| 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 |
| 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 |
| 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 |
| 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 |
| social bacteria and asocial eukaryotes. | | 2008 | 18199122 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| analyzing the catalytic mechanism of the fe-type nitrile hydratase from comamonas testosteroni ni1. | in order to gain insight into the catalytic mechanism of fe-type nitrile hydratases (nhase), the ph and temperature dependence of the kinetic parameters k cat, k m, and k cat/ k m along with the solvent isotope effect were examined for the fe-type nhase from comamonas testosteroni ni1 ( ctnhase). ctnhase was found to exhibit a bell-shaped curve for plots of relative activity vs ph over ph values 4-10 for the hydration of acrylonitrile and was found to display maximal activity at ph approximately ... | 2008 | 18942853 |
| cis- and trans-regulatory elements of 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase as biosensor system for steroid determination in the environment. | 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase from comamonas testosteroni is a key enzyme in the degradation of steroids in the environment. the encoding gene, hsda, is expressed only at very low levels in the absence of steroids, but undergoes a several fold induction in the presence of steroid substrates. in previous investigations, we have elucidated the mechanism of hsda regulation that involves several activators and repressors. in the present study, the hsda gene was replaced by t ... | 2009 | 19000658 |
| isolation of the phe-operon from g. stearothermophilus comprising the phenol degradative meta-pathway genes and a novel transcriptional regulator. | geobacillus stearothermophilus is able to utilize phenol as a sole carbon source. a dna fragment encoding a phenol hydroxylase catalyzing the first step in the meta-pathway has been isolated previously. based on these findings a pcr-based dna walk was performed initially to isolate a catechol 2,3-dioxygenase for biosensoric applications but was continued to elucidate the organisation of the genes encoding the proteins for the metabolization of phenol. | 2008 | 19014555 |
| 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase as a tool for isolation and characterization of a new marine steroid degrading bacterial strain. | steroid contamination of sea water is an ever growing problem and impacts population dynamics of all kinds of sea animals. we have long experience with the soil bacterium comamonas testosteroni which is able to catabolize a variety of steroids and polycyclic aromatic hydrocarbons, and which might be used in the bioremediation of contaminated soil. for our studies, we use 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase (3 alpha-hsd/cr) as an indicator system, since it is a key enzyme in ad ... | 2009 | 19026617 |
| microbial iron redox cycling in a circumneutral-ph groundwater seep. | the potential for microbially mediated redox cycling of iron (fe) in a circumneutral-ph groundwater seep in north central alabama was studied. incubation of freshly collected seep material under anoxic conditions with acetate-lactate or h(2) as an electron donor revealed the potential for rapid fe(iii) oxide reduction (ca. 700 to 2,000 micromol liter(-1) day(-1)). fe(iii) reduction at lower but significant rates took place in unamended controls (ca. 300 micromol liter(-1) day(-1)). culture-based ... | 2009 | 19047399 |
| [microbial community structure of beer wastewater treatment plants analyzed by pcr-dgge technique]. | the microbial community structure of beer wastewater treatment plants with hydrolyze-acidification and sbr process was studied by pcr amplification and denaturing gradient gel electrophoresis (dgge) based 16s rdna. activated sludge samples were collected from both hydrolyze-acidification tank and sbr tank at different depth and disposal period. the total dna was extracted and the 16s rdna was amplified by universal primer. the microbial community structure was analyzed by denaturing gradient gel ... | 2008 | 19143400 |
| 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 |
| thiosulfate oxidation by comamonas sp. s23 isolated from a sulfur spring. | a bacterial isolate s23 capable of oxidizing thiosulfate was isolated from a sulfur spring. strain s23 is gram-negative, aerobic, and motile. the g + c content of dna is 61.4 mol%. the fatty acid composition and phylogenetic analysis of the 16s rrna gene sequence of strain s23 showed that it is related to the members of the genus comamonas, and most closely related to comamonas testosteroni (99.9% sequence similarity). the isolate s23 exhibited thiosulfate oxidation under a mixotrophic growth co ... | 2009 | 19189181 |
