Publications

bacterial transcriptional regulators for degradation pathways of aromatic compounds.	human activities have resulted in the release and introduction into the environment of a plethora of aromatic chemicals. the interest in discovering how bacteria are dealing with hazardous environmental pollutants has driven a large research community and has resulted in important biochemical, genetic, and physiological knowledge about the degradation capacities of microorganisms and their application in bioremediation, green chemistry, or production of pharmacy synthons. in addition, regulation ...	2004	15353566
assimilation of nitrogen from nitrite and trinitrotoluene in pseudomonas putida jlr11.	pseudomonas putida jlr11 releases nitrogen from the 2,4,6-trinitrotoluene (tnt) ring as nitrite or ammonium. these processes can occur simultaneously, as shown by the observation that a nasb mutant impaired in the reduction of nitrite to ammonium grew at a slower rate than the parental strain. nitrogen from tnt is assimilated via the glutamine syntethase-glutamate synthase (gs-gogat) pathway, as evidenced by the inability of gogat mutants to use tnt. this pathway is also used to assimilate ammon ...	2005	15601726
alkaline cyanide biodegradation by pseudomonas pseudoalcaligenes cect5344.	pseudomonas pseudoalcaligenes cect5344 uses cyanide, cyanate, beta-cyanoalanine, and other cyanoderivatives as nitrogen sources under alkaline conditions, which prevents volatile hcn (pk(a) 9.2) formation. the cyanide consumed by this strain is stoichiometrically converted into ammonium. in addition, this bacterium grows with the heavy metal, cyanide-containing waste water generated by the jewellery industry, and is also a cyanide-resistant strain which induces an alternative oxidase and a sider ...	2005	15667296
effect of temperature and additional carbon sources on phenol degradation by an indigenous soil pseudomonad.	a new indigenous soil bacterium pseudomonas sp. growing on phenol and on a mixture of phenol, toluene, o-cresol, naphthalene and 1,2,3-trimethylbenzene (1,2,3-tmb) was isolated and characterized. phylogenetic analysis suggested its classification to pseudomonadaceae family and showed 99.8% dna sequence identity to pseudomonas pseudoalcaligenes species. the isolate was psychrotroph, with growth temperatures ranging from ca. 0 to 40 degrees c. the gc-ms structural analysis of metabolic products of ...	2005	15865154
genetic variation in clones of pseudomonas pseudoalcaligenes after ten months of selection in different thermal environments in the laboratory.	the random amplification of polymorphic dna (rapd) method was used to examine genetic variation in experimental clones of pseudomonas pseudoalcaligenes in two experimental groups, as well as their common ancestor. six clones derived from a single colony of p. pseudoalcaligenes were cultured in two different thermal regimes for 10 months. three clones in the control group were cultured at constant temperature of 35 degrees c and another three clones in the high temperature (ht) group were propaga ...	2005	15886916
identification of bacteria isolated from an oligotrophic lake with pesticide removal capacities.	we studied the growth and capacities for pesticides removal of bacterial strains isolated from the laguna grande, an oligotrophic lake at the south of spain (archidona, málaga). strains were isolated from water samples amended with 10 and 50 microg/ml of nine pesticides: organochlorinated insecticides (aldrin and lindane), organophosphorous insecticides (dimetoate, methyl-parathion and methidation), s-triazine herbicides (simazine and atrazine), fungicide (captan) and diflubenzuron (1-(-4-chloro ...	2005	15943106
influence of inorganic nitrogen management regime on the diversity of nitrite-oxidizing bacteria in agricultural grassland soils.	to assess links between the diversity of nitrite-oxidizing bacteria (nob) in agricultural grassland soils and inorganic n fertilizer management, nob communities in fertilized and unfertilized soils were characterized by analysis of clone libraries and denaturing gradient gel electrophoresis (dgge) of 16s rrna gene fragments. previously uncharacterized nitrospira-like sequences were isolated from both long-term-fertilized and unfertilized soils, but dgge migration patterns indicated the presence ...	2005	16332819
hydrocarbon biodegradation in oxygen-limited sequential batch reactors by consortium from weathered, oil-contaminated soil.	we studied the use of sequential batch reactors under oxygen limitation to improve and maintain consortium ability to biodegrade hydrocarbons. air-agitated tubular reactors (2.5 l) were operated for 20 sequential 21-day cycles. maya crude oil-paraffin mixture (13,000 mg/l) was used as the sole carbon source. the reactors were inoculated with a consortium from the rhizosphere of cyperus laxus, a native plant that grows naturally in weathered, contaminated soil. oxygen limitation was induced in th ...	2005	15920621
microbial diversity in ultra-high-pressure rocks and fluids from the chinese continental scientific drilling project in china.	microbial communities in ultra-high-pressure (uhp) rocks and drilling fluids from the chinese continental scientific drilling project were characterized. the rocks had a porosity of 1 to 3.5% and a permeability of approximately 0.5 mdarcy. abundant fluid and gas inclusions were present in the minerals. the rocks contained significant amounts of fe2o3, feo, p2o5, and nitrate (3 to 16 ppm). acridine orange direct counting and phospholipid fatty acid analysis indicated that the total counts in the ...	2005	15933024
protein engineering of the archetypal nitroarene dioxygenase of ralstonia sp. strain u2 for activity on aminonitrotoluenes and dinitrotoluenes through alpha-subunit residues leucine 225, phenylalanine 350, and glycine 407.	naphthalene dioxygenase (ndo) from ralstonia sp. strain u2 has not been reported to oxidize nitroaromatic compounds. here, saturation mutagenesis of ndo at position f350 of the alpha-subunit (nagac) created variant f350t that produced 3-methyl-4-nitrocatechol from 2,6-dinitrotoluene (26dnt), that released nitrite from 23dnt sixfold faster than wild-type ndo, and that produced 3-amino-4-methyl-5-nitrocatechol and 2-amino-4,6-dinitrobenzyl alcohol from 2-amino-4,6-dinitrotoluene (2a46dnt) (wild-ty ...	2005	15866914
bacterial degradation of cyanide and its metal complexes under alkaline conditions.	a bacterial strain able to use cyanide as the sole nitrogen source under alkaline conditions has been isolated. the bacterium was classified as pseudomonas pseudoalcaligenes by comparison of its 16s rna gene sequence to those of existing strains and deposited in the coleccion espanola de cultivos tipo (spanish type culture collection) as strain cect5344. cyanide consumption is an assimilative process, since (i) bacterial growth was concomitant and proportional to cyanide degradation and (ii) the ...	2005	15691951
crystal structure of the terminal oxygenase component of cumene dioxygenase from pseudomonas fluorescens ip01.	the crystal structure of the terminal component of the cumene dioxygenase multicomponent enzyme system of pseudomonas fluorescens ip01 (cumdo) was determined at a resolution of 2.2 a by means of molecular replacement by using the crystal structure of the terminal oxygenase component of naphthalene dioxygenase from pseudomonas sp. strain ncib 9816-4 (nphdo). the ligation of the two catalytic centers of cumdo (i.e., the nonheme iron and rieske [2fe-2s] centers) and the bridging between them in nei ...	2005	15774891
first isolation of blavim-2 in an environmental isolate of pseudomonas pseudoalcaligenes.		2005	15855549
