| role of heterotrophic bacteria in complete mineralization of trichloroethylene by methylocystis sp. strain m. | biodegradation experiments with radioactively labeled trichloroethylene showed that 32% of the radioactive carbon was converted to glyoxylic acid, dichloroacetic acid and trichloroacetic acid and that the same percentage was converted to co2 and co after 140 h of incubation by a pure culture of a type ii methane-utilizing bacterium, methylocystis sp. strain m, isolated from a mixed culture, mu-81, in our laboratory. in contrast, these water-soluble (14c)trichloroethylene degradation products wer ... | 1992 | 1444420 |
| degradation of 1,2-dichloroethane by ancylobacter aquaticus and other facultative methylotrophs. | cultures of the newly isolated bacterial strains ad20, ad25, and ad27, identified as strains of ancylobacter aquaticus, were capable of growth on 1,2-dichloroethane (dce) as the sole carbon and energy source. these strains, as well as two other new dce utilizers, were facultative methylotrophs and were also able to grow on 2-chloroethanol, chloroacetate, and 2-chloropropionate. in all strains tested, dce was degraded by initial hydrolytic dehalogenation to 2-chloroethanol, followed by oxidation ... | 1992 | 1575500 |
| characterization of the haloacid dehalogenase from xanthobacter autotrophicus gj10 and sequencing of the dhlb gene. | the haloacid dehalogenase of the 1,2-dichloroethane-utilizing bacterium xanthobacter autotrophicus gj10 was purified from a mutant with an eightfold increase in expression of the enzyme. the mutant was obtained by selecting for enhanced resistance to monobromoacetate. the enzyme was purified through (nh4)2so4 fractionation, deae-cellulose chromatography, and hydroxylapatite chromatography. the molecular mass of the protein was 28 kda as determined with sodium dodecyl sulfate-polyacrylamide gel e ... | 1991 | 1744048 |
| involvement of a large plasmid in the degradation of 1,2-dichloroethane by xanthobacter autotrophicus. | xanthobacter autotrophicus gj10 is a bacterium that can degrade short-chain halogenated aliphatic compounds such as 1,2-dichloroethane. a 200-kb plasmid, pxau1, was isolated from this strain and shown to contain the dhla gene, which codes for haloalkane dehalogenase, the first enzyme in the degradation pathway of 1,2-dichloroethane by gj10. loss of pxau1 resulted in loss of haloalkane dehalogenase activity, significantly decreased chloroacetaldehyde dehydrogenase activity, and loss of resistance ... | 1991 | 1872615 |
| crystal structure of haloalkane dehalogenase: an enzyme to detoxify halogenated alkanes. | haloalkane dehalogenase from xanthobacter autotrophicus gj10 converts 1-haloalkanes to the corresponding alcohols and halide ions with water as the sole cosubstrate and without any need for oxygen or cofactors. the three-dimensional structure has been determined by multiple isomorphous replacement techniques using three heavy atom derivatives. the structure has been refined at 2.4 a resolution to an r-factor of 17.9%. the monomeric enzyme is a spherical molecule and is composed to two domains: d ... | 1991 | 2026135 |
| 13c-urea breath test for helicobacter pylori infection. | | 1991 | 2040481 |
| cloning of 1,2-dichloroethane degradation genes of xanthobacter autotrophicus gj10 and expression and sequencing of the dhla gene. | a gene bank from the chlorinated hydrocarbon-degrading bacterium xanthobacter autotrophicus gj10 was prepared in the broad-host-range cosmid vector plafr1. by using mutants impaired in dichloroethane utilization and strains lacking dehalogenase activities, several genes involved in 1,2-dichloroethane metabolism were isolated. the haloalkane dehalogenase gene dhla was subcloned, and it was efficiently expressed from its own constitutive promoter in strains of a pseudomonas sp., escherichia coli, ... | 1989 | 2687254 |
| degradation of halogenated aliphatic compounds by xanthobacter autotrophicus gj10. | a bacterium that is able to utilize a number of halogenated short-chain hydrocarbons and halogenated carboxylic acids as sole carbon source for growth was identified as a strain of xanthobacter autotrophicus. the organism constitutively produces two different dehalogenases. one enzyme is specific for halogenated alkanes, whereas the other, which is more heat stable and has a higher ph optimum, is specific for halogenated carboxylic acids. haloalkanes were hydrolyzed in cell extracts to produce a ... | 1985 | 3994371 |
| purification and characterization of hydrolytic haloalkane dehalogenase from xanthobacter autotrophicus gj10. | a new enzyme, haloalkane dehalogenase, was isolated from the 1,2-dichloroethane-utilizing bacterium xanthobacter autotrophicus gj10. the purified enzyme catalyzed the hydrolytic dehalogenation of n-halogenated c1 to c4 alkanes, including chlorinated, brominated, and iodinated compounds. the highest activity was found with 1,2-dichloroethane, 1,3-dichloropropane, and 1,2-dibromoethane. the enzyme followed michaelis-menten kinetics, and the km for 1,2-dichloroethane was 1.1 mm. maximum activity wa ... | 1985 | 4019411 |
| adaptation of xanthobacter autotrophicus gj10 to bromoacetate due to activation and mobilization of the haloacetate dehalogenase gene by insertion element is1247. | monobromoacetate (mba) is toxic for the 1,2-dichloroethane-degrading bacterium xanthobacter autotrophicus gj10 at concentrations higher than 5 mm. mutants which are able to grow on higher concentrations of mba were isolated and found to overexpress haloacid dehalogenase, which is encoded by the dhlb gene. in mutant gj10m50, a dna fragment (designated is1247) had copied itself from a position on the chromosome that was not linked to the dhlb region to a site immediately upstream of dhlb, resultin ... | 1995 | 7868610 |
| comparative studies of genes encoding thermostable l-2-halo acid dehalogenase from pseudomonas sp. strain yl, other dehalogenases, and two related hypothetical proteins from escherichia coli. | we have determined the nucleotide sequence of the gene encoding thermostable l-2-halo acid dehalogenase (l-dex) from the 2-chloroacrylate-utilizable bacterium pseudomonas sp. strain yl. the open reading frame consists of 696 nucleotides corresponding to 232 amino acid residues. the protein molecular weight was estimated to be 26,179, which was in good agreement with the subunit molecular weight of the enzyme. the gene was efficiently expressed in the recombinant escherichia coli cells: the amoun ... | 1994 | 7944368 |
| influence of organic nutrients and cocultures on the competitive behavior of 1,2-dichloroethane-degrading bacteria. | the effects of organic nutrients and cocultures on substrate removal by and competitive behavior of 1,2-dichloroethane-degrading bacteria were investigated. xanthobacter autotrophicus gj10 needed biotin for optimal growth on 1,2-dichloroethane. in continuous culture, dilution of biotin to a concentration below 0.2 nm resulted in washout. growth could be restored by inoculation with the 2-chloroethanol utilizer pseudomonas sp. strain gj1, leading to a new steady state in which about 1% of the mix ... | 1993 | 8250561 |
| crystallization and preliminary x-ray analysis of l-2-haloacid dehalogenase from xanthobacter autotrophicus gj10. | haloacid dehalogenases are enzymes that cleave carbon-chlorine or carbon-bromine bonds of 2-haloalkanoates. x-ray-quality crystals of l-2-haloacid dehalogenase from the 1,2-dichloroethane-degrading bacterium xanthobacter autotrophicus gj10 have been grown at room temperature from 20% peg 8000, 200 mm sodium formate at ph 6.8-7.0, using macroseeding techniques. the crystals, which diffract in the x-ray beam up to 2.0 a resolution, belong to the spacegroup c2221. cell parameters are a = 58.8 a, b ... | 1995 | 8580854 |
