Publications

positive selection for mutations affecting bioconversion of aromatic compounds in agrobacterium tumefaciens: analysis of spontaneous mutations in the protocatechuate 3,4-dioxygenase gene.	a positive selection method for mutations affecting bioconversion of aromatic compounds was applied to a mutant strain of agrobacterium tumefaciens a348. the nucleotide sequence of the a348 pcahgb genes, which encode protocatechuate 3,4-dioxygenase (pcahg) and beta-carboxy-cis,cis-muconate cycloisomerase (pcab) for the first two steps in catabolism of the diphenolic protocatechuate, was determined. an omega element was introduced into the pcab gene of a348, creating strain ado2077. in the presen ...	2000	11029436
[respiratory activity of bacteria acinetobacter calcoaceticus tm-31 during assimilation of alkane hydrocarbons].	the respiratory activity of acinetobacter calcoaceticus tm-31 with resect to alkane hydrocarbons was studied. the dynamics of oxygen consumption by the cells while assimilating n-hexadecane was assayed by a modified technique using an oxygen electrode. the dependence of cell respiratory activity on the amount of n-hexadecane within the concentration range of 0.03-0.66% was determined. it was demonstrated that the cells also displayed respiratory activity towards other medium-chain n-alkanes: hex ...	2000	11042879
benr, a xyls homologue, regulates three different pathways of aromatic acid degradation in pseudomonas putida.	pseudomonas putida converts benzoate to catechol using two enzymes that are encoded on the chromosome and whose expression is induced by benzoate. benzoate also binds to the regulator xyls to induce expression of the tol (toluene degradation) plasmid-encoded meta pathway operon for benzoate and methylbenzoate degradation. finally, benzoate represses the ability of p. putida to transport 4-hydroxybenzoate (4-hba) by preventing transcription of pcak, the gene encoding the 4-hba permease. here we i ...	2000	11053377
the malonate decarboxylase operon of acinetobacter calcoaceticus kccm 40902 is regulated by malonate and the transcriptional repressor mdcy.	a regulatory gene-like open reading frame oriented oppositely to mdcl, coined mdcy, was found upstream from the structural genes of the mdclmacdegbh operon in acinetobacter calcoaceticus kccm 40902. to elucidate the function of this gene, mdcy was expressed in escherichia coli, and the mdcy protein was purified to homogeneity. its dna binding activity and binding site were examined by gel retardation and footprinting assays in vitro and by site-directed mutagenesis of the binding sites in vivo. ...	2000	11053382
key aromatic-ring-cleaving enzyme, protocatechuate 3,4-dioxygenase, in the ecologically important marine roseobacter lineage.	aromatic compound degradation in six bacteria representing an ecologically important marine taxon of the alpha-proteobacteria was investigated. initial screens suggested that isolates in the roseobacter lineage can degrade aromatic compounds via the beta-ketoadipate pathway, a catabolic route that has been well characterized in soil microbes. six roseobacter isolates were screened for the presence of protocatechuate 3,4-dioxygenase, a key enzyme in the beta-ketoadipate pathway. all six isolates ...	2000	11055908
recognition of two novel phenons of the genus acinetobacter among non-glucose-acidifying isolates from human specimens.	genomic species diversity among 147 acinetobacter clinical isolates not belonging to the a. calcoaceticus- a. baumannii (acb) complex was investigated by phenotypic and genotypic identification methods. the isolates were obtained between 1991 and 1999 from numerous diagnostic laboratories in the czech republic and were studied by numerical probabilistic identification using two biochemical frequency matrices and amplified rdna restriction analysis (ardra). their final identification was derived ...	2000	11060048
emergence and rapid spread of carbapenem resistance during a large and sustained hospital outbreak of multiresistant acinetobacter baumannii.	beginning in 1992, a sustained outbreak of multiresistant acinetobacter baumannii infections was noted in our 1,000-bed hospital in barcelona, spain, resulting in considerable overuse of imipenem, to which the organisms were uniformly susceptible. in january 1997, carbapenem-resistant (cr) a. baumannii strains emerged and rapidly disseminated in the intensive care units (icus), prompting us to conduct a prospective investigation. it was an 18-month longitudinal intervention study aimed at the id ...	2000	11060073
acinetobacter baumannii-infected vascular catheters collected from horses in an equine clinic.	acinetobacter baumannii was isolated from tips clipped from seven intravenous jugular catheters collected from horses in the ghent university equine clinic. they originated from seven different horses. three of the seven showed evidence of local infection.	2000	11060112
inducible metabolism of phenolic acids in pediococcus pentosaceus is encoded by an autoregulated operon which involves a new class of negative transcriptional regulator.	pediococcus pentosaceus displays a substrate-inducible phenolic acid decarboxylase (pad) activity on p-coumaric acid. based on dna sequence homologies between the three pads previously cloned, a dna probe of the lactobacillus plantarum pdc gene was used to screen a p. pentosaceus genomic library in order to clone the corresponding gene of this bacteria. one clone detected with this probe displayed a low pad activity. subcloning of this plasmid insertion allowed us to determine the part of the in ...	2000	11073918
the 4-oxalomesaconate hydratase gene, involved in the protocatechuate 4,5-cleavage pathway, is essential to vanillate and syringate degradation in sphingomonas paucimobilis syk-6.	sphingomonas paucimobilis syk-6 is able to grow on various dimeric lignin compounds, which are converted to vanillate and syringate by the actions of unique lignin degradation enzymes in this strain. vanillate and syringate are degraded by the o-demethylase and converted into protocatechuate (pca) and 3-o-methylgallate (3mga), respectively. pca is further degraded via the pca 4,5-cleavage pathway, while the results suggested that 3mga is degraded through another pathway in which pca 4,5-dioxygen ...	2000	11092855
mutations in catb, the gene encoding muconate cycloisomerase, activate transcription of the distal ben genes and contribute to a complex regulatory circuit in acinetobacter sp. strain adp1.	mutants of the bacterium acinetobacter sp. strain adp1 were selected to grow on benzoate without the benm transcriptional activator. in the wild type, benm responds to benzoate and cis,cis-muconate to activate expression of the benabcde operon, which is involved in benzoate catabolism. this operon encodes enzymes that convert benzoate to catechol, a compound subsequently degraded by cat gene-encoded enzymes. in this report, four spontaneous mutants were found to carry catb mutations that enabled ...	2000	11092867
thermostable nadp(+)-dependent medium-chain alcohol dehydrogenase from acinetobacter sp. strain m-1: purification and characterization and gene expression in escherichia coli.	nadph-dependent alkylaldehyde reducing enzyme, which was greatly induced by n-hexadecane, from acinetobacter sp. strain m-1 was purified and characterized. the purified enzyme had molecular masses of 40 kda as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and 160 kda as determined by gel filtration chromatography. the enzyme, which was shown to be highly thermostable, was most active toward n-heptanal and could use n-alkylaldehydes ranging from c(2) to c(14) and several ...	2000	11097895
