| characterization of protocatechuate 4,5-dioxygenase induced from p-hydroxybenzoate-cultured pseudomonas sp. k82. | pseudomonas sp. k82 has been reported to be an aniline-assimilating soil bacterium. however, this strain can use not only aniline as a sole carbon and energy source, but can also utilize benzoate, p-hydroxybenzoate, and aniline analogues. the strain accomplishes this metabolic diversity by using different aerobic pathways. pseudomonas sp. k82, when cultured in p-hydroxybenzoate, showed extradiol cleavage activity of protocatechuate. in accordance with those findings, our study attempted the puri ... | 2004 | 15357311 |
| [comamonas testosteroni strain ti as a potential base for a microbial sensor detecting surfactants]. | strain comamonas testosteroni ti, capable of degrading the nonionic surfactant (nis) nonylphenolethoxylate (op-10), was used for constructing a pilot cellular biosensor. the lower nis detection limit for the biosensor was 0.25 mg/l. we studied the substrate specificity of the biosensor with respect to a wide range of organic compounds: surfactants, polyaromatic compounds (pac), carbohydrates, alcohols, etc. it was shown that the biosensor based on comamonas testosteroni ti did not respond to glu ... | 2004 | 15455722 |
| steroid degradation gene cluster of comamonas testosteroni consisting of 18 putative genes from meta-cleavage enzyme gene tesb to regulator gene tesr. | steroid degradation genes of comamonas testosteroni ta441 are encoded in at least two gene clusters: one containing the meta-cleavage enzyme gene tesb and orf1, 2, 3; and another consisting of orf18, 17, tesi, h, a2, and tesa1, d, e, f, g (tesa2 to orf18 and tesa1 to tesg are encoded in opposite directions). analysis of transposon mutants with low steroid degradation revealed 13 orfs and a gene (orf4, 5, 21, 22, 23, 25, 26, 27, 28, 30, 31, 32, 33, and tesr) involved in steroid degradation in the ... | 2004 | 15474469 |
| steady-state kinetics and inhibition of anaerobically purified human homogentisate 1,2-dioxygenase. | hgo (homogentisate 1,2-dioxygenase; ec 1.13.11.5) catalyses the o2-dependent cleavage of hga (homogentisate) to maleylacetoacetate in the catabolism of tyrosine. anaerobic purification of heterologously expressed fe(ii)-containing human hgo yielded an enzyme preparation with a specific activity of 28.3+/- 0.6 micromol x min(-1) x mg(-1) (20 mm mes, 80 mm nacl, ph 6.2, 25 degrees c), which is almost twice that of the most active preparation described to date. moreover, the addition of reducing ag ... | 2005 | 15479158 |
| the completely sequenced plasmid pest4011 contains a novel incp1 backbone and a catabolic transposon harboring tfd genes for 2,4-dichlorophenoxyacetic acid degradation. | the herbicide 2,4-dichlorophenoxyacetic acid (2,4-d)-degrading bacterium achromobacter xylosoxidans subsp. denitrificans strain est4002 contains plasmid pest4011. this plasmid ensures its host a stable 2,4-d(+) phenotype. we determined the complete 76,958-bp nucleotide sequence of pest4011. this plasmid is a deletion and duplication derivative of pd2m4, the 95-kb highly unstable laboratory ancestor of pest4011, and was self-generated during different laboratory manipulations performed to increas ... | 2004 | 15489427 |
| the "intracellular" poly(3-hydroxybutyrate) (phb) depolymerase of rhodospirillum rubrum is a periplasm-located protein with specificity for native phb and with structural similarity to extracellular phb depolymerases. | rhodospirillum rubrum possesses a putative intracellular poly(3-hydroxybutyrate) (phb) depolymerase system consisting of a soluble phb depolymerase, a heat-stable activator, and a 3-hydroxybutyrate dimer hydrolase (j. m. merrick and m. doudoroff, j. bacteriol. 88:60-71, 1964). in this study we reinvestigated the soluble r. rubrum phb depolymerase (phaz1). it turned out that phaz1 is a novel type of phb depolymerase with unique properties. purified phaz1 was specific for amorphous short-chain-len ... | 2004 | 15489436 |
| tour-mediated effector-independent growth phase-dependent activation of the sigma54 ptou promoter of pseudomonas stutzeri ox1. | transcription of the catabolic touabcdef operon, encoding the toluene-o-xylene monooxygenase of pseudomonas stutzeri ox1, is driven by the sigma(54)-dependent ptou promoter, whose activity is controlled by the phenol-responsive ntrc-like activator tour. in this paper we describe for the first time a peculiar characteristic of this system, namely, that ptou transcription is activated in a growth phase-dependent manner in the absence of genuine effectors of the cognate tour regulator. this phenome ... | 2004 | 15489447 |
| characterization of bacterial community diversity in cystic fibrosis lung infections by use of 16s ribosomal dna terminal restriction fragment length polymorphism profiling. | progressive loss of lung function resulting from the inflammatory response to bacterial colonization is the leading cause of mortality in cystic fibrosis (cf) patients. a greater understanding of these bacterial infections is needed to improve lung disease management. as culture-based diagnoses are associated with fundamental drawbacks, we used terminal restriction fragment (t-rf) length polymorphism profiling and 16s rrna clone data to characterize, without prior cultivation, the bacterial comm ... | 2004 | 15528712 |
| interactions in biofilms between listeria monocytogenes and resident microorganisms from food industry premises. | twenty nine bacterial strains were grown as binary culture biofilms with listeria monocytogenes to assess their influence on the settlement of the latter on stainless steel coupons. most of the strains had been isolated from food processing plants after cleaning and disinfection and were tentatively identified by the apilab plus 3.3.3 database (biomerieux). sixteen of them decreased l. monocytogenes biofilm colony forming units (cfu) counts. three strains, bacillus sp. ccl 9 an unidentified gram ... | 2004 | 15541798 |
| the genes encoding the hydroxylase of 3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione in steroid degradation in comamonas testosteroni ta441. | steroid degradation genes of comamonas testosteroni ta441 are encoded in at least two gene clusters: one containing the meta-cleavage enzyme gene tesb; and another consisting of orf18, 17, tesi, h, orf11, 12, and tesdefg. tesh and i are, respectively, the delta(1)- and delta(4)(5alpha)-dehydrogenase of the 3-ketosteroid, tesd is the hydrolase for the product of meta-cleavage reaction, and tesefg degrade one of the product of tesd. in this report, we describe the identification of the function of ... | 2004 | 15555908 |
| mechanistic roles of ser-114, tyr-155, and lys-159 in 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase from comamonas testosteroni. | 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase (3alpha-hsd/cr) from comamonas testosteroni, a short chain dehydrogenase/reductase, catalyzes the oxidation of androsterone with nad+ to form androstanedione and nadh. a catalytic triad of ser-114, tyr-155, and lys-159 in 3alpha-hsd/cr has been proposed based on structural analysis and sequence alignment of the short chain dehydrogenase/reductase family. the 3alpha-hsd/cr-catalyzed reaction has not been kinetically analyzed in detail, howeve ... | 2004 | 15572373 |
