Publications

the crystal structure of benzoylformate decarboxylase at 1.6 a resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes.	the crystal structure of the thiamin diphosphate (thdp)-dependent enzyme benzoylformate decarboxylase (bfd), the third enzyme in the mandelate pathway of pseudomonas putida, has been solved by multiple isomorphous replacement at 1.6 a resolution and refined to an r-factor of 15.0% (free r = 18.6%). the structure of bfd has been compared to that of other thdp-dependent enzymes, including pyruvate decarboxylase. the overall architecture of bfd resembles that of the other family members, and cofact ...	1998	9665697
active monomeric and dimeric forms of pseudomonas putida glyoxalase i: evidence for 3d domain swapping.	3d domain swapping of proteins involves the interconversion of a monomer containing a single domain-domain interface and a 2-fold symmetrical dimer containing two equivalent intermolecular interfaces. human glyoxalase i has the structure of a domain-swapped dimer [cameron, a. d., olin, b., ridderström, m., mannervik, b., and jones, t. a. (1997) embo j. 16, 3386-3395] but pseudomonas putida glyoxalase i has been reported to be monomeric [rhee, h.-i., murata, k., and kimura, a. (1986) biochem. bio ...	1998	9671502
sensorial and microbial effects of gaseous ozone on fresh scad (trachurus trachurus).	the bactericidal activity of gaseous ozone was investigated using a commercial ozone generator. five species of fish bacteria, pseudomonas putida, shewanella putrefaciens, brochothrix thermosphacta, enterobacter sp. and lactobacillus plantarum, were inoculated on agar surfaces and exposed to different ozonation times in a gas chamber. results showed ozone in relatively low concentrations (< 0.27 x 10(-3) g l-1) was an effective bactericide of vegetative cells of the five fish bacteria. the age o ...	1998	9674134
bacterial poly(3-hydroxyalkanoates) bearing carbon-carbon triple bonds.	production of poly(3-hydroxyalkanoates), phas, by pseudomonas oleovorans (p. oleovorans) and pseudomonas putida (p. putida) grown with mixtures of nonanoic acid, na, and 10-undecynoic acid, 10-und( identical with), were investigated. both microorganisms produced phas containing carbon-carbon triple bonds in fractions from 0 to 100%, depending on the composition of the carbon substrate mixture. the amounts of unsaturated repeating units in phas produced by p. oleovorans were higher than those in ...	1998	9680410
biochemical properties and substrate specificities of a recombinantly produced azotobacter vinelandii alginate lyase.	alginate is a polysaccharide composed of beta-d-mannuronic acid (m) and alpha-l-guluronic acid (g). an azotobacter vinelandii alginate lyase gene, algl, was cloned, sequenced, and expressed in escherichia coli. the deduced molecular mass of the corresponding protein is 41.4 kda, but a signal peptide is cleaved off, leaving a mature protein of 39 kda. sixty-three percent of the amino acids in this mature protein are identical to those in algl from pseudomonas aeruginosa. algl was partially purifi ...	1998	9683471
physical and genetic map of the obligate intracellular bacterium coxiella burnetii.	pulsed-field gel electrophoresis and pcr techniques have been used to construct a noti macrorestriction map of the obligate intracellular bacterium coxiella burnetii nine mile. the size of the chromosome has been determined to be 2,103 kb comprising 29 noti restriction fragments. the average resolution is 72.5 kb, or about 3. 5% of the genome. experimental data support the presence of a linear chromosome. published genes were localized on the physical map by southern hybridization. one gene, rec ...	1998	9683477
genetic analysis of dioxin dioxygenase of sphingomonas sp. strain rw1: catabolic genes dispersed on the genome.	the dioxin dioxygenase of sphingomonas sp. strain rw1 activates dibenzo-p-dioxin and dibenzofuran for further metabolism by introducing two atoms of oxygen at a pair of vicinal carbon atoms, one of which is involved in one of the bridges between the two aromatic rings, i.e., an angular dioxygenation. the dxna1 and dxna2 cistrons encoding this dioxygenase have been cloned and shown to be located just upstream of a hydrolase gene which specifies an enzyme involved in the subsequent step of the dib ...	1998	9683494
rapid detection and evaluation of clinical characteristics of emerging multiple-drug-resistant gram-negative rods carrying the metallo-beta-lactamase gene blaimp.	gram-negative rods (gnr) carrying the transferable carbapenem resistance gene blaimp, including pseudomonas aeruginosa and serratia marcescens, have been isolated from more than 20 hospitals in japan. although the emergence of such multiple-drug-resistant bacteria is of utmost clinical concern, little information in regard to the distribution of blaimp-positive gnr in hospitals and the clinical characteristics of infected patients is available. to address this, a system for the rapid detection o ...	1998	9687398
a glutathione s-transferase with activity towards cis-1, 2-dichloroepoxyethane is involved in isoprene utilization by rhodococcus sp. strain ad45.	rhodococcus sp. strain ad45 was isolated from an enrichment culture on isoprene (2-methyl-1,3-butadiene). isoprene-grown cells of strain ad45 oxidized isoprene to 3,4-epoxy-3-methyl-1-butene, cis-1, 2-dichloroethene to cis-1,2-dichloroepoxyethane, and trans-1, 2-dichloroethene to trans-1,2-dichloroepoxyethane. isoprene-grown cells also degraded cis-1,2-dichloroepoxyethane and trans-1, 2-dichloroepoxyethane. all organic chlorine was liberated as chloride during degradation of cis-1,2-dichloroepox ...	1998	9687433
influence of carbon source on nitrate removal by nitrate-tolerant klebsiella oxytoca cect 4460 in batch and chemostat cultures.	the nitrate-tolerant organism klebsiella oxytoca cect 4460 tolerates nitrate at concentrations up to 1 m and is used to treat wastewater with high nitrate loads in industrial wastewater treatment plants. we studied the influence of the c source (glycerol or sucrose or both) on the growth rate and the efficiency of nitrate removal under laboratory conditions. with sucrose as the sole c source the maximum specific growth rate was 0.3 h-1, whereas with glycerol it was 0.45 h-1. in batch cultures k. ...	1998	9687459
conversion of phenylalanine to benzaldehyde initiated by an aminotransferase in lactobacillus plantarum	the production of benzaldehyde from phenylalanine has been studied in various microorganisms, and several metabolic pathways have been proposed in the literature for the formation of this aromatic flavor compound. in this study, we describe benzaldehyde formation from phenylalanine by using a cell extract of lactobacillus plantarum. phenylalanine was initially converted to phenylpyruvic acid by an aminotransferase in the cell extract, and the keto acid was further transformed to benzaldehyde. ho ...	1998	9687465
