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Mol Cell Biol. Sep 2007; 27(18): 6433–6445.
Published online Jul 16, 2007. doi:  10.1128/MCB.00135-07
PMCID: PMC2099619

Phosphorylation of Slx4 by Mec1 and Tel1 Regulates the Single-Strand Annealing Mode of DNA Repair in Budding Yeast[down-pointing small open triangle]

Abstract

Budding yeast (Saccharomyces cerevisiae) Slx4 is essential for cell viability in the absence of the Sgs1 helicase and for recovery from DNA damage. Here we report that cells lacking Slx4 have difficulties in completing DNA synthesis during recovery from replisome stalling induced by the DNA alkylating agent methyl methanesulfonate (MMS). Although DNA synthesis restarts during recovery, cells are left with unreplicated gaps in the genome despite an increase in translesion synthesis. In this light, epistasis experiments show that SLX4 interacts with genes involved in error-free bypass of DNA lesions. Slx4 associates physically, in a mutually exclusive manner, with two structure-specific endonucleases, Rad1 and Slx1, but neither of these enzymes is required for Slx4 to promote resistance to MMS. However, Rad1-dependent DNA repair by single-strand annealing (SSA) requires Slx4. Strikingly, phosphorylation of Slx4 by the Mec1 and Tel1 kinases appears to be essential for SSA but not for cell viability in the absence of Sgs1 or for cellular resistance to MMS. These results indicate that Slx4 has multiple functions in responding to DNA damage and that a subset of these are regulated by Mec1/Tel1-dependent phosphorylation.

The RecQ helicases are important regulators of genome stability. Human cells have several RecQ family helicases, including BLM and WRN, that are mutated in Werner's and Bloom's syndromes, respectively (19, 25). Yeasts have a single RecQ helicase: Sgs1 in Saccharomyces cerevisiae and Rqh1 in Schizosaccharomyces pombe. Cells lacking Sgs1 or Rqh1 exhibit high rates of chromosome loss and rearrangements, an elevated incidence of loss of heterozygosity, increased rates of sister chromatid exchange, hypersensitivity to agents that damage DNA, and defects in meiosis (15, 25, 30, 48, 50). Sgs1 is also important for preventing recombination between divergent sequences in the single-strand annealing (SSA) mode of double-strand break (DSB) repair (32, 42, 43). Sgs1 interacts with DNA topoisomerase III (Top3), and together Sgs1 and Top3 can dissolve double Holliday junctions (dHJs) in vitro (49). It is thought that this activity promotes the resolution of recombination intermediates during restart of stalled or blocked replisomes (25).

Replisomes blocked by DNA damage can bypass lesions by at least two different mechanisms: translesion synthesis (TLS) across the damaged base by TLS polymerases and error-free bypass, also known as “template switching” (34, 47). Template switching is thought to involve unpairing of the nascent strands from the parental template and their subsequent annealing (20, 39). The nascent strand that had been blocked is then elongated using the nascent sister strand as template. The resulting structures may be converted to pseudo-dHJs, in a Rad51/Rad52-dependent manner, and cells lacking Sgs1 accumulate these pseudo-dHJs presumably because it normally helps to dissolve them (27). There is experimental evidence to support template switching at blocked replisomes in yeast (53), but the mechanisms involved are unclear, as are many of the relevant genes.

Despite these important roles, Sgs1 is not essential for cell viability. However, a screen for genes required for viability in the absence of SGS1 (or TOP3) identified six “SLX” genes. The products of these genes form three heterodimeric complexes in cells: Slx2 (Mms4)/Slx3 (Mus81), Slx5/Slx8, and Slx1/Slx4 (31). The precise cellular roles of Slx5 and Slx8 are unclear, although cells lacking either protein showed an increased rate of gross chromosomal rearrangements (52). Mms4-Mus81 is a structure-specific endonuclease that, at least in vitro, preferentially cleaves branched DNA structures resembling structures that arise during recombinational processing of stalled replication forks (2, 23). The synthetic lethality of sgs1 mus81 cells is suppressed when RAD52 is deleted (2, 10), suggesting Mus81 cleaves dHJs when they are not dissolved by Sgs1 during recombinational processing of stalled replisomes.

Slx1-Slx4 from budding yeast and fission yeast is also a structure-specific endonuclease with preference in vitro for branched DNA substrates, especially simple-Y, 5′-flap, or replication fork-like structures (7, 14). Slx1-Slx4 is likely to define a pathway distinct from Mms4-Mus81, because the synthetic lethality of sgs1Δ slx1Δ or sgs1Δ slx4Δ cells cannot be rescued by deletion of RAD52 (2, 10). Slx4 has no obvious catalytic or structural motifs, apart from a cryptic SAP domain, but Slx1 has a PHD-type zinc finger and is the founding member of a conserved family of nucleases defined by a UvrC-intron-endonuclease (URI) domain (14).

While some of the cellular functions of Slx1 and Slx4 proteins are likely to overlap, given that these proteins interact and are both required for viability in the absence of Sgs1, cells lacking Slx4 are hypersensitive to DNA alkylation damage whereas cells lacking Slx1 are not (5, 31). Furthermore, phosphorylation of Esc4/Rtt107 is defective in cells lacking Slx4 but not in cells lacking Slx1 (36). Moreover, Slx4 is required for recovery from methyl methanesulfonate (MMS)-induced replisome stalling but Slx1 is not (36). Therefore, at least a subset of the cellular roles of Slx1 and Slx4 appears to be distinct.

