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Molecular and Cellular Biology, October 2004, p. 8576-8585, Vol. 24, No. 19
0270-7306/04/$08.00+0 DOI: 10.1128/MCB.24.19.8576-8585.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Fengyu Qiao,1,
James B. Wilson,2 Anthony A. High,3 Melanie J. Schroeder,3 Peter T. Stukenberg,4 Amy Moss,1 Jeffrey Shabanowitz,3 Donald F. Hunt,3,5 Nigel J. Jones,2 and Gary M. Kupfer1,6*
Departments of Microbiology,1 Pediatrics,6 Biochemistry and Molecular Genetics,4 Pathology University of Virginia Health System,5 Department of Chemistry University of Virginia, Charlottesville, Virginia,3 School of Biological Sciences, University of Liverpool, Liverpool, United Kingdom2
Received 10 June 2004/ Returned for modification 5 July 2004/ Accepted 7 July 2004
| ABSTRACT |
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| INTRODUCTION |
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The one biological characteristic of FA is that cells in culture as well as the patients themselves exhibit hypersensitivity to DNA cross-linking agents. Indeed, such sensitivity results in chromosomal breakage, a phenotype utilized in a clinical test for FA. The reaction to cross-linking may also be manifest by the exhibition of G2 delay, which has been shown by some to be an S-phase defect in FA cells (12, 24, 28). Nonetheless, no biochemical mechanism has been elucidated to explain these findings.
Protein-protein interactions have shown that the FA proteins are interrelated and participate in at least two complexes (29, 36, 55). The first, termed the FA core complex, is nuclear and is comprised of FANCA, FANCC, FANCE, FANCF, FANCG, and FANCL (6, 9, 18, 34, 51). The second is made up of FANCD2 and FANCE. FANCD2 coimmunoprecipitates BRCA1 and is monoubiquitinated in an FA core complex, DNA damage, and S-phase-dependent fashion (19). In addition, BRCA2 has been shown to be the FANCD1 protein (21).
Only a few protein modifications have been reported for FA proteins, but they appear to be functionally important. FANCA, FANCD2, and FANCG have all been reported to be phosphorylated (16, 48, 55). For example, FANCA is phosphorylated only in wild-type, corrected, or mutant FA-D2 cells (1, 16, 40, 55). Also, it was recently found that FANCG is phosphorylated at serine 7 (40a). Knockout of this site results in impaired ability to correct FA-G cells.
Some evidence for activation of FA proteins has emerged in recent reports. The FANCD2 protein has been shown to be monoubiquitinated in response to DNA damage and during S phase (19). Others have shown links to S phase and to DNA repair complexes (1, 39, 42, 47). In addition, Pang et al. have demonstrated that STAT1 undergoes FANCC-dependent phosphorylation in response to
-interferon (37). Recent work has revealed that at least a subset of the FA proteins resides in the nucleus bound to chromatin, where increased protein binding occurs in response to DNA damage. In addition, it was shown that during the cell cycle the FA proteins detach from chromatin during mitosis and FANCG becomes phosphorylated, all the while remaining part of the complex (40).
It was previously shown that the G2-M kinase cdc2 binds to FANCC (27) and that it is part of the FA core complex, as detected by mass spectrometry (49). In this paper we have defined the sites in FANCG that are phosphorylated at mitosis. These events are tightly related to the cell cycle and regulate localization of the entire FA complex. By using mass spectrometry, subsequent mutagenesis of candidate amino acids, and phosphospecific antibodies we show that FANCG is phosphorylated at serines 383 and 387. In particular, S387 is phosphorylated by cdc2, which is consistent with previous findings that cdc2 is part of the FA core complex.
| MATERIALS AND METHODS |
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Cell culture. Cells were grown at 37°C in a 5% CO2 incubator. HeLa cells were grown in Dulbecco's modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS). FA-G mutant cells (326SV) were grown in DMEM plus 15% FBS. 293GPG producer cells were grown as described previously (40). HeLa cells were also transduced with pMMP-Flag-FANCA, and the resulting cells were selected with puromycin. EUFA143 FA-G mutant lymphoblasts were grown in RPMI 1640 plus 15% FBS. The Chinese hamster ovary (CHO) FANCG/XRCC9 mutant cell line NM3 was maintained in DMEM with 10% FBS, as described previously (54).
