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PubMed1982

Permeability of Dictyostelium discoideum to fucose and uracil following growth-arrest induced by starvation, hadacidin, and cerulenin.

The uptake of fucose and uracil by Dictyostelium discoideum in either a starvation or drug-induced growth-arrest state was studied. For both nutrients, the uptake was an energy-dependent process. The rate of fucose uptake remained constant for over four hours, while the uracil rate declined after about one hour, in starvation-induced growth-arrest. Under these conditions, fucose was found to be incorporated into membrane-associated glycoproteins and glycolipids, while uracil was incorporated into RNA. The rate of fucose uptake was the same for starvation or hadacidin-induced growth-arrest, but significantly lower for cerulenin-treated cells. In contrast, uracil uptake was slower in hadacidin-treated cells as opposed to starvation or cerulenin-induced growth-arrest cells. Further experiments showed that the incorporation rate of uracil into RNA was faster in hadacidin-treated cells than controls, and the cerulenin-treated cells were slower. The data suggest that the cells arrested in growth by nutrient deprivation retain the capacity to take-up and incorporate nutrients such as fucose and uracil and that pinocytosis is probably the process responsible for uptake.

Antifungal Agents↗
PubMed1990

De novo synthesis of uracil nucleotides in mouse liver and intestine studied using [15N]alanine.

The amount of newly synthesized uracil nucleotides in mouse liver and intestine was determined by analysis of 15N incorporation into the uracil nucleotide pool of these tissues after intraperitoneal infusion of 15N-labelled amino acids. The appearance of newly synthesized uracil nucleotides was linear with time, and essentially independent of the rate of infusion of L-[15N]alanine. Varying the amino acid used in the infusion could affect the enrichment in the uracil ring nitrogens, but had no significant effect on the calculated amount of de novo synthesis. These results demonstrate the utility of this method in measuring de novo uracil nucleotide synthesis in mouse liver and intestine in vivo. The method should be a valuable tool in the effort to understand the regulation and pharmacological manipulation of de novo uracil nucleotide synthesis.

Alanine↗
PubMed2001

Anticancer agent E7070 inhibits amino acid and uracil transport in fission yeast.

E7070 is a novel sulfonamide anticancer agent that inhibits cell cycle progression in G1 in mammalian cells, but its action targets are not known. We recently employed the genetically amenable fission yeast Schizosaccharomyces pombe as a model organism to search for its targets. Here, we show that E7070 inhibits imports of amino acid and uracil into S. pombe cells. Unlike their prototrophic counterparts, leucine- and uracil-auxotrophic strains are sensitive to E7070 and are unable to proliferate with a delayed G1-S transition in low-glucose yeast extract-polypeptone medium containing this drug because this chemical markedly inhibits the uptake of leucine and uracil in low glucose medium. Furthermore, addition of leucine or uracil to the culture medium or overexpression of genes encoding an amino acid or uracil transporter suppresses the E7070-imposed growth inhibition of these auxotrophic strains. Thus, some of the molecular targets for E7070 action in S. pombe are likely to be leucine and uracil transporters.

Amino Acid Transport Systems↗
PubMed2000

Anti-Epstein-Barr virus (EBV) activity of beta-L-5-iododioxolane uracil is dependent on EBV thymidine kinase.

beta-L-5-Iododioxolane uracil was shown to have potent anti-Epstein-Barr virus (EBV) activity (50% effective concentration = 0.03 microM) with low cytotoxicity (50% cytotoxic concentration = 1,000 microM). It exerts its antiviral activity by suppressing replicative EBV DNA and viral protein synthesis. This compound is phosphorylated in cells where the EBV is replicating but not in cells where the EBV is latent. EBV-specific thymidine kinase could phosphorylate beta-L-5-iododioxolane uracil to the monophosphate metabolite. The K(m) of beta-L-5-iododioxolane uracil with EBV thymidine kinase was estimated to be 5.5 microM, which is similar to that obtained with thymidine but about fivefold higher than that obtained with 2' fluoro-5-methyl-beta-L-arabinofuranosyl uracil, the first L-nucleoside analogue discovered to have anti-EBV activity. The relative V(max) is seven times higher than that of thymidine. The anti-EBV activity of beta-L-5-iododioxolane uracil and its intracellular phosphorylation could be inhibited by 5'-ethynylthymidine, a potent EBV thymidine kinase inhibitor. The present study suggests that beta-L-5-iododioxolane uracil exerts its action after phosphorylation; therefore, EBV thymidine kinase is critical for the antiviral action of this drug.