Slx4 has been also shown to interact physically with proteins other than Slx1. A genome-wide two-hybrid screen identified the Rad1 endonuclease as an Slx4 interactor (22). Rad1 catalyzes DNA incision on the 5′ side of UV-induced lesions and cleaves nonhomologous tails generated by DNA end resection during the SSA mode of DNA repair, responsible for repair of double-strand breaks between repeated sequences (1, 11). However, it is not clear if the endogenous cellular form of Slx4 interacts with Rad1 or if this impacts on the function of either protein. Several groups reported that Slx4 interacts with Esc4/Rtt107 (6, 36, 51). Esc4 was originally identified in a screen for genes that regulate retrotransposition in yeast (40) and in global genome screens for genes required for resistance to MMS (5, 17). Esc4 was subsequently shown to be required for completion of chromosome replication after replisome stalling (36, 37), but it is not yet known how it fulfills this task. Cells lacking Esc4 are hypersensitive to a wide range of agents that cause replisome stalling: camptothecin (CPT; causes S-phase-specific DSBs and replisome collapse) and hydroxyurea (HU; slows replication down by depleting deoxynucleoside triphosphates), as well as MMS, whereas cells lacking Slx4 are not hypersensitive to CPT or HU, suggesting that Esc4 has cellular roles not shared by Slx4. However, esc4Δ and slx4Δ cells show a comparable level of hypersensitivity to MMS and are epistatic in this regard, suggesting that they share a similar role in promoting resistance to MMS.

Slx4 becomes phosphorylated in response to a wide range of different types of DNA damage, at all cell cycle stages, and this requires both the Mec1 and Tel1 protein kinases (12). These kinases, the yeast orthologues of ATR and ATM in higher eukaryotes, respectively, belong to the PIKK family of kinases, which also includes DNA-dependent protein kinase (DNA-PK) (45). Mec1 and Tel1 phosphorylate target proteins, including the Chk1 and Rad53 kinases, on Ser/Thr-Gln (S/T-Q) motifs and are critically important regulators of several aspects of the cellular response to DNA damage and stalled replisomes (45). The Slx4 residues phosphorylated by Mec1 and Tel1 and the functional significance of Slx4 phosphorylation are not yet known. Here we report that Slx4 has at least three independent cellular functions that appear to require different Slx4-interacting proteins, and we show that one of these functions is regulated by Slx4 phosphorylation.

MATERIALS AND METHODS

Yeast strains, plasmids, and antibodies.

All strains used in this study are listed in Table Table1.1. Disruption of SLX4 was carried out by transforming the relevant strains with the KAN-MX-disrupted SLX4 gene amplified from strain SFY008. Gene disruption was tested where possible by screening for MMS hypersensitivity and then verified by PCR. PEP4 disruption was achieved by transforming cells with a PCR product corresponding to the LEU2-disrupted PEP4, amplified from genomic DNA of strain GA1701 (9). PEP4 disruption was found to curtail Slx4 degradation in native cell extracts. Strain SFY013 was constructed by replacing the KANMX cassette in strain SFY008 with a NAT resistance gene. To make plasmid pSLX4, the SLX4 open reading frame plus 1 kb of 5′ sequence was cloned into pRS413, and the SLX4 start ATG was mutated to an NcoI site. After digestion with NcoI, 13 copies of a MYC epitope tag were ligated into the NcoI site. All mutations in SLX4 were introduced using the QuikChange site-directed mutagenesis kit (Stratagene). Mouse monoclonal antibodies against Myc (clone 9E10) and hemagglutinin (HA) were from Roche, and antibodies against Rad1 were from Santa Cruz Biotechnology. Antibodies against Rad10 were a kind gift from Errol Friedberg.

TABLE 1.
Yeast strains used in this study

Analysis of chromosomes by PFGE.

Cells were grown to early log phase (optical density [OD600], 0.5) in yeast extract-peptone-dextrose (YPD) at 30°C and arrested in G1 by addition of α-factor (5 μg/ml). When budded cells accounted for less than 5% of the population, cells were released from arrest by filtration and extensive washing and incubated in YPD for 10 min before addition of MMS (0.05%). After 45 min in MMS, cells were filtered, washed extensively with YPD containing 2.5% (wt/vol) sodium thiosulfate, and incubated in YPD at 30°C. At the times indicated, 1 × 108 cells were removed and fixed in 70% ethanol at 4°C overnight before preparation of chromosomes, exactly as described in the CHEF DRII instruction manual (Bio-Rad). Pulsed-field gel electrophoresis (PFGE) was carried out using a Bio-Rad CHEF DRII apparatus at 14°C in a 1% agarose gel (pulsed-field certified; Bio-Rad) in 0.5× Tris-borate-EDTA for 24 h at 6 V/cm using a 120o included angle with a 6.8- to 158-s switch-time ramp. Gels were stained with 10 μg/ml ethidium bromide for 30 min and washed for 2 min in water before DNA was visualized.

Measurement of spontaneous mutation frequency.

The frequency of forward mutations at the CAN1 gene locus was determined by the frequency of appearance of canavanine-resistant colonies that grew on selective minimal medium plates lacking Arg but containing canavanine (60 μg/ml) (for example, see reference 42a). Cultures were grown to stationary phase for 24 h in minimal medium lacking Arg. The OD600 of cultures was measured, and from the same culture, in parallel, approximately 2 × 107 cells were plated onto canavanine plates and 2 × 102 cells were plated onto YPD plates. The colonies were counted after incubation at 30°C for 3 days. To calculate spontaneous mutation frequencies, the number of canavanine-resistant colonies per ml of culture was divided by the number of CFU (on YPD) per ml of culture. Mutation frequencies represented the average from three independent triplicate experiments, and the relative frequency was calculated from the increase or decrease in mutation frequency in comparison to the wild-type strain.

