A protonmotive force as the source of energy for galactoside transport in energy depletedEscherichia Coli

Summary Uracil transport inSaccharomyces cerevisiae is mediated by a specific permease which does not recognize other pyrimidines such as uridine, cytosine, thymine, 2-hydroxypyrimidine or 5-amino-uracil; hypoxanthine and 6-amino-uracil slightly inhibit the uptake of uracil in a strain lacking cytosine permease activity. Wild type cells concentrate extracellular uracil before its transformation into UMP and subsequent incorporation into nucleic acids. A strain lacking UMP pyrophosphorylase and uridine ribohydrolase (strainfur 1–8 rh, in which the endogenous production as well as the utilization of uracil are lacking) is able to concentrate¹⁴C-2 uracil from the medium. At the same time no other¹⁴C-2 labelled compound could be detected in this strain, thus suggesting that the uptake of uracil in yeast occurs by active transport which is not coupled to the UMP pyrophosphorylase. The optimal pH of uracil uptake in standard growth conditions was 4.3. It was deduced from experiments performed on strainfur 1–8 rh with³H-5 and¹⁴C-2 uracil that the intracellular pool of uracil is recycled once the steady-state has been reached. First order kinetics with similar rate constants were observed for uracil efflux in strainfur 1–8 rh (k min^–1=0.75±0.08) as well as in the strain lacking uracil permease,fur 1–8 rh fur 4–6 (k min^–1=0.60±0.08). The intracellular pool of¹⁴C-2 uracil can be chased in strainfur 1–8 rh by addition of³H uracil without inducing a large initial acceleration of the exit rate (the rate constant remained at 0.60). 2-4-dinitrophenol inhibits the uptake of uracil but also reduces the efflux of uracil in strainfur 1–8 rh fur 4–6. These data and the comparison with cytosine transport in the same organism support the hypothesis that, whereas uracil uptake is a permease mediated active transport, the efflux of uracil does not involve the uracil uptake permease. A coefficient of permeability of 7.4×10^–7 cm sec^–1 was calculated for uracil.     

Optimization of uracil addition for curdlan (β-1→3-glucan) production by Agrobacterium sp.

Uracil, acting as a precursor of UDP-glucose, served as an activator on the production of curdlan with Agrobacterium sp. (ATCC 31750). The time of adding uracil was important to improve curdlan production. When uracil was added after ammonium depletion (at 26 h), it was used as a nitrogen source for cell growth. Although the cell concentration increased, the curdlan production was decreased. If uracil was added at 46 h, then uracil was degraded slowly but still activated curdlan production. With the addition of both sucrose (200 g) and uracil (1.5 g), the curdlan production was increased up to 93 g l^–1 after 160 h fermentation.     

Measurement of plasma uracil using gas chromatography–mass spectrometry in normal individuals and in patients receiving inhibitors of dihydropyrimidine dehydrogenase

A sensitive gas chromatographic–mass spectrometric method is described for reliably measuring endogenous uracil in 100 μl of human plasma. Validation of this assay over a wide concentration range, 0.025 μM to 250 μM (0.0028 μg/ml to 28 μg/ml), allowed for the determination of plasma uracil in patients treated with agents such as eniluracil, an inhibitor of the pyrimidine catabolic enzyme, dihydropyrimidine dehydrogenase. Calibration standards were prepared in human plasma using the stable isotope, [¹⁵N₂]uracil, to avoid interference from endogenous uracil and 10 μM 5-chlorouracil was added as the internal standard.     

Mutations affecting uridine monophosphate pyrophosphorylase or the argR gene in Escherichia coli. Effects on carbamoyl phosphate and pyrimidine biosynthesis and on uracil uptake

Summary In the course of experiments directed towards the isolation of mutants of Escherichia coli K12 with altered regulation of the synthesis of carbamoylphosphate synthetase, two types of mutations were found to affect the cumulative repression of this enzyme by arginine and uracil. Alteraction of the arginine pathway regulatory gene, argR, was shown to reduce the repressibility of the enzyme by both end products while mutations affecting uridine monophosphate pyrophosphorylase (upp) besides affecting uracil uptake preclude enzyme repression by uracil or cytosine in the biosynthesis of carbamoylphosphate and the pyrimidines. The upp mutations were located on the chromosome near the gua operon. Mutations previously designated as uraP are shown to belong to this class.The relation that could exist between the loss of uridine monophosphate pyrophosphorylase and the impairment of uracil uptake is discussed.A new method for isolating argR mutants in arginine-less strains is described.     

