Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
|---|
| cloning, dna sequencing and expression of (3-17)beta hydroxysteroid dehydrogenase from pseudomonas testosteroni. | we describe the cloning, sequencing and overexpression of the (3-17)beta hydroxysteroid dehydrogenase gene of pseudomonas testosteroni. a genomic library of ps. testosteroni total dna constructed from sauiiia digests ligated to a lambda gt11 vector was probed with polyclonal antibody raised against purified enzyme. subclones derived from a recombinant phage containing a 2661-base-pair insert were sequenced and found to contain an open reading frame of 765 base pairs that corresponds to a protein ... | 1993 | 8382516 |
| telluria mixta (pseudomonas mixta bowman, sly, and hayward 1988) gen. nov., comb. nov., and telluria chitinolytica sp. nov., soil-dwelling organisms which actively degrade polysaccharides. | pseudomonas mixta (type strain, acm 1762 [= atcc 49108], an actively dextranolytic species that possesses both lateral and polar flagella, was compared with the strictly aerobic, rod-shaped, chitinolytic bacterium "pseudomonas chitinolytica" acm 3522t (= cncm i-804) (t = type strain), which has a similar flagellation pattern, by performing phenotypic characterization and dna-dna hybridization studies and by analyzing dna base compositions and 16s rrna sequences. our results indicated that "p. ch ... | 1993 | 8427803 |
| uptake of 4-toluene sulfonate by comamonas testosteroni t-2. | the mechanism of transport of the xenobiotic 4-toluene sulfonate (ts) in comamonas testosteroni t-2 was investigated. rapid uptake of ts was observed only in cells grown with ts or 4-methylbenzoate as a carbon and energy source. initial uptake rates under aerobic conditions showed substrate saturation kinetics, with an apparent affinity constant (kt) of 88 microm and a maximal velocity (vmax) of 26.5 nmol/min/mg of protein. uptake of ts was inhibited completely by uncouplers and only marginally ... | 1993 | 8432701 |
| environments and mechanistic roles of the tyrosine residues of delta 5-3-ketosteroid isomerase. | delta 5-3-ketosteroid isomerase (ec 5.3.3.1) from pseudomonas testosteroni converts delta 5-3-ketosteroids to delta 4-3-ketosteroids by a stereoselective and conservative transfer of the 4 beta-proton to the 6 beta-position. the 10(9.5)-fold enzymatic rate acceleration can be attributed to a concerted rate-limiting enolization in which tyr-14 and asp-38, positioned orthogonally, act as general acid and base, respectively. the pka value of the phenolic hydroxyl group of tyr-14 of the y55f/y88f do ... | 1993 | 8439542 |
| microbial metabolism of quinoline and related compounds. xvii. degradation of 3-methylquinoline by comamonas testosteroni 63. | a bacterial strain which utilizes 3-methylquinoline as sole source of carbon, nitrogen and energy was isolated from activated sludge. on the basis of its morphological and physiological characteristics, this isolate was classified as comamonas testosteroni. four metabolites of 3-methylquinoline degradation were isolated from the culture supernatant and identified as 3-methyl-2-oxo-1,2-dihydroquinoline, 6-hydroxy-3-methyl-2-oxo-1,2-dihydroquinoline, 5,6-dihydroxy-3-methyl-2-oxo-1,2-dihydroquinoli ... | 1993 | 8489738 |
| carbonyl reduction by 3 alpha-hsd from comamonas testosteroni--new properties and its relationship to the scad family. | 1993 | 8493916 | |
| molecular analysis of isophthalate and terephthalate degradation by comamonas testosteroni yzw-d. | comamonas testosteroni yzw-d was isolated from passaic river sediment for its ability to degrade isophthalate and terephthalate. degradation of the two isomeric compounds proceeds via separately inducible catabolic pathways that converge at protocatechuate. analysis of the catabolic pathways by which these two isomers are degraded demonstrated that a cis-dihydrodiol intermediate is involved in both pathways. the genes for the conversion of isophthalate and terephthalate to protocatechuate were c ... | 1995 | 8565920 |
| molecular cloning of novel genes for polycyclic aromatic hydrocarbon degradation from comamonas testosteroni gz39. | three strains of comamonas testosteroni were isolated from river sediment for the ability to degrade phenanthrene; two of the strains also grew on naphthalene, and one strain also grew on anthracene. the homology of the genes for polycyclic aromatic hydrocarbon degradation in these strains to the classical genes (nah) for naphthalene degradation from pseudomonas putida ncib 9816-4 was determined. the three c. testosteroni strains showed no homology to the nah gene probe even under low-stringency ... | 1996 | 8572701 |
| biodegradation of polychlorinated biphenyls by rhizobia: a novel finding. | metabolism of simple aromatic compounds in rhizobial strains has been a subject of study for a few decades, due either to the significance of nutritional diversity in the inoculum survival during agricultural applications or to the importance of plant phenolics in the microbe-plant cross-talk and signal-transduction. here, we report the capability of rhizobial strains to catabolize polychlorinated biphenyls (pcbs). in order to identify the genes in these strains that mediate the catabolism of pc ... | 1996 | 8579613 |
| purification and characterization of the 3-ketosteroid-delta 1-dehydrogenase of arthrobacter simplex produced in streptomyces lividans. | the 3-ketosteroid-delta 1-dehydrogenase (ks1dh) gene of arthrobacter simplex ifo12069 cloned in streptomyces lividans was overexpressed, resulting in production of the enzyme both extracellularly and intracellularly. the enzyme was purified by ammonium sulfate fractionation and chromatographies using deae-toyopearl, butyl-toyopearl and toyopearl hw55s from the supernatant of culture broth and cell-free extracts of s. lividans, and both preparations showed the same characteristics. the n-terminal ... | 1995 | 8586617 |
| crystallization and crystal packing of recombinant 3 (or 17) beta-hydroxysteroid dehydrogenase from comamonas testosteroni attc 11996. | the enzyme 3 (or 17) beta-hydroxysteroid dehydrogenase from comamonas testosteroni was crystallized. crystals, of up to 0.6 mm in their longest dimension and suitable for a crystallographic analysis have been obtained by the vapour diffusion method. they belong to the orthorhombic lattice type and diffract to a maximum resolution of 0.23 nm. a final data set obtained by merging data from three crystals resulted in a completeness of 90% with an rmerge of 6%. a molecular replacement search carried ... | 1996 | 8617258 |
| characterization of active recombinant his-tagged oxygenase component of comamonas testosteroni b-356 biphenyl dioxygenase. | biphenyl (bph) dioxygenase oxidizes bph to 2,3-dihydro-2,3-dihydroxybiphenyl in comamonas testosteroni b-356. the enzyme comprises a two-subunit iron-sulfur protein (ispbph), a ferredoxin ferbph, and a ferredoxin reductase redbph. redbph and ferbph transfer electrons from nadh to an fe-s active center of ispbph which activates molecular oxygen for insertion into the substrate. in this work b-356 ispbph complex and its alpha and beta subunits were purified from recombinant escherichia coli strain ... | 1996 | 8626504 |
| chemical structure of lipid a isolated from comamonas testosteroni lipopolysaccharide. | the chemical structure of lipid a of lipopolysaccharide isolated from comamonas testosteroni was determined by quantitative analysis, methylation analysis, mass spectrometry and nmr spectroscopy. the lipid a backbone was found to consist of 6-o-(2-deoxy-2-amino-beta-d-glucopyranosyl)-2-deoxy-2-amino-alpha-d-g luc ose which was phosphorylated in positions 1 and 4'. hydroxyl groups at positions 4 and 6' were unsubstituted, and position 6' of the non-reducing terminal residue was identified as the ... | 1996 | 8647087 |
