate (3mga), respectively. pca is further degraded via the pca 4,5-cleavage pathway, while the results suggested that 3mga is degraded through another pathway in which pca 4,5-dioxygen ...	2000	11092855
functional expression and characterization of the two cyclic amidohydrolase enzymes, allantoinase and a novel phenylhydantoinase, from escherichia coli.	a superfamily of cyclic amidohydrolases, including dihydropyrimidinase, allantoinase, hydantoinase, and dihydroorotase, all of which are involved in the metabolism of purine and pyrimidine rings, was recently proposed based on the rigidly conserved structural domains in identical positions of the related enzymes. with these conserved domains, two putative cyclic amidohydrolase genes from escherichia coli, flanked by related genes, were identified and characterized. from the genome sequence of e. ...	2000	11092864
mutations in catb, the gene encoding muconate cycloisomerase, activate transcription of the distal ben genes and contribute to a complex regulatory circuit in acinetobacter sp. strain adp1.	mutants of the bacterium acinetobacter sp. strain adp1 were selected to grow on benzoate without the benm transcriptional activator. in the wild type, benm responds to benzoate and cis,cis-muconate to activate expression of the benabcde operon, which is involved in benzoate catabolism. this operon encodes enzymes that convert benzoate to catechol, a compound subsequently degraded by cat gene-encoded enzymes. in this report, four spontaneous mutants were found to carry catb mutations that enabled ...	2000	11092867
transcription activation by a variety of arac/xyls family activators does not depend on the class ii-specific activation determinant in the n-terminal domain of the rna polymerase alpha subunit.	the n-terminal domain of the rna polymerase alpha subunit (alpha-ntd) was tested for a role in transcription activation by a variety of arac/xyls family members. based on substitutions at residues 162 to 165 and an extensive genetic screen we conclude that alpha-ntd is not an activation target for these activators.	2000	11092872
characterization of gtpase activity of trme, a member of a novel gtpase superfamily, from thermotoga maritima.	a gene encoding a putative gtp-binding protein, a trme homologue that is highly conserved in both prokaryotes and eukaryotes, was cloned from thermotoga maritima, a hyperthermophilic bacterium. t. maritima trme was overexpressed in escherichia coli and purified. trme has a gtpase activity but no atpase activity. the gtpase activity can be competed with gtp, gdp, and dgtp but not with gmp, atp, ctp, or utp. k(m) and k(cat) at 70 degrees c were 833 microm and 9.3 min(-1), respectively. our results ...	2000	11092873
crystallization and preliminary crystallographic characterization of recombinant l-methionine-alpha-deamino-gamma-mercaptomethane lyase (methioninase).	l-methionine-alpha-deamino-gamma-mercaptomethane lyase (rmetase) is involved in the alpha,gamma-elimination of methionine to alpha-ketobutyrate, methanethiol and ammonia. the reaction catalyzed by rmetase reduces the methionine concentration of methionine-dependent tumor cells, arresting their growth. towards the goal of developing rmetase into an effective antitumor therapeutic and also to understand the catalytic mechanism of this enzyme, rmetase from pseudomonas putida has been expressed, pur ...	2000	11092940
sequence of pha synthase gene from two strains of rhodospirillum rubrum and in vivo substrate specificity of four pha synthases across two heterologous expression systems.	a 3.0-kb genomic fragment has been isolated from rhodospirillum rubrum (atcc 25903) that contains an open reading frame (orf) with strong homology to other known polyhydroxyalkanoate (pha) synthase genes. this orf has lower homology to the r. rubrum strain ha pha synthase than would be expected within the same species. we have conducted a series of heterologous expression studies evaluating the in vivo substrate specificity of pha synthase genes from rhodobacter sphaeroides, ralstonia eutropha ( ...	2000	10803898
identification of an effector specificity subregion within the aromatic-responsive regulators dmpr and xylr by dna shuffling.	the pseudomonas derived sigma(54)-dependent regulators dmpr and xylr control the expression of genes involved in catabolism of aromatic compounds. binding to distinct, nonoverlapping groups of aromatic effectors controls the activities of these transcriptional activators. previous work has derived a common mechanistic model for these two regulators in which effector binding by the n-terminal 210 residues (the a-domain) of the protein relieves repression of an intrinsic atpase activity essential ...	2000	10809676
a complex insertion sequence cluster at a point of interaction between the linear plasmid scp1 and the linear chromosome of streptomyces coelicolor a3(2).	the giant linear plasmid scp1 can integrate into the central region of the linear chromosome of streptomyces coelicolor a3(2). nucleotide sequence analysis around the target site for scp1 integration in strain m145 identified a total of five copies of four insertion sequences (iss) in a 6.5-kb dna stretch. three of the four (is468, is469, and is470) are new is elements, and the other is is466. all of these elements contain one open reading frame which encodes a transposase-like protein. two copi ...	2000	10809688
cloning and expression of ntnd, encoding a novel nad(p)(+)-independent 4-nitrobenzyl alcohol dehydrogenase from pseudomonas sp. strain tw3.	pseudomonas sp. strain tw3 is able to metabolize 4-nitrotoluene to 4-nitrobenzoate and toluene to benzoate aerobically via a route analogous to the upper pathway of the tol plasmids. we report the cloning and characterization of a benzyl alcohol dehydrogenase gene (ntnd) which encodes the enzyme for the catabolism of 4-nitrobenzyl alcohol and benzyl alcohol to 4-nitrobenzaldehyde and benzaldehyde, respectively. the gene is located downstream of the previously reported ntn gene cluster. ntnd bear ...	2000	10809692
branched-chain alpha-keto acid catabolism via the gene products of the bkd operon in enterococcus faecalis: a new, secreted metabolite serving as a temporary redox sink.	recently the bkd gene cluster from enterococcus faecalis was sequenced, and it was shown that the gene products constitute a pathway for the catabolism of branched-chain alpha-keto acids. we have now investigated the regulation and physiological role of this pathway. primer extension analysis identified the presence of a single promoter upstream of the bkd gene cluster. furthermore, a putative catabolite-responsive element was identified in the promoter region, indicative of catabolite repressio ...	2000	10809705
