Publications
| Title | Abstract | Year(sorted ascending) Filter | PMID Filter |
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| degradation of aromatics and chloroaromatics by pseudomonas sp. strain b13: cloning, characterization, and analysis of sequences encoding 3-oxoadipate:succinyl-coenzyme a (coa) transferase and 3-oxoadipyl-coa thiolase. | 3-oxoadipate:succinyl-coenzyme a (coa) transferase and 3-oxoadipyl-coa thiolase carry out the ultimate steps in the conversion of benzoate and 3-chlorobenzoate to tricarboxylic acid cycle intermediates in bacteria utilizing the 3-oxoadipate pathway. this report describes the characterization of dna fragments with the overall length of 5.9 kb from pseudomonas sp. strain b13 that encode these enzymes. dna sequence analysis revealed five open reading frames (orfs) plus an incomplete one. orf1, of u ... | 2002 | 11741863 |
| molecular cloning and expression of mn(2+)-dependent sphingomyelinase/hemolysin of an aquatic bacterium, pseudomonas sp. strain tk4. | we report here the molecular cloning and expression of a hemolytic sphingomyelinase from an aquatic bacterium, pseudomonas sp. strain tk4. the sphingomyelinase gene was found to consist of 1,548 nucleotides encoding 516 amino acid residues. the recombinant 57.7-kda enzyme hydrolyzed sphingomyelin but not phosphatidylcholine, phosphatidylserine, phosphatidylglycerol, phosphatidic acid, or phosphatidylethanolamine, indicating that the enzyme is a sphingomyelin-specific sphingomyelinase c. the hydr ... | 2002 | 11751833 |
| novel alkylsulfatases required for biodegradation of the branched primary alkyl sulfate surfactant 2-butyloctyl sulfate. | recent reports show that contrary to common perception, branched alkyl sulfate surfactants are readily biodegradable in standard biodegradability tests. we report here the isolation of bacteria capable of biodegrading 2-butyloctyl sulfate and the identification of novel enzymes that initiate the process. enrichment culturing from activated sewage sludge yielded several strains capable of growth on 2-butyloctyl sulfate. of these, two were selected for further study and identified as members of th ... | 2002 | 11772605 |
| 16s rrna-based analysis of microbiota from the cecum of broiler chickens. | the microbiota of the intestinal tract of chickens plays an important role in inhibiting the establishment of intestinal pathogens. earlier culturing and microscopic examinations indicated that only a fraction of the bacteria in the cecum of chickens could be grown in the laboratory. therefore, a survey of cecal bacteria was done by retrieval of 16s rrna gene sequences from dna isolated from the cecal content and the cecal mucosa. the ribosomal gene sequences were amplified with universal primer ... | 2002 | 11772618 |
| l-glucitol catabolism in stenotrophomonas maltophilia ac. | the carbohydrate catabolism of the bacterium stenotrophomonas maltophilia ac (previously named pseudomonas sp. strain ac), which is known to convert the unnatural polyol l-glucitol to d-sorbose during growth on the former as the sole source of carbon and energy, was studied in detail. all enzymes operating in a pathway that channels l-glucitol via d-sorbose into compounds of the intermediary metabolism were demonstrated, and for some prominent reactions the products of conversion were identified ... | 2002 | 11823194 |
| molecular characterization and substrate specificity of nitrobenzene dioxygenase from comamonas sp. strain js765. | comamonas sp. strain js765 can grow with nitrobenzene as the sole source of carbon, nitrogen, and energy. we report here the sequence of the genes encoding nitrobenzene dioxygenase (nbdo), which catalyzes the first step in the degradation of nitrobenzene by strain js765. the components of nbdo were designated reductase(nbz), ferredoxin(nbz), oxygenase(nbzalpha), and oxygenase(nbzbeta), with the gene designations nbzaa, nbzab, nbzac, and nbzad, respectively. sequence analysis showed that the comp ... | 2002 | 11823201 |
| production of diamino propionic acid ammonia lyase by a new strain of salmonella typhimurium pu011. | seeds of the legume plant lathyrus sativus, which is grown in arid and semi arid tropical regions, contain diamino propionic acid (dap). dap is a neurotoxin, which, when consumed, causes a disease called lathyrism. lathryrism may manifest as neurolathyrism or osteolathyrism, in which the nervous system, and bone formation respectively, are affected. dap ammonia lyase is produced by a few microorganisms such as salmonella typhi, salmonella typhimurium and pseudomonas, and is capable of detoxifyin ... | 2002 | 11914133 |