| cloning and sequencing of a 2,5-dichlorohydroquinone reductive dehalogenase gene whose product is involved in degradation of gamma-hexachlorocyclohexane by sphingomonas paucimobilis. | sphingomonas (formerly pseudomonas) paucimobilis ut26 utilizes gamma-hexachlorocyclohexane (gamma-hch), a halogenated organic insecticide, as a sole carbon and energy source. in a previous study, we showed that gamma-hch is degraded to 2,5-dichlorohydroquinone (2,5-dchq) (y. nagata, r. ohtomo, k. miyauchi, m. fukuda, k. yano, and m. takagi, j. bacteriol. 176:3117-3125, 1994). in the present study, we cloned and characterized a gene, designated lind, directly involved in the degradation of 2,5-dc ... | 1998 | 9515900 |
| the atrazine catabolism genes atzabc are widespread and highly conserved. | pseudomonas strain adp metabolizes the herbicide atrazine via three enzymatic steps, encoded by the genes atzabc, to yield cyanuric acid, a nitrogen source for many bacteria. here, we show that five geographically distinct atrazine-degrading bacteria contain genes homologous to atza, -b, and -c. the sequence identities of the atz genes from different atrazine-degrading bacteria were greater than 99% in all pairwise comparisons. this differs from bacterial genes involved in the catabolism of othe ... | 1998 | 9537398 |
| multiple beta-ketothiolases mediate poly(beta-hydroxyalkanoate) copolymer synthesis in ralstonia eutropha. | polyhydroxyalkanoates (phas) are a class of carbon and energy storage polymers produced by numerous bacteria in response to environmental limitation. the type of polymer produced depends on the carbon sources available, the flexibility of the organism's intermediary metabolism, and the substrate specificity of the pha biosynthetic enzymes. ralstonia eutropha produces both the homopolymer poly-beta-hydroxybutyrate (phb) and, when provided with the appropriate substrate, the copolymer poly(beta-hy ... | 1998 | 9555876 |
| chloromethane metabolism by methylobacterium sp. strain cm4 | methylobacterium sp. strain cm4 metabolized chloromethane quantitatively with a molar yield of 2.8 g of whole-cell protein/mol of c. this value was similar to that observed after growth with methanol (2.9 g of protein/mol of c) and about three times larger than the yield with formate (0.94 g of protein/mol of c). chloromethane dehalogenation activity was inducible. minitn5 transposon insertion mutants with altered growth characteristics with chloromethane and other c1 compounds were isolated and ... | 1998 | 9572975 |
| structures of homologous composite transposons carrying cbaabc genes from europe and north america. | is1071 is a class ii transposable element carrying a tnpa gene related to the transposase genes of the tn3 family. copies of is1071 that are conserved with more than 99% nucleotide sequence identity have been found as direct repeats flanking a remarkable variety of catabolic gene sequences worldwide. the sequences of chlorobenzoate catabolic transposons found on pbrc60 (tn5271) in niagara falls, n.y., and on pcpe3 in bologna, italy, show that these transposons were formed from highly homologous ... | 1998 | 9572977 |
| degradation of 1,3-dichloropropene by pseudomonas cichorii 170. | the gram-negative bacterium pseudomonas cichorii 170, isolated from soil that was repeatedly treated with the nematocide 1, 3-dichloropropene, could utilize low concentrations of 1, 3-dichloropropene as a sole carbon and energy source. strain 170 was also able to grow on 3-chloroallyl alcohol, 3-chloroacrylic acid, and several 1-halo-n-alkanes. this organism produced at least three different dehalogenases: a hydrolytic haloalkane dehalogenase specific for haloalkanes and two 3-chloroacrylic acid ... | 1998 | 9687453 |
| limonene-1,2-epoxide hydrolase from rhodococcus erythropolis dcl14 belongs to a novel class of epoxide hydrolases. | an epoxide hydrolase from rhodococcus erythropolis dcl14 catalyzes the hydrolysis of limonene-1,2-epoxide to limonene-1,2-diol. the enzyme is induced when r. erythropolis is grown on monoterpenes, reflecting its role in the limonene degradation pathway of this microorganism. limonene-1,2-epoxide hydrolase was purified to homogeneity. it is a monomeric cytoplasmic enzyme of 17 kda, and its n-terminal amino acid sequence was determined. no cofactor was required for activity of this colorless enzym ... | 1998 | 9748436 |
| degradation of 1,2-dibromoethane by mycobacterium sp. strain gp1. | the newly isolated bacterial strain gp1 can utilize 1, 2-dibromoethane as the sole carbon and energy source. on the basis of 16s rrna gene sequence analysis, the organism was identified as a member of the subgroup which contains the fast-growing mycobacteria. the first step in 1,2-dibromoethane metabolism is catalyzed by a hydrolytic haloalkane dehalogenase. the resulting 2-bromoethanol is rapidly converted to ethylene oxide by a haloalcohol dehalogenase, in this way preventing the accumulation ... | 1999 | 10094681 |
| the alkene monooxygenase from xanthobacter strain py2 is closely related to aromatic monooxygenases and catalyzes aromatic monohydroxylation of benzene, toluene, and phenol. | the genes encoding the six polypeptide components of the alkene monooxygenase from xanthobacter strain py2 (xamo) have been located on a 4.9-kb fragment of chromosomal dna previously cloned in cosmid pny2. sequencing and analysis of the predicted amino acid sequences indicate that the components of xamo are homologous to those of the aromatic monooxygenases, toluene 2-, 3-, and 4-monooxygenase and benzene monooxygenase, and that the gene order is identical. the genes and predicted polypeptides a ... | 1999 | 10103255 |
| investigation of two evolutionarily unrelated halocarboxylic acid dehalogenase gene families. | dehalogenases are key enzymes in the metabolism of halo-organic compounds. this paper describes a systematic approach to the isolation and molecular analysis of two families of bacterial alpha-halocarboxylic acid (alphaha) dehalogenase genes, called group i and group ii deh genes. the two families are evolutionarily unrelated and together represent almost all of the alphaha deh genes described to date. we report the design and evaluation of degenerate pcr primer pairs for the separate amplificat ... | 1999 | 10198020 |
| monooxygenase-mediated 1,2-dichloroethane degradation by pseudomonas sp. strain dca1. | a bacterial strain, designated pseudomonas sp. strain dca1, was isolated from a 1,2-dichloroethane (dca)-degrading biofilm. strain dca1 utilizes dca as the sole carbon and energy source and does not require additional organic nutrients, such as vitamins, for optimal growth. the affinity of strain dca1 for dca is very high, with a km value below the detection limit of 0.5 microm. instead of a hydrolytic dehalogenation, as in other dca utilizers, the first step in dca degradation in strain dca1 is ... | 1999 | 10347028 |
| characterization and nucleotide sequence of a klebsiella oxytoca cryptic plasmid encoding a cmy-type beta-lactamase: confirmation that the plasmid-mediated cephamycinase originated from the citrobacter freundii ampc beta-lactamase. | plasmid ptkh11, originally obtained by electroporation of a klebsiella oxytoca plasmid preparation into escherichia coli xac, expressed a high level of an ampc-like beta-lactamase. the enzyme, designated cmy-5, conferred resistance to extended-spectrum beta-lactams in e. coli; nevertheless, the phenotype was cryptic in the k. oxytoca donor. determination of the complete nucleotide sequence of ptkh11 revealed that the 8,193-bp plasmid encoded seven open reading frames, including that for the cmy- ... | 1999 | 10348751 |