| characterization of the gene encoding quinohaemoprotein ethanol dehydrogenase of comamonas testosteroni. | the gene encoding quinohaemoprotein ethanol dehydrogenase type i (qh-edhi) from comamonas testosteroni has been cloned and sequenced. comparison of the amino acid sequence deduced from this with that determined for the n-terminal amino acid stretch of purified qh-edhi, suggests that the gene also contains a leader sequence of 31 residues. based on this information, the molecular mass of the apo-enzyme, i.e. the enzyme without the cofactors pyrroloquinoline quinone (pqq) and haem c, and without t ... | 1996 | 8654419 |
| comamonas testosteroni 3-ketosteroid-delta 4(5 alpha)-dehydrogenase: gene and protein characterization. | comamonas testosteroni delta 4(5 alpha)- and delta1-dehydrogenases [delta4(5alpha)- and delta1dh] are key enzymes in the degradation of steroids having an a:b ring fusion in a trans configuration. we previously reported the isolation of the delta1dh gene (p. plesiat, m. grandguillot, s. harayama, s. vragar, and y. michel briand, j. bacteriol. 173:7219-7227, 1991). in this study, the gene encoding delta 4(5 alpha)dh was cloned in escherichia coli on a 16-kbp bamhi fragment by screening a genomic ... | 1996 | 8655514 |
| [cloning of genes coding for 3-alpha-hydroxysteroid dehydrogenase and for (3-17)-beta-hydroxysteroid dehydrogenase from pseudomonas testosteroni]. | a genomic library of pseudomonas testosteroi total dna constructed from sauiiia digests ligated to a lambda gt11 vector was probed with different polyclonal antibodies raised against purified 3 alpha-hsd and (3 beta-17 beta)-hsd. two different clones reacting with one antibody were selected. the clone reacting with (3-17)beta-hsd antibody contained a 2,661-base pair insert and was found to contained an open reading frame of 765 base pair that corresponds to a protein of 254 amino-acid residues. ... | 1995 | 8673621 |
| comamonas testosteroni colony phenotype influences exopolysaccharide production and coaggregation with yeast cells. | a comamonas testosteroni strain was isolated from activated sludge on the basis of its ability to coaggregate with yeast cells. on agar plates the following two types of colonies were formed: colonies with a mucoid appearance and colonies with a nonmucoid appearance. on plates this strain alternated between the two forms, making sectored colonies. in liquid medium with constant agitation no such change was observed. in the absence of agitation and in contact with a glass surface a culture with p ... | 1996 | 8702260 |
| characterization of active recombinant 2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase from comamonas testosteroni b-356 and sequence of the encoding gene (bphb). | 2,3-dihydro-2,3-dihydroxybiphenyl-2,3-dehydrogenase (b2,3d) catalyzes the second step in the biphenyl degradation pathway. the nucleotide sequence of comamonas testosteroni b-356 bphb, which encodes b2,3d, was determined. structural analysis showed that the dehydrogenases involved in the bacterial degradation of aromatic compounds are related to each other and that their phylogenetic relationships are very similar to the relationships observed for dioxygenases that catalyze the initial reaction ... | 1996 | 8702262 |
| antibiotic resistance and enhanced insecticide catabolism as consequences of steroid induction in the gram-negative bacterium comamonas testosteroni. | the effects of steroid induction on antibiotic resistance against the fungal steroid fusidic acid (ramycin; 16-(acetyloxy)-3 alpha,11 alpha-dihydroxy-29-dammara-17(20), 24-dien-21-oic-acid) as well as on carbonyl reduction and degradation of the novel anti-insect agent nki 42255 (2-(1-imidazolyl)-1-(4-methoxyphenyl)-2-methyl-1-propanone) were studied in the gram-negative soil bacterium comamonas testosteroni strain atcc 11996. cells grown with testosterone as inducing agent showed a 5-6-fold ele ... | 1996 | 8809204 |
| degradative pathways for p-toluenecarboxylate and p-toluenesulfonate and their multicomponent oxygenases in comamonas testosteroni strains psb-4 and t-2. | three multicomponent oxygenases involved in the degradation of p-toluenesulfonate and p-toluenecarboxylate and the regulation of their synthesis have been examined in three strains (t-2, psb-4 and ter-1) of comamonas testosteroni. strain t-2 utilizes p-toluenesulfonate as a source of carbon and energy for growth via p-sulfobenzoate and protocatechuate, and p-toluenecarboxylate via terephthalate and protocatechuate, and has the unusual property of requiring the reductase (tsab) of the toluenesulf ... | 1996 | 8828208 |
| sequencing of comamonas testosteroni strain b-356-biphenyl/chlorobiphenyl dioxygenase genes: evolutionary relationships among gram-negative bacterial biphenyl dioxygenases. | in a previous work, all three components of comamonas testosteroni b-356 biphenyl (bph)/chlorobiphenyls (pcbs) dioxygenase (dox) have been purified and characterized. they include an iron-sulphur protein (ispbph) which is the terminal oxygenase composed of two subunits (encoded by bpha and bphe), a ferredoxin (ferbph) encoded by bphf and a reductase (redbph) encoded by bphg. bphg is not located in the neighbourhood of bphaef in b-356. we are reporting the cloning of b-356-bphg and the sequencing ... | 1996 | 8890734 |
| characterization of a 3 alpha-hydroxysteroid dehydrogenase/carbonyl reductase from the gram-negative bacterium comamonas testosteroni. | a new form of the nad(p)-dependent 3 alpha-hydroxysteroid dehydrogenases (3 alpha-hsds), present in the gram-negative bacterium comamonas testosteroni atcc 11996, was isolated from a testosterone-induced bacterial extract and characterized. the enzyme (hsd 28) has a monomeric molecular mass of 28 kda. it belongs to the protein superfamily of short-chain dehydrogenases/reductases (sdr) as established by n-terminal sequence analysis. along with the 3 alpha-hydroxysteroid dehydrogenase and 3-oxo-re ... | 1996 | 8944761 |
| rp4::mu3a-mediated in vivo cloning and transfer of a chlorobiphenyl catabolic pathway. | chromosomal dna fragments encoding the ability to utilize biphenyl as sole carbon source (bph+) were mobilized by means of plasmid rp4::mu3a from strain jb1 (tentatively identified as burkholderia sp.) to alcaligenes eutrophus ch34 at a frequency of 10(-3) per transferred plasmid. the mobilized dna integrated into the recipient chromosome or was recovered as catabolic prime plasmids. three bph+ prime plasmids were transferred from a. eutrophus to escherichia coli and back to a. eutrophus without ... | 1996 | 8969525 |
| active site directed mutagenesis of 3 beta/17 beta-hydroxysteroid dehydrogenase establishes differential effects on short-chain dehydrogenase/reductase reactions. | mutagenetic replacements of conserved residues within the active site of the short-chain dehydrogenase/reductase (sdr) superfamily were studied using prokaryotic 3 beta/17 beta-hydroxysteroid dehydrogenase (3 beta/17 beta-hsd) from comamonas testosteroni as a model system. the results provide novel data to establish ser 138 as a member of a catalytically important "triad" of residues also involving tyr151 and lys155. a ser-->ala exchange at position 138 results in an almost complete (> 99.9%) lo ... | 1997 | 8993315 |
