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When to investigate for purine and pyrimidine disorders. Introduction and review of clinical and laboratory indications.

When to suspect and thus investigate for inborn errors of purine and pyrimidine metabolism is a dilemma for even the most observant investigator. Often parents of affected children, or a history involving siblings, can provide valuable clues. The recognition of new purine and pyrimidine disorders requires skill and serendipity. But even identifying known disorders can prove difficult, since they cover a broad spectrum of illnesses, can have more than one symptom, or lead to early death. This problem is compounded by the fact that they are relatively recently described and therefore often little known, either in the clinic or laboratory. The considerable heterogeneity in clinical expression within families as well as between families means that asymptomatic homozygotes may not be recognized or can present at any time from early childhood through adolescence up to their eighth decade. Consequently, all siblings should be screened. These disorders should be suspected in any case of unexplained anaemia, failure to thrive, susceptibility to recurrent infection, or neurological deficits with no current diagnosis, including autism, cerebral palsy, delayed development, deafness, epilepsy, self-mutilation, muscle weakness, the inability to walk or talk, and-unusual in children and adolescents-gout, sometimes with renal disease. Some disorders present with radiolucent kidney stones, in acute or chronic renal failure, alone or with any of the above, or as an intolerance/sensitivity to therapy (e.g. 5-fluorouracil in malignancies or azathioprine immunosuppression in organ transplantation), often with life-threatening consequences. Several parameters need to be evaluated to ensure correct diagnosis. Pitfalls which can mask diagnosis using only a single test are renal failure, blood transfusion, diet or drugs.

Biomarkers↗

Inherited defects of purine and pyrimidine metabolism: laboratory methods for diagnosis.

The diagnosis of the majority of the known inherited defects of purine and pyrimidine metabolism can be achieved by analysing urinary excretion profiles. A quantitative measurement of the urinary uric acid/creatinine ratio should be the first approach for purine defects. The general screening system involves separation of the bases and nucleosides by reversed-phase high-performance liquid chromatography and multiwavelength UV detection. The catabolic defects of pyrimidine degradation can be diagnosed by gas chromatography-mass spectrometry as used for organic acids. For the detection of adenylosuccinase deficiency, several simple but effective thin-layer chromatographic methods are available. Techniques such as liquid chromatography-mass spectrometry, direct nega-tiveion fast-atom bombardment mass spectrometry, and proton nuclear magnetic resonance spectroscopy give promising results, but are not yet being used on a large scale. Patients should keep to a simple diet and preferably be free of medication in order to allow a reliable interpretation of the analytical data.

Animals↗

Pyrimidine dimers in DNA initiate systemic immunosuppression in UV-irradiated mice.

Exposing the skin of mice to UV radiation interferes with the induction of delayed and contact hypersensitivity immune responses initiated at nonirradiated sites. The identity of the molecular target in the skin for these immunosuppressive effects of UV radiation remains controversial. To test the hypothesis that DNA is the target for UV-induced systemic immunosuppression, we exposed C3H mice to UV radiation and then used liposomes to deliver a dimer-specific excision repair enzyme into the epidermis in situ. The application of T4 endonuclease V encapsulated in liposomes to UV-irradiated mouse skin decreased the number of cyclobutane pyrimidine dimers in the epidermis and prevented suppression of both delayed and contact hypersensitivity responses. Moreover, the formation of suppressor lymphoid cells was inhibited. Control, heat-inactivated endonuclease encapsulated in liposomes had no effect. These studies demonstrate that DNA is the major target of UV radiation in the generation of systemic immunosuppression and suggest that the primary molecular event mediating these types of immunosuppression by UV radiation is the formation of pyrimidine dimers. Furthermore, they illustrate that the delivery of lesion-specific DNA repair enzymes to living skin after UV irradiation is an effective tool for restoring immune function and suggest that this approach may be broadly applicable to preventing other alterations caused by DNA damage.

Analysis of Variance↗

E.S.R. of spin-trapped radicals in aqueous solutions of pyrimidine nucleosides and nucleotides. Reactions of the hydroxyl radical.

