When is uracil found in dna

So during the larval stages, uracil-DNA is produced and seems not to be corrected in tissues that are to be degraded during the pupal stage. As these insects lack the main uracil-DNA glycosylase enzyme, at the pupal stage, additional uracil-DNA-specific factors may recognise this accumulated uracil as a signal to initiate cell death.

We have already identified an insect-specific protein that seems to be capable of degrading uracil-DNA, and we are investigating whether this enzyme is used to initiate programmed cell death. Uracil in DNA, however, can also be found closer to home — in the immune system of vertebrates like us. Part of our immune system, the adaptive immune system, produces a large number of different antibodies that are trained to protect us from specific pathogens. To increase the number of different antibodies that can be created, we shuffle the DNA sequence in the regions that code for them, not only by recombining the existing sequences in the cells but also by creating new ones through vastly increased mutation rates, known as hypermutation.

This system is very strictly regulated, however, as if it got out of hand, it would lead to cancer. When considering the question of why uracil or why thymine, we need to consider the evolutionary context. Living organisms have evolved in a continuously changing environment, facing a dynamic set of challenges. Thus, a solution that avoids mistakes being incorporated into DNA is advantageous to most organisms and most cells, which explains why thymine-DNA became the norm.

Download this article as a PDF. In , she began a PhD on the regulation of uracil-DNA repair and uracil processing in pupating insects.

She is continuing her work as a postdoctoral scientist, and was a school ambassador in the SET-Routes programme www. Since , she has been the head of a laboratory focusing on genome metabolism and repair at the Institute of Enzymology, Budapest, Hungary. This article demonstrates that science never sleeps, shaking up the dogma that uracil only exists in RNA. As the article explains, this is not always the case. And even when it is, why should that be? Uracil in DNA: error or signal? Understand article.

The authors thus proposed that Pa -UDGb represented a fifth UDG family, that evolved in organisms living at elevated temperatures to counteract the mutagenic threat of both cytosine and adenine deamination. The classification of DNA glycosylases into superfamilies, can be based on characteristic sequence motifs as defined in the Pfam database Bateman et al. MBD4 belongs to the HhH—GPD family, members of which remove a large variety of lesions, including uracil, oxidised bases and certain mismatches, particularly A mismatched to G or 8-oxoG.

The phylogenetic distribution of DNA repair genes has been discussed in detail by Eisen and Hanawalt , while Aravind and Koonin have specifically analysed the UDG superfamily. The HhH—GPD glycosylases are widespread in both Archaea, bacteria and eukaryotes, and are believed to represent a very ancient gene family. However, the UDG superfamily shows a more non-even distribution pattern.

It is distantly related to the AUDG gene family, which is mainly found in Archaea and bacteria, and it seems likely that they share an ancient ancestor.

SMUG1 has so far been found only in some eukaryotes. Based on the conservation pattern in the minor-groove intercalation loop it was suggested that SMUG1 may have evolved from an UNG-like enzyme by rapid divergence, possibly to meet special requirements for repair in multicellular animals Aravind and Koonin, These studies are based on relatively few sequences with low similarity.

This makes alignment and analysis difficult, and the interpretation of these data should be done with caution. The origin of SMUG1 therefore remains an open question. UNG is very widespread in bacteria, and has also been identified in most eukaryotes. It has been suggested that UNG was introduced into eukaryotes by horizontal gene transfer Aravind and Koonin, , possibly from the mitochondrial genome Eisen and Hanawalt, UNG is also the only of these gene families that is found in a large number of viruses, indicating another possible mechanism for horizontal gene transfer.

A Blast search Altschul et al. Sequence comparison of the different gene families within the UDG superfamily identifies several conserved sequence motifs, indicating a common 3D-fold for all UDG-type proteins. It therefore seems realistic to assume that all UDG-type proteins share this common fold. The essential part of the proline-rich motif that is in direct contact with the DNA backbone is structurally conserved in MUG.

However, the actual region seems to be well conserved in most sequences, the variation is mainly with respect to the specific residues found at each position. The motif contributes to uracil recognition by hydrogen bonding to polar atoms of the uracil ring. In the uracil binding pocket there is also a favourable stacking interaction between uracil and a well-conserved phenylalanine residue found between the water-activating and the proline-rich motifs, in addition to the tyrosine from the water-activating motif mentioned above.

This motif is also involved in DNA interaction. In particular the glycine is well conserved, probably because a side chain at this position would interfere with the close contact between the protein and the DNA backbone. This motif shows some variation, but the histidine and the first proline are conserved in most sequences, except in SMUG1. The histidine is one of the active site residues, and forms hydrogen bond with uracil.

This architecture family is a very large one, with 70 topologies listed in CATH. The 3D structure for MBD4 is not known. However, structures are available for several other members of this superfamily, and it can be assumed that important structural features are conserved.