| rhodococcus erythropolis atcc 25544 as a suitable source of cholesterol oxidase: cell-linked and extracellular enzyme synthesis, purification and concentration. | the suitability of the strain rhodococcus erythropolis atcc 25544 grown in a two-liter fermentor as a source of cholesterol oxidase has been investigated. the strain produces both cell-linked and extracellular cholesterol oxidase in a high amount, that can be extracted, purified and concentrated by using the detergent triton x-114. | 2002 | 11914155 |
| species-specific repetitive extragenic palindromic (rep) sequences in pseudomonas putida. | pseudomonas putida kt2440 is a soil bacterium that effectively colonises the roots of many plants and degrades a variety of toxic aromatic compounds. its genome has recently been sequenced. we describe that a 35 bp sequence with the structure of an imperfect palindrome, originally found repeated three times downstream of the rpoh gene terminator, is detected more than 800 times in the chromosome of this strain. the structure of this dna segment is analogous to that of the so-called enterobacteri ... | 2002 | 11937637 |
| genes from pseudomonas sp. strain bs involved in the conversion of l-2-amino-delta(2)-thiazolin-4-carbonic acid to l-cysteine. | dl-2-amino-delta(2)-thiazolin-4-carbonic acid (dl-atc) is a substrate for cysteine synthesis in some bacteria, and this bioconversion has been utilized for cysteine production in industry. we cloned a dna fragment containing the genes involved in the conversion of l-atc to l-cysteine from pseudomonas sp. strain bs. the introduction of this dna fragment into escherichia coli cells enabled them to convert l-atc to cysteine via n-carbamyl-l-cysteine (l-ncc) as an intermediate. the smallest recombin ... | 2002 | 11976087 |
| transformation of isopropylamine to l-alaninol by pseudomonas sp. strain kie171 involves n-glutamylated intermediates. | pseudomonas sp. strain kie171 was able to grow with isopropylamine or l-alaninol [s-(+)-2-amino-1-propanol] as the sole carbon source, but not with d-alaninol. to investigate the hypothesis that l-alaninol is an intermediate in the degradation of isopropylamine, two mini-tn5 mutants unable to utilize both isopropylamine and l-alaninol were isolated. whereas mutant kie171-bi transformed isopropylamine to l-alaninol, mutant kie171-bii failed to do so. the two genes containing a transposon insertio ... | 2002 | 11976110 |
| role of glucose in enhancing the temperature-dependent growth inhibition of escherichia coli o157:h7 atcc 43895 by a pseudomonas sp. | growth of escherichia coli o157:h7 strain atcc 43895 was monitored at 5, 10, 15, and 25 degrees c in both pure and mixed (1:1) cultures with a gluconate-producing pseudomonas sp. found in meat to evaluate the effect of the absence and presence of 1% glucose in broth on temperature-dependent competition. the number of colonies of the pseudomonas strain exceeded 9 log cfu/ml under all conditions tested. the pathogen grew better as the temperature increased from 10 to 15 and 25 degrees c and grew b ... | 2002 | 11976143 |
| biochemical properties of a keratan sulphate/chondroitin sulphate proteoglycan expressed in primate pluripotent stem cells. | we previously identified a pericellular matrix keratan sulphate/chondroitin sulphate proteoglycan present on the surface of human embryonal carcinoma stem cells, cells whose differentiation mimics early development. antibodies reactive with various epitopes on this molecule define a cluster of differentiation markers for primate pluripotent stem cells. we describe the purification of a form of this molecule which is secreted or shed into the culture medium. biochemical analysis of the secreted f ... | 2002 | 12033730 |
| cloning, sequencing and heterologous expression of the gene for lupanine hydroxylase, a quinocytochrome c from a pseudomonas sp. | the gene encoding the enzyme lupanine hydroxylase was isolated by pcr using chromosomal dna from a lupanine-utilizing pseudomonas sp. as template and primers based on the sequences of the n- and c-termini of the purified protein. the derived sequence for the mature gene product gave a protein with an m (r) of 72256, in good agreement with the value found by sds/page of the pure enzyme, and contained the sequences of several peptides obtained after endoproteinase lys-c digestion of the pure enzym ... | 2002 | 12119046 |