Free radicals produced by the reactions of OH radicals with ribose phosphates, pyrimidine nucleosides and nucleotides in aqueous solutions have been investigated by e.s.r. and spin-trapping techniques. OH radicals were generated by U.V. -photolysis of hydrogen peroxide and short-lived free radicals of the samples were spin-trapped by t-nitrosobutane and identified by e.s.r. spectroscopy. For ribose-5'-phosphate and 2' -deoxyribose-5' -phosphate, e.s.r. spectra observed consisted mainly of singles due to -C(5')H2 radicals which were initiated by H-abstraction from the sugar at the C-4' position and formed by the radical transfer to the C-5' position. It has also been shown that OH radicals abstract a hydrogen atom from the sugar at C-1' and C-5' positions. For cytidine, deoxycytidine, 5'-CMP, 3' -CMP and 5' -dCMP, four radicals have been observed and for uridine, deoxyuridine, 5' -UMP, 3' -UMP and 5' -dUMP, the existence of at least three radical species have been established. In contrast to the case of ribose phosphates, no signals due to -C(5')H2 radicals were detected for pyrimidine nucleosides and nucleotides. The results are discussed in relation to a recent mechanism which described OH-induced strand breaks of DNA.

Electron Spin Resonance Spectroscopy↗

Kinetics and mechanism of electron transfer between purines and pyrimidines, their dinucleotides and polynucleotides after reaction with hydrated electrons; a pulse radiolysis study.

The radical spectra of mixtures of thymidine 5'-monophosphate (TMP) or uridine 5'-monophosphate (UMP) with adenine 5'-monophosphate (AMP) after hydrated electron attack, measured from 5 to 3000 microsecond after pulse radiolysis, can only be described in terms of the radical spectra of the nucleotides if an electron transfer is taken into account from the purine radical anion to the pyrimidine, resulting in the formation of a pyrimidine radical anion. From analysis of the spectra of the dinucleoside phosphates ApU, dApT and dCpdA after eaq- attack it follows that the electron-donating species is the purine radical anion (A-.) rather than the protonated purine radical. The electron transfer competes with the fast protonation of the purine radical anion: A-. + py----A + py.- and A-. + H2O in equilibrium AH. respectively. The electron transfer is found to have a diffusion-controlled reaction rate constant of approximately 1.2 X 10(10) for TMP and 3.5 X 10(9) dm3 mol-1 s-1 for UMP.

Electron Transport↗

Synthesis and biological activity of 2'-deoxy-4'-thio-pyrazolo[3,4-d]pyrimidine nucleosides.

The coupling of 4-aminopyrazolo [3, 4-d]pyrimidine with the appropriate thio sugar gave a 3:1 ratio of alpha,beta blocked 4-amino-1-(2-deoxy-4-thio-D-erythropentofuranosyl)-1H pyrazolo[3,4-d]pyrimidine nucleosides. The mixture was deblocked, both the anomers were separated, and the beta-anomer was readily deaminated by adenosine deaminase. The nucleosides have been characterized, and their anomeric configurations have been determined by proton NMR. All three nucleosides were evaluated against a panel of human tumor cell lines for cytotoxicity in vitro. The details of a convenient and high yielding synthesis of these nucleosides are described.

Adenosine↗

Functionalization of pyrimidine and purine nucleosides at C4 and C6: C-nucleophilic substitution of their C4- and C6-(1,2,4-triazol-1-yl) derivatives.

A study of C-nucleophilic substitution at the C4-position on pyrimidine and C6-position on 2'-deoxyguanosine to produce novel nucleosides is presented with the spectroscopic properties of their respective substitution products. C4-(1,2,4-triazol-1-yl) pyrimidine nucleosides 1 were treated with nitroalkanes, malononitrile, acetylacetone, ethyl nitroacetate, acetoacetate and cyanoacetate at 100 degrees C in dioxane in the presence of DBU resulting in the production of novel nucleosides 2-11. To explore the application of this methodology to purine chemistry, this approach was used to produce novel analogs from 2'-deoxyguanosine. We found that the triazolo derivative 12 undergoes C-nucleophilic substitution with nitromethane, malononitrile, acetylacetone, ethyl nitroacetate and cyanoacetate in the presence of potassium carbonate (K2CO3) in DMF at 100 degrees C to give novel nucleosides 13-17.

