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J. Biol. Chem., Vol. 282, Issue 44, 32243-32255, November 2, 2007
The Mre11/Rad50/Nbs1 Complex Plays an Important Role in the Prevention of DNA Rereplication in Mammalian Cells*
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| ABSTRACT |
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| INTRODUCTION |
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DNA replication is strictly regulated by the licensing mechanism, which allows formation of prereplication complexes (pre-RCs) only in late mitosis and prior to S phase (1, 5). Licensing begins with the recruitment of Cdc6 and Cdt1 to origins by chromatin-bound ORC, which in turn facilitates chromatin loading of the MCM2–7 complexes. Two protein kinases, cyclin-dependent kinase (CDK) and Dbf4-dependent kinase (DDK), are required to activate the licensed origins to initiate DNA replication by stimulating DNA unwinding from the origins. After the onset of replication initiation, the origins are converted to an unlicensed state by disassembling the pre-RCs, which leaves only ORC bound to chromatin.
To avoid a second round of DNA initiation, multiple mechanisms are involved in the prevention of reassembly of pre-RCs within the same cell cycle. Among these mechanisms, control of Cdt1 activity in a cell cycle-regulated manner has been shown to be critical (2, 5). Cdt1 is stable in G1 and is targeted for degradation at the onset of S-phase (6–9). Geminin, expressed after cells enter S-phase, binds to Cdt1 and directly inhibits Cdt1 function at origins (10, 11). Recent studies demonstrated that overexpression of Cdt1 or down-regulation of geminin disrupts the licensing control and induces rereplication, which consequently causes genome instability (12–14). Unbalanced expression of Cdt1 or other replication licensing factors as well as DNA hyperreplication has been observed to be associated with tumorigenesis (3, 4, 15, 16).
DNA rereplication causes accumulation of DNA lesions and triggers DNA damage responses observed in multiple organisms (12, 13, 17–20). The activation of damage checkpoint inhibits the extent of rereplication (19) and arrests cell cycle at the G2/M stages (13, 20). Our recent studies demonstrated that upon Cdt1 overexpression, single-stranded DNA (ssDNA)3 is accumulated prior to the appearance of DSBs, which activates the ATR pathway that effectively prevents further rereplication (75). Therefore, cell cycle checkpoint is not only capable of detecting abnormal DNA structures when the licensing control is compromised, but is also actively involved in inhibiting rereplication.
The Mre11/Rad50/Nbs1 complex (MRN) is a highly conserved protein complex that plays major roles in the maintenance of genome stability (21, 22). Hypomorphic mutations in Nbs1 and Mre11 result in autosomal recessive diseases Nijmegen breakage syndrome (NBS) and ataxia-telangiectasia-like disorder (ATLD), respectively (23, 24). The radioresistant DNA synthesis (RDS) phenotype of NBS and ATLD cells suggests a critical role of MRN in mediating the intra-S-phase checkpoint (23, 25). MRN binds directly to ATM and stimulates ATM kinase activity to phosphorylate its multiple substrates (26–28). Meanwhile, Nbs1 is also a downstream substrate of ATM, with ATM-dependent phosphorylation of Nbs1 at least at serine residue 343 (Ser343) is required for mediating the intra-S-phase checkpoint (29–32). Recently, our studies demonstrated that a direct interaction of MRN with RPA is required for IR-induced suppression of DNA synthesis, suggesting that RPA is a target of MRN to mediate the intra-S-phase checkpoint (33). Although substantial evidence suggests that MRN plays a key role in the ATM pathway in responses to DSBs, a connection between MRN and ATR was also described recently. MRN was co-purified with ATR (34) and is a direct substrate of ATR under replication stress (35, 36). MRN is required for replication restart during the recovery from fork stalling and G2/M arrest following HU treatment, similar to the requirement of ATR in these damage responses (37–39). It has also been suggested that MRN is involved in facilitating ATR-mediated phosphorylation events, although the mechanism remains unclear (35, 37, 39).