| the atomic resolution structure of methanol dehydrogenase from methylobacterium extorquens. | the crystal structure of methanol dehydrogenase (mdh) from methylobacterium extorquens has been refined without stereochemical restraints at a resolution of 1.2 a. the high-resolution data have defined the conformation of the tricyclic pyrroloquinoline quinone (pqq) cofactor ring as entirely planar. the detailed definition of the active-site geometry has shown many features that are similar to the quinohaemo-protein alcohol dehydrogenases from comamonas testosteroni and pseudomonas putida, both ... | 2004 | 15608378 |
| effects of ph amendment on metal working fluid wastewater biological treatment using a defined bacterial consortium. | the aim of this study was to determine whether ph amendment of a highly alkaline metal working fluid (mwf) wastewater would improve biological treatment in a bioreactor system following introduction of a bacterial inoculum (comprised of the following strains: agrobacterium radiobacter, comamonas testosteroni, methylobacterium mesophilicum, microbacterium esteraromaticum, and microbacterium saperdae). the ph values tested were 6, 7, 8, and 9. three replicate batch mode bioreactors inoculated with ... | 2005 | 15625673 |
| preliminary evaluation of the api 20ne and rapid nf plus systems for rapid identification of burkholderia pseudomallei and b. mallei. | we evaluated the api 20ne and the rapid nf plus systems with 58 burkholderia pseudomallei and 23 b. mallei strains for identification of these agents, but neither was reliable for confirmatory identification, with only 0 to 60% strains identified accurately. a greater diversity of strains in the system databases would be beneficial. | 2005 | 15635021 |
| protocatechuate 4,5-dioxygenase from comamonas testosteroni t-2: biochemical and molecular properties of a new subgroup within class iii of extradiol dioxygenases. | comamonas testosteroni t-2 degraded at least eight aromatic compounds via protocatechuate (pca), whose extradiol ring cleavage to 2-hydroxy-4-carboxymuconate semialdehyde (hcms) was catalysed by pca 4,5-dioxygenase (pmdab). this inducible, heteromultimeric enzyme was purified. it contained two subunits, alpha (pmda) and beta (pmdb), and the molecular masses of the denatured proteins were 18 kda and 31 kda, respectively. pca was converted stoichiometrically to hcms with an apparent k(m) of 55 mum ... | 2005 | 15650824 |
| over-expression in escherichia coli of a thermally stable and regio-selective nitrile hydratase from comamonas testosteroni 5-mgam-4d. | the genes encoding a thermally stable and regio-selective nitrile hydratase (nhase) and an amidase from comamonas testosteroni 5-mgam-4d have been cloned and sequenced, and active nhase has been over-produced in escherichia coli. maximal activity requires co-expression of a small open reading frame immediately downstream from the nhase beta subunit gene. compared to the native organism, the e. coli biocatalyst has nearly threefold more nhase activity on a dry cell weight basis, and this activity ... | 2005 | 15668757 |
| metabolism of dibenzofuran and dibenzo-p-dioxin by the biphenyl dioxygenase of burkholderia xenovorans lb400 and comamonas testosteroni b-356. | we examined the metabolism of dibenzofuran (df) and dibenzo-p-dioxin (dd) by the biphenyl dioxygenase (bpdo) of comamonas testosteroni b-356 and compared it with that of burkholderia xenovorans lb400. data showed that both enzymes oxygenated df at a low rate, but escherichia coli cells expressing lb400 bpdo degraded df at higher rate (30 nmol in 18 h) compared with cells expressing b-356 bpdo (2 nmol in 18 h). furthermore, both bpdos produced dihydro-dihydroxy-dibenzofuran as a major metabolite, ... | 2005 | 15700128 |
| quantitative molecular assay for fingerprinting microbial communities of wastewater and estrogen-degrading consortia. | a quantitative fingerprinting method, called the real-time terminal restriction fragment length polymorphism (real-time-t-rflp) assay, was developed for simultaneous determination of microbial diversity and abundance within a complex community. the real-time-t-rflp assay was developed by incorporating the quantitative feature of real-time pcr and the fingerprinting feature of t-rflp analysis. the assay was validated by using a model microbial community containing three pure strains, an escherich ... | 2005 | 15746346 |
| medium composition affects the degree and pattern of cadmium inhibition of naphthalene biodegradation. | metals have been reported to inhibit organic pollutant biodegradation; however, widely varying degrees and patterns of inhibition have been reported. to investigate the roles of medium composition and metal bioavailability on these different degrees and patterns of inhibition, we assessed the impact of cadmium on naphthalene biodegradation by a newly isolated strain of comamonas testosteroni in three chemically-defined minimal salts media (msm): tris-buffered msm, pipes-buffered msm, and bushnel ... | 2005 | 15823325 |
| [isolation and identification of comamonas testosteroni: cloning and overexpression of 3alpha-hydroxysteroid dehydrogenase in e.coli]. | to isolate and identify 3alpha-hydroxysteroid dehydrogenase (3alpha-hsd) producing comamonas testosteroni from soil, and to clone and overexpress 3alpha-hsd in e.coli. | 2005 | 15841157 |
| depolymerisation and biodegradation of a synthetic tanning agent by activated sludges, the bacteria arthrobacter globiformis and comamonas testosteroni, and the fungus cunninghamella polymorpha. | degradation of a synthetic tanning agent cnsf (a condensation product of 2-naphthalenesulfonic acid (2-nsa) and formaldehyde) by four activated sludges, two previously characterised bacterial strains, arthrobacter sp. 2ac and comamonas sp. 4bc, and the fungus cunninghamella polymorpha, was studied in batch culture at 25 degrees c by determining the changes in the concentrations of cnsf and its component monomers and oligomers (n2-n11). the loss of individual oligomers was correlated with the len ... | 2005 | 15865336 |
| comamonas (pseudomonas) testosteroni endocarditis. | comamonas testosteroni has rarely been implicated as a human pathogen. we report a case of infectious endocarditis due to this organism, occurring in a 49-year-old man. the posterior leaflet of the mitral valve contained a 1 x 1 cm vegetation and showed myxoid degeneration and acute inflammation. the patient had no evidence of reinfection after 32 months. the infection was almost certainly community acquired, as is usually true for this organism. | 2005 | 15914299 |
| cooperative effect of two surface amino acid mutations (q252l and e170k) in glucose dehydrogenase from bacillus megaterium iwg3 on stabilization of its oligomeric state. | a thermostable glucose dehydrogenase (glcdh) mutant of bacillus megaterium iwg3 harboring the q252l substitution (y. makino, s. negoro, i. urabe, and h. okada, j. biol. chem. 264:6381-6385, 1989) is stable at ph values above 9, but only in the presence of 2 m nacl. another glcdh mutant exhibiting increased stability at an alkaline ph in the absence of nacl has been isolated previously (s.-h. baik, t. ide, h. yoshida, o. kagami, and s. harayama, appl. microbiol. biotechnol. 61:329-335, 2003). thi ... | 2005 | 15933031 |
| isolation of soil bacteria adapted to degrade humic acid-sorbed phenanthrene. | the goal of these studies was to determine how sorption by humic acids affected the bioavailability of polynuclear aromatic hydrocarbons (pahs) to pah-degrading microbes. micellar solutions of humic acid were used as sorbents, and phenanthrene was used as a model pah. enrichments from pah-contaminated soils established with nonsorbed phenanthrene yielded a total of 25 different isolates representing a diversity of bacterial phylotypes. in contrast, only three strains of burkholderia spp. and one ... | 2005 | 16000791 |