Immunoprecipitation. For whole-cell lysate, pelleted cells were extracted in 50 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1% Triton X-100, protease inhibitors (1 µg of leupeptin/ml, 1 µg of aprotinin/ml, 1 µg of pepstatin/ml, 50 µg of phenylmethylsulfonyl fluoride/ml), and phosphatase inhibitors (1 mM sodium orthovanadate, 1 mM sodium pyrophosphate). The extract was tested for protein concentration by the Bradford assay. Two milligrams of protein in 1 ml of the respective buffer containing protease and phosphatase inhibitors was incubated with 50 µl of anti-Flag affinity gel (Sigma) for 1 h at 4°C with rotation. The beads were then washed three times in Tris-buffered saline (TBS; 50 mM Tris-HCl [pH 8.0], 150 mM NaCl) containing 0.1% Triton X-100 and protease and phosphatase inhibitors and was dried. Fifty microliters of loading buffer was added (29). For the immunoprecipitations in which cdc2 was detected, Tween 20 was used as the detergent.
SDS-PAGE and immunoblotting. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was conducted, followed by gel transfer in 25 mM Tris and 200 mM glycine onto nylon-supported nitrocellulose. Filters were blocked for 1 h in 5% bovine serum albumin in TBS and then were incubated overnight at room temperature in TBS plus Tween 20 (TBS-T) containing primary antibody. Filters were then washed in TBS-T, incubated with horseradish peroxidase-linked secondary antibody (Amersham), washed again, and visualized by chemiluminescence (29).
Immunoblotting was performed with FANCG and FANCA antisera, as previously described (40). Rabbit polyclonal phosphospecific antibodies made against synthetic peptides were obtained from Upstate USA, Incorporated. Phosphospecific crude serum was successively passed over columns (Pierce) containing unphosphorylated and phosphorylated peptides, respectively. The antibody attached to the phosphorylated peptide column was eluted with glycine (0.1 M, pH 3.5).
Fusion protein expression and thrombin cleavage. Glutathione S-transferase (GST)-FANCG(N) terminal and GST-FANCG(C) proteins were expressed as previously described (41a). Thrombin was added to 1 µg of fusion protein in TBS (Tris 50 mM, 150 mM NaCl, pH 8.0), and the resulting mixture was incubated overnight at room temperature. After SDS-PAGE the gel was stained with Coomassie and a 14-kDa fragment from FANCG(C) was excised.
Mass spectrometry analysis. Trypsin in-gel digestion and extraction of peptides from the 14-kDa FANCG(C) band was performed as described by Shevchenko (44). Peptides were separated on microcapillary columns by reverse-phase nanoflow high-performance liquid chromatography (HPLC) (Applied Biosystems or Agilent HPLC) with a gradient consisting of 0.1 M acetic acid and 70% acetonitrile with 0.1 M acetic acid on either an Applied Biosystems or Agilent HPLC as previously described (43). Online analysis of the chromatographically separated tryptic peptides was performed by microelectrospray ionization interfaced to a ThermoFinnigan LCQ ion trap mass spectrometer. Data-dependent analysis was performed in which one full mass spectrometry scan from m/z of 300 to 2,000 was performed followed by five mass spectrometry/mass spectrometry scans of the most abundant ions present in the full mass scan. All mass spectrometry/mass spectrometry scans were performed with an isolation window of 3 Da (precursor m/z ± 1.5 Da) and using 35% collision energy.
ProteinFarm in-house software was used as an interface between the raw mass spectrometric information and a database searching program, SEQUEST (13). After deletion of poor quality spectra and conversion to .dta file format, SEQUEST was used to search against a FANCG database. The corresponding spectra of peptides with a cross-correlation score above 2 were manually confirmed for protein validation.
In vitro kinase assays.
In vitro kinase reactions were performed by incubation of a solution containing 1 µg of GST fusion proteins and 10 µCi of [
-32P]ATP and also containing either 1 µl of extract or 10 U of recombinant cdc2 (New England Biolabs) in 25 µl of buffer (50 mM Tris [pH 7.5], 10 mM MgCl2, 1 mM dithiothreitol, 10 µM cold ATP) (25, 53). The reaction was stopped by addition of equal volumes of loading buffer, and the entire content was run on SDS-PAGE. The gel was transferred to membrane (Biotrace) and was subsequently exposed to film for autoradiography and immunoblotting, respectively.
For peptide-based assays FANCG peptides were synthesized with a series of lysines at the N terminus and encompassing FANCG amino acids 378 to 392, with singly mutated peptides at S383A and S387A and doubly mutated peptide S383A/S387A. The reaction mixture consisted of buffer, 10 µCi of [
-32P]ATP, 10 µM cold ATP, and 10 U of recombinant cdc2 (New England Biolabs). The assay was incubated for specified times at 30°C. The reaction mixture was then spotted onto P81 paper (Whatman), which was then washed in 0.75% phosphoric acid and acetone. The paper was then analyzed by scintillation counter.
