new bacterial pathway for 4- and 5-chlorosalicylate degradation via 4-chlorocatechol and maleylacetate in pseudomonas sp. strain mt1.pseudomonas sp. strain mt1 is capable of degrading 4- and 5-chlorosalicylates via 4-chlorocatechol, 3-chloromuconate, and maleylacetate by a novel pathway. 3-chloromuconate is transformed by muconate cycloisomerase of mt1 into protoanemonin, a dominant reaction product, as previously shown for other muconate cycloisomerases. however, kinetic data indicate that the muconate cycloisomerase of mt1 is specialized for 3-chloromuconate conversion and is not able to form cis-dienelactone. protoanemonin ...200314617643
nitrogen control of atrazine utilization in pseudomonas sp. strain adp.pseudomonas sp. strain adp uses the herbicide atrazine as the sole nitrogen source. we have devised a simple atrazine degradation assay to determine the effect of other nitrogen sources on the atrazine degradation pathway. the atrazine degradation rate was greatly decreased in cells grown on nitrogen sources that support rapid growth of pseudomonas sp. strain adp compared to cells cultivated on growth-limiting nitrogen sources. the presence of atrazine in addition to the nitrogen sources did not ...200314660340
bacterial synergism or antagonism in a gel cassette system.the growth and the metabolic activity of shewanella putrfaciens, brochothrix thermosphacta, and pseudomonas sp., when cultured individually or in all possible combinations in gel cassettes system supplemented with 0.1% glucose at 5 degrees c, were investigated. the overall outcome was that the coexistence of the above-mentioned microorganisms affected not only each growth rate but also their type of metabolic end products compared to the control cultures. these effects were varied and depended o ...200314660367
clinical predictors of severe gallbladder complications in acute acalculous evaluate the relationship between clinical information (including age, laboratory data, and sonographic findings) and severe complications, such as gangrene, perforation, or abscess, in patients with acute acalculous cholecystitis (aac).200314669342
nitrobenzoates and aminobenzoates are chemoattractants for pseudomonas strains.three pseudomonas strains were tested for the ability to sense and respond to nitrobenzoate and aminobenzoate isomers in chemotaxis assays. pseudomonas putida prs2000, a strain that grows on benzoate and 4-hydroxybenzoate by using the beta-ketoadipate pathway, has a well-characterized beta-ketoadipate-inducible chemotactic response to aromatic acids. prs2000 was chemotactic to 3- and 4-nitrobenzoate and all three isomers of aminobenzoate when grown under conditions that induce the benzoate chemo ...200414711654
coexpression of genetically engineered 3-ketoacyl-acp synthase iii (fabh) and polyhydroxyalkanoate synthase (phac) genes leads to short-chain-length-medium-chain-length polyhydroxyalkanoate copolymer production from glucose in escherichia coli jm109.polyhydroxyalkanoates (phas) can be divided into three main types based on the sizes of the monomers incorporated into the polymer. short-chain-length (scl) phas consist of monomer units of c3 to c5, medium-chain-length (mcl) phas consist of monomer units of c6 to c14, and scl-mcl phas consist of monomers ranging in size from c4 to c14. although previous studies using recombinant escherichia coli have shown that either scl or mcl pha polymers could be produced from glucose, this study presents t ...200414766582
simultaneous degradation of atrazine and phenol by pseudomonas sp. strain adp: effects of toxicity and adaptation.the strain pseudomonas sp. strain adp is able to degrade atrazine as a sole nitrogen source and therefore needs a single source for both carbon and energy for growth. in addition to the typical c source for pseudomonas, na(2)-succinate, the strain can also grow with phenol as a carbon source. phenol is oxidized to catechol by a multicomponent phenol hydroxylase. catechol is degraded via the ortho pathway using catechol 1,2-dioxygenase. it was possible to stimulate the strain in order to degrade ...200415066779
growth of polychlorinated-biphenyl-degrading bacteria in the presence of biphenyl and chlorobiphenyls generates oxidative stress and massive accumulation of inorganic polyphosphate.inorganic polyphosphate (polyp) plays a significant role in increasing bacterial cell resistance to unfavorable environmental conditions and in regulating different biochemical processes. using transmission electron microscopy of the polychlorinated biphenyl (pcb)-degrading bacterium pseudomonas sp. strain b4 grown in defined medium with biphenyl as the sole carbon source, we observed large and abundant electron-dense granules at all stages of growth and following a shift from glucose to bipheny ...200415128568
albusin b, a bacteriocin from the ruminal bacterium ruminococcus albus 7 that inhibits growth of ruminococcus approximately 32-kda protein (albusin b) that inhibited growth of ruminococcus flavefaciens fd-1 was isolated from culture supernatants of ruminococcus albus 7. traditional cloning and gene-walking pcr techniques revealed an open reading frame (albb) encoding a protein with a predicted molecular mass of 32,168 da. a blast search revealed two homologs of albb from the unfinished genome of r. albus 8 and moderate similarity to llpa, a recently described 30-kda bacteriocin from pseudomonas sp. s ...200415128585
the structure of chondroitin b lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery.chondroitinase b from pedobacter heparinus is the only known enzyme strictly specific for dermatan sulfate and is a widely used enzymatic tool for the structural characterization of glycosaminoglycans. this beta-helical polysaccharide lyase belongs to family pl-6 and cleaves the beta(1,4) linkage of dermatan sulfate in a random manner, yielding 4,5-unsaturated dermatan sulfate disaccharides as the product. the previously reported structure of its complex with a dermatan sulfate disaccharide prod ...200415155751
molecular analysis of the microflora associated with dental caries.molecular techniques have revealed many novel, presumed unculturable, taxa in oral infections. the aim of this study was to characterize the bacterial community of the middle and advancing front of carious dental lesions by cultural and molecular analyses. samples were collected with a hand excavator from five teeth with carious lesions involving dentine. samples were cultured on blood agar and rogosa agar incubated in air plus 5% co(2) and on fastidious anaerobe agar anaerobically. dna was also ...200415243054
biochemical characterization of styab from pseudomonas sp. strain vlb120 as a two-component flavin-diffusible monooxygenase.pseudomonas sp. vlb120 uses styrene as a sole source of carbon and energy. the first step in this metabolic pathway is catalyzed by an oxygenase (stya) and a nadh-flavin oxidoreductase (styb). both components have been isolated from wild-type pseudomonas strain vlb120 as well as from recombinant escherichia coli. stya from both sources is a dimer, with a subunit size of 47 kda, and catalyzes the enantioselective epoxidation of cc double bonds. styrene is exclusively converted to s-styrene oxide ...200415292130
use of 16s ribosomal dna pcr and denaturing gradient gel electrophoresis for analysis of the microfloras of healing and nonhealing chronic venous leg ulcers.the bacterial microfloras of 8 healing and 10 nonhealing chronic venous leg ulcers were compared by using a combination of cultural analysis and denaturing gradient gel electrophoresis (dgge) of pcr-amplified 16s rrna gene products. cultural analysis of the microflora revealed that the majority of both wound types carried the aerobes staphylococcus and pseudomonas spp. (89 and 80%, respectively). sequencing of 16s ribosomal dnas selected on the basis of dgge profiling allowed the identification ...200415297496
