The Saccharomyces cerevisiae RAD9, RAD17, RAD24 and MEC3 Genes Are Required for Tolerating Irreparable, Ultraviolet-Induced DNA Damage

Corresponding author: L. H. Hartwell, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., LY301, Seattle, WA 98109-1024., lhartwel{at}fhcrc.org (E-mail).

Communicating editor: M. D. ROSE

	ABSTRACT

TOP ABSTRACT MATERIALS AND METHODS RESULTS DISCUSSION LITERATURE CITED

In wild-type Saccharomyces cerevisiae, a checkpoint slows the rate of progression of an ongoing S phase in response to exposure to a DNA-alkylating agent. Mutations that eliminate S phase regulation also confer sensitivity to alkylating agents, leading us to suggest that, by regulating the S phase rate, cells are either better able to repair or better able to replicate damaged DNA. In this study, we determine the effects of mutations that impair S phase regulation on the ability of excision repair-defective cells to replicate irreparably UV-damaged DNA. We assay survival after UV irradiation, as well as the genetic consequences of replicating a damaged template, namely mutation and sister chromatid exchange induction. We find that RAD9, RAD17, RAD24, and MEC3 are required for UV-induced (although not spontaneous) mutagenesis, and that RAD9 and RAD17 (but not REV3, RAD24, and MEC3) are required for maximal induction of replication-dependent sister chromatid exchange. Therefore, checkpoint genes not only control cell cycle progression in response to damage, but also play a role in accommodating DNA damage during replication.

WE previously showed that in wild-type Saccharomyces cerevisiae, the rate of progression of an ongoing S phase is slowed in the presence of a DNA-alkylating agent (PAULOVICH and HARTWELL 1995 ). In contrast, checkpoint mutants replicate damaged and undamaged DNA at comparable rates. This regulation is dependent on the RAD9, RAD17, RAD24, RAD53, MEC1, MEC3, PRI1, RFA1, and RFC5 genes (PAULOVICH and HARTWELL 1995 ; LONGHESE et al. 1996A , LONGHESE et al. 1996B ; MARINI et al. 1997 ; PAULOVICH et al. 1997 ; SUGIMOTO et al. 1997 ), but is not dependent on genes from a variety of DNA repair pathways, including base and nucleotide excision repair, recombinational repair, mismatch repair, and postreplication repair (PAULOVICH et al. 1997 ). Mutations that eliminate S phase regulation also confer sensitivity to alkylating agents, leading us to suggest that, by regulating the S phase rate, cells are either better able to repair or better able to tolerate DNA damage (PAULOVICH et al. 1997 ). Mutating known repair genes, singly or in combination, causes further slowing of the S phase rate rather than eliminating S phase regulation (PAULOVICH et al. 1997 ), suggesting that S phase slowing may be a result of accommodating unrepaired lesions during replication rather than the result of repairing lesions.

Others have shown that rad1 mutants, despite a global defect in nucleotide excision repair (REYNOLDS and FRIEDBERG 1981 ; WILCOX and PRAKASH 1981 ), are able to replicate damaged DNA and survive after low levels of UV irradiation (JAMES et al. 1978 ). Therefore, rad1 cells must have some mechanism for tolerating irreparable DNA damage. However, there are genetic consequences to replicating the damaged DNA template. Daughter strand gaps are formed (PRAKASH 1981 ), presumably straddling polymerase-blocking lesions in the template strand, and both mutation (JAMES et al. 1978 ) and sister chromatid exchange (SCE; KADYK and HARTWELL 1993 ) are induced (Figure 1).

View larger version (18K): In this window In a new window Download PPT slide   Figure 1. Model proposed to explain how cells replicate despite the presence of irreparable, UV-induced, covalent modification of the DNA template. Thin lines represent nascent strands, and arrows represent 3' ends. Mechanisms proposed for RAD52-dependent SCE (inside box) are hypotheses and are not based on data from yeast. The reader is referred to the Introduction for a discussion of the model. Note that the existence of a RAD52-dependent recombination pathway and a REV3-dependent mutagenic pathway does not preclude the existence of other nonrecombinational, nonmutagenic pathways of DNA damage tolerance.

The reconstitution of high-molecular-weight DNA after daughter strand gap formation in rad1 cells is called postreplication repair, and it has been shown to be dependent on RAD6, RAD18, and RAD52 (PRAKASH 1981 ). The molecular mechanism responsible for reconstituting intact daughter strands in rad1 yeast has not been elucidated, and two models (Figure 1, box) have been proposed (reviewed in NAEGELI 1994 ; FRIEDBERG et al. 1995 ). In the first model, the free 3' end of the daughter strand gap invades the sister chromatid and a Holliday junction is formed. Branch migration could then occur across the damaged template, resulting in recombinational bypass of the lesion without the need to replicate across it. Resolution of the junction would result in SCE (a combination of gene conversion and reciprocal exchange). In the second model, the free 3' end of the daughter strand gap invades the sister chromatid duplex, ultimately using the nascent strand of the sister chromatid as a template on which to replicate around the lesion. A second template switch would then occur downstream of the lesion, allowing the polymerase to replicationally bypass the lesion and resulting in SCE (exclusively gene conversion).

More is known about the UV induction of mutations. REV3 encodes an inessential DNA polymerase necessary for UV-induced mutagenesis in vivo (LEMONTT 1971 ; MORRISON et al. 1989 ). Rev3p and Rev7p form a complex called Pol, which in vitro is able to replicate over a damaged template much more efficiently than other major replicases (NELSON et al. 1996 ). Replication across a damaged template results in the insertion of noncognate nucleotides. This is the so-called error-prone pathway that results in mutation (Figure 1).

We hypothesized that the mutagenic and/or recombinogenic mechanisms of accommodating lesions in the template may require special modes of replication that are slower than normal replicative DNA synthesis and that may depend on checkpoint gene function. This could explain why checkpoint mutants fail to slow the rate of ongoing replication in response to DNA damage and would predict that checkpoint mutants would be defective in replication-dependent SCE and/or induced mutagenesis. To test this hypothesis, we assayed the induction of SCE and mutation in checkpoint mutants in a rad1 excision repair-defective background after UV irradiation. We chose to work in a rad1 background because in wild-type cells, most lesions can be repaired before replication. We find that RAD9, RAD17, RAD24, and MEC3 are all required for UV-induced mutagenesis, and that RAD9 and RAD17 (but not REV3, RAD24, and MEC3) are required for maximal UV induction of SCE in rad1 cells.

	MATERIALS AND METHODS

TOP ABSTRACT MATERIALS AND METHODS RESULTS DISCUSSION LITERATURE CITED

Media and growth conditions:
YEPD and dropout media have been described (SHERMAN et al. 1981 ). YM-1 is described in HARTWELL 1967 .

Yeast strains:
All strains used in this study were constructed in the A364a background. The rad9::URA3 (yMP11498), rad17::URA3 (yMP11474), and rad24::URA3 (yMP11477) strains were constructed by PCR-based gene replacement (BAUDIN et al. 1993 ) using oligonucleotides designed to delete >90% of the coding sequences. The oligonucleotides used for each deletion were as follows: rad9::URA3 (yMP11498), OLIGO 1: 5'-CAT AGT GAG AAA ATC TTC AAC ATC AGG GCT ATG TCA GGC CGG AAA CAG CTA TGA TG-3' and OLIGO 2: 5'-CAT CTA ACC TCA GAA ATA GTG TTG TAT ATA TCA TTG TCC GTG TAA AAC GAC GGC CAG T-3'; rad17::URA3 (yMP11474), OLIGO 1: 5'-CGG TGT GGA AAC AAA GTA GTT GAA GGA TTT CAA CTA TGC GGG AAA CAG CTA TGA CCA TG-3' and OLIGO 2: 5'-GAA TGA AGT TCT GCG TTT TCT GCG ATG CTG GAT ATT GAC TTG TAA AAC GAC GGC CAG T-3'; and rad24::URA3 (yMP11477), OLIGO 1: 5'-CAC CAC TAA TTA TCA AGT TTG TTC CTG TCT GAA TGA TAT GGG GAA ACA GCT ATG ACC ATG-3' and OLIGO 2: 5'-CCT GGG GTT TTC TCG TCA AAT TTA AAG AGT AAA AAG TTA GAG TGT AAA ACG ACG GCC AGT-3'. PCR using pJJ242 (JONES and PRAKASH 1990 ) as a template generated an intact URA3 gene flanked by sequence homology to either RAD9, RAD17, or RAD24. Each PCR product was used to transform the parent strain yMP10502, resulting in the construction of rad9::URA3 (yMP11498), rad17::URA3 (yMP11474), and rad24::URA3 (yMP11477) derivatives by one-step gene replacement (ROTHSTEIN 1983 ). Each deletion strain was confirmed by PCR analysis of genomic DNA followed by diagnostic restriction mapping (data not shown).

