Main

Damaged DNA and the mitotic apparatus (mitotic spindle, centromeres and centrosome) represent major sites of poly(ADP-ribose) accumulation5. The specific targeting of proteins to these sites is dependent on the recognition of poly(ADP-ribose) (PAR) by defined PAR-binding motifs or modules. Until now, only two such motifs have been described. One is found in proteins such as p53, histones and XRCC1, and is characterized by a 20 amino acid motif containing a basic residue-rich cluster and a pattern of hydrophobic amino acids interspersed with basic residues6,7; the second is a conserved ∼190-residue domain known as the macro domain, and is found in the poly(ADP-ribose) polymerases PARP9, PARP14 and PARP15 (ref. 8).

CHFR is a ubiquitin ligase that functions in the antephase checkpoint by actively delaying passage into mitosis in response to microtubule poisons9,10. It is frequently mutated in human epithelial cancers10, and CHFR-deficient mice develop spontaneous tumours11,12, but a detailed understanding of its function is still emerging. Analysis of the primary sequence of CHFR revealed a conserved putative C2H2 zinc-finger motif at its carboxy terminus. Using homology and pattern searches, similar motifs were found in other eukaryotic DNA repair and checkpoint control proteins (Supplementary Fig. 1a, b). Similarities between a subset of these proteins have been noted13,14,15, but the function of the motif was not elucidated.

The putative C2H2 zinc-finger is separated by a 6–8 amino acid spacer and has the consensus [K/R]xxCx[F/Y]GxxCxbbxxxxHxxx[F/Y]xH (Supplementary Fig. 1b). On the basis of the data that follows, the motif will be referred to as PBZ. The phylogenetic distribution of the PBZ motif is limited to eukaryotes, excluding yeast, and, as such, its occurrence coincides with the presence of poly(ADP-ribose) polymerases (PARPs). Because the majority of proteins containing PBZ motifs are either directly or indirectly associated with PAR metabolism, we analysed the PAR-binding ability of two human representatives, CHFR and APLF. APLF (C2 or f13) is an FHA-domain protein involved in the DNA damage response13,14,15. The modular structures of CHFR and APLF revealed one and two PBZ motifs, respectively (Fig. 1a). Additionally, Caenorhabditis elegans DNA ligase III, containing a single PBZ motif at its C terminus, was also analysed. Purified recombinant proteins were dot-blotted onto a nitrocellulose membrane and tested for their ability to bind 32P-labelled poly(ADP-ribose). PAR binding was observed with all three proteins, and was resistant to extensive washing with 1 M salt (Fig. 1b, lanes 1–3). The interaction with PAR was equal to, or better than, that observed with XRCC1, which binds PAR with high affinity (lane 4)6,16.

Figure 1: PAR binding/modification mediated by the PBZ zinc finger motif.
figure 1

a, Schematic diagram of the PBZ motifs in CHFR and APLF. Mutations are indicated in red. b, PAR binding by APLF, CHFR and C. elegans DNA ligase III (lig3) as determined by dot-blot analysis. XRCC1 and BSA were used as controls. c, PAR-binding is abolished by mutations in the PBZ motif. WT, wild type. d, PAR-binding is dependent on zinc. e, Analysis of PAR binding by surface plasmon resonance. f, In vitro poly(ADP-ribosyl)ation of APLF and CHFR by PARP1. g, PAR binding by the APLF and CHFR PBZ mutants.

Full size image

Mutation of the conserved cysteine residues in the single putative PBZ motif within CHFR (Fig. 1a, indicated in red) resulted in the inability of the CHFR*PBZ mutant to bind PAR (Fig. 1c, compare lanes 5 and 6). With APLF, PAR-binding was abolished by mutation of both putative zinc-finger motifs (APLF*PBZ), but not by mutation of a single motif (APLF*PBZ1 and APLF*PBZ2) (Fig. 1c, lanes 1–4). The tandem motifs of APLF, when purified as a recombinant glutathione S-transferase (GST)-tagged protein, exhibited PAR binding (Fig. 1c, lane 7).