| engineering of coenzyme specificity of formate dehydrogenase from saccharomyces cerevisiae. | a eukaryotic formate dehydrogenase (ec 1.2.1.2, fdh) with its substrate specificity changed from nad(+) to nadp(+) has been constructed by introducing two single-point mutations, asp(196)-->ala (d196a) and tyr(197)-->arg (y197r). the mutagenesis was based on the results of homology modelling of a nad(+)-specific fdh from saccharomyces cerevisiae (scefdh) using the pseudomonas sp.101 fdh (psefdh) crystal structure as a template. the resulting model structure suggested that asp(196) and tyr(197) m ... | 2002 | 12144528 |
| purification, substrate range, and metal center of atzc: the n-isopropylammelide aminohydrolase involved in bacterial atrazine metabolism. | n-isopropylammelide isopropylaminohydrolase, atzc, the third enzyme in the atrazine degradation pathway in pseudomonas sp. strain adp, catalyzes the stoichiometric hydrolysis of n-isopropylammelide to cyanuric acid and isopropylamine. the atzc gene was cloned downstream of the tac promoter and expressed in escherichia coli, where the expressed enzyme comprised 36% of the soluble protein. atzc was purified to homogeneity by ammonium sulfate precipitation and phenyl column chromatography. it has a ... | 2002 | 12218024 |
| genes coding for a new pathway of aerobic benzoate metabolism in azoarcus evansii. | a new pathway for aerobic benzoate oxidation has been postulated for azoarcus evansii and for a bacillus stearothermophilus-like strain. benzoate is first transformed into benzoyl coenzyme a (benzoyl-coa), which subsequently is oxidized to 3-hydroxyadipyl-coa and then to 3-ketoadipyl-coa; all intermediates are coa thioesters. the genes coding for this benzoate-induced pathway were investigated in the beta-proteobacterium a. evansii. they were identified on the basis of n-terminal amino acid sequ ... | 2002 | 12399500 |
| cloning and characterization of a gene cluster involved in cyclopentanol metabolism in comamonas sp. strain ncimb 9872 and biotransformations effected by escherichia coli-expressed cyclopentanone 1,2-monooxygenase. | cyclopentanone 1,2-monooxygenase, a flavoprotein produced by pseudomonas sp. strain ncimb 9872 upon induction by cyclopentanol or cyclopentanone (m. griffin and p. w. trudgill, biochem. j. 129:595-603, 1972), has been utilized as a biocatalyst in baeyer-villiger oxidations. to further explore this biocatalytic potential and to discover new genes, we have cloned and sequenced a 16-kb chromosomal locus of strain 9872 that is herein reclassified as belonging to the genus comamonas: sequence analysi ... | 2002 | 12406764 |
| a third transposable element, isppu12, from the toluene-xylene catabolic plasmid pww0 of pseudomonas putida mt-2. | a 3,372-bp insertion sequence, isppu12, has been identified on the archetypal toluene-xylene tol catabolic plasmid pww0 from pseudomonas putida mt-2. the insertion sequence element is located on the plasmid between bases 84397 and 87768 in a region which also contains the termini and transposase genes of the catabolic transposons tn4651 and tn4653 (a. greated, l. lambertson, p. a. williams, and c. m. thomas, environ. microbiol., in press). isppu12 has terminal inverted repeats of 24 bp with thre ... | 2002 | 12426346 |
| lipopeptide production in pseudomonas sp. strain dss73 is regulated by components of sugar beet seed exudate via the gac two-component regulatory system. | pseudomonas sp. strain dss73 isolated from the sugar beet rhizosphere produces the cyclic lipopeptide amphisin, which inhibits the growth of plant-pathogenic fungi. by tn5::luxab mutagenesis, we obtained two nonproducing mutant strains, dss73-15c2 and dss73-12h8. the gene interrupted by the transposon in strain dss73-15c2 (amsy) encoded a protein with homology to peptide synthetases that was designated amphisin synthetase. dss73-12h8 carried the transposon in a regulatory gene encoding a protein ... | 2002 | 12200307 |
| identification of bacteria in drinking and purified water during the monitoring of a typical water purification system. | a typical purification system that provides purified water which meets ionic and organic chemical standards, must be protected from microbial proliferation to minimize cross-contamination for use in cleaning and preparations in pharmaceutical industries and in health environments. | 2002 | 12182763 |
