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PubMed2000

Screening for pyrimidine metabolism disorders using dried filter-paper urine samples: method development and a pilot study in Nagoya City, Japan.

A screening system for pyrimidine metabolism disorders by measurement with high-performance liquid chromatography using dried filter-paper urine samples is presented. This system permits the simultaneous determination of dihydrouracil, uracil, orotic acid and pseudouridine. The coefficient of variations for the four compounds on the filter-paper urine samples were 0.010 approximately 0.069 and the recoveries were 98.5 approximately 107.1%. The detection limits of the four compounds were 2 approximately 20 micromol/liter. The correlation between the filter-paper urine samples and liquid urine samples was excellent (0.938-0.988). We supeculated that this method could be used to detect pyrimidine metabolism disorders, such as dihydropyrimidinuria, dihydropyrimidine dehydrogenase deficiency and hereditary orotic aciduria. As a pilot study, we have analyzed dried filter-paper urine samples from 34, 200 healthy Japanese, and found three cases of dihydropyrimidinuria without clinical symptoms.

Drug Stability↗
PubMed1971

Development of Pyrimidine-metabolizing Enzymes in Cotyledons of Germinating Peas.

Mechanisms controlling conversion of orotic acid-6-(14)C to uridine-5'-phosphate in cotyledons of germinating Alaska peas (Pisum sativum L.) were investigated. The content of 5-phosphoribosyl-1-pyrophosphate was very low in dry seeds, increased to a maximum after about 12 hours of imbibition, and then rapidly declined. Orotidine-5'-phosphate pyrophosphorylase and orotidine-5'-phosphate decarboxylase activities more than doubled during the first 24 hours of germination and then also decreased. These results do not account for the continuous increases of orotate anabolism in such cotyledons as we observed previously. The initial increases in activities of these two enzymes were unaffected by cycloheximide, while the subsequent decreases were less rapid in the presence of this inhibitor. Activities of cotyledonary cytidine deaminase and uridine hydrolase also increased during imbibition, but the activity of only the latter showed a decrease after imbibition was completed. Cycloheximide inhibited the initial rapid increase in uridine hydrolase activity but had little effect on its subsequent decline. Cycloheximide had only slight inhibitory effects on the development of cytidine deaminase activity during the first 62 hours. The evidence suggests that uridine hydrolase might be synthesized de novo during the first few days of germination, but that the other three enzymes might not be.

Journal Article↗
PubMed1989

A reversible selection system for UMP synthase gene amplification and deamplification.

The bifunctional enzyme UMP synthase provides a unique reversible selection system whereby cells that have amplified the UMP synthase gene can be isolated from a wild-type population and cells that have deleted the extra genes can be selected from a population with amplified copies of the gene. UMP synthase catalyzes the conversion of orotic acid to orotidine 5'-monophosphate (OMP) and then OMP to UMP. In the amplification step, Chinese hamster lung cells are selected for resistance to pyrazofurin and 6-azauridine, two inhibitors of the orotidine 5'-decarboxylase activity that converts OMP to UMP. The resistant cells have increased levels of both activities of UMP synthase as a result of a stable amplification of the UMP synthase gene. The deamplification step depends on 5-fluorouracil (5FU), which is converted to its monophosphate form by the orotate phosphoribosyltransferase activity of UMP synthase. Thus cells with increases in this activity are more sensitive to 5FU cytotoxicity, permitting single-step selection of revertants that have lost their amplified UMP synthase genes. These 5FU-selected cells are similar to the parental cell line in their level of UMP synthase activity and number of UMP synthase gene copies. Reselection in increasing concentrations of pyrazofurin and 6-azauridine allows one to isolate cells that have reamplified the UMP synthase gene. The ability to cycle cells of a single lineage through states of amplification and deamplification will facilitate study of the gene amplification process and the factors that influence the composition and stability of amplified regions.

Amides↗
PubMed1990

Biosynthesis and scavenging of pyrimidines by pathogenic mycobacteria.