| bacterial 2,4-dioxygenases: new members of the alpha/beta hydrolase-fold superfamily of enzymes functionally related to serine hydrolases. | 1h-3-hydroxy-4-oxoquinoline 2,4-dioxygenase (qdo) from pseudomonas putida 33/1 and 1h-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase (hod) from arthrobacter ilicis rü61a catalyze an n-heterocyclic-ring cleavage reaction, generating n-formylanthranilate and n-acetylanthranilate, respectively, and carbon monoxide. amino acid sequence comparisons between qdo, hod, and a number of proteins belonging to the alpha/beta hydrolase-fold superfamily of enzymes and analysis of the similarity between the predict ... | 1999 | 10482514 |
| distribution of tetrahydromethanopterin-dependent enzymes in methylotrophic bacteria and phylogeny of methenyl tetrahydromethanopterin cyclohydrolases. | the methylotrophic proteobacterium methylobacterium extorquens am1 possesses tetrahydromethanopterin (h(4)mpt)-dependent enzymes, which are otherwise specific to methanogenic and sulfate-reducing archaea and which have been suggested to be involved in formaldehyde oxidation to co(2) in m. extorquens am1. the distribution of h(4)mpt-dependent enzyme activities in cell extracts of methylotrophic bacteria from 13 different genera are reported. h(4)mpt-dependent activities were detected in all of th ... | 1999 | 10482517 |
| detoxification of environmental mutagens and carcinogens: structure, mechanism, and evolution of liver epoxide hydrolase. | the crystal structure of recombinant murine liver cytosolic epoxide hydrolase (ec 3.3.2.3) has been determined at 2.8-a resolution. the binding of a nanomolar affinity inhibitor confirms the active site location in the c-terminal domain; this domain is similar to that of haloalkane dehalogenase and shares the alpha/beta hydrolase fold. a structure-based mechanism is proposed that illuminates the unique chemical strategy for the activation of endogenous and man-made epoxide substrates for hydroly ... | 1999 | 10485878 |
| cloning and characterization of a cryptic haloacid dehalogenase from burkholderia cepacia mba4. | burkholderia cepacia mba4 has been shown to produce a single dehalogenase batch culture. moreover, other cryptic dehalogenases were also detected when the cells were grown in continuous culture. in this paper, we report the cloning and characterization of one of the cryptic dehalogenases in mba4. this cryptic haloacid dehalogenase, designated chd1, was expressed constitutively in escherichia coli. this recombinant chd1 had a relative molecular weight of 58,000 and existed predominantly as a dime ... | 1999 | 10498712 |
| halomethane:bisulfide/halide ion methyltransferase, an unusual corrinoid enzyme of environmental significance isolated from an aerobic methylotroph using chloromethane as the sole carbon source. | a novel dehalogenating/transhalogenating enzyme, halomethane:bisulfide/halide ion methyltransferase, has been isolated from the facultatively methylotrophic bacterium strain cc495, which uses chloromethane (ch(3)cl) as the sole carbon source. purification of the enzyme to homogeneity was achieved in high yield by anion-exchange chromatography and gel filtration. the methyltransferase was composed of a 67-kda protein with a corrinoid-bound cobalt atom. the purified enzyme was inactive but was act ... | 1999 | 10508052 |
| utilization of trihalogenated propanes by agrobacterium radiobacter ad1 through heterologous expression of the haloalkane dehalogenase from rhodococcus sp. strain m15-3. | trihalogenated propanes are toxic and recalcitrant organic compounds. attempts to obtain pure bacterial cultures able to use these compounds as sole carbon and energy sources were unsuccessful. both the haloalkane dehalogenase from xanthobacter autotrophicus gj10 (dhla) and that from rhodococcus sp. strain m15-3 (dhaa) were found to dehalogenate trihalopropanes to 2,3-dihalogenated propanols, but the kinetic properties of the latter enzyme are much better. broad-host-range dehalogenase expressio ... | 1999 | 10508091 |
| cloning and sequencing of a novel meta-cleavage dioxygenase gene whose product is involved in degradation of gamma-hexachlorocyclohexane in sphingomonas paucimobilis. | sphingomonas (formerly pseudomonas) paucimobilis ut26 utilizes gamma-hexachlorocyclohexane (gamma-hch), a halogenated organic insecticide, as a sole source of carbon and energy. in a previous study, we showed that gamma-hch is degraded to chlorohydroquinone (chq) and then to hydroquinone (hq), although the rate of reaction from chq to hq was slow (k. miyauchi, s. k. suh, y. nagata, and m. takagi, j. bacteriol. 180:1354-1359, 1998). in this study, we cloned and characterized a gene, designated li ... | 1999 | 10542173 |
| dehalogenation of haloalkanes by mycobacterium tuberculosis h37rv and other mycobacteria. | haloalkane dehalogenases convert haloalkanes to their corresponding alcohols by a hydrolytic mechanism. to date, various haloalkane dehalogenases have been isolated from bacteria colonizing environments that are contaminated with halogenated compounds. a search of current databases with the sequences of these known haloalkane dehalogenases revealed the presence of three different genes encoding putative haloalkane dehalogenases in the genome of the human parasite mycobacterium tuberculosis h37rv ... | 2000 | 10618227 |
| roles of horizontal gene transfer and gene integration in evolution of 1,3-dichloropropene- and 1,2-dibromoethane-degradative pathways. | the haloalkane-degrading bacteria rhodococcus rhodochrous ncimb13064, pseudomonas pavonaceae 170, and mycobacterium sp. strain gp1 share a highly conserved haloalkane dehalogenase gene (dhaa). here, we describe the extent of the conserved dhaa segments in these three phylogenetically distinct bacteria and an analysis of their flanking sequences. the dhaa gene of the 1-chlorobutane-degrading strain ncimb13064 was found to reside within a 1-chlorobutane catabolic gene cluster, which also encodes a ... | 2000 | 10735862 |
| haloalkane-utilizing rhodococcus strains isolated from geographically distinct locations possess a highly conserved gene cluster encoding haloalkane catabolism. | the sequences of the 16s rrna and haloalkane dehalogenase (dhaa) genes of five gram-positive haloalkane-utilizing bacteria isolated from contaminated sites in europe, japan, and the united states and of the archetypal haloalkane-degrading bacterium rhodococcus sp. strain ncimb13064 were compared. the 16s rrna gene sequences showed less than 1% sequence divergence, and all haloalkane degraders clearly belonged to the genus rhodococcus. all strains shared a completely conserved dhaa gene, suggesti ... | 2000 | 10781539 |
| cloning and sequencing of the gene encoding an aldehyde dehydrogenase that is induced by growing alteromonas sp. strain ke10 in a low concentration of organic nutrients. | the protein composition of alteromonas sp. strain ke10 cultured at two different organic-nutrient concentrations was determined by using two-dimensional polyacrylamide gel electrophoresis. the cellular levels of three proteins, olga, -b, and -c, were considerably higher in cells grown in a low concentration of organic nutrient medium (lon medium; 0.2 mg of carbon per liter) than cells grown in a high concentration of organic nutrient medium (hon; 200 mg of c liter(-1)) or cells starved for organ ... | 2000 | 10788355 |
