Publications

a survey of orphan enzyme activities.	using computational database searches, we have demonstrated previously that no gene sequences could be found for at least 36% of enzyme activities that have been assigned an enzyme commission number. here we present a follow-up literature-based survey involving a statistically significant sample of such "orphan" activities. the survey was intended to determine whether sequences for these enzyme activities are truly unknown, or whether these sequences are absent from the public sequence databases ...	2007	17623104
similar enzymes, different structures: phthalate dioxygenase is an alpha3alpha3 stacked hexamer, not an alpha3beta3 trimer like "normal" rieske oxygenases.	phthalate dioxygenase (pdo) is a member of a class of bacterial oxygenases that contain both rieske [2fe-2s] and fe(ii) mononuclear centers. recent crystal structures of several rieske dioxygenases showed that they exist as alpha(3)beta(3) multimers with subunits arranged head-to-tail in alpha and beta stacked planar rings. the structure of pdo, which consists of only alpha-subunits, remains to be solved. although similar to other rieske dioxygenases in many aspects, pdo was shown to differ in t ...	2007	17764654
finding intermediates in the o2 activation pathways of non-heme iron oxygenases.	intermediates in the reaction cycle of an oxygenase are usually very informative with respect to the chemical mechanism of o 2 activation and insertion. however, detection of these intermediates is often complicated by their short lifetime and the regulatory mechanism of the enzyme designed to ensure specificity. here, the methods used to detect the intermediates in an extradiol dioxygenase, a rieske cis-dihydrodiol dioxygenase, and soluble methane monooxygenase are discussed. the methods includ ...	2007	17567087
conformationally constrained analogues of 2-arachidonoylglycerol.	novel monocyclic analogues of 2-arachidonoylglycerol (2-ag) were designed in order to explore the pharmacophoric conformations of this endocannabinoid ligand at the key cannabinergic proteins. all 2-arachidonoyl esters of 1,2,3-cyclohexanetriol [meso-7 (am5504), (+/-)-8 (am5503), and meso-9 (am5505)] were synthesized by regioselective acylation of 2,3-dihydroxycyclohexanone followed by selective reductions. the optically active isomers (+)-8 (am4434) and (-)-8 (am4435) were synthesized from (2s, ...	2007	17826996
outcome of life-threatening malaria in african children requiring endotracheal intubation.	little is known about children undergoing critical care for malaria. the purpose of this survey was to evaluate the outcome in african children requiring endotracheal intubation for life-threatening malaria.	2007	17470294
biochemical and crystallographic analysis of substrate binding and conformational changes in acetyl-coa synthetase.	the adenylate-forming enzymes, including acyl-coa synthetases, the adenylation domains of non-ribosomal peptide synthetases (nrps), and firefly luciferase, perform two half-reactions in a ping-pong mechanism. we have proposed a domain alternation mechanism for these enzymes whereby, upon completion of the initial adenylation reaction, the c-terminal domain of these enzymes undergoes a 140 degrees rotation to perform the second thioester-forming half-reaction. structural and kinetic data of mutan ...	2007	17497934
metabolomic and genetic analysis of biomarkers for peroxisome proliferator-activated receptor alpha expression and activation.	peroxisome proliferator-activated receptor alpha (pparalpha) is a nuclear receptor with manifold effects on intermediary metabolism. to define a set of urinary biomarkers that could be used to determine the efficacy of pparalpha agonists, a metabolomic investigation was undertaken in wild-type and pparalpha-null mice fed for 2 wk either a regular diet or a diet containing the pparalpha ligand wy-14,643 ([4-chloro-6-(2,3-xylidino)-2-pyrimidinylthio] acetic acid), and their urine was analyzed by u ...	2007	17550978
dissimilatory iodate reduction by marine pseudomonas sp. strain sct.	bacterial iodate (io(3)(-)) reduction is poorly understood largely due to the limited number of available isolates as well as the paucity of information about key enzymes involved in the reaction. in this study, an iodate-reducing bacterium, designated strain sct, was newly isolated from marine sediment slurry. sct is phylogenetically closely related to the denitrifying bacterium pseudomonas stutzeri and reduced 200 microm iodate to iodide (i(-)) within 12 h in an anaerobic culture containing 10 ...	2007	17644635
hydroxyatrazine n-ethylaminohydrolase (atzb): an amidohydrolase superfamily enzyme catalyzing deamination and dechlorination.	hydroxyatrazine [2-(n-ethylamino)-4-hydroxy-6-(n-isopropylamino)-1,3,5-triazine] n-ethylaminohydrolase (atzb) is the sole enzyme known to catalyze the hydrolytic conversion of hydroxyatrazine to n-isopropylammelide. atzb, therefore, serves as the point of intersection of multiple s-triazine biodegradative pathways and is completely essential for microbial growth on s-triazine herbicides. here, atzb was cloned from pseudomonas sp. strain adp and its product was purified to homogeneity and charact ...	2007	17660279
a novel sampling method for the investigation of gut mirobiota.	in order to characterize the qualitative and quantitative microorganisms in different sites of the lower digestive tract (ldt) in healthy volunteers, a specific technique was developed for collecting mucous of the distal ileum, colon and rectum.	2007	17663516
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
c-myc interacts with trf1/pin2 and regulates telomere length.	telomere, the end of linear chromosome, is protected by dna-protein complexes. these complexes cap the linear chromosome and play an important role in the maintenance of genomic stability. trf1/pin2, a double-stranded dna-binding protein is known to regulate telomere length by not only protecting telomere but also blocking the access of telomerase to telomere in cis. to better understand the mechanism through which trf1/pin2 regulates telomere length, we performed the yeast two-hybrid screening ...	2007	17765874
plp catabolism: identification of the 4-pyridoxic acid dehydrogenase gene in mesorhizobium loti maff303099.	the function of the mlr6793 gene from mesorhizobium loti maff303099 has been identified. this gene encodes 4-pyridoxic acid dehydrogenase, an enzyme involved in the catabolism of plp (vitamin b6). this enzyme was overexpressed in escherichia coli and characterized. 4-pyridoxic acid dehydrogenase is a 33kda protein that catalyzes the four electron oxidation of 4-pyridoxic acid to 3-hydroxy-2-methylpyridine-4,5-dicarboxylate, using nicotinamide adenine dinucleotide as a cofactor. the k cat for nad ...	2007	17868768
production of l-carnitine by secondary metabolism of bacteria.	abstract: the increasing commercial demand for l-carnitine has led to a multiplication of efforts to improve its production with bacteria. the use of different cell environments, such as growing, resting, permeabilized, dried, osmotically stressed, freely suspended and immobilized cells, to maintain enzymes sufficiently active for l-carnitine production is discussed in the text. the different cell states of enterobacteria, such as escherichia coli and proteus sp., which can be used to produce l- ...	2007	17910757
