Deoxycytidylate aminohydrolase. II. Kinetic properties. The activatory effect of deoxycytidine triphosphate and the inhibitory effect of deoxythymidine triphosphate

The Genomic Impact of DNA CpG Methylation on Gene Expression; Relationships in Prostate Cancer

The process of DNA CpG methylation has been extensively investigated for over 50 years and revealed associations between changing methylation status of CpG islands and gene expression. As a result, DNA CpG methylation is implicated in the control of gene expression in developmental and homeostasis processes, as well as being a cancer-driver mechanism. The development of genome-wide technologies and sophisticated statistical analytical approaches has ushered in an era of widespread analyses, for example in the cancer arena, of the relationships between altered DNA CpG methylation, gene expression, and tumor status. The remarkable increase in the volume of such genomic data, for example, through investigators from the Cancer Genome Atlas (TCGA), has allowed dissection of the relationships between DNA CpG methylation density and distribution, gene expression, and tumor outcome. In this manner, it is now possible to test that the genome-wide correlations are measurable between changes in DNA CpG methylation and gene expression. Perhaps surprisingly is that these associations can only be detected for hundreds, but not thousands, of genes, and the direction of the correlations are both positive and negative. This, perhaps, suggests that CpG methylation events in cancer systems can act as disease drivers but the effects are possibly more restricted than suspected. Additionally, the positive and negative correlations suggest direct and indirect events and an incomplete understanding. Within the prostate cancer TCGA cohort, we examined the relationships between expression of genes that control DNA methylation, known targets of DNA methylation and tumor status. This revealed that genes that control the synthesis of S-adenosyl-l-methionine (SAM) associate with altered expression of DNA methylation targets in a subset of aggressive tumors.

Deoxyuridine analog nucleotides in deoxycytidine analog treatment: secondary active metabolites?

Deoxycytidine analogs (dCa's) are nucleosides widely used in anticancer and anti (retro) viral therapies. Intracellularly phosphorylated dCa anabolites are considered to be their main active metabolites. This article reviews the literature on the formation and pharmacological activity of deaminated dCa nucleotides. Most dCa's are rapidly deaminated into deoxyuridine analogs (dUa's) which are only slowly phosphorylated and therefore relatively inactive. dUa nucleotides are, however, also formed via deamination of dCa monophosphates by deoxycytidine monophosphate deaminase (dCMPD). dUa-monophosphates can interact with thymidylate synthase (TS), whereas dUa-triphosphates are incorporated into nucleic acids and interfere with polymerases. Administration of dCa's as monophosphate prodrugs or co-administration of the cytidine deaminase inhibitor tetrahydrouridine (THU) does not prevent dUa nucleotide formation which is, on the other hand, influenced by the dose and dCMPD activity. Taken together, these observations show that the formation of dUa nucleotides is a common phenomenon in treatment with dCa's and these compounds may play a role in treatment outcome. We conclude that more attention should be given to these relatively unknown, but potentially important metabolites.

DNA methylation as a target for drug design

DNA methylation is essential for normal embryonic development. Distinctive genomic methylation patterns must be formed and maintained with high fidelity to ensure the inactivities of specific promoters during development. The mutagenic and epigenetic aspects of DNA methylation are especially interesting because they may lead to the inactivation of genes which are involved in human carcinogenesis. The mutagenicity of 5-Methylcytosine (5mC) and the role of promoter hypermethylation in gene silencing, particularly in cancer, suggest a clinical significance for the design of novel DNA methylation inhibitors which may be utilized to reverse the effects of DNA methylation.

Hill coefficient ratios give binding ratios of allosteric enzyme effectors; inhibition, activation, and squatting in deoxycytidylate aminohydrolase (EC 3.5.4.12)

The ratio of the steady-state kinetic Hill coefficients of two different effectors equals (under some rather weak general assumptions) the ratio in which the effectors displace each other from an enzyme. This principle can make implications of experimental allosteric enzyme kinetic data immediately apparent. We can use it to find that one molecule of the allosteric inhibitor of dCMP aminohydrolase, at moderately high effector concentrations, displaces one molecule of substrate, or one molecule of activator, whereas at very high concentrations, one molecule of inhibitor displaces two of substrate. Further use of the principle suggests that substrate, at high concentrations, binds binds to activator sites. However, ratios of substrate, activator, and inhibitor Hill coefficients are incompatible with a simple model of activation in which substrate and activator are bound to the same conformation.

