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Sample records for 5-phosphoribosyl 1-pyrophosphate prpp

  1. Hydrophilic-interaction liquid chromatography-tandem mass spectrometric determination of erythrocyte 5-phosphoribosyl 1-pyrophosphate in patients with hypoxanthine-guanine phosphoribosyltransferase deficiency.

    PubMed

    Hasegawa, Hiroshi; Shinohara, Yoshihiko; Nozaki, Sayako; Nakamura, Makiko; Oh, Koei; Namiki, Osamu; Suzuki, Kiyotaka; Nakahara, Akihiko; Miyazawa, Mari; Ishikawa, Ken; Himeno, Takahiro; Yoshida, Sayaka; Ueda, Takanori; Yamada, Yasukazu; Ichida, Kimiyoshi

    2015-01-22

    Mutations in the gene encoding hypoxanthine-guanine phosphoribosyltransferase (HPRT) cause Lesch-Nyhan disease (LND) and its variants (LNV). Due to the technical problems for measuring the HPRT activity in vitro, discordances between the residual HPRT activity and the clinical severity were found. 5-Phosphoribosyl 1-pyrophosphate (PRPP) is a substrate for HPRT. Since increased PRPP concentrations were observed in erythrocytes from patients with LND and LNV, we have turned our attention to erythrocyte PRPP as a biomarker for the phenotype classification. In the present work, a method for determination of PRPP concentration in erythrocyte was developed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) with multiple reaction monitoring (MRM). Packed erythrocyte samples were deproteinized by heating and the supernatants were injected into the LC-MS/MS system. All measurement results showed good precision with RSD <6%. PRPP concentrations of nine normal male subjects, four male patents with LND and six male patients with LNV were compared. The PRPP concentrations in erythrocyte from patients with LND were markedly increased compared with those from normal subjects, and those from patients with LNV were also increased but the degree was smaller than those with LND. The increase pattern of PRPP concentration in erythrocyte from patients with HPRT deficiency was consistent with the respective phenotypes and was correlated with the disease severity. PRPP concentration was suggested to give us supportive information for the diagnosis and the phenotype classification of LND and LNV.

  2. Biochemical characterization of the Mycobacterium tuberculosis phosphoribosyl-1-pyrophosphate synthetase

    PubMed Central

    Alderwick, Luke J; Lloyd, Georgina S; Lloyd, Adrian J; Lovering, Andrew L; Eggeling, Lothar; Besra, Gurdyal S

    2011-01-01

    Mycobacterium tuberculosis arabinogalactan (AG) is an essential cell wall component. It provides a molecular framework serving to connect peptidoglycan to the outer mycolic acid layer. The biosynthesis of the arabinan domains of AG and lipoarabinomannan (LAM) occurs via a combination of membrane bound arabinofuranosyltransferases, all of which utilize decaprenol-1-monophosphorabinose as a substrate. The source of arabinose ultimately destined for deposition into cell wall AG or LAM originates exclusively from phosphoribosyl-1-pyrophosphate (pRpp), a central metabolite which is also required for other essential metabolic processes, such as de novo purine and pyrimidine biosyntheses. In M. tuberculosis, a single pRpp synthetase enzyme (Mt-PrsA) is solely responsible for the generation of pRpp, by catalyzing the transfer of pyrophosphate from ATP to the C1 hydroxyl position of ribose-5-phosphate. Here, we report a detailed biochemical and biophysical study of Mt-PrsA, which exhibits the most rapid enzyme kinetics reported for a pRpp synthetase. PMID:21045009

  3. Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance.

    PubMed

    Hove-Jensen, Bjarne; Andersen, Kasper R; Kilstrup, Mogens; Martinussen, Jan; Switzer, Robert L; Willemoës, Martin

    2017-03-01

    Phosphoribosyl diphosphate (PRPP) is an important intermediate in cellular metabolism. PRPP is synthesized by PRPP synthase, as follows: ribose 5-phosphate + ATP → PRPP + AMP. PRPP is ubiquitously found in living organisms and is used in substitution reactions with the formation of glycosidic bonds. PRPP is utilized in the biosynthesis of purine and pyrimidine nucleotides, the amino acids histidine and tryptophan, the cofactors NAD and tetrahydromethanopterin, arabinosyl monophosphodecaprenol, and certain aminoglycoside antibiotics. The participation of PRPP in each of these metabolic pathways is reviewed. Central to the metabolism of PRPP is PRPP synthase, which has been studied from all kingdoms of life by classical mechanistic procedures. The results of these analyses are unified with recent progress in molecular enzymology and the elucidation of the three-dimensional structures of PRPP synthases from eubacteria, archaea, and humans. The structures and mechanisms of catalysis of the five diphosphoryltransferases are compared, as are those of selected enzymes of diphosphoryl transfer, phosphoryl transfer, and nucleotidyl transfer reactions. PRPP is used as a substrate by a large number phosphoribosyltransferases. The protein structures and reaction mechanisms of these phosphoribosyltransferases vary and demonstrate the versatility of PRPP as an intermediate in cellular physiology. PRPP synthases appear to have originated from a phosphoribosyltransferase during evolution, as demonstrated by phylogenetic analysis. PRPP, furthermore, is an effector molecule of purine and pyrimidine nucleotide biosynthesis, either by binding to PurR or PyrR regulatory proteins or as an allosteric activator of carbamoylphosphate synthetase. Genetic analyses have disclosed a number of mutants altered in the PRPP synthase-specifying genes in humans as well as bacterial species.

  4. Implementation of the PR&PP methodology: the role of formal expert elicitations

    SciTech Connect

    Pilat, Joseph F

    2010-01-01

    The application of the methodology developed by the GenIV International Forum's (GIF's) Proliferation Resistance and Physical Protection (PR&PP) Working Group is an expert elicitation. Although the framework of the methodology is structured and systematic, it does not by itself constitute or require a formal elicitation. However, formal elicitation can be utilized in the PR&PP context to provide a systematic, credible and transparent qualitative analysis and develop input for quantitative analyses. This section provides an overview of expert elicitations, a discussion of the role formal expert elicitations can play in the PR&PP methodology, an outline of the formal expert elicitation process and a brief practical guide to conducting formal expert elicitations. Expert elicitation is a process utilizing knowledgeable people in cases, for example, when an assessment is needed but physically based data is absent or open to interpretation. More specifically, it can be used to: (1) predict future events; (2) provide estimates on new, rare, complex or poorly understood phenomena; (3) integrate or interpret existing information; or (4) determine what is currently known, how well it is known or what is worth learning in a field. Expert elicitation can be informal or formal. The informal application of expert judgment is frequently used. Although it can produce good results, it often provides demonstrably biased or otherwise flawed answers to problems. This along with the absence of transparency can result in a loss of confidence when experts speak on issues. More formal expert elicitation is a structured process that makes use of people knowledgeable in certain areas to make assessments. The reason for advocating formal use is that the quality and accuracy of expert judgment comes from the completeness of the expert's understanding of the phenomena and the process used to elicit and analyze the data. The use of a more formal process to obtain, lU1derstand and analyze expert

  5. Very High-Temperature Reactor (VHTR) Proliferation Resistance and Physical Protection (PR&PP)

    SciTech Connect

    Moses, David Lewis

    2011-10-01

    This report documents the detailed background information that has been compiled to support the preparation of a much shorter white paper on the design features and fuel cycles of Very High-Temperature Reactors (VHTRs), including the proposed Next-Generation Nuclear Plant (NGNP), to identify the important proliferation resistance and physical protection (PR&PP) aspects of the proposed concepts. The shorter white paper derived from the information in this report was prepared for the Department of Energy Office of Nuclear Science and Technology for the Generation IV International Forum (GIF) VHTR Systems Steering Committee (SSC) as input to the GIF Proliferation Resistance and Physical Protection Working Group (PR&PPWG) (http://www.gen-4.org/Technology/horizontal/proliferation.htm). The short white paper was edited by the GIF VHTR SCC to address their concerns and thus may differ from the information presented in this supporting report. The GIF PR&PPWG will use the derived white paper based on this report along with other white papers on the six alternative Generation IV design concepts (http://www.gen-4.org/Technology/systems/index.htm) to employ an evaluation methodology that can be applied and will evolve from the earliest stages of design. This methodology will guide system designers, program policy makers, and external stakeholders in evaluating the response of each system, to determine each system's resistance to proliferation threats and robustness against sabotage and terrorism threats, and thereby guide future international cooperation on ensuring safeguards in the deployment of the Generation IV systems. The format and content of this report is that specified in a template prepared by the GIF PR&PPWG. Other than the level of detail, the key exception to the specified template format is the addition of Appendix C to document the history and status of coated-particle fuel reprocessing technologies, which fuel reprocessing technologies have yet to be deployed

  6. The effects of 1% pyrophosphate and 0.02% sodium fluoride on artificial caries lesions in vivo.

    PubMed

    Mellberg, J R; Petrou, I D; Deutchman, M; Grote, N

    1988-12-01

    We evaluated the potential of a pyrophosphate-fluoride solution to affect the remineralizing-demineralizing equilibrium, i.e., caries-inhibiting/-promoting effects on enamel in vivo. Fifteen subjects carried dentin blocks and enamel thin sections with artificial caries lesions in removable partial dentures for periods of two weeks, during which time they rinsed twice daily in a double-blind, randomized cross-over design with solutions containing (a) 90 ppm F, (b) 90 ppm F and 1% pyrophosphate, or (c) no active agents (placebo). A severe cariogenic challenge provided to the lesions by plaque under a stainless steel mesh cover resulted in the placebo-treated lesions losing 70.2% +/- 72.1% mineral. The pyrophosphate rinse with fluoride held the mineral loss to only 28.1 +/- 52.8%, while the fluoride rinse without pyrophosphate held the loss to 24.2 +/- 50.1%. The differences between the fluoride and placebo results were significant (p less than 0.01), but the difference between the two fluoride groups was not. A large amount of fluoride was deposited in the dentin lesions. In the surface layer, the concentration was increased from 1000 ppm F to more than 2300 ppm F by both fluoride treatments. The concentration of fluoride in both groups of fluoride-treated lesions further increased to more than 3500 ppm F in the approximate center of the lesion before declining in deeper layers toward the level found in the placebo-treated group. The findings from both mineral change and fluoride uptake phases of this study show that in the presence of 90 ppm F, 1% pyrophosphate did not promote demineralization of artificial caries lesions.

  7. Comprehensive X-Ray Structural Studies of the Quinolinate Phosphoribosyl Transferase (BNA6) From Saccharomyces Cerevisiae

    SciTech Connect

    di Luccio, E.; Wilson, D.K.

    2009-05-14

    Quinolinic acid phosphoribosyl transferase (QAPRTase, EC 2.4.2.19) is a 32 kDa enzyme encoded by the BNA6 gene in yeast and catalyzes the formation of nicotinate mononucleotide from quinolinate and 5-phosphoribosyl-1-pyrophosphate (PRPP). QAPRTase plays a key role in the tryptophan degradation pathway via kynurenine, leading to the de novo biosynthesis of NAD{sup +} and clearing the neurotoxin quinolinate. To improve our understanding of the specificity of the eukaryotic enzyme and the course of events associated with catalysis, we have determined the crystal structures of the apo and singly bound forms with the substrates quinolinate and PRPP. This reveals that the enzyme folds in a manner similar to that of various prokaryotic forms which are {approx}30% identical in sequence. In addition, the structure of the Michaelis complex is approximated by PRPP and the quinolinate analogue phthalate bound to the active site. These results allow insight into the kinetic mechanism of QAPRTase and provide an understanding of structural diversity in the active site of the Saccharomyces cerevisiae enzyme when compared to prokaryotic homologues.

  8. Effects of Sheng-Mai injection on the PRPP synthetase activity in BFU-es and CFU-es from bone marrows of mice with benzene-induced aplastic anemia.

    PubMed

    Liu, L P; Liu, J F; Lu, Y Q

    2001-08-10

    160 Kunming mice were divided at random into 3 groups. Group 1: normal control (40 mice). Group 2: aplastic anemia (AA) control (60 mice); benzene inhalation was carried out for 2.5 months and sterilized normal saline was injected i.p. for another 6 weeks. Group 3: treated AA (60 mice); benzene was administered by inhalation in a similar manner, Sheng-Mai Injection (SMI) was administered i.p. for 6 weeks after the AA models were established. SMI is a famous Chinese traditional prescription of Panax ginseng C.A. Meyer (0.1 g/ml), Ophiopogon japonicus (Thunb.) Ker-Gawl (0.312 g/ml) and Fructus Schisandrae (0.158 g/ml). Activities of phosphoribosylpyrophosphate (PRPP) synthetase in BFU-Es and CFU-Es were estimated by ion pair reversed phase HPLC (IPrHPLC). Accompanying the sharp drop in counts of erythroid progenitor cells, the PRPP synthetase activity in CFU-Es of AA mice was reduced significantly (P<0.01), whereas there were no remarkable changes of this enzyme activity in their BFU-Es compared with the control group. Both the counts of erythroid progenitor cells and PRPP synthetase activity in CFU-Es returned nearly to normal levels following treatment with SMI of mice in Group 3 (P<0.01). Our results suggest that the attenuation of PRPP synthetase activity in peripheral erythrocytes of AA patients may originate from the weakening of activity of this enzyme in CFU-Es from their bone marrow. The impairment of PRPP formation would explain ATP depletion and disorders of energy metabolism in AA erythrocytes. SMI can distinctly increase the reduced quantity of erythroid progenitor cells and promote rapid restoration of PRPP synthetase activity in CFU-Es of AA mice.

  9. Adenine phosphoribosyltransferase from Sulfolobus solfataricus is an enzyme with unusual kinetic properties and a crystal structure that suggests it evolved from a 6-oxopurine phosphoribosyltransferase.

    PubMed

    Jensen, Kaj Frank; Hansen, Michael Riis; Jensen, Kristine Steen; Christoffersen, Stig; Poulsen, Jens-Christian Navarro; Mølgaard, Anne; Kadziola, Anders

    2015-04-14

    The adenine phosphoribosyltransferase (APRTase) encoded by the open reading frame SSO2342 of Sulfolobus solfataricus P2 was subjected to crystallographic, kinetic, and ligand binding analyses. The enzyme forms dimers in solution and in the crystals, and binds one molecule of the reactants 5-phosphoribosyl-α-1-pyrophosphate (PRPP) and adenine or the product adenosine monophosphate (AMP) or the inhibitor adenosine diphosphate (ADP) in each active site. The individual subunit adopts an overall structure that resembles a 6-oxopurine phosphoribosyltransferase (PRTase) more than known APRTases implying that APRT functionality in Crenarchaeotae has its evolutionary origin in this family of PRTases. Only the N-terminal two-thirds of the polypeptide chain folds as a traditional type I PRTase with a five-stranded β-sheet surrounded by helices. The C-terminal third adopts an unusual three-helix bundle structure that together with the nucleobase-binding loop undergoes a conformational change upon binding of adenine and phosphate resulting in a slight contraction of the active site. The inhibitor ADP binds like the product AMP with both the α- and β-phosphates occupying the 5'-phosphoribosyl binding site. The enzyme shows activity over a wide pH range, and the kinetic and ligand binding properties depend on both pH and the presence/absence of phosphate in the buffers. A slow hydrolysis of PRPP to ribose 5-phosphate and pyrophosphate, catalyzed by the enzyme, may be facilitated by elements in the C-terminal three-helix bundle part of the protein.

