Publications
| Title | Abstract | Year Filter | PMID(sorted descending) Filter |
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| antibacterial activity of some plant extracts used in folk medicine. | in the present work, selected plants were screened for their potential antibacterial activity. for evaluating antibacterial activity, both aqueous and organic solvent methanol was used. the plants screened were ocimum sanctum, jatropha gossypifolia, boerhavia diffusa, azadirachta indica, solidago virgaurea, and commelina benghalensis. the antibacterial activity was assessed against six bacterial strains--pseudomonas testosteroni, staphylococcus epidermidis, klebsiella pneumoniae, bacillus subtil ... | 2007 | 18928141 |
| regulation of testosterone degradation in comamonas testosteroni. | recently, we have identified a gene encoding a luxr-type factor, teir (testosterone-inducible regulator), which positively regulates steroid degradation in comamonas testosteroni. herein, we demonstrate that teir interacts in vivo with steroid catabolic gene promoters. the presence of testosterone induces a significant teir protein increase at the early logarithmic phase of growth. interestingly, it is not until the early stationary phase where the activation of a steroid-inducible gene promoter ... | 2008 | 18852046 |
| expression of a fused fpg gene in e. coli and engineering a strain comamonas testosteroni zd4-1-fpg for environmental application. | a fused fpg gene composed of phe b and gfp gene, which encoded catechol 2,3-dioxygenase (c23o) and green fluorescence protein (gfp), respectively, was expressed in e. coli to investigate its functional intactness. the expression results showed that c23o activity was detected in the induced bacterial cells and the e. coli cells containing the fusion protein emitted green fluorescence under epifluorescence microscopy, indicating that the fused fpg gene expressed correctly in e. coli. after express ... | 2008 | 18780218 |
| cloning the bacterial bphc gene into nicotiana tabacum to improve the efficiency of pcb phytoremediation. | the aim of this work is to increase the efficiency of the biodegradation of polychlorinated biphenyls (pcbs) by the introduction of bacterial genes into the plant genome. for this purpose, we selected the bphc gene encoding 2,3-dihydroxybiphenyl-1,2-dioxygenase from pseudomonas testosteroni b-356 to be cloned into tobacco plants. the dihydroxybiphenyldioxygenase enzyme is the third enzyme in the biphenyl degradation pathway, and its unique function is the cleavage of biphenyl. three different co ... | 2009 | 18683252 |
| high crystallizability under air-exclusion conditions of the full-length lysr-type transcriptional regulator tsar from comamonas testosteroni t-2 and data-set analysis for a miras structure-solution approach. | the full-length lysr-type transcriptional regulator tsar from comamonas testosteroni t-2 was heterologously overexpressed in escherichia coli, purified and stabilized under conditions that favoured its rapid crystallization using the microbatch-under-oil technique. the purified protein was highly crystallizable and two different crystal forms were readily obtained. however, only monoclinic crystals gave diffraction beyond 2 a and there was a slight variation in unit-cell parameters between cryst ... | 2008 | 18678953 |
| comamonas testosteroni meningitis in a homeless man. | we report a case of meningitis caused by comamonas testosteroni in a 54-year-old, alcoholic, homeless man. he, as a pedestrian, was struck by a car and suffered multiple fractures of the facial bones including the left frontal sinus. over the course of 2-week hospitalization, he was clinically diagnosed with multiple cerebral and cerebellar infarcts resulting in altered mental status. he was pronounced dead 15 days after the injury. at the time of autopsy, diffuse purulent meningitis was found o ... | 2008 | 18637874 |
| crystal structure of a carbonyl reductase from candida parapsilosis with anti-prelog stereospecificity. | a novel short-chain (s)-1-phenyl-1,2-ethanediol dehydrogenase (scr) from candida parapsilosis exhibits coenzyme specificity for nadph over nadh. it catalyzes an anti-prelog type reaction to reduce 2-hydroxyacetophenone into (s)-1-phenyl-1,2-ethanediol. the coding gene was overexpressed in escherichia coli and the purified protein was crystallized. the crystal structure of the apo-form was solved to 2.7 a resolution. this protein forms a homo-tetramer with a broken 2-2-2 symmetry. the overall fol ... | 2008 | 18566346 |