increased mesquite gum formation in nodal explants cultures after treatment with a microbial biomass preparation.	prosopis laevigata nodal explants cultures were established in murashige and skoog medium. simultaneously these cultures were subjected to stress with biotic elicitors and an environmental factor (temperature increase to promote heat stress) in order to promote and increase exuded mesquite gum production. the biotic elicitors were: aspergillus nidulans and pseudomonas pseudoalcaligenes both used in concentrations of 10, 20 and 30 mg, whereas the environmental condition was different incubation t ...	2005	16198591
diversity of alkaliphilic and alkalitolerant bacteria cultivated from decomposing reed rhizomes in a hungarian soda lake.	bacterial communities associated with decomposing rhizomes of phragmites australis were investigated in lake ferto (neusiedlersee, hungary). alkaliphilic and alkalitolerant strains were isolated on cellulose-containing alkaline medium spread with dilutions of scrapings taken from the surface of the decaying plant material. fifty-one strains were grouped by numerical analysis based on physiological tests and biolog sole carbon source utilization data. the strains identified by 16s rdna sequence c ...	2005	16132425
alcaligenes faecalis subsp. phenolicus subsp. nov. a phenol-degrading, denitrifying bacterium isolated from a graywater bioprocessor.	a gram (-) coccobacillary bacterium, j(t), was isolated from a graywater bioprocessor. 16s rrna and biochemical analysis has revealed strain j(t) closely resembles alcaligenes faecalis atcc 8750t and a. faecalis subsp. parafaecalis dsm 13975t, but is a distinct, previously uncharacterized isolate. strain j(t), along with the type strain of a. faecalis and its previously described subspecies share the ability to aerobically degrade phenol. the degradation rates of phenol for strain j(t) and refer ...	2005	16094869
resistance of marine bacterioneuston to solar radiation.	a total of 90 bacterial strains were isolated from the sea surface microlayer (i.e., bacterioneuston) and underlying waters (i.e., bacterioplankton) from two sites of the northwestern mediterranean sea. the strains were identified by sequence analysis, and growth recovery was investigated after exposure to simulated solar radiation. bacterioneuston and bacterioplankton isolates were subjected to six different exposure times, ranging from 0.5 to 7 h of simulated noontime solar radiation. followin ...	2005	16151115
epoxide formation on the aromatic b ring of flavanone by biphenyl dioxygenase of pseudomonas pseudoalcaligenes kf707.	prokaryotic dioxygenase is known to catalyze aromatic compounds into their corresponding cis-dihydrodiols without the formation of an epoxide intermediate. biphenyl dioxygenase from pseudomonas pseudoalcaligenes kf707 showed novel monooxygenase activity by converting 2(r)- and 2(s)-flavanone to their corresponding epoxides (2-(7-oxabicyclo[4.1.0]hepta-2,4-dien-2-yl)-2, 3-dihydro-4h-chromen-4-one), whereby the epoxide bond was formed between c2' and c3' on the b ring of the flavanone. the enzyme ...	2005	16151125
pleiotropic costs of niche expansion in the rna bacteriophage phi 6.	natural and experimental systems have failed to universally demonstrate a trade-off between generalism and specialism. when a trade-off does occur it is difficult to attribute its cause to antagonistic pleiotropy without dissecting the genetic basis of adaptation, and few previous experiments provide these genetic data. here we investigate the evolution of expanded host range (generalism) in the rna virus phi6, an experimental model system allowing adaptive mutations to be readily identified. we ...	2006	16299384
steady-state kinetic characterization of evolved biphenyl dioxygenase, which acquired novel degradation ability for benzene and toluene.	biphenyl dioxygenase (bph dox) catalyzes initial oxygenation in the bacterial biphenyl degradation pathway. bph dox in pseudomonas pseudoalcaligenes kf707 is a rieske type three-component enzyme in which a large subunit (encoded by the bpha1 gene) plays an important role in the substrate specificity of bph dox. steady-state kinetic assays using purified enzyme components demonstrated that kf707 bph dox had a kcat/km of 33.1 x 10(3) (m(-1) s(-1)) for biphenyl. evolved 1072 bph dox generated by th ...	2006	16636475
characterization of genes involved in the initial reactions of 4-chloronitrobenzene degradation in pseudomonas putida zwl73.	the genes encoding enzymes involved in the initial reactions during degradation of 4-chloronitrobenzene (4cnb) were characterized from the 4cnb utilizer pseudomonas putida zwl73, in which a partial reductive pathway was adopted. a dna fragment containing genes coding for chloronitrobenzene nitroreductase (cnba) and hydroxylaminobenzene mutase (cnbb) were pcr-amplified and subsequently sequenced. these two genes were actively expressed in escherichia coli, and recombinant e. coli cells catalyzed ...	2006	16642329
biodegradation of pyridine in a completely mixed activated sludge process.	a potential bacterial culture (p1), isolated from garden soil and identified as pseudomonas pseudoalcaligenes-kpn, was used as a starter seed to develop the biomass in a completely mixed activated sludge (cmas) reactor and the system was evaluated for treatment of wastewater containing pyridine. the results of this study indicate that pyridine could be degraded efficiently at a loading of 0.251 kg pyridine kg mlss(-1) d(-1) (0.156 kg toc kg mlss(-1) d(-1)) and at an optimal hydraulic retention t ...	2006	16084081
cross-regulation of biphenyl- and salicylate-catabolic genes by two regulatory systems in pseudomonas pseudoalcaligenes kf707.	pseudomonas pseudoalcaligenes kf707 grows on biphenyl and salicylate as sole sources of carbon. the biphenyl-catabolic (bph) genes are organized as bphr1a1a2(orf3)a3a4bcx0x1x2x3d, encoding the enzymes for conversion of biphenyl to acetyl coenzyme a. in this study, the salicylate-catabolic (sal) gene cluster encoding the enzymes for conversion of salicylate to acetyl coenzyme a were identified 6.6-kb downstream of the bph gene cluster along with a second regulatory gene, bphr2. both the bph and s ...	2006	16788178
application of a microfluidic reactor for screening cancer prodrug activation using silica-immobilized nitrobenzene nitroreductase.	the nitroreductase-catalyzed conversion of a strong electron-withdrawing nitro group to the corresponding electron-donating hydroxylamine is useful in a variety of biotechnological applications. activation of prodrugs for cancer treatments or antibiotic therapy are the most common applications. here, we show that a bacterial nitrobenzene nitroreductase (nbza) from pseudomonas pseudoalcaligenes js45 activates the dinitrobenzamide cancer prodrug cb1954 and the proantibiotic nitrofurazone. nbza was ...	2006	16961327
expression of organophosphorus hydrolase ophc2 in pichia pastoris: purification and characterization.	organophosphorus hydrolase is able to hydrolyze phosphoester bonds and reduce the toxicity of organophosphorus compounds. in this work, recombinant organophosphorus hydrolase ophc2 was successfully produced by pichia pastoris at a high expression level (approximately 5.5 g/l) using 3 l high-cell-density fermentation. the expression level is higher than those produced in other expression systems. the results of the sds-page and the western blot analyses showed a major 36 kda polypeptide band, whi ...	2006	16769224
high nitrogen removal from wastewater with several new aerobic bacteria isolated from diverse ecosystems.	three new bacteria hs-03, hs-043 and hs-047 isolated from different ecosystems were found capable of aerobic denitrification. the potential application of these strains in wastewater treatment under aerobic conditions was investigated. these three bacteria all presented high nitrogen removal from wastewater that more than 98% of 10 mmol/l nitrate could be removed in 12-24 h by adding cheap external carbon source and low concentration of iron as well as molybdate. the mechanism at molecular level ...	2006	17294651