| post-operative endophthalmitis due to an unusual pathogen, comamonas testosteroni. | here, we describe the first report of post-operative endophthalmitis due to comamonas testosteroni in an elderly diabetic patient after complicated cataract surgery. the isolate was identified by using mini api strips. the patient was successfully treated with intravitreal ceftazidime and oral ciprofloxacin. | 2009 | 19208890 |
| principles of bone marrow transplantation (bmt): providing optimal veterinary and husbandry care to irradiated mice in bmt studies. | bone marrow transplantation (bmt) is the treatment of choice for many leukemias, solid tumors, and metabolic diseases. the field of bone marrow research is highly dependent on in vivo experimentation, because in vitro techniques do not mimic these complicated in vivo systems. therefore, understanding the medical and husbandry care needs of these transiently immunodeficient bone marrow recipient animals is crucial for researchers, veterinary and animal care personnel. here we discuss the principl ... | 2009 | 19245745 |
| bioaugmentation of activated sludge towards 3-chloroaniline removal with a mixed bacterial population carrying a degradative plasmid. | a bioaugmentation approach combining several strategies was applied to achieve degradation of 3-chloroaniline (3ca) in semicontinuous activated sludge reactors. in a first step, a 3ca-degrading comamonas testosteroni strain carrying the degradative plasmid pnb2 was added to a biofilm reactor, and complete 3ca degradation together with spread of the plasmid within the indigenous biofilm population was achieved. a second set of reactors was then bioaugmented with either a suspension of biofilm cel ... | 2009 | 19268574 |
| population growth of a rhabditid nematode on plant growth promoting bacteria from potato tubers and rhizosphere soil. | nine bacterial isolates from the rhizosphere and(or) tubers of potato (solanum tuberosum cv. kennebec) at a field site on prince edward island were assessed as food sources for a bacteria-feeding nematode species tentatively identified as diplogaster lheritieri. this species was the most common rhabditid nematode recovered from soil around potato roots at the same site. in laboratory feeding trials, an isolate of comamonas testosteroni recovered from soil was an excellent food source for d. lher ... | 1996 | 19277195 |
| 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 |
| 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 |
| pseudomonas aeruginosa pao1 preferentially grows as aggregates in liquid batch cultures and disperses upon starvation. | in both natural and artificial environments, bacteria predominantly grow in biofilms, and bacteria often disperse from biofilms as freely suspended single-cells. in the present study, the formation and dispersal of planktonic cellular aggregates, or 'suspended biofilms', by pseudomonas aeruginosa in liquid batch cultures were closely examined, and compared to biofilm formation on a matrix of polyester (pe) fibers as solid surface in batch cultures. plankton samples were analyzed by laser-diffrac ... | 2009 | 19436737 |
| 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 |
| role of s114 in the nadh-induced conformational change and catalysis of 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase from comamonas testosteroni. | 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase reversibly catalyzes the oxidation of androsterone with nad(+) to form androstanedione and nadh. in this study, we characterize the role of the conserved residue s114 in cofactor binding and catalysis, using site-directed mutagenesis, steady-state kinetics, fluorescence quenching and anisotropy measurements. the catalytic efficiency of v/k(nadh)et for wild-type and s114a is 1.5 x10(7) and 3.8 x 10(3) m(-1) s(-1), respectively, suggesting tha ... | 2009 | 19520191 |
| igr genes and mycobacterium tuberculosis cholesterol metabolism. | recently, cholesterol was identified as a physiologically important nutrient for mycobacterium tuberculosis survival in chronically infected mice. however, it remained unclear precisely when cholesterol is available to the bacterium and what additional bacterial functions are required for its metabolism. here, we show that the igr locus, which we previously found to be essential for intracellular growth and virulence of m. tuberculosis, is required for cholesterol metabolism. while igr-deficient ... | 2009 | 19542286 |