the hotdog fold: wrapping up a superfamily of thioesterases and dehydratases.the hotdog fold was initially identified in the structure of escherichia coli faba and subsequently in 4-hydroxybenzoyl-coa thioesterase from pseudomonas sp. strain cbs. since that time structural determinations have shown a number of other apparently unrelated proteins also share the hotdog fold.200415307895
rational proteomics ii: electrostatic nature of cofactor preference in the short-chain oxidoreductase (scor) enzyme family.the dominant role of long-range electrostatic interatomic interactions in nicotinamide adenine dinucleotide/nicotinamide adenine dinucleotide phosphate (nad/nadp) cofactor recognition has been shown for enzymes of the short-chain oxidoreductase (scor) family. an estimation of cofactor preference based only on the contribution of the electrostatic energy term to the total energy of enzyme-cofactor interaction has been tested for approximately 40 known three-dimensional (3d) crystal complexes and ...200415340916
comparison of atpase-encoding type iii secretion system hrcn genes in biocontrol fluorescent pseudomonads and in phytopathogenic proteobacteria.type iii protein secretion systems play a key role in the virulence of many pathogenic proteobacteria, but they also occur in nonpathogenic, plant-associated bacteria. certain type iii protein secretion genes (e.g., hrcc) have been found in pseudomonas sp. strain sbw25 (and other biocontrol pseudomonads), but other type iii protein secretion genes, such as the atpase-encoding gene hrcn, have not been found. using both colony hybridization and a pcr approach, we show here that hrcn is nevertheles ...200415345390
involvement of linear plasmids in aerobic biodegradation of vinyl chloride.pseudomonas putida strain aj and ochrobactrum strain td were isolated from hazardous waste sites based on their ability to use vinyl chloride (vc) as the sole source of carbon and energy under aerobic conditions. strains aj and td also use ethene and ethylene oxide as growth substrates. strain aj contained a linear megaplasmid (approximately 260 kb) when grown on vc or ethene, but it contained no circular plasmids. while strain aj was growing on ethylene oxide, it was observed to contain a 100-k ...200415466555
isolation of lightning-competent soil bacteria.artificial transformation is typically performed in the laboratory by using either a chemical (cacl(2)) or an electrical (electroporation) method. however, laboratory-scale lightning has been shown recently to electrotransform escherichia coli strain dh10b in soil. in this paper, we report on the isolation of two "lightning-competent" soil bacteria after direct electroporation of the nycodenz bacterial ring extracted from prairie soil in the presence of the pbhcrec plasmid (tc(r), sp(r), sm(r)). ...200415466589
transferable antibiotic resistance elements in haemophilus influenzae share a common evolutionary origin with a diverse family of syntenic genomic islands.transferable antibiotic resistance in haemophilus influenzae was first detected in the early 1970s. after this, resistance spread rapidly worldwide and was shown to be transferred by a large 40- to 60-kb conjugative element. bioinformatics analysis of the complete sequence of a typical h. influenzae conjugative resistance element, icehin1056, revealed the shared evolutionary origin of this element. icehin1056 has homology to 20 contiguous sequences in the national center for biotechnology inform ...200415547285
integron carrying a novel metallo-beta-lactamase gene, blaimp-16, and a fused form of aminoglycoside-resistant gene aac(6')-30/aac(6')-ib': report from the sentry antimicrobial surveillance program.since january 2002 pseudomonas sp. strains resistant to carbapenems and ceftazidime have been routinely screened as part of the sentry antimicrobial surveillance program for metallo-beta-lactamase production, and their resistance determinants have been analyzed. pseudomonas aeruginosa index strain 101-4704, which harbors a novel bla(imp) variant, bla(imp-16), was isolated in april 2002 from a 60-year-old man in brasilia, brazil. bla(imp-16) was found on the chromosome of the p. aeruginosa index ...200415561846
regulation of the pseudomonas sp. strain adp cyanuric acid degradation operon.pseudomonas sp. strain adp is the model strain for studying bacterial degradation of the s-triazine herbicide atrazine. in this work, we focused on the expression of the atzdef operon, involved in mineralization of the central intermediate of the pathway, cyanuric acid. expression analysis of atzd-lacz fusions in pseudomonas sp. strain adp and pseudomonas putida showed that atzdef is subjected to dual regulation in response to nitrogen limitation and cyanuric acid. the gene adjacent to atzd, orf ...200515601699
molecular nature of spontaneous modifications in gacs which cause colony phase variation in pseudomonas sp. strain pcl1171.pseudomonas sp. strain pcl1171 displays colony phase variation between opaque phase i and translucent phase ii colonies, thereby regulating the production of secondary metabolites and exoenzymes. complementation and sequence analysis of 26 phase ii mutants and of 13 wild-type phase ii sectors growing out of phase i colonies showed that in all these cases the phase ii phenotype is caused by spontaneous mutations in gaca or/and gacs. mutation of gac reduced both the length of the lag phase and the ...200515629930
characterization and performance of a toluene-degrading biofilm developed on pumice stones.background: hydrocarbon-degrading biofilms in the treatment of contaminated groundwaters have received increasing attention due to the role played in the so-called "biobarriers". these are bioremediation systems in which a microbial consortium adherent to a solid support is placed across the flow of a contaminated plume, thus promoting biodegradation of the pollutant. results: a microbial consortium adherent to pumice granules (biofilm) developed from a toluene-enriched microflora in a mini-scal ...200515655073
use of pyrosequencing of 16s rrna fragments to differentiate between bacteria responsible for neonatal sepsis.infants admitted to neonatal intensive care units for suspicion of bacterial sepsis receive at least two broad-spectrum antibiotics for a minimum of 48 to 72 hours to cover both gram-positive and gram-negative organisms while awaiting blood culture results. on average, bacterial growth becomes detectable within 12 to 24 hours, with an additional 24 to 48 hours required for identification. we have previously described using a 16s rrna pcr assay for screening neonatal blood for bacterial dna. comb ...200515681481
molecular and biochemical characterization of an endo-beta-1,3-glucanase from the pinewood nematode bursaphelenchus xylophilus acquired by horizontal gene transfer from bacteria.we report the cloning and functional characterization of an endo-beta-1,3-glucanase from the pinewood nematode bursaphelenchus xylophilus acquired by horizontal gene transfer from bacteria. this is the first gene of this type from any nematode species. we show that a similar cdna is also present in another closely related species b. mucronatus, but that similar sequences are not present in any other nematode studied to date. the b. xylophilus gene is expressed solely in the oesophageal gland cel ...200515727561