active-site engineering of biphenyl dioxygenase: effect of substituted amino acids on substrate specificity and regiospecificity.	biphenyl dioxygenase (bph dox) catalyzes the initial dioxygenation step in the metabolism of biphenyl. the large subunit (bpha1) of bph dox plays a crucial role in the determination of the substrate specificity of biphenyl-related compounds including polychlorinated biphenyls (pcbs). previously, the substitution of asn at thr-376 near the active-site iron in the bpha1 of pseudomonas pseudoalcaligenes kf707 expanded the oxidation range and altered the regiospecificity of bph dox for pcbs. in this ...	2006	16217654
cyanide metabolism of pseudomonas pseudoalcaligenes cect5344: role of siderophores.	cyanide is one of the most potent and toxic chemicals produced by industry. the jewelry industry of córdoba (spain) generates a wastewater (residue) that contains free cyanide, as well as large amounts of cyano-metal complexes. cyanide is highly toxic to living systems because it forms very stable complexes with transition metals that are essential for protein function. in spite of its extreme toxicity, some organisms have acquired mechanisms to avoid cyanide poisoning. the biological assimilati ...	2006	16417508
identification of nif genes in n2-fixing bacterial strains isolated from rice fields along the yangtze river plain.	the aim of this research was to identify nifh and nifhdkye ' genes in twenty strains of n2-fixing heterotrophic bacteria isolated from rice fields in the yangtze river plain. southern hybridization of the total dna from each strain was performed with the klebsiella pneumoniae nifhdkye ' gene probe (6.2 kb eco ri fragment from psa30) and the azospirillum brasilense nifh gene probe (0.6 kb eco ri-hin diii fragment from phu8). we found that eco ri fragments of total dna from aeromonas hydrophila hy ...	2006	16463319
[transformation of embryogenic calli of siberian wildrye grass (elymus sibiricus l. cv. chuancao no.2) mediated by agrobacterium].	formation of embryogenic calli of siberian wildrye grass (elymus sibiricus l. cv. chuancao no.2) was induced from mature seeds as explants, and proliferated on ms medium containing 2,4-d 5.0 mg/l and kt 0.05 mg/l. an effective and stable callus regeneration system was established by optimizing the culture conditions (tables 1, 2 and fig.2). after the calli were subcultured 8 weeks, selected the whitish-yellow-coloured compact nodular calli that transformed with plasmid pcambia1304 carrying hygro ...	2006	16477130
novel partial reductive pathway for 4-chloronitrobenzene and nitrobenzene degradation in comamonas sp. strain cnb-1.	comamonas sp. strain cnb-1 grows on 4-chloronitrobenzene (4-cnb) and nitrobenzene as sole carbon and nitrogen sources. in this study, two genetic segments, cnbb-orf2-cnba and cnbr-orf1-cnbcacbdefghi, located on a newly isolated plasmid, pcnb1 (ca. 89 kb), and involved in 4-cnb/nitrobenzene degradation, were characterized. seven genes (cnba, cnbb, cnbca, cnbcb, cnbd, cnbg, and cnbh) were cloned and functionally expressed in recombinant escherichia coli, and they were identified as encoding 4-cnb ...	2006	16517619
16s rrna gene sequencing versus the api 20 ne system and the vitek 2 id-gnb card for identification of nonfermenting gram-negative bacteria in the clinical laboratory.	over a period of 26 months, we have evaluated in a prospective fashion the use of 16s rrna gene sequencing as a means of identifying clinically relevant isolates of nonfermenting gram-negative bacilli (non-pseudomonas aeruginosa) in the microbiology laboratory. the study was designed to compare phenotypic with molecular identification. results of molecular analyses were compared with two commercially available identification systems (api 20 ne, vitek 2 fluorescent card; biomérieux, marcy l'etoil ...	2006	16597863
the locus coding for the 3-nitrobenzoate dioxygenase of comamonas sp. strain js46 is flanked by is1071 elements and is subject to deletion and inversion events.	in comamonas sp. strain js46, 3-nitrobenzoate (3nba) is initially oxidized at the 3,4 position by a dioxygenase, which results in release of nitrite and production of protocatechuate. the locus coding for the 3nba dioxygenase (designated mnb, for m-nitrobenzoate) was mobilized from strain js46 using a plasmid capture method, cloned, and sequenced. the 3nba dioxygenase (mnba) is a member of the phthalate family of aromatic oxygenases. an open reading frame designated mnbb that codes for an nad(p) ...	2006	16597970
pseudomonad cyclopentadecanone monooxygenase displaying an uncommon spectrum of baeyer-villiger oxidations of cyclic ketones.	baeyer-villiger monooxygenases (bvmos) are biocatalysts that offer the prospect of high chemo-, regio-, and enantioselectivity in the organic synthesis of lactones or esters from a variety of ketones. in this study, we have cloned, sequenced, and overexpressed in escherichia coli a new bvmo, cyclopentadecanone monooxygenase (cpdb or cpdmo), originally derived from pseudomonas sp. strain hi-70. the 601-residue primary structure of cpdb revealed only 29% to 50% sequence identity to those of known ...	2006	16597975
assessment of toluene/biphenyl dioxygenase gene diversity in benzene-polluted soils: links between benzene biodegradation and genes similar to those encoding isopropylbenzene dioxygenases.	the pcr-single-strand conformation polymorphism (sscp) technique was used to assess the diversity and distribution of rieske nonheme iron oxygenases of the toluene/biphenyl subfamily in soil dna and bacterial isolates recovered from sites contaminated with benzene, toluene, ethylbenzene, and xylenes (btex). the central cores of genes encoding the catalytic alpha subunits were targeted, since they are responsible for the substrate specificities of these enzymes. sscp functional genotype fingerpri ...	2006	16672497
multiniche screening reveals the clinically relevant metallo-beta-lactamase vim-2 in pseudomonas aeruginosa far from the hospital setting: an ongoing dispersion process?	a screening study of the presence of metallo-beta-lactamases (imp and vim types and spm-1) in isolates from different nonhospital sources was conducted, and it revealed the presence of bla(vim-2), associated with the in58 class 1 integron, in two unrelated pseudomonas aeruginosa strains from aquatic habitats. the results suggest that the hospital setting was the possible origin of these bla(vim-2)-carrying strains.	2006	16672526
a glutathione s-transferase catalyzes the dehalogenation of inhibitory metabolites of polychlorinated biphenyls.	bphk is a glutathione s-transferase of unclear physiological function that occurs in some bacterial biphenyl catabolic (bph) pathways. we demonstrated that bphk of burkholderia xenovorans strain lb400 catalyzes the dehalogenation of 3-chloro 2-hydroxy-6-oxo-6-phenyl-2,4-dienoates (hopdas), compounds that are produced by the cometabolism of polychlorinated biphenyls (pcbs) by the bph pathway and that inhibit the pathway's hydrolase. a one-column protocol was developed to purify heterologously pro ...	2006	16740949
protein engineering of the 4-methyl-5-nitrocatechol monooxygenase from burkholderia sp. strain dnt for enhanced degradation of nitroaromatics.	4-methyl-5-nitrocatechol (4m5nc) monooxygenase (dntb) from burkholderia sp. strain dnt catalyzes the second step of 2,4-dinitrotoluene degradation by converting 4m5nc to 2-hydroxy-5-methylquinone with the concomitant removal of the nitro group. dntb is a flavoprotein that has a very narrow substrate range. here, error-prone pcr was used to create variant dntb m22l/l380i, which accepts the two new substrates 4-nitrophenol (4np) and 3-methyl-4-nitrophenol (3m4np). at 300 microm of 4np, the initial ...	2006	16751499
