Deoxyribonucleotide Synthesis Research Articles

Bringing Individuality to Public Health Recommendations

The data generated from the human genome project offers unprecedented opportunities to elucidate the etiology of chronic diseases and developmental anomalies that arise from deleterious genome-diet interactions. Folate metabolism is an attractive system to explore such relationships. Folate is necessary for the synthesis of purine and thymidine deoxyribonucleotides and S-adenosylmethionine, a cofactor required for DNA methylation. Impaired folate metabolism results from primary folate deficiency, alcohol, gastrointestinal disorders that result in malabsorption, single nucleotide polymorphisms, increased folate catabolism and secondary nutrient deficiencies in vitamin B-6, vitamin B-12 and iron arising from a variety of pathologies. Any of these conditions singly or in combination influence DNA synthesis, DNA integrity, allelic-specific gene expression, chromatin structure and DNA mutation rates. Biochemical manifestations of impaired folate metabolism include increased uracil uptake into DNA, altered DNA methylation status and elevated homocysteine and S-adenosylhomocysteine in serum and tissues. These biochemical changes are associated with risk for cancer, cardiovascular disease, neural tube defects and some neuropathies and anemia, although direct causative mechanisms have not been established in all cases. Interactions between folate and the genome are reciprocal; polymorphisms in key genes influence folate nutritional requirements, indicating that dietary folate adequacy likely exerts selective pressure and thereby influences genetic variation. Other studies indicate that exposure to excess folate, perhaps at levels that occur at the upper end of the intake distribution curve, may have unintended consequences in promoting embryo viability. Therefore individualizing folic acid dietary recommendations necessitates a detailed understanding of all genetic and physiological variables that influence the interaction of folate with the genome and their relationship to the disease process.

Catalytic Properties, Thiol p K Value, and Redox Potential of Trypanosoma brucei Tryparedoxin

The dithiol protein tryparedoxin is a component of the unique trypanothione/trypanothione reductase metabolism of trypanosomatids and is involved in the parasite synthesis of deoxyribonucleotides and the detoxication of hydroperoxides. Tryparedoxin is a highly abundant protein in all life stages of Trypanosoma brucei, the causative agent of African sleeping sickness. As shown here, its functional properties are intermediate between those of classical thioredoxins and glutaredoxins. The redox potential of T. brucei tryparedoxin of -249 mV was determined by protein-protein redox equilibration with Escherichia coli thioredoxin. The trypanothione/tryparedoxin couple is probably the most significant factor determining the cytosolic redox potential of the parasites. The pK value of Cys(40), the first thiol in the WCPPC motif, is 7.2 as derived from the thiolate absorption at 240 nm and the rate of carboxymethylation. Alteration of the active site into that of thioredoxin (CGPC) did not affect the pK value. In contrast, in the mutant with the glutaredoxin motif (CPYC) the pK dropped to < or =4.0. The fact that the pK value of tryparedoxin coincides with the intracellular pH of the parasite may contribute to the reactivity of tryparedoxin in thiol disulfide exchange reactions.

Ribonucleotide reductase subunits from the yellow fever mosquito, Aedes aegypti: cloning and expression

Ribonucleotide reductase catalyses the de novo synthesis of deoxyribonucleotides. Class I reductases use an iron center to generate a tyrosyl free radical that can initiate formation of the deoxyribonucleotide. These reductases are α2β2 holoenzymes, and the subunits are denoted as R1 and R2. R1 contains the allosteric binding site and the active site, whereas R2 contains a binuclear iron center that initiates formation of the tyrosyl radical. We have cloned and sequenced the cDNAs encoding the R1 and R2 subunit in the yellow fever mosquito, Aedes aegypti. The messages for these proteins are increased in response to blood-feeding.