| a novel mammalian expression system derived from components coordinating nicotine degradation in arthrobacter nicotinovorans pao1. | we describe the design and detailed characterization of 6-hydroxy-nicotine (6hnic)-adjustable transgene expression (nice) systems engineered for lentiviral transduction and in vivo modulation of angiogenic responses. arthrobacter nicotinovorans pao1 encodes a unique catabolic machinery on its plasmid pao1, which enables this gram-positive soil bacterium to use the tobacco alkaloid nicotine as the exclusive carbon source. the 6hnic-responsive repressor-operator (hdnor-o(nic)) interaction, control ... | 2005 | 16002786 |
| molecular cloning and structural analysis of quinohemoprotein alcohol dehydrogenase adh-iig from pseudomonas putida hk5. | depending on the alcohols used as growth substrates, pseudomonas putida hk5 produces two distinct quinohemoprotein alcohol dehydrogenases, adh-iib and adh-iig, both of which contain pyrroloquinoline quinone (pqq) and heme c as the prosthetic groups but show different substrate specificities, especially for diol substrates. molecular cloning of the gene of adh-iib and its crystal structure are already reported. here, molecular cloning of the gene, qgda, and solution of the three-dimensional struc ... | 2005 | 16061256 |
| superiority of molecular techniques for identification of gram-negative, oxidase-positive rods, including morphologically nontypical pseudomonas aeruginosa, from patients with cystic fibrosis. | phenotypic identification of gram-negative bacteria from cystic fibrosis (cf) patients carries a high risk of misidentification. therefore, we compared the results of biochemical identification by api 20ne with 16s rrna gene sequencing in 88 gram-negative, oxidase-positive rods, other than morphologically and biochemically typical p. aeruginosa, from respiratory secretions of cf patients. the api 20ne allowed correct identification of the bacterial species in 15 out of 88 (17%) isolates investig ... | 2005 | 16081953 |
| biosynthesis of medium chain length poly(3-hydroxyalkanoates) (mcl-phas) by comamonas testosteroni during cultivation on vegetable oils. | comamonas testosteroni has been studied for its ability to synthesize and accumulate medium chain length poly(3-hydroxyalkanoates) (mcl-phas) during cultivation on vegetable oils available in the local market. castor seed oil, coconut oil, mustard oil, cotton seed oil, groundnut oil, olive oil and sesame oil were supplemented in the mineral medium as a sole source of carbon for growth and phas accumulation. the composition of phas was analysed by a coupled gas chromatography/mass spectroscopy (g ... | 2005 | 16084364 |
| plasmid-mediated bioaugmentation of activated sludge bacteria in a sequencing batch moving bed reactor using pnb2. | the applicability of plasmid pnb2 for bioaugmentation of bacteria in model wastewater treatment reactors receiving 3-chloroaniline (3-ca) was investigated. | 2005 | 16108914 |
| impact of membrane fatty acid composition on the uncoupling sensitivity of the energy conservation of comamonas testosteroni atcc 17454. | the fatty acid composition of pyruvate-grown comamonas testosteroni atcc 17454 was analyzed after growth at 30 and 20 degrees c and after half-maximum growth inhibition caused by different membrane-active chemicals at 30 degrees c. palmitic acid (16:0), palmitoleic acid (16:1 omega7c) and vaccenic acid (18:1 omega7c) were the dominant fatty acids. at 20 degrees c, the proportion of palmitic acid decreased and those of palmitoleic and vaccenic acid increased. saturation degree was also lowered wh ... | 2006 | 16133339 |
| a second 5-carboxyvanillate decarboxylase gene, ligw2, is important for lignin-related biphenyl catabolism in sphingomonas paucimobilis syk-6. | a lignin-related biphenyl compound, 5,5'-dehydrodivanillate (ddva), is degraded to 5-carboxyvanillate (5cva) by the enzyme reactions catalyzed by ddva o-demethylase (ligx), meta-cleavage oxygenase (ligz), and meta-cleavage compound hydrolase (ligy) in sphingomonas paucimobilis syk-6. 5cva is then transformed to vanillate by a nonoxidative 5cva decarboxylase and is further degraded through the protocatechuate 4,5-cleavage pathway. a 5cva decarboxylase gene, ligw, was isolated from syk-6 (x. peng, ... | 2005 | 16151081 |
| new chitosan-degrading strains that produce chitosanases similar to choa of mitsuaria chitosanitabida. | the betaproteobacterium mitsuaria chitosanitabida (formerly matsuebacter chitosanotabidus) 3001 produces a chitosanase (choa) that is classified in glycosyl hydrolase family 80. while many chitosanase genes have been isolated from various bacteria to date, they show limited homology to the m. chitosanitabida 3001 chitosanase gene (choa). to investigate the phylogenetic distribution of chitosanases analogous to choa in nature, we identified 67 chitosan-degrading strains by screening and investiga ... | 2005 | 16151097 |
| identification of 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid, 4-hydroxy-2-oxohexanoic acid, and 2-hydroxyhexa-2,4-dienoic acid and related enzymes involved in testosterone degradation in comamonas testosteroni ta441. | comamonas testosteroni ta441 utilizes testosterone via aromatization of the a ring followed by meta-cleavage of the ring. the product of the meta-cleavage reaction, 4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-dien-4-oic acid, is degraded by a hydrolase, tesd. we directly isolated and identified two products of tesd as 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid and (2z,4z)-2-hydroxyhexa-2,4-dienoic acid. the latter was a pure 4z isomer. 2-hydroxyhexa-2,4-dienoic acid was con ... | 2005 | 16151114 |
| rrna sequence-based scanning electron microscopic detection of bacteria. | a new scanning electron microscopic method was developed for gaining both phylogenetic and morphological information about target microbes using in situ hybridization with rrna-targeted oligonucleotide probes (sem-ish). target cells were hybridized with oligonucleotide probes after gold labeling. gold enhancement was used for amplification of probe signals from hybridized cells. the hybridized cells released a strong backscatter electron signal due to accumulation of gold atoms inside cells. sem ... | 2005 | 16151145 |
| characterization of floating activity of indigenous diesel-assimilating bacterial isolates. | six diesel-degrading bacterial strains were isolated from oil-polluted sites located in central taiwan. the floating activity of the isolates in an oil-supplemented liquid medium was monitored. cell-surface hydrophobicity as well as cell-free and cell-residue emulsification activities were also investigated. three isolates, identified as gordonia alkanivorans cc-jg 39, rhodococcus erythropolis cc-bc 04, and r. erythropolis cc-bc 11, were found to float and grow near the diesel layer on the surfa ... | 2005 | 16233818 |
| replacement of tyrosine 181 by phenylalanine in gentisate 1,2-dioxygenase i from pseudomonas alcaligenes ncimb 9867 enhances catalytic activities. | xlne, encoding gentisate 1,2-dioxygenase (ec 1.13.11.4), from pseudomonas alcaligenes (p25x) was mutagenized by site-directed mutagenesis. the mutant enzyme, y181f, demonstrated 4-, 3-, 6-, and 16-fold increases in relative activity towards gentisate and 3-fluoro-, 4-methyl-, and 3-methylgentisate, respectively. the specific mutation conferred a 13-fold higher catalytic efficiency (k(cat)/km) on y181f towards 3-methylgentisate than that of the wild-type enzyme. | 2005 | 16237038 |