Depletion of zinc, by incubation of wild-type CHFR and APLF with the metal-chelating agent EDTA, resulted in a severe reduction in the ability of each protein to bind PAR (Fig. 1d, lanes 2 and 5). Subsequent incubation with excess zinc, however, restored PAR-binding ability to CHFR (lane 6) and C. elegans DNA ligase III (data not shown), but not to APLF which was irreversibly inactivated (lane 3). We conclude that PAR binding is dependent on the presence of zinc, and define this newly identified motif as a PAR-binding zinc-finger or PBZ module. To our knowledge, this is the first description of a zinc finger that is involved in PAR binding.

Interactions between PAR and recombinant CHFR and APLF were further analysed by surface plasmon resonance (Fig. 1e). Wild-type CHFR and APLF bound PAR efficiently, and the kinetics of binding and dissociation are shown in Fig. 1e and Supplementary Table 1. The interactions of PAR with CHFR and APLF were significantly more stable than that observed with XRCC1. The binding of PAR by CHFR*PBZ or APLF*PBZ was not detectable (Fig. 1e).

To investigate whether APLF and CHFR were themselves substrates for poly(ADP-ribosyl)ation, they were incubated with PARP1 in the presence of 32P-labelled NAD (Fig. 1f). PARP1 poly(ADP-ribosyl)ated wild-type APLF and CHFR, as well as APLF*PBZ2 (lanes 2, 3 and 5), whereas the CHFR*PBZ and APLF*PBZ mutants remained unmodified (lanes 4 and 6). Thus, an intact PBZ motif is required for poly(ADP-ribosyl)ation.

Mutational analysis of the PBZ motif revealed that the conserved arginine preceding the zinc finger was required for PAR-binding in both APLF (APLF*R1) and CHFR (CHFR*R1) (Fig. 1g, lanes 6 and 12). Furthermore, mutations at residues following the second cysteine of PBZ compromised PAR binding to CHFR*R2, CHFR*Q, APLF*Y, APLF*R2 and APLF*R2K (lanes 2, 3, 8, and 10, and Supplementary Fig. 2). All APLF mutants deficient for PAR-binding were not poly(ADP-ribosyl)ated by PARP1 in vitro (Supplementary Fig. 2).

We next determined whether APLF and CHFR associate with PAR in vivo. When Flag-tagged APLF and CHFR proteins were transiently expressed in HEK293T cells, we found that the Flag pull downs of each protein contained PAR, as detected by western blotting (Fig. 2a, lanes 3 and 7). The PBZ-inactivating mutations severely reduced or abolished the associations of both APLF and CHFR with PAR (Fig. 2a, lanes 4 and 8, and Fig. 2b, lanes 3, 4, 6 and 7). Interestingly, PARP1 was present in both the APLF and the APLF*PBZ immunoprecipitates (Fig. 2a, lanes 3 and 4), but not in the CHFR pull downs (lanes 7 and 8). We also found that expression of green fluorescent protein (GFP)–APLF and GFP–CHFR fusion proteins in HEK293T cells resulted in the formation of distinct nuclear foci that co-localized with PAR (Fig. 2c), even in the absence of DNA damage. The co-localization of PAR with GFP–APLF and GFP–CHFR, but not with their PBZ mutant derivatives, indicates that the overexpressed wild-type proteins are poly(ADP-ribosyl)ated in vivo. We do not, however, rule out the possibility that the overexpressed proteins might recruit other poly(ADP-ribosyl)ated proteins leading to the observed signals. In control experiments, PAR failed to localize with GFP when expressed without CHFR or APLF (data not shown).