tolerance of the rieske-type [2fe-2s] cluster in recombinant ferredoxin bpha3 from pseudomonas sp. kks102 to histidine ligand mutations.bpha3 from pseudomonas sp. kks102 is a rieske-type [2fe-2s] ferredoxin that transfers electrons from an nadh-dependent oxidoreductase, bpha4, to a biphenyl dioxygenase complex. a high-level expression and purification system for the recombinant bpha3 in escherichia coli was constructed. two histidine ligands of the rieske-type cluster in bpha3, were each replaced with serine, cysteine, asparagine and tyrosine. the single mutants, in which either his44 or his65 was replaced with a cysteine residu ...200515733056
mice have a transcribed l-threonine aldolase/gly1 gene, but the human gly1 gene is a non-processed pseudogene.there are three pathways of l-threonine catabolism. the enzyme l-threonine aldolase (ta) has been shown to catalyse the conversion of l-threonine to yield glycine and acetaldehyde in bacteria, fungi and plants. low levels of ta enzymatic activity have been found in vertebrates. it has been suggested that any detectable activity is due to serine hydroxymethyltransferase and that mammals lack a genuine threonine aldolase.200515757516
crystal structure of the terminal oxygenase component of cumene dioxygenase from pseudomonas fluorescens ip01.the crystal structure of the terminal component of the cumene dioxygenase multicomponent enzyme system of pseudomonas fluorescens ip01 (cumdo) was determined at a resolution of 2.2 a by means of molecular replacement by using the crystal structure of the terminal oxygenase component of naphthalene dioxygenase from pseudomonas sp. strain ncib 9816-4 (nphdo). the ligation of the two catalytic centers of cumdo (i.e., the nonheme iron and rieske [2fe-2s] centers) and the bridging between them in nei ...200515774891
inactivation of hiv-1 in breast milk by treatment with the alkyl sulfate microbicide sodium dodecyl sulfate (sds).reducing transmission of hiv-1 through breast milk is needed to help decrease the burden of pediatric hiv/aids in society. we have previously reported that alkyl sulfates (i.e., sodium dodecyl sulfate, sds) are microbicidal against hiv-1 at low concentrations, are biodegradable, have little/no toxicity and are inexpensive. therefore, they may be used for treatment of hiv-1 infected breast milk. in this report, human milk was artificially infected by adding to it hiv-1 (cell-free or cell-associat ...200515888210
purification and characterization of allophanate hydrolase (atzf) from pseudomonas sp. strain adp.atzf, allophanate hydrolase, is a recently discovered member of the amidase signature family that catalyzes the terminal reaction during metabolism of s-triazine ring compounds by bacteria. in the present study, the atzf gene from pseudomonas sp. strain adp was cloned and expressed as a his-tagged protein, and the protein was purified and characterized. atzf had a deduced subunit molecular mass of 66,223, based on the gene sequence, and an estimated holoenzyme molecular mass of 260,000. the acti ...200515901697
the crystal structure of pffabz, the unique beta-hydroxyacyl-acp dehydratase involved in fatty acid biosynthesis of plasmodium falciparum.the unique beta-hydroxyacyl-acp dehydratase in plasmodium falciparum, pffabz, is involved in fatty acid biosynthesis and catalyzes the dehydration of beta-hydroxy fatty acids linked to acyl carrier protein. the structure was solved by single anomalous dispersion (sad) phasing using a quick-soaking experiment with potassium iodide and refined to a resolution of 2.1 a. the crystal structure represents the first structure of a plasmodium beta-hydroxyacyl-acp dehydratase with broad substrate specifi ...200515930004
emergent mechanistic diversity of enzyme-catalysed beta-diketone cleavage.the enzymatic cleavage of c-c bonds in beta-diketones is, comparatively, a little studied biochemical process, but one that has important relevance to human metabolism, bioremediation and preparative biocatalysis. in recent studies, four types of enzymes have come to light that cleave c-c bonds in the beta-diketone functionality using different chemical mechanisms. oph [oxidized poly(vinyl alcohol) hydrolase from pseudomonas sp. strain vm15c], which cleaves nonane-4,6-dione to butyrate and penta ...200515934927
recd plays an essential function during growth at low temperature in the antarctic bacterium pseudomonas syringae lz4w.the antarctic psychrotrophic bacterium pseudomonas syringae lz4w has been used as a model system to identify genes that are required for growth at low temperature. transposon mutagenesis was carried out to isolate mutant(s) of the bacterium that are defective for growth at 4 degrees but normal at 22 degrees . in one such cold-sensitive mutant (cs1), the transposon-disrupted gene was identified to be a homolog of the recd gene of several bacteria. trans-complementation and freshly targeted gene d ...200515956672
signature proteins that are distinctive of alpha proteobacteria.the alpha (alpha) proteobacteria, a very large and diverse group, are presently characterized solely on the basis of 16s rrna trees, with no known molecular characteristic that is unique to this group. the genomes of three alpha-proteobacteria, rickettsia prowazekii (rp), caulobacter crescentus (cc) and bartonella quintana (bq), were analyzed in order to search for proteins that are unique to this group.200515960851
purification, characterization, and crystallization of the components of the nitrobenzene and 2-nitrotoluene dioxygenase enzyme systems.the protein components of the 2-nitrotoluene (2nt) and nitrobenzene dioxygenase enzyme systems from acidovorax sp. strain js42 and comamonas sp. strain js765, respectively, were purified and characterized. these enzymes catalyze the initial step in the degradation of 2-nitrotoluene and nitrobenzene. the identical shared reductase and ferredoxin components were monomers of 35 and 11.5 kda, respectively. the reductase component contained 1.86 g-atoms iron, 2.01 g-atoms sulfur, and one molecule of ...200516000792
amino acids in positions 48, 52, and 73 differentiate the substrate specificities of the highly homologous chlorocatechol 1,2-dioxygenases cbna and tcbc.chlorocatechol 1,2-dioxygenase (ccd) is the first-step enzyme of the chlorocatechol ortho-cleavage pathway, which plays a central role in the degradation of various chloroaromatic compounds. two ccds, cbna from the 3-chlorobenzoate-degrader ralstonia eutropha nh9 and tcbc from the 1,2,4-trichlorobenzene-degrader pseudomonas sp. strain p51, are highly homologous, having only 12 different amino acid residues out of identical lengths of 251 amino acids. but cbna and tcbc are different in substrate ...200516030237
novel lectin-like bacteriocins of biocontrol strain pseudomonas fluorescens pf-5.bacteriocin llpa, produced by pseudomonas sp. strain bw11m1, is a peculiar antibacterial protein due to its homology to mannose-binding lectins mostly found in monocots (a. h. a. parret, g. schoofs, p. proost, and r. de mot, j. bacteriol. 185:897-908, 2003). biocontrol strain pseudomonas fluorescens pf-5 contains two llpa-like genes, named llpa1(pf-5) and llpa2(pf-5). recombinant escherichia coli cells expressing llpa1(pf-5) or llpa2(pf-5) acquired bacteriocin activity and secreted a 31-kda prot ...200516151105
improving the activity and stability of gl-7-aca acylase ca130 by site-directed the present study, glutaryl-7-amino cephalosporanic acid acylase from pseudomonas sp. strain 130 (ca130) was mutated to improve its enzymatic activity and stability. based on the crystal structure of ca130, two series of amino acid residues, one from those directly involved in catalytic function and another from those putatively involved in surface charge, were selected as targets for site-directed mutagenesis. in the first series of experiments, several key residues in the substrate-binding ...200516151116