| characterization of the p-toluenesulfonate operon tsambcd and tsar in comamonas testosteroni t-2. | comamonas testosteroni t-2 uses a standard, if seldom examined, attack on an aromatic compound and oxygenates the side chain of p-toluenesulfonate (ts) (or p-toluenecarboxylate) to p-sulfobenzoate (or terephthalate) prior to complete oxidation. the expression of the first three catabolic enzymes in the pathway, the ts methyl-monooxygenase system (comprising reductase b and oxygenase m; tsamb), p-sulfobenzyl alcohol dehydrogenase (tsac), and p-sulfobenzaldehyde dehydrogenase (tsad), is coregulate ... | 1997 | 9006050 |
| d-lysine production from l-lysine by successive chemical racemization and microbial asymmetric degradation. | in order to develop a practical process for d-lysine production from l-lysine, successive chemical racemization and microbial asymmetric degradation were investigated. the racemization of l-lysine proceeded quantitatively at elevated temperatures. a sample of 1000 strains of bacteria, fungi, yeast and actinomyces were screened for the ability to degrade l-lysine asymmetrically. microorganisms belonging to the achromobacter, agrobacterium, candida, comamonas, flavobacterium, proteus, providencia, ... | 1997 | 9163947 |
| conjugative plasmids and the degradation of arylsulfonates in comamonas testosteroni. | comamonas testosteroni t-2 degrades p-toluenesulfonate (tsa) via p-sulfobenzoate (psb) and protocatechuate and degrades toluenecarboxylate via terephthalate (ter) and protocatechuate. the appropriate genes are expressed in at least five regulatory units, some of which are also found in c. testosteroni psb-4 (f. junker, r. kiewitz, and a. m. cook, j. bacteriol. 179:919-927, 1997). c. testosteroni t-2 was found to contain two plasmids, ptsa (85 kbp) and pt2t (50 kbp); a tsa- mutant (strain ter-1) ... | 1997 | 9172362 |
| biodegradation of the mixtures of 4-chlorophenol and phenol by comamonas testosteroni cpw301. | a 4-chlorophenol (4-cp)-degrading bacterium, strain cpw301, was isolated from soil and identified as comamonas testosteroni. this strain dechlorinated and degraded 4-cp via a meta-cleavage pathway. cpw301 could also utilize phenol as a carbon and energy source without the accumulation of any metabolites via the same meta-cleavage pathway. when phenol was added as an additional substrate, cpw301 could degrade 4-cp and phenol simultaneously. the addition of phenol greatly accelerated the degradati ... | 1996 | 9188195 |
| highly efficient control of iron-containing nitrile hydratases by stoichiometric amounts of nitric oxide and light. | the reaction of two iron-containing nitrile hydratases (nhase) with no has been studied: nhase from rhodococcus sp. r312, which is probably similar to the photosensitive n771 nhase, and the new nhase from comamonas testosteroni ni1 whose aminoacid sequence is quite different from those of br312 and n771 nhases. both enzymes are equally inactivated after addition of stoichiometric amounts of no added as an anaerobic solution or produced in situ under physiological conditions by a rat brain no-syn ... | 1997 | 9202148 |
| chemoenzymatic synthesis of chiral biologically active heterocycles. | the chemoenzymatic approach to the preparation of some chiral biologically active heterocycles is discussed. synthetic strategies took advantage of enantioselective bioconversion processes carried out on suitable reaction intermediates. reductions of carbonyl compounds catalyzed by different alcohol dehydogenases (tbadh from thermoanaerobium brockii, 20 beta-hsdh from streptomyces hydrogenans, beta-hsdh from pseudomonas testosteroni) allowed the preparation with high enantiomeric purity of the e ... | 1997 | 9274001 |
| testosterone-regulated expression of enzymes involved in steroid and aromatic hydrocarbon catabolism in comamonas testosteroni. | the effect of testosterone as the sole carbon source on protein expression was analyzed in comamonas testosteroni. testosterone simultaneously induced the expression of steroid- and aromatic hydrocarbon-catabolizing enzymes and repressed one amino acid-degrading enzyme. it is suggested that steroids play a regulative role in catabolic enzyme synthesis during adaptive growth of c. testosteroni. | 1997 | 9294458 |
| cloning of the gene for poly(3-hydroxybutyric acid) depolymerase of comamonas testosteroni and functional analysis of its substrate-binding domain. | a poly(3-hydroxybutyric acid) (phb) depolymerase gene of comamonas testosteroni ym1004 was cloned on sau3ai fragment from genomic dna into escherichia coli dh5. nucleotide sequence analysis dedicated a 1539 bp open reading frame encoding a protein 513 amino acid with a putative 25 residue signal peptide for secretion. the deduced amino acid sequence was very similar to that of phb depolymerase of comamonas sp. in order to understand the characteristics of substrate-binding domain of the depolyme ... | 1997 | 9297825 |
| high-resolution crystal structures of delta5-3-ketosteroid isomerase with and without a reaction intermediate analogue. | bacterial delta5-3-ketosteroid isomerase (ksi) catalyzes a stereospecific isomerization of steroid substrates at an extremely fast rate, overcoming a large disparity of pka values between a catalytic residue and its target. the crystal structures of ksi from pseudomonas putida and of the enzyme in complex with equilenin, an analogue of the reaction intermediate, have been determined at 1.9 and 2.5 a resolution, respectively. the structures reveal that the side chains of tyr14 and asp99 (a newly ... | 1997 | 9369474 |
| analysis of changes in congener selectivity during pcb degradation by burkholderia sp. strain tsn101 with increasing concentrations of pcb and characterization of the bphbcd genes and gene products. | we isolated and characterized a gram-negative bacterium, burkholderia sp. strain tsn101, that can degrade polychlorinated biphenyls (pcbs) at concentrations as high as 150 microg kaneclor 300/ml, a pcb mixture equivalent to aroclor 1242. growing cells of strain tsn101 degraded most of the tri- and tetrachlorobiphenyls in medium containing 25 microg kaneclor 300/ml. using pcb concentrations of 50-150 microg of kaneclor 300/ml, the congener selectivity pattern was different and the pattern of chlo ... | 1998 | 9396836 |
| degradation of tetrahydrofurfuryl alcohol by ralstonia eutropha is initiated by an inducible pyrroloquinoline quinone-dependent alcohol dehydrogenase. | an organism tentatively identified as ralstonia eutropha was isolated from enrichment cultures containing tetrahydrofurfuryl alcohol (thfa) as the sole source of carbon and energy. the strain was able to tolerate up to 200 mm thfa in mineral salt medium. the degradation was initiated by an inducible ferricyanide-dependent alcohol dehydrogenase (adh) which was detected in the soluble fraction of cell extracts. the enzyme catalyzed the oxidation of thfa to the corresponding tetrahydrofuran-2-carbo ... | 1997 | 9406410 |
| substrate ambiguity of 3-deoxy-d-manno-octulosonate 8-phosphate synthase from neisseria gonorrhoeae in the context of its membership in a protein family containing a subset of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthases. | 3-deoxy-d-manno-octulosonate 8-phosphate (kdop) synthase and 3-deoxy-d-arabino-heptulosonate 7-phosphate (dahp) synthase catalyze similar phosphoenolpyruvate-utilizing reactions. the genome of neisseria gonorrhoeae contains one gene encoding kdop synthase and one gene encoding dahp synthase. of the two nonhomologous dahp synthase families known, the n. gonorrhoeae protein belongs to the family i assemblage. kdop synthase exhibited an ability to replace arabinose-5-p with either erythrose-4-p or ... | 1998 | 9422601 |