| degradation of aromatics and chloroaromatics by pseudomonas sp. strain b13: purification and characterization of 3-oxoadipate:succinyl-coenzyme a (coa) transferase and 3-oxoadipyl-coa thiolase. | the degradation of 3-oxoadipate in pseudomonas sp. strain b13 was investigated and was shown to proceed through 3-oxoadipyl-coenzyme a (coa) to give acetyl-coa and succinyl-coa. 3-oxoadipate:succinyl-coa transferase of strain b13 was purified by heat treatment and chromatography on phenyl-sepharose, mono-q, and superose 6 gels. estimation of the native molecular mass gave a value of 115,000 +/- 5,000 da with a superose 12 column. polyacrylamide gel electrophoresis under denaturing conditions res ... | 2002 | 11741862 |
| strategies for helicase recruitment and loading in bacteria. | dna replication initiation in prokaryotes and eukaryotes requires the recruitment and loading of a helicase at the replication origin. to subsequently unwind the double-stranded dna, the helicase must be properly positioned on the separated dna strands. several studies have revealed similarities and differences in the mechanisms used by different autonomously replicating dna elements (replicons) for recruitment and activation of the appropriate helicase. of particular interest are plasmid replic ... | 2003 | 12524518 |
| novel approach to the improvement of biphenyl and polychlorinated biphenyl degradation activity: promoter implantation by homologous recombination. | to improve the capabilities of microorganisms relevant for biodegradation, we developed a new genetic approach and applied it to the bph operon (bphegf[orf4]a1a2a3cd[orf1]a4r) of pseudomonas sp. strain kks102 to enhance its biphenyl- and polychlorinated biphenyl (pcb)-degrading activity. a native promoter of the bph operon, which was under control, was replaced through homologous recombination by a series of promoters that had constitutive activity. by testing a series of promoters with various ... | 2003 | 12513989 |
| plant lectin-like bacteriocin from a rhizosphere-colonizing pseudomonas isolate. | rhizosphere isolate pseudomonas sp. strain bw11m1, which belongs to the pseudomonas putida cluster, secretes a heat- and protease-sensitive bacteriocin which kills p. putida gr12-2r3. the production of this bacteriocin is enhanced by dna-damaging treatment of producer cells. we isolated a tnmod mutant of strain bw11m1 that had lost the capacity to inhibit the growth of strain gr12-2r3. a wild-type genomic fragment encompassing the transposon insertion site was shown to confer the bacteriocin phe ... | 2003 | 12533465 |
| synergistic degradation of linuron by a bacterial consortium and isolation of a single linuron-degrading variovorax strain. | the bacterial community composition of a linuron-degrading enrichment culture and the role of the individual strains in linuron degradation have been determined by a combination of methods, such as denaturing gradient gel electrophoresis of the total 16s rrna gene pool, isolation and identification of strains, and biodegradation assays. three strains, variovorax sp. strain wdl1, delftia acidovorans wdl34, and pseudomonas sp. strain wdl5, were isolated directly from the linuron-degrading culture. ... | 2003 | 12620840 |
| prokaryotic homologs of the eukaryotic 3-hydroxyanthranilate 3,4-dioxygenase and 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase in the 2-nitrobenzoate degradation pathway of pseudomonas fluorescens strain ku-7. | the 2-nitrobenzoic acid degradation pathway of pseudomonas fluorescens strain ku-7 proceeds via a novel 3-hydroxyanthranilate intermediate. in this study, we cloned and sequenced a 19-kb dna locus of strain ku-7 that encompasses the 3-hydroxyanthranilate meta-cleavage pathway genes. the gene cluster, designated nbaexhjigfcdr, is organized tightly and in the same direction. the nbac and nbad gene products were found to be novel homologs of the eukaryotic 3-hydroxyanthranilate 3,4-dioxygenase and ... | 2003 | 12620844 |
| bacterial conversion of hydroxylamino aromatic compounds by both lyase and mutase enzymes involves intramolecular transfer of hydroxyl groups. | hydroxylamino aromatic compounds are converted to either the corresponding aminophenols or protocatechuate during the bacterial degradation of nitroaromatic compounds. the origin of the hydroxyl group of the products could be the substrate itself (intramolecular transfer mechanism) or the solvent water (intermolecular transfer mechanism). the conversion of hydroxylaminobenzene to 2-aminophenol catalyzed by a mutase from pseudomonas pseudoalcaligenes js45 proceeds by an intramolecular hydroxyl tr ... | 2003 | 12732549 |