DNA combing.

Wild-type and slx4Δ cells containing the human nucleotide transporter hENT1 on a centromeric plasmid (pRS415) and seven copies of the herpes simplex thymidine kinase gene were synchronized in late G1 for 2.5 h with 2 μg/ml α-factor (GenePep). Cells were released in S phase with 50 mg/ml Pronase (Calbiochem) in the presence of 30 μg/ml bromodeoxyuridine (BrdU) and 0.05% MMS. After 60 min, MMS was quenched with sodium thiosulfate and cells were resuspended in fresh medium containing 30 μg/ml BrdU. Genomic DNA was extracted in LMP agarose plugs (800 ng/plug) and was stained with YOYO-1 (Molecular Probes). DNA was resuspended in 50 mM morpholineethanesulfonic acid, pH 5.7, to a final concentration of 150 ng/ml. DNA fibers were stretched on silanized coverslips as described elsewhere (29) and were denatured for 25 min in 1 N NaOH. BrdU was detected with a rat monoclonal antibody (clone BU1/75; AbCys) and a secondary antibody coupled to Alexa 488 (Molecular Probes). DNA molecules were counterstained with an antiguanosine antibody (Argene) and an anti-mouse IgG coupled to Alexa 546 (Molecular Probes). Images were recorded with a Leica DM6000B microscope coupled to a CoolSNAP HQ charge-coupled device camera (Roper Scientific) and were processed as described previously (33). MetaMorph v6.2 (Universal Imaging Corp.) was used to measure BrdU signals and DNA fibers, and statistical analysis was performed with Prism 4 (GraphPad Software, Inc.).

Antibody production.

All peptides were synthesized by Graham Bloomberg, University of Bristol. Antibodies against phosphorylation sites in Slx4 were raised at the Scottish Antibody Production Unit (Lanarkshire, Scotland) by immunizing sheep with the following peptides coupled to keyhole limpet hemocyanin: AQKSPMpTQETTKN (phospho-Thr-72), LDNQESpSQQRLWT (phospho-Ser-289), and VNFLSLpSQVMDDK (phospho-Ser-329), where pS and pT are phospho-Ser and phospho-Thr, respectively. Antibodies were purified by affinity chromatography on CH-Sepharose to which the phosphopeptide immunogen had been covalently coupled. Phospho-specific antibodies were used at a final concentration of 4 μg/ml in the presence of 50 μg/ml non-phospho peptide in a Western blot analysis.

Miscellaneous methods.

Western blotting of extracts prepared by the trichloroacetic acid lysis method (38), preparation of native cell extracts and Myc-Slx4 immunoprecipitation, measurement of SSA induced by a run of trinucleotide repeats placed between direct repeats (13), measurement of HO-induced SSA (16) and fluorescence-activated cell sorter (FACS) analysis (12) were all carried out as described previously.

RESULTS

Analysis of DNA replication during recovery from MMS-induced replisome stalling in cells lacking Slx4.

The major DNA lesion induced by MMS, N3-methyl adenine, potently blocks replisome progression (3). Roberts et al. showed that Slx4 is required for recovery of DNA replication after MMS-induced replisome stalling (36). We obtained similar data (Fig. (Fig.1A).1A). Cells were released from G1 arrest into S phase in the presence of MMS. After 45 min in MMS, all cells were still in S phase as judged by FACS analysis (Fig. (Fig.1B),1B), and since chromosomes were not completely replicated, they did not enter the gel (Fig. (Fig.1A,1A, lanes 2, 7, 12, and 17) due to the presence of forks and bubbles that impede chromosome migration (8, 18). When cells were washed free of MMS, chromosome replication recovered and was almost complete after 5 hours in wild-type cells (Fig. (Fig.1B),1B), enabling chromosomes to enter the gel (Fig. (Fig.1A).1A). In contrast, there was a major defect in recovery of chromosome replication in slx4Δ cells and in sgs1Δ cells (46), but not in cells lacking Slx1 (Fig. (Fig.1A1A).

FIG. 1.FIG. 1.
Analysis of DNA replication during recovery from MMS-induced replisome stalling in slx4Δ cells. (A) Strains BY4741 (wild type), SFY008 (slx4Δ), SFY009 (slx1Δ), and SFY010 (sgs1Δ) were grown to mid-log phase, arrested in ...