oxidation of trichloroethylene, 1,1-dichloroethylene, and chloroform by toluene/o-xylene monooxygenase from pseudomonas stutzeri ox1.	toluene/o-xylene monooxygenase (tomo) from pseudomonas stutzeri ox1, which oxidizes toluene and o-xylene, was examined for its ability to degrade the environmental pollutants trichloroethylene (tce), 1, 1-dichloroethylene (1,1-dce), cis-1,2-dce, trans-1,2-dce, chloroform, dichloromethane, phenol, 2,4-dichlorophenol, 2,4,5-trichlorophenol, 2,4,6-trichlorophenol, 2,3,5,6-tetrachlorophenol, and 2,3,4,5, 6-pentachlorophenol. escherichia coli jm109 that expressed tomo from genes on plasmid pbz1260 un ...	1998	9687467
the requirement of rpon (sigma factor sigma54) in denitrification by pseudomonas stutzeri is indirect and restricted to the reduction of nitrite and nitric oxide.	the rpon region of pseudomonas stutzeri was cloned, and an rpon null mutant was constructed. rpon was not essential for denitrification in this bacterium but affected the expression levels and enzymatic activities of cytochrome cd1 nitrite reductase and nitric oxide reductase, whereas those of respiratory nitrate reductase and nitrous oxide reductase were comparable to wild-type levels. since the transcription of the structural genes nirs and norcb, coding for nitrite reductase and the nitric ox ...	1998	9687481
effect of humic fractions and clay on biodegradation of phenanthrene by a pseudomonas fluorescens strain isolated from soil.	the mineralization of phenanthrene in pure cultures of a pseudomonas fluorescens strain, isolated from soil, was measured in the presence of soil humic fractions and montmorillonite. humic acid and clay, either separately or in combination, shortened the acclimation phase. a higher mineralization rate was measured in treatments with humic acid at 100 microg/ml. humic acid at 10 microg/ml stimulated the transformation only in the presence of 10 g of clay per liter. we suggest that sorption of phe ...	1998	9687489
a silent abc transporter isolated from streptomyces rochei f20 induces multidrug resistance.	in the search for heterologous activators for actinorhodin production in streptomyces lividans, 3.4 kb of dna from streptomyces rochei f20 (a streptothricin producer) were characterized. subcloning experiments showed that the minimal dna fragment required for activation was 0.4 kb in size. the activation is mediated by increasing the levels of transcription of the actii-orf4 gene. sequencing of the minimal activating fragment did not reveal any clues about its mechanism; nevertheless, it was sho ...	1998	9696745
biochemical and genetic characterization of a gentisate 1, 2-dioxygenase from sphingomonas sp. strain rw5.	a 4,103-bp long dna fragment containing the structural gene of a gentisate 1,2-dioxygenase (ec 1.13.11.4), gtda, from sphingomonas sp. strain rw5 was cloned and sequenced. the gtda gene encodes a 350-amino-acid polypeptide with a predicted size of 38.85 kda. comparison of the gtda gene product with protein sequences in databases, including those of intradiol or extradiol ring-cleaving dioxygenases, revealed no significant homology except for a low similarity (27%) to the 1-hydroxy-2-naphthoate d ...	1998	9696766
arginine catabolism and the arginine succinyltransferase pathway in escherichia coli.	arginine catabolism produces ammonia without transferring nitrogen to another compound, yet the only known pathway of arginine catabolism in escherichia coli (through arginine decarboxylase) does not produce ammonia. our aims were to find the ammonia-producing pathway of arginine catabolism in e. coli and to examine its function. we showed that the only previously described pathway of arginine catabolism, which does not produce ammonia, accounted for only 3% of the arginine consumed. a search fo ...	1998	9696779
amplification of putative chlorocatechol dioxygenase gene fragments from alpha- and beta-proteobacteria.	redundant primers were designed for the pcr amplification of dna from chlorocatechol dioxygenase genes. these primers were used successfully to amplify 270- to 279-bp fragments from a variety of 2,4-dichlorophenoxyacetate- and cholorobenzoate-degrading strains, including species of sphingomonas. three groups of closely related sequences were amplified: one from chlorobenzoate degraders that was 86% similar to the amino acid sequence of the protein coded by the tfdc gene of ralstonia eutropha jmp ...	1998	9699302
[features of the production of cryiiia delta-endotoxin from bacillus thuringiensis in a recombinant strain of pseudomonas putida under control of pm and xyls regulatory elements].	the addition of 3-methyl benzoate to the culture of the recombinant strain pseudomonas putida ipm-36 (bearing the cryiiia gene of b. thuringiensis subsp, tenebrionis under the control of the pm promoter and the regulator gene xyls) slowed down the growth rate of the recombinant strain and increased, under non-selective conditions, the number of plasmid-free cells. intense synthesis of the coleoptera-specific delta-endotoxin encoded by the cryiiia gene began 6-8 h after the addition of the induce ...	1998	9702728
controlled comparative evaluation of bact/alert fan and esp 80a aerobic media as means for detecting bacteremia and fungemia.	during a one-year period, a total of 6,305 blood cultures were processed in a tertiary-care teaching hospital; 6 to 12 ml of blood was inoculated into both a bact/alert fan aerobic bottle and an esp 80a aerobic bottle. the fan aerobic bottle contains an antimicrobial-absorbing material; the 80a aerobic bottle does not. bottles were processed on their respective continuous-monitoring blood culture instruments for up to five days of incubation. four hundred thirty-three cultures (6.9%) representin ...	1998	9705414
the tomato cf-9 disease resistance gene functions in tobacco and potato to confer responsiveness to the fungal avirulence gene product avr 9	the cf-9 gene encodes an extracytoplasmic leucine-rich repeat protein that confers resistance in tomato to races of the fungus cladosporium fulvum that express the corresponding avirulence gene avr 9. we investigated whether the genomic cf-9 gene functions in potato and tobacco. transgenic tobacco and potato plants carrying cf-9 exhibit a rapid hypersensitive cell death response (hr) to avr 9 peptide injection. cf 9 tobacco plants were reciprocally crossed to avr 9-producing tobacco. a developme ...	1998	9707527
comparison of sample sequences of the salmonella typhi genome to the sequence of the complete escherichia coli k-12 genome.	raw sequence data representing the majority of a bacterial genome can be obtained at a tiny fraction of the cost of a completed sequence. to demonstrate the utility of such a resource, 870 single-stranded m13 clones were sequenced from a shotgun library of the salmonella typhi ty2 genome. the sequence reads averaged over 400 bases and sampled the genome with an average spacing of once every 5,000 bases. a total of 339,243 bases of unique sequence was generated (approximately 7% representation). ...	1998	9712782