bacterial colonization of disposable soft contact lenses is greater during corneal infiltrative events than during asymptomatic extended lens wear.	microorganisms, especially gram-negative bacteria, are considered to play a role in the etiology of certain corneal infiltrative events (cies) observed during soft contact lens wear. this study explored the possibility of microbial colonization of soft contact lenses as a risk factor leading to cies. in a clinical trial conducted from march 1993 to january 1996, 330 subjects wore disposable soft contact lenses on a 6-night extended-wear and disposal schedule. during this period, 4,321 lenses (11 ...	2000	11101574
substrate range and genetic analysis of acinetobacter vanillate demethylase.	an acinetobacter sp. genetic screen was used to probe structure-function relationships in vanillate demethylase, a two-component monooxygenase. mutants with null, leaky, and heat-sensitive phenotypes were isolated. missense mutations tended to be clustered in specific regions, most of which make known contributions to catalytic activity. the vanillate analogs m-anisate, m-toluate, and 4-hydroxy-3,5-dimethylbenzoate are substrates of the enzyme and weakly inhibit the metabolism of vanillate by wi ...	2000	10671462
evolution of arginine biosynthesis in the bacterial domain: novel gene-enzyme relationships from psychrophilic moritella strains (vibrionaceae) and evolutionary significance of n-alpha-acetyl ornithinase.	in the arginine biosynthetic pathway of the vast majority of prokaryotes, the formation of ornithine is catalyzed by an enzyme transferring the acetyl group of n-alpha-acetylornithine to glutamate (ornithine acetyltransferase [oatase]) (argj encoded). only two exceptions had been reported-the enterobacteriaceae and myxococcus xanthus (members of the gamma and delta groups of the class proteobacteria, respectively)-in which ornithine is produced from n-alpha-acetylornithine by a deacylase, acetyl ...	2000	10692366
transformation of acinetobacter sp. strain bd413(pfg4deltanptii) with transgenic plant dna in soil microcosms and effects of kanamycin on selection of transformants.	here we show that horizontal transfer of dna, extracted from transgenic sugar beets, to bacteria, based on homologous recombination, can occur in soil. restoration of a 317-bp-deleted nptii gene in acinetobacter sp. strain bd413(pfg4) cells incubated in sterile soil microcosms was detected after addition of nutrients and transgenic plant dna encoding a functional nptii gene conferring bacterial kanamycin resistance. selective effects of the addition of kanamycin on the population dynamics of aci ...	2000	10698801
comparison of different pcr approaches for typing of francisella tularensis strains.	in this study, we evaluated three pcr methods for epidemiological typing of francisella tularensis: repetitive extragenic palindromic element pcr (rep-pcr), enterobacterial repetitive intergenic consensus sequence pcr (eric-pcr), and random amplified polymorphic dna (rapd) assay with both m13 and t3-t7 primers. the analysis was performed with 40 strains of f. tularensis isolated from hares, humans, ticks, and a vole. on the basis of the combination of rep, eric, and rapd fingerprints, f. tularen ...	2000	10698989
improved repetitive-element pcr fingerprinting of salmonella enterica with the use of extremely elevated annealing temperatures.	modified thermal cycling conditions were explored in an effort to improve the reproducibility and resolving power of repetitive-element pcr (rep-pcr) fingerprinting. assay performance was rigorously evaluated under standard and modified cycling conditions, using as a test set 12 strains putatively representing 12 serovars of salmonella enterica. for all three fingerprint types (eric2, boxa1r, and composite fingerprints), the use of extremely elevated annealing temperatures plus an initial "touch ...	2000	10702502
aminoacyl-trna synthetases, the genetic code, and the evolutionary process.	the aminoacyl-trna synthetases (aarss) and their relationship to the genetic code are examined from the evolutionary perspective. despite a loose correlation between codon assignments and aars evolutionary relationships, the code is far too highly structured to have been ordered merely through the evolutionary wanderings of these enzymes. nevertheless, the aarss are very informative about the evolutionary process. examination of the phylogenetic trees for each of the aarss reveals the following. ...	2000	10704480
postoperative endophthalmitis caused by sequestered acinetobacter calcoaceticus.	to describe postoperative endophthalmitis caused by sequestered acinetobacter calcoaceticus.	2000	10704562
purification of a jojoba embryo fatty acyl-coenzyme a reductase and expression of its cdna in high erucic acid rapeseed.	the jojoba (simmondsia chinensis) plant produces esters of long-chain alcohols and fatty acids (waxes) as a seed lipid energy reserve. this is in contrast to the triglycerides found in seeds of other plants. we purified an alcohol-forming fatty acyl-coenzyme a reductase (far) from developing embryos and cloned the cdna encoding the enzyme. expression of a cdna in escherichia coli confers far activity upon those cells and results in the accumulation of fatty alcohols. the far sequence shows signi ...	2000	10712526
sinorhizobium meliloti puta gene regulation: a new model within the family rhizobiaceae.	proline dehydrogenase (puta) is a bifunctional enzyme that catalyzes the oxidation of proline to glutamate. in sinorhizobium meliloti, as in other microorganisms, the puta gene is transcriptionally activated in response to proline. in rhodobacter capsulatus, agrobacterium, and most probably in bradyrhizobium, this activation is dependent on an lrp-like protein encoded by the putr gene, located immediately upstream of puta. interestingly, sequence and genetic analysis of the region upstream of th ...	2000	10715000
sal genes determining the catabolism of salicylate esters are part of a supraoperonic cluster of catabolic genes in acinetobacter sp. strain adp1.	a 5-kbp region upstream of the are-ben-cat genes was cloned from acinetobacter sp. strain adp1, extending the supraoperonic cluster of catabolic genes to 30 kbp. four open reading frames, sala, salr, sale, and sald, were identified from the nucleotide sequence. reverse transcription-pcr studies suggested that these open reading frames are organized into two convergent transcription units, salar and salde. the sale gene, encoding a protein of 239 residues, was ligated into expression vector pet5a ...	2000	10715011
nucleotide sequence of the bla(rtg-2) (carb-5) gene and phylogeny of a new group of carbenicillinases.	we determined the nucleotide sequence of the bla gene for the acinetobacter calcoaceticus beta-lactamase previously described as carb-5. alignment of the deduced amino acid sequence with those of known beta-lactamases revealed that carb-5 possesses an rtg triad in box vii, as described for the proteus mirabilis gn79 enzyme, instead of the rsg consensus characteristic of the other carbenicillinases. phylogenetic studies showed that these rtg enzymes constitute a new, separate group, possibly ance ...	2000	10722515
secreted enzymatic activities of wild-type and pild-deficient legionella pneumophila.	legionella pneumophila, the agent of legionnaires' disease, is an intracellular pathogen of protozoa and macrophages. previously, we had determined that the legionella pild gene is involved in type iv pilus biogenesis, type ii protein secretion, intracellular infection, and virulence. since the loss of pili and a protease do not account for the infection defect exhibited by a pild-deficient strain, we sought to define other secreted proteins absent in the mutant. based upon the release of p-nitr ...	2000	10722574