| [degradation of p-toluenesulfonate by immobilized comamonas testosteroni bs1310 (pbs1010) cells]. | parameters of degradation of p-toluenesulfonate (ts) by free and agar-embedded comamonas testosteroni bs1310 (pbs1010) cells were determined. the maximum rate of ts degradation was 25% lower in by immobilized than free cells, equaling 11 nmol x min(-1) x mg(-1) cells. degradation of ts by both free and immobilized cells was associated with molecular oxygen consumption (molar ratio, 1 : 2). in a plug-flow reactor, the degradation rate was 10.4 nmol x min(-1) x mg(-1) cells. the results can be app ... | 2005 | 16240649 |
| recognition of individual genes in diverse microorganisms by cycling primed in situ amplification. | cycling primed in situ amplification-fluorescent in situ hybridization (cprins-fish) was developed to recognize individual genes in a single bacterial cell. in cprins, the amplicon was long single-stranded dna and thus retained within the permeabilized microbial cells. fish with a multiply labeled fluorescent probe set enabled significant reduction in nonspecific background while maintaining high fluorescence signals of target bacteria. the ampicillin resistance gene in escherichia coli, chloram ... | 2005 | 16269764 |
| bacterial decarboxylation of o-phthalic acids. | the decarboxylation of phthalic acids was studied with bacillus sp. strain fo, a marine mixed culture on-7, and pseudomonas testosteroni. the mixed culture on-7, when grown anaerobically on phthalate but incubated aerobically with chloramphenicol, quantitatively converted phthalic acid to benzoic acid. substituted phthalic acids were also decarboxylated: 4,5-dihydroxyphthalic acid to protocatechuic acid; 4-hydroxyphthalic and 4-chlorophthalic acids to 3-hydroxybenzoic and 3-chlorobenzoic acids, ... | 1983 | 16346440 |
| transfer and expression of the catabolic plasmid pbrc60 in wild bacterial recipients in a freshwater ecosystem. | 3-chlorobenzoate (3cba)-degrading bacteria were isolated from the waters and sediments of flowthrough mesocosms dosed with various concentrations of 3cba and inoculated with a 3cba-degrading alcaligenes sp., strain br60. bacteria capable of 3cba degradation which were distinct from br60 were isolated. they carried pbrc60, a plasmid introduced with alcaligenes sp. strain br60 that carries a transposable element (tn5271) encoding 3cba degradation. the isolates expressed these genes in different wa ... | 1991 | 16348493 |
| nitrospira-like bacteria associated with nitrite oxidation in freshwater aquaria. | oxidation of nitrite to nitrate in aquaria is typically attributed to bacteria belonging to the genus nitrobacter which are members of the alpha subdivision of the class proteobacteria. in order to identify bacteria responsible for nitrite oxidation in aquaria, clone libraries of rrna genes were developed from biofilms of several freshwater aquaria. analysis of the rdna libraries, along with results from denaturing gradient gel electrophoresis (dgge) on frequently sampled biofilms, indicated the ... | 1998 | 16349486 |
| purification and properties of a polyester polyurethane-degrading enzyme from comamonas acidovorans tb-35. | a polyester polyurethane (pur)-degrading enzyme, pur esterase, derived from comamonas acidovorans tb-35, a bacterium that utilizes polyester pur as the sole carbon source, was purified until it showed a single band in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (sds-page). this enzyme was bound to the cell surface and was extracted by addition of 0.2% n,n-bis(3-d-gluconamidopropyl)deoxycholamide (deoxy-bigchap). the results of gel filtration and sds-page showed that the pur esteras ... | 1998 | 16349494 |
| identification of hydrocarbon-degrading bacteria in soil by reverse sample genome probing. | bacteria with limited genomic cross-hybridization were isolated from soil contaminated with c5+, a mixture of hydrocarbons, and identified by partial 16s rrna sequencing. filters containing denatured genomic dnas were used in a reverse sample genome probe (rsgp) procedure for analysis of the effect of an easily degradable compound (toluene) and a highly recalcitrant compound (dicyclopentadiene [dcpd]) on community composition. hybridization with labeled total-community dna isolated from soil exp ... | 1998 | 16349504 |
| dimerization and enzymatic activity of fungal 17beta-hydroxysteroid dehydrogenase from the short-chain dehydrogenase/reductase superfamily. | 17beta-hydroxysteroid dehydrogenase from the fungus cochliobolus lunatus (17beta-hsdcl) is a member of the short-chain dehydrogenase/reductase (sdr) superfamily. sdr proteins usually function as dimers or tetramers and 17beta-hsdcl is also a homodimer under native conditions. | 2005 | 16359545 |
| functional analysis of unique class ii insertion sequence is1071. | various xenobiotic-degrading genes on many catabolic plasmids are often flanked by two copies of an insertion sequence, is1071. this 3.2-kb is element has long (110-bp) terminal inverted repeats (irs) and a transposase gene that are phylogenetically related to those of the class ii transposons. however, the transposition mechanism of is1071 has remained unclear. our study revealed that is1071 was only able to transpose at high frequencies in two environmental beta-proteobacterial strains, comamo ... | 2006 | 16391056 |
| transmission of nephridial bacteria of the earthworm eisenia fetida. | the lumbricid earthworms (annelid family lumbricidae) harbor gram-negative bacteria in their excretory organs, the nephridia. comparative 16s rrna gene sequencing of bacteria associated with the nephridia of several earthworm species has shown that each species of worm harbors a distinct bacterial species and that the bacteria from different species form a monophyletic cluster within the genus acidovorax, suggesting that there is a specific association resulting from radiation from a common bact ... | 2006 | 16391117 |
| microbiology of airway disease in a cohort of patients with cystic fibrosis. | recent reports document an increasing incidence of new gram-negative pathogens such as stenotrophomonas maltophilia and alcaligenes xylosoxidans isolated from patients with cystic fibrosis, along with an increase in common gram-negative pathogens such as pseudomonas aeruginosa and burkholderia cepacia complex. furthermore, the increase in multidrug-resistance of such organisms makes the therapeutic management of these patients more problematic. therefore, careful isolation and identification, an ... | 2006 | 16405721 |
| treatment of naphthalene-2-sulfonic acid from tannery wastewater by a granular activated carbon fixed bed inoculated with bacterial isolates arthrobacter globiformis and comamonas testosteroni. | the kinetics of naphthalene-2-sulfonic acid (2-nsa) adsorption by granular activated carbon (gac) were measured and the relationships between adsorption, desorption, bioavailability and biodegradation assessed. the conventional langmuir model fitted the experimental sorption isotherm data and introduced 2-nsa degrading bacteria, established on the surface of the gac, did not interfere with adsorption. the potential value of gac as a microbial support in the aerobic degradation of 2-nsa by arthro ... | 2006 | 16427119 |