  10. Biosynthesis of D-arabinose in mycobacteria - a novel bacterial pathway with implications for antimycobacterial therapy.

    PubMed

    Wolucka, Beata A

    2008-06-01

    Decaprenyl-phospho-arabinose (beta-D-arabinofuranosyl-1-O-monophosphodecaprenol), the only known donor of d-arabinose in bacteria, and its precursor, decaprenyl-phospho-ribose (beta-D-ribofuranosyl-1-O-monophosphodecaprenol), were first described in 1992. En route to D-arabinofuranose, the decaprenyl-phospho-ribose 2'-epimerase converts decaprenyl-phospho-ribose to decaprenyl-phospho-arabinose, which is a substrate for arabinosyltransferases in the synthesis of the cell-wall arabinogalactan and lipoarabinomannan polysaccharides of mycobacteria. The first step of the proposed decaprenyl-phospho-arabinose biosynthesis pathway in Mycobacterium tuberculosis and related actinobacteria is the formation of D-ribose 5-phosphate from sedoheptulose 7-phosphate, catalysed by the Rv1449 transketolase, and/or the isomerization of d-ribulose 5-phosphate, catalysed by the Rv2465 d-ribose 5-phosphate isomerase. d-Ribose 5-phosphate is a substrate for the Rv1017 phosphoribosyl pyrophosphate synthetase which forms 5-phosphoribosyl 1-pyrophosphate (PRPP). The activated 5-phosphoribofuranosyl residue of PRPP is transferred by the Rv3806 5-phosphoribosyltransferase to decaprenyl phosphate, thus forming 5'-phosphoribosyl-monophospho-decaprenol. The dephosphorylation of 5'-phosphoribosyl-monophospho-decaprenol to decaprenyl-phospho-ribose by the putative Rv3807 phospholipid phosphatase is the committed step of the pathway. A subsequent 2'-epimerization of decaprenyl-phospho-ribose by the heteromeric Rv3790/Rv3791 2'-epimerase leads to the formation of the decaprenyl-phospho-arabinose precursor for the synthesis of the cell-wall arabinans in Actinomycetales. The mycobacterial 2'-epimerase Rv3790 subunit is similar to the fungal D-arabinono-1,4-lactone oxidase, the last enzyme in the biosynthesis of D-erythroascorbic acid, thus pointing to an evolutionary link between the D-arabinofuranose- and L-ascorbic acid-related pathways. Decaprenyl-phospho-arabinose has been a lead compound for the

  11. Biochemical characterization of quinolinic acid phosphoribosyltransferase from Mycobacterium tuberculosis H37Rv and inhibition of its activity by pyrazinamide.

    PubMed

    Kim, Hyun; Shibayama, Keigo; Rimbara, Emiko; Mori, Shigetarou

    2014-01-01

    Quinolinic acid phosphoribosyltransferase (QAPRTase, EC 2.4.2.19) is a key enzyme in the de novo pathway of nicotinamide adenine dinucleotide (NAD) biosynthesis and a target for the development of new anti-tuberculosis drugs. QAPRTase catalyzes the synthesis of nicotinic acid mononucleotide from quinolinic acid (QA) and 5-phosphoribosyl-1-pyrophosphate (PRPP) through a phosphoribosyl transfer reaction followed by decarboxylation. The crystal structure of QAPRTase from Mycobacterium tuberculosis H37Rv (MtQAPRTase) has been determined; however, a detailed functional analysis of MtQAPRTase has not been published. Here, we analyzed the enzymatic activities of MtQAPRTase and determined the effect on catalysis of the anti-tuberculosis drug pyrazinamide (PZA). The optimum temperature and pH for MtQAPRTase activity were 60°C and pH 9.2. MtQAPRTase required bivalent metal ions and its activity was highest in the presence of Mg2+. Kinetic analyses revealed that the Km values for QA and PRPP were 0.08 and 0.39 mM, respectively, and the kcat values for QA and PRPP were 0.12 and 0.14 [s-1], respectively. When the amino acid residues of MtQAPRTase, which may interact with QA, were substituted with alanine residues, catalytic activity was undetectable. Further, PZA, which is an anti-tuberculosis drug and a structural analog of QA, markedly inhibited the catalytic activity of MtQAPRTase. The structure of PZA may provide the basis for the design of new inhibitors of MtQAPRTase. These findings provide new insights into the catalytic properties of MtQAPRTase.

  12. De novo purine biosynthesis by two pathways in Burkitt lymphoma cells and in human spleen.

    PubMed

    Reem, G H

    1972-05-01

    This study was designed to answer the question whether human lymphocytes and spleen cells were capable of de novo purine biosynthesis. Experiments were carried out in cell-free extracts prepared from human spleen, and from a cell line established from Burkitt lymphoma. Burkitt lymphoma cells and human spleen cells could synthesize the first and second intermediates of the purine biosynthetic pathway. Cell-free extracts of all cell lines studied contained the enzyme systems which catalyze the synthesis of phosphoribosyl-1-amine, the first intermediate unique to the purine biosynthetic pathway and of phosphoribosyl glycinamide, the second intermediate of this pathway. Phosphoribosyl-1-amine could be synthesized in cell-free extracts from alpha-5-phosphoribosyl-1-pyrophosphate (PRPP) and glutamine, from PRPP and ammonia, and by an alternative pathway, directly from ribose-5-phosphate and ammonia. These findings suggest that extrahepatic tissues may be an important source for the de novo synthesis of purine ribonucleotide in man. They also indicate that ammonia may play an important role in purine biosynthesis. The alternative pathway for the synthesis of phosphoribosyl-1-amine from ribose-5-phosphate and ammonia was found to be subject to inhibition by the end products of the purine synthetic pathway, particularly by adenylic acid and to a lesser degree by guanylic acid. The alternative pathway for phosphoribosyl-1-amine synthesis from ribose-5-phosphate and ammonia may contribute significantly towards the regulation of the rate of de novo purine biosynthesis in the normal state, in metabolic disorders in which purines are excessively produced and in myeloproliferative diseases.

  13. Phenolic amides are potent inhibitors of De Novo nucleotide biosynthesis

    DOE PAGES

    Pisithkul, Tippapha; Jacobson, Tyler B.; O'Brien, Thomas J.; ...

    2015-06-12

    An outstanding challenge toward efficient production of biofuels and value-added chemicals from plant biomass is the impact that lignocellulose-derived inhibitors have on microbial fermentations. Elucidating the mechanisms that underlie their toxicity is critical for developing strategies to overcome them. Here, using Escherichia coli as a model system, we investigated the metabolic effects and toxicity mechanisms of feruloyl amide and coumaroyl amide, the predominant phenolic compounds in ammonia-pretreated biomass hydrolysates. Using metabolomics, isotope tracers, and biochemical assays, we showed that these two phenolic amides act as potent and fast-acting inhibitors of purine and pyrimidine biosynthetic pathways. Feruloyl or coumaroyl amide exposuremore » leads to (i) a rapid buildup of 5-phosphoribosyl-1-pyrophosphate (PRPP), a key precursor in nucleotide biosynthesis, (ii) a rapid decrease in the levels of pyrimidine biosynthetic intermediates, and (iii) a long-term generalized decrease in nucleotide and deoxynucleotide levels. Tracer experiments using 13C-labeled sugars and [15N]ammonia demonstrated that carbon and nitrogen fluxes into nucleotides and deoxynucleotides are inhibited by these phenolic amides. We found that these effects are mediated via direct inhibition of glutamine amidotransferases that participate in nucleotide biosynthetic pathways. In particular, feruloyl amide is a competitive inhibitor of glutamine PRPP amidotransferase (PurF), which catalyzes the first committed step in de novo purine biosynthesis. Finally, external nucleoside supplementation prevents phenolic amide-mediated growth inhibition by allowing nucleotide biosynthesis via salvage pathways. Furthermore, the results presented here will help in the development of strategies to overcome toxicity of phenolic compounds and facilitate engineering of more efficient microbial producers of biofuels and chemicals.« less

  14. Phenolic Amides Are Potent Inhibitors of De Novo Nucleotide Biosynthesis

    PubMed Central

    Pisithkul, Tippapha; Jacobson, Tyler B.; O'Brien, Thomas J.; Stevenson, David M.

    2015-01-01

    An outstanding challenge toward efficient production of biofuels and value-added chemicals from plant biomass is the impact that lignocellulose-derived inhibitors have on microbial fermentations. Elucidating the mechanisms that underlie their toxicity is critical for developing strategies to overcome them. Here, using Escherichia coli as a model system, we investigated the metabolic effects and toxicity mechanisms of feruloyl amide and coumaroyl amide, the predominant phenolic compounds in ammonia-pretreated biomass hydrolysates. Using metabolomics, isotope tracers, and biochemical assays, we showed that these two phenolic amides act as potent and fast-acting inhibitors of purine and pyrimidine biosynthetic pathways. Feruloyl or coumaroyl amide exposure leads to (i) a rapid buildup of 5-phosphoribosyl-1-pyrophosphate (PRPP), a key precursor in nucleotide biosynthesis, (ii) a rapid decrease in the levels of pyrimidine biosynthetic intermediates, and (iii) a long-term generalized decrease in nucleotide and deoxynucleotide levels. Tracer experiments using 13C-labeled sugars and [15N]ammonia demonstrated that carbon and nitrogen fluxes into nucleotides and deoxynucleotides are inhibited by these phenolic amides. We found that these effects are mediated via direct inhibition of glutamine amidotransferases that participate in nucleotide biosynthetic pathways. In particular, feruloyl amide is a competitive inhibitor of glutamine PRPP amidotransferase (PurF), which catalyzes the first committed step in de novo purine biosynthesis. Finally, external nucleoside supplementation prevents phenolic amide-mediated growth inhibition by allowing nucleotide biosynthesis via salvage pathways. The results presented here will help in the development of strategies to overcome toxicity of phenolic compounds and facilitate engineering of more efficient microbial producers of biofuels and chemicals. PMID:26070680

  15. Phenolic amides are potent inhibitors of De Novo nucleotide biosynthesis

    SciTech Connect

    Pisithkul, Tippapha; Jacobson, Tyler B.; O'Brien, Thomas J.; Stevenson, David M.; Amador-Noguez, Daniel

    2015-06-12

    An outstanding challenge toward efficient production of biofuels and value-added chemicals from plant biomass is the impact that lignocellulose-derived inhibitors have on microbial fermentations. Elucidating the mechanisms that underlie their toxicity is critical for developing strategies to overcome them. Here, using Escherichia coli as a model system, we investigated the metabolic effects and toxicity mechanisms of feruloyl amide and coumaroyl amide, the predominant phenolic compounds in ammonia-pretreated biomass hydrolysates. Using metabolomics, isotope tracers, and biochemical assays, we showed that these two phenolic amides act as potent and fast-acting inhibitors of purine and pyrimidine biosynthetic pathways. Feruloyl or coumaroyl amide exposure leads to (i) a rapid buildup of 5-phosphoribosyl-1-pyrophosphate (PRPP), a key precursor in nucleotide biosynthesis, (ii) a rapid decrease in the levels of pyrimidine biosynthetic intermediates, and (iii) a long-term generalized decrease in nucleotide and deoxynucleotide levels. Tracer experiments using 13C-labeled sugars and [15N]ammonia demonstrated that carbon and nitrogen fluxes into nucleotides and deoxynucleotides are inhibited by these phenolic amides. We found that these effects are mediated via direct inhibition of glutamine amidotransferases that participate in nucleotide biosynthetic pathways. In particular, feruloyl amide is a competitive inhibitor of glutamine PRPP amidotransferase (PurF), which catalyzes the first committed step in de novo purine biosynthesis. Finally, external nucleoside supplementation prevents phenolic amide-mediated growth inhibition by allowing nucleotide biosynthesis via salvage pathways. Furthermore, the results presented here will help in the development of strategies to overcome toxicity of phenolic compounds and facilitate engineering of more efficient microbial producers of biofuels and chemicals.

  16. Structure of dimeric, recombinant Sulfolobus solfataricus phosphoribosyl diphosphate synthase: a bent dimer defining the adenine specificity of the substrate ATP.

    PubMed

    Andersen, Rune W; Leggio, Leila Lo; Hove-Jensen, Bjarne; Kadziola, Anders

    2015-03-01

    The enzyme 5-phosphoribosyl-1-α-diphosphate (PRPP) synthase (EC 2.7.6.1) catalyses the Mg(2+)-dependent transfer of a diphosphoryl group from ATP to the C1 hydroxyl group of ribose 5-phosphate resulting in the production of PRPP and AMP. A nucleotide sequence specifying Sulfolobus solfataricus PRPP synthase was synthesised in vitro with optimised codon usage for expression in Escherichia coli. Following expression of the gene in E. coli PRPP synthase was purified by heat treatment and ammonium sulphate precipitation and the structure of S. solfataricus PRPP synthase was determined at 2.8 Å resolution. A bent dimer oligomerisation was revealed, which seems to be an abundant feature among PRPP synthases for defining the adenine specificity of the substrate ATP. Molecular replacement was used to determine the S. solfataricus PRPP synthase structure with a monomer subunit of Methanocaldococcus jannaschii PRPP synthase as a search model. The two amino acid sequences share 35 % identity. The resulting asymmetric unit consists of three separated dimers. The protein was co-crystallised in the presence of AMP and ribose 5-phosphate, but in the electron density map of the active site only AMP and a sulphate ion were observed. Sulphate ion, reminiscent of the ammonium sulphate precipitation step of the purification, seems to bind tightly and, therefore, presumably occupies and blocks the ribose 5-phosphate binding site. The activity of S. solfataricus PRPP synthase is independent of phosphate ion.