a novel phenanthrene dioxygenase from nocardioides sp. strain kp7: expression in escherichia coli.	nocardioides sp. strain kp7 grows on phenanthrene but not on naphthalene. this organism degrades phenanthrene via 1-hydroxy-2-naphthoate, o-phthalate, and protocatechuate. the genes responsible for the degradation of phenanthrene to o-phthalate (phd) were found by southern hybridization to reside on the chromosome. a 10.6-kb dna fragment containing eight phd genes was cloned and sequenced. the phda, phdb, phdc, and phdd genes, which encode the alpha and beta subunits of the oxygenase component, ...	2000	10735855
type iv pilus genes pila and pilc of pseudomonas stutzeri are required for natural genetic transformation, and pila can be replaced by corresponding genes from nontransformable species.	pseudomonas stutzeri lives in terrestrial and aquatic habitats and is capable of natural genetic transformation. after transposon mutagenesis, transformation-deficient mutants were isolated from a p. stutzeri jm300 strain. in one of them a gene which coded for a protein with 75% amino acid sequence identity to pilc of pseudomonas aeruginosa, an accessory protein for type iv pilus biogenesis, was inactivated. the presence of type iv pili was demonstrated by susceptibility to the type iv pilus-dep ...	2000	10735861
genetic and biochemical characterization of the pathway in pantoea citrea leading to pink disease of pineapple.	pink disease of pineapple, caused by pantoea citrea, is characterized by a dark coloration on fruit slices after autoclaving. this coloration is initiated by the oxidation of glucose to gluconate, which is followed by further oxidation of gluconate to as yet unknown chromogenic compounds. to elucidate the biochemical pathway leading to pink disease, we generated six coloration-defective mutants of p. citrea that were still able to oxidize glucose into gluconate. three mutants were found to be af ...	2000	10735866
flow cytometric techniques to characterise physiological states of acinetobacter calcoaceticus.	monitoring biotechnological processes involves acquiring information about key metabolic events and, ideally, single cell states should be determined to obtain comprehensive data on the physiological status of the surveyed population. in this paper, growth stages of the strain acinetobacter calcoaceticus 69-v were characterised at the single cell level using flow cytometry. four methods for analysing bacterial cellular characteristics by fluorescence were compared with respect to their sensitivi ...	2000	10739345
characterization of the protocatechuic acid catabolic gene cluster from streptomyces sp. strain 2065.	protocatechuate 3,4-dioxygenase (ec 1.13.11.3) catalyzes the ring cleavage step in the catabolism of aromatic compounds through the protocatechuate branch of the beta-ketoadipate pathway. a protocatechuate 3,4-dioxygenase was purified from streptomyces sp. strain 2065 grown in p-hydroxybenzoate, and the n-terminal sequences of the beta- and alpha-subunits were obtained. pcr amplification was used for the cloning of the corresponding genes, and dna sequencing of the flanking regions showed that t ...	2000	10742233
opinion: the clinical use of selective digestive decontamination.	several recent meta-analyses have shown that the use of sdd can reduce the occurrence of nosocomial pneumonia among ventilated patients in the intensive care unit (icu) setting. however, the use of sdd has also been demonstrated to increase subsequent patient colonization and infection with antibiotic-resistant bacteria, particularly gram-positive cocci. therefore, the routine use of sdd cannot be advocated at the present time. the mortality benefit of sdd appears to occur in surgical/trauma pat ...	2000	11123875
intrathecal use of colistin.		2000	11203334
biological modification of the fatty acid group in an emulsan by supplementing fatty acids under conditions inhibiting fatty acid biosynthesis.	when the concentration of the antibiotic cerulenin was increased up to 3.0 mg/l in medium containing ethanol as a carbon source, the specific growth rate of acinetobacter calcoaceticus and the fatty acid content of the emulsan decreased from 0.179 h(-1) and 13.9% to 0.015 h(-1) and 3.4%, respectively. the emulsifying activity in medium containing cerulenin decreased with increasing cerulenin concentration. in the culture containing 3.0 mg/l cerulenin, fatty acid biosynthesis was inhibited. vario ...	2000	16232861
cloning and sequence analysis of the esta gene encoding enzyme for producing (r)-beta-acetylmercaptoisobutyric acid from pseudomonas aeruginosa 1001.	the esta gene encoding the enzyme that catalyzes the production of (r)-beta-acetylmercaptoisobutyric acid from (r,s)-ester from pseudomonas aeruginosa 1001, was cloned in escherichia coli and its nucleotide sequence was determined, revealing the presumed open reading frame encoding a polypeptide of 316 amino acid residues (948 nucleotides). the overall a + t and c + g compositions were 32.59% and 67.41%, respectively. the amino acid sequence of the esta gene product showed a significant similari ...	2000	16232934
horizontal transfer of an exopolymer complex from one bacterial species to another.	alasan, the exocellular polymeric emulsifier produced by acinetobacter radioresistens ka53 was shown to bind to the surface of sphingomonas paucimobilis epa505 and acinetobacter calcoaceticus rag-1. the presence of alasan on the surface of s. paucimobilis epa505 and a. calcoaceticus rag-1 caused a decrease in their cell-surface hydrophobicities. binding was proportional to the concentration of recipient cells and input alasan. at the highest concentration of a. calcoaceticus rag-1 (4 x 10(9) ml( ...	2000	11234924
the bacterial enhancer-dependent sigma(54) (sigma(n)) transcription factor.		2000	10894718
microbial biofilms: from ecology to molecular genetics.	biofilms are complex communities of microorganisms attached to surfaces or associated with interfaces. despite the focus of modern microbiology research on pure culture, planktonic (free-swimming) bacteria, it is now widely recognized that most bacteria found in natural, clinical, and industrial settings persist in association with surfaces. furthermore, these microbial communities are often composed of multiple species that interact with each other and their environment. the determination of bi ...	2000	11104821
a functional-phylogenetic classification system for transmembrane solute transporters.	a comprehensive classification system for transmembrane molecular transporters has been developed and recently approved by the transport panel of the nomenclature committee of the international union of biochemistry and molecular biology. this system is based on (i) transporter class and subclass (mode of transport and energy coupling mechanism), (ii) protein phylogenetic family and subfamily, and (iii) substrate specificity. almost all of the more than 250 identified families of transporters in ...	2000	10839820
bacteria are not what they eat: that is why they are so diverse.		2000	10629168
