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Biochemistry and Biophysics |
Department of Pathology, Brigham and Womens Hospital, Harvard Medical School, Boston, Massachusetts 02115
| ABSTRACT |
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| INTRODUCTION |
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BRCA1 is a component of the RNA holo-pol3 (1 , 2) . The holo-pol contains the core RNA polymerase II enzyme plus many accessory factors. BRCA1 fused to a DNA-binding domain activates transcription in cell-free systems to a similar extent as does the powerful activator, VP16 (3 , 4) . Many transcriptional regulators have been reported to interact with BRCA1, e.g., RNA Pol II, RNA helicase A, p53, STAT1, myc, CtIP, ZBRK1, ATF family members, and estrogen receptor (3 , 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15) . The presence of BRCA1 in the main mRNA synthesizing transcription machine, the holo-pol complex, and BRCA1 association with regulators of transcription highlight the importance of BRCA1 transcription function.
BARD1, the BRCA1-associated RING domain protein, has been identified as a protein that associates with the NH2 terminus of BRCA1 (16) . BARD1 protein has a RING finger motif and BRCT repeat, as has BRCA1. After DNA damage, BRCA1-BARD1 association is stimulated, and the polyadenylation of mRNA transcripts is repressed (17) . BRCA1 has ubiquitin polymerase activity by itself, and the BARD1 association significantly enhances the ubiquitin polymerase activity (18, 19, 20) . Specific targets of BRCA1-mediated ubiquitination have not been identified. The potential importance of ubiquitination in BRCA1 function is also suggested by the association of the NH2 terminus of BRCA1 with a de-ubiquitinating enzyme known as BRCA1-associated protein 1 (BAP1; Ref. 21 ).
Subcellular localization of BRCA1 changes are dynamically dependent on the cell cycle or DNA damage. In S-phase of cell cycle, BRCA1 localizes to discrete nuclear foci (dots) with BARD1 and Rad51 (22, 23, 24) . The protein complexes in the nuclear foci are unknown. It is unknown which BRCA1 domain is important for the structure of nuclear dots and whether BRCA1 changes of subcellular positions correlate with the holo-pol association.
In this study, we analyzed the BRCA1 association with holo-pol using deletion mutants of BRCA1. We found that BARD1 is a component of the holo-pol, and deletion of the BRCA1 NH2 terminus severely limits the association of the mutant BRCA1 protein with the holo-pol complex. This deletion mutant also fails to form nuclear foci, leading to the suggestion that the nuclear foci might contain holo-pol, although other protein complexes associated with the BRCA1 NH2 terminus may be responsible for the BRCA1 nuclear dot formation. Our data suggest that BRCA1 is involved in the function of Pol II in several ways via association with the holo-pol and possibly via subnuclear localization.
| MATERIALS AND METHODS |
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Adenovirus Construction.
HA-epitope tagged full-length and deleted mutants BRCA1 were inserted into AdEasy (Quantum Biotechnology, Inc.) shuttle vectors such that the BRCA1 gene would be under the control of the cytomegalovirus promoter. Full-length HA-epitope tagged BRCA1, with the tag fused to the NH2 terminus (HA-BRCA1) or to the COOH terminus (BRCA1-HA), were subcloned from constructs in the pcDNA3 vector (22)
. The 1302 deletion was constructed by digestion of HindIII and EcoRI from BRCA1-HA and then ligated for insertion of the following forward (F) and reverse (R) linkers: F, 5'-AGCTTATAATGACCGGTG-3'; and R, 5'-AATTCACCGGTCATTATA-3'. The 305770 deletion was constructed by digestion of EcoRI and KpnI from HA-BRCA1 and then ligated for insertion of the following forward (F) and reverse (R) linkers: F, 5'-AATTCGGACCAAAGAAGAAGCGTAAGACCGGTCTGGTAC-3'; and R, 5'-CAGACCGGTCTTACGCTTCTTCTTTGGTCCACCG-3'. The 775-1292 deletion has been described previously (25)
. The 15271863 deletion mutant was generated by digestion of full-length HA-BRCA1 of pcDNA35' HA-BRCA1 with HindIII and SacI, and then this fragment was inserted into the AdEasy shuttle vector. With each shuttle vector construct, recombination occurred in bacteria to recover adenoviral genomic DNA with the BRCA1 gene, and virus was recovered following transfection into 293A cells. In two of the deletion mutants,
305770 and
7751292, the linker that replaced the BRCA1 sequences also contained the nuclear localization sequence from the SV40 large T antigen, Pro-Lys-Lys-Lys-Arg-Lys.
