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J. Biol. Chem., Vol. 281, Issue 50, 38472-38477, December 15, 2006
The Tandem BRCT Domain of 53BP1 Is Not Required for Its Repair Function*
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| ABSTRACT |
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| INTRODUCTION |
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The repair defect in 53BP1-deficient cells can be quantified by assessing PIKK-dependent phosphorylation of the histone H2A variant, H2AX, a component of the nucleosome core structure (14, 15). In response to DNA damage, H2AX is reversibly phosphorylated at megabase regions flanking the sites of DNA DSBs (16). Once repair has been completed, the histone mark is removed from the chromatin with the help of protein phosphatase 2A (17, 18).
Previous studies showed that relocalization of 53BP1 to the sites of DNA DSBs depends on a region upstream of the BRCT domains (10, 19, 20). This region includes a tandem Tudor domain, which was recently proposed to be required for the initial recruitment of 53BP1 to chromatin by its direct binding to a methylated histone mark (21, 22), as well as an adjacent region required for 53BP1 accumulation (20). However, it is unknown to what extent the 53BP1 BRCT motifs or the multiple N-terminal (S/T)Q sites are needed for the repair function of 53BP1. To address these questions, we stably expressed various 53BP1-deletion mutants in 53BP1-defcient MEFs and analyzed the repair capacity of these cells by determining the numbers of residual P-H2AX foci following treatment with ionizing radiation. Moreover, we fine-mapped the region required for 53BP1 oligomerization and, using the same approach, assessed the role of 53BP1 oligomerization in DNA DSB repair.
| EXPERIMENTAL PROCEDURES |
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Repair and Checkpoint AssaysFor the DNA DSB repair assay, cells were plated onto coverslips and grown to confluency. Once the cells had stopped dividing, they were irradiated with 1 or 2 Gy using a 137Cs source and allowed to recover for up to 27 h prior to immunostaining with anti-phopsho H2AX antibodies (24). The cells were viewed on a Nikon Eclipse 800 microscope, and the number of P-H2AX foci was assessed in 100-200 cells/sample. To analyze the integrity of the intra-S-phase checkpoint, logarithmically growing cells were plated into 96-well plates and grown at 37 °C for 2 days in medium containing 10 nCi of [14C]thymidine (ICN Radiochemicals) per ml. Radioactive medium was replaced overnight with fresh medium to chase 14C-labeled precursors into DNA prior exposure of cells to 0, 5, 10, and 20 Gy of IR. 30 min later, [3H]thymidine was added to the medium (20 µCi/ml), and the cells were incubated for another 30 min at 37 °C. After removal of the radioactive medium and two washes with cold phosphate-buffered saline, the cells were trypsinized, harvested on filter paper, and analyzed on a scintillation counter. For the low dose G2/M checkpoint assay, cells were either untreated or irradiated with 0.5 Gy and then incubated for 1 h at 37°C prior to fixation and staining with anti-phospho-histone H3 antibodies (Upstate%20Biotechnology">Upstate Biotechnology) and propidium iodide. The number of mitotic cells was assessed by immunofluorescence microscopy.
Immunoprecipitation and ImmunoblottingCells were lysed in lysis buffer (20 mM Tris-HCl, pH 8, 100 mM NaCl, 1 mM EDTA, 0.5% Nonidet P-40) supplemented with 1 mM phenylmethanesulfonyl fluoride, 2 µg/ml aprotinin, 50 mM NaF, 40 mM
-glycerolphosphate, and 2 mM Na3VO4, and extracts were incubated with the indicated primary antibodies and protein G-Sepharose beads (Amersham Biosciences) or S-agarose beads (EMD Biosciences) for 1 h at 4°C. The beads were then gently washed three times with lysis buffer, and the precipitated complexes were resuspended in 2x Laemmli buffer. After boiling, the samples were resolved by sodium dodecyl sulfate polyacrylamide gel electrophoresis, transferred to polyvinylidene difluoride membrane, and immunoblotted with various antibodies. Monoclonal antibodies against the FLAG (M2) and HA epitope (HA.11) were purchased from Sigma and Covance, respectively. Anti-p53 antibodies DO1 and 421 were purchased from Oncogene, whereas the polyclonal anti-53BP1 antibody was raised against the N terminus of 53BP1 (7).