In our previous studies, we demonstrated that Nbs1 inhibits the simian virus 40 (SV40) large T antigen-induced hyperreplication of chromosomal DNA and SV40 origin-containing replicons, suggesting a possible role of Nbs1 in limiting inappropriate DNA rereplication events (40). Here, we demonstrate that in mammalian cells, MRN plays an important role in the prevention of rereplication when the licensing control is disrupted by Cdt1 overexpression. Loss of Mre11 or Nbs1 function does not only increase levels of rereplication in rereplication-susceptible cell lines but also leads to substantial rereplication in the cell lines that are normally resistant to Cdt1 overexpression-induced rereplication. We also showed that a major mechanism by which MRN inhibits rereplication is through regulating the ATR pathway. MRN facilitates ATR activation to phosphorylate Chk1 upon Cdt1 overexpression, an event that appears to be important for inhibiting rereplication (19, 75). Nbs1 phosphorylation at Ser343 by ATR is observed at an early stage after Cdt1 is overexpressed, and this phosphorylation is needed for the inhibition of rereplication. Moreover, the interaction of MRN with RPA that is required for mediating the intra-S-phase checkpoint (33) is also required for the inhibition of rereplication. Collectively, these data suggest that MRN acts through the activation of the S-phase checkpoint in the ATR pathway to suppress DNA rereplication.
| EXPERIMENTAL PROCEDURES |
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Silencing of endogenous Mre11, Nbs1, or ATR in U2OS, T98G, or A549 cells was performed by two rounds of retroviral infection using pMKO vector (42) that expressed two different Mre11, Nbs1, or ATR shRNA target sequences. The shRNA retrovirus plasmids constructed by inserting annealed and phosphorylated shRNA oligos into pMKO retroviral vector. The shRNA target sequences used were Mre11: GAUGAGAACUCUUGGUUUAAC, and GAGUAUAGAUUUAGCAGAACA; Nbs1: GGAGGAAGAUGUCAAUGUUAG and GAAGAAACGUGAACUCAAGGA; ATR: CGAGACTTCTGCGGATTGCAG and AACCTCCGTGATGTTGCTTGA (43).
Adenovirus Construction and Infection—Production of recombinant adenoviruses is conducted by using the AdEasy system method (44). Adenovirus plasmids constructed by inserting, full-length hCdt1, Nbs1 N-terminal fragment (Nbs1-N-1–478), full-length Mre11, and Mre11
521–543 into pAd-track-CMV shuttle vector. Then, in vivo recombination was performed by transforming pAd-track-CMV plasmid together with pAd-Easy-1 adenoviral vector into BJ5813 competent cell by electroporation (44). The recombinant adenoviral plasmids were transfected into 293 cells to generate corresponding recombinant adenoviruses. Large scale purification of adenoviruses from 293 cells was accomplished by CsCI density gradient centrifugation. The concentration of purified virus was measured A260 using the equation 1A260
1012 pfu (12).
Immunoblot Analysis and Antibodies—Cells were lysed in NETN (150 mM NaCl, 1 mM EDTA, 20 mM Tris-Cl pH 8.0, 0.5% Nonidet P-40 (v/v)) containing protease and phosphatase inhibitors (1.0 mM sodium orthovanadate, 50 µM sodium fluoride). For immunoblot analysis, proteins were separated by SDS-PAGE, transferred to nitrocellulose membranes (Bio-Rad), incubated overnight in primary antibodies followed by 1 h of incubation in horseradish peroxidase-conjugated secondary antibodies.
Antibodies used in this study are listed as follows: antibodies to Cdt1 (8), Mre11 ((D27; Ref. 40), and Nbs1 (D29; Ref. 29) were described earlier, antibody to phospho-Chk1 (Ser317) was obtained from R & D Systems, phospho-Chk2 (Thr68) and phospho-Nbs1 (Ser343) antibodies were from Cell Signaling, antibodies to Chk1, Chk2, and Ku70 were purchased from Santa Cruz Biotechnology, RPA2 and ATR antibodies were from Oncogene, and Rad50 and
-H2AX (Ser139) were from Upstate%20Biotechnology">Upstate Biotechnology.