We wished to test if this lack of recovery from MMS-induced replisome stalling in the absence of Slx4 reflected an inability to resume DNA synthesis or whether instead cells could resume DNA replication but could not complete it. Cells were released from α-factor arrest into S phase in the presence of MMS and then washed free of MMS. FACS analysis (Fig. (Fig.1B)1B) revealed that, like wild-type cells, slx4Δ cells had an apparently 2C DNA content by 4 h postrecovery, indicating that the majority of the chromosomes in these cells had been replicated. More than 90% of slx4Δ cells were viable at this time point (data not shown). DNA replication during recovery from MMS-induced replisome stalling in slx4Δ cells was investigated further by DNA combing (28, 29). Cells were released from G1 into MMS-containing medium in the presence of BrdU. After 45 min, MMS was washed out and cells were allowed to recover for 90 min or 130 min in fresh medium in the continued presence of BrdU. After combing, chromosome fibers were stained with anti-DNA antibodies (red) or anti-BrdU antibodies (green) (Fig. (Fig.1C).1C). This analysis revealed striking defects associated with loss of Slx4. BrdU tracks were almost 50% shorter in slx4Δ cells than in wild-type cells 90 and 130 min after recovery (Fig. 1C and D), suggesting that DNA replication during recovery from MMS is slower in slx4Δ cells. Even so, at 130 min after release of cells from MMS, more than 90% of the stalled replisomes had resumed DNA replication in the absence of Slx4 (Fig. 1C and E). However, unreplicated gaps were observed in around 26% of the fibers in slx4Δ cells, compared with around 8% in wild-type cells (Fig. (Fig.1E).1E). These data are reminiscent of the defects seen in cells lacking the cullin Rtt101, which is also required for recovery from DNA alkylation damage (45). In rtt101Δ cells, unreplicated gaps were detected in 22% of chromosome fibers, compared with only 2% in wild-type cells, and CldU tracks were 50% shorter as observed in slx4Δ cells (45). We also noticed that DNA fibers isolated from slx4Δ cells were significantly shorter than those isolated from wild-type cells (Fig. (Fig.1E),1E), presumably because they are more fragile and break during the combing process due to the persistence of unreplicated chromosomal gaps and stalled replisomes. Taken together, these data indicate that although cells lacking Slx4 restart DNA synthesis when replisomes stall, DNA replication is slower than normal. Also, at the latest time point examined, chromosomes from slx4Δ cells are left with unreplicated gaps. This would account for the inability of chromosomes to enter pulsed-field gels (Fig. (Fig.1A1A).

SLX4 interacts with genes involved in error-free DNA damage bypass genes.

One possible explanation for the recovery defect described above could be that Slx4 promotes repair of DNA alkylation damage. Epistasis analysis with mutants defective in base excision repair (BER), the principal pathway for repair of DNA alkylation damage, was carried out. Cells lacking both SLX4 and methyladenine DNA glycosylase (MAG1), a BER factor that cleaves methylated bases to leave an abasic site in DNA, are more sensitive to MMS than either of the respective single mutants (Fig. (Fig.2A).2A). Similar results were obtained with APN1 (Fig. (Fig.2A),2A), which is also required for BER. We conclude that BER or nucleotide excision repair (NER) (data not shown) is unlikely to be the major function of SLX4.

FIG. 2.
SLX4 interacts with genes involved in DNA damage bypass. Strains BY4741 (wild type), SFY008 (slx4Δ), SFY022 (apn1Δ), SFY023 (apn1Δ slx4Δ), SFY020 (mag1Δ), SFY021 (mag1Δ slx4Δ), SFY036 (pol30k164r ...

Alternatively, Slx4 could promote recovery from replisome stalling by regulating bypass of fork-blocking lesions. Bypass requires Rad6/Rad18-dependent ubiquitination of Lys164 of proliferating cell nuclear antigen (PCNA) (34, 47). Consequently, cells in which Lys164 of PCNA (Pol30 in budding yeast) is mutated to Arg are hypersensitive to MMS (21). When SLX4 was disrupted in pol30 lys164arg mutant cells, the double mutants were not more sensitive to MMS than the most sensitive single mutant (Fig. (Fig.2B,2B, top panel). Consistent with this, disruption of SLX4 did not further sensitize rad18Δ or rad6Δ cells to MMS (Fig. (Fig.2B,2B, lower panel). Therefore SLX4 has an epistatic relationship with genes that regulate DNA damage bypass.

There are two major pathways in cells for bypassing DNA lesions: TLS and error-free bypass (47). TLS occurs by transient recruitment to stalled replisomes of specialized TLS DNA polymerases that, unlike the replicative polymerases δ and epsilon, can replicate across DNA lesions (47). Rad6/Rad18-dependent mono-ubiquitination of PCNA at Lys164 is thought to recruit TLS polymerases to stalled replisomes. Error-free bypass requires the addition of further ubiquitin moieties to mono-Ub PCNA, and this is catalyzed by the Rad5/Mms2/Ubc13 complex (47). We sought to determine which of these bypass pathways is regulated by SLX4. The major error-prone translesion polymerase in budding yeast is polymerase ζ (Pol ζ), comprising Rev3, the catalytic subunit, and Rev7 (35, 47). The MMS sensitivity of slx4Δ rev3Δ cells was greater than that of the single mutants (Fig. (Fig.2C),2C), suggesting that SLX4 is not involved in error-prone translesion synthesis and pointing instead to error-free bypass. Consistent with this, slx4Δ mms2Δ double mutants were not more sensitive to MMS (Fig. (Fig.2D)2D) than the most sensitive single mutants. These data suggest that the inability of slx4Δ cells to complete DNA synthesis after replisome stalling may be due to an inability to carry out error-free bypass.

Translesion synthesis by Pol ζ is responsible for 50 to 75% of spontaneous cell mutations, and so deletion of Rev3 decreases cell mutation frequencies (26). In contrast, mutations in error-free bypass factors increase spontaneous mutation frequency because of compensatory increases in TLS (4, 41). We reasoned that if Slx4 regulates error-free bypass, then Slx4 deficiency should increase the frequency of spontaneous mutation. Therefore, the frequency of forward mutation in the CAN1 gene, which gives rise to canavanine resistance, was measured. In the genetic background used in this study, deletion of REV3 decreased spontaneous mutation frequency, whereas disruption of UBC13 caused an approximately 8.5-fold increase in mutation frequency (Table (Table2),2), consistent with previous reports (4). Cells lacking Slx4 showed an approximately fivefold increase in the frequency of mutation, and this was abrogated by deletion of Rev3 (Table (Table2).2). Therefore, cells lacking Slx4 have a “mutator” phenotype that is caused by increased translesion synthesis, like cells lacking error-free bypass factors. This is consistent with, but does not prove, a role for Slx4 in error-free DNA damage avoidance.

