Publications

low-frequency horizontal transfer of an element containing the chlorocatechol degradation genes from pseudomonas sp. strain b13 to pseudomonas putida f1 and to indigenous bacteria in laboratory-scale activated-sludge microcosms.	the possibilities for low-frequency horizontal transfer of the self-transmissible chlorocatechol degradative genes (clc) from pseudomonas sp. strain b13 were investigated in activated-sludge microcosms. when the clc genes were transferred into an appropriate recipient bacterium such as pseudomonas putida f1, a new metabolic pathway for chlorobenzene degradation was formed by complementation which could be selected for by the addition of mono- or 1, 4-dichlorobenzene (cb). under optimized conditi ...	1998	9603824
cloning and sequencing of the sphingomonas (pseudomonas) paucimobilis gene essential for the o demethylation of vanillate and syringate.	sphingomonas (pseudomonas) paucimobilis syk-6 is able to grow on 5,5'-dehydrodivanillic acid (ddva), syringate, vanillate, and other dimeric model compounds of lignin as a sole carbon source. nitrosoguanidine mutagenesis of s. paucimobilis syk-6 was performed, and two mutants with altered ddva degradation pathways were isolated. the mutant strain nt-1 could not degrade ddva, but could degrade syringate, vanillate, and 2,2',3'-trihydroxy-3-methoxy-5,5'-dicarboxybiphenyl (oh-ddva). strain dc-49 co ...	1998	9501423
development of a direct in situ pcr method for detection of specific bacteria in natural environments.	we applied hnpp (2-hydroxy-3-naphthoic acid-2'-phenylanilide phosphate) to direct in situ pcr for the routine detection of specific bacterial cells at the single-cell level. pcr was performed on glass slides with digoxigenin-labeled dutp. the digoxigenin-labeled pcr products were detected with alkaline phosphatase-labeled antidigoxigenin antibody and hnpp which was combined with fast red tr. a bright red fluorescent signal was produced from conversion to hnp (dephosphorylated form) by alkaline p ...	1998	9546190
establishment of new genetic traits in a microbial biofilm community.	conjugational transfer of the tol plasmid (pwwo) was analyzed in a flow chamber biofilm community engaged in benzyl alcohol degradation. the community consisted of three species, pseudomonas putida ri, acinetobacter sp. strain c6, and an unidentified isolate, d8. only p. putida ri could act as a recipient for the tol plasmid. cells carrying a chromosomally integrated laciq gene and a lacp-gfp-tagged version of the tol plasmid were introduced as donor strains in the biofilm community after its fo ...	1998	9603843
alginate lyase promotes diffusion of aminoglycosides through the extracellular polysaccharide of mucoid pseudomonas aeruginosa.	we demonstrated that a 2% suspension of pseudomonas aeruginosa alginate completely blocked the diffusion of gentamicin and tobramycin, but not that of carbenicillin, illustrating how alginate production can help protect p. aeruginosa growing within alginate microcolonies in patients with cystic fibrosis (cf) from the effects of aminoglycosides. this aminoglycoside diffusion barrier was degraded with a semipurified preparation of p. aeruginosa alginate lyase, suggesting that this enzyme deserves ...	1998	9559826
modular fluorescent-labeled siderophore analogues.	biomimetic analogues 1 of the microbial siderophore (iron carrier) ferrichrome were labeled via piperazine with various fluorescent markers at a site not interfering with iron binding or receptor recognition (compounds 10-12). these iron carriers were built from a tetrahedral carbon symmetrically extended with three strands, each containing an amino acid (g = glycyl, a = alanyl, l = leucyl and p = phenylalanyl) and terminated by a hydroxamic acid, which together define an octahedral iron-binding ...	1998	9572892
a gene system for glucitol transport and metabolism in clostridium beijerinckii ncimb 8052.	the gutd gene of clostridium beijerinckii ncimb 8052 encoding glucitol 6-phosphate dehydrogenase was cloned on a 5.7-kbp chromosomal dna fragment by complementing an escherichia coli gutd mutant strain and selecting for growth on glucitol. five open reading frames (orfs) in the order guta1 guta2 orfx gutb gutd were identified in a 4.0-kbp region of the cloned dna. the deduced products of four of these orfs were homologous to components of the glucitol phosphotransferase system (pts) and glucitol ...	1998	9572925
use of inducible feedback-resistant n-acetylglutamate synthetase (arga) genes for enhanced arginine biosynthesis by genetically engineered escherichia coli k-12 strains.	the goal of this work was to construct escherichia coli strains capable of enhanced arginine production. the arginine biosynthetic capacity of previously engineered e. coli strains with a derepressed arginine regulon was limited by the availability of endogenous ornithine (m. tuchman, b. s. rajagopal, m. t. mccann, and m. h. malamy, appl. environ. microbiol. 63:33-38, 1997). ornithine biosynthesis is limited due to feedback inhibition by arginine of n-acetylglutamate synthetase (nags), the produ ...	1998	9572954
oxidation of methyl-substituted naphthalenes: pathways in a versatile sphingomonas paucimobilis strain	aromatic compounds with alkyl substituents are abundant in fossil fuels. these compounds become important environmental sources of soluble toxic products, developmental inhibitors, etc. principally through biological activities. to assess the effect of methyl substitution on the completeness of mineralization and accumulation of pathway products, an isolate from a phenanthrene enrichment culture, sphingomonas paucimobilis 2322, was used. washed cell suspensions containing cells grown on 2,6-dime ...	1998	9572967
characterization of a protocatechuate catabolic gene cluster from rhodococcus opacus 1cp: evidence for a merged enzyme with 4-carboxymuconolactone-decarboxylating and 3-oxoadipate enol-lactone-hydrolyzing activity.	the catechol and protocatechuate branches of the 3-oxoadipate pathway, which are important for the bacterial degradation of aromatic compounds, converge at the common intermediate 3-oxoadipate enol-lactone. a 3-oxoadipate enol-lactone-hydrolyzing enzyme, purified from benzoate-grown cells of rhodococcus opacus (erythropolis) 1cp, was found to have a larger molecular mass under denaturing conditions than the corresponding enzymes previously purified from gamma-proteobacteria. sequencing of the n ...	1998	9495744
evolutionary relationship between chlorocatechol catabolic enzymes from rhodococcus opacus 1cp and their counterparts in proteobacteria: sequence divergence and functional convergence.	biochemical investigations of the muconate and chloromuconate cycloisomerases from the chlorophenol-utilizing strain rhodococcus opacus (erythropolis) 1cp had previously indicated that the chlorocatechol catabolic pathway of this strain may have developed independently from the corresponding pathways of proteobacteria. to test this hypothesis, we cloned the chlorocatechol catabolic gene cluster of strain 1cp by using pcr with primers derived from sequences of n termini and peptides of purified c ...	1998	9495745
characterization of the hcnabc gene cluster encoding hydrogen cyanide synthase and anaerobic regulation by anr in the strictly aerobic biocontrol agent pseudomonas fluorescens cha0.	the secondary metabolite hydrogen cyanide (hcn) is produced by pseudomonas fluorescens from glycine, essentially under microaerophilic conditions. the genetic basis of hcn synthesis in p. fluorescens cha0 was investigated. the contiguous structural genes hcnabc encoding hcn synthase were expressed from the t7 promoter in escherichia coli, resulting in hcn production in this bacterium. analysis of the nucleotide sequence of the hcnabc genes showed that each hcn synthase subunit was similar to kno ...	1998	9620970