| glycosylation of fluorophenols by plant cell cultures. | fluoroaromatic compounds are used as agrochemicals and released into environment as pollutants. glycosylation of 2-, 3-, and 4-fluorophenols using plant cell cultures of nicotiana tabacum was investigated to elucidate their potential to metabolize these compounds. cultured n. tabacum cells converted 2-fluorophenol into its beta-glucoside (60%) and beta-gentiobioside (10%). 4-fluorophenol was also glycosylated to its beta-glucoside (32%) and beta-gentiobioside (6%) by n. tabacum cells. on the oth ... | 2009 | 19564930 |
| antibiotic susceptibility profiles of uncommon bacterial species causing severe infections in italy. | this study presents the results of the italian "severe infections project" involving bacteria that can be considered rare causes of disease. we isolated 30 uncommon human pathogens from a total of 60 strains (1.2% of all the isolates). the most frequent sources of uncommon human pathogens were primary bloodstream infections (48.3%) and pneumonia (20%). species such as comamonas testosteroni, enterococcus hirae, kluyvera ascorbata, kluyvera cryocrescens, leclercia adecarboxylata and ochrobactrum ... | 2009 | 19567344 |
| broad-range pcr, cloning and sequencing of the full 16s rrna gene for detection of bacterial dna in synovial fluid samples of tunisian patients with reactive and undifferentiated arthritis. | broad-range rdna pcr provides an alternative, cultivation-independent approach for identifying bacterial dna in reactive and other form of arthritis. the aim of this study was to use broad-range rdna pcr targeting the 16s rrna gene in patients with reactive and other forms of arthritis and to screen for the presence of dna from any given bacterial species in synovial fluid (sf) samples. | 2009 | 19570210 |
| amidation of bioactive peptides: the structure of the lyase domain of the amidating enzyme. | many neuropeptides and peptide hormones require amidation of their carboxy terminal for full biological activity. the enzyme peptidyl-alpha-hydroxyglycine alpha-amidating lyase (pal; ec 4.3.2.5) catalyzes the second and last step of this reaction, n-dealkylation of the peptidyl-alpha-hydroxyglycine to generate the alpha-amidated peptide and glyoxylate. here we report the x-ray crystal structure of the pal catalytic core (palcc) alone and in complex with the nonpeptidic substrate alpha-hydroxyhip ... | 2009 | 19604476 |
| airway infection with a novel cupriavidus species in persons with cystic fibrosis. | we describe the recovery and identification of a bacterium that represents a new species of the genus cupriavidus from cultures of respiratory tract specimens from two patients with cystic fibrosis (cf). the elucidation of the role of this species in cf lung disease will require an evaluation of a greater number of cases. | 2009 | 19605576 |
| 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 |
| 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 |
| dna-stable isotope probing integrated with metagenomics for retrieval of biphenyl dioxygenase genes from polychlorinated biphenyl-contaminated river sediment. | stable isotope probing with [(13)c]biphenyl was used to explore the genetic properties of indigenous bacteria able to grow on biphenyl in pcb-contaminated river raisin sediment. a bacterial 16s rrna gene clone library generated from [(13)c]dna after a 14-day incubation with [(13)c]biphenyl revealed the dominant organisms to be members of the genera achromobacter and pseudomonas. a library built from pcr amplification of genes for aromatic-ring-hydroxylating dioxygenases from the [(13)c]dna fract ... | 2009 | 19648381 |
| metabolic analysis of the soil microbe dechloromonas aromatica str. rcb: indications of a surprisingly complex life-style and cryptic anaerobic pathways for aromatic degradation. | initial interest in dechloromonas aromatica strain rcb arose from its ability to anaerobically degrade benzene. it is also able to reduce perchlorate and oxidize chlorobenzoate, toluene, and xylene, creating interest in using this organism for bioremediation. little physiological data has been published for this microbe. it is considered to be a free-living organism. | 2009 | 19650930 |