Insight on specificity of uracil permeases of the NAT/NCS2 family from analysis of the transporter encoded in the pyrimidine utilization operon of Escherichia coli

The uracil permease UraA of Escherichia coli is a structurally known prototype for the ubiquitous Nucleobase‐Ascorbate Transporter (NAT) or Nucleobase‐Cation Symporter‐2 (NCS2) family and represents a well‐defined subgroup of bacterial homologs that remain functionally unstudied. Here, we analyze four of these homologs, including RutG of E. coli which shares 35% identity with UraA and is encoded in the catabolic rut (pyr imidine ut ilization) operon. Using amplified expression in E. coli K‐12, we show that RutG is a high‐affinity permease for uracil, thymine and, at low efficiency, xanthine and recognizes also 5‐fluorouracil and oxypurinol. In contrast, UraA and the homologs from Acinetobacter calcoaceticus and Aeromonas veronii are permeases specific for uracil and 5‐fluorouracil. Molecular docking indicates that thymine is hindered from binding to UraA by a highly conserved Phe residue which is absent in RutG. Site‐directed replacement of this Phe with Ala in the three uracil‐specific homologs allows high‐affinity recognition and/or transport of thymine, emulating the RutG profile. Furthermore, all RutG orthologs from enterobacteria retain an Ala at this position, implying that they can use both uracil and thymine and, possibly, xanthine as substrates and provide the bacterial cell with a range of catabolizable nucleobases.     

Binding and structural studies of the complexes of type 1 ribosome inactivating protein from Momordica balsamina with uracil and uridine

Ribosome inactivating protein (RIP) catalyzes the cleavage of glycosidic bond formed between adenine and ribose sugar of ribosomal RNA to inactivate ribosomes. Previous structural studies have shown that RNA bases, adenine, guanine, and cytosine tend to bind to RIP in the substrate binding site. However, the mode of binding of uracil with RIP was not yet known. Here, we report crystal structures of two complexes of type 1 RIP from Momordica balsamina (MbRIP1) with base, uracil and nucleoside, uridine. The binding studies of MbRIP1 with uracil and uridine as estimated using fluorescence spectroscopy showed that the equilibrium dissociation constants (K_D) were 1.2 × 10⁻⁶ M and 1.4 × 10⁻⁷ M respectively. The corresponding values obtained using surface plasmon resonance (SPR) were found to be 1.4 × 10⁻⁶ M and 1.1 × 10⁻⁷ M, respectively. Structures of the complexes of MbRIP1 with uracil (Structure-1) and uridine (Structure-2) were determined at 1.70 and 1.98 Å resolutions respectively. Structure-1 showed that uracil bound to MbRIP1 at the substrate binding site but its mode of binding was significantly different from those of adenine, guanine and cytosine. However, the mode of binding of uridine was found to be similar to those of cytidine. As a result of binding of uracil to MbRIP1 at the substrate binding site, three water molecules were expelled while eight water molecules were expelled when uridine bound to MbRIP1.     

Repair of uracil residues closely spaced on the opposite strands of plasmid DNA results in double-strand break and deletion formation

Summary The role of closely spaced lesions on both DNA strands in the induction of double-strand breaks and formation of deletions was studied. For this purpose a polylinker sequence flanked by 165 by direct repeats was inserted within the tet gene of pBR327. This plasmid was used to construct DNA containing one or two uracil residues which replaced cytosine residues in the Kpnl restriction site of the polylinker. Incubation of the plasmid DNA construct with Escherichia coli cell-free extracts showed that double-strand breaks occurred as a result of excision repair of the opposing uracil residues by uracil-DNA glycosylase (in extracts from ung ⁺ but not in extracts from ung ^– E. coli strains). Recombination of direct repeats, induced by double-strand breakage of plasmid DNA, can lead to the deletion of the polylinker and of one of the direct repeats, thus restoring the tet ⁺ gene function which can be detected by the appearance of tetracycline-resistant colonies of transformants. Transformation of E. coli cells with single or double uracil-containing DNAs demonstrated that DNA containing two closely spaced uracil residues was tenfold more effective in the induction of deletions than DNA containing only a single uracil residue. The frequency of deletions is increased tenfold in an ung ⁺ E. coli strain in comparison with an ung ^– strain, suggesting that deletions are induced by double-strand breakage of plasmid DNA which occurs in vivo as a result of the excision of opposing uracil residues.     

