PubMed HealthSearch

SEARCH · PubMed Health

Results for “uracil”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources

Biochemical mechanism of uracil uptake regulation in Escherichia coli B. Allosteric effects on uracil phosphoribosyltransferase under stringent conditions.

The regulation of uracil uptake in bacteria was studied in bacteriophage T4-infected cells, where host-specific, stable RNA synthesis is completely shut-off by phage, and where phage-specific RNA synthesis, which is not stringently regulated, could be followed by a continuous incorporation of uracil. This incorporation into phage RNA was found to be dependent on the allelic state of the rel gene and it was thus severely restricted under stringent conditions. This was not the case with adenine, which was incorported into RNA to almost the same extent under stringent and relaxed conditions, respectively. The inhibition of uracil uptake under proceeding RNA formation, which was furthermore found to be reversed by addition of chloramphenicol, indicated a specific mechanism governing the cellular entry of uracil. This is suggested to involve the allosteric regulation of uracil phosphoribosyltransferase (EC 2.4.2.9.). The enzyme was partially purified by ammonium sulfate precipitation and gel chromatography. The dependence on GDP and GTP as positive effectors was demonstrated. The stimulatory effect of GTP was abolished in vitro by the addition of guanosine 5'-diphosphate 3-diphosphate, which is known to accumulate during amino acid starvation in stringent bacteria. The reversible inactivation of the enzyme by dilution suggested a subunit structure of uracil phosphoribosyltransferase.

Adenine

Uracil incorporation: a source of pulse-labeled DNA fragments in the replication of the Escherichia coli chromosome.

Uracil is incorporated into newly synthesized DNA by mutants of Escherichia coli with reduced levels of dUTPase (dUTP nucleotidohydrolase; EC 3.6.1.23). Excision-repair of the incorporated uracil results in the generation of labeled DNA fragments that appear after brief pulses with [(3)H]thymidine [Tye, B-K., Nyman, P.-D., Lehman, I. R., Hochhauser, S. & Weiss, B. (1977) Proc. Natl. Acad. Sci. USA 74, 154-157]. Uracil is also incorporated into the newly synthesized DNA of strains of E. coli that contain normal levels of dUTPase. DNA fragments generated by the postreplication excision-repair of uracil may therefore contribute to the pool of nascent DNA (Okazaki) fragments that normally appear in wild-type strains. Discontinuous DNA replication has been examined in the absence of uracil excision by comparing Okazaki fragments in strains that are defective in DNA polymerase I (polA(-)) and polA(-) strains that are also defective in uracil N-glycosidase, an enzyme required for the excision-repair of uracil in DNA (polA(-)ung(-)). Little or no difference was detected in the level of Okazaki fragments in the polA(-) strain as compared with the polA(-)ung(-) strain. Thus, the uracil-induced cleavage of DNA cannot be the sole mechanism for the generation of Okazaki fragments. Mutants that are defective both in dUTPase and in uracil N-glycosidase incorporate uracil into their DNA with a high frequency (up to 1 per 100 nucleotides). These uracil residues, once incorporated, persist in the DNA without an adverse affect on the growth of the cells.

Chromosomes

Uracil metabolism in golden hamster after irradiation.

The catabolism of uracil and the total balance of excreted radioactivity were studied in golden hamsters after a peroral application of 14C-uracil. Twenty-four hours after administration most of the radioactivity taken up appeared in expired carbon dioxide. The percent proportion of radioactivity in carbon dioxide was independent of the amount of uracil administered. On the other hand, the percentage of radioactivity excreted in urine depended on the amount of uracil taken up, high doses of the compound causing up to eight-fold increase in urine-excreted radioactivity. Most of the exogenously-administered uracil was catabolized within the first 5 hours. Irradiation had no substantial effect on the dynamics of uracil catabolism. Analysis of urine revealed that most urine-excreted radioactivity is in the form of uracil. On peroral application of high doses of uracil to irradiated hamsters, their urine was found to contain barbituric acid which originated from uracil.

