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polycyclic aromatic hydrocarbon degradation by a new marine bacterium, neptunomonas naphthovorans gen. nov., sp. nov.two strains of bacteria were isolated from creosote-contaminated puget sound sediment based on their ability to utilize naphthalene as a sole carbon and energy source. when incubated with a polycyclic aromatic hydrocarbon (pah) compound in artificial seawater, each strain also degraded 2-methylnaphthalene and 1-methylnaphthalene; in addition, one strain, nag-2n-113, degraded 2,6-dimethylnaphthalene and phenanthrene. acenaphthene was not degraded when it was used as a sole carbon source but was d ...19999872786
the chlorocatechol-catabolic transposon tn5707 of alcaligenes eutrophus nh9, carrying a gene cluster highly homologous to that in the 1,2,4-trichlorobenzene-degrading bacterium pseudomonas sp. strain p51, confers the ability to grow on 3-chlorobenzoate.alcaligenes eutrophus (ralstonia eutropha) nh9, isolated in japan, utilizes 3-chlorobenzoate as its sole source of carbon and energy. sequencing of the relevant region of plasmid penh91 from strain nh9 revealed that the genes for the catabolic enzymes were homologous to the genes of the modified ortho-cleavage pathway. the genes from strain nh9 (cbnr-abcd) showed the highest homology (89 to 100% identity at the nucleotide level) to the tcbr-cdef genes on plasmid pp51 of the 1,2,4-trichlorobenzen ...19999925607
molecular characterization of the genes pcag and pcah, encoding protocatechuate 3,4-dioxygenase, which are essential for vanillin catabolism in pseudomonas sp. strain hr199.pseudomonas sp. strain hr199 is able to utilize eugenol (4-allyl-2-methoxyphenol), vanillin (4-hydroxy-3-methoxybenzaldehyde), or protocatechuate as the sole carbon source for growth. mutants of this strain which were impaired in the catabolism of vanillin but retained the ability to utilize eugenol or protocatechuate were obtained after nitrosoguanidine mutagenesis. one mutant (sk6169) was used as recipient of a pseudomonas sp. strain hr199 genomic library in cosmid pvk100, and phenotypic compl ...199910049847
contrasting effects of a nonionic surfactant on the biotransformation of polycyclic aromatic hydrocarbons to cis-dihydrodiols by soil bacteria.the biotransformation of the polycyclic aromatic hydrocarbons (pahs) naphthalene and phenanthrene was investigated by using two dioxygenase-expressing bacteria, pseudomonas sp. strain 9816/11 and sphingomonas yanoikuyae b8/36, under conditions which facilitate mass-transfer limited substrate oxidation. both of these strains are mutants that accumulate cis-dihydrodiol metabolites under the reaction conditions used. the effects of the nonpolar solvent 2,2,4, 4,6,8,8-heptamethylnonane (hmn) and the ...199910049904
aspartate 205 in the catalytic domain of naphthalene dioxygenase is essential for activity.the naphthalene dioxygenase enzyme system carries out the first step in the aerobic degradation of naphthalene by pseudomonas sp. strain ncib 9816-4. the crystal structure of naphthalene dioxygenase (b. kauppi, k. lee, e. carredano, r. e. parales, d. t. gibson, h. eklund, and s. ramaswamy, structure 6:571-586, 1998) indicates that aspartate 205 may provide the most direct route of electron transfer between the rieske [2fe-2s] center of one alpha subunit and mononuclear iron in the adjacent alpha ...199910074076
the periplasmic nitrate reductase in pseudomonas sp. strain g-179 catalyzes the first step of denitrification.both membrane-bound and periplasmic nitrate reductases have been found in denitrifying bacteria. yet the role of periplasmic nitrate reductase in denitrification has not been clearly defined. to analyze the function of the periplasmic nitrate reductase in pseudomonas sp. strain g-179, the nap gene cluster was identified and found to be linked to genes involved in reduction of nitrite and nitric oxide and anaerobic heme biosynthesis. mutation in the nap region rendered the cells incapable of grow ...199910217771
diverse oxygenations catalyzed by carbazole 1,9a-dioxygenase from pseudomonas sp. strain ca10.carbazole 1,9a-dioxygenase (cardo) from pseudomonas sp. strain ca10 is a multicomponent enzyme that catalyzes the angular dioxygenation of carbazole, dibenzofuran, and dibenzo-p-dioxin. it was revealed by gas chromatography-mass spectrometry and 1h and 13c nuclear magnetic resonance analyses that xanthene and phenoxathiin were converted to 2,2',3-trihydroxydiphenylmethane and 2,2',3-trihydroxydiphenyl sulfide, respectively. thus, for xanthene and phenoxathiin, angular dioxygenation by cardo occu ...199910322011
monooxygenase-mediated 1,2-dichloroethane degradation by pseudomonas sp. strain dca1.a bacterial strain, designated pseudomonas sp. strain dca1, was isolated from a 1,2-dichloroethane (dca)-degrading biofilm. strain dca1 utilizes dca as the sole carbon and energy source and does not require additional organic nutrients, such as vitamins, for optimal growth. the affinity of strain dca1 for dca is very high, with a km value below the detection limit of 0.5 microm. instead of a hydrolytic dehalogenation, as in other dca utilizers, the first step in dca degradation in strain dca1 is ...199910347028