The rad9 (7835-25b), rad17 (DLY279), and rad24 (DLY270) strains (A364a) were kindly provided by TED WEINERT and DAVID LYDALL (WEINERT and HARTWELL 1990 ; WEINERT et al. 1994 ; LYDALL and WEINERT 1995 ) and subsequently crossed to other strains in the A364a background to generate the checkpoint deletion strains used in this study. The identities of all strains used in the experiments in this study were confirmed by complementation testing with our newly constructed rad9::URA3 (yMP11498), rad17::URA3 (yMP11474), and rad24::URA3 (yMP11477) strains (described above), using methyl methanesulfonate (MMS) sensitivity as an assay.

The rad6 disruption (A364a background) was kindly provided by BARBARA GARVIK. It was derived from yMP10381 by one-step gene replacement (ROTHSTEIN 1983 ) using a 2-kb BamHI-HindIII fragment of plasmid pJJ211 (kindly provided by LOUISE PRAKASH), which contains an allele of RAD6 in which an internal 0.6-kb EcoRI fragment is replaced with LEU2. The deletion was confirmed by genomic Southern blotting (data not shown).

The rad52 disruption was constructed by PCR-based gene replacement (BAUDIN et al. 1993 ) using oligonucleotides designed to delete >90% of the coding sequences. The oligonucleotides used were as follows: OLIGO 1: 5'-GAA AAA TAT AGC GGC GGG CGG GTT ACG CGA CCG GTA TCG AAG GAA ACA GCT ATG ACC ATG-3' and OLIGO 2: 5'-GAT GCA AAT TTT TTA TTT GTT TCG GCC AGG AAG CGT TTC AGT TGT AAA ACG ACG GCC AGT-3'. PCR using pJJ250 (JONES and PRAKASH 1990 ) as a template generated an intact LEU2 gene flanked by sequence homology to RAD52. The PCR product was used to transform parent strain yMP10381, resulting in the construction of rad52::LEU2 (yMP11450) by one-step gene replacement (ROTHSTEIN 1983 ). The deletion strain was confirmed by PCR analysis of genomic DNA followed by diagnostic restriction mapping (data not shown).

The rad27 (yMP11400) strain was kindly provided by ELIZABETH JENSEN of the Seattle Project. It was constructed by PCR-based gene replacement (BAUDIN et al. 1993 ) using oligonucleotides designed to delete >90% of the coding sequences. The oligonucleotides used were as follows: OLIGO 1: 5'-TGG AAA GAA ATA GGA AAC GGA CAC CGG AAG AAA AAA TAT GAG GAA ACA GCT ATG ACC ATG-3' and OLIGO 2: 5'-CCC TCA TCT TCT TCC CTT TGT GAC TTT ATT CTT ATT TTT GGT TGT AAA ACG ACG GCC AGT-3'. PCR using pJJ250 (JONES and PRAKASH 1990 ) as a template generated an intact LEU2 gene flanked by sequence homology to RAD27. The PCR product was used to transform parent strain yMP10381, resulting in the construction of rad27::LEU2 (yMP11450) by one-step gene replacement (ROTHSTEIN 1983 ). The deletion strain was confirmed by PCR analysis of genomic DNA followed by diagnostic restriction mapping (data not shown). As this strain was temperature sensitive for mitotic growth at 30°, all manipulations with this mutant were done at 23°.

YEF615 was kindly provided by ERIC FOSS. It was derived from yMP11450 by selecting for a His⁺ sister chromatid recombinant and then subsequently for a Ura^- derivative of the recombinant.

The msh2, rad18, and rev3 constructions were described in PAULOVICH et al. 1997 . The SCR::URA3 construct and the rad1 allele were introduced in all strains in this study by genetic crosses originating with either 8202SCR or 8271-1a (A364a derivatives), which are listed in Table 1 and described in KADYK and HARTWELL 1992 , KADYK and HARTWELL 1993 .

Detection of SCEs:
The SCR::URA3 sister chromatid recombination substrate has been described and diagrammed previously in detail (KADYK and HARTWELL 1992 , KADYK and HARTWELL 1993 ). Briefly, tandem, nonidentical ade3 deletions, oriented head-to-tail and containing a 305-bp region of overlap, were integrated near the centromere of chromosome III between LEU2 and HIS4. All strains used in this study also contain the ade3-130 deletion mutation, which prevents recombination between the endogenous ade3-130 locus and the SCE substrate (KADYK and HARTWELL 1992 ). Both the endogenous ade3-130 mutation and the tandem ade3 deletions in the recombination substrate confer auxotrophy for both adenine and histidine (KADYK and HARTWELL 1992 ). Strains bearing these ade3 alleles arrest within one cell cycle of being plated on C-His medium, and, therefore, all recombinants studied occur in the same cell cycle that receives irradiation (KADYK and HARTWELL 1992 ). Either an unequal reciprocal recombination event or a gene conversion event between tandem deletions on sister chromatids can reconstitute a functional ADE3 gene, and, hence, these events can be selected on C-His medium (KADYK and HARTWELL 1992 ). Intrachromosomal recombination cannot be detected in our assay because it results in the formation of an episome containing ADE3 and URA3 but lacking a centromere and an origin of replication. These recombinants are not recovered as viable His+ colonies (see KADYK and HARTWELL 1992 ).

Kill curves, UV-induced mutagenesis, and UV-induced SCE rates:
Cells (4 x 10⁸) were harvested by centrifugation from log phase cultures grown overnight at 30° in YM-1 + 2% glucose medium. Cells were resuspended in 133 ml YM-1 + 2% glucose medium and synchronized in the G1 phase by the addition of factor to a final concentration of 5 µM. After a 2.5-hr incubation at 30°, cells were harvested by centrifugation and resuspended in 20 ml H₂O that had been precooled to 4° to inhibit cell cycle progression during subsequent UV irradiation. After sonication to separate cells, an additional 190 ml of precooled H₂O (4°) was added to the cells. We determined in pilot experiments (data not shown) that cell densities >10⁷ cells/ml resulted in a decrease in the effective dose of UV irradiation that each cell was exposed to (based on cell killing), presumably as a result of the cells shielding each other from the UV source. Therefore, 10-ml aliquots (~4 x 10⁶ cells/ml) were transferred to standard 100 x 15-mm plastic petri dishes and exposed, individually and while constantly swirling, to varying doses of UV irradiation. UV irradiation was delivered by a UVP source (model UVS-28; Upland, CA) at a dose rate of 0.04 J/m²/sec (0–5 J/m² total dose range), 0.083 J/m²/sec (5–10 J/m² total dose range), or 0.84 J/m²/sec (10–75 J/m² total dose range). Typically, to obtain enough irradiated cells, three aliquots were irradiated for each UV dose examined in a given experiment. The three aliquots were pooled on ice immediately after UV exposure. Pooled, irradiated samples for each UV dose were harvested by centrifugation and resuspended in 1 ml H₂O (4°) + 0.1 mg/ml pronase to degrade residual factor. (Cells were maintained at 4° to inhibit their dividing before plating.) After resonication and dilution into sterile normal saline (4°), total cell concentration was determined using a Coulter channelizer (Coulter Electronics, Hialeah, FL). Viable cells per milliliter were determined by plating serial dilutions onto C + 2% glucose medium and scoring the number of colony-forming units (CFU) after 3 days of growth at 30°. Viability was calculated as CFU per milliliter per total cells per milliliter. SCE rates were determined by plating serial dilutions onto C-His + 2% glucose medium, selecting for sister chromatid recombinants. SCE rates were expressed as His⁺ cells per 10⁶ viable cells for each UV dose tested. Mutation rates were determined by plating serial dilutions onto C-Arg-Ser + canavanine + 2% glucose medium, selecting for forward mutation to canavanine resistance. Mutation rates were expressed as canavanine-resistant cells per 10⁶ viable cells for each UV dose tested. For both mutation and SCE, the rates after UV induction were determined by subtracting the observed rate of events (SCE or mutation) in the starting culture (0 J/m²) from the observed rate after exposure to a given dose of UV irradiation. In a few cases, where the numbers of recombinants or mutants recovered were small (in mutants defective in these processes), the difference between the observed rate after UV exposure and the observed rate of events (SCE or mutation) in the starting culture (0 J/m²) gave a low negative number; in these cases, the point was plotted as zero events induced. Error bars on all kill curve data were calculated as described previously (PAULOVICH et al. 1997 ). All incubations after UV irradiation were done in the dark to minimize the effects of photoreactivation.