Figure 2: Interactions of APLF and CHFR with PAR are mediated by the PBZ motif.
figure 2

a, Immunoprecipitation of Flag-tagged APLF and CHFR from HEK293T extracts. Inputs (10%) and Flag-precipitates were blotted using PAR, APLF and CHFR antibodies. Ubi-CHFR indicates ubiquitylated CHFR. b, Association of PAR with wild-type and PBZ-mutated Flag-tagged APLF. c, Co-localization of wild-type APLF and CHFR proteins with PAR in HEK293T cells transfected with GFP-tagged APLF and CHFR wild-type and mutant constructs. Scale bar, 10 µm.

Full size image

To examine the functional importance of the PBZ motif, we analysed its requirement for the CHFR-dependent antephase checkpoint in Ptk1 cells. Following treatment with microtubule poisons (such as colcemid), late G2 and prophase cells with an intact checkpoint delay entry to mitosis and decondense their chromosomes, while the nuclear envelope remains intact9,17. However, a CHFR deletion mutant lacking the amino-terminal FHA domain (CHFRΔFHA) acts as a trans-dominant inhibitor of endogenous CHFR function10, and its expression abrogates the mitotic delay. We found that mutations of the cysteine residues in the PBZ motif of CHFRΔFHA (CHFR*PBZΔFHA) abolished its ability to act as a trans-dominant inhibitor (Fig. 3a, b, and Supplementary videos 1 and 2). All prophase cells expressing CHFRΔFHA failed to exhibit an antephase checkpoint when exposed to colcemid (9 out of 9 cells), whereas those expressing CHFR*PBZΔFHA returned to interphase (6 out of 6 cells). Thus, the ability of CHFRΔFHA to act as a dominant negative relies on PBZ, which in turn suggests an involvement of the PBZ motif in regulating CHFR actions.

Figure 3: Checkpoint functions, but not ubiquitylation, of CHFR are affected by PBZ mutations.
figure 3

a, Ptk1 cells expressing CFP-tagged CHFRΔFHA (top panels) or CHFR*PBZΔFHA (lower panels) were treated with 15 µM colcemid (0 min) and their behaviour was monitored by time-lapse DIC and fluorescence microscopy at 3-min intervals. Scale bar, 10 µm. b, Quantification of the data from a. c, HeLa cells expressing wild-type or mutant CHFR and untransfected cells were treated with colcemid and the mitotic indices (±s.d., n = 3) were determined at two-hourly intervals. d, Auto-ubiquitylation of CHFR does not impair PAR-binding. Wild-type and mutant CHFR were ubiquitylated in vitro and analysed for PAR binding (upper panels) or by western blotting (lower panels). e, Analysis of Ptk1 cells pre-treated with the PARP inhibitor KU-0058948 (1 µM), or PBS for 1 h, and challenged with 15 µM colcemid. Their behaviour was monitored by time-lapse DIC.

Full size image

HeLa cells do not express CHFR and therefore lack an intact antephase checkpoint9,18, leading us to use them as the parental cell line in a direct test of the physiological significance of PBZ in the antephase checkpoint. When HeLa cells were transfected with either wild-type or PBZ-mutated cyan fluorescent protein (CFP)-tagged CHFR and treated with colcemid, we found that expression of wild-type but not mutant CHFR restored the checkpoint defect, as indicated by a decrease in the mitotic index (Fig. 3c). Importantly, the auto-ubiquitylation activity of CHFR, both in vivo and in vitro, was unaffected by mutations in the PBZ motif (Fig. 2a, lanes 7 and 8, and Fig. 3d, lanes 7 and 11). Furthermore, auto-ubiquitylation of wild-type CHFR did not impair its PAR-binding potential (Fig. 3d, lanes 1 and 2). Hence, the disparity between CHFR and its PBZ-mutated variant in the antephase checkpoint most probably reflects differences in their PAR-related functions.

Finally, a direct link between PAR metabolism and the antephase checkpoint was established by treating Ptk1 cells with the specific PARP inhibitor KU-005894819. We found that the PARP inhibitor compromised the ability of Ptk1 cells to delay nuclear envelope breakdown in response to microtubule poisons (Fig. 3e and Supplementary video 3). Instead, the majority of the treated cells continued into mitosis. These results show that inhibition of PAR synthesis compromises the antephase checkpoint, and demonstrate a connection between the PAR-related functions of PBZ and its requirement for CHFR checkpoint regulation.