Fluorescence-activated Cell Sorting (FACS) Analysis—Cells were rinsed with phosphate-buffered saline, collected by trypsinization and fixed with 70% ethanol overnight at 4 °C. After fixation, cells were stained with propidium iodide solution which containing 38 mM sodium citrate, 10 µg/ml RNase A and 15 µg/ml propidium iodide (Sigma). The labeled cells were analyzed with a Becton-Dickinson flow cytometer using Cellquest software.
Plasmids and Mutagenesis—To generate mutations in Nbs1 (S343A, R28A(FHA), Y176A(BRCT), R28A/Y176A (FHA/BRCT)) and Mre11 (NAAIRS, D543A/D544A), Myc-tagged full-length Nbs1 and Mre11 cloned into mammalian expression vector pcDNA3
was used as template for site-directed mutagenesis (QuikChange, Stratagene). Wild-type and mutant forms of Myc-tagged Nbs1 and Mre11 were cloned into the retroviral vector pBabepuro.
Single Cell Gel Electrophoresis (Comet Assay)—The neutral comet assay was performed as described (45) with minor modifications (46). Briefly, after treatment harvested cells were washed two times with cold phosphate-buffered saline at a concentration of 4 x 106 cells/ml. Cells were then resuspended in 0.8% low melting point agarose and spread on microscopic slides. Slides were incubated for 30 min in lysis solution (2.5 M NaCl, 100 mM EDTA, 10 mM Tris-Cl pH 10.0, 1% sodium N-lauroyl sarcosine, and 1% Triton X-100). Subsequently, Slides were subjected to electrophoresis in Tris borate-EDTA buffer at 1 V/cm for 20 min. After electrophoresis, the slides were dried, stained with ethidium bromide, and viewed under a fluorescent microscope. The presence of a tail (comet) reflects DNA damage (DSBs) in the cells. For quantitative measurement, nuclei with a comet tail larger than 2 nuclear diameters were counted as positive for DNA damage. The percentage of nuclei with tails was the number of positive for DNA damage divided by the total number of nuclei counted. Results are presented as range of at least three independent experiments.
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| RESULTS |
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2-fold more) and rereplication. Silencing Mre11 by shRNAs prior to the depletion of DDB1 or Cdt2 significantly increased the rereplication levels compared with Mre11-proficient cells (Fig. 1B). These data suggest that MRN is involved in the suppression of rereplication when licensing control is disrupted.
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Rereplication generates both ssDNA and DSBs and these two kinds of DNA lesions activate ATR and ATM, respectively (13, 14, 20, 75). MRN plays a critical role in the activation of ATM in response to DSBs (26, 27, 50). Recent studies showed that after ATM activation, MRN is also important for processing the DSBs to generate RPA-bound ssDNA, leading to ATR activation (51). Thus, compromised ATR activation observed in MRN-deficient cells after Cdt1 overexpression could be caused by a loss of MRN function in the processing of DSBs that is required for ATR activation.
To examine this possibility, we performed a time course analysis to monitor the activation of ATR and ATM after Cdt1 overexpression in Mre11-deficient and proficient cells. Consistent with our previous findings (75), in vector-infected cells, ATR-mediated Chk1 phosphorylation at Ser317 occurred at 12-h postinfection (hpi) while ATM-mediated Chk2 phosphorylation at Thr68 was not detected until 24 hpi in vector-infected U2OS cells (Fig. 2C, left panel), suggesting the ATR-Chk1 pathway is activated prior to the ATM-Chk2 pathway. H2AX phosphorylation, an indicator of DSB accumulation (52), appeared at similar time points as Chk2 phosphorylation at the 24-h time point (75), suggesting that Cdt1 overexpression-induced DSB formation is likely a signal to activate the ATM-Chk2 pathway. Importantly, when Mre11 was silenced, ATR-mediated Chk1 phosphorylation at the early stage of Cdt1 overexpression, before DSB formation, was significantly impaired (Fig. 2C, right panel). These data suggest that after Cdt1 overexpression, MRN is involved in promoting ATR activation before the accumulation of DSBs and the activation of ATM, thereby revealing an important role of MRN in facilitating ATR activation in a separate pathway from ATM activation in rereplication control. The Chk2 phosphorylation that occurred at late stages after Cdt1 overexpression was also diminished Fig. 2C, right panel). Similar results were obtained when the expression of Nbs1 was suppressed by shRNAs (data not shown). These data suggest that MRN is required for activating both ATR-Chk1 and ATM-Chk2 pathways. However, given a critical role of the ATR-Chk1 pathway, but not the ATM-Chk2 pathway in restraining rereplication at the early stage of the loss of licensing control (75), these data suggest that one role of MRN in the prevention of rereplication is mediated by facilitating ATR-mediated activation of Chk1 when Cdt1 is overexpressed.