identification and sequencing of beta-myrcene catabolism genes from pseudomonas sp. strain m1.the m1 strain, able to grow on beta-myrcene as the sole carbon and energy source, was isolated by an enrichment culture and identified as a pseudomonas sp. one beta-myrcene-negative mutant, called n22, obtained by transposon mutagenesis, accumulated (e)-2-methyl-6-methylen-2,7-octadien-1-ol (or myrcen-8-ol) as a unique beta-myrcene biotransformation product. this compound was identified by gas chromatography-mass spectrometry. we cloned and sequenced the dna regions flanking the transposon and u ...199910388678
two moles of o2 consumption and one mole of h2o2 formation during cholesterol peroxidation with cholesterol oxidase from pseudomonas sp. strain st-200.cholesterol oxidase from pseudomonas sp. strain st-200 oxidized cholesterol and cholestanol to 6beta-hydroperoxycholest-4-en-3-one and 5alpha-cholestan-3-one respectively. the former was converted spontaneously to several oxysteroids such as 6-hydroxycholest-4-en-3-one and cholest-4-ene-3,6-dione, with the consumption of 2 mol of o(2) and the formation of 1 mol of h(2)o(2) for each mole of cholesterol oxidized. an oxidized form of the cholesterol oxidase dehydrogenates cholesterol, probably to t ...199910417325
degradation of 3-phenoxybenzoic acid in soil by pseudomonas pseudoalcaligenes pob310(ppob) and two modified pseudomonas strains.pseudomonas pseudoalcaligenes pob310(ppob) and pseudomonas sp. strains b13-d5(pd30.9) and b13-st1(ppob) were introduced into soil microcosms containing 3-phenoxybenzoic acid (3-pob) in order to evaluate and compare bacterial survival, degradation of 3-pob, and transfer of plasmids to a recipient bacterium. strain pob310 was isolated for its ability to use 3-pob as a growth substrate; degradation is initiated by pob-dioxygenase, an enzyme encoded on ppob. strain b13-d5 contains pd30.9, a cloning ...199910427019
heterologous expression and characterization of the purified oxygenase component of rhodococcus globerulus p6 biphenyl dioxygenase and of chimeras derived from it.in this work, we have purified the his-tagged oxygenase (ht-oxygenase) component of rhodococcus globerulus p6 biphenyl dioxygenase. the alpha or beta subunit of p6 oxygenase was exchanged with the corresponding subunit of pseudomonas sp. strain lb400 or of comamonas testosteroni b-356 to create new chimeras that were purified ht-proteins and designated ht-alpha(p6)beta(p6), ht-alpha(p6)beta(lb400), ht-alpha(p6)beta(b-356), ht-alpha(lb400)beta(p6), and ht-alpha(b-356)beta(p6). ht-alpha(p6)beta(p6 ...199910438748
genotypic and phenotypic relationships between clinical and environmental isolates of stenotrophomonas maltophilia.while the gram-negative bacterium stenotrophomonas maltophilia is used in biotechnology (e.g., for biological control of plant pathogens and for bioremediation), the number of s. maltophilia diseases in humans has dramatically increased in recent years. a total of 40 s. maltophilia isolates from clinical and environmental sources (plant associated and water) was investigated to determine the intraspecies diversity of the group and to determine whether or not the strains could be grouped based on ...199910523559
transcriptional activation of the chlorocatechol degradative genes of ralstonia eutropha nh9.ralstonia eutropha (formerly alcaligenes eutrophus) nh9 degrades 3-chlorobenzoate via the modified ortho-cleavage pathway. a ca. 5.7-kb six-gene cluster is responsible for chlorocatechol degradation: the cbnabcd operon encoding the degradative enzymes (including orfx of unknown function) and the divergently transcribed cbnr gene encoding the lysr-type transcriptional regulator of the cbn operon. the cbnrab orfxcd gene cluster is nearly identical to the chlorocatechol genes (tcbrcd orfxef) of the ...199910542171
biochemical and genetic analyses of ferulic acid catabolism in pseudomonas sp. strain hr199.the gene loci fcs, encoding feruloyl coenzyme a (feruloyl-coa) synthetase, ech, encoding enoyl-coa hydratase/aldolase, and aat, encoding beta-ketothiolase, which are involved in the catabolism of ferulic acid and eugenol in pseudomonas sp. strain hr199 (dsm7063), were localized on a dna region covered by two ecori fragments (e230 and e94), which were recently cloned from a pseudomonas sp. strain hr199 genomic library in the cosmid pvk100. the nucleotide sequences of parts of fragments e230 and e ...199910543794
flagellate predation on a bacterial model community: interplay of size-selective grazing, specific bacterial cell size, and bacterial community composition.the influence of grazing by the bacterivorous nanoflagellate ochromonas sp. strain ds on the taxonomic and morphological structures of a complex bacterial community was studied in one-stage chemostat experiments. a bacterial community, consisting of at least 30 different strains, was fed with a complex carbon source under conditions of low growth rate (0.5 day(-1) when nongrazed) and low substrate concentration (9 mg liter(-1)). before and after the introduction of the predator, the bacterial co ...199910543797