characteristics of acinetobacter strains (phenotype classification, antibiotic susceptibility and production of beta-lactamases) isolated from haemocultures from patients at the teaching hospital in olomouc.	a total of 85 strains of the genus acinetobacter were isolated from haemocultures at the institute of microbiology of the teaching hospital in olomouc over the period january 1993 to june 1997. sixty-two (73.0%) strains of the acinetobacter calcoaceticus-baumannii complex (acb complex) were the most frequent. in 3 (3.5%) strains it was impossible to decide whether they belonged to the acb complex. other acinetobacter species were represented by 20 (23.5%) strains. the greatest amount (28.2%) of ...	1999	10743729
[the clinical picture, treatment and prognosis of meningitis due to anaerobic and nonfermentative bacteria].	the study of incidence, clinical manifestations and prognosis of meningitis with anaerobic and non-fermentative bacteria.	1999	10756944
evidence for a chemiosmotic model of dehalorespiration in desulfomonile tiedjei dcb-1.	desulfomonile tiedjei dcb-1, a sulfate-reducing bacterium, conserves energy for growth from reductive dehalogenation of 3-chlorobenzoate by an uncharacterized chemiosmotic process. respiratory electron transport components were examined in d. tiedjei cells grown under conditions for reductive dehalogenation, pyruvate fermentation, and sulfate reduction. reductive dehalogenation was inhibited by the respiratory quinone inhibitor 2-heptyl-4-hydroxyquinoline n-oxide, suggesting that a respiratory q ...	1999	9864310
genetic and biochemical characterization of a 2-pyrone-4, 6-dicarboxylic acid hydrolase involved in the protocatechuate 4, 5-cleavage pathway of sphingomonas paucimobilis syk-6.	sphingomonas paucimobilis syk-6 is able to grow on a wide variety of dimeric lignin compounds with guaiacyl moieties, which are converted into protocatechuate by the actions of lignin degradation enzymes in this strain. protocatechuate is a key metabolite in the syk-6 degradation of lignin compounds with guaiacyl moieties, and it is thought that it degrades to pyruvate and oxaloacetate via the protocatechuate 4,5-cleavage pathway. in a 10.5-kb ecori fragment carrying the protocatechuate 4,5-diox ...	1999	9864312
characterization of biosynthetic enzymes for ectoine as a compatible solute in a moderately halophilic eubacterium, halomonas elongata.	1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid (ectoine) is an excellent osmoprotectant. the biosynthetic pathway of ectoine from aspartic beta-semialdehyde (asa), in halomonas elongata, was elucidated by purification and characterization of each enzyme involved. 2,4-diaminobutyrate (daba) aminotransferase catalyzed reversively the first step of the pathway, conversion of asa to daba by transamination with l-glutamate. this enzyme required pyridoxal 5'-phosphate and potassium ions for i ...	1999	9864317
use of a murine o-antigen-specific monoclonal antibody to identify acinetobacter strains of unnamed genomic species 13 sensu tjernberg and ursing.	a monoclonal antibody against the o-antigenic polysaccharide chain of the lipopolysaccharide (lps) of acinetobacter strains belonging to the unnamed genomic species 13 sensu tjernberg and ursing (13tu) was obtained after immunization of balb/c mice with heat-killed bacteria and was characterized by enzyme immunoassay and western blot analysis, by use of lps and proteinase k-treated bacterial lysates, analyses in which the antibody was shown to be highly specific for the homologous antigen. in ad ...	1999	10325309
genotypic and phenotypic similarity of multiresistant acinetobacter baumannii isolates in the czech republic.	the diversity of 103 clinical isolates of the acinetobacter calcoaceticus-acinetobacter baumannii complex obtained between 1991 and 1997 from 17 czech hospitals was studied by ribotyping, biotyping, plasmid profiling and antibiotic susceptibility testing. according to the ecori ribotypes, all but one of these isolates were identified to the dna group level: 77 isolates were allocated to dna group 2 (a. baumannii), 14 to dna group 3, 10 to dna group 13 sensu tjernberg and ursing and one to dna gr ...	1999	10334596
allylic or benzylic stabilization is essential for catalysis by bacterial benzyl alcohol dehydrogenases.	benzyl alcohol dehydrogenase from acinetobacter calcoaceticus (ac-badh) and tol plasmid-encoded benzyl alcohol dehydrogenase from pseudomonas putida (tol-badh) have previously been shown to oxidize a variety of aromatic alcohols but not aliphatic substrates. here, we have expressed the genes for ac-badh and tol-badh in escherichia coli, purified the resulting over-expressed enzymes, and shown that each is an effective catalyst of both benzylic and allylic alcohol oxidation, but not of oxidation ...	1999	10334943
induction of heat shock proteins in response to primary alcohols in acinetobacter calcoaceticus.	cells of acinetobacter calcoaceticus 69-v, a species able to metabolize a range of aliphatic hydrocarbons and alcohols, were confronted with ethanol, butanol, hexanol or heat shock during growth on acetate as sole source of carbon and energy. the primary alcohols and the heat shock led to the synthesis of new proteins or amplified expression of specific, common and general proteins, which were detected by silver staining after two-dimensional gel electrophoresis. some of the alcohol-inducible pr ...	1999	10344248
structures and properties of gellan polymers produced by sphingomonas paucimobilis atcc 31461 from lactose compared with those produced from glucose and from cheese whey	the dairy industry produces large quantities of whey as a by-product of cheese production and is increasingly looking for new ways to utilize this waste product. gellan gum is reliably produced by sphingomonas paucimobilis in growth media containing lactose, a significant component of cheese whey, as a carbon source. we studied and compared polysaccharide biosynthesis by s. paucimobilis atcc 31461 in media containing glucose, lactose (5 to 30 g/liter), and sweet cheese whey. we found that alteri ...	1999	10347031
characterization of a pseudomonas putida allylic alcohol dehydrogenase induced by growth on 2-methyl-3-buten-2-ol.	we have been working to develop an enzymatic assay for the alcohol 2-methyl-3-buten-2-ol (232-mb), which is produced and emitted by certain pines. to this end we have isolated the soil bacterium pseudomonas putida mb-1, which uses 232-mb as a sole carbon source. strain mb-1 contains inducible 3-methyl-2-buten-1-ol (321-mb) and 3-methyl-2-buten-1-al dehydrogenases, suggesting that 232-mb is metabolized by isomerization to 321-mb followed by oxidation. 321-mb dehydrogenase was purified to near-hom ...	1999	10347052
enhancement of solubilization and biodegradation of polyaromatic hydrocarbons by the bioemulsifier alasan.	alasan, a high-molecular-weight bioemulsifier complex of an anionic polysaccharide and proteins that is produced by acinetobacter radioresistens ka53 (s. navon-venezia, z. zosim, a. gottlieb, r. legmann, s. carmeli, e. z. ron, and e. rosenberg, appl. environ. microbiol. 61:3240-3244, 1995), enhanced the aqueous solubility and biodegradation rates of polyaromatic hydrocarbons (pahs). in the presence of 500 microg of alasan ml-1, the apparent aqueous solubilities of phenanthrene, fluoranthene, and ...	1999	10347063
in vivo efficacies of combinations of beta-lactams, beta-lactamase inhibitors, and rifampin against acinetobacter baumannii in a mouse pneumonia model.	the effects of various regimens containing combinations of beta-lactams, beta-lactam inhibitor(s), and rifampin were assessed in a recently described mouse model of acinetobacter baumannii pneumonia (m. l. joly-guillou, m. wolff, j. j. pocidalo, f. walker, and c. carbon, antimicrob. agents chemother. 41:345-351, 1997). two aspects of the therapeutic response were studied: the kinetics of the bactericidal effect (treatment was initiated 3 h after intratracheal inoculation, and bacterial counts we ...	1999	10348761
