The effects of the ring fragmentation product of thymidine C5-hydrate on phosphodiesterases and klenow (exo-) fragment

Unexpected role for Helicobacter pylori DNA polymerase I as a source of genetic variability

Helicobacter pylori, a human pathogen infecting about half of the world population, is characterised by its large intraspecies variability. Its genome plasticity has been invoked as the basis for its high adaptation capacity. Consistent with its small genome, H. pylori possesses only two bona fide DNA polymerases, Pol I and the replicative Pol III, lacking homologues of translesion synthesis DNA polymerases. Bacterial DNA polymerases I are implicated both in normal DNA replication and in DNA repair. We report that H. pylori DNA Pol I 5′- 3′ exonuclease domain is essential for viability, probably through its involvement in DNA replication. We show here that, despite the fact that it also plays crucial roles in DNA repair, Pol I contributes to genomic instability. Indeed, strains defective in the DNA polymerase activity of the protein, although sensitive to genotoxic agents, display reduced mutation frequencies. Conversely, overexpression of Pol I leads to a hypermutator phenotype. Although the purified protein displays an intrinsic fidelity during replication of undamaged DNA, it lacks a proofreading activity, allowing it to efficiently elongate mismatched primers and perform mutagenic translesion synthesis. In agreement with this finding, we show that the spontaneous mutator phenotype of a strain deficient in the removal of oxidised pyrimidines from the genome is in part dependent on the presence of an active DNA Pol I. This study provides evidence for an unexpected role of DNA polymerase I in generating genomic plasticity.

Helicobacter pylori is the main cause of ulcers and gastric cancers. One the characteristics of this bacterial species is that it displays an amazing capacity to change its genetic information. This genetic variability provides H. pylori with an adaptation potential that allows it to successfully colonise the stomach of about half the human population. Here we identified a surprising source of genomic plasticity in an enzyme also involved in the maintenance of DNA integrity. Indeed, we show that DNA polymerase I, one of the only two DNA polymerases that are found in H. pylori, although essential for DNA replication and repair, contributes to mutagenesis due to its biochemical characteristics.

Biological consequences of free radical-damaged DNA bases

The principal oxidized cytosine bases, uracil glycol, 5-hydroxycytosine, and 5-hydroxyuracil, are readily bypassed, miscode, and are thus important premutagenic lesions. Similarly the principal oxidation product of guanine, 8-oxoguanine, miscodes with A and is a premutagenic lesion. Most of the thymine and adenine products that retain their ring structure primarily pair with their cognate bases and are not potent premutagenic lesions. Although thymine glycol pairs with its cognate base and is not mutagenic it significantly distorts the DNA molecule and is a lethal lesion. Ring fragmentation, ring contraction, and ring open products of both pyrimidines and purines block DNA polymerases and are potentially lethal lesions. Although these breakdown products have the potential to mispair during translesion synthesis, the mutational spectra of prokaryotic mutants defective in the pyrimidine-specific and/or purine-specific DNA glycosylases do not reflect that expected of the breakdown products. Taken together, the data suggest that the principal biological consequences of endogenously produced and unrepaired free radical-damaged DNA bases are mutations.

DNA substrates containing defined oxidative base lesions and their application to study substrate specificities of base excision repair enzymes

Reactive oxygen species generate structurally diverse base lesions in DNA. These lesions are primarily removed by base excision repair (BER) enzymes in prokaryotic and eukaryotic cells. Biochemical properties of BER enzymes such as substrate specificity, enzymatic parameters, and action mechanisms can be best studied by employing defined oligonucleotide and DNA substrates. Currently available methods are listed to prepare defined DNA substrates containing oxidative base damage and analogs. BER enzymes for oxidative base damage are classified into two subgroups that recognize pyrimidine lesions (Endo III homologs) and purine lesions (Fpg homologs), though E. coli Fpg exhibits weak repair activity for certain pyrimidine damage. Recently, several interesting findings have been reported in relation to the substrate specificity of BER enzymes. Saccharomyces cerevisiae Endo III homologs (NTG1 and NTG2) have been shown to recognize formamidopyrimidine (Fapy) lesions that are derived from purine. Endo III and Endo VIII have a very weak activity to dihydrothymine in comparison with thymine glycol. Excision of 7,8-dihydro-8-oxoguanine by Fpg and human OGG1 is paired-base-dependent, whereas that of Fapy is essentially paired-base-independent. The repair efficiency of BER enzymes is affected by surrounding sequence contexts. In general, the sequence context effect appears to be more pronounced for Fpg homologs than Endo III homologs.