| RESULTS |
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1052-1302 and
Tudor 1477-1632), which are unable to relocate in response to DNA damage, showed the same repair defect as 53BP1-deficient cells (Fig. 1). Moreover, reconstitution with h53BP1 full-length protein (FL) restored the DSB repair to levels that were similar to the ones observed in the 53BP1 wild-type line (Fig. 1, wt), suggesting that human 53BP1 can fully replace its murine counterpart in DNA DSB repair.
The N terminus of 53BP1 contains no functionally defined protein region but has several (S/T)Q sites, which represent potential target sites for ATM or other PIKKs. In fact, we and others had previously shown that 53BP1 becomes hyperphoshorylated in an ATM-dependent manner in response to DNA damage, and we mapped Ser-6, Ser-25, Ser-29, and Ser-784 as inducible in vivo ATM phosphorylation sites (7, 9, 20). To test whether phosphorylation of these four sites is required for the repair function of 53BP1, we transiently transfected 53BP1-deficient MEFs with a quadruple serine to alanine mutant (S6A,S25A,S29A,S784A). Interestingly, the expression of this particular 53BP1 phospho-mutant almost restored the repair efficiency to wild-type levels, whereas cells expressing the
1-1052 mutant showed the repair defect similar to 53BP1-null cells (53BP1-/-, 5.20 ± 0.26; FL, 1.83 ± 0.13; S6A,S25A,S29A,S784A, 2.10 ± 0.18;
1-1052, 5.24 ± 0.31, mean ± S.E.).
There are at least two possible explanations for this result. One is that there are additional redundant phosphorylation sites at the N terminus of 53BP1. Phosphorylation of those sites is sufficient for mediating DNA DSB repair. Alternatively, 53BP1 phosphorylation could be independent from the repair function of 53BP1 and might contribute to checkpoint or other function of 53BP1. To distinguish these two possibilities, we analyzed a series of MEF lines stably expressing increasing N-terminal deletions (
1-165,
1-334,
1-500,
1-659,
1-1052) or a phospho-mutant (10) with all 15 conserved (S/T)Q sites being changed to AQ sites (15AQ) (Fig. 2A). Using the same residual P-H2AX foci assay, we observed a gradual increase in repair deficiency with increasing length of the deletion (Fig. 2B). Consistent with this finding, transient expression of two internal deletion mutants,
170-499 and
334-659, resulted only in a partial rescue of the repair deficiency (data not shown). Moreover, expression of the 15AQ mutant could not salvage the repair defect in 53BP1-null MEFs, although the average number of residual P-H2AX foci was slightly lower than that observed in the parental line or in cells expressing the
1-1052 deletion mutant (Fig. 2B). Based on these observations, we believe that phosphorylation of 53BP1 at multiple sites within the 53BP1 N terminus is required for efficient DNA DSB repair.
To test whether 53BP1 phosphorylation would be involved in checkpoint control, we analyzed the ability of cells to repress DNA synthesis in the presence of DNA damage (radio-resistant DNA synthesis (RDS) assay). However, unlike ATM-deficient control cells, neither 53BP1-null nor 53BP1-reconstituted MEFs showed a significant RDS phenotype in response to 5, 10, or 20 Gy IR (Fig. S1 in supplemental materials and data not shown). These findings corroborated our former conclusion that 53BP1 does not play a major role in cell cycle checkpoint control (11).
