Uracil in DNA—General mutagen, but normal intermediate in acquired immunity
Introduction
The RNA base uracil may be present in DNA in small amounts as a result of cytosine deamination or misincorporation of dUMP during DNA replication. Such lesions are normally faithfully repaired by base excision repair (BER) initiated by a uracil-DNA glycosylase [1]. Contrary to expectations, mice deficient in the major uracil-DNA glycosylase encoded by the Ung-gene are viable, fertile and develop normally [2]. This is probably due to the existence of at least three alternative uracil-DNA glycosylases named SMUG1 (single strand selective monofunctional uracil-DNA glycosylase), TDG (thymine/uracil mismatch DNA glycosylase) and MBD4 (methyl binding domain 4 protein) [1]. These apparently have specialized functions but may also serve as backups for each other. Surprisingly, uracil in DNA and uracil-DNA glycosylase encoded by the UNG gene also have functions in the acquired immune system [3], [4], as well as in the innate immune system in defense against retroviral infections [5]. Thus, there is important crosstalk between the ancient DNA repair mechanisms and the innate immune system, as well as the much younger acquired immune system that came with vertebrates. For the acquired immune system mismatch repair proteins and proteins required for double strand break repair are also involved. This demonstrates that the interactions between these defense systems are in fact quite extensive [6]. While Ung-deficient mice have no overt phenotype macroscopically, they develop B-cell lymphomas late in life [7], [8]. In this review we will present the current knowledge about the origins of uracil in DNA and discuss functional characteristics of the quantitatively dominating glycosylases removing uracil and some closely related oxidative lesions. Finally, we will discuss the role of uracil and uracil-DNA glycosylase UNG2 in the Ig diversification process.
Section snippets
Uracil in DNA
Uracil in DNA is in several ways a rather special case among DNA lesions. First, it is a normal constituent in RNA but not in cellular DNA. Second, template uracil in U:G mispairs is a non-blocking, but 100% mutagenic lesion that results in mutation in one of the two daughter cells if it is replicated across. Incorporation of dUMP from the normal nucleotide dUTP results in U:A pairs that themselves are not mutagenic. However, chromosomal abasic sites resulting from uracil-removal are mutagenic
Removal of uracil by uracil-DNA glycosylases
At least four different uracil-DNA glycosylases (UDGs) have been identified in mammalian cells. These are UNG1/UNG2, SMUG1, TDG and MBD4 [30]. In addition, mouse NEIL1 has also been demonstrated to excise uracil and thymine from mismatches [31], but the biological significance of this remains unclear. Among the UDGs, UNG, SMUG1 and TDG belong to the same protein superfamily, possess the same fold and have probably evolved from the same ancestral gene [32]. Although our knowledge of the
Role of uracil and UNG in immunoglobulin gene diversification
The acquired immune system performs its main function through immunoglobulin (Ig) molecules. A primary repertoire of low affinity antibodies (IgM) is generated by the RAG1/RAG2 dependent V(D)J recombination process in the bone marrow [62]. The Ig based defense mechanism is adaptive and responds dynamically during the course of infection. This is achieved by three additional somatic Ig gene diversification processes; gene conversion (GC), somatic hypermutation (SHM) and class switch
Future perspectives
Although our understanding of the uracil-DNA glycosylases has advanced considerably over the last decade, several aspects remain to be elucidated. A major question is how UNG2 may initiate either repair of uracil, or induce mutations or recombination via SHM and CSR, respectively. It is very likely that UNG2, as well as many of the other factors involved in these processes are subject to extensive post-translational regulation that direct assembly of specific and higher order protein complexes.
Acknowledgements
This work was supported by The Research Council of Norway, the National Program in Functional Genomics (FUGE) administered by The Research Council of Norway, The Norwegian Cancer Society, The Cancer Fund at St.Olav's Hospital, Trondheim, The Svanhild and Arne Must Fund for Medical Research and The European Union Program DNA Repair.
References (97)
- et al.
Uracil-DNA glycosylase (UNG)-deficient mice reveal a primary role of the enzyme during DNA replication
Mol. Cell.
(2000) - et al.
Immunoglobulin isotype switching is inhibited and somatic hypermutation perturbed in UNG-deficient mice
Curr. Biol.
(2002) - et al.
Monoclonal B-cell hyperplasia and leukocyte imbalance precede development of B-cell malignancies in uracil-DNA glycosylase deficient mice
DNA Repair (Amst.)
(2005) - et al.
Human genetic defects in class-switch recombination (hyper-IgM syndromes)
Curr. Opin. Immunol.
(2001) - et al.
Mutagenicity, toxicity and repair of DNA base damage induced by oxidation
Mutat. Res.
(2003) - et al.
RNA editing enzyme APOBEC1 and some of its homologs can act as DNA mutators
Mol. Cell.
(2002) - et al.
The human dUTPase gene encodes both nuclear and mitochondrial isoforms. Differential expression of the isoforms and characterization of a cDNA encoding the mitochondrial species
J. Biol. Chem.
(1997) - et al.
Base excision repair of DNA in mammalian cells
FEBS Lett.
(2000) - et al.
A back-up glycosylase in Nth1 knock-out mice is a functional Nei (endonuclease VIII) homologue
J. Biol. Chem.
(2002) Structure and function in the uracil-DNA glycosylase superfamily
Mutat. Res.
(2000)