Adenoviruses were prepared using standard protocols, and virus titers were determined by the TCID50 method (Quantum Biotechnologies, Inc.). The MOI for each virus, when using 293 cells was: HA-BRCA1 (full-length, NH2-terminal tag), 0.8 pfu/cell; BRCA1-HA (full-length, COOH-terminal tag), 1.0 pfu/cell; HA-BRCA1(
1302), 1.0 pfu/cell; HA-BRCA1(
305770), 0.6 pfu/cell; HA-BRCA1(
7751292), 0.4 pfu/cell; and HA-BRCA1(
15271863), 0.6 pfu/cell. The MOI for each virus, when using MCF-10A cells was: HA-BRCA1 (full-length, amino-terminal tag), 120 pfu/cell; HA-BRCA1(
1302), 130 pfu/cell; HA-BRCA1(
305770), 50 pfu/cell; HA-BRCA1(
7751292), 80 pfu/cell; and HA-BRCA1(
15271863), 80 pfu/cell. These MOIs were selected for equivalent levels of HA-tagged protein expression. With 293S cells infected at an MOI of
1, we estimated that
70% of the cells in the culture are infected. With MCF-10A cells infected at MOIs ranging from 50 to 130 pfu/cell, all cells in the culture were infected.
IP.
One hundred fifty µl of eluted protein from the Biorex70 column was immunoprecipitated with the specific antibody for human Med17 (26)
. Seven hundred fifty µl of binding reactions were incubated with rotation for overnight at 4°C in buffer H [20 mM Tris-OAc (pH 7.9), 1 mM EDTA, and 5% glycerol, 0.12 M KOAc, 0.1% NP40, 0.1 mM DTT, 0.2 mg/ml BSA, and 0.5 mM phenylmethylsulfonyl fluoride] in the presence of protein extract, 5 µl of antibody, and 20 µl of protein A beads. These steps are performed with or without antigenic peptide (0.1 mg/ml). With all IPs, supernatant was removed, and protein beads were then washed three times using 800 µl of wash buffer [120 mM KOAc, 20 mM Tris-OAc (pH 7.9), 0.1% NP40, 0.1 mM DTT, and 0.5 mM phenylmethylsulfonyl fluoride]. For Western blot analysis, samples were subjected to electrophoresis in 5% SDS-polyacrylamide gels and immunoblotted using the indicated antibodies.
Immunocytochemistry.
293A cells were grown in DMEM supplemented with 5% FBS, 100 µg/ml penicillin and streptomycin, and infected with recombinant adenoviruses to express full-length HA-BRCA1, HA-BRCA1(
1302), HA-BRCA1(
305770), HA-BRCA1(
7751292), and HA-BRCA1(
15271863). Cells were fixed for 10 min in PBS-buffered 3% paraformaldehyde and 2% sucrose solution, followed by 5-min permeabilization on ice in Triton buffer [0.5% Triton X-100 in 20 mM HEPES (pH 7.4), 50 mM NaCl, 3 mM MgCl2, and 300 mM sucrose]. HA-BRCA1 was visualized with affinity-purified monoclonal antibody, HA.11 (Covance) as primary antibody, and FITC-conjugated secondary antibody. All images were collected by confocal microscopy.