a comprehensive set of plasmids for vanillate- and xylose-inducible gene expression in caulobacter crescentus.	caulobacter crescentus is widely used as a powerful model system for the study of prokaryotic cell biology and development. analysis of this organism is complicated by a limited selection of tools for genetic manipulation and inducible gene expression. this study reports the identification and functional characterization of a vanillate-regulated promoter (p(van)) which meets all requirements for application as a multi-purpose expression system in caulobacter, thus complementing the established x ...	2007	17959646
gene identification and structural characterization of the pyridoxal 5'-phosphate degradative protein 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase from mesorhizobium loti maff303099.	the function of the mlr6791 gene from mesorhizobium loti maff303099 has been identified. this gene encodes 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase (hmpddc), an enzyme involved in the catabolism of pyridoxal 5'-phosphate (vitamin b6). this enzyme was overexpressed in escherichia coli and characterized. hmpddc is a 26 kda protein that catalyzes the decarboxylation of 3-hydroxy-2-methylpyridine-4,5-dicarboxylate to 3-hydroxy-2-methylpyridine-5-carboxylate. the km and kcat were fo ...	2007	17973403
molecular analysis of the subgingival microbiota in health and disease.	this investigation provides molecular analyses of the periodontal microbiota in health and disease. subgingival samples from 47 volunteers with healthy gingivae or clinically diagnosed chronic periodontitis were characterized by pcr-denaturing gradient gel electrophoresis (dgge) with primers specific for the v2-v3 region of the eubacterial 16s rrna gene. a hierarchical dendrogram was constructed from band patterns. all unique pcr amplicons (dgge bands) were sequenced for identity. samples were a ...	2007	17085691
novel macrolide resistance module carried by the incp-1beta resistance plasmid prsb111, isolated from a wastewater treatment plant.	the macrolide resistance plasmid prsb111 was isolated from bacteria residing in the final effluents of a wastewater treatment plant. the 47-kb plasmid confers resistance to azithromycin, clarithromycin, erythromycin, roxithromycin, and tylosin when it is carried by pseudomonas sp. strain b13 and is very similar to prototype incp-1beta plasmid pb3, which was previously isolated from an activated-sludge bacterial community of a wastewater treatment plant. the two plasmids differ in their accessory ...	2007	17101677
a gene cluster involved in degradation of substituted salicylates via ortho cleavage in pseudomonas sp. strain mt1 encodes enzymes specifically adapted for transformation of 4-methylcatechol and 3-methylmuconate.	pseudomonas sp. strain mt1 has recently been reported to degrade 4- and 5-chlorosalicylate by a pathway assumed to consist of a patchwork of reactions comprising enzymes of the 3-oxoadipate pathway. genes encoding the initial steps in the degradation of salicylate and substituted derivatives were now localized and sequenced. one of the gene clusters characterized (sal) showed a novel gene arrangement, with sala, encoding a salicylate 1-hydroxylase, being clustered with salcd genes, encoding muco ...	2007	17172348
adaptation of pseudomonas sp. strain 7-6 to quaternary ammonium compounds and their degradation via dual pathways.	pseudomonas sp. strain 7-6, isolated from active sludge obtained from a wastewater facility, utilized a quaternary ammonium surfactant, n-dodecyltrimethylammonium chloride (dtac), as its sole carbon, nitrogen, and energy source. when initially grown in the presence of 10 mm dtac medium, the isolate was unable to degrade dtac. the strain was cultivated in gradually increasing concentrations of the surfactant until continuous exposure led to high tolerance and biodegradation of the compound. based ...	2007	17261523
the role of laterally transferred genes in adaptive evolution.	bacterial genomes develop new mechanisms to tide them over the imposing conditions they encounter during the course of their evolution. acquisition of new genes by lateral gene transfer may be one of the dominant ways of adaptation in bacterial genome evolution. lateral gene transfer provides the bacterial genome with a new set of genes that help it to explore and adapt to new ecological niches.	2007	17288581
proteoglycan synthesis by human corneal explants submitted to laser in situ keratomileusis (lasik).	to evaluate the acute effects of laser in situ keratomileusis (lasik) upon the synthesis of proteoglycans (pgs) and collagen fibril organization in human corneal explants.	2007	17293778
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
structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from sphingobium yanoikuyae b1.	the initial step involved in oxidative hydroxylation of monoaromatic and polyaromatic compounds by the microorganism sphingobium yanoikuyae strain b1 (b1), previously known as sphingomonas yanoikuyae strain b1 and beijerinckia sp. strain b1, is performed by a set of multiple terminal rieske non-heme iron oxygenases. these enzymes share a single electron donor system consisting of a reductase and a ferredoxin (bpdo-fb1). one of the terminal rieske oxygenases, biphenyl 2,3-dioxygenase (bpdo-ob1), ...	2007	17349044
x-ray structure of a hydroxylase-regulatory protein complex from a hydrocarbon-oxidizing multicomponent monooxygenase, pseudomonas sp. ox1 phenol hydroxylase.	phenol hydroxylase (ph) belongs to a family of bacterial multicomponent monooxygenases (bmms) with carboxylate-bridged diiron active sites. included are toluene/o-xylene (tomo) and soluble methane (smmo) monooxygenase. ph hydroxylates aromatic compounds, but unlike smmo, it cannot oxidize alkanes despite having a similar dinuclear iron active site. important for activity is formation of a complex between the hydroxylase and a regulatory protein component. to address how structural features of bm ...	2006	17176061
mechanistic studies of the flavoenzyme tryptophan 2-monooxygenase: deuterium and 15n kinetic isotope effects on alanine oxidation by an l-amino acid oxidase.	tryptophan 2-monooxygenase (tmo) from pseudomonas savastanoi catalyzes the oxidative decarboxylation of l-tryptophan during the biosynthesis of indoleacetic acid. structurally and mechanistically, the enzyme is a member of the family of l-amino acid oxidases. deuterium and 15n kinetic isotope effects were used to probe the chemical mechanism of l-alanine oxidation by tmo. the primary deuterium kinetic isotope effect was ph independent over the ph range 6.5-10, with an average value of 6.0 +/- 0. ...	2006	17176107
identification of potential cepr regulated genes using a cep box motif-based search of the burkholderia cenocepacia genome.	the burkholderia cenocepacia cepir quorum sensing system has been shown to positively and negatively regulate genes involved in siderophore production, protease expression, motility, biofilm formation and virulence. in this study, two approaches were used to identify genes regulated by the cepir quorum sensing system. transposon mutagenesis was used to create lacz promoter fusions in a cepi mutant that were screened for differential expression in the presence of n-acylhomoserine lactones. a bioi ...	2006	17187664