Next, we investigated to what extent the C-terminal BRCT repeats contribute to the function of 53BP1 in DNA DSB repair. 53BP1 had been identified and named based on the in vitro interaction of its C terminus with the central DNA-binding domain of p53 (3). Although this original observation was made in yeast cells overexpressing these two proteins, subsequent structural analyses confirmed that the first BRCT motif together with the inter-repeat linker bind to the DNA-binding surface of p53 (26). We also observed an interaction of endogenous 53BP1 and p53 in human cells (Fig. 3B). However, the functional significance of this tandem BRCT domain has not been addressed.
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BRCT 1700-1972, Fig. 3A) were analyzed for residual P-H2AX foci 27 h after exposure to 2 Gy. Interestingly, expression of the BRCT truncation mutant completely rescued the repair defect in 53BP1-null cells (Fig. 3C). The same observation was made in cells transiently transfected with the
BRCT 1700-1972 construct (data not shown). Moreover, the average number of P-H2AX foci in unirradiated
BRCT cells was similar to that found in cells expressing full-length 53BP1. In contrast, 53BP1-deficient cells or cells that expressed the N-terminal deletion mutant (
1-1052) showed higher baseline levels indicative of a higher number of unrepaired endogenous lesions (Fig. 3C). The rescue effect of the
BRCT mutant was not restricted to a late stage of repair but could be seen as early as 1 h following irradiation with 1 Gy (see Fig. S2A in supplemental materials). In addition, a low dose G2/M checkpoint assay showed that the 53BP1 BRCT domains are not involved cell cycle checkpoint control (Fig. S2B in supplemental materials). Together, these findings indicate that the 53BP1 BRCT domains are not required for efficient DSB repair or checkpoint control.
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Dimer (
1231-1270) construct and performed a double-transfection assay. 293T cells were co-transfected with S-FLAG-tagged full-length 53BP1 and the HA-
Dimer mutant or an HA-tagged control plasmid. 48 h later, aliquots of the cells were collected. Cell lysates were immunoprecipitated with either anti-HA or anti-S antibodies and analyzed by Western blotting using anti-FLAG and anti-HA antibodies, respectively. S-FLAG-53BP1 FL could be readily detected in the HA-FL and HA-
1-1052 precipitates but not in the HA-
Dimer (
1231-1270) and HA-
1052-1302 precipitates. Correspondingly, HA-FL and HA-
1-1052, but not HA-
Dimer or HA-
1052-1302, co-immunoprecipitated with S-FLAG-FL 53BP1 (Fig. 4B). These data confirm that the region comprising residues 1231-1270 is required for 53BP1 oligomerization.
Next, we transfected 53BP1-null MEFs with the
Dimer (
1231-1270) construct and asked whether deletion of the oligomerization region would affect 53BP1 accumulation at the sites of DNA DSBs. Notably, cells expressing the deletion mutant still formed IRIF, although the deleted region resides within the region required for 53BP1 foci formation (Fig. 4, A and C). However, expression of
Dimer (
1231-1270) could not rescue the repair defect in stably transfected 53BP1-deficient MEFs (Fig. 4D). Collectively, these findings suggest that oligomerization of 53BP1 is critical for its function in DNA DSB repair.