Deoxyribonucleotide synthesis in anaerobic microorganisms: The class III ribonucleotide reductase

For growth under oxygen-free atmosphere, some strict or facultative anaerobes depend on a class III ribonucleotide reductase for the synthesis of deoxyribonucleotides, the DNA precursors. Prototypes for this class of enzymes are ribonucleotide reductases from Escherichia coli and bacteriophage T4. This review article describes their structural and mechanistic properties as well as their complex allosteric regulation. Their evolutionnary relationship to class I and class II ribonucleotide reductases is also discussed.

Molecular characterization of ribonucleotide reductase from Cryptosporidium parvum.

The Apicomplexan enteric parasite, Cryptosporidium, infects a broad range of mammals, birds, fish and reptiles. Cryptosporidium parvum, the principal causative agent of human cryptosporidiosis, has emerged as a major contributor to waterborne outbreaks of this disease. The absence of effective drugs against C. parvum has necessitated the search for new drug targets. One attractive class of target enzymes is ribonucleotide reductase, an essential enzyme required for the de novo synthesis of deoxyribonucleotides. We report the cloning and sequencing of the small and large subunits of ribonucleotide reductase from a C. parvum genotype 2 isolate, GCH1. Southern blot analysis showed that these subunits are encoded by single copy genes. Both subunits have been expressed as recombinant proteins in Escherichia coli.

The Anaerobic Ribonucleotide Reductase from Lactococcus lactis

Deoxyribonucleotide synthesis by anaerobic class III ribonucleotide reductases requires two proteins, NrdD and NrdG. NrdD contains catalytic and allosteric sites and, in its active form, a stable glycyl radical. This radical is generated by NrdG with its [4Fe-4S](+) cluster and S-adenosylmethionine. We now find that NrdD and NrdG from Lactobacillus lactis anaerobically form a tight alpha(2)beta(2) complex, suggesting that radical generation by NrdG and radical transfer to the specific glycine residue of NrdD occurs within the complex. Activated NrdD was separated from NrdG by anaerobic affinity chromatography on dATP-Sepharose without loss of its glycyl radical. NrdD alone then catalyzed the reduction of CTP with formate as the electron donor and ATP as the allosteric effector. The reaction required Mg(2+) and was stimulated by K(+) but not by dithiothreitol. Thus NrdD is the actual reductase, and NrdG is an activase, making class III reductases highly similar to pyruvate formate lyase and its activase and suggesting a common root for the two anaerobic enzymes during early evolution. Our results further support the contention that ribonucleotide reduction during transition from an RNA world to a DNA world started with a class III-like enzyme from which other reductases evolved when oxygen appeared on earth.

Activation of caspases and induction of apoptosis by novel ribonucleotide reductase inhibitors amidox and didox

Amidox and didox are two polyhydroxy-substituted benzohydroxamic acid derivatives that belong to a new class of ribonucleotide reductase (RR) inhibitors. RR is the rate-limiting enzyme for de novo deoxyribonucleotide synthesis, and its activity is significantly increased in tumor cells in proportion to the proliferation rate. Therefore, RR is a target for antitumor therapy. HL-60 and K562 leukemia cells were treated with increasing doses of amidox and didox. Thereafter, the mode of cytotoxic drug action was determined by Hoechst 33258/propidium iodide (HO/PI) double staining, annexin binding, DNA fragmentation, and caspase activation. This was correlated to the decrease in dNTP levels. Staining with HO/PI and binding of fluorescein isothiocyanate-conjugated annexin V to externalized phosphatidylserine were used to quantify apoptosis. Low doses of amidox or didox resulted in an increase of apoptotic HL-60 cells within 48 hours. Higher doses (50 microM amidox or 250 microM didox) led to rapid induction of apoptosis, which could be detected as early as 4 hours after treatment. After 48 hours with these concentrations, almost 100% of the HL-60 cells died by apoptosis without an increase in necrosis. K562 cells were found to be resistant to amidox but not to didox. In HL-60 cells, upstream caspase 8 is processed in response to didox, whereas caspases 8 and 9 are processed upon amidox treatment. Didox-induced apoptosis, but not amidox-induced apoptosis, can be correlated with the decrease in dNTP levels. The results suggests that amidox induces several apoptosis mechanisms in HL-60 cells. In contrast, only caspase 9 is activated by didox in K562 cells, and because amidox hardly induces apoptosis in this cell line, no caspase cleavage is observed. Didox triggers distinct apoptosis pathways in HL-60 and K562 cells.