Uracil synthesisvia HCN oligomerization

Uracil is released from HCN oligomers upon acid hydrolysis in concentrations of 0.001% for 1M HCN solutions to 0.005% for 0.1M solutions. This yield is comparable with earlier reported, minor or nonbiological pyrimidines such as 5-hydroxyuracil and orotic acid. This is the first report of uracil itselfvia HCN oligomerization. Data are presented which establish that the observed uracil is not formed by decarboxylation of previously formed orotic acid, butvia acid hydrolysis of at least two other precursors.     

Specific Labeling of Intracellular Toxoplasma gondii with Uracil*

SYNOPSIS 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.     

Verwertung von Pyrimidinderivaten durch Hydrogenomonas facilis

Zusammenfassung Nach Behandlung mit 1-Nitroso-3-nitro-1-methylguanidin und nach Anreicherung in einem penicillinhaltigen Medium wurden von Hydrogenomonas facilis 35 Mutanten isoliert, die Uracil nicht mehr als N-Quelle zu nutzen vermochten. Eine Gruppe dieser Mutanten bildete keine Dihydrouracil-Dehydrogenase und verwertete Thymin, Orotsäure und Uracil nicht mehr. Eine zweite Gruppe hatte die Fähigkeit verloren, Dihydrouracil-Hydrase zu bilden und konnte Uracil, Orotsäure, Thymin, Dihydrouracil und Dihydrothymin nicht mehr verwerten. Während des Wachstums mit Cytosin wurde durch die erste Gruppe dieser Mutanten Uracil und durch die zweite Gruppe Dihydrouracil in das Nährmedium ausgeschieden.Die Enzyme Dihydrouracil-Dehydrogenase und Dihydrouracil-Hydrase waren in Zellen, die mit Cytosin, Uracil, Thymin oder Orotsäure angezogen worden waren, mit wesentlich höherer spezifischer Aktivität nachweisbar als in Zellen, die mit Ammoniumchlorid gewachsen waren. Dihydroorotsäure-Dehydrogenase und Dihydroorotsäure-Hydrase waren in den zellfreien Extrakten in keinem Fall nachweisbar. Die Befunde weisen daraufhin, daß Uracil und Thymin bei H. facilis durch eine unspezifische Dehydrogenase und Dihydrouracil und Dihydrothymin durch eine unspezifische Hydrase umgesetzt werden, und daß diese Enzyme in Gegenwart von Uracil, Thymin oder Orotsäure induktiv gebildet werden.

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Utilization of pyrimidine derivatives by Hydrogenomonas facilis II. Degradation of thymine and uracil by wild type and mutants

Summary 35 mutant strains, unable to utilize uracil as a nitrogen source, were isolated from Hydrogenomonas facilis following treatment with 1-nitroso-3-nitro-1-methylguanidine and enrichment in a penicillin containing medium. One group of these mutants lacked dihydrouracil dehydrogenase and did not utilize thymine, orotic acid and uracil. A second group of mutants had lost the ability to form dehydrouracil hydrase and was unable to utilize uracil, orotic acid, thymine, dihydrouracil and dihydrothymine. The first group of these mutants excreted uracil, the second group dihydrouracil into the medium during growth with cytosine.The enzymes dihydrouracil dehydrogenase and dihydrouracil hydrase were present in much higher specific enzyme activities in cells grown with cytosine, uracil, thymine or orotic acid than in ammonia grown cells. Dihydroorotic dehydrogenase and dihydroorotase could not be demonstrated in cell-free extracts. These data indicate that both uracil and thymine are utilized as substrates by a non-specific hydrogenase and that both dihydrouracil and dihydrothymine are utilized by a non-specific hydrase. Both these enzymes are induced in presence of uracil, thymine or orotic acid in cells of Hydrogenomonas facilis.

