Uracil in DNA – occurrence, consequences and repair

Krokan, Hans E.; Drabløs, Finn; Slupphaug, Geir

doi:10.1038/sj.onc.1205996

Cited by 443 publications

(366 citation statements)

References 109 publications

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“…The first DNA glycosylase to be discovered was uracil DNA glycosylase (UDG) in E. coli after searching for an enzymatic activity that would recognize uracil whose presence in DNA as a G•U pair would be mutagenic because U is generated due to deamination of cytosine [19]. Subsequently, similar enzyme activities were identified in other bacteria, yeast, plants and mammalian cells, and mitochondria-specific UDGs were also characterized [20]. In contrast to the promiscuity of most DNA glycosylases for diverse substrates, UDG is highly specific for U which tightly fits into UDG's catalytic pocket.…”

Section: Dna Glycosylase a Key Enzyme In Bermentioning

confidence: 99%

Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells

2008

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Base excision repair (BER) is an evolutionarily conserved process for maintaining genomic integrity by eliminating several dozen damaged (oxidized or alkylated) or inappropriate bases that are generated endogenously or induced by genotoxicants, predominantly, reactive oxygen species (ROS). BER involves 4-5 steps starting with base excision by a DNA glycosylase, followed by a common pathway usually involving an AP-endonuclease (APE) to generate 3′ OH terminus at the damage site, followed by repair synthesis with a DNA polymerase and nick sealing by a DNA ligase. This pathway is also responsible for repairing DNA single-strand breaks with blocked termini directly generated by ROS. Nearly all glycosylases, far fewer than their substrate lesions particularly for oxidized bases, have broad and overlapping substrate range, and could serve as back-up enzymes in vivo. In contrast, mammalian cells encode only one APE, APE1, unlike two APEs in lower organisms. In spite of overall similarity, BER with distinct subpathways in the mammals is more complex than in E. coli. The glycosylases form complexes with downstream proteins to carry out efficient repair via distinct subpathways one of which, responsible for repair of strand breaks with 3′ phosphate termini generated by the NEIL family glycosylases or by ROS, requires the phosphatase activity of polynucleotide kinase instead of APE1. Different complexes may utilize distinct DNA polymerases and ligases. Mammalian glycosylases have nonconserved extensions at one of the termini, dispensable for enzymatic activity but needed for interaction with other BER and non-BER proteins for complex formation and organelle targeting. The mammalian enzymes are sometimes covalently modified which may affect activity and complex formation. The focus of this review is on the early steps in mammalian BER for oxidized damage.

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Section: Dna Glycosylase a Key Enzyme In Bermentioning

confidence: 99%

Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells

2008

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“…UNG1 is apparently the only mitochondrial uracil-DNA glycosylase. The sources of uracil in mammalian nuclear genomes, and the uracil-DNA glycosylases processing these uracils, are modelled in figure 2. (a) Members of the UNG family Nuclear UNG2 and mitochondrial UNG1 are both encoded by the UNG gene (Ung in the mouse), which is representative of the classical large family of conserved uracil-DNA glycosylases found in vertebrates, yeast, most bacteria and some viruses (herpes and pox families), but not in insect cells (Krokan et al 1997(Krokan et al , 2002. Alternative N-terminal sequences in UNG2 and UNG1 determine nuclear and mitochondrial targeting, respectively.…”

