Consensus sequences for good and poor removal of uracil from double stranded DNA by uracil-DNA glycosylase

Counteracting the mutagenic effect of hydrolytic deamination of DNA 5-methylcytosine residues at high temperature: DNA mismatch N-glycosylase Mig.Mth of the thermophilic archaeon Methanobacterium thermoautotrophicum THF

Spontaneous hydrolytic deamination of DNA 5-methylcytosine residues gives rise to T/G mismatches which are pre-mutagenic lesions requiring DNA repair. For fundamental reasons, the significance of this and other processes lowering genetic fidelity must be accentuated at elevated temperatures, making thermophilic organisms attractive objects for studying how cells cope with thermal noise threatening the integrity of their genetic information. Gene mig of Methanobacterium thermoautotrophicum THF, an anaerobic archaeon with an optimal growth temperature of 65 degrees C, was isolated and its product (Mig.Mth; EC3.2.2-) shown to be a T/G-selective DNA thymine N-glycosylase with the properties required for counteracting the mutagenic effect of hydrolytic 5-meC deamination. The enzyme acts on T/G and U/G oppositions with similar efficiency; G/G, A/G, T/C and U/C are minor substrates; no other opposition of common nucleobases is attacked and no removal of U from single-stranded DNA is observed. Substrate preferences are modulated by sequence context. Together with the results presented here, one example of an enzyme directed against the hydrolytic deamination damage of 5-meC is known from each of the three phylogenetic kingdoms; entry into the repair pathway is glycosylytic in the eukaryotic and the archaeal case, whereas the eubacterial repair starts with an endonucleolytic DNA incision.

Methylation inhibitors can increase the rate of cytosine deamination by (cytosine-5)-DNA methyltransferase

The target cytosines of (cytosine-5)-DNA methyltransferases in prokaryotic and eukaryotic DNA show increased rates of C-->T transition mutations compared to non-target cytosines. These mutations are induced either by the spontaneous deamination of 5-mC-->T generating inefficiently repaired G:T rather than G:U mismatches, or by the enzyme-induced C-->U deamination which occurs under conditions of reduced levels of S-adenosylmethionine (AdoMet) and S-adenosylhomocysteine (AdoHcy). We tested whether various inhibitors of (cytosine-5)-DNA methyltransferases analogous to AdoMet and AdoHcy would affect the rate of enzyme-induced deamination of the target cytosine by M.HpaII and M.SssI. Interestingly, we found two compounds, sinefungin and 5'-amino-5'-deoxyadenosine, that increased the rate of deamination 10(3)-fold in the presence and 10(4)-fold in the absence of AdoMet and AdoHcy. We have therefore identified the first mutagenic compounds specific for the target sites of (cytosine-5)-DNA methyltransferases. A number of analogs of AdoMet and AdoHcy have been considered as possible antiviral, anticancer, antifungal and antiparasitic agents. Our findings show that chemotherapeutic agents with affinities to the cofactor binding pocket of (cytosine-5)-DNA methyltransferase should be tested for their potential mutagenic effects.

Modified substrates as probes for studying uracil-DNA glycosylase

In order to study the mechanism of action of uracil-DNA glycosylase (UDG) from human placenta, single-stranded (ss) and double-stranded (ds) oligodeoxyribonucleotides (oligos), containing deoxyuridine (dU) and a wide variety of their analogs were used. It was shown that UDG has a twofold preference for ss oligos over ds oligos and a twofold preference for intermolecular duplexes over similar hairpin-like duplexes. The replacement of dU with 1-(beta-D-2'-deoxy-threo-pentofuranosil)uracil (xU) or 1-(beta-D-3'-deoxy-threo-pentofuranosil)uracil (tU), which results in a change in sugar hydroxyl configuration, has no influence on UDG binding to such substrates, but inhibits uracil removal. A oligo containing 2'-deoxy-2'-fluorouridine (flU), with a 3'-endo conformation of modified sugar is recognized by UDG 100-200-fold less efficiently than the natural ones. F or Br atoms or a methyl group were introduced at position 5 of a dU residue in an oligo. It was shown that the nature of a substituent at this position is essential for UDG function.