cloning and comparison of flic genes and identification of glycosylation in the flagellin of pseudomonas aeruginosa a-type strains.	pseudomonas aeruginosa a-type strains produce flagellin proteins which vary in molecular weight between strains. to compare the properties of a-type flagellins, the flagellin genes of several pseudomonas aeruginosa a-type strains, as determined by interaction with specific anti-a monoclonal antibody, were cloned and sequenced. pcr amplification of the a-type flagellin gene fragments from five strains each yielded a 1.02-kb product, indicating that the gene size is not likely to be responsible fo ...	1998	9620973
new unstable variants of green fluorescent protein for studies of transient gene expression in bacteria.	use of the green fluorescent protein (gfp) from the jellyfish aequorea victoria is a powerful method for nondestructive in situ monitoring, since expression of green fluorescence does not require any substrate addition. to expand the use of gfp as a reporter protein, new variants have been constructed by the addition of short peptide sequences to the c-terminal end of intact gfp. this rendered the gfp susceptible to the action of indigenous housekeeping proteases, resulting in protein variants w ...	1998	9603842
effect of bacterial distribution and activity on conjugal gene transfer on the phylloplane of the bush bean (phaseolus vulgaris).	conjugal plasmid transfer was examined on the phylloplane of bean (phaseolus vulgaris) and related to the spatial distribution pattern and metabolic activity of the bacteria. the donor (pseudomonas putida kt2442) harbored a derivative of the tol plasmid, which conferred kanamycin resistance and had the gfp gene inserted downstream of a lac promoter. a chromosomal insertion of laciq prevented expression of the gfp gene. the recipient (p. putida kt2440) had a chromosomal tetracycline resistance ma ...	1998	9572970
heterogeneity in levels of vacuolating cytotoxin gene (vaca) transcription among helicobacter pylori strains.	broth culture supernatants from tox+ helicobacter pylori strains induce vacuolation of hela cells in vitro and contain vaca in concentrations that are higher than those found in supernatants from tox- h. pylori strains. to investigate the basis for this phenomenon, we analyzed the transcription of the vacuolating cytotoxin gene (vaca) in eight tox+ strains (each with a type s1/m1 vaca genotype) and nine tox- strains (each with a type s2/m2 vaca genotype). most of the tox+ and tox- strains tested ...	1998	9632570
structures of homologous composite transposons carrying cbaabc genes from europe and north america.	is1071 is a class ii transposable element carrying a tnpa gene related to the transposase genes of the tn3 family. copies of is1071 that are conserved with more than 99% nucleotide sequence identity have been found as direct repeats flanking a remarkable variety of catabolic gene sequences worldwide. the sequences of chlorobenzoate catabolic transposons found on pbrc60 (tn5271) in niagara falls, n.y., and on pcpe3 in bologna, italy, show that these transposons were formed from highly homologous ...	1998	9572977
short-run tests for determining harmful effects of pcb-containing engine oils on cells.	our main objective was to set up reproducible methods for a rapid determination of harmful effects of pcb-containing engine oils on cells. we used a plate method and scenedesmus quadricauda, saccharomyces cerevisiae, rhodotorula glutinis and pseudomonas putida as test organisms.	1998	9867477
isolation and characterization of toluene-sensitive mutants from pseudomonas putida ih-2000.	two toluene-sensitive mutants were generated from pseudomonas putida ih-2000, the first known toluene-tolerant isolate, by tn5 transposon mutagenesis. these mutants were unable to grow in the presence of toluene (log p(ow) 2.8) but they could grow in medium overlaid with organic solvents having a log p(ow) value higher than that of toluene such as p-xylene (log p(ow) 3.1), cyclohexane (log p(ow) 3.4) and n-hexane (log p(ow) 3.9). the tn5 transposable element knocked out a cyob-like gene in one m ...	1998	9868765
simultaneous degradation of chloro- and methyl-substituted aromatic compounds: competition between pseudomonas strains using the ortho and meta pathway or the ortho pathway exclusively.	pseudomonas sp. d7-4 and pseudomonas sp. b13 fr1(pfrc20p) degraded mixtures of chloro- and methyl-substituted benzoates exclusively via an extended ortho pathway, whereas in pseudomonas putida wr 201 both ortho and meta fission were induced by mixtures of 3-chloro- and 3-methylbenzoate or even by 3-chloro-benzoate alone. the competition behaviour of these strains was compared in batch and in chemostat cultures.. despite misrouting of metabolites, strain wr201 was competitive, in a lot of the com ...	1998	9840960
phosphate starvation-independent 2-aminoethylphosphonic acid biodegradation in a newly isolated strain of pseudomonas putida, ng2.	a strain of pseudomonas putida that utilized the biogenic organophosphonate 2-aminoethylphosphonic acid as sole carbon and energy, nitrogen and phosphorus source contained 2-aminoethylphosphonic acid: pyruvate aminotransferase and phosphonoacetaldehyde hydrolase (phosphonatase) activities which were inducible by the presence of 2-aminoethylphosphonic acid in the culture medium, regardless of the phosphate status of the cells. neither of these activities were induced in their phosphate-free or ph ...	1998	9841125
bacterial iron transport: 1h nmr determination of the three-dimensional structure of the gallium complex of pyoverdin g4r, the peptidic siderophore of pseudomonas putida g4r.	among the fluorescent pseudomonas species, pseudomonas putida is a rare case of a nitrogen-fixing bacterium that transforms nitrogen into ammonia. when grown under iron-deficient conditions, it produces two major pyoverdins: pyoverdin g4r and pyoverdin g4ra. their primary structures have been established using fab-ms and one- and two-dimensional 15n, 13c, and 1h nmr on both the unlabeled and 15n-labeled compounds [salah el din, a. l. m., et al. (1997) tetrahedron 53, 12539-12552]. the two pyover ...	1998	9843403
siderotyping of fluorescent pseudomonads: characterization of pyoverdines of pseudomonas fluorescens and pseudomonas putida strains from antarctica.	five independent fluorescent pseudomonad isolates originating from antarctica were analysed for their pyoverdine systems. a pyoverdine-related siderotyping, which involved pyoverdine-induced growth stimulation, pyoverdine-mediated iron uptake, pyoverdine analysis by electrophoresis and isoelectric focusing, revealed three different pyoverdine-related siderotypes among the five isolates. one siderotype, including pseudomonas fluorescens 1w and p. fluorescens 10cw, was identical to that of p. fluo ...	1998	9846748
sequence diversity of the opri gene, coding for major outer membrane lipoprotein i, among rrna group i pseudomonads.	the sequence of opri, the gene coding for the major outer membrane lipoprotein i, was determined by pcr sequencing for representatives of 17 species of rrna group i pseudomonads, with a special emphasis on pseudomonas aeruginosa and pseudomonas fluorescens. within the p. aeruginosa species, opri sequences for 25 independent isolates were found to be identical, except for one silent substitution at position 96. the opri sequences diverged more for the other rrna group i pseudomonads (85 to 91% si ...	1998	9851998
the modified beta-ketoadipate pathway in rhodococcus rhodochrous n75: enzymology of 3-methylmuconolactone metabolism.	rhodococcus rhodochrous n75 is able to metabolize 4-methylcatechol via a modified beta-ketoadipate pathway. this organism has been shown to activate 3-methylmuconolactone by the addition of coenzyme a (coa) prior to hydrolysis of the butenolide ring. a lactone-coa synthetase is induced by growth of r. rhodochrous n75 on p-toluate as a sole source of carbon. the enzyme has been purified 221-fold by ammonium sulfate fractionation, hydrophobic chromatography, gel filtration, and anion-exchange chro ...	1998	9852013