  17. Crystal structure of human nicotinic acid phosphoribosyltransferase.

    PubMed

    Marletta, Ada Serena; Massarotti, Alberto; Orsomando, Giuseppe; Magni, Giulio; Rizzi, Menico; Garavaglia, Silvia

    2015-01-01

    Nicotinic acid phosphoribosyltransferase (EC 2.4.2.11) (NaPRTase) is the rate-limiting enzyme in the three-step Preiss-Handler pathway for the biosynthesis of NAD. The enzyme catalyzes the conversion of nicotinic acid (Na) and 5-phosphoribosyl-1-pyrophosphate (PRPP) to nicotinic acid mononucleotide (NaMN) and pyrophosphate (PPi). Several studies have underlined the importance of NaPRTase for NAD homeostasis in mammals, but no crystallographic data are available for this enzyme from higher eukaryotes. Here, we report the crystal structure of human NaPRTase that was solved by molecular replacement at a resolution of 2.9 Å in its ligand-free form. Our structural data allow the assignment of human NaPRTase to the type II phosphoribosyltransferase subfamily and reveal that the enzyme consists of two domains and functions as a dimer with the active site located at the interface of the monomers. The substrate-binding mode was analyzed by molecular docking simulation and provides hints into the catalytic mechanism. Moreover, structural comparison of human NaPRTase with the other two human type II phosphoribosyltransferases involved in NAD biosynthesis, quinolinate phosphoribosyltransferase and nicotinamide phosphoribosyltransferase, reveals that while the three enzymes share a conserved overall structure, a few distinctive structural traits can be identified. In particular, we show that NaPRTase lacks a tunnel that, in nicotinamide phosphoribosiltransferase, represents the binding site of its potent and selective inhibitor FK866, currently used in clinical trials as an antitumoral agent.

  18. Crystal structure of human nicotinic acid phosphoribosyltransferase

    PubMed Central

    Marletta, Ada Serena; Massarotti, Alberto; Orsomando, Giuseppe; Magni, Giulio; Rizzi, Menico; Garavaglia, Silvia

    2015-01-01

    Nicotinic acid phosphoribosyltransferase (EC 2.4.2.11) (NaPRTase) is the rate-limiting enzyme in the three-step Preiss–Handler pathway for the biosynthesis of NAD. The enzyme catalyzes the conversion of nicotinic acid (Na) and 5-phosphoribosyl-1-pyrophosphate (PRPP) to nicotinic acid mononucleotide (NaMN) and pyrophosphate (PPi). Several studies have underlined the importance of NaPRTase for NAD homeostasis in mammals, but no crystallographic data are available for this enzyme from higher eukaryotes. Here, we report the crystal structure of human NaPRTase that was solved by molecular replacement at a resolution of 2.9 Å in its ligand-free form. Our structural data allow the assignment of human NaPRTase to the type II phosphoribosyltransferase subfamily and reveal that the enzyme consists of two domains and functions as a dimer with the active site located at the interface of the monomers. The substrate-binding mode was analyzed by molecular docking simulation and provides hints into the catalytic mechanism. Moreover, structural comparison of human NaPRTase with the other two human type II phosphoribosyltransferases involved in NAD biosynthesis, quinolinate phosphoribosyltransferase and nicotinamide phosphoribosyltransferase, reveals that while the three enzymes share a conserved overall structure, a few distinctive structural traits can be identified. In particular, we show that NaPRTase lacks a tunnel that, in nicotinamide phosphoribosiltransferase, represents the binding site of its potent and selective inhibitor FK866, currently used in clinical trials as an antitumoral agent. PMID:26042198

  19. Crystallization and preliminary X-ray diffraction study of phosphoribosyl pyrophosphate synthetase from E. Coli

    SciTech Connect

    Timofeev, V. I. Abramchik, Yu. A. Zhukhlistova, N. E. Kuranova, I. P.

    2015-09-15

    Enzymes of the phosphoribosyl pyrophosphate synthetase family (PRPPS, EC 2.7.6.1) catalyze the formation of 5-phosphoribosyl pyrophosphate (5-PRPP) from adenosine triphosphate and ribose 5-phosphate. 5-Phosphoribosyl pyrophosphate is an important intermediate in the synthesis of purine, pyrimidine, and pyridine nucleotides, as well as of the amino acids histidine and tryptophan. The crystallization conditions for E. coli PRPPS were found by the vapor-diffusion technique and were optimized to apply the capillary counter-diffusion technique. The X-ray diffraction data set was collected from the crystals grown by the counter-diffusion technique using a synchrotron radiation source to 3.1-Å resolution. The crystals of PRPPS belong to sp. gr. P6{sub 3}22 and have the following unit-cell parameters: a = b = 104.44 Å, c = 124.98 Å, α = β = 90°, γ = 120°. The collected X-ray diffraction data set is suitable for the solution of the three-dimensional structure of PRPPS at 3.1-Å resolution.

  20. Crystallization and preliminary X-ray diffraction study of phosphoribosyl pyrophosphate synthetase from E. Coli

    NASA Astrophysics Data System (ADS)

    Timofeev, V. I.; Abramchik, Yu. A.; Zhukhlistova, N. E.; Kuranova, I. P.

    2015-09-01

    Enzymes of the phosphoribosyl pyrophosphate synthetase family (PRPPS, EC 2.7.6.1) catalyze the formation of 5-phosphoribosyl pyrophosphate (5-PRPP) from adenosine triphosphate and ribose 5-phosphate. 5-Phosphoribosyl pyrophosphate is an important intermediate in the synthesis of purine, pyrimidine, and pyridine nucleotides, as well as of the amino acids histidine and tryptophan. The crystallization conditions for E. coli PRPPS were found by the vapor-diffusion technique and were optimized to apply the capillary counter-diffusion technique. The X-ray diffraction data set was collected from the crystals grown by the counter-diffusion technique using a synchrotron radiation source to 3.1-Å resolution. The crystals of PRPPS belong to sp. gr. P6322 and have the following unit-cell parameters: a = b = 104.44 Å, c = 124.98 Å, α = β = 90°, γ = 120°. The collected X-ray diffraction data set is suitable for the solution of the three-dimensional structure of PRPPS at 3.1-Å resolution.

  1. Implications for advanced safeguards derived from PR&PP case study results

    SciTech Connect

    Boyer, Brian D

    2009-01-01

    The proliferation resistance and physical protection (PR and PP) working group produced a case study on the Example Sodium Fast Reactor (ESFR). The ESFR is a hypothetical nuclear energy system consisting of four sodium-cooled fast reactors of medium size collocated with an on-site dry fuel storage facility and a spent fuel reprocessing facility using pyroprocessing technology. This study revealed how safeguards would be applied at such site consisting of integrated multiple fuel cycle facilities and the implications of what safeguards technology and safeguards concepts would need to be adapted and developed to safeguard successfully this Generation IV nuclear energy system concept. The major safeguards concepts driving our safeguards analysis are timeliness goals and material quantity goals. Because the fresh transuranic (TRU) fuel to be produced in the ESFR fuel fabrication facility contains plutonium, the ESFR will be reprocessing, using in the reactor, and storing material on site that will have IAEA defined 'direct-use material' in it with stringent timeliness goals and material quantity goals that drive the safeguards implementation. Specifically, the TRU fresh fuel, pyroprocessing in process material, LWR spent fuel sent to the ESFR, and TRU spent fuel will contain plutonium. This material will need to be verified at interim intervals four times per year because the irradiated direct-use material, as defined previously, has three-month timeliness goals and 8 kg material quantity goals for plutonium. The TRU in-process material is, of course, irradiated direct-use material as defined by the IAEA. Keeping the plutonium and uranium together with TRu products should provide a radiation barrier. this radiation barrier slows down the ability to reprocess the fuel. Furthermore, the reprocessing technique, if it has some intrinsic proliferation resistance, will need major modifications to be able to separate plutonium from the uranium and TRU mixture. The ESFR design should have such features in it if it is seen to have intrinsic proliferation resistance. The technical difficulty in diverting material from the ESFR is at least as strongly impacted by the adversaries overall technical capabilities as it is by the effort required to overcome those barriers intrinsic to the nuclear fuel cycle. The intrinsic proliferation resistance of the ESFR will affect how extrinsic measures in the safeguards approach for the ESFR will provide overall proliferation resistance.

  2. A Qualitative Assessment of Diversion Scenarios for an Example Sodium Fast Reactor Using the GEN IV PR&PP Methodology

    SciTech Connect

    Zentner, Michael D.; Coles, Garill A.; Therios, Ike

    2012-01-20

    FAST REACTORS;NUCLEAR ENERGY;NUCLEAR MATERIALS MANAGEMENT;PROLIFERATION;SAFEGUARDS;THEFT; A working group was created in 2002 by the Generation IV International Forum (GIF) for the purpose of developing an internationally accepted methodology for assessing the Proliferation Resistance of a nuclear energy system (NES) and its individual elements. A two year case study is being performed by the experts group using this methodology to assess the proliferation resistance of a hypothetical NES called the Example Sodium Fast Reactor (ESFR). This work demonstrates how the PR and PP methodology can be used to provide important information at various levels of details to NES designers, safeguard administrators and decision makers. The study analyzes the response of the complete ESFR nuclear energy system to different proliferation and theft strategies. The challenges considered include concealed diversion, concealed misuse and 'break out' strategies. This paper describes the work done in performing a qualitative assessment of concealed diversion scenarios from the ESFR.

  3. Pathway Aggregation in the Risk Assessment of Proliferation Resistance and Physical Protection (PR&PP) of Nuclear Energy Systems

    SciTech Connect

    Aldemir, Tunc; Denning, Richard; Catalyurek, Umit; Yilmaz, Alper; Yue, Meng; Cheng, Lap-Yan

    2015-01-23

    The framework for Proliferation Resistance and Physical Protection (PR & PP) evaluation is to define a set of challenges, to obtain the system responses, and to assess the outcomes. The assessment of outcomes heavily relies on pathways, defined as sequences of events or actions that could potentially be followed by a State or a group of individuals in order to achieve a proliferation objective, with the defined threats as initiating events. There may be large number of segments connecting pathway stages (e.g. acquisition, processing, and fabrication for PR) which can lead to even larger number of pathways or scenarios through possible different combinations of segment connections, each with associated probabilities contributing to the overall risk. Clustering of these scenarios in specified stage attribute intervals is important for their tractable analysis and outcome assessment. A software tool for scenario generation and clustering (OSUPR) is developed that utilizes the PRCALC code developed at the Brookhaven National Laboratory for scenario generation and the K- means, mean shift and adaptive mean shift algorithms as possible clustering schemes. The results of the study using the Example Sodium Fast Breeder as an example system show that clustering facilitates the probabilistic or deterministic analysis of scenarios to identify system vulnerabilities and communication of the major risk contributors to stakeholders. The results of the study also show that the mean shift algorithm has the most potential for assisting the analysis of the scenarios generated by PRCALC.

  4. Crystal structures of Toxoplasma gondii uracil phosphoribosyltransferase reveal the atomic basis of pyrimidine discrimination and prodrug binding.

    PubMed Central

    Schumacher, M A; Carter, D; Scott, D M; Roos, D S; Ullman, B; Brennan, R G

    1998-01-01

    Uracil phosphoribosyltransferase (UPRTase) catalyzes the transfer of a ribosyl phosphate group from alpha-D-5-phosphoribosyl-1-pyrophosphate to the N1 nitrogen of uracil. The UPRTase from the opportunistic pathogen Toxoplasma gondii is a rational target for antiparasitic drug design. To aid in structure-based drug design studies against toxoplasmosis, the crystal structures of the T.gondii apo UPRTase (1.93 A resolution), the UPRTase bound to its substrate, uracil (2.2 A resolution), its product, UMP (2.5 A resolution), and the prodrug, 5-fluorouracil (2.3 A resolution), have been determined. These structures reveal that UPRTase recognizes uracil through polypeptide backbone hydrogen bonds to the uracil exocyclic O2 and endocyclic N3 atoms and a backbone-water-exocyclic O4 oxygen hydrogen bond. This stereochemical arrangement and the architecture of the uracil-binding pocket reveal why cytosine and pyrimidines with exocyclic substituents at ring position 5 larger than fluorine, including thymine, cannot bind to the enzyme. Strikingly, the T. gondii UPRTase contains a 22 residue insertion within the conserved PRTase fold that forms an extended antiparallel beta-arm. Leu92, at the tip of this arm, functions to cap the active site of its dimer mate, thereby inhibiting the escape of the substrate-binding water molecule. PMID:9628859

  5. Targeted disruption of the mouse adenine phosphoribosyltransferase (aprt) gene and the production of APRT-deficient mice

    SciTech Connect

    Engle, S.J.; Chen, J.; Tischfield, J.A.

    1994-09-01

    Adenine phosphoribosyltransferase (APRT: EC 2.4.2.7), a ubiquitously expressed purine salvage enzyme, catalyzes the synthesis of AMP and inorganic pyrophosphate from existing adenine and 5-phosphoribosyl-1-pyrophosphate. Deficiency of this enzyme in humans results in the accumulation of 2,8-dihydroxyadenine leading to crystalluria and nephrolithiasis. In order to facilitate our study of this rare, autosomal recessive disorder, we applied the advances in gene targeting technology and mouse embryonic stem (ES) cell culture to the production of APRT-deficient mice. A positive-negative targeting strategy was used. The tageting vector contain 5.6 kb of the mouse APRT gene, a neomycin resistance gene in exon 3 as a positive selection marker, and a HSV thymidine kinase gene at the 3{prime} end of the homology as a negative selection marker. The vector was introduced into D3 ES cells by electroporation and the cells were selected for G418 and ganciclovir (GANC) resistance. G418-GANC resistant clones were screened by Southern blot. One of several correctly targeted clones was expanded and used for blastocyst microinjection to produce chimeric mice. Chimeric animals were bred and agouti progeny heterozygous for the targeted allele were obtained. Heterozygous animals have been bred to produce APRT-deficient animals. Matings are currently underway to determine the phenotype of APRT/HPRT-deficient animals.

  6. Small elevations of glucose concentration redirect and amplify the synthesis of guanosine 5'-triphosphate in rat islets.

