Effect of Uridine on de Novo Pyrimidine Biosynthesis in Rat Hepatoma Cells in Culture

Structure-Based Prototyping of Allosteric Inhibitors of Human Uridine/Cytidine Kinase 2 (UCK2)

Pyrimidine nucleotide biosynthesis in humans is a promising chemotherapeutic target for infectious diseases caused by RNA viruses. Because mammalian cells derive pyrimidine ribonucleotides through a combination of de novo biosynthesis and salvage, combined inhibition of dihydroorotate dehydrogenase (DHODH; the first committed step in de novo pyrimidine nucleotide biosynthesis) and uridine/cytidine kinase 2 (UCK2; the first step in salvage of exogenous nucleosides) strongly attenuates viral replication in infected cells. However, while several pharmacologically promising inhibitors of human DHODH are known, to date there are no reports of medicinally viable leads against UCK2. Here, we use structure-based drug prototyping to identify two classes of promising leads that noncompetitively inhibit UCK2 activity. In the process, we have identified a hitherto unknown allosteric site at the intersubunit interface of this homotetrameric enzyme. By reducing the k_cat of human UCK2 without altering its K_M, these new inhibitors have the potential to enable systematic dialing of the fractional inhibition of pyrimidine salvage to achieve the desired antiviral effect with minimal host toxicity.

Dietary feedback regulation of purine and pyrimidine biosynthesis in man

Ten days after a healthy person has consumed a purine-free isoenergetic diet, the excretion of (endogenous) uric acid reaches a minimum and remains constant thereafter. Purines are absorbed in different degrees from various biochemical sources added to such a diet--little from DNA, nearly all from ribomononucleotides--presumably owing to different rates of hydrolysis. There is always a linear relationship between dietary purine content and uric acid excretion, independent of the source of purine. The findings suggest that dietary purines play a minor role (if any) in the regulation of purine synthesis, contrary to the conclusions of other workers. The demonstration that oral administration of uridine diminishes the oroticaciduria in patients with hereditary oroticaciduria suggested dietary feedback regulation of pyrimidine biosynthesis by pyrimidine nucleosides in the diet. The reduction of allopurinol-induced oroticaciduria by dietary RNA pointed in the same direction. Closer analysis with RNA hydrolysate and isolated purine as well as pyrimidine nucleotides, however, revealed that not only pyrimidine derivatives but also purine mononucleotides diminish oroticaciduria. The nucleotides had no influence on the change in the activity of orotidine-5'-phosphate decarboxylase (EC 4.1.1.23), induced by allopurinol; this makes an effect on the decarboxylase unlikely. The feedback regulation is assumed to act by inhibition of an earlier step.

Uridine in the Prevention and Treatment of Nrti-Related Mitochondrial Toxicity

Long-term side effects of antiretroviral therapy are attributed to the mitochondrial (mt) toxicity of nucleoside analogue reverse transcriptase inhibitors (NRTIs) and their ability to deplete mtDNA. Studies in hepatocytes suggest that uridine is able to prevent and treat mtDNA depletion by pyrimidine NRTIs [zalcitabine (ddC) and stavudine (d4T)] and to fully abrogate hepatocyte death, elevated lactate production and intracellular steatosis. Uridine was also found to improve the liver and haematopoietic toxicities of zidovudine (AZT), which are unrelated to mtDNA depletion, and to prevent neuronal cell death induced by ddC. Most recently, uridine was found to prevent the onset of a lipoatrophic phenotype (reduced intracellular lipids, increased apoptosis, mtDNA depletion and mt depolarization) in adipocytes incubated long-term with d4T and AZT. Various steps of mt nucleoside utilization may be involved in the protective effect, but competition of uridine metabolites with NRTIs at polymerase y or other enzymes is a plausible explanation. Pharmacokinetic studies suggest that uridine serum levels can be safely increased in humans to achieve concentrations which are protective in vitro (50–200 μM). Uridine was not found to interfere with the antiretroviral activity of NRTIs. Mitocnol, a sugar cane extract which effectively increases uridine in human serum, was beneficial in individual HIV patients with mt toxicity and is now being tested in placebo-controlled randomized trials. Until these data become available, the risk-benefit calculation of using uridine should be individualized. The current safety data justify the closely monitored use of uridine in individuals who suffer from mt toxicity but who cannot be switched to less toxic NRTIs.