| degradation of chloroaromatics: purification and characterization of a novel type of chlorocatechol 2,3-dioxygenase of pseudomonas putida gj31. | a purification procedure for a new kind of extradiol dioxygenase, termed chlorocatechol 2,3-dioxygenase, that converts 3-chlorocatechol productively was developed. structural and kinetic properties of the enzyme, which is part of the degradative pathway used for growth of pseudomonas putida gj31 with chlorobenzene, were investigated. the enzyme has a subunit molecular mass of 33.4 kda by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. estimation of the native mr value under nondenatur ... | 1998 | 9440519 |
| a new comamonas testosteroni steroid-inducible gene: cloning and sequence analysis. | comamonas testosteroni can grow on a variety of steroid compounds as the sole carbon and energy source. in a previous study, we cloned and sequenced the testosterone-inducible betahsd gene from c. testosteroni (genti-raimondi, s., tolmasky, m., patrito, l., flury, a. and actis, l., molecular cloning and expression of the beta-hydroxysteroid dehydrogenase gene from pseudomonas testosteroni. gene, 1991, 105, 43-49.). herein we report the cloning and characterization of another steroid-inducible ge ... | 1997 | 9449210 |
| genetics of naphthalene and phenanthrene degradation by comamonas testosteroni. | naphthalene and phenanthrene have long been used as model compounds to investigate the ability of bacteria to degrade polycyclic aromatic hydrocarbons. the catabolic pathways have been determined, several of the enzymes have been purified to homogeneity, and genes have been cloned and sequenced. however, the majority of this work has been performed with fast growing pseudomonas strains related to the archetypal naphthalene-degrading p. putida strains g7 and ncib 9816-4. recently comamonas testos ... | 1997 | 9451837 |
| identification of bacterial isolates obtained from intestinal contents associated with 12,000-year-old mastodon remains. | mastodon (mammut americanum) remains unearthed during excavation of ancient sediments usually consist only of skeletal material, due to postmortem decomposition of soft tissues by microorganisms. two recent excavations of skeletal remains in anoxic sediments in ohio and michigan, however, have uncovered organic masses which appear to be remnants of the small and large intestines, respectively. macrobotanical examinations of the composition of these masses revealed assemblages of plant material r ... | 1998 | 9464403 |
| bacterial community dynamics during start-up of a trickle-bed bioreactor degrading aromatic compounds. | this study was performed with a laboratory-scale fixed-bed bioreactor degrading a mixture of aromatic compounds (solvesso100). the starter culture for the bioreactor was prepared in a fermentor with a wastewater sample of a care painting facility as the inoculum and solvesso100 as the sole carbon source. the bacterial community dynamics in the fermentor and the bioreactor were examined by a conventional isolation procedure and in situ hybridization with fluorescently labeled rrna-targeted oligon ... | 1998 | 9501433 |
| biphenyl-associated meta-cleavage dioxygenases from comamonas testosteroni b-356. | in addition to 2,3-dihydroxybiphenyl 1,2-dioxygenase (b1,2o), biphenyl-grown cells of comamonas testosteroni b-356 were shown to produce a catechol 2,3-dioxygenase (c2,3o). b1,2o showed strong sequence homology with b1,2os found in other biphenyl catabolic pathways, while partial sequence analysis of the c2,3o of b-356 suggested a relationship with xyleii-encoded c2,3o. the coexistence of two meta-cleavage dioxygenases in this strain prompted a comparison between the catalytic properties of the ... | 1998 | 9522448 |
| population dynamics of phenol-degrading bacteria in activated sludge determined by gyrb-targeted quantitative pcr. | a method for quantifying bacterial populations introduced into an activated-sludge microbial community is described. the method involves extraction of dna from activated sludge, appropriate dilution of the extracted dna with dna extracted from nonintroduced activated sludge, pcr amplification of a gyrb gene fragment from the introduced strain with a set of strain-specific primers, and quantification of the electrophoresed pcr product by densitometry. the adequacy of the method was examined by an ... | 1998 | 9546154 |
| microbiology of a nitrite-oxidizing bioreactor. | the microbiology of the biomass from a nitrite-oxidizing sequencing batch reactor (nosbr) fed with an inorganic salts solution and nitrite as the sole energy source that had been operating for 6 months was investigated by microscopy, by culture-dependent methods, and by molecular biological methods, and the seed sludge that was used to inoculate the nosbr was investigated by molecular biological methods. the nosbr sludge comprised a complex and diverse microbial community containing gram-negativ ... | 1998 | 9572966 |
| chloromethane metabolism by methylobacterium sp. strain cm4 | methylobacterium sp. strain cm4 metabolized chloromethane quantitatively with a molar yield of 2.8 g of whole-cell protein/mol of c. this value was similar to that observed after growth with methanol (2.9 g of protein/mol of c) and about three times larger than the yield with formate (0.94 g of protein/mol of c). chloromethane dehalogenation activity was inducible. minitn5 transposon insertion mutants with altered growth characteristics with chloromethane and other c1 compounds were isolated and ... | 1998 | 9572975 |
| structures of homologous composite transposons carrying cbaabc genes from europe and north america. | is1071 is a class ii transposable element carrying a tnpa gene related to the transposase genes of the tn3 family. copies of is1071 that are conserved with more than 99% nucleotide sequence identity have been found as direct repeats flanking a remarkable variety of catabolic gene sequences worldwide. the sequences of chlorobenzoate catabolic transposons found on pbrc60 (tn5271) in niagara falls, n.y., and on pcpe3 in bologna, italy, show that these transposons were formed from highly homologous ... | 1998 | 9572977 |
| 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 |
| catalytic contribution of phenylalanine-101 of 3-oxo-delta 5-steroid isomerase. | 3-oxo-delta 5-steroid isomerase (ksi, ec 5.3.3.1) from pseudomonas testosteroni catalyzes the isomerization of a variety of 3-oxo-delta 5-steroids to their conjugated delta4-isomers through the formation of an intermediate dienolate ion. it has previously been found in our laboratory that the aromatic ring of phe-101 is important for catalysis. the present work extends these studies. two double-mutant ksis (d38e/f101l and d38e/f101a) were prepared to compare the free energy profiles for the reac ... | 1998 | 9578560 |
| the adsorption of substrate-binding domain of phb depolymerases to the surface of poly(3-hydroxybutyric acid). | the binding characteristic of phb depolymerase has been studied by using glutathione s-transferase (gst) fusion proteins with substrate-binding domain of three bacterial phb depolymerases, alcaligenes faecalis, comamonas acidovorans and comamonas testosteroni. analysis using immuno-gold labeling technique and transmission electron microscopy indicated that a novel gst fusion protein derived from a. faecalis enzyme adsorbed to the surface of poly(3-hydroxybutyric acid) (p(3hb)) single crystals li ... | 1998 | 9585889 |
| two nearly identical aromatic compound hydrolase genes in a strong polychlorinated biphenyl degrader, rhodococcus sp. strain rha1. | the two 2-hydroxy-6-oxohepta-2,4-dienoate (hohd) hydrolase genes, etbd1 and etbd2, were cloned from a strong polychlorinated biphenyl (pcb) degrader, rhodococcus sp. strain rha1, and their nucleotide sequences were determined. the etbd2 gene was located in the vicinity of bpha gene homologs and encoded an enzyme whose amino-terminal sequence was very similar to the amino-terminal sequence of the hohd hydrolase which was purified from rha1. using the etbd2 gene fragment as a probe, we cloned the ... | 1998 | 9603807 |