cis-chlorobenzene dihydrodiol dehydrogenase (tcbb) from pseudomonas sp. strain p51, expressed in escherichia coli dh5alpha(ptcb149), catalyzes enantioselective dehydrogenase reactions.cis-chlorobenzene dihydrodiol dehydrogenase (cdd) from pseudomonas sp. strain p51, cloned into escherichia coli dh5alpha(ptcb149) was able to oxidize cis-dihydrodihydroxy derivatives (cis-dihydrodiols) of dihydronaphthalene, indene, and four para-substituted toluenes to the corresponding catechols. during the incubation of a nonracemic mixture of cis-1,2-indandiol, only the (+)-cis-(1r,2s) enantiomer was oxidized; the (-)-cis-(s,2r) enantiomer remained unchanged. cdd oxidized both enantiomers of ...199910583971
the extracellular regions of psma and the transferrin receptor contain an aminopeptidase domain: implications for drug design.the aeromonas proteolytica aminopeptidase (amp), pseudomonas sp. (rs-16) carboxypeptidase g2 (cpg2), and streptomyces griseus aminopeptidase (sgap) are zinc dependent proteolytic enzymes with cocatalytic zinc ion centers and a conserved aminopeptidase fold. a blast search with the sequence of the solved amp structure indicated that a similar domain could be found in prostate-specific membrane antigen (psma) and the transferrin receptor (tfr). when the psma or tfr sequence was input into the thre ...199910595564
generation of novel bacterial regulatory proteins that detect priority pollutant phenols.the genetic systems of bacteria that have the ability to use organic pollutants as carbon and energy sources can be adapted to create bacterial biosensors for the detection of industrial pollution. the creation of bacterial biosensors is hampered by a lack of information about the genetic systems that control production of bacterial enzymes that metabolize pollutants. we have attempted to overcome this problem through modification of dmpr, a regulatory protein for the phenol degradation pathway ...200010618218
in vitro analysis of roles of a disulfide bridge and a calcium binding site in activation of pseudomonas sp. strain kwi-56 lipase.the expression of lipase from pseudomonas sp. strain kwi-56 (recently reclassified as burkholderia cepacia) had been found to be dependent on an activator gene (act) downstream of its structural gene (lip). in this work, the mature lipase was synthesized in an enzymatically active form with a cell-free escherichia coli s30 coupled transcription-translation system by expressing a recombinant lipase gene (rlip) encoding the mature lipase in the presence of its purified activator or by coexpression ...200010629173
estimation of the yield coefficient of pseudomonas sp. strain dp-4 with a low substrate (2,4-dichlorophenol [dcp]) concentration in a mineral medium from which uncharacterized organic compounds were eliminated by a non-dcp-degrading organism.the yield coefficient (yc) of pseudomonas sp. strain dp-4, a 2, 4-dichlorophenol (dcp)-degrading organism, was estimated from the number of cfu produced at the expense of 1 unit amount of dcp at low concentrations. at a low concentration of dcp, the yc can be overestimated in pure culture, because dp-4 assimilated not only dcp but also uncharacterized organic compounds contaminating a mineral salt medium. the concentration of these uncharacterized organic compounds was nutritionally equivalent t ...200010653719
substrate specificity of naphthalene dioxygenase: effect of specific amino acids at the active site of the enzyme.the three-component naphthalene dioxygenase (ndo) enzyme system carries out the first step in the aerobic degradation of naphthalene by pseudomonas sp. strain ncib 9816-4. the three-dimensional structure of ndo revealed that several of the amino acids at the active site of the oxygenase are hydrophobic, which is consistent with the enzyme's preference for aromatic hydrocarbon substrates. although ndo catalyzes cis-dihydroxylation of a wide range of substrates, it is highly regio- and enantiosele ...200010692370
roles of horizontal gene transfer and gene integration in evolution of 1,3-dichloropropene- and 1,2-dibromoethane-degradative pathways.the haloalkane-degrading bacteria rhodococcus rhodochrous ncimb13064, pseudomonas pavonaceae 170, and mycobacterium sp. strain gp1 share a highly conserved haloalkane dehalogenase gene (dhaa). here, we describe the extent of the conserved dhaa segments in these three phylogenetically distinct bacteria and an analysis of their flanking sequences. the dhaa gene of the 1-chlorobutane-degrading strain ncimb13064 was found to reside within a 1-chlorobutane catabolic gene cluster, which also encodes a ...200010735862
role of tfdc(i)d(i)e(i)f(i) and tfdd(ii)c(ii)e(ii)f(ii) gene modules in catabolism of 3-chlorobenzoate by ralstonia eutropha jmp134(pjp4).the enzymes chlorocatechol-1,2-dioxygenase, chloromuconate cycloisomerase, dienelactone hydrolase, and maleylacetate reductase allow ralstonia eutropha jmp134(pjp4) to degrade chlorocatechols formed during growth in 2,4-dichlorophenoxyacetate or 3-chlorobenzoate (3-cb). there are two gene modules located in plasmid pjp4, tfdc(i)d(i)e(i)f(i) (module i) and tfdd(ii)c(ii)e(ii)f(ii) (module ii), putatively encoding these enzymes. to assess the role of both tfd modules in the degradation of chloroaro ...200010742248