| RESULTS |
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7751292) has been described previously (25)
. Infected whole cell extracts were prepared by standard procedures (2)
. Expression levels of full-length BRCA1 and the four deletions of HA-tagged BRCA1 in whole cell extracts were examined by immunoblot for the HA-epitope (Fig. 1B)
5-fold higher than endogenous BRCA1 in these extracts (data not shown). Important for analyzing protein complexes containing an overexpressed protein, cell localization data revealed no pool of cells with abnormally localized HA-BRCA1 (see Fig. 5
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10% of the total tagged full-length BRCA1 protein (factoring in the large volume of the flow-through fraction). Fractionation results were similar for the BRCA1 containing the epitope tag fused to the COOH terminus (data not shown). On the other hand, 4050% of HA-BRCA1(
305770) and HA-BRCA1(
7751292) were fractionated in the 0.6 M KOAc fraction and about 4050% in the 0.15 M KOAc flow through. In the case of the COOH-terminal deletion mutant (
15271863), 65% was eluted in the 0.15 M KOAc flow through and about 30% in the 0.6 M KOAc peak, lower than the other two internal deletion mutants. By contrast, 98% of the NH2-terminal deletion mutant, BRCA1(
1302), was fractionated primarily in the 0.15 M KOAc flow through. In this sample, endogenous BRCA1 was mainly eluted in the 0.6 M KOAc fraction, as is normally observed (data not shown). Clearly, deletion of the BRCA1 NH2 terminus reduced the association of BRCA1 with the holo-pol-containing fraction 50-fold. The COOH-terminal deletion resulted in a minor,
2-fold, decrease in association with the holo-pol-containing fraction.
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1302), which had little fractionation in the 0.6 M salt elution, where the holo-pol is typically found. Using the holo-pol-specific, affinity-purified antibody against Med17 to immunopurify holo-pol from the flow-through fraction, we found that only a small amount of the Pol II in that fraction was associated with the holo-pol (Fig. 3A)
1302), which primarily eluted in the flow through, had only background levels of binding to the holo-pol in that fraction (Fig. 3A)
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15271863) required prolonged exposure to visualize Pol II. We infer from the last observation that BRCA1 may be involved in the turnover of Pol II.
We next fractionated the 0.6 M KOAc fractions that contain holo-pol using sucrose gradient sedimentation and analyzed by immunoblotting using antibody specific for the HA-tag and Pol II (Fig. 2C)
. The full-length protein sediments in two protein peaks, the fraction 5 complex and the holo-pol, consistent with our prior observations (25)
. The fractionation patterns of HA-BRCA1(
305770) and HA-BRCA1(
7751292) were similar, and they made three peaks of HA-BRCA1. As we described in a previous report (25)
, these three peaks are the >60S fraction 5 complex, the 30S holo-pol complex, and the smaller HUIC. The COOH-terminal deletion mutant (
15271863) sedimented similarly as did the full-length HA-BRCA1 in only two complexes, the fraction 5 complex and the holo-pol. Because the NH2-terminal deletion mutant, HA-BRCA1(
1302), was fractionated primarily in the 0.15 M KOAc flow through, we analyzed twice the amount of protein sample, and Western blots for HA-epitope required prolonged exposure to visualize HA-BRCA1. Although HA-BRCA1(
1302) was fractionated broadly, it has three sedimentation peaks, consistent with a subset of this deletion mutant associated with the holo-pol. Clearly, most of the BRCA1(
1302) protein does not cosediment with the holo-pol or the fraction 5 complex, although there is a minor peak of BRCA1(
1302) that cosediments with the holo-pol in fractions 1317. Recall that the vast majority of the expressed BRCA1(
1302) did not copurify with the holo-pol on the first chromatographic step, making the results of the sedimentation profile suggest that only a little of this BRCA1 mutant associates with the holo-pol. BRCA1(
1302) does cosediment in fractions 2127, which contain the HUIC. Because we have identified BARD1 as a component of the HUIC, this is surprising for the BRCA1 mutant, which should not bind BARD1. The level of purification in fractions 2127 was not high, indicating the likelihood that the cosedimentation of BRCA1(
1302) with the HUIC was coincidental. Fractionation patterns of Pol II were consistent with previous observations of a broad peak typically centering on fraction 15. The pattern of the Pol II sedimentation was largely unchanged by the expression BRCA1 deletion mutants. The one exception was in the extract expressing HA-BRCA1(
305770); the peak of Pol II shifted slightly to a lower molecular weight, suggesting an alteration in the polymerase content in the holo-pol complex. These results suggest that, with the exception of HA-BRCA1(
1302), the deletion mutants of HA-BRCA1 copurify with holo-pol over two purification steps.