Regional mapping of the gene encoding dihydroorotate dehydrogenase, an enzyme involved in UMP synthesis, electron transport, and superoxide generation, to human chromosome region 16q22

De novo UMP synthesis is a critical metabolic pathway for nucleic acid synthesis and for a variety of metabolic pathways. The pathway is a target for many widely used cancer chemotherapy agents, several of which are pyrimidine analogs. Humans and cattle have been described with mutations in UMP synthesis that lead to serious inborn errors of metabolism. Dihydroorotate dehydrogenase (EC 1.3.3.1) (DHODH) carries out the fourth committed step in the pathway and may also be important for mitochondrial electron transport and oxygen radical metabolism. We report here that the gene encoding this enzyme in humans is located in the chromosomal region 16q22. With the mapping of DHODH, the mapping of all the steps of UMP synthesis is complete. All three genes involved map to different human chromosomes. This information is important in consideration of regulation of UMP synthesis in mammals, including humans.

Posttranscriptional regulation of the expression of CAD gene during differentiation of F9 teratocarcinoma cells by induction with retinoic acid and dibutyryl cyclic AMP

We have studied the regulation of expression of the carbamoyl-phosphate synthetase II-aspartate transcarbamylase-dihydroorotase gene in F9 teratocarcinoma cells during their differentiation into parietal endoderm cells by induction with a combination of retinoic acid and dibutyryl cyclic AMP. Steady-state levels of CAD mRNA decreased by 7-fold in F9 cells following 120 h of retinoic acid and dibutyryl cyclic AMP induction as compared to levels in uninduced cells. Conversely, no apparent changes were found in the steady-state levels of beta-actin mRNA between induced and uninduced cells. Despite a 7-fold decrease in the steady-state levels of CAD mRNA, its rate of transcription remained the same between induced and uninduced cells, indicating a role for posttranscriptional mechanisms for its down regulation during retinoic acid- and dibutyryl cyclic AMP-induced differentiation of F9 cells. The cellular growth rate of F9 cells as determined by [3H]thymidine uptake and parallel cell counting decreased markedly during their induction with retinoic acid and dibutyryl cyclic AMP. Taken together, it is apparent that the expression of the CAD gene is cell-growth-dependent and its regulation in this system is at the posttranscriptional level.

Comparative activity of erythrocyte adenosine deaminase and orotidine decarboxylase in Diamond-Blackfan anemia

It previously has been reported that red blood cells (RBC) of patients with Diamond-Blackfan syndrome (DBS) have increased activity of orotidine decarboxylase (ODC) and adenosine deaminase (ADA). The studies reported here compared the activity of these two enzymes in DBS erythrocytes, cord blood, and reticulocytes. The activity of ODC, although increased in some DBS erythrocytes, was not significantly different from that seen in cord RBC or reticulocytes. In contrast, RBC-ADA activity was increased in 23 of 26 DBS patients; and this enzyme elevation was distinct from that seen in cord blood and reticulocytes. Moreover, ADA activity was normal in 26 of 27 patients with transient erythroblastopenia of childhood (TEC). Taken together, these data indicate RBC-ADA activity is more sensitive than ODC as a marker of DBS. In addition, RBC-ADA activity continues to be useful for distinguishing DBS and TEC in most patients with RBC hypoplasia.

A 13C tracer method for quantitating de novo pyrimidine biosynthesis in vitro and in vivo

Gas chromatographic/mass spectrometric methods for the measurement of the flux through the de novo pyrimidine biosynthetic pathway by quantitating the incorporation of [13C]bicarbonate and 13CO2 into the uracil nucleotide pool in L1210 tumors are reported. Simultaneous measurements of the incorporation of [13C]bicarbonate and the more commonly used [14C]bicarbonate into uridine of L1210 cells in vitro showed that the two methods were comparable. A modification of the method was applied to in vivo studies where the incorporation of 13CO2 into the uracil nucleotide pool of L1210 tumors in mice was quantitated. The measurements were used to determine changes in the flux through the de novo pyrimidine pathway in animals pretreated with known inhibitors of the pathway. A comparison of control animals with those pretreated with 6-azauridine, acivicin, and pyrazofurin resulted in mean percentage inhibitions of 87, 95, and 94%, respectively. This technique should allow investigation of the respective contributions of salvage and de novo synthesis in the formation of pyrimidines in vivo and the effects of agents designed as enzyme inhibitors of the de novo pathway.

Activity of orotate metabolizing enzyme complex and various urea-cycle enzymes in mutant mice with ornithine transcarbamylase deficiency

The overall activity of the enzyme complex consisting of orotate phosphoribosyl transferase and orotidine monophosphate decarboxylase, and of various enzymes of the urea cycle, has ben studied in sparse-fur (spf) mutant mice with ornithine transcarbamylase deficiency. The enzyme complex has a lower overall activity, which could be caused by disturbed pyrimidine metabolism due to hyperammonemia. Other enzymes of the urea cycle do not show any significant change.

