Publications

metabolism of 2,2'- and 3,3'-dihydroxybiphenyl by the biphenyl catabolic pathway of comamonas testosteroni b-356.	the purpose of this investigation was to examine the capacity of the biphenyl catabolic enzymes of comamonas testosteroni b-356 to metabolize dihydroxybiphenyls symmetrically substituted on both rings. data show that 3,3'-dihydroxybiphenyl is by far the preferred substrate for strain b-356. however, the dihydrodiol metabolite is very unstable and readily tautomerizes to a dead-end metabolite or is dehydroxylated by elimination of water. the tautomerization route is the most prominent. thus, a ve ...	2004	14711640
teir, a luxr-type transcription factor required for testosterone degradation in comamonas testosteroni.	we have identified a new steroid-inducible gene (designated teir [testosterone-inducible regulator]) in comamonas testosteroni that is required for testosterone degradation. nucleotide sequence analysis of teir predicts a 391-amino-acid protein which shows homology between residues 327 and 380 (c-terminal domain) to the luxr helix-turn-helix dna binding domain and between residues 192 and 227 to the pas sensor domain. this domain distribution resembles that described for trar, a specific transcr ...	2004	14973025
molecular breeding of 2,3-dihydroxybiphenyl 1,2-dioxygenase for enhanced resistance to 3-chlorocatechol.	3-chlorobiphenyl is known to be mineralized by biphenyl-utilizing bacteria to 3-chlorobenzoate, which is further metabolized to 3-chlorocatechol. an extradiol dioxygenase, 2,3-dihydroxybiphenyl 1,2-dioxygenase (dhb12o; ec 1.13.11.39), which is encoded by the bphc gene, catalyzes the third step of the upper pathway of 3-chlorobiphenyl degradation. in this study, two full-length bphcs and nine partial fragments of bphcs fused to the 3' end of bphc in pseudomonas pseudoalcaligenes kf707 were cloned ...	2004	15113829
herbaspirillum chlorophenolicum sp. nov., a 4-chlorophenol-degrading bacterium.	a 4-chlorophenol-degrading bacterial strain, formerly designated as a strain of comamonas testosteroni, was reclassified as a member of the genus herbaspirillum based on its phenotypic and chemotaxonomic characteristics, as well as phylogenetic analysis using 16s rdna sequences. phylogenetic inference based on 16s rdna sequences showed that strain cpw301(t) clusters in a phylogenetic branch that contains herbaspirillum species. 16s rdna sequence similarity of strain cpw301(t) to species of the g ...	2004	15143035
a novel outer-membrane anion channel (porin) as part of a putatively two-component transport system for 4-toluenesulphonate in comamonas testosteroni t-2.	inducible mineralization of tsa (4-toluenesulphonate) by comamonas testosteroni t-2 is initiated by a secondary transport system, followed by oxygenation and oxidation by tsambcd to 4-sulphobenzoate under the regulation of tsar and tsaq. evidence is presented for a novel, presumably two-component transport system (tsast). it is proposed that tsat, an outer-membrane porin, formed an anion-selective channel that works in co-operation with the putative secondary transporter, tsas, located in the in ...	2004	15176949
kinetic property and phylogenic relationship of 2-hydroxymuconic semialdehyde dehydrogenase encoded in tomc gene of burkholderia cepacia g4.	2-hydroxymuconic semialdehyde (2-hms) dehydrogenase catalyzes the conversion of 2-hms to 4-oxalocrotonate, which is a step in the meta cleavage pathway of aromatic hydrocarbons in bacteria. a tomc gene that encodes 2-hms dehydrogenase of burkholderia cepacia g4, a soil bacterium that can grow on toluene, cresol, phenol, or benzene, was overexpressed into e. coli hb101, and its gene product was characterized in this study. 2-hms dehydrogenase from b. cepacia g4 has a high catalytic efficiency in ...	2004	15202565
structural double-mutant cycle analysis of a hydrogen bond network in ketosteroid isomerase from pseudomonas putida biotype b.	ksi (ketosteroid isomerase) catalyses an allylic isomerization reaction at a diffusion-controlled rate. a hydrogen bond network, asp(99).water(504).tyr(14).tyr(55).tyr(30), connects two critical catalytic residues, tyr(14) and asp(99), with tyr(30), tyr(55) and a water molecule in the highly apolar active site of the pseudomonas putida ksi. in order to characterize the interactions among these amino acids in the hydrogen bond network of ksi, double-mutant cycle analysis was performed, and the cr ...	2004	15228388