Antiviral Agents↗
PubMed1975

Isolation and initial characterization of a uracil auxotroph of the blue-green alga Anacystis nidulans.

A uracil-requiring auxotroph of Anacystis nidulans was isolated after treatment with N-methyl-N'-nitrosoguanidine. Neither precursors in the de novo pyrimidine pathway nor compounds of "salvage" or degradative pathways could replace the uracil requirement. The reversion frequency for mutation to a nonuracil requirement for growth was 2.0 times 10(-8). The calculated average rate of uracil utilization was 1.1 times 10(-17) mol of uracil per unit cell mass/h. The amount of uracil required for the synthesis of a unit cell mass was 3.8 times 10(-17) mol of uracil.

Cyanobacteria↗
PubMed1979

Specificity of uracil uptake in Neurospora crassa.

The specificity of uracil uptake was investigated in germinating wild-type conidia of Neurospora crassa. From comparative inhibition studies, several generalizations concerning the specificity of uracil uptake can be made. (i) The tautomeric forms of uracil analogs is an important determinant of recognition by the uptake system. (ii) Substituents at the 5 position of the pyrimidine ring may impose steric constraints on binding. (iii) The presence of a negative charge results in the loss of recognition. (iv) The double bond between the 5 and 6 carbons appears to be important for recognition. (v) Purine bases do not inhibit uracil uptake. Crude extracts of the transport-deficient mutant strain uc-5 pyr-1 were shown to have uridine 5'-monophosphate pyrophosphorylase activity comparable to that of the wild-type strain, suggesting that uracil uptake in Neurospora does not occur by a group translocation mechanism involving phosphoribosylation. Specificity studies of uridine 5'-monophosphate pyrophosphorylase indicated that phosphoribosylation was not an important determinant of the specificity of uracil uptake.

Biological Transport, Active↗
PubMed1981

Synthesis and metabolism of uracil-containing deoxyribonucleic acid in Escherichia coli.

Significant amounts of uracil were found in the deoxyribonucleic acids (DNAs) of Escherichia coli mutants deficient in both uracil-DNA glycosylase (ung) and deoxyuridine 5'-triphosphate nucleotidohydrolase (dut) activities, whereas little uracil was found in the DNAs of wild-type cells and cells deficient in only one of these two activities. The amounts of uracil found in the DNAs of dut ung mutants were directly related to the growth temperature of the cultures, apparently because the deoxyuridine 5'-triphosphate nucleotidohydrolase synthesized by dut mutants was temperature sensitive. The dut mutant used failed to grow exponentially, became filamentous at temperatures above 25 degrees C, and exhibited a hyperrec phenotype; however, the ung mutation suppressed all of these effects. Although the dut ung mutants grew exponentially at all temperatures, their growth rates were always slower than the growth rate of the wild type. Since pool size measurements indicated that both deoxyuridine triphosphate and deoxythymidine triphosphate pools were markedly elevated in dut mutants, the reduced growth rate of dut ung cells apparently was due to the actual presence of uracil in the DNA, rather than to a deficiency of deoxyuridine triphosphate and deoxyribosylthymine triphosphate for DNA synthesis. The presence of uracil in E. coli donor DNA also markedly reduced the recombination frequency when the recipient cells were ung+, indicating that DNA repair commenced before the entering DNA could be replicated.

DNA Glycosylases↗
PubMed1975

Model of the antimicrobial silver uracil.

A model is proposed for the antimicrobial agent, silver uracil, whereby silver interacts with uracil forming a silver uracil combination with the silver in the +1 state intercalating between stacked uracils in a manner similar to a 'sandwich' model. The uracils maintain stability by hydrogen bonding with the water solvent, and 'flip-flop' through an antiparallism mode at 220 degrees. The silver bonds to the uracil by a charge transfer mechanism, increasing the nuclear shielding field of the pyrimidine. The presence of the water (solvent) is necessary for the structure.

Anti-Bacterial Agents↗
PubMed2002

H-NMR studies of duplex DNA decamer containing a uracil cyclobutane dimer: implications regarding the high UV mutagenecity of CC photolesions.