pseudomonas segetis sp. nov., isolated from soil.	a gram-negative, aerobic bacterium, designated strain fr1439t, was isolated from the soil of dokdo in the republic of korea. the cells of strain fr1439t were catalase- and oxidase-positive, motile and rod-shaped. phylogenetic analysis of the 16s rrna gene sequence revealed that it represents a distinct line of descent within the genus pseudomonas. the levels of dna-dna relatedness between strain fr1439t and type strains of phylogenetically related species, namely pseudomonas flavescens, pseudomo ...	2006	17082397
haloalkane dehalogenase linb is responsible for beta- and delta-hexachlorocyclohexane transformation in sphingobium indicum b90a.	incubation of resting cells of sphingobium indicum b90a, sphingobium japonicum ut26, and sphingobium francense sp+ showed that they were able to transform beta- and delta-hexachlorocyclohexane (beta- and delta-hch, respectively), the most recalcitrant hexachlorocyclohexane isomers, to pentachlorocyclohexanols, but only resting cells of strain b90a could further transform the pentachlorocyclohexanol intermediates to the corresponding tetrachlorocyclohexanediols. moreover, experiments with resting ...	2006	16957186
evaluation of pyrrolidonyl arylamidase for the identification of nonfermenting gram-negative rods.	to evaluate the activity of pyrrolidonyl arylamidase (pyr) for the differentiation and identification of nonfermenting gram negative rods (nfgnr), 293 isolates were tested. a 24 h culture of each test organism was prepared. from this a 108-109 cfu/ml suspension was added to 0.25 ml of sterile physiologic solution. a pyr disk was then added and the test was incubated for 30 minutes at 35-37 degrees c, at environmental atmosphere. reading was done by adding 1 drop of cinnamaldehyde reagent. strain ...	2007	16822636
multiple-level regulation of genes for protocatechuate degradation in acinetobacter baylyi includes cross-regulation.	the bacterium acinetobacter baylyi uses the branched beta-ketoadipate pathway to metabolize aromatic compounds. here, the multiple-level regulation of expression of the pca-qui operon encoding the enzymes for protocatechuate and quinate degradation was studied. it is shown that both activities of the iclr-type regulator protein pcau at the structural gene promoter pcaip, namely protocatechuate-dependent activation of pca-qui operon expression as well as repression in the absence of protocatechua ...	2007	17085716
multiple-level regulation of genes for protocatechuate degradation in acinetobacter baylyi includes cross-regulation.	the bacterium acinetobacter baylyi uses the branched beta-ketoadipate pathway to metabolize aromatic compounds. here, the multiple-level regulation of expression of the pca-qui operon encoding the enzymes for protocatechuate and quinate degradation was studied. it is shown that both activities of the iclr-type regulator protein pcau at the structural gene promoter pcaip, namely protocatechuate-dependent activation of pca-qui operon expression as well as repression in the absence of protocatechua ...	2007	17085716
the thiol:disulfide oxidoreductase dsbb mediates the oxidizing effects of the toxic metalloid tellurite (teo32-) on the plasma membrane redox system of the facultative phototroph rhodobacter capsulatus.	the highly toxic oxyanion tellurite (teo3(2-)) is a well known pro-oxidant in mammalian and bacterial cells. this work examines the effects of tellurite on the redox state of the electron transport chain of the facultative phototroph rhodobacter capsulatus, in relation to the role of the thiol:disulfide oxidoreductase dsbb. under steady-state respiration, the addition of tellurite (2.5 mm) to membrane fragments generated an extrareduction of the cytochrome pool (c- and b-type hemes); further, in ...	2007	17098900
the thiol:disulfide oxidoreductase dsbb mediates the oxidizing effects of the toxic metalloid tellurite (teo32-) on the plasma membrane redox system of the facultative phototroph rhodobacter capsulatus.	the highly toxic oxyanion tellurite (teo3(2-)) is a well known pro-oxidant in mammalian and bacterial cells. this work examines the effects of tellurite on the redox state of the electron transport chain of the facultative phototroph rhodobacter capsulatus, in relation to the role of the thiol:disulfide oxidoreductase dsbb. under steady-state respiration, the addition of tellurite (2.5 mm) to membrane fragments generated an extrareduction of the cytochrome pool (c- and b-type hemes); further, in ...	2007	17098900
family shuffling of soil dna to change the regiospecificity of burkholderia xenovorans lb400 biphenyl dioxygenase.	previous work has shown that the c-terminal portion of bpha, especially two amino acid segments designated region iii and region iv, influence the regiospecificity of the biphenyl dioxygenase (bpdo) toward 2,2'-dichlorobiphenyl (2,2'-cb). in this work, we evolved bpdo by shuffling bpha genes amplified from polychlorinated biphenyl-contaminated soil dna. sets of approximately 1-kb dna fragments were amplified with degenerate primers designed to amplify the c-terminal portion of bpha. these fragme ...	2007	17142386
family shuffling of soil dna to change the regiospecificity of burkholderia xenovorans lb400 biphenyl dioxygenase.	previous work has shown that the c-terminal portion of bpha, especially two amino acid segments designated region iii and region iv, influence the regiospecificity of the biphenyl dioxygenase (bpdo) toward 2,2'-dichlorobiphenyl (2,2'-cb). in this work, we evolved bpdo by shuffling bpha genes amplified from polychlorinated biphenyl-contaminated soil dna. sets of approximately 1-kb dna fragments were amplified with degenerate primers designed to amplify the c-terminal portion of bpha. these fragme ...	2007	17142386
a gene cluster involved in degradation of substituted salicylates via ortho cleavage in pseudomonas sp. strain mt1 encodes enzymes specifically adapted for transformation of 4-methylcatechol and 3-methylmuconate.	pseudomonas sp. strain mt1 has recently been reported to degrade 4- and 5-chlorosalicylate by a pathway assumed to consist of a patchwork of reactions comprising enzymes of the 3-oxoadipate pathway. genes encoding the initial steps in the degradation of salicylate and substituted derivatives were now localized and sequenced. one of the gene clusters characterized (sal) showed a novel gene arrangement, with sala, encoding a salicylate 1-hydroxylase, being clustered with salcd genes, encoding muco ...	2007	17172348
a gene cluster involved in degradation of substituted salicylates via ortho cleavage in pseudomonas sp. strain mt1 encodes enzymes specifically adapted for transformation of 4-methylcatechol and 3-methylmuconate.	pseudomonas sp. strain mt1 has recently been reported to degrade 4- and 5-chlorosalicylate by a pathway assumed to consist of a patchwork of reactions comprising enzymes of the 3-oxoadipate pathway. genes encoding the initial steps in the degradation of salicylate and substituted derivatives were now localized and sequenced. one of the gene clusters characterized (sal) showed a novel gene arrangement, with sala, encoding a salicylate 1-hydroxylase, being clustered with salcd genes, encoding muco ...	2007	17172348
a novel deaminase involved in chloronitrobenzene and nitrobenzene degradation with comamonas sp. strain cnb-1.	comamonas sp. strain cnb-1 degrades nitrobenzene and chloronitrobenzene via the intermediates 2-aminomuconate and 2-amino-5-chloromuconate, respectively. deamination of these two compounds results in the release of ammonia, which is used as a source of nitrogen for bacterial growth. in this study, a novel deaminase was purified from comamonas strain cnb-1, and the gene (cnbz) encoding this enzyme was cloned. the n-terminal sequence and peptide fingerprints of this deaminase were determined, and ...	2007	17259310