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
the clc element of pseudomonas sp. strain b13, a genomic island with various catabolic properties.	pseudomonas sp. strain b13 is a bacterium known to degrade chloroaromatic compounds. the properties to use 3- and 4-chlorocatechol are determined by a self-transferable dna element, the clc element, which normally resides at two locations in the cell's chromosome. here we report the complete nucleotide sequence of the clc element, demonstrating the unique catabolic properties while showing its relatedness to genomic islands and integrative and conjugative elements rather than to other known cata ...	2006	16484212
crystal structure of 3-hydroxyanthranilic acid 3,4-dioxygenase from saccharomyces cerevisiae: a special subgroup of the type iii extradiol dioxygenases.	3-hydroxyanthranilic acid 3,4-dioxygenase (3hao) is a non-heme ferrous extradiol dioxygenase in the kynurenine pathway from tryptophan. it catalyzes the conversion of 3-hydroxyanthranilate (haa) to quinolinic acid (quin), an endogenous neurotoxin, via the activation of n-methyl-d-aspartate (nmda) receptors and the precursor of nad(+) biosynthesis. the crystal structure of 3hao from s. cerevisiae at 2.4 a resolution shows it to be a member of the functionally diverse cupin superfamily. the struct ...	2006	16522801
pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine crenarchaeota.	marine crenarchaeota represent an abundant component of oceanic microbiota with potential to significantly influence biogeochemical cycling in marine ecosystems. prior studies using specific archaeal lipid biomarkers and isotopic analyses indicated that planktonic crenarchaeota have the capacity for autotrophic growth, and more recent cultivation studies support an ammonia-based chemolithoautotrophic energy metabolism. we report here analysis of fosmid sequences derived from the uncultivated mar ...	2006	16533068
adding selectivity to antimicrobial peptides: rational design of a multidomain peptide against pseudomonas spp.	currently available antimicrobials exhibit broad killing with regard to bacterial genera and species. indiscriminate killing of microbes by these conventional antibiotics can disrupt the ecological balance of the indigenous microbial flora, often resulting in negative clinical consequences. species-specific antimicrobials capable of precisely targeting pathogenic bacteria without damaging benign microorganisms provide a means of avoiding this problem. in this communication, we report the success ...	2006	16569868
aerobic benzoyl-coenzyme a (coa) catabolic pathway in azoarcus evansii: conversion of ring cleavage product by 3,4-dehydroadipyl-coa semialdehyde dehydrogenase.	benzoate, a strategic intermediate in aerobic aromatic metabolism, is metabolized in various bacteria via an unorthodox pathway. the intermediates of this pathway are coenzyme a (coa) thioesters throughout, and ring cleavage is nonoxygenolytic. the fate of the ring cleavage product 3,4-dehydroadipyl-coa semialdehyde was studied in the beta-proteobacterium azoarcus evansii. cell extracts contained a benzoate-induced, nadp(+)-specific aldehyde dehydrogenase, which oxidized this intermediate. a pos ...	2006	16585753
natural pseudomonas sp. strain n3 in artificial soil microcosms.	the lightning-competent pseudomonas sp. strain n3, recently isolated from soil, has been used to study the extent of natural electrotransformation (net) or lightning transformation as a horizontal gene transfer mechanism in soil. the variation of electrical fields applied to the soil with a laboratory-scale lightning system provides an estimate of the volume of soil affected by net. based on the range of the electric field that induces net of pseudomonas strain n3, the volume of soil, where net ...	2006	16597934
purification and characterization of trzf: biuret hydrolysis by allophanate hydrolase supports growth.	trzf, the allophanate hydrolase from enterobacter cloacae strain 99, was cloned, overexpressed in the presence of a chaperone protein, and purified to homogeneity. native trzf had a subunit molecular weight of 65,401 and a subunit stoichiometry of alpha(2) and did not contain significant levels of metals. trzf showed time-dependent inhibition by phenyl phosphorodiamidate and is a member of the amidase signature protein family. trzf was highly active in the hydrolysis of allophanate but was not a ...	2006	16597948
pseudomonad cyclopentadecanone monooxygenase displaying an uncommon spectrum of baeyer-villiger oxidations of cyclic ketones.	baeyer-villiger monooxygenases (bvmos) are biocatalysts that offer the prospect of high chemo-, regio-, and enantioselectivity in the organic synthesis of lactones or esters from a variety of ketones. in this study, we have cloned, sequenced, and overexpressed in escherichia coli a new bvmo, cyclopentadecanone monooxygenase (cpdb or cpdmo), originally derived from pseudomonas sp. strain hi-70. the 601-residue primary structure of cpdb revealed only 29% to 50% sequence identity to those of known ...	2006	16597975
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
coregulation by phenylacetyl-coenzyme a-responsive paax integrates control of the upper and lower pathways for catabolism of styrene by pseudomonas sp. strain y2.	the p(stya) promoter of pseudomonas sp. strain y2 controls expression of the styabcd genes, which are required for the conversion of styrene to phenylacetate, which is further catabolized by the products of two paa gene clusters. two paax repressor proteins (paax1 and paax2) regulate transcription of the paa gene clusters of this strain. in silico analysis of the p(stya) promoter region revealed a sequence located just within stya that is similar to the reported paax binding sites of escherichia ...	2006	16788190
purification of outer membrane vesicles from pseudomonas aeruginosa and their activation of an il-8 response.	considerable lung injury results from the inflammatory response to pseudomonas aeruginosa infections in patients with cystic fibrosis (cf). the p. aeruginosa laboratory strain pao1, an environmental isolate, and isolates from cf patients were cultured in vitro and outer membrane vesicles from those cultures were quantitated, purified, and characterized. vesicles were produced throughout the growth phases of the culture and vesicle yield was strain-independent. strain-dependent differences in the ...	2006	16807039
mineralization of paraoxon and its use as a sole c and p source by a rationally designed catabolic pathway in pseudomonas putida.	organophosphate compounds, which are widely used as pesticides and chemical warfare agents, are cholinesterase inhibitors. these synthetic compounds are resistant to natural degradation and threaten the environment. we constructed a strain of pseudomonas putida that can efficiently degrade a model organophosphate, paraoxon, and use it as a carbon, energy, and phosphorus source. this strain was engineered with the pnp operon from pseudomonas sp. strain env2030, which encodes enzymes that transfor ...	2006	17021221