rapid monitoring method to assess efficacy of sanitizers against pseudomonas putida biofilms.	biofilms of luminescent pseudomonas putida were developed on rubber surfaces by incubation in brain heart infusion (bhi) broth. scanning electron microscopy (sem) and epifluorescence microscopy (efm) were used to examine biofilm formation. to test the efficacy of two sanitizers commonly employed in dairy plants for cip (cleaning in place) procedures, a novel bioluminescence method and aerobic plating were used to enumerate cells. immediately after the sanitizer treatments an apparent 5-log reduc ...	1998	9713769
mechanism for biotransformation of nonylphenol polyethoxylates to xenoestrogens in pseudomonas putida.	a strain of pseudomonas putida isolated from activated sewage grew aerobically on the xenoestrogen precursor, nonylphenol polyethoxylate (npeox, where x is the number of ethoxylate units) as sole carbon source. comparative growth yields on npeoav6, npeoav9, and npeoav20 (mixtures with average ethoxylate numbers as indicated) were consistent with utilization of all but two ethoxylate units, and the final accumulating metabolite was identified by gas chromatography-mass spectroscopy as nonylphenol ...	1998	9721266
chromosomal integration, tandem amplification, and deamplification in pseudomonas putida f1 of a 105-kilobase genetic element containing the chlorocatechol degradative genes from pseudomonas sp. strain b13.	analysis of chlorobenzene-degrading transconjugants of pseudomonas putida f1 which had acquired the genes for chlorocatechol degradation (clc) from pseudomonas sp. strain b13 revealed that the clc gene cluster was present on a 105-kb amplifiable genetic element (named the clc element). in one such transconjugant, p. putida rr22, a total of seven or eight chromosomal copies of the entire genetic element were present when the strain was cultivated on chlorobenzene. chromosomal integrations of the ...	1998	9721270
purification and characterization of the coniferyl aldehyde dehydrogenase from pseudomonas sp. strain hr199 and molecular characterization of the gene.	the coniferyl aldehyde dehydrogenase (caldh) of pseudomonas sp. strain hr199 (dsm7063), which catalyzes the nad+-dependent oxidation of coniferyl aldehyde to ferulic acid and which is induced during growth with eugenol as the carbon source, was purified and characterized. the native protein exhibited an apparent molecular mass of 86,000 +/- 5,000 da, and the subunit mass was 49.5 +/- 2.5 kda, indicating an alpha2 structure of the native enzyme. the optimal oxidation of coniferyl aldehyde to feru ...	1998	9721273
similarities between the antabc-encoded anthranilate dioxygenase and the benabc-encoded benzoate dioxygenase of acinetobacter sp. strain adp1.	acinetobacter sp. strain adp1 can use benzoate or anthranilate as a sole carbon source. these structurally similar compounds are independently converted to catechol, allowing further degradation to proceed via the beta-ketoadipate pathway. in this study, the first step in anthranilate catabolism was characterized. a mutant unable to grow on anthranilate, acn26, was selected. the sequence of a wild-type dna fragment that restored growth revealed the antabc genes, encoding 54-, 19-, and 39-kda pro ...	1998	9721284
purification, characterization, and sequence analysis of 2-aminomuconic 6-semialdehyde dehydrogenase from pseudomonas pseudoalcaligenes js45.	2-aminonumconic 6-semialdehyde is an unstable intermediate in the biodegradation of nitrobenzene and 2-aminophenol by pseudomonas pseudoalcaligenes js45. previous work has shown that enzymes in cell extracts convert 2-aminophenol to 2-aminomuconate in the presence of nad+. in the present work, 2-aminomuconic semialdehyde dehydrogenase was purified and characterized. the purified enzyme migrates as a single band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis with a molecular mass of ...	1998	9721300
active recruitment of sigma54-rna polymerase to the pu promoter of pseudomonas putida: role of ihf and alphactd.	the sequence elements determining the binding of the sigma54-containing rna polymerase (sigma54-rnap) to the pu promoter of pseudomonas putida have been examined. contrary to previous results in related systems, we show that the integration host factor (ihf) binding stimulates the recruitment of the enzyme to the -12/-24 sequence motifs. such a recruitment, which is fully independent of the activator of the system, xylr, requires the interaction of the c-terminal domain of the alpha subunit of r ...	1998	9724648
evolution of an enzyme active site: the structure of a new crystal form of muconate lactonizing enzyme compared with mandelate racemase and enolase.	muconate lactonizing enzyme (mle), a component of the beta-ketoadipate pathway of pseudomonas putida, is a member of a family of related enzymes (the "enolase superfamily") that catalyze the abstraction of the alpha-proton of a carboxylic acid in the context of different overall reactions. new untwinned crystal forms of mle were obtained, one of which diffracts to better than 2.0-a resolution. the packing of the octameric enzyme in this crystal form is unusual, because the asymmetric unit contai ...	1998	9724714
cloning, nucleotide sequence, and expression in escherichia coli of levansucrase genes from the plant pathogens pseudomonas syringae pv. glycinea and p. syringae pv. phaseolicola.	plant-pathogenic bacteria produce various extracellular polysaccharides (epss) which may function as virulence factors in diseases caused by these bacteria. the eps levan is synthesized by the extracellular enzyme levansucrase in pseudomonas syringae, erwinia amylovora, and other bacterial species. the lsc genes encoding levansucrase from p. syringae pv. glycinea pg4180 and p. syringae pv. phaseolicola ncppb 1321 were cloned, and their nucleotide sequences were determined. heterologous expressio ...	1998	9726857
contribution of indole-3-acetic acid production to the epiphytic fitness of erwinia herbicola	erwinia herbicola 299r produces large quantities of indole-3-acetic acid (iaa) in culture media supplemented with l-tryptophan. to assess the contribution of iaa production to epiphytic fitness, the population dynamics of the wild-type strain and an iaa-deficient mutant of this strain on leaves were studied. strain 299xyle, an isogenic iaa-deficient mutant of strain 299r, was constructed by insertional interruption of the indolepyruvate decarboxylase gene of strain 299r with the xyle gene, which ...	1998	9726868
substrate specificity of and product formation by muconate cycloisomerases: an analysis of wild-type enzymes and engineered variants.	muconate cycloisomerases play a crucial role in the bacterial degradation of aromatic compounds by converting cis,cis-muconate, the product of catechol ring cleavage, to (4s)-muconolactone. chloromuconate cycloisomerases catalyze both the corresponding reaction and a dehalogenation reaction in the transformation of chloroaromatic compounds. this study reports the first thorough examination of the substrate specificity of the muconate cycloisomerases from pseudomonas putida prs2000 and acinetobac ...	1998	9726873
