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J Biol Chem, Vol. 274, Issue 31, 22060-22064, July 30, 1999


Roles of Replication Protein A and DNA-dependent Protein Kinase in the Regulation of DNA Replication following DNA Damage*

Ya WangDagger , Xiang-Yang Zhou, Hongyan Wang, M. Saiful Huq, and George Iliakis

From the Department of Radiation Oncology, Kimmel Cancer Center of Jefferson Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 19107

    ABSTRACT
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS AND DISCUSSION
REFERENCES

Exposure of mammalian cells to DNA damage-inducing agents (DDIA) inhibits ongoing DNA replication. The molecular mechanism of this inhibition remains to be elucidated. We employed a simian virus 40 (SV40) based in vitro DNA replication assay to study biochemical aspects of this inhibition. We report here that the reduced DNA replication activity in extracts of DDIA-treated cells is partly caused by a reduction in the amount of replication protein A (RPA). We also report that the dominant inhibitory effect is caused by the DNA-dependent protein kinase (DNA-PK) which inactivates SV40 T antigen (TAg) by phosphorylation. The results demonstrate that RPA and DNA-PK are involved in the regulation of viral DNA replication after DNA damage and suggest that analogous processes regulate cellular DNA replication with the DNA-PK targeting the functional homologues of TAg.

    INTRODUCTION
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS AND DISCUSSION
REFERENCES

Inhibition of DNA replication in eukaryotic cells is one of the earliest effects of radiation to be reported. Camptothecin (CPT)1 and other DNA damage-inducing agents (DDIA) exert similar inhibitory effects on DNA replication in actively growing cells. It has been documented that a major component of this inhibition derives from a delay in the initiation of unreplicated origins (1, 2). Although this response was first observed several decades ago, the underlying molecular mechanisms remain largely unknown but ATM is thought to play an important role. More recently, evidence has been presented suggesting that the inhibition observed in DNA replication in response to DDIA is equivalent to the activation of a checkpoint in the S-phase and that it requires in yeast the products of MEC1 and RAD53 genes, homologues of ATM and Chk2, respectively (3-6). It is important to establish the mechanisms of regulation of DNA replication after DNA damage and the biochemical functions of the above genes in the process. We investigated the regulation of DNA replication after DNA damage using a simian virus 40 (SV40) based in vitro DNA replication assay, and have shown that extracts of cells exposed to DDIA have reduced activity for in vitro DNA replication and inhibit, in a dominant fashion, the ability of extracts from nontreated cells to promote in vitro DNA replication (7, 8).

In the SV40-based DNA replication assay, replication of plasmids containing the SV40 origin of DNA (ori+ DNA) replication is accomplished in vitro with either crude cytoplasmic extracts or proteins purified from such extracts with SV40 T antigen (TAg) as the only noncellular protein (9-13). It is believed that all cellular proteins required in this assay function in a manner similar to that in vivo (10-14). We have reported that the degree of inhibition of DNA replication in cells exposed either to x-rays or CPT is comparable with that measured in vitro using extracts prepared from cells exposed to these agents (7, 8). We subsequently focused on the molecular characterization of this inhibition. In the present study, we provide evidence that following DNA damage two processes contribute to the inhibition of in vitro DNA replication: reduced availability of replication protein A (RPA) and activation of DNA-dependent protein kinase (DNA-PK).

    EXPERIMENTAL PROCEDURES
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS AND DISCUSSION
REFERENCES

Cell Culture, X-ray Radiation, and CPT Treatment-- HeLa cell culture, x-ray radiation, and CPT treatment are as described (7, 8). MO59J cells were grown in Dulbecco's modified Eagle's medium-F-12 supplemented with 10% iron-supplemented calf serum (Hyclone).

Cytoplasmic Extract Preparation and Extract Modification-- Procedures used for cytoplasmic extract preparation either in large scale (109 cells) or in small scale (107 cells) have been described previously (7, 8, 15). In some experiments, double-stranded DNA (dsDNA) fragments (Stratagene, sonicated salmon sperm DNA, length range from 0.5 to 2 kilobase pairs) in TE buffer (10 mM Tris·Cl, pH 7.5, 1 mM EDTA) were added in the cytoplasmic extracts at 30 °C for 10 min. Wortmannin (Sigma) was added to the extracts (20 µM) at 30 °C for 10 min before assembling replication reactions. In some experiments, purified recombined RPA (rRPA) or TAg was added to the extracts at 30 °C for 10 min before assembling the reactions. RPA, wild type or mutant forms, were prepared as described (8). Detection of RPA was by Western blotting using standard procedures.