diverse responses to uv-b radiation and repair mechanisms of bacteria isolated from high-altitude aquatic environments.	acinetobacter johnsonii a2 isolated from the natural community of laguna azul (andean mountains at 4,560 m above sea level), serratia marcescens mf42, pseudomonas sp. strain mf8 isolated from the planktonic community, and cytophaga sp. strain mf7 isolated from the benthic community from laguna pozuelos (andean puna at 3,600 m above sea level) were subjected to uv-b (3,931 j m-2) irradiation. in addition, a marine pseudomonas putida strain, 2idinh, and a second acinetobacter johnsonii strain, atc ...	2006	17056692
sequence analysis and structure prediction of type ii pseudomonas sp. usm 4-55 pha synthase and an insight into its catalytic mechanism.	polyhydroxyalkanoates (pha), are biodegradable polyesters derived from many microorganisms such as the pseudomonads. these polyesters are in great demand especially in the packaging industries, the medical line as well as the paint industries. the enzyme responsible in catalyzing the formation of pha is pha synthase. due to the limited structural information, its functional properties including catalysis are lacking. therefore, this study seeks to investigate the structural properties as well as ...	2006	17076907
evaluation of chiral alpha-cyanoesters as general fluorescent substrates for screening enantioselective esterases.	esterases play a crucial role in industrial chemical synthesis, maintaining normal physiological metabolism and detoxifying exogenous ester-containing toxicants. to meet the rapidly increasing industrial need for all kinds of esterases, especially enantioselective esterases used to generate highly pure chiral compounds, general substrates are necessary for rapid screening, monitoring, purification, and characterization. in this study, general fluorescent substrates including phenolic derivatives ...	2006	16448170
comparative genomics of regulation of heavy metal resistance in eubacteria.	heavy metal resistance (hmr) in eubacteria is regulated by a variety of systems including transcription factors from the merr family (cog0789). the hmr systems are characterized by the complex signal structure (strong palindrome within a 19 or 20 bp promoter spacer), and usually consist of transporter and regulator genes. some hmr regulons also include detoxification systems. the number of sequenced bacterial genomes is constantly increasing and even though hmr resistance regulons of the cog0789 ...	2006	16753059
neutrophil apoptosis: a marker of disease severity in sepsis and sepsis-induced acute respiratory distress syndrome.	apoptosis of neutrophils (polymorphonuclear neutrophils [pmns]) may limit inflammatory injury in sepsis and acute respiratory distress syndrome (ards), but the relationship between the severity of sepsis and extent of pmn apoptosis and the effect of superimposed ards is unknown. the objective of this study was to correlate neutrophil apoptosis with the severity of sepsis and sepsis-induced ards.	2006	17092345
questions about the use of antibiotics in acute pancreatitis.	the use of antibiotics in acute pancreatitis despite recent clinical trials remains controversial. the aim of this study is to review the latest clinical trials and guidelines about antibiotics in acute pancreatitis and determine its proper use.	2006	16820058
peritonitis - the eastern experience.	peritonitis is a common emergency encountered by surgeons the world over. this paper aims to provide an overview of the spectrum of peritonitis seen in the east. studies dealing with the overall spectrum of secondary peritonitis in various countries of this region were identified using pubmed and google. these were analyzed for the site and cause of perforation and the mortality. it was observed that perforation of duodenal ulcers was the most the commonly encountered perforations. these are fol ...	2006	16759427
kinetics of dithionite-dependent reduction of cytochrome p450 3a4: heterogeneity of the enzyme caused by its oligomerization.	to explore the basis of apparent conformational heterogeneity of cytochrome p450 3a4 (cyp3a4), the kinetics of dithionite-dependent reduction was studied in solution, in proteoliposomes, and in nanodiscs. in cyp3a4 oligomers in solution the kinetics obeys a three-exponential equation with similar amplitudes of each of the phases. addition of substrate (bromocriptine) displaces the phase distribution toward the slow phase at the expense of the fast one, while the middle phase remains unaffected. ...	2005	16229479
health considerations regarding horizontal transfer of microbial transgenes present in genetically modified crops.	the potential effects of horizontal gene transfer on human health are an important item in the safety assessment of genetically modified organisms. horizontal gene transfer from genetically modified crops to gut microflora most likely occurs with transgenes of microbial origin. the characteristics of microbial transgenes other than antibiotic-resistance genes in market-approved genetically modified crops are reviewed. these characteristics include the microbial source, natural function, function ...	2005	16489267
crystallization and preliminary x-ray crystallographic analysis of 2-methyl-3-hydroxypyridine-5-carboxylic acid (mhpc) oxygenase from pseudomonas sp. ma-1.	2-methyl-3-hydroxypyridine-5-carboxylic acid (mhpc) oxygenase (mhpco) catalyzes the conversion of an aromatic substrate, mhpc, to an aliphatic compound, alpha-(n-acetylaminomethylene)-succinic acid, and is involved in the degradation of vitamin b6 by the soil bacterium pseudomonas sp. ma-1. using only fad as a cofactor, mhpco is unique in catalyzing hydroxylation and subsequent aromatic ring cleavage without requiring a metal-ion cofactor. here, the crystallization of mhpco is reported together ...	2005	16511028
regulation of the pseudomonas sp. strain adp cyanuric acid degradation operon.	pseudomonas sp. strain adp is the model strain for studying bacterial degradation of the s-triazine herbicide atrazine. in this work, we focused on the expression of the atzdef operon, involved in mineralization of the central intermediate of the pathway, cyanuric acid. expression analysis of atzd-lacz fusions in pseudomonas sp. strain adp and pseudomonas putida showed that atzdef is subjected to dual regulation in response to nitrogen limitation and cyanuric acid. the gene adjacent to atzd, orf ...	2005	15601699
molecular nature of spontaneous modifications in gacs which cause colony phase variation in pseudomonas sp. strain pcl1171.	pseudomonas sp. strain pcl1171 displays colony phase variation between opaque phase i and translucent phase ii colonies, thereby regulating the production of secondary metabolites and exoenzymes. complementation and sequence analysis of 26 phase ii mutants and of 13 wild-type phase ii sectors growing out of phase i colonies showed that in all these cases the phase ii phenotype is caused by spontaneous mutations in gaca or/and gacs. mutation of gac reduced both the length of the lag phase and the ...	2005	15629930
