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DNA Repair: DNA Polymerase ζ and Rev1 Break in

2006; Elsevier BV; Volume: 16; Issue: 8 Linguagem: Inglês

10.1016/j.cub.2006.03.043

1879-0445

Nadine K. Kolas, Daniel Durocher,

Microtubule and mitosis dynamics

DNA polymerase zeta and Rev1 play key roles in replication past DNA lesions. New work shows that the yeast checkpoint kinase Mec1 recruits a complex consisting of polymerase zeta and Rev1 to DNA double-strand breaks. This study highlights the role of polymerases that mediate translesion synthesis in the response to DNA double-strand breaks. DNA polymerase zeta and Rev1 play key roles in replication past DNA lesions. New work shows that the yeast checkpoint kinase Mec1 recruits a complex consisting of polymerase zeta and Rev1 to DNA double-strand breaks. This study highlights the role of polymerases that mediate translesion synthesis in the response to DNA double-strand breaks. DNA double-strand breaks are the most lethal form of DNA damage and are intermediates in numerous gross chromosomal rearrangements. When a DNA double-strand break occurs and is recognised by a cell, a signaling cascade ensues which orchestrates a complex response aimed at maintaining cell viability and genome integrity (reviewed in [1Rouse J. Jackson S.P. Interfaces between the detection, signaling, and repair of DNA damage.Science. 2002; 297: 547-551Crossref PubMed Scopus (545) Google Scholar]). This signaling cascade, often known as the DNA damage checkpoint, is controlled in large part by PI(3) kinase-like kinases: ATR and ATM in human cells; Mec1 and Tel1 in budding yeast. Checkpoint signaling modulates DNA double-strand break repair in part by regulating protein recruitment to sites of DNA damage. The recruited proteins can be detected either by their accumulation in subnuclear structures called 'foci' or by chromatin immunoprecipitation [2Lisby M. Rothstein R. Localization of checkpoint and repair proteins in eukaryotes.Biochimie. 2005; 87: 579-589Crossref PubMed Scopus (51) Google Scholar]. A major challenge in recent years has been to catalogue those proteins that localize to DNA double-strand breaks, to understand the molecular and temporal basis of their recruitment, and to elucidate their contribution to the DNA damage response. Recent work has added to the list a complex composed of DNA polymerase zeta (Polζ) and Rev1, two translesion synthesis polymerases. Polζ is an error-prone polymerase, made up of Rev3 and Rev7 subunits, which plays an important role in translesion synthesis by virtue of its ability to extend mispaired primer termini or primer termini opposite DNA lesions [3Rattray A.J. Strathern J.N. Error-prone DNA polymerases: when making a mistake is the only way to get ahead.Annu. Rev. Genet. 2003; 37: 31-66Crossref PubMed Scopus (136) Google Scholar, 4Prakash S. Johnson R.E. Prakash L. Eukaryotic translesion synthesis DNA polymerases: specificity of structure and function.Annu. Rev. Biochem. 2005; 74: 317-353Crossref PubMed Scopus (791) Google Scholar]. The function of Polζ during translesion synthesis requires Rev1 [5Lawrence C.W. Christensen R.B. Ultraviolet-induced reversion of cyc1 alleles in radiation-sensitive strains of yeast. III. rev3 mutant strains.Genetics. 1979; 92: 397-408Crossref PubMed Google Scholar, 6Lawrence C.W. Nisson P.E. Christensen R.B. UV and chemical mutagenesis in rev7 mutants of yeast.Mol. Gen. Genet. 1985; 200: 86-91Crossref PubMed Scopus (46) Google Scholar], a member of the Y family of polymerases. Although Rev1 has its own catalytic activity, this appears to make little contribution to lesion bypass; in contrast, Rev1's translesion synthesis activity is diminished by the rev1-1 mutation, which affects the protein's amino-terminal BRCT domain while leaving its catalytic activity relatively intact [3Rattray A.J. Strathern J.N. Error-prone DNA polymerases: when making a mistake is the only way to get ahead.Annu. Rev. Genet. 2003; 37: 31-66Crossref PubMed Scopus (136) Google Scholar, 4Prakash S. Johnson R.E. Prakash L. Eukaryotic translesion synthesis DNA polymerases: specificity of structure and function.Annu. Rev. Biochem. 