In Vitro Assay for DNA Replication-- The plasmid, pSV01Delta EP, carrying the minimal origin of SV40 DNA replication (ori+) was used as a template in the replication reactions. The reaction mixture was incubated at 37 °C for 1 h. Activity present in acid-insoluble material was determined (6, 7). Replication products were analyzed by agarose gel electrophoresis as described (7, 8).

Single-stranded DNA (ssDNA) Binding-- A 25-mer DNA oligonucleotide (5'-GATCCTCCTCACTACTTCTGGAATG-3' was end-labeled by T4 polynucleotide kinase using 5 pmol of [gamma -32P]ATP (Life Technologies, Inc.). Extracts were prepared as described above. Binding reactions were performed at 37 °C for 15 min with 30 fmol of radiolabeled probe (2000 cpm/fmol) and 10 µg of total cell protein as described (16). Bound and free probes were separated on 10% native polyacrylamide gels in 0.25 × TBE buffer (45 mM Tris borate, 1 mM EDTA). Gels were dried and exposed to autoradiography film. A monoclonal antibody against RPA 70 subunit was used during DNA binding reactions when indicated.

DNA-PK Activity-- DNA-PK activity was assayed by using a commercially available kit following the manufacture's protocols (SignaTECT DNA-PK assay system, Promega).

TAg Phosphorylation by DNA-PK-- The reaction mixture (25 µl) containing 1 µg of purified TAg, 20 units of DNA-PK (Promega), 25 mM HEPES-KOH, pH 7.5, 12.5 mM MgCl2, 20% glycerol, 0.1% Nonidet P-40, 1 mM dithiothreitol, and 50 mM KCl, [gamma -32P]ATP (3000 Ci/mmol, 10 µCi/µl, 0.05 µl/sample), 0.25 mM cold ATP, and (when indicated) 0.6 µg of ori+ plasmid DNA were incubated at 30 °C for 10 min. Then the reactions were either mixed with the 2× electrophoresis sample loading buffer and electrophoresed in 10% SDS-polyacrylamide gel electrophoresis for autoradiography or supplemented with 12.5 µl of termination buffer (7.5 M guanidine hydrochloride) for 32P phosphorylation counting. The gels for the former samples were subsequently dried and exposed to autoradiography film. The latter samples were collected onto Whatman GF-C glass fiber filters, washed with 10% trichloroacetic acid followed by repeated washing with deionized water. 32P phosphorylation was determined by liquid scintillation counting. The phosphorylation activity of TAg is calculated in picomoles of ATP/minute/20 units of DNA-PK.

    RESULTS AND DISCUSSION
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS AND DISCUSSION
REFERENCES

RPA, a ssDNA-binding protein, is a heterotrimeric complex with subunits of 70, 34, and 14 kDa required in the initiation stages of in vitro DNA replication and for multiple other processes of DNA metabolism (17-20). To test whether RPA plays a role in the inhibition of DNA replication in the in vitro DNA replication assay, we measured, by immunoblotting, its abundance in the extracts of cells treated with radiation or CPT. The amount of RPA p70, the subunit responsible for ssDNA binding, was reduced by approximately 50% (Fig. 1a, top). In line with a reduction in RPA p70, the binding activity of RPA to ssDNA was also reduced by about 50% in the same extracts (Fig. 1a, bottom, lanes 4 and 5). Post-translational modifications of RPA p34 have been implicated in cell cycle regulation and S-phase checkpoint activation (21, 22). We observed phosphorylation of RPA p34 (8), but could not establish alterations in the level of this subunit after DNA damage, probably due to the presence of a form not associated with the RPA holoenzyme (23). A monoclonal anti-RPA p70 antibody slowed the mobility of the DNA-protein complex in reactions assembled using cell extracts, as well as in reactions assembled with rRPA (Fig. 1b, lanes 2 and 4), confirming that the ssDNA binding protein is RPA. The amount of RPA p70 in the whole cell lysates of treated cells was similar to that of nontreated cells (data not shown). Therefore, we hypothesized that RPA may bind to DNA damage sites after exposure of cells to DDIA and be retained in the nucleus during extract preparation, reducing thus its level in the cytoplasmic component. In support of this hypothesis, addition of dsDNA fragments reduced RPA binding to ssDNA (Fig. 1c). It is possible that competition for RPA between damage sites and replication sites contributes to the inhibition of DNA replication in DDIA-treated cells.