To determine the origin of the UV-specific CC to TT tandem mutation at the CC site, we made a duplex DNA decamer containing a uracil cis-syn cyclobutane dimer (CBD) as the deaminated model of a cytosine dimer. Two-dimensional 1H-NMR spectroscopy studies were performed on this sequence where two adenines (Ade) were opposite to the uracil dimer. Two imino protons of the uracil dimer were found to retain Watson-Crick hydrogen bonding with the opposite Ade, although the 5'-U(NH) of the dimer site showed unusual upfield shift like that of the 5'-T(NH) of the TT dimer, which seemed to be associated with deshielding by the flanking base rather than with reduced hydrogen bonding. (McAteer et al. 1998, J. Mol. Biol. 282:1013-1032). Hydrogen bondings at the dimer site were also supported by detecting typical strong nuclear Overhauser effects (NOE) between two imino protons and the opposite Ade H2 or NH2. But sequential NOE interactions of base protons with sugar protons were absent at the two flanking nucleotides of the 5' side of the uracil dimer and at the intradimer site, contrasting with its thymine analog where sequential NOE was absent only at the A4-T5 step. In addition, NOE cross peak for U5(NH) <--> A4(H2) was detected, although the NOE interactions of U6(NH) with A7(H2) and A17(H2) were not observed in contrast to the thymine dimer duplex. This different local structural alteration may be affected by the induced right-hand twisted puckering mode of cis-syn cyclobutane ring of the uracil dimer in the B-DNA duplex, even though the isolated uracil dimer had left-hand twisted puckering rigidly. In parallel, these observations may be correlated with observed differences in mutagenic properties between cis-syn UU dimer and cis-syn TT dimer.

Base Sequence↗
PubMed1990

Misincorporation of uracil into DNA as possible contributor to neuronal aging and abiotrophy.

Neuronal aging and abiotrophy may be related to the abnormal presence of uracil in DNA. Evidence which could support this hypothesis exists: 1) DNA polymerase beta, the only nuclear DNA polymerase present in adult neurons which is able to repair damaged DNA, incorporates dUTP or dTTP with the same efficiency. This suggests that in adult neurons the incorporation of dUTP into DNA is solely dependent on the relative intracellular concentration of dUTP; 2) uracil into DNA also arises from cytosine deamination; 3) at birth, when neurons stop proliferating, uracil DNA-glycosylase, the enzyme responsible of the removal of uracil from DNA, nearly disappears; 4) a significant replacement of thymine by uracil in DNA could produce genetic instability which in turn could affect the recognition of DNA sequences by enzymes and/or by regulatory DNA binding proteins. Thus enzymatic defects which might alter the intracellular dUTP pool, in different neuronal systems, could account for the multiplicity of the clinical manifestations of aging and neurodegenerative disorders. The increase of the age-specific rate of abiotrophic diseases may be due to accumulation with time of uracil containing DNA.

Cell Survival↗
PubMed1995

Reaction of bromotrichloromethane derived free radicals with uracil in a model system. Structures of products formed.

Free radicals generated by benzoyl peroxide-mediated catalytic decomposition of bromotrichloromethane (eg. trichloromethyl) were allowed to react under nitrogen or under air with uracil. Under nitrogen two reaction products were formed, one was identified as 5-chlorouracil and the other as a 5-bromouracil. Under air, besides the above two products other nine were also formed: 5,6-dihydrouracil; 5-hydroxyuracil; a chlorohydroxy adduct of uracil; a bromohydroxy derivative of uracil having the 5,6 bond in the saturated form; other bromohydroxy derivative of uracil having the double bond intact; 5,6-dihydroxyuracil; two dihalogenated hydroxylated uracil derivatives and one peak we were not able to descipher its structure. No single reaction product formed had carbon centered radicals (eg. trichloromethyl) added from CBrCl3 and consequently would be missed in 'in vivo' covalent binding studies where 14C haloalkane (CBrCl3 or carbon tetrachloride) were employed. If similar reaction products resulted during interaction of CBrCl3 reactive metabolites with uracil in RNAs, significant deleterious effects in their function would be expected. That possibility, however, remains to be established.

Aerobiosis↗
PubMed1999

Only one of the charged amino acids located in membrane-spanning regions is important for the function of the Saccharomyces cerevisiae uracil permease.

The transport of uracil into the yeast Saccharomyces cerevisiae is mediated by uracil permease, a specific co-transporter encoded by the FUR4 gene. Uracil permease is a multispan membrane protein that is delivered to the plasma membrane via the secretory pathway. Experimental results led to the proposal of a two-dimensional model of the protein's topology. According to this model, the membrane domain of Fur4p contains three charged amino acid residues (Glu-243, Lys-272 and Glu-539) that are conserved in the members of the FUR family of yeast transporters. We have previously shown that a mis-sense mutation leading to the replacement of Lys-272 by Glu severely impairs the function of uracil permease. In the present paper, the role of the three charged residues present in the membrane-spanning regions of Fur4p was further investigated by using site-directed mutagenesis. The variant permeases were correctly targeted to the plasma membrane and their stabilities were similar to that of the wild-type permease. The effect of the mutations was studied by measuring the uptake constants for uracil on whole cells and equilibrium binding parameters on plasma membrane-enriched fractions. We found no evidence for ionic interaction between either of the glutamic residues in transmembrane segments 3 and 9 and the lysine residue in transmembrane segment 4. Of the three charged residues, only Lys-272 was important for the transport activity of the transporter. Its replacement by Ala, Glu or even Arg strongly impaired both the binding and the translocation of uracil.