    PubMed Central

    Metz, S A; Meredith, M; Rabaglia, M E; Kowluru, A

    1993-01-01

    Recent studies suggest a permissive requirement for guanosine 5'-triphosphate (GTP) in insulin release, based on the use of GTP synthesis inhibitors (such as myocophenolic acid) acting at inosine monophosphate (IMP) dehydrogenase; herein, we examine the glucose dependency of GTP synthesis. Mycophenolic acid inhibited insulin secretion equally well after islet culture at 7.8 or 11.1 mM glucose (51% inhibition) but its effect was dramatically attenuated when provided at < or = 6.4 mM glucose (13% inhibition; P < 0.001). These observations were explicable by a stimulation of islet GTP synthesis derived from IMP since, at high glucose: (a) total GTP content was augmented; (b) a greater decrement in GTP (1.75 vs. 1.05 pmol/islet) was induced by mycophenolic acid; and (c) a smaller "pool" of residual GTP persisted after drug treatment. Glucose also accelerated GTP synthesis from exogenous guanine ("salvage" pathway) and increased content of a pyrimidine, uridine 5'-triphosphate (UTP), suggesting that glucose augments production of a common regulatory intermediate (probably 5-phosphoribosyl-1-pyrophosphate). Pathway-specific radiolabeling studies confirmed that glucose tripled both salvage and de novo synthesis of nucleotides. We conclude that steep changes in the biosynthesis of cytosolic pools of GTP occur at modest changes in glucose concentrations, a finding which may have relevance to the adaptive (patho) physiologic responses of islets to changes in ambient glucose levels. PMID:8349822

  7. Aldolase as a Chirality Intersection of L-Amino Acids and D-Sugars

    NASA Astrophysics Data System (ADS)

    Munegumi, Toratane

    2015-06-01

    Aldolase plays an important role in glycolysis and gluconeogenesis to produce D-fructose-1,6-bisphosphate (D-FBP) from dihydroxyacetone phosphate (DHP) and D-glyceraldehyde-3-phosphate (D-GAP). This reaction is stereoselective and retains the D-GAP 2R configuration and yields D-FBP (with the configuration: 3S, 4S, 5R). The 3- and 4-position carbons are the newly formed chiral carbons because the 5-position carbon of D-FBP comes from the 2-position of D-GAP. Although four diastereomeric products, ( 3S, 4R, 5R), ( 3R, 4R, 5R), ( 3R, 4S, 5R), ( 3S, 4S, 5R), are expected in the nonenzymatic reaction, only the ( 3S, 4S, 5R) diastereomer (D-FBP) is obtained. Therefore, the chirality in the 3- and 4-positions is induced by the chirality of the enzyme composed of L-amino acid residues. D-Glucose-6-phosphate (D-G6P), which is generated from D-FBP in the gluconeogenesis pathway, produces D-ribose-5-phosphate (D-R5P) in the pentose phosphate pathway. D-R5P is converted to PRPP (5-phosphoribosyl-α-pyrophosphate), which is used for the de novo synthesis of nucleotides. Ribonucleic acid (RNA) uses the nucleotides as building blocks. The configurations of the 4R-carbon and of the 3S-carbon are retained. The stereochemical structure of RNA is based on 3S as well as 4R (D). The consideration above suggests that aldolase is a key enzyme that determines the 3S configuration in D-R5P. It is thus a chirality intersection between amino acids and sugars, because the sugar chirality is determined by the chiral environment of an L-amino acid protein, aldolase, to produce D-FBP.

  8. Glutamine-dependent carbamoyl-phosphate synthetase and other enzyme activities related to the pyrimidine pathway in spleen of Squalus acanthias (spiny dogfish).

    PubMed

    Anderson, P M

    1989-07-15

    The first two steps of urea synthesis in liver of marine elasmobranchs involve formation of glutamine from ammonia and of carbamoyl phosphate from glutamine, catalysed by glutamine synthetase and carbamoyl-phosphate synthetase, respectively [Anderson & Casey (1984) J. Biol. Chem. 259, 456-462]; both of these enzymes are localized exclusively in the mitochondrial matrix. The objective of this study was to establish the enzymology of carbamoyl phosphate formation and utilization for pyrimidine nucleotide biosynthesis in Squalus acanthias (spiny dogfish), a representative elasmobranch. Aspartate carbamoyltransferase could not be detected in liver of dogfish. Spleen extracts, however, had glutamine-dependent carbamoyl-phosphate synthetase, aspartate carbamoyltransferase, dihydro-orotase, and glutamine synthetase activities, all localized in the cytosol; dihydro-orotate dehydrogenase, orotate phosphoribosyltransferase, and orotidine-5'-decarboxylase activities were also present. Except for glutamine synthetase, the levels of all activities were very low. The carbamoyl-phosphate synthetase activity is inhibited by UTP and is activated by 5-phosphoribosyl 1-pyrophosphate. The first three enzyme activities of the pyrimidine pathway were eluted in distinctly different positions during gel filtration chromatography under a number of different conditions; although complete proteolysis of inter-domain regions of a multifunctional complex during extraction cannot be excluded, the evidence suggests that in dogfish, in contrast to mammalian species, these three enzymes of the pyrimidine pathway exist as individual polypeptide chains. These results: (1) establish that dogfish express two different glutamine-dependent carbamoyl-phosphate synthetase activities, (2) confirm the report [Smith, Ritter & Campbell (1987) J. Biol. Chem. 262, 198-202] that dogfish express two different glutamine synthetases, and (3) provide indirect evidence that glutamine may not be available in liver for

  9. Uracil salvage pathway in Lactobacillus plantarum: Transcription and genetic studies.

    PubMed

    Arsène-Ploetze, Florence; Nicoloff, Hervé; Kammerer, Benoît; Martinussen, Jan; Bringel, Françoise

    2006-07-01

    The uracil salvage pathway in Lactobacillus plantarum was demonstrated to be dependent on the upp-pyrP gene cluster. PyrP was the only high-affinity uracil transporter since a pyrP mutant no longer incorporated low concentrations of radioactively labeled uracil and had increased resistance to the toxic uracil analogue 5-fluorouracil. The upp gene encoded a uracil phosphoribosyltransferase (UPRT) enzyme catalyzing the conversion of uracil and 5-phosphoribosyl-alpha-1-pyrophosphate to UMP and pyrophosphate. Analysis of mutants revealed that UPRT is a major cell supplier of UMP synthesized from uracil provided by preformed nucleic acid degradation. In a mutant selection study, seven independent upp mutants were isolated and all were found to excrete low amounts of pyrimidines to the growth medium. Pyrimidine-dependent transcription regulation of the biosynthetic pyrimidine pyrR1-B-C-Aa1-Ab1-D-F-E operon was impaired in the upp mutants. Despite the fact that upp and pyrP are positioned next to each other on the chromosome, they are not cotranscribed. Whereas pyrP is expressed as a monocistronic message, the upp gene is part of the lp_2376-glyA-upp operon. The lp_2376 gene encodes a putative protein that belongs to the conserved protein family of translation modulators such as Sua5, YciO, and YrdC. The glyA gene encodes a putative hydroxymethyltransferase involved in C1 unit charging of tetrahydrofolate, which is required in the biosynthesis of thymidylate, pantothenate, and purines. Unlike upp transcription, pyrP transcription is regulated by exogenous pyrimidine availability, most likely by the same mechanism of transcription attenuation as that of the pyr operon.

  10. Identification, Heterologous Expression, and Functional Characterization of Bacillus subtilis YutF, a HAD Superfamily 5'-Nucleotidase with Broad Substrate Specificity

    PubMed Central

    Zakataeva, Natalia P.; Romanenkov, Dmitriy V.; Yusupova, Yuliya R.; Skripnikova, Victoria S.; Asahara, Takayuki; Gronskiy, Sergey V.

    2016-01-01

    5'-nucleotidases (EC 3.1.3.5) catalyze the hydrolytic dephosphorylation of 5'-ribonucleotides and 5'-deoxyribonucleotides as well as complex nucleotides, such as uridine 5'-diphosphoglucose (UDP-glucose), nicotinamide adenine dinucleotide and flavin adenine dinucleotide, to their corresponding nucleosides plus phosphate. These enzymes have been found in diverse species in intracellular and membrane-bound, surface-localized forms. Soluble forms of 5'-nucleotidases belong to the ubiquitous haloacid dehalogenase superfamily (HADSF) and have been shown to be involved in the regulation of nucleotide, nucleoside and nicotinamide adenine dinucleotide (NAD+) pools. Despite the important role of 5'-nucleotidases in cellular metabolism, only a few of these enzymes have been characterized in the Gram-positive bacterium Bacillus subtilis, the workhorse industrial microorganism included in the Food and Drug Administration’s GRAS (generally regarded as safe) list. In the present study, we report the identification of a novel 5'-nucleotidase gene from B. subtilis, yutF, which comprises 771 bp encoding a 256-amino-acid protein belonging to the IIA subfamily of the HADSF. The gene product is responsible for the major p-nitrophenyl phosphatase activity in B. subtilis. The yutF gene was overexpressed in Escherichia coli, and its product fused to a polyhistidine tag was purified and biochemically characterized as a soluble 5'-nucleotidase with broad substrate specificity. The recombinant YutF protein was found to hydrolyze various purine and pyrimidine 5'-nucleotides, showing preference for 5'-nucleoside monophosphates and, specifically, 5'-XMP. Recombinant YutF also exhibited phosphohydrolase activity toward nucleotide precursors, ribose-5-phosphate and 5-phosphoribosyl-1-pyrophosphate. Determination of the kinetic parameters of the enzyme revealed a low substrate specificity (Km values in the mM concentration range) and modest catalytic efficiencies with respect to substrates. An

  11. The Kinetics of Intramolecular Distribution of 15N in Uric Acid after Administration of [15N]Glycine A REAPPRAISAL OF THE SIGNIFICANCE OF PREFERENTIAL LABELING OF N-(3 + 9) OF URIC ACID IN PRIMARY GOUT

    PubMed Central

    Sperling, Oded; Wyngaarden, James B.; Starmer, C. Frank

    1973-01-01

    The concept of an abnormality of glutamine metabolism in primary gout was first proposed on the basis of isotope data: when [15N]glycine was administered to gouty subjects, there was disproportionately great enrichment of N-(3 + 9) of uric acid, which derive from the amide-N of glutamine. An unduly high concentration of 15N in glutamine was postulated, and attributed to a hypothetical defect in catabolism of glutamine. Excess glutamine was proposed as the driving force of uric acid overproduction. We have reexamined this proposition in four gouty subjects: one mild overproducer of uric acid with “idiopathic gout,” one marked overproducer with high-grade but “partial” hypoxanthine-guanine phosphoribosyl-transferase deficiency, and two extraordinary overproducers with superactive phosphoribosylpyrophosphate synthetases. In the last three, the driving force of excessive purine biosynthesis is a known surplus of α-5-phosphoribosyl-1-pyrophosphate. Disproportionately high labeling of N-(3 + 9) was present in all four gouty subjects, most marked in the most flamboyant overproducers. The precursor glucine pool was sampled by periodic administration of benzoic acid and isolation of urinary hippuric acid. Similarly, the precursor glutamine pool was sampled by periodic administration of phenylacetic acid and isolation of the amide-N of urinary phenylacetylglutamine. The time course of 15N enrichment of hippurate differed from that of the amide-N of glutamine. Whereas initial enrichment values of hippurate were very high, those of glutamine-amide-N were low, increasing to a maximum at about 3 h, and then declining less rapidly than those of hippurate. However, enrichment values of hippurate and of phenacetyl glutamine were normal in all of the gouty subjects studied. Thus, preferential enrichment of N-(3 + 9) in gouty overproducers given [15N]glycine does not necessarily reflect a specific abnormality of glutamine metabolism, but rather appears to be a kinetic

  12. DEVELOPMENT OF A METHODOLOGY TO ASSESS PROLIFERATION RESISTANCE AND PHYSICAL PROTECTION FOR GENERATION IV SYSTEMS

    SciTech Connect

    Nishimura, R.; Bari, R.; Peterson, P.; Roglans-Ribas, J.; Kalenchuk, D.

    2004-10-06

    Enhanced proliferation resistance and physical protection (PR&PP) is one of the technology goals for advanced nuclear concepts, such as Generation IV systems. Under the auspices of the Generation IV International Forum, the Office of Nuclear Energy, Science and Technology of the U.S. DOE, the Office of Nonproliferation Policy of the National Nuclear Security Administration, and participating organizations from six other countries are sponsoring an international working group to develop an evaluation methodology for PR&PP. This methodology will permit an objective PR&PP comparison between alternative nuclear systems (e.g., different reactor types or fuel cycles) and support design optimization to enhance robustness against proliferation, theft and sabotage. The paper summarizes the proposed assessment methodology including the assessment framework, measures used to express the PR&PP characteristics of the system, threat definition, system element and target identification, pathway identification and analysis, and estimation of the measures.

  13. Transcriptome analysis guided metabolic engineering of Bacillus subtilis for riboflavin production.

    PubMed

    Shi, Shuobo; Chen, Tao; Zhang, Zhigang; Chen, Xun; Zhao, Xueming

    2009-01-01

    A comparative transcriptome profiling between a riboflavin-producing Bacillus subtilis strain RH33 and the wild-type strain B. subtilis 168 was performed, complemented with metabolite pool and nucleotide sequence analysis, to rationally identify new targets for improving riboflavin production. The pur operon (purEKBCSQLFMNHD) together with other PurR-regulated genes (glyA, guaC, pbuG, xpt-pbuX, yqhZ-folD, and pbuO) was all down-regulated in RH33, which consequently limited the supply of the riboflavin precursors. As 5-phospho-ribosyl-1(a)-pyrophosphate (PRPP) strongly inhibits the binding of PurR to its targets, it was inferred that the reduced expression of PurR-regulated genes might be caused by a low PRPP pool, which was subsequently confirmed by metabolite analysis. Thus, we selected and co-overexpressed prs and ywlF genes in RH33, which are involved in the biosynthetic pathway of PRPP from ribulose-5-phosphate. This co-amplification led to an elevated PRPP pool and thus the increased transcript abundances of PurR-regulated genes participated in riboflavin precursor biosynthesis. The riboflavin titer was increased by 25% (up to 15 g l(-1)) in fed-batch fermentation.

  14. Metabolic Engineering of the Purine Pathway for Riboflavin Production in Ashbya gossypii†

    PubMed Central

    Jiménez, Alberto; Santos, María A.; Pompejus, Markus; Revuelta, José L.