Animals

Effect of coadministration of uracil or cytosine on the anti-tumor activity of clinical doses of 1-(2-tetrahydrofuryl)-5-fluorouracil and level of 5-fluorouracil in rodents.

Concentration of 5-fluorouracil (5-FU) in the tumor, blood, and various organs of AH130-bearing rats after administration of clinical doses of 1-(2-tetrahydrofuryl)-5-fluorouracil (FT-207) and uracil was examined. The concentration of 5-FU in blood was less than 0.02 microgram/ml with all combinations of FT-207 and uracil except high molar ratios of uracil to FT-207 (ratio, 5 and 10), whereas high concentrations of up to a maximum of 0.200 microgram/g on administration of uracil plus 5 or 7.5 mg/kg of FT-207 (ratio, 4), was found in the tumor. On oral administration of FT-207 plus uracil in various combinations, the highest T/B (ratio of concentration of 5-FU in the tumor to that in blood) value was obtained at a ratio of uracil to FT-207 of 4. With this combination, 5-FU concentration in the tumor, muscle, and spleen was higher than that after administration of FT-207 alone (5 mg/kg). These results suggest that at the clinical doses the optimum molar ratio of uracil to FT-207 is 4. Coadministration of cytosine enhanced the antitumor activity of FT-207 on sarcoma-180 in mice. However, cytosine enhanced the antitumor activity of FT-207 less than uracil and its coadministration resulted in a lower concentration of 5-FU in the tumor than coadministration of uracil.

Administration, Oral

Uracil incorporation into nascent DNA of thymine-requiring mutant of Bacillus subtilis 168.

A thymine-requiring mutant of Bacillus subtilis strain 168 accumulates short DNA chains after brief pulses with [(3)H]thymidine. Reversion of the thy mutation to thy(+) abolishes the accumulation of short DNA chains, suggesting that the accumulation is related to the thy mutation. The reason for this accumulation has been further investigated by analysis of a mutant with a defective uracil-DNA glycosidase activity (urg). The accumulation of short DNA chains in thy(-) cells is abolished by the deficiency of uracil-DNA glycosidase activity. In thy(+) cells, the deficiency of the glycosidase activity does not change the sedimentation profile of pulse-labeled DNA. DNA isolated from thy(-)urg(-) cells is fragmented by successive treatment with purified uracil-DNA glycosidase and alkali, indicating that uracil residues are present in this DNA. DNA isolated from thy(+)urg(-) cells is not fragmented by the same treatment. Significant radioactivity is detected in the dUMP region, when [(3)H]uridine-labeled DNA from thy(-)urg(-) cells is hydrolyzed and analyzed by thin-layer chromatography. Only a trace amount of radioactivity, which is not influenced by the deficiency of uracil-DNA glycosidase activity, is found in the dUMP region in DNA hydrolysates from thy(+) cells. These results suggest that, in thy(-) cells, uracil is incorporated into DNA and the accumulation of short DNA chains results from the excision-repair of this uracil whereas in thy(+) cells, uracil is seldom, if ever, incorporated into DNA.

Bacillus subtilis

Selective inhibition of uracil tRNA methylases of E. coli by ethionine.

L-ethionine has been found to inhibit uracil tRNA methylating enzymes in vitro under conditions where methylation of other tRNA bases is unaffected. No selective inhibitor for uracil tRNA methylases has been identified previously. 15 mM L-ethionine or 30 mM D,L-ethionine caused about 40% inhibition of tRNA methylation catalyzed by enzyme extracts from E. coli B or E. coli M3S (mixtures of methylases for uracil, guanine, cytosine, and adenine) but did not inhibit the activity of preparations from an E. coli mutant that lacks uracil tRNA methylase. Analysis of the 14CH3 bases in methyl-deficient E. coli tRNA after its in vitro methylation with E. coli B3 enzymes in the presence or absence of ethionine showed that ethionine inhibited 14CH3 transfer to uracil in tRNA, but did not diminish significantly the 14CH3 transfer to other tRNA bases. Under similar conditions 0.6 mM S-adenosylethionine and 0.2 mM ethylthioadenosine inhibited the overall tRNA base methylating activity of E. coli B preparations about 50% but neither of these ethionine metabolites preferentially inhibited uracil methylation. Ethionine was not competitive with S-adenosyl methionine. Uracil methylation was not inhibited by alanine, valine, or ethionine sulfoxide. It is suggested that the thymine deficiency that we found earlier in tRNA from ethionine-treated E. coli B cells, resulted from base specific inhibition by the amino acid, ethionine, of uracil tRNA methylation in vivo.