the yvyd gene of bacillus subtilis is under dual control of sigmab and sigmah.	during a search by computer-aided inspection of two-dimensional (2d) protein gels for sigmab-dependent general stress proteins exhibiting atypical induction profiles, a protein initially called hst23 was identified as a product of the yvyd gene of bacillus subtilis. in addition to the typical sigmab-dependent, stress- and starvation-inducible pattern, yvyd is also induced in response to amino acid depletion. by primer extension of rna isolated from the wild-type strain and appropriate mutants ca ...	1998	9852014
active efflux of organic solvents by pseudomonas putida s12 is induced by solvents.	induction of the membrane-associated organic solvent efflux system srpabc of pseudomonas putida s12 was examined by cloning a 312-bp dna fragment, containing the srp promoter, in the broad-host-range reporter vector pkrz-1. compounds that are capable of inducing expression of the srpabc genes include aromatic and aliphatic solvents and alcohols. general stress conditions such as ph, temperature, nacl, or the presence of organic acids did not induce srp transcription. although the solvent efflux ...	1998	9852029
protein binding in vivo to op2 promoter of the pseudomonas putida tol plasmid.	the transcription of op2 encoding enzymes for m-toluate catabolism on the pseudomonas putida tol plasmid is activated by basal-level xyls protein in the presence of m-toluate or by overproduced xyls protein in the absence of m-toluate. in this study, in vivo dimethyl sulfate (dms) footprinting was performed to understand the mechanism of transcriptional regulation of op2 promoter by xyls. in the presence of overproduced xyls without m-toluate, several protected nucleotides were observed, indicat ...	1998	9861447
mobilization of broad host range plasmid from pseudomonas putida to established biofilm of bacillus azotoformans. i. experiments.	a strain of pseudomonas putida harboring plasmids rk2 and pdlb101 was exposed to a pure culture biofilm of bacillus azotoformans grown in a rotating annular reactor under three different concentrations of the limiting nutrient, succinate. experimental results demonstrated that the broad host range rsf1010 derivative pdlb101 was transferred to and expressed by b. azotoformans. at the lower concentrations, donor mediated plasmid transfer increased with increasing nutrient levels, but the highest n ...	1998	10099203
lithocholic acid side-chain cleavage to produce 17-keto or 22-aldehyde steroids by pseudomonas putida strain st-491 grown in the presence of an organic solvent, diphenyl ether.	we devised a method to screen for microorganisms capable of growing on bile acids in the presence of organic solvents and producing organic solvent-soluble derivatives. pseudomonas putida biovar a strain st-491 isolated in this study produced decarboxylated derivatives from the bile acids. strain st-491 grown on 0.5% lithocholic acid catabolized approximately 30% of the substrate as a carbon source, and transiently accumulated in the medium androsta-1,4-diene-3,17-dione in an amount of correspon ...	1998	9972239
rational engineering of the tol meta-cleavage pathway	the meta-cleavage pathway of pseudomonas putida mt-2 was simulated using a biochemical systems simulation developed by regan (1996). a non-competitive inhibition term for catechol-2,3-dioxygenase (c23o) by 2-oh-pent-2,4-dienoate (ki = 150 μm) was incorporated into the model. the simulation predicted steady state accumulation levels in the μm range for metabolites pre-meta-cleavage, and in the mm range for metabolites post-meta-cleavage. the logarithmic gains l[v-i, xj] and l[x-i, xj] clearly ind ...	1998	10191395
evolution of enzymatic activities in the enolase superfamily: partitioning of reactive intermediates by (d)-glucarate dehydratase from pseudomonas putida.	glucarate dehydratase (glucd) from pseudomonas putida catalyzes the dehydration of both (d)-glucarate and (l)-idarate to 3-deoxy-(l)-threo-2-hexulosarate as well as their epimerization. (d)-[6-13c]glucarate and (l)-[6-13c]idarate have been synthesized for use in continuous assay of the reactions catalyzed by glucd by both 13c and 1h nmr spectroscopies, thereby allowing the simultaneous measure of both the dehydration and epimerization reactions. substrate and solvent isotope effects for the dehy ...	1998	9772160
use of 13c nuclear magnetic resonance and gas chromatography to examine methionine catabolism by lactococci.	formation of methanethiol from methionine is widely believed to play a significant role in development of cheddar cheese flavor. however, the catabolism of methionine by cheese-related microorganisms has not been well characterized. two independent methionine catabolic pathways are believed to be present in lactococci, one initiated by a lyase and the other initiated by an aminotransferase. to differentiate between these two pathways and to determine the possible distribution between the pathway ...	1998	9835547
cloning and characterization of nadp-mannitol dehydrogenase cdna from the button mushroom, agaricus bisporus, and its expression in response to nacl stress.	mannitol, a six-carbon sugar alcohol, is the main storage carbon in the button mushroom, agaricus bisporus. given the physiological importance of mannitol metabolism in growth, fruit body development, and salt tolerance of a. bisporus, the enzyme responsible for mannitol biosynthesis, nadp-dependent mannitol dehydrogenase (mtdh) (ec 1.1.1.138), was purified to homogeneity, and mtdh cdna was cloned, sequenced, and characterized. to our knowledge, this represents the first report on the isolation ...	1998	9835550
evolution of enzymatic activities in the enolase superfamily: crystal structure of (d)-glucarate dehydratase from pseudomonas putida.	the structure of (d)-glucarate dehydratase from pseudomonas putida (glucd) has been solved at 2.3 a resolution by multiple isomorphous replacement and refined to a final r-factor of 19.0%. the protein crystallizes in the space group i222 with one subunit in the asymmetric unit. the unit cell dimensions are a = 69.6 a, b = 108.8 a, and c = 122.6 a. the crystals were grown using the batch method where the primary precipitant was poly(ethylene glycol) 1000. the structure reveals that glucd is a tet ...	1998	9772161
differential scanning calorimetric study of poly(3-hydroxyoctanoate) inclusions in bacterial cells.	medium chain length polyhydroxyalkanoates, mcl-phas, produced by bacteria as inclusion bodies or granules were analyzed in situ by differential scanning calorimetry (dsc) without isolation from the cells. the kinetic dsc study of pha granules, which contained mostly 3-hydroxyoctanoate units (pho), in pseudomonas putida bm01 cells showed that the polymer within the granules existed in an amorphous state, but it crystallized after dehydration of the cells under freeze-drying condition (below -50 d ...	1998	9777703
psychrotolerant bacteria isolated from arctic soil that degrade polychlorinated biphenyls at low temperatures	psychrotolerant polychlorinated biphenyl (pcb)-degrading bacteria were isolated at 7 degreesc from pcb-contaminated arctic soil by using biphenyl as the sole organic carbon source. these isolates were distinguished from each other by differences in substrates that supported growth and substrates that were oxidized. 16s ribosomal dna sequences suggest that these isolates are most closely related to the genus pseudomonas. total removal of aroclor 1242, and rates of removal of selected pcb congener ...	1998	9835569