| implanted-port-catheter-related sepsis caused by acidovorax avenae and methicillin-sensitive staphylococcus aureus. | acidovorax avenae is a gram-negative rod in the family comamonadaceae and a phytopathogen found in the environment. human infections caused by members of the comamonadaceae are extremely rare. we report a case of implanted-port-catheter-related sepsis caused by acidovorax avenae and methicillin (meticillin)-sensitive staphylococcus aureus (mssa). | 2009 | 19710279 |
| 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 |
| the complete genome of comamonas testosteroni reveals its genetic adaptations to changing environments. | members of the gram-negative, strictly aerobic genus comamonas occur in various environments. here we report the complete genome of comamonas testosteroni strain cnb-2. strain cnb-2 has a circular chromosome that is 5,373,643 bp long and has a g+c content of 61.4%. a total of 4,803 open reading frames (orfs) were identified; 3,514 of these orfs are functionally assigned to energy production, cell growth, signal transduction, or transportation, while 866 orfs encode hypothetical proteins and 423 ... | 2009 | 19734336 |
| identification of comamonas species using 16s rrna gene sequence. | a bacterial strain bz02 was isolated from a water sample collected from river gomti at the indian city of lucknow. we characterized the strain using 16s rrna sequence. phylogenetic analysis showed that the strain formed a monophyletic clade with members of the genus comamonas. the closest phylogenetic relative was comamonas testosteroni with 95% 16s rrna gene sequence similarity. it is proposed that the identified strain bz02 be assigned as the type strain of a species of the genus comamonas (co ... | 2009 | 19759812 |
| expression, purification, crystallization and preliminary x-ray analysis of para-nitrophenol 4-monooxygenase from pseudomonas putida dll-e4. | para-nitrophenol 4-monooxygenase (pnpa) plays an important role in bacterial degradation of para-nitrophenol by oxidative release of the nitro group from the aromatic ring to form p-benzoquinone. in order to understand the structural basis of the function of this enzyme, pnpa was cloned, expressed in escherichia coli and purified. pnpa was crystallized by the hanging-drop vapour-diffusion technique with peg 4000 as precipitant. the pnpa crystals belonged to space group p2(1)2(1)2(1), with unit-c ... | 2009 | 19851007 |
| homology modeling and docking studies of comamonas testosteroni b-356 biphenyl-2,3-dioxygenase involved in degradation of polychlorinated biphenyls. | biphenyl dioxygenase is a microbial enzyme which catalyzes the stereospecific dioxygenation of aromatic rings of biphenyl congeners leading to their degradation. hence, it has attracted the attention of researchers due to its ability to oxidize chlorinated biphenyls, which are one of the serious environmental contaminants. in the present study, the three-dimensional model of alpha-subunit of biphenyl dioxygenase (bpha) from comamonas testosteroni b-356 has been constructed. the resulting model w ... | 2010 | 19879892 |
| the missing link in linear alkylbenzenesulfonate surfactant degradation: 4-sulfoacetophenone as a transient intermediate in the degradation of 3-(4-sulfophenyl)butyrate by comamonas testosteroni kf-1. | biodegradation of the laundry surfactant linear alkylbenzenesulfonate (las) involves complex bacterial communities. the known heterotrophic community has two tiers. first, all las congeners are oxygenated and oxidized to about 50 sulfophenylcarboxylates (spc). second, the spcs are mineralized. comamonas testosteroni kf-1 mineralizes 3-(4-sulfophenyl)butyrate (3-c4-spc). during growth of strain kf-1 with 3-c4-spc, two transient intermediates were detected in the culture medium. one intermediate w ... | 2010 | 19915037 |
| characterization of the isophthalate degradation genes of comamonas sp. strain e6. | the isophthalate (ipa) degradation gene cluster (iphacbdr) responsible for the conversion of ipa into protocatechuate (pca) was isolated from comamonas sp. strain e6, which utilizes phthalate isomers as sole carbon and energy sources via the pca 4,5-cleavage pathway. based on amino acid sequence similarity, the ipha, iphc, iphb, iphd, and iphr genes were predicted to code for an oxygenase component of ipa dioxygenase (ipado), a periplasmic ipa binding receptor, a 1,2-dihydroxy-3,5-cyclohexadiene ... | 2010 | 19933340 |
| characterization of the isophthalate degradation genes of comamonas sp. strain e6. | the isophthalate (ipa) degradation gene cluster (iphacbdr) responsible for the conversion of ipa into protocatechuate (pca) was isolated from comamonas sp. strain e6, which utilizes phthalate isomers as sole carbon and energy sources via the pca 4,5-cleavage pathway. based on amino acid sequence similarity, the ipha, iphc, iphb, iphd, and iphr genes were predicted to code for an oxygenase component of ipa dioxygenase (ipado), a periplasmic ipa binding receptor, a 1,2-dihydroxy-3,5-cyclohexadiene ... | 2010 | 19933340 |