| identification of genes involved in inversion of stereochemistry of a c-12 hydroxyl group in the catabolism of cholic acid by comamonas testosteroni ta441. | comamonas testosteroni ta441 degrades steroids such as testosterone via aromatization of the a ring, followed by meta-cleavage of the ring. in the dna region upstream of the meta-cleavage enzyme gene tesb, two genes required during cholic acid degradation for the inversion of an alpha-oriented hydroxyl group on c-12 were identified. a dehydrogenase, stea, converts 7 alpha,12 alpha-dihydroxyandrosta-1,4-diene-3,17-dione to 7 alpha-hydroxyandrosta-1,4-diene-3,12,17-trione, and a hydrogenase, steb, ... | 2008 | 18539741 |
| crystal structure and mutagenic analysis of gdosp, a gentisate 1,2-dioxygenase from silicibacter pomeroyi. | dioxygenases catalyze dioxygen incorporation into various organic compounds and play a key role in the complex degradation pathway of mono- and polycyclic aromatic and hetero-aromatic compounds. here we report the crystal structure of gentisate 1,2-dioxygenase from silicibacter pomeroyi (gdosp) at a 2.8 a resolution. the enzyme possessed a conserved three-dimensional structure of the bicupin family, forming a homotetramerization. however, each subunit of gdosp unusually contained two ferrous cen ... | 2008 | 18505738 |
| protocol to determine accurate absorption coefficients for iron-containing transferrins. | an accurate protein concentration is an essential component of most biochemical experiments. the simplest method to determine a protein concentration is by measuring the a(280) using an absorption coefficient (epsilon) and applying the beer-lambert law. for some metalloproteins (including all transferrin family members), difficulties arise because metal binding contributes to the a(280) in a nonlinear manner. the edelhoch method is based on the assumption that the epsilon of a denatured protein ... | 2008 | 18471984 |
| 15n nmr relaxation studies of y14f mutant of ketosteroid isomerase: the influence of mutation on backbone mobility. | the backbone dynamics of y14f mutant of delta(5)-3-ketosteroid isomerase (ksi) from comamonas testosteroni has been studied in free enzyme and its complex with a steroid analogue, 19-nortestosterone hemisuccinate (19-nths), by 15n nmr relaxation measurements. model-free analysis of the relaxation data showed that the single-point mutation induced a substantial decrease in the order parameters (s2) in free y14f ksi, indicating that the backbone structures of y14f ksi became significantly mobile b ... | 2008 | 18424811 |
| biphenyl dioxygenase from an arctic isolate is not cold adapted. | biphenyl dioxygenase from the psychrotolerant bacterium pseudomonas sp. strain cam-1 (bpdo(cam-1)) was purified and found to have an apparent k(cat) for biphenyl of 1.1 +/- 0.1 s(-1) (mean +/- standard deviation) at 4 degrees c. in contrast, bpdo(lb400) from the mesophile burkholderia xenovorans lb400 had no detectable activity at this temperature. at 57 degrees c, the half-life of the bpdo(cam-1) oxygenase was less than half that of the bpdo(lb400) oxygenase. nevertheless, bpdo(cam-1) appears t ... | 2008 | 18424535 |
| testosterone-inducible regulator is a kinase that drives steroid sensing and metabolism in comamonas testosteroni. | the mechanism of gene regulation by steroids in bacteria is still a mystery. we use steroid-inducible 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase (3alpha-hsd/cr) as a reporter system to study steroid signaling in comamonas testosteroni. in previous investigations we cloned and characterized the 3alpha-hsd/cr-encoding gene, hsda. in addition, we identified two negative regulator genes (repa and repb) in the vicinity of hsda, the protein products which repress hsda expression on the lev ... | 2008 | 18424443 |
| examination and expansion of the substrate range of m-hydroxybenzoate hydroxylase. | the gene encoding m-hydroxybenzoate hydroxylase (moba) was cloned from comamonas testosteroni gz39. moba converts m-hydroxybenzoate and to a lesser extent p-hydroxybenzoate to protocatechuate. to explore the structural and functional relationships in phenolic acid monooxygenases, moba was subjected to in vitro mutagenesis by error-prone pcr and the mutant mobas were screened for their ability to oxidize phenol or 3-aminophenol. a mutant moba with a single v257a substitution was able to transform ... | 2008 | 18417078 |