assessment of changes in microbial community structure during operation of an ammonia biofilter with molecular tools.	biofiltration has been used for two decades to remove odors and various volatile organic and inorganic compounds in contaminated off-gas streams. although biofiltration is widely practiced, there have been few studies of the bacteria responsible for the removal of air contaminants in biofilters. in this study, molecular techniques were used to identify bacteria in a laboratory-scale ammonia biofilter. both 16s rrna and ammonia monooxygenase (amoa) genes were used to characterize the heterotrophi ...	1998	9835577
characterization of cell lysis in pseudomonas putida induced upon expression of heterologous killing genes.	active biological containment systems are based on the controlled expression of killing genes. these systems are of interest for the pseudomonadaceae because of the potential applications of these microbes as bioremediation agents and biopesticides. the physiological effects that lead to cell death upon the induction of expression of two different heterologous killing genes in nonpathogenic pseudomonas putida kt2440 derivatives have been analyzed. p. putida cmc4 and cmc12 carry in their chromoso ...	1998	9835581
maintenance of a pseudomonas fluorescens plasmid in heterologous hosts: metabolic burden as a more reliable variable to predict plasmid instability.	the stability of a large, multiresistance plasmid, pscl of p. fluorescens cas102 was studied in pseudomonas putida and e. coli under various non-stress conditions. both the strains lost the plasmid within 25 days when repeatedly subcultured in lb broth without any antibiotic. the transformants survived in sterile soil and water without any marked reduction in the viability. in sterile soil, p. putida lost 93% and e. coli, 98% of their plasmid containing population in 30 days, while in sterile wa ...	1998	9782786
high expression, purification, and properties of recombinant homocysteine alpha, gamma-lyase.	homocysteine alpha,gamma-lyase from the anaerobic protozoan parasite trichomonas vaginalis has been cloned from genomic dna using pcr methods and expressed in escherichia coli with a vector containing the t7 promoter. the recombinant homocysteine alpha,gamma-lyase (rhcyase) is expressed as the major protein in the host e. coli cells. the enzyme was purified to approximately 90% purity using heat treatment at 50 degreesc, precipitation steps with polyethyleneimine, polyethylene glycol 8000, and h ...	1998	9790890
species-specific oligonucleotides for enumeration of pseudomonas putida f1, burkholderia sp. strain js150, and bacillus subtilis atcc 7003 in biodegradation experiments.	species-specific sequences were identified within the v4 variable region of 16s rrna of two bacterial species capable of aromatic hydrocarbon metabolism, pseudomonas putida f1 and burkholderia sp. strain js150, and a third, bacillus subtilis atcc 7003, that can function as a secondary degrader. fluorescent in situ hybridization (fish) with species-specific oligonucleotides was used for direct counting of these species throughout a phenol biodegradation experiment in batch culture. traditional di ...	1998	9835594
recombinant klebsiella oxytoca strains with improved efficiency in removal of high nitrate loads	klebsiella oxytoca cect 4460 removes high nitrate loads from industrial wastewaters without accumulation of nitrite under optimal culture conditions; however, under nonoptimal conditions nitrite accumulates. this situation reflects an in vivo-limited functioning of nitrite reductase in this strain. as a way to overcome this limitation, an increase in the nitrite reductase gene dose in k. oxytoca cect 4460 was considered. to achieve this, we cloned and transferred into this strain the klebsiella ...	1998	9835599
construction of a bioluminescent reporter strain to detect polychlorinated biphenyls	a bioluminescent reporter strain, ralstonia eutropha env307(putk60), was constructed for the detection of polychlorinated biphenyls by inserting the biphenyl promoter upstream of the bioluminescence genes. in the presence of a nonionic surfactant, which enhances the solubility of chlorinated biphenyls, bioluminescence was induced three- to fourfold over background by biphenyl, monochlorinated biphenyls, and aroclor 1242. the minimum detection limits for these compounds ranged from 0.15 mg/liter ...	1998	9835601
induction of the tod operon by trichloroethylene in pseudomonas putida tva8.	bioluminescence, mrna levels, and toluene degradation rates in pseudomonas putida tva8 were measured as a function of various concentrations of toluene and trichloroethylene (tce). tva8 showed an increasing bioluminescence response to increasing tce and toluene concentrations. compared to uninduced tva8 cultures, todc1 mrna levels increased 11-fold for tce-treated cultures and 13-fold for toluene-treated cultures. compared to uninduced p. putida f1 cultures, todc1 mrna levels increased 4.4-fold ...	1998	9835608
molecular characterization and regulation of an operon encoding a system for transport of arginine and ornithine and the argr regulatory protein in pseudomonas aeruginosa.	the complete nucleotide sequence for the aot operon of pseudomonas aeruginosa pao1 was determined. this operon contains six open reading frames. the derived sequences for four of these, aotj, aotq, aotm, and aotp, show high similarity to those of components of the periplasmic binding protein-dependent abc (atp binding cassette) transporters of enteric bacteria. transport studies with deletion derivatives established that these four genes function in arginine-inducible uptake of arginine and orni ...	1998	9791103
wound-released chemical signals may elicit multiple responses from an agrobacterium tumefaciens strain containing an octopine-type ti plasmid.	the vir regions of octopine-type and nopaline-type ti plasmids direct the transfer of oncogenic t-dna from agrobacterium tumefaciens to the nuclei of host plant cells. previous studies indicate that at least two genetic loci at the left ends of these two vir regions are sufficiently conserved to form heteroduplexes visible in the electron microscope. to initiate an investigation of these genetic loci, we determined the dna sequences of these regions of both ti plasmids and identified both conser ...	1998	9791116
molecular genetics of the genus paracoccus: metabolically versatile bacteria with bioenergetic flexibility.	paracoccus denitrificans and its near relative paracoccus versutus (formerly known as thiobacilllus versutus) have been attracting increasing attention because the aerobic respiratory system of p. denitrificans has long been regarded as a model for that of the mitochondrion, with which there are many components (e.g., cytochrome aa3 oxidase) in common. members of the genus exhibit a great range of metabolic flexibility, particularly with respect to processes involving respiration. prominent exam ...	1998	9841665
the virulence plasmid of yersinia, an antihost genome.	the 70-kb virulence plasmid enables yersinia spp. (yersinia pestis, y. pseudotuberculosis, and y. enterocolitica) to survive and multiply in the lymphoid tissues of their host. it encodes the yop virulon, an integrated system allowing extracellular bacteria to disarm the cells involved in the immune response, to disrupt their communications, or even to induce their apoptosis by the injection of bacterial effector proteins. this system consists of the yop proteins and their dedicated type iii sec ...	1998	9841674
gene organization in the trxa/b-oric region of the streptomyces coelicolor chromosome and comparison with other eubacteria.	the gene organization was determined in the trxa/b-rnpa region of the streptomyces coelocolor chromosome, near to the origin of replication, oric. previously, we showed that the trxa and trxb genes, coding for thioredoxin and thioredoxin reductase, respectively, occur in s. coelicolor as a gene cluster and are contained on a cosmid h24 that carries oric and several genes involved in dna replication. here we show that the trxa/b locus is positioned approx. 9.4kb from oric, present the nucleotide ...	1998	9795152