Measurement of spontaneous SCE rates:
Spontaneous SCE rates were determined by the method of the median (LEA and COULSON 1948 ). Liquid cultures were grown to saturation in YM-1 + 2% glucose at 30°, sonicated, diluted into sterile normal saline, and plated onto C + 2% glucose medium at a density of ~100 CFU per standard 100 x 15-mm plastic petri dish. After 3 days of growth at 30°, 20 individual colonies per strain were dissected on agar slabs using a sterile scalpel. Each agar slab (containing one individual colony) was transferred into 3 ml sterile normal saline, vortexed vigorously to resuspend the cells, and subjected to sonication to individualize the cells. Exactly 100 µl was removed from each of the 20 samples, and all 20 aliquots (100 µl each) were pooled in a separate tube to be used to assess the average CFU/colony. The pooled sample (2.0 ml) was diluted serially into sterile normal saline, plated onto C + 2% glucose medium, and incubated at 30° for 3 days to determine the average number of viable cells (CFU) in the 20 colonies examined. The remainder (2.9 ml) of each of the 20 samples was processed individually to determine the number of sister chromatid recombinants per colony. Each 2.9-ml sample was harvested by centrifugation and resuspended in 100 µl sterile normal saline, and the entire 100-µl sample was plated onto C-His medium to select for sister chromatid recombinants. After incubation at 30° for 3 days, the number of His⁺ colonies was scored for each of the 20 plates, and the median number of His⁺ colonies for all 20 plates was determined. The rate of production of recombinants was then calculated by the method of the median (LEA and COULSON 1948 ). Standard deviations were obtained by determination of SCE rates as described above for multiple isolates of any given mutant examined, as indicated in the Table 2 legend.

Measurement of spontaneous mutation rates:
Spontaneous mutation rates were determined by the method of the median (LEA and COULSON 1948 ). Liquid cultures were grown to saturation in YM-1 + 2% glucose at 30°, sonicated, diluted into sterile normal saline, and plated onto C + 2% glucose medium at a density of ~100 CFU per standard 100 x 15-mm plastic petri dish. After 3 days of growth at 30°, 20 individual colonies per strain were dissected on agar slabs using a sterile scalpel. Each agar slab (containing one individual colony) was transferred into 5 ml C + 2% glucose medium, vortexed vigorously to resuspend the cells, and subjected to sonication to individualize the cells. Each of the 20 samples was then incubated at 30° for ~24 hr to allow further expansion of the population so that a significant number of Can^r mutants could be obtained. (This extra step was not necessary during measurement of spontaneous SCE rates, which are ~10-fold higher than spontaneous mutation rates.) After this additional 24-hr incubation, exactly 100 µl was removed from each of the 20 samples, and all 20 aliquots (100 µl each) were pooled in a separate tube to be used to assess the average CFU per colony. The pooled sample (2.0 ml) was diluted serially into sterile normal saline, and aliquots were plated onto C + 2% glucose medium and incubated at 30° for 5 days to determine the average number of viable cells (CFU) in the 20 colonies examined.

The remainder (4.9 ml) of each of the 20 samples was processed individually to determine the number of Can^r mutants per culture. Exactly 0.3 ml was removed from each sample, sonicated, and plated onto C-Arg-Ser + canavanine + 2% glucose medium to select for Can^r mutants. After incubation at 30° for 5 days, the number of Can^r colonies was scored for each of the 20 plates, and the median number of Can^r colonies for all 20 plates was determined. The rate of production of mutants was then calculated by the method of the median (LEA and COULSON 1948 ). Standard deviations were obtained by determination of mutation rates as described above for multiple isolates of any given strain examined, as indicated in the Table 2 legend.

	RESULTS

TOP ABSTRACT MATERIALS AND METHODS RESULTS DISCUSSION LITERATURE CITED

After low-dose UV irradiation, rad1 mutants survive but undergo induction of SCE and mutation:
Because rad1 mutants are completely defective in the incision step of nucleotide excision repair (REYNOLDS and FRIEDBERG 1981 ; WILCOX and PRAKASH 1981 ), UV irradiation of rad1 mutants results in the introduction of irreparable covalent changes in the DNA molecule. Therefore, to proliferate after UV irradiation, rad1 cells are forced to replicate a damaged DNA template, resulting in stimulation of both SCE (KADYK and HARTWELL 1993 ) and mutation (JAMES et al. 1978 ; Figure 1).

For the series of experiments described in this study, we designed an excision repair-defective rad1 haploid yeast strain in which we were able to measure the induction of SCE and the induction of mutation. To ensure that all strains studied were distributed uniformly in the cell cycle, cells were synchronized in the G1 phase with factor before UV irradiation. Hence, in our experiments, SCE is induced during or after the ensuing S phase, when sister chromatids are present.

As reported previously (COX and PARRY 1968 ), the rad1 mutant is extremely sensitive to the killing effects of UV irradiation (Figure 2A). Doses of irradiation that do not lower the viability of the wild-type, excision repair-proficient strain are highly lethal to the rad1 excision repair-defective strain. Furthermore, there is a dramatic stimulation of mutation and SCE at this low dose range (KADYK and HARTWELL 1993 ) in the excision-defective strain, but not in the wild-type strain (Figure 2B and Figure C), and we conclude that the rad1 mutant is hypermutable and hyperrecombinogenic in response to UV irradiation. Interestingly, excision repair-defective human XP-A cells are also hypermutable compared with wild-type mammalian cells in response to UV irradiation (KONZE-THOMAS et al. 1982 ). These data are consistent with the model in which irreparable lesions can be accommodated during replication by processes that result in SCE and mutagenesis (Figure 1).

View larger version (14K): In this window In a new window Download PPT slide   Figure 2. Excision repair-defective rad1 cells that survive exposure to UV irradiation undergo induction of SCE and mutation. RAD1 or rad1 cells were synchronized in the G1 phase of the cell cycle and exposed to varying doses of UV irradiation. After UV irradiation, cells were processed as described in MATERIALS AND METHODS to determine viability (A), induction of forward mutation to Canr (B), and induction of SCE (C). All curves are the mean of at least three independent experiments that were performed on independent segregants (as indicated below). The standard deviation is shown for each data point, although in some cases, it is concealed under the symbol used for the data point. Strains used are as follows: wild type (yMP10381, yMP10625, yMP10628); rad1 (yMP10619, yMP10621, yMP10633).

SCE and mutation are also induced in the wild-type strain, although at much higher doses of UV irradiation:
Wild-type cells arrest in the G1 phase in response to UV irradiation, maximizing the probability that nucleotide excision repair of UV photoproducts will be completed before replication begins (SIEDE et al. 1993 , SIEDE et al. 1994 ). Therefore, if SCE and mutagenesis result from replication over unrepaired lesions, one might predict that wild-type cells, benefitting from DNA excision repair and the G1 checkpoint, may not undergo induction of mutation and SCE. Alternatively, at high doses of UV irradiation, some lesions in wild-type cells might escape repair and therefore need to be accommodated during replication, just as irreparable lesions must be accommodated in rad1 cells. This model predicts that SCE and mutation should be induced in the wild type at high doses of UV.