| identification of signature and primers specific to genus pseudomonas using mismatched patterns of 16s rdna sequences. | pseudomonas, a soil bacterium, has been observed as a dominant genus that survives in different habitats with wide hostile conditions. we had a basic assumption that the species level variation in 16s rdna sequences of a bacterial genus is mainly due to substitutions rather than insertion or deletion of bases. keeping this in view, the aim was to identify a region of 16s rdna sequence and within that focus on substitution prone stretches indicating species level variation and to derive patterns ... | 2003 | 12769821 |
| aerobic denitrifying bacteria that produce low levels of nitrous oxide. | most denitrifiers produce nitrous oxide (n(2)o) instead of dinitrogen (n(2)) under aerobic conditions. we isolated and characterized novel aerobic denitrifiers that produce low levels of n(2)o under aerobic conditions. we monitored the denitrification activities of two of the isolates, strains tr2 and k50, in batch and continuous cultures. both strains reduced nitrate (no(3)(-)) to n(2) at rates of 0.9 and 0.03 micro mol min(-1) unit of optical density at 540 nm(-1) at dissolved oxygen (o(2)) (d ... | 2003 | 12788710 |
| assessment of bioavailability of soil-sorbed atrazine. | bioavailability of pesticides sorbed to soils is an important determinant of their environmental fate and impact. mineralization of sorbed atrazine was studied in soil and clay slurries, and a desorption-biodegradation-mineralization (dbm) model was developed to quantitatively evaluate the bioavailability of sorbed atrazine. three atrazine-degrading bacteria that utilized atrazine as a sole n source (pseudomonas sp. strain adp, agrobacterium radiobacter strain j14a, and ralstonia sp. strain m91- ... | 2003 | 12788728 |
| molecular diversity of denitrifying genes in continental margin sediments within the oxygen-deficient zone off the pacific coast of mexico. | to understand the composition and structure of denitrifying communities in the oxygen-deficient zone off the pacific coast of mexico, the molecular diversity of nir genes from sediments obtained at four stations was examined by using a pcr-based cloning approach. a total of 50 operational taxonomic units (otus) for nirk and 82 otus for nirs were obtained from all samples. forty-four of the nirs clones and 31 of the nirk clones were sequenced; the levels of similarity of the nirs clones were 52 t ... | 2003 | 12788762 |
| on the origins of cyanuric acid hydrolase: purification, substrates, and prevalence of atzd from pseudomonas sp. strain adp. | cyanuric acid hydrolase (atzd) from pseudomonas sp. strain adp was purified to homogeneity. of 22 cyclic amides and triazine compounds tested, only cyanuric acid and n-methylisocyanuric acid were substrates. other cyclic amidases were found not to hydrolyze cyanuric acid. ten bacteria that use cyanuric acid as a sole nitrogen source for growth were found to contain either atzd or trzd, but not both genes. | 2003 | 12788776 |
| unusual integrase gene expression on the clc genomic island in pseudomonas sp. strain b13. | an unusual type of gene expression from an integrase promoter was found in cultures of the bacterium pseudomonas sp. strain b13. the promoter controls expression of the intb13 integrase gene, which is present near the right end of a 105-kb conjugative genomic island (the clc element) encoding catabolism of aromatic compounds. the enzymatic activity of integrase intb13 is essential for site-specific integration of the clc element into the bacterial host's chromosome. by creating transcription fus ... | 2003 | 12867462 |
| alteration of chain length substrate specificity of aeromonas caviae r-enantiomer-specific enoyl-coenzyme a hydratase through site-directed mutagenesis. | aeromonas caviae r-specific enoyl-coenzyme a (enoyl-coa) hydratase (phaj(ac)) is capable of providing (r)-3-hydroxyacyl-coa with a chain length of four to six carbon atoms from the fatty acid beta-oxidation pathway for polyhydroxyalkanoate (pha) synthesis. in this study, amino acid substitutions were introduced into phaj(ac) by site-directed mutagenesis to investigate the feasibility of altering the specificity for the acyl chain length of the substrate. a crystallographic structure analysis of ... | 2003 | 12902277 |