     

Pyrimidine metabolism during somatic embryo development in white spruce (Picea glauca)

Pyrimidine metabolism was investigated at various stages ofsomatic embryo development of white spruce (Picea glauca). The contribution of thede novo and the salvage pathways of pyrimidine biosynthesis to nucleotide and nucleic acid formation and the catabolism of pyrimidine was estimated by the exogenously supplied [6-¹⁴C]orotic acid, an intermediate of thede novo pathway, and with [2-¹⁴C]uridine and [2-¹⁴C]uracil, substrates of the salvage pathways. Thede novo pathway was very active throughout embryo development. More than 80 percnt; of [6-¹⁴C]orotic acid taken up by the tissue was utilized for nucleotide and nucleic acid synthesis in all stages of this process. The salvage pathways of uridine and uracil were also operative. Relatively high nucleic acid biosynthesis from uridine was observed, whereas the contribution of uracil salvage to the pyrimidine nucleotide and nucleic acid synthesis was extremely limited. A large proportion of uracil was degraded as ¹⁴CO₂, probably via β-ureidopropionate. Among the enzymes of pyrimidine metabolism, orotate phosphoribosyltransferase was high during the initial phases of embryo development, after which it gradually declined. Uridine kinase, responsible for the salvage of uridine, showed an opposite pattern, since its activity increased as embryos developed. Low activities of uracil phosphoribosyltransferase and non-specific nucleoside phosphotransferase were also detected throughout the developmental period. These results suggest that the flux of thede novo and salvage pathways of pyrimidine nucleotide biosynthesisin vivo is roughly controlled by the amount of these enzymes. However, changing patterns of enzyme activity during embryo development that were measuredin vitro did not exactly correlate with the flux estimated by the radioactive precursors. Therefore, other fine control mechanisms, such as the fluctuation of levels of substrates and/or effectors may also participate to the real control of pyrimidine metabolism during white spruce somatic embryo development.     

Importance of determining viability ofMycobacterium leprae inside macrophages—anin vitro method using uracil

It has been demonstrated thatMycobacterium leprae, are caPable of taking uP uracil and incorPorating it into trichloroacetic acid-insoluble materials, both as free susPension of bacteria, as well as when they are inside the macrophages, a host cell for theirin vivo survival. Same amount of bacteria show better incorPoration inside macroPhages than as free bacterial susPension. Both tyPes of incorPoration are inhibited by rifamPicin an antileProsy drug and an RNA synthesis inhibitor. Thus uracil uPtake byMycobacterium lePrae inside macroPhages has been used for standardising a raPidin vitro viability assay for the leProsy causing bacteria.     

Growth inhibition of Saccharomyces cerevisiae by the immunosuppressant leflunomide is due to the inhibition of uracil uptake via Fur4p

The immunosuppressant leflunomide inhibits cytokine-stimulated proliferation of lymphoid cells in vitro and also inhibits the growth of the eukaryotic microorganism Saccharomyces cerevisiae. To elucidate the molecular mechanism of action of the drug, two yeast genes which suppress the anti-proliferative effect when present in multiple copies were cloned and designated MLF1 and MLF2 for multicopy suppressor of leflunomide sensitivity. DNA sequencing analysis revealed that the MLF1 gene is identical to the FUR4 gene, which encodes a uracil permease and functions to import uracil efficiently. The MLF2 was found to be identical to the URA3 gene. Excess exogenous uracil also overcomes the anti-proliferative effect of leflunomide on yeast cells. Uracil prototrophy also conferred resistance to leflunomide. Uracil uptake was inhibited by leflunomide. Thus, the growth inhibition by leflunomide seen in a S. cerevisiae ura3 auxotroph is due to the inhibition of the entry of exogenous uracil via the Fur4 uracil permease. Received: 7 May 1998 / Accepted: 16 July 1998     

Effect of uracil on colonial morphology ofNeisseria gonorrhoeae

The production of cells ofNeisseria gonorrhoeae that form type-T4 colonies in cultures started with cells that originally formed only type-T2 colonies was inhibited by calf thymus RNA. Guanosine and uracil were the only nucleic acid constituents that significantly reduced the T2 to T4 shift. Uracil gave the best results in degree of inhibition. It was found that some tritiated uracil was incorporated into the RNA of growing cells ofN. gonorrhoeae but that much more was incorporated into DNA probably after conversion to guanine and adenine. The data show that the shift from T2 to T4 can be progressively inhibited by increasing the concentration of uracil in the growth medium.     

