DNA glycosylases

CUX2 protein functions as an accessory factor in the repair of oxidative DNA damage

CUX1 and CUX2 proteins are characterized by the presence of three highly similar regions called Cut repeats 1, 2, and 3. Although CUX1 is ubiquitously expressed, CUX2 plays an important role in the specification of neuronal cells and continues to be expressed in postmitotic neurons. Cut repeats from the CUX1 protein were recently shown to stimulate 8-oxoguanine DNA glycosylase 1 (OGG1), an enzyme that removes oxidized purines from DNA and introduces a single strand break through its apurinic/apyrimidinic lyase activity to initiate base excision repair. Here, we investigated whether CUX2 plays a similar role in the repair of oxidative DNA damage. Cux2 knockdown in embryonic cortical neurons increased levels of oxidative DNA damage. In vitro, Cut repeats from CUX2 increased the binding of OGG1 to 7,8-dihydro-8-oxoguanine-containing DNA and stimulated both the glycosylase and apurinic/apyrimidinic lyase activities of OGG1. Genetic inactivation in mouse embryo fibroblasts or CUX2 knockdown in HCC38 cells delayed DNA repair and increased DNA damage. Conversely, ectopic expression of Cut repeats from CUX2 accelerated DNA repair and reduced levels of oxidative DNA damage. These results demonstrate that CUX2 functions as an accessory factor that stimulates the repair of oxidative DNA damage. Neurons produce a high level of reactive oxygen species because of their dependence on aerobic oxidation of glucose as their source of energy. Our results suggest that the persistent expression of CUX2 in postmitotic neurons contributes to the maintenance of genome integrity through its stimulation of oxidative DNA damage repair.

Location of abasic sites in oligodeoxynucleotides by tandem mass spectrometry and by a chemical cleavage initiated by an unusual reaction of the ODN with MALDI matrix

We describe two approaches employing electrospray ionization (ESI) tandem mass spectrometry (MS/MS) and matrix assisted laser desorption/ionization (MALDI) post-source decay (PSD) for determining the location of an abasic site in modified oligodeoxynucleotides (ODNs). With MS/MS, we found both complementary fragment ions (a(n)' and w(n)') produced at the abasic site were predominant in the mass spectra and allowed the location to be determined. Under MALDI conditions, most ODNs carrying an abasic site are singly charged, and PSD gives predominately w(n)' ions at the abasic sites, revealing their location. We also describe another approach for identifying and locating abasic sites in model ODNs; namely, an "in situ" derivatization coupled with MALDI mass spectrometry (MS). In general, an ODN n-mer containing an abasic site at the m-th position from the 5-terminus can react with the matrix component, anthranilic acid, to form a Schiff base. The adduct upon MALDI breaks into 3' and 5' fragments (w(n-m), b(m), a(m), d(m-1)) at the abasic site, revealing its location. ESI MS methods are also applicable for detecting the hydrazone derivatives of abasic sites, and the fragmentation of hydrazones shows the location of the abasic site.

A mollicute (mycoplasma) DNA repair enzyme: purification and characterization of uracil-DNA glycosylase

The DNA repair enzyme uracil-DNA glycosylase from Mycoplasma lactucae (831-C4) was purified 1,657-fold by using affinity chromatography and chromatofocusing techniques. The only substrate for the enzyme was DNA that contained uracil residues, and the Km of the enzyme was 1.05 +/- 0.12 microM for dUMP containing DNA. The product of the reaction was uracil, and it acted as a noncompetitive inhibitor of the uracil-DNA glycosylase with a Ki of 5.2 mM. The activity of the enzyme was insensitive to Mg2+, Mn2+, Zn2+, Ca2+, and Co2+ over the concentration range tested, and the activity was not inhibited by EDTA. The enzyme activity exhibited a biphasic response to monovalent cations and to polyamines. The enzyme had a pI of 6.4 and existed as a nonspherical monomeric protein with a molecular weight of 28,500 +/- 1,200. The uracil-DNA glycosylase from M. lactucae was inhibited by the uracil-DNA glycosylase inhibitor from bacteriophage PBS-2, but the amount of inhibitor required for 50% inhibition of the mycoplasmal enzyme was 2.2 and 8 times greater than that required to cause 50% inhibition of the uracil-DNA glycosylases from Escherichia coli and Bacillus subtilis, respectively. Previous studies have reported that some mollicutes lack uracil-DNA glycosylase activity, and the results of this study demonstrate that the uracil-DNA glycosylase from M. lactucae has a higher Km for uracil-containing DNA than those of the glycosylases of other procaryotic organisms. Thus, the low G + C content of the DNA from some mollicutes and the A.T-biased mutation pressure observed in these organisms may be related to their decreased capacity to remove uracil residues from DNA.