novel dna sequences from natural strains of the nitrogen-fixing symbiotic bacterium sinorhizobium meliloti.variation in genome size and content is common among bacterial strains. identifying these naturally occurring differences can accelerate our understanding of bacterial attributes, such as ecological specialization and genome evolution. in this study, we used representational difference analysis to identify potentially novel sequences not present in the sequenced laboratory strain rm1021 of the nitrogen-fixing bacterium sinorhizobium meliloti. using strain rm1021 as the driver and the type strain ...200516269751
adaptation of alcaligenes eutrophus b9 and pseudomonas sp. b13 to 2-fluorobenzoate as growth substrate.alcaligenes eutrophus b9 and pseudomonas sp. b13 could be adapted to 2-fluorobenzoate as the sole source of carbon and energy. the ability of the a. eutrophus b9 to use this new substrate is clearly based on the defective dihydrodihydroxybenzoate dehydrogenase. nontoxic 6-fluoro-3,5-cyclohexadiene-1,2-diol-1-carboxylic acid is accumulated instead of 3-fluorocatechol. about 84% of the substrate is dioxygenated to catechol and utilized via the 3-oxoadipate pathway. during continuous adaptation of ...198016345497
root-associated n(2) fixation (acetylene reduction) by enterobacteriaceae and azospirillum strains in cold-climate spodosols.n(2) fixation by bacteria in associative symbiosis with washed roots of 13 poaceae and 8 other noncultivated plant species in finland was demonstrated by the acetylene reduction method. the roots most active in c(2)h(2) reduction were those of agrostis stolonifera, calamagrostis lanceolata, elytrigia repens, and phalaris arundinacea, which produced 538 to 1,510 nmol of c(2)h(4).g (dry weight). h when incubated at po(2) 0.04 with sucrose (ph 6.5), and 70 to 269 nmol of c(2)h(4). g (dry weight).h ...198116345687
symbiotic utilization of polyvinyl alcohol by mixed cultures.polyvinyl alcohol (pva)-utilizing cultures were obtained from various sources. they were mixed cultures even after cyclical transfer to liquid and plate media with pva as a sole source of carbon. component bacteria were isolated from the several mixed cultures, and it was shown that pva was utilized symbiotically by two bacterial members which could not utilize pva in each respective pure culture. from a mixed culture, strains vm15, vm15a (pseudomonas putida) and vm15c (pseudomonas sp.) were iso ...198116345693
nitrogenase activity (acetylene reduction) of root-associated, cold-climate azospirillum, enterobacter, klebsiella, and pseudomonas species during growth on various carbon sources and at various partial pressures of oxygen.a comprehensive view of the diazotrophic bacterial flora of plants requires that attention be paid to the appropriate carbon and oxygen requirements during isolation of the bacteria. twenty compounds (monosaccharides, disaccharides, polyols, and organic acids) were therefore examined as carbon and energy sources for nitrogenase activity in semisolid stab cultures at po(2) values of 0.21, 0.02, and </=0.002 with 12 strains of diazotrophic root-associated bacteria. with the facultatively anaerobic ...198316346205
iron-chelating compounds produced by soil pseudomonads: correlation with fungal growth inhibition.strains of pseudomonas putida, pseudomonas sp., and pseudomonas aeruginosa were examined for their ability to grow in the presence of the iron chelator, ethylenediamine-di-(o-hydroxyphenylacetic acid). in vitro fungal inhibition assays showed that the isolates varied in their ability to inhibit the growth of representative fungal plant pathogens. fungal inhibition in vitro was superior to that of previously reported pseudomonas sp. studies with fusarium oxysporum forma sp. lycopersici and a susc ...198316346334
isolation of a pseudomonas sp. which utilizes the phosphonate herbicide glyphosate.a strain of bacteria has been isolated which rapidly and efficiently utilizes the herbicide glyphosate (n-phosphonomethylglycine) as its sole phosphorus source in a synthetic medium. the strain (pg2982) was isolated by subculturing pseudomonas aeruginosa atcc 9027 in a synthetic broth medium containing glyphosate as the sole phosphorus source. strain pg2982 differs from the culture of p. aeruginosa in that it is nonflagellated, does not produce pyocyanin, and has an absolute requirement for thia ...198316346357
mixed continuous cultures of polyvinyl alcohol-utilizing symbionts pseudomonas putida vm15a and pseudomonas sp. strain vm15c.stable mixed continuous cultures of pseudomonas sp. strain vm15c and pseudomonas putida vm15a, the former of which produced a polyvinyl alcohol (pva)-degrading enzyme and the latter of which produced an essential growth factor for pva utilization by strain vm15c, were established with pva as the sole source of carbon and energy with chemostat cultivation. a high extent of pva degradation was achieved at dilution rates of less than 0.030/h. the predominant strain in the cultures was the primary m ...198416346642
localization of polyvinyl alcohol oxidase produced by a bacterial symbiont, pseudomonas sp. strain axenic culture of a polyvinyl alcohol (pva)-degrading symbiont, pseudomonas sp. strain vm15c, was established on pva with a crude preparation of the growth factor (factor a) produced by the symbiotic partner pseudomonas putida vm15a. an increase of factor a in the culture medium enhanced the cell-associated pva oxidase activity as well as the growth rate, but decreased production of extracellular pva oxidase. pva oxidase in cells grown on pva was present in the periplasmic space at a higher r ...198516346711
enhancement of pyrroloquinoline quinone production and polyvinyl alcohol degradation in mixed continuous cultures of pseudomonas putida vm15a and pseudomonas sp. strain vm15c with mixed carbon a mixed continuous culture of pseudomonas putida vm15a and pseudomonas sp. strain vm15c with polyvinyl alcohol (pva) as the sole source of carbon, growth of the pva-degrading bacterium vm15c and, hence, pva degradation were limited by the growth factor, pyrroloquinoline quinone, produced by vm15a. feeding of a carbon source for vm15a, ethanol, with pva enhanced pyrroloquinoline quinone production and caused increases in the vm15c population and pva degradation in a mixed continuous culture. t ...198516346804
effects of chemical speciation on the mineralization of organic compounds by microorganisms.the mineralization of 1.0 to 100 ng each of four complexing compounds-oxalate, citrate, nitrilotriacetate (nta), and edta-per ml was tested in media prepared in accordance with equilibrium calculations by a computer program so that the h, ca, mg, fe, or al complex (chemical species) was predominant. sewage microorganisms mineralized calcium citrate more rapidly than iron, aluminum, or hydrogen citrate, and magnesium citrate was degraded slowest. aluminum, hydrogen, and iron oxalates were mineral ...198516346854
isolation of endoglucanase genes from pseudomonas fluorescens subsp. cellulosa and a pseudomonas sp.endoglucanase genes from pseudomonas fluorescens subsp. cellulosa and pseudomonas sp. were cloned and characterized. dna hybridization studies showed that these genes are homologous and that each species has one copy of the gene per genome. the dna fragment from pseudomonas sp. codes for, at most, a 23-kilodalton endoglucanase.198616347092