a bacterial sensor of plant cell contact controls the transcriptional induction of ralstonia solanacearum pathogenicity genes.	the hrp genes of the plant pathogen ralstonia solanacearum are key pathogenicity determinants; they encode a type iii protein secretion machinery involved in the secretion of mediators of the bacterium-plant interaction. these hrp genes are under the genetic control of the hrpb regulatory gene, expression of which is induced when bacteria are co-cultivated with plant cell suspensions. in this study, we used hrp-gfp transcriptional fusions to demonstrate that the expression of the hrpb and type i ...	2000	10811621
domain organization and flavin adenine dinucleotide-binding determinants in the aerotaxis signal transducer aer of escherichia coli.	aerotactic responses in escherichia coli are mediated by the membrane transducer aer, a recently identified member of the superfamily of pas domain proteins, which includes sensors of light, oxygen, and redox state. initial studies of aer suggested that it might use a flavin adenine dinucleotide (fad) prosthetic group to monitor cellular redox changes. to test this idea, we purified lauryl maltoside-solubilized aer protein by his-tag affinity chromatography and showed by high performance liquid ...	2000	10811894
metabolic pathways for cytotoxic end product formation from glutamate- and aspartate-containing peptides by porphyromonas gingivalis.	metabolic pathways involved in the formation of cytotoxic end products by porphyromonas gingivalis were studied. the washed cells of p. gingivalis atcc 33277 utilized peptides but not single amino acids. since glutamate and aspartate moieties in the peptides were consumed most intensively, a dipeptide of glutamate or aspartate was then tested as a metabolic substrate of p. gingivalis. p. gingivalis cells metabolized glutamylglutamate to butyrate, propionate, acetate, and ammonia, and they metabo ...	2000	10940008
in vivo and in vitro effects of (p)ppgpp on the sigma(54) promoter pu of the tol plasmid of pseudomonas putida.	the connection between the physiological control of the sigma(54)-dependent pu promoter of the tol plasmid pww0 of pseudomonas putida and the stringent response mediated by the alarmone (p)ppgpp has been examined in vivo an in vitro. to this end, the key regulatory elements of the system were faithfully reproduced in an escherichia coli strain and assayed as lacz fusions in various genetic backgrounds lacking (p)ppgpp or overexpressing rela. neither the responsiveness of pu to 3-methyl benzylalc ...	2000	10940009
genetic analysis of a gene cluster for cyclohexanol oxidation in acinetobacter sp. strain se19 by in vitro transposition.	biological oxidation of cyclic alcohols normally results in formation of the corresponding dicarboxylic acids, which are further metabolized and enter the central carbon metabolism in the cell. we isolated an acinetobacter sp. from an industrial wastewater bioreactor that utilized cyclohexanol as a sole carbon source. a cosmid library was constructed from acinetobacter sp. strain se19, and oxidation of cyclohexanol to adipic acid was demonstrated in recombinant escherichia coli carrying a se19 d ...	2000	10940013
mutations in each of the tol genes of pseudomonas putida reveal that they are critical for maintenance of outer membrane stability.	the outer membrane of gram-negative bacteria functions as a permeability barrier that protects cells against a large number of antibacterial agents. oprl protein of pseudomonas putida has been shown to be crucial to maintain the stability of this cell component (j. j. rodríguez-herva, m.-i. ramos-gonzález, and j. l. ramos. j. bacteriol. 178:1699-1706, 1996). in the present study we cloned and mutagenized the orf1, tolq, tolr, tola, and tolb genes from p. putida kt2440, which were located upstrea ...	2000	10940016
entry into and release of solvents by escherichia coli in an organic-aqueous two-liquid-phase system and substrate specificity of the acrab-tolc solvent-extruding pump.	growth of escherichia coli is inhibited upon exposure to a large volume of a harmful solvent, and there is an inverse correlation between the degree of inhibition and the log p(ow) of the solvent, where p(ow) is the partition coefficient measured for the partition equilibrium established between the n-octanol and water phases. the acrab-tolc efflux pump system is involved in maintaining intrinsic solvent resistance. we inspected the solvent resistance of delta acrab and/or delta tolc mutants in ...	2000	10940021
identification of the gene encoding sulfopyruvate decarboxylase, an enzyme involved in biosynthesis of coenzyme m.	the products of two adjacent genes in the chromosome of methanococcus jannaschii are similar to the amino and carboxyl halves of phosphonopyruvate decarboxylase, the enzyme that catalyzes the second step of fosfomycin biosynthesis in streptomyces wedmorensis. these two m. jannaschii genes were recombinantly expressed in escherichia coli, and their gene products were tested for the ability to catalyze the decarboxylation of a series of alpha-ketoacids. both subunits are required to form an alpha( ...	2000	10940029
genetic evidence that transcription activation by rhas involves specific amino acid contacts with sigma 70.	rhas activates transcription of the escherichia coli rhabad and rhat operons in response to l-rhamnose and is a member of the arac/xyls family of transcription activators. we wished to determine whether sigma(70) might be an activation target for rhas. we found that sigma(70) k593 and r599 appear to be important for rhas activation at both rhabad and rhat, but only at truncated promoters lacking the binding site for the second activator, crp. to determine whether these positively charged sigma(7 ...	2000	10940041
versatile biosensor vectors for detection and quantification of mercury.	three different whole cell biosensor constructs were made by fusing the mercury inducible promoter, p(mer), and its regulatory gene, merr, from transposon tn21 with reporter genes luxcdabe, laczya, or gfp. in escherichia coli these biosensor constructs responded to low levels of mercury by producing light, beta-galactosidase or green fluorescent protein, respectively. since the responses were quantitative, the constructs were used to quantify bioavailable mercury in different environments. the c ...	2000	11094290