TABLE 2.
Analysis of the frequency of spontaneous mutations in slx4Δ cellsa

Slx4 interacts with Slx1 and with Rad1-Rad10 in a mutually exclusive manner.

Slx4 does not have any catalytic motifs that could provide clues as to how it may participate in DNA processing reactions at blocked replisomes. However, Slx4 interacts with the Slx1 structure-specific endonuclease that can cleave branched structures, such as flaps, in vitro (14, 31). Genome-wide two-hybrid analysis revealed the Rad1 subunit of the Rad1-Rad10 endonuclease as a putative Slx4-interactor (22). We tested if cellular Slx4 could interact with Rad1 and if Slx1 was found in the same complex. Endogenous Slx4 was tagged at the C terminus with 13 copies of the Myc epitope in cells in which Slx1 was tagged at the N terminus with 12 copies of the HA epitope. Disruption of Sgs1 did not cause lethality in this background and the cells were not more sensitive to MMS than wild-type cells, strongly suggesting that epitope tagging did not affect the function of Slx4 or Slx1 (data not shown). As shown in Fig. Fig.3B,3B, Slx1, Rad1, and Rad10 were detected in anti-Myc (Slx4) immunoprecipitates before and after exposure of cells to MMS or ionizing radiation (IR). In contrast, Slx4 was detected in Slx1 immunoprecipitates, but Rad1 and Rad10 were not. Consistent with this observation, Slx4 and Rad10 were detected in anti-Rad1 immunoprecipitates but Slx1 was not. These data indicate that Slx4 interacts with Slx1 and with Rad1-Rad10 in a mutually exclusive manner. This is consistent with the previous observation that Slx1 (31), but not Rad1 (48), is synthetically lethal with Sgs1. In addition, although both Slx4 and Slx1 interact with Esc4 (36, 51), neither Rad1 nor Rad10 was found in anti-Esc4 immunoprecipitates (Fig. (Fig.3A).3A). Taken together, these data demonstrate that Slx4 exists in cells in at least two complexes: Slx1-Slx4-Esc4 and Slx4-Rad1-Rad10.

FIG. 3.
Slx4 interacts with Rad1-Rad10 and is required for SSA. (A) Cells expressing Myc13-Slx4 and HA6-Slx4 (in which PEP4 was disrupted) or cells expressing Slx4 were grown to mid-exponential phase in liquid culture and left untreated or incubated with MMS ...

It is easy to envisage how the catalytic activity of Rad1 and Slx1 could be useful during error-free bypass. However, cells lacking Slx1 (Fig. (Fig.1A)1A) or Rad1 (data not shown) are not defective in recovery from MMS-induced replisome stalling and are not hypersensitive to MMS (Fig. (Fig.3B).3B). To rule out redundancy between Slx1 and Rad1, a strain lacking both nucleases was made. However, slx1Δ rad1Δ cells were not more hypersensitive to MMS than wild-type cells, and slx1Δ rad1Δ slx4Δ cells were not more hypersensitive to MMS than slx4Δ cells (Fig. (Fig.3B).3B). Therefore, the role of Slx4 in promoting cellular resistance to MMS, which may involve regulating error-free bypass, appears to be independent of Slx1 and Rad1.

Slx4 regulates single-strand annealing.

The observation that Slx4 interacts physically with Rad1-Rad10 in cells prompted us to test the role of Slx4 in Rad1-Rad10-dependent processes. Rad1-Rad10 is involved in NER, but as slx4Δ cells are not hypersensitive to UV (data not shown), Slx4 does not appear to be involved in NER. Rad1-Rad10 also plays an important role during the SSA mode of DSB repair that can repair a DSB between repeated sequences (Fig. (Fig.3D).3D). After resection of the ends, complementary strands of the homologous regions flanking the DSB can anneal, producing an intermediate that has two nonhomologous 3′-ended tails. Rad1 cleaves the 3′ single-strand tails, and the resulting nicks are sealed by ligation (1, 11). Thus, SSA results in deletion of one copy of the repeat plus the sequence located between the repeats.

Zakian and colleagues reported a system for measuring SSA repair of DSBs induced by a hairpin placed between two direct repeats (Fig. (Fig.3C,3C, top) (13). When a run of 250 tandem CTG trinucleotide repeats (TNRs) and the URA3 gene are placed between two direct repeats (Fig. (Fig.3C,3C, top), the TNRs form a hairpin that causes replisome stalling and DSB formation. These breaks are repaired by SSA in a manner dependent on RAD1and RAD52, resulting in loss of the URA3 marker from between the direct repeats and, consequently, cells become resistant to 5-fluoroorotic acid (5-FOA); no marker loss was observed in the absence of CTG repeats (13). As shown in Fig. Fig.3C3C (bottom), a high frequency of URA3 loss is observed in when TNRs (CTG-250) are located between the direct repeats, but not in the absence of TNRs (CTG-0). Disruption of Slx4, however, like disruption of Rad1 (13), causes a severe reduction in SSA in this assay (Fig. (Fig.3C).3C). However, disruption of MMS2 that regulates error-free bypass did not have a statistically significant effect on marker loss (Fig. (Fig.3C,3C, bottom), and this demonstrates that marker loss in this assay is not due to sister strand slippage caused by template switching at the TNRs. Furthermore, disruption of Slx1 had no effect on SSA (Fig. (Fig.3C,3C, bottom). This argues that Slx4 regulates Rad1-dependent SSA independently of Slx1 and independently of its role in error-free bypass.