cloning and expression of ntnd, encoding a novel nad(p)(+)-independent 4-nitrobenzyl alcohol dehydrogenase from pseudomonas sp. strain tw3.pseudomonas sp. strain tw3 is able to metabolize 4-nitrotoluene to 4-nitrobenzoate and toluene to benzoate aerobically via a route analogous to the upper pathway of the tol plasmids. we report the cloning and characterization of a benzyl alcohol dehydrogenase gene (ntnd) which encodes the enzyme for the catabolism of 4-nitrobenzyl alcohol and benzyl alcohol to 4-nitrobenzaldehyde and benzaldehyde, respectively. the gene is located downstream of the previously reported ntn gene cluster. ntnd bear ...200010809692
bacterial community structure and physiological state within an industrial phenol bioremediation system.the structure of bacterial populations in specific compartments of an operational industrial phenol remediation system was assessed to examine bacterial community diversity, distribution, and physiological state with respect to the remediation of phenolic polluted wastewater. rapid community fingerprinting by pcr-based denaturing gradient gel electrophoresis (dgge) of 16s rdna indicated highly structured bacterial communities residing in all nine compartments of the treatment plant and not exclu ...200010831417
influence of chlorine substituents on rates of oxidation of chlorinated biphenyls by the biphenyl dioxygenase of burkholderia sp. strain lb400.biphenyl dioxygenase from burkholderia (pseudomonas) sp. strain lb400 catalyzes the first reaction of a pathway for the degradation of biphenyl and a broad range of chlorinated biphenyls (cbs). the effect of chlorine substituents on catalysis was determined by measuring the specific activity of the enzyme with biphenyl and 18 congeners. the catalytic oxygenase component was purified and incubated with individual cbs in the presence of electron transport proteins and cofactors that were required ...200010877788
characterization of s-triazine herbicide metabolism by a nocardioides sp. isolated from agricultural soils.atrazine, a herbicide widely used in corn production, is a frequently detected groundwater contaminant. nine gram-positive bacterial strains able to use this herbicide as a sole source of nitrogen were isolated from four farms in central canada. the strains were divided into two groups based on repetitive extragenic palindromic (rep)-pcr genomic fingerprinting with eric and boxa1r primers. based on 16s ribosomal dna sequence analysis, both groups were identified as nocardioides sp. strains. none ...200010919761
identification of the dimerization domain of dehalogenase iva of burkholderia cepacia mba4.haloacid dehalogenases are enzymes that catalyze the hydrolytic removal of halogens from haloalkanoic acids. dehalogenase iva (dehiva) from burkholderia cepacia mba4 and dehalogenase ci (dehci) from pseudomonas sp. strain cbs3 exhibit 68% identity. despite their similarity dehiva is a dimeric enzyme while dehci is a monomer. in this work, we describe the identification of the domain that confers the dimerization function of dehiva. recombinant dna molecules were constructed by fusion of the resp ...200010919767
chromosomal integration of tcb chlorocatechol degradation pathway genes as a means of expanding the growth substrate range of bacteria to include haloaromatics.the tcbr-tcbcdef gene cluster, coding for the chlorocatechol ortho-cleavage pathway in pseudomonas sp. strain p51, has been cloned into a tn5-based minitransposon. the minitransposon carrying the tcb gene cluster and a kanamycin resistance gene was transferred to pseudomonas putida kt2442, and chromosomal integration was monitored by selection either for growth on 3-chlorobenzoate or for kanamycin resistance. transconjugants able to utilize 3-chlorobenzoate as a sole carbon source were obtained, ...200010919778
regioselectivity and enantioselectivity of naphthalene dioxygenase during arene cis-dihydroxylation: control by phenylalanine 352 in the alpha subunit.the naphthalene dioxygenase (ndo) system catalyzes the first step in the degradation of naphthalene by pseudomonas sp. strain ncib 9816-4. the enzyme has a broad substrate range and catalyzes several types of reactions including cis-dihydroxylation, monooxygenation, and desaturation. substitution of valine or leucine at phe-352 near the active site iron in the alpha subunit of ndo altered the stereochemistry of naphthalene cis-dihydrodiol formed from naphthalene and also changed the region of ox ...200010986254
substrate specificity of atrazine chlorohydrolase and atrazine-catabolizing bacteria.bacterial atrazine catabolism is initiated by the enzyme atrazine chlorohydrolase (atza) in pseudomonas sp. strain adp. other triazine herbicides are metabolized by bacteria, but the enzymological basis of this is unclear. here we begin to address this by investigating the catalytic activity of atza by using substrate analogs. purified atza from pseudomonas sp. strain adp catalyzed the hydrolysis of an atrazine analog that was substituted at the chlorine substituent by fluorine. atza did not cat ...200011010866