The HhH—GPD-fold consists of a four-helix bundle domain and a six-helix barrel domain, with the active site and the HhH motif located at the interface between these domains.

Whereas most DNA-binding proteins seem to use a charged surface rich in lysine and arginine residues to bind backbone phosphates, the DNA binding surface of OGG1 is nearly charge neutral. UNG-proteins are highly selective for uracil, but remove 5-fluorouracil and certain oxidised pyrimidines with very low efficiency Krokan et al. The efficient removal of uracil from single-stranded DNA is puzzling since it leaves a non-informative lesion without the information in a complementary strand.

Single-stranded DNA is probably mainly found temporarily in transcribed genes and very close to the replication fork. Abasic sites resulting from uracil-removal in single-stranded DNA at the replication fork could be handled by at least three different mechanisms; i regression of the replication fork and repair by short patch or long patch BER, ii recombination repair using the old strand at the other side of the fork, iii translesion DNA synthesis.

Regression of a replication fork stalled at a single-strand lesion is well established in E. It may in principle apply to all types of lesions that stall the replication fork, including abasic sites Robu et al. Recombination using information from the sister chromatid at stalled replication forks Gruss and Michel, , as well as translesion synthesis across abasic sites are well established processes in bacteria. Interestingly, repair of abasic sites in chromosomal DNA in E. Therefore, abasic sites resulting from the action of UNG at the replication fork is possibly unlikely to be dealt with by BER alone.

For more comprehensive overviews, the reader should consult other recent reviews Dogliotti et al. The presumed major track is the short patch pathway. The alternative long patch pathway largely uses replication proteins Dogliotti et al. As shown in Figure 2 , uracil in DNA may be present in different positions relative to a replication fork, and in addition the sequence context may vary.

It seems likely that the type of uracil-DNA glycosylase, as well as the mechanism of repair in the subsequent steps will depend on these factors. Uracil present in the fork prior to replication, e. Among the uracil-DNA glycosylases, only UNG2 specifically accumulates in the replication foci during S phase, and as discussed, all experimental evidence suggests that UNG2 has an important role in the removal of misincorporated uracil in replication foci.

Uracil in different positions relative to the replication fork, and proposed mechanisms of repair in different positions. One important problem is the following: How are deaminated cytosines that escape repair prior to replication repaired, if at all?

However, UNG2 efficiently removes uracil from single-stranded DNA and may thus generate an abasic site that blocks replication. The stalled replication fork may recruit proteins required for fork regression and homologous recombination, which are alternative mechanisms to short patch repair and long patch repair in the downstream steps subsequent to uracil removal.

Involvement of recombination in the repair of abasic sites has been documented for E. Furthermore, induction of deamination of cytosine by NO is strongly cytotoxic in E. The finding that recombination factors are required for processing of abasic sites in bacteria suggests that this may also be the case in mammalian cells, since this basic process is highly likely to be conserved. We therefore propose that uracil in single-stranded DNA at the replication fork is incised by UNG2 and repaired by recombination or fork regression, which are both processes requiring recombination proteins.

Aravind L, Koonin EV. Bartsch H, Nair J. Bellacosa A. Cell Physiol. USA 96 : — Brown TC, Jiricny J. Nucleic Acids Res. NY Acad. Google Scholar. Gruss A, Michel B.

USA 95 : — USA 98 : — Hendrich B, Bird A. Supplier Information. Molfile expand Molfile. Read full article at Wikipedia. Average Mass. Monoisotopic Mass. Metabolite of Species. Mus musculus NCBI:txid Daphnia magna NCBI:txid Jones, Nathalie Dom, Julian L.

Saccharomyces cerevisiae NCBI:txid Retrovirology volume 5 , Article number: 45 Cite this article. Metrics details.

In cellular organisms, such lesions are faithfully cleared out through several universal DNA repair mechanisms, thus preventing genome injury. However, several recent studies have brought some pieces of evidence that introduction of uracil bases in viral genomic DNA intermediates during genome replication might be a way of innate immune defence against some viruses. This review will present the current knowledge about the cellular and viral countermeasures against uracils in DNA and the implications of these uracils as weapons against viruses.

Uracils in DNA may arise either from incorporation of dUTP in place of thymidine 5'-triphosphate dTTP or from the generation of uracils in DNA consecutive to spontaneous or enzymatic deaminations of cytosines which, if unrepaired, will lead to non-mutagenic U:A or mutagenic U:G mispairs, respectively.

The end point of this process is the appearance of strand breaks and the loss of DNA integrity. Consequently, viruses that replicate in this adverse cellular context have a high probability to incorporate dUTP in their genome during viral replication.