Mycobacterium microti incorporated a wide range of exogenously supplied pyrimidines into its nucleic acids. M. avium incorporated a relatively narrow range of pyrimidines but both M. avium and M. microti when recovered after growth in vivo incorporated a slightly wider range of pyrimidines than the same strains grown in vitro. M. microti and M. leprae could not take up uridine nucleotides directly but could utilize the pyrimidines by hydrolysing them to uridine and then taking up the uridine. Pyrimidine biosynthesis, judged by the ability to incorporate carbon from CO2 or aspartate into pyrimidines was readily detected in non-growing suspensions of M. microti and M. avium harvested from Dubos medium, which does not contain pyrimidines. The biosynthetic activity was diminished in mycobacteria grown in vivo when there is likely to be a source of pyrimidines which they might use. Relative activities for pyrimidine biosynthesis de novo in M. microti were 100 for cells isolated from Dubos medium, 6 for cells isolated from Dubos medium containing the pyrimidine cytidine and 11 from cells recovered after growth in mice. In contrast, relative activities for a scavenging reaction, uracil incorporation, were 100, 71 and 59, respectively. Three key enzymes in the pathway of pyrimidine biosynthesis de novo were detected in M. microti and M. avium. Two, dihydroorotate synthase and orotate phosphoribosyltransferase appeared to be constitutive in M. microti and M. avium. Aspartate transcarbamoylase activity was higher in these mycobacteria grown in vivo than in Dubos medium but it was repressed in M. microti or M. avium grown in Dubos medium in the presence of 50 microM-pyrimidine. Aspartate transcarbamoylase was strongly inhibited by the feedback inhibitors ATP, CTP and UTP. Enzymes for scavenging pyrimidines were detected at low specific activities in all mycobacteria studied. Activities of phosphoribosyltransferases, enzymes that convert bases directly to nucleotides, were not related to the ability of intact mycobacteria to take up pyrimidine bases while activities of pyrimidine nucleoside kinases were generally related to the ability of intact mycobacteria to take up nucleosides. Phosphoribosyltransferase activity for uracil, cytosine, orotic acid and--in organisms grown in Dubos medium with 50 microM-uridine-thymine, as well as kinases for uridine, deoxyuridine, cytidine and thymidine were detected in M. microti. However, M. avium only contained uracil and orotate phosphoribosyltransferase, uridine, cytidine and thymidine kinase, and additionally deoxyuridine kinase when grown axenically with 50 microM-uracil, reflecting its more limited abilities in pyrimidine scavenging.

Animals↗
PubMed2002

Equilibrium of formation of the 6-carbanion of UMP, a potential intermediate in the action of OMP decarboxylase.

There has been some speculation that the C-6 position in UMP may be unusually acidic, stabilizing a carbanion that is generated at this position during OMP decarboxylation. On the basis of the rate of OH- catalyzed deuterium exchange at elevated temperatures we estimate that the pKa value for ionization at C-6 of dimethyl uracil is 34 +/- 2 in water. The same method yields a value of 37 +/- 2 for ionization at C-2 of thiophene in good agreement with the value determined by polarographic methods. The barrier to proton release (46 kcal/mol) is even higher than that for CO2 release from orotic acid derivatives.

Deuterium↗
PubMed1978

Changes in the free and membrane-bound ribosomes in maternal rat liver during starvation.

Free and membrane-bound ribosomal ribonucleic acid (RNA) from maternal rat liver was measured in virgin rats and in variously dated pregnant animals that were either fed or starved for one to four days. The total amounts of free and membrane-bound ribosomal RNA differed between pregnant and nonpregnant rats, but the free ribosomal RNA progressively decreased only in the nonpregnant animals. A similar conservation of membrane-bound ribosomal RNA was observed with starvation among the pregnant rats except for the very early dated pregnant rats. Radioisotope labeling experiments using 3H-labeled orotic acid demonstrated a slower increase in specific activity among fed rats, irrespective of pregnancy state. However, metabolic and physiologic changes associated with pregnancy imposed additional complicating factors to the study.

Animals↗
PubMed1988

Rates of rat liver RNA degradation in vivo as determined from cytidine release during brief cyclic perfusion in situ.

