Uracil-N-glycosylase

Fig. 6. Schematic representation of the dUTP/uracil-N-glycosylase sterilization procedure. Reprinted with the permission of Sninsky et al. (Sll).

Whereas DNA contains the nucleotide base thymine, RNA contains the nucleotide base uracil instead, and the reason is that the base cytosine, also present in both DNA and RNA, will convert to uracil, which would then cause a nucleotide mismatch if uracil had originally been present in the DNA (Voet and Voet, 1995, p. 1049). And such mismatches mean that mutations would occur. However, if any uracil shows up in the DNA, it is normally converted or excised by the enzyme uracil N-glycosylase, to be replaced by cytosine. (Uracyl A-glycosylase is also involved in DNA replication.) In other words, nature hopefully can correct itself at the DNA level. 

Poly [d(A-T)] containing a few [a-32p, uracil-3H]dUMP residues has been prepared using [a-32p, uracil- HldUTP as a substrate for Klenow fragment, and then treated successively with uracil N-glycosylase and T4 UV endonuclease V to afford polydeoxyribonucleotide chains with deoxyribose 5-[32p] phosphate residues at the... 

In prokaryotic DNA the major methylated bases are N -methyladenine (mA) and to a lesser extent Nl-methylcytosine. Methylation in bacteria occurs at specific sites. In E. coli, methylation of A residues in the sequence 5 -GATC-3 is involved in mismatch error correction, and it plays a role in controlling initiation of DNA replication. Methylation at other sites protects DNA against cleavage by restriction endonucleases (described here). Structural studies on a bacterial DNA methylase have shown that the bases undergoing methylation rotate completely out of the DNA duplex and into a catalytic pocket within the enzyme structure. Other enzymes that work on bases, such as uracil-N-glycosylase, operate similarly. 

C-5 cytosine can spontaneously deaminate just as cytosine can. When C-5 cytosine deaminates, it forms thymidine, not uracil. Therefore uracil N-glycosylase, a DNA repair enzyme, will not recognize this product of deamination as an inappropriate base and will not remove it from the DNA, causing a transition mutation. 

CSR and not SHM (Manis et al., 2002b). In the case of CSR, transcription through an S region would generate single-stranded stretches of DNA on which AID could deaminate C bases, any of which could be converted into a single-stranded break by the subsequent action of a uracil N-glycosylase (UNG) and AP-endonuclease (Rada et al, 2002). 

Uracil N-glycosylase activity abolished. Mutant permits incorporation of uracil residues into DNA. In mg host, the U residues in U-DNA are removed, leaving abasic sites Mutation in D-xylose isomerase, rendering the strain unable to utilize xylose... 

Error reduction systems include proofreading (see here) and the uracil-DNA N-glycosylase system (see here), which protects against mutation arising from deamination of cytosine. Other processes for repairing DNA that is altered either by uncorrected replicative errors or by environmental damage are listed below. Cellular repair systems include the following ... 

Second, the enzyme uracil-DNA N-glycosylase removes any dUMP residues that make it into DNA. Figure 24.35 shows how this repair system works. As seen in the figure, the uracil base is clipped from the sugar, followed by an adjacent nick in the DNA strand which contained the uracil. Nick translation by DNA polymerase I removes the apyrimidinic moiety and replaces it with dXMP. Finally, DNA ligase (see here) reseals the nick. 

DNA Replication Overview Replication Fork E. coli DNA Polymerases Eukaryotic DNA Polymerases Other Replication Proteins Topoisomerases Uracil-DNA N-Glycosylase Replication Complexes Initiation of DNA Replication Replication of Linear Genomes Fidelity of DNA Replication... 

Uracil-DNA N-Glycosylase Removal of Incorporated Uracil (Figure 24.35) Reconstruction of Replication Machines (Figure 24.6, Figure 24.36)... 

Figure 13.11 Reaction sequence of the base excision repair pathway. The base excision repair (BER) pathway is exemplified for the uracil excision-repair reactions. Only the lesioned (e.g. uracil) part of one strand nucleotide structure of the dsDNA is shown. The excision of uracil by uracil DNA glycosylase without associated AP-lyase generally follows AP-endonuclease and 5 -deoxyribophosphodiesterase which cleave the nucleotide chain. The repair with N-glycosylase is associated with AP-lyase (P-elimination reaction catalyzed by AP-lyase converts the deoxyribose residue to aldehyde form) and 3 -phosphodiesterase. The single nucleotide gap is filled by DNA polymerase (dCTP is required to replace uracil) and DNA ligase...

Imai, K., Slupphaug, G., Lee, W. I., Revy, P., Nonoyama, S., Catalan, N., Yel, L., Forveille, M., Kavli, B., Krokan, H. E., Ochs, H. D., Fischer, A., and Durandy, A. (2003b). Human uracil-DNA glycosylase deficiency associated with profoundly impaired immunoglobulin class-switch recombination. Nat. Immunol. 4, 1023-1028. 

Base-excision repair requires the recognition and removal of inappropriate bases such as uracil, hypoxanthine, and xanthine from DNA. The DNA glycosylases are enzymes that remove the aberrant base by cleaving the N-glycosyl bond. Direct repair is different than the other repair mechanism in that the mutated base is repaired directly, without removal of the nucleotide. The protein 06-methylguanine DNA methyltransferase, for example, carries our direct repair. 

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