Rna synthesis and processing during cytodifferentiation in fetal rat pancreas

In fetal rat pancreas cytodifferentiation occurs between day 14 and day 20 of gestation and is accompanied by an exponential increase in the cellular accumulation of tissue specific proteins and an elaboration of the cellular organelles associated with their synthesis and secretion. Evaluation of RNA synthesis by [3H] uridine incorporation into trichloroacetic acid precipitable material showed that during this period the apparent rate of RNA synthesis increased 7.5 fold from 2 x 10(3) dpm/micrograms DNA/h on day 15 to 1.5 x 10(4) dpm/micrograms DNA/h on day 19; [3H] leucine uptake showed that the rate of protein synthesis increased about the same extent with the major difference being that the maximum rate of protein synthesis occurred on day 19, one day after the maximum rate of RNA synthesis. The soluble pyrimidine nucleotide pools decreased from 122 pmol/micrograms DNA on day 14 to 15 pmol/micrograms DNA on day 16 followed by an increase to 104 pmol/micrograms DNA on day 19; the purine nucleotide pools decreased from 367 pmol/micrograms DNA on day 14 to 286 pmol/micrograms DNA on day 16 and then increased to 635 pmol/micrograms DNA on day 19. These values roughly paralleled the transitions observed in the rates of RNA and protein synthesis. Agarose-acrylamide slab gel electrophoresis showed an increase in RNA synthesis and an increase in ribosomal RNA synthesis and processing with cytodifferentiation.

Uridine and cytidine metabolism following inhibition of de novo pyrimidine synthesis by pyrazofurin

Pyrazofurin, an inhibitor of orotidylate decarboxylase, imposes an absolute nutritional requirement for exogenous uridine to maintain normal growth of L5178Y, P388, L1210, W256 and S180 cells in vitro. The amount of uridine necessary for cell division when de novo uridine nucleotide synthesis is inhibited by pyrazofurin is: L5178Y, 30.5; P388, 39.7; L1210, 53.3: W256, 70.6; and S180, 886 fmol/cell. Cytidine, which can be deaminated to uridine, will substitute for uridine to maintain normal cell growth in the presence of growth-inhibitory concentrations of pyrazofurin (5 microM). The requirements for cytidine and uridine are identical. If cytidine deamination is prevented by tetrahydrouridine (100 microM), cytidine can no longer support growth in the presence of pyrazofurin. Cytidine and uridine, as expected, are additive in their effect to permit normal growth of pyrazofurin treated cells. Tetrahydrouridine does not alter this additive effect, indicating that when both nucleotides are added to pyrazofurin treated cells each nucleotide replenishes their respective nucleotide pools and cytidine deamination is unnecessary to allow cell growth. Incorporation of [14C]uridine into the acid insoluble cell fraction of L5178Y cells was 25 fmol/cell at 48 h and remained constant during the remaining growth of the pyrazofurin treated cell suspension. The [14C]uridine acid soluble pool of 4 fmol/cell also was maximum at 48 h but declined during the subsequent growth of the suspension culture to approx. 2 fmol/cell at 96 h. This decline in the acid soluble pool is correlated with a 42% decrease in modal cell volume during this phase of cell growth which would maintain a constant specific activity of uridine in this pool. This may explain the decline in the acid soluble pool while the acid insoluble pool remains constant during growth of suspension cultures of L51878Y cells. The block in pyrimidine synthesis de novo induced by pyrazofurin provides a useful and quick method for the evaluation of uridine and cytidine metabolism of tumor cell specimens.

Isolation and characterization of 5-fluorouracil-resistant mutants of Chinese hamster ovary cells deficient in the activities of orotate phosphoribosyltransferase and orotidine 5'-monophosphate decarboxylase

A rapid, simple method for isolation of large numbers of Chinese hamster ovary cell (CHO-K1) mutants deficient in the final two enzymes of UMP biosynthesis, orotate phosphoribosyltransferase (EC 2.4.2.10), and OMP decarboxylase (EC 4.1.1.23) is described. The method takes advantage of the fact that CHO-K1 cells require orotate phosphoribosyltransferase to activate the pyrimidine analog 5-fluorouracil to its active form; hence, mutants lacking thhe relevance of these observations to the metabolism of this cancer chemotheraputic agent, to the study of the structure of the protein(s) involved in catalyzing the last two steps of UMP biosynthesis, to the study of the structure of the gene(s) coding for this protein, and to analysis of the human genetic disease orotic aciduria is discussed.