    2005-01-01

    Purine nucleotides are essential precursors for living organisms because they are involved in many important processes, such as nucleic acid synthesis, energy supply, and the biosynthesis of several amino acids and vitamins such as riboflavin. GTP is the immediate precursor for riboflavin biosynthesis, and its formation through the purine pathway is subject to several regulatory mechanisms in different steps. Extracellular purines repress the transcription of most genes required for de novo ATP and GTP synthesis. Additionally, three enzymes of the pathway, phosphoribosyl pyrophosphate (PRPP) amidotransferase, adenylosuccinate synthetase, and IMP dehydrogenase, are subject to feedback inhibition by their end products. Here we report the characterization and manipulation of the committed step in the purine pathway of the riboflavin overproducer Ashbya gossypii. We report that phosphoribosylamine biosynthesis in A. gossypii is negatively regulated at the transcriptional level by extracellular adenine. Furthermore, we show that ATP and GTP exert a strong inhibitory effect on the PRPP amidotransferase from A. gossypii. We constitutively overexpressed the AgADE4 gene encoding PRPP amidotransferase in A. gossypii, thereby abolishing the adenine-mediated transcriptional repression. In addition, we replaced the corresponding residues (aspartic acid310, lysine333, and alanine417) that have been described to be important for PRPP amidotransferase feedback inhibition in other organisms by site-directed mutagenesis. With these manipulations, we managed to enhance metabolic flow through the purine pathway and to increase the production of riboflavin in the triple mutant strain 10-fold (228 mg/liter). PMID:16204483

  15. Studies on the energy metabolism of opossum (Didelphis virginiana) erythrocytes: V. Utilization of hypoxanthine for the synthesis of adenine and guanine nucleotides in vitro

    SciTech Connect

    Bethlenfalvay, N.C.; White, J.C.; Chadwick, E.; Lima, J.E. )

    1990-06-01

    High pressure liquid radiochromatography was used to test the ability of opossum erythrocytes to incorporate tracer amounts of (G-{sup 3}H) hypoxanthine (Hy) into ({sup 3}H) labelled triphosphates of adenine and guanine. In the presence of supraphysiologic (30 mM) phosphate which is optimal for PRPP synthesis, both ATP and GTP are extensively labelled. When physiologic (1 mM) medium phosphate is used, red cells incubated under an atmosphere of nitrogen accumulate ({sup 3}H) ATP in a linear fashion suggesting ongoing PRPP synthesis in red cells whose hemoglobin is deoxygenated. In contrast, a lesser increase of labelled ATP is observed in cells incubated under oxygen, suggesting that conditions for purine nucleotide formation from ambient Hy are more favorable in the venous circulation.

  16. Crystal structure of a chimera of human and Plasmodium falciparum hypoxanthine guanine phosphoribosyltransferases provides insights into oligomerization.

    PubMed

    Gayathri, P; Sujay Subbayya, I N; Ashok, Chethan S; Selvi, T Senthamizh; Balaram, Hemalatha; Murthy, M R N

    2008-12-01

    The crystal structure of a chimera of Plasmodium falciparum (Pf) and human hypoxanthine guanine phosphoribosyltransferases (HGPRT), which consists of the core of the protein from the human enzyme and the hood region from the Pf enzyme, has been determined as a complex with the product guanosine monophosphate (GMP). The chimera can utilize hypoxanthine, guanine, and xanthine as substrates, similar to the Pf enzyme. It exists as a monomer-dimer mixture in solution, but shifts to a tetramer on addition of phosphoribosyl pyrophosphate (PRPP). The structural studies reveal that the asymmetric unit of the crystal consists of two monomers of the chimeric HGPRT. Surprisingly, the dimer interface of the chimera is the less extensive AC interface of the parent HGPRTs. An analysis of the crystal structures of the various human HGPRTs provides an explanation for the oligomeric characteristics of the chimera. Pro93 and Tyr197 form part of crucial interactions holding together the AB interface in the unliganded or GMP-bound forms of HGPRT, while Pro93 and His26 interact at the interface after binding of PRPP. Replacement of Tyr197 of human HGPRT by Ile207 in the chimera disrupts the interaction at the AB interface in the absence of PRPP. In the presence of PRPP, the interaction between Pro93 and His26 could restore the AB interface, shifting the chimeric enzyme to a tetrameric state. The structure provides valuable insights into the differences in the AB interface between Pf and human HGPRTs, which may be useful for designing selective inhibitors against the parasite enzyme.

  17. Mechanisms of Oxygen Toxicity at the Cellular Level.

    DTIC Science & Technology

    1980-07-30

    phosphoribosyltransferase, which uses PRPP as a substrate. (3) Relationship of thiamine to oxygen toxicity. Thiamine is protective for E coli exposed to hyperoxia. Oxygen...exposure appears to poison an enzyme in the pathway for synthesis of hydroxymethyl pyrimidine, required for thiamine synthesis. Other enzymes in the...and its relationship to item (2). In addition, 3 we have completed a proposed study of effects of thiamine which had been delayed bacause of

  18. Aviation Forecasts. Fiscal Years 1976-1987

    DTIC Science & Technology

    1975-09-01

    international scheduled carriers continued to show a poor profit picture when looked at as a group . The international trunk car- riers decreased from... blg AVAIL1 + bj- PILOTS + IL PILB »104 b20 VrPRPP-t b2] IFRFF + U10 ACON »u4 I),,., IFRDF ♦ Vu PP t12 ♦ b23 L1PP * b24 LLSTD - b26 CLEAN

  19. Thermal stability of Artemia HGPRT: effect of substrates on inactivation kinetics.

    PubMed

    Montero, C; Llorente, P; Argomaniz, L; Menendez, M

    1996-06-01

    Hypoxanthine-guanine phosphoribosyltransferase (HGPRT, E.C.2.4.2.8) from Artemia cysts exhibits maximum activity at 70 degrees C. Its thermal stability has been examined following enzymatic activity as a function of temperature. Cold-induced renaturation experiments of samples heated at increasing temperatures showed that reversibility of thermal inactivation depends on the incubation time and final temperature. Prolonged incubation of the thermoinactivated enzyme at 0 degree C did not afford any further increase of the catalytic activity at 37 degrees C. The complex substrate PRPP:Mg protects HGPRT from thermal inactivation. However, incubations with hypoxanthine rendered a less thermostable enzyme at any temperature tested. The irreversible inactivation of HGPRT proceeds in two exponential steps. The analysis of the apparent rate constants for the fast and the slow phases, lambda 1 and lambda 2 as per the Lumry and Eyring model suggests the existence of more than three states in the thermal denaturation pathway of the free enzyme. In the presence of PRPP:Mg the irreversible process follows a single exponential and proceeds very slowly below 70 degrees C. PRPP:Mg also protects the enzyme from inactivation by NEM and pCMB, suggesting that -SH groups may be in the vicinity of the active site.

  20. Challenges to Integration of Safety and Reliability with Proliferation Resistance and Physical Protection for Generation IV Nuclear Energy Systems

    SciTech Connect

    H. Khalil; P. F. Peterson; R. Bari; G. -L. Fiorini; T. Leahy; R. Versluis

    2012-07-01

    The optimization of a nuclear energy system's performance requires an integrated consideration of multiple design goals - sustainability, safety and reliability (S&R), proliferation resistance and physical protection (PR&PP), and economics - as well as careful evaluation of trade-offs for different system design and operating parameters. Design approaches motivated by each of the goal areas (in isolation from the other goal areas) may be mutually compatible or in conflict. However, no systematic methodology approach has yet been developed to identify and maximize synergies and optimally balance conflicts across the possible design configurations and operating modes of a nuclear energy system. Because most Generation IV systems are at an early stage of development, design, and assessment, designers and analysts are only beginning to identify synergies and conflicts between PR&PP, S&R, and economics goals. The close coupling between PR&PP and S&R goals has motivated early attention within the Generation IV International Forum to their integrated consideration to facilitate the optimization of their effects and the minimization of potential conflicts. This paper discusses the status of this work.

  1. Methodology Development and Applications of Proliferation Resistance and Physical Protection Evaluation.

    SciTech Connect

    Bari, R.A.; Peterson, P.F., Therios, I.U., Whitlock, J.J.

    2010-04-11

    We present an overview of the program on the evaluation methodology for proliferation resistance and physical protection (PR&PP) of advanced nuclear energy systems (NESs) sponsored by the Generation IV International Forum (GIF). For a proposed NES design, the methodology defines a set of challenges, analyzes system response to these challenges, and assesses outcomes. The challenges to the NES are the threats posed by potential actors (proliferant States or sub-national adversaries). The characteristics of Generation IV systems, both technical and institutional, are used to evaluate the response of the system and to determine its resistance against proliferation threats and robustness against sabotage and terrorism threats. The outcomes of the system response are expressed in terms of a set of measures, which are the high-level PR&PP characteristics of the NES. The methodology is organized to allow evaluations to be performed at the earliest stages of system design and to become more detailed and more representative as the design progresses. It can thus be used to enable a program in safeguards by design or to enhance the conceptual design process of an NES with regard to intrinsic features for PR&PP.

  2. Effects of different substrate composition on biosynthesis of polyhydroxybutyrate-co-hydroxyvalerate by recombinant Escherichia coli.

    PubMed

    Chien, Chih-Ching; Li, Hsiu-Hsiung; Soo, Po-Chi; Chen, Shan-Yu; Wei, Yu-Hong; Chen, Wen-Ming

    2012-02-01

    Cupriavidus necator is well known for its ability to accumulate polyhydroxybutyrate (PHB). When supplemented with propionic acid (or sodium propionate) in the growth medium, the bacterium is also able to synthesize polyhydroxybutyrate-co-hydroxyvalerate (PHBV). In order to increase the fraction of 3-hydroxyvalerate (3HV) in PHBV, we cloned the propionate permease gene prpP from C. necator and the propionyl-CoA synthase gene prpE from Cupriavidus taiwanensis and transformed into an Escherichia coli containing phaCAB operon of C. necator. The effects on PHBV accumulation in cells co-expressed with phaCAB and prpE or prpP in the media contained mixed carbon sources (glucose and sodium propionate) were evaluated. The HV fraction in PHBV increased when prpE or prpP was overexpressed in the cells. Concentrations of yeast extracts could also affect the fraction of HV. In addition, when glucose was replaced by sodium pyruvate, sodium succinate, or sodium gluconate, only PHB were detected in the recombinant strains.

  3. Crystal structure of human phosphoribosylpyrophosphate synthetase 1 reveals a novel allosteric site.

    PubMed

    Li, Sheng; Lu, Yongcheng; Peng, Baozhen; Ding, Jianping

    2007-01-01

    PRPP (phosphoribosylpyrophosphate) is an important metabolite essential for nucleotide synthesis and PRS (PRPP synthetase) catalyses synthesis of PRPP from R5P (ribose 5-phosphate) and ATP. The enzymatic activity of PRS is regulated by phosphate ions, divalent metal cations and ADP. In the present study we report the crystal structures of recombinant human PRS1 in complexes with SO4(2-) ions alone and with ATP, Cd2+ and SO4(2-) ions respectively. The AMP moiety of ATP binds at the ATP-binding site, and a Cd2+ ion binds at the active site and in a position to interact with the beta- and gamma-phosphates of ATP. A SO4(2-) ion, an analogue of the activator phosphate, was found to bind at both the R5P-binding site and the allosteric site defined previously. In addi-tion, an extra SO4(2-) binds at a site at the dimer interface between the ATP-binding site and the allosteric site. Binding of this SO4(2-) stabilizes the conformation of the flexible loop at the active site, leading to the formation of the active, open conformation which is essential for binding of ATP and initiation of the catalytic reaction. This is the first time that structural stabilization at the active site caused by binding of an activator has been observed. Structural and biochemical data show that mutations of some residues at this site influence the binding of SO4(2-) and affect the enzymatic activity. The results in the present paper suggest that this new SO4(2-)-binding site is a second allosteric site to regulate the enzymatic activity which might also exist in other eukaryotic PRSs (except plant PRSs of class II), but not in bacterial PRSs.

  4. MARKOV Model Application to Proliferation Risk Reduction of an Advanced Nuclear System

    SciTech Connect

    Bari,R.A.

    2008-07-13

    The Generation IV International Forum (GIF) emphasizes proliferation resistance and physical protection (PR&PP) as a main goal for future nuclear energy systems. The GIF PR&PP Working Group has developed a methodology for the evaluation of these systems. As an application of the methodology, Markov model has been developed for the evaluation of proliferation resistance and is demonstrated for a hypothetical Example Sodium Fast Reactor (ESFR) system. This paper presents the case of diversion by the facility owner/operator to obtain material that could be used in a nuclear weapon. The Markov model is applied to evaluate material diversion strategies. The following features of the Markov model are presented here: (1) An effective detection rate has been introduced to account for the implementation of multiple safeguards approaches at a given strategic point; (2) Technical failure to divert material is modeled as intrinsic barriers related to the design of the facility or the properties of the material in the facility; and (3) Concealment to defeat or degrade the performance of safeguards is recognized in the Markov model. Three proliferation risk measures are calculated directly by the Markov model: the detection probability, technical failure probability, and proliferation time. The material type is indicated by an index that is based on the quality of material diverted. Sensitivity cases have been done to demonstrate the effects of different modeling features on the measures of proliferation resistance.

  5. Difficulties with multitasking on return to work after TBI: a critical case study.

    PubMed

    Bootes, Kylie; Chapparo, Christine

    2010-01-01

    Work performance research highlights that psychometric cognitive measures and cognitive component information processing measures are strong predictors of success in multitasking work environments [14]. People with a mild to moderate traumatic brain injury (TBI) returning to a job requiring multitasking, may have difficulty succeeding despite pre-morbid equivalent cognitive scores. A critical case study is presented to begin to determine what aspects of information processing contribute to difficulties in multitasking work performance, for people with a TBI. The Perceive Recall Plan and Perform (PRPP) System of Task Analysis: Workplace Interview (i.e. PRPP@WORK) is used with the employer to obtain information processing scores. Results indicate substantial information processing deficits were perceived by the employer for the employee with a TBI. Future larger studies of people with a TBI who return to work that requires multitasking are needed to more clearly indicate: the level of multitasking they perform; what aspects of information processing hinder their work performance; the impact on performance of perceived cognitive load by the person with a TBI and the type and impact of support provided to improve their work performance.

  6. Limiting Future Proliferation and Security Risks

    SciTech Connect

    Bari, R.

    2011-03-13

    A major new technical tool for evaluation of proliferation and security risks has emerged over the past decade as part the activities of the Generation IV International Forum. The tool has been developed by a consensus group from participating countries and organizations and is termed the Proliferation Resistance and Physical Protection (PR&PP) Evaluation Methodology. The methodology defines a set of challenges, analyzes system response to these challenges, and assesses outcomes. The challenges are the threats posed by potential actors (proliferant states or sub-national adversaries). It is of paramount importance in an evaluation to establish the objectives, capabilities, resources, and strategies of the adversary as well as the design and protection contexts. Technical and institutional characteristics are both used to evaluate the response of the system and to determine its resistance against proliferation threats and robustness against sabotage and terrorism threats. The outcomes of the system response are expressed in terms of a set of measures, which thereby define the PR&PP characteristics of the system. This paper summarizes results of applications of the methodology to nuclear energy systems including reprocessing facilities and large and small modular reactors. The use of the methodology in the design phase a facility will be discussed as it applies to future safeguards concepts.

  7. Generation IV PR and PP Methods and Applications

    SciTech Connect

    Bari,R.A.