mineralization of individual congeners of linear alkylbenzenesulfonate by defined pairs of heterotrophic bacteria.	parvibaculum lavamentivorans ds-1(t) utilized the commercial surfactant linear alkylbenzenesulfonate (las) (20 congeners with c(10) to c(13) side chains) as a carbon and energy source by shortening the side chain, and sulfophenylcarboxylates (spcs) and similar compounds (e.g., alpha,beta-unsaturated spcs [spc-2hs]) were excreted with quantitative recovery of the sulfophenyl moiety. 2-(4-sulfophenyl)decane (2-c10-las) was converted largely to 3-(4-sulfophenyl)butyrate (3-c4-spc), as were 2-c12-la ...	2004	15240283
detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays.	to effectively monitor biodegrading populations, a comprehensive 50-mer-based oligonucleotide microarray was developed based on most of the 2,402 known genes and pathways involved in biodegradation and metal resistance. this array contained 1,662 unique and group-specific probes with <85% similarity to their nontarget sequences. based on artificial probes, our results showed that under hybridization conditions of 50 degrees c and 50% formamide, the 50-mer microarray hybridization can differentia ...	2004	15240314
removal of nitriles from synthetic wastewater by acrylonitrile utilizing bacteria.	this study describes the ability of two bacteria strains, isolated from an abs resin manufacturing wastewater treatment system, to remove high acrylonitrile concentrations. straight chain aliphatic nitrile compound (propionitrile, allyl cyanide); branch chain aliphatic nitrile compound (isobutyronitrilc) and aromatic nitrile compound (benzonitrile) removal by comamonas testosteroni and acidovorax sp. was also investigated. the results are: comamonas testosteroni and acidovorax sp. can remove acr ...	2004	15242125
characterization of the 3-o-methylgallate dioxygenase gene and evidence of multiple 3-o-methylgallate catabolic pathways in sphingomonas paucimobilis syk-6.	sphingomonas paucimobilis syk-6 is able to grow on various lignin-derived biaryls as the sole source of carbon and energy. these compounds are degraded to vanillate and syringate by the unique and specific enzymes in this strain. vanillate and syringate are converted to protocatechuate (pca) and 3-o-methylgallate (3mga), respectively, by the tetrahydrofolate-dependent o-demethylases. previous studies have suggested that these compounds are further degraded via the pca 4,5-cleavage pathway. howev ...	2004	15262932
measurement of bile acid in serum and bile with arylamine-glass-bound 3alpha-hydroxysteroid dehydrogenase and diaphorase.	3alpha-hydroxysteroid dehydrogenase (3-hsd) from pseudomonas testosteroni and diaphorase (lipoyl dehydrogenase) from clostridium spp. have been immobilized individually onto arylamine glass beads through diazotization. a cost-effective enzymic colorimetric method for determination of bile acid in serum and bile employing a mixture of these immobilized enzymes was developed. the method is based on measurement of reduced nicotinamide adenine dinucleotide generated from bile acid in serum/bile by i ...	2004	15301946
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
crystal structure of a baeyer-villiger monooxygenase.	flavin-containing baeyer-villiger monooxygenases employ nadph and molecular oxygen to catalyze the insertion of an oxygen atom into a carbon-carbon bond of a carbonylic substrate. these enzymes can potentially be exploited in a variety of biocatalytic applications given the wide use of baeyer-villiger reactions in synthetic organic chemistry. the catalytic activity of these enzymes involves the formation of two crucial intermediates: a flavin peroxide generated by the reaction of the reduced fla ...	2004	15328411
ability of bacterial biphenyl dioxygenases from burkholderia sp. lb400 and comamonas testosteroni b-356 to catalyse oxygenation of ortho-hydroxychlorobiphenyls formed from pcbs by plants.	capacity of enzymes of the biphenyl/chlorobiphenyl pathway, especially biphenyl dioxygenase (bpdo) of two polychlorinated biphenyls (pcb) degrading bacteria, burkholderia sp. lb400 and comamonas testosteroni b-356, to metabolize ortho-substituted hydroxybiphenyls was tested.,these compounds found among plant products of pcb metabolism, are carrying chlorine atoms on the hydroxyl-substituted ring. the abilities of his-tagged purified lb400 and b-356 bpdos to catalyze the oxygenation of 2-hydroxy- ...	2004	14553993
first comprehensively documented case of paracoccus yeei infection in a human.	paracoccus yeei was isolated in pure culture from an aerobic blood culture and bulla fluid from a 67-year-old male. the biochemical identification scheme for this recently described species is outlined. because of its reaction pattern it is not unlikely that p. yeei is underdiagnosed.	2004	15243119
