Publications

dechlorination of atrazine by a rhizobium sp. isolate.	a rhizobium sp. strain, named patr, was isolated from an agricultural soil and found to actively degrade the herbicide atrazine. incubation of patr in a basal liquid medium containing 30 mg of atrazine liter(sup-1) resulted in the rapid consumption of the herbicide and the accumulation of hydroxyatrazine as the only metabolite detected after 8 days of culture. experiments performed with ring-labeled [(sup14)c]atrazine indicated no mineralization. the enzyme responsible for the hydroxylation of a ...	1997	16535552
isolation and characterization of a chlorinated-pyridinol-degrading bacterium.	the isolation of a pure culture of bacteria able to use 3,5,6-trichloro-2-pyridinol (tcp) as a sole source of carbon and energy under aerobic conditions was achieved for the first time. the bacterium was identified as a pseudomonas sp. and designated atcc 700113. [2,6-(sup14)c]tcp degradation yielded (sup14)co(inf2), chloride, and unidentified polar metabolites.	1997	16535719
molecular basis of a bacterial consortium: interspecies catabolism of atrazine.	pseudomonas sp. strain adp contains the genes, atza, -b, and -c, that encode three enzymes which metabolize atrazine to cyanuric acid. atrazine-catabolizing pure cultures isolated from around the world contain genes homologous to atza, -b, and -c. the present study was conducted to determine whether the same genes are present in an atrazine-catabolizing bacterial consortium and how the genes and metabolism are subdivided among member species. the consortium contained four or more bacterial speci ...	1998	16349478
initial reductive reactions in aerobic microbial metabolism of 2,4,6-trinitrotoluene.	because of its high electron deficiency, initial microbial transformations of 2,4,6-trinitrotoluene (tnt) are characterized by reductive rather than oxidation reactions. the reduction of the nitro groups seems to be the dominating mechanism, whereas hydrogenation of the aromatic ring, as described for picric acid, appears to be of minor importance. thus, two bacterial strains enriched with tnt as a sole source of nitrogen under aerobic conditions, a gram-negative strain called tnt-8 and a gram-p ...	1998	16349484
identification of hydrocarbon-degrading bacteria in soil by reverse sample genome probing.	bacteria with limited genomic cross-hybridization were isolated from soil contaminated with c5+, a mixture of hydrocarbons, and identified by partial 16s rrna sequencing. filters containing denatured genomic dnas were used in a reverse sample genome probe (rsgp) procedure for analysis of the effect of an easily degradable compound (toluene) and a highly recalcitrant compound (dicyclopentadiene [dcpd]) on community composition. hybridization with labeled total-community dna isolated from soil exp ...	1998	16349504
light-mediated nitrite accumulation during denitrification by pseudomonas sp. strain jr12.	the effect of light on the denitrifying characteristics of a nonphotosynthetic denitrifier, pseudomonas sp. strain jr12, was examined. already at low light intensities, nitrite accumulated as a result of light inhibition of nitrite but not of nitrate reduction rates. exposure of this bacterium to light caused a photooxidation of cytochrome c, an intermediate electron carrier in its respiratory pathway. photoinhibition of nitrite reduction was reversible, as nitrite reduction rates returned to pr ...	1998	16349525
atzc is a new member of the amidohydrolase protein superfamily and is homologous to other atrazine-metabolizing enzymes.	pseudomonas sp. strain adp metabolizes atrazine to cyanuric acid via three plasmid-encoded enzymes, atza, atzb, and atzc. the first enzyme, atza, catalyzes the hydrolytic dechlorination of atrazine, yielding hydroxyatrazine. the second enzyme, atzb, catalyzes hydroxyatrazine deamidation, yielding n-isopropylammelide. in this study, the third gene in the atrazine catabolic pathway, atzc, was cloned from a pseudomonas sp. strain adp cosmid library as a 25-kb ecori dna fragment in escherichia coli. ...	1998	9422605
detoxification of protoanemonin by dienelactone hydrolase.	protoanemonin is a toxic metabolite which may be formed during the degradation of some chloroaromatic compounds, such as polychlorinated biphenyls, by natural microbial consortia. we show here that protoanemonin can be transformed by dienelactone hydrolase of pseudomonas sp. strain b13 to cis-acetylacrylate. although similar km values were observed for cis-dienelactone and protoanemonin, the turnover rate of protoanemonin was only 1% that of cis-dienelactone. this indicates that at least this pe ...	1998	9440530