    2008-10-13

    This paper presents an evaluation methodology for proliferation resistance and physical protection (PR&PP) of Generation IV nuclear energy systems (NESs). For a proposed NES design, the methodology defines a set of challenges, analyzes system response to these challenges, and assesses outcomes. The challenges to the NES are the threats posed by potential actors (proliferant States or sub-national adversaries). The characteristics of Generation IV systems, both technical and institutional, are used to evaluate the response of the system and determine its resistance against proliferation threats and robustness against sabotage and terrorism threats. The outcomes of the system response are expressed in terms of six measures for PR and three measures for PP, which are the high-level PR&PP characteristics of the NES. The methodology is organized to allow evaluations to be performed at the earliest stages of system design and to become more detailed and more representative as design progresses. Uncertainty of results are recognized and incorporated into the evaluation at all stages. The results are intended for three types of users: system designers, program policy makers, and external stakeholders. Particular current relevant activities will be discussed in this regard. The methodology has been illustrated in a series of demonstration and case studies and these will be summarized in the paper.

  8. A structured model for vegetative growth and sporulation in Bacillus thuringiensis.

    PubMed

    Starzak, M; Bajpai, R K

    1991-01-01

    A mathematical model has been developed for the delta-endotoxin producing Bacillus thuringiensis. The structure of the model involves the processes taking place during vegetative growth, those leading to the initiation of sporulation under conditions of carbon and/or nitrogen limitation, and the sporulation events. The key features in the model are the pools of compounds, such as PRPP, IMP, ADP/ATP, GDP/GTP, pyrimidine nucleotides, NAD/NADH2, amino acids, nucleic acids, cell wall, and vegetative and sporulation proteins. These, along with sigma-factors that control the nature of RNA-polymerase during the different phases, effectively stimulate the vegetative growth and sporulation. The initiation of sporulation is controlled by the intracellular concentration of GTP. Results of simulation of vegetative growth, initiation of sporulation, spore protein formation, and production of delta-endotoxin under C- or N-limitation are presented.

  9. A structured model for vegetative growth and sporulation in Bacillus thuringiensis

    SciTech Connect

    Starzak, M.; Bajpai, R.K.

    1991-12-31

    A mathematical model has been developed for the 6-endotoxin producing Bacillus thuringiensis. The structure of the model involves the processes taking place during vegetative growth, those leading to the initiation of sporulation under conditions of carbon and/or nitrogen limitation, and the sporulation events. The key features in the model are the pools of compounds, such as PRPP, IMP, ADP/ATP, GDP/GTP, pyrimidine nucleotides, NAD/NADH{sub 2}, amino acids, nucleic acids, cell wall, and vegetative and sporulation proteins. These, along with a-factors that control the nature of RNA-polymerase during the different phases, effectively stimulate the vegetative growth and sporulation. The initiation of sporulation is controlled by the intracellular concentration of GTP. Results of simulation of vegetative growth, initiation of sporulation, spore protein formation, and production of {delta}-endotoxin under C- or N-limitation are presented.

  10. A Comparison of the Safety Analysis Process and the Generation IV Proliferation Resistance/Physical Protection Assessment Methodology

    SciTech Connect

    T. A. Bjornard; M. D. Zentner

    2006-05-01

    The Generation IV International Forum (GIF) is a vehicle for the cooperative international development of future nuclear energy systems. The Generation IV program has established primary objectives in the areas of sustainability, economics, safety and reliability, and Proliferation Resistance and Physical Protection (PR&PP). In order to help meet the latter objective a program was launched in December 2002 to develop a rigorous means to assess nuclear energy systems with respect to PR&PP. The study of Physical Protection of a facility is a relatively well established methodology, but an approach to evaluate the Proliferation Resistance of a nuclear fuel cycle is not. This paper will examine the Proliferation Resistance (PR) evaluation methodology being developed by the PR group, which is largely a new approach and compare it to generally accepted nuclear facility safety evaluation methodologies. Safety evaluation methods have been the subjects of decades of development and use. Further, safety design and analysis is fairly broadly understood, as well as being the subject of federally mandated procedures and requirements. It is therefore extremely instructive to compare and contrast the proposed new PR evaluation methodology process with that used in safety analysis. By so doing, instructive and useful conclusions can be derived from the comparison that will help to strengthen the PR methodological approach as it is developed further. From the comparison made in this paper it is evident that there are very strong parallels between the two processes. Most importantly, it is clear that the proliferation resistance aspects of nuclear energy systems are best considered beginning at the very outset of the design process. Only in this way can the designer identify and cost effectively incorporate intrinsic features that might be difficult to implement at some later stage. Also, just like safety, the process to implement proliferation resistance should be a dynamic

  11. Functional identification of MSMEG_6402 protein from Mycobacterium smegmatis in decaprenylphosphoryl-D-arabinose biosynthesis.

    PubMed

    Jiang, Tao; Cai, Lina; Zhao, Xiaojiao; He, Lianqi; Ma, Yufang; Zang, Shizhu; Zhang, Cuili; Li, Xinli; Xin, Yi

    2014-11-01

    The arabinogalactan (AG) of the mycobacterial cell wall consists of an arabinan region, a galactan region and a disaccharide linker. Decaprenylphosphoryl-D-arabinose (DPA) is the donor for arabinofuran residues, which are formed from phosphoribose diphosphate (PRPP) and decaprenyl phosphate (DP). DP is sequentially catalyzed by a three-step process that involves a transferase, a phosphatase and an epimerase. Rv3807c is a putative phospholipid phosphatase that might generate the intermediate product of decaprenyl-phosphoryl-ribose (DPR) in DPA biosynthesis. Mycobacterium smegmatis MSMEG_6402 is a homolog gene of Mycobacterium tuberculosis Rv3807c and was substituted for the functional identification of Rv3807c. Previously, we generated a conditional MSMEG_6402 gene knockout strain (M. sm-ΔM_6402) that exhibited significantly affected cell wall structure. To understand the function of MSMEG_6402 in DPA biosynthesis, this gene was amplified and expressed, and the resulting protein was identified and purified using a His-tagged approach. A MSMEG_6402 enzymatic reaction system with PRPP and DP as substrates was utilized, and the reaction products were separated using thin layer chromatography (TLC). The results revealed a specific lipid-linked sugar band that appeared in the reaction with the addition of MSMEG_6402. Furthermore, ESI-MS detection was utilized in this study, and the results revealed that the enzymatic reaction products involving MSMEG_6402 included DPPR and a sodium ion adduct of DPR. Additionally, the phosphatase activity of MSMEG_6402 was also determined through phosphate group detection using the colorimetric method. Based on our results together with the results of previous studies, including the functional identification and bioinformatics analysis of M. tuberculosis Rv3807c, we propose that MSMEG_6402, as a phosphatase, has an intimate relationship with DPA biosynthesis.

  12. Dynamic diversity of the tryptophan pathway in chlamydiae: reductive evolution and a novel operon for tryptophan recapture

    PubMed Central

    Xie, Gary; Bonner, Carol A; Jensen, Roy A

    2002-01-01

    Background Complete genomic sequences of closely related organisms, such as the chlamydiae, afford the opportunity to assess significant strain differences against a background of many shared characteristics. The chlamydiae are ubiquitous intracellular parasites that are important pathogens of humans and other organisms. Tryptophan limitation caused by production of interferon-γ by the host and subsequent induction of indoleamine dioxygenase is a key aspect of the host-parasite interaction. It appears that the chlamydiae have learned to recognize tryptophan depletion as a signal for developmental remodeling. The consequent non-cultivable state of persistence can be increasingly equated to chronic disease conditions. Results The genes encoding enzymes of tryptophan biosynthesis were the focal point of this study. Chlamydophila psittaci was found to possess a compact operon containing PRPP synthase, kynureninase, and genes encoding all but the first step of tryptophan biosynthesis. All but one of the genes exhibited translational coupling. Other chlamydiae (Chlamydia trachomatis, C. muridarum and Chlamydophila pneumoniae) lack genes encoding PRPP synthase, kynureninase, and either lack tryptophan-pathway genes altogether or exhibit various stages of reductive loss. The origin of the genes comprising the trp operon does not seem to have been from lateral gene transfer. Conclusions The factors that accommodate the transition of different chlamydial species to the persistent (chronic) state of pathogenesis include marked differences in strategies deployed to obtain tryptophan from host resources. C. psittaci appears to have a novel mechanism for intercepting an early intermediate of tryptophan catabolism and recycling it back to tryptophan. In effect, a host-parasite metabolic mosaic has evolved for tryptophan recycling. PMID:12225590

  13. Structure of Salmonella typhimurium OMP synthase in a complete substrates complex

    PubMed Central

    Grubmeyer, Charles; Hansen, Michael Riis; Fedorov, Alexander A.; Almo, Steven C.

    2012-01-01

    Dimeric Salmonella typhimurium orotate phosphoribosyltransferase (OMP synthase, E.C. 2.4.2.10), a key enzyme in de novo pyrimidine nucleotide synthesis, has been co-crystallized in a complete substrate complex of E•MgPRPP•orotate, and the structure solved to 2.2 Å resolution. This structure resembles that for Saccharomyces cerevisiae OMP synthase in showing a dramatic and asymmetric reorganization around the active site-bound ligands, but shares the same basic topology previously observed in complexes of OMP synthase from S. typhimurium and Escherichia coli. The catalytic loop (residues 99–109) contributed by subunit A is reorganized to close the active site situated in subunit B and to sequester it from solvent. Furthermore, the overall structure of subunit B is more compact, due to movements of the amino-terminal hood and elements of the core domain. The catalytic loop of subunit B remains open and disordered, and subunit A retains the more relaxed conformation observed in loop-open S. typhimurium OMP synthase structures. A non-proline cis-peptide formed between Ala71 and Tyr72 is seen in both subunits. The loop-closed catalytic site of subunit B reveals that both the loop and the hood interact directly with the bound pyrophosphate group of PRPP. In contrast to dimagnesium hypoxanthine-guanine phosphoribosyltransferases, OMP synthase contains a single catalytic Mg2+ in the closed active site. The remaining pyrophosphate charges of PRPP are neutralized by interactions with Arg99A, Lys100B, Lys103A, and His105A. The new structure confirms the importance of loop movement in catalysis by OMP synthase, and identifies several additional movements that must be accomplished in each catalytic cycle. A catalytic mechanism based on enzymic and substratea-ssisted stabilization of the previously documented oxocarbenium transition state structure is proposed. PMID:22531064

  14. Molecular dynamics perspective on the protein thermal stability: a case study using SAICAR synthetase.

    PubMed

    Manjunath, Kavyashree; Sekar, Kanagaraj

    2013-09-23

    The enzyme SAICAR synthetase ligates aspartate with CAIR (5'-phosphoribosyl-4-carboxy-5-aminoimidazole) forming SAICAR (5-amino-4-imidazole-N-succinocarboxamide ribonucleotide) in the presence of ATP. In continuation with our previous study on the thermostability of this enzyme in hyper-/thermophiles based on the structural aspects, here, we present the dynamic aspects that differentiate the mesophilic (E. coli, E. chaffeensis), thermophilic (G. kaustophilus), and hyperthermophilic (M. jannaschii, P. horikoshii) SAICAR synthetases by carrying out a total of 11 simulations. The five functional dimers from the above organisms were simulated using molecular dynamics for a period of 50 ns each at 300 K, 363 K, and an additional simulation at 333 K for the thermophilic protein. The basic features like root-mean-square deviations, root-mean-square fluctuations, surface accessibility, and radius of gyration revealed the instability of mesophiles at 363 K. Mean square displacements establish the reduced flexibility of hyper-/thermophiles at all temperatures. At the simulations time scale considered here, the long-distance networks are considerably affected in mesophilic structures at 363 K. In mesophiles, a comparatively higher number of short-lived (having less percent existence time) Cα, hydrogen bonds, hydrophobic interactions are formed, and long-lived (with higher percentage existence time) contacts are lost. The number of time-averaged salt-bridges is at least 2-fold higher in hyperthermophiles at 363 K. The change in surface accessibility of salt-bridges at 363 K from 300 K is nearly doubled in mesophilic protein compared to proteins from other temperature classes.

  15. Identification of a gene cluster in Klebsiella pneumoniae which includes citX, a gene required for biosynthesis of the citrate lyase prosthetic group.

    PubMed

    Schneider, Karin; Kästner, Christopher N; Meyer, Margareta; Wessel, Mirja; Dimroth, Peter; Bott, Michael

    2002-05-01

    The biosynthesis of the 2'-(5"-phosphoribosyl)-3'-dephospho-coenzyme A (CoA) prosthetic group of citrate lyase (EC 4.1.3.6), a key enzyme of citrate fermentation, proceeds via the initial formation of the precursor 2'-(5"-triphosphoribosyl)-3'-dephospho-CoA and subsequent transfer to apo-citrate lyase with removal of pyrophosphate. In Escherichia coli, the two steps are catalyzed by CitG and CitX, respectively, and the corresponding genes are part of the citrate lyase gene cluster, citCDEFXG. In the homologous citCDEFG operon of Klebsiella pneumoniae, citX is missing. A search for K. pneumoniae citX led to the identification of a second genome region involved in citrate fermentation which comprised the citWX genes and the divergent citYZ genes. The citX gene was confirmed to encode holo-citrate lyase synthase, whereas citW was shown to encode a citrate carrier, the third one identified in this species. The citYZ genes were found to encode a two-component system consisting of the sensor kinase CitY and the response regulator CitZ. Remarkably, both proteins showed >or=40% sequence identity to the citrate-sensing CitA-CitB two-component system, which is essential for the induction of the citrate fermentation genes in K. pneumoniae. A citZ insertion mutant was able to grow anaerobically with citrate, indicating that CitZ is not essential for expression of citrate fermentation genes. CitX synthesis was induced to a basal level under anaerobic conditions, independent of citrate, CitB, and CitZ, and to maximal levels during anaerobic growth with citrate as the sole carbon source. Similar to the other citrate fermentation enzymes, CitX synthesis was apparently subject to catabolite repression.

  16. Deregulation of purine pathway in Bacillus subtilis and its use in riboflavin biosynthesis

    PubMed Central

    2014-01-01

    Background Purine nucleotides are essential metabolites for living organisms because they are involved in many important processes, such as nucleic acid synthesis, energy supply, and biosynthesis of several amino acids and riboflavin. Owing to the pivotal roles of purines in cell physiology, the pool of intracellular purine nucleotides must be maintained under strict control, and hence the de novo purine biosynthetic pathway is tightly regulated by transcription repression and inhibition mechanism. Deregulation of purine pathway is essential for this pathway engineering in Bacillus subtilis. Results Deregulation of purine pathway was attempted to improve purine nucleotides supply, based on a riboflavin producer B. subtilis strain with modification of its rib operon. To eliminate transcription repression, the pur operon repressor PurR and the 5’-UTR of pur operon containing a guanine-sensing riboswitch were disrupted. Quantitative RT-PCR analysis revealed that the relative transcription levels of purine genes were up-regulated about 380 times. Furthermore, site-directed mutagenesis was successfully introduced into PRPP amidotransferase (encoded by purF) to remove feedback inhibition by homologous alignment and analysis. Overexpression of the novel mutant PurF (D293V, K316Q and S400W) significantly increased PRPP amidotransferase activity and triggered a strong refractory effect on purine nucleotides mediated inhibition. Intracellular metabolite target analysis indicated that the purine nucleotides supply in engineered strains was facilitated by a stepwise gene-targeted deregulation. With these genetic manipulations, we managed to enhance the metabolic flow through purine pathway and consequently increased riboflavin production 3-fold (826.52 mg/L) in the purF-VQW mutant strain. Conclusions A sequential optimization strategy was applied to deregulate the rib operon and purine pathway of B. subtilis to create genetic diversities and to improve riboflavin production

  17. Crystallization and preliminary X-ray diffraction analysis of recombinant phosphoribosylpyrophosphate synthetase from the Thermophilic thermus thermophilus strain HB27

    NASA Astrophysics Data System (ADS)

    Abramchik, Yu. A.; Timofeev, V. I.; Muravieva, T. I.; Sinitsyna, E. V.; Esipov, R. S.; Kuranova, I. P.