| distal cleavage of 3-chlorocatechol by an extradiol dioxygenase to 3-chloro-2-hydroxymuconic semialdehyde. | a 2,3-dihydroxybiphenyl 1,2-dioxygenase from the naphthalenesulfonate-degrading bacterium sphingomonas sp. strain bn6 oxidized 3-chlorocatechol to a yellow product with a strongly ph-dependent absorption maximum at 378 nm. a titration curve suggested (de)protonation of an ionizable group with a pka of 4.4. the product was isolated, purified, and converted, by treatment with diazomethane, to a dimethyl derivative and, by incubation with ammonium chloride, to a picolinic acid derivative. mass spec ... | 1998 | 9603871 |
| characterization of the hca cluster encoding the dioxygenolytic pathway for initial catabolism of 3-phenylpropionic acid in escherichia coli k-12. | we have identified, cloned, and sequenced the hca cluster encoding the dioxygenolytic pathway for initial catabolism of 3-phenylpropionic acid (pp) in escherichia coli k-12. this cluster maps at min 57.5 of the chromosome and is composed of five catabolic genes arranged as a putative operon (hcaa1a2cbd) and two additional genes transcribed in the opposite direction that encode a potential permease (hcat) and a regulator (hcar). sequence comparisons revealed that while hcaa1a2cd genes encode the ... | 1998 | 9603882 |
| homology model of the quinohaemoprotein alcohol dehydrogenase from comamonas testosteroni. | a molecular model of qh-adh, the quinohaemoprotein alcohol dehydrogenase from comamonas testosteroni, has been built by homology modelling. sequence similarity of n-terminal residues 1-570 with the alpha-subunit of quinoprotein methanol dehydrogenases (mdhs) from methylophilus methylotrophus w3a1 and methylobacterium extorquens provided a basis for the design of the pqq-binding domain of qh-adh. minimal sequence similarity with cytochrome c551 from ectothiorhodospira halophila and cytochrome c5 ... | 1998 | 9613842 |
| diverse and related 16s rrna-encoding dna sequences in prostate tissues of men with chronic prostatitis. | treatment of chronic prostatitis/chronic pelvic pain syndrome is often empirical because clinical culture methods fail to detect prostate-associated pathogens in >90% of patients. previously, we tested a variety of specific-microorganism pcrs and began a dna sequence study after we found that 77% of prostatitis patients were pcr positive for prokaryotic rrna-encoding dna sequences (rdnas) despite negative cultures using optimal techniques. in the present study, 36 rdna clones from 23 rdna-positi ... | 1998 | 9620394 |
| crystal structure and enzyme mechanism of delta 5-3-ketosteroid isomerase from pseudomonas testosteroni. | bacterial delta 5-3-ketosteroid isomerase (ksi) from pseudomonas testosteroni has been intensively studied as a prototype for understanding an enzyme-catalyzed allylic rearrangement involving intramolecular proton transfer. asp38 serves as a general base to abstract the proton from the steroid c4-h, which is a much stronger base than the carboxyl group of this residue. this unfavorable proton transfer requires 11 kcal/mol of energy which has to be provided by favorable interactions between catal ... | 1998 | 9622484 |
| enantioselective uptake and degradation of the chiral herbicide dichlorprop [(rs)-2-(2,4-dichlorophenoxy)propanoic acid] by sphingomonas herbicidovorans mh. | sphingomonas herbicidovorans mh was able to completely degrade both enantiomers of the chiral herbicide dichlorprop [(rs)-2-(2,4-dichlorophenoxy)propanoic acid], with preferential degradation of the (s) enantiomer over the (r) enantiomer. these results are in agreement with the recently reported enantioselective degradation of mecoprop [(rs)-2-(4-chloro-2-methylphenoxy)propanoic acid] by this bacterium (c. zipper, k. nickel, w. angst, and h.-p. e. kohler, appl. environ. microbiol. 62:4318-4322, ... | 1998 | 9642189 |
| a highly selective pcr protocol for detecting 16s rrna genes of the genus pseudomonas (sensu stricto) in environmental samples. | pseudomonas species are plant, animal, and human pathogens; exhibit plant pathogen-suppressing properties useful in biological control; or express metabolic versatilities valued in biotechnology and bioremediation. specific detection of pseudomonas species in the environment may help us gain a more complete understanding of the ecological significance of these microorganisms. the objective of this study was to develop a pcr protocol for selective detection of pseudomonas (sensu stricto) in envir ... | 1998 | 9647828 |
| spatial and temporal variation of phenanthrene-degrading bacteria in intertidal sediments. | phenanthrene-degrading bacteria were isolated from a 1-m2 intertidal sediment site in boston harbor. samples were taken six times over 2 years. a total of 432 bacteria were isolated and characterized by biochemical testing. when clustered on the basis of phenotypic characteristics, the isolates could be separated into 68 groups at a similarity level of approximately 70%. several groups (a total of 200 isolates) corresponded to well-characterized species belonging the genera vibrio and pseudomona ... | 1998 | 9647830 |
| intergeneric transfer of conjugative and mobilizable plasmids harbored by escherichia coli in the gut of the soil microarthropod folsomia candida (collembola). | the gut of the soil microarthropod folsomia candida provides a habitat for a high density of bacterial cells (t. thimm, a. hoffmann, h. borkott, j. c. munch, and c. c. tebbe, appl. environ. microbiol. 64:2660-2669, 1998). we investigated whether these gut bacteria act as recipients for plasmids from escherichia coli. filter mating with e. coli donor cells and collected feces of f. candida revealed that the broad-host-range conjugative plasmid prp4-luc (prp4 with a luciferase marker gene) transfe ... | 1998 | 9647844 |
| high-efficiency incorporation in vivo of tyrosine analogues with altered hydroxyl acidity in place of the catalytic tyrosine-14 of delta 5-3-ketosteroid isomerase of comamonas (pseudomonas) testosteroni: effects of the modifications on isomerase kinetics. | versions of the y55f/y88f modified form of delta 5-3-ketosteroid isomerase in which the active-site tyrosine-14 is replaced by 2-fluorotyrosine, 3-fluorotyrosine, and 2,3-difluorotyrosine, amino acids having progressively greater acidity of their phenolic hydroxyls, have been expressed in an escherichia coli host and purified to high homogeneity. the steady-state kinetic properties of y55f/y88f ksi and its fluorotyrosine modified forms have been determined. the mechanistic implications of the re ... | 1998 | 9657686 |
| the regulated outer membrane protein omp21 from comamonas acidovorans is identified as a member of a new family of eight-stranded beta-sheet proteins by its sequence and properties. | omp21, a minor outer membrane protein of the soil bacterium comamonas acidovorans, was purified from a spontaneous mutant lacking a surface layer and long-chain lipopolysaccharide. omp21 synthesis is enhanced by oxygen depletion, and the protein has a variable electrophoretic mobility in sodium dodecyl sulfate-polyacrylamide gel electrophoresis due to its heat-modifiable behavior. the structural gene omp21 encodes a precursor of 204 amino acids with a putative signal peptide of 21 amino acids. m ... | 1998 | 9683466 |