commensal interactions in a dual-species biofilm exposed to mixed organic compounds.there is limited knowledge of interspecies interactions in biofilm communities. in this study, pseudomonas sp. strain gj1, a 2-chloroethanol (2-ce)-degrading organism, and pseudomonas putida dmp1, a p-cresol-degrading organism, produced distinct biofilms in response to model mixed waste streams composed of 2-ce and various p-cresol concentrations. the two organisms maintained a commensal relationship, with dmp1 mitigating the inhibitory effects of p-cresol on gj1. a triple-labeling technique com ...200011010902
development and dynamics of pseudomonas sp. biofilms.pseudomonas sp. strain b13 and pseudomonas putida ous82 were genetically tagged with the green fluorescent protein and the discosoma sp. red fluorescent protein, and the development and dynamics occurring in flow chamber-grown two-colored monospecies or mixed-species biofilms were investigated by the use of confocal scanning laser microscopy. separate red or green fluorescent microcolonies were formed initially, suggesting that the initial small microcolonies were formed simply by growth of subs ...200011053394
rhizosphere competitiveness of trichloroethylene-degrading, poplar-colonizing recombinant bacteria.indigenous bacteria from poplar tree (populus canadensis var. eugenei 'imperial carolina') and southern california shrub rhizospheres, as well as two tree-colonizing rhizobium strains (atcc 10320 and atcc 35645), were engineered to express constitutively and stably toluene o-monooxygenase (tom) from burkholderia cepacia g4 by integrating the tom locus into the chromosome. the poplar and rhizobium recombinant bacteria degraded trichloroethylene at a rate of 0.8 to 2.1 nmol/min/mg of protein and w ...200011055909
purification and characterization of streptomyces griseus catechol o-methyltransferase.a soluble (100,000 x g supernatant) methyltransferase catalyzing the transfer of the methyl group of s-adenosyl-l-methionine to catechols was present in cell extracts of streptomyces griseus. a simple, general, and rapid catechol-based assay method was devised for enzyme purification and characterization. the enzyme was purified 141-fold by precipitation with ammonium sulfate and successive chromatography over columns of deae-cellulose, deae-sepharose, and sephacryl s-200. the purified cytoplasm ...200011055938
adaptive mutation: implications for evolution.adaptive mutation is defined as a process that, during nonlethal selections, produces mutations that relieve the selective pressure whether or not other, nonselected mutations are also produced. examples of adaptive mutation or related phenomena have been reported in bacteria and yeast but not yet outside of microorganisms. a decade of research on adaptive mutation has revealed mechanisms that may increase mutation rates under adverse conditions. this article focuses on mechanisms that produce a ...200011084622
bacterial biodegradation of extractives and patterns of bordered pit membrane attack in pine wood.wood extractives, commonly referred to as pitch, cause major problems in the manufacturing of pulp and paper. treatment of nonsterile southern yellow pine chips for 14 days with pseudomonas fluorescens, pseudomonas sp., xanthomonas campestris, and serratia marcescens reduced wood extractives by as much as 40%. control treatments receiving only water lost 11% of extractives due to the growth of naturally occurring microorganisms. control treatments were visually discolored after the 14-day incuba ...200011097890
relationship between nitrite reduction and active phosphate uptake in the phosphate-accumulating denitrifier pseudomonas sp. strain jr 12.phosphate uptake by the phosphate-accumulating denitrifier pseudomonas sp. jr12 was examined with different combinations of electron and carbon donors and electron acceptors. phosphate uptake in acetate-supplemented cells took place with either oxygen or nitrate but did not take place when nitrite served as the final electron acceptor. furthermore, nitrite reduction rates by this denitrifier were shown to be significantly reduced in the presence of phosphate. phosphate uptake assays in the prese ...200011097896
role of the dmpr-mediated regulatory circuit in bacterial biodegradation properties in methylphenol-amended soils.pathway substrates and some structural analogues directly activate the regulatory protein dmpr to promote transcription of the dmp operon genes encoding the (methyl)phenol degradative pathway of pseudomonas sp. strain cf600. while a wide range of phenols can activate dmpr, the location and nature of substituents on the basic phenolic ring can limit the level of activation and thus utilization of some compounds as assessed by growth on plates. here we address the role of the aromatic effector res ...200111133441
nag genes of ralstonia (formerly pseudomonas) sp. strain u2 encoding enzymes for gentisate catabolism.ralstonia sp. strain u2 metabolizes naphthalene via gentisate to central metabolites. we have cloned and sequenced a 21.6-kb region spanning the nag genes. upstream of the pathway genes are nagy, homologous to chemotaxis proteins, and nagr, a regulatory gene of the lysr family. divergently transcribed from nagr are the genes for conversion of naphthalene to gentisate (nagaaghabacadbfcqed) (s. l. fuenmayor, m. wild, a. l. boyes, and p. a. williams, j. bacteriol. 180:2522-2530, 1998), which except ...200111133965