cofactor regeneration by a soluble pyridine nucleotide transhydrogenase for biological production of hydromorphone.	we have applied the soluble pyridine nucleotide transhydrogenase of pseudomonas fluorescens to a cell-free system for the regeneration of the nicotinamide cofactors nad and nadp in the biological production of the important semisynthetic opiate drug hydromorphone. the original recombinant whole-cell system suffered from cofactor depletion resulting from the action of an nadp(+)-dependent morphine dehydrogenase and an nadh-dependent morphinone reductase. by applying a soluble pyridine nucleotide ...	2000	11097884
zoospore homing and infection events: effects of the biocontrol bacterium burkholderia cepacia ammdr1 on two oomycete pathogens of pea (pisum sativum l.).	burkholderia cepacia ammdr1 is a biocontrol agent that protects pea and sweet corn seeds from pythium damping-off in field experiments. the goal of this work was to understand the effect of b. cepacia ammdr1 on pythium aphanidermatum and aphanomyces euteiches zoospore homing events and on infection of pea seeds or roots. in vitro, b. cepacia ammdr1 caused zoospore lysis, prevented cyst germination, and inhibited germ tube growth of both oomycetes. b. cepacia ammdr1 also reduced the attractivenes ...	2000	11097889
control of expression of divergent pseudomonas putida put promoters for proline catabolism.	pseudomonas putida kt2440 uses proline as the sole c and n source. utilization of this amino acid involves its uptake, which is mediated by the putp protein, and its conversion into glutamate, mediated by the puta protein. sequence analysis revealed that the puta and putp genes are transcribed divergently. expression from the putp and puta genes was analyzed at the mrna level in different host backgrounds in the absence and presence of proline. expression from the put promoters was induced by pr ...	2000	11097893
relationship between nitrite reduction and active phosphate uptake in the phosphate-accumulating denitrifier pseudomonas sp. strain jr 12.	phosphate uptake by the phosphate-accumulating denitrifier pseudomonas sp. jr12 was examined with different combinations of electron and carbon donors and electron acceptors. phosphate uptake in acetate-supplemented cells took place with either oxygen or nitrate but did not take place when nitrite served as the final electron acceptor. furthermore, nitrite reduction rates by this denitrifier were shown to be significantly reduced in the presence of phosphate. phosphate uptake assays in the prese ...	2000	11097896
composition of soil microbial communities enriched on a mixture of aromatic hydrocarbons.	soil contaminated with c5+, which contained benzene (45%, wt/wt), dicyclopentadiene (dcpd) plus cyclopentadiene (together 20%), toluene (6%), styrene (3%), xylenes (2%), naphthalene (2%), and smaller quantities of other compounds, served as the source for isolation of 55 genomically distinct bacteria (standards). use of benzene as a substrate by these bacteria was most widespread (31 of 44 standards tested), followed by toluene (23 of 44), xylenes (14 of 44), styrene (10 of 44), and naphthalene ...	2000	11097903
fatty acid competition as a mechanism by which enterobacter cloacae suppresses pythium ultimum sporangium germination and damping-off.	interactions between plant-associated microorganisms play important roles in suppressing plant diseases and enhancing plant growth and development. while competition between plant-associated bacteria and plant pathogens has long been thought to be an important means of suppressing plant diseases microbiologically, unequivocal evidence supporting such a mechanism has been lacking. we present evidence here that competition for plant-derived unsaturated long-chain fatty acids between the biological ...	2000	11097912
uptake and active efflux of polycyclic aromatic hydrocarbons by pseudomonas fluorescens lp6a.	the mechanism of transport of polycyclic aromatic hydrocarbons (pahs) by pseudomonas fluorescens lp6a, a pah-degrading bacterium, was studied by inhibiting membrane transport and measuring the resulting change in cellular uptake. three cultures were used: wild-type lp6a which carried a plasmid for pah degradation, a transposon mutant lacking the first enzyme in the pathway for pah degradation, and a cured strain without the plasmid. washed cells were mixed with aqueous solutions of radiolabelled ...	2000	11097918
diversity of l-methionine catabolism pathways in cheese-ripening bacteria.	enzymatic activities that could be involved in methanethiol generation in five cheese-ripening bacteria were assayed, and the major sulfur compounds produced were identified. l-methionine and alpha-keto-gamma-methyl-thio-butyric acid demethiolating activities were detected in whole cells and cell extracts (cfes) of all the bacteria tested. no l-methionine deaminase activity could be detected in any of the ripening bacteria and l-methionine aminotransferase was detected in cfes of brevibacterium ...	2000	11097940
bacterial toxin-antitoxin gene system as containment control in yeast cells.	the potential of a bacterial toxin-antitoxin gene system for use in containment control in eukaryotes was explored. the escherichia coli rele and relb genes were expressed in the yeast saccharomyces cerevisiae. expression of the rele gene was highly toxic to yeast cells. however, expression of the relb gene counteracted the effect of rele to some extent, suggesting that toxin-antitoxin interaction also occurs in s. cerevisiae. thus, bacterial toxin-antitoxin gene systems also have potential appl ...	2000	11097943
isolation and characterisation of ethoprophos-degrading bacteria.	an enrichment culture technique was used to isolate bacteria responsible for the enhanced biodegradation of ethoprophos in a soil from northern greece. restriction fragment length polymorphism patterns of the 16s rrna gene, partial 16s rrna sequence analysis, and sodium dodecylsulfate-polyacrylamide gel electrophoresis total protein profile analysis were used to characterise the isolated bacteria. two of the three ethoprophos-degrading cultures were pure and both isolates were classified as stra ...	2000	11098072