Isolation of a herpes simplex virus cDNA encoding the DNA repair enzyme uracil-DNA glycosylase

Activity of the DNA repair enzyme uracil-DNA glycosylase has been shown to increase in herpes simplex virus type 2 (HSV-2)-infected cells. When mRNA derived from either HSV-1- or HSV-2-infected HeLa S3 cells was translated in an in vitro translation system, significant uracil-DNA glycosylase activity could be detected in the lysate. This activity was specific for the removal of uracil from DNA. Lysates from in vitro translation of mRNA derived from uninfected HeLa cells did not contain measurable glycosylase activity. A cDNA library was constructed with mRNA derived from HSV-2-infected cells 10 h postinfection. Pooled isolates from this library were used in hybrid-arrest and in vitro translation reactions to isolate a uracil-DNA glycosylase-specific cDNA. In vitro translation of hybrid-selected RNA, by using this cDNA, produced glycosylase activity in the lysate. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of radiolabeled products from this translation reaction showed a protein component with a molecular weight of 39,000. This is consistent with the molecular weight determinations of the purified glycosylase enzyme derived from either uninfected or HSV-infected HeLa cells. Northern (RNA blot) analysis of HSV-derived RNA, by using the glycosylase cDNA as a probe, revealed five overlapping transcripts of 3.4, 2.8, 2.4, 1.7, and 1.0 kilobases. Southern analysis indicated that the DNA sequence encoding the HSV-specific uracil-DNA glycosylase was located between 0.065 and 0.08 map units on the prototypic arrangement of the HSV genome.

The incorporation of deoxyuridine monophosphate into DNA increases the sister-chromatid exchange yield

The effect of a treatment with 5-fluoro-2'-deoxyuridine (FdUrd) in combination with 2'-deoxyuridine (dUrd) on cell proliferation, incorporation of DNA precursors into DNA and sister-chromatid exchanges (SCEs) has been analyzed in Allium cepa meristem cells. FdUrd in the range 10(-9)-5 X 10(-7) M produced a dose- and time-dependent decrease in the amount of cells in mitosis. This inhibitory effect could be reversed by 70-80% in short-term (6 h) experiments, by exogenously supplied dUrd at a concentration of 10(-4) M. However, at the highest FdUrd dose tested (10(-7) M), 10(-4) M dUrd could not reverse the FdUrd effect in long-term experiments (20 h, about one cell cycle interval), as shown by analyzing the kinetics of synchronous cell populations. DNA extracted from cells pulsed with [6-3H]dUrd in the presence of FdUrd and 6-amino-uracil (6-AU), an inhibitor of uracil-DNA glycosylase, contained a small amount of label (at least 3% of the total radioactivity incorporated into DNA) in the form of [6-3H]dUMP. Thus, we conclude that, under our experimental conditions, exogenously supplied dUrd may be metabolized intracellularly to 2'-deoxyuridine triphosphate (dUTP) and that this deoxynucleotide may eventually be mis-incorporated into DNA. As far as the formation of SCEs is concerned, analysis of second division chromosomes showed that 2'-deoxyuridine monophosphate (dUMP) residues present in newly-synthesized DNA strands are probably not relevant to SCE formation. However, by analyzing SCE levels in third division chromosomes of cells treated with FdUrd and dUrd during their second cycle, we have scored a 6-fold increase in the reciprocal SCE level which demonstrates that the replication of a dUMP-containing DNA template leads to a higher SCE yield.

Uracil-DNA glycosylase activity from Dictyostelium discoideum

We have isolated and partially characterized a uracil-DNA glycosylase activity from the cellular slime mold, Dictyostelium discoideum. This glycosylase has a broad pH optimum (6.5-8.5) and is fully active in 10 mM EDTA or in 5 mM Mg2+. Its molecular weight by gel filtration is about 55 000. This enzyme activity may work in concert with previously described apurinic/apyrimidinic (AP) endonuclease activities in the excision repair of uracil from the DNA of this lower eukaryote.

Deoxyuridine misincorporation causes site-specific mutational lesions in the lacI gene of Escherichia coli

Spontaneous forward mutation in lacI was analyzed by DNA sequencing in a Dut- strain of E. coli. Hyperuracil incorporation into DNA due to the defect in deoxyuridinetriphosphatase caused a 5-fold increase in mutation frequency. Deletion, duplication and base-substitution frequencies were all enhanced in the Dut- strain. However, the analysis of the specificity of mutation revealed a remarkable site- and class-specificity. For example, base substitutions at a single site, a G:C = greater than A:T transition (Ochre 34) accounted for 55% of the base substitutions recovered. The spontaneous A:T = greater than G:C hotspot at position +6 at the lac operator was also recovered at an enhanced frequency in the Dut- strain where it accounted for 25% of the base substitutions. Many of the deletion and duplication events were recovered more than once; most had endpoints in A/T rich regions. The spontaneous frameshift hotspot involving the gain or loss of 5'-CTGG-3' in a region where this tetramer is tandemly repeated 3 times, was also greatly enhanced. No frameshifts involving a single base pair nor IS1 insertions were identified among the 86 lacI mutants sequenced. The analysis of these events reveals them to be generally consistent with a mechanism involving AP sites generated by the removal of misincorporated uracil by uracil-N-glycosylase. Considering the number of potential AP sites (approximately 1 per 170 base pairs) E. coli is remarkably refractory to mutational consequences of deoxyuridine misincorporation in place of thymidine.