| chemical structure of lipid a isolated from flavobacterium meningosepticum lipopolysaccharide. | the chemical structure of the lipid a of the lipopolysaccharide component isolated from flavobacterium meningosepticum ifo 12535 was elucidated. methylation and nuclear magnetic resonance analyses showed that two kinds of hydrophilic backbone exist in the free lipid a: a beta (1-->6)-linked 2-amino-2-deoxy-d-glucose, which is usually present in enterobacterial lipid a's, and a 2-amino-6-o-(2, 3-diamino-2,3-dideoxy-beta-d-glucopyranosyl)-2-deoxy-d-glucose, in a molar ratio of 1.00:0.35. both back ... | 1998 | 9683486 |
| genetic analysis of dioxin dioxygenase of sphingomonas sp. strain rw1: catabolic genes dispersed on the genome. | the dioxin dioxygenase of sphingomonas sp. strain rw1 activates dibenzo-p-dioxin and dibenzofuran for further metabolism by introducing two atoms of oxygen at a pair of vicinal carbon atoms, one of which is involved in one of the bridges between the two aromatic rings, i.e., an angular dioxygenation. the dxna1 and dxna2 cistrons encoding this dioxygenase have been cloned and shown to be located just upstream of a hydrolase gene which specifies an enzyme involved in the subsequent step of the dib ... | 1998 | 9683494 |
| analysis of beta-subgroup proteobacterial ammonia oxidizer populations in soil by denaturing gradient gel electrophoresis analysis and hierarchical phylogenetic probing | a combination of denaturing gradient gel electrophoresis (dgge) and oligonucleotide probing was used to investigate the influence of soil ph on the compositions of natural populations of autotrophic beta-subgroup proteobacterial ammonia oxidizers. pcr primers specific to this group were used to amplify 16s ribosomal dna (rdna) from soils maintained for 36 years at a range of ph values, and pcr products were analyzed by dgge. genus- and cluster-specific probes were designed to bind to sequences w ... | 1998 | 9687457 |
| biochemical and genetic characterization of a gentisate 1, 2-dioxygenase from sphingomonas sp. strain rw5. | a 4,103-bp long dna fragment containing the structural gene of a gentisate 1,2-dioxygenase (ec 1.13.11.4), gtda, from sphingomonas sp. strain rw5 was cloned and sequenced. the gtda gene encodes a 350-amino-acid polypeptide with a predicted size of 38.85 kda. comparison of the gtda gene product with protein sequences in databases, including those of intradiol or extradiol ring-cleaving dioxygenases, revealed no significant homology except for a low similarity (27%) to the 1-hydroxy-2-naphthoate d ... | 1998 | 9696766 |
| molybdopterin radical in bacterial aldehyde dehydrogenases. | the epr spectra of three different molybdoprotein aldehyde dehydrogenases, one purified from comamonas testosteroni and two purified from amycolatopsis methanolica, showed in their oxidized state a novel type of signal. these three enzymes contain two different [2fe-2s] centers, one flavin and one molybdopterin cytosine dinucleotide, as cofactors all of which are expected to be epr silent in the oxidized state. the new epr signal is isotropic with g = 2.004 both at x-band and q-band frequencies, ... | 1998 | 9698384 |
| microvirgula aerodenitrificans gen. nov., sp. nov., a new gram-negative bacterium exhibiting co-respiration of oxygen and nitrogen oxides up to oxygen-saturated conditions. | a denitrifier micro-organism was isolated from an upflow denitrifying filter inoculated with an activated sludge. the cells were gram-negative, catalase- and oxidase-positive curved rods and very motile. they were aerobic as well as anoxic heterotrophs that had an atypical respiratory type of metabolism in which oxygen and nitrogen oxides were used simultaneously as terminal electron acceptors. the g&c content was 65 mol%. our isolate was phenotypically similar to comamonas testosteroni, accordi ... | 1998 | 9734031 |
| 3-ketosteroid-delta1-dehydrogenase of rhodococcus rhodochrous: sequencing of the genomic dna and hyperexpression, purification, and characterization of the recombinant enzyme. | the gene encoding 3-ketosteroid-delta1-dehydrogenase from rhodococcus rhodochrous was cloned and sequenced. the gene (ksdd) consists of 1,536 nucleotides and encodes an enzyme protein of 511 amino acid residues. the amino terminal methionine residue was deleted in the mature protein. the amino acids involved in the flavin binding site are conserved in the dehydrogenase sequence. the deduced amino acid sequence is highly homologous to that from arthrobacter simplex but less so to that from pseudo ... | 1998 | 9792929 |
| molecular detection, isolation, and physiological characterization of functionally dominant phenol-degrading bacteria in activated sludge. | dna was isolated from phenol-digesting activated sludge, and partial fragments of the 16s ribosomal dna (rdna) and the gene encoding the largest subunit of multicomponent phenol hydroxylase (lmph) were amplified by pcr. an analysis of the amplified fragments by temperature gradient gel electrophoresis (tgge) demonstrated that two major 16s rdna bands (bands r2 and r3) and two major lmph gene bands (bands p2 and p3) appeared after the activated sludge became acclimated to phenol. the nucleotide s ... | 1998 | 9797297 |
| in situ detection of bacteria in continuous-flow cultures of seawater sediment suspensions with fluorescently labelled rrna-directed oligonucleotide probes. | rrna-targeted and fluorescently labelled oligonucleotide probes were used to study the composition of natural bacterial populations in continuous-flow cultures of seawater sediment suspensions. the cultures were run as enrichment cultures with increasing dilution rates, and hexadecane as the sole carbon source. total cell numbers were analysed by counting dapi (4',6-diamidino-2-phenylindole)-stained cells. to differentiate the population composition, oligonucleotide probes for eubacteria, for cy ... | 1998 | 9802019 |
| adaptation of comamonas testosteroni ta441 to utilize phenol: organization and regulation of the genes involved in phenol degradation. | comamonas testosteroni ta441 was not able to grow on phenol as a sole carbon and energy source, but it gained the ability to utilize phenol after a 2-3-week incubation in a medium containing phenol. phenol hydroxylase (ph) and catechol 2,3-dioxygenase (c230) were highly induced by phenol in the adapted strain designated as strain p1, suggesting that phenol was degraded via the meta-pathway. gene clusters for phenol degradation were isolated from both strains ta441 and p1. the structural genes en ... | 1998 | 9802031 |
| purification and properties of a novel sulfatase from pseudomonas testosteroni that hydrolyzed 3 beta-hydroxy-5-cholenoic acid 3-sulfate. | a novel sulfatase hydrolyzing the sulfate ester bond in 3 beta-hydroxy-5-cholenoic acid 3-sulfate (delta 5-3 beta-sulfate) was purified from pseudomonas testosteroni atcc 11996 as the second bile acid sulfatase. the molecular weight was 95,000 and the molecule was composed of a homodimer of a subunit of which the molecular weight was 46,000. this sulfatase hydrolyzed delta 5-3 beta-sulfate to 3 alpha-hydroxy-5-cholenoic acid and sulfuric acid with inversion of beta- to alpha-configuration of the ... | 1998 | 9805374 |
| 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 |
| molecular cloning, overexpression, and characterization of steroid-inducible 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase from comamonas testosteroni. a novel member of the short-chain dehydrogenase/reductase superfamily. | 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase (3alpha-hsd/cr) from comamonas testosteroni, a bacterium that is able to grow on steroids as the sole carbon source, catalyzes the oxidoreduction at position 3 of a variety of c19-27 steroids and the carbonyl reduction of a variety of nonsteroidal aldehydes and ketones. the gene of this steroid-inducible 3alpha-hsd/cr was cloned by screening a c. testosteroni gene bank with a homologous dna probe that was obtained by polymerase chain reactio ... | 1998 | 9812981 |