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Fig. 1.   RPA DNA binding activities and in vitro DNA replication in cytoplasmic extracts of DDIA treated cells. a: top, Western blot for RPA p70 level in cytoplasmic extracts of HeLa cells (C, control; R, irradiated, CPT, CPT-treated). Extracts prepared as described under "Experimental Procedures." a: bottom, RPA binding to ssDNA measured by a gel-shift assay with the same extracts. rRPA was used as a positive control. b, a monoclonal anti-RPA antibody against p70 supershifts the DNA-protein complex in HeLa cell extracts and in a reaction assembled with rRPA. c, as in a, but for reactions incubated in the presence of different amounts of dsDNA fragments (0, 1, 5, 10, 20, 50, and 100 ng in lanes 1, 2, 3, 4, 5, 6, and 7, respectively). d, SV40 DNA replication reactions (25 µl) were assembled using the indicated amount of extracts (S-100) from untreated, irradiated (upper gel) or CPT-treated (lower gel) cells. Shown are the effects of added rRPA (2 µg) and wortmannin (20 µM) on DNA replication activity. Results of reactions assembled by mixing extracts of treated (R or CPT) and nontreated cells are also shown. Reactions assembled without TAg were included in all experiments and consistently showed only background levels of DNA synthesis (about 1 pmol incorporation; results not shown).

Although the amount of RPA was reduced in extracts from DDIA-treated HeLa cells, addition of rRPA could not recover DNA replication activity (Fig. 1d, compare lanes 7 and 8). Also, a small amount of such extracts mixed with control extracts strongly inhibited DNA replication (Fig. 1d, compare lanes 1 and 6). We discovered that the inhibition of DNA replication could be reversed when extracts of DDIA-treated HeLa cells were preincubated with wortmannin, a nonspecific inhibitor of protein kinases, and were supplemented with RPA (Fig. 1d, lane 10). A similar reversion of DNA replication inhibition was also observed when extracts of DDIA-treated cells were preincubated with wortmannin and mixed with control extracts (Fig. 1d, lane 11). Thus, the reduction in DNA replication activity observed in cytoplasmic extracts of cells exposed to ionizing radiation or CPT is the combined result of a reduction in RPA activity and an activation of a wortmannin-sensitive kinase. Other factors essential for in vitro SV40 DNA replication remain practically unaffected in such extracts.

As mentioned above, dsDNA fragments could reduce RPA binding to ssDNA. We examined whether addition of dsDNA fragments to extracts of nontreated cells could simulate some of the characteristics of inhibition observed in extracts of treated cells. The presence of dsDNA fragments in the extracts of nontreated cells inhibited DNA replication in a dose-dependent manner (Fig. 2a, HeLa), and the inhibition reached a plateau at 50 ng (Fig. 2a, HeLa). Addition of rRPA relieved somewhat the observed inhibition, but the effect was relatively small (Fig. 2a, HeLa, and Fig. 2b, lane 7). Pretreatment of extracts with wortmannin did not affect the inhibition caused by 50 ng of dsDNA (Fig. 2b, lane 6). However, addition of rRPA to wortmannin-pretreated extracts completely reversed DNA replication inhibition (Fig. 2b, lane 8). Thus, dsDNA fragments inhibit in vitro DNA replication via a mechanism similar to that identified for extracts of cells exposed to radiation or CPT, i.e. by sequestering RPA and by activating a wortmannin-sensitive kinase. In subsequent experiments, dsDNA fragments were added to the extracts of untreated cells to mimic the DNA damage effect.


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Fig. 2.   Effect of wortmannin and RPA on dsDNA-induced inhibition of in vitro DNA replication in reactions assembled with extracts of untreated cells. a, extracts of HeLa (open circle , ) or MO59J (down-triangle, black-down-triangle ) cells were preincubated with different amounts of dsDNA fragments for 10 min at 30 °C and were then added to the reaction mixture without (open circle , down-triangle) or with 2 µg of rRPA (, black-down-triangle ) for in vitro DNA replication. The results have been normalized to the replication activity measured in reactions assembled in the absence of dsDNA fragments. b, the products of in vitro DNA replication in reactions assembled with HeLa cell extracts in the presence or absence of 50 ng of dsDNA fragments. The effect of rRPA and wortmannin on DNA replication activity is indicated.