| isolation and characterization of 2,3-dichloro-1-propanol-degrading rhizobia. | 2,3-dichloro-1-propanol is more chemically stable than its isomer, 1, 3-dichloro-2-propanol, and is therefore more difficult to degrade. the isolation of bacteria capable of complete mineralization of 2, 3-dichloro-1-propanol was successful only from enrichments at high ph. the bacteria thus isolated were found to be members of the alpha division of the proteobacteria in the rhizobium subdivision, most likely agrobacterium sp. they could utilize both dihaloalcohol substrates and 2-chloropropioni ... | 2000 | 10877782 |
| identification of the dimerization domain of dehalogenase iva of burkholderia cepacia mba4. | haloacid dehalogenases are enzymes that catalyze the hydrolytic removal of halogens from haloalkanoic acids. dehalogenase iva (dehiva) from burkholderia cepacia mba4 and dehalogenase ci (dehci) from pseudomonas sp. strain cbs3 exhibit 68% identity. despite their similarity dehiva is a dimeric enzyme while dehci is a monomer. in this work, we describe the identification of the domain that confers the dimerization function of dehiva. recombinant dna molecules were constructed by fusion of the resp ... | 2000 | 10919767 |
| the importance of reactant positioning in enzyme catalysis: a hybrid quantum mechanics/molecular mechanics study of a haloalkane dehalogenase. | hybrid quantum mechanics/molecular mechanics calculations using austin model 1 system-specific parameters were performed to study the s(n)2 displacement reaction of chloride from 1,2-dichloroethane (dce) by nucleophilic attack of the carboxylate of acetate in the gas phase and by asp-124 in the active site of haloalkane dehalogenase from xanthobacter autotrophicus gj10. the activation barrier for nucleophilic attack of acetate on dce depends greatly on the reactants having a geometry resembling ... | 2000 | 10963662 |
| evidence of substantial carbon isotope fractionation among substrate, inorganic carbon, and biomass during aerobic mineralization of 1, 2-dichloroethane by xanthobacter autotrophicus. | carbon isotope fractionation during aerobic mineralization of 1, 2-dichloroethane (1,2-dca) by xanthobacter autotrophicus gj10 was investigated. a strong enrichment of (13)c in residual 1,2-dca was observed, with a mean fractionation factor alpha +/- standard deviation of 0.968 +/- 0.0013 to 0.973 +/- 0.0015. in addition, a large carbon isotope fractionation between biomass and inorganic carbon occurred. a mechanistic model that links the fractionation factor alpha to the rate constants of the f ... | 2000 | 11055937 |
| chloromethane utilization gene cluster from hyphomicrobium chloromethanicum strain cm2(t) and development of functional gene probes to detect halomethane-degrading bacteria. | hyphomicrobium chloromethanicum cm2(t), an aerobic methylotrophic member of the alpha subclass of the class proteobacteria, can grow with chloromethane as the sole carbon and energy source. h. chloromethanicum possesses an inducible enzyme system for utilization of chloromethane, in which two polypeptides (67-kda cmua and 35-kda cmub) are expressed. previously, four genes, cmua, cmub, cmuc, and puru, were shown to be essential for growth of methylobacterium chloromethanicum on chloromethane. the ... | 2001 | 11133460 |
| reductive, coenzyme a-mediated pathway for 3-chlorobenzoate degradation in the phototrophic bacterium rhodopseudomonas palustris. | we isolated a strain of rhodopseudomonas palustris (rcb100) by selective enrichment in light on 3-chlorobenzoate to investigate the steps that it uses to accomplish anaerobic dechlorination. analyses of metabolite pools as well as enzyme assays suggest that r. palustris grows on 3-chlorobenzoate by (i) converting it to 3-chlorobenzoyl coenzyme a (3-chlorobenzoyl-coa), (ii) reductively dehalogenating 3-chlorobenzoyl-coa to benzoyl-coa, and (iii) degrading benzoyl-coa to acetyl-coa and carbon diox ... | 2001 | 11229940 |
| evidence that a linear megaplasmid encodes enzymes of aliphatic alkene and epoxide metabolism and coenzyme m (2-mercaptoethanesulfonate) biosynthesis in xanthobacter strain py2. | the bacterial metabolism of propylene proceeds by epoxidation to epoxypropane followed by a sequence of three reactions resulting in epoxide ring opening and carboxylation to form acetoacetate. coenzyme m (2-mercaptoethanesulfonic acid) (com) plays a central role in epoxide carboxylation by serving as the nucleophile for epoxide ring opening and the carrier of the c(3) unit that is ultimately carboxylated to acetoacetate, releasing com. in the present work, a 320-kb linear megaplasmid has been i ... | 2001 | 11244054 |
| genetic characterization and evolutionary implications of a car gene cluster in the carbazole degrader pseudomonas sp. strain ca10. | the nucleotide sequences of the 27,939-bp-long upstream and 9,448-bp-long downstream regions of the caraaaababbcac(orf7)ad genes of carbazole-degrading pseudomonas sp. strain ca10 were determined. thirty-two open reading frames (orfs) were identified, and the car gene cluster was consequently revealed to consist of 10 genes (caraaaababbcacaddfe) encoding the enzymes for the three-step conversion of carbazole to anthranilate and the degradation of 2-hydroxypenta-2,4-dienoate. the high identities ... | 2001 | 11371531 |
| trans-3-chloroacrylic acid dehalogenase from pseudomonas pavonaceae 170 shares structural and mechanistic similarities with 4-oxalocrotonate tautomerase. | the genes (caad1 and caad2) encoding the trans-3-chloroacrylic acid dehalogenase (caad) of the 1,3-dichloropropene-utilizing bacterium pseudomonas pavonaceae 170 were cloned and heterologously expressed in escherichia coli and pseudomonas sp. strain gj1. caad is a protein of 50 kda that is composed of alpha-subunits of 75 amino acid residues and beta-subunits of 70 residues. it catalyzes the hydrolytic cleavage of the beta-vinylic carbon-chlorine bond in trans-3-chloroacrylic acid with a turnove ... | 2001 | 11418568 |
| bef(3)(-) acts as a phosphate analog in proteins phosphorylated on aspartate: structure of a bef(3)(-) complex with phosphoserine phosphatase. | protein phosphoaspartate bonds play a variety of roles. in response regulator proteins of two-component signal transduction systems, phosphorylation of an aspartate residue is coupled to a change from an inactive to an active conformation. in phosphatases and mutases of the haloacid dehalogenase (had) superfamily, phosphoaspartate serves as an intermediate in phosphotransfer reactions, and in p-type atpases, also members of the had family, it serves in the conversion of chemical energy to ion gr ... | 2001 | 11438683 |
| mechanism of chloride elimination from 3-chloro- and 2,4-dichloro-cis,cis-muconate: new insight obtained from analysis of muconate cycloisomerase variant catb-k169a. | chloromuconate cycloisomerases of bacteria utilizing chloroaromatic compounds are known to convert 3-chloro-cis,cis-muconate to cis-dienelactone (cis-4-carboxymethylenebut-2-en-4-olide), while usual muconate cycloisomerases transform the same substrate to the bacteriotoxic protoanemonin. formation of protoanemonin requires that the cycloisomerization of 3-chloro-cis,cis-muconate to 4-chloromuconolactone is completed by protonation of the exocyclic carbon of the presumed enol/enolate intermediate ... | 2001 | 11443090 |