Amino Acids

Depression of uracil uptake by ammonium in Neurospora crassa.

The mechanism of uracil uptake and one aspect of its regulation were studied in germinated conidia of Neurospora crassa. Uracil was found to be taken up by a transport mechanism that did not exhibit Michaelis-Menten kinetics. Rather, the kinetic patterns indicated two separate systems or a single transport mechanism with negative cooperativity. Cytosine and thymine inhibited uracil uptake, but uridine did not. The mutant strain uc-5-pyr-1, which failed to transport uracil, was used in reversion studies and to map the uc-5 locus. Spontaneous reversion rates at the uc-5 locus were found to be approximately 2 x 10(-8), indicating that the uc-5 lesion results from a single mutation. Loss of the uracil transport function through a single mutation favors the model of a single transport mechanism with negative cooperativity. Uracil uptake was significantly decreased in the presence of NH 4+, and evidence is presented for repression by NH4+ of a uracil transport system. Growth rates of pyrimidine-requiring and wild-type strains measured in the presence and absence of NH4+, with uracil as the pyrimidine supplement, showed that NH4+ decreased the growth rates of the pyrimidine-requiring strains significantly, while having no effect on wild-type growth rates.

Ammonia

The properties of a bacteriophage T5 mutant unable to induce deoxyuridine 5'-triphosphate nucleotidohydrolase. Synthesis of uracil-containing T5 deoxyribonucleic acid.

Bacteriophage T5 induces a deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) activity during infection of Escherichia coli. A T5 mutant (T5 dut) unable to induce this dUTPase activity has been isolated. Although this mutant is viable, the E. coli dUTPase activity is not sufficiently active to exclude uracil from the progeny DNA and about 3% of the thymine is replaced by uracil. When the mutant is grown in an E. coli dut host about 12% of the thymine in the progeny DNA is replaced by uracil. T5 phage containing 12% uracil can replicate in uracil-DNA glycosylase-deficient (ung) hosts with high efficiency, but fail to replicate in ung+ hosts. The amount of thymine replaced by uracil in the progeny produced in dut hosts is nearly independent of the ung genotype, indicating that the host uracil-DNA glycosylase-dependent repair pathway is not operating efficiently to remove uracil from T5 progeny DNA.

Coliphages

Reaction of uracil and thymine derivatives with sodium bisulfite. Studies on the mechanism and reduction of the adduct.

The rates and equilibria for the addition of sodium bisulfite to uracil, thymine, and their nucleosides have been studied for the pH range 3-9.5. The rate of addition for uracil is proportional to the concentration of sulfite ion and unionized uracil. The equilibrium constant (25 degrees C) for the reaction is (1.0 +/- 0.15) X 10(3) 1 - mol-1 for uracil and 0.62 +/- 0.03 1- mol-1 for thymine. A pH of 6-7, with a high bisulfite concentration is suggested for biochemical applications of the uracil reaction. The uracil reaction, which proceeds readily under physiological conditions and has a high equilibrium constant, may be a contributing cause of the biochemical effects of bisulfite and sulfur dioxide. Additional evidence on the structure of the thymine-bisulfite adduct has been obtained by nuclear magnetic resonance spectroscopy. This spectrum supports the assignment of structure as dihydrothymine-6-sulfonate. The uracil-bisulfite adduct is reduced by sodium borohydride to sodium 3-ureido-propanol-2-sulfonate. This reaction is suggested for the chemical modification of nucleic acids.