| the naphthalene catabolic (nag) genes of polaromonas naphthalenivorans cj2: evolutionary implications for two gene clusters and novel regulatory control. | polaromonas naphthalenivorans cj2, found to be responsible for the degradation of naphthalene in situ at a coal tar waste-contaminated site (c.-o. jeon et al., proc. natl. acad. sci. usa 100:13591-13596, 2003), is able to grow on mineral salts agar media with naphthalene as the sole carbon source. beginning from a 484-bp nagac-like region, we used a genome walking strategy to sequence genes encoding the entire naphthalene degradation pathway andadditional flanking regions. we found that the naph ... | 2006 | 16461653 |
| pyrroloquinoline quinone-dependent dehydrogenases from ketogulonicigenium vulgare catalyze the direct conversion of l-sorbosone to l-ascorbic acid. | a novel enzyme, l-sorbosone dehydrogenase 1 (sndh1), which directly converts l-sorbosone to l-ascorbic acid (l-aa), was isolated from ketogulonicigenium vulgare dsm 4025 and characterized. this enzyme was a homooligomer of 75-kda subunits containing pyrroloquinoline quinone (pqq) and heme c as the prosthetic groups. two isozymes of sndh, sndh2 consisting of 75-kda and 55-kda subunits and sndh3 consisting of 55-kda subunits, were also purified from the bacterium. all of the sndhs produced l-aa, a ... | 2006 | 16461703 |
| the clc element of pseudomonas sp. strain b13, a genomic island with various catabolic properties. | pseudomonas sp. strain b13 is a bacterium known to degrade chloroaromatic compounds. the properties to use 3- and 4-chlorocatechol are determined by a self-transferable dna element, the clc element, which normally resides at two locations in the cell's chromosome. here we report the complete nucleotide sequence of the clc element, demonstrating the unique catabolic properties while showing its relatedness to genomic islands and integrative and conjugative elements rather than to other known cata ... | 2006 | 16484212 |
| 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 |
| characterization of the terephthalate degradation genes of comamonas sp. strain e6. | we isolated comamonas sp. strain e6, which utilizes terephthalate (tpa) as the sole carbon and energy source via the protocatechuate (pca) 4,5-cleavage pathway. two almost identical tpa degradation gene clusters, tphricia2ia3ibia1i and tphriiciia2iia3iibiia1ii, were isolated from this strain. based on amino acid sequence similarity, the genes tphr, tphc, tpha2, tpha3, tphb, and tpha1 were predicted to code, respectively, for an iclr-type transcriptional regulator, a periplasmic tpa binding recep ... | 2006 | 16517628 |
| degradation of 4-chlorophenol via the meta cleavage pathway by comamonas testosteroni jh5. | comamonas testosteroni jh5 used 4-chlorophenol (4-cp) as its sole source of energy and carbon up to a concentration of 1.8 mm, accompanied by the stoichiometric release of chloride. the degradation of 4-cp mixed with the isomeric 2-cp by resting cells led to the accumulation of 3-chlorocatechol (3-cc), which inactivated the catechol 2,3-dioxygenase. as a result, further 4-cp breakdown was inhibited and 4-cc accumulated as a metabolite. in the crude extract of 4-cp-grown cells, catechol 1,2-dioxy ... | 1997 | 16535738 |
| expression, crystallization and preliminary x-ray crystallographic studies of the outer membrane protein ompw from escherichia coli. | ompw is an eight-stranded 21 kda molecular-weight beta-barrel protein from the outer membrane of gram-negative bacteria. it is a major antigen in bacterial infections and has implications in antibiotic resistance and in the oxidative degradation of organic compounds. ompw from escherichia coli was cloned and the protein was expressed in inclusion bodies. a method for refolding and purification was developed which yields properly folded protein according to circular-dichroism measurements. the pr ... | 2006 | 16582500 |
| degradation of aroclor 1242 dechlorination products in sediments by burkholderia xenovorans lb400(ohb) and rhodococcus sp. strain rha1(fcb). | burkholderia xenovorans strain lb400, which possesses the biphenyl pathway, was engineered to contain the oxygenolytic ortho dehalogenation (ohb) operon, allowing it to grow on 2-chlorobenzoate and to completely mineralize 2-chlorobiphenyl. a two-stage anaerobic/aerobic biotreatment process for aroclor 1242-contaminated sediment was simulated, and the degradation activities and genetic stabilities of lb400(ohb) and the previously constructed strain rha1(fcb), capable of growth on 4-chlorobenzoat ... | 2006 | 16597946 |
| 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 |
| testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole. | a longstanding proposal in enzymology is that enzymes are electrostatically and geometrically complementary to the transition states of the reactions they catalyze and that this complementarity contributes to catalysis. experimental evaluation of this contribution, however, has been difficult. we have systematically dissected the potential contribution to catalysis from electrostatic complementarity in ketosteroid isomerase. phenolates, analogs of the transition state and reaction intermediate, ... | 2006 | 16602823 |
| characterization of the replication, maintenance, and transfer features of the incp-7 plasmid pcar1, which carries genes involved in carbazole and dioxin degradation. | isolated from pseudomonas resinovorans ca10, pcar1 is a 199-kb plasmid that carries genes involved in the degradation of carbazole and dioxin. the nucleotide sequence of pcar1 has been determined previously. in this study, we characterized pcar1 in terms of its replication, maintenance, and conjugation. by constructing miniplasmids of pcar1 and testing their establishment in pseudomonas putida ds1, we show that pcar1 replication is due to the repa gene and its upstream dna region. the repa gene ... | 2006 | 16672459 |
| 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 |
| metabolism of isovanillate, vanillate, and veratrate by comamonas testosteroni strain br6020. | in comamonas testosteroni strain br6020, metabolism of isovanillate (ivan; 3-hydroxy-4-methoxybenzoate), vanillate (van; 4-hydroxy-3-methoxybenzoate), and veratrate (ver; 3,4-dimethoxybenzoate) proceeds via protocatechuate (pca; 3,4-dihydroxybenzoate). a 13.4-kb locus coding for the catabolic enzymes that channel the three substrates to pca was cloned. o demethylation is mediated by the phthalate family oxygenases ivaa (converts ivan to pca and ver to van) and vana (converts van to pca and ver t ... | 2006 | 16707678 |
| oxidative stress by biphenyl metabolites induces inhibition of bacterial cell separation. | cell-cell separation of a polychlorinated biphenyl (pcb)-degrading bacterium comamonas testosteroni tk102 was monitored by flow cytometry. when monohydroxy metabolites of biphenyl (bp) (2-hydroxybiphenyl and 3-hydroxybiphenyl) were added to the culture, cell-cell separation of strain tk102 was inhibited at stationary phase. this inhibition was reproduced on non-pcb degrading bacteria such as pseudomonas putida ppy101 and escherichia coli mv1184, but was not observed on pseudomonas aeruginosa pao ... | 2006 | 16733731 |
| analysis of amino acid residues involved in catalysis of polyethylene glycol dehydrogenase from sphingopyxis terrae, using three-dimensional molecular modeling-based kinetic characterization of mutants. | polyethylene glycol dehydrogenase (pegdh) from sphingopyxis terrae (formerly sphingomonas terrae) is composed of 535 amino acid residues and one flavin adenine dinucleotide per monomer protein in a homodimeric structure. its amino acid sequence shows 28.5 to 30.5% identity with glucose oxidases from aspergillus niger and penicillium amagasakiense. the adp-binding site and the signature 1 and 2 consensus sequences of glucose-methanol-choline oxidoreductases are present in pegdh. based on three-di ... | 2006 | 16751555 |