aerobic growth on nitroglycerin as the sole carbon, nitrogen, and energy source by a mixed bacterial culture.	nitroglycerin (glycerol trinitrate [gtn]), an explosive and vasodilatory compound, was metabolized by mixed microbial cultures from aeration tank sludge previously exposed to gtn. aerobic enrichment cultures removed gtn rapidly in the absence of a supplemental carbon source. complete denitration of gtn, provided as the sole c and n source, was observed in aerobic batch cultures and proceeded stepwise via the dinitrate and mononitrate isomers, with successive steps occurring at lower rates. the d ...	1998	9726874
conversion of methionine to thiols by lactococci, lactobacilli, and brevibacteria	methanethiol has been strongly associated with desirable cheddar cheese flavor and can be formed from the degradation of methionine (met) via a number of microbial enzymes. methionine gamma-lyase is thought to play a major role in the catabolism of met and generation of methanethiol in several species of bacteria. other enzymes that have been reported to be capable of producing methanethiol from met in lactic acid bacteria include cystathionine beta-lyase and cystathionine gamma-lyase. the objec ...	1998	9726877
purification and characterization of l-methionine gamma-lyase from brevibacterium linens bl2	l-methionine gamma-lyase (ec 4.4.1.11) was purified to homogeneity from brevibacterium linens bl2, a coryneform bacterium which has been used successfully as an adjunct bacterium to improve the flavor of cheddar cheese. the enzyme catalyzes the alpha,gamma elimination of methionine to produce methanethiol, alpha-ketobutyrate, and ammonia. it is a pyridoxal phosphate-dependent enzyme, with a native molecular mass of approximately 170 kda, consisting of four identical subunits of 43 kda each. the ...	1998	9726878
genotypic and phenotypic responses of a riverine microbial community to polycyclic aromatic hydrocarbon contamination.	the phenotypic and genotypic adaptation of a freshwater sedimentary microbial community to elevated (22 to 217 microgram [dry weight] of sediment-1) levels of polycyclic aromatic hydrocarbons (pahs) was determined by using an integrated biomolecular approach. central to the approach was the use of phospholipid fatty acid (plfa) profiles to characterize the microbial community structure and nucleic acid analysis to quantify the frequency of degradative genes. the study site was the little scioto ...	1998	9726892
pseudomonas sp. strain 273, an aerobic alpha, omega-dichloroalkanedegrading bacterium.	a gram-negative, aerobic bacterium was isolated from soil; this bacterium grew in 50% (vol/vol) suspensions of 1,10-dichlorodecane (1,10-dcd) as the sole source of carbon and energy. phenotypic and small-subunit ribosomal rna characterizations identified the organism, designated strain 273, as a member of the genus pseudomonas. after induction with 1,10-dcd, pseudomonas sp. strain 273 released stoichiometric amounts of chloride from c5 to c12 alpha, omega-dichloroalkanes in the presence of oxyge ...	1998	9726906
a new metabolic link between fatty acid de novo synthesis and polyhydroxyalkanoic acid synthesis. the phag gene from pseudomonas putida kt2440 encodes a 3-hydroxyacyl-acyl carrier protein-coenzyme a transferase.	to investigate the metabolic link between fatty acid de novo synthesis and polyhydroxyalkanoic acid (pha) synthesis, we isolated mutants of pseudomonas putida kt2440 deficient in this metabolic route. the gene phag was cloned by phenotypic complementation of these mutants; it encoded a protein of 295 amino acids with a molecular mass of 33,876 da, and the amino acid sequence exhibited 44% amino acid identity to the primary structure of the rhla gene product, which is involved in the rhamnolipid ...	1998	9727022
molecular regulation of beta-lactam biosynthesis in filamentous fungi.	the most commonly used beta-lactam antibiotics for the therapy of infectious diseases are penicillin and cephalosporin. penicillin is produced as an end product by some fungi, most notably by aspergillus (emericella) nidulans and penicillium chrysogenum. cephalosporins are synthesized by both bacteria and fungi, e.g., by the fungus acremonium chrysogenum (cephalosporium acremonium). the biosynthetic pathways leading to both secondary metabolites start from the same three amino acid precursors an ...	1998	9729600
nutrient uptake by microorganisms according to kinetic parameters from theory as related to cytoarchitecture.	the abilities of organisms to sequester substrate are described by the two kinetic constants specific affinity, a degrees, and maximal velocity vmax. specific affinity is derived from the frequency of substrate-molecule collisions with permease sites on the cell surface at subsaturating concentrations of substrates. vmax is derived from the number of permeases and the effective residence time, tau, of the transported molecule on the permease. the results may be analyzed with affinity plots (v/s ...	1998	9729603
growth kinetics of suspended microbial cells: from single-substrate-controlled growth to mixed-substrate kinetics.	growth kinetics, i.e., the relationship between specific growth rate and the concentration of a substrate, is one of the basic tools in microbiology. however, despite more than half a century of research, many fundamental questions about the validity and application of growth kinetics as observed in the laboratory to environmental growth conditions are still unanswered. for pure cultures growing with single substrates, enormous inconsistencies exist in the growth kinetic data reported. the low q ...	1998	9729604
aerobic anoxygenic phototrophic bacteria.	the aerobic anoxygenic phototrophic bacteria are a relatively recently discovered bacterial group. although taxonomically and phylogenetically heterogeneous, these bacteria share the following distinguishing features: the presence of bacteriochlorophyll a incorporated into reaction center and light-harvesting complexes, low levels of the photosynthetic unit in cells, an abundance of carotenoids, a strong inhibition by light of bacteriochlorophyll synthesis, and the inability to grow photosynthet ...	1998	9729607
insertion sequences.	insertion sequences (iss) constitute an important component of most bacterial genomes. over 500 individual iss have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. the last 10 years have also seen some striking advances in our understanding of the transposition process itself. not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic e ...	1998	9729608
linkage map of escherichia coli k-12, edition 10: the traditional map.	this map is an update of the edition 9 map by berlyn et al. (m. k. b. berlyn, k. b. low, and k. e. rudd, p. 1715-1902, in f. c. neidhardt et al., ed., escherichia coli and salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). it uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. the latter are included as ...	1998	9729611