Binding Sites

Excision of uracil from bromodeoxyuridine-substituted and U.V.-irradiated DNA in cultured mouse lymphoma cells.

A uracil-DNA glycosylase activity was detected in cell-free extracts from cultured mouse lymphoma L5178 cells. We investigated whether or not this enzyme plays a role in the removal of uracil from chromosomal DNA. U.V. light (254nm) irradiation of the cells with BUdR-substituted DNA produced not only single-strand breaks but also 'internal' uracil residues that were recognized as substrate sites by uracil-DNA glycosylase. These 'internal' uracil residues were lost from the DNA upon reincubation of the irradiated cells. The product released from the DNA was identified as uracil. Thus, the intracellular action of the uracil-DNA glycosylase was demonstrated and the subsequent reconstitution of the DNA strand was inferred in cultured mammalian cells.

Animals

Role of uracil-DNA glycosylase in the repair of deaminated cytosine residues of DNA in Escherichia coli.

Uracil-DNA glycosylase, which acts specifically on uracil-containing DNA, was purified 250-fold from an extract of Escherichia coli 1100. The enzyme releases free uracil from DNA, producing alkali-labile apyrimidinic sites in the DNA. The enzyme is active on both native and heat-denatured DNA of phage PBS1, which contains uracil in place of thymine. piX174 DNA which had been treated with bisulfite and then at alkaline pH was susceptible to the action of uracil-DNA glycosylase. Since DNA treated with bisulfite alone was less susceptible to the enzyme, it is likely that the enzyme recognizes deaminated cytosine, namely uracil, but not bisulfite adducts of uracil and cytosine in the treated DNA. DNA treated with nitrite or hydroxylamine was not attacked by the enzyme. Enzyme activity acting on bisulfite-treated DNA was absent from an extract of E. coli mutant BD10 (ung). The mutant exhibited higher sensitivity to bisulfite than did the wild-type strain and was unable to reactivate phage T1 pre-exposed to bisulfite and weak alkali.

Binding Sites

In vivo synthesis and properties of uracil-containing DNA.

T4 bacteriophage DNA containing as much as 30% of its thymine replaced by uracil can be synthesised in Escherichia coli deficient in both dUTPase and uracil--DNA glycosidase. This uracil-containing DNA is competent for RNA transcription, and can be packaged into phage which are viable, if the host cells are deficient in uracil--DNA glycosidase activity. If the host cells are not deficient in this glycosidase activity the infecting phage DNA is rapidly attacked, resulting in more than 50% acid-solubilisation of the DNA. The infected cells are inefficiently killed, presumably because of very limited, if any, expression of the phage DNA. These results indicate that this replacement of thymine by uracil in DNA does not seriously impair the biological functionality of T4 DNA, provided the DNA is not subjected to the breakdown (repair) pathway initiated by uracil--DNA glycosidase.

Bacteriolysis

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

Pyrimidine nucleoside analogues.X. 5-Substituted 1-(1,3-dihydroxypropyl-2) uracils.

A convenient method is suggested for synthesis of uracil-1-malonic acid diethyl ester by alkylating 2,4-bis(trimethylsilyl) uracil with bromo-malonic acid diethyl ester. This compound has been shown to hydrolyze with NaOH yielding either uracil or uracil-1-acetic acid, depending on reaction conditions. Similarly, thymine-1-malinic acid diethyl ester and 5-fluorouracil-1,3-dimalonic acid tetraethyl ester were obtained. 1-(1,3-Dihydroxypropyl)uracil has been obtained by reducing uracil-1-malonic acid diethyl ester with NaBH4.

Hydrogen-Ion Concentration

Specific labeling of intracellular Toxoplasma gondii with uracil.