| preliminary crystallographic analysis of salicylate 1,2-dioxygenase from pseudaminobacter salicylatoxidans. | salicylate 1,2-dioxygenase, a new ring-fission dioxygenase from the naphthalenesulfonate-degrading strain pseudaminobacter salicylatoxidans which oxidizes salicylate to 2-oxohepta-3,5-dienedioic acid by a novel ring-fission mechanism, has been crystallized. diffraction-quality crystals of salicylate 1,2-dioxygenase were obtained using the sitting-drop vapour-diffusion method at 277 k from a solution containing 10%(w/v) ethanol, 6%(w/v) peg 400, 0.1 m sodium acetate ph 4.6. crystals belong to the ... | 2006 | 16754979 |
| crystallization and preliminary x-ray analysis of the complex of nadh and 3alpha-hydroxysteroid dehydrogenase from pseudomonas sp. b-0831. | the nad(p)(+)-dependent enzyme 3alpha-hydroxysteroid dehydrogenase (3alpha-hsd) catalyzes the reversible interconversion of hydroxyl and oxo groups at position 3 of the steroid nucleus. the complex of nadh and 3alpha-hsd from pseudomonas sp. b-0831 was crystallized by the hanging-drop vapour-diffusion method. refinement of crystallization conditions with microseeding improved the quality of the x-ray diffraction data to a resolution of 1.8 a. the crystals belonged to the orthorhombic space group ... | 2006 | 16754984 |
| degradation characteristics and metabolic pathway of 17alpha-ethynylestradiol by sphingobacterium sp. jcr5. | a 17alpha-ethynylestradiol (ee2)-degrading bacterium was isolated from the activated sludge of the wastewater treatment plant (wwtp) of an oral contraceptives producing factory in beijing, china. on the basis of its morphology, biochemical properties and the 16s rdna sequence analysis, this strain was identified as sphingobacterium sp. jcr5. this strain grew on ee2 as sole source of carbon and energy, and metabolized up to 87% of the substrate added (30 mgl-1) within 10 d at 30 degrees c. in add ... | 2007 | 16766017 |
| design and evaluation of 16s rrna sequence based oligonucleotide probes for the detection and quantification of comamonas testosteroni in mixed microbial communities. | the beta-proteobacterial species comamonas testosteroni is capable of biotransformation and also biodegradation of a range of chemical compounds and thus potentially useful in chemical manufacturing and bioremediation. the ability to detect and quantify members of this species in mixed microbial communities thus may be desirable. | 2006 | 16772028 |
| cloning and expression of the gene for periplasmic poly(vinyl alcohol) dehydrogenase from sphingomonas sp. strain 113p3, a novel-type quinohaemoprotein alcohol dehydrogenase. | a gene for periplasmic poly(vinyl alcohol) (pva) dehydrogenase (pvadh) was cloned, based on the n-terminal amino acid sequence of the purified pvadh from sphingomonas sp. 113p3 and the sequence of the gene for pvadh (pvaa, genbank accession no. ab190288). the recombinant pvadh tagged with hexahistidine was expressed in escherichia coli and purified to homogeneity. the recombinant enzyme had the same characteristics as the purified enzyme from sphingomonas sp. strain 113p. in addition to pva, the ... | 2006 | 16804170 |
| purification and characterization of an arene cis-dihydrodiol dehydrogenase endowed with broad substrate specificity toward polycyclic aromatic hydrocarbon dihydrodiols. | initial reactions involved in the bacterial degradation of polycyclic aromatic hydrocarbons (pahs) include a ring-dihydroxylation catalyzed by a dioxygenase and a subsequent oxidation of the dihydrodiol products by a dehydrogenase. in this study, the dihydrodiol dehydrogenase from the pah-degrading sphingomonas strain chy-1 has been characterized. the bphb gene encoding pah dihydrodiol dehydrogenase (pddh) was cloned and overexpressed as a his-tagged protein. the recombinant protein was purified ... | 2006 | 16820465 |
| method for assessment of viability and morphological changes of bacteria in the early stage of colony formation on a simulated natural environment. | a quantitative analysis of changes in the physiological status of bacterial cells is a fundamental type of study in microbiological research. we devised a method for measuring the viability of bacteria in the early stage of colony formation on a simulated natural environment. in this method, a solid medium containing soil extract was used, and the formation of bacterial microcolonies on a membrane filter was determined by use of a laser scanning cytometer combined with live-dead fluorescent dyes ... | 2006 | 16820503 |
| molecular detection and diversity of medium-chain-length polyhydroxyalkanoates-producing bacteria enriched from activated sludge. | knowledge of the species composition of complex bacterial communities is still very limited. the main objectives of this study were to identify medium-chain-length polyhydroxyalkanoates (mcl-phas)-producing bacteria from activated sludge fed with methanol as well as to characterize their pha operon. | 2006 | 16834606 |
| bioremediation of soil contaminated with pentachlorophenol (pcp) using humic acids bound on zeolite. | we determined the toxicity of various chlorophenols, especially pentachlorophenol (pcp), on five bacterial strains and studied pcp biodegradation in soils amended with an organomineral complex (omc) prepared from humic acids (organic part) bound on zeolite (inorganic part). both components of omc have excellent sorption properties and are of natural origin and therefore suitable to be used in the environment. toxicity of chlorophenols depends not only on the number of chlorine atoms but also on ... | 2007 | 16876229 |
| orf18-disrupted mutant of comamonas testosteroni ta441 accumulates significant amounts of 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid and its derivatives after incubation with steroids. | in a steroid degradation gene cluster of comamonas testosteroni ta441 consisting of orf18, 17 and tesiha2a1defg, orf18 was implicated in encoding a coa-transferase by database searches, but the matching substrate was not clear. in this study, orf18 was shown to be necessary for conversion of 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid, a product of hydrolysis of 4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-dien-4-oic acid in steroid degradation by ta441. the orf18-disrupted m ... | 2006 | 16891113 |
| effects of mutations in the substrate-binding domain of poly[(r)-3-hydroxybutyrate] (phb) depolymerase from ralstonia pickettii t1 on phb degradation. | poly[(r)-3-hydroxybutyrate] (phb) depolymerase from ralstonia pickettii t1 (phaz(rpit1)) adsorbs to denatured phb (dphb) via its substrate-binding domain (sbd) to enhance dphb degradation. to evaluate the amino acid residues participating in dphb adsorption, phaz(rpit1) was subjected to a high-throughput screening system consisting of pcr-mediated random mutagenesis targeted to the sbd gene and a plate assay to estimate the effects of mutations in the sbd on dphb degradation by phaz(rpit1). gene ... | 2006 | 16963553 |