| catalytic function of an alpha/beta hydrolase is required for energy stress activation of the sigma(b) transcription factor in bacillus subtilis. | the general stress response of bacillus subtilis is controlled by the sigma(b) transcription factor, which is activated in response to diverse energy and environmental stresses. these two classes of stress are transmitted by separate signaling pathways which converge on the direct regulators of sigma(b), the rsbv anti-anti-sigma factor and the rsbw anti-sigma factor. the energy signaling branch involves the rsbp phosphatase, which dephosphorylates rsbv in order to trigger the general stress resp ... | 2001 | 11591687 |
| persistently conserved positions in structurally similar, sequence dissimilar proteins: roles in preserving protein fold and function. | many protein pairs that share the same fold do not have any detectable sequence similarity, providing a valuable source of information for studying sequence-structure relationship. in this study, we use a stringent data set of structurally similar, sequence-dissimilar protein pairs to characterize residues that may play a role in the determination of protein structure and/or function. for each protein in the database, we identify amino-acid positions that show residue conservation within both cl ... | 2002 | 11790845 |
| molecular method to assess the diversity of burkholderia species in environmental samples. | in spite of the importance of many members of the genus burkholderia in the soil microbial community, no direct method to assess the diversity of this genus has been developed so far. the aim of this work was the development of soil dna-based pcr-denaturing gradient gel electrophoresis (dgge), a powerful tool for studying the diversity of microbial communities, for detection and analysis of the burkholderia diversity in soil samples. primers specific for the genus burkholderia were developed bas ... | 2002 | 11916673 |
| generating segmental mutations in haloalkane dehalogenase: a novel part in the directed evolution toolbox. | directed evolution techniques allow us to genuinely mimic molecular evolution in vitro. to enhance this imitation of natural evolutionary processes on a laboratory scale in even more detail, we developed an in vitro method for the generation of random deletions and repeats. the pairwise fusion of two fragments of the same gene that are truncated by exonuclease bal-31 either at the 3' or 5' side results in a deletion or a repeat at the fusion point. although in principle the method randomly cover ... | 2002 | 11937643 |
| functionally relevant motions of haloalkane dehalogenases occur in the specificity-modulating cap domains. | one-nanosecond molecular dynamics trajectories of three haloalkane dehalogenases (dhla, linb, and dhaa) are compared. the main domain was rigid in all three dehalogenases, whereas the substrate specificity-modulating cap domains showed considerably higher mobility. the functionally relevant motions were spread over the entire cap domain in dhla, whereas they were more localized in linb and dhaa. the highest amplitude of essential motions of dhla was noted in the alpha4'-helix-loop-alpha4-helix r ... | 2002 | 11967377 |
| biochemical, molecular, and genetic analyses of the acetone carboxylases from xanthobacter autotrophicus strain py2 and rhodobacter capsulatus strain b10. | acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalyzing the condensation of acetone and co(2) to form acetoacetate. in this study, the acetone carboxylase of the purple nonsulfur photosynthetic bacterium rhodobacter capsulatus was purified to homogeneity and compared to that of xanthobacter autotrophicus strain py2, the only other organism from which an acetone carboxylase has been purified. the biochemical properties of the enzymes were virtually indistinguishable, wit ... | 2002 | 12003937 |
| biodegradation of 1,2,3-trichloropropane through directed evolution and heterologous expression of a haloalkane dehalogenase gene. | using a combined strategy of random mutagenesis of haloalkane dehalogenase and genetic engineering of a chloropropanol-utilizing bacterium, we constructed an organism that is capable of growth on 1,2,3-trichloropropane (tcp). this highly toxic and recalcitrant compound is a waste product generated from the manufacture of the industrial chemical epichlorohydrin. attempts to select and enrich bacterial cultures that can degrade tcp from environmental samples have repeatedly been unsuccessful, proh ... | 2002 | 12089046 |
| gene discovery within the planctomycete division of the domain bacteria using sequence tags from genomic dna libraries. | the planctomycetes comprise a distinct group of the domain bacteria, forming a separate division by phylogenetic analysis. the organization of their cells into membrane-defined compartments including membrane-bounded nucleoids, their budding reproduction and complete absence of peptidoglycan distinguish them from most other bacteria. a random sequencing approach was applied to the genomes of two planctomycete species, gemmata obscuriglobus and pirellula marina, to discover genes relevant to thei ... | 2002 | 12093378 |
| cloning and expression of the haloalkane dehalogenase gene dhma from mycobacterium avium n85 and preliminary characterization of dhma. | haloalkane dehalogenases are microbial enzymes that catalyze cleavage of the carbon-halogen bond by a hydrolytic mechanism. until recently, these enzymes have been isolated only from bacteria living in contaminated environments. in this report we describe cloning of the dehalogenase gene dhma from mycobacterium avium subsp. avium n85 isolated from swine mesenteric lymph nodes. the dhma gene has a g+c content of 68.21% and codes for a polypeptide that is 301 amino acids long and has a calculated ... | 2002 | 12147465 |
| the n-terminal domain of mammalian soluble epoxide hydrolase is a phosphatase. | the mammalian soluble epoxide hydrolase (seh) is an enzyme with multiple functions, being implicated in detoxification of xenobiotic epoxides as well as in regulation of physiological processes such as blood pressure. the enzyme is a homodimer, in which each subunit is composed of two domains. the 35-kda c-terminal domain has an alpha/beta hydrolase fold and harbors the catalytic center for the eh activity. the 25-kda n-terminal domain has a different alpha/beta fold and belongs to the haloacid ... | 2003 | 12574508 |
| new insertion sequence elements in the upstream region of cfia in imipenem-resistant bacteroides fragilis strains. | the 747-bp cfia gene, which encodes a metallo-beta-lactamase, and the regions flanking cfia in six imipenem-resistant and four imipenem-susceptible bacteroides fragilis strains isolated in japan were analyzed by pcr and dna sequencing. the nucleotide sequences of the cfia genes (designated cfia(1) to cfia(10)) of all 10 strains tested varied from that of the standard cfia gene from b. fragilis tal2480. however, putative proteins encoded by the cfia variants contained conserved amino acid residue ... | 2003 | 12604530 |
| reconstruction of mycobacterial dehalogenase rv2579 by cumulative mutagenesis of haloalkane dehalogenase linb. | the homology model of protein rv2579 from mycobacterium tuberculosis h37rv was compared with the crystal structure of haloalkane dehalogenase linb from sphingomonas paucimobilis ut26, and this analysis revealed that 6 of 19 amino acid residues which form an active site and entrance tunnel are different in linb and rv2579. to characterize the effect of replacement of these six amino acid residues, mutations were introduced cumulatively into the six amino acid residues of linb. the sixfold mutant, ... | 2003 | 12676719 |