Radioactive uracil was not significantly incorporated into the nucleic acids of human fibroblast cells. Infection of these cells with Toxoplasma gondii resulted in an exponential increase in the rate of uracil incorporation that paralleled the exponential growth of the parasite. One day after infection the rate of uracil incorporation was increased 100-fold. It was established by autoradiography that all of the [3H] uracil was incorporated into the intracellular parasites. A possible explanation for this difference in ability to use uracil is our observation that the specific activity of uridine phosphorylase was 100-fold greater in partially purified parasites than in the host cell.

Animals

Isolation and characterization of a Bacillus subtilis mutant with a defective N-glycosidase activity for uracil-containing deoxyribonucleic acid.

Crude cell extracts of Bacillus subtilis 168T exhibit enzyme activity capable of releasing free uracil from phage PBS1 deoxyribonucleic acid (DNA) in the presence of ethylenediaminetetraacetate. By measuring the enzyme activity in 300 clones that emanated from mutagenized cells, we obtained a mutant strain that did not show this N-glycosidase activity. The mutant strain, designated as TKJ6901 (urg-1) exhibited no physiological abnormalities. We observed the intracellular action of the enzyme by following the fate of uracil-containing DNA in cells from wild-type and mutant cultures. When infection with phage PBS1 was allowed in the presence of chloramphenicol, extensive degradation of phage DNA was observed only in the wild-type cells. When bromouracil residues were converted to uracil residues by ultraviolet light irradiation in the presence of cysteamine, the DNA was extensively fragmented in the wild-type cells. These single-strand breaks were rejoined upon postirradiation incubation. In contrast, such fragmentation of the DNA was not observed in the mutant cells, indicating that the uracil residues were not removed from the DNA. This demonstrated that the N-glycosidase activity was involved in the excision of uracil in DNA. A transformation assay with four types of recipient strains with combinations of N-glycosidase and DNA polymerase I deficiencies indicated that DNA polymerase I was involved in the later steps of this base excision repair pathway initiated by the action of the N-glycosidase.

Bacillus subtilis

Escherichia coli K-12 mutants deficient in uracil-DNA glycosylase.

A new assay specific for uracil-DNA glycosylase is described, Escherichia coli mutants partially and totally deficient in uracil-DNA glycosylase activity have been isolated by using this assay in mass-screening procedures. These have been designated ung mutants. The ung gene maps between tyrA and nadB on the E. coli chromosome. T4 phage containing uracil in their DNA grow on the most glycosylase-deficient hosts but are unable to grow on wild-type bacteria. This provides a simple spot test for the ung genotype. The ung mutants show slightly higher rates of spontaneous mutation to antibiotic resistance. Taken together, these results suggest a central role for uracil-DNA glycosylase in the initiation of an excision repair pathway for the exclusion of uracil from DNA.

Chromosome Mapping

Isolation of Escherichia coli mutants with changed regulation of uracil uptake.

The incorporation of uracil into the pyrimidine ribonucleotide pools of Escherichia coli is strongly restricted under stringent conditions. Previously, we have suggested that this inhibition can be explained by the allosteric properties of uracil phosphoribosyltransferase. It has been proposed that this enzyme performs the uptake of uracil into the cell by transporting it across the cytoplasmic membrane, with the stimultaenous formation of UMP. To test this hypothesis it would be helpful to have mutants with changed regulation of uracil uptake, and in the present work, a method is introduced for the selection of such mutants. This method is based on phenotypic suppression of amber mutations by 5-fluorouracil (5FU). Mutants were isolated in an arginine-requiring strain of E. coli carrying an amber mutation in argI, the ornithine transcarbamylase gene. To facilitate the phenotypic rescue of this defective gene, mutants which overproduced ornithine transcarbamylase mRNA were isolated as a first step. The absence of exogenously added arginine causes stringent conditions, and phenotypic rescue by 5FU is, thus, prevented, unless the 5FU uptake mechanism is mutationally changed in such a manner that the drug is taken up into the cell. Three mutants in which the growth could be supported by 5FU in the absence of arginine were isolated. Two of them had acquired an increased ability to take up uracil under stringent conditions.

Arginine