| generation of useful insertionally blocked sterol degradation pathway mutants of fast-growing mycobacteria and cloning, characterization, and expression of the terminal oxygenase of the 3-ketosteroid 9alpha-hydroxylase in mycobacterium smegmatis mc(2)155. | integration of the pcg79 temperature-sensitive plasmid carrying tn611 was used to generate libraries of mutants with blocked sterol-transforming ability of the sterol-utilizing strains mycobacterium smegmatis mc(2)155 and mycobacterium phlei m51-ept. of the 10,000 insertional mutants screened from each library, 4 strains with altered activity of the sterol-degrading enzymes were identified. a blocked 4-androstene-3,17-dione-producing m. phlei mutant transformed sitosterol to 23,24-dinorcholane d ... | 2006 | 17021205 |
| coping with polychlorinated biphenyl (pcb) toxicity: physiological and genome-wide responses of burkholderia xenovorans lb400 to pcb-mediated stress. | the biodegradation of polychlorinated biphenyls (pcbs) relies on the ability of aerobic microorganisms such as burkholderia xenovorans sp. lb400 to tolerate two potential modes of toxicity presented by pcb degradation: passive toxicity, as hydrophobic pcbs potentially disrupt membrane and protein function, and degradation-dependent toxicity from intermediates of incomplete degradation. we monitored the physiological characteristics and genome-wide expression patterns of lb400 in response to the ... | 2006 | 17021212 |
| the complete genome of rhodococcus sp. rha1 provides insights into a catabolic powerhouse. | rhodococcus sp. rha1 (rha1) is a potent polychlorinated biphenyl-degrading soil actinomycete that catabolizes a wide range of compounds and represents a genus of considerable industrial interest. rha1 has one of the largest bacterial genomes sequenced to date, comprising 9,702,737 bp (67% g+c) arranged in a linear chromosome and three linear plasmids. a targeted insertion methodology was developed to determine the telomeric sequences. rha1's 9,145 predicted protein-encoding genes are exceptional ... | 2006 | 17030794 |
| crystal structure of 3-hydroxybenzoate hydroxylase from comamonas testosteroni has a large tunnel for substrate and oxygen access to the active site. | the 3-hydroxybenzoate hydroxylase (mhbh) from comamonas testosteroni kh122-3s is a single-component flavoprotein monooxygenase, a member of the glutathione reductase (gr) family. it catalyzes the conversion of 3-hydroxybenzoate to 3,4-dihydroxybenzoate with concomitant requirements for equimolar amounts of nadph and molecular oxygen. the production of dihydroxy-benzenoid derivative by hydroxylation is the first step in the aerobic degradation of various phenolic compounds in soil microorganisms. ... | 2006 | 17045293 |
| characterization of mobr, the 3-hydroxybenzoate-responsive transcriptional regulator for the 3-hydroxybenzoate hydroxylase gene of comamonas testosteroni kh122-3s. | comamonas testosteroni kh122-3s is an aerobic soil bacterium that utilizes 3-hydroxybenzoate as a sole carbon and energy source. in this strain, 3-hydroxybenzoate hydroxylase (moba) acts on the initial step of the degradation to produce 3,4-dihydroxybenzoate, which is subsequently subjected to the meta-cleavage pathway leading to tricarboxylic acid cycle intermediates. gene walking analysis of the upstream region of moba revealed an open reading frame (mobr) that encodes a transcriptional regula ... | 2006 | 17046018 |
| bacterial diversity in aortic aneurysms determined by 16s ribosomal rna gene analysis. | aortic aneurysms are common vascular conditions that cause considerable morbidity and mortality. understanding of the mechanisms involved in the pathogenesis of the condition remains limited. recently, infection has been suggested as possible contributor in the development of the disease. the aim of the present study was to examine aortic aneurysms for the presence of bacterial dna using polymerase chain reaction (pcr) targeting the 16s ribosomal rna (rrna) gene, followed by cloning and sequenci ... | 2006 | 17098542 |
| autoregulator protein phar for biosynthesis of polyhydroxybutyrate [p(3hb)] possibly has two separate domains that bind to the target dna and p(3hb): functional mapping of amino acid residues responsible for dna binding. | phar from paracoccus denitrificans functions as a repressor or autoregulator of the expression of genes encoding phasin protein (phap) and phar itself, both of which are components of polyhydroxyalkanoate (pha) granules (a. maehara, s. taguchi, t. nishiyama, t. yamane, and y. doi, j. bacteriol. 184:3992-4002, 2002). phar is a unique regulatory protein in that it also has the ability to bind tightly to an effector molecule, pha polyester. in this study, by using a quartz crystal microbalance, we ... | 2007 | 17122335 |
| autoregulator protein phar for biosynthesis of polyhydroxybutyrate [p(3hb)] possibly has two separate domains that bind to the target dna and p(3hb): functional mapping of amino acid residues responsible for dna binding. | phar from paracoccus denitrificans functions as a repressor or autoregulator of the expression of genes encoding phasin protein (phap) and phar itself, both of which are components of polyhydroxyalkanoate (pha) granules (a. maehara, s. taguchi, t. nishiyama, t. yamane, and y. doi, j. bacteriol. 184:3992-4002, 2002). phar is a unique regulatory protein in that it also has the ability to bind tightly to an effector molecule, pha polyester. in this study, by using a quartz crystal microbalance, we ... | 2007 | 17122335 |
| 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 |
| transcriptomic analysis reveals a bifurcated terephthalate degradation pathway in rhodococcus sp. strain rha1. | phthalate isomers and their esters are important pollutants whose biodegradation is not well understood. rhodococcus sp. strain rha1 is notable for its ability to degrade a wide range of aromatic compounds. rha1 was previously shown to degrade phthalate (pth) and to have genes putatively encoding terephthalate (tpa) degradation. transcriptomic analysis of 8,213 genes indicated that 150 were up-regulated during growth on pth and that 521 were up-regulated during growth on tpa. distinct ring cleav ... | 2007 | 17142403 |
| transcriptomic analysis reveals a bifurcated terephthalate degradation pathway in rhodococcus sp. strain rha1. | phthalate isomers and their esters are important pollutants whose biodegradation is not well understood. rhodococcus sp. strain rha1 is notable for its ability to degrade a wide range of aromatic compounds. rha1 was previously shown to degrade phthalate (pth) and to have genes putatively encoding terephthalate (tpa) degradation. transcriptomic analysis of 8,213 genes indicated that 150 were up-regulated during growth on pth and that 521 were up-regulated during growth on tpa. distinct ring cleav ... | 2007 | 17142403 |
| biochemical and genetic analysis of the gamma-resorcylate (2,6-dihydroxybenzoate) catabolic pathway in rhizobium sp. strain mtp-10005: identification and functional analysis of its gene cluster. | we identified a gene cluster that is involved in the gamma-resorcylate (2,6-dihydroxybenzoate) catabolism of the aerobic bacterium rhizobium sp. strain mtp-10005. the cluster consists of the grardafcbek genes, and graa, grab, grac, and grad were heterologously expressed in escherichia coli. enzymological studies showed that grad, graa, grac, and grab encode the reductase (grad) and oxygenase (graa) components of a resorcinol hydroxylase (ec 1.14.13.x), a maleylacetate reductase (grac) (ec 1.3.1. ... | 2007 | 17158677 |