Nbs1 Phosphorylation at Ser343 by ATR Is Required for the Prevention of Rereplication When Cdt1 Is Overexpressed—Nbs1 is phosphorylated at Ser343 by ATM in response to IR or by ATR under replication stress (30, 31, 35). Because phosphorylation of Nbs1-S343 is important for mediating the intra-S-phase checkpoint by down-regulation of DNA replication (29–32), we examined whether this regulation might also be used in inhibiting Cdt1 overexpression-induced rereplication. We observed that Nbs1 was phosphorylated at Ser343 after Cdt1 overexpression, similar to that after IR and UV treatment (Fig. 3A). Importantly, the phosphorylation of Nbs1 at Ser343 occurred at an early stage after Cdt1 overexpression (Fig. 3B), approximately at the same time when Chk1 was phosphorylated (Fig. 2B), indicating that ATR is probably the kinase that phosphorylates Nbs1.
To examine whether Nbs1 phosphorylation at Ser343 is indeed dependent upon ATR after Cdt1 overexpression, we inhibited ATR expression by expressing ATR-shRNAs in U2OS cells (Fig. 3C, right). Because ATM may also be activated to phosphorylate Nbs1 at Ser343 when DSBs are generated, we examined Nbs1 phosphorylation at Ser343 in ATR deficient cells at 16 and 20 hpi after Ad-Cdt1 infection when DSBs were absent as revealed by H2AX phosphorylation (Fig. 2B). We observed that phosphorylation of Nbs1 at Ser343 and Chk1 at Ser317 was significantly reduced when ATR was silenced (Fig. 3C, left). Similar results were obtained when a fibroblast cell line, GM847-ATR-KD (41), expressing a doxycycline-inducible kinase inactive allele of ATR (ATR-KD) was used (Fig. 3D). Collectively, these results suggest that ATR kinase activity is required for phosphorylation of Nbs1 at Ser343, especially at the initial stage after Cdt1 overexpression in mammalian cell lines.
Because ATM- or ATR-directed Nbs1-S343 phosphorylation is required for mediating IR- or UV-induced down-regulation of DNA replication (30, 31, 35), the early appearance of Nbs1-S343 phosphorylation after Cdt1 overexpression prompted us to examine whether this ATR-dependent phosphorylation event might play a role in mediating the inhibition of rereplication. Myc-tagged wild type Nbs1 or Nbs1-S343A with silent mutations at the shRNA-targeted sites were expressed in U2OS cells by retroviral infection and endogenous Nbs1 was silenced by Nbs1-shRNAs (Fig. 3E, right). Intriguingly, overexpression of Cdt1 in the Nbs1-S343A mutant led to a significant increase of the extent of rereplication than in Nbs1-WT-expressing cells (Fig. 3E, left), suggesting that ATR-mediated Nbs1 phosphorylation at Ser343 is important for inhibiting rereplication. These data also suggest that in addition to MRN acting upstream of ATR to regulate the activation of ATR-Chk1, Nbs1 is also a downstream effector of ATR to inhibit rereplication.