Section: Mammalian Uracil-dna Glycosylases and Their Assumed Functionsmentioning

confidence: 99%

Uracil in DNA and its processing by different DNA glycosylases

Visnes

Doseth

Pettersen

et al. 2008

Phil. Trans. R. Soc. B

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111

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Uracil in DNA may result from incorporation of dUMP during replication and from spontaneous or enzymatic deamination of cytosine, resulting in U:A pairs or U:G mismatches, respectively. Uracil generated by activation-induced cytosine deaminase (AID) in B cells is a normal intermediate in adaptive immunity. Five mammalian uracil-DNA glycosylases have been identified; these are mitochondrial UNG1 and nuclear UNG2, both encoded by the UNG gene, and the nuclear proteins SMUG1, TDG and MBD4. Nuclear UNG2 is apparently the sole contributor to the post-replicative repair of U:A lesions and to the removal of uracil from U:G contexts in immunoglobulin genes as part of somatic hypermutation and class-switch recombination processes in adaptive immunity. All uracil-DNA glycosylases apparently contribute to U:G repair in other cells, but they are likely to have different relative significance in proliferating and non-proliferating cells, and in different phases of the cell cycle. There are also some indications that there may be species differences in the function of the uracil-DNA glycosylases.

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“…In vivo studies have shown that misincorporation of dUMP during DNA synthesis introduces a significant amount of uracil residues into the DNA of many organisms (2)(3)(4). However, the levels of uracil actually remaining in DNA, Ϸ10-15 residues per human genome (5), are lower because of the DNA base excision repair (BER) process, which is responsible for the rapid uracil removal and repair (1). The BER pathway is initiated by uracil-DNA glycosylase (UDG), which cleaves the N-glycosidic bond, generating an apurinic-apyrimidinic (AP) site, which is then repaired through the sequential action of AP endonuclease (Ape), DNA polymerase, and DNA ligase.…”

mentioning

confidence: 99%

“…Thus, our data support a model in which protein p56 ensures an efficient viral DNA replication, preventing the deleterious effect caused by UDG when it eliminates uracil residues present in the 29 genome. 29 DNA polymerase ͉ DNA repair ͉ protein-primed replication ͉ dUMP incorporation U racil residues are introduced into genomic DNA either by incorporation of dUMP in place of dTMP during replication or deamination of existing dCMP residues (1). In vivo studies have shown that misincorporation of dUMP during DNA synthesis introduces a significant amount of uracil residues into the DNA of many organisms (2)(3)(4).…”

mentioning

confidence: 99%

Phage φ29 protein p56 prevents viral DNA replication impairment caused by uracil excision activity of uracil-DNA glycosylase

Serrano‐Heras

Bravo

Salas

2008

Proc. Natl. Acad. Sci. U.S.A.

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Protein p56 encoded by the Bacillus subtilis phage 29 inhibits host uracil-DNA glycosylase (UDG) activity. In previous studies, we suggested that this inhibition is likely a defense mechanism developed by phage 29 to prevent the action of UDG if uracilation occurs in DNA either from deamination of cytosine or the incorporation of dUMP during viral DNA replication. In this work, we analyzed the ability of 29 DNA polymerase to insert dUMP into DNA. Primer extension analysis showed that viral DNA polymerase incorporates dU opposite dA with a catalytic efficiency only 2-fold lower than that for dT. Using the 29 DNA amplification system, we found that 29 DNA polymerase is also able to carry out the extension of the dA:dUMP pair and replicate past uracil. Additionally, UDG and apurinic-apyrimidinic endonuclease treatment of viral DNA isolated from 29-infected cells revealed that uracil residues arise in 29 DNA during replication, probably as a result of misincorporation of dUMP by the 29 DNA polymerase. On the other hand, the action of UDG on uracil-containing 29 DNA impaired in vitro viral DNA replication, which was prevented by the presence of protein p56. Furthermore, transfection activity of uracil-containing 29 DNA was significantly higher in cells that constitutively synthesized p56 than in cells lacking this protein. Thus, our data support a model in which protein p56 ensures an efficient viral DNA replication, preventing the deleterious effect caused by UDG when it eliminates uracil residues present in the 29 genome.29 DNA polymerase ͉ DNA repair ͉ protein-primed replication ͉ dUMP incorporation

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Uracil in DNA – occurrence, consequences and repair

Cited by 443 publications

References 109 publications

Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells

Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells

Uracil in DNA and its processing by different DNA glycosylases

Phage φ29 protein p56 prevents viral DNA replication impairment caused by uracil excision activity of uracil-DNA glycosylase

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