In this work, we have defined a novel PAR-interaction motif present in a number of proteins associated with the DNA damage response and checkpoint regulation. Although two functionally equivalent domains have previously been reported, this is the first example of a zinc-dependent motif implicated in PAR binding and poly(ADP-ribosyl)ation. Zinc fingers were originally identified as nucleic acid recognition elements20, but can also mediate protein–protein interactions21. Owing to its chemical composition, PAR may be considered as the third type of nucleic acid3, a notion supported by the base stacking and hydrogen-bonding potential of its constituting ADP-ribose residues. Moreover, long PAR chains were postulated to adopt helical conformations, reminiscent of those found with DNA and RNA22. In light of this, the evolution of zinc-fingers into PAR-binding elements may seem a suitable consequence of diversification.

The use of the PBZ motif is widespread amongst eukaryotes, and is particularly prominent in Dictyostelium discoideum (Supplementary Fig. 1). The absence of the motif in organisms lacking PARP metabolism (such as prokaryotes and yeasts) may suggest the co-evolution of this motif with PARPs. Importantly, all the PBZ motifs identified in this study were found in proteins potentially regulated by poly(ADP-ribosyl)ation. The majority are DNA damage response proteins, including several PARPs, PARP-related proteins, Ku, Chk2, RAD17, APLF, and proteins involved in single-strand break and base-excision repair (for example, tyrosyl-DNA phosphodiesterase, DNA ligase III and uracil DNA glycosylase). The modulation of DNA ligase III activity by PAR and interactions with poly(ADP-ribosyl)ated PARP1 have been described previously23. Similarly, Ku and PARP1 form a complex, the properties of which are changed on its poly(ADP-ribosyl)ation24.

Using CHFR, we established the functional importance of the PBZ motif, demonstrating that specific PBZ-targeted mutations abrogate CHFR function in the antephase checkpoint and that treatment with a PARP inhibitor abolished this checkpoint in CHFR-proficient cells. Thus, PAR assumes a major role in modulating CHFR activity, and consequently in regulation of the antephase checkpoint in response to microtubule poisons. The physiological importance of the PBZ motif is further supported by observations that APLF localizes at sites of DNA damage, by a mechanism dependent on the region of APLF containing the PBZ motif and on PAR synthesis13,14,15. Given that APLF interacts directly with poly(ADP-ribosyl)ated PARP1, we propose that this association defines a role for APLF in DNA break repair.

In general, PAR modifications regulate a dynamic network of intermolecular associations. It has been estimated that PARP1-associated PAR constitutes the major fraction of PAR within the cell25. Consequently, automodified PARP1 is likely to attract proteins with PAR-binding motifs, the subsequent poly(ADP-ribosyl)ation of which may be a secondary effect that provides an additional level of regulation. This would be consistent with our results demonstrating efficient binding of PAR by APLF and CHFR, and the ability of these proteins to be poly(ADP-ribosyl)ated by PARP1. Collectively, these data define a novel poly(ADP-ribose)-binding zinc finger and indicate a mechanism by which cells use modification-dependent interactions to orchestrate the assembly of regulatory pathways.

Methods Summary

All proteins were purified after expression in Escherichia coli. Modification by PARP1 was carried out using a PARP activity assay kit (Trevigen). PAR binding was assessed in dot-blot assays and quantitated by Surface Plasmon Resonance using a BIACORE 3000. Off-rates were determined in the presence of PAR. Transient expression of Flag-tagged proteins in human embryonic kidney 293T cells allowed the co-immunoprecipitation of protein–PAR and protein–protein complexes. Transiently expressed GFP-/CFP-tagged proteins and PAR-specific antibodies were used in immunofluoresence studies. CHFR checkpoints in Ptk1 and Hela cells treated with colcemid were analysed by time-lapse differential interference contrast (DIC) and fluorescence microscopy. In vitro CHFR auto-ubiquitylation was performed as described26. Detailed experimental procedures are found in Supplementary Information and Methods.