automated confocal laser scanning microscopy and semiautomated image processing for analysis of biofilms.	the purpose of this study was to develop and apply a quantitative optical method suitable for routine measurements of biofilm structures under in situ conditions. a computer program was designed to perform automated investigations of biofilms by using image acquisition and image analysis techniques. to obtain a representative profile of a growing biofilm, a nondestructive procedure was created to study and quantify undisturbed microbial populations within the physical environment of a glass flow ...	1998	9797255
malonate decarboxylase of pseudomonas putida is composed of five subunits.	two different forms of malonate decarboxylase were purified from pseudomonas putida. the active form was composed of the five different subunits alpha (60 kda), beta (33 kda), gamma (28 kda), delta (13 kda), and epsilon (30 kda) and the inactive form was composed of the four subunits lacking the epsilon subunit. the former catalyzed the decarboxylation of malonate to acetate, but the latter could not, although it retained both activities of acetyl-coa:malonate coa transferase and malonyl-coa dec ...	1998	9851033
cloning and molecular analysis of the poly(3-hydroxybutyrate) and poly(3-hydroxybutyrate-co-3-hydroxyalkanoate) biosynthesis genes in pseudomonas sp. strain 61-3.	two types of polyhydroxyalkanoate (pha) biosynthesis gene loci (phb and pha) of pseudomonas sp. strain 61-3, which produces a blend of poly(3-hydroxybutyrate) [p(3hb)] homopolymer and a random copolymer (poly(3-hydroxybutyrate-co-3-hydroxyalkanoate) [p(3hb-co-3ha]) consisting of 3ha units of 4 to 12 carbon atoms, were cloned and analyzed at the molecular level. in the phb locus, three open reading frames encoding polyhydroxybutyrate (phb) synthase (phbcps), beta-ketothiolase (phbaps), and nadph- ...	1998	9851987
novel organization of the genes for phthalate degradation from burkholderia cepacia dbo1.	burkholderia cepacia dbo1 is able to utilize phthalate as the sole source of carbon and energy for growth. two overlapping cosmid clones containing the genes for phthalate degradation were isolated from this strain. subcloning and activity analysis localized the genes for phthalate degradation to two separate regions on the cosmid clones. analysis of the nucleotide sequence of these two regions showed that the genes for phthalate degradation are arranged in at least three transcriptional units. ...	1998	9851995
incp plasmids are unusually effective in mediating conjugation of escherichia coli and saccharomyces cerevisiae: involvement of the tra2 mating system.	mobilizable shuttle plasmids containing the origin-of-transfer (orit) region of plasmids f (incfi), colib-p9 (inci1), and rp4/rp1 (incpalpha) were constructed to test the ability of the cognate conjugation system to mediate gene transfer from escherichia coli to saccharomyces cerevisiae. only the palpha system caused detectable mobilization to yeast, giving peak values of 5 x 10(-5) transconjugants per recipient cell in 30 min. transfer of the shuttle plasmid required carriage of orit in cis and ...	1998	9851996
ratios of carbon isotopes in microbial lipids as an indicator of substrate usage.	the occurrence and abundance of microbial fatty acids have been used for the identification of microorganisms in microbial communities. however, these fatty acids can also be used as indicators of substrate usage. for this, a systematic investigation of the discrimination of the stable carbon isotopes by different microorganisms is necessary. we grew 11 strains representing major bacterial and fungal species with four different isotopically defined carbon sources and determined the isotope ratio ...	1998	9797266
accumulation of alpha-keto acids as essential components in cyanide assimilation by pseudomonas fluorescens ncimb 11764.	pyruvate (pyr) and alpha-ketoglutarate (alphakg) accumulated when cells of pseudomonas fluorescens ncimb 11764 were cultivated on growth-limiting amounts of ammonia or cyanide and were shown to be responsible for the nonenzymatic removal of cyanide from culture fluids as previously reported (j.-l. chen and d. a. kunz, fems microbiol. lett. 156:61-67, 1997). the accumulation of keto acids in the medium paralleled the increase in cyanide-removing activity, with maximal activity (760 micromol of cy ...	1998	9797306
a small, dilute-cytoplasm, high-affinity, novel bacterium isolated by extinction culture and having kinetic constants compatible with growth at ambient concentrations of dissolved nutrients in seawater.	dilutions of raw seawater produced a bacterial isolate capable of extended growth in unamended seawater. its 2.9-mb genome size and 40-fg dry mass were similar to values for many naturally occurring aquatic organotrophs, but water and dna comprised a large portion of this small chemoheterotroph, as compared to escherichia coli. the isolate used only a few aromatic hydrocarbons and acetate, and glucose and amino acid incorporation were entirely absent, although many membrane and cytoplasmic prote ...	1998	9797308
a novel screening method for isolating exopolysaccharide-deficient mutants.	a screening method based on differential staining of the wild type and exopolysaccharide-deficient mutants of rhizobium (sinorhizobium) meliloti by the lipophilic dye sudan black b is described. mutants defective in the production of either succinoglycan or eps ii (galactoglucan) were isolated by using this method, which might also prove useful for isolating exopolysaccharide-defective derivatives of other bacteria.	1998	9797329
transcriptional activation of the catechol and chlorocatechol operons: variations on a theme.	the ortho-cleavage pathways of catechol and 3-chlorocatechol are central catabolic pathways of pseudomonas putida that convert aromatic and chloroaromatic compounds to tricarboxylic acid (tca)-cycle intermediates. they are encoded by the evolutionarily related catbca and clcabd operons, respectively. expression of the cat and clc operons requires the lysr-type transcriptional activators catr and clcr, and the inducer molecules cis,cis-muconate and 2-chloro-cis,cis-muconate. in addition to sequen ...	1998	9858745
quantitative structure/activity relationship for the rate of conversion of c4-substituted catechols by catechol-1,2-dioxygenase from pseudomonas putida (arvilla) c1.	the influence of various c4/c5 substituents in catechol (1,2-dihydroxybenzene) derivatives on the overall rate of conversion by catechol-1,2-dioxygenase from pseudomonas putida (arvilla) c1 was investigated. using catechol, 4-methylcatechol, 4-fluorocatechol, 4-chlorocatechol, 4-bromocatechol, 4,5-difluorocatechol and 4-chloro-5-fluorocatechol, it could be demonstrated that substituents at the c4 and/or c5 position decrease the rate of conversion, from 62% (4-methylcatechol) down to 0.7% (4-chlo ...	1998	9799107
cloning and nucleotide sequence of amidase gene from pseudomonas putida.	amidases are a class of enzymes which convert amides to acids and have potential value in the development of commercial bioprocesses for the production of useful chemicals. a gene encoding an amidase in pseudomonas putida 5b has been cloned, sequenced, and overexpressed in escherichia coli. an additional open reading frame (p38k) encoding a putative protein of 38 kda was found immediately upstream of the amidase gene. this work continues our characterization of a p. putida operon, which now appe ...	1998	9809753