Pyrimidine biosynthesis in Aspergillus nidulans. Isolation and characterisation of mutants resistant to fluoropyrimidines.

Summary Mutants resistant to 5-fluorouracil, 5-fluorouridine and 5-fluorodeoxyuridine have been selected in Aspergillus nidulans. Growth tests combined with genetic analysis showed that mutations conferring resistance to fluoropyrimidines could occur in at least seven genes. Three of these, fulE, fulF and furA were concerned with either the uptake of pyrimidines or their conversion to uridine monophosphate. The other four genes did not affect these functions. Mutations in fulA probably confer resistance by lowering ornithine transcarbamoylase, thereby making the normally arginine-specific carbamoyl phosphate pool available for increased uracil synthesis. Mutations in fulD may make the arginine-specific carbamoyl phosphate synthetase insensitive to inhibition or repression by arginine, and so lead to increased carbamoyl phosphate pool sizes, and increased uracil synthesis. Both fulA and fulD mutants suppress pyrA mutants which lack the uracil-specific carbamoyl phosphate synthetase. Mutations in fulB and fulC do not suppress pyrA, and so may act more directly to increase uracil synthesis. The synthesis of aspartate carbamoyl transferase in fulB7 strains is not repressed by uracil. fulC mutants are closely linked to the pyrA, B, C, N region which codes for the first two enzymes of pyrimidine biosynthesis, and may result in these enzymes being less sensitive to inhibition by uracil.Abbreviations used 5FU 5-fluorouracil - 5FUR 5-fluorouridine - 5FdUR 5-fluorodeoxyuridine     

Identification of the Orotidine-5′-Phosphate Decarboxylase Gene and Development of a Transformation System in the Yeast Saccharomyces exiguus Yp74L-3

To investigate the uracil biosynthetic pathway of the yeast Saccharomyces exiguus Yp74L-3, uracil auxotrophic mutants were isolated. Using conventional genetic techniques, four mutant genes concerned in uracil biosynthesis were identified and denoted as ura1, ura2, ura3, and ura4. Mutations in the URA3 and URA4 genes were specifically selected with 5-fluoroorotic acid (5-FOA). Vector plasmids containing the URA3 gene and an autonomously replicating sequence (ARS) of S. cerevisiae produced sufficient amounts of Ura⁺ transformants from the ura4 mutant of S. exiguus. This fact indicates that the S. exiguus URA4 gene encodes orotidine-5′-phosphate decarboxylase (OMP decarboxylase) and demonstrates that vector plasmids for S. cerevisiae are also usable in S. exiguus.     

Incorporation of Uracil by Synchronous Chlorella

Light-dark synchronized Chlorella fusca was used to study the incorporation of radioactive uracil into the trichloroacetic acid insoluble fraction. In autospores the incorporation measured in darkened cells usually started immediately after uraci addition, and the time course showed three distinct linear phases with abrupt transitions between them. Chromatographic analyses of the radioactive pool components showed that the total amounts of monophosphate, diphosphate and triphosphate nucleotides of uracil did not limit the incorporation and thus did not cause the abrupt rate shifts. In autospores, 5, 9 and 14 h old cells, the initial incorporation rate increased with increasing initial uracil concentration to reach a constant value above 0.5 μ.M. Addition of glucose to the cells increased the incorporation rate over the whole uracil concentration range tested with autospores, but did not influence the rates of the other cells. The incorporation rate varied during the synchronous cycle in a manner which closely resembled the pattern for uptake and degradation rates, with the most pronounced similarity from 9 h onwards.     

Degradation of pyrimidine bases in Clostridium sticklandii

Resting cells of Clostridium sticklandii took up thymine or uracil, when grown in a medium containing 40 mM serine and 20 mM thymine or uracil. The uptake was much lower, when the cells had been grown in a complex medium. Cell-free extracts from cells grown in the complex medium reduced the two bases to the dihydro compounds and decomposed dihydrothymine to -ureidoisobutyrate, as indicated by thin-layer chromatography. Uptake and degradation were stimulated by both NADH and NADPH. Further breakdown did not occur, as ¹⁴CO₂ was not evolved from C-2-labelled thymine or uracil. The rates of pyrimidine uptake and breakdown of C. sticklandii were lower than those reported for C. sporogenes (Hilton et al., 1975).