Online Methods

Proteins

APLF and CHFR clones were obtained from the RZPD German Resource Centre for Genome Research, whereas a C. elegans DNA ligase III construct was purchased from Geneservice. Tandem zinc finger motifs were subcloned from APLF complementary DNA (bases 1,102–1,332) to construct GST–PBZ. Mutations in APLF and CHFR were introduced using the QuickChange II site-directed mutagenesis kit (Stratagene). APLF and DNA ligase III were overexpressed as N-terminally His-tagged proteins using the Gateway pDEST17 vector (Invitrogen), whereas GST- and His-tagged CHFR and GST-PBZ proteins were produced using pET41a (Novagen). All proteins were expressed in E. coli BL21-CodonPlus cells. The cultures were induced at 30 °C with 0.2 mM IPTG for 2 h for APLF expression, or overnight at 18 °C with 0.01 mM IPTG for CHFR, GST–PBZ and DNA ligase III. Recombinant proteins were purified over nickel-NTA-agarose (Qiagen) (APLF and DNA ligase III), or on glutathione Sepharose (GE Healthcare) (CHFR, GST–PBZ). Mutant proteins were overexpressed and purified according to the procedures defined for the wild-type variants. XRCC1 protein was a gift from T. Lindahl.

Antibodies

Rabbit anti-APLF polyclonal antibodies were raised against purified recombinant APLF protein prepared from E. coli. Mouse monoclonal and rabbit polyclonal anti-PAR antibodies (Trevigen), rabbit anti-CHFR antibody and anti-PARP1 (Abcam), and monoclonal anti-ubiquitin antibody (Abcam) were purchased.

Modification by PARP1 in vitro

Recombinant proteins were modified using a PARP activity assay kit (Trevigen). Typically, reactions (10 µl) contained 30 ng of purified PARP1, 1 µM substrate protein, and 100 µM of NAD+ spiked with [32P]-labelled NAD+ (Amersham Biosciences). Reactions were incubated for 10 min at room temperature. Modified proteins were analysed by SDS–PAGE and visualized by autoradiography.

PAR-binding assay

Proteins (2 pmol) were spotted onto a nitrocellulose membrane, which was subsequently blocked with TBS-T buffer (Tris-HCl, pH 7.5, 150 mM NaCl, 0.05% Tween) supplemented with 5% milk. Radioactively labelled PAR was prepared from 200 ng of automodified PARP1 as described8. PAR polymer was detached from PARP1 using DNase I and proteinase K and extracted using phenol–chloroform. The water-soluble polymer was then diluted in 10 ml with TBS-T and incubated with the nitrocellulose membrane. The membrane was extensively washed with TBS-T, and TBS-T containing 1 M NaCl, then air-dried and subjected to autoradiography.

For the zinc-depletion experiments, proteins were incubated with 20 mM EDTA overnight at 4 °C. For zinc rebinding, the proteins were desalted and incubated with 1 mM ZnSO4.

Surface plasmon resonance

Biotinylated PAR was coupled to streptavidin-coated BIACORE sensor chips, and assays were carried in 20 mM HEPES, pH 7.2, 150 mM NaCl and 0.005% P20 surfactant. Off rates were measured in the presence of 5 µM PAR (defined in monomeric units) using the coinject function of the Biocore. Biotinylated PAR was produced using 10 µM biotinylated NAD (Trevigen) and 100 µM NAD, as described for the modification by PARP1 in vitro. Proteins to be analysed (1 nM–1 µM) were injected at a flow rate of 20 µl min-1. Binding events were measured in response units.