| the binding and release of oxygen and hydrogen peroxide are directed by a hydrophobic tunnel in cholesterol oxidase. | the usage by enzymes of specific binding pathways for gaseous substrates or products is debated. the crystal structure of the redox enzyme cholesterol oxidase, determined at sub-angstrom resolution, revealed a hydrophobic tunnel that may serve as a binding pathway for oxygen and hydrogen peroxide. this tunnel is formed by a cascade of conformational rearrangements and connects the active site with the exterior surface of the protein. to elucidate the relationship between this tunnel and gas bind ... | 2008 | 18410129 |
| a new classification system for bacterial rieske non-heme iron aromatic ring-hydroxylating oxygenases. | rieske non-heme iron aromatic ring-hydroxylating oxygenases (rhos) are multi-component enzyme systems that are remarkably diverse in bacteria isolated from diverse habitats. since the first classification in 1990, there has been a need to devise a new classification scheme for these enzymes because many rhos have been discovered, which do not belong to any group in the previous classification. here, we present a scheme for classification of rhos reflecting new sequence information and interactio ... | 2008 | 18387195 |
| architecture and spatial organization in a triple-species bacterial biofilm synergistically degrading the phenylurea herbicide linuron. | members of a triple-species 3-(3,4-dichlorophenyl)-1-methoxy-1-methyl urea (linuron)-mineralizing consortium, i.e. the linuron- and 3,4-dichloroaniline-degrading variovorax sp. wdl1, the 3,4-dichloroaniline-degrading comamonas testosteroni wdl7 and the n,o-dimethylhydroxylamine-degrading hyphomicrobium sulfonivorans wdl6, were cultivated as mono- or multi-species biofilms in flow cells irrigated with selective or nonselective media, and examined with confocal laser scanning microscopy. in contra ... | 2008 | 18373685 |
| crystal structure of human spermine synthase: implications of substrate binding and catalytic mechanism. | the crystal structures of two ternary complexes of human spermine synthase (ec 2.5.1.22), one with 5'-methylthioadenosine and spermidine and the other with 5'-methylthioadenosine and spermine, have been solved. they show that the enzyme is a dimer of two identical subunits. each monomer has three domains: a c-terminal domain, which contains the active site and is similar in structure to spermidine synthase; a central domain made up of four beta-strands; and an n-terminal domain with remarkable s ... | 2008 | 18367445 |
| novel aromatic ring-hydroxylating dioxygenase genes from coastal marine sediments of patagonia. | polycyclic aromatic hydrocarbons (pahs), widespread pollutants in the marine environment, can produce adverse effects in marine organisms and can be transferred to humans through seafood. our knowledge of pah-degrading bacterial populations in the marine environment is still very limited, and mainly originates from studies of cultured bacteria. in this work, genes coding catabolic enzymes from pah-biodegradation pathways were characterized in coastal sediments of patagonia with different levels ... | 2008 | 18366740 |
| different bacterial strategies to degrade taurocholate. | aerobic enrichment cultures with taurocholate or alkanesulfonates as sole sources of carbon and energy for growth were successful and yielded nine bacterial isolates, all of which utilized taurocholate. growth was complex and involved not only many, usually transient, excretion products but also sorption of taurocholate and cholate to cells. three metabolic strategies to dissimilate taurocholate were elucidated, all of which involved bile salt hydrolase cleaving taurocholate to cholate and tauri ... | 2008 | 18320171 |
| degradation of 4-fluorophenol by arthrobacter sp. strain if1. | a gram-positive bacterial strain capable of aerobic biodegradation of 4-fluorophenol (4-fp) as the sole source of carbon and energy was isolated by selective enrichment from soil samples collected near an industrial site. the organism, designated strain if1, was identified as a member of the genus arthrobacter on the basis of 16s ribosomal rna gene sequence analysis. arthrobacter strain if1 was able to mineralize 4-fp up to concentrations of 5 mm in batch culture. stoichiometric release of fluor ... | 2008 | 18228015 |