The inhibition of DNA replication after DNA damage is thought of as an active process that favors DNA repair. To identify the target of wortmannin in the extracts from DDIA-treated cells, we tested DNA replication activity in extracts of repair-deficient cell lines. MO59J cells are deficient in dsDNA break rejoining and sensitive to ionizing radiation-induced cell killing (24). We found that when MO59J cell extracts were supplemented with DNA fragments, both RPA binding to ssDNA (Fig. 1c, MO59J) and in vitro DNA replication (Fig. 2a, MO59J) were reduced to a degree similar to that observed in HeLa cell extracts. However, contrary to the results with the extracts of HeLa cells, RPA alone completely reversed this inhibition (Fig. 2a, MO59J, and Fig. 3a). These results indicated that the wortmannin-sensitive protein kinase was absent from MO59J cell extracts.


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Fig. 3.   Effect of DNA-PK on in vitro DNA replication. a, the products of in vitro DNA replication in reactions assembled with MO59J cell extracts in the presence of 50 ng of dsDNA fragments. b, DNA-PK activity in extracts of HeLa or MO59J cells (C, CPT, R, and C+dsDNA: control extracts plus 100 ng of DNA fragments). The DNA-PK activity is expressed as picomoles of [gamma -32P]ATP transferred to the substrate peptide/minute/milligram of protein. Data are the average from three independent experiments. c, 150 µg of MO59J cell extracts were preincubated with 100 ng of dsDNA fragments in the presence of 40 units of DNA-PK (Promega), at 30 °C for 10 min. Subsequently, 20 µM wortmannin was added, and the mixture used to assemble DNA replication reactions was incubated at 37 °C for 1 h in the presence of 2 µg of rRPA. Data are the average from three independent experiments.

It has been reported that MO59J cells lack any detectable DNA-PK activity (25) and have a low expression of ATM (26). It is well known that AT cells show reduced inhibition of DNA replication after DNA damage (27). At the concentration used (20 µM), wortmannin inhibits both DNA-PK and ATM kinase. To examine whether wortmannin acts in MO59J cell extracts by inhibiting ATM or by inhibiting DNA-PK, we prepared extracts from AT cells and performed experiments similar to those outlined with M059J cell extracts. Unexpectedly, restoration of DNA replication in AT cell extracts after addition of DNA fragments required both RPA and wortmannin, indicating that the inhibitory mechanism of in vitro DNA replication does not utilize ATM (data not shown). We measured, therefore, the DNA-PK activity in the extracts of DDIA-treated HeLa cells. The DNA-PK activity was higher in the extracts of treated HeLa cells than in control extracts when no activating dsDNA was added to the reactions (Fig. 3b, in control buffer). Importantly, addition of purified DNA-PK to M059J cell extracts supplemented with DNA fragments re-established the wortmannin requirement for the restoration of DNA replication activity (Fig. 3c). These results identify the wortmannin-sensitive kinase that inhibits DNA in vitro replication as DNA-PK.

DNA-PK (28, 29) is a serine/threonine kinase consisting of a 465-kDa catalytic subunit (DNA-PKcs) and a heterodimeric regulatory complex termed Ku. As targets of DNA-PK we considered two essential factors for in vitro SV40 DNA replication: RPA and TAg. Both proteins are known to be phosphorylated by DNA-PK and have been implicated in regulatory steps of DNA replication (29, 30). To investigate whether RPA or TAg contribute to the inhibition of DNA replication observed in extracts of DDIA-treated HeLa cells, we separately preincubated these proteins with a small amount of extract from treated HeLa cells to allow for possible post-translational modifications. The mixture was then used to assemble reactions with extracts of nontreated cells. Wortmannin was added to these reactions after the end of the preincubation period to neutralize the inhibitory effect of the treated cell extract that accompanied RPA or TAg. The results indicated that this preincubation did not alter RPA activity (data not shown), but dramatically reduced TAg activity for DNA replication (Fig. 4a). To further confirm that the modulation of RPA by DNA-PK has no effect on the DNA replication activity, we used a mutant RPA with a deletion in the N-terminal domain of RPA p34. The deletion removes DNA-PK phosphorylation sites without affecting the activity of the enzyme for in vitro DNA replication (31, 32). The effect of this mutant protein (data not shown) on DNA replication was practically identical to the effect of the wild type protein. This suggests that phosphorylation of RPA by DNA-PK does not modify its activity in supporting DNA replication in extracts of either treated or nontreated cells. Despite the fact that in vitro observations suggest no role for phosphorylated RPA in the regulation of DNA replication after DNA damage, the possibility that this form of RPA plays a role in vivo should be left open.