a cold-adapted lipase of an alaskan psychrotroph, pseudomonas sp. strain b11-1: gene cloning and enzyme purification and characterization.	a psychrotrophic bacterium producing a cold-adapted lipase upon growth at low temperatures was isolated from alaskan soil and identified as a pseudomonas strain. the lipase gene (lipp) was cloned from the strain and sequenced. the amino acid sequence deduced from the nucleotide sequence of the gene (924 bp) corresponded to a protein of 308 amino acid residues with a molecular weight of 33,714. lipp also has consensus motifs conserved in other cold-adapted lipases, i.e., lipase 2 from antarctic m ...	1998	9464382
biochemical and genetic characterization of trans-2'-carboxybenzalpyruvate hydratase-aldolase from a phenanthrene-degrading nocardioides strain.	trans-2'-carboxybenzalpyruvate hydratase-aldolase was purified from a phenanthrene-degrading bacterium, nocardioides sp. strain kp7, and characterized. the purified enzyme was found to have molecular masses of 38 kda by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and 113 kda by gel filtration chromatography. thus, the homotrimer of the 38-kda subunit constituted an active enzyme. the km and kcat values of this enzyme for trans-2'-carboxybenzalpyruvate were 50 microm and 13 s(-1), r ...	1998	9473051
genetic and functional analysis of the styrene catabolic cluster of pseudomonas sp. strain y2.	the chromosomal region of pseudomonas sp. strain y2 involved in the conversion of styrene to phenylacetate (upper catabolic pathway) has been cloned and sequenced. four catabolic genes, styabcd, and two regulatory genes, stysr, were identified. this gene cluster when transferred to escherichia coli w confers to this phenylacetate-degrading host the ability to grow on styrene as the sole carbon and energy source. genes styabcd are homologous to those encoding the styrene upper catabolic pathway i ...	1998	9495743
enzyme specificity of 2-nitrotoluene 2,3-dioxygenase from pseudomonas sp. strain js42 is determined by the c-terminal region of the alpha subunit of the oxygenase component.	biotransformations with recombinant escherichia coli expressing the genes encoding 2-nitrotoluene 2,3-dioxygenase (2ntdo) from pseudomonas sp. strain js42 demonstrated that 2ntdo catalyzes the dihydroxylation and/or monohydroxylation of a wide range of aromatic compounds. extremely high nucleotide and deduced amino acid sequence identity exists between the components from 2ntdo and the corresponding components from 2,4-dinitrotoluene dioxygenase (2,4-dntdo) from burkholderia sp. strain dnt (form ...	1998	9495758
anti-mitochondrial antibodies in patients with dilated cardiomyopathy (anti-m7) are directed against flavoenzymes with covalently bound fad.	anti-mitochondrial antibodies (anti-m7) in sera from patients with dilated cardiomyopathy and myocarditis recognize, besides mitochondrial antigens, bacterial sarcosine dehydrogenase. the common target antigen was identified as the covalently bound fad of mitochondrial and bacterial flavoenzymes. thus, anti-m7-positive serum reacted on western blots exclusively with covalently flavinylated enzymes. the antigenic specificity of anti-m7 sera was reproduced by an antiserum raised in rabbits with 6- ...	1998	9528896
ntn genes determining the early steps in the divergent catabolism of 4-nitrotoluene and toluene in pseudomonas sp. strain tw3.	pseudomonas sp. strain tw3 is able to oxidatively metabolize 4-nitrotoluene and toluene via a route analogous to the upper pathway of the tol plasmids. we report the sequence and organization of five genes, ntnwcmab*, which are very similar to and in the same order as the xyl operon of tol plasmid pww0 and present evidence that they encode enzymes which are expressed during growth on both 4-nitrotoluene and toluene and are responsible for their oxidation to 4-nitrobenzoate and benzoate, respecti ...	1998	9555884
a gene cluster encoding steps in conversion of naphthalene to gentisate in pseudomonas sp. strain u2.	pseudomonas sp. strain u2 was isolated from oil-contaminated soil in venezuela by selective enrichment on naphthalene as the sole carbon source. the genes for naphthalene dioxygenase were cloned from the plasmid dna of strain u2 on an 8.3-kb bamhi fragment. the genes for the naphthalene dioxygenase genes nagaa (for ferredoxin reductase), nagab (for ferredoxin), and nagac and nagad (for the large and small subunits of dioxygenase, respectively) were located by southern hybridizations and by nucle ...	1998	9573207