| distribution of the coenzyme m pathway of epoxide metabolism among ethene- and vinyl chloride-degrading mycobacterium strains. | an epoxyalkane:coenzyme m (com) transferase (eacomt) enzyme was recently found to be active in the aerobic vinyl chloride (vc) and ethene assimilation pathways of mycobacterium strain js60. in the present study, eacomt activity and genes were investigated in 10 different mycobacteria isolated on vc or ethene from diverse environmental samples. in all cases, epoxyethane metabolism in cell extracts was dependent on com, with average specific activities of eacomt between 380 and 2,910 nmol/min/mg o ... | 2003 | 14532060 |
| propane monooxygenase and nad+-dependent secondary alcohol dehydrogenase in propane metabolism by gordonia sp. strain ty-5. | a new isolate, gordonia sp. strain ty-5, is capable of growth on propane and n-alkanes with c(13) to c(22) carbon chains as the sole source of carbon. in whole-cell reactions, significant propane oxidation to 2-propanol was detected. a gene cluster designated prmabcd, which encodes the components of a putative dinuclear-iron-containing multicomponent monooxygenase, including the large and small subunits of the hydroxylase, an nadh-dependent acceptor oxidoreductase, and a coupling protein, was cl ... | 2003 | 14645271 |
| molecular and culture-based analyses of aerobic carbon monoxide oxidizer diversity. | isolates belonging to six genera not previously known to oxidize co were obtained from enrichments with aquatic and terrestrial plants. dna from these and other isolates was used in pcr assays of the gene for the large subunit of carbon monoxide dehydrogenase (coxl). coxl and putative coxl fragments were amplified from known co oxidizers (e.g., oligotropha carboxidovorans and bradyrhizobium japonicum), from novel co-oxidizing isolates (e.g., aminobacter sp. strain cox, burkholderia sp. strain lu ... | 2003 | 14660374 |
| isecp1b-mediated transposition of blactx-m in escherichia coli. | several expanded-spectrum beta-lactamase bla(ctx-m) genes are associated with isecp1-like elements in enterobacteriaceae. we found that isecp1b was able to mobilize the adjacent bla(ctx-m-19) gene by a transpositional mechanism in escherichia coli by recognizing a variety of dna sequences as right inverted repeats. | 2005 | 15616333 |
| diversity of green-like and red-like ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes (cbbl) in differently managed agricultural soils. | a pcr-based approach was developed to detect ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) form i large-subunit genes (cbbl) as a functional marker of autotrophic bacteria that fix carbon dioxide via the calvin-benson-bassham cycle. we constructed two different primer sets, targeting the green-like and red-like phylogenetic groups of cbbl genes. the diversity of these cbbl genes was analyzed by the use of three differently managed agricultural soils from a long-term field experiment. ... | 2005 | 15640185 |
| cloning, expression, and site-directed mutagenesis of the propene monooxygenase genes from mycobacterium sp. strain m156. | propene monooxygenase has been cloned from mycobacterium sp. strain m156, based on hybridization with the amoabcd genes of rhodococcus corallinus b276. sequencing indicated that the mycobacterial enzyme is a member of the binuclear nonheme iron monooxygenase family and, in gene order and sequence, is most similar to that from r. corallinus b-276. attempts were made to express the pmoabcd operon in escherichia coli and mycobacterium smegmatis mc(2)155. in the former, there appeared to be a proble ... | 2005 | 15812019 |
| catalysis of potato epoxide hydrolase, steh1. | the kinetic mechanism of epoxide hydrolase (ec 3.3.2.3) from potato, steh1 (solanum tuberosum epoxide hydrolase 1), was studied by presteady-state and steady-state kinetics as well as by ph dependence of activity. the specific activities towards the different enantiomers of tso (trans-stilbene oxide) as substrate were 43 and 3 micromol x min(-1) x mg(-1) with the r,r- or s,s-isomers respectively. the enzyme was, however, enantioselective in favour of the s,s enantiomer due to a lower k(m) value. ... | 2005 | 15882148 |
| indications for acquisition of reductive dehalogenase genes through horizontal gene transfer by dehalococcoides ethenogenes strain 195. | the genome of dehalococcoides ethenogenes strain 195, an anaerobic dehalorespiring bacterium, contains 18 copies of putative reductive dehalogenase genes, including the well-characterized tcea gene, whose gene product functions as the key enzyme in the environmentally important dehalorespiration process. the genome of d. ethenogenes was analyzed using a bioinformatic tool based on the frequency of oligonucleotides. the results in the form of a genomic signature revealed several local disruptions ... | 2005 | 15932990 |
| the tetr family of transcriptional repressors. | we have developed a general profile for the proteins of the tetr family of repressors. the stretch that best defines the profile of this family is made up of 47 amino acid residues that correspond to the helix-turn-helix dna binding motif and adjacent regions in the three-dimensional structures of tetr, qacr, cprb, and ethr, four family members for which the function and three-dimensional structure are known. we have detected a set of 2,353 nonredundant proteins belonging to this family by scree ... | 2005 | 15944459 |
| analysis of gene islands involved in methanopterin-linked c1 transfer reactions reveals new functions and provides evolutionary insights. | in this study, the occurrence and chromosomal clustering of genes encoding c(1) transfer reactions linked to tetrahydromethanopterin (h(4)mpt) were analyzed in a variety of proteobacteria and in representatives of the planctomycetes via genomic analysis or via partial sequencing by cosmid walking. although a tendency for clustering was found common for the genes of interest, significant variations in gene order and the degree of clustering were uncovered both between and within different groups ... | 2005 | 15968072 |
| elucidation of a carotenoid biosynthesis gene cluster encoding a novel enzyme, 2,2'-beta-hydroxylase, from brevundimonas sp. strain sd212 and combinatorial biosynthesis of new or rare xanthophylls. | a carotenoid biosynthesis gene cluster mediating the production of 2-hydroxyastaxanthin was isolated from the marine bacterium brevundimonas sp. strain sd212 by using a common crti sequence as the probe dna. a sequence analysis revealed this cluster to contain 12 open reading frames (orfs), including the 7 known genes, crtw, crty, crti, crtb, crte, idi, and crtz. the individual orfs were functionally analyzed by complementation studies using escherichia coli that accumulated various carotenoid p ... | 2005 | 16085816 |
| two rhizobial strains, mesorhizobium loti maff303099 and bradyrhizobium japonicum usda110, encode haloalkane dehalogenases with novel structures and substrate specificities. | haloalkane dehalogenases are key enzymes for the degradation of halogenated aliphatic pollutants. two rhizobial strains, mesorhizobium loti maff303099 and bradyrhizobium japonicum usda110, have open reading frames (orfs), mlr5434 and blr1087, respectively, that encode putative haloalkane dehalogenase homologues. the crude extracts of escherichia coli strains expressing mlr5434 and blr1087 showed the ability to dehalogenate 18 halogenated compounds, indicating that these orfs indeed encode haloal ... | 2005 | 16085827 |
| cloning, biochemical properties, and distribution of mycobacterial haloalkane dehalogenases. | haloalkane dehalogenases are enzymes that catalyze the cleavage of the carbon-halogen bond by a hydrolytic mechanism. genomes of mycobacterium tuberculosis and m. bovis contain at least two open reading frames coding for the polypeptides showing a high sequence similarity with biochemically characterized haloalkane dehalogenases. we describe here the cloning of the haloalkane dehalogenase genes dmba and dmbb from m. bovis 5033/66 and demonstrate the dehalogenase activity of their translation pro ... | 2005 | 16269704 |