Cytotoxicity assays. For human fibroblast lines, cells were plated at density to achieve 10 to 100 colonies per plate in a 6-well dish. Mitomycin C (MMC) was added in the indicated doses. Midway through a 7-day incubation, the cells were washed and MMC was re-added. After being washed the cells were stained with crystal violet followed by extraction in SDS-methanol. Absorbance was measured at an optical density of 595 nm (OD595). For the hamster lines, the cells were similarly plated but the colonies were counted with the microscope.
For lymphoblasts, 2 ml of cells was seeded into flasks at a density of 2 x 105 cells/ml. MMC was added at the indicated doses (0 to 300 nM) with duplicate or triplicate flasks being prepared for each dose. Following 24 h of incubation at 37°C, a further 2 ml of growth medium was added, along with sufficient MMC to maintain the indicated (starting) dose. This process was repeated for a further 2 days (i.e., the volume of medium in the flask was doubled each 24 h while maintaining the MMC concentration). After four days, 4 ml of the resulting 16-ml cultures was transferred to new flasks. Twelve milliliters of fresh medium containing MMC was added, and the cells were incubated for a further 3 to 4 days. Resulting cell densities in each individual culture were determined by hemocytometer counts (a minimum of four counts for each culture) and were normalized to the cell numbers obtained in untreated cultures. MMC sensitivity in CHO cell lines was determined by clonal survival assays as described previously (54).
Cell cycle analysis. A total of 500,000 EUFA143 cells with various constructs of FANCG were treated with 1 µM MMC. After being washed in phosphate-buffered saline, the cells were resuspended in a solution containing 0.1% citrate, 0.03% NP-40, 100 µg of propidium iodide/ml, and 10 µg of RNase/ml and were analyzed by fluorescence-activated cell sorting (FACS) (45).
| RESULTS |
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-32P]ATP. The reaction was then run over SDS-PAGE. The proteins were transferred to membrane. Immunoblotting with anti-FANCG(C) and autoradiography showed that not only was the carboxyl terminus phosphorylated but also that the signal was chiefly restricted to a 14-kDa thrombin cleavage product (Fig. 2). The FANCG(C) mixture was also Coomassie stained to show the full-length FANCG(C) and the thrombin cleavage products.
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No obvious cdc2 consensus sequence for phosphorylation exists in any of the FANCG protein. In order to determine if any amino acids appeared likely to be phosphorylated, we analyzed FANCG (amino acids 374 to 504) by using a kinase predictor program (www.kinase.com). This analysis revealed that three amino acids were the most likely candidates for phosphorylation: S383, S387, and T487.
S383 and S387 are phosphorylated at mitosis. Based on the analysis of the most likely amino acids to be phosphorylated in FANCG (374 to 504), we used PCR-directed mutagenesis to mutate S383, S387, and T487 to alanine. Each mutant FANCG was then introduced into HeLa cells, which were then forced into mitosis by using nocodazole. Subsequent immunoblotting revealed that mutating S383A (lane 4) and S387A (lane 5) each eliminated one of the mitotic isoforms of FANCG (Fig. 3A). Indeed, the double S383A/S387A (lane 6) resulted in the removal of both isoforms, suggesting that S383 and S387 may be the phosphoamino acids of FANCG during mitosis. The T487A (lane 7) mutant did not affect the expression of the mitotic isoforms. None of the FANCG mutants affected the ability to bind to FANCA, suggesting that the FA complex remains intact, although decreased affinity for or diminished stability of FANCA may have resulted in the case of FANCG(S387A) (17).
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S383 and S387 are functionally important in FANCG. To show that S383 and S387 not only were phosphorylated but also were functionally important, we introduced Flag-FANCG(S383A), Flag-FANCG(S387A), and Flag-FANCG(S383A/S387A) constructs into FA-G mutant EUFA143 cells. Cell survival assays measuring sensitivity to MMC revealed that knockout of S383 and/or S387 resulted in the inability to fully correct FA-G mutant cells (Fig. 4A). Equal expression of mutant FANCG species was demonstrated by immunoblotting of FANCG in EUFA143 cell lysates (Fig. 4B). Ku80 immunoblotting showed equal loading. Thus, not only are S383 and S387 phosphorylated, but they are also functionally important to the FA pathway.
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Another phenotype associated with FA cells is increased G2 accumulation after MMC treatment (12, 24, 28). To assess the effect of these mitotic phosphorylation mutations on cell cycle, we subjected the EUFA143 cells to FACS analysis after MMC treatment. Corrected cells displayed markedly lower G2 accumulation than all the mutants (Fig. 4E). These data are consistent with the cytotoxicity results that S383 and S387 are functionally important phosphoamino acids.