towards a biocatalyst for (s)-styrene oxide production: characterization of the styrene degradation pathway of pseudomonas sp. strain vlb120.	in order to design a biocatalyst for the production of optically pure styrene oxide, an important building block in organic synthesis, the metabolic pathway and molecular biology of styrene degradation in pseudomonas sp. strain vlb120 was investigated. a 5.7-kb xhoi fragment, which contained on the same strand of dna six genes involved in styrene degradation, was isolated from a gene library of this organism in escherichia coli by screening for indigo formation. t7 rna polymerase expression expe ...	1998	9603811
low-frequency horizontal transfer of an element containing the chlorocatechol degradation genes from pseudomonas sp. strain b13 to pseudomonas putida f1 and to indigenous bacteria in laboratory-scale activated-sludge microcosms.	the possibilities for low-frequency horizontal transfer of the self-transmissible chlorocatechol degradative genes (clc) from pseudomonas sp. strain b13 were investigated in activated-sludge microcosms. when the clc genes were transferred into an appropriate recipient bacterium such as pseudomonas putida f1, a new metabolic pathway for chlorobenzene degradation was formed by complementation which could be selected for by the addition of mono- or 1, 4-dichlorobenzene (cb). under optimized conditi ...	1998	9603824
the atzabc genes encoding atrazine catabolism are located on a self-transmissible plasmid in pseudomonas sp. strain adp.	pseudomonas sp. strain adp initiates atrazine catabolism via three enzymatic steps, encoded by atza, -b, and -c, which yield cyanuric acid, a nitrogen source for many bacteria. in-well lysis, southern hybridization, and plasmid transfer studies indicated that the atza, -b, and -c genes are localized on a 96-kb self-transmissible plasmid, padp-1, in pseudomonas sp. strain adp. high-performance liquid chromatography analyses showed that cyanuric acid degradation was not encoded by padp-1. padp-1 w ...	1998	9603862
utility of gram's stain and efficacy of quantitative cultures for posttraumatic pneumonia: a prospective study.	this prospective trial examined the efficacy of using bronchoalveolar lavage (bal) for the diagnosis of pneumonia (pn) and the utility of gram's stain (gs) for dictating empiric therapy.	1998	9605666
construction and use of an ipb dna module to generate pseudomonas strains with constitutive trichloroethene and isopropylbenzene oxidation activity.	pseudomonas sp. strain jr1 exhibits trichloroethene (tce) oxidation activity with isopropylbenzene (ipb) as the inducer substrate. we previously reported the genes encoding the first three enzymes of the ipb-degradative pathway (ipba1, ipba2, ipba3, ipba4, ipbb, and ipbc) and identified the initial ipb dioxygenase (ipba1 a2a3a4) as responsible for tce cooxidation (u. pflugmacher, b. averhoff, and g. gottschalk, appl. environ. microbiol. 62:3967-3977, 1996). primer extension analyses revealed mul ...	1998	9647815
cloning of a sphingomonas paucimobilis syk-6 gene encoding a novel oxygenase that cleaves lignin-related biphenyl and characterization of the enzyme.	sphingomonas paucimobilis syk-6 transforms 2,2'-dihydroxy-3,3'-dimethoxy-5,5'-dicarboxybiphenyl (ddva), a lignin-related biphenyl compound, to 5-carboxyvanillic acid via 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl (oh-ddva) as an intermediate (15). the ring fission of oh-ddva is an essential step in the ddva degradative pathway. a 15-kb ecori fragment isolated from the cosmid library complemented the growth deficiency of a mutant on oh-ddva. subcloning and deletion analysis showed that a ...	1998	9647824
chromosomal integration, tandem amplification, and deamplification in pseudomonas putida f1 of a 105-kilobase genetic element containing the chlorocatechol degradative genes from pseudomonas sp. strain b13.	analysis of chlorobenzene-degrading transconjugants of pseudomonas putida f1 which had acquired the genes for chlorocatechol degradation (clc) from pseudomonas sp. strain b13 revealed that the clc gene cluster was present on a 105-kb amplifiable genetic element (named the clc element). in one such transconjugant, p. putida rr22, a total of seven or eight chromosomal copies of the entire genetic element were present when the strain was cultivated on chlorobenzene. chromosomal integrations of the ...	1998	9721270