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Fig. 4.   Effect of DNA-PK on SV40 TAg. a, 75 µg of HeLa cell extract (C, CPT, R, and C+dsDNA) were preincubated with 0.5 µg of TAg at 30 °C for 10 min in half-strength DNA-PK sample buffer (Promega) in the presence of 5 mM ATP. Subsequently, wortmannin was added (20 µM), and the mixture in the presence of 100 µg of extracts from untreated HeLa cells was assembled DNA replication reactions at 37 °C for 1 h. Data are the average from three independent experiments. b, different amounts of DNA-PK (Promega) were preincubated with TAg at 30 °C as in a in the presence of 50 ng of dsDNA fragments for 10 min. Subsequently, wortmannin was added (20 µM), and the mixture was assembled DNA replication reactions in the presence of 150 µg of extracts from untreated HeLa cells without (open circle ) or with () 1 µg of additional TAg at 37 °C for 1 h. c, effect of ori+ DNA on the phosphorylation of TAg by DNA-PK. TAg was incubated with purified DNA-PK with or without ori+ DNA as described in b but with [gamma -32P]ATP (3000 Ci/mmol, 10 µCi/µl, 0.05 µl/sample) and 0.25 mM cold ATP. Top, autoradiograph of TAg phosphorylated by DNA-PK. Bottom, phosphorylation activity of TAg calculated in picomoles ATP/minute/20 units of DNA-PK. Data are the average from three independent experiments.

To confirm that the modification of TAg in extracts of treated HeLa cells was mediated by DNA-PK, we preincubated TAg with purified DNA-PK. The in vitro DNA replication activity decreased dramatically in reactions assembled using TAg preincubated with DNA-PK, and this inhibition could be completely reversed by nontreated TAg (Fig. 4b). Addition of [gamma -32P]ATP during the preincubation period confirmed phosphorylation of TAg by DNA-PK (Fig. 4c). Phosphorylation and inactivation of TAg for DNA replication was inhibited by the presence of ori+ DNA in the preincubation reaction (Fig. 4c), suggesting that binding of TAg to the replication origin reduced the phosphorylation of TAg and thus its inactivation.

The results presented here provide evidence that following DNA damage two processes contribute to the inhibition of in vitro DNA replication: reduced availability of RPA and activation of DNA-PK. Similar processes may also be involved and partly regulate cellular or viral DNA replication in vivo after exposure of cells to DDIA. DNA-PK may inhibit DNA replication by phosphorylating functional homologues of TAg. Recruitment of RPA to DNA damage sites may contribute to this down-regulation. The latter pathway may explain the inhibition of DNA replication in irradiated MO59J cells, which is found to be similar to that observed in cell lines with normal DNA-PK activity (24). The results shown in Fig. 2a support this hypothesis.

There is strong evidence that severe combined immunodeficiency mice have greatly reduced DNA-PK activity (33-35) and are as a result hypersensitive to radiation and deficient in DNA double strand breaks rejoining. Recently it has been reported that DNA-PK may play a role in tumor suppression (36). Here, we report yet another function of DNA-PK: the regulation DNA replication after DNA damage. Although our results did not implicate ATM in the inhibition of in vitro DNA replication following DNA damage, the evidence for an important role of this kinase in the regulation of DNA replication in vivo is overwhelming and suggests that multiple processes regulate DNA replication after DNA damage. The in vitro assay allowed us to study one specific aspect of this regulation.

    ACKNOWLEDGEMENTS

We thank Drs. M. J. Allalunis-Turner for MO59J cells, J. Hurwitz for pSV01Delta EP plasmid and hybridoma cells producing antibodies against RPA P34 or RPA P70, and M. Wold for p11d-tRPA and ptRPA 25 32Delta 1-33 constructs.

    FOOTNOTES

* This work was supported by Grants CA76203 (to Y. W.), CA56706 (to G. I.), and P30-CA56036 and T32-CA09137 (to X. Y. Z) from the NCI, DHHS.The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

Dagger To whom correspondence and reprint requests should be addressed. Tel.: 215-955-2045; Fax: 215-955-2052; E-mail: ya.wang@mail.tju.edu.

    ABBREVIATIONS

The abbreviations used are: CPT, camptothecin; DDIA, DNA damage-inducing agents; SV40, simian virus 40; RPA, replication protein A; DNA-PK, DNA-dependent protein kinase; ori+, SV40 origin of DNA; TAg, SV40 T antigen; rRPA, recombined RPA; ssDNA, single stranded DNA; dsDNA, double-stranded DNA; DNA-PKcs, DNA-PK catalytic subunit.

    REFERENCES
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS AND DISCUSSION
REFERENCES

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