| degradation of halogenated aliphatic compounds by xanthobacter autotrophicus gj10. | [this corrects the article on p. 674 in vol. 49.]. | 1985 | 16346827 |
| kinetics of bacterial growth on chlorinated aliphatic compounds. | with the pure bacterial cultures ancylobacter aquaticus ad20 and ad25, xanthobacter autotrophicus gj10, and pseudomonas sp. strain ad1, monod kinetics was observed during growth in chemostat cultures on 1,2-dichloroethane (ad20, ad25, and gj10), 2-chloroethanol (ad20 and gj10), and 1,3-dichloro-2-propanol (ad1). both the michaelis-menten constants (k(m)) of the first catabolic (dehalogenating) enzyme and the monod half-saturation constants (k(s)) followed the order 2-chloroethanol, 1,3-dichloro- ... | 1993 | 16348981 |
| identification of chloroacetaldehyde dehydrogenase involved in 1,2-dichloroethane degradation. | the degradation of 1,2-dichloroethane and 2-chloroethanol by xanthobacter autotrophicus gj10 proceeds via chloroacetaldehyde, a reactive and potentially toxic intermediate. the organism produced at least three different aldehyde dehydrogenases, of which one is plasmid encoded. two mutants of strain gj10, designated gj10m30 and gj10m41, could no longer grow on 2-chloroethanol and were found to lack the nad-dependent aldehyde dehydrogenase that is the predominant protein in wild-type cells growing ... | 1994 | 16349259 |
| crystal structure of the probable haloacid dehalogenase ph0459 from pyrococcus horikoshii ot3. | ph0459, from the hyperthermophilic archaeon pyrococcus horikoshii ot3, is a probable haloacid dehalogenase with a molecular mass of 26,725 da. here, we report the 2.0 a crystal structure of ph0459 (pdb id: 1x42) determined by the multiwavelength anomalous dispersion method. the core domain has an alpha/beta structure formed by a six-stranded parallel beta-sheet flanked by six alpha-helices and three 3(10)-helices. one disulfide bond, cys186-cys212, forms a bridge between an alpha-helix and a 3(1 ... | 2006 | 16385007 |
| multicopy integration and expression of heterologous genes in methylobacterium extorquens atcc 55366. | high-level expression of chromosomally integrated genes in methylobacterium extorquens atcc 55366 was achieved under the control of the strong m. extorquens am1 methanol dehydrogenase promoter (pmxaf) using the mini-tn7 transposon system. stable maintenance and expression of the integrated genes were obtained in the absence of antibiotic selective pressure. furthermore, using this technology, a multicopy integration protocol for m. extorquens was also developed. chromosomal integration of one to ... | 2006 | 16391115 |
| emergence of dha-1-producing klebsiella spp. in the parisian region: genetic organization of the ampc and ampr genes originating from morganella morganii. | eleven klebsiella pneumoniae clinical isolates and one klebsiella oxytoca clinical isolate showing various pulsed-field gel electrophoresis types and producing an inducible dha-1 class c beta-lactamase were isolated in the parisian region between 1998 and 2003. the aim of this study was to compare the genetic organization of the bla(dha-1) genes in this collection of clinical isolates. in four isolates, the morganella morganii-derived genomic region containing bla(dha-1) was inserted in an entir ... | 2006 | 16436717 |
| diversity and biocatalytic potential of epoxide hydrolases identified by genome analysis. | epoxide hydrolases play an important role in the biodegradation of organic compounds and are potentially useful in enantioselective biocatalysis. an analysis of various genomic databases revealed that about 20% of sequenced organisms contain one or more putative epoxide hydrolase genes. they were found in all domains of life, and many fungi and actinobacteria contain several putative epoxide hydrolase-encoding genes. multiple sequence alignments of epoxide hydrolases with other known and putativ ... | 2006 | 16597997 |
| rna-based stable isotope probing and isolation of anaerobic benzene-degrading bacteria from gasoline-contaminated groundwater. | stable isotope probing (sip) of benzene-degrading bacteria in gasoline-contaminated groundwater was coupled to denaturing gradient gel electrophoresis (dgge) of dna fragments amplified by reverse transcription-pcr from community 16s rrna molecules. supplementation of the groundwater with [(13)c(6)]benzene together with an electron acceptor (nitrate, sulfate, or oxygen) showed that a phylotype affiliated with the genus azoarcus specifically appeared in the (13)c-rna fraction only when nitrate was ... | 2006 | 16672506 |
| the alkyl tert-butyl ether intermediate 2-hydroxyisobutyrate is degraded via a novel cobalamin-dependent mutase pathway. | fuel oxygenates such as methyl and ethyl tert-butyl ether (mtbe and etbe, respectively) are degraded only by a limited number of bacterial strains. the aerobic pathway is generally thought to run via tert-butyl alcohol (tba) and 2-hydroxyisobutyrate (2-hiba), whereas further steps are unclear. we have now demonstrated for the newly isolated beta-proteobacterial strains l108 and l10, as well as for the closely related strain cip i-2052, that 2-hiba was degraded by a cobalamin-dependent enzymatic ... | 2006 | 16751524 |
| stability and performance of xanthobacter autotrophicus gj10 during 1,2-dichloroethane biodegradation. | a nucleic acid-based approach was used to investigate the dynamics of a microbial community dominated by xanthobacter autotrophicus gj10 in the degradation of synthetic wastewater containing 1,2-dichloroethane (dce). this study was performed over a 140-day period in a nonsterile continuous stirred-tank bioreactor (cstb) subjected to different operational regimens: nutrient-limiting conditions, baseline operation, and the introduction of glucose as a cosubstrate. the microbial community was analy ... | 2006 | 16751558 |
| evolution of enzymatic activity in the tautomerase superfamily: mechanistic and structural consequences of the l8r mutation in 4-oxalocrotonate tautomerase. | 4-oxalocrotonate tautomerase (4-ot) and trans-3-chloroacrylic acid dehalogenase (caad) are members of the tautomerase superfamily, a group of structurally homologous proteins that share a beta-alpha-beta fold and a catalytic amino-terminal proline. 4-ot, from pseudomonas putida mt-2, catalyzes the conversion of 2-oxo-4-hexenedioate to 2-oxo-3-hexenedioate through the dienol intermediate 2-hydroxymuconate in a catabolic pathway for aromatic hydrocarbons. caad, from pseudomonas pavonaceae 170, cat ... | 2006 | 16784221 |
| caver: a new tool to explore routes from protein clefts, pockets and cavities. | the main aim of this study was to develop and implement an algorithm for the rapid, accurate and automated identification of paths leading from buried protein clefts, pockets and cavities in dynamic and static protein structures to the outside solvent. | 2006 | 16792811 |
| characterization of 2-bromoethanesulfonate as a selective inhibitor of the coenzyme m-dependent pathway and enzymes of bacterial aliphatic epoxide metabolism. | bacterial growth with short-chain aliphatic alkenes requires coenzyme m (com) (2-mercaptoethanesulfonic acid), which serves as the nucleophile for activation and conversion of epoxide products formed from alkene oxidation to central metabolites. in the present work the com analog 2-bromoethanesulfonate (bes) was shown to be a specific inhibitor of propylene-dependent growth of and epoxypropane metabolism by xanthobacter autotrophicus strain py2. bes (at low [millimolar] concentrations) completel ... | 2006 | 16997966 |