Radicals and the Birth and Death of DNA

Radicals have important functions in the enzymatic synthesis of deoxyribonucleotides and their destruction by antibiotics. The chemical basis for these reactions is that radicals dramatically speed up ionic reactions. Nature has developed methods to generate these radicals under mild conditions in water as solvent. The 'catalytic' effect of these reactive intermediates is described.

Trypanothione-dependent Synthesis of Deoxyribonucleotides by Trypanosoma brucei Ribonucleotide Reductase

Trypanosoma brucei, the causative agent of African sleeping sickness, synthesizes deoxyribonucleotides via a classical eukaryotic class I ribonucleotide reductase. The unique thiol metabolism of trypanosomatids in which the nearly ubiquitous glutathione reductase is replaced by a trypanothione reductase prompted us to study the nature of thiols providing reducing equivalents for the parasite synthesis of DNA precursors. Here we show that the dithiol trypanothione (bis(glutathionyl)spermidine), in contrast to glutathione, is a direct reductant of T. brucei ribonucleotide reductase with a K(m) value of 2 mm. This is the first example of a natural low molecular mass thiol directly delivering reducing equivalents for ribonucleotide reduction. At submillimolar concentrations, the reaction is strongly accelerated by tryparedoxin, a 16-kDa parasite protein with a WCPPC active site motif. The K(m) value of T. brucei ribonucleotide reductase for T. brucei tryparedoxin is about 4 micrometer. The disulfide form of trypanothione is a powerful inhibitor of the tryparedoxin-mediated reaction that may represent a physiological regulation of deoxyribonucleotide synthesis by the redox state of the cell. The trypanothione/tryparedoxin system is a new system providing electrons for a class I ribonucleotide reductase, in addition to the well known thioredoxin and glutaredoxin systems described in other organisms.

Predictive molecular markers in non-small cell lung cancer.

Recent biotechnologic knowledge has enabled the discovery of a cornucopia of genetic abnormalities commonly involved not only in cancer but also in other diseases ranging from the plague to arteriosclerosis. The wealth of possibilities uncovered by this knowledge inspires the hope that today's dream of a unified concept of common treatment for multiple diseases could become a future reality. This review arbitrarily categorizes recent findings into five major areas. First, cisplatin resistance associated with the nucleotide excision repair pathway can help clinical oncologists to choose between cisplatin and noncisplatin combinations. Second, the relevant role of nuclear factor-kappa B as a predictor of chemosensitivity can lead to the development of new drugs abrogating nuclear factor-kappa B expression. Third, the presence of tubulin mutations, which are directly involved in resistance to microtubule-interactive drugs, can guide chemotherapy based on taxane or nontaxane combinations. In addition, certain chromosomal deletions affect genes involved in deoxyribonucleotide synthesis, like ribonucleotide reductase, that intervene in gemcitabine metabolism; this raises interest in investigating deletion at chromosome 11p15.5 as a potential mechanism of gemcitabine resistance. Finally, an overwhelming number of publications have analyzed genes involved in cell cycle regulation and development as predictive markers of survival; however, where these pieces fit into the puzzle of cancer management is still unclear.

Role of the glutathione/glutaredoxin and thioredoxin systems in yeast growth and response to stress conditions.