purification and characterization of the coniferyl aldehyde dehydrogenase from pseudomonas sp. strain hr199 and molecular characterization of the gene.	the coniferyl aldehyde dehydrogenase (caldh) of pseudomonas sp. strain hr199 (dsm7063), which catalyzes the nad+-dependent oxidation of coniferyl aldehyde to ferulic acid and which is induced during growth with eugenol as the carbon source, was purified and characterized. the native protein exhibited an apparent molecular mass of 86,000 +/- 5,000 da, and the subunit mass was 49.5 +/- 2.5 kda, indicating an alpha2 structure of the native enzyme. the optimal oxidation of coniferyl aldehyde to feru ...	1998	9721273
pseudomonas sp. strain 273, an aerobic alpha, omega-dichloroalkanedegrading bacterium.	a gram-negative, aerobic bacterium was isolated from soil; this bacterium grew in 50% (vol/vol) suspensions of 1,10-dichlorodecane (1,10-dcd) as the sole source of carbon and energy. phenotypic and small-subunit ribosomal rna characterizations identified the organism, designated strain 273, as a member of the genus pseudomonas. after induction with 1,10-dcd, pseudomonas sp. strain 273 released stoichiometric amounts of chloride from c5 to c12 alpha, omega-dichloroalkanes in the presence of oxyge ...	1998	9726906
identification and characterization of is1411, a new insertion sequence which causes transcriptional activation of the phenol degradation genes in pseudomonas putida.	a new insertion sequence (is element), is1411, was identified downstream of the phenol degradation genes pheba that originated from plasmid dna of pseudomonas sp. strain est1001. according to sequence analysis, is1411 belongs to a new family of is elements that has recently been named the isl3 family (j. mahillon and m. chandler, microbiol. mol. biol. rev. 62:725-774, 1998). is1411 generates 8-bp duplication of the target dna and carries 24-bp inverted repeats (irs), highly homologous to the irs ...	1998	9765560
int-b13, an unusual site-specific recombinase of the bacteriophage p4 integrase family, is responsible for chromosomal insertion of the 105-kilobase clc element of pseudomonas sp. strain b13.	pseudomonas sp. strain b13 carries the clcrabde genes encoding chlorocatechol-degradative enzymes on the self-transmissible 105-kb clc element. the element integrates site and orientation specifically into the chromosomes of various bacterial recipients, with a glycine trna structural gene (glyv) as the integration site. we report here the localization and nucleotide sequence of the integrase gene and the activity of the integrase gene product in mediating site-specific integration. the integras ...	1998	9791097
molecular cloning, expression and site-directed mutagenesis of glutathione s-transferase from ochrobactrum anthropi.	the gene coding for a novel glutathione s-transferase (gst) has been isolated from the bacterium ochrobactrum anthropi. a pcr fragment of 230 bp was obtained using oligonucleotide primers deduced from n-terminal and 'internal' sequences of the purified enzyme. the gene was obtained by screening of a genomic dna partial library from o. anthropi constructed in pbluescript with a pcr fragment probe. the gene encodes a protein (oagst) of 201 amino acids with a calculated molecular mass of 21738 da. ...	1998	9794797
identification of a marine agarolytic pseudoalteromonas isolate and characterization of its extracellular agarase	the phenotypic and agarolytic features of an unidentified marine bacteria that was isolated from the southern pacific coast was investigated. the strain was gram negative, obligately aerobic, and polarly flagellated. on the basis of several phenotypic characters and a phylogenetic analysis of the genes coding for the 16s rrna, this strain was identified as pseudoalteromonas antarctica strain n-1. in solid agar, this isolate produced a diffusible agarase that caused agar softening around the colo ...	1998	9797294
involvement of the terminal oxygenase beta subunit in the biphenyl dioxygenase reactivity pattern toward chlorobiphenyls.	biphenyl dioxygenase (bph dox) oxidizes biphenyl on adjacent carbons to generate 2,3-dihydro-2,3-dihydroxybiphenyl in comamonas testosteroni b-356 and in pseudomonas sp. strain lb400. the enzyme comprises a two-subunit (alpha and beta) iron sulfur protein (ispbph), a ferredoxin (ferbph), and a ferredoxin reductase (redbph). b-356 bph dox preferentially catalyzes the oxidation of the double-meta-substituted congener 3,3'-dichlorobiphenyl over the double-para-substituted congener 4,4'-dichlorobiph ...	1998	9811638