a bioluminescent derivative of pseudomonas putida kt2440 for deliberate release into the environment.	recombinant derivatives of pseudomonas putida strain kt2440 are of potential interest as microbial inoculants to be deliberately released for agricultural applications. to facilitate tracking of this strain and its derivatives after introduction into the environment, a mini-tn5-'luxab transposon was introduced into the chromosome of p. putida kt2440, yielding strain p. putida s1b1. sequencing of the dna region located upstream of the 'luxab genes and similarity search with the p. putida kt2440 g ...	2000	11102686
pseudo-outbreak of pseudomonas putida in a hospital outpatient clinic originating from a contaminated commercial anti-fog solution--vancouver, british columbia.		2000	11107658
directed evolution of toluene dioxygenase from pseudomonas putida for improved selectivity toward cis-indandiol during indene bioconversion.	toluene dioxygenase (tdo) from pseudomonas putida f1 converts indene to a mixture of cis-indandiol (racemic), 1-indenol, and 1-indanone. the desired product, cis-(1s,2r)-indandiol, is a potential key intermediate in the chemical synthesis of indinavir sulfate (crixivan), merck's hiv-1 protease inhibitor for the treatment of aids. to reduce the undesirable byproducts 1-indenol and 1-indanone formed during indene bioconversion, the recombinant tdo expressed in escherichia coli was evolved by direc ...	2000	11120645
use of substrate responsive-direct viable counts to visualize naphthalene degrading bacteria in a coal tar-contaminated groundwater microbial community.	a microscopy-based method was developed to distinguish naphthalene-degrading bacteria within the microbial community of a coal tar-contaminated groundwater system. pure cultures of pseudomonas putida ncib 9816-4 were used to develop the substrate responsive-direct viable count (sr-dvc) method. cells were concentrated on membrane filters, placed on agar plates of stanier's minimal basal salts media containing antibiotics (nalidixic acid, piromidic acid, pipemidic acid, and cephalexin), and expose ...	2000	11121606
role of yersinia intermedia and pseudomonas putida in the development of a fruity off-flavour in pasteurized milk.	analysis by gas chromatography-mass spectrometry of pasteurized milk with a fruity (pineapple like) off odour and a sour, rancid and soapy taste indicated the presence of concentrations at microg/ml levels of ethyl butanoate, ethyl hexanoate, ethyl octanoate, ethyl decanoate, octanoic acid, decanoic acid and dodecanoic acid. the off-odour and taste were attributed to the presence of these compounds in the milk. microbiological examination confirmed that the milk was also contaminated with a seri ...	2000	11131069
genetic transformation and biotechnological application of the yeast arxula adeninivorans.	the relatively unknown, non-pathogenic, dimorphic, haploid, ascomycetous yeast arxula adeninivorans exhibits some unusual properties which are of biotechnological interest. the yeast is able to assimilate and ferment many compounds as sole source of carbon and/or nitrogen, it utilises n-alkanes and degrades starch efficiently. a. adeninivorans features such as thermo- and haloresistance as well as the yeast's uncommon growth and secretion behaviour should be especially emphasised. in media conta ...	2000	11131385
homologous functional expression of cryptic phag from pseudomonas oleovorans establishes the transacylase-mediated polyhydroxyalkanoate biosynthetic pathway.	various pseudomonads are capable of the synthesis of polyhydroxyalkanoate (pha), composed of medium chain length (mcl) 3-hydroxy fatty acids (c6-c14), when grown on simple carbon sources such as, for example, gluconate or acetate. in pseudomonas putida, the fatty acid de novo synthesis and pha synthesis are linked by the transacylase phag. southern hybridization experiments with digoxigenin-labeled phag(pp) from p. putida and genomic dna from various pseudomonads indicate that phag homologues ar ...	2000	11131392
the solvent efflux system of pseudomonas putida s12 is not involved in antibiotic resistance.	the active efflux system contributing to the solvent tolerance of pseudomonas putida s12 was characterized physiologically. the mutant p. putida jk1, which lacks the active efflux system, was compared with the wild-type organism. none of 20 known substrates of common multi-drug-resistant pumps had a stronger growth-inhibiting effect on the mutant than on the wild type. the amount of [14c]toluene accumulating in p. putida s12 increased in the presence of the solvent xylene and in the presence of ...	2000	11131400
evaluation of mycobacterium tuberculosis genes involved in resistance to killing by human macrophages.	a coinfection assay was developed to examine mycobacterium tuberculosis genes suspected to be involved in resistance to killing by human macrophages. thp-1 macrophages were infected with a mixture of equal numbers of recombinant mycobacterium smegmatis lr222 bacteria expressing an m. tuberculosis gene and wild-type m. smegmatis lr222 bacteria expressing the xyle gene. at various times after infection, the infected macrophages were lysed and the bacteria were plated. the resulting colonies were s ...	2000	10603413
bacillus subtilis lrpc is a sequence-independent dna-binding and dna-bending protein which bridges dna.	genetic evidence suggests that the bacillus subtilis lrpc gene product participates in cell growth and sporulation. the purified lrpc protein, which has a predicted molecular mass of 16.4 kda, is a tetramer in solution. lrpc binds with higher affinity ( k (app) approximately 80 nm) to intrinsically curved dna than to non-curved dna ( k (app) approximately 700 nm). dnase i footprinting and the supercoiling of relaxed circular plasmid dna in the presence of topoisomerase i revealed that lrpc induc ...	2000	10606655
an aerotaxis transducer gene from pseudomonas putida.	an aerotaxis gene, aer, was cloned from pseudomonas putida prs2000. a p. putida aer mutant displayed an altered aerotactic response in a capillary assay. wild-type p. putida clustered at the air/liquid interface. in contrast, the aer mutant did not cluster at the interface, but instead formed a diffuse band at a distance from the meniscus. wild-type aer, provided in trans, complemented the aer mutant to an aerotactic response that was stronger than wild-type. the p. putida aer sequence is simila ...	2000	10612751