Analysis of competition for substrate sites in an allosteric enzyme with co-operative kinetics. Effects of dAMP and dUMP on donkey spleen deoxycytidylate aminohydrolase

Hypotheses about the interactions of effectors with conformations of allosteric enzymes having co-operative kinetics can be tested simply and exactly without knowledge of the nature of the intersubunit co-operativity by using a linkage approach to the analysis of steady-state kinetics. Applying this approach to competition for substrate sites in the allosteric enzyme donkey spleen dCMP aminohydrolase, we show that the kinetics are consistent with the hypothesis that the substrate dCMP and the competitor dAMP, as well as the allosteric activator dCTP, bind exclusively to the same conformation of the enzyme subunits. The linkage test can be applied in the presence of other effectors without knowledge of how these interact with the enzyme. Our tests showed that dCMP and DAMP are still bound exclusively to this same conformation in the presence of the product dUMP or of the allosteric inhibitor dTTP. We give evidence that dUMP binds to the same conformation as dCMP, but that it is also bound to other conformation(s). The advantages of the linkage approach, and some general problems in steady-state kinetics of allosteric enzymes, are discussed.

Kinetic behaviour and allosteric regulation of human deoxycytidylate deaminase derived from leukemic cells

Deoxycytidylate deaminase has been highly purified (1232-fold) from human leukemia CCRF-CEM cells. The native molecular weight of the enzyme is 108 000 and subunit molecular weight 50 500, suggesting that the native enzyme exists as a dimer. The enzyme exhibits a sigmoidal initial velocity vs substrate concentration curve and is regulated by allosteric effectors, dCTP and TTP. The curve relating substrate concentration to initial velocity was changed from a sigmoidal shape to a hyperbolic one by the activator dCTP, while the inhibitor TTP increased the sigmoidicity of the curve. The molecular weight of deoxycytidylate deaminase was unchanged in the presence of allosteric effectors, indicating that aggregation-disaggregation is not the basis of regulation. Deoxycytidylate deaminase exhibited the greatest affinity for the substrate dCMP, with lesser affinity for ara-CMP, and least affinity for CMP. Ara-CMP was an effective substrate in the presence of dCTP concentrations exceeding 4 microM. These data indicate that human neoplastic cell deoxycytidylate deaminase is a highly regulated allosteric enzyme, which is likely to have a significant influence on cellular dUMP, dCTP and TTP pools. These findings further suggest, that the enzyme through its influence on dUMP levels is likely to modulate the biochemical effects of pyrimidine antimetabolites active against the thymidylate synthetase reaction and in the presence of elevated dCTP pools will promote deamination of ara-CMP to the inactive ara-UMP.

Interaction of normal and unusually modified microbial DNA with cultured mammalian cells. Breakdown and reincorporation vs. uptake of polymerized DNA

The uptake of radioactively labeled bacterial and phage DNA and the incorporation of acid-soluble DNAase I digests of these DNAs by cultures of human foreskin and 3T3 cells were studied. The presence of large amounts of unusually modified pyrimidine residues in donor phage DNAs allowed radioactive donor DNA in the nuclei of DNA-treated cells to be distinguished from host DNA labeled with breakdown products derived from donor DNA. This distinction could be made because it was found that radioactively labeled 5-methylcytosine residues in predigested XP-12 DNA and glucosylated 5-hydroxymethylcytosine residues in predigested T4 DNA could not be incorporated in an unaltered form into animal cell DNA. The results obtained from the study of uptake of these DNAs suggest that approx. 4--40 ng of phage DNA per 10(6) cells was transported to the nuclei of DEAE-dextran-pretreated cells during 3 days of incubation in medium after treatment with the DNA. However, interpretation of the results is complicated by the finding of considerable amounts of donor DNA binding to and persisting at the cell surface, which might attach to nuclei during subcellular fractionation.