The breakdown of RNA and of long-lived proteins in rat liver is believed to occur largely within the lysosomal-vacuolar system. Both processes are induced by amino acid lack and suppressed by insulin, and in all circumstances a consistent lag of 15-20 min was observed between the introduction of a physiological regulator and onset of the degradative response. This lag has allowed us to determine rates of liver RNA degradation in vivo during brief cyclic perfusions, as was done previously for long-lived-protein breakdown [Hutson & Mortimore (1982) J. Biol. Chem. 257, 9548-9554]. Degradation was measured from the release of [14C]cytidine in livers of rats previously labelled in vivo with [6-14C]orotic acid. Release was linear and unaffected by physiological regulators between 2 and 12 min of perfusion. In contrast with protein breakdown, no short-lived component was observed. In animals trained to feed between 16:00 and 20:00 h, the content of liver RNA fell at an average rate of 0.26 mg/h per 100 g initial body wt. between 07:00 and 16:00 h, a loss that was within 9% of that predicted from the net release (total release minus reutilization) of cytidine in vivo. In addition, the total rate of RNA degradation determined at the end of the meal was only 12% of that at the start of the post-absorptive period 14 h later (2.1 versus 17.1%/day). This finding is fully consistent with a lysosomal mechanism for RNA degradation, since autophagy is strongly suppressed by food intake. This approach provides a comparatively simple means of approximating moment-to-moment rates of RNA degradation in the rat liver in vivo.

Amino Acids↗
PubMed1995

Use of polymerase chain reaction epitope tagging for protein tagging in Saccharomyces cerevisiae.

Epitope tagging is the insertion of a short stretch of amino acids constituting an epitope into another protein. Tagged proteins can be identified by Western, immunoprecipitation and immunofluorescence assays using pre-existing antibodies. We have designed vectors containing the URA3 gene flanked by direct repeats of epitope tags. We use the polymerase chain reaction (PCR) to amplify the tag-URA3-tag cassette such that the ends of the PCR fragments possess homology to the gene of interest. In vivo recombination is then used to direct integration of the fragment to the location of interest, and transformants are selected by their Ura+ phenotype. Finally, selection for Ura- cells on 5-fluoro-orotic acid plates yields cells where recombination between the repeated epitopes has 'popped out' the URA3 gene, leaving a single copy of the epitope at the desired location. PCR epitope tagging (PET) provides a rapid and direct technique for tagging that does not require any cloning steps. We have used PET to tag three Saccharomyces cerevisiae proteins, Cln1, Sic1 and Est1.

Amino Acid Sequence↗
PubMed1982

Acid-soluble nucleotides of human milk at different stages of lactation.

The acid-soluble ribonucleotides of human milk were measured by enzymic and ion-exchange chromatographic procedures at different stages of lactation. Human colostrum and milk contained CMP, AMP, GMP, UMP, GDP-mannose, UDP-N-acetyl-glucosamine, UDP-N-acetyl-galactosamine, UDP-glucose, UDP-galactose, UDP and other minor nucleotides. Cytidine and adenosine derivatives were present in relatively higher amounts than in milk from ruminant species. The nucleotide concentration decreased with advancing lactation. Human milk at 3 months of lactation contained about 10 mumol/100 ml nucleotides, which represented about 75% of the amount of nucleotides present in human colostrum. Human milk did not contain orotic acid. The UDP-glucose/UDP-galactose ratio was constant during lactation and was similar to that of milks from ruminant species.

Adenosine Monophosphate↗
PubMed1987

Optimization of a high-performance liquid chromatographic method for the determination of nucleosides and their catabolites. Application to cat and rabbit heart perfusates.

A high-performance liquid chromatographic method is described for the separation of nucleosides and related compounds in a single isocratic run. The separation of a standard mixture of at least thirteen compounds is achieved within 15 min on a new type of reversed-phase column 25 cm long, filled with 5-micron particles of Select B. Pre-treatment of the silica particles before silanization has given this type of reversed-phase material unique characteristics for basic and acidic compounds. Chromatograms are shown to compare the effectiveness of the Select B column for the separation of nucleosides with that of other C18 and C8 phases. The separation is achieved with 0.3 M ammonium dihydrogen phosphate (pH 4.00) and a mixture of methanol, acetonitrile and tetrahydrofuran. Detection is carried out with a variable-wavelength UV detector at 254 nm. Sample preparation and the influence of the organic solvents, pH and buffer concentration are described. To illustrate the applicability of the method, representative chromatograms are shown of perfusates of Langendorff preparations and the working hearts of cats and rabbits. Remarkable differences were obtained before and after ischaemia and before and after treatment with a nucleoside transport inhibitor. Baseline separation of cytosine, orotic acid, cytidine, uracil, uric acid, hypoxanthine, xanthine, inosine, guanosine, xanthosine, allopurinol, thymine and adenosine was achieved. The detection limit for these compounds was less than 1 ng per injection.