| social bacteria and asocial eukaryotes. | 2008 | 18199122 | |
| comamonas composti sp. nov., isolated from food waste compost. | a bacterial strain designated yy287(t), isolated from food waste compost, was investigated by 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 were the type strains comamonas testosteroni dsm 50244(t) (96.5 ... | 2008 | 18175717 |
| contributions of a disulfide bond to the structure, stability, and dimerization of human igg1 antibody ch3 domain. | recombinant human monoclonal antibodies have become important protein-based therapeutics for the treatment of various diseases. the antibody structure is complex, consisting of beta-sheet rich domains stabilized by multiple disulfide bridges. the dimerization of the c(h)3 domain in the constant region of the heavy chain plays a pivotal role in the assembly of an antibody. this domain contains a single buried, highly conserved disulfide bond. this disulfide bond was not required for dimerization, ... | 2008 | 18156469 |
| distinct roles for two cyp226 family cytochromes p450 in abietane diterpenoid catabolism by burkholderia xenovorans lb400. | the 80-kb dit cluster of burkholderia xenovorans lb400 encodes the catabolism of abietane diterpenoids. this cluster includes ditq and ditu, predicted to encode cytochromes p450 (p450s) belonging to the poorly characterized cyp226a subfamily. using proteomics, we identified 16 dit-encoded proteins that were significantly more abundant in lb400 cells grown on dehydroabietic acid (dha) or abietic acid (aba) than in succinate-grown cells. a key difference in the catabolism of dha and aba lies in th ... | 2008 | 18156276 |
| distinct roles for two cyp226 family cytochromes p450 in abietane diterpenoid catabolism by burkholderia xenovorans lb400. | the 80-kb dit cluster of burkholderia xenovorans lb400 encodes the catabolism of abietane diterpenoids. this cluster includes ditq and ditu, predicted to encode cytochromes p450 (p450s) belonging to the poorly characterized cyp226a subfamily. using proteomics, we identified 16 dit-encoded proteins that were significantly more abundant in lb400 cells grown on dehydroabietic acid (dha) or abietic acid (aba) than in succinate-grown cells. a key difference in the catabolism of dha and aba lies in th ... | 2008 | 18156276 |
| study of anoxic and oxic cholesterol metabolism by sterolibacterium denitrificans. | the initial enzymes and genes involved in the anoxic metabolism of cholesterol were studied in the denitrifying bacterium sterolibacterium denitrificans chol-1s(t). the second enzyme of the proposed pathway, cholest-4-en-3-one-delta1-dehydrogenase (acmb), was partially purified. based on amino acid sequence analysis, a gene probe was derived to screen a cosmid library of chromosomal dna for the acmb gene. a positive clone comprising a 43-kbp dna insert was sequenced. in addition to the acmb gene ... | 2008 | 18039763 |
| study of anoxic and oxic cholesterol metabolism by sterolibacterium denitrificans. | the initial enzymes and genes involved in the anoxic metabolism of cholesterol were studied in the denitrifying bacterium sterolibacterium denitrificans chol-1s(t). the second enzyme of the proposed pathway, cholest-4-en-3-one-delta1-dehydrogenase (acmb), was partially purified. based on amino acid sequence analysis, a gene probe was derived to screen a cosmid library of chromosomal dna for the acmb gene. a positive clone comprising a 43-kbp dna insert was sequenced. in addition to the acmb gene ... | 2008 | 18039763 |
| establishment and characterization of dual-species biofilms formed from a 3,5-dinitrobenzoic-degrading strain and bacteria with high biofilm-forming capabilities. | in this study, the possibility of establishing a dual-species biofilm from a bacterium with a high biofilm-forming capability and a 3,5-dinitrobenzoic acid (3,5-dnba)-degrading bacterium, comamonas testosteroni a3, was investigated. our results showed that the combinations of strain a3 with each of five strains with a high biofilm-forming capability (pseudomonas sp. m8, pseudomonas putida m9, bacillus cereus m19, pseudomonas plecoglossicida m21 and aeromonas hydrophila m22) presented different l ... | 2008 | 18034834 |