We determined the response of wild-type cells to higher doses of UV irradiation than rad1 cells can tolerate. To achieve comparable killing in wild-type and rad1 backgrounds, wild-type cells must be exposed to approximately sevenfold higher doses of UV irradiation (Figure 3A), as compared to rad1 cells (Figure 2A). Although there was only a small induction of mutation in wild-type cells at low doses of UV irradiation (see Figure 2B), at higher doses, wild-type cells undergo mutation induction at least as effectively as rad1 cells (Figure 3B). Similarly, although there was very little induction of SCE in wild-type cells at low doses of UV irradiation (see Figure 2C), at higher doses (Figure 3C), wild-type cells undergo SCE induction as effectively as rad1 cells (Figure 2C). In fact, both rad1 and wild-type cells reach comparable mutation induction (~75–100 Can^r mutants per 10⁶ viable cells) and SCE induction (~100 recombinants per 10⁶ viable cells) at roughly the same level (50% viability) of survival (compare Figure 2 and Figure 3). These data are consistent with a model in which damage that cannot be repaired in a rad1 cell or that is replicated before completion of repair in a RAD1 cell may be accommodated using SCE and induced mutagenesis.

View larger version (13K): In this window In a new window Download PPT slide   Figure 3. Wild-type cells that survive exposure to UV irradiation undergo induction of SCE and mutation. Rad+ cells were synchronized in the G1 phase of the cell cycle and exposed to varying doses of UV irradiation. After UV irradiation, cells were processed as described in MATERIALS AND METHODS to determine viability (A), induction of forward mutation to Canr (B), and induction of SCE (C). All curves are the mean of at least three independent experiments performed on independent segregants (as indicated below). The standard deviation is shown for each data point, although in some cases, it is concealed under the symbol used for the data point. Strains used are yMP10381, yMP10625, and yMP10628.

REV3 is required for the induction of mutation, but not for the induction of SCE in a rad1 background after UV irradiation:
It had previously been shown that the rev3 mutant is defective in UV-induced mutagenesis (LEMONTT 1971 ; MORRISON et al. 1989 ), and that in vitro, Rev3p and Rev7p form a complex called Pol that is able to replicate over damaged template much more efficiently than other major replicases (NELSON et al. 1996 ). To confirm that mutation induction in our rad1 strains is dependent on REV3, we constructed the rad1 rev3 double mutant and determined its response to UV irradiation. The rad1 rev3 double mutant is more sensitive to UV damage than either the rad1 or the rev3 single mutants (Figure 4A), consistent with the hypothesis that Rev3p is required for translesion synthesis across sites of unrepaired damage. Also consistent with this hypothesis, mutation induction in the rad1 background is dependent on REV3 (Figure 4B).

View larger version (14K): In this window In a new window Download PPT slide   Figure 4. REV3 is required for the induction of mutation, but not for the induction of SCE in a rad1 background after UV irradiation. rad1 or rad1 rev3 cells were synchronized in the G1 phase of the cell cycle and exposed to varying doses of UV irradiation. After UV irradiation, cells were processed as described in MATERIALS AND METHODS to determine viability (A), induction of forward mutation to Canr (B), and induction of SCE (C). All curves are the mean of at least three independent experiments performed on independent segregants (as indicated below). The standard deviation is shown for each data point, although in some cases, it is concealed under the symbol used for the data point. Strains used are as follows: rad1 (yMP10619, yMP10621, yMP10633); rad1 rev3 (yMP10618, yMP10622, yMP11463).

Because it was possible that the Rev3 polymerase replaced the replicative polymerase at sites of damage, and because all UV-induced SCE in a rad1 background were previously shown to be replication dependent (KADYK and HARTWELL 1993 ), it was possible that Rev3p also carried out bypass synthesis at sites of damage, resulting in SCE (see Figure 1). This model predicts that the induction of SCE should be dependent on REV3. However, we found that the rad1 rev3 double mutant induced the same level of SCE as the rad1 single mutant after UV irradiation (Figure 4C). Therefore, we conclude that REV3 is not required for replication-dependent SCE in a rad1 background in response to UV irradiation.

RAD52 is required for the induction of SCE, but not for the induction of mutation in a rad1 background after UV irradiation:
It had previously been shown that the rad1 rad52 mutant is defective in SCE (KADYK and HARTWELL 1993 ). To confirm that SCE induction in our rad1 strains is dependent on RAD52, we constructed the rad1 rad52 double mutant and determined its response to UV irradiation. The rad1 rad52 double mutant is more sensitive to UV damage than either the rad1 or the rad52 single mutants (Figure 5A; KADYK and HARTWELL 1993 ), consistent with the hypothesis that Rad52p is required for recombinational bypass of irreparable damage (see Figure 1). Also consistent with this hypothesis, SCE induction in the rad1 background is completely dependent on RAD52 (Figure 5C; KADYK and HARTWELL 1993 ).

View larger version (14K): In this window In a new window Download PPT slide   Figure 5. RAD52 is required for the induction of SCE, but not for the induction of mutation in a rad1 background after UV irradiation. rad1 or rad1 rad52 cells were synchronized in the G1 phase of the cell cycle and exposed to varying doses of UV irradiation. After UV irradiation, cells were processed as described in MATERIALS AND METHODS to determine viability (A), induction of forward mutation to Canr (B), and induction of SCE (C). All curves are the mean of at least three independent experiments performed on independent segregants (as indicated below). The standard deviation is shown for each data point, although in some cases, it is concealed under the symbol used for the data point. Strains used are as follows: rad1 (yMP10619, yMP10621, yMP10633); rad1 rad52 (yMP11458, yMP11459, yMP11461).

In contrast, the rad1 rad52 mutant was proficient at induced mutagenesis (Figure 5B). In fact, the double mutant is actually hypermutable because it reaches comparable levels of mutagenesis at lower doses of UV irradiation than the rad1 single mutant. The high induction of mutation in the rad1 rad52 mutant is consistent with a model in which lesions that cannot be tolerated recombinationally (because of deletion of RAD52) are channeled into a mutagenic repair pathway. Interestingly, both rad1 and rad1 rad52 mutants reach comparable mutation induction (~65 Can^r mutants per 10⁶ viable cells) at roughly the same level (40% viability) of survival (compare Figure 2A and Figure B, and Figure 5A and Figure B), raising the possibility that accumulation of lethal mutations is what kills the cells.

Deletion of RAD50 does not suppress the UV sensitivity of rad1 rad52:
One possible explanation for the extreme sensitivity of rad1 rad52 is that cells are attempting to execute SCE at sites of lesions, but that in the absence of Rad52p, lethal recombination intermediates are formed. This phenomenon has been observed in spo13 rad52 yeast mutants attempting homologue recombination in meiosis (MALONE et al. 1991 ). Spore viability of a spo13 rad52 homozygous diploid can be rescued by deletion of RAD50, which blocks an earlier step in recombination and prevents formation of lethal recombination intermediates (MALONE et al. 1991 ). We tested the possibility that this was occurring in our experiments by assaying sensitivity to UV irradiation in a rad1 rad50 rad52 triple mutant. If the UV sensitivity of the rad1 rad52 mutant resulted from the accumulation of RAD50-dependent lethal recombination intermediates, then we would expect deletion of RAD50 to partially suppress the UV sensitivity of this strain. However, the rad1 rad50 and rad1 rad50 rad52 mutants had identical UV kill curves (data not shown), making this model unlikely.

RAD9, RAD17, RAD24, and MEC3 function to help rad1 cells tolerate irreparable UV-induced damage:
To investigate whether RAD9, RAD17, RAD24, and MEC3 [all of which play a role in the S phase DNA damage response (LONGHESE et al. 1996A ; PAULOVICH et al. 1997 )] are required for the survival of rad1 cells after UV irradiation, we determined the sensitivity of double mutants to UV damage. rad1 rad9, rad1 rad17, rad1 rad24, and rad1 mec3 double mutants are all 5 to 10 times more sensitive to UV irradiation than the rad1 single mutant (see Figure 6A, 10 J/m²/sec dose; note that the rad1 rad9 mutant is slightly less sensitive than the others). We conclude that in the absence of nucleotide excision repair, checkpoint genes must play some essential role in tolerating UV-induced damage. A similar result has been seen in a rad16 excision repair-defective background (KISER and WEINERT 1996 ).