Elevation of pyrimidine enzyme activities in the RBC of patients with congenital hypoplastic anaemia and their parents

The activities of orotate phosphoribosyl transferase (OPRT) and orotidine monophosphate decarboxylase (ODC) were significantly elevated (P less than 0.001) in erythrocytes (RBC) from five patients with prednisone-responsive congenital hypoplastic anaemia (CHA). (OPRT: patients - 10.1--64.2 nmol/h/10(9) RBC; controls - 2.8 +/- 0.3 (mean +/- SEM, n = 37); ODC: patients = 30--124 nmol/h/10(9) RBC; controls = 10.2 +/- 0.7 (mean SEM, n = 37).) Two patients had a less pronounced, but significant, increase of aspartate transcarbamylase activity and three patients had marginal increases of dihydroorotase activity. Dihydroorotate dehydrogenase activity was not detected in any CHA patient or control. In one patient prior to prednisone therapy, the OPRT and ODT activities were elevated 10-fold and remained elevated 3-fold after 16 months of therapy. An elevated enzyme pattern similar to that of RBC from CHA patients was observed in three parents of three CHA patients, but not in three parents of two other CHA patients. The activities of all five pyrimidine enzymes were normal for one patient with transient erythroblastopenia of childhood. In contrast, the activities of all the pyrimidine biosynthetic enzymes were elevated in blood from patients with a young RBC population: sickle cell anaemia, sickle-beta-thalassaemia, hereditary spherocytosis, and DiGuglielmo syndrome and from the newborn. It is postulated that factors which affect the activities of pyrimidine enzymes in CHA may also result in diminished erythropoiesis.

Pyrimidine biosynthesis in normal and transformed cells

We have developed procedures for sensitive measurement of specific radioactivities of pyrimidine nucleosides excreted from cells in culture. The changes in the observed values reflect dilution of the added isotope through de novo biosynthesis of nonradioactive pyrimidine nucleosides or by shifting and equilibration of other nucleotide pools into the free uridine pool. It is thus possible to monitor uridine biosynthesis occurring in intact cells without destroying or disrupting the cell population. On comparing a series of normal and and transformed lines, we have observed several growth-dependent patterns of change in specific activity and levels of uridine excretion and the temporal appearance of these changes. Hamster embryo fibroblasts slows pyrimidine biosynthesis at mid-growth while the hamster cell line V79 continues to dilute the pyrimidine pool at about 7% of the rate observed during exponential growth at confluence. Both cells exhibit Urd excretion beginning at one-half maximal growth. Passageable normal rat liver cells (IARC-20) also show a cessation of pyrimidine biosynthesis with a prior increase in uridine excretion. Two chemically transformed lines IARC-28 and IARC-19 derived from IARC-20 show different patterns. IARC-19 begins uridine excretion in early log growth and the specific activity continues to decrease at about 2% of the rate observed during exponential growth at confluence. The IARC-28 cells also begin excretion in early log growth but pyrimidine biosynthesis stops at about midlog. This method may prove to be an additional aid in recognizing and differentiating transformed cells in culture that do not exhibit the transformed phenotype.

Response of the pyrimidine pathway of Escherichia coli K 12 to exogenous adenine and uracil

The effect of exogenous adenine or uracil upon the de novo pathway for synthesis of pyrimidine nucleotides in Escherichia coli K12 was investigated. Parameters studied were levels of the enzymes carbamoyl phosphate synthase (EC 2.7.2.9), aspartate carbamoyltransferase (EC 2.1.3.2) and orotate phosphoribosyltransferase (EC 2.4.2.10) and the intermediates carbamoyl phosphate, aspartate and orotate, together with the contributions of exogenous uracil and aspartate to intracellular pyrimidine nucleotide. Taken with earlier data [Bagnara, A.S. & Finch, L. R. (1974) Eur. J. Biochem- 41, 421--430] on contents of UTP, CTP and 5-phosphoribosyl 1-diphosphate in cultures of this strain after the addition of adenine or uracil, the results obtained provide new insights into the regulatory mechanisms operating on the pathway in vivo. These insights enable evaluation of the contributions of such factors as limitation for a substrate, feed-back allosteric control by end products and enzyme repression/depression mechanisms. The evidence presented indicates that depressed levels of orotate phosphoribosyltransferase in E. coli K12 result in the wasteful ultilization of asparatate for excess synthesis of pyrimidine nucleotide precursors during balanced growth of the strain in minimal medium. Exogenous adenine increases the excessive accumulation of these precursors by lowering the intracellular content of 5-phosphoribosyl 1-diphosphate (Bagnara and Finch, 1974). This causes a decrease in the conversion of orotate to orotidine 5'-monophosphate, thus lowering the utilization or orotate and its precursors for synthesis of pyrimidine nucleotides. Further, since the contents of these nucleotide end products are thereby decreased (Bagnara nad Finch, 1974), theri feed-back on the early steps in the pathway is diminished and the production of the precursors is increased. It is postulated that growth of E. coli K12 under these conditions is limited by a compound that is metabolically related to precursors to aspartate.