Repair of oxidized purines and damaged pyrimidines by E. coli Fpg protein: different roles of proline 2 and lysine 57 residues

The Escherichia coli Fpg protein is involved in the repair of oxidized purines, including the highly mutagenic 7,8-dihydro-8-oxoguanine (8-oxoG). The Fpg protein also excises various oxidized pyrimidines with high efficiency. We examined, by targeted mutagenesis, the role of two highly conserved amino acid residues, proline 2 (P2) and lysine 57 (K57), on the catalytic activities of the Fpg protein toward a ring-fragmentation product of thymine (alpha RT) and 5,6-dihydrothymine (dHT). The following E. coli mutant Fpg proteins were investigated: lysine 57 --> glycine (FpgK57G), proline 2 --> glycine (FpgP2G), and proline 2 --> glutamic acid (FpgP2E). The FpgK57G protein had barely detectable alpha RT and dHT-DNA glycosylase activities and produced minute amounts of a Schiff-base complex upon reaction with alpha RT containing DNA. In contrast, the activity of an FpgP2G mutant toward alpha RT was comparable to the wild type activity and produced a Schiff-base complex with this substrate. FpgP2E was completely inactive in all the assays, in contrast, to the other mutants. The crystal structure of a homologous Fpg protein from an extreme thermophile, Thermus thermophilus HB8, reveals that it is composed of two distinct domains connected by a flexible hinge (Sugahara et al. [2000]: EMBO J 19:3857-3869). The N-terminal proline, one primary residue for enzymatic catalysis, is positioned at the bottom of a cleft in close proximity to lysine 52 (analogous to K57 of the E. coli Fpg). Based on the biochemical assays, together with the crystal structure of T. thermophilus HB8 Fpg protein, we propose a two-nucleophile model for the enzymatic catalysis.

Oxidative base damage to DNA: specificity of base excision repair enzymes

Base excision repair (BER) is likely to be the main mechanism involved in the enzymatic restoration of oxidative base lesions within the DNA of both prokaryotic and eukaryotic cells. Emphasis was placed in early studies on the determination of the ability of several bacterial DNA N-glycosylases, including Escherichia coli endonuclease III (endo III) and formamidopyrimidine DNA N-glycosylase (Fpg), to recognize and excise several oxidized pyrimidine and purine bases. More recently, the availability of related DNA repair enzymes from yeast and human has provided new insights into the enzymatic removal of several.OH-mediated modified DNA bases. However, it should be noted that most of the earlier studies have involved globally modified DNA as the substrates. This explains, at least partly, why there is a paucity of accurate kinetic data on the excision rate of most of the modified bases. Interestingly, several oxidized pyrimidine and purine nucleosides have been recently inserted into defined sequence oligonucleotides. The use of the latter substrates, together with overexpressed DNA N-glycosylases, allows detailed studies on the efficiency of the enzymatic release of the modified bases. This was facilitated by the development of accurate chromatographic and mass spectrometric methods aimed at measuring oxidized bases and nucleosides. As one of the main conclusions, it appears that the specificity of both endo III and Fpg proteins is much broader than expected a few years ago.

Inhibition of klenow fragment (exo-) catalyzed DNA polymerization by (5R)-5,6-dihydro-5-hydroxythymidine and structural analogue 5,6-dihydro-5-methylthymidine

Oligonucleotides containing 5R-5,6-dihydro-5-hydroxythymidine (5R-3) and structural analogue 5,6-dihydro-5-methylthymidine (9) at defined sites were chemically synthesized via a method that obviates the use of NH4OH. Oligonucleotides prepared by this method were used to examine the effects of 5R-3 and 9 on the fidelity of Klenow (exo-) in vitro. The presence of lesions 5R-3 and 9 in DNA templates was shown to inhibit polymerization of primers hybridized to these templates. Inhibition was observed for both translesional synthesis and extension one nucleotide past the lesion, with the latter being more pronounced. The fidelity of Klenow (exo-) was reduced only slightly when utilizing substrates containing either dihyropyrimidine nucleotide. These results provide the first experimental verification of computational studies carried out on the effects of 3 on DNA templates, and are consistent with a structural model in which the C5-methyl group of 5R-3 adopts a pseudoaxial orientation resulting in a disruption in base stacking.

Substrate and mispairing properties of 5-formyl-2'-deoxyuridine 5'-triphosphate assessed by in vitro DNA polymerase reactions

5-Formyluracil (fU) is one of the thymine lesions produced by reactive oxygen radicals in DNA and its constituents. In this work, 5-formyl-2'-deoxyuridine 5'-triphosphate (fdUTP) was chemically synthesized and extensively purified by HPLC. The electron withdrawing 5-formyl group facilitated ionization of fU. Thus, p K a of the base unit of fdUTP was 8.6, significantly lower than that of parent thymine (p K a = 10.0 as dTMP). fdUTP efficiently replaced dTTP during DNA replication catalyzed by Escherichia coli DNA polymerase I (Klenow fragment), T7 DNA polymerase (3'-5'exonuclease free) and Taq DNA polymerase. fU-specific cleavage of the replication products by piperidine revealed that when incorporated as T, incorporation of fU was virtually uniform, suggesting minor sequence context effects on the incorporation frequency of fdUTP. fdUTP also replaced dCTP, but with much lower efficiency than that for dTTP. The substitution efficiency for dCTP increased with increasing pH from 7.2 to 9.0. The parallel correlation between ionization of the base unit of fdUTP (p K a = 8.6) and the substitution efficiency for dCTP strongly suggests that the base-ionized form of fdUTP is involved in mispairing with template G. These data indicate that fU can be specifically introduced into DNA as unique lesions by in vitro DNA polymerase reactions. In addition, fU is potentially mutagenic since this lesion is much more prone to form mispairing with G than parent thymine.