abundance of dioxygenase genes similar to ralstonia sp. strain u2 nagac is correlated with naphthalene concentrations in coal tar-contaminated freshwater sediments.	we designed a real-time pcr assay able to recognize dioxygenase large-subunit gene sequences with more than 90% similarity to the ralstonia sp. strain u2 nagac gene (nagac-like gene sequences) in order to study the importance of organisms carrying these genes in the biodegradation of naphthalene. sequencing of pcr products indicated that this real-time pcr assay was specific and able to detect a variety of nagac-like gene sequences. one to 100 ng of contaminated-sediment total dna in 25-microl r ...	2004	15240274
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
rational proteomics ii: electrostatic nature of cofactor preference in the short-chain oxidoreductase (scor) enzyme family.	the dominant role of long-range electrostatic interatomic interactions in nicotinamide adenine dinucleotide/nicotinamide adenine dinucleotide phosphate (nad/nadp) cofactor recognition has been shown for enzymes of the short-chain oxidoreductase (scor) family. an estimation of cofactor preference based only on the contribution of the electrostatic energy term to the total energy of enzyme-cofactor interaction has been tested for approximately 40 known three-dimensional (3d) crystal complexes and ...	2004	15340916
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
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
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
regulation of tetralin biodegradation and identification of genes essential for expression of thn operons.	the tetralin biodegradation genes of sphingomonas macrogolitabida strain tfa are clustered in two closely linked and divergent operons. to analyze expression of both operons under different growth conditions, transcriptional and translational gene fusions of the first genes of each operon to lacz have been constructed in plasmids unable to replicate in sphingomonas and integrated by recombination into the genome of strain tfa. expression analysis indicated that the transcription of both genes is ...	2004	15342579
bacterial transcriptional regulators for degradation pathways of aromatic compounds.	human activities have resulted in the release and introduction into the environment of a plethora of aromatic chemicals. the interest in discovering how bacteria are dealing with hazardous environmental pollutants has driven a large research community and has resulted in important biochemical, genetic, and physiological knowledge about the degradation capacities of microorganisms and their application in bioremediation, green chemistry, or production of pharmacy synthons. in addition, regulation ...	2004	15353566
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
conjugal transfer of plasmid pnb2 to activated sludge bacteria leads to 3-chloroaniline degradation in enrichment cultures.	the involvement of the aniline-degradative plasmid pnb2 in degradation of 3-chloroaniline (3-ca) was investigated.	2004	15130151
identification of a novel steroid inducible gene associated with the beta hsd locus of comamonas testosteroni.	comamonas testosteroni is a soil bacterium, which can use a variety of steroids as carbon and energy source. even if it can be estimated that the complete degradation of the steroid nucleus requires more than 20 enzymatic reactions, the complete molecular characterization of the genes encoding these steroid degradative enzymes as well as the genetic organization of them remain to be elucidated. we have previously reported the cloning and nucleotide sequence of two steroid-inducible genes, beta h ...	2004	15026087
pqq glucose dehydrogenase with novel electron transfer ability.	pqq glucose dehydrogenase from acinetobacter calcoaceticus (gdh-b) is one of the most industrially attractive enzymes, as a sensor constituent for glucose sensing, because of its high catalytic activity and insensitivity to oxygen. we attempted to engineer gdh-b to enable electron transfer to the electrode in the absence of artificial electron mediator by mimicking the domain structure of the quinohemoprotein ethanol dehydrogenase (qh-edh) from comamonas testosteroni, which is composed of a pqq- ...	2004	14741705
biphenyl dioxygenases: functional versatilities and directed evolution.		2004	15292119
brassinosteroid deficiency due to truncated steroid 5alpha-reductase causes dwarfism in the lk mutant of pea.	the endogenous brassinosteroids in the dwarf mutant lk of pea (pisum sativum) were quantified by gas chromatography-selected ion monitoring. the levels of castasterone, 6-deoxocastasterone, and 6-deoxotyphasterol in lk shoots were reduced 4-, 70-, and 6-fold, respectively, compared with those of the wild type. the fact that the application of brassinolide restored the growth of the mutant indicated that the dwarf mutant lk is brassinosteroid deficient. gas chromatography-selected ion monitoring ...	2004	15286289