isolation and characterization of two cryptic plasmids in the ammonia-oxidizing bacterium nitrosomonas sp. strain eni-11.	two plasmids were discovered in the ammonia-oxidizing bacterium nitrosomonas sp. strain eni-11, which was isolated from activated sludge. the plasmids, designated pays and payl, were relatively small, being approximately 1.9 kb long. they were cryptic plasmids, having no detectable plasmid-linked antibiotic resistance or heavy metal resistance markers. the complete nucleotide sequences of pays and payl were determined, and their physical maps were constructed. there existed two major open readin ...	1999	10348848
a functional 4-hydroxysalicylate/hydroxyquinol degradative pathway gene cluster is linked to the initial dibenzo-p-dioxin pathway genes in sphingomonas sp. strain rw1.	the bacterium sphingomonas sp. strain rw1 is able to use dibenzo-p-dioxin, dibenzofuran, and several hydroxylated derivatives as sole sources of carbon and energy. we have determined and analyzed the nucleic acid sequence of a 9,997-bp hindiii fragment downstream of cistrons dxna1a2, which encode the dioxygenase component of the initial dioxygenase system of the corresponding catabolic pathways. this fragment contains 10 colinear open reading frames (orfs), apparently organized in one compact op ...	1999	10348858
genetic analysis of a chromosomal region containing vana and vanb, genes required for conversion of either ferulate or vanillate to protocatechuate in acinetobacter.	vana and vanb form an oxygenative demethylase that converts vanillate to protocatechuate in microorganisms. ferulate, an abundant phytochemical, had been shown to be metabolized through a vanillate intermediate in several pseudomonas isolates, and biochemical evidence had indicated that vanillate also is an intermediate in ferulate catabolism by acinetobacter. genetic evidence supporting this conclusion was obtained by characterization of mutant acinetobacter strains blocked in catabolism of bot ...	1999	10348863
the physiological contribution of acinetobacter pcak, a transport system that acts upon protocatechuate, can be masked by the overlapping specificity of vank.	vank is the fourth member of the ubiquitous major facilitator superfamily of transport proteins to be identified that, together with pcak, benk, and muck, contributes to aromatic catabolism in acinetobacter sp. strain adp1. vank and pcak have overlapping specificity for p-hydroxybenzoate and, most clearly, for protocatechuate: inactivation of both proteins severely impairs growth with protocatechuate, and the activity of either protein alone can mask the phenotype associated with inactivation of ...	1999	10348864
distribution of acinetobacter species on skin of healthy humans.	the distribution of the 19 currently known genospecies of acinetobacter on human skin, i.e. forehead, forearm and toe webs, was determined. three selective media were compared for their specificity for all genospecies of acinetobacter. a minimal-salts agar supplemented with 1% acetate proved to be more efficient than the leeds medium for the isolation of most genospecies in mixed culture with other bacterial species. acinetobacter isolates were provisionally identified using biochemical tests an ...	1999	10357050
epidemiological study of an acinetobacter baumannii outbreak by using a combination of antibiotyping and ribotyping.	from june to november 1994 (period 1) and from february to june 1995 (period 2), multiresistant acinetobacter baumannii strains were isolated in intensive care units and surgical wards of the amiens teaching hospital center (amiens, france). eighteen isolates were obtained from 17 (1%) of 1,706 patients admitted during both of these periods, giving an incidence rate of nosocomial infection per 1,000 patient days of 0.6%. of 17 infected patients, 9 had pneumonia, 3 had urinary tract infection, 2 ...	1999	10364581
the 1.7 a crystal structure of the apo form of the soluble quinoprotein glucose dehydrogenase from acinetobacter calcoaceticus reveals a novel internal conserved sequence repeat.	the crystal structure of a dimeric apo form of the soluble quinoprotein glucose dehydrogenase (s-gdh) from acinetobacter calcoaceticus has been solved by multiple isomorphous replacement followed by density modification, and was subsequently refined at 1. 72 a resolution to a final crystallographic r-factor of 16.5% and free r-factor of 20.8% [corrected]. the s-gdh monomer has a beta-propeller fold consisting of six four-stranded anti-parallel beta-sheets aligned around a pseudo 6-fold symmetry ...	1999	10366508
[trends in resistant bacteria isolated from a tube smear in intubated patients in intensive care].	long standing antibiotics therapy has resulted in growing bacteria resistance. we took a tube smear and prepared culture with antibiogram from the fifty intubated patients in the intensive care unit in the war period. gram-negative germs were the dominant ones in total sum, and among them the acinetobacter calcoaceticus (no 21), pseudomonas aeruginosa (no 18), klebsiella pneumoniae (no 18), were isolated most frequently. pseudomonas aeruginosa showed high resistance to gentamicin (64%), amikacin ...	1999	10386042
cell surface analysis techniques: what do cell preparation protocols do to cell surface properties?	cell surface analysis often requires manipulation of cells prior to examination. the most commonly employed procedures are centrifugation at different speeds, changes of media during washing or final resuspension, desiccation (either air drying for contact angle measurements or freeze-drying for sensitive spectroscopic analysis, such as x-ray photoelectron spectroscopy), and contact with hydrocarbon (hydrophobicity assays). the effects of these procedures on electrophoretic mobility, adhesion to ...	1999	10388679
physiological adaptations involved in alkane assimilation at a low temperature by rhodococcus sp. strain q15.	we examined physiological adaptations which allow the psychrotroph rhodococcus sp. strain q15 to assimilate alkanes at a low temperature (alkanes are contaminants which are generally insoluble and/or solid at low temperatures). during growth at 5 degrees c on hexadecane or diesel fuel, strain q15 produced a cell surface-associated biosurfactant(s) and, compared to glucose-acetate-grown cells, exhibited increased cell surface hydrophobicity. a transmission electron microscopy examination of strai ...	1999	10388690
structure of the soluble methane monooxygenase regulatory protein b.	the soluble methane monooxygenase (smmo; ec 1.14.13.25) from the pseudothermophile methylococcus capsulatus (bath) is a three-component enzyme system that catalyzes the selective oxidation of methane to methanol. we have used nmr spectroscopy to produce a highly refined structure of mmob, the 16-kda regulatory protein of this system. this structure has a unique and intricate fold containing seven beta-strands forming two beta-sheets oriented perpendicular to each other and bridged by three alpha ...	1999	10393915
specificity of the lipase-specific foldases of gram-negative bacteria and the role of the membrane anchor.	folding of lipases that are secreted by pseudomonads and other gram-negative bacteria via the type ii secretion pathway is facilitated by dedicated chaperones, called lipase-specific foldases (lifs). lifs are membrane-anchored proteins with a large periplasmic domain. the functional interaction between the lif and its cognate lipase is specific, since the pseudomonas aeruginosa lif was found not to substitute for lifs from burkholderia glumae or acinetobacter calcoaceticus. however, the p. aerug ...	1999	10394914