identification of diazotrophs in the culturable bacterial community associated with roots of lasiurus sindicus, a perennial grass of thar desert, india.	lasiurus sindicus is a highly nutritive, drought-tolerant, perennial grass that is endemic to the thar desert of rajasthan, india. analysis of 16s rrna coding genes of the bacterial isolates enriched in nitrogen-free semisolid medium, from the surface-sterilized roots of l. sindicus, showed predominance of gram-negative over gram-positive bacteria. according to comparative sequence analysis of 16s rdna sequence data, gram-positive bacteria with low gc content (staphylococcus warneri and bacillus ...	2007	17264993
synthesis of highly hydroxylated aromatics by evolved biphenyl dioxygenase and subsequent dihydrodiol dehydrogenase.	the evolved bpha1 (2049) gene, in which nine amino acids from the pseudomonas pseudoalcaligenes kf707 bpha1 were changed to those from the burkholderia xenovorans lb400 bpha1 (m247i, h255q, v258i, g268a, d303e, -313g, s324t, v325i, and t376n), was expressed in escherichia coli along with the bpha2a3a4 and bphb genes derived from strain kf707. this recombinant e. coli cells converted biphenyl and several heterocyclic aromatic compounds into the highly hydroxylated products such as biphenyl-2,3,2' ...	2007	17401562
the cyanotrophic bacterium pseudomonas pseudoalcaligenes cect5344 responds to cyanide by defence mechanisms against iron deprivation, oxidative damage and nitrogen stress.	two-dimensional (2-d) electrophoresis approach has been used to test protein expression changes in response to cyanide in the alkaliphilic bacterium pseudomonas pseudoalcaligenes cect5344. this is a cyanide-assimilating strain which also grows in media containing cyanide-enriched effluent from the jewellery industry. the bacterium efficiently uses this residue as the sole nitrogen source for aerobic growth under alkaline ph with negligible nitrogen losses as hcn. cell-free extracts isolated from ...	2007	17504491
evaluation of the colorimetric vitek 2 card for identification of gram-negative nonfermentative rods: comparison to 16s rrna gene sequencing.	ninety strains of a collection of well-identified clinical isolates of gram-negative nonfermentative rods collected over a period of 5 years were evaluated using the new colorimetric vitek 2 card. the vitek 2 colorimetric system identified 53 (59%) of the isolates to the species level and 9 (10%) to the genus level; 28 (31%) isolates were misidentified. an algorithm combining the colorimetric vitek 2 card and 16s rrna gene sequencing for adequate identification of gram-negative nonfermentative r ...	2007	17507509
essential role of cytochrome bd-related oxidase in cyanide resistance of pseudomonas pseudoalcaligenes cect5344.	pseudomonas pseudoalcaligenes cect5344 grows in minimal medium containing cyanide as the sole nitrogen source. under these conditions, an o2-dependent respiration highly resistant to cyanide was detected in cell extracts. the structural genes for the cyanide-resistant terminal oxidase, cioa and ciob, are clustered and encode the integral membrane proteins that correspond to subunits i and ii of classical cytochrome bd, although the presence of heme d in the membrane could not be detected by diff ...	2007	17574992
molecular characterization of a novel ortho-nitrophenol catabolic gene cluster in alcaligenes sp. strain nyz215.	alcaligenes sp. strain nyz215 was isolated for its ability to grow on ortho-nitrophenol (onp) as the sole source of carbon, nitrogen, and energy and was shown to degrade onp via a catechol ortho-cleavage pathway. a 10,152-bp dna fragment extending from a conserved region of the catechol 1,2-dioxygenase gene was obtained by genome walking. of seven complete open reading frames deduced from this fragment, three (onpabc) have been shown to encode the enzymes involved in the initial reactions of onp ...	2007	17616586
carbapenemases: the versatile beta-lactamases.	carbapenemases are beta-lactamases with versatile hydrolytic capacities. they have the ability to hydrolyze penicillins, cephalosporins, monobactams, and carbapenems. bacteria producing these beta-lactamases may cause serious infections in which the carbapenemase activity renders many beta-lactams ineffective. carbapenemases are members of the molecular class a, b, and d beta-lactamases. class a and d enzymes have a serine-based hydrolytic mechanism, while class b enzymes are metallo-beta-lactam ...	2007	17630334
bacterial toxicity of potassium tellurite: unveiling an ancient enigma.	biochemical, genetic, enzymatic and molecular approaches were used to demonstrate, for the first time, that tellurite (teo(3) (2-)) toxicity in e. coli involves superoxide formation. this radical is derived, at least in part, from enzymatic teo(3) (2-) reduction. this conclusion is supported by the following observations made in k(2)teo(3)-treated e. coli bw25113: i) induction of the ibpa gene encoding for the small heat shock protein ibpa, which has been associated with resistance to superoxide ...	2007	17299591
evidence for a tellurite-dependent generation of reactive oxygen species and absence of a tellurite-mediated adaptive response to oxidative stress in cells of pseudomonas pseudoalcaligenes kf707.	tellurite (teo3(2-)) is the most toxic and soluble oxyanion among tellurium (te) compounds. the effects of the metalloid anion on the oxidative stress response of the obligate aerobe pseudomonas pseudoalcaligenes kf707 were investigated. cells treated with sub-lethal concentrations of teo3(2-) showed neither adaptation to it nor cross-protection against oxidants such as 1,1'-4,4'-bipyridinium dichloride (paraquat, pq2+), diazenedicarboxylic acid bis-n,n-dimethylamide (diamide), tert-butyl hydrop ...	2007	17013634
enzymology and evolution of the pyruvate pathway to 2-oxobutyrate in methanocaldococcus jannaschii.	the archaeon methanocaldococcus jannaschii uses three different 2-oxoacid elongation pathways, which extend the chain length of precursors in leucine, isoleucine, and coenzyme b biosyntheses. in each of these pathways an aconitase-type hydrolyase catalyzes an hydroxyacid isomerization reaction. the genome sequence of m. jannaschii encodes two homologs of each large and small subunit that forms the hydrolyase, but the genes are not cotranscribed. the genes are more similar to each other than to p ...	2007	17449626
selection for biocontrol bacteria antagonistic toward rosellinia necatrix by enrichment of competitive avocado root tip colonizers.	biological control of soil-borne pathogens is frequently based on the application of antagonistic microorganisms selected solely for their ability to produce in vitro antifungal factors. the aim of this work was to select bacteria that efficiently colonize the roots of avocado plants and display antagonism towards rosellinia necatrix, the causal agent of avocado white root rot. a high frequency of antagonistic strains (ten isolates, 24.4%) was obtained using a novel procedure based on the select ...	2007	17467245
screening of delta-aminolevulinic acid dehydratase from pseudomonas strains as biosensor for lead and some other metals contamination.	delta-aminolevulinic acid dehydratase (alad; e.c. 4.2.1.24) is a metalloprotein and plays a crucial role in heme synthesis. its sensitivity to toxic metals depends on the metallic co-factors. in this study the effects of some heavy metals on alads activity of five pseudomonas isolates from akarçay stream (afyonkarahisar) have been studied in order to determine whether their alads could be used as biosensor for lead and other heavy metals contamination. the data obtained from the study were analy ...	2007	17975741