Sulphydryl groups (-SH) play a remarkably broad range of roles in the cell, and the redox status of cysteine residues can affect both the structure and the function of numerous enzymes, receptors and transcription factors. The intracellular milieu is usually a reducing environment as a result of high concentrations of the low-molecular-weight thiol glutathione (GSH). However, reactive oxygen species (ROS), which are the products of normal aerobic metabolism, as well as naturally occurring free radical-generating compounds, can alter this redox balance. A number of cellular factors have been implicated in the regulation of redox homeostasis, including the glutathione/glutaredoxin and thioredoxin systems. Glutaredoxins and thioredoxins are ubiquitous small heat-stable oxidoreductases that have proposed functions in many cellular processes, including deoxyribonucleotide synthesis, repair of oxidatively damaged proteins, protein folding and sulphur metabolism. This review describes recent findings in the lower eukaryote Saccharomyces cerevisiae that are leading to a better understanding of their role in redox homeostasis in eukaryotic cell metabolism.

The anticytomegaloviral activity of raltitrexed is abrogated in quiescent mouse fibroblasts that overexpress thymidylate synthase

Cytomegalovirus (CMV) replication in non-proliferating cells requires the coordinated expression of the host enzymes responsible for deoxyribonucleotide synthesis. Thymidylate synthase (TS) is an essential cellular enzyme that catalyzes de novo synthesis of thymidylic acid (dTMP). In this report we show that murine CMV (MCMV) replication and DNA synthesis are inhibited in quiescent 3T6 fibroblasts by raltitrexed, a quinazoline-based folate analog that specifically inhibits TS. This antiviral activity was abrogated in LU3-7 cells, a 3T6 derivative that overproduces TS by about 50-fold. These observations indicate that the anticytomegaloviral activity of raltitrexed is associated with TS inhibition and suggest that cellular TS activity is required for efficient CMV replication in quiescent cells.

Nucleotides, Part LXVII, The 2-Cyanoethyl and (2-Cyanoethoxy)carbonyl Group for Base Protection in Nucleoside and Nucleotide Chemistry

The amino functions of the common 2′-deoxyribo- and ribonucleosides were blocked by the (2-cyanoethoxy)carbonyl group on treatment with 2-cyanoethyl carbonochloridate (5) or 1-[(2-cyanoethoxy)carbonyl]-3-methyl-1H-imidazolium chloride (6) leading to 7, 18, 8, 19, 9, and 20. In 2′-deoxyguanosine, the amide group was additionally blocked at the O6 position by the 2-cyanoethyl (→27) and 2-(4-nitrophenyl)ethyl group (→31, 32). Comparative kinetic studies regarding the cleavage of the ce/ceoc and npe/npeoc group by β-elimination revealed valuable information about the ease and sequential deprotection of the various blocking groups at different sites of the nucleobases. Besides the 5′-O-(dimethoxytrityl)-protected 3′-(2-cyanoethyl diisopropylphosphoramidites) 38 and 39 of N4-[(2-cyanoethoxy)carbonyl]-2′-deoxycytidine and N6-[(2-cyanoethoxy)carbonyl]-2′-deoxyadenosine, respectively, the N2-[(2-cyanoethoxy)carbonyl]-2′-deoxy-O6-[2-(4-nitrophenyl)ethyl]guanosine analog 40 is recommended as building block for oligo-2′-deoxyribonucleotide synthesis.

Occurrence of multiple ribonucleotide reductase classes in gamma-proteobacteria species.

Ribonucleotide reductase (RNR) is central to de novo synthesis of deoxyribonucleotides and essential for all living cells. Three classes have been described; class I is oxygen dependent and represented by two subclasses, Ia (NrdAB) and Ib (NrdEF); class II (NrdJ) is indifferent to oxygen; and class III (NrdDG) is oxygen sensitive. More than one class can be found in an organism, reflecting the oxygen status of its environment. We have investigated, by using PCR and Southern blot, the occurrence of the different classes among species of the gamma-Proteobacteria. Class III are present in all species tested, but the presence of the other classes varies. Some species contain one unique additional enzyme, class Ia, Ib, or II, whereas others contain two additional enzymes, class Ia and Ib, or class Ia and II.