Active site directed effectors of allosteric enzymes

This communication introduces the concept of an active site directed effector, in terms of the two state model of Monod et al. (Monod, J., Wyman, J. and Changeux, J.-P. (1965) J. Mol. Biol. 12, 88-118), a consideration made necessary by the observation that the activity of a number of enzymes of the control type is modulated by effector molecules whose structure is similar to that of the substrate. We present equations which describe the kinetic responses obtained in its absence; this seemingly paradoxical activation, at low (S), is not tions the v versus (S) plot obtained in the presence of the effector crosses that obtained in its absence; this seemingly paradoxial activation, at low (S), is not explainable by the other frequently used two state models (Monod, J., Wyman, J. and Changeux, J.-P. (1965) J. Mol. Biol. 12, 88-118; Rubin, M.M. and Changeux, J.-P. (1966) J. Mol. Biol. 21, 265-274; Frieden, C. (1967) J. Biol. Chem. 242, 4045-4052; Dalziel, K. (1968) FEBS Lett. 1, 346-348 and Nichol, L.W., O'Dea, K. and Baghurst, P.A. (1972) J. Theor. Biol. 34, 255-263). The model is discussed using examples taken from the literature and successfully used to reanalyse published data on the enzyme deoxythymidine diphosphate D-glucose pyrophosphorylase (Frieden, C. (1967) J. Biol. Chem. 242, 4045-4052).

Bacteriophage PBS2-induced deoxycytidine triphosphate deaminase in Bacillus subtilis

The dCTP deaminase induced by Bacillus subtilis bacteriophage PBS2, whose DNA contains uracil instead of thymine, requires metal ion and thiol activators and has a molecular weight of 125,000. The enzyme displays sigmoidal substrate saturation kinetics and inhibition by dUTP, consistent with the deaminase's proposed role of providing balanced levels of dUTP and dCTP for PBS2 uracil-DNA synthesis.

Deoxycytidylate deaminase. Properties of the enzyme from cultured kidney cells of baby hamster

dCMP deaminase was partially purified from BHK-21/C13 cells grown in culture. The molecular weight of the enzyme was estimated by gel filtration and gradient centrifugation to be 130000 and 115000 respectively. The enzyme had a pH optimum of 8.4. Its activity versus substrate concentration curve was sigmoid, the substrate concentration at half-maximal velocity being 4.4mm. dCTP activated the deaminase maximally at 40mum, gave a hyperbolic curve for activity versus dCMP concentration and a K(m) value for dCMP of 0.91mm. dCTP activation required the presence of Mg(2+) or Mn(2+) ions. dTTP inhibited the deaminase maximally at 15mum; the inhibition required the presence of Mg(2+) or Mn(2+) ions. The enzyme was very heat-labile but could be markedly stabilized by dCTP at 0.125mm and ethylene glycol at 20% (v/v).

Deoxycytidine triphosphate deaminase: identification and function in Salmonella typhimurium

The biosynthesis of 2'-deoxyuridine monophosphate (dUMP) has been studied in a cytidine- and uracil-requiring mutant of Salmonella typhimurium (DP-55). The dUMP pool and the thymidine monophosphate (dTMP) pool of DP-55, grown in the presence of (3)H-uracil and unlabeled cytidine, are found to have the same specific activities. However, only 30% of the dUMP and the dTMP is synthesized from a uridine nucleotide. Seventy per cent is derived directly from a cytosine compound. The identification and partial purification of a Mg(2+)-dependent 2'-deoxycytidine triphosphate (dCTP) deaminase from S. typhimurium suggests that the combined action of dCTP deaminase and 2'-deoxyuridine triphosphate pyrophosphatase accounts for 70% of the dUMP, and therefore the dTMP, synthesized in vivo. The introduction of a thymine requirement (i.e., a block in thymidylate synthetase) into DP-55 results in a 100-fold increase in the size of the dUMP pool. However, the relative contribution of the uridine and cytidine pathways to dUMP synthesis is unaltered. The high dUMP pool is accompanied by extensive catabolism of dUMP to uracil. Partial thymine starvation of the cells results in a significant increase in the dUMP and dCTP pools. Moreover, an increase in the contribution of the dCTP pathway to dUMP synthesis is observed. As a result of these changes the catabolism of dUMP to uracil is augmented.