Animals↗
PubMed2000

Cloning and expression of beta1,4-galactosyltransferase gene from Helicobacter pylori.

Helicobacter pylori, which is a human pathogen associated with gastric and duodenal ulcer, has been shown to express human oncofetal antigens Lewis X and Lewis Y. Although the mammalian glycosyltransferases that synthesize these structures are well characterized, little is known about the corresponding bacterial enzymes. We report that a novel beta1,4-galactosyltransferase gene (HpgalT) involved in the biosynthesis of lipopolysaccharides in H. pylori has been cloned and expressed in Escherichia coli. The deduced amino acid sequence of the protein (HpGal-T) encoded by HpgalT consists of 274 residues with the calculated molecular mass of 31,731 Da, which does not show significant similarity to those of beta1,4-galactosyltransferases from mammalian sources and Neisseria It was confirmed that HpGal-T catalyzed the introduction of galactose from UDP-Gal in a beta1,4 linkage to accepting N-acetylglucosamine (GlcNAc) residues by means of high-performance anion-exchange chromatography with pulsed amperometric detection (HPAEC-PAD). When the E.coli cells which overexpressed HpgalT was coupled with the UDP-Gal production system, which consisted of recombinant E.coli cells overexpressing its UDP-Gal biosynthetic genes and Corynebacterium ammoniagenes, N-acetyllactosamine, a core structure of lipopolysaccharide of H.pylori, was efficiently produced from orotic acid, galactose, and GlcNAc.

Amino Acid Sequence↗
PubMed1999

Aberrations of ammonia metabolism in ornithine carbamoyltransferase-deficient spf-ash mice and their prevention by treatment with urea cycle intermediate amino acids and an ornithine aminotransferase inactivator.

Sparse fur with abnormal skin and hair (spf-ash) mice are deficient in ornithine carbamoyltransferase (OCT) activity, but their OCT protein is kinetically normal. We administered ammonium chloride to spf-ash mice, in order to analyze ammonia metabolism and to find a rationale for the therapy of OCT deficiency. Ammonia concentration in the liver of spf-ash mice increased to a level much higher than in the control. Ammonium chloride injection caused an increase in ornithine (Orn) 5 min after injection and an increase in the sum of Orn, citrulline (Cit) and arginine (Arg) for at least 15 min in the liver of control mice, but no increase in Orn, Cit and Arg in the liver of spf-ash mice. Treatment of spf-ash mice with Arg 5-20 min prior to the injection of ammonium chloride kept the hepatic ammonia concentration at a level comparable to that without the load. A significant reciprocal relationship between ammonia and Orn concentrations in the liver of spf-ash mice 5 min after an ammonium chloride load with or without Arg strongly suggests that ammonia disposal is dependent on the supply of Orn. In spf-ash mice loaded with tryptone as a nitrogen source, Arg supplementation showed a dramatic decrease in urinary orotic acid excretion in a dose-dependent manner. Similar effects were observed with Cit and Orn at the same dose, and a long-lasting effect with an ornithine aminotransferase inactivator, 5-(fluoromethyl)ornithine, at a much lower dose. The rate of urea formation in liver perfused with ammonium chloride was lower in spf-ash mice than in controls, but with the addition of Orn to the medium it increased to a similar level in control and spf-ash mice. These results indicate that OCT is not saturated with Orn in vivo under physiological conditions and that the administration or enrichment of the urea cycle intermediate amino acids enhances the OCT reaction so that the ammonia metabolism of OCT-deficient spf-ash mice is at least partially normalized.

Amino Acid Metabolism, Inborn Errors↗
PubMed1994

Localization of uridine monophosphate synthase (UMPS) gene to river buffalo chromosomes by FISH.

Uridine monophosphate synthase plays an important role in pyrimidine synthesis, converting orotic acid to uridine 5' monophosphate. In cattle, UMPS deficiency is inherited as a monogenic autosomal recessive trait. While heterozygous carriers are phenotypically normal, homozygotes are lethal in utero (Shanks et al. 1992). UMPS has been mapped to human chromosome 3q13 (Qumsiyeh et al. 1989), sheep chromosome 1q (Burkin et al. 1993) and cattle chromosome 1q31 (Ryan et al. 1994). In the present study we used a cattle genomic probe to localize UMPS to river buffalo chromosomes by fluorescence in situ hybridization.