They have thus acquired strategies consisting in concentrating dUTPase or UNG activities in close proximity to their replication machinery. In the following we will focus on the different ways by which uracils are introduced into cellular and viral DNA and on the resulting biological consequences when uracils remain unrepaired, with a special attention to HIV-1 lentivirus. However, HIV-1 fights the detrimental uracilation of its genome induced by members of the APOBEC family, which are cytosine deaminases able to convert cytosine to uracil residues, through the Vif protein.

The U:A pair in DNA results from the incorporation of dUTP by polymerases and constitutes a non-mutagenic event per se that can nonetheless alters promoters functions [ 1 ].

However, U:A pair may be a cytotoxic lesion or even become a mutagenic event when chromosomal abasic sites AP-sites are generated after the removal of uracils by cellular repair mechanisms [ 2 ]. The U:G mispair is a non-blocking DNA replication lesion and occurs after the deamination of a cytosine to uracil. This lesion is mutagenic, leading to a G-to-A transition mutation in one of the two daughter strands after DNA replication. The incorporation of dUTP into DNA during replication has been estimated to be up to 10 4 uracil residues in human genome per day [ 3 ] and represents the major source of uracils in DNA [ 4 ].

Thus the incorporation of dUTP directly depends on its intracellular concentration. However, some cell types such as HT29 cell line, primary spleen cells, macrophages or quiescent lymphocytes display significantly higher dUTP levels that can even exceed those of dTTP [ 6 — 8 ]. Biosynthesis pathways of ribonucleotides and deoxyribonucleotides in mammalian cells and the possible consequence of the misincorporation and repair of uracil residues in DNA. The deamination of cytosine residues to uracil residues in DNA can arise either from a spontaneous non-enzymatic or an enzymatic process.

Spontaneous deamination is a frequent event that has been estimated by chemical measurements and genetic assays to occur between 70 to times per cell per day [ 9 ]. In addition to cytosine deaminases, the mammalian genome encodes two distinct enzymes able to convert cytosine to uracil, namely the cytosine-5 -methyltransferase and the APOBEC cytidine deaminase. The cytosine-5 -methyltransferase, is in charge of the conversion of cytosines within CpG islets to 5-methylcytosines.

The conversion starts with the formation of a covalent bond between the enzyme and the cytosine, leading to a transient dihydropyrimidine intermediate product that is quickly subjected to spontaneous deamination. The enzyme next catalyzes the transfer of a methyl group to the cytosine. This latter reaction uses the S-adenosylmethionine SAM molecule as a methyl donor. Thus, a cytosine deamination to uracil may occur in the case of the abortive catalysis by cytosine-5 -methyltransferase [ 11 ] or in the presence of a low cellular concentration of SAM [ 12 ].

The first member of this family, APOBEC1 apolipoprotein B mRNA editing catalytic subunit 1 , has been identified as the enzyme responsible for the tissue-specific deamination of the C of the apolipoprotein B mRNA, leading to a premature stop codon and the expression of a truncated form of the apolipoprotein B lipid-transport protein in gastrointestinal tissues [ 13 , 14 ].

The AID protein, whose expression is restricted to activated mature B cells, has been identified as a key factor of antibody diversification [ 17 ]. AID is required to deaminate specifically some cytosines in ssDNA of variable and switch regions of the Ig gene locus, allowing somatic hypermutation SHM and the class-switch recombination CSR processes that are needed to generate antibody diversity in response to antigens [ 18 — 21 ].

However, a recent study reported that this previously described antiviral effect of the deaminase-defective APOBEC3G mutants was negligible as compared to the wild-type protein when equal amounts of these proteins were packaged into viral particles [ 31 ]. Accordingly, several studies support the notion that one of the cellular functions of APOBEC3 proteins could be to prevent the propagation of mobile elements in their host genomes.

In a general way, uracils coming from the action of the AID or the APOBEC3 proteins appear to be central actors in the adaptive or innate immune response, respectively. APOBEC3 family members and their associated roles in exogenous viruses and endogenous retroelements restriction. Data are compiled from [27, 77, 87, 90, ]. Eukaryotic and prokaryotic cells have evolved in setting up two mechanisms to impede the presence of uracils in DNA, bringing to light the highly deleterious effects of genomic uracils if unrepaired.

The dUTPase is a ubiquitous enzyme that is well conserved in all organisms. This protein maintains a low level of intracellular dUTP by converting dUTP to dUMP and inorganic pyrophosphate and also allows the biosynthesis of nucleotides derived from thymidine [ 32 ] Fig. The human dUTPase gene encodes, through alternative splicing, two isoforms that localize to either the mitochondrion or nucleus [ 33 ].

The expression of the nuclear form is cell-cycle regulated with a high expression in the S phase of dividing cells that contrasts to a nearly undetectable expression in differentiated and non-dividing cells [ 34 ]. In addition, partial deficiency leads to enhanced frequency of spontaneous mutations, recombinations and DNA fragmentation [ 35 — 39 ]. The DNA repair process has been extensively subjected to reviews [ 40 ] and will be shortly introduced here.