| degradation of polychlorinated biphenyl metabolites by naphthalene-catabolizing enzymes. | the ability of the dehydrogenase and ring cleavage dioxygenase of the naphthalene degradation pathway to transform 3,4-dihydroxylated biphenyl metabolites was investigated. 1,2-dihydro-1, 2-dihydroxynaphthalene dehydrogenase was expressed as a histidine-tagged protein. the purified enzyme transformed 2, 3-dihydro-2,3-dihydroxybiphenyl, 3,4-dihydro-3,4-dihydroxybiphenyl, and 3,4-dihydro-3,4-dihydroxy-2,2',5,5'-tetrachlorobiphenyl to 2, 3-dihydroxybiphenyl, 3,4-dihydroxybiphenyl (3,4-dhb), and 3, ... | 1998 | 9835542 |
| isolation of marine polycyclic aromatic hydrocarbon (pah)-degrading cycloclasticus strains from the gulf of mexico and comparison of their pah degradation ability with that of puget sound cycloclasticus strains. | phenanthrene- and naphthalene-degrading bacteria were isolated from four offshore and nearshore locations in the gulf of mexico by using a modified most-probable-number technique. the concentrations of these bacteria ranged from 10(2) to 10(6) cells per ml of wet surficial sediment in mildly contaminated and noncontaminated sediments. a total of 23 strains of polycyclic aromatic hydrocarbon (pah)-degrading bacteria were obtained. based on partial 16s ribosomal dna sequences and phenotypic charac ... | 1998 | 9835552 |
| purification and characterization of gallic acid decarboxylase from pantoea agglomerans t71 | oxygen-sensitive gallic acid decarboxylase from pantoea (formerly enterobacter) agglomerans t71 was purified from a cell extract after stabilization by reducing agents. this enzyme has a molecular mass of approximately 320 kda and consists of six identical subunits. it is highly specific for gallic acid. gallic acid decarboxylase is unique among similar decarboxylases in that it requires iron as a cofactor, as shown by plasma emission spectroscopy (which revealed an iron content of 0.8 mol per m ... | 1998 | 9835557 |
| psychrotolerant bacteria isolated from arctic soil that degrade polychlorinated biphenyls at low temperatures | psychrotolerant polychlorinated biphenyl (pcb)-degrading bacteria were isolated at 7 degreesc from pcb-contaminated arctic soil by using biphenyl as the sole organic carbon source. these isolates were distinguished from each other by differences in substrates that supported growth and substrates that were oxidized. 16s ribosomal dna sequences suggest that these isolates are most closely related to the genus pseudomonas. total removal of aroclor 1242, and rates of removal of selected pcb congener ... | 1998 | 9835569 |
| enumeration and detection of anaerobic ferrous iron-oxidizing, nitrate-reducing bacteria from diverse european sediments. | anaerobic, nitrate-dependent microbial oxidation of ferrous iron was recently recognized as a new type of metabolism. in order to study the occurrence of three novel groups of ferrous iron-oxidizing, nitrate-reducing bacteria (represented by strains brg1, brg2, and brg3), 16s rrna-targeted oligonucleotide probes were developed. in pure-culture experiments, these probes were shown to be suitable for fluorescent in situ hybridization, as well as for hybridization analysis of denaturing gradient ge ... | 1998 | 9835573 |
| assessment of changes in microbial community structure during operation of an ammonia biofilter with molecular tools. | biofiltration has been used for two decades to remove odors and various volatile organic and inorganic compounds in contaminated off-gas streams. although biofiltration is widely practiced, there have been few studies of the bacteria responsible for the removal of air contaminants in biofilters. in this study, molecular techniques were used to identify bacteria in a laboratory-scale ammonia biofilter. both 16s rrna and ammonia monooxygenase (amoa) genes were used to characterize the heterotrophi ... | 1998 | 9835577 |
| flow cytometric analysis of the in situ accessibility of escherichia coli 16s rrna for fluorescently labeled oligonucleotide probes. | in situ identification of whole fixed bacterial cells by hybridization with fluorescently labeled, rrna-targeted oligonucleotide probes is often limited by low signal intensities. in addition to an impermeability of the cell periphery and a low cellular rrna content, the three-dimensional structure of the ribosome may hinder the access of oligonucleotides to their target sites. until now, a systematic study on the accessibility of 16s rrna target sites had not been done. here, we report fluoresc ... | 1998 | 9835591 |
| a natural view of microbial biodiversity within hot spring cyanobacterial mat communities. | this review summarizes a decade of research in which we have used molecular methods, in conjunction with more traditional approaches, to study hot spring cyanobacterial mats as models for understanding principles of microbial community ecology. molecular methods reveal that the composition of these communities is grossly oversimplified by microscopic and cultivation methods. for example, none of 31 unique 16s rrna sequences detected in the octopus spring mat, yellowstone national park, matches t ... | 1998 | 9841675 |
| novel organization of the genes for phthalate degradation from burkholderia cepacia dbo1. | burkholderia cepacia dbo1 is able to utilize phthalate as the sole source of carbon and energy for growth. two overlapping cosmid clones containing the genes for phthalate degradation were isolated from this strain. subcloning and activity analysis localized the genes for phthalate degradation to two separate regions on the cosmid clones. analysis of the nucleotide sequence of these two regions showed that the genes for phthalate degradation are arranged in at least three transcriptional units. ... | 1998 | 9851995 |
| rapid identification of burkholderia pseudomallei by latex agglutination based on an exopolysaccharide-specific monoclonal antibody. | we recently identified a constitutively expressed exopolysaccharide of burkholderia pseudomallei which is composed of a unique linear tetrasaccharide repeating unit consisting of three galactose residues and one 3-deoxy-d-manno-2-octulosonic acid residue. in this study we developed a latex agglutination test based on monoclonal antibody 3015, which is specific for this exopolysaccharide, and evaluated this test for rapid identification of b. pseudomallei grown on agar plates. all 74 environmenta ... | 1999 | 9854098 |
| microdermatology: cell surface in the interaction of microbes with the external world. | 1999 | 9864305 | |
| genetic and biochemical characterization of a 2-pyrone-4, 6-dicarboxylic acid hydrolase involved in the protocatechuate 4, 5-cleavage pathway of sphingomonas paucimobilis syk-6. | sphingomonas paucimobilis syk-6 is able to grow on a wide variety of dimeric lignin compounds with guaiacyl moieties, which are converted into protocatechuate by the actions of lignin degradation enzymes in this strain. protocatechuate is a key metabolite in the syk-6 degradation of lignin compounds with guaiacyl moieties, and it is thought that it degrades to pyruvate and oxaloacetate via the protocatechuate 4,5-cleavage pathway. in a 10.5-kb ecori fragment carrying the protocatechuate 4,5-diox ... | 1999 | 9864312 |
| 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 |