characterization of the endogenous plasmid from pseudomonas alcaligenes ncib 9867: dna sequence and mechanism of transfer.	the endogenous plasmid pra2 from pseudomonas alcaligenes ncib 9867 was determined to have 32,743 bp with a g+c content of 59.8%. sequence analysis predicted a total of 29 open reading frames, with approximately half of them contributing towards the functions of plasmid replication, mobilization, and stability. the pac25i restriction-modification system and two mobile elements, tn5563 and is1633, were physically localized. an additional eight open reading frames with unknown functions were also d ...	2000	10613866
proline catabolism by pseudomonas putida: cloning, characterization, and expression of the put genes in the presence of root exudates.	pseudomonas putida kt2442 is a root-colonizing strain which can use proline, one of the major components in root exudates, as its sole carbon and nitrogen source. a p. putida mutant unable to grow with proline as the sole carbon and nitrogen source was isolated after random mini-tn5-km mutagenesis. the mini-tn5 insertion was located at the puta gene, which is adjacent to and divergent from the putp gene. the puta gene codes for a protein of 1,315 amino acid residues which is homologous to the pu ...	2000	10613867
hbar, a 4-hydroxybenzoate sensor and fnr-crp superfamily member, regulates anaerobic 4-hydroxybenzoate degradation by rhodopseudomonas palustris.	under anaerobic conditions, structurally diverse aromatic compounds are catabolized by bacteria to form benzoyl-coenzyme a (benzoyl-coa), the starting compound for a central reductive pathway for aromatic ring degradation. the structural genes required for the conversion of 4-hydroxybenzoate (4-hba) to benzoyl-coa by rhodopseudomonas palustris have been identified. here we describe a regulatory gene, hbar, that is part of the 4-hba degradation gene cluster. an hbar mutant that was constructed wa ...	2000	10613868
identification of a new class of 5'-adenylylsulfate (aps) reductases from sulfate-assimilating bacteria.	a gene was cloned from burkholderia cepacia dbo1 that is homologous with escherichia coli cysh encoding 3'-phosphoadenylylsulfate (paps) reductase. the b. cepacia gene is the most recent addition to a growing list of cysh homologs from a diverse group of sulfate-assimilating bacteria whose products show greater homology to plant 5'-adenylylsulfate (aps) reductase than they do to e. coli cysh. the evidence reported here shows that the cysh from one of the species, pseudomonas aeruginosa, encodes ...	2000	10613872
convenient test for screening metallo-beta-lactamase-producing gram-negative bacteria by using thiol compounds.	a simple disk diffusion test was constructed for detection of imp-1-type metallo-beta-lactamase-producing gram-negative bacteria. two kirby-bauer disks containing ceftazidime (caz) and a filter disk containing a metallo-beta-lactamase inhibitor were used in this test. several imp-1 inhibitors such as thiol compounds including 2-mercaptopropionic acid, heavy metal salts, and edta were evaluated for this test. two caz disks were placed on a mueller-hinton agar plate on which a bacterial suspension ...	2000	10618060
differentiation of phylogenetically related slowly growing mycobacteria by their gyrb sequences.	the conventional methods for identifying mycobacterial species are based on their phenotypic characterization. since some problematic species are slow growers, their taxonomy takes several weeks or months to identify. the ribosomal dna (rdna) sequence-based identification strategy has been adopted to solve this problem. more recently, the gyrb sequences have been shown to be useful phylogenetic markers for the identification of species. we determined the gyrb sequences of 43 slowly growing strai ...	2000	10618105
importance of pfka for rapid growth of enterobacter cloacae during colonization of crop seeds.	enterobacter cloacae a-11 is a prototrophic, glycolytic mutant of strain 501r3 with a single transposon insertion in pfka. the populations of strain a-11 on cucumber and radish seeds were smaller than the populations of strain 501r3 in natural soil, but the populations of these two strains on pea, soybean, sunflower, and sweet corn seeds were similar (d. p. roberts, p. d. dery, i. yucel, j. buyer, m. a. holtman, and d. y. kobayashi, appl. environ. microbiol. 65:2513-2519, 1999). the net effect o ...	2000	10618207
the ntrb and ntrc genes are involved in the regulation of poly-3-hydroxybutyrate biosynthesis by ammonia in azospirillum brasilense sp7.	azospirillum brasilense sp7 and its ntra (rpon), ntrbc, and ntrc mutants have been evaluated for their capabilities of poly-3-hydroxybutyrate (phb) accumulation in media with high and low ammonia concentrations. it was observed that the ntrbc and ntrc mutants can produce phb in both low- and high-c/n-ratio media, while no significant phb production was observed for the wild type or the ntra mutant in low-c/n-ratio media. further investigation by fermentation analysis indicated that the ntrbc and ...	2000	10618211
generation of novel bacterial regulatory proteins that detect priority pollutant phenols.	the genetic systems of bacteria that have the ability to use organic pollutants as carbon and energy sources can be adapted to create bacterial biosensors for the detection of industrial pollution. the creation of bacterial biosensors is hampered by a lack of information about the genetic systems that control production of bacterial enzymes that metabolize pollutants. we have attempted to overcome this problem through modification of dmpr, a regulatory protein for the phenol degradation pathway ...	2000	10618218
production and comparison of peptide siderophores from strains of distantly related pathovars of pseudomonas syringae and pseudomonas viridiflava lmg 2352.	the production of peptide siderophores and the variation in siderophore production among strains of pseudomonas syringae and pseudomonas viridiflava were investigated. an antibiose test was used to select a free amino acid-containing agar medium favorable for production of fluorescent siderophores by two p. syringae strains. a culture technique in which both liquid and solid asparagine-containing culture media were used proved to be reproducible and highly effective for inducing production of si ...	2000	10618243