characterization and performance of a toluene-degrading biofilm developed on pumice stones.	background: hydrocarbon-degrading biofilms in the treatment of contaminated groundwaters have received increasing attention due to the role played in the so-called "biobarriers". these are bioremediation systems in which a microbial consortium adherent to a solid support is placed across the flow of a contaminated plume, thus promoting biodegradation of the pollutant. results: a microbial consortium adherent to pumice granules (biofilm) developed from a toluene-enriched microflora in a mini-scal ...	2005	15655073
use of pyrosequencing of 16s rrna fragments to differentiate between bacteria responsible for neonatal sepsis.	infants admitted to neonatal intensive care units for suspicion of bacterial sepsis receive at least two broad-spectrum antibiotics for a minimum of 48 to 72 hours to cover both gram-positive and gram-negative organisms while awaiting blood culture results. on average, bacterial growth becomes detectable within 12 to 24 hours, with an additional 24 to 48 hours required for identification. we have previously described using a 16s rrna pcr assay for screening neonatal blood for bacterial dna. comb ...	2005	15681481
molecular and biochemical characterization of an endo-beta-1,3-glucanase from the pinewood nematode bursaphelenchus xylophilus acquired by horizontal gene transfer from bacteria.	we report the cloning and functional characterization of an endo-beta-1,3-glucanase from the pinewood nematode bursaphelenchus xylophilus acquired by horizontal gene transfer from bacteria. this is the first gene of this type from any nematode species. we show that a similar cdna is also present in another closely related species b. mucronatus, but that similar sequences are not present in any other nematode studied to date. the b. xylophilus gene is expressed solely in the oesophageal gland cel ...	2005	15727561
tolerance of the rieske-type [2fe-2s] cluster in recombinant ferredoxin bpha3 from pseudomonas sp. kks102 to histidine ligand mutations.	bpha3 from pseudomonas sp. kks102 is a rieske-type [2fe-2s] ferredoxin that transfers electrons from an nadh-dependent oxidoreductase, bpha4, to a biphenyl dioxygenase complex. a high-level expression and purification system for the recombinant bpha3 in escherichia coli was constructed. two histidine ligands of the rieske-type cluster in bpha3, were each replaced with serine, cysteine, asparagine and tyrosine. the single mutants, in which either his44 or his65 was replaced with a cysteine residu ...	2005	15733056
mice have a transcribed l-threonine aldolase/gly1 gene, but the human gly1 gene is a non-processed pseudogene.	there are three pathways of l-threonine catabolism. the enzyme l-threonine aldolase (ta) has been shown to catalyse the conversion of l-threonine to yield glycine and acetaldehyde in bacteria, fungi and plants. low levels of ta enzymatic activity have been found in vertebrates. it has been suggested that any detectable activity is due to serine hydroxymethyltransferase and that mammals lack a genuine threonine aldolase.	2005	15757516
crystal structure of the terminal oxygenase component of cumene dioxygenase from pseudomonas fluorescens ip01.	the crystal structure of the terminal component of the cumene dioxygenase multicomponent enzyme system of pseudomonas fluorescens ip01 (cumdo) was determined at a resolution of 2.2 a by means of molecular replacement by using the crystal structure of the terminal oxygenase component of naphthalene dioxygenase from pseudomonas sp. strain ncib 9816-4 (nphdo). the ligation of the two catalytic centers of cumdo (i.e., the nonheme iron and rieske [2fe-2s] centers) and the bridging between them in nei ...	2005	15774891
inactivation of hiv-1 in breast milk by treatment with the alkyl sulfate microbicide sodium dodecyl sulfate (sds).	reducing transmission of hiv-1 through breast milk is needed to help decrease the burden of pediatric hiv/aids in society. we have previously reported that alkyl sulfates (i.e., sodium dodecyl sulfate, sds) are microbicidal against hiv-1 at low concentrations, are biodegradable, have little/no toxicity and are inexpensive. therefore, they may be used for treatment of hiv-1 infected breast milk. in this report, human milk was artificially infected by adding to it hiv-1 (cell-free or cell-associat ...	2005	15888210
purification and characterization of allophanate hydrolase (atzf) from pseudomonas sp. strain adp.	atzf, allophanate hydrolase, is a recently discovered member of the amidase signature family that catalyzes the terminal reaction during metabolism of s-triazine ring compounds by bacteria. in the present study, the atzf gene from pseudomonas sp. strain adp was cloned and expressed as a his-tagged protein, and the protein was purified and characterized. atzf had a deduced subunit molecular mass of 66,223, based on the gene sequence, and an estimated holoenzyme molecular mass of 260,000. the acti ...	2005	15901697
the crystal structure of pffabz, the unique beta-hydroxyacyl-acp dehydratase involved in fatty acid biosynthesis of plasmodium falciparum.	the unique beta-hydroxyacyl-acp dehydratase in plasmodium falciparum, pffabz, is involved in fatty acid biosynthesis and catalyzes the dehydration of beta-hydroxy fatty acids linked to acyl carrier protein. the structure was solved by single anomalous dispersion (sad) phasing using a quick-soaking experiment with potassium iodide and refined to a resolution of 2.1 a. the crystal structure represents the first structure of a plasmodium beta-hydroxyacyl-acp dehydratase with broad substrate specifi ...	2005	15930004
emergent mechanistic diversity of enzyme-catalysed beta-diketone cleavage.	the enzymatic cleavage of c-c bonds in beta-diketones is, comparatively, a little studied biochemical process, but one that has important relevance to human metabolism, bioremediation and preparative biocatalysis. in recent studies, four types of enzymes have come to light that cleave c-c bonds in the beta-diketone functionality using different chemical mechanisms. oph [oxidized poly(vinyl alcohol) hydrolase from pseudomonas sp. strain vm15c], which cleaves nonane-4,6-dione to butyrate and penta ...	2005	15934927
recd plays an essential function during growth at low temperature in the antarctic bacterium pseudomonas syringae lz4w.	the antarctic psychrotrophic bacterium pseudomonas syringae lz4w has been used as a model system to identify genes that are required for growth at low temperature. transposon mutagenesis was carried out to isolate mutant(s) of the bacterium that are defective for growth at 4 degrees but normal at 22 degrees . in one such cold-sensitive mutant (cs1), the transposon-disrupted gene was identified to be a homolog of the recd gene of several bacteria. trans-complementation and freshly targeted gene d ...	2005	15956672
signature proteins that are distinctive of alpha proteobacteria.	the alpha (alpha) proteobacteria, a very large and diverse group, are presently characterized solely on the basis of 16s rrna trees, with no known molecular characteristic that is unique to this group. the genomes of three alpha-proteobacteria, rickettsia prowazekii (rp), caulobacter crescentus (cc) and bartonella quintana (bq), were analyzed in order to search for proteins that are unique to this group.	2005	15960851
purification, characterization, and crystallization of the components of the nitrobenzene and 2-nitrotoluene dioxygenase enzyme systems.	the protein components of the 2-nitrotoluene (2nt) and nitrobenzene dioxygenase enzyme systems from acidovorax sp. strain js42 and comamonas sp. strain js765, respectively, were purified and characterized. these enzymes catalyze the initial step in the degradation of 2-nitrotoluene and nitrobenzene. the identical shared reductase and ferredoxin components were monomers of 35 and 11.5 kda, respectively. the reductase component contained 1.86 g-atoms iron, 2.01 g-atoms sulfur, and one molecule of ...	2005	16000792
amino acids in positions 48, 52, and 73 differentiate the substrate specificities of the highly homologous chlorocatechol 1,2-dioxygenases cbna and tcbc.	chlorocatechol 1,2-dioxygenase (ccd) is the first-step enzyme of the chlorocatechol ortho-cleavage pathway, which plays a central role in the degradation of various chloroaromatic compounds. two ccds, cbna from the 3-chlorobenzoate-degrader ralstonia eutropha nh9 and tcbc from the 1,2,4-trichlorobenzene-degrader pseudomonas sp. strain p51, are highly homologous, having only 12 different amino acid residues out of identical lengths of 251 amino acids. but cbna and tcbc are different in substrate ...	2005	16030237
novel lectin-like bacteriocins of biocontrol strain pseudomonas fluorescens pf-5.	bacteriocin llpa, produced by pseudomonas sp. strain bw11m1, is a peculiar antibacterial protein due to its homology to mannose-binding lectins mostly found in monocots (a. h. a. parret, g. schoofs, p. proost, and r. de mot, j. bacteriol. 185:897-908, 2003). biocontrol strain pseudomonas fluorescens pf-5 contains two llpa-like genes, named llpa1(pf-5) and llpa2(pf-5). recombinant escherichia coli cells expressing llpa1(pf-5) or llpa2(pf-5) acquired bacteriocin activity and secreted a 31-kda prot ...	2005	16151105
improving the activity and stability of gl-7-aca acylase ca130 by site-directed mutagenesis.	in the present study, glutaryl-7-amino cephalosporanic acid acylase from pseudomonas sp. strain 130 (ca130) was mutated to improve its enzymatic activity and stability. based on the crystal structure of ca130, two series of amino acid residues, one from those directly involved in catalytic function and another from those putatively involved in surface charge, were selected as targets for site-directed mutagenesis. in the first series of experiments, several key residues in the substrate-binding ...	2005	16151116
novel dna sequences from natural strains of the nitrogen-fixing symbiotic bacterium sinorhizobium meliloti.	variation in genome size and content is common among bacterial strains. identifying these naturally occurring differences can accelerate our understanding of bacterial attributes, such as ecological specialization and genome evolution. in this study, we used representational difference analysis to identify potentially novel sequences not present in the sequenced laboratory strain rm1021 of the nitrogen-fixing bacterium sinorhizobium meliloti. using strain rm1021 as the driver and the type strain ...	2005	16269751
nitrobenzoates and aminobenzoates are chemoattractants for pseudomonas strains.	three pseudomonas strains were tested for the ability to sense and respond to nitrobenzoate and aminobenzoate isomers in chemotaxis assays. pseudomonas putida prs2000, a strain that grows on benzoate and 4-hydroxybenzoate by using the beta-ketoadipate pathway, has a well-characterized beta-ketoadipate-inducible chemotactic response to aromatic acids. prs2000 was chemotactic to 3- and 4-nitrobenzoate and all three isomers of aminobenzoate when grown under conditions that induce the benzoate chemo ...	2004	14711654
coexpression of genetically engineered 3-ketoacyl-acp synthase iii (fabh) and polyhydroxyalkanoate synthase (phac) genes leads to short-chain-length-medium-chain-length polyhydroxyalkanoate copolymer production from glucose in escherichia coli jm109.	polyhydroxyalkanoates (phas) can be divided into three main types based on the sizes of the monomers incorporated into the polymer. short-chain-length (scl) phas consist of monomer units of c3 to c5, medium-chain-length (mcl) phas consist of monomer units of c6 to c14, and scl-mcl phas consist of monomers ranging in size from c4 to c14. although previous studies using recombinant escherichia coli have shown that either scl or mcl pha polymers could be produced from glucose, this study presents t ...	2004	14766582
simultaneous degradation of atrazine and phenol by pseudomonas sp. strain adp: effects of toxicity and adaptation.	the strain pseudomonas sp. strain adp is able to degrade atrazine as a sole nitrogen source and therefore needs a single source for both carbon and energy for growth. in addition to the typical c source for pseudomonas, na(2)-succinate, the strain can also grow with phenol as a carbon source. phenol is oxidized to catechol by a multicomponent phenol hydroxylase. catechol is degraded via the ortho pathway using catechol 1,2-dioxygenase. it was possible to stimulate the strain in order to degrade ...	2004	15066779
growth of polychlorinated-biphenyl-degrading bacteria in the presence of biphenyl and chlorobiphenyls generates oxidative stress and massive accumulation of inorganic polyphosphate.	inorganic polyphosphate (polyp) plays a significant role in increasing bacterial cell resistance to unfavorable environmental conditions and in regulating different biochemical processes. using transmission electron microscopy of the polychlorinated biphenyl (pcb)-degrading bacterium pseudomonas sp. strain b4 grown in defined medium with biphenyl as the sole carbon source, we observed large and abundant electron-dense granules at all stages of growth and following a shift from glucose to bipheny ...	2004	15128568
albusin b, a bacteriocin from the ruminal bacterium ruminococcus albus 7 that inhibits growth of ruminococcus flavefaciens.	an approximately 32-kda protein (albusin b) that inhibited growth of ruminococcus flavefaciens fd-1 was isolated from culture supernatants of ruminococcus albus 7. traditional cloning and gene-walking pcr techniques revealed an open reading frame (albb) encoding a protein with a predicted molecular mass of 32,168 da. a blast search revealed two homologs of albb from the unfinished genome of r. albus 8 and moderate similarity to llpa, a recently described 30-kda bacteriocin from pseudomonas sp. s ...	2004	15128585
the structure of chondroitin b lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery.	chondroitinase b from pedobacter heparinus is the only known enzyme strictly specific for dermatan sulfate and is a widely used enzymatic tool for the structural characterization of glycosaminoglycans. this beta-helical polysaccharide lyase belongs to family pl-6 and cleaves the beta(1,4) linkage of dermatan sulfate in a random manner, yielding 4,5-unsaturated dermatan sulfate disaccharides as the product. the previously reported structure of its complex with a dermatan sulfate disaccharide prod ...	2004	15155751
molecular analysis of the microflora associated with dental caries.	molecular techniques have revealed many novel, presumed unculturable, taxa in oral infections. the aim of this study was to characterize the bacterial community of the middle and advancing front of carious dental lesions by cultural and molecular analyses. samples were collected with a hand excavator from five teeth with carious lesions involving dentine. samples were cultured on blood agar and rogosa agar incubated in air plus 5% co(2) and on fastidious anaerobe agar anaerobically. dna was also ...	2004	15243054
biochemical characterization of styab from pseudomonas sp. strain vlb120 as a two-component flavin-diffusible monooxygenase.	pseudomonas sp. vlb120 uses styrene as a sole source of carbon and energy. the first step in this metabolic pathway is catalyzed by an oxygenase (stya) and a nadh-flavin oxidoreductase (styb). both components have been isolated from wild-type pseudomonas strain vlb120 as well as from recombinant escherichia coli. stya from both sources is a dimer, with a subunit size of 47 kda, and catalyzes the enantioselective epoxidation of cc double bonds. styrene is exclusively converted to s-styrene oxide ...	2004	15292130
use of 16s ribosomal dna pcr and denaturing gradient gel electrophoresis for analysis of the microfloras of healing and nonhealing chronic venous leg ulcers.	the bacterial microfloras of 8 healing and 10 nonhealing chronic venous leg ulcers were compared by using a combination of cultural analysis and denaturing gradient gel electrophoresis (dgge) of pcr-amplified 16s rrna gene products. cultural analysis of the microflora revealed that the majority of both wound types carried the aerobes staphylococcus and pseudomonas spp. (89 and 80%, respectively). sequencing of 16s ribosomal dnas selected on the basis of dgge profiling allowed the identification ...	2004	15297496
the hotdog fold: wrapping up a superfamily of thioesterases and dehydratases.	the hotdog fold was initially identified in the structure of escherichia coli faba and subsequently in 4-hydroxybenzoyl-coa thioesterase from pseudomonas sp. strain cbs. since that time structural determinations have shown a number of other apparently unrelated proteins also share the hotdog fold.	2004	15307895
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
comparison of atpase-encoding type iii secretion system hrcn genes in biocontrol fluorescent pseudomonads and in phytopathogenic proteobacteria.	type iii protein secretion systems play a key role in the virulence of many pathogenic proteobacteria, but they also occur in nonpathogenic, plant-associated bacteria. certain type iii protein secretion genes (e.g., hrcc) have been found in pseudomonas sp. strain sbw25 (and other biocontrol pseudomonads), but other type iii protein secretion genes, such as the atpase-encoding gene hrcn, have not been found. using both colony hybridization and a pcr approach, we show here that hrcn is nevertheles ...	2004	15345390
involvement of linear plasmids in aerobic biodegradation of vinyl chloride.	pseudomonas putida strain aj and ochrobactrum strain td were isolated from hazardous waste sites based on their ability to use vinyl chloride (vc) as the sole source of carbon and energy under aerobic conditions. strains aj and td also use ethene and ethylene oxide as growth substrates. strain aj contained a linear megaplasmid (approximately 260 kb) when grown on vc or ethene, but it contained no circular plasmids. while strain aj was growing on ethylene oxide, it was observed to contain a 100-k ...	2004	15466555
isolation of lightning-competent soil bacteria.	artificial transformation is typically performed in the laboratory by using either a chemical (cacl(2)) or an electrical (electroporation) method. however, laboratory-scale lightning has been shown recently to electrotransform escherichia coli strain dh10b in soil. in this paper, we report on the isolation of two "lightning-competent" soil bacteria after direct electroporation of the nycodenz bacterial ring extracted from prairie soil in the presence of the pbhcrec plasmid (tc(r), sp(r), sm(r)). ...	2004	15466589
transferable antibiotic resistance elements in haemophilus influenzae share a common evolutionary origin with a diverse family of syntenic genomic islands.	transferable antibiotic resistance in haemophilus influenzae was first detected in the early 1970s. after this, resistance spread rapidly worldwide and was shown to be transferred by a large 40- to 60-kb conjugative element. bioinformatics analysis of the complete sequence of a typical h. influenzae conjugative resistance element, icehin1056, revealed the shared evolutionary origin of this element. icehin1056 has homology to 20 contiguous sequences in the national center for biotechnology inform ...	2004	15547285
integron carrying a novel metallo-beta-lactamase gene, blaimp-16, and a fused form of aminoglycoside-resistant gene aac(6')-30/aac(6')-ib': report from the sentry antimicrobial surveillance program.	since january 2002 pseudomonas sp. strains resistant to carbapenems and ceftazidime have been routinely screened as part of the sentry antimicrobial surveillance program for metallo-beta-lactamase production, and their resistance determinants have been analyzed. pseudomonas aeruginosa index strain 101-4704, which harbors a novel bla(imp) variant, bla(imp-16), was isolated in april 2002 from a 60-year-old man in brasilia, brazil. bla(imp-16) was found on the chromosome of the p. aeruginosa index ...	2004	15561846
molecular modeling of family gh16 glycoside hydrolases: potential roles for xyloglucan transglucosylases/hydrolases in cell wall modification in the poaceae.	family gh16 glycoside hydrolases can be assigned to five subgroups according to their substrate specificities, including xyloglucan transglucosylases/hydrolases (xths), (1,3)-beta-galactanases, (1,4)-beta-galactanases/kappa-carrageenases, "nonspecific" (1,3/1,3;1,4)-beta-d-glucan endohydrolases, and (1,3;1,4)-beta-d-glucan endohydrolases. a structured family gh16 glycoside hydrolase database has been constructed (http://www.ghdb.uni-stuttgart.de) and provides multiple sequence alignments with fu ...	2004	15557263
novel approach to the improvement of biphenyl and polychlorinated biphenyl degradation activity: promoter implantation by homologous recombination.	to improve the capabilities of microorganisms relevant for biodegradation, we developed a new genetic approach and applied it to the bph operon (bphegf[orf4]a1a2a3cd[orf1]a4r) of pseudomonas sp. strain kks102 to enhance its biphenyl- and polychlorinated biphenyl (pcb)-degrading activity. a native promoter of the bph operon, which was under control, was replaced through homologous recombination by a series of promoters that had constitutive activity. by testing a series of promoters with various ...	2003	12513989
strategies for helicase recruitment and loading in bacteria.	dna replication initiation in prokaryotes and eukaryotes requires the recruitment and loading of a helicase at the replication origin. to subsequently unwind the double-stranded dna, the helicase must be properly positioned on the separated dna strands. several studies have revealed similarities and differences in the mechanisms used by different autonomously replicating dna elements (replicons) for recruitment and activation of the appropriate helicase. of particular interest are plasmid replic ...	2003	12524518