Biochemical genetic analysis of pyrimidine biosynthesis in mammalian cells: I. Isolation of a mutant defective in the early steps of de novo pyrimidine synthesis

The isolation and characterization of a new mutant of Chinese hamster ovary cells is described. This mutant, Urd-A, shows an absolute requirement for exogenously added pyrimidines for growth. Complementation analysis indicates that the lesion in this mutant is recessive. Revertants can be isolated at frequencies suggesting that it is a single gene alteration. Biochemical analysis of cell-free extracts of CHO-K1 (Urd+) and Urd-A revealed that Urd-A possesses no more than 10% of wild-type levels of carbamyl phosphate synthetase (EC 2.7.2.9) activity, no more than 1% of wild-type levels of aspartate transcarbamylase (EC 1.2.3.2) activity, and undetectable levels of dihydroorotase (EC 3.5.2.3) activity. Thus, this mutant appears simultaneously to possess marked or complete deficiencies in the activities of the first three enzymes of pyrimidine biosynthesis. Activities of the other enzymes of the pathway appear normal. The use of this mutant for biochemical-genetic studies of pyrimidine biosynthesis is discussed.

Stable mutants of mammalian cells that overproduce the first three enzymes of pyrimidine nucleotide biosynthesis

Upon exposure to 0.1 mM N-phosphonacetyl-L-aspartate (PALA), a transition state analog inhibitor of aspartate transcarbamylase, most cells of a simian virus 40 (SV40)-transformed Syrian hamster line are killed within a few days, but resistant mutants form spontaneously with frequency 2-5 X 10(-5) in a stochastic process not dependent upon the presence of the inhibitor. The resistant phenotype is stable for many months in the absence of PALA. Other cell lines also give resistant mutants, but with substantially lower frequencies. Serial selection with PALA at concentrations up to 25 mM has yielded clones with more than 100 times the original aspartate transcarbamylase activity. The activities of carbamyl-P synthetase and dihydroorotase, which co-purify with aspartate transcarbamylase as a three-enzyme complex, increase in parallel with aspartate transcarbamylase activity in each resistant clone tested, but there is no substantial change in the activities of the last three enzymes of the de novo pathway, which are not in this complex. In each of the three resistant clones tested, there is an increase in the number of aspartate transcarbamylase active sites, determined by titration with 3H-PALA, which closely parallels the increase in enzyme activity. In one resistant clone tested, there is no change in the Ki for PALA or the Km for carbamyl-P. The only mechanism detected for achieving resistance to PALA is an increase in the steady state amount of the three enzyme complex.

Control of pyrimidine biosynthesis in the perfused liver. Feedback inhibition of glutamine-dependent carbamoyl phosphate synthetase

The site of feedback inhibition of the biosynthesis of pyrimidine nucleotides de novo was investigated in the isolated perfused rat liver. Hepatic uridine phosphate contents were specifically depleted by use of D-galactosamine. The effective activities of enzymes involved in the synthetic pathway were deduced from the rats of incorporation of labeled precursors into the acid-soluble uracil nucleotide pool and into some intermediates of the pathway. The labeling of hepatic urea was also monitored. When the uridine phosphate contents were less than 20% of controls, the incorporation of [14-C]-bicarbonate was stimulated about 20-fold. Label from [U-14C]oxaloacetate used as permeable precursor of intrace-lular aspartate was introduced into the uridylates to the same extent in normal and UTP-depleted livers. Similar results were obtained with labeled carbamoyl phosphate although the uptake of this compound by the liver was rather low. The lack of labeling of urea from exogenous carbamoyl phosphate does not indicate a free exchange of extra- and intramitochondrial carbamoyl phosphate. [ureido-14C]Ureidosuccinate produced in normal and D-galactosamine-treated livers almost identical labeling patterns of dihydroorotate, orotate and orotidine 5'-phosphate. The steady state concentrations of these intermediates were all below 15 nmol/g liver wet weight.