site-directed mutagenesis study on the thermal stability of a chimeric pqq glucose dehydrogenase and its structural interpretation.	we have previously reported that a chimeric pyrroloquinoline quinone (pqq) glucose dehydrogenase (gdh), e97a3, which was made up of 97% of escherichia coli pqqgdh sequence and 3% of acinetobacter calcoaceticus pqqgdh, showed increased thermal stability compared with both parental enzymes. site-directed mutagenesis studies were carried out in order to investigate the role of amino-acid substitution at the c-terminal region, ser771, of a chimeric pqqgdhs on their thermal stability. a series of ser ...	1999	10399272
the genes ruba and rubb for alkane degradation in acinetobacter sp. strain adp1 are in an operon with estb, encoding an esterase, and oxyr.	alkanes are oxidized in acinetobacter sp. strain adp1 by a three-component alkane monooxygenase, composed of alkane hydroxylase, rubredoxin, and rubredoxin reductase. ruba and rubb encode rubredoxin and a nad(p)h-dependent rubredoxin reductase. we demonstrate here that single base pair substitutions in ruba or rubb lead to defects in alkane degradation, showing that both genes are essential for alkane utilization. differences in the degradation capacity for hexadecane and dodecane in these mutan ...	1999	10400587
areabc genes determine the catabolism of aryl esters in acinetobacter sp. strain adp1.	acinetobacter sp. strain adp1 is able to grow on a range of esters of aromatic alcohols, converting them to the corresponding aromatic carboxylic acids by the sequential action of three inducible enzymes: an area-encoded esterase, an areb-encoded benzyl alcohol dehydrogenase, and an arec-encoded benzaldehyde dehydrogenase. the are genes, adjacent to each other on the chromosome and transcribed in the order arecba, were located 3.5 kbp upstream of benk. benk, encoding a permease implicated in ben ...	1999	10419955
nosocomial meningitis in children after ventriculoperitoneal shunt insertion.	this study reviews 33 cases of ventriculoperitoneal shunt (vps) meningitis among 415 children after 540 shunt insertions within 8 y, in 9 paediatric intensive care units from 5 centres in slovakia. the incidence of vps meningitis was 6.3% per insertion. the most common organisms isolated from cerebrospinal fluid (csf) and shunt were coagulase-negative staphylococci (52.8%), followed by staphylococcus aureus (13.1%) and pseudomonas aeruginosa (7.5%). seven of 15 assessed risk factors were signifi ...	1999	10426184
proton-nuclear magnetic resonance analyses of the substrate specificity of a beta-ketolase from pseudomonas putida, acetopyruvate hydrolase.	a revised purification of acetopyruvate hydrolase from orcinol-grown pseudomonas putida orc is described. this carbon-carbon bond hydrolase, which is the last inducible enzyme of the orcinol catabolic pathway, is monomeric with a molecular size of approximately 38 kda; it hydrolyzes acetopyruvate to equimolar quantities of acetate and pyruvate. we have previously described the aqueous-solution structures of acetopyruvate at ph 7.5 and several synthesized analogues by (1)h-nuclear magnetic resona ...	1999	10438778
fluorescence in situ hybridization assay using peptide nucleic acid probes for differentiation between tuberculous and nontuberculous mycobacterium species in smears of mycobacterium cultures.	tb pna fish is a new fluorescence in situ hybridization (fish) method using peptide nucleic acid (pna) probes for differentiation between species of the mycobacterium tuberculosis complex (mtc) and nontuberculous mycobacteria (ntm) in acid-fast bacillus-positive (afb+) cultures is described. the test is based on fluorescein-labelled pna probes that target the rrna of mtc or ntm species applied to smears of afb+ cultures for microscopic examination. parallel testing with the two probes serves as ...	1999	10449448
skin carriage of acinetobacters in hong kong.	we studied the carriage of acinetobacter spp. at five superficial sites in 79 patients from two hospitals, in 133 healthy controls from the community (medical students and new nurses), and in 198 student nurses in different classes. a total of 431 isolates from 364 positive sites of 201 subjects and 124 blood culture isolates (1997 to 1998) were genospeciated by amplified ribosomal dna restriction analysis. genospecies 3 was the most common species. the carriage rate of student nurses (42 of 131 ...	1999	10449482
legionella pneumophila invasion of mrc-5 cells induces tyrosine protein phosphorylation.	after uptake and intracellular multiplication of legionella pneumophila in mrc-5 lung fibroblasts, important cytoskeletal filament structures, like actin, tubulin, or vimentin, and a cell membrane-associated fibronectin were rearranged during early infection, resulting in a loss of cell adhesion and collapse of the cytoskeleton. dysregulation of the cellular phosphorylation and dephosphorylation cascade may contribute to the observed changes and may support intracellular survival and multiplicat ...	1999	10456891
polyphosphate kinase of acinetobacter sp. strain adp1: purification and characterization of the enzyme and its role during changes in extracellular phosphate levels.	polyphosphate (polyp) is a ubiquitous biopolymer whose function and metabolism are incompletely understood. the polyphosphate kinase (ppk) of acinetobacter sp. strain adp1, an organism that accumulates large amounts of polyp, was purified to homogeneity and characterized. this enzyme, which adds the terminal phosphate from atp to a growing chain of polyp, is a 79-kda monomer. ppk is sensitive to magnesium concentrations, and optimum activity occurs in the presence of 3 mm mgcl(2). the optimum ph ...	1999	10473375
bacterial growth state distinguished by single-cell protein profiling: does chlorination kill coliforms in municipal effluent?	municipal effluent is the largest reservoir of human enteric bacteria. its public health significance, however, depends upon the physiological status of the wastewater bacterial community. a novel immunofluorescence assay was developed and used to examine the bacterial growth state during wastewater disinfection. quantitative levels of three highly conserved cytosolic proteins (dnak, dps, and fis) were determined by using enterobacterium-specific antibody fluorochrome-coupled probes. enterobacte ...	1999	10473432
stereochemical course of biotin-independent malonate decarboxylase catalysis.	malonate decarboxylases, which catalyze the conversion of malonate to acetate, can be classified into biotin-dependent and biotin-independent enzymes. in order to reveal the stereochemical course of the reactions catalyzed by the biotin-independent enzymes from acinetobacter calcoaceticus and pseudomonas fluorescens, a chiral substrate, malonate carrying (13)c in one carboxyl group and (3)h at one of the methylene positions, was prepared and used in the reactions catalyzed by these two enzymes. ...	1999	10496981
characterization of the phthalate permease ophd from burkholderia cepacia atcc 17616.	the ophd gene, encoding a permease for phthalate transport, was cloned from burkholderia cepacia atcc 17616. expression of the gene in escherichia coli results in the ability to transport phthalate rapidly into the cell. uptake inhibition experiments show that 4-hydroxyphthalate, 4-chlorophthalate, 4-methylphthalate, and cinchomeronate compete for the phthalate permease. an ophd knockout mutant of 17616 grows slightly more slowly on phthalate but is still able to take up phthalate at rates equiv ...	1999	10498738