| expression, purification, crystallization and initial crystallographic characterization of the p-hydroxybenzoate hydroxylase from corynebacterium glutamicum. | p-hydroxybenzoate hydroxylase (phbh) is an fad-dependent monooxygenase that catalyzes the hydroxylation of p-hydroxybenzoate (pohb) to 3,4-dihydroxybenzoate in an nadph-dependent reaction and plays an important role in the biodegradation of aromatic compounds. phbh from corynebacterium glutamicum was crystallized using the hanging-drop vapour-diffusion method in the presence of nah(2)po(4) and k(2)hpo(4) as precipitants. x-ray diffraction data were collected to a maximum resolution of 2.5 a on a ... | 2007 | 18007046 |
| the fto (fat mass and obesity associated) gene codes for a novel member of the non-heme dioxygenase superfamily. | genetic variants in the fto (fat mass and obesity associated) gene have been associated with an increased risk of obesity. however, the function of its protein product has not been experimentally studied and previously reported sequence similarity analyses suggested the absence of homologs in existing protein databases. here, we present the first detailed computational analysis of the sequence and predicted structure of the protein encoded by fto. | 2007 | 17996046 |
| cholest-4-en-3-one-delta 1-dehydrogenase, a flavoprotein catalyzing the second step in anoxic cholesterol metabolism. | the anoxic metabolism of cholesterol was studied in the denitrifying bacterium sterolibacterium denitrificans, which was grown with cholesterol and nitrate. cholest-4-en-3-one was identified before as the product of cholesterol dehydrogenase/isomerase, the first enzyme of the pathway. the postulated second enzyme, cholest-4-en-3-one-delta(1)-dehydrogenase, was partially purified, and its n-terminal amino acid sequence and tryptic peptide sequences were determined. based on this information, the ... | 2008 | 17993555 |
| cholest-4-en-3-one-delta 1-dehydrogenase, a flavoprotein catalyzing the second step in anoxic cholesterol metabolism. | the anoxic metabolism of cholesterol was studied in the denitrifying bacterium sterolibacterium denitrificans, which was grown with cholesterol and nitrate. cholest-4-en-3-one was identified before as the product of cholesterol dehydrogenase/isomerase, the first enzyme of the pathway. the postulated second enzyme, cholest-4-en-3-one-delta(1)-dehydrogenase, was partially purified, and its n-terminal amino acid sequence and tryptic peptide sequences were determined. based on this information, the ... | 2008 | 17993555 |
| evolution and functional characterization of the rh50 gene from the ammonia-oxidizing bacterium nitrosomonas europaea. | the family of ammonia and ammonium channel proteins comprises the amt proteins, which are present in all three domains of life with the notable exception of vertebrates, and the homologous rh proteins (rh50 and rh30) that have been described thus far only in eukaryotes. the existence of an rh50 gene in bacteria was first revealed by the genome sequencing of the ammonia-oxidizing bacterium nitrosomonas europaea. here we have used a phylogenetic approach to study the evolution of the n. europaea r ... | 2007 | 17921289 |
| purification and characterization of a three-component salicylate 1-hydroxylase from sphingomonas sp. strain chy-1. | in the bacterial degradation of polycyclic aromatic hydrocarbons (pahs), salicylate hydroxylases catalyze essential reactions at the junction between the so-called upper and lower catabolic pathways. unlike the salicylate 1-hydroxylase from pseudomonads, which is a well-characterized flavoprotein, the enzyme found in sphingomonads appears to be a three-component fe-s protein complex, which so far has not been characterized. here, the salicylate 1-hydroxylase from sphingomonas sp. strain chy-1 wa ... | 2007 | 17905882 |
| convergent evolution of a new arsenic binding site in the arsr/smtb family of metalloregulators. | acidithiobacillus ferrooxidans has an arsenic resistance operon that is controlled by an as(iii)-responsive transcriptional repressor, afarsr, a member of the arsr/smtb family of metalloregulators. afarsr lacks the as(iii) binding site of the arsrs from plasmid r773 and escherichia coli, which have a cys(32)-val-cys(34)-asp-leu-cys(37) sequence in the dna binding site. in contrast, it has three cysteine residues, cys(95), cys(96), and cys(102), that are not present in the r773 and e. coli arsrs. ... | 2007 | 17897948 |