| novel tn4371-ice like element in ralstonia pickettii and genome mining for comparative elements. | integrative conjugative elements (ices) are important factors in the plasticity of microbial genomes. an element related to the ice tn4371 was discovered during a bioinformatic search of the ralstonia pickettii 12j genome. this element was analysed and further searches carried out for additional elements.a pcr method was designed to detect and characterise new elements of this type based on this scaffold and a culture collection of fifty-eight ralstonia pickettii and ralstonia insidiosa strains ... | 2009 | 19941653 |
| structure and ligand binding properties of the epoxidase component of styrene monooxygenase . | styrene monooxygenase (smo) is a two-component flavoprotein monooxygenase that transforms styrene to styrene oxide in the first step of the styrene catabolic and detoxification pathway of pseudomonas putida s12. the crystal structure of the n-terminally histidine-tagged epoxidase component of this system, nsmoa, determined to 2.3 a resolution, indicates the enzyme exists as a homodimer in which each monomer forms two distinct domains. the overall architecture is most similar to that of p-hydroxy ... | 2010 | 20055497 |
| structural studies on the full-length lysr-type regulator tsar from comamonas testosteroni t-2 reveal a novel open conformation of the tetrameric lttr fold. | lysr-type transcriptional regulators (lttrs) constitute the largest family of regulators in prokaryotes. the full-length structures of the lttr tsar from comamonas testosteroni t-2 and its complex with the natural inducer para-toluensulfonate have been characterized by x-ray diffraction. both ligand-free and complexed forms reveal a dramatically different quaternary structure from that of cbnr from ralstonia eutropha, or a putative lysr-type regulator from pseudomonas aeruginosa, the only other ... | 2010 | 20059681 |
| molecular diversity of katg genes in the soil bacteria comamonas. | three complete katg genes coding for bifunctional catalase-peroxidases (katgs) from the beta-proteobacterium comamonas terrigena and two related strains of comamonas testosteroni have been cloned and sequenced. catalase-peroxidases are unique bifunctional enzymes known to be expressed in these soil bacteria in response to environmental and/or oxidative stress. the evolutionary and structural diversity of these enzymes is investigated based on multiple sequence alignment and comprehensive phyloge ... | 2010 | 20062977 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| structural insight into the catalytic mechanism of gluconate 5-dehydrogenase from streptococcus suis: crystal structures of the substrate-free and quaternary complex enzymes. | gluconate 5-dehydrogenase (ga5dh) is an nadp(h)-dependent enzyme that catalyzes a reversible oxidoreduction reaction between d-gluconate and 5-keto-d-gluconate, thereby regulating the flux of this important carbon and energy source in bacteria. despite the considerable amount of physiological and biochemical knowledge of ga5dh, there is little physical or structural information available for this enzyme. to this end, we herein report the crystal structures of ga5dh from pathogenic streptococcus ... | 2009 | 19177572 |
| structure of the plp degradative enzyme 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase from mesorhizobium loti maff303099 and its mechanistic implications. | a vitamin b(6) degradative pathway has recently been identified and characterized in mesorhizobium loti maff303099. one of the enzymes on this pathway, 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (mhpco), is a flavin-dependent enzyme and catalyzes the oxidative ring-opening of 2-methyl-3-hydroxypyridine-5-carboxylic acid to form e-2-(acetamino-methylene)succinate. the gene for this enzyme has been cloned, and the corresponding protein has been overexpressed in escherichia coli and pur ... | 2009 | 19317437 |
| chaperone-fusion expression plasmid vectors for improved solubility of recombinant proteins in escherichia coli. | the enteric bacterium escherichia coli is the most extensively used prokaryotic organism for production of proteins of therapeutic or commercial interest. however, it is common that heterologous over-expressed recombinant proteins fail to properly fold resulting in formation of insoluble aggregates known as inclusion bodies. complex systems have been developed that employ simultaneous over-expression of chaperone proteins to aid proper folding and solubility during bacterial expression. here we ... | 2009 | 19328840 |