| the biphenyl- and 4-chlorobiphenyl-catabolic transposon tn4371, a member of a new family of genomic islands related to incp and ti plasmids. | the nucleotide sequence of the biphenyl catabolic transposon tn4371 has been completed and analyzed. it confirmed that the element has a mosaic structure made of several building blocks. in addition to previously identified genes coding for a tyrosine recombinase related to phage integrases and for biphenyl degradation enzymes very similar to those of achromobacter georgiopolitanum kks102, tn4371 carries many plasmid-related genes involved in replication, partition, and other, as-yet-unknown, pl ... | 2003 | 12902278 |
| biotransformation of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (cl-20) by denitrifying pseudomonas sp. strain fa1. | the microbial and enzymatic degradation of a new energetic compound, 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (cl-20), is not well understood. fundamental knowledge about the mechanism of microbial degradation of cl-20 is essential to allow the prediction of its fate in the environment. in the present study, a cl-20-degrading denitrifying strain capable of utilizing cl-20 as the sole nitrogen source, pseudomonas sp. strain fa1, was isolated from a garden soil. studies with inta ... | 2003 | 12957905 |
| low-temperature isolation of disease-suppressive bacteria and characterization of a distinctive group of pseudomonads. | the influence of environmental factors during isolation on the composition of potential biocontrol isolates is largely unknown. bacterial isolates that efficiently suppressed wheat seedling blight caused by fusarium culmorum were found by isolating psychrotrophic, root-associated bacteria and by screening them in a bioassay that mimicked field conditions. the impact of individual isolation factors on the disease-suppressive index (dsi) of almost 600 isolates was analyzed. the bacteria originated ... | 2003 | 14602601 |
| 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 ... | 2003 | 14617643 |
| 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 ... | 2003 | 14660340 |
| 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 ... | 2003 | 14660367 |
| clinical predictors of severe gallbladder complications in acute acalculous cholecystitis. | to 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). | 2003 | 14669342 |
| 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 ... | 2004 | 14711654 |
| 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 ... | 2004 | 14766582 |
| 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 ... | 2004 | 15066779 |
| 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 ... | 2004 | 15128568 |
| 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 ... | 2004 | 15155751 |
| 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 ... | 2004 | 15243054 |
| 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 ... | 2004 | 15292130 |
| 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 ... | 2004 | 15297496 |
| 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. | 2004 | 15307895 |
| 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 ... | 2004 | 15340916 |
| 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 ... | 2004 | 15345390 |
| 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 ... | 2004 | 15466555 |
| 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 ... | 2004 | 15547285 |
| 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 ... | 2004 | 15561846 |
| albusin b, a bacteriocin from the ruminal bacterium ruminococcus albus 7 that inhibits growth of ruminococcus flavefaciens. | an 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 ... | 2004 | 15128585 |
| 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)). ... | 2004 | 15466589 |
| molecular modeling of family gh16 glycoside hydrolases: potential roles for xyloglucan transglucosylases/hydrolases in cell wall modification in the poaceae. | family gh16 glycoside hydrolases can be assigned to five subgroups according to their substrate specificities, including xyloglucan transglucosylases/hydrolases (xths), (1,3)-beta-galactanases, (1,4)-beta-galactanases/kappa-carrageenases, "nonspecific" (1,3/1,3;1,4)-beta-d-glucan endohydrolases, and (1,3;1,4)-beta-d-glucan endohydrolases. a structured family gh16 glycoside hydrolase database has been constructed (http://www.ghdb.uni-stuttgart.de) and provides multiple sequence alignments with fu ... | 2004 | 15557263 |