    2017-01-01

    Phosphoribosylpyrophosphate synthetases (PRPP synthetases) are among the key enzymes essential for vital functions of organisms and are involved in the biosynthesis of purine and pyrimidine nucleotides, coenzymes, and the amino acids histidine and tryptophan. These enzymes are used in biotechnology for the combined chemoenzymatic synthesis of natural nucleotide analogs. Recombinant phosphoribosylpyrophosphate synthetase I from the thermophilic strain HB27 of the bacterium Thermus thermophilus ( T. th HB27) has high thermal stability and shows maximum activity at 75°C, due to which this enzyme holds promise for biotechnological applications. In order to grow crystals and study them by X-ray crystallography, an enzyme sample, which was produced using a highly efficient producer strain, was purified by affinity and gel-filtration chromatography. The screening of crystallization conditions was performed by the vapor-diffusion technique. The crystals of the enzyme suitable for X-ray diffraction were grown by the counter-diffusion method through a gel layer. These crystals were used to collect the X-ray diffraction data set at the SPring-8 synchrotron radiation facility (Japan) to 3-Å resolution. The crystals belong to sp. gr. P21 and have the following unitcell parameters: a = 107.7 Å, b = 112.6 Å, c = 110.2 Å, α = γ = 90°, β = 116.6°. The X-ray diffraction data set is suitable for determining the three-dimensional structure of the enzyme at 3.0-Å resolution.

  18. An exploration of the ecological validity of the Virtual Action Planning-Supermarket (VAP-S) with people with schizophrenia.

    PubMed

    Aubin, Ginette; Béliveau, Marie-France; Klinger, Evelyne

    2015-08-28

    People with schizophrenia often have functional limitations that affect their daily activities due to executive function deficits. One way to assess these deficits is through the use of virtual reality programmes that reproduce real-life instrumental activities of daily living (IADLs). One such programme is the Virtual Action Planning-Supermarket (VAP-S). This exploratory study aimed to examine the ecological validity of this programme, specifically, how task performance in both virtual and natural environments compares. Case studies were used and involved five participants with schizophrenia, who were familiar with grocery shopping. They were assessed during both the VAP-S shopping task and a real-life grocery shopping task using an observational assessment tool, the Perceive, Recall, Plan and Perform (PRPP) System of Task Analysis. The results show that when difficulties were present in the virtual task, difficulties were also observed in the real-life task. For some participants, greater difficulties were observed in the virtual task. These difficulties could be explained by the presence of perceptual deficits and problems remembering the required sequenced actions in the virtual task. In conclusion, performance on the VAP-S by these five participants was generally comparable to the performance in a natural environment.

  19. Synthesis and cytotoxicity of substituted ethyl 2-phenacyl-3-phenylpyrrole-4-carboxylates.

    PubMed

    Evans, Michael A; Smith, Daniel C; Holub, Justin M; Argenti, Anthony; Hoff, Mafoloe; Dalglish, Gerard A; Wilson, Donna L; Taylor, Brett M; Berkowitz, Joshua D; Burnham, Bruce S; Krumpe, Keith; Gupton, John T; Scarlett, Tanya C; Durham Jr, Richard W; Hall, Iris H

    2003-06-01

    The substituted ethyl-2-phenacyl-3-phenylpyrrole-4-carboxylates were synthesized by a condensation of a beta-chloroenal and an alpha-aminoketone under neutral conditions. They proved to be potent cytotoxic agents against the growth of murine L1210 and P388 leukemias and human HL-60 promyelocytic leukemia, HuT-78 lymphoma, and HeLa-S(3) uterine carcinoma. Selective compounds were active against the growth of Tmolt(3) and Tmolt(4) leukemias and THP-1 acute monocytic leukemia, liver Hepe-2, ovary 1-A9, ileum HCT-8 adenocarcinoma, and osteosarcoma HSO. A mode of action study in HL-60 cells demonstrated that DNA and protein syntheses were inhibited after 60 min at 100 microM. DNA and RNA polymerases, PRPP-amido transferase, dihydrofolate reductase, thymidylate synthase, and TMP kinase activities were interfered with by the agent with reduction of d[NTP] pools. Nonspecific interaction with the bases of DNA and cross-linking of the DNA may play a role in the mode of action of these carboxylates.

  20. Structure of pyrR (Rv1379) from Mycobacterium tuberculosis: A persistence gene and protein drug target

    SciTech Connect

    Kantardjieff, K A; Vasquez, C; Castro, P; Warfel, N M; Rho, B; Lekin, T; Kim, C; Segelke, B W; Terwilliger, T C; Rupp, B

    2004-09-24

    The 1.9 {angstrom} native structure of pyrimidine biosynthesis regulatory protein encoded by the Mycobacterium tuberculosis pyrR gene (Rv1379) is reported. Because pyrimidine biosynthesis is an essential step in the progression of TB, pyrR is an attractive antitubercular drug target. The Mycobacterium tuberculosis pyrR gene (Rv1379) encodes a protein that regulates expression of pyrimidine nucleotide biosynthesis (pyr) genes in a UMP-dependent manner. Because pyrimidine biosynthesis is an essential step in the progression of TB, the gene product pyrR is an attractive antitubercular drug target. We report the 1.9 {angstrom} native structure of Mtb pyrR determined by the TB Structural Genomics Consortium facilities (PDB entry 1W30) in trigonal space group P3{sub 1}21, with cell dimensions at 120K of a = 66.64 {angstrom}, c = 154.72 {angstrom}, and two molecules in the asymmetric unit. The 3D structure and residual uracil phosphoribosyltransferase activity point to a common PRTase ancestor for pyrR. However, while PRPP and UMP binding sites have been retained in Mtb pyrR, a novel dimer interaction among subunits creates a deep, positively charged cleft capable of binding pyr mRNA. In silico screening of pyrimidine nucleoside analogs has revealed a number of potential leads compounds that, if bound to Mtb pyrR, could facilitate transcriptional attenuation, particularly cyclopentenyl nucleosides.

  1. Modulation of hexa-acyl pyrophosphate lipid A population under Escherichia coli phosphate (Pho) regulon activation.

    PubMed

    Lamarche, Martin G; Kim, Sang-Hyun; Crépin, Sébastien; Mourez, Michael; Bertrand, Nicolas; Bishop, Russell E; Dubreuil, J Daniel; Harel, Josée

    2008-08-01

    Environmental phosphate is an important signal for microorganism gene regulation, and it has recently been shown to trigger some key bacterial virulence mechanisms. In many bacteria, the Pho regulon is the major circuit involved in adaptation to phosphate limitation. The Pho regulon is controlled jointly by the two-component regulatory system PhoR/PhoB and by the phosphate-specific transport (Pst) system, which both belong to the Pho regulon. We showed that a pst mutation results in virulence attenuation in extraintestinal pathogenic Escherichia coli (ExPEC) strains. Our results indicate that the bacterial cell surface of the pst mutants is altered. In this study, we show that pst mutants of ExPEC strains display an increased sensitivity to different cationic antimicrobial peptides and vancomycin. Remarkably, the hexa-acylated 1-pyrophosphate form of lipid A is significantly less abundant in pst mutants. Among differentially expressed genes in the pst mutant, lpxT coding for an enzyme that transfers a phosphoryl group to lipid A, forming the 1-diphosphate species, was found to be downregulated. Our results strongly suggest that the Pho regulon is involved in lipid A modifications, which could contribute to bacterial surface perturbations. Since the Pho regulon and the Pst system are conserved in many bacteria, such a lipid A modification mechanism could be widely distributed among gram-negative bacterial species.

  2. Fluorescent substrate analog for monitoring chain elongation by undecaprenyl pyrophosphate synthase in real time.

    PubMed

    Teng, Kuo-Hsun; Chen, Annie P-C; Kuo, Chih-Jung; Li, Yu-Chin; Liu, Hon-Ge; Chen, Chao-Tsen; Liang, Po-Huang

    2011-10-01

    Farnesyl pyrophosphate (FPP) is a common substrate for a variety of prenyltransferases for synthesizing isoprenoid compounds. In this study, (2E,6E)-8-O-(N-methyl-2-aminobenzoyl)-3,7-dimethyl-2,6-octandien-1-pyrophosphate (MANT-O-GPP), a fluorescent analog of FPP, was synthesized and demonstrated as a satisfactory substrate for Escherichia coli undecaprenyl pyrophosphate synthase (UPPS) with a K(m) of 1.5 μM and a k(cat) of 1.2s(-1) based on [(14)C]IPP consumption. Interesting, we found that its emission fluorescence intensity at 420 nm increased remarkably during chain elongation, thereby useful for real-time monitoring kinetics of UPPS to yield a K(m) of 1.1 μM and a k(cat) of 1.0 s(-1), consistent with those measured using radiolabeled substrate. Using this assay, the IC(50) of a known UPPS inhibitor farnesyl thiopyrophosphate (FsPP) was confirmed. Our studies provide a convenient and environmentally friendly alternative for kinetics and inhibition studies on UPPS drug target.

  3. Phosphorylation of Cytokinin by Adenosine Kinase from Wheat Germ 1

    PubMed Central

    Chen, Chong-Maw; Eckert, Richard L.

    1977-01-01

    Adenosine kinase was partially purified from wheat germ. This enzyme preparation, which was devoid of adenine phosphoribosyltransferase and nearly free of adenosine deaminase but contained adenylate kinase, rapidly phosphorylated adenosine and a cytokinin, N6-(δ2-isopentenyl)adenosine. Electrophoretic analysis indicated that only N6-(δ2-isopentenyl)adenosine-monophosphate was formed from the cytokinin while about 55% AMP, 45% ADP, and a trace of ATP were formed from adenosine. The biosynthesized nucleoside monophosphates were quantitatively hydrolyzed to the corresponding nucleosides by 5′-nucleotidase and the isopentenyl side chain of the phosphorylated cytokinin was not cleaved. The enzyme did not catalyze phosphorylation of inosine. The phosphorylation of the cytokinin and adenosine required ATP and Mg2+. The pH optimum was from 6.8 to 7.2 for both the cytokinin and adenosine. At pH 7 and 37 C the Km and Vmax for the cytokinin were 31 μm and 8.3 nmoles per mg protein per minute, and the values for adenosine were 8.7 μm and 46 nmoles per mg protein per minute. Crude enzyme preparations from tobacco callus tissue and wheat germ phosphorylated N6-(δ2-isopentenyl)adenosine. These preparations also phosphorylated N6-(δ2-isopentenyl)adenine when 5-phosphorylribose-1-pyrophosphate was present. PMID:16659870

  4. Proliferation resistance: issues, initiatives and evaluation

    SciTech Connect

    Pilat, Joseph F

    2009-01-01

    The vision of a nuclear renaissance has highlighted the issue of proliferation resistance. The prospects for a dramatic growth in nuclear power may depend on the effectiveness of, and the resources devoted to, plans to develop and implement technologies and approaches that strengthen proliferation resistance. The GenIV International Forum (GIF) and others have devoted attention and resources to proliferation resistance. However, the hope of finding a way to make the peaceful uses of nuclear energy resistant to proliferation has reappeared again and again in the history of nuclear power with little practical consequence. The concept of proliferation resistance has usually focused on intrinsic (technological) as opposed to extrinsic (institutional) factors. However, if there are benefits that may yet be realized from reactors and other facilities designed to minimize proliferation risks, it is their coupling with effective safeguards and other nonproliferation measures that likely will be critical. Proliferation resistance has also traditionally been applied only to state threats. Although there are no technologies that can wholly eliminate the risk of proliferation by a determined state, technology can play a limited role in reducing state threats and perhaps in eliminating many non-state threats. These and other issues are not academic. They affect efforts to evaluate proliferation resistance, including the methodology developed by GIF's Proliferation Resistance and Physical Protection (PR&PP) Working Group as well as the proliferation resistance initiatives that are being pursued or may be developed in the future. This paper will offer a new framework for thinking about proliferation resistance issues, including the ways the output of the methodology could be developed to inform the decisions that states, the International Atomic Energy (IAEA) and others will have to make in order to fully realize the promise of a nuclear renaissance.

  5. Proliferation resistance assessments during the design phase of a recycling facility as a means of reducing proliferation risks

    SciTech Connect

    Lindell, M.A.; Grape, S.; Haekansson, A.; Jacobsson Svaerd, S.