toluene induction and uptake kinetics and their inclusion in the specific-affinity relationship for describing rates of hydrocarbon metabolism.the kinetics of concentration-dependent toluene metabolism were examined by evaluating each term in the second-order rate equation. marine and freshwater pseudomonads were used. uptake for pseudomonas sp. strain t2 was characterized by a completely saturatable system with small transport constant (k(t) = 44 mug/liter) and large specific affinity. kinetics for pseudomonas putida ppf1 were similar. induction had little effect on k(t), but it caused the specific affinity to increase from about 0.03 ...198716347440
hydrogen and formate oxidation coupled to dissimilatory reduction of iron or manganese by alteromonas putrefaciens.the ability of alteromonas putrefaciens to obtain energy for growth by coupling the oxidation of various electron donors to dissimilatory fe(iii) or mn(iv) reduction was investigated. a. putrefaciens grew with hydrogen, formate, lactate, or pyruvate as the sole electron donor and fe(iii) as the sole electron acceptor. lactate and pyruvate were oxidized to acetate, which was not metabolized further. with fe(iii) as the electron acceptor, a. putrefaciens had a high affinity for hydrogen and format ...198916347876
copper resistance gene homologs in pathogenic and saprophytic bacterial species from tomato.copper-resistant strains of xanthomonas campestris pv. vesicatoria, pseudomonas cichorii, pseudomonas putida, pseudomonas fluorescens, and a yellow pseudomonas sp. were isolated from tomato plants or seeds. in southern hybridizations, dna from each strain showed homology with the copper resistance (cop) operon previously cloned from pseudomonas syringae pv. tomato pt23. homology was associated with plasmid and chromosomal dna in x. compestris pv. vesicatoria, p. putida, and the yellow pseudomona ...199016348118
enhanced growth of wheat and soybean plants inoculated with azospirillum brasilense is not necessarily due to general enhancement of mineral uptake.the capacity of azospirillum brasilense to enhance the accumulation of k, p, ca, mg, s, na, mn, fe, b, cu, and zn in inoculated wheat and soybean plants was evaluated by using two different analytical methods with five a. brasilense strains originating from four distinct geographical regions. a pseudomonas isolate from the rhizosphere of zea mays seedlings was included as a control. all a. brasilense strains significantly improved wheat and soybean growth by increasing root and shoot dry weight ...199016348150
transfer and expression of the catabolic plasmid pbrc60 in wild bacterial recipients in a freshwater ecosystem.3-chlorobenzoate (3cba)-degrading bacteria were isolated from the waters and sediments of flowthrough mesocosms dosed with various concentrations of 3cba and inoculated with a 3cba-degrading alcaligenes sp., strain br60. bacteria capable of 3cba degradation which were distinct from br60 were isolated. they carried pbrc60, a plasmid introduced with alcaligenes sp. strain br60 that carries a transposable element (tn5271) encoding 3cba degradation. the isolates expressed these genes in different wa ...199116348493
enhancement of the potential to utilize octopine in the nonfluorescent pseudomonas sp. strain 92.the nonfluorescent pseudomonas sp. strain 92 requires the presence of a supplementary carbon source for growth on octopine, whereas the spontaneous mutant rb100 has acquired the capacity to utilize this opine as the sole carbon and nitrogen source. insertional mutagenesis of rb100 with transposon tn5 generated mutants which were unable to grow on octopine and others which grew slowly on this substrate. both types of mutants yielded revertants that had regained the ability to utilize octopine. so ...199116348533
kinetics of bacterial growth on chlorinated aliphatic compounds.with the pure bacterial cultures ancylobacter aquaticus ad20 and ad25, xanthobacter autotrophicus gj10, and pseudomonas sp. strain ad1, monod kinetics was observed during growth in chemostat cultures on 1,2-dichloroethane (ad20, ad25, and gj10), 2-chloroethanol (ad20 and gj10), and 1,3-dichloro-2-propanol (ad1). both the michaelis-menten constants (k(m)) of the first catabolic (dehalogenating) enzyme and the monod half-saturation constants (k(s)) followed the order 2-chloroethanol, 1,3-dichloro- ...199316348981
a biological sensor for iron available to bacteria in their habitats on plant surfaces.a sensor responsive to iron was constructed by fusing a promoterless ice nucleation activity gene (inaz) to an iron-regulated promoter of a genomic region involved in pyoverdine (fluorescent siderophore) (pvd) production in pseudomonas syringae. cells of pseudomonas fluorescens and p. syringae that contained the pvd-inaz fusion expressed iron-responsive ice nucleation activity in the bean rhizosphere and phyllosphere, respectively, and in culture. addition of fe(iii) to leaves or soil reduced th ...199416349283
quantification of frankia strains and other root-associated bacteria in pure cultures and in the rhizosphere of axenic seedlings by high-performance liquid chromatography-based muramic acid assay.application of a high-performance liquid chromatography-based muramic acid assay with precolumn fluorescence derivatization to quantification of root-associated bacteria was studied both in pure cultures and in the rhizosphere of axenic festuca rubra seedlings. quantities of muramic acid from acid-hydrolyzed cells of frankia strains, streptomyces griseoviridis, enterobacter agglomerans, klebsiella pneumoniae, pseudomonas sp., and bacillus polymyxa were mostly proportional to the respective cell ...199416349413
molecular basis of a bacterial consortium: interspecies catabolism of atrazine.pseudomonas sp. strain adp contains the genes, atza, -b, and -c, that encode three enzymes which metabolize atrazine to cyanuric acid. atrazine-catabolizing pure cultures isolated from around the world contain genes homologous to atza, -b, and -c. the present study was conducted to determine whether the same genes are present in an atrazine-catabolizing bacterial consortium and how the genes and metabolism are subdivided among member species. the consortium contained four or more bacterial speci ...199816349478
initial reductive reactions in aerobic microbial metabolism of 2,4,6-trinitrotoluene.because of its high electron deficiency, initial microbial transformations of 2,4,6-trinitrotoluene (tnt) are characterized by reductive rather than oxidation reactions. the reduction of the nitro groups seems to be the dominating mechanism, whereas hydrogenation of the aromatic ring, as described for picric acid, appears to be of minor importance. thus, two bacterial strains enriched with tnt as a sole source of nitrogen under aerobic conditions, a gram-negative strain called tnt-8 and a gram-p ...199816349484
identification of hydrocarbon-degrading bacteria in soil by reverse sample genome probing.bacteria with limited genomic cross-hybridization were isolated from soil contaminated with c5+, a mixture of hydrocarbons, and identified by partial 16s rrna sequencing. filters containing denatured genomic dnas were used in a reverse sample genome probe (rsgp) procedure for analysis of the effect of an easily degradable compound (toluene) and a highly recalcitrant compound (dicyclopentadiene [dcpd]) on community composition. hybridization with labeled total-community dna isolated from soil exp ...199816349504
light-mediated nitrite accumulation during denitrification by pseudomonas sp. strain jr12.the effect of light on the denitrifying characteristics of a nonphotosynthetic denitrifier, pseudomonas sp. strain jr12, was examined. already at low light intensities, nitrite accumulated as a result of light inhibition of nitrite but not of nitrate reduction rates. exposure of this bacterium to light caused a photooxidation of cytochrome c, an intermediate electron carrier in its respiratory pathway. photoinhibition of nitrite reduction was reversible, as nitrite reduction rates returned to pr ...199816349525