We tested the effect of disruption of Slx4 in a different assay for SSA that did not rely on TNRs for formation of DSBs. Instead, the HO endonuclease was induced to create a single DSB between 205-bp repeated segments of the URA3 gene (Fig. (Fig.3D)3D) (43). Induction of a GAL::HO gene efficiently induced SSA in wild-type cells and created deletion products that could be monitored by Southern hybridization (Fig. (Fig.3E),3E), and it is well established that this requires Rad1-Rad10 (11). Strikingly, disruption of Slx4 in this background also abolishes SSA. Taken together, the data in this section indicate that Slx4 interacts with Rad1-Rad10 and promotes repair of DSBs by SSA.

Phosphorylation of Slx4 by Mec1 and Tel1 regulates SSA.

DNA damage induces Mec1/Tel1-dependent phosphorylation of Slx4 that is independent of Rad53 and Chk1 (12). Mec1/Tel1, ATR/ATM, and DNA-PK all have identical specificity in vitro, and even though DNA-PK is not found in yeasts, it phosphorylates the same motifs in vitro in Slx4 as Mec1 and Tel1 (45). Since DNA-PK is readily available, we determined the residues in Slx4 phosphorylated by DNA-PK in vitro as a starting point to ultimately find the residues phosphorylated in vivo by Mec1/Tel1. Incubation of recombinant His6-Slx4 with DNA-PK resulted in phosphorylation of His6-Slx4 with a stoichiometry of approximately 6 moles of phosphate per mole of Slx4 (data not shown). The sites phosphorylated in Slx4 were identified by a combination of mass spectrometry and Edman degradation (data not shown). These analyses revealed that Slx4 is phosphorylated in vitro by DNA-PK on the following six residues: Thr72, Thr113, Ser289, Thr319, Ser329, and Ser355, and all of these conformed to the S/T-Q consensus sequence (Table (Table33).

TABLE 3.
Sequences surrounding residues in Slx4 phosphorylated by DNA-PK in vitro

To test whether Slx4 is phosphorylated on these residues in vivo, phospho-specific antibodies were raised. Phosphopeptides corresponding to Thr113, Ser355, and Thr319 failed to generate antibodies capable of recognizing the phosphopeptide immunogen (data not shown). In contrast, dot blot analysis showed that affinity-purified phospho-specific antibodies raised against Thr72, Ser289, and Ser329 recognized the correct phosphopeptide immunogen but not the corresponding non-phospho peptide (Fig. (Fig.4B).4B). Native extracts from cells in which endogenous Slx4 was tagged at the C terminus with 13 copies of the Myc epitope and that lacked the Pep4 protease to curtail Slx4 degradation were prepared (12). Slx4-Myc was immunoprecipitated and subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) followed by Western blotting with the Slx4 phospho-specific antibodies. This showed clearly that Slx4 is phosphorylated on Thr72, Ser289, and Ser329 after exposure of cells to MMS (Fig. (Fig.4C).4C). Phosphorylation of Slx4 on Thr72 was evident 15 min after MMS treatment and was much stronger after 90 min (Fig. (Fig.4D).4D). In addition, Thr72 became phosphorylated after exposure of cells to CPT, which causes double-strand breaks during S phase (Fig. (Fig.4D).4D). Slx4-Myc was then immunoprecipitated from cells lacking both Mec1 and Tel1, and precipitates were subjected to SDS-PAGE followed by Western blotting. As shown in Fig. Fig.4E,4E, no phosphorylation of Thr72, Ser289, and Ser329 was observed in mec1Δ tel1Δ cells. Phosphorylation of these residues occurred at wild-type levels in cells lacking either Mec1 or Tel1 and in cells lacking both Rad53 and Chk1 (data not shown). Thus, both Mec1 and Tel1 phosphorylate Slx4 on several S/T-Q motifs after DNA damage in vivo.

FIG. 4.
Identification of Ser/Thr residues in Slx4 phosphorylated by Mec1 and Tel1 after DNA damage. (A) Schematic diagram of Slx4. Sites phosphorylated by DNA-PK are indicated. Asterisks denote all S/T-Q motifs. (B) Different amounts of phosphopeptide (“phospho”) ...

To test the potential role of Mec1/Tel1-mediated phosphorylation in regulating Slx4, different combinations of point mutations were introduced into the SLX4 gene expressed under the control of its own promoter from a low-copy-number plasmid. Initially, the three residues in Slx4 that were shown to be phosphorylated by Mec1 and Tel1 in vivo—Thr72, Ser289, and Ser329 (Fig. (Fig.4C)—were4C)—were all mutated to alanines, resulting in pSLX4-MUT3. In another mutant, these three sites plus the three other sites phosphorylated in vitro by DNA-PK, Thr113, Thr319, and Ser355, were mutated to Ala (pSLX4-MUT6). When these plasmids and wild-type pSLX4 were introduced into slx4Δ cells, the Slx4 mutants were expressed at similar levels to wild-type Slx4 (data not shown).

We tested if the Slx4 phosphorylation site mutants could rescue the MMS hypersensitivity of slx4Δ cells. Cells expressing Slx4-Mut3 (data not shown) or Slx4-Mut6 (Fig. (Fig.5A)5A) were no more sensitive to MMS than cells expressing wild-type Slx4. However, it was possible that phosphorylation of Slx4 by Mec1/Tel1 at S/T-Q sites other than those mutated in pSLX4-MUT6 may have provided resistance to MMS. This is unlikely, since mutation of 16 of the total 18 S/T-Q motifs in Slx4 had no effect on the ability of Slx4 to rescue the MMS hypersensitivity of slx4Δ cells (data not shown). Thus, it is highly unlikely that Mec1/Tel1-dependent phosphorylation of Slx4 is required for its ability to promote resistance to MMS or, therefore, error-free bypass. However, we reasoned that phosphorylation of Slx4 may affect an aspect of its function other than cellular resistance to MMS, such as SSA or the ability to maintain cell viability in the absence of Sgs1. Therefore, we investigated the role of phosphorylation in regulating these aspects of Slx4 function.