active-site characterization of candida boidinii formate dehydrogenase.nad+-dependent formate dehydrogenase (fdh) from candida boidinii was cloned and expressed to a high level in escherichia coli (20% of soluble e. coli protein). molecular modelling studies were used to create a three-dimensional model of c. boidinii fdh, based on a known structure of the pseudomonas sp. 101 enzyme. this model was used for investigating the catalytic mechanism by site-directed mutagenesis. eleven forms of c. boidinii fdh were characterized by steady-state kinetic analysis: the wil ...200111171126
analysis of bacterial community structure in sulfurous-oil-containing soils and detection of species carrying dibenzothiophene desulfurization (dsz) genes.the selective effects of sulfur-containing hydrocarbons, with respect to changes in bacterial community structure and selection of desulfurizing organisms and genes, were studied in soil. samples taken from a polluted field soil (a) along a concentration gradient of sulfurous oil and from soil microcosms treated with dibenzothiophene (dbt)-containing petroleum (fsl soil) were analyzed. analyses included plate counts of total bacteria and of dbt utilizers, molecular community profiling via soil d ...200111229891
melamine deaminase and atrazine chlorohydrolase: 98 percent identical but functionally different.the gene encoding melamine deaminase (tria) from pseudomonas sp. strain nrrl b-12227 was identified, cloned into escherichia coli, sequenced, and expressed for in vitro study of enzyme activity. melamine deaminase displaced two of the three amino groups from melamine, producing ammeline and ammelide as sequential products. the first deamination reaction occurred more than 10 times faster than the second. ammelide did not inhibit the first or second deamination reaction, suggesting that the lower ...200111274097
map of the incp1beta plasmid ptsa encoding the widespread genes (tsa) for p-toluenesulfonate degradation in comamonas testosteroni t-2.the catabolic incp1beta plasmid ptsa from comamonas testosteroni t-2 was mapped by subtractive analysis of restriction digests, by sequencing outwards from the tsa operon (toluenesulfonate degradation), and by generating overlapping, long-distance-pcr amplification products. the plasmid was estimated to comprise 72 +/- 4 kb. the tsa region was found to be a composite transposon flanked by two is1071 elements. a cryptic tsa operon was also present in the tsa transposon. those backbone genes and r ...200111282598
genetic characterization and evolutionary implications of a car gene cluster in the carbazole degrader pseudomonas sp. strain ca10.the nucleotide sequences of the 27,939-bp-long upstream and 9,448-bp-long downstream regions of the caraaaababbcac(orf7)ad genes of carbazole-degrading pseudomonas sp. strain ca10 were determined. thirty-two open reading frames (orfs) were identified, and the car gene cluster was consequently revealed to consist of 10 genes (caraaaababbcacaddfe) encoding the enzymes for the three-step conversion of carbazole to anthranilate and the degradation of 2-hydroxypenta-2,4-dienoate. the high identities ...200111371531
trans-3-chloroacrylic acid dehalogenase from pseudomonas pavonaceae 170 shares structural and mechanistic similarities with 4-oxalocrotonate tautomerase.the genes (caad1 and caad2) encoding the trans-3-chloroacrylic acid dehalogenase (caad) of the 1,3-dichloropropene-utilizing bacterium pseudomonas pavonaceae 170 were cloned and heterologously expressed in escherichia coli and pseudomonas sp. strain gj1. caad is a protein of 50 kda that is composed of alpha-subunits of 75 amino acid residues and beta-subunits of 70 residues. it catalyzes the hydrolytic cleavage of the beta-vinylic carbon-chlorine bond in trans-3-chloroacrylic acid with a turnove ...200111418568
dual-bioaugmentation strategy to enhance remediation of cocontaminated soil.although metals are thought to inhibit the ability of microorganisms to degrade organic pollutants, several microbial mechanisms of resistance to metal are known to exist. this study examined the potential of cadmium-resistant microorganisms to reduce soluble cadmium levels to enhance degradation of 2,4-dichlorophenoxyacetic acid (2,4-d) under conditions of cocontamination. four cadmium-resistant soil microorganisms were examined in this study. resistant up to a cadmium concentration of 275 micr ...200111425743
organization and regulation of meta cleavage pathway genes for toluene and o-xylene derivative degradation in pseudomonas stutzeri ox1.pseudomonas stutzeri ox1 meta pathway genes for toluene and o-xylene catabolism were analyzed, and loci encoding phenol hydroxylase, catechol 2,3-dioxygenase, 2-hydroxymuconate semialdehyde dehydrogenase, and 2-hydroxymuconate semialdehyde hydrolase were mapped. phenol hydroxylase converted a broad range of substrates, as it was also able to transform the nongrowth substrates 2,4-dimethylphenol and 2,5-dimethylphenol into 3,5-dimethylcatechol and 3,6-dimethylcatechol, respectively, which, howeve ...200111425758