Solid-phase synthesis of deoxyribonucleotides having a cap structure analog.

In this study, the solid-phase synthesis of oligodeoxyribonucleotides having a guanosine pyrophosphate cap structure (Gpp-) was achieved by using a new guanosine monophosphate unit having the DMTr group capable of estimation of coupling efficiency of the pyrophosphate bond formation. Since 7-methylguanosine base was unstable under basic conditions, Gpp-capped DNA oligomers were synthesized by using a new linker having a silanediyl bond, which allowed to release the DNA chain from the solid support by treatment with fluoride anion under neutral conditions.

Trimidox, an inhibitor of ribonucleotide reductase, induces apoptosis and activates caspases in HL-60 promyelocytic leukemia cells.

Ribonucleotide reductase (RR) is the rate-limiting enzyme for the de novo synthesis of deoxyribonucleotides. Its activity is significantly increased in tumor cells related to the proliferation rate. Therefore, the enzyme is considered to be an excellent target for cancer chemotherapy. In the present study, we investigated whether the antineoplastic effects of trimidox (3,4, 5-trihydroxybenzamidoxime), a novel inhibitor of RR, were due to induction of apoptosis.HL-60 cells were incubated with various concentrations of trimidox. Consequently, cell morphology, DNA condensation, annexin binding, DNA fragmentation, and signature type cleavage of poly(ADP-ribose)polymerase and gelsolin were determined. We also tested the involvement of CD95 and CD95 ligand in apoptosis induction. Furthermore, we examined the c-myc expression of HL-60 cells after incubation with trimidox in order to elucidate a possible association between c-myc expression and induction of apoptosis in the case of trimidox. Trimidox incubation caused a time-dependent increase of c-myc RNA expression and this was accompanied by the induction of apoptosis. Apoptosis was triggered independently of CD95 by the activation of caspases and PARP cleavage. We conclude that trimidox is able to induce programmed cell death. The induction of apoptosis was demonstrated by various biochemical and morphological methods and seems to be associated with the induction of c-myc. Apoptosis was induced by the activation of caspases and without change of the CD95 and CD95 ligand expression.

Mammalian S-phase checkpoint integrity is dependent on transformation status and purine deoxyribonucleosides.

In eukaryotic cells arrested in S-phase, checkpoint controls normally restrain mitosis until after replication. We have identified an array of previously unsuspected factors that modulate this restraint, using transformed hamster cells in which cycle controls are known to be altered in S-phase arrest. Arrested cells accumulate cyclin B, the regulatory partner of the mitotic p34(cdc2) kinase, which is normally not abundant until late G(2) phase; treatment of arrested cells with caffeine produces rapid S-phase condensation. We show here that such S-phase checkpoint slippage, as visualised through caffeine-dependent S-phase condensation, correlates with rodent origin and transformed status, is opposed by reverse transformation, and is favoured by c-src and opposed by wnt1 overexpression. Slippage is also dependent on a prolonged replicative arrest, and is favoured by arrest with hydroxyurea, which inhibits ribonucleotide reductase. This last is a key enzyme in deoxyribonucleotide synthesis, recently identified as a determinant of malignancy. Addition of deoxyribonucleosides shows that rapid S-phase condensation is suppressed by a novel checkpoint mechanism: purine (but not pyrimidine) deoxyribonucleosides, like reverse transformation, suppress cyclin B/p34(cdc2) activation by caffeine, but not cyclin B accumulation. Thus, ribonucleotide reductase has an unexpectedly complex role in mammalian cell cycle regulation: not only is it regulated in response to cycle progression, but its products can also reciprocally influence cell cycle control kinase activation.