physiological and molecular biological characterization of ammonia oxidation of the heterotrophic nitrifier pseudomonas putida.	the heterotrophic nitrifier pseudomonas putida aerobically oxidized ammonia to hydroxylamine, nitrite, and nitrate. product formation was accompanied by a small but significant release of no, whereas n2o evolution could not be detected under the assay conditions employed. the isolate reduced nitrate to nitrite and partially further to no under anaerobic conditions. aerobically grown cells utilized gamma-aminobutyrate as a carbon source and as a n-source by ammonification. the physiological exper ...	1998	9732537
phylogenetic relationships of pseudomonas putida strains deduced from the nucleotide sequences of gyrb, rpod and 16s rrna genes.	phylogenetic analysis of 20 pseudomonas strains (pseudomonas putida, pseudomonas fluorescens and pseudomonas chlororaphis) was conducted by using the nucleotide sequences of the genes for 16s rna, dna gyrase b subunit (gyrb) and rna polymerase delta 70 factor (rpod), which have been determined by the direct sequencing of pcr-amplified fragments. on the basis of gyrb and rpod sequences, these strains were split into two major clusters: one including the type strain of p. putida and all biovar a s ...	1998	9734035
influence of the tonb energy-coupling protein on efflux-mediated multidrug resistance in pseudomonas aeruginosa.	tonb couples the energized state of the cytoplasmic membrane to the operation of outer membrane receptors responsible for fe(iii) siderophore uptake across the outer membrane of gram-negative bacteria. a tonb mutant of pseudomonas aeruginosa deficient in iron siderophore uptake was shown in the present study to be hypersusceptible to a wide variety of antibiotics, reminiscent of the phenotype of mutants defective in the mexab-oprm antibiotic efflux operon. this was not related to influences of a ...	1998	9736539
outbreak of pseudomonas fluorescens bacteremia among oncology patients.	from 7 to 24 march 1997, four patients developed pseudomonas fluorescens bacteremia at the hospital; one on the oncology ward and the other three in the chemotherapy room. these patients all had underlying malignancies and had the port-a-cath (smiths industries medical systems, deltec, inc., st. paul, minn.) implants. three patients had primary bacteremia, and one had port-a-cath-related infection. none of these patients had received a blood transfusion before the episodes of bacteremia. all pat ...	1998	9738043
the rpos gene regulates op2, an operon for the lower pathway of xylene catabolism on the tol plasmid, and the stress response in pseudomonas putida mt-2.	operon op2 on the pseudomonas putida tol plasmid encodes enzymes for m-toluate catabolism; transcription of this operon is activated by xyls in the presence of m-toluate. because transcriptional activation of op2 specifically occurs in the stationary phase of growth both in p. putida and in escherichia coli, we suspected that its transcription is dependent on rpos (sigmas). therefore, we constructed a rpos disruption strain of p. putida mt-2, and assayed op2 expression and other phenotypes. op2 ...	1998	9738882
colicin import into escherichia coli cells.		1998	9748429
mutation analysis of pobr and pcau, closely related transcriptional activators in acinetobacter.	acinetobacter pobr and pcau are transcriptional activators that closely resemble each other in primary structure, dna-binding sites, metabolic modulators, and physiological function. pobr responds to the inducer-metabolite p-hydroxybenzoate and activates transcription of poba, the structural gene for the enzyme that converts p-hydroxybenzoate to protocatechuate. this compound, differing from p-hydroxybenzoate only in that it contains an additional oxygen atom, binds to pcau and thereby specifica ...	1998	9748437
carbon-source-dependent expression of the palkb promoter from the pseudomonas oleovorans alkane degradation pathway.	pseudomonas oleovorans gpo1 can metabolize medium-chain-length alkanes by means of an enzymatic system whose induction is regulated by the alks protein. in the presence of alkanes, alks activates the expression of promoter palkb, from which most of the genes of the pathway are transcribed. in addition, expression of the first enzyme of the pathway, alkane hydroxylase, is known to be influenced by the carbon source present in the growth medium, indicating the existence of an additional overimpose ...	1998	9748457
nucleotide sequence and characterization of cdra, a cell division-related gene of helicobacter pylori.	we identified cell division-related gene cdra in helicobacter pylori hpk5. the putative gene product, cdra, is a 367-amino-acid polypeptide that exhibited a high level of homology to conserved hypothetical atp-binding protein hp0066 of h. pylori 26695, except in the n-terminal region, and showed some similarity to the ftsk/spoiiie family proteins. we isolated a cdra-disrupted mutant by allelic exchange mutagenesis. because of the low transformation frequency, the possibility that a suppressing m ...	1998	9748467
growth medium-dependent regulation of myxococcus xanthus fatty acid content is controlled by the esg locus.	we compared the cellular fatty acid profiles of myxococcus xanthus cells grown in either a casitone-based complex medium or a chemically defined medium. the cells grown in the complex medium had a much higher content of the abundant branched-chain fatty acid iso-15:0 and several other branched-chain species. the higher branched-chain fatty acid content of the cells grown in the complex medium was dependent on the esg locus, which encodes the e1alpha and e1beta components of a branched-chain keto ...	1998	9748468
[evaluation of antibacterial activities of various antibiotics against glucose non-fermentative gram-negative rods other than pseudomonas aeruginosa].	mics of piperacillin, sulbactam/cefoperazone, minocycline (mino), gentamicin, amikacin, flomoxef, ceftazidime, cefozopran, cefsulodin and imipenem were determined, against 189 clinical isolated strains of glucose non-fermentative gram-negative rods (nfgnr; acinetobacter baumannii (44), alcaligenes faecalis (5), alcaligenes xylosoxidans (25), burkholderia cepacia (12), chryseobacterium indologenes (23), chryseobacterium meningosepticum (9), pseudomonas fluorescens (8), pseudomonas putida (12), st ...	1998	9755431
crystallization and preliminary x-ray diffraction studies of the oxygenating subunit of 3,6-diketocamphane monooxygenase from pseudomonas putida.	the oxygenating constituent of the 3,6-diketocamphane monooxygenase isozyme from pseudomonas putida ncimb 10007 has been crystallized under two different conditions. crystals were initially grown from polyethylene glycol (peg) 8000 and sodium acetate using the vapour-phase diffusion method. the crystals were of orthorhombic p212121 space group, with cell dimensions a = 55.8, b = 94.5 and c = 163.7 a and diffracted to 2.8 a resolution. more recently, improved crystals, which diffracted beyond 2 a ...	1998	9757131