biotreatment of waste gas containing pyridine in a biofilter.	industrial waste gas emissions containing pyridine are generated from pyridine manufacturing industries, and in industrial operations where pyridine is used as a solvent, as an intermediate for synthesis and as a catalyst for a variety of applications. pyridine has unpleasant fishy odor with an odor index of 2390 and waste gaseous emissions containing pyridine require proper treatment prior to discharge. a biofilter, packed with compost and wood chips and inoculated with pseudomonas pseudoalcali ...	2007	16815008
[transformation of core pseudomonas pseudoalcaligene insecticidal protein gene and its insecticidal expression in tobacco].	we studied the effect of the signal peptide sequence (sps) on the expression of pseudomonas pseudoalcaligenes insecticidal protein gene (ppip).	2008	19062644
description of a novel indole-oxidizing bacterium pseudomonas indoloxydans sp. nov., isolated from a pesticide-contaminated site.	a gram-negative, deep brown-pigmented gammaproteobacteria, strain ipl-1(t), capable of oxidizing indole was isolated from a lindane-contaminated site and subjected to a polyphasic taxonomic study. most of the physiological and biochemical properties, major fatty acids (c(18:1)omega7c, c(16:1)omega7c/iso c(15:0) 2oh and c(16:0)), estimated dna g+c content (67.2mol%) and 16s rrna gene sequence analysis showed that strain ipl-1(t) belonged to the genus pseudomonas. strain ipl-1(t) exhibited highest ...	2008	18406094
pseudomonas pseudoalcaligenes kf707 upon biofilm formation on a polystyrene surface acquire a strong antibiotic resistance with minor changes in their tolerance to metal cations and metalloid oxyanions.	the susceptibility to various biocides was examined in planktonic cells and biofilms of the obligate aerobe, pcbs degrader, pseudomonas pseudoalcaligenes kf707. the toxicity of two antibiotics, amikacin and rifampicin, three metalloid oxyanions (aso2(-), seo3(2-), teo3(2-)) and three metal cations (cd2+, ni2+, al3+) was tested at two stages of the biofilm-development (4 and 24 h) and compared to planktonic cells susceptibility. mature biofilms formed in rich (lb, luria-bertani) medium were thick ...	2008	18437359
identifying competing aerobic nitrobenzene biodegradation pathways by compound-specific isotope analysis.	nitroaromatic compounds that contaminate soil and groundwater can be biodegraded by different, sometimes competing reaction pathways. we evaluated the combined use of compound-specific stable c and n isotope analysis to distinguish between enzymatic nitrobenzene oxidation by comamonas sp. strain js765 and partial reduction by pseudomonas pseudoalcaligenes strain js45 under aerobic conditions. bulk 13c and 15n enrichment factors for nitrobenzene dioxygenation with js765 were -3.9 per thousand +/- ...	2008	18678003
two similar enhanced root-colonizing pseudomonas strains differ largely in their colonization strategies of avocado roots and rosellinia necatrix hyphae.	pseudomonas alcaligenes avo73 and pseudomonas pseudoalcaligenes avo110 were selected previously as efficient avocado root tip colonizers, displaying in vitro antagonism towards rosellinia necatrix, causal agent of avocado white root rot. despite the higher number of antagonistic properties shown in vitro by avo73, only avo110 demonstrated significant protection against avocado white root rot. as both strains are enhanced root colonizers, and as colonization is crucial for the most likely biocont ...	2008	18684119
protein engineering on biphenyl dioxygenase for conferring activity to convert 7-hydroxyflavone and 5,7-dihydroxyflavone (chrysin).	a central part (amino-acid position 268-397 of 458 amino-acid residues) of the biphenyl dioxygenase large (alpha) subunit, bpha1, from pseudomonas pseudoalcaligenes strain kf707 was exchanged with the corresponding part of bpha1 from another biphenyl-degrading bacterium, pseudomonas putida strain kf715, to construct hybrid bpha1, bpha1 (715-707). when expressed in escherichia coli together with the bpha2a3a4bc genes from strain kf707, this enzyme was shown to possess activity for degrading both ...	2008	18804053
biphenyl dioxygenase from an arctic isolate is not cold adapted.	biphenyl dioxygenase from the psychrotolerant bacterium pseudomonas sp. strain cam-1 (bpdo(cam-1)) was purified and found to have an apparent k(cat) for biphenyl of 1.1 +/- 0.1 s(-1) (mean +/- standard deviation) at 4 degrees c. in contrast, bpdo(lb400) from the mesophile burkholderia xenovorans lb400 had no detectable activity at this temperature. at 57 degrees c, the half-life of the bpdo(cam-1) oxygenase was less than half that of the bpdo(lb400) oxygenase. nevertheless, bpdo(cam-1) appears t ...	2008	18424535
diversity of the c-terminal portion of the biphenyl dioxygenase large subunit.	the biphenyl dioxygenase (bpdo) catalyses a stereospecific dioxygenation of biphenyl and analogs of it. aside from being involved in the destruction and detoxification of toxic pollutants in soil, in the context of the green chemistry concept, this enzyme is a promising biocatalyst to design new more selective and more environmentally friendly approaches to manufacture fine chemicals. at this time, most of our knowledge about the variability of key residues determining the substrate specificity ...	2008	18685267
characterization of the pseudomonas pseudoalcaligenes cect5344 cyanase, an enzyme that is not essential for cyanide assimilation.	cyanase catalyzes the decomposition of cyanate into co(2) and ammonium, with carbamate as an unstable intermediate. the cyanase of pseudomonas pseudoalcaligenes cect5344 was negatively regulated by ammonium and positively regulated by cyanate, cyanide, and some cyanometallic complexes. cyanase activity was not detected in cell extracts from cells grown with ammonium, even in the presence of cyanate. nevertheless, a low level of cyanase activity was detected in nitrogen-starved cells. the cyn gen ...	2008	18708510
hydroquinone dioxygenase from pseudomonas fluorescens acb: a novel member of the family of nonheme-iron(ii)-dependent dioxygenases.	hydroquinone 1,2-dioxygenase (hqdo), an enzyme involved in the catabolism of 4-hydroxyacetophenone in pseudomonas fluorescens acb, was purified to apparent homogeneity. ligandation with 4-hydroxybenzoate prevented the enzyme from irreversible inactivation. hqdo was activated by iron(ii) ions and catalyzed the ring fission of a wide range of hydroquinones to the corresponding 4-hydroxymuconic semialdehydes. hqdo was inactivated by 2,2'-dipyridyl, o-phenanthroline, and hydrogen peroxide and inhibi ...	2008	18502867
antibacterial and preliminary phytochemical and physico-chemical analysis of eucalyptus citriodora hk leaf.	the present communication deals with some studies on the antibacterial, physico-chemical and phytochemical parameters of different extracts of eucalyptus citriodora leaf. the antibacterial study was performed using the agar ditch method on some clinically important bacteria, namely pseudomonas pseudoalcaligenes, proteus vulgaris, citrobacter freundii, staphylococcus subflava, bacillus megaterium, and enterobacter aerogenes. physico-chemical parameters namely water, methanol, 1,4-dioxane, dmf, ac ...	2008	18569717
degradation of fluorobiphenyl by pseudomonas pseudoalcaligenes kf707.	the biphenyl-degrading bacterium pseudomonas pseudoalcaligenes kf707 can use 2- and 4-fluorobiphenyl as sole carbon and energy sources. accumulation of fluorinated catabolites was determined by fluorine-19 nuclear magnetic spectroscopy (19f nmr) and revealed that growth on 4-fluorobiphenyl yielded 4-fluorobenzoate and 4-fluoro-1,2-dihydro-1,2-dihydroxybenzoate as major fluorometabolites; 2-fluorobenzoate and 2-fluoromuconic acid were observed in 2-fluorobiphenyl-grown cultures. pseudomonas pseud ...	2008	18616594