View larger version (45K): In this window In a new window Download PPT slide   Figure 6. Role of RAD9, RAD17, RAD24, and MEC3 in SCE and induced mutagenesis in UV-treated rad1 cells. rad1 rad9, rad1 rad17, rad1 rad24, or rad1 mec3 double-mutant cells were synchronized in the G1 phase of the cell cycle and exposed to varying doses of UV irradiation. After UV irradiation, cells were processed as described in MATERIALS AND METHODS to determine viability (A), induction of forward mutation to Canr (B), and induction of SCE (C). All curves are the mean of at least three independent experiments performed on independent segregants (as indicated below). The standard deviation is shown for each data point, although in some cases, it is concealed under the symbol used for the data point. Strains used are as follows: wild type (yMP10381, yMP10625, yMP10628); rad1 (yMP10619, yMP10621, yMP-10633); rad1 rad9 (yMP11048, yMP11049, yMP11050); rad1 rad17 (yMP11095, yMP11096, yMP11100); rad1 rad24 (yMP11005, yMP11007, yMP11013); rad1 mec3 (yMP11430, yMP11434, yMP11444).

RAD9, RAD17, RAD24, and MEC3 are required for UV-induced mutagenesis in a rad1 background:
Because RAD9, RAD17, RAD24, and MEC3 are required for slowing S phase progression in response to DNA damage (PAULOVICH et al. 1997 ), and because replicating irreparably damaged DNA results in mutation (JAMES et al. 1978 ), we examined whether these genes are necessary for induced mutagenesis in rad1 cells. We measured the rates of forward mutation at the CAN1 locus after UV irradiation in rad1 rad9, rad1 rad17, rad1 rad24, and rad1 mec3 double mutants. CAN1 encodes an arginine permease (AHMAD and BUSSEY 1986 ), and any loss-of-function mutation at this locus confers resistance to canavanine. Hence, there should be no bias as to the spectrum of mutation we can detect. We found that deletion of any one of these four checkpoint genes drastically reduces induced mutagenesis (Figure 6B), comparable to deletion of the REV3 locus (Figure 4B). Furthermore, we found that all possible combinations of rad9, rad17, and rad24 in a rad1 background also confer complete defects in induced mutagenesis (see Figure 7B). We conclude that RAD9, RAD17, RAD24, and MEC3 are required for REV3-dependent, UV-induced mutagenesis in a rad1 background.

View larger version (46K): In this window In a new window Download PPT slide   Figure 7. Effects of combining checkpoint deletions on UV induction of SCE and mutagenesis in a rad1 background. rad1 rad9 rad17, rad1 rad9 rad24, rad1 rad17 rad24, or rad1 rad9 rad17 rad24 cells were synchronized in the G1 phase of the cell cycle and exposed to varying doses of UV irradiation. After UV irradiation, cells were processed as described in MATERIALS AND METHODS to determine viability (A), induction of forward mutation to Canr (B), and induction of SCE (C). All curves are the average or mean of two to three independent experiments performed on independent segregants (as indicated below). The range or standard deviation is shown for each data point, although in some cases, it is concealed under the symbol used for the data point. Strains used are as follows: wild type (yMP10381, yMP10625, yMP10628); rad1 (yMP10619, yMP10621, yMP10633); rad1 rad9 rad17 (yMP11550, yMP11557); rad1 rad9 rad24 (yMP11436, yMP11438); rad1 rad17 rad24 (yMP11452, yMP11453, yMP11454); rad1 rad9 rad17 rad24 (yMP11554, yMP11556).

RAD9 and RAD17, but neither RAD24 nor MEC3, are required for maximal UV induction of replication-dependent SCE in a rad1 background:
Because RAD9, RAD17, RAD24, and MEC3 are required for slowing S phase progression in response to DNA damage (PAULOVICH et al. 1997 ), and because replicating damaged DNA results in SCE (KADYK and HARTWELL 1993 ), we were interested in asking whether these genes are necessary for UV-induced SCE. We measured the induction of SCE after UV irradiation in rad1 rad9, rad1 rad17, rad1 rad24, and rad1 mec3 double mutants. We found that rad1 rad24 and rad1 mec3 double mutants induce levels of SCE comparable to the rad1 single mutant after UV irradiation (Figure 6C). However, rad1 rad9 and rad1 rad17 mutants induce only about half of the level of SCE induced in the rad1 single mutant (Figure 6C). We conclude that UV-induced SCE in a rad1 background is not dependent on RAD24 and MEC3, but is partially dependent on RAD9 and RAD17.

The partial SCE defects of rad9 and rad17 are not additive:
We determined whether Rad9p and Rad17p were acting in the same pathway for SCE by constructing the rad1 rad9 rad17 triple mutant and measuring its SCE profile. As can be seen in Figure 7C, the rad1 rad9 rad17 mutant has a partial defect in the induction of SCE that is comparable to that of either the rad1 rad9 or rad1 rad17 mutants (see Figure 6C). We conclude that the SCE induction defects in rad1 rad9 and rad1 rad17 are not additive, and, hence, that Rad9p and Rad17p act in the same pathway of SCE induction.

UV induction of SCE in rad1 rad24 is partially dependent on RAD9 and suppressed by RAD17:
As shown in Figure 6C, rad1 rad24 has the same SCE profile as the rad1 single mutant, in contrast to the rad1 rad9 and rad1 rad17 mutants, which show partial defects in induction of SCE (Figure 6C). To determine if the SCE observed in the rad1 rad24 mutant was induced via the RAD9- and RAD17-dependent pathway, we measured induction in rad1 rad9 rad24 and rad1 rad17 rad24 triple mutants. The rad1 rad9 rad24 triple mutant showed the same induction kinetics as the rad1 rad9 mutant (compare Figure 6C and Figure 7C), and, therefore, we conclude that SCE that is induced in rad1 rad24, just like that which is induced in the rad1 single mutant, is partially dependent on RAD9.

Surprisingly, the rad1 rad17 rad24 triple mutant showed a hyper-recombination phenotype (Figure 7C), stimulating an SCE level several times higher than any strain examined so far. We conclude that RAD17 suppresses SCE in the rad1 rad24 mutant. [Interestingly, the rad17 single mutant has a similar hyper-recombinogenic phenotype in response to UV (see below and Figure 8C).]

View larger version (41K): In this window In a new window Download PPT slide   Figure 8. Effects of checkpoint deletions on UV induction of SCE and mutagenesis in an excision repair-proficient background. rad9, rad17, rad24, and mec3 single mutants were synchronized in the G1 phase of the cell cycle and exposed to varying doses of UV irradiation. After UV irradiation, cells were processed as described in MATERIALS AND METHODS to determine viability (A), induction of forward mutation to Canr (B), and induction of SCE (C). All curves are the average or mean of two to three independent experiments performed on independent segregants (as indicated below). The range or standard deviation is shown for each data point, although in some cases, it is concealed under the symbol used for the data point. Strains used are as follows: wild type (yMP10381, yMP10625, yMP10628); rad9 (yMP10899, yMP11030, yMP11038); rad17 (yMP11089, yMP11094, yMP11097); rad24 (yMP10533, yMP11006, yMP11011, yMP11020); mec3 (yMP11446, yMP11447).

The hyper-recombinogenic phenotype of rad1 rad17 rad24 is partially dependent on RAD9:
To test whether the SCE in rad1 rad17 rad24 was induced through the RAD9-dependent SCE pathway, we constructed the rad1 rad9 rad17 rad24 mutant and measured its response to UV irradiation. The quadruple mutant has an approximately fourfold lower level of induction of SCE than the rad1 rad17 rad24 triple mutant (Figure 7C). Hence, the hyper-recombination phenotype of the rad1 rad17 rad24 mutant is partially dependent on RAD9, and we conclude that SCE induced in rad1 rad17 rad24 is partially occurring through the RAD9-dependent pathway. Interestingly, however, the maximal induction in the quadruple mutant is still two to four times greater than the maximal level of induction in either a rad1 (Figure 2C), rad1 rad9 (Figure 6C), or a rad1 rad9 rad24 mutant (Figure 7C), suggesting that the hyper-recombination in the triple mutant occurs through a non-RAD9-dependent mechanism.