shewanella putrefaciens mtrb encodes an outer membrane protein required for fe(iii) and mn(iv) reduction.	iron and manganese oxides or oxyhydroxides are abundant transition metals, and in aquatic environments they serve as terminal electron acceptors for a large number of bacterial species. the molecular mechanisms of anaerobic metal reduction, however, are not understood. shewanella putrefaciens is a facultative anaerobe that uses fe(iii) and mn(iv) as terminal electron acceptors during anaerobic respiration. transposon mutagenesis was used to generate mutants of s. putrefaciens, and one such mutan ...	1998	9829939
cloning and molecular analysis of the poly(3-hydroxybutyrate) and poly(3-hydroxybutyrate-co-3-hydroxyalkanoate) biosynthesis genes in pseudomonas sp. strain 61-3.	two types of polyhydroxyalkanoate (pha) biosynthesis gene loci (phb and pha) of pseudomonas sp. strain 61-3, which produces a blend of poly(3-hydroxybutyrate) [p(3hb)] homopolymer and a random copolymer (poly(3-hydroxybutyrate-co-3-hydroxyalkanoate) [p(3hb-co-3ha]) consisting of 3ha units of 4 to 12 carbon atoms, were cloned and analyzed at the molecular level. in the phb locus, three open reading frames encoding polyhydroxybutyrate (phb) synthase (phbcps), beta-ketothiolase (phbaps), and nadph- ...	1998	9851987
the method of contact angle measurements and estimation of work of adhesion in bioleaching of metals.	in this paper, we present our method for the measurement of contact angles on the surface of minerals during the bioleaching process because the standard deviation obtained in our measurements achieved unexpectedly low error. construction of a goniometer connected with a specially prepared computer program allowed us to repeat measurements several times over a short time course, yielding excellent results.after defining points on the outline of the image of a drop and its baseline as well of the ...	1998	12734596
the method of contact angle measurements and estimation of work of adhesion in bioleaching of metals.	in this paper, we present our method for the measurement of contact angles on the surface of minerals during the bioleaching process because the standard deviation obtained in our measurements achieved unexpectedly low error. construction of a goniometer connected with a specially prepared computer program allowed us to repeat measurements several times over a short time course, yielding excellent results.after defining points on the outline of the image of a drop and its baseline as well of the ...	1998	12734596
infectious pulmonary disease in patients receiving immunosuppressive therapy for organ transplantation.		1999	10398512
genetic and biochemical analyses of the tec operon suggest a route for evolution of chlorobenzene degradation genes.	the teca broad-spectrum chlorobenzene dioxygenase of burkholderia sp. strain ps12 catalyzes the first step in the mineralization of 1,2,4, 5-tetrachlorobenzene. the catabolic genes were localized on a small plasmid that belongs to the incpbeta incompatibility group. pcr analysis of the genetic environment of the tec genes indicated high similarity to the transposon-organized catabolic tcb chlorobenzene degradation genes of pseudomonas sp. strain p51. sequence analysis of the regions flanking the ...	1999	9864349
thermal gradient gel electrophoresis analysis of bioprotection from pollutant shocks in the activated sludge microbial community.	we used a culture-independent approach, namely, thermal gradient gel electrophoresis (tgge) analysis of ribosomal sequences amplified directly from community dna, to determine changes in the structure of the microbial community following phenol shocks in the highly complex activated sludge ecosystem. parallel experimental model sewage plants were given shock loads of chlorinated and methylated phenols and simultaneously were inoculated (i) with a genetically engineered microorganism (gem) able t ...	1999	9872766
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 ...	1999	9872786
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 ...	1999	9925607
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 ...	1999	10049847
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 ...	1999	10049904
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 ...	1999	10074076
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 ...	1999	10217771
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 ...	1999	10322011
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 ...	1999	10347028
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 ...	1999	10388678
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 ...	1999	10417325
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 ...	1999	10427019
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 ...	1999	10438748
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 ...	1999	10523559