a new classification system for bacterial rieske non-heme iron aromatic ring-hydroxylating oxygenases.	rieske non-heme iron aromatic ring-hydroxylating oxygenases (rhos) are multi-component enzyme systems that are remarkably diverse in bacteria isolated from diverse habitats. since the first classification in 1990, there has been a need to devise a new classification scheme for these enzymes because many rhos have been discovered, which do not belong to any group in the previous classification. here, we present a scheme for classification of rhos reflecting new sequence information and interactio ...	2008	18387195
important discoveries from analysing bacterial phenotypes.	the ability to test hundreds to thousands of cellular phenotypes in a single experiment has opened up new avenues of investigation and exploration and led to important discoveries in very diverse applications of microbiological research and development. the information provided by global phenotyping is complementary to, and often more easily interpretable than information provided by global molecular analytical methods such as gene chips and proteomics. this report summarizes advances presented ...	2008	18681942
cloning and characterisation of (r)-3-hydroxyacyl-acyl carrier protein-coenzyme a transferase gene (phag) from pseudomonas sp. usm 4-55.	the (r)-3-hydroxyacyl-acp-coa transferase catalyses the conversion of (r)-3-hydroxyacyl-acp to (r)-3-hydroxyacyl-coa derivatives, which serves as the ultimate precursor for polyhydroxyalkanoate (pha) polymerisation from unrelated substrates in pseudomonads. phag was found to be responsible for channelling precursors for polyhydroxyalkanoate (pha) synthase from a de novo fatty acid biosynthesis pathway when cultured on carbohydrates, such as glucose or gluconate. the phag gene was cloned from pse ...	2009	24575175
spread of metallo-β-lactamases: screening reveals the presence of abla spm-1 gene in hospital sewage in southern brazil.	of 396 pseudomonas aeruginosa strains isolated from hospital sewage, the blaspm-1 gene was confirmed in nine. this is the first report of environmental p. aeruginosa strains carrying the blaspm-1 gene in brazil. the carbapenem resistance, already disseminated among clinical isolates, has been detected among environmental isolates.	2009	24031322
microbial degradation of pyridine and alpha-picoline using a strain of the genera pseudomonas and nocardia sp.	biodegradation of pyridine and alpha-picoline (2-methyl pyridine) by pseudomonas pseudoalcaligenes-kpn and nocardia sp. isolated from garden soil were investigated in batch culture experiments. pyridine and alpha-picoline (50-200 mg l(-1)) were used as sole source of carbon and energy in the investigation. the kinetic constants were evaluated for pyridine and alpha-picoline degradation under optimized nutritional (c, n, p) and environmental (ph, temperature) conditions. the values of bio-kinetic ...	2009	18987898
metabolomic investigation of the bacterial response to a metal challenge.	pseudomonas pseudoalcaligenes kf707 is naturally resistant to the toxic metalloid tellurite, but the mechanisms of resistance are not known. in this study we report the isolation of a kf707 mutant (t5) with hyperresistance to tellurite. in order to characterize the bacterial response and the pathways leading to tolerance, we utilized phenotype microarray technology (biolog) and a metabolomic technique based on nuclear magnetic resonance spectroscopy. the physiological states of kf707 wild-type a ...	2009	19047385
effects of biocides and other metal removal fluid constituents on mycobacterium immunogenum.	cells of mycobacterium immunogenum are significantly more resistant to biocides and antimicrobial compounds used for disinfection of metal removal fluids (mrfs) than cells of the gram-negative bacterium pseudomonas pseudoalcaligenes. to ensure accurate measurement of m. immunogenum susceptibility, a biocide inactivation step must be included to prevent an overestimation of killing for short-term exposures. cell suspensions in 5% mrf for 30 min rather than direct plating following biocide exposur ...	2009	19201985
the gaf-like-domain-containing transcriptional regulator dfdr is a sensor protein for dibenzofuran and several hydrophobic aromatic compounds.	dibenzofuran (df) is one of the dioxin carbon skeletal compounds used as a model to study the microbial degradation of dioxins. this study analyzed the transcriptional regulation of the df dioxygenase genes dfda1 to dfda4 in the df-utilizing actinomycetes rhodococcus sp. strain yk2 and terrabacter sp. strain yk3. an open reading frame designated dfdr was detected downstream of the dfdc genes. the c-terminal part of the dfdr amino acid sequence has high levels of similarity to several luxr-type d ...	2009	18952799
the gaf-like-domain-containing transcriptional regulator dfdr is a sensor protein for dibenzofuran and several hydrophobic aromatic compounds.	dibenzofuran (df) is one of the dioxin carbon skeletal compounds used as a model to study the microbial degradation of dioxins. this study analyzed the transcriptional regulation of the df dioxygenase genes dfda1 to dfda4 in the df-utilizing actinomycetes rhodococcus sp. strain yk2 and terrabacter sp. strain yk3. an open reading frame designated dfdr was detected downstream of the dfdc genes. the c-terminal part of the dfdr amino acid sequence has high levels of similarity to several luxr-type d ...	2009	18952799
pseudomonas tuomuerensis sp. nov., isolated from a bird's nest.	strain 78-123t was isolated from a sample of a bird's nest situated on the bank of qiongtailan river in the region of tuomuer peak of tianshan mountain in the xin-jiang uygur autonomous region in north-western china. phylogenetic analysis based on 16s rrna gene sequence similarity showed that strain 78-123t was related to members of the genus pseudomonas. 16s rrna gene sequence similarity between strain 78-123t and pseudomonas mendocina atcc 25411t, pseudomonas pseudoalcaligenes jcm 5968t and ps ...	2009	19126738
pseudomonas caeni sp. nov., a denitrifying bacterium isolated from the sludge of an anaerobic ammonium-oxidizing bioreactor.	two gram-negative, rod-shaped, motile, aerobic bacterial strains designated hy-14(t) and hy-24 were isolated from the sludge of an anaerobic ammonium-oxidizing bioreactor. the strains could not grow with 5 % (w/v) nacl, did not produce acid from d-glucose or utilize d-glucose, gluconate or citrate as a sole carbon source. summed feature 3 and c(16 : 0) were the most abundant fatty acids; hydroxyl fatty acids c(12 : 0) 3-oh and c(10 : 0) 3-oh were also present. fatty acid c(12 : 0) 2-oh was absen ...	2009	19622647
a new atisane-type diterpene from the bark of the mangrove plant excoecaria agallocha.	a new atisane-type diterpene, ent-16alpha-hydroxy-atisane-3,4-lactone (4) and three known diterpenes, ent-16alpha-hydroxy-atisane-3-one (1), ent-atisane-3beta,16alpha-diol (2), ent-3,4-seco-16alpha-hydroxyatis- 4(19)-en -3-oic acid (3) were isolated from the bark of the mangrove plant excoecaria agallocha. their structures and relative stereochemistry were elucidated by means of extensive nmr and ms analysis. compound 3 exhibited significant anti-microfouling activity against the adherence of ps ...	2009	19158653