The FHA and BRCT Domains of Nbs1 Are Important for Nbs1-mediated Inhibition of Rereplication through Regulating Nbs1 Phosphorylation at Ser343—We previously demonstrated that synthesis of an N-terminal Nbs1 fragment (amino acids 1–478) enhanced SV40 T-mediated hyperreplication and also induced profound DNA rereplication and tetraploidy in NBS-deficient cells in the absence of SV40 T (40). These results suggest that expression of this Nbs1 N-terminal fragment disrupts the cellular mechanism to prevent DNA rereplication, but the mechanism was unknown. To examine whether this Nbs1 N-terminal fragment might influence Cdt1-induced rereplication, we infected U2OS cells with a recombinant adenovirus (Ad-Nbs1-(1–478)) prior to Ad-Cdt1 infection. Overexpression of Nbs1-(1–478) significantly enhanced Cdt1-induced rereplication, while overexpression of this fragment alone did not induce rereplication (Fig. 4A). These studies suggested that overexpression of the Nbs1-(1–478) fragment is not sufficient to override the cellular control to prevent rereplication, but it facilitates Cdt1-induced rereplication.
The Nbs1-(1–478) fragment contains the FHA and BRCT domains and both are important for various functions of Nbs1 including damage-induced Nbs1 phosphorylation at Ser343 and foci formation (53, 54). One scenario is that overexpression of the Nbs1-(1–478) fragment may impair the function of the FHA/BRCT domains by a dominant negative effect, thus leading to more severe rereplication after Cdt1 overexpression. Because the FHA/BRCT domains are important for IR-induced Ser343 phosphorylation (53, 54), and phosphorylation of Nbs1 at Ser343 is important for limiting Cdt1-induced rereplication (Fig. 3E), we examined whether overexpression of the Nbs1-(1–478) fragment would affect Cdt1 overexpression-induced phosphorylation of Nbs1-Ser343. We first examined phosphorylation of endogenous Nbs1-S343 when the Nbs1-(1–478) fragment was overexpressed prior to Cdt1 overexpression. As shown in Fig. 4B, Cdt1-induced Nbs1 phosphorylation at Ser343 was indeed inhibited by overexpressing the Nbs1-(1–478) fragment. Thus, a possible mechanism causing more replication by overexpression of the Nbs1-(1–478) fragment is through the disruption of Nbs1 phosphorylation at Ser343.
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Our previous studies demonstrated that MRN interacts with RPA via a specific site on Mre11 covering residues 540 to 545 on Mre11 (33). Substitution of residues 540 to 545 with a NAAIRS sequence (56) or replacement of the two conserved Asp543 and Asp544 with alanines completely abolished the interaction of MRN with RPA (33). To test whether the interaction of MRN and RPA is important for rereplication control, we used U2OS cells expressing Myc-Mre11 wild type or the RPA-binding mutants, Myc-Mre11-NAAIRS (changing amino acids 540–545) and Mre11-DD (D543A and D544A) with endogenous Mre11 silenced by Mre11-shRNAs (Fig. 5A). Overexpression of Cdt1 induced higher levels of rereplication in the Mre11-NAAIRS and Mre11-DD mutants compared with Mre11-wild type (Fig. 5B). These data suggest that the interaction of MRN with RPA is important for inhibiting Cdt1-induced rereplication.
We have shown that MRN facilitates the activation of ATR-mediated S-phase checkpoint, thereby contributing to the inhibition of Cdt1-induced rereplication. In addition to a critical role of RPA in DNA replication, RPA also binds to ssDNA accumulated upon DNA damage and serves as a sensor to activate the ATR-mediated S-phase checkpoint (57). This raised a possibility that the interaction of MRN and RPA may be important for activating ATR when Cdt1 is overexpressed and thus is needed to prevent rereplication. To test this, we examined phosphorylation of both ATR and ATM substrates after infecting the U2OS cell lines with Ad-Cdt1. As shown in Fig. 5C, ATR-mediated phosphorylation of Chk1 at Ser317 and RPA2, as well as ATM-mediated phosphorylation of Chk2 at Thr68 induced by Cdt1 overexpression remained at similar levels in the Myc-Mre11-wild-type, Myc-Mre11-NAAIRS, or Myc-Mre11-DD expressing cell lines with endogenous Mre11 silenced. These results suggest that MRN does not require its association with RPA to sense DNA lesions and activate the ATR- or ATM-mediated S-phase checkpoint when Cdt1 is overexpressed. Because Cdt1-induced Nbs1 phosphorylation at Ser343 was also not affected in the Mre11 mutant cell lines defective in RPA binding (Fig. 5C), MRN/RPA probably acts as a downstream effector to mediate the inhibition of rereplication after Nbs1 Ser343 is phosphorylated by ATR. It is conceivable that the interaction of MRN with RPA may directly modulate RPA replication activities to inhibit Cdt1-induced rereplication.