Acetates↗

Synthesis of racemic and enantiomeric 3-pyrrolidinyl derivatives of purine and pyrimidine nucleobases.

The present work relates to the synthesis of pyrrolidine nucleoside analogs. Starting from malic acid, we have elaborated a high-yield synthesis of racemic and enantiomeric N-protected 3-pyrrolidinols and their O-mesyl derivatives as key compounds for alkylations of purine and pyrimidine nucleobases. On varying base and solvent, we have found conditions providing both satisfactory N-/O-regioisomeric ratio and acceptable yield for pyrimidine compounds.

Antineoplastic Agents↗

Sequence specificity of cyclobutane pyrimidine dimers in DNA treated with solar (ultraviolet B) radiation.

Cyclobutane pyrimidine dimers were quantified at the sequence level after irradiation with solar ultraviolet (UVB) and nonsolar ultraviolet (UVC) light sources. The yield of photoproducts at specific sites was dependent on the nucleotide composition in and around the potential lesion as well as on the wavelength of ultraviolet light used to induce the damage. Induction was greater in the presence of 5' flanking pyrimidines than purines; 5' guanine inhibited induction more than adenine. UVB irradiation increased the induction of cyclobutane dimers containing cytosine relative to thymine homodimers. At the single UVC and UVB fluences used, the ratio of thymine homodimers (T mean value of T) to dimers containing cytosine (C mean value of T, T mean value of C, C mean value of C) was greater after UVC compared to UVB irradiation.

Base Sequence↗

X-ray structure of T4 endonuclease V: an excision repair enzyme specific for a pyrimidine dimer.

The x-ray structure of T4 endonuclease V, an enzyme responsible for the first step of a pyrimidine-dimer-specific excision-repair pathway, was determined at a 1.6-angstrom resolution. The enzyme consists of a single compact domain classified into an all-alpha structure. This single domain has two distinct catalytic activities; it functions as a pyrimidine dimer glycosylase and as an apurinic-apyrimidinic endonuclease. The amino-terminal segment penetrates between two major helices and prevents their direct contact. The refined structure suggests the residues involved in the substrate binding and the catalysis of the glycosylation reaction.

Amino Acid Sequence↗

ENZYMES OF THE PYRIMIDINE PATHWAY IN ESCHERICHIA COLI. II. INTRACELLULAR LOCALIZATION AND PROPERTIES OF DIHYDROOROTIC DEHYDROGENASE.

Taylor, W. Herman (Portland State College, Portland, Ore.), and Mary L. Taylor. Enzymes of the pyrimidine pathway in Escherichia coli. II. Intracellular localization and properties of dihydroorotic dehydrogenase. J. Bacteriol. 88:105-111. 1964.-Intracellular localization of three enzymes of the pyrimidine pathway in Escherichia coli was studied. Dihydroorotic dehydrogenase was found to be associated with the membrane portion of lysed spheroplasts. Centrifugal fractionation of cell-free extracts showed all the dihydroorotic dehydrogenase activity to be associated with large structures, probably cell wall-membrane fragments. In contrast, all orotidylic decarboxylase activity was found in the cytoplasm in both lysed spheroplasts and cell-free extracts. Aspartate transcarbamylase activity appeared to be particulate in repressed cells, but only 25% was particulate in derepressed cells. Dihydroorotic dehydrogenase was shown to be bound to oxidative particles by oxygen uptake and orotate production from dihydroorotate. A ferricyanide reduction assay, suitable for measuring soluble and particulate enzyme, was devised for dihydroorotic dehydrogenase. Soluble dihydroorotic dehydrogenase was prepared by use of deoxycholate. A 20-fold purification of the enzyme compared to whole-cell activity was achieved by ammonium sulfate fractionation of the deoxycholate-soluble enzyme. Although cytochromes were implicated by cyanide inhibition of aerobic orotate production by particles, the purified enzyme appeared to be separated from the cytochromes, as shown by lack of cyanide inhibition in the ferricyanide assay. The purified soluble enzyme did not react in the aerobic assay previously used by others for assay of this enzyme. In contrast to the degradative dihydroorotic dehydrogenases reported by other workers, the biosynthetic dihydroorotic dehydrogenase of E. coli did not link to pyridine nucleotides.