c-type cytochromes and manganese oxidation in pseudomonas putida mnb1.	pseudomonas putida mnb1 is an isolate from an mn oxide-encrusted pipeline that can oxidize mn(ii) to mn oxides. we used transposon mutagenesis to construct mutants of strain mnb1 that are unable to oxidize manganese, and we characterized some of these mutants. the mutants were divided into three groups: mutants defective in the biogenesis of c-type cytochromes, mutants defective in genes that encode key enzymes of the tricarboxylic acid cycle, and mutants defective in the biosynthesis of tryptop ...	1998	9758766
the cytochrome c maturation operon is involved in manganese oxidation in pseudomonas putida gb-1.	a pseudomonas putida strain, strain gb-1, oxidizes mn2+ to mn oxide in the early stationary growth phase. it also secretes a siderophore (identified as pyoverdine) when it is subjected to iron limitation. after transposon (tn5) mutagenesis several classes of mutants with differences in mn2+ oxidation and/or secretion of the mn2+-oxidizing activity were identified. preliminary analysis of the tn5 insertion site in one of the nonoxidizing mutants suggested that a multicopper oxidase-related enzyme ...	1998	9758767
secondary metabolite- and endochitinase-dependent antagonism toward plant-pathogenic microfungi of pseudomonas fluorescens isolates from sugar beet rhizosphere	forty-seven isolates representing all biovars of pseudomonas fluorescens (biovars i to vi) were collected from the rhizosphere of field-grown sugar beet plants to select candidate strains for biological control of preemergence damping-off disease. the isolates were tested for in vitro antagonism toward the plant-pathogenic microfungi pythium ultimum and rhizoctonia solani in three different plate test media. mechanisms of fungal inhibition were elucidated by tracing secondary-metabolite producti ...	1998	9758768
analysis of the gene cluster encoding toluene/o-xylene monooxygenase from pseudomonas stutzeri ox1.	the toluene/o-xylene monooxygenase cloned from pseudomonas stutzeri ox1 displays a very broad range of substrates and a very peculiar regioselectivity, because it is able to hydroxylate more than one position on the aromatic ring of several hydrocarbons and phenols. the nucleotide sequence of the gene cluster coding for this enzymatic system has been determined. the sequence analysis revealed the presence of six open reading frames (orfs) homologous to other genes clustered in operons coding for ...	1998	9758777
plasmids responsible for horizontal transfer of naphthalene catabolism genes between bacteria at a coal tar-contaminated site are homologous to pdtg1 from pseudomonas putida ncib 9816-4	the presence of a highly conserved nahac allele among phylogenetically diverse bacteria carrying naphthalene-catabolic plasmids provided evidence for in situ horizontal gene transfer at a coal tar-contaminated site (j. b. herrick, k. g. stuart-keil, w. c. ghiorse, and e. l. madsen, appl. environ. microbiol. 63:2330-2337, 1997). the objective of the present study was to identify and characterize the different-sized naphthalene-catabolic plasmids in order to determine the probable mechanism of hor ...	1998	9758778
a plant growth-promoting bacterium that decreases nickel toxicity in seedlings	a plant growth-promoting bacterium, kluyvera ascorbata sud165, that contained high levels of heavy metals was isolated from soil collected near sudbury, ontario, canada. the bacterium was resistant to the toxic effects of ni2+, pb2+, zn2+, and cro4-, produced a siderophore(s), and displayed 1-aminocyclopropane-1-carboxylic acid deaminase activity. canola seeds inoculated with this bacterium and then grown under gnotobiotic conditions in the presence of high concentrations of nickel chloride were ...	1998	9758782
optimization of differential display of prokaryotic mrna: application to pure culture and soil microcosms.	the differential display (dd) technique, which is widely used almost exclusively for eukaryotic gene discovery, was optimized to detect differential mrna transcription from both pure-culture and soil-derived bacterial rna. a model system which included toluene induction of todc1 in pseudomonas putida f1 was used to optimize the procedure. at 24-h tod induction was determined to be approximately 8 x 10(7) transcripts/microg or 0.08% of the total mrna. the primer concentration, primer length, anne ...	1998	9758787
biocatalyst engineering by assembly of fatty acid transport and oxidation activities for in vivo application of cytochrome p-450bm-3 monooxygenase.	the application of whole cells containing cytochrome p-450bm-3 monooxygenase [ec 1.14.14.1] for the bioconversion of long-chain saturated fatty acids to omega-1, omega-2, and omega-3 hydroxy fatty acids was investigated. we utilized pentadecanoic acid and studied its conversion to a mixture of 12-, 13-, and 14-hydroxypentadecanoic acids by this monooxygenase. for this purpose, escherichia coli recombinants containing plasmid pcyp102 producing the fatty acid monooxygenase cytochrome p-450bm-3 wer ...	1998	9758800
degradation of 1,2,3,4-tetrachlorobenzene by pseudomonas chlororaphis rw71	pseudomonas chlororaphis rw71 mineralized 1,2,3,4-tetrachlorobenzene, a highly recalcitrant pollutant hitherto not known to be degraded by pure cultures, as a sole source of carbon and energy, thereby releasing stoichiometric amounts of chloride. the transient excretion of tetrachlorocatechol in the early growth phase suggests an initial attack by a dioxygenase to form the corresponding dihydrodiol which rearomatizes to the catechol. the activity of chlorocatechol 1,2-dioxygenase in crude cell e ...	1998	9758802
determination of the biomasses of small bacteria at low concentrations in a mixture of species with forward light scatter measurements by flow cytometry	the forward light scatter intensity of bacteria analyzed by flow cytometry varied with their dry mass, in accordance with theory. a standard curve was formulated with rayleigh-gans theory to accommodate cell shape and alignment. it was calibrated with an extinction-culture isolate of the small marine organism cycloclasticus oligotrophus, for which dry weight was determined by chn analysis and 14c-acetate incorporation. increased light scatter intensity due to formaldehyde accumulation in preserv ...	1998	9758817
characterization of genes involved in biosynthesis of a novel antibiotic from burkholderia cepacia bc11 and their role in biological control of rhizoctonia solani.	genetic manipulation of fluorescent pseudomonads has provided major insight into their production of antifungal molecules and their role in biological control of plant disease. burkholderia cepacia also produces antifungal activities, but its biological control activity is much less well characterized, in part due to difficulties in applying genetic tools. here we report genetic and biochemical characterization of a soil isolate of b. cepacia relating to its production of an unusual antibiotic t ...	1998	9758823