| 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 |
| involvement of the cynabds operon and the co2-concentrating mechanism in the light-dependent transport and metabolism of cyanate by cyanobacteria. | the cyanobacteria synechococcus elongatus strain pcc7942 and synechococcus sp. strain utex625 decomposed exogenously supplied cyanate (nco-) to co2 and nh3 through the action of a cytosolic cyanase which required hco3- as a second substrate. the ability to metabolize nco- relied on three essential elements: proteins encoded by the cynabds operon, the biophysical activity of the co2-concentrating mechanism (ccm), and light. inactivation of cyns, encoding cyanase, and cyna yielded mutants unable t ... | 2007 | 17122352 |
| involvement of the cynabds operon and the co2-concentrating mechanism in the light-dependent transport and metabolism of cyanate by cyanobacteria. | the cyanobacteria synechococcus elongatus strain pcc7942 and synechococcus sp. strain utex625 decomposed exogenously supplied cyanate (nco-) to co2 and nh3 through the action of a cytosolic cyanase which required hco3- as a second substrate. the ability to metabolize nco- relied on three essential elements: proteins encoded by the cynabds operon, the biophysical activity of the co2-concentrating mechanism (ccm), and light. inactivation of cyns, encoding cyanase, and cyna yielded mutants unable t ... | 2007 | 17122352 |
| the orphan response regulator hp1021 of helicobacter pylori regulates transcription of a gene cluster presumably involved in acetone metabolism. | helicobacter pylori is a gastric pathogen for which no nonhuman reservoir is known. in accordance with the tight adaptation to its unique habitat, the human stomach, h. pylori is endowed with a very restricted repertoire of regulatory proteins. nevertheless, the three complete two-component systems of h. pylori were shown to be involved in the regulation of important virulence traits like motility and acid resistance and in the control of metal homeostasis. hp1021 is an orphan response regulator ... | 2007 | 17220217 |
| heterologous expression and identification of the genes involved in anaerobic degradation of 1,3-dihydroxybenzene (resorcinol) in azoarcus anaerobius. | azoarcus anaerobius, a strictly anaerobic, gram-negative bacterium, utilizes resorcinol as a sole carbon and energy source with nitrate as an electron acceptor. previously, we showed that resorcinol degradation by this bacterium is initiated by two oxidative steps, both catalyzed by membrane-associated enzymes that lead to the formation of hydroxyhydroquinone (hhq; 1,2,4-benzenetriol) and 2-hydroxy-1,4-benzoquinone (hbq). this study presents evidence for the further degradation of hbq in cell ex ... | 2007 | 17369298 |
| 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 |
| quorum sensing has an unexpected role in virulence in the model pathogen citrobacter rodentium. | the bacterial mouse pathogen citrobacter rodentium causes attaching and effacing (ae) lesions in the same manner as pathogenic escherichia coli, and is an important model for this mode of pathogenesis. quorum sensing (qs) involves chemical signalling by bacteria to regulate gene expression in response to cell density. e. coli has never been reported to have n-acylhomoserine lactone (ahl) qs, but it does utilize luxs-dependent signalling. we found production of ahl qs signalling molecules by an a ... | 2007 | 17557113 |
| dark matter in a deep-sea vent and in human mouth. | | 2007 | 17803764 |
| biodegradation of bis(2-chloroethyl) ether by xanthobacter sp. strain env481. | degradation of bis(2-chloroethyl) ether (bcee) was observed to occur in two bacterial strains. strain env481, a xanthobacter sp. strain, was isolated by enrichment culturing of samples from a superfund site located in the northeastern united states. the strain was able to grow on bcee or 2-chloroethylethyl ether as the sole source of carbon and energy. bcee degradation in strain env481 was facilitated by sequential dehalogenation reactions resulting in the formation of 2-(2-chloroethoxy)ethanol ... | 2007 | 17873075 |
| crystallization and preliminary x-ray studies of ton_1713 from thermococcus onnurineus na1, a putative member of the haloacid dehalogenase superfamily. | the haloacid dehalogenase (had) protein superfamily is one of the largest enzyme families and shows hydrolytic activity towards diverse substrates. structural analyses of enzymes belonging to the had family are required to elucidate the molecular basis underlying their broad substrate specificity and reaction mechanism. for this purpose, ton_1713, a hypothetical protein from thermococcus onnurineus that is a member of the had superfamily, was expressed in escherichia coli, purified and crystalli ... | 2007 | 18084090 |
| the human gastric pathogen helicobacter pylori has a potential acetone carboxylase that enhances its ability to colonize mice. | helicobacter pylori colonizes the human stomach and is the etiological agent of peptic ulcer disease. all three h. pylori strains that have been sequenced to date contain a potential operon whose products share homology with the subunits of acetone carboxylase (encoded by acxabc) from xanthobacter autotrophicus strain py2 and rhodobacter capsulatus strain b10. acetone carboxylase catalyzes the conversion of acetone to acetoacetate. genes upstream of the putative acxabc operon encode enzymes that ... | 2008 | 18215283 |
| 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 |
| transposable modules generated by a single copy of insertion sequence ispme1 and their influence on structure and evolution of natural plasmids of paracoccus methylutens dm12. | we demonstrated that a single copy of insertion sequence ispme1 can mobilize adjacent segments of genomic dna of paracoccus methylutens dm12, which leads to the generation of diverse transposable elements of various size and dna contents. all elements (named transposable modules [tmos]) contain ispme1 (placed at the 5' ends of the elements) and have variable 3'-end regions of between 0.5 and 5 kb. ispme1 was shown to encode an outwardly oriented promoter, which may activate the transcription of ... | 2008 | 18296518 |
| rcom: a new single-component transcriptional regulator of co metabolism in bacteria. | genomic analysis suggested the existence of a co-sensing bacterial transcriptional regulator that couples an n-terminal pas fold domain to a c-terminal dna-binding lyttr domain. uv/visible-light spectral analyses of heterologously expressed, purified full-length proteins indicated that they contained a hexacoordinated b-type heme moiety that avidly binds co and no. studies of protein variants strongly suggested that the pas domain residues his74 and met104 serve as the heme fe(ii) axial ligands, ... | 2008 | 18326575 |
| structure-function studies on the active site of the coelenterazine-dependent luciferase from renilla. | renilla luciferase (rluc) is a versatile tool for gene expression assays and in vivo biosensor applications, but its catalytic mechanism remains to be elucidated. rluc is evolutionarily related to the alpha/beta hydrolase family. its closest known homologs are bacterial dehalogenases, raising the question of how a protein with a hydrolase fold can function as a decarboxylating oxygenase. molecular docking simulations with the coelenterazine substrate against an rluc homology model as well as a r ... | 2008 | 18359861 |