BARD1 Is a Component of holo-pol, and the NH2-Terminal and the COOH-Terminal Regions of BRCA1 Are Both Important for Association with the holo-pol.
Next, we tested whether these BRCA1 deletion mutants were truly associated with the holo-pol by IP using the holo-pol-specific antibody directed against Med17 (26)
. The antibody was affinity purified, and the input protein was the Biorex70 0.6 M KOAc eluate (Fig. 3B)
. All samples are evaluated in threes: 10% input protein was in the first lane of each trio (Lanes 1, 4, 7, 11, and 14), and IP with Med17 in the presence of its antigenic peptide was in the second lane of each set (Lanes 2, 5, 8, 12, and 15), and Med17 IP in the absence of blocking peptide in the third lane of each set (Lanes 3, 6, 9, 13, and 16). The use of the antigenic peptide in the second lane of each was to control for the specificity of the IP. Immunoblots were stained using antibodies specific for the HA epitope to detect overexpressed BRCA1 (top), endogenous BRCA1 (second from top), Pol II (third panel), SWI/SNF subunit BRG1 (fourth panel), and the BRCA1-interactor BARD1 (bottom panel). With the full-length HA-BRCA1 (Lanes 13), we observed HA-BRCA1, Pol II, BRG1, and BARD1, all associated with the Med17. The first three of these confirmed published results (1
, 2)
, but the identification of BARD1 associated with the holo-pol has never been demonstrated. On Biorex70 column fractionation, the total cellular BARD1 separates into the flow through and 0.6 M eluates, and it was fractionated broadly in sucrose sedimentation, including holo-pol-containing fractions. Furthermore, these fractionation patterns of BARD1 did not change by overexpressing any of the BRCA1 full-length or deletion proteins (data not shown). These results suggest that, because BARD1 can be found in protein fractions that do not contain BRCA1, not all of the BARD1 in the cells is bound to BRCA1. Rad50, although present in the input sample, was negative for immunopurification by Med17 antibody (data not shown).
We next asked whether the BRCA1 deletion mutant proteins competed with endogenous BRCA1 for binding to the holo-pol. When analyzing the full-length HA-BRCA1, it comigrated with endogenous BRCA1, making it impossible to determine which BRCA1 protein was associated with the holo-pol. The deletion mutants HA-BRCA1(
305770) and HA-BRCA1(
7751292) were not different from the full-length BRCA1 with regard to association with Med17. Of interest in this analysis, because these mutants migrate faster than the endogenous BRCA1, we observed that these mutants competed with the endogenous BRCA1 for binding to the holo-pol (Fig. 3
, Lanes 49). This result suggests that there exist in holo-pol complex a limited number of BRCA1 binding sites, and the overexpressed BRCA1 protein competed with the endogenous BRCA1 for binding. This competition for BRCA1 binding to the holo-pol attests to the specificity of the interaction between BRCA1 and the transcription complex.
The NH2-terminal-deleted HA-BRCA1(
1302) was not enriched in the 0.6 M KOAc fraction (Fig. 2)
; thus, this mutant was not significantly present in the input. The small amount of HA-BRCA1(
1302) present in this sample does in fact appear to be associated with the holo-pol because a weak band was present in the IP (Lane 13). This residual binding is consistent with our prior observation that the COOH terminus of BRCA1 is important for binding the holo-pol (2)
. The very low amounts of HA-BRCA1(
1302) in the sample suggest, however, that there exist two domains of BRCA1 important for binding to the holo-pol, the NH2 terminus and the COOH terminus. The NH2 and COOH termini are partially redundant for association with the holo-pol, but much less of the total cellular BRCA1(
1302) was in the holo-pol than was true for the other mutants. Endogenous BRCA1 was fractionated in the 0.6 M KOAc fraction and was not competed by low amount of HA- BRCA1(
1302) for binding the holo-pol (Fig. 3
, Lanes 1113). These BRCA1 purification and binding data, taken together with the presence of BARD1 in the holo-pol, suggest that both the BRCA1 NH2 terminus and the COOH terminus are very important for association with the holo-pol.