| configurational entropy in protein-peptide binding: computational study of tsg101 ubiquitin e2 variant domain with an hiv-derived ptap nonapeptide. | configurational entropy is thought to influence biomolecular processes, but there are still many open questions about this quantity, including its magnitude, its relationship to molecular structure, and the importance of correlation. the mutual information expansion (mie) provides a novel and systematic approach to extracting configurational entropy changes due to correlated motions from molecular simulations. we present the first application of the mie method to protein-ligand binding using mul ... | 2009 | 19362095 |
| fido, a novel ampylation domain common to fic, doc, and avrb. | the vibrio parahaemolyticus type iii secreted effector vops contains a fic domain that covalently modifies rho gtpase threonine with amp to inhibit downstream signaling events in host cells. the vops fic domain includes a conserved sequence motif (hpfx[d/e]gn[g/k]r) that contributes to ampylation. fic domains are found in a variety of species, including bacteria, a few archaea, and metazoan eukaryotes. | 2009 | 19503829 |
| bacillus subtilis as potential producer for polyhydroxyalkanoates. | abstract: polyhydroxyalkanoates (phas) are biodegradable polymers produced by microbes to overcome environmental stress. commercial production of phas is limited by the high cost of production compared to conventional plastics. another hindrance is the brittle nature and low strength of polyhydroxybutyrate (phb), the most widely studied pha. the needs are to produce phas, which have better elastomeric properties suitable for biomedical applications, preferably from inexpensive renewable sources ... | 2009 | 19619289 |
| homotaurine metabolized to 3-sulfopropanoate in cupriavidus necator h16: enzymes and genes in a patchwork pathway. | homotaurine (3-aminopropanesulfonate), a natural product and an analogue of gaba (4-aminobutyrate), was found to be a sole source of nitrogen for cupriavidus necator (ralstonia eutropha) h16, whose genome sequence is known. homotaurine nitrogen was assimilated into cell material, and the quantitative fate of the organosulfonate was sulfopropanoate, which was recovered in the growth medium. the first scalar reaction was shown to be inducible homotaurine:2-oxoglutarate aminotransferase, which rele ... | 2009 | 19648235 |
| phenotypic and molecular characterization of solobacterium moorei isolates from patients with wound infection. | though seldom reported, solobacterium moorei, which was first described in 2000, has been identified in specimens from patients with root canals, periradicular lesions, periodontal disease, dentoalveolar abscesses, bacteremia, septic thrombophlebitis, and halitosis. in the present study, we describe 9 cases of mixed wound infection, from a pool of 400 surgical wound infections that we have studied, in which s. moorei was isolated or found in a clone library. all isolates of s. moorei were identi ... | 2010 | 20071554 |
| crystal structure analysis reveals pseudomonas pily1 as an essential calcium-dependent regulator of bacterial surface motility. | several bacterial pathogens require the "twitching" motility produced by filamentous type iv pili (t4p) to establish and maintain human infections. two cytoplasmic atpases function as an oscillatory motor that powers twitching motility via cycles of pilus extension and retraction. the regulation of this motor, however, has remained a mystery. we present the 2.1 a resolution crystal structure of the pseudomonas aeruginosa pilus-biogenesis factor pily1, and identify a single site on this protein r ... | 2010 | 20080557 |
| crystal structure analysis reveals pseudomonas pily1 as an essential calcium-dependent regulator of bacterial surface motility. | several bacterial pathogens require the "twitching" motility produced by filamentous type iv pili (t4p) to establish and maintain human infections. two cytoplasmic atpases function as an oscillatory motor that powers twitching motility via cycles of pilus extension and retraction. the regulation of this motor, however, has remained a mystery. we present the 2.1 a resolution crystal structure of the pseudomonas aeruginosa pilus-biogenesis factor pily1, and identify a single site on this protein r ... | 2010 | 20080557 |