identification and characterization of come and comf, two novel pilin-like competence factors involved in natural transformation of acinetobacter sp. strain bd413.	although the high level of competence for natural transformation of acinetobacter sp. strain bd413 has been the subject of numerous studies, only two competence genes, comc and comp, have been identified to date. by chromosomal walking analysis we found two overlapping open reading frames, designated come and comf, starting 61 bp downstream of comc. come and comf are expressed as stable proteins in escherichia coli, thus proving that they are indeed coding regions, but expression was successful ...	1999	10508090
substitution, insertion, deletion, suppression, and altered substrate specificity in functional protocatechuate 3,4-dioxygenases.	protocatechuate 3,4-dioxygenase is a member of a family of bacterial enzymes that cleave the aromatic rings of their substrates between two adjacent hydroxyl groups, a key reaction in microbial metabolism of varied environmental chemicals. in an appropriate genetic background, it is possible to select for acinetobacter strains containing spontaneous mutations blocking expression of pcah or -g, genes encoding the alpha and beta subunits of protocatechuate 3, 4-dioxygenase. the crystal structure o ...	1999	10515940
active-site structure of the soluble quinoprotein glucose dehydrogenase complexed with methylhydrazine: a covalent cofactor-inhibitor complex.	soluble glucose dehydrogenase (s-gdh) from the bacterium acinetobacter calcoaceticus is a classical quinoprotein. it requires the cofactor pyrroloquinoline quinone (pqq) to catalyze the oxidation of glucose to gluconolactone. the precise catalytic role of pqq in s-gdh and several other pqq-dependent enzymes has remained controversial because of the absence of comprehensive structural data. we have determined the crystal structure of a ternary complex of s-gdh with pqq and methylhydrazine, a comp ...	1999	10518528
rapid identification of burkholderia pseudomallei in blood cultures by a monoclonal antibody assay.	burkholderia pseudomallei is the causative agent of melioidosis. in northeast thailand, this gram-negative bacterium is a major cause of mortality from septicemia. the definitive diagnosis of this disease is made by bacterial culture. in this study, we produced a monoclonal antibody (mab) specific to the 30-kda protein of b. pseudomallei by in vivo and in vitro immunization of balb/c mice with a crude culture filtrate antigen. the mab could directly agglutinate with all 243 clinical isolates of ...	1999	10523570
ciprofloxacin in treatment of nosocomial meningitis in neonates and in infants: report of 12 cases and review.	twelve cases of neonatal and infant nosocomial meningitis treated with intravenous ciprofloxacin in doses of 10 to 60 mg/kg/day are described. four neonates were 21 to 28 days old and eight infants were 2 to 6 months old. six presented with gram-negative meningitis: escherichia coli (2), salmonella enteritidis (1), acinetobacter calcoaceticus (1), two with two organisms, and (h. influenzae plus staphylococcus epidermidis, acinetobacter spp. plus s. epidermidis), and six were attributable to gram ...	1999	10529884
a protein residing at the subunit interface of the bacterial ribosome.	surface labeling of escherichia coli ribosomes with the use of the tritium bombardment technique has revealed a minor unidentified ribosome-bound protein (spot y) that is hidden in the 70s ribosome and becomes highly labeled on dissociation of the 70s ribosome into subunits. in the present work, the n-terminal sequence of the protein y was determined and its gene was identified as yfia, an orf located upstream the phe operon of e. coli. this 12.7-kda protein was isolated and characterized. an af ...	1999	10535924
bacterial populations in an anthropogenically disturbed stream: comparison of different seasons.	abstract to determine the effects of environmental changes on stream bacterial populations, assemblage- and population-level measurements were compared between an anthropogenically disturbed stream and an undisturbed reference stream during different seasons. physical and chemical variables monitored at two disturbed sites from a stream affected by multiple environmental perturbations confirmed discernibly different water quality from three reference sites: two from an adjacent, undisturbed wate ...	1999	10541785
cloning and sequencing of a novel meta-cleavage dioxygenase gene whose product is involved in degradation of gamma-hexachlorocyclohexane in sphingomonas paucimobilis.	sphingomonas (formerly pseudomonas) paucimobilis ut26 utilizes gamma-hexachlorocyclohexane (gamma-hch), a halogenated organic insecticide, as a sole source of carbon and energy. in a previous study, we showed that gamma-hch is degraded to chlorohydroquinone (chq) and then to hydroquinone (hq), although the rate of reaction from chq to hq was slow (k. miyauchi, s. k. suh, y. nagata, and m. takagi, j. bacteriol. 180:1354-1359, 1998). in this study, we cloned and characterized a gene, designated li ...	1999	10542173
identification of a transcriptional activator (chnr) and a 6-oxohexanoate dehydrogenase (chne) in the cyclohexanol catabolic pathway in acinetobacter sp. strain ncimb 9871 and localization of the genes that encode them.	we identified chnr, a gene encoding an arac-xyls type of transcriptional activator that regulates the expression of chnb, the structural gene for cyclohexanone monooxygenase (chmo) in acinetobacter sp. strain ncimb 9871. the gene sequence of chne, which encodes an nadp(+)-linked 6-oxohexanoate dehydrogenase, the enzyme catalyzing the fifth step of cyclohexanol degradation, was also determined. the gene arrangement is chnb-chne-chnr. the predicted molecular masses of the three polypeptides were v ...	1999	10543838
a novel lipolytic enzyme located in the outer membrane of pseudomonas aeruginosa.	a lipase-negative deletion mutant of pseudomonas aeruginosa pao1 still showed extracellular lipolytic activity toward short-chain p-nitrophenylesters. by screening a genomic dna library of p. aeruginosa pao1, an esterase gene, esta, was identified, cloned, and sequenced, revealing an open reading frame of 1,941 bp. the product of esta is a 69.5-kda protein, which is probably processed by removal of an n-terminal signal peptide to yield a 67-kda mature protein. a molecular mass of 66 kda was dete ...	1999	10559163
transcriptional analysis of the rubrerythrin and superoxide dismutase genes of clostridium perfringens.	we cloned and sequenced a 2.7-kb fragment of chromosomal dna from clostridium perfringens containing the superoxide dismutase-encoding gene, sod. previously, rubrerythrin from c. perfringens had been isolated and its gene (rbr) had been cloned (y. lehmann, l. meile, and m. teuber, j. bacteriol. 178:7152-7158, 1996). northern blot experiments revealed a length of approximately 800 bases for each transcript of rbr and sod of c. perfringens. thus, rbr and sod each represent a monocistronic operon. ...	1999	10559182
functional evaluation of the genes involved in malonate decarboxylation by acinetobacter calcoaceticus.	the genomic locus containing the potential repressor gene mdcy (inactivated by a putative is3 element) and the mdclmacdegbh genes from acinetobacter calcoaceticus was cloned and sequenced. in order to evaluate the biochemical function of the protein components, the genes were expressed independently and their activities predicted by database analysis. the mdca gene product, the alpha subunit, was found to be malonate/acetyl-coa transferase and the mdcd gene product, the beta subunit, was found t ...	1999	10561613