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 ...	1999	10542171
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 ...	1999	10543794
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 ...	1999	10543797
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 ...	1999	10583971
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 ...	1999	10595564
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 ...	2000	10618218
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 ...	2000	10629173
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 ...	2000	10653719
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 ...	2000	10692370
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 ...	2000	10735862
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 ...	2000	10742248
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 ...	2000	10809692
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 ...	2000	10831417
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 ...	2000	10877788
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 ...	2000	10919761
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 ...	2000	10919767
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, ...	2000	10919778
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 ...	2000	10986254
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 ...	2000	11010866
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 ...	2000	11010902
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 ...	2000	11053394
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 ...	2000	11055909
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 ...	2000	11055938
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 ...	2000	11084622
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 ...	2000	11097890
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 ...	2000	11097896
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 ...	2001	11133441
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 ...	2001	11133965
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 ...	2001	11171126
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 ...	2001	11229891
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 ...	2001	11274097
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 ...	2001	11282598
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 ...	2001	11371531
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 ...	2001	11418568
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 ...	2001	11425743
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 ...	2001	11425758
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 ...	2001	11472901
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) ...	2001	11472925
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 ...	2001	11472935
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 ...	2001	11472938
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 ...	2001	11489860
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 ...	2001	11526006
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 ...	2001	11527999
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 ...	2001	11544232
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 ...	2001	11566993
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 ...	2001	11571137
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 ...	2001	11571141
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 ...	2001	11571196
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 ...	2001	11679330
phylogenetic relationships among group ii intron orfs.	group ii introns are widely believed to have been ancestors of spliceosomal introns, yet little is known about their own evolutionary history. in order to address the evolution of mobile group ii introns, we have compiled 71 open reading frames (orfs) related to group ii intron reverse transcriptases and subjected their derived amino acid sequences to phylogenetic analysis. the phylogenetic tree was rooted with reverse transcriptases (rts) of non-long terminal repeat retroelements, and the infer ...	2001	11222775
the metacyc database.	metacyc is a metabolic-pathway database that describes 445 pathways and 1115 enzymes occurring in 158 organisms. metacyc is a review-level database in that a given entry in metacyc often integrates information from multiple literature sources. the pathways in metacyc were determined experimentally, and are labeled with the species in which they are known to occur based on literature references examined to date. metacyc contains extensive commentary and literature citations. applications of metac ...	2002	11752254