FIG. 5.
Phosphorylation of Slx4 promotes SSA. (A) Wild-type cells (strain HP30) transformed with pRS413 (empty vector) or slx4Δ cells (SFY018) transformed with empty vector or plasmids pSLX4 or pSLX4-MUT6 were grown to saturation in liquid culture. Tenfold ...

Cells lacking both sgs1Δ and slx4Δ are inviable but can be kept alive by a low-copy-number [pSGS1-URA3-ADE] plasmid expressing SGS1. These cells are sensitive to killing by FOA, which is converted to toxic intermediates by Ura3, since cells cannot lose the SGS1 plasmid (30, 31). sgs1Δ slx4Δ ade2 ade3 [pSGS1-URA3-ADE] cells (strain NJY561) (5) were transformed with the following HIS3 plasmids: empty plasmid (pRS413), pSLX4, or pSLX4-MUT6. Cells were then restreaked to YPD plates with or without 5-FOA. Cells transformed with empty plasmid (pRS413) are FOA sensitive and red (since they cannot lose the ADE3 gene). Introduction of SLX4 on a low-copy-number plasmid allowed sgs1Δ slx4Δ [pSGS1-URA3-ADE] cells to grow on FOA (Fig. (Fig.5B)5B) and caused red-white sectoring on low-adenine plates (data not shown), since cells could now lose the SGS1-URA3 plasmid. Introduction of pSLX4-MUT6, like wild-type SLX4, resulted in FOA resistance (Fig. (Fig.5B).5B). This indicates Slx4 phosphorylation is not essential for viability in sgs1Δ cells. We next tested the impact of Slx4 phosphorylation on SSA. Whereas wild-type Slx4 could rescue the decrease in SSA observed in slx4Δ cells, the Slx4-Mut3 or Slx4-Mut6 phospho site mutants could not (Fig. (Fig.5C).5C). This is consistent with previous observations that cells lacking Mec1 show reduced SSA (24). Taken together, the data in this section indicate that Mec1/Tel1-mediated phosphorylation of Slx4 regulates SSA but not cell viability in the absence of Sgs1 or cellular resistance to MMS.

DISCUSSION

In this study we showed that Slx4 has at least three apparently independent cellular functions: protecting cells when Sgs1 is not functional, promoting cellular resistance to MMS, and SSA. We also demonstrated that phosphorylation of Slx4 by Mec1 and Tel1 regulates SSA but is not required for viability in sgs1Δ cells and is not required for cellular resistance to MMS.

The inability of slx4Δ cells to recover from MMS-induced replisome stalling (Fig. (Fig.1A)1A) (36) prompted us to investigate if DNA replication could resume in these cells during recovery or whether problems arose instead in completing S phase. We found that although DNA replication can resume after replisome stalling in cells lacking Slx4 (Fig. (Fig.1B),1B), DNA synthesis is slow and there is a major defect in the completion of replication, resulting in unreplicated gaps in the genome (Fig. 1C to E). Precisely why slx4Δ cells have problems in completing DNA replication is not yet clear. However, in this study we found that SLX4 interacts with genes involved in error-free DNA damage bypass, and several lines of evidence suggest that Slx4 might regulate this process. Firstly, Slx4 is epistatic with error-free bypass genes in terms of MMS hypersensitivity (Fig. (Fig.2).2). Secondly, cells lacking a known error-free DNA damage bypass factor, Mms2, have a similar recovery defect to that seen in slx4Δ cells (data not shown). Thirdly, the spontaneous mutation frequency is elevated in slx4Δ cells, caused by a compensatory increase in TLS. This also occurs in known error-free bypass mutants (Table (Table2)2) and probably masks the real severity of the consequences of disrupting Slx4, especially given the additive effect of disrupting REV3 in slx4Δ cells (Fig. (Fig.2C2C).

Error-free bypass is thought to involve template switching initiated by unpairing and annealing of the blocked nascent strand with the intact nascent sister strand, but the mechanisms and gene products involved are not clear. After replication past the blockage, the nascent strands would unpair again and reanneal with the parental strands (20, 39). There is experimental evidence to support template switching at blocked replisomes in yeast (53), but since the mechanisms involved are unclear, as are many of the relevant genes, it is difficult to speculate about the potential role of Slx4. Template switching should involve the action of helicases and nucleases, and it is possible that Slx4 recruits one or more catalytic activities to replisomes blocked by DNA lesions. In this light, it is interesting that Slx4 interacts with Slx1 that in vitro cleaves structures that resemble those that may arise during error-free bypass. However, Slx1 is not required for cellular resistance to MMS. Genome-wide analysis revealed the Rad1 subunit of the Rad1-Rad10 nuclease as a potential Slx4 interactor, and in this study we demonstrated that cellular Slx4 interacts with Rad1-Rad10 (Fig. (Fig.3A).3A). However, rad1Δ cells recover normally from MMS (data not shown) and are not MMS sensitive (Fig. (Fig.3B).3B). It is unlikely, therefore, that Rad1 and Slx1 function redundantly in error-free bypass since slx1Δ rad1Δ cells are not hypersensitive to MMS (Fig. (Fig.3B3B).