crystal structure of the probable haloacid dehalogenase ph0459 from pyrococcus horikoshii ot3.ph0459, from the hyperthermophilic archaeon pyrococcus horikoshii ot3, is a probable haloacid dehalogenase with a molecular mass of 26,725 da. here, we report the 2.0 a crystal structure of ph0459 (pdb id: 1x42) determined by the multiwavelength anomalous dispersion method. the core domain has an alpha/beta structure formed by a six-stranded parallel beta-sheet flanked by six alpha-helices and three 3(10)-helices. one disulfide bond, cys186-cys212, forms a bridge between an alpha-helix and a 3(1 ...200616385007
the clc element of pseudomonas sp. strain b13, a genomic island with various catabolic properties.pseudomonas sp. strain b13 is a bacterium known to degrade chloroaromatic compounds. the properties to use 3- and 4-chlorocatechol are determined by a self-transferable dna element, the clc element, which normally resides at two locations in the cell's chromosome. here we report the complete nucleotide sequence of the clc element, demonstrating the unique catabolic properties while showing its relatedness to genomic islands and integrative and conjugative elements rather than to other known cata ...200616484212
health considerations regarding horizontal transfer of microbial transgenes present in genetically modified crops.the potential effects of horizontal gene transfer on human health are an important item in the safety assessment of genetically modified organisms. horizontal gene transfer from genetically modified crops to gut microflora most likely occurs with transgenes of microbial origin. the characteristics of microbial transgenes other than antibiotic-resistance genes in market-approved genetically modified crops are reviewed. these characteristics include the microbial source, natural function, function ...200516489267
crystallization and preliminary x-ray crystallographic analysis of 2-methyl-3-hydroxypyridine-5-carboxylic acid (mhpc) oxygenase from pseudomonas sp. ma-1.2-methyl-3-hydroxypyridine-5-carboxylic acid (mhpc) oxygenase (mhpco) catalyzes the conversion of an aromatic substrate, mhpc, to an aliphatic compound, alpha-(n-acetylaminomethylene)-succinic acid, and is involved in the degradation of vitamin b6 by the soil bacterium pseudomonas sp. ma-1. using only fad as a cofactor, mhpco is unique in catalyzing hydroxylation and subsequent aromatic ring cleavage without requiring a metal-ion cofactor. here, the crystallization of mhpco is reported together ...200516511028
crystal structure of 3-hydroxyanthranilic acid 3,4-dioxygenase from saccharomyces cerevisiae: a special subgroup of the type iii extradiol dioxygenases.3-hydroxyanthranilic acid 3,4-dioxygenase (3hao) is a non-heme ferrous extradiol dioxygenase in the kynurenine pathway from tryptophan. it catalyzes the conversion of 3-hydroxyanthranilate (haa) to quinolinic acid (quin), an endogenous neurotoxin, via the activation of n-methyl-d-aspartate (nmda) receptors and the precursor of nad(+) biosynthesis. the crystal structure of 3hao from s. cerevisiae at 2.4 a resolution shows it to be a member of the functionally diverse cupin superfamily. the struct ...200616522801
pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine crenarchaeota.marine crenarchaeota represent an abundant component of oceanic microbiota with potential to significantly influence biogeochemical cycling in marine ecosystems. prior studies using specific archaeal lipid biomarkers and isotopic analyses indicated that planktonic crenarchaeota have the capacity for autotrophic growth, and more recent cultivation studies support an ammonia-based chemolithoautotrophic energy metabolism. we report here analysis of fosmid sequences derived from the uncultivated mar ...200616533068
localization and characterization of the carbon tetrachloride transformation activity of pseudomonas sp. strain kc.previous research has established that pseudomonas sp. strain kc rapidly transforms carbon tetrachloride (ct) to carbon dioxide (45 to 55%), a nonvolatile fraction (45 to 55%), and a cell-associated fraction ((equiv)5%) under denitrifying, iron-limited conditions. the present study provides additional characterization of the nonvolatile fraction, demonstrates that electron transfer plays a role in the transformation, and establishes the importance of both extracellular and intracellular factors. ...199516534941
isolation and characterization of a pseudomonas sp. that mineralizes the s-triazine herbicide atrazine.a bacterium that was capable of metabolizing atrazine at very high concentrations (>1,000 ppm) was isolated from a herbicide spill site. the organism was differentiated by observing clearing zones on indicator agar plates containing 1,000 ppm atrazine. detailed taxonomic studies identified the organism as a pseudomonas sp., designated adp, that was dissimilar to currently known species. pseudomonas sp. strain adp metabolized atrazine as its sole nitrogen source. nongrowing suspended cells also m ...199516534995
transformation of substituted fluorenes and fluorene analogs by pseudomonas sp. strain f274.pseudomonas sp. strain f274, previously shown to catabolize fluorene via fluorenone and its angular dioxygenation, 2(prm1),3(prm1)-dihydroxy-2-carboxybiphenyl, phthalate, and protocatechuate, was examined for its ability to transform substituted fluorenes and s- and n-heterocyclic analogs. halogen- and methyl-substituted fluorenes were metabolized to correspondingly substituted phthalates via attack on the unsubstituted ring. in the case of 1-methylfluorene, initial oxidation of the methyl group ...199516535132
uptake of benzoic acid and chloro-substituted benzoic acids by alcaligenes denitrificans bri 3010 and bri 6011.the mechanism of uptake of benzoic and 2,4-dichlorobenzoic acid (2,4-dcba) by alcaligenes denitrificans bri 3010 and bri 6011 and pseudomonas sp. strain b13, three organisms capable of degrading various isomers of chlorinated benzoic acids, was investigated. in all three organisms, uptake of benzoic acid was inducible. for benzoic acid uptake into bri 3010, monophasic saturation kinetics with apparent k(infm) and v(infmax) values of 1.4 (mu)m and 3.2 nmol/min/mg of cell dry weight, respectively, ...199516535175
transformation of low concentrations of 3-chlorobenzoate by pseudomonas sp. strain b13: kinetics and residual concentrations.the transformation of 3-chlorobenzoate (3cb) and acetate at initial concentrations in the wide range of 10 nm to 16 mm was studied in batch experiments with pseudomonas sp. strain b13. transformation rates of 3cb at millimolar concentrations could be described by michaelis-menten kinetics (k(infm), 0.13 mm; v(infmax), 24 nmol (middot) mg of protein(sup-1) (middot) min(sup-1)). experiments with nanomolar and low micromolar concentrations of 3cb indicated the possible existence of two different tr ...199616535232
atropine metabolism by pseudomonas sp. strain at3: evidence for nortropine as an intermediate in tropine breakdown and reactions leading to succinate.pseudomonas strain at3, isolated by elective culture with atropine, hydrolyzed atropine and grew diauxically, first on the tropic acid and then on the tropine. tropine was also used as a sole carbon and energy source. the methyl group of tropine was eliminated as formaldehyde, and the nortropine thus formed was a precursor of 6-hydroxycyclohepta-1,4-dione. ammonia was detected as a product of nitrogen elimination. 6-hydroxycyclohepta-1,4-dione was oxidized to cyclohepta-1,3,5-trione by an induce ...199616535398