HhaI and HpaII DNA methyltransferases bind DNA mismatches, methylate uracil and block DNA repair

The hydrolytic deamination of 5-methylcytosine (5-mC) to thymine (T) is believed to be responsible for the high mutability of the CpG dinucleotide in DNA. We have shown a possible alternate mechanism for mutagenesis at CpG in which HpaII DNA-(cytosine-5) methyltransferase (M.HpaII) can enzymatically deaminate cytosine (C) to uracil (U) in DNA [Shen, J.-C., Rideout, W.M., III and Jones, P.A., Cell, 71, 1073-1080, (1992)]. Both the hydrolytic deamination of 5-mC and enzymatic deamination of C create premutagenic DNA mismatches (G:U and G:T) with the guanine (G) originally paired to the normal C. Surprisingly, we found that DNA-(cytosine-5) methyltransferases have higher affinities for these DNA mismatches than for their normal G:C targets and are capable of transferring a methyl group to the 5-position of U, creating T at low efficiencies. This binding by methyltransferase to mismatches at the recognition site prevented repair of G:U mismatches by uracil DNA glycosylase in vitro.

Sequence specificity for removal of uracil from U.A pairs and U.G mismatches by uracil-DNA glycosylase from Escherichia coli, and correlation with mutational hotspots

The rate of removal of uracil from different positions in double-stranded DNA by uracil-DNA glycosylase from Escherichia coli varied more than 15-fold. Consensus sequences for good and poor removal were 5'-(A/T)UA(A/T)-3' and 5'-(G/C)U(T/G/C)-3', respectively. In general, the sequence context surrounding U was more important for the rate of removal than whether U was present in U.A pairs or U.G mispairs. Rates of removal of U from sites of amber mutations in the lacI gene, where mutation frequencies and deamination rates were known, indicated that the observed variation in removal is biologically significant.

The structural basis of specific base-excision repair by uracil-DNA glycosylase

The 1.75-A crystal structure of the uracil-DNA glycosylase from herpes simplex virus type-1 reveals a new fold, distantly related to dinucleotide-binding proteins. Complexes with a trideoxynucleotide, and with uracil, define the DNA-binding site and allow a detailed understanding of the exquisitely specific recognition of uracil in DNA. The overall structure suggests binding models for elongated single- and double-stranded DNA substrates. Conserved residues close to the uracil-binding site suggest a catalytic mechanism for hydrolytic base excision.

Inefficient excision of uracil from loop regions of DNA oligomers by E. coli uracil DNA glycosylase

Kinetic parameters for uracil DNA glycosylase (E. coli)-catalysed excision of uracil from DNA oligomers containing dUMP in different structural contexts were determined. Our results show that single-stranded oligonucleotides (unstructured) are used as somewhat better substrates than the double-stranded oligonucleotides. This is mainly because of the favourable Vmax value of the enzyme for single-stranded substrates. More interestingly, however, we found that uracil release from loop regions of DNA hairpins is extremely inefficient. The poor efficiency with which uracil is excised from loop regions is a result of both increased Km and lowered Vmax values. This observation may have significant implications in uracil DNA glycosylase-directed repair of DNA segments that can be extruded as hairpins. In addition, these studies are useful in designing oligonucleotides for various applications in DNA research where the use of uracil DNA glycosylase is sought.

Efficient removal of uracil from G.U mispairs by the mismatch-specific thymine DNA glycosylase from HeLa cells

The uracil DNA glycosylases (EC 3.2.2.3) characterized to date remove uracil from DNA irrespective of whether it is base paired with adenine or mispaired with guanine in double-stranded substrates or whether it is found in single-stranded DNA. We report here the characterization of uracil glycosylase activity that can remove the base solely from a mispair with guanine. It does not recognize uracil either in A.U pairs or in single-stranded substrates. The enzyme, a 55-kDa polypeptide, was previously characterized as a mismatch-specific thymine DNA glycosylase and was thought to be responsible solely for the correction (to G.C) of G.T mispairs that arise as a result of spontaneous hydrolytic deamination of 5-methylcytosine to thymine. Given the broader substrate specificity of the enzyme (in addition to uracil and thymine, the protein can also remove 5-bromouracil from mispairs with guanine), we propose that its biological role in vivo may also include the correction of a subset of G.U mispairs inefficiently removed by the more abundant ubiquitous uracil glycosylases, such as those arising from cytosine deamination in G+C-rich regions of the genome.