biotransformation of various substituted aromatic compounds to chiral dihydrodihydroxy derivatives.the biotransformation of four different classes of aromatic compounds by the escherichia coli strain dh5alpha(ptcb 144), which contained the chlorobenzene dioxygenase (cdo) from pseudomonas sp. strain p51, was examined. cdo oxidized biphenyl as well as monochlorobiphenyls to the corresponding cis-2,3-dihydro-2,3-dihydroxy derivatives, whereby oxidation occurred on the unsubstituted ring. no higher substituted biphenyls were oxidized. the absolute configurations of several monosubstituted cis-ben ...200111472901
multiphasic kinetics of transformation of 1,2,4-trichlorobenzene at nano- and micromolar concentrations by burkholderia sp. strain ps14.the transformation of 1,2,4-trichlorobenzene (1,2,4-tcb) at initial concentrations in nano- and micromolar ranges was studied in batch experiments with burkholderia sp. strain ps14. 1,2,4-tcb was metabolized from nano- and micromolar concentrations to below its detection limit of 0.5 nm. at low initial 1,2,4-tcb concentrations, a first-order relationship between specific transformation rate and substrate concentration was observed with a specific affinity (a(0)(a)) of 0.32 liter. mg (dry weight) ...200111472925
methane oxidation and the competition for oxygen in the rice rhizosphere.a mechanistic approach is presented to describe oxidation of the greenhouse gas methane in the rice rhizosphere of flooded paddies by obligate methanotrophic bacteria. in flooded rice paddies these methanotrophs compete for available o(2) with other types of bacteria. soil incubation studies and most-probable-number (mpn) counts of oxygen consumers show that microbial oxygen consumption rates were dominated by heterotrophic and methanotrophic respiration. mpn counts of methanotrophs showed large ...200111472935
degradation of chlorinated dibenzofurans and dibenzo-p-dioxins by two types of bacteria having angular dioxygenases with different features.two kinds of bacteria having different-structured angular dioxygenases-a dibenzofuran (df)-utilizing bacterium, terrabacter sp. strain dbf63, and a carbazole (car)-utilizing bacterium, pseudomonas sp. strain ca10-were investigated for their ability to degrade some chlorinated dibenzofurans (cdfs) and chlorinated dibenzo-p-dioxins (cdds) (or, together, cdf/ds) using either wild-type strains or recombinant escherichia coli strains. first, it was shown that car 1,9a-dioxygenase (cardo) catalyzed an ...200111472938
genetic and structural organization of the aminophenol catabolic operon and its implication for evolutionary process.the aminophenol (ap) catabolic operon in pseudomonas putida hs12 mineralizing nitrobenzene was found to contain all the enzymes responsible for the conversion of ap to pyruvate and acetyl coenzyme a via extradiol meta cleavage of 2-aminophenol. the sequence and functional analyses of the corresponding genes of the operon revealed that the ap catabolic operon consists of one regulatory gene, nbzr, and the following nine structural genes, nbzjcacbdgfeih, which encode catabolic enzymes. the nbzr pr ...200111489860
low-temperature lipase from psychrotrophic pseudomonas sp. strain kb700a.we have previously reported that a psychrotrophic bacterium, pseudomonas sp. strain kb700a, which displays sigmoidal growth even at -5 degrees c, produced a lipase. a genomic dna library of strain kb700a was introduced into escherichia coli tg1, and screening on tributyrin-containing agar plates led to the isolation of the lipase gene. sequence analysis revealed an open reading frame (kb-lip) consisting of 1,422 nucleotides that encoded a protein (kb-lip) of 474 amino acids with a molecular mass ...200111526006
biological degradation of 2,4,6-trinitrotoluene.nitroaromatic compounds are xenobiotics that have found multiple applications in the synthesis of foams, pharmaceuticals, pesticides, and explosives. these compounds are toxic and recalcitrant and are degraded relatively slowly in the environment by microorganisms. 2,4,6-trinitrotoluene (tnt) is the most widely used nitroaromatic compound. certain strains of pseudomonas and fungi can use tnt as a nitrogen source through the removal of nitrogen as nitrite from tnt under aerobic conditions and the ...200111527999
complete nucleotide sequence and organization of the atrazine catabolic plasmid padp-1 from pseudomonas sp. strain adp.the complete 108,845-nucleotide sequence of catabolic plasmid padp-1 from pseudomonas sp. strain adp was determined. plasmid padp-1 was previously shown to encode atza, atzb, and atzc, which catalyze the sequential hydrolytic removal of s-triazine ring substituents from the herbicide atrazine to yield cyanuric acid. computational analyses indicated that padp-1 encodes 104 putative open reading frames (orfs), which are predicted to function in catabolism, transposition, and plasmid maintenance, t ...200111544232
lipase and its modulator from pseudomonas sp. strain kfcc 10818: proline-to-glutamine substitution at position 112 induces formation of enzymatically active lipase in the absence of the modulator.a lipase gene, lipk, and a lipase modulator gene, limk, of pseudomonas sp. strain kfcc 10818 have been cloned, sequenced, and expressed in escherichia coli. the limk gene is located immediately downstream of the lipk gene. enzymatically active lipase was produced only in the presence of the limk gene. the effect of the lipase modulator limk on the expression of active lipase was similar to those of the pseudomonas subfamily i.1 and i.2 lipase-specific foldases (lifs). the deduced amino acid sequ ...200111566993