| in situ, real-time catabolic gene expression: extraction and characterization of naphthalene dioxygenase mrna transcripts from groundwater. | we developed procedures for isolating and characterizing in situ-transcribed mrna from groundwater microorganisms catabolizing naphthalene at a coal tar waste-contaminated site. groundwater was pumped through 0.22-microm-pore-size filters, which were then frozen in dry ice-ethanol. rna was extracted from the frozen filters by boiling sodium dodecyl sulfate lysis and acidic phenol-chloroform extraction. transcript characterization was performed with a series of pcr primers designed to amplify nah ... | 1999 | 9872763 |
| morphological and biochemical properties of a sphaerotilus sp. isolated from paper mill slimes. | four strains of filamentous bacteria were isolated from slimes collected in different paper mill factories. morphological and physiological characterization of the isolates indicated an affiliation with the genus sphaerotilus. however, while the physiological properties of the isolates were almost identical, pronounced physiological differences between the isolates and sphaerotilus natans dsm 6575(t), dsm 565, and dsm 566 with respect to their ability to metabolize complex polysaccharides, sugar ... | 1999 | 9872774 |
| cloning and characterization of the polyhydroxybutyrate depolymerase gene of pseudomonas stutzeri and analysis of the function of substrate-binding domains. | the extracellular polyhydroxybutyrate (phb) depolymerase gene (phazpst) of pseudomonas stutzeri was cloned and sequenced. phazpst was composed of 1,728 bp encoding a protein of 576 amino acids. analyses of the n-terminal amino acid sequence and the matrix-assisted laser desorption/ionization-time-of-flight (maldi-tof) mass spectrum of the purified enzyme showed that the mature enzyme consisted of 538 amino acids with a deduced molecular mass of 57,506 da. analysis of the deduced amino acid seque ... | 1999 | 9872779 |
| 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 |
| phylogenetic affinity of a wide, vacuolate, nitrate-accumulating beggiatoa sp. from monterey canyon, california, with thioploca spp. | environmentally dominant members of the genus beggiatoa and thioploca spp. are united by unique morphological and physiological adaptations (s. c. mchatton, j. p. barry, h. w. jannasch, and d. c. nelson, appl. environ. microbiol. 62:954-958, 1996). these adaptations include the presence of very wide filaments (width, 12 to 160 microm), the presence of a central vacuole comprising roughly 80% of the cellular biovolume, and the capacity to internally concentrate nitrate at levels ranging from 150 ... | 1999 | 9872789 |
| the alpha subunit of toluene dioxygenase from pseudomonas putida f1 can accept electrons from reduced ferredoxintol but is catalytically inactive in the absence of the beta subunit. | the oxygenase component of toluene dioxygenase from pseudomonas putida f1 is an iron-sulfur protein (isptol) consisting of alpha (todc1) and beta (todc2) subunits. purified todc1 gave absorbance and electron paramagnetic resonance spectra identical to those given by purified isptol. todc1 was reduced by nadh and catalytic amounts of reductasetol and ferredoxintol. reduced todc1 did not oxidize toluene, and catalysis was strictly dependent on the presence of purified todc2. | 1999 | 9872799 |
| the phn genes of burkholderia sp. strain rp007 constitute a divergent gene cluster for polycyclic aromatic hydrocarbon catabolism. | cloning and molecular ecological studies have underestimated the diversity of polycyclic aromatic hydrocarbon (pah) catabolic genes by emphasizing classical nah-like (nah, ndo, pah, and dox) sequences. here we report the description of a divergent set of pah catabolic genes, the phn genes, which although isofunctional to the classical nah-like genes, show very low homology. this phn locus, which contains nine open reading frames (orfs), was isolated on an 11.5-kb hindiii fragment from phenanthre ... | 1999 | 9882667 |
| phylogenetic differences between particle-associated and planktonic ammonia-oxidizing bacteria of the beta subdivision of the class proteobacteria in the northwestern mediterranean sea. | the aim of this study was to determine if there were differences between the types of ammonia-oxidizing bacteria of the beta subdivision of the class proteobacteria associated with particulate material and planktonic samples obtained from the northwestern mediterranean sea. a nested pcr procedure performed with ammonia oxidizer-selective primers was used to amplify 16s rrna genes from extracted dna. the results of partial and full-length sequence analyses of 16s rrna genes suggested that differe ... | 1999 | 9925616 |
| conversion of 3-chlorocatechol by various catechol 2,3-dioxygenases and sequence analysis of the chlorocatechol dioxygenase region of pseudomonas putida gj31. | pseudomonas putida gj31 contains an unusual catechol 2,3-dioxygenase that converts 3-chlorocatechol and 3-methylcatechol, which enables the organism to use both chloroaromatics and methylaromatics for growth. a 3.1-kb region of genomic dna of strain gj31 containing the gene for this chlorocatechol 2,3-dioxygenase (cbze) was cloned and sequenced. the cbze gene appeared to be plasmid localized and was found in a region that also harbors genes encoding a transposase, a ferredoxin that was homologou ... | 1999 | 9973359 |
| complete sequence of a 184-kilobase catabolic plasmid from sphingomonas aromaticivorans f199. | the complete 184,457-bp sequence of the aromatic catabolic plasmid, pnl1, from sphingomonas aromaticivorans f199 has been determined. a total of 186 open reading frames (orfs) are predicted to encode proteins, of which 79 are likely directly associated with catabolism or transport of aromatic compounds. genes that encode enzymes associated with the degradation of biphenyl, naphthalene, m-xylene, and p-cresol are predicted to be distributed among 15 gene clusters. the unusual coclustering of gene ... | 1999 | 10049392 |
| purification and characterization of gentisate 1,2-dioxygenases from pseudomonas alcaligenes ncib 9867 and pseudomonas putida ncib 9869. | two 3-hydroxybenzoate-inducible gentisate 1,2-dioxygenases were purified to homogeneity from pseudomonas alcaligenes ncib 9867 (p25x) and pseudomonas putida ncib 9869 (p35x), respectively. the estimated molecular mass of the purified p25x gentisate 1, 2-dioxygenase was 154 kda, with a subunit mass of 39 kda. its structure is deduced to be a tetramer. the pi of this enzyme was established to be 4.8 to 5.0. the subunit mass of p35x gentisate 1, 2-dioxygenase was 41 kda, and this enzyme was deduced ... | 1999 | 10049846 |
| molecular analysis of a novel methanesulfonic acid monooxygenase from the methylotroph methylosulfonomonas methylovora. | methylosulfonomonas methylovora m2 is an unusual gram-negative methylotrophic bacterium that can grow on methanesulfonic acid (msa) as the sole source of carbon and energy. oxidation of msa by this bacterium is carried out by a multicomponent msa monooxygenase (msamo). cloning and sequencing of a 7.5-kbp sphi fragment of chromosomal dna revealed four tightly linked genes encoding this novel monooxygenase. analysis of the deduced msamo polypeptide sequences indicated that the enzyme contains a tw ... | 1999 | 10094704 |
| selection of clc, cba, and fcb chlorobenzoate-catabolic genotypes from groundwater and surface waters adjacent to the hyde park, niagara falls, chemical landfill. | the frequency of isolation of three nonhomologous chlorobenzoate catabolic genotypes (clc, cba, and fcb) was determined for 464 isolates from freshwater sediments and groundwater in the vicinity of the hyde park industrial landfill site in the niagara watershed. samples were collected from both contaminated and noncontaminated sites during spring, summer, and fall and enriched at 4, 22, or 32 degrees c with micromolar to millimolar concentrations of chlorobenzoates and 3-chlorobiphenyl (m. c. pe ... | 1999 | 10103260 |