Overexpression of MRN Inhibits Cdt1-induced Rereplication through Its Interaction with RPA—Because Nbs1 or Mre11 deficiency led to a significant increase of rereplication induced by Cdt1 overexpression, we tested whether overexpression of MRN might suppress Cdt1-induced rereplication. To do this, we infected U2OS cells with Ad-Mre11 prior to Ad-Cdt1 infection. When Mre11 was overexpressed, the levels of Nbs1 and Rad50 as well as endogenous Mre11 were significantly increased (Fig. 6B) and more MRN complexes were present as demonstrated by co-immunoprecipitation (data not shown). Stabilization of Nbs1 and Rad50 by Mre11 overexpression is probably due to a critical role of Mre11 to stabilize the MRN complex, which is supported by the observation that in Mre11 deficient cells, Nbs1 and Rad50 protein levels are significantly reduced (25). Interestingly, overexpression of Mre11 almost completely inhibited Cdt1-overexpression-induced rereplication (Fig. 6A). These data suggest that MRN is not only required for the prevention of rereplication, but is also a limiting factor to inhibit massive rereplication that is induced by Cdt1.
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521–543, an RPA-binding mutant of Mre11 prior to Ad-Cdt1 infection. Strikingly, contrary to wild-type Mre11, the Mre11
521–543 mutant failed to suppress Cdt1-induced rereplication, suggesting that the suppression of rereplication by Mre11 overexpression is indeed through an interaction with RPA. These studies highlight a critical role of the interaction of MRN with RPA to prevent rereplication and support the idea that MRN directly inhibits RPA activities that are required for rereplication. MRN Is Important for Preventing DSB Accumulation When Cdt1 Is Overexpressed—DNA rereplication causes accumulation of DSBs that are the source for inducing genetic instability. The MRN complex plays a critical role in DSB repair (58, 59), and depletion of Mre11 in Xenopus egg extracts leads to accumulation of DSBs in S-phase (60). As described, DSBs are generated in rereplicating cells either when Cdt1 is overexpressed or geminin is depleted (13, 14, 20). In addition to the role of MRN in the inhibition of rereplication, we also investigated its involvement in the prevention of DSB accumulation during rereplication. We performed single cell gel electrophoresis analysis (Comet assay) and under neutral conditions this assay mainly detects DSBs (61). Because loss of Mre11 led to more severe rereplication (Fig. 1), we used different titers of Ad-Cdt1 to infect Mre11-proficient or -deficient U2OS cells to achieve similar levels of rereplication (Fig. 7A). Under neutral conditions, the Comet assay detected significantly more comet tails in Mre11-deficient cells than in control cells when similar levels of rereplication was induced (Fig. 7, B and C). These data suggest that more DSBs are accumulated in Mre11-deficient cells, suggesting a critical role of MRN in the prevention of DSBs during rereplication.