effect of selected polysaccharide-producing soil bacteria on hyperhydricity control in oregano tissue cultures.hyperhydricity, or vitrification, is a physiological malformation affecting tissue culture-generated plants. this malformation is associated with excessive hydration and poor lignification and results in poor regeneration of plants. we have tested hyperhydricity prevention in oregano by several nonspecific polysaccharide-producing rhizosphere bacteria. among these bacteria, pseudomonas mucidolens and another pseudomonas sp. prevented hyperhydricity and improved acclimation of oregano clones. the ...199716535525
dechlorination of atrazine by a rhizobium sp. isolate.a rhizobium sp. strain, named patr, was isolated from an agricultural soil and found to actively degrade the herbicide atrazine. incubation of patr in a basal liquid medium containing 30 mg of atrazine liter(sup-1) resulted in the rapid consumption of the herbicide and the accumulation of hydroxyatrazine as the only metabolite detected after 8 days of culture. experiments performed with ring-labeled [(sup14)c]atrazine indicated no mineralization. the enzyme responsible for the hydroxylation of a ...199716535552
isolation and characterization of a chlorinated-pyridinol-degrading bacterium.the isolation of a pure culture of bacteria able to use 3,5,6-trichloro-2-pyridinol (tcp) as a sole source of carbon and energy under aerobic conditions was achieved for the first time. the bacterium was identified as a pseudomonas sp. and designated atcc 700113. [2,6-(sup14)c]tcp degradation yielded (sup14)co(inf2), chloride, and unidentified polar metabolites.199716535719
adding selectivity to antimicrobial peptides: rational design of a multidomain peptide against pseudomonas spp.currently available antimicrobials exhibit broad killing with regard to bacterial genera and species. indiscriminate killing of microbes by these conventional antibiotics can disrupt the ecological balance of the indigenous microbial flora, often resulting in negative clinical consequences. species-specific antimicrobials capable of precisely targeting pathogenic bacteria without damaging benign microorganisms provide a means of avoiding this problem. in this communication, we report the success ...200616569868
aerobic benzoyl-coenzyme a (coa) catabolic pathway in azoarcus evansii: conversion of ring cleavage product by 3,4-dehydroadipyl-coa semialdehyde dehydrogenase.benzoate, a strategic intermediate in aerobic aromatic metabolism, is metabolized in various bacteria via an unorthodox pathway. the intermediates of this pathway are coenzyme a (coa) thioesters throughout, and ring cleavage is nonoxygenolytic. the fate of the ring cleavage product 3,4-dehydroadipyl-coa semialdehyde was studied in the beta-proteobacterium azoarcus evansii. cell extracts contained a benzoate-induced, nadp(+)-specific aldehyde dehydrogenase, which oxidized this intermediate. a pos ...200616585753
natural pseudomonas sp. strain n3 in artificial soil microcosms.the lightning-competent pseudomonas sp. strain n3, recently isolated from soil, has been used to study the extent of natural electrotransformation (net) or lightning transformation as a horizontal gene transfer mechanism in soil. the variation of electrical fields applied to the soil with a laboratory-scale lightning system provides an estimate of the volume of soil affected by net. based on the range of the electric field that induces net of pseudomonas strain n3, the volume of soil, where net ...200616597934
purification and characterization of trzf: biuret hydrolysis by allophanate hydrolase supports growth.trzf, the allophanate hydrolase from enterobacter cloacae strain 99, was cloned, overexpressed in the presence of a chaperone protein, and purified to homogeneity. native trzf had a subunit molecular weight of 65,401 and a subunit stoichiometry of alpha(2) and did not contain significant levels of metals. trzf showed time-dependent inhibition by phenyl phosphorodiamidate and is a member of the amidase signature protein family. trzf was highly active in the hydrolysis of allophanate but was not a ...200616597948
pseudomonad cyclopentadecanone monooxygenase displaying an uncommon spectrum of baeyer-villiger oxidations of cyclic ketones.baeyer-villiger monooxygenases (bvmos) are biocatalysts that offer the prospect of high chemo-, regio-, and enantioselectivity in the organic synthesis of lactones or esters from a variety of ketones. in this study, we have cloned, sequenced, and overexpressed in escherichia coli a new bvmo, cyclopentadecanone monooxygenase (cpdb or cpdmo), originally derived from pseudomonas sp. strain hi-70. the 601-residue primary structure of cpdb revealed only 29% to 50% sequence identity to those of known ...200616597975
crystallization and preliminary x-ray analysis of the complex of nadh and 3alpha-hydroxysteroid dehydrogenase from pseudomonas sp. b-0831.the nad(p)(+)-dependent enzyme 3alpha-hydroxysteroid dehydrogenase (3alpha-hsd) catalyzes the reversible interconversion of hydroxyl and oxo groups at position 3 of the steroid nucleus. the complex of nadh and 3alpha-hsd from pseudomonas sp. b-0831 was crystallized by the hanging-drop vapour-diffusion method. refinement of crystallization conditions with microseeding improved the quality of the x-ray diffraction data to a resolution of 1.8 a. the crystals belonged to the orthorhombic space group ...200616754984
coregulation by phenylacetyl-coenzyme a-responsive paax integrates control of the upper and lower pathways for catabolism of styrene by pseudomonas sp. strain y2.the p(stya) promoter of pseudomonas sp. strain y2 controls expression of the styabcd genes, which are required for the conversion of styrene to phenylacetate, which is further catabolized by the products of two paa gene clusters. two paax repressor proteins (paax1 and paax2) regulate transcription of the paa gene clusters of this strain. in silico analysis of the p(stya) promoter region revealed a sequence located just within stya that is similar to the reported paax binding sites of escherichia ...200616788190
purification of outer membrane vesicles from pseudomonas aeruginosa and their activation of an il-8 response.considerable lung injury results from the inflammatory response to pseudomonas aeruginosa infections in patients with cystic fibrosis (cf). the p. aeruginosa laboratory strain pao1, an environmental isolate, and isolates from cf patients were cultured in vitro and outer membrane vesicles from those cultures were quantitated, purified, and characterized. vesicles were produced throughout the growth phases of the culture and vesicle yield was strain-independent. strain-dependent differences in the ...200616807039
mineralization of paraoxon and its use as a sole c and p source by a rationally designed catabolic pathway in pseudomonas putida.organophosphate compounds, which are widely used as pesticides and chemical warfare agents, are cholinesterase inhibitors. these synthetic compounds are resistant to natural degradation and threaten the environment. we constructed a strain of pseudomonas putida that can efficiently degrade a model organophosphate, paraoxon, and use it as a carbon, energy, and phosphorus source. this strain was engineered with the pnp operon from pseudomonas sp. strain env2030, which encodes enzymes that transfor ...200617021221