2005; 74: 317-353Crossref PubMed Scopus (791) Google Scholar]. The implication is that Rev1 has a more structural role in translesion synthesis. Rev1 has recently been shown to be part of a tight physical complex with Polζ in two independent studies [7Acharya N. Haracska L. Johnson R.E. Unk I. Prakash S. Prakash L. Complex formation of yeast Rev1 and Rev7 proteins: a novel role for the polymerase-associated domain.Mol. Cell Biol. 2005; 25: 9734-9740Crossref PubMed Scopus (66) Google Scholar, 8Hirano Y. Sugimoto K. ATR-homolog Mec1 controls association of DNA polymerase zeta-Rev1 complex with regions near a double-strand break.Curr. Biol. 2006; 16: 586-590Abstract Full Text Full Text PDF PubMed Scopus (65) Google Scholar], including that of Hirano and Sugimoto [8Hirano Y. Sugimoto K. ATR-homolog Mec1 controls association of DNA polymerase zeta-Rev1 complex with regions near a double-strand break.Curr. Biol. 2006; 16: 586-590Abstract Full Text Full Text PDF PubMed Scopus (65) Google Scholar] recently published in Current Biology. It is likely that Rev1 interacts with the intact Polζ complex, as the association of Rev1 with either Rev3 or Rev7 is disrupted when either REV7 or REV3 are deleted. The interaction with Polζ is mediated by the polymerase-associated domain close to Rev1's carboxyl terminus [7Acharya N. Haracska L. Johnson R.E. Unk I. Prakash S. Prakash L. Complex formation of yeast Rev1 and Rev7 proteins: a novel role for the polymerase-associated domain.Mol. Cell Biol. 2005; 25: 9734-9740Crossref PubMed Scopus (66) Google Scholar], and does not require the Rev1 BRCT domain, as both the Rev1-1 or Rev1BRCTΔ proteins interact with Polζ [7Acharya N. Haracska L. Johnson R.E. Unk I. Prakash S. Prakash L. Complex formation of yeast Rev1 and Rev7 proteins: a novel role for the polymerase-associated domain.Mol. Cell Biol. 2005; 25: 9734-9740Crossref PubMed Scopus (66) Google Scholar, 8Hirano Y. Sugimoto K. ATR-homolog Mec1 controls association of DNA polymerase zeta-Rev1 complex with regions near a double-strand break.Curr. Biol. 2006; 16: 586-590Abstract Full Text Full Text PDF PubMed Scopus (65) Google Scholar]. There is increasing evidence that error-prone polymerases are also involved in the repair of DNA double-strand breaks. For example, the X family polymerases are involved in non-homologous end-joining [9Nick McElhinny S.A. Ramsden D.A. Sibling rivalry: competition between Pol X family members in V(D)J recombination and general double strand break repair.Immunol. Rev. 2004; 200: 156-164Crossref PubMed Scopus (48) Google Scholar], whereas the Y family Polη is involved in DNA synthesis during homologous recombination in vertebrates [10Kawamoto T. Araki K. Sonoda E. Yamashita Y.M. Harada K. Kikuchi K. Masutani C. Hanaoka F. Nozaki K. Hashimoto N. et al.Dual roles for DNA polymerase eta in homologous DNA recombination and translesion DNA synthesis.Mol. Cell. 2005; 20: 793-799Abstract Full Text Full Text PDF PubMed Scopus (191) Google Scholar, 11McLlwraith M.J. Vaisman A. Liu Y. Fanning E. Woodgate R. West S.C. Human DNA polymerase eta promotes DNA synthesis from strand invasion intermediates of homologous recombination.Mol. Cell. 2005; 20: 783-792Abstract Full Text Full Text PDF PubMed Scopus (243) Google Scholar]. The Polζ–Rev1 complex has been functionally linked with DNA double-strand breaks, as it is required for the elevated rates of mutations associated with recombinational DNA double-strand break repair in yeast [12Rattray A.J. Shafer B.K. McGill C.B. Strathern J.N. The roles of REV3 and RAD57 in double-strand-break-repair-induced mutagenesis of Saccharomyces cerevisiae.Genetics. 2002; 162: 1063-1077PubMed Google Scholar]. From observations, Hirano and Sugimoto [8Hirano Y. Sugimoto K. ATR-homolog Mec1 controls association of DNA polymerase zeta-Rev1 complex with regions near a double-strand break.Curr. Biol. 2006; 16: 586-590Abstract Full Text Full Text PDF PubMed Scopus (65) Google Scholar] surmised that Polζ–Rev1 may physically associate with DNA double-strand breaks. To test this prediction, Hirano and Sugimoto [8Hirano Y. Sugimoto K. ATR-homolog Mec1 controls association of DNA polymerase zeta-Rev1 complex with regions near a double-strand break.Curr. Biol. 2006; 16: 586-590Abstract Full Text Full Text PDF PubMed Scopus (65) Google Scholar] used chromatin immunoprecipitation to examine protein recruitment in the vicinity of a DNA double-strand break delivered by the homothallic (HO) endonuclease [13Haber J.E. Uses and abuses of HO endonuclease.Methods Enzymol. 