Immunoprecipitation

Human embryonic kidney 293T cells were transiently transfected using Lipofectamine 2000 (Invitrogen), according to the manufacturer’s specifications, with Flag-tagged wild-type and mutant APLF and CHFR constructs. Following transfection (24 h), cells were solubilized in lysis buffer (50 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1% Triton X-100, 1 mM dithiothreitol, 1 mM EDTA) supplemented with 50 U µl-1 benzonase (Novagen) and protein inhibitors (Sigma). Whole cell extracts were clarified by centrifugation and incubated with anti-Flag M2 agarose (Sigma) for 2 h at 4 °C. Following repeated washes with lysis buffer, the immunoprecipitates were boiled in SDS–PAGE loading buffer and analysed by immunoblotting.

Immunofluorescence

HEK293T cells grown on glass coverslips were transfected with GFP-fusion constructs of the wild-type and mutant APLF and CHFR proteins. Lipofectamine 2000 was used as a transfecting agent. Post transfection (24 h), the cells were fixed in 4% paraformaldehyde for 10 min, permeabilized with 0.1% Triton X-100 in PBS and blocked with 2% BSA in PBS. Following incubation with the monoclonal anti-PAR antibody, and Alexa Fluor 546 goat anti-mouse IgG secondary antibody (Invitrogen), the cells were analysed using a Deltavision system.

Ubiquitylation assays

Auto-ubiquitylation was performed essentially as described26. Typically, a 100 µl reaction contained 10 ng E1, 200 ng E2 ubiquitin-conjugating enzyme (UbcH5B), 1 µg ubiquitin, 5 pmol GST-tagged CHFR, 4 mM ATP, 20 mM Tris-HCl, pH 7.5, 50 mM NaCl, 0.2 mM DTT and 10 mM MgCl2. Reactions were incubated for 30 min at 30 °C and half the sample was analysed for PAR binding by dot blotting. The other half was mixed with glutathione Sepharose beads for retention of GST–CHFR, and after extensive washing the beads were boiled in SDS–PAGE loading buffer and the proteins resolved by gel electrophoresis.

CHFR checkpoint assays

Ptk1 cells were cultured on 0.15 mm ΔT dishes (Bioptechs) at 37 °C in Ham’s F-12 medium (Gibco), 10% FBS, 100 U ml-1 penicillin, 0.1 mg ml-1 streptomycin, 1 mM Na Pyruvate, and 0.1% (v/v) Fungizone (Gibco). Approximately 5% of the cell volume of CFP-tagged wild-type or mutant CHFRΔFHA constructs (30 ng µl-1) was injected into Ptk1 cells using a semiautomatic microinjector (Eppendorf) attached to a microscope (model DMIRBE; Leica). Once cells entered into prophase, they were treated with colcemid (15 µM) and their progress followed by time-lapse DIC and fluorescence microscopy at 3-min intervals. Early prophase Ptk1 cells were identified by the beginnings of chromosome condensation, as visualized by DIC microscopy.

HeLa cells were transfected with CFP-tagged wild-type or mutant CHFR by electoroporation (250 V, 1,500 mF, Easyject, Equibio). Following electroporation (18 to 24 h), the medium was replaced with Leibovitz’s L-15 medium (Invitrogen). Colcemid (Sigma) was added to the medium at time 0 at a concentration of 15 µM and the DIC and fluorescence images were taken every 15 min for 18 h on a Leica DMIRB microscope equipped with a 40× 1.2 numerical aperture lens and a CoolSNAP HQ camera (Photometrics) controlled by Slidebook software (Intelligent Imaging Innovations). In these experiments (Fig. 3c), the data are presented as mean ± standard deviation. The statistical significance was determined using a pairwise comparison at 2 and 4 h using a t-test (the antephase delay is about 4 h). The data indicated a significant difference between the untransfected cells and those transfected with wild-type CHFR (P = 0.067 and 0.15).

In the PARP inhibition experiments, Ptk1 cells were pre-treated with 1 µM KU-0058948 or PBS for 1 h and challenged with 15 µM colcemid. Prophase cells that decondensed their chromosomes were scored as returning to interphase, and cells that broke down their nuclear envelopes were scored as continuing to mitosis.