The effect of 5-fluorouracil on DNA chain elongation in intact bone marrow cells

The effect of 5-fluorouracil (FUra) on DNA elongation was assessed in intact bone marrow cells that had been pulsed for 1 hr with [3H]-dThd in the absence or presence of FUra, chased in fresh media from 0 to 3 hr, and then analyzed on alkaline sucrose gradients. While DNA from control cells elongated at an average rate of 86 nucleotides per sec over a 3 hr interval, DNA from FUra-treated cells did not elongate and in contrast decreased in size over the same interval. In a parallel study to examine what happens to the FUra that was incorporated into DNA, bone marrow cells were pulsed for 1 hr with 50 microM [3H]-FUra, and then chased in fresh media from 0 to 2 hr. An aliquot of cells from each time point was lysed on an alkaline sucrose gradient to assess the size of [3H]-FUra-containing DNA, while another aliquot of cells from each time point was analyzed for radioactivity remaining in total DNA. The percentage of replicon-size DNA (greater than or equal to 100S) containing radiolabel decreased over the 2 hr chase while the percentage of small molecular weight DNA (greater than or equal to 7.2S) increased over the same interval. These changes in DNA size were accompanied by a decrease in radioactivity in total DNA. These studies suggest that excision of FUra from nascent DNA chains may prevent further elongation of DNA.

The occurrence and consequences of deoxyuridine in DNA

Deoxyuridine can become resident in the DNA of prokaryotic and eukaryotic cells via two general mechanisms - deamination of cytosine to uracil, and nucleotide pool changes that lead to misincorporation of deoxyuridine in place of thymidine. In this paper we have examined the chemical basis of deamination reactions in DNA and discussed a possible mechanism for an increased rate of deamination by means of cross-strand protonation of cytosine by alkylated guanine. In addition, we have examined the genetic and drug-induced conditions that lead to dUMP misincorporation into DNA in place of thymidine and have presented experimental evidence indicating that the antifolate-induced lesion is a general drug-dose dependent lesion of human blood cells. Finally, the toxic and genetic impact of this lesion has been evaluated within the context of a review of the repair mechanisms elicited by dUMP in DNA.

Properties of a human lymphoblast AP-endonuclease associated with activity for DNA damaged by ultraviolet light, gamma-rays, or osmium tetroxide

An endonuclease activity for UV-irradiated DNA, gamma-irradiated DNA, and OsO4-treated DNA that was partially purified from human lymphoblasts was found to have associated with it an endonuclease activity for partially depurinated DNA. When this apurinic endonuclease (Endo A) was characterized and compared with the cells' major apurinic endonuclease (Endo B), several notable differences were observed. (1) Endo A bound to oxidized DNA-Sepharose under conditions where Endo B did not. (2) Endo A did not require Mg2+, retaining full activity in 10 mM ethylenediamine-tetraacetic acid, while Endo B showed an absolute requirement for Mg2+. (3) Whereas the nicks made in depurinated DNA by Endo B were efficient priming sites for Escherichia coli polymerase I, those made by Endo A were not. Further characterization of the nicks indicated that Endo A incises depurinated DNA 3' to apurinic sites, leaving 3'-terminal deoxyribose, a poor priming site for DNA synthesis. Endo A action on UV-irradiated DNA produced nicks that resembled those it made in depurinated DNA, suggesting that the UV endonuclease activity acts through an apurinic/apyrimidinic site intermediate.

Reaction of apurinic/apyrimidinic sites with [14C]methoxyamine. A method for the quantitative assay of AP sites in DNA

A simple and rapid method is described for the determination of AP (apurinic/apyrimidinic) sites in DNA. The method involves the reaction of [14C]methoxyamine with the aldehyde group present in the deoxyribose moiety after a base loss. Studies with alkylated-depurinated DNA and with uracil-containing polydeoxyribonucleotides depyrimidinated by uracil-DNA glycosylase show that methoxyamine reacts with both apurinic and apyrimidinic sites in a rapid and exhaustive way. Under standard conditions (30-min incubation with 5 mM methoxyamine at 37 degrees C, pH 7.2) untreated DNA is almost unreactive and the [14C]methoxyamine incorporation in DNA is proportional to the number of AP sites. Since the methoxyamine reaction is free from any degradative effect on DNA, AP sites may be estimated from a simple determination of the acid-insoluble radioactivity.