2002; 350: 141-164Crossref PubMed Scopus (42) Google Scholar] at a single site in the yeast genome. They found that Polζ and Rev1 are both enriched at the locus surrounding the DNA double-strand break, interdependently of each other. Interestingly, the recruitment of Polζ–Rev1 to damaged chromatin was found to be independent of Rev1's catalytic activity but entirely dependent on integrity of its BRCT domain, as a complex containing the Rev1-1 protein failed to localize to the vicinity of the HO-induced DNA double-strand break. The processivity factor PCNA, a ring-shaped protein that connects topologically to DNA, plays an essential role in Polζ-dependent translesion synthesis; it has been shown that this requires mono-ubiquitination of PCNA on Lys164 by the Rad6–Rad18 complex [14Stelter P. Ulrich H.D. Control of spontaneous and damage-induced mutagenesis by SUMO and ubiquitin conjugation.Nature. 2003; 425: 188-191Crossref PubMed Scopus (657) Google Scholar, 15Haracska L. Torres-Ramos C.A. Johnson R.E. Prakash S. Prakash L. Opposing effects of ubiquitin conjugation and SUMO modification of PCNA on replicational bypass of DNA lesions in Saccharomyces cerevisiae.Mol. Cell Biol. 2004; 24: 4267-4274Crossref PubMed Scopus (172) Google Scholar], which permits recruitment of other family polymerases to stalled replication forks (for example, see [16Kannouche P.L. Wing J. Lehmann A.R. Interaction of human DNA polymerase eta with monoubiquitinated PCNA: a possible mechanism for the polymerase switch in response to DNA damage.Mol. Cell. 2004; 14: 491-500Abstract Full Text Full Text PDF PubMed Scopus (680) Google Scholar] and Figure 1A). To determine if Polζ–Rev1 is recruited to DNA double-strand breaks in a similar manner, Hirano and Sugimoto [8Hirano Y. Sugimoto K. ATR-homolog Mec1 controls association of DNA polymerase zeta-Rev1 complex with regions near a double-strand break.Curr. Biol. 2006; 16: 586-590Abstract Full Text Full Text PDF PubMed Scopus (65) Google Scholar] examined the contribution of PCNA ubiquitination to Polζ–Rev1 DNA double-strand break localization. Perhaps surprisingly, they found that PCNA ubiquitination-deficient yeast strains are fully able to recruit Polζ–Rev1 to sites of DNA double-strand breaks. Hirano and Sugimoto [8Hirano Y. Sugimoto K. ATR-homolog Mec1 controls association of DNA polymerase zeta-Rev1 complex with regions near a double-strand break.Curr. Biol. 2006; 16: 586-590Abstract Full Text Full Text PDF PubMed Scopus (65) Google Scholar] also tested the contribution of the 9-1-1 complex, a checkpoint signaling heterotrimer analogous to the PCNA 'sliding clamp' which has also been linked to the recruitment of polymerases to damaged chromatin. Again they found that Polζ–Rev1 recruitment to DNA double-strand breaks is independent of clamp function. But an intact checkpoint signaling cascade is required for Polζ–Rev1 recruitment to DNA double-strand breaks: the authors found that Mec1 is essential for the association between Polζ–Rev1 and the chromatin surrounding the break. These results are particularly compelling as BRCT domains are known to bind to phosphorylated sites on proteins [17Manke I.A. Lowery D.M. Nguyen A. Yaffe M.B. BRCT repeats as phosphopeptide-binding modules involved in protein targeting.Science. 2003; 302: 636-639Crossref PubMed Scopus (520) Google Scholar, 18Yu X. Chini C.C. He M. Mer G. Chen J. The BRCT domain is a phospho-protein binding domain.Science. 2003; 302: 639-642Crossref PubMed Scopus (648) Google Scholar], and the Rev1 BRCT domain may have some phosphopeptide-binding activity [18Yu X. Chini C.C. He M. Mer G. Chen J. The BRCT domain is a phospho-protein binding domain.Science. 