molecular characterization of the toxic cyanobacterium cylindrospermopsis raciborskii and design of a species-specific pcr.	cylindrospermopsis raciborskii is a toxic-bloom-forming cyanobacterium that is commonly found in tropical to subtropical climatic regions worldwide, but it is also recognized as a common component of cyanobacterial communities in temperate climates. genetic profiles of c. raciborskii were examined in 19 cultured isolates originating from geographically diverse regions of australia and represented by two distinct morphotypes. a 609-bp region of rpoc1, a dna-dependent rna polymerase gene, was ampl ...	2000	10618244
role of leaf surface sugars in colonization of plants by bacterial epiphytes.	the relationship between nutrients leached onto the leaf surface and the colonization of plants by bacteria was studied by measuring both the abundance of simple sugars and the growth of pseudomonas fluorescens on individual bean leaves. data obtained in this study indicate that the population size of epiphytic bacteria on plants under environmentally favorable conditions is limited by the abundance of carbon sources on the leaf surface. sugars were depleted during the course of bacterial coloni ...	2000	10618250
quantification of different eubacterium spp. in human fecal samples with species-specific 16s rrna-targeted oligonucleotide probes.	species-specific 16s rrna-targeted, cy3 (indocarbocyanine)-labeled oligonucleotide probes were designed and validated to quantify different eubacterium species in human fecal samples. probes were directed at eubacterium barkeri, e. biforme, e. contortum, e. cylindroides (two probes), e. dolichum, e. hadrum, e. lentum, e. limosum, e. moniliforme, and e. ventriosum. the specificity of the probes was tested with the type strains and a range of common intestinal bacteria. with one exception, none of ...	2000	10618251
dual labeling with green fluorescent proteins for confocal microscopy.	we report a dual labeling technique involving two green fluorescent protein (gfp) variants that is compatible with confocal microscopy. two lasers were used to obtain images of (i) mixed cultures of cells, where one species contained gfpuv and another species contained gfpmut2 or gfpmut3, and (ii) a single species containing both gfpuv and gfpmut2 in the same cell. this method shows promise for monitoring gene expression and as a nondestructive and in situ technique for confocal microscopy of mu ...	2000	10618256
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
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
srpdb (signal recognition particle database).	the signal recognition particle database (srpdb) is maintained at the university of texas health science center at tyler, texas, and organizes srp-related information about srp rna, srp proteins and the srp receptor. srpdb is accessible on the www at the url http://psyche.uthct.edu/dbs/srpdb/srpdb.++ +html. a mirror site of the srpdb is located in europe at the university of göteborg, sweden (http://www.medkem. gu.se/dbs/srpdb/srpdb.html ). this release of srpdb adds 10 new srp rna sequences (a ...	2000	10592215
cloning of a gene for d-sorbitol dehydrogenase from gluconobacter oxydans g624 and expression of the gene in pseudomonas putida ifo3738.	we have cloned a novel gene for d-sorbitol dehydrogenase (sldh), which efficiently converted d-sorbitol to l-sorbose, from gluconobacter oxydans g624 (ferm bp-4415). a cosmid library of the genomic dna was screened by assaying sldh activity. the inserted dna from a positive clone was downsized by subcloning into charomid and pucp plasmid, successively. sequencing analysis of the dna responsible for sldh activity revealed an open reading frame of 1455 bp coding for 485 amino acid residues with a ...	2000	16232778
metabolic engineering study on the direct fermentation of 2-keto-l-gulonic acid, a key intermediate of l-ascorbic acid in pseudomonas putida ifo3738.	we have achieved production of 2-keto-l-gulonic acid (2-klga) in recombinant pseudomonas putida ifo3738. firstly, the genes for sorbose dehydrogenase (sdh)/sorbosone dehydrogenase (sndh) were introduced into p. putida. the recombinant p. putida/pbbr-sdh produced 0.7 mg/ml of 2-klga in a culture broth containing 5% l-sorbose. replacement of the native sndh promoter by the escherichia coli tufb promoter (pbbr-sdh-tufb) improved the productivity of 2-klga up to 11.4 mg/ml. secondly, the sorbitol de ...	2000	16232848
[characteristic of mutants of pseudomonas putida ipm-36 recombinant strains, selected by anticipating growth on a media containing an inducer of cry3a gene expression].	induction of the expression of the delta-endotoxin gene from bacillus thuringiensis var. tenebrionis in the recombinant strain pseudomonas putida ipm-36 negatively affected the viability and the growth rate of the culture. in order to optimize the insecticide production by the recombinant strain, mutant clones exhibiting anticipating growth on an inducer-containing medium were selected and studied. these clones differed in such aspects as the localization of mutations (either in plasmid pbtn11, ...	2000	11315669
[isolation and study of acinetobacter sp. mutant strains defective in production of exopolysaccharides].	nitrosoguanidine-induced mutants of acinetobacter sp. defective in exopolysaccharide biosynthesis did not differ from the parent strain in distinguishing physiological and biochemical properties, such as requirements for growth factors, utilization of mono- and disaccharides, and resistance to antibiotics. the genetic relation of parent and mutant strains was shown by 16s rrna pcr analysis. the comparative study of parent and mutant strains with respect to resistance to unfavorable environmental ...	2000	11315670
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
expression of marker rnas in pseudomonas putida.	a broad-host-range vector that expresses a unique artificial rna in pseudomonas putida has been developed. this vector was derived from the plasmid pbbr1mcs and incorporates regulatory regions from the escherichia coli ribosomal operon, rrnb. these include the promoters p1 and p2, and the terminators t1 and t2. the gene for the artificial rna was derived from vibrio proteolyticus 5s rrna. the artificial rna product accumulates to a level that is 10-20% of the total 5s rrna in p. putida. the rna ...	2000	10594220