The COOH-terminal-deleted HA-BRCA1 was associated with the Med17-containing holo-pol complex, and a low amount of endogenous BRCA1 was associated with the Med17 complex. By comparing the level of competition with endogenous BRCA1 for binding the holo-pol complex, the deletion mutants HA-BRCA1(
305770) and HA-BRCA1(
7751292) bound to the holo-pol with higher affinity than did the COOH-terminal-deleted BRCA1. This result suggests that the COOH-terminal deletion does in fact bind to the holo-pol, possibly because of the interaction of the NH2 terminus of BRCA1 with the holo-pol, although the amount bound with holo-pol is reduced relative to the deletion mutants HA-BRCA1(
305770) and HA-BRCA1(
7751292) (Fig. 3
, Lanes 1416). Importantly, deletion of the NH2 terminus of BRCA1 was found to have the most profound effect on associating with the holo-pol.
The NH2-Terminus of BRCA1 Is Important for Formation of Nuclear Dots.
Because BRCA1 has known to localize in nuclear dots in the S-phase of cell cycle (27)
, we tested which domain of BRCA1 affects this localization. 293A cells were infected with recombinant adenoviruses to express full-length HA-BRCA1 and each deletion variant (Fig. 4)
. Cells were stained with the anti-HA, monoclonal antibody HA.11, to visualize the expressed tagged HA-BRCA1 (Fig. 4, AE)
and stained with 4',6-diamidino-2-phenylindole to show the nucleus (Fig. 4, FJ)
. Expression of full-length HA-BRCA1, HA-BRCA1(
305770), HA-BRCA1(
7751292), and HA-BRCA1(
15271863) and followed by probing cells using anti-HA antibody detected nuclear dots in
10% cells. In all of these cases, we detected diffuse nuclear staining with 3050 foci of recombinant BRCA1. Staining of cells expressing HA-BRCA1(
1302) revealed only homogenous nuclear staining without foci (Fig. 4B)
. The staining patterns were specific because immunofluorescence was negative when we used anti-HA antibody preincubated with its antigenic HA-peptide for 1 h on ice (data not shown). Staining by another monoclonal anti-HA antibody, 12CA5, and anti-BRCA1(Ab-1) yielded similar results. The Ab-1 antibody detected endogenous BRCA1 in nuclear foci, even in cells expressing HA-BRCA1(
1302), indicating that this mutant did not interfere with dot formation (data not shown). The results in Fig. 4
were typical for those seen on each monolayer, but accurate counts of stained cells were not possible using the 293 cells because these adhered poorly to the solid support. These results suggest that the NH2 terminus of BRCA1, the deletion of which results in the most severe loss of interaction with holo-pol complex, is important in the formation of nuclear dots in S-phase.
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1302), which does not copurify with the holo-pol, was exclusively nuclear, regardless of leptomycin B. This was likely attributable to deletion of the characterized nuclear export sequence in BRCA1 residues 89100 (28)
. This result argues strongly that the failure of the BRCA1(
1302) to associate with the holo-pol is not merely the result of abnormal shunting of the protein to the wrong cellular compartment but rather the deletion mutant is present in high concentration in the vicinity of the holo-pol. The other deletion mutants, which readily associate with the holo-pol, were observed to have the same subcellular distribution and response to leptomycin B, as did the full-length BRCA1 (Fig. 5A)
We determined the number of MCF-10A cells that form BRCA1 speckles when overexpressing tagged BRCA1 deletion proteins (Fig. 5B)
. We found that BRCA1-associated nuclear speckles were present in
40% of the cells with nuclear staining when expressing full-length HA-BRCA1, BRCA1(
305770), BRCA1(
7751292), or BRCA1(
15271863) (Fig. 5B)
. The subcellular distribution and nuclear foci formation results were similar to those obtained in 293 cells, from which the protein preparations were derived, but in the latter case accurate cell counts were not possible because of the propensity of the cells to float.