| comamonas testosteroni bacteremia in a patient with perforated acute appendicitis. short communication. | comamonas testosteroni is an uncommon isolate in the clinical laboratory as a human pathogen. c. testosteroni most commonly emerges in abdominal pathologies especially in perforated appendicitis. in turkey we report first time a case of bacteremia due to this organism, in a 22-year-old man with perforated acute appendicitis. the organism was shown to be susceptible to routine antibiotics so it was easily eliminated even after having caused a bacteremia. | 2007 | 17896478 |
| mechanism of proton transfer in the 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase from comamonas testosteroni. | 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase from comamonas testosteroni catalyzes the oxidation of androsterone with nad(+) to form androstanedione and nadh with a concomitant releasing of protons to bulk solvent. to probe the proton transfer during the enzyme reaction, we used mutagenesis, chemical rescue, and kinetic isotope effects to investigate the release of protons. the kinetic isotope effects of (d)v and (d(2)o)v for wild-type enzyme are 1 and 2.1 at pl 10.4 (where l represent ... | 2007 | 17893142 |
| comparative transcriptome analysis of methylibium petroleiphilum pm1 exposed to the fuel oxygenates methyl tert-butyl ether and ethanol. | high-density whole-genome cdna microarrays were used to investigate substrate-dependent gene expression of methylibium petroleiphilum pm1, one of the best-characterized aerobic methyl tert-butyl ether (mtbe)-degrading bacteria. differential gene expression profiling was conducted with pm1 grown on mtbe and ethanol as sole carbon sources. based on microarray high scores and protein similarity analysis, an mtbe regulon located on the megaplasmid was identified for further investigation. putative f ... | 2007 | 17890343 |
| host-plant selectivity of rhizobacteria in a crop/weed model system. | belowground microorganisms are known to influence plants' performance by altering the soil environment. plant pathogens such as cyanide-producing strains of the rhizobacterium pseudomonas may show strong host-plant selectivity. we analyzed interactions between different host plants and pseudomonas strains and tested if these can be linked to the cyanide sensitivity of host plants, the cyanide production of bacterial strains or the plant identity from which strains had been isolated. eight strain ... | 2007 | 17786217 |
| ligand specificity of mobr, a transcriptional regulator for the 3-hydroxybenzoate hydroxylase gene of comamonas testosteroni kh122-3s. | mobr from comamonas testosteroni kh122-3s is a member of the marr family of transcriptional regulators and functions as a repressor for the moba gene that encodes a 3-hydroxybenzoate 4-hydroxylase. 3-hydroxybenzoate binds to mobr as a ligand, resulting in an efficient induction of moba. various 3-hydroxybenzoate analogues were examined for their inducibilities using the moba::lacz transcriptional fusion system. beta-galactosidase was induced by the addition of 2,3-dihydroxybenzoate or 3,5-dihydr ... | 2007 | 17707338 |
| human wild-type alanine:glyoxylate aminotransferase and its naturally occurring g82e variant: functional properties and physiological implications. | human hepatic peroxisomal agt (alanine:glyoxylate aminotransferase) is a plp (pyridoxal 5'-phosphate)-dependent enzyme whose deficiency causes primary hyperoxaluria type i, a rare autosomal recessive disorder. to acquire experimental evidence for the physiological function of agt, the k(eq),(overall) of the reaction, the steady-state kinetic parameters of the forward and reverse reactions, and the pre-steady-state kinetics of the half-reactions of the plp form of agt with l-alanine or glycine an ... | 2007 | 17696873 |