The Anaerobic Ribonucleotide Reductase from Escherichia coli: THE SMALL PROTEIN IS AN ACTIVATING ENZYME CONTAINING A [4Fe-4S]2+ CENTER

For deoxyribonucleotide synthesis during anaerobic growth, Escherichia coli cells depend on an oxygen-sensitive class III ribonucleotide reductase. The enzyme system consists of two proteins: protein alpha, on which ribonucleotides bind and are reduced, and protein beta, of which the function is to introduce a catalytically essential glycyl radical on protein alpha. Protein beta can assemble one [4Fe-4S] center per polypeptide enjoying both the [4Fe-4S](2+) and [4Fe-4S](1+) redox state, as shown by iron and sulfide analysis, Mössbauer spectroscopy (delta = 0.43 mm.s(-1), DeltaE(Q) = 1.0 mm.s(-1), [4Fe-4S](2+)), and EPR spectroscopy (g = 2. 03 and 1.93, [4Fe-4S](1+)). This iron center is sensitive to oxygen and can decompose into stable [2Fe-2S](2+) centers during exposure to air. This degraded form is nevertheless active, albeit to a lesser extent because of the conversion of the cluster into [4Fe-4S] forms during the strongly reductive conditions of the assay. Furthermore, protein beta has the potential to activate several molecules of protein alpha, suggesting that protein beta is an activating enzyme rather than a component of an alpha(2)beta(2) complex as previously claimed.

Lung cancer and the human gene for ribonucleotide reductase subunit M1 (RRM1)

LOH11A is a region of Chromosome (Chr) 11p15.5 where 75% of lung cancers show loss of heterozygosity (LOH). Clinical and cell biological studies suggest that LOH11A contains a tumor/metastasis suppressor gene. We have mapped this region (650 kb) using overlapping genomic P1/PAC/BAC clones, and one of the genes that we have identified is RRM1. This gene encodes the large subunit (M1) of ribonucleotide reductase, the heterodimeric enzyme that catalyzes the rate-limiting step in deoxyribonucleotide synthesis. By comparing our genomic sequences with the previously published cDNA, we have found that the human gene is composed of 19 exons. It is oriented telomere to centromere and is Alu rich. In order to verify that RRM1 maps within the boundaries of LOH11A, we assessed the frequency of LOH at a SacI polymorphism within intron IX of the gene. We observed LOH in 48% (15/31) of informative lung tumor specimens. To determine whether RRM1 was mutated in tumors, SSCP analysis of the 19 RRM1 exons was performed. No mutations were revealed in 12 pairs of normal and tumor DNA samples. Immunoblots on protein extracts from normal/tumor pairs indicated that a protein of the expected size was present in both. Our conclusion is that RRM1 lies within the LOH11A region, but that its exons are not mutated in tumors. The potential for RRM1 to act as a tumor suppressor is discussed.

Evidence by Mutagenesis that Tyr370 of the Mouse Ribonucleotide Reductase R2 Protein Is the Connecting Link in the Intersubunit Radical Transfer Pathway

Ribonucleotide reductase catalyzes all de novo synthesis of deoxyribonucleotides. The mammalian enzyme consists of two non-identical subunits, the R1 and R2 proteins, each inactive alone. The R1 subunit contains the active site, whereas the R2 protein harbors a binuclear iron center and a tyrosyl free radical essential for catalysis. It has been proposed that the radical properties of the R2 subunit are transferred approximately 35 A to the active site of the R1 protein, through a coupled electron/proton transfer along a conserved hydrogen-bonded chain, i.e. a radical transfer pathway (RTP). To gain a better insight into the properties and requirements of the proposed RTP, we have used site-directed mutagenesis to replace the conserved tyrosine 370 in the mouse R2 protein with tryptophan or phenylalanine. This residue is located close to the flexible C terminus, known to be essential for binding to the R1 protein. Our results strongly indicate that Tyr(370) links the RTP between the R1 and R2 proteins. Interruption of the hydrogen-bonded chain in Y370F inactivates the enzyme complex. Alteration of the same chain in Y370W slows down the RTP, resulting in a 58 times lower specific activity compared with the native R2 protein and a loss of the free radical during catalysis.