Carboxy-Lyases↗

ENZYMES OF THE PYRIMIDINE PATHWAY IN ESCHERICHIA COLI. I. SYNTHESIS BY CELLS AND SPHEROPLASTS.

Taylor, W. Herman (Portland State College, Portland, Ore.), and G. David Novelli. Enzymes of the pyrimidine pathway in Escherichia coli. I. Synthesis by cells and spheroplasts. J. Bacteriol. 88:99-104. 1964.-Upon release from repression, cells and spheroplasts of two mutants of Escherichia coli efficiently synthesized aspartate transcarbamylase and ornithine transcarbamylase, whereas only cells synthesized dihydroorotic dehydrogenase. Ethylenediaminetetraacetate treatment and sucrose incubation of cells were found to be responsible for the loss of dihydroorotic dehydrogenase synthesis. Spheroplasts required the addition of amino acids and an energy source for the synthesis of aspartate transcarbamylase. Uracil repressed synthesis of aspartate transcarbamylase in spheroplasts as well as in cells. Chloramphenicol inhibition and amino acid requirement for increased aspartate transcarbamylase activity in spheroplasts indicated de novo protein synthesis. E. coli 15, R185-482, and E. coli K-12, 496, were used to study the effect of carbon source and stimulation by orotate and dihydroorotate on synthesis of dihydroorotic dehydrogenase. Only E. coli 15, R185-482, showed any stimulation of dihydroorotic dehydrogenase synthesis. When glucose was the carbon source, orotate but not dihydroorotate stimulated; with glycerol as carbon source, dihydroorotate stimulated and orotate acted as a repressor. These results are discussed in terms of induction and pyrimidine supply to the cells.

Amino Acids↗

den V gene of bacteriophage T4 determines a DNA glycosylase specific for pyrimidine dimers in DNA.

Endonuclease V of bacteriophage T4 has been described as an enzyme, coded for by the denV gene, that incises UV-irradiated DNA. It has recently been proposed that incision of irradiated DNA by this enzyme and the analogous "correndonucleases" I and II of Micrococcus luteus requires the sequential action of a pyrimidine dimer-specific DNA glycosylase and an apyrimidinic/apurinic endonuclease. In support of this two-step mechanism, we found that our preparations of T4 endonuclease V contained a DNA glycosylase activity that produced alkali-labile sites in irradiated DNA and an apyrimidinic/apurinic endonuclease activity that converted these sites to nicks. Both activities could be detected in the presence of 10 mM EDTA. In experiments designed to determine which of the activities is coded by the denV gene, we found that the glycosylase was more heat labile in extracts of Escherichia coli infected with either of two thermosensitive denV mutants than in extracts of cells infected with wild-type T4. In contrast, apyrimidinic/apurinic endonuclease activity was no more heat labile in extracts of the former than in extracts of the latter. Our results indicate that the denV gene codes for a DNA glycosylase specific for pyrimidine dimers.

DNA↗

Atomic structure of a pyrimidine-dimer specific excision-repair enzyme from bacteriophage T4.

T4 endonuclease V is an enzyme responsible for the first step of a pyrimidine-dimer specific excision-repair process. The three-dimensional structure of this enzyme has been determined at 1.6A resolution by X-ray crystallography. The enzyme consists of one single compact domain classified into the all alpha structure. This single domain possesses two distinct catalytic activities, a pyrimidine-dimer glycosylase and an apurinic/apyrimidinic endonuclease. The backbone of the enzyme represents a unique folding scheme incompatible with close packing of alpha-helices. The refined structure suggests possible residues that participate in interactions with DNA.

Amino Acid Sequence↗

Early steps of excision repair of cyclobutane pyrimidine dimers by the Micrococcus luteus endonuclease. A three-step incision model.