survival rate of microbes after freeze-drying and long-term storage.	the survival rates of 10 species of microorganisms were investigated after freeze-drying and preserving in a vacuum at 5 degrees c. the survival rates varied with species. the survival rates immediately after freeze-drying were different among yeast, gram-positive bacteria, and gram-negative bacteria, and the change in the 10-year survival rate was species-specific. the survival rate of yeast, saccharomyces cerevisiae, was about 10% immediately after drying, and the rate did not decrease signifi ...	2000	11161557
identification and characterization of the dnaa upstream region of thermus thermophilus.	the gene order in the dnaa region of thermus thermophilus was determined. previously, we showed that the putative oric of t. thermophilus is located in the dnaa-dnan intergenic region. in the 4 kb region upstream of the dnaa gene four orfs were found, all orientated in the same direction which is opposite to that of dnaa. the orfs were identified as t. thermophilus homologs of gida, gidb, soj and spo0j of bacillus subtilis. the gene order spo0j-soj-gidb-gida-dnaa-dnan resembles that of b. subtil ...	2000	11167017
distribution of catabolic pathways in some hydrocarbon-degrading bacteria from a subsurface polluted soil.	enrichment cultures on naphtha solvent were used to select aromatic hydrocarbon-degrading bacteria from a btex (benzene, toluene, ethylbenzene, xylene)-contaminated subsoil obtained from beneath a paint factory located in milan, italy. fifteen isolated strains were studied for their different biodegradative capacities. among these, 13 were able to grow on naphtha solvent. ten were identified as pseudomonas putida and three as pseudomonas aureofaciens. two other degraders were identified as pseud ...	2000	11191814
role of tyrosine 114 of l-methionine gamma-lyase from pseudomonas putida.	l-methionine gamma-lyase from pseudomonas putida has a conserved tyrosine residue (tyr114) in the active site as in all known sequences of y-family pyridoxal 5'-phosphate dependent enzymes. a mutant form of l-methionine y-lyase in which tyr114 was replaced by phenylalanine (y114f) resulted in 910-fold decrease in kcat for alpha,gamma-elimination of l-methionine, while the km remained the same as the wild type enzyme. the y114f mutant had the reduced kcat by only 28- and 16-fold for substrates wi ...	2000	11193400
[degradation of phenanthrene by mutant strains--naphthalene degraders].	five naphthalene- and salicylate-utilizing pseudomonas putida strains cultivated for a long time on phenanthrene produced mutants capable of growing on this substrate and 1-hydroxy-2-naphthoate as the sole sources of carbon and energy. the mutants catabolize phenanthrene with the formation of 1-hydroxy-2-naphthoate, 2-hydroxy-1-naphthoate, salicylate, and catechol. the latter products are further metabolized by the meta- and ortho-cleavage pathways. in all five mutants, naphthalene and phenanthr ...	2000	11195577
biodegradation and biosorption of acid anthraquinone dye.	the acid anthraquinone dye tectilon blue (tb4r) is a major coloured component from the aqueous effluent of a carpet printing plant in northern ireland. the aerobic biodegradation of tb4r has been investigated experimentally in batch systems, using three strains of bacteria, namely, bacillus gordonae (ncimb 12553), bacillus benzeovorans (ncimb 12555) and pseudomonas putida (ncimb 9776). all three strains successfully decolourised the dye, and results were correlated using michaelis-menten kinetic ...	2000	15092952
evaluation of the galega-rhizobium galegae system for the bioremediation of oil-contaminated soil.	the bioremediation potential of a nitrogen-fixing leguminous plant, galega orientalis, and its microsymbiont rhizobium galegae was evaluated in btx (benzene, toluene, xylene)-contaminated soils in microcosm and mesocosm scale. to measure the intrinsic tolerance of the organisms to m-toluate, a model compound representing btx, g. orientalis and r. galegae were cultivated under increasing concentrations of m-toluate alone and in association with pseudomonas putida pwwo, a bacterial strain able to ...	2000	15093001
competitiveness in root colonization by pseudomonas putida requires the rpos gene.	the rpos gene in pseudomonas putida was essential for plant root colonization under competitive conditions from other microbes. the rpos- mutant survived less well than the wild-type strain in culture medium, and unlike the wild-type, failed to colonize the roots in a peat matrix containing an established diverse microflora. the rpos-deficient p. putida isolate was generated by insertion of a glucuronidase-npt cassette into the rpos gene. the rpos mutant had dose-dependent increased sensitivity ...	2001	15049448
the influence of preculture conditions and food quality on the ingestion and digestion process of three species of heterotrophic nanoflagellates.	the influence of prey characteristics such as motility and size as well as of predator characteristics such as satiation and preculturing diet on the feeding process of interception feeding heterotrophic nanoflagellates was investigated. three species of gram-negative bacteria, one species of gram-positive bacteria, two species of cyanobacteria (synechococcus) and inert latex particles were fed as prey particles for three species of heterotrophic nanoflagellates (spumella, ochromonas, cafeteria) ...	2001	12024279
molecular cloning and transcriptional analysis of the alkyl hydroperoxide reductase genes from pseudomonas putida kt2442.	pseudomonas putida kt2442tol (formerly designated tol), a toluene-resistant variant of strain kt2442 constitutively overexpressed several proteins. the most abundantly produced 24-kda soluble protein was found to be similar to ahpc, the small subunit of alkyl hydroperoxide reductase. molecular cloning of the p. putida ahpc based on the n-terminal sequence allowed cloning of closely located ahpf, the large subunit of alkyl hydroperoxide reductase. the deduced amino acid sequences of these genes s ...	2001	12483614
induction of 2-amino-d2-thiazoline-4-carboxylic acid hydrolase and n-carbamoyl-l-cysteine amidohydrolase by s-compounds in pseudomonas putida aj3865.	the induction of 2-amino-delta(2)-thiazoline-4-carboxylic acid hydrolase (atcase) and n-carbamoylcysteine amidohydrolase (nccase), both of which are involved in the conversion step of 2-amino-delta(2)-thiazoline carboxylic acid (atc) to cysteine, was studied with pseudomonas putida aj3865. we found that l-atc induced l-atcase and l-nccase, but that d-atc induced only l-nccase, whereas l- or d-ncc and thiazoline derivatives did not induce both enzymes. the bacterium showed neither d-atcase nor d- ...	2001	12483619