Animals↗
PubMed1982

Enzymes of purine and pyrimidine metabolism from the human malaria parasite, Plasmodium falciparum.

Plasmodium falciparum trophozoites were isolated by mechanical rupture of infected human erythrocytes followed by a series of differential centrifugation steps. After lysis with sonication, the 100 000 x g supernatant of parasites and uninfected host cells was used to determine the specific activities of a number of enzymes involved in purine and pyrimidine metabolism. P. falciparum possessed the purine salvage enzymes: adenosine deaminase, purine nucleoside phosphorylase, hypoxanthine-guanine phosphoribosyltransferase (PRTase), xanthine PRTase, adenine PRTase, adenosine kinase. The last two enzymes, however, were present at much lower activity levels. Hypoxanthine was converted (presumably via IMP) into adenine and guanine nucleotides only in the presence both of supernatant and membrane fractions of P. falciparum. Two enzymes involved in the de novo synthesis of pyrimidines, orotic acid PRTase, and orotidine 5'-phosphate decarboxylase, were present in parasite extracts as were the enzymes for pyrimidine nucleotide phosphorylation: UMP-CMP kinase, dTMP kinase, nucleoside diphosphate kinase. Xanthine oxidase, CTP synthetase, cytidine deaminase and several kinases for the salvage of pyrimidine nucleosides were not detected in the parasites. Both phosphoribosyl pyrophosphate synthetase and uracil PRTase were present but at low activity levels. Human erythrocytes displayed similar but not identical enzyme patterns. Enzyme specific activities, however, were generally much lower than those of the corresponding parasite enzymes.

Adenosine Deaminase↗
PubMed1976

Purification, size, and properties of the complex of orotate phosphoribosyltransferase: orotidylate decarboxylase from mouse Ehrlich ascites carcinoma.

Complex U, which contains the last two enzymes (orotate phosphoribosyltransferase (EC 2.4.2.10) and orotidylate decarboxylase (EC 4.1.23)) of the six enzymes for the de novo biosynthesis of UMP, has been purified 200-fold from mouse Ehrlich ascites cells. The specific activity of the orotate phosphoribosyltransferase and the orotidylate decarboxylase activities of the complex were 0.115 and 0.290 mumol of product/mg of protein/min; the recovery of the activities was high being 20 to 30%. The rate of the two activities remained similar to that of the homogenate. At the sixth step of the fractionation, one can obtain a fraction that has lost phosphoribosyltransferase activity but retains decarboxylase activity. The apparent molecular weights, as determined by density gradient centrifugation, of the native complex and the fraction containing only decarboxylase activity are identical, 55,700 +/- 4,000. Both activities of complex U are labile to very mild treatments such as dilution, dialysis, or storage at 3 degrees. Dithiothreitol and 5-phosphoribosyl-1-pyrophosphate (PP-Rib-P), but not orotic acid or MgCl2, can stabilize either or both of the enzyme activities. The degree of stabilization by three of these chemicals varies with the reagent(s) used, with the nature of the treatment, and with the concentration of Complex U. When PP-Rib-P, Mg2+ and dithiothreitol are present in the diluting buffer the activity losses were slowed and then followed by a partial recovery of the phosphoribosyltransferase activity. Maximum activities of both enzymes are observed by adding undiluted complex to a complete reaction mixture without preincubation. The complex cannot be exposed to pH values of 4 or below, or pH 9 or above. The stability studies have led to the development of conditions that permit one, for the first time, to subject the complex to electrophoresis and to recover a large percentage of both enzyme activities, rather than only decarboxylase activity as has occurred in the past. The electrophoretic studies indicate that PP-Rib-P produces a complex whose conformation and/or net charge differ significantly from that of the complex in the absence of PP-Rib-P. Kinetic characteristics of the transferase are a pH optimum between 6.5 and 7.5, apparent Km values for orotate, PP-Rib-P, and Mg2+ of 1.9 muM, 16 muM, and 2.9 mM, respectively; for the decarboxylase, a sharp pH optimum of 7.0 is observed, and a Km value for orotidine 5'-phosphate of 0.8 muM.