resistance to tellurite as a selection marker for genetic manipulations of pseudomonas strains.	resistance to the toxic compound potassium tellurite (telr) has been employed as a selection marker built into a set of transposon vectors and broad-host-range plasmids tailored for genetic manipulations of pseudomonas strains potentially destined for environmental release. in this study, the activated telr determinants encoded by the cryptic telab genes of plasmid rk2 were produced, along with the associated kila gene, as dna cassettes compatible with cognate vectors. in one case, the telr dete ...	1998	9758838
evidence for interspecies gene transfer in the evolution of 2,4-dichlorophenoxyacetic acid degraders.	small-subunit ribosomal dna (ssu rdna) from 20 phenotypically distinct strains of 2,4-dichlorophenoxyacetic acid (2,4-d)-degrading bacteria was partially sequenced, yielding 18 unique strains belonging to members of the alpha, beta, and gamma subgroups of the class proteobacteria. to understand the origin of 2,4-d degradation in this diverse collection, the first gene in the 2,4-d pathway, tfda, was sequenced. the sequences fell into three unique classes found in various members of the beta and ...	1998	9758850
substrate selectivity and biochemical properties of 4-hydroxy-2-keto-pentanoic acid aldolase from escherichia coli.	4-hydroxy-2-keto-pentanoic acid aldolase from escherichia coli was identified as a class i aldolase. the enzyme was found to be highly selective for the acetaldehyde acceptor but would accept alpha-ketobutyric acid or phenylpyruvic acid in place of the pyruvic acid carbonyl donor.	1998	9758851
crystallization and preliminary x-ray studies of pseudomonas putida histidine ammonium-lyase.	histidine ammonium-lyase from p. putida was expressed in escherichia coli, purified to homogeneity, and crystallized by the vapour-diffusion method using polyethylene glycol 3350 as the precipitant. the crystals, which diffract to at least 2.5 a resolution, exhibit the symmetry of space group p212121, with unit-cell parameters a = 89.7, b = 138.2 and c = 164.8 a. the asymmetric unit contains a tetramer, and the crystals have a vm value of 2.41 a3 da-1.	1998	9761874
crystallographic study of azurin from pseudomonas putida.	azurin from pseudomonas putida is a blue copper protein which functions as an electron carrier. two crystal forms of azurin were grown, one in the presence and the other in the absence of zinc acetate; each belongs to space group p21 and contains two molecules per asymmetric unit. the zinc-free crystals have cell dimensions a = 43.25, b = 50.65, c = 54.60 a, beta = 107.79 degrees, while the crystals grown from zinc-containing solution have cell dimensions a = 40.76, b = 51.22, c = 54.96 a, beta ...	1998	9761890
iron-responsive gene regulation in a campylobacter jejuni fur mutant.	the expression of iron-regulated systems in gram-negative bacteria is generally controlled by the fur protein, which represses the transcription of iron-regulated promoters by using fe2+ as a cofactor. mutational analysis of the campylobacter jejuni fur gene was carried out by generation of a set of mutant copies of fur which had a kanamycin or chloramphenicol resistance gene introduced into the regions encoding the n and c termini of the fur protein. the mutated genes were recombined into the c ...	1998	9765558
identification and characterization of is1411, a new insertion sequence which causes transcriptional activation of the phenol degradation genes in pseudomonas putida.	a new insertion sequence (is element), is1411, was identified downstream of the phenol degradation genes pheba that originated from plasmid dna of pseudomonas sp. strain est1001. according to sequence analysis, is1411 belongs to a new family of is elements that has recently been named the isl3 family (j. mahillon and m. chandler, microbiol. mol. biol. rev. 62:725-774, 1998). is1411 generates 8-bp duplication of the target dna and carries 24-bp inverted repeats (irs), highly homologous to the irs ...	1998	9765560
a chaperone in the hsp70 family controls production of extracellular fibrils in myxococcus xanthus.	three independent tn5-lac insertions in the s1 locus of myxococcus xanthus inactivate the sglk gene, which is nonessential for growth but required for social motility and multicellular development. the sequence of sglk reveals that it encodes a homologue of the chaperone hsp70 (dnak). the sglk gene is cotranscribed with the upstream grps gene, which encodes a grpe homologue. unlike sglk, grps is not required for social motility or development. wild-type m. xanthus is encased in extracellular pol ...	1998	9765567
influence of the mexab-oprm multidrug efflux system on quorum sensing in pseudomonas aeruginosa.	pseudomonas aeruginosa nalb mutants which hyperexpress the mexab-oprm multidrug efflux system produce reduced levels of several extracellular virulence factors known to be regulated by quorum sensing. such mutants also produce less acylated homoserine lactone autoinducer pai-1, consistent with an observed reduction in lasi expression. these data suggest that pai-1 is a substrate for mexab-oprm, and its resulting exclusion from cells hyperexpressing mexab-oprm limits pai-1-dependent activation of ...	1998	9765578
the nine genes of the nocardia lactamdurans cephamycin cluster are transcribed into large mrnas from three promoters, two of them located in a bidirectional promoter region.	the nine biosynthesis genes of the nocardia lactamdurans cephamycin cluster are expressed as three different mrnas initiating at promoters latp, cefdp, and pcbabp, as shown by low-resolution s1 nuclease protection assays and northern blotting analysis. bidirectional expression occurred from divergent promoters (latp and cefdp) located in a 629-bp intergenic region that contains three heptameric direct repeats similar to those recognized by members of the sarp (streptomyces antibiotic regulatory ...	1998	9765587
isolation of a soil psychrotrophic toluene-degrading pseudomonas strain: influence of temperature on the growth characteristics on different substrates.	two psychrotrophic toluene-degrading pseudomonas putida strains were isolated at low temperature from a toluene-polluted soil, thereby demonstrating that toluene degradation at low temperature occurred in nature, a finding of possible interest for soil bioremediation procedures. in one of these strains, two aromatic compounds (toluene and benzoate) were degraded, most likely through different pathways. to study the effect of the growth temperature on the metabolism of these substrates, we studie ...	1997	9765796
production of substituted naphthalene dihydrodiols by engineered escherichia coli containing the cloned naphthalene 1,2-dioxygenase gene from pseudomonas fluorescens n3.	naphthalene dioxygenase, a key enzyme in the dihydroxylation of naphthalene, is encoded by the plasmid pn3, responsible for naphthalene metabolism in pseudomonas fluorescens n3. the naphthalene dioxygenase, including all the sequences for its expression and the regulatory region, has been localized on the 4.3-kb hindiii-clai fragment and on the 3.5-kb hindiii fragment of the plasmid pn3, by southern analysis using as probes naha and nahr genes, the homologous genes of the plasmid nah7 from pseud ...	1997	9765814