targeted mutagenesis of sigma54 activator proteins in myxococcus xanthus.	myxococcus xanthus dna segments related to the highly conserved central sequence of sigma54 activator proteins have been investigated. a genetic technique designed to inactivate a gene that encodes such an activator by inserting a plasmid-borne internal fragment of the putative gene has been tested. when the internal fragment inserted by homologous recombination into the corresponding chromosomal locus, the expected duplication of the gene was observed by southern hybridization. the single restr ...	1998	9811647
synthesis of medium-chain-length polyhydroxyalkanoates in arabidopsis thaliana using intermediates of peroxisomal fatty acid beta-oxidation.	polyhydroxyalkanoate (pha) is a family of polymers composed primarily of r-3-hydroxyalkanoic acids. these polymers have properties of biodegradable thermoplastics and elastomers. medium-chain-length phas (mcl-phas) are synthesized in bacteria by using intermediates of the beta-oxidation of alkanoic acids. to assess the feasibility of producing mcl-phas in plants, arabidopsis thaliana was transformed with the phac1 synthase from pseudomonas aeruginosa modified for peroxisome targeting by addition ...	1998	9811811
the atrazine catabolism genes atzabc are widespread and highly conserved.	pseudomonas strain adp metabolizes the herbicide atrazine via three enzymatic steps, encoded by the genes atzabc, to yield cyanuric acid, a nitrogen source for many bacteria. here, we show that five geographically distinct atrazine-degrading bacteria contain genes homologous to atza, -b, and -c. the sequence identities of the atz genes from different atrazine-degrading bacteria were greater than 99% in all pairwise comparisons. this differs from bacterial genes involved in the catabolism of othe ...	1998	9537398
occurrence of homologs of the escherichia coli lytb gene in gram-negative bacterial species.	the escherichia coli lytb protein regulates the activity of guanosine 3',5'-bispyrophosphate synthetase i (rela). a southern blot analysis of chromosomal dna with the e. coli lytb gene as a probe revealed the presence of lytb homologs in all of the gram-negative bacterial species examined but not in gram-positive species. the lytb homologs from enterobacter aerogenes and pseudomonas fluorescens complemented the e. coli lytb44 mutant allele.	1998	9537400
nonstereospecific transamination catalyzed by pyridoxal phosphate-dependent amino acid racemases of broad substrate specificity.	pyridoxal 5'-phosphate-dependent amino acid racemases of broad substrate specificity catalyze transamination as a side reaction. we studied the stereospecificities for hydrogen abstraction from c-4' of the bound pyridoxamine 5'-phosphate during transamination from pyridoxamine 5'-phosphate to pyruvate catalyzed by three amino acid racemases of broad substrate specificity. when the enzymes were incubated with (4's)- or (4'r)-[4'-3h]pyridoxamine 5'-phosphate in the presence of pyruvate, tritium wa ...	1998	9461589
a new 4-nitrotoluene degradation pathway in a mycobacterium strain.	mycobacterium sp. strain hl 4-nt-1, isolated from a mixed soil sample from the stuttgart area, utilized 4-nitrotoluene as the sole source of nitrogen, carbon, and energy. under aerobic conditions, resting cells of the mycobacterium strain metabolized 4-nitrotoluene with concomitant release of small amounts of ammonia; under anaerobic conditions, 4-nitrotoluene was completely converted to 6-amino-m-cresol. 4-hydroxylaminotoluene was converted to 6-amino-m-cresol by cell extracts and thus could be ...	1998	9464378
alkane hydroxylase from acinetobacter sp. strain adp1 is encoded by alkm and belongs to a new family of bacterial integral-membrane hydrocarbon hydroxylases.	degradation of long-chain alkanes by acinetobacter sp. strain adp1 involves rubredoxin and rubredoxin reductase. we complemented a mutant deficient in alkane utilization and sequenced four open reading frames (orfs) on the complementing dna. each of these orfs was disrupted by insertional mutagenesis on the chromosome. as determined from sequence comparisons, orf1 and orf4 seem to encode a rotamase of the ppic type and an acyl coenzyme a dehydrogenase, respectively. disruption of these orfs does ...	1998	9546151
effects of bacterial host and dichloromethane dehalogenase on the competitiveness of methylotrophic bacteria growing with dichloromethane.	methylobacterium sp. strain dm4 and methylophilus sp. strain dm11 can grow with dichloromethane (dcm) as the sole source of carbon and energy by virtue of homologous glutathione-dependent dcm dehalogenases with markedly different kinetic properties (the kcat values of the enzymes of these strains are 0.6 and 3.3 s-1, respectively, and the km values are 9 and 59 microm, respectively). these strains, as well as transconjugant bacteria expressing the dcm dehalogenase gene (dcma) from dm11 or dm4 on ...	1998	9546153
population dynamics of phenol-degrading bacteria in activated sludge determined by gyrb-targeted quantitative pcr.	a method for quantifying bacterial populations introduced into an activated-sludge microbial community is described. the method involves extraction of dna from activated sludge, appropriate dilution of the extracted dna with dna extracted from nonintroduced activated sludge, pcr amplification of a gyrb gene fragment from the introduced strain with a set of strain-specific primers, and quantification of the electrophoresed pcr product by densitometry. the adequacy of the method was examined by an ...	1998	9546154
alcaligenes eutrophus as a bacterial chromate sensor.	in alcaligenes eutrophus ch34, determinants encoding inducible resistance to chromate (chr) and to cobalt and nickel (cnr) are located adjacent to each other on plasmid pmol28. to develop metal-sensing bacterial strains, a cloned part of plasmid pmol28, which contains both determinants, was mutated with tn5-lacz. the chr::lacz fusions were specifically induced by chromium; cnr was induced best by ni2+ but was also induced by co2+, mn2+, chromate, cu2+, cd2+, and zn2+. the broad-host-range incp1 ...	1998	9464379
cloning and nucleotide sequence of the gyrb gene of vibrio parahaemolyticus and its application in detection of this pathogen in shrimp.	because biochemical testing and 16s rrna sequence analysis have proven inadequate for the differentiation of vibrio parahaemolyticus from closely related species, we employed the gyrase b gene (gyrb) as a molecular diagnostic probe. the gyrb genes of v. parahaemolyticus and closely related vibrio alginolyticus were cloned and sequenced. oligonucleotide pcr primers were designed for the amplification of a 285-bp fragment from within gyrb specific for v. parahaemolyticus. these primers recognized ...	1998	9464408
engineering of quasi-natural pseudomonas putida strains for toluene metabolism through an ortho-cleavage degradation pathway.	to construct a bacterial catalyst for bioconversion of toluene and several alkyl and chloro- and nitro-substituted derivatives into the corresponding benzoates, the upper tol operon of plasmid pww0 of pseudomonas putida was fully reassembled as a single gene cassette along with its cognate regulatory gene, xylr. the corresponding dna segment was then targeted to the chromosome of a p. putida strain by using a genetic technique that allows deletion of all recombinant tags inherited from previous ...	1998	9464417
biodegradation of metal-edta complexes by an enriched microbial population.	a mixed culture utilizing edta as the sole carbon source was isolated from a mixed inoculum of water from the river mersey (united kingdom) and sludge from an industrial effluent treatment plant. fourteen component organisms were isolated from the culture, including representatives of the genera methylobacterium, variovorax, enterobacter, aureobacterium, and bacillus. the mixed culture biodegraded metal-edta complexes slowly; the biodegradability was in the order fe > cu > co > ni > cd. by incor ...	1998	9546167