The early steps of excision repair of cyclobutane pyrimidine dimers are investigated. It is demonstrated that the apurinic/apyrimidinic endonuclease associated with the Micrococcus luteus uv-specific endonuclease cleaves the phosphodiester bond on the 3' side of the deoxyribose leaving a 3' hydroxy terminus and a 5' phosphoryl terminus. This nick is not a substrate for T4 polynucleotide ligase. The 3' base-free deoxyribose terminus is not a substrate for either the polymerase or the 3' to 5' exonuclease activities of Escherichia coli DNA polymerase I. However, the 3' terminus of the nick is converted to a substrate for DNA polymerization by the action of a 5' apurinic/apyrimidinic endonuclease. A three-step model for the incision step of excision repair of cyclobutane pyrimidine dimers is presented.

Alkaline Phosphatase↗

Activities of various enzymes of pyrimidine nucleotide and DNA syntheses in normal and neoplastic human tissues.

The activities of the key enzymes of pyrimidine nucleotide and DNA syntheses in 43 human tumors and 28 normal human tissues were investigated. The activities of cytidine triphosphate synthetase, deoxycytidine monophosphate deaminase, uridine kinase, thymidine kinase, thymidine monophosphate kinase and DNA polymerase were markedly increased in tumor tissues, compared with those in the corresponding normal tissues, while the activities of deoxycytidine kinase, cytidine deaminase and deoxycytidine deaminase were only slightly increased. The use of thymidine and deoxyuridine as substrates of human pyrimidine nucleoside phosphorylase gave 1 to 2 orders of magnitude higher activity than that of uridine.

Carbon-Nitrogen Ligases↗

Specificity of pyrimidine nucleoside phosphorylases and the phosphorolysis of 5-fluoro-2'-deoxyuridine.

Isoelectric focusing and studies with 1-(2'-deoxy-beta-D-glucopyranosyl)thymine (GPT), a specific inhibitor of uridine phosphorylase activity, were used to determine the substrate specificities of mammalian pyrimidine nucleoside phosphorylases and their cleavage of 5-fluoro-2'-deoxyuridine (FdUrd). Isoelectric focusing profiles for the cytosol fractions from Ehrlich ascites cells and from Novikoff hepatoma cells each consisted essentially of one peak of nucleoside phosphorylase activity [isoelectric points (pl) 5.4 and 5.8, respectively] that cleaved both uridine and thymidine (dThd), as well as FdUrd. By contrast, cytosol fractions from HeLa (S3) cells, mouse liver, and normal human leukocytes each exhibited a major peak of activity (pl 4.6, 6.5, and 4.9, respectively) that cleaved only dThd and FdUrd, while mouse liver exhibited a second peak (pl 5.2) that cleaved primarily uridine. To distinguish clearly between (a) uridine phosphorylases that cleave primarily uridine and that are inhibited by GPT and (b)dThd phosphorylases that cleave only deoxynucleosides and that are not inhibited by GPT, we propose the term "uridine-deoxyuridine phosphorylases" to define those pyrimidine nucleoside phosphorylases that cleave both uridine and dThd and that are inhibited by GPT. On the basis of this definition and studies with GPT in nonfocused cytosol preparations, we conclude that FdUrd is cleaved to 5-fluorouracil by uridine-deoxyuridine phosphorylase activity in Ehrlich ascites cells and in Novikoff hepatoma cells, and by dThd phosphorylases in mouse liver, in normal human leukocytes, and in HeLa (S3) cells.

Animals↗

[Crystal structure and function of pyrimidine dimer specific excision repair enzyme: T4 endonuclease V].

Bacteriophage T4 endonuclease V is an enzyme which plays an important role in pyrimidine dimer specific excision repair of DNA. This enzyme possesses two distinct catalytic activities, pyrimidine dimer glycosylase and apyrimidinic endonuclease. The three dimensional structure (3D) of the wild type enzyme was determined at 1.45A resolution by X-ray crystallography. In combination with the results of site-directed mutagenesis, the refined structure revealed that Glu23 and the surrounding basic residues constitute the catalytic center of this enzyme. Furthermore, the 3D structure of active site mutants were determined and compared with that of the wild type. The results suggest that a precise configuration of Glu23 residue is required for glycosylation and that Arg3 plays an important role in the substrate binding.

Amino Acid Sequence↗