    2013-07-01

    The sustainability criterion for Gen IV nuclear energy systems inherently presumes the availability of efficient fuel recycling capabilities. One area for research on advanced fuel recycling concerns safeguards aspects of this type of facilities. Since a recycling facility may be considered as sensitive from a non-proliferation perspective, it is important to address these issues early in the design process, according to the principle of Safeguards By Design. Presented in this paper is a mode of procedure, where assessments of the proliferation resistance (PR) of a recycling facility for fast reactor fuel have been performed so as to identify the weakest barriers to proliferation of nuclear material. Two supplementing established methodologies have been applied; TOPS (Technological Opportunities to increase Proliferation resistance of nuclear power Systems) and PR-PP (Proliferation Resistance and Physical Protection evaluation methodology). The chosen fuel recycling facility belongs to a small Gen IV lead-cooled fast reactor system that is under study in Sweden. A schematic design of the recycling facility, where actinides are separated using solvent extraction, has been examined. The PR assessment methodologies make it possible to pinpoint areas in which the facility can be improved in order to reduce the risk of diversion. The initial facility design may then be slightly modified and/or safeguards measures may be introduced to reduce the total identified proliferation risk. After each modification of design and/or safeguards implementation, a new PR assessment of the revised system can then be carried out. This way, each modification can be evaluated and new ways to further enhance the proliferation resistance can be identified. This type of iterative procedure may support Safeguards By Design in the planning of new recycling plants and other nuclear facilities. (authors)

  6. Is ZMP the toxic metabolite in Lesch-Nyhan disease?

    PubMed

    López, José M

    2008-11-01

    The genetic deficiency of hypoxanthine-guanine phosphoribosyltransferase (HPRT), located on the X chromosome, causes a severe neurological disorder in man, known as Lesch-Nyhan disease (LND). The enzyme HPRT is part of the savage pathway of purine biosynthesis and catalyzes the conversion of hypoxanthine and guanine to their respective nucleotides, IMP and GMP. HPRT deficiency is associated with a relatively selective dysfunction of brain dopamine systems. Several metabolites that accumulate in the patients (phosphoribosylpyrophosphate (PRPP), hypoxanthine, guanine, xanthine, and Z-nucleotides) have been proposed as toxic agents in LND. Some authors have pointed that Z-riboside, derived from the accumulation of ZMP, could be the toxic metabolite in LND. However, the available experimental data support a better hypothesis. I suggest that ZMP (and not Z-riboside) is the key toxic metabolite in LND. ZMP is an inhibitor of the bifunctional enzyme adenylosuccinate lyase, and a deficiency of this enzyme causes psychomotor and mental retardation in humans. Moreover, it has been reported that ZMP inhibits mitochondrial oxidative phosphorylation and induces apoptosis in certain cell types. ZMP is also an activator of the AMP-activated protein kinase (AMPK), a homeostatic regulator of energy levels in the cell. The AMPK has been implicated in the regulation of cell viability, catecholamine biosynthesis and cell structure. I propose that accumulation of ZMP will induce a pleiotropic effect in the brain by (1) a direct inhibition of mitochondrial respiration and the bifunctional enzyme adenylosuccinate lyase, and (2) a sustained activation of the AMPK which in turns would reduce cell viability, decrease dopamine synthesis, and alters cell morphology. In addition, a mechanism to explain the accumulation of ZMP in LND is presented. The knowledge of the toxic metabolite, and the way it acts, would help to design a better therapy.

  7. Investigation of reductive dechlorination supported by natural organic carbon

    USGS Publications Warehouse

    Rectanus, H.V.; Widdowson, M.A.; Chapelle, F.H.; Kelly, C.A.; Novak, J.T.

    2007-01-01

    Because remediation timeframes using monitored natural attenuation may span decades or even centuries at chlorinated solvent sites, new approaches are needed to assess the long-term sustainability of reductive dechlorination in ground water systems. In this study, extraction procedures were used to investigate the mass of indigenous organic carbon in aquifer sediment, and experiments were conducted to determine if the extracted carbon could support reductive dechlorination of chloroethenes. Aquifer sediment cores were collected from a site without an anthropogenic source of organic carbon where organic carbon varied from 0.02% to 0.12%. Single extraction results showed that 1% to 28% of sediment-associated organic carbon and 2% to 36% of the soft carbon were removed depending on nature and concentration of the extracting solution (Nanopure water; 0.1%, 0.5%, and 1.0% sodium pyrophosphate; and 0.5 N sodium hydroxide). Soft carbon is defined as organic carbon oxidized with potassium persulfate and is assumed to serve as a source of biodegradable carbon within the aquifer. Biodegradability studies demonstrated that 20% to 40% of extracted organic carbon was biodegraded aerobically and anaerobically by soil microorganisms in relatively brief tests (45 d). A five-step extraction procedure consisting of 0.1% pyrophosphate and base solutions was investigated to quantify bioavailable organic carbon. Using the extracted carbon as the sole electron donor source, tetrachloroethene was transformed to cis-1,2- dichloroethene and vinyl chloride in anaerobic enrichment culture experiments. Hydrogen gas was produced at levels necessary to sustain reductive dechlorination (>1 nM). ?? 2007 National Ground Water Association.

  8. Phase I/II study of adoptive transfer of γδ T cells in combination with zoledronic acid and IL-2 to patients with advanced renal cell carcinoma.

    PubMed

    Kobayashi, Hirohito; Tanaka, Yoshimasa; Yagi, Junji; Minato, Nagahiro; Tanabe, Kazunari

    2011-08-01

    Human Vγ2 Vδ2-bearing T cells have recently received much attention in cancer immunotherapy. In this study, we conducted a phase I/II clinical trial of the adoptive transfer of γδ T cells to patients with advanced renal cell carcinoma. Eleven patients who had undergone nephrectomy and had lung metastasis were enrolled. Peripheral blood γδ T cells obtained from the patients were stimulated ex vivo with 2-methyl-3-butenyl-1-pyrophosphate (2M3B1PP), a synthetic pyrophosphomonoester antigen, and transferred in combination with zoledronic acid (Zol) and teceleukin (recombinant human interleukin-2). Expanded γδ T cells exhibited potent cytotoxic activity against tumor cells in vitro, and the proportion of peripheral blood γδ T cells among CD3(+) cells typically peaked three to 5 days after transfer. Tumor doubling time was prolonged in all 11 patients, and the best overall responses were 1 CR, 5 SD, and 5 PD, as defined based on Response Evaluation Criteria in Solid Tumors (RECIST). Although ten patients developed adverse reactions of grade ≥3, they were likely to have been the result of the concomitant infusion of Zol and IL-2, and most symptoms swiftly reverted to normal during the course of treatment. In conclusion, this clinical trial demonstrated that our regimen for the adoptive transfer of γδ T cells in combination with Zol and IL-2 was well tolerated and that objective clinical responses could be achieved in some patients with advanced renal cell carcinoma.

  9. Myocardial infarction determined by technetium-99m pyrophosphate single-photon tomography complicating elective coronary artery bypass grafting for angina pectoris

    SciTech Connect

    Burns, R.J.; Gladstone, P.J.; Tremblay, P.C.; Feindel, C.M.; Salter, D.R.; Lipton, I.H.; Ogilvie, R.R.; David, T.E.

    1989-06-15

    The incidence of acute myocardial infarction (AMI) complicating coronary artery bypass grafting (CABG) has previously been based on concordance of electrocardiographic, enzymatic and scintigraphic criteria. Technetium-99m pyrophosphate (Tc-PPi) single-photon emission computed tomography now enables detection of AMI with high sensitivity and specificity. Using this technique, perioperative AMI was detected in 12 of 58 patients (21%) undergoing successful elective CABG for stable angina pectoris. Stepwise multivariate logistic regression analysis was performed to compare the predictive value of preoperative (New York Heart Association class, left ventricular ejection fraction and use of beta blockers) and intraoperative (number of grafts constructed, use of internal mammary anastomoses, use of sequential saphenous vein grafts, smallest grafted distal vessel lumen caliber and aortic cross-clamp time) variables. Preoperative New York Association class (p = 0.04) and smallest grafted distal vessel lumen caliber (p = 0.03) were significant multivariate predictors of perioperative AMI. Only 1 perioperative patient with AMI (and 1 pyrophosphate-negative patient) developed new Q waves. Serum creatine kinase-MB was higher in patients with AMI by repeated measures analysis of variance (p = 0.0003). Five AMIs occurred in myocardial segments revascularized using sequential saphenous vein grafts, and 7 in segments perfused by significantly stenosed epicardial vessels with distal lumen diameter and perfusion territory considered too small to warrant CABG. At 6-month follow-up, the mean left ventricular ejection fraction increased from 0.61 to 0.65 in Tc-PPI-negative patients (p = 0.01), but not in perioperative patients with AMI.

  10. EVALUATION METHODOLOGY FOR PROLIFERATION RESISTANCE AND PHYSICAL PROTECTION OF GENERATION IV NUCLEAR ENERGY SYSTEMS: AN OVERVIEW.

    SciTech Connect

    BARI, R.; ET AL.

    2006-03-01

    This paper provides an overview of the methodology approach developed by the Generation IV International Forum Expert Group on Proliferation Resistance & Physical Protection for evaluation of Proliferation Resistance and Physical Protection robustness of Generation IV nuclear energy systems options. The methodology considers a set of alternative systems and evaluates their resistance or robustness to a collection of potential threats. For the challenges considered, the response of the system to these challenges is assessed and expressed in terms of outcomes. The challenges to the system are given by the threats posed by potential proliferant States and sub-national adversaries on the nuclear systems. The characteristics of the Generation IV systems, both technical and institutional, are used to evaluate their response to the threats and determine their resistance against the proliferation threats and robustness against sabotage and theft threats. System response encompasses three main elements: (1) System Element Identification. The nuclear energy system is decomposed into smaller elements (subsystems) at a level amenable to further analysis. (2) Target Identification and Categorization. A systematic process is used to identify and select representative targets for different categories of pathways, within each system element, that actors (proliferant States or adversaries) might choose to use or attack. (3) Pathway Identification and Refinement. Pathways are defined as potential sequences of events and actions followed by the proliferant State or adversary to achieve its objectives (proliferation, theft or sabotage). For each target, individual pathway segments are developed through a systematic process, analyzed at a high level, and screened where possible. Segments are connected into full pathways and analyzed in detail. The outcomes of the system response are expressed in terms of PR&PP measures. Measures are high-level characteristics of a pathway that include

  11. Evaluation Methodology For Proliferation Resistance And Physical Protection Of Generation IV Nuclear Energy Systems: An Overview

    SciTech Connect

    T. Bjornard; R. Bari; R. Nishimura; P. Peterson; J. Roglans; D. Bley; J. Cazalet; G.G.M. Cojazzi; P. Delaune; M. Golay; G. Rendad; G. Rochau; M. Senzaki; I. Therios; M. Zentner

    2006-05-01

    This paper provides an overview of the methodology approach developed by the Generation IV International Forum Expert Group on Proliferation Resistance & Physical Protection for evaluation of Proliferation Resistance and Physical Protection robustness of Generation IV nuclear energy systems options. The methodology considers a set of alternative systems and evaluates their resistance or robustness to a collection of potential threats. For the challenges considered, the response of the system to these challenges is assessed and expressed in terms of outcomes. The challenges to the system are given by the threats posed by potential proliferant States and sub-national adversaries on the nuclear systems. The characteristics of the Generation IV systems, both technical and institutional, are used to evaluate their response to the threats and determine their resistance against the proliferation threats and robustness against sabotage and theft threats. System response encompasses three main elements: 1.System Element Identification. The nuclear energy system is decomposed into smaller elements (subsystems) at a level amenable to further analysis. 2.Target Identification and Categorization. A systematic process is used to identify and select representative targets for different categories of pathways, within each system element, that actors (proliferant States or adversaries) might choose to use or attack. 3.Pathway Identification and Refinement. Pathways are defined as potential sequences of events and actions followed by the proliferant State or adversary to achieve its objectives (proliferation, theft or sabotage). For each target, individual pathway segments are developed through a systematic process, analyzed at a high level, and screened where possible. Segments are connected into full pathways and analyzed in detail. The outcomes of the system response are expressed in terms of PR&PP measures. Measures are high-level characteristics of a pathway that include

  12. Cardiopulmonary Function, Exercise Capacity, and Echocardiography Finding of Pediatric Patients With Kawasaki Disease: An Observational Study.

    PubMed

    Tuan, Sheng-Hui; Li, Min-Hui; Hsu, Miao-Ju; Tsai, Yun-Jeng; Chen, Yin-Han; Liao, Tin-Yun; Lin, Ko-Long

    2016-01-01

    assess and monitor cardiovascular risk of KD patients. Max-Z of CA correlates with PRPP modest inversely and might be used as a follow-up indicator of CA reserve during exercise after acute stage of KD.

  13. Teleconference highlights-NE-NA proliferation resistance review

    SciTech Connect

    Miller, Michael C

    2009-01-01

    Herczeg gave a readout from the kickoff meeting with Paul Lisowski - namely develop a common definition of proliferation resistance (for use by S-1, other upper management, public affairs, etc.), and to evaluate possible framework where a metric could be assigned for fuel cycle comparisons (integral, easy to communicate). Sprinkle raised concern about 'trivializing' notion of proliferation resistance (PR), with idea of making sure we don't lose the concept that strong safeguards and security are required within a nonproliferation framework that support U.S. policy goals. Integrated Safeguards by Design notion was brought up in this context. Round table discussion of the term PR, its misuse (even unintentional), fact that Chu is using term and apparently in context of proliferation proof. It was noted that there has been much work already done in this area and we should not reinvent the wheel. One of the first tasks needs to be gathering up old reports (TOPS, Como, PRPP, etc) and distributing to group (action item for all). It was also noted that there are multiple definitions of PR, including the recent NPIA, supporting the need for this type of activity. Miller described the current work package under AFCI, with $50k of funding from the campaign management account. Herczeg asked about additional funds should it become clear that a larger effort is required (tension between current program and getting something out relatively soon). Goldner to look into potential additional funds. Miller notes that within current work package, easy to engage LANL participants and that Per Peterson can participate under UCB funding (a new center is being established with UC fee awards from LANL and LLNL - the Berkeley Nuclear Research Center). Consensus that Per would be a good external member of the group. Sprinkle notes that held like to coordinate the NE and NA work packages. Miller and Sprinkle to work offline. Wallace talked about the possibility of being more quantitative in

  14. Facility Safeguardability Analysis In Support of Safeguards-by-Design

    SciTech Connect

    Philip Casey Durst; Roald Wigeland; Robert Bari; Trond Bjornard; John Hockert; Michael Zentner

    2010-07-01

    The following report proposes the use of Facility Safeguardability Analysis (FSA) to: i) compare and evaluate nuclear safeguards measures, ii) optimize the prospective facility safeguards approach, iii) objectively and analytically evaluate nuclear facility safeguardability, and iv) evaluate and optimize barriers within the facility and process design to minimize the risk of diversion and theft of nuclear material. As proposed by the authors, Facility Safeguardability Analysis would be used by the Facility Designer and/or Project Design Team during the design and construction of the nuclear facility to evaluate and optimize the facility safeguards approach and design of the safeguards system. Through a process of “Safeguards-by-Design” (SBD), this would be done at the earliest stages of project conceptual design and would involve domestic and international nuclear regulators and authorities, including the International Atomic Energy Agency (IAEA). The benefits of the Safeguards-by-Design approach is that it would clarify at a very early stage the international and domestic safeguards requirements for the Construction Project Team, and the best design and operating practices for meeting these requirements. It would also minimize the risk to the construction project, in terms of cost overruns or delays, which might otherwise occur if the nuclear safeguards measures are not incorporated into the facility design at an early stage. Incorporating nuclear safeguards measures is straight forward for nuclear facilities of existing design, but becomes more challenging with new designs and more complex nuclear facilities. For this reason, the facility designer and Project Design Team require an analytical tool for comparing safeguards measures, options, and approaches, and for evaluating the “safeguardability” of the facility. The report explains how preliminary diversion path analysis and the Proliferation Resistance and Physical Protection (PRPP) evaluation