| biochemical and genetic investigation of initial reactions in aerobic degradation of the bile acid cholate in pseudomonas sp. strain chol1. | bile acids are surface-active steroid compounds with toxic effects for bacteria. recently, the isolation and characterization of a bacterium, pseudomonas sp. strain chol1, growing with bile acids as the carbon and energy source was reported. in this study, initial reactions of the aerobic degradation pathway for the bile acid cholate were investigated on the biochemical and genetic level in strain chol1. these reactions comprised a-ring oxidation, activation with coenzyme a (coa), and beta-oxida ... | 2007 | 17693490 |
| 4-sulfomuconolactone hydrolases from hydrogenophaga intermedia s1 and agrobacterium radiobacter s2. | the 4-carboxymethylen-4-sulfo-but-2-en-olide (4-sulfomuconolactone) hydrolases from hydrogenophaga intermedia strain s1 and agrobacterium radiobacter strain s2 are part of a modified protocatechuate pathway responsible for the degradation of 4-sulfocatechol. in both strains, the hydrolase-encoding genes occur downstream of those encoding the enzymes that catalyze the lactonization of 3-sulfomuconate. the deduced amino acid sequences of the 4-sulfomuconolactone hydrolases demonstrated the highest ... | 2007 | 17660282 |
| a survey of orphan enzyme activities. | using computational database searches, we have demonstrated previously that no gene sequences could be found for at least 36% of enzyme activities that have been assigned an enzyme commission number. here we present a follow-up literature-based survey involving a statistically significant sample of such "orphan" activities. the survey was intended to determine whether sequences for these enzyme activities are truly unknown, or whether these sequences are absent from the public sequence databases ... | 2007 | 17623104 |
| 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 |
| molecular characterization of class 3 integrons from delftia spp. | two environmental strains, delftia acidovorans c17 and delftia tsuruhatensis a90, were found to carry class 3 integrons, which have seldom been reported and then only from pathogens in which they are associated with antibiotic resistance genes. the delftia integrons comprised a highly conserved class 3 integrase gene, upstream and oppositely oriented from a set of three or four gene cassettes that encoded unidentified functions. the a90 integron had one more gene cassette than the c17 integron, ... | 2007 | 17573473 |
| nucleotide sequence of plasmid pcnb1 from comamonas strain cnb-1 reveals novel genetic organization and evolution for 4-chloronitrobenzene degradation. | the nucleotide sequence of a new plasmid pcnb1 from comamonas sp. strain cnb-1 that degrades 4-chloronitrobenzene (4cnb) was determined. pcnb1 belongs to the incp-1beta group and is 91,181 bp in length. a total of 95 open reading frames appear to be involved in (i) the replication, maintenance, and transfer of pcnb1; (ii) resistance to arsenate and chromate; and (iii) the degradation of 4cnb. the 4cnb degradative genes and arsenate resistance genes were located on an extraordinarily large transp ... | 2007 | 17526790 |
| characterization of biphenyl dioxygenase of pandoraea pnomenusa b-356 as a potent polychlorinated biphenyl-degrading enzyme. | biphenyl dioxygenase (bpdo) catalyzes the aerobic transformation of biphenyl and various polychlorinated biphenyls (pcbs). in three different assays, bpdo(b356) from pandoraea pnomenusa b-356 was a more potent pcb-degrading enzyme than bpdo(lb400) from burkholderia xenovorans lb400 (75% amino acid sequence identity), transforming nine congeners in the following order of preference: 2,3',4-trichloro approximately 2,3,4'-trichloro > 3,3'-dichloro > 2,4,4'-trichloro > 4,4'-dichloro approximately 2, ... | 2007 | 17526697 |
| evaluation of the colorimetric vitek 2 card for identification of gram-negative nonfermentative rods: comparison to 16s rrna gene sequencing. | ninety strains of a collection of well-identified clinical isolates of gram-negative nonfermentative rods collected over a period of 5 years were evaluated using the new colorimetric vitek 2 card. the vitek 2 colorimetric system identified 53 (59%) of the isolates to the species level and 9 (10%) to the genus level; 28 (31%) isolates were misidentified. an algorithm combining the colorimetric vitek 2 card and 16s rrna gene sequencing for adequate identification of gram-negative nonfermentative r ... | 2007 | 17507509 |