localization of f plasmid sopb protein to positions near the poles of escherichia coli cells.	the subcellular localization of the sopb protein, which is encoded by the escherichia coli f plasmid and is involved in the partition of the single-copy plasmid, was directly visualized through the expression of the protein fused to the jellyfish green fluorescent protein (gfp). the fusion protein, but not gfp itself, was found to localize to positions close but not at the poles of exponentially growing cells. neither the presence of other f-encoded proteins nor the binding of sopb to its recogn ...	1998	9465048
ntn genes determining the early steps in the divergent catabolism of 4-nitrotoluene and toluene in pseudomonas sp. strain tw3.	pseudomonas sp. strain tw3 is able to oxidatively metabolize 4-nitrotoluene and toluene via a route analogous to the upper pathway of the tol plasmids. we report the sequence and organization of five genes, ntnwcmab*, which are very similar to and in the same order as the xyl operon of tol plasmid pww0 and present evidence that they encode enzymes which are expressed during growth on both 4-nitrotoluene and toluene and are responsible for their oxidation to 4-nitrobenzoate and benzoate, respecti ...	1998	9555884
availability of o2 as a substrate in the cytoplasm of bacteria under aerobic and microaerobic conditions.	the growth rates of pseudomonas putida kt2442 and mt-2 on benzoate, 4-hydroxybenzoate, or 4-methylbenzoate showed an exponential decrease with decreasing oxygen tensions (partial o2 tension [po2] values). the oxygen tensions resulting in half-maximal growth rates were in the range of 7 to 8 mbar of o2 (corresponding to 7 to 8 microm o2) (1 bar = 10(5) pa) for aromatic compounds, compared to 1 to 2 mbar for nonaromatic compounds like glucose or succinate. the decrease in the growth rates coincide ...	1998	9555896
the tfdk gene product facilitates uptake of 2,4-dichlorophenoxyacetate by ralstonia eutropha jmp134(pjp4).	uptake of 2,4-dichlorophenoxyacetate (2,4-d) by ralstonia eutropha jmp134(pjp4) was studied and shown to be an energy-dependent process. the uptake system was inducible with 2,4-d and followed saturation kinetics in a concentration range of up to 60 microm, implying the involvement of a protein in the transport process. we identified an open reading frame on plasmid pjp4, which was designated tfdk, whose translation product tfdk was highly hydrophobic and showed resemblance to transport proteins ...	1998	9555911
overexpression, purification, and characterization of the cloned metallo-beta-lactamase l1 from stenotrophomonas maltophilia.	the metallo-beta-lactamase l1 from stenotrophomonas maltophilia was cloned, overexpressed, and characterized by spectrometric and biochemical techniques. results of metal analyses were consistent with the cloned enzyme having 2 mol of tightly bound zn(ii) per monomer. gel filtration chromatography demonstrated that the cloned enzyme exists as a tightly held tetramer with a molecular mass of ca. 115 kda, and matrix-assisted laser desorption ionization and time-of-flight mass spectrometry indicate ...	1998	9559809
luxi- and luxr-homologous genes of rhizobium etli cnpaf512 contribute to synthesis of autoinducer molecules and nodulation of phaseolus vulgaris.	autoinduction plays an important role in intercellular communication among symbiotic and pathogenic gram-negative bacteria. we report here that a nitrogen-fixing symbiont of phaseolus vulgaris, rhizobium etli cnpaf512, produces at least seven different autoinducer molecules. one of them exhibits a growth-inhibitory effect like that of the bacteriocin small [n-(3r-hydroxy-7-cis-tetradecanoyl)-l-homoserine lactone]. at least two of the other autoinducers are synthesized by a luxi-homologous autoin ...	1998	9473034
a novel phenol hydroxylase and catechol 2,3-dioxygenase from the thermophilic bacillus thermoleovorans strain a2: nucleotide sequence and analysis of the genes.	the new thermophilic bacillus thermoleovorans strain a2 degrades phenol and cresols via the meta cleavage pathway. the first two enzymes involved in this process, the phenol hydroxylase and catechol 2,3-dioxygenase, encoded by the phea and pheb genes respectively, were cloned and sequenced. the deduced amino acid sequence of phea contains 524 amino acids with a theoretical m(r) of 59,602 da and displays less than 10% amino acid identity to known phenol hydroxylases. the greatest amino acid ident ...	1998	9561730
is1491 from pseudomonas alcaligenes ncib 9867: characterization and distribution among pseudomonas species.	a new insertion sequence, is1491, has been cloned and sequenced. the 2489-bp is1491 was isolated from a pseudomonas alcaligenes ncib 9867 (strain p25x) 4.8-kb psti chromosomal fragment. is1491 is flanked by an imperfect inverted repeat of 23 bp and carries two overlapping open reading frames, orf1 and orf2. both orf1 and orf2 displayed homology to the ista-like and istb-like transposases encoded by the is21 family of insertion sequences, which include two is elements previously isolated from p. ...	1998	9571135
polyethylene glycol conjugation of recombinant methioninase for cancer therapy.	recombinant methioninase (rmetase) is a homotetrameric pyridoxal 5'-phosphate enzyme of 172-kda molecular mass derived from pseudomonas putida and cloned in escherichia coli. rmetase has been found previously to be an effective, anti-tumor agent in vitro and in vivo. the enzyme targets the elevated minimal methionine requirement seen in all tumor types. in order to prevent immunological reactions which might be produced by multiple dosing of rmetase and to prolong the serum half-life of rmetase, ...	1998	9473456
the primitive protozoon trichomonas vaginalis contains two methionine gamma-lyase genes that encode members of the gamma-family of pyridoxal 5'-phosphate-dependent enzymes.	methionine gamma-lyase, the enzyme that catalyzes the breakdown of methionine by an alpha,gamma-elimination reaction and is a member of the gamma-family of pyridoxal 5'-phosphate-dependent enzymes, is present in high activity in the primitive protozoan parasite trichomonas vaginalis but is absent from mammals. two genes, mgl1 and mgl2, encoding methionine gamma-lyase, have now been isolated from t. vaginalis. they are both single copy, encode predicted proteins (mgl1 and mgl2) of 43 kda, have 69 ...	1998	9488680
two new mycobacterium strains and their role in toluene degradation in a contaminated stream.	two toluene-degrading strains, t103 and t104, were isolated from rock surface biomass in a freshwater stream contaminated with toluene. the strains exhibit different capacities for degradation of toluene and other aromatic compounds and have characteristics of the genus mycobacterium. both are aerobic, rod-shaped, gram-positive, nonmotile, and acid-alcohol fast and produce yellow pigments. they have mainly straight-chain saturated and monounsaturated fatty acids with 10 to 20 carbon atoms and la ...	1998	9572941
a mixed culture recovery method indicates that enteric bacteria do not enter the viable but nonculturable state.	a new method, called the mixed culture recovery (mcr) method, has been developed to determine whether recovery of culturable bacterial cells from a population of largely nonculturable cells is due to resuscitation of the nonculturable cells from a viable but nonculturable state or simply to growth of residual culturable cells. the mcr method addresses this issue in that it involves the mixing of two easily distinguishable strains (e.g., lactose positive and negative) in such a way that large num ...	1998	9572945
molecular characterization of benzyl alcohol dehydrogenase and benzaldehyde dehydrogenase ii of acinetobacter calcoaceticus.	the nucleotide sequences of xylb and xylc from acinetobacter calcoaceticus, the genes encoding benzyl alcohol dehydrogenase and benzaldehyde dehydrogenase ii, were determined. the complete nucleotide sequence indicates that these two genes form part of an operon and this was supported by heterologous expression and physiological studies. benzaldehyde dehydrogenase ii is a 51654 da protein with 484 amino acids per subunit and it is typical of other prokaryotic and eukaryotic aldehyde dehydrogenas ...	1998	9494109