| dissecting the paradoxical effects of hydrogen bond mutations in the ketosteroid isomerase oxyanion hole. | the catalytic importance of enzyme active-site interactions is frequently assessed by mutating specific residues and measuring the resulting rate reductions. this approach has been used in bacterial ketosteroid isomerase to probe the energetic importance of active-site hydrogen bonds donated to the dienolate reaction intermediate. the conservative tyr16phe mutation impairs catalysis by 10(5)-fold, far larger than the effects of hydrogen bond mutations in other enzymes. however, the less-conserva ... | 2010 | 20080683 |
| liquid chromatography-mass spectrometry (lc-ms) of steroid hormone metabolites and its applications. | advances in liquid chromatography-mass spectrometry (lc-ms) can be used to measure steroid hormone metabolites in vitro and in vivo. we find that lc-electrospray ionization (esi)-ms using a lcq ion trap mass spectrometer in the negative ion mode can be used to monitor the product profile that results from 5alpha-dihydrotestosterone (dht)-17beta-glucuronide, dht-17beta-sulfate, and tibolone-17beta-sulfate reduction catalyzed by human members of the aldo-keto reductase (akr) 1c subfamily and assig ... | 2010 | 20083198 |
| cloning, expression and functional analysis of nicotinate dehydrogenase gene cluster from comamonas testosteroni ja1 that can hydroxylate 3-cyanopyridine. | a nicotinate dehydrogenase (nadh) gene cluster was cloned from comamonas testosteroni ja1. the enzyme, termed nadh(ja1), is composed of 21, 82, and 46 kda subunits, respectivley containing [2fe2s], mo(v) and cytochrome c domains. the recombinant nadh(ja1) can catalyze the hydroxylation of nicotinate and 3-cyanopyridine. nadh(ja1) protein exhibits 52.8% identity to the amino acid sequence of nadh(kt2440) from p. putida kt2440. sequence alignment analysis showed that the [2fe2s] domain in nadh(ja1 ... | 2010 | 20119845 |
| proton affinity of the oxyanion hole in the active site of ketosteroid isomerase. | the absorption spectra of a series of inhibitors bound at the active site of delta(5)-3-ketosteroid isomerase from pseudomonas putida were found to exhibit substantial variations in the contributions of the protonated and deprotonated forms. systematic variation of the inhibitor solution pk(a) combined with a method of quantifying the contributions of each protonation state showed the oxyanion hole in the active site of wild-type delta(5)-3-ketosteroid isomerase to have a proton affinity equal t ... | 2010 | 20143849 |
| characterization of comamonas thiooxidans sp. nov., and comparison of thiosulfate oxidation with comamonas testosteroni and comamonas composti. | comamonas thiooxidans (strain s23(t)) capable of oxidizing thiosulfate under a mixotrophic growth condition was isolated from a sulfur spring. dna-dna homology study showed 55% similarity with comamonas testosteroni kctc2990(t) and 52% with comamonas composti lmg24008(t), the nearest phylogenetic relative (16s rrna sequence similarity <97%). comparative genomic fingerprinting by using eric and rep-pcr further delineated species identity of the strain s23(t) for which comamonas thiooxidans sp. no ... | 2010 | 20148250 |
| construction and application of variants of the pseudomonas fluorescens ebc191 arylacetonitrilase for increased production of acids or amides. | the arylacetonitrilase from pseudomonas fluorescens ebc191 differs from previously studied arylacetonitrilases by its low enantiospecificity during the turnover of mandelonitrile and by the large amounts of amides that are formed in the course of this reaction. in the sequence of the nitrilase from p. fluorescens, a cysteine residue (cys163) is present in direct neighborhood (toward the amino terminus) to the catalytic active cysteine residue, which is rather unique among bacterial nitrilases. t ... | 2010 | 20382812 |
| initial steps in anoxic testosterone degradation by steroidobacter denitrificans. | steroid compounds have many important physiological activities in higher organisms. testosterone and related steroids are important environmental contaminants that disrupt the endocrine systems of animals. the degradation of steroids, especially under anoxic conditions, is challenging because of their complex chemical structure. a denitrifying gamma-proteobacterium, steroidobacter denitrificans, able to grow anaerobically on a variety of steroids as the sole carbon and energy source was adopted ... | 2010 | 20413554 |