Amino Acid Sequence↗
PubMed1992

The presence of uracil-DNA glycosylase in insects is dependent upon developmental complexity.

The metamorphosis of insects can, in a general way, be divided between those organisms that undergo pupation accompanied by cellular histolysis and those that gradually develop into adults without an intervening pupal stage of development. In the former case, the death of a cell population is an integral part of development that is tightly associated with massive DNA degradation during pupation. In that regard, it has been suggested that uracil-containing DNA acts as a target for the nucleolytic breakdown of DNA during histolysis in insects (Deutsch, W. A. (1987) Mutat. Res. 184, 209-215), thus placing into question how compatible the existence of uracil-DNA glycosylases would be for this form of developmental signal. As a result, we tested for the presence of a uracil-DNA glycosylase in insects representative of those having an intervening pupal stage of development and those that do not. We show here that a nonpupating insect contains a uracil-DNA glycosylase activity. Conversely, crude extracts of Drosophila melanogaster, as well as of three other insect populations that undergo pupation similar to that found in Drosophila, do not contain detectable levels of this DNA repair activity. Thus, there appears to be a consistent correlation between cellular destruction during development and the absence of a uracil-DNA glycosylase, which supports the possibility that uracil-containing DNA may play an important role in those cells targeted for death.

Animals↗
PubMed1981

Induction of uracil-DNA glycosylase and dUTP nucleotidohydrolase activity in herpes simplex virus-infected human cells.

HeLa BU cells infected with either the type 1 or the type 2 forms of herpes simplex virus show an increase in the activities of uracil-DNA glycosylase and dUTP nucleotidohydrolase. Under optimal conditions, uracil-DNA glycosylase activity increases approximately 40-fold in HSV type 2-infected cells. In herpes simplex virus (HSV) type 1-infected cells, uracil-DNA glycosylase activity increases only 6-fold. At a KCl concentration of 100 mM, uracil-DNA glycosylase derived from HSV type 2-infected cells is activated 2-fold, while the glycosylase extracted from mock infected HeLa BU cells is inhibited almost 90% at 100 mM KCl. dUTP nucleotidohydrolase activity increases 4-fold and 3-fold, respectively, in HSV type 1- and HSV type 2-infected HeLa BU cells. Nondenaturing polyacrylamide gel electrophoresis of extracts derived from the type 1- and type 2-infected cells indicates distinct electrophoretic mobilities from the host cell enzyme. dUTP nucleotidohydrolase RF values for the mock infected cells, HSV type 1, and HSV type 2 are 0.5, 0.25, and 0.33, respectively. Serum from rabbits immunized against cells infected with herpes simplex virus type 1 or type 2 specifically neutralizes the dUTPase and uracil-DNA glycosylase activities extracted from herpes simplex virus-infected cells. This serum does not neutralize dUTPase or uracil-DNA glycosylase activity derived from mock infected cells.

Cell Transformation, Viral↗
PubMed1993

Dihydropyrimidine dehydrogenase. Kinetic mechanism for reduction of uracil by NADPH.

Steady-state and pre-steady-state kinetic data were used to determine the kinetic mechanism for bovine liver dihydropyrimidine dehydrogenase (DPDase). Steady-state kinetic data suggested a random rapid-equilibrium mechanism with Km values for NADPH and uracil of 0.12 microM and 0.8 microM, respectively, and a kcat of 1.6 s-1 in Tris buffer at pH 8.0 and 37 degrees C. The dissociation constant of DPDase for NADPH at 25 degrees C in the absence of uracil (0.09 microM) was similar to the Km for NADPH. DPDase also catalyzed the exchange of tritium in [4S-3H,4R-1H]NADP3H with solvent protons in the absence of uracil. DPDase inactivated by 5-ethynyluracil, which covalently modifies the enzyme at the uracil binding site, catalyzed the exchange reaction at the same rate (1 s-1) as native enzyme. Thus, the interaction of NADPH with DPDase was independent of the uracil binding site. Because DPDase catalyzed the exchange of deuterium in [4S-2H,4R-1H]NADP2H with solvent protons with a rate constant of 5.4 s-1, which was significantly larger than that for tritium, the analogous rate constant for exchange of the 4-hydrogen in NADPH must be significantly larger than 5 s-1. Consequently, intermediates on the exchange pathway were kinetically competent to participate in the reduction of uracil by NADPH (kcat = 1.6 s-1). Rate constants for reduction of DPDase by NADPH and 5,6-dihydrouracil were several orders of magnitude greater than kcat. The rate constants for dissociation of E.NADP+ (15 s-1) and for dissociation of E.5,6-dihydrouracil (> 250 s-1) were also greater than kcat. These results supported a random rapid-equilibrium kinetic mechanism and suggested kcat was an internal electron transfer between enzymic prosthetic groups.