| DISCUSSION |
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MRN Facilitates ATR Checkpoint Signaling to Limit Rereplication—DNA rereplication causes accumulation of DSBs and ssDNA, leading to the activation of both ATM- and ATR-mediated checkpoints (12, 13, 20). We showed previously that the ATR-Chk1 pathway is activated prior to the activation of the ATM-Chk2 pathway, and the ATR-Chk1 pathway plays a predominant role in restraining DNA rereplication while the ATM-Chk2 pathway is largely not needed for rereplication control (75). This is consistent with the observation that the deletion of MEC1 (the ortholog of ATR) and RAD17 in budding yeast increased the extent of rereplication (17, 62). Our studies demonstrated that multiple substrates of ATR including Chk1, Rad17, and RPA2, are phosphorylated in a manner that is dependent on Mre11 and Nbs1. More importantly, the activation of ATR at the early stage after Cdt1 overexpression, before the activation of ATM, requires MRN function. This suggests that one important function of MRN in rereplication control is to facilitate the activation of ATR, which in turn suppresses DNA rereplication. The activation of ATM after Cdt1 overexpression is also dependent on MRN, but this requirement is likely not involved in rereplication control, because ATM is dispensable for suppressing rereplication (75). As revealed by Chk2 and H2AX phosphorylation, ATM activation occurs at the late stage of Cdt1 overexpression when DSBs are present (Fig. 2C). This MRN-dependent ATM activation may contribute to the repair of DSBs that are associated with DNA rereplication.
A connection of MRN with ATR in response to DNA damage was established recently. Co-purification of MRN and ATR was observed and the interaction of MRN with ATR was stimulated after HU treatment (34, 35). In response to IR, MRN was required for processing the DSB ends, leading to ssDNA formation and ATR activation (34, 51). Under replication stress, MRN facilitated ATR-mediated phosphorylation events in a substrate and damage dose-dependent manner (35, 37, 39, 63). However, MRN-independent Chk1 phosphorylation by ATR was also reported (34, 51). Our studies demonstrated that activation of the ATR pathway due to a loss of replication licensing control requires MRN activities, thus providing another piece of evidence that MRN is important for facilitating ATR activation.
ATR-dependent Phosphorylation of Nbs1 at Ser343 Is Important for the Suppression of Rereplication—Nbs1 is phosphorylated at Ser343 by ATM in response to DSBs (29–32) and by ATR under replication stress (35). This phosphorylation is required for the inhibition of DNA replication after IR and UV treatment (30, 31), suggesting that Nbs1 phosphorylation at Ser343 triggers the inactivation of late origin firing, an event essential for mediating the intra-S-phase checkpoint. We observed that Nbs1 is phosphorylated at Ser343 in an ATR-dependent manner after Cdt1 overexpression. Mutating this Ser343 phosphorylation site significantly enhanced Cdt1 overexpression-induced rereplication. These studies suggest that in addition to its role in facilitating ATR activation, MRN is also a target of ATR, serving as a downstream effector to mediate the suppression of rereplication, which is similar to the involvement of MRN in the intra-S phase checkpoint control (35). Because inhibition of late origin firing is believed as a major pathway to mediate the intra-S phase checkpoint (64), the involvement of Nbs1 phosphorylation at Ser343 in preventing rereplication suggests that controlling origin firing is likely one of the important mechanisms to suppress rereplication.
We also observed that the phosphorylation of Nbs1 at Ser343 occurs at the early stage after Cdt1 overexpression before DSB accumulation and ATM activation, which raises two important points. First, ATR effectively phosphorylates Nbs1 to suppress DNA rereplication before DSBs are accumulated. It was proposed that one important mechanism underlying the DSB formation during rereplication is the head-to-tail fork collision (65). Suppression of rereplication by ATR-mediated Nbs1 phosphorylation at an early stage when licensing control is disrupted would considerably minimize DSB formation, which is important for the maintenance of genome stability. Second, this ATR-mediated phosphorylation of Nbs1 occurs before DSB formation, suggesting that DSB is not necessarily required for inducing the phosphorylation of Nbs1, although a major function of MRN is believed to be involved in chromosome DSB metabolism (66). Our findings as well as other accumulating evidence support the notion that MRN also plays an important role in the DNA damage responses other than DSB-associated events (35, 37).