diverse responses to uv-b radiation and repair mechanisms of bacteria isolated from high-altitude aquatic environments.acinetobacter johnsonii a2 isolated from the natural community of laguna azul (andean mountains at 4,560 m above sea level), serratia marcescens mf42, pseudomonas sp. strain mf8 isolated from the planktonic community, and cytophaga sp. strain mf7 isolated from the benthic community from laguna pozuelos (andean puna at 3,600 m above sea level) were subjected to uv-b (3,931 j m-2) irradiation. in addition, a marine pseudomonas putida strain, 2idinh, and a second acinetobacter johnsonii strain, atc ...200617056692
sequence analysis and structure prediction of type ii pseudomonas sp. usm 4-55 pha synthase and an insight into its catalytic mechanism.polyhydroxyalkanoates (pha), are biodegradable polyesters derived from many microorganisms such as the pseudomonads. these polyesters are in great demand especially in the packaging industries, the medical line as well as the paint industries. the enzyme responsible in catalyzing the formation of pha is pha synthase. due to the limited structural information, its functional properties including catalysis are lacking. therefore, this study seeks to investigate the structural properties as well as ...200617076907
molecular analysis of the subgingival microbiota in health and disease.this investigation provides molecular analyses of the periodontal microbiota in health and disease. subgingival samples from 47 volunteers with healthy gingivae or clinically diagnosed chronic periodontitis were characterized by pcr-denaturing gradient gel electrophoresis (dgge) with primers specific for the v2-v3 region of the eubacterial 16s rrna gene. a hierarchical dendrogram was constructed from band patterns. all unique pcr amplicons (dgge bands) were sequenced for identity. samples were a ...200717085691
novel macrolide resistance module carried by the incp-1beta resistance plasmid prsb111, isolated from a wastewater treatment plant.the macrolide resistance plasmid prsb111 was isolated from bacteria residing in the final effluents of a wastewater treatment plant. the 47-kb plasmid confers resistance to azithromycin, clarithromycin, erythromycin, roxithromycin, and tylosin when it is carried by pseudomonas sp. strain b13 and is very similar to prototype incp-1beta plasmid pb3, which was previously isolated from an activated-sludge bacterial community of a wastewater treatment plant. the two plasmids differ in their accessory ...200717101677
a gene cluster involved in degradation of substituted salicylates via ortho cleavage in pseudomonas sp. strain mt1 encodes enzymes specifically adapted for transformation of 4-methylcatechol and 3-methylmuconate.pseudomonas sp. strain mt1 has recently been reported to degrade 4- and 5-chlorosalicylate by a pathway assumed to consist of a patchwork of reactions comprising enzymes of the 3-oxoadipate pathway. genes encoding the initial steps in the degradation of salicylate and substituted derivatives were now localized and sequenced. one of the gene clusters characterized (sal) showed a novel gene arrangement, with sala, encoding a salicylate 1-hydroxylase, being clustered with salcd genes, encoding muco ...200717172348
x-ray structure of a hydroxylase-regulatory protein complex from a hydrocarbon-oxidizing multicomponent monooxygenase, pseudomonas sp. ox1 phenol hydroxylase.phenol hydroxylase (ph) belongs to a family of bacterial multicomponent monooxygenases (bmms) with carboxylate-bridged diiron active sites. included are toluene/o-xylene (tomo) and soluble methane (smmo) monooxygenase. ph hydroxylates aromatic compounds, but unlike smmo, it cannot oxidize alkanes despite having a similar dinuclear iron active site. important for activity is formation of a complex between the hydroxylase and a regulatory protein component. to address how structural features of bm ...200617176061
mechanistic studies of the flavoenzyme tryptophan 2-monooxygenase: deuterium and 15n kinetic isotope effects on alanine oxidation by an l-amino acid oxidase.tryptophan 2-monooxygenase (tmo) from pseudomonas savastanoi catalyzes the oxidative decarboxylation of l-tryptophan during the biosynthesis of indoleacetic acid. structurally and mechanistically, the enzyme is a member of the family of l-amino acid oxidases. deuterium and 15n kinetic isotope effects were used to probe the chemical mechanism of l-alanine oxidation by tmo. the primary deuterium kinetic isotope effect was ph independent over the ph range 6.5-10, with an average value of 6.0 +/- 0. ...200617176107
identification of potential cepr regulated genes using a cep box motif-based search of the burkholderia cenocepacia genome.the burkholderia cenocepacia cepir quorum sensing system has been shown to positively and negatively regulate genes involved in siderophore production, protease expression, motility, biofilm formation and virulence. in this study, two approaches were used to identify genes regulated by the cepir quorum sensing system. transposon mutagenesis was used to create lacz promoter fusions in a cepi mutant that were screened for differential expression in the presence of n-acylhomoserine lactones. a bioi ...200617187664
adaptation of pseudomonas sp. strain 7-6 to quaternary ammonium compounds and their degradation via dual pathways.pseudomonas sp. strain 7-6, isolated from active sludge obtained from a wastewater facility, utilized a quaternary ammonium surfactant, n-dodecyltrimethylammonium chloride (dtac), as its sole carbon, nitrogen, and energy source. when initially grown in the presence of 10 mm dtac medium, the isolate was unable to degrade dtac. the strain was cultivated in gradually increasing concentrations of the surfactant until continuous exposure led to high tolerance and biodegradation of the compound. based ...200717261523
the role of laterally transferred genes in adaptive evolution.bacterial genomes develop new mechanisms to tide them over the imposing conditions they encounter during the course of their evolution. acquisition of new genes by lateral gene transfer may be one of the dominant ways of adaptation in bacterial genome evolution. lateral gene transfer provides the bacterial genome with a new set of genes that help it to explore and adapt to new ecological niches.200717288581
proteoglycan synthesis by human corneal explants submitted to laser in situ keratomileusis (lasik).to evaluate the acute effects of laser in situ keratomileusis (lasik) upon the synthesis of proteoglycans (pgs) and collagen fibril organization in human corneal explants.200717293778
generation by a widely applicable approach of a hybrid dioxygenase showing improved oxidation of polychlorobiphenyls.recently, a sequence-based approach has been developed for the fast isolation and characterization of class ii aryl-hydroxylating dioxygenase activities (s. kahl and b. hofer, microbiology 149:1475-1481, 2003). it comprises the pcr amplification of segments of alpha subunit genes of unknown sequence that encode the catalytic center and their fusion with sequences of the bpha gene cluster of burkholderia xenovorans lb400. one of the resulting chimeric enzymes, harboring the core segment of a diox ...200717322323
structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from sphingobium yanoikuyae b1.the initial step involved in oxidative hydroxylation of monoaromatic and polyaromatic compounds by the microorganism sphingobium yanoikuyae strain b1 (b1), previously known as sphingomonas yanoikuyae strain b1 and beijerinckia sp. strain b1, is performed by a set of multiple terminal rieske non-heme iron oxygenases. these enzymes share a single electron donor system consisting of a reductase and a ferredoxin (bpdo-fb1). one of the terminal rieske oxygenases, biphenyl 2,3-dioxygenase (bpdo-ob1), ...200717349044
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