Animals↗
PubMed1993

Synthesis of brain-targeted 1-(2-deoxy-2-fluoro-beta-D-ribofuranosyl)-(E)-5-(2-iodovinyl)uracil coupled to a dihydropyridine <---> pyridinium salt redox chemical-delivery system.

1-(2-Deoxy-2-fluoro-beta-D-ribofuranosyl-(E)-5-(2-iodovinyl)uracil (IVFRU) was coupled to a dihydropyridine <---> pyridinium salt redox chemical-delivery system (CDS) via a cleavable sugar-ester linkage as a site-directed approach to increase diffusion of the parent nucleoside into the central nervous system. Treatment of 1-(2-deoxy-2-fluoro-beta-D-ribofuranosyl)uracil with Bu(t)Me(2)SiCl in the presence of imidazole in DMF yielded the protected 5-O-tert-butyldimethylsilyl derivative. Subsequent reaction with nicotinoyl chloride hydrochloride in pyridine afforded 1-[5-O-tert-butyldimethylsilyl-2-deoxy-2-fluoro-3-O-(3-pyridylcarbony l )-beta-D-ribofuranosyl]uracil. Reaction with iodine monochloride in methanol simultaneously cleaved the silyl ether moiety and iodinated the uracil ring at the 5-position. Coupling with (E)-Bu(3)Sn-CH = CH-SiMe(3) in the presence of (Ph3P)2Pd2(II)Cl2 in THF gave 1-[2-deoxy-2-fluoro-3-O-(3-pyridylcarbonyl)-beta-D-ribofuranosyl]- (E)-5-(2-trimethylsilylvinyl)uracil. Quaternization with iodomethane in acetone yielded the N-methylpyridinium iodide salt. Ionation of the reactive (E)-trimethylsilylvinyl moiety with iodine monochloride in acetonitrile and reduction of the quaternary pyridinium iodide salt with sodium dithionite in the presence of sodium hydrogen carbonate was carried out as a one-pot procedure to afford 1-[2-deoxy-2-fluoro-3-O-(1-methyl-1,4-dihydropyridyl-3-carbonyl)-b eta-D-ribofuranosyl]-(E)-5-(2-iodovinyl)uracil (IVFRU-CDS). This synthetic strategy is readily amenable to the high specific-activity radioiodination of IVFRU.

Animals↗
PubMed2005

Theoretical study of guanine-Cu and uracil-Cu (neutral, anionic, and cationic). Is it possible to carry out a photoelectron spectroscopy experiment?

The structure and bonding of guanine-Cu and uracil-Cu (neutral, anionic, and cationic) are discussed on the basis of the calculated structures and energies. The interaction of the metal atom with guanine and uracil has been analyzed using the B3LYP density-functional approach. The removal of one electron from the neutral complexes produces the stabilization of one of the isomers, while the addition of one electron leads to a system where the metal atom is weakly bounded to guanine or uracil, according to the metal-bases bond distance that is long (2.29-2.90). For guanine-Cu and uracil-Cu, the vertical ionization energy of the anion is close to the dissociation energy of one hydrogen atom from guanine-Cu or uracil-Cu. In these cases, it could be possible to produce the detachment of one electron from the anion and also the removal of one hydrogen atom. This is important since the photoelectron spectroscopy of atomic or mixed-atomic cluster anions has proven to be a very effective tool in the study of small systems. For the analysis of copper atoms with DNA bases such as guanine and uracil, it is expected that the photoelectron spectra of the anion-bases complexes strongly resemble the spectrum of Cu(-1), just shifted to higher electron binding energies due to the product stabilization. Hopefully, this information will be useful for the experimental groups.

Journal Article↗
PubMed1998

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

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.

Amino Acid Sequence↗