| a polyomic approach to elucidate the fluoranthene-degradative pathway in mycobacterium vanbaalenii pyr-1. | mycobacterium vanbaalenii pyr-1 is capable of degrading a wide range of high-molecular-weight polycyclic aromatic hydrocarbons (pahs), including fluoranthene. we used a combination of metabolomic, genomic, and proteomic technologies to investigate fluoranthene degradation in this strain. thirty-seven fluoranthene metabolites including potential isomers were isolated from the culture medium and analyzed by high-performance liquid chromatography, gas chromatography-mass spectrometry, and uv-visibl ... | 2007 | 17449607 |
| [study on the structure and function of a stable methane-oxidizing mixed microbial consortium]. | from an agricultural sample taken in chongqing, a stable methane-oxidizing mixed microbial consortium was established by enrichment culture with methane as a sole source of carbon and energy. the mixed consortium showed high capability of phenol degradation and 1,2-epoxypropane production from propene. more than 99% of phenol at an initial concentration of 600mg/l could be degraded by the mixed microbial consortium after 11 h of cultivation. the productivity of 1, 2-epoxypropane could be increas ... | 2007 | 17436634 |
| a tale of two oxidation states: bacterial colonization of arsenic-rich environments. | microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. finding a means of preserving natural environments-including ground and surface waters-from arsenic constitutes a major challenge facing modern society. although this metalloid is ubiquitous on earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. in-depth exploration of the genome of the beta ... | 2007 | 17432936 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| application of smartgene idns software to partial 16s rrna gene sequences for a diverse group of bacteria in a clinical laboratory. | laboratories often receive clinical isolates for bacterial identification that have ambiguous biochemical profiles by conventional testing. with the emergence of 16s rrna gene sequencing as an identification tool, we evaluated the usefulness of smartgene idns, a 16s rrna sequence database and software program for microbial identification. identification by conventional methods of a diverse group of bacterial clinical isolates was compared with gene sequences interrogated by the smartgene and mic ... | 2006 | 17050811 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| quantitative determination of free-dna uptake in river bacteria at the single-cell level by in situ rolling-circle amplification. | detection of plasmid dna uptake in river bacteria at the single-cell level was carried out by rolling-circle amplification (rca). uptake of a plasmid containing the green fluorescent protein gene (gfp) by indigenous bacteria from two rivers in osaka, japan, was monitored for 506 h using this in situ gene amplification technique with optimized cell permeabilization conditions. plasmid uptake determined by in situ rca was compared to direct counts of cells expressing gfp under fluorescence microsc ... | 2006 | 16957252 |
| 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 |
| improved in situ hybridization efficiency with locked-nucleic-acid-incorporated dna probes. | low signal intensity due to poor probe hybridization efficiency is one of the major drawbacks of rrna-targeted in situ hybridization. there are two major factors affecting the hybridization efficiency: probe accessibility and affinity to the targeted rrna molecules. in this study, we demonstrate remarkable improvement in in situ hybridization efficiency by applying locked-nucleic-acid (lna)-incorporated oligodeoxynucleotide probes (lna/dna probes) without compromising specificity. fluorescently ... | 2006 | 16885281 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| microbial dioxygenase gene population shifts during polycyclic aromatic hydrocarbon biodegradation. | the degradation of polycyclic aromatic hydrocarbons (pahs) by bacteria has been widely studied. while many pure cultures have been isolated and characterized for their ability to grow on pahs, limited information is available on the diversity of microbes involved in pah degradation in the environment. we have designed generic pcr primers targeting the gene fragment encoding the rieske iron sulfur center common to all pah dioxygenase enzymes. these rieske primers were employed to track dioxygenas ... | 2006 | 16751518 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |