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 ...200717644635
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 ...200717550978
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 ...200717660279
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 ...200717693490
a novel sampling method for the investigation of gut 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.200717663516
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.200717293778
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.200717288581
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 ...200717959646
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 ...200717973403
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 ...200717765874
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- ...200717910757
a novel caffeine dehydrogenase in pseudomonas sp. strain cbb1 oxidizes caffeine to trimethyluric acid.a unique heterotrimeric caffeine dehydrogenase was purified from pseudomonas sp. strain cbb1. this enzyme oxidized caffeine to trimethyluric acid stoichiometrically and hydrolytically, without producing hydrogen peroxide. the enzyme was not nad(p)(+) dependent; coenzyme q(0) was the preferred electron acceptor. the enzyme was specific for caffeine and theobromine and showed no activity with xanthine.200817981969
efficient display of active lipase lipb52 with a pichia pastoris cell surface display system and comparison with the lipb52 displayed on saccharomyces cerevisiae cell surface.for industrial bioconversion processes, the utilization of surface-displayed lipase in the form of whole-cell biocatalysts is more advantageous, because the enzymes are displayed on the cell surface spontaneously, regarded as immobilized enzymes.200818221563
functional role of the additional domains in inulosucrase (isla) from leuconostoc citreum cw28.inulosucrase (isla) from leuconostoc citreum cw28 belongs to a new subfamily of multidomain fructosyltransferases (ftfs), containing additional domains from glucosyltransferases. it is not known what the function of the additional domains in this subfamily is.200818237396
survey of bacterial diversity in chronic wounds using pyrosequencing, dgge, and full ribosome shotgun sequencing.chronic wound pathogenic biofilms are host-pathogen environments that colonize and exist as a cohabitation of many bacterial species. these bacterial populations cooperate to promote their own survival and the chronic nature of the infection. few studies have performed extensive surveys of the bacterial populations that occur within different types of chronic wound biofilms. the use of 3 separate16s-based molecular amplifications followed by pyrosequencing, shotgun sanger sequencing, and denatur ...200818325110
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 ...200717868768
nadh availability limits asymmetric biocatalytic epoxidation in a growing recombinant escherichia coli strain.styrene can efficiently be oxidized to (s)-styrene oxide by recombinant escherichia coli expressing the styrene monooxygenase genes styab from pseudomonas sp. strain vlb120. targeting microbial physiology during whole-cell redox biocatalysis, we investigated the interdependency of styrene epoxidation, growth, and carbon metabolism on the basis of mass balances obtained from continuous two-liquid-phase cultures. full induction of styab expression led to growth inhibition, which could be attenuate ...200818192422
sub-grouping and sub-functionalization of the rifin multi-copy protein family.parasitic protozoans possess many multicopy gene families which have central roles in parasite survival and virulence. the number and variability of members of these gene families often make it difficult to predict possible functions of the encoded proteins. the families of extra-cellular proteins that are exposed to a host immune response have been driven via immune selection to become antigenically variant, and thereby avoid immune recognition while maintaining protein function to establish a ...200818197962
the majority of in vitro macrophage activation exhibited by extracts of some immune enhancing botanicals is due to bacterial lipoproteins and lipopolysaccharides.we have identified potent monocyte/macrophage activating bacterial lipoproteins within commonly used immune enhancing botanicals such as echinacea, american ginseng and alfalfa sprouts. these bacterial lipoproteins, along with lipopolysaccharides, were substantially more potent than other bacterially derived components when tested in in vitro monocyte/macrophage activation systems. in experiments using raw 264.7 and mouse peritoneal macrophages the majority (85-98%) of the activity within extrac ...200818486914
genes and enzymes of azetidine-2-carboxylate metabolism: detoxification and assimilation of an antibiotic.l-(-)-azetidine-2-carboxylate (ac) is a toxic, natural product analog of l-proline. this study revealed the genes and biochemical strategy employed by pseudomonas sp. strain a2c to detoxify and assimilate ac as its sole nitrogen source. the gene region from pseudomonas sp. strain a2c required for detoxification was cloned into escherichia coli and sequenced. the 7.0-kb region contained eight identifiable genes. four encoded putative transporters or permeases for gamma-amino acids or drugs. anoth ...200818487339
the binary protein interactome of treponema pallidum--the syphilis spirochete.protein interaction networks shed light on the global organization of proteomes but can also place individual proteins into a functional context. if we know the function of bacterial proteins we will be able to understand how these species have adapted to diverse environments including many extreme habitats. here we present the protein interaction network for the syphilis spirochete treponema pallidum which encodes 1,039 proteins, 726 (or 70%) of which interact via 3,649 interactions as revealed ...200818509523
novel aromatic ring-hydroxylating dioxygenase genes from coastal marine sediments of patagonia.polycyclic aromatic hydrocarbons (pahs), widespread pollutants in the marine environment, can produce adverse effects in marine organisms and can be transferred to humans through seafood. our knowledge of pah-degrading bacterial populations in the marine environment is still very limited, and mainly originates from studies of cultured bacteria. in this work, genes coding catabolic enzymes from pah-biodegradation pathways were characterized in coastal sediments of patagonia with different levels ...200818366740
action for child survival: elimination of haemophilus influenzae type b meningitis in guide immunization policy, we determined the public health benefit of introducing haemophilus influenzae type b (hib) vaccine in uganda and estimated the vaccine effectiveness.200818438518
the plant-associated bacterium stenotrophomonas rhizophila expresses a new enzyme for the synthesis of the compatible solute glucosylglycerol.the rhizobacterium stenotrophomonas rhizophila accumulates the compatible solutes glucosylglycerol (gg) and trehalose under salt stress conditions. the complete gene for the gg synthesis enzyme was cloned and sequenced. this enzyme from s. rhizophila represented a novel fusion protein composed of a putative c-terminal gg-phosphate synthase domain and an n-terminal putative gg-phosphate phosphatase domain, which was named ggpps. a similar gene was cloned from pseudomonas sp. strain oa146. the ggp ...200818586931
biphenyl dioxygenase from an arctic isolate is not cold adapted.biphenyl dioxygenase from the psychrotolerant bacterium pseudomonas sp. strain cam-1 (bpdo(cam-1)) was purified and found to have an apparent k(cat) for biphenyl of 1.1 +/- 0.1 s(-1) (mean +/- standard deviation) at 4 degrees c. in contrast, bpdo(lb400) from the mesophile burkholderia xenovorans lb400 had no detectable activity at this temperature. at 57 degrees c, the half-life of the bpdo(cam-1) oxygenase was less than half that of the bpdo(lb400) oxygenase. nevertheless, bpdo(cam-1) appears t ...200818424535
identification and characterization of bacterial cutinase.cutinase, which exists in both fungi and bacteria, catalyzes the cleavage of the ester bonds of cutin. fungal cutinases have been extensively studied, however, reports on bacterial cutinases have been limited due to the lack of knowledge concerning the identity of their open reading frames. in the present study, the cutinase from thermobifida fusca was induced by cutin and purified to homogeneity by following p-nitrophenyl butyrate hydrolyzing activity. peptide mass fingerprinting analysis of th ...200818658138
the dape-encoded n-succinyl-l,l-diaminopimelic acid desuccinylase from haemophilus influenzae contains two active-site histidine residues.the catalytic and structural properties of the h67a and h349a dape-encoded n-succinyl-l,l-diaminopimelic acid desuccinylase (dape) from haemophilus influenzae were investigated. on the basis of sequence alignment with the carboxypeptidase from pseudomonas sp. strain rs-16, both h67 and h349 were predicted to be zn(ii) ligands. the h67a dape enzyme exhibited a decreased catalytic efficiency (180-fold) compared with wild-type (wt) dape towards n-succinyldiaminopimelic acid. no catalytic activity w ...200918712420
a genome-scale metabolic reconstruction of pseudomonas putida kt2440: ijn746 as a cell factory.pseudomonas putida is the best studied pollutant degradative bacteria and is harnessed by industrial biotechnology to synthesize fine chemicals. since the publication of p. putida kt2440's genome, some in silico analyses of its metabolic and biotechnology capacities have been published. however, global understanding of the capabilities of p. putida kt2440 requires the construction of a metabolic model that enables the integration of classical experimental data along with genomic and high-through ...200818793442
poly-3-hydroxybutyrate synthase from the periplasm of escherichia coli.this is the first report of a poly-3-hydroxybutyrate (phb) synthase in escherichia coli. the enzyme was isolated from the periplasm using ammonium sulfate fractionation, hydrophobic, and size-exclusion chromatography and identified by lc/ms/ms as ydcs, a component of a putative abc transporter. green fluorescent protein-tagged ydcs, purified by 2d native gel electrophoresis, also exhibited phb synthase activity. optimal conditions for enzyme activity were 37 degrees c, ph 6.8-7.5, 100 mm kcl. k( ...200818640095
crystal structure of a carbonyl reductase from candida parapsilosis with anti-prelog stereospecificity.a novel short-chain (s)-1-phenyl-1,2-ethanediol dehydrogenase (scr) from candida parapsilosis exhibits coenzyme specificity for nadph over nadh. it catalyzes an anti-prelog type reaction to reduce 2-hydroxyacetophenone into (s)-1-phenyl-1,2-ethanediol. the coding gene was overexpressed in escherichia coli and the purified protein was crystallized. the crystal structure of the apo-form was solved to 2.7 a resolution. this protein forms a homo-tetramer with a broken 2-2-2 symmetry. the overall fol ...200818566346
the transcriptional repressor protein nsrr senses nitric oxide directly via a [2fe-2s] cluster.the regulatory protein nsrr, a member of the rrf2 family of transcription repressors, is specifically dedicated to sensing nitric oxide (no) in a variety of pathogenic and non-pathogenic bacteria. it has been proposed that no directly modulates nsrr activity by interacting with a predicted [fe-s] cluster in the nsrr protein, but no experimental evidence has been published to support this hypothesis. here we report the purification of nsrr from the obligate aerobe streptomyces coelicolor. we demo ...200818989365
a novel transposon, tn6009, composed of a tn916 element linked with a staphylococcus aureus mer operon.the aim of this study was to characterize a novel conjugative transposon tn6009 composed of a tn916 linked to a staphylococcus aureus mer operon in representative gram-positive and gram-negative bacteria isolated in nigeria and portugal.200818583328
the 1.6 a crystal structure of mycobacterium smegmatis mshc: the penultimate enzyme in the mycothiol biosynthetic pathway.mycobacterium smegmatis mshc catalyzes the atp-dependent condensation of glcn-ins and l-cysteine to form l-cys-glcn-ins, the penultimate step in mycothiol biosynthesis. attempts to crystallize the native, full-length mshc have been unsuccessful. however, incubation of the enzyme with the cysteinyl adenylate analogue, 5'-o-[n-(l-cysteinyl)-sulfamonyl]adenosine (csa), followed by a 24-h limited trypsin proteolysis yielded an enzyme preparation that readily crystallized. the three-dimensional struc ...200819053270
variability in in vitro macrophage activation by commercially diverse bulk echinacea plant material is predominantly due to bacterial lipoproteins and lipopolysaccharides.we previously reported that the majority of in vitro monocyte/macrophage activation exhibited by extracts of echinacea and other botanicals depends upon bacterial lipopolysaccharides and braun-type bacterial lipoproteins. we determined the contribution made by these bacterial components to the overall immune-enhancing activity detected in e. purpurea and e. angustifolia bulk root and aerial material obtained from six major growers/suppliers in north america. substantial variation in activity (up ...200818942831
anenpi: identification and annotation of analogous enzymes.enzymes are responsible for the catalysis of the biochemical reactions in metabolic pathways. analogous enzymes are able to catalyze the same reactions, but they present no significant sequence similarity at the primary level, and possibly different tertiary structures as well. they are thought to have arisen as the result of independent evolutionary events. a detailed study of analogous enzymes may reveal new catalytic mechanisms, add information about the origin and evolution of biochemical pa ...200819091081
a modeling study by response surface methodology and artificial neural network on culture parameters optimization for thermostable lipase production from a newly isolated thermophilic geobacillus sp. strain arm.thermostable bacterial lipases occupy a place of prominence among biocatalysts owing to their novel, multifold applications and resistance to high temperature and other operational conditions. the capability of lipases to catalyze a variety of novel reactions in both aqueous and nonaqueous media presents a fascinating field for research, creating interest to isolate novel lipase producers and optimize lipase production. the most important stages in a biological process are modeling and optimizat ...200819105837
resolving genetic functions within microbial populations: in situ analyses using rrna and mrna stable isotope probing coupled with single-cell raman-fluorescence in situ hybridization.prokaryotes represent one-half of the living biomass on earth, with the vast majority remaining elusive to culture and study within the laboratory. as a result, we lack a basic understanding of the functions that many species perform in the natural world. to address this issue, we developed complementary population and single-cell stable isotope ((13)c)-linked analyses to determine microbial identity and function in situ. we demonstrated that the use of rrna/mrna stable isotope probing (sip) rec ...200918997025
export of recombinant proteins in escherichia coli using abc transporter with an attached lipase abc transporter recognition domain (lard).abstract:200919178697
structure of a sigma28-regulated nonflagellar virulence protein from campylobacter jejuni.campylobacter jejuni, a gram-negative motile bacterium, is a leading cause of human gastrointestinal infections. although the mechanism of c.jejuni-mediated enteritis appears to be multifactorial, flagella play complex roles in the virulence of this human pathogen. cj0977 is a recently identified virulence factor in c. jejuni and is expressed by a sigma(28) promoter that controls late genes in the flagellar regulon. a cj0977 mutant strain is fully motile but significantly reduced in the invasion ...200818835274
identification and characterization of catabolic para-nitrophenol 4-monooxygenase and para-benzoquinone reductase from pseudomonas sp. strain wbc-3.pseudomonas sp. strain wbc-3 utilizes para-nitrophenol (pnp) as a sole source of carbon, nitrogen, and energy. in order to identify the genes involved in this utilization, we cloned and sequenced a 12.7-kb fragment containing a conserved region of nad(p)h:quinone oxidoreductase genes. of the products of the 13 open reading frames deduced from this fragment, pnpa shares 24% identity to the large component of a 3-hydroxyphenylacetate hydroxylase from pseudomonas putida u and pnpb is 58% identical ...200919218392
the mechanisms of human hotdog-fold thioesterase 2 (hthem2) substrate recognition and catalysis illuminated by a structure and function based analysis.the focus of this paper is the hotdog-fold thioesterase them2 from human (hthem2; swiss-prot entry q9npj3 ). in an earlier communication (cheng, z., song, f., shan, x., wei, z., wang, y., dunaway-mariano, d., and gong, w. (2006) crystal structure of human thioesterase superfamily member 2, biochem. biophys. res. commun. 349, 172-177) we reported the apo crystal structure of hthem2. herein, we report the results of an extensive hthem2 substrate screen, the structure determination of hthem2 comple ...200919170545
structural analysis reveals dna binding properties of rv2827c, a hypothetical protein from mycobacterium tuberculosis.tuberculosis (tb) is a major global health threat caused by mycobacterium tuberculosis (mtb). it is further fueled by the hiv pandemic and by increasing incidences of multidrug resistant mtb-strains. rv2827c, a hypothetical protein from mtb, has been implicated in the survival of mtb in the macrophages of the host. the three-dimensional structure of rv2827c has been determined by the three-wavelength anomalous diffraction technique using bromide-derivatized crystals and refined to a resolution o ...200919184528
a tn5051-like mer-containing transposon identified in a heavy metal tolerant strain achromobacter sp. ao22.achromobacter sp. ao22 (formerly alcaligenes sp. ao22), a bacterial strain isolated from a lead-contaminated industrial site in australia, was previously found to be resistant to moderate to high levels of mercury, copper and other heavy metals. however, the nature and location of the genetic basis for mercuric ion resistance in this strain, had not been previously identified.200919284535
synthesis of rhamnolipid biosurfactant and mode of hexadecane uptake by pseudomonas species.abstract:200919284586
molecular determinants of the regioselectivity of toluene/o-xylene monooxygenase from pseudomonas sp. strain ox1.bacterial multicomponent monooxygenases (bmms) are a heterogeneous family of di-iron monooxygenases which share the very interesting ability to hydroxylate aliphatic and/or aromatic hydrocarbons. each bmm possesses defined substrate specificity and regioselectivity which match the metabolic requirements of the strain from which it has been isolated. pseudomonas sp. strain ox1, a strain able to metabolize o-, m-, and p-cresols, produces the bmm toluene/o-xylene monooxygenase (tomo), which convert ...200919074607
structure of the plp degradative enzyme 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase from mesorhizobium loti maff303099 and its mechanistic implications.a vitamin b(6) degradative pathway has recently been identified and characterized in mesorhizobium loti maff303099. one of the enzymes on this pathway, 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (mhpco), is a flavin-dependent enzyme and catalyzes the oxidative ring-opening of 2-methyl-3-hydroxypyridine-5-carboxylic acid to form e-2-(acetamino-methylene)succinate. the gene for this enzyme has been cloned, and the corresponding protein has been overexpressed in escherichia coli and pur ...200919317437
the sensor kinase tods operates by a multiple step phosphorelay mechanism involving two autokinase domains.expression of the pseudomonas putida tod operon, which encodes enzymes for toluene metabolism, takes place from the p(todx) promoter and is mediated by the tods/todt two component system. the sensor kinase tods has a complex domain arrangement containing two functional modules, each harboring a sensor- and an autokinase domain and separated by a receiver domain. based on site-directed mutagenesis of phosphoaccepting his-190, asp-500, and his-760 and in vitro transphosphorylation experiments with ...200919240030
the mechanism of domain alternation in the acyl-adenylate forming ligase superfamily member 4-chlorobenzoate: coenzyme a ligase.4-chlorobenzoate:coa ligase (cbl) belongs to the adenylate-forming family of enzymes that catalyze a two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme a or an acyl-carrier protein. the active site is located at the interface of a large n-terminal domain and a smaller c-terminal domain. crystallographic structures have been determined at multiple steps along the reaction pathway and form the ba ...200919320426
constitutive and regulated expression vectors to construct polyphosphate deficient bacteria.inorganic polyphosphate (polyp), a polymer of tens or hundreds of phosphate residues linked by atp-like bonds, is found in all organisms and performs a wide variety of functions. polyp is synthesized in bacterial cells by the actions of polyphosphate kinases (ppk1 and ppk2) and degraded by an exopolyphosphatase (ppx). bacterial cells with polyp deficiencies are impaired in many structural and important cellular functions such as motility, quorum sensing, biofilm formation and virulence. knockout ...200919323822
performance of a yeast-mediated biological fuel cell.saccharomyces cerevisiae present in common baker's yeast was used in a microbial fuel cell in which glucose was the carbon source. methylene blue was used as the electronophore in the anode compartment, while potassium ferricyanide and methylene blue were tested as electron acceptors in the cathode compartment. microbes in a mediator-free environment were used as the control. the experiment was performed in both open and closed circuit configurations under different loads ranging from 100 komega ...200819325724
co2 production as an indicator of biofilm metabolism.biofilms are important in aquatic nutrient cycling and microbial proliferation. in these structures, nutrients like carbon are channeled into the production of extracellular polymeric substances or cell division; both are vital for microbial survival and propagation. the aim of this study was to assess carbon channeling into cellular or noncellular fractions in biofilms. growing in tubular reactors, biofilms of our model strain pseudomonas sp. strain ct07 produced cells to the planktonic phase f ...200919346353
a rapid crosstalk of human gammadelta t cells and monocytes drives the acute inflammation in bacterial infections.vgamma9/vdelta2 t cells are a minor subset of t cells in human blood and differ from other t cells by their immediate responsiveness to microbes. we previously demonstrated that the primary target for vgamma9/vdelta2 t cells is (e)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (hmb-pp), an essential metabolite produced by a large range of pathogens. here we wished to study the consequence of this unique responsiveness in microbial infection. the majority of peripheral vgamma9/vdelta2 t cells share ...200919229322
two small ncrnas jointly govern virulence and transmission in legionella transit from intra- to extracellular environments, legionella pneumophila differentiates from a replicative/non-virulent to a transmissive/virulent form using the two-component system leta/lets and the global repressor protein csra. while investigating how both regulators act co-ordinately we characterized two ncrnas, rsmy and rsmz, that link the leta/lets and csra regulatory networks. we demonstrate that leta directly regulates their expression and show that rsmy and rsmz are functional in e ...200919400772
biodegradation of the high explosive hexanitrohexaazaiso-wurtzitane (cl-20).the aerobic biodegradability of the high explosive cl-20 by activated sludge and the white rot fungus phanerochaete chrysosporium has been investigated. although activated sludge is not effective in degrading cl-20 directly, it can mineralize the alkaline hydrolysis products. phanerochaete chrysosporium degrades cl-20 in the presence of supplementary carbon and nitrogen sources. biodegradation studies were conducted using various nutrient media under diverse conditions. variables included the cl ...200919440524
the stat pathway mediates late-phase immunity against plasmodium in the mosquito anopheles gambiae.the stat family of transcription factors activates expression of immune system genes in vertebrates. the ancestral stat gene (agstat-a) appears to have duplicated in the mosquito anopheles gambiae, giving rise to a second intronless stat gene (agstat-b), which we show regulates agstat-a expression in adult females. agstat-a participates in the transcriptional activation of nitric oxide synthase (nos) in response to bacterial and plasmodial infection. activation of this pathway, however, is not e ...200919454353
distal end of 105-125 loop--a putative reductase binding domain of phthalate dioxygenase.the phthalate dioxygenase system consists of the dioxygenase, pdo, which contains a rieske [2fe-2s] center and a fe(ii)-mononuclear center, and the reductase, pdr. involvement of the distal end of the 105-125 loop of pdo in its interaction with pdr was tested by substituting charged residues in the loop with alanines and by replacing the conserved tryptophan-94. compared to wild-type pdo, all variants had lower catalytic activity and the rieske centers were reduced more slowly by reduced pdr. th ...200919464996
analysis of proteins with the 'hot dog' fold: prediction of function and identification of catalytic residues of hypothetical proteins.the hot dog fold has been found in more than sixty proteins since the first report of its existence about a decade ago. the fold appears to have a strong association with fatty acid biosynthesis, its regulation and metabolism, as the proteins with this fold are predominantly coenzyme a-binding enzymes with a variety of substrates located at their active sites.200919473548
modeling of solvent-dependent conformational transitions in burkholderia cepacia lipase.the characteristic of most lipases is the interfacial activation at a lipid interface or in non-polar solvents. interfacial activation is linked to a large conformational change of a lid, from a closed to an open conformation which makes the active site accessible for substrates. while for many lipases crystal structures of the closed and open conformation have been determined, the pathway of the conformational transition and possible bottlenecks are unknown. therefore, molecular dynamics simula ...200919476626
identification of a novel self-sufficient styrene monooxygenase from rhodococcus opacus 1cp.sequence analysis of a 9-kb genomic fragment of the actinobacterium rhodococcus opacus 1cp led to identification of an open reading frame encoding a novel fusion protein, stya2b, with a putative function in styrene metabolism via styrene oxide and phenylacetic acid. gene cluster analysis indicated that the highly related fusion proteins of nocardia farcinica ifm10152 and arthrobacter aurescens tc1 are involved in a similar physiological process. whereas 413 amino acids of the n terminus of stya2 ...200919482928
inhibition of human folylpolyglutamate synthetase by diastereomeric phosphinic acid mimics of the tetrahedral intermediate.phosphorus-containing pseudopeptides, racemic at the c-terminal alpha-carbon, are potent mechanism-based inhibitors of folylpolyglutamate synthetase (fpgs). they are mimics of the tetrahedral intermediate postulated to form during fpgs-catalyzed biosynthesis of poly(gamma-l-glutamates). in the present paper, the fpgs inhibitory activity of each diastereomer coupled to three heterocycles is reported. the high r(f) pseudopeptide containing the 5,10-dideazatetrahydropteroyl (ddah(4)pte) heterocycle ...200919563773
medical bioremediation of age-related diseases.abstract: catabolic insufficiency in humans leads to the gradual accumulation of a number of pathogenic compounds associated with age-related diseases, including atherosclerosis, alzheimer's disease, and macular degeneration. removal of these compounds is a widely researched therapeutic option, but the use of antibodies and endogenous human enzymes has failed to produce effective treatments, and may pose risks to cellular homeostasis. another alternative is "medical bioremediation," the use of m ...200919358742
studies of a ring-cleaving dioxygenase illuminate the role of cholesterol metabolism in the pathogenesis of mycobacterium tuberculosis.mycobacterium tuberculosis, the etiological agent of tb, possesses a cholesterol catabolic pathway implicated in pathogenesis. this pathway includes an iron-dependent extradiol dioxygenase, hsac, that cleaves catechols. immuno-compromised mice infected with a deltahsac mutant of m. tuberculosis h37rv survived 50% longer than mice infected with the wild-type strain. in guinea pigs, the mutant disseminated more slowly to the spleen, persisted less successfully in the lung, and caused little pathol ...200919300498
bacterial chemotaxis to atrazine and related s-triazines.pseudomonas sp. strain adp utilizes the human-made s-triazine herbicide atrazine as the sole nitrogen source. the results reported here demonstrate that atrazine and the atrazine degradation intermediates n-isopropylammelide and cyanuric acid are chemoattractants for strain adp. in addition, the nonmetabolized s-triazine ametryn was also an attractant. the chemotactic response to these s-triazines was not specifically induced during growth with atrazine, and atrazine metabolism was not required ...200919581468
increased diversity of predacious bdellovibrio-like organisms (blos) as a function of eutrophication in kumaon lakes of india.predation by bdellovibrio-like organisms (blos) results in bacterial community succession in aquatic ecosystems. the effects of nutrient loading on the distribution and phylogeny of blos remain largely unknown. to this end, we present our findings on blo diversity from four north-indian lakes that are variable in their trophic status; nainital is eutrophic, both, bhimtal and naukuchiatal are mesotrophic and sattal remains oligotrophic, respectively. initially, total heterotrophic bacteria and bl ...200919319600
the role of the conserved phenylalanine in the sigma54-interacting gaftga motif of bacterial enhancer binding proteins.sigma(54)-dependent transcription requires activation by bacterial enhancer binding proteins (bebps). bebps are members of the aaa+ (atpases associated with various cellular activities) protein family and typically form hexameric structures that are crucial for their atpase activity. the precise mechanism by which the energy derived from atp hydrolysis is coupled to biological output has several unknowns. here we use escherichia coli pspf, a model bebp involved in the transcription of stress res ...200919692583
metagenomics reveals diversity and abundance of meta-cleavage pathways in microbial communities from soil highly contaminated with jet fuel under air-sparging bioremediation.the extradiol dioxygenase diversity of a site highly contaminated with aliphatic and aromatic hydrocarbons under air-sparging treatment was assessed by functional screening of a fosmid library in escherichia coli with catechol as substrate. the 235 positive clones from inserts of dna extracted from contaminated soil were equivalent to one extradiol dioxygenase-encoding gene per 3.6 mb of dna screened, indicating a strong selection for genes encoding this function. three subfamilies were identifi ...200919575758
distribution of bacterial keratitis and emerging resistance to antibiotics in china from 2001 to study on the distribution of bacterial keratitis isolates and the resistance to antibiotics in china from 2001 to 2004.200819668756
arsenic accumulation by pseudomonas stutzeri and its response to some thiol chelators.the aim of this study is to examine arsenic accumulation by pseudomonas stutzeri and its response to some thiol chelators, dmps and miadmsa.200819568912
isolation and characterization of a novel 2-sec-butylphenol-degrading bacterium pseudomonas sp. strain ms-1.a novel bacterium capable of utilizing 2-sec-butylphenol as the sole carbon and energy source, pseudomonas sp. strain ms-1, was isolated from freshwater sediment. within 30 h, strain ms-1 completely degraded 1.5 mm 2-sec-butylphenol in basal salt medium, with concomitant cell growth. a pathway for the metabolism of 2-sec-butylphenol by strain ms-1 was proposed on the basis of the identification of 3 internal metabolites-3-sec-butylcatechol, 2-hydroxy-6-oxo-7-methylnona-2,4-dienoic acid, and 2-me ...201019705287
oral microbial and respiratory status of persons with mental retardation/intellectual and developmental disability: an observational cohort study.the objective of this study was to determine the prevalence of select microorganisms in oral biofilms and to investigate relationships between oral and respiratory status in persons with mental retardation/intellectual and developmental disabilities (idd).200919748295
the effects of maturation on the colonic microflora in infancy and childhood.the composition of colonic mircoflora and its changes with maturation have rarely been investigated in large samples. methods. we used conventional microbiological testing to analyse the colonic flora (kyberstatus, institut formicroecology, herborn, germany) of stool samples from 12 484 children with different intestinal and nonintestinal diagnoses. stool samples were analysed for total colony forming units (cfu) (per g stool) and the abundance of bifidobacteria, bacteroides sp., escherichia col ...200919763278
incidence and severity of respiratory syncytial virus pneumonia in rural kenyan children identified through hospital surveillance.although necessary for developing a rationale for vaccination, the burden of severe respiratory syncytial virus (rsv) disease in children in resource-poor settings remains poorly defined.200919788358
initial insight into the function of the lysosomal 66.3 kda protein from mouse by means of x-ray crystallography.the lysosomal 66.3 kda protein from mouse is a soluble, mannose 6-phosphate containing protein of so far unknown function. it is synthesized as a glycosylated 75 kda precursor that undergoes limited proteolysis leading to a 28 kda n- and a 40 kda c-terminal fragment.200919706171
prevalence of renal anomalies after urinary tract infections in hospitalized infants less than 2 months of age.our aim was to determine the incidence of anatomical abnormalities after a urinary tract infection (uti) in infants <2 months of age hospitalized in the neonatal intensive care unit (nicu).201019812586
prevalence of renal anomalies after urinary tract infections in hospitalized infants less than 2 months of age.our aim was to determine the incidence of anatomical abnormalities after a urinary tract infection (uti) in infants <2 months of age hospitalized in the neonatal intensive care unit (nicu).201019812586
organic acid production in vitro and plant growth promotion in maize under controlled environment by phosphate-solubilizing fluorescent pseudomonas.phosphorus deficiency is a major constraint to crop production due to rapid binding of the applied phosphorus into fixed forms not available to the plants. microbial solubilization of inorganic phosphates has been attributed mainly to the production of organic acids. phosphate-solubilizing microorganisms enhance plant growth under conditions of poor phosphorus availability by solubilizing insoluble phosphates in the soil. this paper describes the production of organic acids during inorganic phos ...200919698133
health-care associated infections rates, length of stay, and bacterial resistance in an intensive care unit of morocco: findings of the international nosocomial infection control consortium (inicc).most studies related to healthcare-associated infection (hai) were conducted in the developed countries. we sought to determine healthcare-associated infection rates, microbiological profile, bacterial resistance, length of stay (los), and extra mortality in one icu of a hospital member of the international infection control consortium (inicc) in morocco.200919811636
temperature-dependent expression of phzm and its regulatory genes lasi and ptsp in rhizosphere isolate pseudomonas sp. strain m18.pseudomonas sp. strain m18, an effective biological control agent isolated from the melon rhizosphere, has a genetic background similar to that of the opportunistic human pathogen pseudomonas aeruginosa pao1. however, the predominant phenazine produced by strain m18 is phenazine-1-carboxylic acid (pca) rather than pyocyanin (pyo); the quantitative ratio of pca to pyo is 105 to 1 at 28 degrees c in strain m18, while the ratio is 1 to 2 at 37 degrees c in strain pao1. we first provided evidence th ...200919717631
tonb-dependent transporters and their occurrence in cyanobacteria.different iron transport systems evolved in gram-negative bacteria during evolution. most of the transport systems depend on outer membrane localized tonb-dependent transporters (tbdts), a periplasma-facing tonb protein and a plasma membrane localized machinery (exbbd). so far, iron chelators (siderophores), oligosaccharides and polypeptides have been identified as substrates of tbdts. for iron transport, three uptake systems are defined: the lactoferrin/transferrin binding proteins, the porphyr ...200919821963
function-biased choice of additives for optimization of protein crystallization - the case of the putative thioesterase pa5185 from pseudomonas aeruginosa pao1.the crystal structure of pa5185, a putative thioesterase from pseudomonas aeruginosa strain pao1, was solved using multi-wavelength anomalous diffraction to 2.4 a. analysis of the structure and information about the putative function of the protein were used to optimize crystallization conditions. the crystal growth was optimized by applying additives with chemical similarity to a fragment of a putative pa5185 substrate (coa or its derivative). using new crystallization conditions containing thi ...200819898606
novel insights about class 2 integrons from experimental and genomic order to contribute to the knowledge of the architecture and epidemiology of class 2 integrons, we performed a class 2 integron molecular survey in which we analyzed 726 isolates in two bacterial populations from environmental and nonepidemiologically related clinical samples, respectively, collected from 1982 to 2007. we recovered the inti2 gene from 130 of 726 isolates, most of which were clinical isolates, and only 1 (a psychrophilic pseudomonas sp.) was from a water sample. unlike the wid ...201019917745
the vaginal bacterial communities of japanese women resemble those of women in other racial determine whether different racial groups shared common types of vaginal microbiota, we characterized the composition and structure of vaginal bacterial communities in asymptomatic and apparently healthy japanese women in tokyo, japan, and compared them with those of white and black women from north america. the composition of vaginal communities was compared based on community profiles of terminal restriction fragments of 16s rrna genes and phylogenetic analysis of cloned 16s rrna gene seque ...201019912342
the vaginal bacterial communities of japanese women resemble those of women in other racial determine whether different racial groups shared common types of vaginal microbiota, we characterized the composition and structure of vaginal bacterial communities in asymptomatic and apparently healthy japanese women in tokyo, japan, and compared them with those of white and black women from north america. the composition of vaginal communities was compared based on community profiles of terminal restriction fragments of 16s rrna genes and phylogenetic analysis of cloned 16s rrna gene seque ...201019912342
crystal structure and functional analysis of the extradiol dioxygenase lapb from a long-chain alkylphenol degradation pathway in pseudomonas.lapb is a non-heme fe(ii)-dependent 2,3-dioxygenase that catalyzes the second step of a long-chain alkylphenol (lap) degradation pathway in pseudomonas sp. kl28 and belongs to the superfamily of type i extradiol dioxygenases. in this study, the crystal structures of substrate-free lapb and its complexes with a substrate or product were determined, along with a functional analysis of the active site residues. structural features of the homotetramer are similar to those of other type i extradiol d ...200919828456
electron transfer in the complex of membrane-bound human cytochrome p450 3a4 with the flavin domain of p450bm-3: the effect of oligomerization of the heme protein and intermittent modulation of the spin equilibrium.we studied the kinetics of nadph-dependent reduction of human cyp3a4 incorporated into nanodiscs (cyp3a4-nd) and proteoliposomes in order to probe the effect of p450 oligomerization on its reduction. the flavin domain of cytochrome p450-bm3 (bmr) was used as a model electron donor partner. unlike cyp3a4 oligomers, where only 50% of the enzyme was shown to be reducible by bmr, cyp3a4-nd could be reduced almost completely. high reducibility was also observed in proteoliposomes with a high lipid-to ...201020026040
electron transfer in the complex of membrane-bound human cytochrome p450 3a4 with the flavin domain of p450bm-3: the effect of oligomerization of the heme protein and intermittent modulation of the spin equilibrium.we studied the kinetics of nadph-dependent reduction of human cyp3a4 incorporated into nanodiscs (cyp3a4-nd) and proteoliposomes in order to probe the effect of p450 oligomerization on its reduction. the flavin domain of cytochrome p450-bm3 (bmr) was used as a model electron donor partner. unlike cyp3a4 oligomers, where only 50% of the enzyme was shown to be reducible by bmr, cyp3a4-nd could be reduced almost completely. high reducibility was also observed in proteoliposomes with a high lipid-to ...201020026040
early and late onset sepsis in late preterm infants.preterm birth is increasing worldwide, and late preterm births, which comprise more than 70% of all preterm births, account for much of the increase. early and late onset sepsis results in significant mortality in extremely preterm infants, but little is known about sepsis outcomes in late preterm infants.200919953725
structure and ligand binding properties of the epoxidase component of styrene monooxygenase .styrene monooxygenase (smo) is a two-component flavoprotein monooxygenase that transforms styrene to styrene oxide in the first step of the styrene catabolic and detoxification pathway of pseudomonas putida s12. the crystal structure of the n-terminally histidine-tagged epoxidase component of this system, nsmoa, determined to 2.3 a resolution, indicates the enzyme exists as a homodimer in which each monomer forms two distinct domains. the overall architecture is most similar to that of p-hydroxy ...201020055497
studies on the mechanism of p-hydroxyphenylacetate 3-hydroxylase from pseudomonas aeruginosa: a system composed of a small flavin reductase and a large flavin-dependent oxygenase.there are two known types of microbial two-component flavin-dependent monooxygenases that catalyze oxygenation of p-hydroxyphenylacetate (hpa), and they are distinguished by having structurally distinct reductases and oxygenases. this paper presents a detailed analysis of the properties of the enzyme from pseudomonas aeruginosa, an example of one group, and compares its properties to those published for the acinetobacter baumannii enzyme, an example of the alternative group. the reductase and ox ...201020000468
antifungal activity of selected indigenous pseudomonas and bacillus from the soybean rhizosphere.the purpose of this study was to isolate and select indigenous soil pseudomonas and bacillus bacteria capable of developing multiple mechanisms of action related to the biocontrol of phytopathogenic fungi affecting soybean crops. the screening procedure consisted of antagonism tests against a panel of phytopathogenic fungi, taxonomic identification, detection by pcr of several genes related to antifungal activity, in vitro detection of the antifungal products, and root colonization assays. two i ...200920016811
new structural and functional defects in polyphosphate deficient bacteria: a cellular and proteomic study.inorganic polyphosphate (polyp), a polymer of tens or hundreds of phosphate residues linked by atp-like bonds, is found in all organisms and performs a wide variety of functions. polyp is synthesized in bacterial cells by the actions of polyphosphate kinases (ppk1 and ppk2) and degraded by exopolyphosphatase (ppx). bacterial cells with polyp deficiencies due to knocking out the ppk1 gene are affected in many structural and important cellular functions such as motility, quorum sensing, biofilm fo ...201020067623
anthranilate-activating modules from fungal nonribosomal peptide assembly lines.fungal natural products containing benzodiazepinone- and quinazolinone-fused ring systems can be assembled by nonribosomal peptide synthetases (nrps) using the conformationally restricted beta-amino acid anthranilate as one of the key building blocks. we validated that the first module of the acetylaszonalenin synthetase of neosartorya fischeri nrrl 181 activates anthranilate to anthranilyl-amp. with this as a starting point, we then used bioinformatic predictions about fungal adenylation domain ...201020225828
annual variations in the diversity, viability, and origin of airborne bacteria.the presence of bacteria in aerosols has been known for centuries, but information on their identity and role in dispersing microbial traits is still limited. this study monitored the airborne bacterial community during an annual survey using samples collected from a 25-m tower near the baltic sea coast. the number of cfu was estimated using agar plates while the most probable number (mpn) of viable bacteria was estimated using dilution-to-extinction culturing assays (dcas). the mpn and cfu valu ...201020228096
a novel hydrolytic dehalogenase for the chlorinated aromatic compound chlorothalonil.dehalogenases play key roles in the detoxification of halogenated aromatics. interestingly, only one hydrolytic dehalogenase for halogenated aromatics, 4-chlorobenzoyl-coenzyme a (coa) dehalogenase, has been reported. here, we characterize another novel hydrolytic dehalogenase for a halogenated aromatic compound from the 2,4,5,6-tetrachloroisophthalonitrile (chlorothalonil)-degrading strain of pseudomonas sp. ctn-3, which we have named chd. chd catalyzes a hydroxyl substitution at the 4-chlorine ...201020363940
bacterial community dynamics during the application of a myxococcus xanthus-inoculated culture medium used for consolidation of ornamental this study, we investigated under laboratory conditions the bacterial communities inhabiting quarry and decayed ornamental carbonate stones before and after the application of a myxococcus xanthus-inoculated culture medium used for consolidation of the stones. the dynamics of the community structure and the prevalence of the inoculated bacterium, m. xanthus, were monitored during the time course of the consolidation treatment (30 days). for this purpose, we selected a molecular strategy combi ...201020393845
phenolic acids act as signaling molecules in plant-microbe symbioses.phenolic acids are the main polyphenols made by plants. these compounds have diverse functions and are immensely important in plant-microbe interactions/symbiosis. phenolic compounds act as signaling molecules in the initiation of legumerhizobia symbioses, establishment of arbuscular mycorrhizal symbioses and can act as agents in plant defense. flavonoids are a diverse class of polyphenolic compounds that have received considerable attention as signaling molecules involved in plant-microbe inter ...201020400851
unique extracellular matrix heparan sulfate from the bivalve nodipecten nodosus (linnaeus, 1758) safely inhibits arterial thrombosis after photochemically induced endothelial lesion.heparin-like glycans with diverse disaccharide composition and high anticoagulant activity have been described in several families of marine mollusks. the present work focused on the structural characterization of a new heparan sulfate (hs)-like polymer isolated from the mollusk nodipecten nodosus (linnaeus, 1758) and on its anticoagulant and antithrombotic properties. total glycans were extracted from the mollusk and fractionated by ethanol precipitation. the main component (>90%) was identifie ...201020053999
mycobacterium tuberculosis nucleoid-associated dna-binding protein h-ns binds with high-affinity to the holliday junction and inhibits strand exchange promoted by reca protein.a number of studies have shown that the structure and composition of bacterial nucleoid influences many a processes related to dna metabolism. the nucleoid-associated proteins modulate not only the dna conformation but also regulate the dna metabolic processes such as replication, recombination, repair and transcription. understanding of how these processes occur in the context of mycobacterium tuberculosis nucleoid is of considerable medical importance because the nucleoid structure may be cons ...201020176569
kinetic and structural characterization of a heterohexamer 4-oxalocrotonate tautomerase from chloroflexus aurantiacus j-10-fl: implications for functional and structural diversity in the tautomerase superfamily .4-oxalocrotonate tautomerase (4-ot) isozymes play prominent roles in the bacterial utilization of aromatic hydrocarbons as sole carbon sources. these enzymes catalyze the conversion of 2-hydroxy-2,4-hexadienedioate (or 2-hydroxymuconate) to 2-oxo-3-hexenedioate, where pro-1 functions as a general base and shuttles a proton from the 2-hydroxyl group of the substrate to the c-5 position of the product. 4-ot, a homohexamer from pseudomonas putida mt-2, is the most extensively studied 4-ot isozyme a ...201020465238
bacteriological study of aerobic isolates from plantar ulcers of paucibacillary leprosy patients.plantar ulcers commonly occur in leprosy patients, which usually recur and cause morbidity in such cases.201020418976
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