removal of copper by pseudomonas putida strain s4 isolated from copper mines.	a bacterial strain, pseudomonas putida s4, was isolated from smelter drainage of copper mines. the strain exhibited resistance to several heavy metals, like aluminium (al), zinc (zn), nickel (ni), cobalt (co) besides copper (cu). strain s4 could accumulate cu from the cu-supplemented growth medium. in the present study, we have demonstrated the cu2+ removal capacity of this strain from various samples such as mine effluent, low-grade ore and ore-tailings, collected from the mining site. moreover ...	2001	12562024
inorganic nutrient utilisation by "adapted" pseudomonas putida strain used in the bioremediation of agricultural soil polluted with crude petroleum.	garden soil samples polluted with crude petroleum were bioremediated by inorganic nutrient monitoring with appropriate adjustment and inoculation with crude oil-adapted strain of pseudomonasputida (pp) isolated from oil-impacted soils. soil samples without pp inoculation served as the control samples to compare the abilities of the native soil microflora with the adapted pp strain in biodegrading crude oil pollutant. in the experimental samples, oil concentration and all the inorganic nutrient s ...	2001	12017254
the use of modified gfp as a reporter for metabolic activity in pseudomonas putida.	many bacteria are now known to enter into a "viable but nonculturable" (vbnc) state in response to various environmental stresses. in this state, the cells are no longer culturable on routine media, but retain viability and in many cases have been shown to be capable of resuscitating to the metabolically active and culturable state. there have been no simple means of measuring the metabolic activity of cells in the vbnc state. the use of green fluorescent protein (gfp) variants with short half-l ...	2001	12032604
plasmid transfer detection in soil using the inducible lpr system fused to eukaryotic luciferase genes.	we report a model system for plasmid transfer analysis using the regulated lambda phage right promoter, lpr, fused to luc and lucor as reporter genes. we have demonstrated that the systems ci857-lpr::luc and ci857-lpr::lucor are temperature-inducible in escherichia coli but not in other gram-negative bacteria analyzed, enabling detection of luminescence when plasmids were mobilized from e. coli to those gram-negative backgrounds. using light for the detection, we have observed plasmid transfer f ...	2001	12032609
detection of small sequence differences using competitive pcr: molecular monitoring of genetically improved, mercury-reducing bacteria.	a quantitative pcr approach is presented to detect small genomic sequence differences for molecular quantification of recombinant dna. the only unique genetic feature of the mercury-reducing, genetically improved pseudomonas putida kt2442::mer73 available to distinguish it from its native mercury-resistant relatives is the dna sequence crossing the border of the insertion site of the introduced dna fragment. the quantification assay is a combination of specific pcr amplification and temperature ...	2001	11196305
biodegradation of phenol in a continuous process: comparative study of stirred tank and fluidized-bed bioreactors.	the paper presents the main results obtained from the study of the biodegradation process of phenol by a pure culture of pseudomonas putida atcc 17484. the experimental work was carried out in two different systems: a stirred tank where cells grew as a suspended culture and a fluidized bed where cells were immobilized within calcium alginate gel beads. the influence of the hydraulic residence time (hrt) and organic loading rate on the removal efficiency of phenol was determined for both bioreact ...	2001	11198177
effectiveness of orbital shaking for the aeration of suspended bacterial cultures in square-deepwell microtiter plates.	growth of heterogeneous culture collections in microtiter plates is advantageous for logistic reasons and also in enabling significant savings in medium costs, labor input and use of equipment during large screening projects. the main hurdles to overcome for aerobic microbial strains are the prevention of cross-contamination and excessive evaporation while assuring sufficient aeration rates. for this purpose we developed a sandwich spongy silicone/cotton wool cover to close the wells of square-d ...	2001	11173298
bioremediation of sterile agricultural soils polluted with crude petroleum by application of the soil bacterium, pseudomonas putida, with inorganic nutrient supplementations.	the effects of bioremediation program of sterile agricultural soils contaminated with crude petroleum were determined with a view to developing a suitable technique for rehabilitation of similar environments upon pollution by oil spillage. sterile soils inoculated with the soil bacterium, pseudomonas putida (pp), with inorganic nutrients monitoring and supplementation constituted the experimental set-ups (esu). the control set-ups (csu) contained all the materials present in esu except that they ...	2001	11178721
an active role for a structured b-linker in effector control of the sigma54-dependent regulator dmpr.	the activities of many prokaryotic sigma54-dependent transcriptional activators are controlled by the n-terminal a-domain of the protein, which is linked to the central transcriptional activation domain via a short b-linker. it used to be thought that these b-linkers simply serve as flexible tethers. here we show that the b-linker of the aromatic-responsive regulator dmpr and many other regulators of the family contain signature heptad repeats with regularly spaced hydrophobic amino acids. mutan ...	2001	11179226
fine-mapping, mutation analyses, and structural mapping of cerebrotendinous xanthomatosis in u.s. pedigrees.	cerebrotendinous xanthomatosis (ctx) is a rare autosomal recessive disorder of bile acid biosynthesis. clinically, ctx patients present with tendon xanthomas, juvenile cataracts, and progressive neurological dysfunction and can be diagnosed by the detection of elevated plasma cholestanol levels. ctx is caused by mutations affecting the sterol 27-hydroxylase gene (cyp27 ). ctx has been identified in a number of populations, but seems to have a higher prevalence in the japanese, sephardic jewish, ...	2001	11181744