Mitotic mutants fail to correct CHO cells. FANCG was first cloned as XRCC9 by using the radiation-sensitive mutant CHO cell line UV40, in which the FANCG homolog XRCC9 is mutant (10, 32). To assess if S383 and S387 have homologous amino acids, we performed alignments against murine and hamster versions of FANCG. This analysis revealed that both S383 and S387 are conserved in both murine and hamster fancg in highly homologous stretches of sequence (Fig. 5A). In contrast, T487 is not conserved.
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cdc2 phosphorylates FANCG at S387. Previous work has demonstrated that FANCC and cdc2 bind and that cdc2 can be detected in the FA core complex by mass spectrometry (8, 27). The data depicted in Fig. 2 show that cdc2 can phosphorylate a 14-kDa thrombin cleavage product of FANCG. To determine if any of the mitotic phosphoamino acids could be phosphorylated by cdc2, we mutated GST-FANCG(C) to alanine at S383, S387, or T487 by PCR-mediated mutagenesis. After thrombin cleavage, we performed an in vitro kinase reaction using recombinant cdc2. While cdc2 could phosphorylate GST-FANCG(S383A) (Fig. 6A, lane 3), albeit at lower intensity, it failed to phosphorylate GST-FANCG(S387A) (lane 4) at all, indicating that S387 was a phosphorylation site for cdc2. Use of recombinant polo-like kinase was able to phosphorylate either mutant form of FANCG, suggesting that it was not a likely kinase for FANCG at mitosis (data not shown). Fifteen amino acid peptides (amino acids 378 to 392) spanning the S383 and S387 sites of FANCG were synthesized that were variably mutated at serines 383 and 387. Using recombinant cdc2 in an in vitro kinase reaction, the wild-type peptide was phosphorylated more than 40-fold (Fig. 6B) by 60 min. Mutation at serine 383 resulted in a greater than 50% diminution of phosphorylation. Interestingly, both mutation at 387 and a doubly mutated 383/0.387 resulted in a completely phosphorylation-dead peptide.
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| DISCUSSION |
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Important examples exist in the literature, as the human SWI/SNF complex is phosphorylated at mitosis concomitant with its egress from the nucleus (35, 41). In addition, the BLM protein is also phosphorylated at mitosis and retains the ability to become dephosphorylated in response to DNA damage during G2-M (11). We will be exploring this same possibility for the FA core complex as well, given the excessive G2-M phenotype noted in FA after DNA damage. Phosphorylated FANCG and regulated exit of the FA core complex may be necessary for proper transit into mitosis. These complexes appear to be preserved and not simply degraded; they stand ready for reuse as cells reenter S phase (J. Mi, submitted for publication). Experiments which track individual complexes in pulse-chase fashion will be necessary to show just how long-lived FA complexes are.
The FA pathway appears to be tied to the cell cycle in some way. First, mutant FA cells accumulate in the G2 phase of the cell excessively after MMC treatment (12, 28). Second, we have shown that cdc2 and FANCC interact and that cdc2 can be detected in the FA core complex by mass spectrometry (27, 49). Third, recent data imply that the FA complex may function at an S-phase checkpoint (1, 2, 19, 38, 39, 42, 47). Thus, while the checkpoint machinery, which causes arrest in FA mutant cells, might be intact, the ability to coordinate a downstream repair function could be impaired.
The notion that S383 and S387 are important amino acids in FANCG is further borne out by the fact that these are conserved amino acids in the mouse and hamster. FANCG was first cloned from a CHO line hypersensitive to ionizing radiation and MMC (10, 32). Thus, the mouse and hamster would be attractive organisms for the performance of transgenic experiments for the expression of these FANCG mutants. Phosphorylation of FANCG is not the first such posttranslational modification to be described. FANCA phosphorylation was shown to be functionally important as well, as it is lacking in all but the FA-D complementation group cell lines (1, 26, 55). No obvious stimulation has been described for this event. Researchers have reported on FANCG phosphorylation (16, 40). We also have mapped a site at FANCG serine 7, but the stimulus for this is unknown. By contrast, FANCG phosphorylation is associated with mitosis. It remains to be seen whether the FA core complex plays a mechanistic role in G2-M or simply that phosphorylation of FANCG signals the end of DNA replication and, thus, the end of FA core complex function in that cell cycle. Our new phosphospecific antibodies should be useful in this regard as well as in immunofluorescence studies of mitotic cells.
| ACKNOWLEDGMENTS |
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We thank Sahana Ananth for technical assistance.
| FOOTNOTES |
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J.M. and F.Q. contributed equally to this work. ![]()
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