changes in populations of rhizosphere bacteria associated with take-all disease of wheat.take-all, caused by gaeumannomyces graminis var. tritici, is one of the most important fungal diseases of wheat worldwide. knowing that microbe-based suppression of the disease occurs in monoculture wheat fields following severe outbreaks of take-all, we analyzed the changes in rhizosphere bacterial communities following infection by the take-all pathogen. several bacterial populations were more abundant on diseased plants than on healthy plants, as indicated by higher counts on a pseudomonas-se ...200111571137
growth of pseudomonas mendocina on fe(iii) (hydr)oxides.although iron (fe) is an essential element for almost all living organisms, little is known regarding its acquisition from the insoluble fe(iii) (hydr)oxides in aerobic environments. in this study a strict aerobe, pseudomonas mendocina, was grown in batch culture with hematite, goethite, or ferrihydrite as a source of fe. p. mendocina obtained fe from these minerals in the following order: goethite > hematite > ferrihydrite. furthermore, fe release from each of the minerals appears to have occur ...200111571141
physical and metabolic interactions of pseudomonas sp. strain ja5-b45 and rhodococcus sp. strain f9-d79 during growth on crude oil and effect of a chemical surfactant on them.methods to enhance crude oil biodegradation by mixed bacterial cultures, for example, (bio)surfactant addition, are complicated by the diversity of microbial populations within a given culture. the physical and metabolic interactions between rhodococcus sp. strain f9-d79 and pseudomonas sp. strain ja5-b45 were examined during growth on bow river crude oil. the effects of a nonionic chemical surfactant, igepal co-630 (nonylphenol ethoxylate), also were evaluated. strain f9-d79 grew attached to th ...200111571196
identification of disulfides from the biodegradation of dibenzothiophene.several investigations have identified benzothiophene-2,3-dione in the organic solvent extracts of acidified cultures degrading dibenzothiophene via the kodama pathway. in solution at neutral ph, the 2,3-dione exists as 2-mercaptophenylglyoxylate, which cyclizes upon acidification and is extracted as the 2,3-dione. the fate of these compounds in microbial cultures has never been determined. this study investigated the abiotic reactions of 2-mercaptophenylglyoxylate incubated aerobically in miner ...200111679330
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 ...200211741862
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 ...200211741863
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 ...200211751833
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 ...200211772605
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 ...200211772618
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 ...200211823194
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 ...200211823201
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 ...200211914133
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-114.200211914155
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 ...200211937637
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 ...200211976087
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 ...200211976110
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 ...200211976143
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 ...200212033730
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 ...200212119046
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 ...200212144528
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.200212182763
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 ...200212200307
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 ...200212218024
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 ...200212399500
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 ...200212406764
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 ...200212426346
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 ...200312513989
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 ...200312524518
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 ...200312533465
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. ...200312620840
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 ...200312620844
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 ...200312732549
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 ...200312769821
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 ...200312788710
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- ...200312788728
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 ...200312788762
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.200312788776
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 ...200312867462
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 ...200312902277
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 ...200312902278
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 ...200312957905
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 ...200314602601
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