Slx4 interacts with Esc4, which is also required for recovery from replisome stalling (36, 37), but unlike Slx4, disruption of Esc4 causes sickness but not lethality in sgs1Δ cells (51). Cells lacking Esc4 are hypersensitive to CPT and HU (44), whereas cells lacking Slx4 are not (data not shown), suggesting that Slx4 and Esc4 have distinct functions. However, esc4Δ and slx4Δ cells show a comparable level of hypersensitivity to MMS and are epistatic in this regard (6, 36). In addition, Slx4 is required for phosphorylation of Esc4 by Mec1 (36), indicating that the Slx4-Esc4 interaction is functionally important. It remains to be determined how the association with Esc4 impacts on Slx4 function in promoting resistance to MMS. It will be of particular importance to examine the ability of these proteins to associate with stalled replisomes and how this is regulated.

Rad1-Rad10 is essential for SSA (1, 11, 13), and because we found that Slx4 interacts with this complex, we tested if Slx4 regulates SSA. Indeed, slx4Δ cells showed a severe reduction in Rad1-Rad10-dependent SSA in two different assays (Fig. (Fig.3).3). It is not yet clear why deletion of Slx4 has such a profound effect on SSA but could reflect a role in Rad1-mediated removal of nonhomologous tails, in annealing of the repeats, or in directing new DNA synthesis prior to ligation of the ends. Since the Slx4-Slx1 complex also cleaves flaps and branched structures, it is tempting to speculate that Slx4 recognizes and binds to these structures in a manner that somehow facilitates cleavage by associated enzymes. However, Slx1 does not appear to be involved in SSA, and the Slx4-Slx1 and Slx4-Rad1-Rad10 complexes appear to be distinct. It is not, therefore, clear how the different complexes recognize the appropriate lesions. Biochemical analysis of these complexes and the identification of separation-of-function mutants may help to elucidate this problem.

In this study we identified six residues in Slx4 phosphorylated by DNA-PK in vitro. Phospho-specific antibodies demonstrated clearly that at least three of these sites—Thr72, Ser289, and Ser329—become phosphorylated in vivo in response to DNA damage but not in cells lacking both Mec1 and Tel1 kinases. Mutation of these three sites in Slx4 phosphorylated in vivo after DNA damage does not affect cell viability in the presence of MMS or viability in cells lacking Sgs1 but does inhibit Rad1-dependent SSA. This suggests that the role of Slx4 in SSA is distinct from its role in promoting cell viability in the absence of Sgs1 and in promoting resistance to MMS (Fig. (Fig.66).

FIG. 6.
Model for cellular roles of Slx4. Slx4 exists in at least two mutually exclusive, functionally distinct Slx4-containing complexes. Esc4-Slx4-Slx1 protects cells in the absence of Sgs1 but is not required for SSA. The Slx4-Rad1-Rad10 complex, on the other ...

The Slx4-Rad1-Rad10 and Slx4-Slx1-Esc4 complexes appear to be functionally distinct, and phosphorylation of Slx4 by Mec1 and Tel1 appears to be required for the function of one of these complexes: Slx4-Rad1-Rad10, which mediates SSA. It will be vitally important to investigate the molecular basis for modulation of Slx4 function by phosphorylation. It is unlikely that phosphorylation promotes the interaction of Slx4 with Rad1-Rad10, since Slx4 interacts with these proteins even in the absence of DNA damage (Fig. (Fig.3A)3A) (22, 31). However, it may be that phosphorylation modulates recruitment of Slx4-Rad1-Rad10 to stalled replisomes or sites of DNA damage, and this will be interesting to investigate.

Based on the data in this study, we postulate the existence of at least two mutually exclusive, functionally distinct Slx4-containing complexes (Fig. (Fig.6A).6A). Esc4-Slx4-Slx1 protects cell viability in the absence of Sgs1 but is not required for SSA. The Slx4-Rad1-Rad10 complex, on the other hand, promotes SSA. The two Slx4-containing complexes appear to be distinct, in that deletion of RAD1 is not synthetically lethal with deletion of SGS1 (48) but deletion of SLX1 is (31). In addition, Rad1-Rad10 but not Slx1 is required for SSA (Fig. 3C and E). The ability of Slx4 to promote cellular resistance to MMS probably involves the Esc4-Slx4-Slx1 complex: even though Slx1 is not required for recovery from MMS (Fig. (Fig.1A),1A), Esc4 and Slx4 are epistatic with regard to MMS hypersensitivity (36). Alternatively, one or more as-yet-unidentified Slx4-interacting proteins may fulfill this task. It will be important to identify such proteins, to examine the dynamics of Slx4-containing complexes and how Slx4 is distributed among them, and to study how Slx4 phosphorylation influences Slx4 function at the molecular level.

Acknowledgments

We thank Helle Ulrich, Michael Fasullo, Virginia Zakian, and EUROSCARF for yeast strains and Steve Brill for useful reagents and advice. We are grateful to Susan Lees-Miller for the kind gift of DNA-PK. We thank the Antibody Production Team and James Hastie and Hilary MacLauchlan in the Division of Signal Transduction Therapy, University of Dundee, for help with raising and purifying antibodies and the DNA sequencing group for technical assistance. We are grateful to Tony Carr, Anton Gartner, and members of the Rouse laboratory for useful discussions and to S. Gasser for technical advice.

S.F. was funded by a predoctoral fellowship from the Medical Research Council (MRC) UK, and work in the Rouse lab is funded by the MRC, the Association for International Cancer Research, and an EMBO Young Investigator Award.

Footnotes

[down-pointing small open triangle]Published ahead of print on 16 July 2007.

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