biochemical and genetic characterization of an extracellular protease from pseudomonas fluorescens cy091.	pseudomonas fluorescens cy091 cultures produce an extracellular protease with an estimated molecular mass of 50 kda. production of this enzyme (designated aprx) was observed in media containing cacl2 or srcl2 but not in media containing zncl2, mgcl2, or mncl2. the requirement of ca2+ (or sr2+) for enzyme production was concentration dependent, and the optimal concentration for production was determined to be 0.35 mm. following ammonium sulfate precipitation and ion-exchange chromatography, the a ...	1998	9501431
development and testing of a bacterial biosensor for toluene-based environmental contaminants.	a bacterial biosensor for benzene, toluene, and similar compounds has been constructed, characterized, and field tested on contaminated water and soil. the biosensor is based on a plasmid incorporating the transcriptional activator xylr from the tol plasmid of pseudomonas putida mt-2. the xylr protein binds a subset of toluene-like compounds and activates transcription at its promoter, pu. a reporter plasmid was constructed by placing the luc gene for firefly luciferase under the control of xylr ...	1998	9501440
identification of a chemotaxis gene region from pseudomonas putida.	pseudomonas putida is chemotactic to a range of organic compounds, including several aromatic compounds. genes involved in this behavioral response were identified by tn5 mutagenesis of p. putida prs2000, resulting in a strain that was nonchemotactic to all chemoattractants tested. cloning and sequencing of the dna at the dna at the tn5 insertion site revealed a 13-kb region that contained 12 open reading frames, 9 of which are homologous to chemotaxis, flagellar and motility genes in other bact ...	1998	9503621
a protein-induced dna bend increases the specificity of a prokaryotic enhancer-binding protein.	control of transcription in prokaryotes often involves direct contact of regulatory proteins with rna polymerase from binding sites located adjacent to the target promoter. alternatively, in the case of genes transcribed by escherichia coli rna polymerase holoenzyme containing the alternate sigma factor sigma54, regulatory proteins bound at more distally located enhancer sites can activate transcription via dna looping by taking advantage of the increasing flexibility of dna over longer distance ...	1998	9512522
cloning and sequencing of a 2,5-dichlorohydroquinone reductive dehalogenase gene whose product is involved in degradation of gamma-hexachlorocyclohexane by sphingomonas paucimobilis.	sphingomonas (formerly pseudomonas) paucimobilis ut26 utilizes gamma-hexachlorocyclohexane (gamma-hch), a halogenated organic insecticide, as a sole carbon and energy source. in a previous study, we showed that gamma-hch is degraded to 2,5-dichlorohydroquinone (2,5-dchq) (y. nagata, r. ohtomo, k. miyauchi, m. fukuda, k. yano, and m. takagi, j. bacteriol. 176:3117-3125, 1994). in the present study, we cloned and characterized a gene, designated lind, directly involved in the degradation of 2,5-dc ...	1998	9515900
pcau, a transcriptional activator of genes for protocatechuate utilization in acinetobacter.	the acinetobacter pcaijfbdkchg operon encodes the six enzymes that convert protocatechuate to citric acid cycle intermediates. directly downstream from the operon are qui and pob genes encoding sets of enzymes that convert quinate and p-hydroxybenzoate, respectively, to protocatechuate. prior to this investigation, the only known regulatory gene in the pca-qui-pob cluster was pobr, which encodes a transcriptional activator that responds to p-hydroxybenzoate and activates transcription of poba. t ...	1998	9515921
characterization of the gene cassette required for biosynthesis of the (alpha1-->6)-linked n-acetyl-d-mannosamine-1-phosphate capsule of serogroup a neisseria meningitidis.	the (alpha1-->6)-linked n-acetyl-d-mannosamine-1-phosphate meningococcal capsule of serogroup a neisseria meningitidis is biochemically distinct from the sialic acid-containing capsules produced by other disease-associated meningococcal serogroups (e.g., b, c, y, and w-135). we defined the genetic cassette responsible for expression of the serogroup a capsule. the cassette comprised a 4,701-bp nucleotide sequence located between the outer membrane capsule transporter gene, ctra, and gale, encodi ...	1998	9515923
biodegradation of cyanides, cyanates and thiocyanates to ammonia and carbon dioxide by immobilized cells of pseudomonas putida.	pseudomonas putida utilizes cyanide as the sole source of carbon and nitrogen. agar, alginate, and carrageenan were screened as the encapsulating matrices for p. putida. alginate-immobilized cells of p. putida degraded sodium cyanide (nacn) more efficiently than non-immobilized cells or cells immobilized in agar or carrageenan. the end products of biodegradation of cyanide were identified as ammonia (nh3) and carbon dioxide (co2). these products changed the medium ph. in bioreactors, the rate of ...	1998	9523454
metalloadsorption by escherichia coli cells displaying yeast and mammalian metallothioneins anchored to the outer membrane protein lamb.	yeast (cup1) and mammalian (hmt-1a) metallothioneins (mts) have been efficiently expressed in escherichia coli as fusions to the outer membrane protein lamb. a 65-amino-acid sequence from the cup1 protein of saccharomyces cerevisiae (yeast [y] mt) was genetically inserted in permissive site 153 of the lamb sequence, which faces the outer medium. a second lamb fusion at position 153 was created with 66 amino acids recruited from the form of human (h) mt that is predominant in the adipose tissue, ...	1998	9573175
2-ketocyclohexanecarboxyl coenzyme a hydrolase, the ring cleavage enzyme required for anaerobic benzoate degradation by rhodopseudomonas palustris.	2-ketocyclohexanecarboxyl coenzyme a (2-ketochc-coa) hydrolase has been proposed to catalyze an unusual hydrolytic ring cleavage reaction as the last unique step in the pathway of anaerobic benzoate degradation by bacteria. this enzyme was purified from the phototrophic bacterium rhodopseudomonas palustris by sequential q-sepharose, phenyl-sepharose, gel filtration, and hydroxyapatite chromatography. the sequence of the 25 n-terminal amino acids of the purified hydrolase was identical to the ded ...	1998	9573182
substrate specificities of hybrid naphthalene and 2,4-dinitrotoluene dioxygenase enzyme systems.	bacterial three-component dioxygenase systems consist of reductase and ferredoxin components which transfer electrons from nad(p)h to a terminal oxygenase. in most cases, the oxygenase consists of two different subunits (alpha and beta). to assess the contributions of the alpha and beta subunits of the oxygenase to substrate specificity, hybrid dioxygenase enzymes were formed by coexpressing genes from two compatible plasmids in escherichia coli. the activities of hybrid naphthalene and 2,4-dini ...	1998	9573183
characterization of the cvaa and cvi promoters of the colicin v export system: iron-dependent transcription of cvaa is modulated by downstream sequences.	secretion of the escherichia coli toxin colicin v was previously determined to be iron regulated via the fur (ferric uptake regulator) protein, based on studies in fur mutants. the iron dependence of transcription and expression of cvaa, which encodes a transporter accessory protein, and cvi, encoding the colicin v immunity protein, was assessed under conditions of iron excess or depletion. immunoblots showed that production of both cvi and cvaa is iron dependent. the iron-dependent transcriptio ...	1998	9537361