terminal-restriction fragment length polymorphism analysis of biphenyl dioxygenase genes from a polychlorinated biphenyl-polluted soil.	polychlorinated biphenyls (pcbs) are ubiquitous persistent organic pollutants that can be co-metabolically biotransformed by biphenyl-utilizing bacteria. in this study, terminal-restriction fragment length polymorphism (t-rflp) was applied to the substrate specificity-determining region of the 2,3-biphenyl dioxygenase encoding genes of a microbial community found in a pcb-polluted soil. notably, both the total biphenyl/pcb-utilizing community and its members actively expressing the 2,3-biphenyl ...	2009	19835952
dna-stable isotope probing integrated with metagenomics for retrieval of biphenyl dioxygenase genes from polychlorinated biphenyl-contaminated river sediment.	stable isotope probing with [(13)c]biphenyl was used to explore the genetic properties of indigenous bacteria able to grow on biphenyl in pcb-contaminated river raisin sediment. a bacterial 16s rrna gene clone library generated from [(13)c]dna after a 14-day incubation with [(13)c]biphenyl revealed the dominant organisms to be members of the genera achromobacter and pseudomonas. a library built from pcr amplification of genes for aromatic-ring-hydroxylating dioxygenases from the [(13)c]dna fract ...	2009	19648381
chemotaxis to pyrimidines and identification of a cytosine chemoreceptor in pseudomonas putida.	we developed a high-throughput quantitative capillary assay and demonstrated that pseudomonas putida strains f1 and prs2000 were attracted to cytosine, but not thymine or uracil. in contrast, pseudomonas aeruginosa pao1 was not chemotactic to any pyrimidines. chemotaxis assays with a mutant strain of f1 in which the putative methyl-accepting chemotaxis protein-encoding gene pput_0623 was deleted revealed that this gene (designated mcpc) encodes a chemoreceptor for positive chemotaxis to cytosine ...	2009	19251854
biotransformations of 2-methylisoborneol by camphor-degrading bacteria.	many camphor-degrading bacteria that are able to transform 2-methylisoborneol (2-mib) have been identified. three of these strains have been examined in detail. rhodococcus ruber t1 metabolizes camphor through 6-hydroxycamphor but converts 2-mib to 3-hydroxy-2-mib. pseudomonas putida g1, which metabolizes camphor through 5-hydroxycamphor, converts mib primarily to 6-hydroxy-2-mib. rhodococcus wratislaviensis dlc-cam converts 2-mib through 5-hydroxy-2-mib to 5-keto-2-mib. together, these three st ...	2009	19060161
biotransformations of 2-methylisoborneol by camphor-degrading bacteria.	many camphor-degrading bacteria that are able to transform 2-methylisoborneol (2-mib) have been identified. three of these strains have been examined in detail. rhodococcus ruber t1 metabolizes camphor through 6-hydroxycamphor but converts 2-mib to 3-hydroxy-2-mib. pseudomonas putida g1, which metabolizes camphor through 5-hydroxycamphor, converts mib primarily to 6-hydroxy-2-mib. rhodococcus wratislaviensis dlc-cam converts 2-mib through 5-hydroxy-2-mib to 5-keto-2-mib. together, these three st ...	2009	19060161
integrated bioprocessing for the ph-dependent production of 4-valerolactone from levulinate in pseudomonas putida kt2440.	enzymes are powerful biocatalysts capable of performing specific chemical transformations under mild conditions, yet as catalysts they remain subject to the laws of thermodynamics, namely, that they cannot catalyze chemical reactions beyond equilibrium. here we report the phenomenon and application of using extracytosolic enzymes and medium conditions, such as ph, to catalyze metabolic pathways beyond their intracellular catalytic limitations. this methodology, termed "integrated bioprocessing" ...	2010	19915035
integrated bioprocessing for the ph-dependent production of 4-valerolactone from levulinate in pseudomonas putida kt2440.	enzymes are powerful biocatalysts capable of performing specific chemical transformations under mild conditions, yet as catalysts they remain subject to the laws of thermodynamics, namely, that they cannot catalyze chemical reactions beyond equilibrium. here we report the phenomenon and application of using extracytosolic enzymes and medium conditions, such as ph, to catalyze metabolic pathways beyond their intracellular catalytic limitations. this methodology, termed "integrated bioprocessing" ...	2010	19915035
characterization of the isophthalate degradation genes of comamonas sp. strain e6.	the isophthalate (ipa) degradation gene cluster (iphacbdr) responsible for the conversion of ipa into protocatechuate (pca) was isolated from comamonas sp. strain e6, which utilizes phthalate isomers as sole carbon and energy sources via the pca 4,5-cleavage pathway. based on amino acid sequence similarity, the ipha, iphc, iphb, iphd, and iphr genes were predicted to code for an oxygenase component of ipa dioxygenase (ipado), a periplasmic ipa binding receptor, a 1,2-dihydroxy-3,5-cyclohexadiene ...	2010	19933340
characterization of the isophthalate degradation genes of comamonas sp. strain e6.	the isophthalate (ipa) degradation gene cluster (iphacbdr) responsible for the conversion of ipa into protocatechuate (pca) was isolated from comamonas sp. strain e6, which utilizes phthalate isomers as sole carbon and energy sources via the pca 4,5-cleavage pathway. based on amino acid sequence similarity, the ipha, iphc, iphb, iphd, and iphr genes were predicted to code for an oxygenase component of ipa dioxygenase (ipado), a periplasmic ipa binding receptor, a 1,2-dihydroxy-3,5-cyclohexadiene ...	2010	19933340
modified 3-oxoadipate pathway for the biodegradation of methylaromatics in pseudomonas reinekei mt1.	catechols are central intermediates in the metabolism of aromatic compounds. degradation of 4-methylcatechol via intradiol cleavage usually leads to the formation of 4-methylmuconolactone (4-ml) as a dead-end metabolite. only a few microorganisms are known to mineralize 4-ml. the mml gene cluster of pseudomonas reinekei mt1, which encodes enzymes involved in the metabolism of 4-ml, is shown here to encode 10 genes found in a 9.4-kb chromosomal region. reverse transcription assays revealed that t ...	2010	20061479
nitroaromatic compounds, from synthesis to biodegradation.	nitroaromatic compounds are relatively rare in nature and have been introduced into the environment mainly by human activities. this important class of industrial chemicals is widely used in the synthesis of many diverse products, including dyes, polymers, pesticides, and explosives. unfortunately, their extensive use has led to environmental contamination of soil and groundwater. the nitro group, which provides chemical and functional diversity in these molecules, also contributes to the recalc ...	2010	20508249
application of a novel bacterial consortium for mineralization of sulphonated aromatic amines.	a novel bacterial consortium (tj-2) for mineralization of aromatic amines resulting from decolorization of azo dyes was developed. three bacterial strains were identified as pseudomonas pseudoalcaligenes (tj-21,eu072476), pseudomonas citronellolis (tj-22,eu072477) and pseudomonas testosterone (tj-23,eu072477) by 16s rrna gene sequence analysis. aromatic amine mineralization under aerobic conditions was observed to be significantly higher with the consortium as compared to pure strains indicating ...	2010	20863689
absolute configuration-dependent epoxide formation from isoflavan-4-ol stereoisomers by biphenyl dioxygenase of pseudomonas pseudoalcaligenes strain kf707.	biphenyl dioxygenase from pseudomonas pseudoalcaligenes strain kf707 expressed in escherichia coli was found to exhibit monooxygenase activity toward four stereoisomers of isoflavan-4-ol. lc-ms and lc-nmr analyses of the metabolites revealed that the corresponding epoxides formed between c2' and c3' on the b-ring of each isoflavan-4-ol substrate were the sole products. the relative reactivity of the stereoisomers was found to be in the order: (3s,4s)-cis-isoflavan-4-ol > (3r,4s)-trans-isoflavan- ...	2010	21063701