| kinetics of dithionite-dependent reduction of cytochrome p450 3a4: heterogeneity of the enzyme caused by its oligomerization. | to explore the basis of apparent conformational heterogeneity of cytochrome p450 3a4 (cyp3a4), the kinetics of dithionite-dependent reduction was studied in solution, in proteoliposomes, and in nanodiscs. in cyp3a4 oligomers in solution the kinetics obeys a three-exponential equation with similar amplitudes of each of the phases. addition of substrate (bromocriptine) displaces the phase distribution toward the slow phase at the expense of the fast one, while the middle phase remains unaffected. ... | 2005 | 16229479 |
| 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 ... | 2005 | 16269751 |
| 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 ... | 2005 | 16489267 |
| 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 ... | 2005 | 16511028 |
| 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 ... | 2005 | 15601699 |
| 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 ... | 2005 | 15629930 |
| 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 ... | 2005 | 15655073 |
| 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 ... | 2005 | 15681481 |
| 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 ... | 2005 | 15727561 |
| 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 ... | 2005 | 15733056 |
| 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. | 2005 | 15757516 |
| 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 ... | 2005 | 15774891 |
| 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 ... | 2005 | 15888210 |
| 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 ... | 2005 | 15901697 |
| 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 ... | 2005 | 15930004 |
| 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 ... | 2005 | 15934927 |
| 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 ... | 2005 | 15956672 |
| 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. | 2005 | 15960851 |
| 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 ... | 2005 | 16000792 |
| 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 ... | 2005 | 16030237 |
| 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 ... | 2005 | 16151105 |
| improving the activity and stability of gl-7-aca acylase ca130 by site-directed mutagenesis. | in 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 ... | 2005 | 16151116 |
| 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 ... | 2006 | 16522801 |
| 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 ... | 2006 | 16533068 |
| 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 ... | 2006 | 17176061 |
| 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. ... | 2006 | 17176107 |
| 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 ... | 2006 | 17187664 |
| 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 ... | 2006 | 16385007 |
| 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 ... | 2006 | 16484212 |
| 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 ... | 2006 | 16569868 |
| 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 ... | 2006 | 16585753 |
| 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 ... | 2006 | 16597934 |
| 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 ... | 2006 | 16597948 |
| 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 ... | 2006 | 16597975 |
| 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 ... | 2006 | 16754984 |
| 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 ... | 2006 | 16788190 |
| 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 ... | 2006 | 16807039 |
| 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 ... | 2006 | 17021221 |
| 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 ... | 2006 | 17056692 |
| 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 ... | 2006 | 17076907 |
| comparative genomics of regulation of heavy metal resistance in eubacteria. | heavy metal resistance (hmr) in eubacteria is regulated by a variety of systems including transcription factors from the merr family (cog0789). the hmr systems are characterized by the complex signal structure (strong palindrome within a 19 or 20 bp promoter spacer), and usually consist of transporter and regulator genes. some hmr regulons also include detoxification systems. the number of sequenced bacterial genomes is constantly increasing and even though hmr resistance regulons of the cog0789 ... | 2006 | 16753059 |