2003; 302: 639-642Crossref PubMed Scopus (648) Google Scholar]. A simple model can be conceived in which the Rev1 BRCT domain recognizes a protein phosphorylated in a Mec1-dependent fashion in the vicinity of DNA double-strand breaks (Figure 1B). There is much debate, however, about whether single BRCT domains can bind to phosphorylated epitopes in a sequence-specific manner, as opposed to tandem BRCT domains, which almost universally display phosphoprotein-binding activity. As Rev1 only has a single BRCT domain, more work will be required to determine whether phospho-dependent protein–protein interactions mediated by the Rev1 BRCT domain influence Polζ–Rev1 recruitment to DNA double-strand breaks. The new work raises some other fascinating questions. Firstly, although Rev1 is unique among the Y family polymerases in having a BRCT domain, Pol X family members in yeast and vertebrates, such as Pol4, Polμ, Polλ and TdT, all have amino-terminal BRCT domains, raising the intriguing possibility that they too can be recruited to DNA double-strand breaks in a PI(3) kinase-like kinase-dependent fashion. Secondly, what is the biological significance of targeting Polζ–Rev1 to DNA double-strand breaks? Although Hirano and Sugimoto [8Hirano Y. Sugimoto K. ATR-homolog Mec1 controls association of DNA polymerase zeta-Rev1 complex with regions near a double-strand break.Curr. Biol. 2006; 16: 586-590Abstract Full Text Full Text PDF PubMed Scopus (65) Google Scholar] provide some evidence that Polζ–Rev1 may be involved in DNA double-strand break repair, the yeast strain used to examine this possibility does not allow conclusive demonstration of a DNA double-strand break repair function, as the non-homologous end-joining events detected by this assay require mutation or deletion of the HO endonuclease recognition site in order to survive the continuous HO expression. The use of more specialized strains will allow the examination of the qualitative and quantitative aspects of DNA double-strand break repair dependent on Polζ–Rev1. Nevertheless, it is notable that data from vertebrate cells are consistent with a role for Polζ and Rev1 in DNA double-strand break repair [19Okada T. Sonoda E. Yoshimura M. Kawano Y. Saya H. Kohzaki M. Takeda S. Multiple roles of vertebrate REV genes in DNA repair and recombination.Mol. Cell Biol. 2005; 25: 6103-6111Crossref PubMed Scopus (93) Google Scholar, 20Sonoda E. Okada T. Zhao G.Y. Tateishi S. Araki K. Yamaizumi M. Yagi T. Verkaik N.S. van Gent D.C. Takata M. et al.Multiple roles of Rev3, the catalytic subunit of polzeta in maintaining genome stability in vertebrates.EMBO J. 2003; 22: 3188-3197Crossref PubMed Scopus (170) Google Scholar]. This role, supported by the function of Polζ–Rev1 in DNA double-strand break-induced mutagenesis and by the study of Hirano and Sugimoto [8Hirano Y. Sugimoto K. ATR-homolog Mec1 controls association of DNA polymerase zeta-Rev1 complex with regions near a double-strand break.Curr. Biol. 2006; 16: 586-590Abstract Full Text Full Text PDF PubMed Scopus (65) Google Scholar], suggests that Polζ–Rev1 may promote DNA synthesis during DNA repair, perhaps in a manner analogous to the model recently described for Polη [10Kawamoto T. Araki K. Sonoda E. Yamashita Y.M. Harada K. Kikuchi K. Masutani C. Hanaoka F. Nozaki K. Hashimoto N. et al.Dual roles for DNA polymerase eta in homologous DNA recombination and translesion DNA synthesis.Mol. Cell. 2005; 20: 793-799Abstract Full Text Full Text PDF PubMed Scopus (191) Google Scholar, 11McLlwraith M.J. Vaisman A. Liu Y. Fanning E. Woodgate R. West S.C. Human DNA polymerase eta promotes DNA synthesis from strand invasion intermediates of homologous recombination.Mol. Cell. 2005; 20: 783-792Abstract Full Text Full Text PDF PubMed Scopus (243) Google Scholar], or may serve to bypass abasic sites or other lesions surrounding double-strand breaks caused by ionizing radiation, an agent known to generate clustered and complex DNA damage. Although much remains to be learned from the role of Polζ–Rev1 in DNA double-strand break repair or associated mutagenesis, the studies of Hirano and Sugimoto [8Hirano Y. Sugimoto K. ATR-homolog Mec1 controls association of DNA polymerase zeta-Rev1 complex with regions near a double-strand break.Curr. Biol. 2006; 16: 586-590Abstract Full Text Full Text PDF PubMed Scopus (65) Google Scholar] further confirm that far from being exceptional and anecdotal, the involvement of error-prone polymerases in DNA double-strand break repair represents an emerging feature of these enzymes and suggest that at least for Polζ–Rev1, this involvement is orchestrated by checkpoint signaling.