Checkpoint mutants in a rad1 background do not have elevated levels of spontaneous SCE or mutagenesis:
Induction of mutation and SCE may be saturable (see Figure 2 Figure 3 Figure 4 Figure 5 Figure 6), and the biological basis for the possible plateau in these induction curves has not been determined. Nonetheless, the possibility that these processes were saturable raised the issue that the reason checkpoint mutants might appear to be defective in UV-induced mutagenesis or SCE was simply that the spontaneous rates of these events were elevated in the checkpoint mutants. If the spontaneous levels were already at saturation, then the mutants would not be able to further induce SCE and mutation in response to UV irradiation and would, therefore, appear in our assay to be defective in these processes. To address this possibility, we determined the spontaneous rates of mutation and of SCE in every single and double mutant examined in this study (Table 2). None of the double mutants examined in this study has a spontaneous rate of SCE that is higher than the rad1 single mutant. We conclude that in no case does an elevated rate of spontaneous SCE explain the UV induction defects observed in the double mutants.

With the exception of rad1 mec3, rad1 rad17, and rad1 rad52, none of the double mutants examined in this study has a spontaneous rate of mutation that is significantly higher than the rad1 single mutant. The rad1 rad17 and rad1 mec3 mutants have slightly higher spontaneous mutation rates (23.66 x 10^-7 and 25.30 x 10^-7, respectively) than the rad1 mutant (15.05 x 10^-7); however, mutagenesis can be induced to at least a rate of >1000 x 10^-7 (Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7), which provides an ample margin to detect induction if the double mutant is proficient. For example, the rad1 rad52 mutant has a higher spontaneous rate (122.58 x 10^-7) than the rad1 mutant (15.05 x 10^-7). Nonetheless, the elevated spontaneous rate in this mutant did not prevent further induced mutagenesis in response to UV, to an even greater extent than in the rad1 single mutant (see Figure 5B). We conclude that in no case does an elevated rate of spontaneous mutagenesis explain the defects in UV induction observed in the double mutants.

RAD9, RAD17, RAD24, and MEC3 are required for UV-induced mutagenesis in an excision repair-proficient background:
UV-induced mutations are fixed at different points in the cell cycle in rad1 and wild-type cells (reviewed in FRIEDBERG et al. 1995 ). Mutations arise with high probability prereplicatively in excision repair-proficient cells and predominantly postreplicatively in excision repair-defective cells (ECKARDT and HAYNES 1977 ; JAMES and KILBEY 1977 ; KILBEY et al. 1978 ; ECKARDT et al. 1980 ; SIEDE et al. 1983 ), suggesting that there may be more than one mechanism of induced mutagenesis (both REV3 dependent).

If there are mechanistic differences between induced mutagenesis in RAD1 and rad1 cells, mutagenesis in these two backgrounds may show different dependencies on the checkpoint genes. Therefore, having determined that RAD9, RAD17, RAD24, and MEC3 are required for mutation induction in a rad1 background (Figure 6B), we determined whether they are required for mutagenesis in an excision repair-proficient background. Previous studies (PRAKASH 1974 ; LAWRENCE and CHRISTENSEN 1976 ) have shown that the rad9 mutant may be defective in UV- and chemically induced mutagenesis in RAD1 cells. rad9, rad17, rad24, and mec3 single mutants display a mild degree (5–10-fold) of sensitivity to UV irradiation, as compared to the wild type (Figure 8A; LYDALL and WEINERT 1995 ). [Interestingly, in this RAD1 background, the rad9 mutant is more UV sensitive than the other single mutants (Figure 8A), whereas in the rad1 background, rad9 conferred a slightly lesser sensitivity to UV irradiation than did the other mutants (Figure 6A).] We find that rad9, rad24, and mec3 mutants show decreased induction of mutation compared to wild type after UV irradiation (Figure 8B). Whereas the rad17 mutant may be slightly hypomutable compared to the wild type, it is not as defective as the other mutants (Figure 8B). Hence, UV-induced mutagenesis in an excision repair-proficient background is largely dependent on RAD9, RAD24, and MEC3, and to a lesser degree dependent on RAD17. Therefore, mutating these checkpoint genes does not allow us to genetically separate the mutagenesis pathway in RAD1 cells from that in rad1 cells.

RAD9, RAD17, RAD24, and MEC3 are not required for UV-induced SCE in an excision repair-proficient background:
In the rad1 mutant, without excision repair and without replication, recombinogenic, single-stranded DNA gaps cannot be generated. Hence, the SCE that occurs in a rad1 background is completely dependent on DNA replication (KADYK and HARTWELL 1993 ). UV-induced SCE in a rad1 mutant is presumably the result of postreplication repair of daughter strand gaps formed during replication across UV lesions in the template strand (see Figure 1 and Introduction).

SCE occurring in wild-type cells synchronized in the G1 phase before irradiation (Figure 3C) may result from the same mechanism (postreplication repair) if some lesions escape surveillance and are replicated before excision repair. However, unlike rad1 cells, wild-type cells have a second possible mechanism for SCE induction. If, in wild-type cells, replication forks were to encounter nucleotide excision repair-induced single-stranded gaps, this could result in the formation of one intact and one broken sister chromatid. After replication, the broken chromatid could then be repaired by homologous recombination using the intact sister as a template.

We have shown that SCE in rad1 cells is partially dependent on RAD9 and RAD17, but not dependent on RAD24 and MEC3. Given the possibility that SCE is induced via different mechanisms in rad1 cells compared to wild type, we determined whether any of these genes are required for SCE in an excision repair-proficient background. We find that none of the checkpoint genes is necessary for SCE induction in a RAD1 background (Figure 8C). Furthermore, the rad17 and mec3 mutants are actually hyper-recombinogenic (Figure 8C). We conclude that none of these checkpoint genes is required for UV-induced SCE in a RAD1 background, and that Rad17p and Mec3p actually suppress SCE in excision repair-proficient cells. These differences in genetic requirements for SCE in wild-type vs. rad1 cells are consistent with the model that SCE occurs at least in part through different mechanisms in nucleotide excision repair-competent and -deficient cells.

RAD1, REV3, RAD9, RAD17, RAD24, and MEC3 are not required for spontaneous SCE or mutation during mitotic growth:
As previously discussed, the apparent defect in induced mutagenesis in these checkpoint mutants could result if the mutants had levels of spontaneous mutagenesis so high that further induction would be impossible, either because of saturation of the mutagenesis system or because of accumulation of lethal mutations. However, as can be seen from the data in Table 2, rad1, rev3, rad9, rad17, rad24, and mec3 single mutants have rates of spontaneous SCE and mutation comparable to that of the wild type. We conclude that in no case can the observed defects in induced mutagenesis in checkpoint mutants be explained by elevated rates of spontaneous mutagenesis. Note that despite the fact that REV3, RAD9, RAD17, RAD24, and MEC3 are required for UV-induced mutagenesis (Figure 6A), none of these genes is necessary for a wild-type rate of spontaneous mutagenesis (Table 2).

Dramatic elevations in the spontaneous mutation rate are seen in the rad1 mutant (15.05 x 10^-7) and especially in the rad52 mutant (45.39 x 10^-7; VON BORSTEL et al. 1971 ) compared to the wild type (4.11 x 10^-7; Table 2). The elevated level observed in the rad52 mutant is consistent with a model in which lesions are channeled into the mutagenic repair pathway when recombinational repair is not available (see Figure 1). Furthermore, the elevation in spontaneous mutation rates in the rad1 and the rad52 single mutants is synergistic because the increase in the rad1 rad52 double mutant is greater than the sum of the increases in the single mutants, consistent with a model in which excision repair and recombination repair may compete for common lesions.

The mutator phenotype of the mismatch repair mutant msh2 is not dependent on RAD17 or RAD24:
msh2 cells, defective in mismatch repair, have an elevated spontaneous mutation rate compared to that of the wild type (Table 2; REENAN and KOLODNER 1992 ). Mutations presumably result when errors made by cellular replicases go unrepaired. Because checkpoint genes are necessary for the S phase DNA damage response (PAULOVICH and HARTWELL 1995 ; LONGHESE et al. 1996A ; PAULOVICH et al. 1997 ), and because they are required for UV-induced mutagenesis, we asked whether the high level of spontaneous mutation in the msh2 mutant was dependent on two representative checkpoint genes, RAD17 or RAD24. We constructed rad17 msh2 and rad24 msh2 double mutants and measured their spontaneous mutation rates. Both double mutants have spontaneous mutation rates similar to the msh2 single mutant (Table 2). We conclude that neither RAD17 nor RAD24 is necessary for spontaneous mutagenesis in the msh2 mutant, and, therefore, that spontaneous damage normally repaired by the MSH2 pathway is not channeled into the RAD17- and RAD24-dependent mutagenic pathway in the msh2 mutant.