representative freshwater bacterioplankton isolated from crater lake, oregon.	high-throughput culturing (htc) methods that rely on dilution to extinction in very-low-nutrient media were used to obtain bacterial isolates from crater lake, oregon. 16s rrna sequence determination and phylogenetic reconstruction were used to determine the potential ecological significance of isolated bacteria, both in crater lake and globally. fifty-five crater lake isolates yielded 16 different 16s rrna gene sequences. thirty of 55 (55%) crater lake isolates had 16s rrna gene sequences with ...	2004	15528517
use of chlorate as a selective inhibitor to distinguish membrane-bound nitrate reductase (nar) and periplasmic nitrate reductase (nap) of dissimilative nitrate reducing bacteria in sediment.	the use of chlorate as a selective inhibitor of dissimilative nitrate reduction was studied using pure cultures of comamonas testosteroni (a denitrifier) and klebsiella pneumoniae (a nitrate-ammonifier) isolated from estuarine sediment, and in sediment slurry. pure culture experiments demonstrated that chlorate selectively inhibited membrane-bound nitrate reductase (nar) activity, probably by blocking nitrate transporters (nark). sediment slurry experiments showed that chlorate inhibited nitrate ...	2004	19712307
performances of vitek 2 colorimetric cards for identification of gram-positive and gram-negative bacteria.	the purpose of this study was to evaluate the new vitek 2 identification cards that use colorimetric reading to identify gram-positive and gram-negative bacteria (gp and gn cards, respectively) in comparison to fluorimetric cards (id-gpc and id-gnb, respectively). a total of 580 clinical isolates and stock collection strains belonging to 116 taxa were included in the study. of the 249 gram-positive strains tested with both the id-gpc and gp cards, 218 (87.5%) and 235 (94.4%) strains were correct ...	2005	16145083
protein subunit interfaces: heterodimers versus homodimers.	protein dimers are either homodimers (complexation of identical monomers) or heterodimers (complexation of non-identical monomers). these dimers are common in catalysis and regulation. however, the molecular principles of protein dimer interactions are difficult to understand mainly due to the geometrical and chemical characteristics of proteins. nonetheless, the principles of protein dimer interactions are often studied using a dataset of 3d structural complexes determined by x-ray crystallogra ...	2005	17597849
soil microbial community responses to additions of organic carbon substrates and heavy metals (pb and cr).	microcosm experiments were conducted with soils contaminated with heavy metals (pb and cr) and aromatic hydrocarbons to determine the effects of each upon microbial community structure and function. organic substrates were added as a driving force for change in the microbial community. glucose represented an energy source used by a broad variety of bacteria, whereas fewer soil species were expected to use xylene. the metal amendments were chosen to inhibit the acute rate of organic mineralizatio ...	2005	16332740
anesthetic interaction with ketosteroid isomerase: insights from molecular dynamics simulations.	the nature and the sites of interactions between anesthetic halothane and homodimeric delta5-3-ketosteroid isomerase (ksi) are characterized by flexible ligand docking and confirmed by 1h-15n nmr. the dynamics consequence of halothane interaction and the implication of the dynamic changes to ksi function are studied by multiple 5-ns molecular dynamics simulations in the presence and absence of halothane. both docking and md simulations show that halothane prefer the amphiphilic dimeric interface ...	2005	16040747
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
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
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
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
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
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
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
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
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
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
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
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
[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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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