| biochemical and genetic analysis of the gamma-resorcylate (2,6-dihydroxybenzoate) catabolic pathway in rhizobium sp. strain mtp-10005: identification and functional analysis of its gene cluster. | we identified a gene cluster that is involved in the gamma-resorcylate (2,6-dihydroxybenzoate) catabolism of the aerobic bacterium rhizobium sp. strain mtp-10005. the cluster consists of the grardafcbek genes, and graa, grab, grac, and grad were heterologously expressed in escherichia coli. enzymological studies showed that grad, graa, grac, and grab encode the reductase (grad) and oxygenase (graa) components of a resorcinol hydroxylase (ec 1.14.13.x), a maleylacetate reductase (grac) (ec 1.3.1. ... | 2007 | 17158677 |
| membrane topology of aspartate:alanine antiporter aspt from comamonas testosteroni. | we cloned the aspt gene encoding the l-aspartate:l-alanine antiporter asptct in comamonas testosteroni genomic dna. analysis of the nucleotide sequence revealed that c. testosteroni has an asp operon containing aspt upstream of the l-aspartate 4-decarboxylase gene, and that the gene order of the asp operon of c. testosteroni is the inverse of that of tetragenococcus halophilus. we used proteoliposomes to confirm the transport processes of asptct. to elucidate the two-dimensional structure of asp ... | 2007 | 17158863 |
| regulated polyploidy in halophilic archaea. | polyploidy is common in higher eukaryotes, especially in plants, but it is generally assumed that most prokaryotes contain a single copy of a circular chromosome and are therefore monoploid. we have used two independent methods to determine the genome copy number in halophilic archaea, 1) cell lysis in agarose blocks and southern blot analysis, and 2) real-time quantitative pcr. fast growing h. salinarum cells contain on average about 25 copies of the chromosome in exponential phase, and their p ... | 2006 | 17183724 |
| rational design of novel mutants of fungal 17beta-hydroxysteroid dehydrogenase. | reduction of 17-ketosteroids is a biocatalytic process of economic significance for the production of steroid drugs. this reaction can be catalyzed by different microbial 17beta-hydroxysteroid dehydrogenases (17beta-hsd), like the 17beta-hsd activity of saccharomyces cerevisiae, pichia faranosa and mycobacterium sp., and by purified 3beta,17beta-hsd from pseudomonas testosteroni. in addition to the bacterial 3beta,17beta-hsd the 17beta-hsd of the filamentous fungus cochliobolus lunatus is the on ... | 2007 | 17196285 |
| understanding oligomerization in 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase from comamonas testosteroni: an in silico approach and evidence for an active protein. | 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase (3alpha-hsd/cr) from comamonas testosteroni belongs to the short chain dehydrogenase/reductase (sdr) protein superfamily and catalyzes the oxidoreduction of a variety of steroid substrates, including the steroid antibiotic fusidic acid. the enzyme also mediates the carbonyl reduction of non-steroidal aldehydes and ketones such as a novel insecticide. it is suggested that 3alpha-hsd/cr contributes to the bioremediation of natural and syntheti ... | 2007 | 17258342 |
| 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 |
| a gene cluster encoding cholesterol catabolism in a soil actinomycete provides insight into mycobacterium tuberculosis survival in macrophages. | rhodococcus sp. strain rha1, a soil bacterium related to mycobacterium tuberculosis, degrades an exceptionally broad range of organic compounds. transcriptomic analysis of cholesterol-grown rha1 revealed a catabolic pathway predicted to proceed via 4-androstene-3,17-dione and 3,4-dihydroxy-9,10-seconandrost-1,3,5(10)-triene-9,17-dione (3,4-dhsa). inactivation of each of the hsac, supab, and mce4 genes in rha1 substantiated their roles in cholesterol catabolism. moreover, the hsac(-) mutant accum ... | 2007 | 17264217 |
| influence of cobalt substitution on the activity of iron-type nitrile hydratase: are cobalt type nitrile hydratases regulated by carbon monoxide? | comamonas testosteroni ni1 nitrile hydratase is a fe-type nitrile hydratase whose native and recombinant forms are identical. here, the iron of ni1 nitrile hydratase was replaced by cobalt using a chaperone based escherichia coli expression system. cobalt (coni1) and iron (feni1) enzymes share identical vmax (30 nmol min(-1) mg(-1)) and km (200 microm) toward their substrate and identical ki values for the known competitive inhibitors of feni1. however, nitrophenols used as inhibitors do display ... | 2007 | 17267045 |
| generation by a widely applicable approach of a hybrid dioxygenase showing improved oxidation of polychlorobiphenyls. | recently, a sequence-based approach has been developed for the fast isolation and characterization of class ii aryl-hydroxylating dioxygenase activities (s. kahl and b. hofer, microbiology 149:1475-1481, 2003). it comprises the pcr amplification of segments of alpha subunit genes of unknown sequence that encode the catalytic center and their fusion with sequences of the bpha gene cluster of burkholderia xenovorans lb400. one of the resulting chimeric enzymes, harboring the core segment of a diox ... | 2007 | 17322323 |
| degradation of alkyl methyl ketones by pseudomonas veronii mek700. | pseudomonas veronii mek700 was isolated from a biotrickling filter cleaning 2-butanone-loaded waste air. the strain is able to grow on 2-butanone and 2-hexanol. the genes for degradation of short chain alkyl methyl ketones were identified by transposon mutagenesis using a newly designed transposon, mini-tn5495, and cloned in escherichia coli. dna sequence analysis of a 15-kb fragment revealed three genes involved in methyl ketone degradation. the deduced amino acid sequence of the first gene, me ... | 2007 | 17351032 |
| comamonas odontotermitis sp. nov., isolated from the gut of the termite odontotermes formosanus. | a bacterial strain, designated dant 3-8(t), isolated from the gut of the termite odontotermes formosanus, was investigated by a polyphasic taxonomic approach. the cells were rod-shaped, gram-negative, non-pigmented, non-spore-forming and non-fermentative. phylogenetic analyses using the 16s rrna gene sequence showed that the strain formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus comamonas, its closest neighbours being comamonas testosteroni ... | 2007 | 17392226 |
| presumed pseudobacteremia outbreak resulting from contamination of proportional disinfectant dispenser. | reported here are the microbiological and epidemiological details of a presumed outbreak of aerobic gram-negative bacilli infections affecting 19 hematological patients, which was traced to contaminated disinfectant. over a 5-month period, the following organisms were isolated from the blood cultures of 19 neutropenic patients: pseudomonas fluorescens (n = 13), achromobacter xylosoxidans (n = 12), comamonas testosteroni (n = 2) or stenotrophomonas maltophilia (n = 1). the affected patients were ... | 2007 | 17393202 |
| characterization of a c-c bond hydrolase from sphingomonas wittichii rw1 with novel specificities towards polychlorinated biphenyl metabolites. | sphingomonas wittichii rw1 degrades chlorinated dibenzofurans and dibenzo-p-dioxins via meta cleavage. we used inverse pcr to amplify dxnb2, a gene encoding one of three meta-cleavage product (mcp) hydrolases identified in the organism that are homologues of bphd involved in biphenyl catabolism. purified dxnb2 catalyzed the hydrolysis of 8-oh 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate (hopda) approximately six times faster than for hopda at saturating substrate concentrations. moreover, the speci ... | 2007 | 17416660 |