Mutation of RAD9, RAD17, or RAD24 is synthetic lethal with mutation of RAD27:
A mutator phenotype has recently been described for the rad27 mutant (TISHKOFF et al. 1997 ). The mutator phenotype of rad27 is not dependent on mismatch repair (TISHKOFF et al. 1997 ). Moreover, the spectrum of mutations that arise in the rad27 mutant is unique (TISHKOFF et al. 1997 ). Because checkpoint genes are necessary for UV-induced mutagenesis, we wanted to determine if the high rate of spontaneous mutation in the rad27 mutant was occurring through the checkpoint-dependent mutational system. When we attempted to construct rad9 rad27, rad17 rad27, and rad24 rad27 double mutants by crossing haploid parent strains carrying either rad27 or a checkpoint gene deletion, viability predominantly segregated 3:1 in these tetrads, and no rad9 rad27, rad17 rad27, or rad24 rad27 double mutants were recovered. (Furthermore, the majority of dead segregants were inferred to be double mutants.) We conclude that mutation of RAD9, RAD17, or RAD24 is synthetic lethal with mutation of RAD27, raising the interesting possibility that spontaneous lesions occurring in a rad27 background might be handled through the checkpoint-dependent mutational system. [Of course, there may also be other functions of checkpoint genes that are essential in rad27 cells. Synthetic lethality between rad9 and rad27 has been shown by others (VALLEN and CROSS 1995 ).]

rad1 rad18 and rad1 rad6 double mutants have low plating efficiency:
Both RAD6 and RAD18 confer severe sensitivity to UV irradiation (COX and PARRY 1968 ; FRIEDBERG et al. 1995 ), and both are necessary for postreplication repair (PRAKASH 1981 ) and for UV-induced mutagenesis (LAWRENCE and CHRISTENSEN 1976 ). Therefore, we wanted to determine whether either gene was necessary for sister chromatid recombination. We crossed a rad1 parent strain to a strain carrying either rad6 or rad18. We were able to recover the double mutants at the expected frequency. However, both the rad1 rad18 and rad1 rad6 double mutants had a severe growth defect in our A364a background that was associated with plating efficiencies of 1.5 and 22%, respectively. The low plating efficiencies of these double mutants made it technically unfeasible to determine their UV induction curves for mutation and SCE.

	DISCUSSION

TOP ABSTRACT MATERIALS AND METHODS RESULTS DISCUSSION LITERATURE CITED

Checkpoint genes are involved in replicating irreparable DNA damage:
The role of RAD9, RAD17, RAD24, and MEC3 in the regulation of cell cycle progression in response to DNA damage is well established (WEINERT and HARTWELL 1988 , WEINERT and HARTWELL 1990 , WEINERT and HARTWELL 1993 ; WEINERT et al. 1994 ). Some of these genes have also been implicated in the processing of DNA damage (LYDALL and WEINERT 1995 ). We find that rad1 rad9, rad1 rad17, rad1 rad24, and rad1 mec3 mutants are all more sensitive to UV-induced killing than the rad1 single mutant, suggesting a role for these genes in helping cells survive DNA damage, even in the absence of nucleotide excision repair (Figure 6A; see KISER and WEINERT 1996 for similar results in rad16 background). Furthermore, we show that mutation induction in rad1 cells is dependent on RAD9, RAD17, RAD24, and MEC3, and that SCE induction is partially dependent on RAD9 and RAD17 (Figure 6B and Figure C). Therefore, checkpoint genes not only control cell cycle progression in response to damage, but they also play a role in accommodating DNA damage during replication.

Checkpoint genes may play either a direct or an indirect role in mutagenesis and replication-dependent SCE:
One possible explanation for the dependence of UV-induced mutagenesis on Rad9p, Rad17p, Rad24p, and Mec3p is that these proteins may be directly involved in translesion synthesis. For example, they may be physically associated with the Rev3p-containing Pol complex. Specifically, because RAD24 contains areas of similarity to RF-C subunits and shows genetic interactions with RFC1 (LYDALL and WEINERT 1997 ), perhaps in response to DNA damage, Rad24p becomes associated with RF-C, and this association results in loading of the Rev3 polymerase rather than the normal replicase. Another possibility is that a putative Rad17p-dependent exonuclease [Rad17p is homologous to a 3'-5' exonuclease from Ustilago; see LYDALL and WEINERT 1995 ] may degrade the 3' end of nascent strands terminated at UV lesions, allowing the Rev3p polymerase the opportunity to load onto the primer and subsequently replicate over the UV lesion. Alternatively, the role of checkpoint genes in induced mutagenesis may be indirect. For example, transcriptional induction of a variety of genes in response to UV irradiation has been shown to be dependent on the checkpoint genes in both excision repair-proficient and excision repair-deficient cells (ABOUSSEKHRA et al. 1996 ; KISER and WEINERT 1996 ). Therefore, it is possible that the dependence of induced mutagenesis on checkpoint genes reflects defects in checkpoint mutants in the transcriptional induction of genes that are directly involved in translesion synthesis.

In contrast to induced mutagenesis, replication-dependent SCE in rad1 cells does not require Rad24p and Mec3p, but does in part depend on Rad9p and Rad17p (Figure 6C). As with mutation induction, Rad9p and Rad17p may play either a direct or an indirect role in SCE. For example, they may associate with the replication complex at sites of damage to facilitate template switching and bypass of lesions (Figure 1, box), or they may be an integral component of the recombinational apparatus involved in repairing daughter strand gaps. The observation that some but not all the checkpoint proteins are required for SCE may favor models of direct involvement in the process over more indirect models, such as a general requirement for transcriptional induction, as discussed above. However, there certainly are documented differences in phenotypes among checkpoint mutants with respect to DNA damage-induced transcription of repair genes (KISER and WEINERT 1996 ). Nonetheless, the possibility that the observed partial defects are caused by transcriptional induction defects in the checkpoint mutants seems less likely because rad1 rad17 rad24 has a hyper-recombinogenic phenotype (Figure 7C), yet it would presumably have at least as much of a transcriptional induction defect as the rad1 rad17 mutant, which is partially defective in SCE (Figure 6C).

What is Rad17p's role in SCE?
RAD17 is unique among all genes examined in that it is required for SCE in some backgrounds, whereas it acts as a suppressor of SCE in other backgrounds. For example, maximal induction of SCE in the rad1 rad17 (Figure 6C) mutant is about half of the maximal induction in the rad1 single mutant, demonstrating partial dependence of replication-dependent SCE on RAD17. Paradoxically, deletion of RAD17 in the rad1 rad24 strain results in a hyper-recombination phenotype, with maximal level of induction of SCE in the rad1 rad17 rad24 triple mutant being four to five times higher than that in the rad1 rad24 double mutant (Figure 7C). Hence, it appears as though, at least in an excision repair-defective background, the ability of the deletion of RAD17 to cause a hyper-recombination phenotype is limited to backgrounds in which RAD24 has also been deleted. These epistatic interactions are depicted in a genetic model (suggested by TED WEINERT) in Figure 9. (Interestingly, Rad9p opposes the activity of a Rad17p-dependent accumulation of single-strand DNA at telomeres in cdc13 cells at nonpermissive temperature, whereas in UV-irradiated rad1 cells, Rad9p and Rad17p act together to facilitate SCE. While we do not understand the biochemical basis of this difference, it may be caused by different substrates in the two systems.)

View larger version (22K): In this window In a new window Download PPT slide   Figure 9. Genetic pathway showing epistatic interactions between RAD9, RAD17, RAD24, MEC3, RAD52, and REV3. (A) In the rad1 mutant, Rad9p, Rad17p, Rad24p, and Rad52p all regulate SCE. Our data can be explained by a model in which Rad9p and Rad52p positively regulate SCE, Rad24p negatively regulates SCE, and Rad17p negatively regulates both Rad24p and SCE. RAD9, RAD17, RAD24, MEC3, and REV3 are all required for UV-induced mutagenesis in the rad1 mutant. (B) In excision repair-proficient (RAD1) cells, Rad17p and Mec3p are suppressors of SCE, and RAD9, RAD17, RAD24, MEC3, and REV3 are all required for UV-induced mutagenesis.