Animals↗
PubMed1991

A comparison of 5-fluorouracil metabolism in human colorectal cancer and colon mucosa.

The metabolism of 5-fluorouracil (5-FU) was studied in biopsy specimens of primary colorectal cancer and healthy colonic mucosa obtained from previously untreated patients immediately after surgical removal. The conversion of 5-FU to anabolites was measured under saturating substrate (5-FU) and cosubstrate concentrations. For all enzymes, the activity was about threefold higher in tumor tissue compared with healthy mucosa of the same patient. The activity of pyrimidine nucleoside phosphorylase with deoxyribose-1-phosphate (dRib-1-P) was about tenfold higher (about 130 and 1200 nmol/hr/mg protein in tumors) than with ribose-1-phosphate (Rib-1-P), both in tumor and mucosa. Synthesis of the active nucleotides (5-fluoro-uridine-5'-monophosphate [FUMP] and 5-fluoro-2'-deoxyuridine-5'-monophosphate [FdUMP]) was studied by adding physiologic concentrations of adenosine triphosphate (ATP) to the reaction mixture; the rate of FdUMP synthesis was 50% of that of FUMP (about 4 and 7 nmol/hr/mg protein in tumors). Direct synthesis of FUMP from 5-FU in the presence of 5-phosphoribosyl-1-pyrophosphate (PRPP) was about 2 nmol/hr/mg protein. With the natural substrate for this reaction, orotic acid, the activity was about 14-fold higher. To obtain insight into the recruitment of precursors for these cosubstrates, the authors also tested the enzyme activity of pyrimidine nucleoside phosphorylase with inosine and ribose-5-phosphate (Rib-5-P, as precursors for Rib-1-P) and deoxyinosine (as a precursor for dRib-1-P); enzyme activities were approximately 7%, 7%, and 3%, respectively, of that with the normal substrates, both in tumors and mucosa. However, when ATP and Rib-5-P were combined, the synthesis of FUMP was about 70% of that with PRPP, but only in tumors. In normal tissues no activity was detectable. These data suggest a preference of colon tumor over colon mucosa for the conversion of 5-FU to active nucleotides by a direct pathway; a selective antitumor effect of 5-FU may be related to this difference.

Adenosine Triphosphate↗
PubMed1999

Motional dynamics of the catalytic loop in OMP synthase.

In de novo pyrimidine biosynthesis, orotate phosphoribosyltransferase catalyzes the formation of orotidine 5'-monophosphate (OMP) from orotic acid and alpha-D-5-phosphoribosyl-1-pyrophosphate (PRPP). The known three-dimensional structure of the dimeric enzyme from Salmonella typhimurium is similar to that of other Type I phosphoribosyltransferases (nucleotide synthases) with a solvent-exposed active site atop a Rossman-type nucleotide binding fold. The three-dimensional structure of an enzyme-inhibitor complex [Henriksen et al. (1996) Biochemistry 35, 3803-3809] indicates that one of the two identical solvent-exposed loops can descend to cover the active site of the adjacent subunit of the dimeric enzyme. Catalytically essential residues are known to reside on this loop. In the present work, sensitivity toward limited proteolysis by trypsin confirms that the loop is solvent-exposed. Protection by PRPP and, to a lesser extent, by OMP demonstrates the existence of a second, trypsin-inaccessible, loop position. Two-dimensional 1H-15N NMR relaxation experiments on [alpha-15N]histidine-labeled WT OPRTase yielded backbone 15N T1 and T2 relaxation times and 15N[1H] NOE for His-105 (a loop residue) that are characteristic of small peptides. These results document that the surface loop is highly flexible in the unliganded enzyme. Addition of a hydrolytically stable PRPP analogue to the enzyme resulted in a significant reduction of His-105 peak intensity, indicating a dramatic change in the dynamic properties of the loop backbone in the analogue-ligated enzyme. 1H NMR titrations on histidine C2 protons, coupled with 1H and 31P titrations monitoring the C1H and 5-phosphate PRPP resonances, allowed the quantitation of the rates of loop movement during product release, and relate protein motion to enzymatic catalysis. These results suggest that loop opening and PRPP release is a two-step process, whose overall rate is partially rate-limiting in the reverse pyrophosphorolysis reaction.

Alanine↗