| DISCUSSION |
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53BP1 has been shown to undergo a dynamic interaction with chromatin following DNA damage. Upon exposure of cells to ionizing radiation, 53BP1 becomes transiently immobilized at the chromosomal regions flanking the DNA DSBs (28). Binding and retention of 53BP1 to chromatin requires an intact Tudor domain, a recently characterized methyl-binding motif (21), as well as a less distinguished upstream region (20). Deletion of the Tudor domain or the preceding region prevent the repair function of 53BP1, indicating that accumulation of 53BP1 at break sites is an absolute requirement for efficient DNA DSB repair. Similarly, mutation of multiple phosphorylation sites at the 53BP1 N terminus impairs DSB repair in an incremental fashion. Although it remains to be determined how many phosphorylation sites have to conspire for full 53BP1 function, it appears that there is no sharp threshold for these phosphorylation events. DNA damage-induced phosphorylation of multiple PIKK sites has also been described in budding yeast Rad9 (29), which is thought to be the homologue of mammalian 53BP1 based on sequence similarities in its tandem BRCT and Tudor motifs. In budding yeast, phosphorylation of Rad9 is required for the survival of genotoxic stress by regulating the activation of the checkpoint kinase Rad53, the functional orthologue of the mammalian signal transducer Chk2 (29). Phosphorylated Rad9 recruits Rad53 to DNA lesions, thus enabling its phosphorylation by the PIKK Mec1. Phosphorylation of Rad53 triggers its activation, autophosphorylation, and subsequent release from Rad9 (30, 31). Similarly, 53BP1 has been shown to interact with Chk2 and promote its phosphorylation (11, 32, 33). However, unlike its yeast counterpart, Chk2 can still be activated in the absence of 53BP1 (11, 34), although the activation or phosphorylation of Chk2 is reduced in 53BP1-deficient cells. These data suggest that 53BP1 is not essential for Chk2 phosphorylation and/or activation following DNA damage, raising the possibility that a more complex and redundant signal adaptor system may be evolved in higher organisms. Indeed, although phosphorylation of Rad9 as well as Rad9-dependent phosphorylation of Rad53 require the C-terminal tandem BRCT domains in budding yeast (35), deletion of the BRCT domains in mammalian 53BP1 did not affect 53BP1 phosphorylation (data not shown) or 53BP1 function in DNA DSB repair. Moreover, homo-oligomerization appears to be the critical function of the Rad9 (budding yeast) or Crb2 (fission yeast) BRCT domains (35, 36), whereas oligomerization of 53BP1 depends on a small region outside of its BRCT domains.
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Unlike budding yeast Rad9 or fission yeast Crb2, which are key players in DNA damage checkpoint control (40, 41), 53BP1 appears to have a limited role in DNA damage checkpoints. Although small interfering RNA-mediated down-regulation of 53BP1 in human cancer lines led to defects in the G2/M and intra-S-phase checkpoints (32, 33), minor or no cell cycle checkpoint defects were detected in 53BP1-deficient mouse and chicken cells (11, 34). These differences between 53BP1 and its proposed yeast homologues could have evolved with the increasing number of BRCT-containing proteins in metazoa. For example, checkpoint proteins MDC1/NFBD1 and MCPH1/BRIT1 are BRCT-containing proteins that do not have any apparent homologues in yeast. These proteins might be evolved to carry out checkpoint functions, whereas 53BP1 gains more importance in DNA DSB repair.
Regardless of their differences, it is still tempting to speculate that the mechanism of action remained similar among 53BP1, budding yeast Rad9, and fission yeast Crb2. All three proteins appear to be oligomeric adaptors that enable/facilitate the activation of effector molecules in response to DNA damage. Further studies will be necessary to elucidate the new role of the 53BP1 BRCT motifs in the complex mammalian damage response network.
| FOOTNOTES |
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The on-line version of this article (available at http://www.jbc.org) contains two supplemental figures. ![]()
1 Both authors contributed equally to this work. ![]()
2 Present address: Department of Therapeutic Radiology, Yale University School of Medicine, P. O. Box 208040, New Haven, CT 06520. ![]()
3 To whom correspondence should be addressed: Dept. of Therapeutic Radiology, Yale University School of Medicine, P. O. Box 208040, New Haven, CT 06520. Tel.: 203-785-3758; Fax: 203-785-7482; E-mail: Junjie.Chen{at}yale.edu.
4 The abbreviations used are: DSB, double strand breaks; BRCT, BRCA1 C-terminal; PIKK, phosphoinositide 3-kinase-related protein kinase; ATM, ataxia telangiectasia mutated; MEF, mouse embryonic fibroblasts; Gy, grays; HA, hemagglutinin; IR, ionizing radiation; IRIF, IR-induced foci; FL, full length protein. ![]()
| ACKNOWLEDGMENTS |
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| REFERENCES |
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