| DISCUSSION |
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BARD1 was found in multiple chromatographic fractions, even some fractions with undetectable BRCA1. BARD1 was associated with the holo-pol complex, BARD1 was purified by holo-pol-specific antibody, and this association was not affected by overexpression of deletion mutants of BRCA1.
The results from the various purification data are summarized in Fig. 6
. The NH2-terminal deletion mutant of BRCA1 interacts poorly with Med17-containing holo-pol complex. Instead, endogenous BRCA1 is interacting with holo-pol complex in this sample. This deletion removes the characterized binding domains for BARD1, BAP1, and part of the domain for binding p53 (6
, 16
, 21)
. It was not determined which component of the holo-pol binds to the NH2 terminus of BRCA1, although BARD1 is a good candidate because it is in the holo-pol and it binds to this domain of BRCA1. It was surprising that deletion of the NH2 terminus of BRCA1 resulted in a >50-fold reduction in holo-pol association, whereas deletion of the BRCA1 COOH-terminal domain resulted in a 2-fold reduction in copurification with the holo-pol. Our published experiments have demonstrated that the COOH terminus of BRCA1 can bind to the holo-pol complex (1
, 2)
. Both domains can independently bind to the holo-pol. Deletion of the BRCA1 COOH terminus does not abrogate interaction with the Med17-containing holo-pol complex, because the BRCA1 NH2 terminus is still present in BRCA1(
15271863). Previous results in which deletion of the COOH-terminal 11 amino acids of BRCA1 resulted in diminished binding to the holo-pol (1)
, probably reflect a smaller fraction of the BRCA1 association with the holo-pol. Such a possibility is consistent with our observation of a quantitative decrease in HA-BRCA1(
15271863) copurifying with the holo-pol. Alternatively, the 11 amino acid truncation could cause misfolding and thus result in a more severe effect than the larger deletion. Previous analyses of the BRCA1 COOH terminus used in vitro binding assays, which reveal domains that function positively to bind. By contrast, in this study, we analyzed deletion mutants in the context of the rest of the BRCA1 and not a fusion protein. The results of this study revealed that although the COOH terminus could bind to the holo-pol, deletion of the NH2 terminus had a more profound effect on holo-pol association.
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| ACKNOWLEDGMENTS |
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| FOOTNOTES |
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1 This work was supported by Research Grant RPG-99-097-01 from the American Cancer Society, a grant from the Elsa U. Pardee Foundation (to J. D. P.), and Fellowship Grant DAMD17-00-0164 from the Department of Defense Breast Cancer Research Program (to N. C.). ![]()
2 To whom requests for reprints should be addressed, at Department of Pathology, Brigham and Womens Hospital, 75 Francis Street, Boston, MA 02115. E-mail: jparvin{at}rics.bwh.harvard.edu ![]()
3 The abbreviations used are: holo-pol, polymerase II holoenzyme; Pol II, polymerase II; BARD1, BRCA1-associated RING domain protein; HUIC, hydroxyurea-induced complex; IP, immunoprecipitation; MOI, multiplicity of infection; pfu, plaque-forming unit. ![]()
Received 12/14/01. Accepted 5/22/02.
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M. Benezra, N. Chevallier, D. J. Morrison, T. K. MacLachlan, W. S. El-Deiry, and J. D. Licht BRCA1 Augments Transcription by the NF-{kappa}B Transcription Factor by Binding to the Rel Domain of the p65/RelA Subunit J. Biol. Chem., July 11, 2003; 278(29): 26333 - 26341. [Abstract] [Full Text] [PDF] |
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