plant lectin-like bacteriocin from a rhizosphere-colonizing pseudomonas isolate.	rhizosphere isolate pseudomonas sp. strain bw11m1, which belongs to the pseudomonas putida cluster, secretes a heat- and protease-sensitive bacteriocin which kills p. putida gr12-2r3. the production of this bacteriocin is enhanced by dna-damaging treatment of producer cells. we isolated a tnmod mutant of strain bw11m1 that had lost the capacity to inhibit the growth of strain gr12-2r3. a wild-type genomic fragment encompassing the transposon insertion site was shown to confer the bacteriocin phe ...	2003	12533465
synergistic degradation of linuron by a bacterial consortium and isolation of a single linuron-degrading variovorax strain.	the bacterial community composition of a linuron-degrading enrichment culture and the role of the individual strains in linuron degradation have been determined by a combination of methods, such as denaturing gradient gel electrophoresis of the total 16s rrna gene pool, isolation and identification of strains, and biodegradation assays. three strains, variovorax sp. strain wdl1, delftia acidovorans wdl34, and pseudomonas sp. strain wdl5, were isolated directly from the linuron-degrading culture. ...	2003	12620840
prokaryotic homologs of the eukaryotic 3-hydroxyanthranilate 3,4-dioxygenase and 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase in the 2-nitrobenzoate degradation pathway of pseudomonas fluorescens strain ku-7.	the 2-nitrobenzoic acid degradation pathway of pseudomonas fluorescens strain ku-7 proceeds via a novel 3-hydroxyanthranilate intermediate. in this study, we cloned and sequenced a 19-kb dna locus of strain ku-7 that encompasses the 3-hydroxyanthranilate meta-cleavage pathway genes. the gene cluster, designated nbaexhjigfcdr, is organized tightly and in the same direction. the nbac and nbad gene products were found to be novel homologs of the eukaryotic 3-hydroxyanthranilate 3,4-dioxygenase and ...	2003	12620844
bacterial conversion of hydroxylamino aromatic compounds by both lyase and mutase enzymes involves intramolecular transfer of hydroxyl groups.	hydroxylamino aromatic compounds are converted to either the corresponding aminophenols or protocatechuate during the bacterial degradation of nitroaromatic compounds. the origin of the hydroxyl group of the products could be the substrate itself (intramolecular transfer mechanism) or the solvent water (intermolecular transfer mechanism). the conversion of hydroxylaminobenzene to 2-aminophenol catalyzed by a mutase from pseudomonas pseudoalcaligenes js45 proceeds by an intramolecular hydroxyl tr ...	2003	12732549
identification of signature and primers specific to genus pseudomonas using mismatched patterns of 16s rdna sequences.	pseudomonas, a soil bacterium, has been observed as a dominant genus that survives in different habitats with wide hostile conditions. we had a basic assumption that the species level variation in 16s rdna sequences of a bacterial genus is mainly due to substitutions rather than insertion or deletion of bases. keeping this in view, the aim was to identify a region of 16s rdna sequence and within that focus on substitution prone stretches indicating species level variation and to derive patterns ...	2003	12769821
aerobic denitrifying bacteria that produce low levels of nitrous oxide.	most denitrifiers produce nitrous oxide (n(2)o) instead of dinitrogen (n(2)) under aerobic conditions. we isolated and characterized novel aerobic denitrifiers that produce low levels of n(2)o under aerobic conditions. we monitored the denitrification activities of two of the isolates, strains tr2 and k50, in batch and continuous cultures. both strains reduced nitrate (no(3)(-)) to n(2) at rates of 0.9 and 0.03 micro mol min(-1) unit of optical density at 540 nm(-1) at dissolved oxygen (o(2)) (d ...	2003	12788710
assessment of bioavailability of soil-sorbed atrazine.	bioavailability of pesticides sorbed to soils is an important determinant of their environmental fate and impact. mineralization of sorbed atrazine was studied in soil and clay slurries, and a desorption-biodegradation-mineralization (dbm) model was developed to quantitatively evaluate the bioavailability of sorbed atrazine. three atrazine-degrading bacteria that utilized atrazine as a sole n source (pseudomonas sp. strain adp, agrobacterium radiobacter strain j14a, and ralstonia sp. strain m91- ...	2003	12788728
molecular diversity of denitrifying genes in continental margin sediments within the oxygen-deficient zone off the pacific coast of mexico.	to understand the composition and structure of denitrifying communities in the oxygen-deficient zone off the pacific coast of mexico, the molecular diversity of nir genes from sediments obtained at four stations was examined by using a pcr-based cloning approach. a total of 50 operational taxonomic units (otus) for nirk and 82 otus for nirs were obtained from all samples. forty-four of the nirs clones and 31 of the nirk clones were sequenced; the levels of similarity of the nirs clones were 52 t ...	2003	12788762
on the origins of cyanuric acid hydrolase: purification, substrates, and prevalence of atzd from pseudomonas sp. strain adp.	cyanuric acid hydrolase (atzd) from pseudomonas sp. strain adp was purified to homogeneity. of 22 cyclic amides and triazine compounds tested, only cyanuric acid and n-methylisocyanuric acid were substrates. other cyclic amidases were found not to hydrolyze cyanuric acid. ten bacteria that use cyanuric acid as a sole nitrogen source for growth were found to contain either atzd or trzd, but not both genes.	2003	12788776
unusual integrase gene expression on the clc genomic island in pseudomonas sp. strain b13.	an unusual type of gene expression from an integrase promoter was found in cultures of the bacterium pseudomonas sp. strain b13. the promoter controls expression of the intb13 integrase gene, which is present near the right end of a 105-kb conjugative genomic island (the clc element) encoding catabolism of aromatic compounds. the enzymatic activity of integrase intb13 is essential for site-specific integration of the clc element into the bacterial host's chromosome. by creating transcription fus ...	2003	12867462
alteration of chain length substrate specificity of aeromonas caviae r-enantiomer-specific enoyl-coenzyme a hydratase through site-directed mutagenesis.	aeromonas caviae r-specific enoyl-coenzyme a (enoyl-coa) hydratase (phaj(ac)) is capable of providing (r)-3-hydroxyacyl-coa with a chain length of four to six carbon atoms from the fatty acid beta-oxidation pathway for polyhydroxyalkanoate (pha) synthesis. in this study, amino acid substitutions were introduced into phaj(ac) by site-directed mutagenesis to investigate the feasibility of altering the specificity for the acyl chain length of the substrate. a crystallographic structure analysis of ...	2003	12902277
the biphenyl- and 4-chlorobiphenyl-catabolic transposon tn4371, a member of a new family of genomic islands related to incp and ti plasmids.	the nucleotide sequence of the biphenyl catabolic transposon tn4371 has been completed and analyzed. it confirmed that the element has a mosaic structure made of several building blocks. in addition to previously identified genes coding for a tyrosine recombinase related to phage integrases and for biphenyl degradation enzymes very similar to those of achromobacter georgiopolitanum kks102, tn4371 carries many plasmid-related genes involved in replication, partition, and other, as-yet-unknown, pl ...	2003	12902278