autoantibodies to brain components and antibodies to acinetobacter calcoaceticus are present in bovine spongiform encephalopathy.	bovine spongiform encephalopathy (bse) is a neurological disorder, predominantly of british cattle, which belongs to the group of transmissible spongiform encephalopathies together with creutzfeldt-jakob disease (cjd), kuru, and scrapie. autoantibodies to brain neurofilaments have been previously described in patients with cjd and kuru and in sheep affected by scrapie. spongiform-like changes have also been observed in chronic experimental allergic encephalomyelitis, at least in rabbits and guin ...	1999	10569779
characterization of activity and expression of isocitrate lyase in mycobacterium avium and mycobacterium tuberculosis.	analysis by two-dimensional gel electrophoresis revealed that mycobacterium avium expresses several proteins unique to an intracellular infection. one abundant protein with an apparent molecular mass of 50 kda was isolated, and the n-terminal sequence was determined. it matches a sequence in the m. tuberculosis database (sanger) with similarity to the enzyme isocitrate lyase of both corynebacterium glutamicum and rhodococcus fascians. only marginal similarity was observed between this open readi ...	1999	10572116
pathophysiology of surgical site infection in total hip arthroplasty.	this article is a case report of a 69-year-old man who underwent a right total hip replacement procedure and developed a surgical site infection. areas of concern in prevention and treatment of hip arthroplasty infection are presented, focusing on the pathophysiologic process involved. a review of the patient risk factors and the pathophysiologic action potentiating risk for infection include host immunity, nutritional status, diabetes, age, use of steroids or immunosuppressive drugs, rheumatoid ...	1999	10586159
a gene involved in quinate metabolism is specific to one dna homology group of xanthomonas campestris.	a gene involved in quinate metabolism was cloned from xanthomonas campestris pv. juglandis strain c5. the gene, quma, located on a 4. 2-kb kpni-ecorv fragment in plasmid pqm38, conferred quinate metabolic activity to x. c. pv. celebensis. tn3-spice insertional analyses further located the quma gene on a region of about 3.0 kb within pqm38. nucleotide sequencing of this 3.0-kb fragment reveals that the coding region of quma is 2373 bp, the deduced amino acid sequence of which closely resembles a ...	1999	10594704
fate of free dna and transformation of the oral bacterium streptococcus gordonii dl1 by plasmid dna in human saliva.	competitive pcr was used to monitor the survival of a 520-bp dna target sequence from a recombinant plasmid, pvacmc1, after admixture of the plasmid with freshly sampled human saliva. the fraction of the target remaining amplifiable ranged from 40 to 65% after 10 min of exposure to saliva samples from five subjects and from 6 to 25% after 60 min of exposure. pvacmc1 plasmid dna that had been exposed to degradation by fresh saliva was capable of transforming naturally competent streptococcus gord ...	1999	9872752
in situ, real-time catabolic gene expression: extraction and characterization of naphthalene dioxygenase mrna transcripts from groundwater.	we developed procedures for isolating and characterizing in situ-transcribed mrna from groundwater microorganisms catabolizing naphthalene at a coal tar waste-contaminated site. groundwater was pumped through 0.22-microm-pore-size filters, which were then frozen in dry ice-ethanol. rna was extracted from the frozen filters by boiling sodium dodecyl sulfate lysis and acidic phenol-chloroform extraction. transcript characterization was performed with a series of pcr primers designed to amplify nah ...	1999	9872763
plasmid-encoded anthranilate synthase (trpeg) in buchnera aphidicola from aphids of the family pemphigidae.	buchnera aphidicola is an obligate intracellular symbiont of aphids. one of its proposed functions is the synthesis of essential amino acids, nutrients required by aphids but deficient in their diet of plant phloem sap. the genetic organization of the tryptophan pathway in buchnera from proliferous aphids of the family aphididae has previously been shown to reflect a capacity to overproduce this essential amino acid (c.-y. lai, l. baumann, and p. baumann, proc. natl. acad. sci. usa 91:3819-3823, ...	1999	9872768
bacterial adhesion to soil contaminants in the presence of surfactants	it has been proposed that addition of surfactants to contaminated soil enhances the solubility of target compounds; however, surfactants may simultaneously reduce the adhesion of bacteria to hydrophobic surfaces. if the latter mechanism is important for the biodegradation of virtually insoluble contaminants, then the use of surfactants may not be beneficial. the adhesion of a mycobacterium strain and a pseudomonas strain, isolated from a creosote-contaminated soil, to the surfaces of highly visc ...	1999	9872775
production of wax esters during aerobic growth of marine bacteria on isoprenoid compounds	this paper describes the production of isoprenoid wax esters during the aerobic degradation of 6,10,14-trimethylpentadecan-2-one and phytol by four bacteria (acinetobacter sp. strain phy9, pseudomonas nautica [ip85/617], marinobacter sp. strain cab [dsmz 11874], and marinobacter hydrocarbonoclasticus [atcc 49840]) isolated from the marine environment. different pathways are proposed to explain the formation of these compounds. in the case of 6,10, 14-trimethylpentadecan-2-one, these esters resul ...	1999	9872783
the alpha subunit of toluene dioxygenase from pseudomonas putida f1 can accept electrons from reduced ferredoxintol but is catalytically inactive in the absence of the beta subunit.	the oxygenase component of toluene dioxygenase from pseudomonas putida f1 is an iron-sulfur protein (isptol) consisting of alpha (todc1) and beta (todc2) subunits. purified todc1 gave absorbance and electron paramagnetic resonance spectra identical to those given by purified isptol. todc1 was reduced by nadh and catalytic amounts of reductasetol and ferredoxintol. reduced todc1 did not oxidize toluene, and catalysis was strictly dependent on the presence of purified todc2.	1999	9872799
the phn genes of burkholderia sp. strain rp007 constitute a divergent gene cluster for polycyclic aromatic hydrocarbon catabolism.	cloning and molecular ecological studies have underestimated the diversity of polycyclic aromatic hydrocarbon (pah) catabolic genes by emphasizing classical nah-like (nah, ndo, pah, and dox) sequences. here we report the description of a divergent set of pah catabolic genes, the phn genes, which although isofunctional to the classical nah-like genes, show very low homology. this phn locus, which contains nine open reading frames (orfs), was isolated on an 11.5-kb hindiii fragment from phenanthre ...	1999	9882667
a sensitive, viable-colony staining method using nile red for direct screening of bacteria that accumulate polyhydroxyalkanoic acids and other lipid storage compounds.	the oxazine dye nile blue a and its fluorescent oxazone form, nile red, were used to develop a simple and highly sensitive staining method to detect poly(3-hydroxybutyric acid) and other polyhydroxyalkanoic acids (phas) directly in growing bacterial colonies. in contrast to previously described methods, these dyes were directly included in the medium at concentrations of only 0.5 microgram/ml, and growth of the cells occurred in the presence of the dyes. this allowed an estimation of the presenc ...	1999	9914303