Relationship between defects in replication-dependent SCE and mutagenesis and defects in S phase regulation:
In response to alkylation damage, wild-type yeast cells dramatically slow the rate at which chromosomal DNA is replicated (PAULOVICH et al. 1995). The mec1-1 and rad53 mutants, in contrast, replicate damaged and undamaged DNA at roughly the same rate. rad9, rad17, and rad24 have an intermediate phenotype; they replicate damaged DNA slower than mec1-1 and rad53, but faster than wild type in response to damage (PAULOVICH et al. 1995, PAULOVICH et al. 1997 ). We have observed similar effects of these mutations during S phase in a rad1 background in response to UV irradiation (data not shown). One model we proposed (PAULOVICH et al. 1997 ) to explain these two different phenotypic classes is that slowing of S phase is the result of cells' replicating over DNA lesions using either translesion or bypass synthesis. If mec1-1 and rad53 were defective in both translesion and bypass synthesis, whereas rad9, rad17, and rad24 were defective in only one of these processes, then these differences could explain the two phenotypic classes of defects in S phase regulation. So far, our data are consistent with this model because, despite the fact that rad9, rad17, and rad24 are defective in UV-induced mutagenesis (Figure 6B), all mutants are able to carry out at least some sister chromatid recombination (Figure 6C). The sister chromatid recombination occurring during S phase in these mutants could account for a partial slowing of S phase in response to damage. It will be interesting to measure UV induction of mutation and SCE in rad1 mec1 and rad1 rad53 strains, as this model predicts that these mutants will be completely defective in both mutation and SCE induction.

Relationship between defects in replication-dependent SCE and mutagenesis and defects in postreplication repair:
UV photoproducts block the progress of DNA polymerases and consequently cause the formation of daughter strand gaps across lesions during replication (PRAKASH 1981 ; reviewed in FRIEDBERG et al. 1995 ). The reconstitution of high molecular weight DNA after daughter strand gap formation is called postreplication repair, and it has been shown to be dependent on RAD6, RAD18, and RAD52 in a rad1 background (PRAKASH 1981 ). Because rad1 rev3 mutants are not defective in postreplication repair (PRAKASH 1981 ) but are defective in UV-induced mutagenesis (MORRISON et al. 1989 ), it appears as though translesion synthesis is not required for the repair of daughter strand gaps. In contrast, the lack of SCE induction in the rad1 rad52 mutant (Figure 5; KADYK and HARTWELL 1993 ) is correlated with its defect in postreplication repair (PRAKASH 1981 ), suggesting that daughter strand gap repair largely reflects recombinational bypass of lesions. Consistent with this conclusion, the rad1 rad52 mutant is hypermutable (and therefore presumably carrying out lots of translesion synthesis), yet has a defect in daughter strand gap repair (PRAKASH 1981 ). Given our finding that rad1 rad9 and rad1 rad17 are partially defective in replication-dependent SCE, it will be of interest to determine if these mutants have a defect in postreplication repair.

Are lesions channeled between mutagenic and recombinogenic pathways?
Others have suggested that DNA lesions may be tolerated by both recombination and mutation, but that cells somehow channel lesions preferentially into one pathway over the other (SCHIESTL et al. 1990 ; RONG et al. 1991 ; ABOUSSEKHRA et al. 1992 ; HEUDE and FABRE 1993 ). Our data are consistent with the hypothesis that the recombination pathway is preferred over the mutation pathway. In wild-type cells, SCE is induced at lower doses of UV than induction of mutation (Figure 2B and Figure C). One might argue that this results from there being more than one type of lesion induced by UV, and that a more prevalent lesion is replicated strictly by the recombinational pathway, whereas a less prevalent lesion is replicated strictly by the mutagenic pathway. However, at least in a rad1 background, when the option of recombination is taken away by deletion of RAD52 (Figure 3B), cells are hypermutable in response to UV irradiation, suggesting that lesions that would have been handled recombinationally are now secondarily channeled to the mutagenic pathway.

Interestingly, the rad1 rev3 mutant is not hyper-recombinogenic in response to UV (Figure 4C), suggesting that lesions normally handled by the REV3 pathway may not be channeled into the SCE pathway. Alternatively, the number of lesions normally handled by the REV3 pathway may be negligible relative to the number of lesions normally handled by SCE. (The SCE rates we measure are likely to underestimate the actual rates because we are only able to detect unequal recombination events.) Therefore, channeling these lesions into SCE (by deletion of REV3) would not result in a detectable increase in the SCE rate.

SCE:
Measurement of SCE induction is widely used to determine the genotoxicity of chemicals in hopes of predicting their carcinogenicity (PERRY and EVANS 1975 ). Additionally, measurement of SCE induction in peripheral blood lymphocytes in people is used to assess the exposure of individuals to DNA-damaging agents (reviewed in TUCKER et al. 1993 ) or to assess the inherent genetic instability of their cells in hopes of correlating cellular phenotypes with disease (e.g., Bloom's syndrome; CHAGANTI et al. 1974 ). Amazingly, despite its widespread use as a marker of genome damage, we know virtually nothing about the molecular mechanisms underlying the process of SCE or its regulation.

Work in yeast has suggested that SCE may occur via more than one mechanism. For example, there are qualitative differences between SCEs induced in excision repair-defective rad1 cells and SCEs induced in wild-type cells. UV-induced SCE that occurs in a rad1 background is completely dependent on lesions being present during DNA replication, whereas SCE in a wild-type background can be induced by UV damage occurring in the G2 phase, without an intervening S phase (KADYK and HARTWELL 1993 ). Furthermore, SCE in the rad1 background is completely caused by gene conversion, whereas SCE in a wild-type background is a mixture of gene conversion and reciprocal recombination (KADYK and HARTWELL 1993 ). We show that SCE in a rad1 background is partially dependent on RAD9 and RAD17, whereas SCE in a wild-type background is independent of these genes. All these observations support the hypothesis that G2 SCE in wild-type cells is mechanistically different from the replication-dependent SCE observed in rad1 strains.

One possible basis of these differences in SCE in wild-type and rad1 cells is that replication-dependent SCE in a rad1 cell and replication-independent (G2) SCE in a wild-type cell are stimulated by different substrates. For example, in the rad1 mutant, in the absence of excision repair and without replication, recombinogenic, single-stranded DNA gaps cannot be generated. Hence, in the rad1 mutant, recombination is dependent on replication over UV lesions, which results in the formation of recombinogenic daughter strand gaps (Figure 1). In this case, the SCE-inducing substrate is presumably a single-stranded gap across a template that contains an irreparable UV photoproduct (Figure 1). In contrast, wild-type cells have at least two mechanisms to generate recombinogenic lesions. Lesions that happened to be replicated rather than repaired could presumably stimulate daughter strand gap formation and SCE in the wild type, just as in the rad1 cells. A second possible source of recombinogenic lesions in wild-type cells is nucleotide excision repair. For example, perhaps in nucleotide excision repair-proficient cells, replication forks occasionally encounter single-stranded excision gaps. This could result in replication fork breakage and the formation of one broken and one intact sister chromatid (reviewed in KUZMINOV 1995 ), followed by repair of the broken sister using SCE in a process that is not dependent on RAD9 and RAD17.

	FOOTNOTES

¹ Present address: Massachusetts General Hospital, Medical Services, Boston, MA 02114.

	ACKNOWLEDGMENTS

We thank RUSSELL DORER and DAVE TOCZYSKI for formative discussions. We thank members of the Hartwell lab for comments on this manuscript, REBECCA MARGULIES for help with pilot experiments during the early stages of this work, NICK TERZOPOULOS for media preparation, and LAURA REITER for tetrad dissection. We especially thank CHRISTOPHER LAWRENCE for helpful comments on this manuscript, and TED WEINERT for helpful comments on the manuscript and for suggesting the epistasis model depicted in Figure 9. This work was supported by General Medical Sciences grant GM-17709 from the National Institutes of Health. A.G.P. was supported by a Merck Distinguished Fellow Award and a Medical Scientist Training Program (MSTP) training grant from the National Institutes of Health. L.H.H. is a Research Professor of the American Cancer Society.

Manuscript received April 7, 1998; Accepted for publication June 5, 1998.

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