It has been described that the FHA and BRCT domains of Nbs1 are important for foci formation and Nbs1 phosphorylation in response to DNA damage (35, 53, 54). We demonstrated that these two domains are also important for the prevention of rereplication through participating in the regulation of Nbs1 phosphorylation at Ser343. Currently, the mechanism underlying the involvement of the FHA/BRCT domains in the regulation of checkpoint-induced Nbs1 phosphorylation is not clear. The requirement of these two domains in the interaction of MRN with ATR may contribute to the regulation that facilitates the ATR-mediated Nbs1 phosphorylation at Ser343 (35).
The Interaction of MRN with RPA Is Required for Inhibiting DNA Rereplication Downstream of the Activation of ATR—MRN forms a complex with replication essential protein RPA and this interaction is important for mediating the intra-S-phase checkpoint (33, 67). Here we demonstrate that this interaction is also required for MRN to inhibit Cdt1-induced rereplication.
In response to DNA damage, RPA binds to ssDNA and activates the ATR pathway (57). One scenario is that RPA recruits MRN to ssDNA via a direct interaction, which places MRN in the vicinity of ATR to facilitate ATR activation. However, our studies showed that the interaction of MRN with RPA is not required for ATR activation when Cdt1 is overexpressed. Thus, the MRN/RPA complex is more likely situated downstream of ATR, serving as an effector to suppress rereplication.
RPA is an essential protein that is required for both replication initiation and elongation (55, 68). We observed that overexpression of MRN suppresses rereplication and this suppression is through the interaction of MRN with RPA. This suggests that the MRN/RPA complex is not only required for MRN to inhibit rereplication, but is also a limiting factor to suppress overt rereplication. One model is that when the S-phase checkpoint is activated by Cdt1 overexpression, MRN suppresses RPA replication activity via the direct interaction, leading to the inhibition of rereplication. Overt rereplication may recruit more RPA to replication centers to support rereplication initiation and elongation, which exceeds the control capacity of MRN by forming a complex with RPA under the normal cell cycle-mediated regulation. Overexpression of MRN may allow more RPA to form a complex with MRN, thus leading to more sufficient inhibition of DNA rereplication. These studies are in support of a downstream effector role of MRN/RPA in the prevention of rereplication.
MRN Prevents DSBs Accumulation When Cdt1 Is Overexpressed—DSBs in mitotic cells are the major source for inducing translocations that are highly associated with tumorigenesis (69, 70). It has been demonstrated that DNA rereplication leads to accumulation of DSBs, possibly through head-to-tail collision during the process of rereplication (65). MRN plays an essential role in homologous recombination-mediated repair of DSBs (58, 59), and our studies showed that MRN activity is also required for preventing and/or repairing DBSs that appear during DNA rereplication.
The involvement of MRN in the prevention of DSB formation during rereplication may be multi-faceted. First, MRN directly participates in the DSB repair. Mre11 carries nuclease activities and is possibly needed for processing DNA ends to promote DSB repair (51, 71). Second, MRN may facilitate DSB repair through activation of the ATM pathway when DSBs are accumulated. Activated ATM directly or indirectly phosphorylates multiple proteins involved in homologous recombination such as BRCA1, FANCD2, Rad51, and BRCA2, thereby stimulating cellular repair activities (72–74).
Taken together, our studies suggest that when licensing control is disrupted, MRN is actively involved in the prevention of DNA rereplication as well as the repair of rereplication-associated DSBs, thus revealing new roles of MRN in the maintenance of genome stability.
| FOOTNOTES |
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The on-line version of this article (available at http://www.jbc.org) contains supplemental Figs. S1 and S2. ![]()
1 Current address: Signal Transduction Program, Burnham Institute for Medical Research, La Jolla, CA 92037. ![]()
2 To whom correspondence should be addressed: Dept. of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Rd., La Jolla, CA 92037. Tel.: 858-784-7910; Fax: 858-784-7978; E-mail: xiaohwu{at}scripps.edu.
3 The abbreviations used are: ssDNA, single-stranded DNA; FACS, fluorescence-activated cell sorting; MRN, Mre11/Nbs1/Rad50 complex; DSB, double-stranded breaks; hpi, hour postinfection; pfu, plague-forming unit. ![]()
| ACKNOWLEDGMENTS |
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