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
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
use of the bact/alert blood culture system for culture of sterile body fluids other than blood.	studies have demonstrated that large-volume culture methods for sterile body fluids other than blood increase recovery compared to traditional plated-medium methods. bact/alert is a fully automated blood culture system for detecting bacteremia and fungemia. in this study, we compared culture in bact/alert standard aerobic and anaerobic bottles, bact/alert fan aerobic and fan anaerobic bottles, and culture on routine media for six specimen types, i.e., continuous ambulatory peritoneal dialysate ( ...	1998	9774578
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
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
cloning of the nocardia corallina polyhydroxyalkanoate synthase gene and production of poly-(3-hydroxybutyrate-co-3-hydroxyhexanoate) and poly-(3-hydroxyvalerate-co-3-hydroxyheptanoate).	the polyhydroxyalkanoate (pha) synthase gene (phacnc) from nocardia corallina was identified in a lambda library on a 6-kb bamhi fragment. a 2.8-kb xhoii subfragment was found to contain the intact pha synthase. this 2.8-kb fragment was subjected to dna sequencing and was found to contain the coding region for the pha synthase and a small downstream open reading frame of unknown function. on the basis of dna sequence, phacnc is closest in homology to the pha synthases (phacpai and phacpaii) of p ...	1998	9783428
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
int-b13, an unusual site-specific recombinase of the bacteriophage p4 integrase family, is responsible for chromosomal insertion of the 105-kilobase clc element of pseudomonas sp. strain b13.	pseudomonas sp. strain b13 carries the clcrabde genes encoding chlorocatechol-degradative enzymes on the self-transmissible 105-kb clc element. the element integrates site and orientation specifically into the chromosomes of various bacterial recipients, with a glycine trna structural gene (glyv) as the integration site. we report here the localization and nucleotide sequence of the integrase gene and the activity of the integrase gene product in mediating site-specific integration. the integras ...	1998	9791097
identification of chlorobenzene dioxygenase sequence elements involved in dechlorination of 1,2,4,5-tetrachlorobenzene.	the teca chlorobenzene dioxygenase and the todcba toluene dioxygenase exhibit substantial sequence similarity yet have different substrate specificities. escherichia coli cells producing recombinant teca enzyme dioxygenate and simultaneously eliminate a halogen substituent from 1,2,4,5-tetrachlorobenzene but show no activity toward benzene, whereas those producing todcba dioxygenate benzene but not tetrachlorobenzene. a hybrid teca dioxygenase variant containing the large alpha-subunit of the to ...	1998	9791099
molecular genetic analysis of phosphite and hypophosphite oxidation by pseudomonas stutzeri wm88.	the first molecular and genetic characterization of a biochemical pathway for oxidation of the reduced phosphorus (p) compounds phosphite and hypophosphite is reported. the pathway was identified in pseudomonas stutzeri wm88, which was chosen for detailed studies from a group of organisms isolated based on their ability to oxidize hypophosphite (+1 valence) and phosphite (+3 valence) to phosphate (+5 valence). the genes required for oxidation of both compounds by p. stutzeri wm88 were cloned on ...	1998	9791102
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
a novel mechanism for resistance to the antimetabolite n-phosphonoacetyl-l-aspartate by helicobacter pylori.	the mechanism of resistance to n-phosphonoacetyl-l-aspartate (pala), a potent inhibitor of aspartate carbamoyltransferase (which catalyzes the first committed step of de novo pyrimidine biosynthesis), in helicobacter pylori was investigated. at a 1 mm concentration, pala had no effects on the growth and viability of h. pylori. the inhibitor was taken up by h. pylori cells and the transport was saturable, with a km of 14.8 mm and a vmax of 19.1 nmol min-1 microliters of cell water-1. by 31p nucle ...	1998	9791105
regio- and stereospecific conversion of 4-alkylphenols by the covalent flavoprotein vanillyl-alcohol oxidase.	the regio- and stereospecific conversion of prochiral 4-alkylphenols by the covalent flavoprotein vanillyl-alcohol oxidase was investigated. the enzyme was active, with 4-alkylphenols bearing aliphatic side chains of up to seven carbon atoms. optimal catalytic efficiency occurred with 4-ethylphenol and 4-n-propylphenols. these short-chain 4-alkylphenols are stereoselectively hydroxylated to the corresponding (r)-1-(4'-hydroxyphenyl)alcohols (f. p. drijfhout, m. w. fraaije, h. jongejan, w. j. h. ...	1998	9791114
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
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
evolution of a pathway for chlorobenzene metabolism leads to natural attenuation in contaminated groundwater	complete metabolism of chlorinated benzenes is not a feature that is generally found in aerobic bacteria but is thought to be due to a novel recombination of two separate gene clusters. such a recombination could be responsible for adaptation of a natural microbial community in response to contamination with synthetic chemicals. this hypothesis was tested in a chlorobenzene (cb)-contaminated aquifer. cb-degrading bacteria from a contaminated site were characterized for a number of years by exami ...	1998	9797264
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
whole-cell kinetics of trichloroethylene degradation by phenol hydroxylase in a ralstonia eutropha jmp134 derivative	the rate, progress, and limits of trichloroethylene (tce) degradation by ralstonia eutropha aek301/pyk3021 whole cells were examined in the absence of aromatic induction. at tce concentrations up to 800 &mgr;m, degradation rates were sustained until tce was no longer detectable. the ks and vmax for tce degradation by aek301/pyk3021 whole cells were determined to be 630 &mgr;m and 22.6 nmol/min/mg of total protein, respectively. the sustained linear rates of tce degradation by aek301/pyk3021 up t ...	1998	9797289
molecular detection, isolation, and physiological characterization of functionally dominant phenol-degrading bacteria in activated sludge.	dna was isolated from phenol-digesting activated sludge, and partial fragments of the 16s ribosomal dna (rdna) and the gene encoding the largest subunit of multicomponent phenol hydroxylase (lmph) were amplified by pcr. an analysis of the amplified fragments by temperature gradient gel electrophoresis (tgge) demonstrated that two major 16s rdna bands (bands r2 and r3) and two major lmph gene bands (bands p2 and p3) appeared after the activated sludge became acclimated to phenol. the nucleotide s ...	1998	9797297