A Role for Saccharomyces cerevisiae Chk1p in the Response to Replication Blocks

Replication blocks and DNA damage incurred during S phase activate the S-phase and intra-S-phase checkpoint responses, respectively, regulated by the Atrp and Chk1p checkpoint kinases in metazoans. In Saccharomyces cerevisiae, these checkpoints are regulated by the Atrp homologue Mec1p and the kinase Rad53p. A conserved role of these checkpoints is to block mitotic progression until DNA replication and repair are completed. In S. cerevisiae, these checkpoints include a transcriptional response regulated by the kinase Dun1p; however, dun1Δ cells are proficient for the S-phase-checkpoint-induced anaphase block. Yeast Chk1p kinase regulates the metaphase-to-anaphase transition in the DNA-damage checkpoint pathway via securin (Pds1p) phosphorylation. However, like Dun1p, yeast Chk1p is not required for the S-phase-checkpoint-induced anaphase block. Here we report that Chk1p has a role in the intra-S-phase checkpoint activated when yeast cells replicate their DNA in the presence of low concentrations of hydroxyurea (HU). Chk1p was modified and Pds1p was transiently phosphorylated in this response. Cells lacking Dun1p were dependent on Chk1p for survival in HU, and chk1Δ dun1Δ cells were defective in the recovery from replication interference caused by transient HU exposure. These studies establish a relationship between the S-phase and DNA-damage checkpoint pathways in S. cerevisiae and suggest that at least in some genetic backgrounds, the Chk1p/securin pathway is required for the recovery from stalled or collapsed replication forks.

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RAD9, RAD17, and RAD24 Are Required for S Phase Regulation in Saccharomyces cerevisiae in Response to DNA Damage

Genetics ◽

10.1093/genetics/145.1.45 ◽

1997 ◽

Vol 145 (1) ◽

pp. 45-62 ◽

Cited By ~ 11

Author(s):

A G Paulovich ◽

R U Margulies ◽

B M Garvik ◽

L H Hartwell

Keyword(s):

Saccharomyces Cerevisiae ◽

Dna Damage ◽

Dna Repair ◽

S Phase ◽

Dna Damage Checkpoint ◽

Wild Type ◽

Alkylation Damage ◽

Checkpoint Pathway ◽

Phase Regulation ◽

Phase Progression

We have previously shown that a checkpoint dependent on MEC1 and RAD53 slows the rate of S phase progression in Saccharomyces cerevisiae in response to alkylation damage. Whereas wild-type cells exhibit a slow S phase in response to damage, mec1-1 and rad53 mutants replicate rapidly in the presence or absence of DNA damage. In this report, we show that other genes (RAD9, RAD17, RAD24) involved in the DNA damage checkpoint pathway also play a role in regulating S phase in response to DNA damage. Furthermore, RAD9, RAD17, and RAD24 fall into two groups with respect to both sensitivity to alkylation and regulation of S phase. We also demonstrate that the more dramatic defect in S phase regulation in the mec1-1 and rad53 mutants is epistatic to a less severe defect seen in rad9Δ, rad17Δ, and rad24Δ. Furthermore, the triple rad9Δ rad17Δ rad24Δ mutant also has a less severe defect than mec1-1 or rad53 mutants. Finally, we demonstrate the specificity of this phenotype by showing that the DNA repair and/or checkpoint mutants mgt1Δ, mag1Δ, apn1Δ, rev3Δ, rad18Δ, rad16Δ, dun1-Δ100, sad4-1, tel1Δ, rad26Δ, rad51Δ, rad52-1, rad54Δ, rad14Δ, rad1Δ, pol30–46, pol30–52, mad3Δ, pds1Δ/esp2Δ, pms1Δ, mlh1Δ, and msh2Δ are all proficient at S phase regulation, even though some of these mutations confer sensitivity to alkylation.

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Orchestration of the S-phase and DNA damage checkpoint pathways by replication forks from early origins

The Journal of Cell Biology ◽

10.1083/jcb.200706009 ◽

2008 ◽

Vol 180 (6) ◽

pp. 1073-1086 ◽

Cited By ~ 8

Author(s):

Julie M. Caldwell ◽

Yinhuai Chen ◽

Kaila L. Schollaert ◽

James F. Theis ◽

George F. Babcock ◽

...

Keyword(s):

Dna Damage ◽

Replication Fork ◽

S Phase ◽

Dna Damage Checkpoint ◽

Replication Forks ◽

Checkpoint Signaling ◽

Checkpoint Pathway ◽

Origin Licensing ◽

Pause Site ◽

S Phase Checkpoint

The S-phase checkpoint activated at replication forks coordinates DNA replication when forks stall because of DNA damage or low deoxyribonucleotide triphosphate pools. We explore the involvement of replication forks in coordinating the S-phase checkpoint using dun1Δ cells that have a defect in the number of stalled forks formed from early origins and are dependent on the DNA damage Chk1p pathway for survival when replication is stalled. We show that providing additional origins activated in early S phase and establishing a paused fork at a replication fork pause site restores S-phase checkpoint signaling to chk1Δ dun1Δ cells and relieves the reliance on the DNA damage checkpoint pathway. Origin licensing and activation are controlled by the cyclin–Cdk complexes. Thus, oncogene-mediated deregulation of cyclins in the early stages of cancer development could contribute to genomic instability through a deficiency in the forks required to establish the S-phase checkpoint.

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Saccharomyces cerevisiae Rrm3p DNA Helicase Promotes Genome Integrity by Preventing Replication Fork Stalling: Viability of rrm3 Cells Requires the Intra-S-Phase Checkpoint and Fork Restart Activities

Molecular and Cellular Biology ◽

10.1128/mcb.24.8.3198-3212.2004 ◽

2004 ◽

Vol 24 (8) ◽

pp. 3198-3212 ◽

Cited By ~ 97

Author(s):

Jorge Z. Torres ◽

Sandra L. Schnakenberg ◽

Virginia A. Zakian

Keyword(s):

Saccharomyces Cerevisiae ◽

Dna Damage ◽

Replication Fork ◽

Opportunity To Learn ◽

Normal Growth ◽

Dna Helicase ◽

S Phase ◽

Exogenous Dna ◽

Fork Stalling ◽

S Phase Checkpoint

ABSTRACT Rrm3p is a 5′-to-3′ DNA helicase that helps replication forks traverse protein-DNA complexes. Its absence leads to increased fork stalling and breakage at over 1,000 specific sites located throughout the Saccharomyces cerevisiae genome. To understand the mechanisms that respond to and repair rrm3-dependent lesions, we carried out a candidate gene deletion analysis to identify genes whose mutation conferred slow growth or lethality on rrm3 cells. Based on synthetic phenotypes, the intra-S-phase checkpoint, the SRS2 inhibitor of recombination, the SGS1/TOP3 replication fork restart pathway, and the MRE11/RAD50/XRS2 (MRX) complex were critical for viability of rrm3 cells. DNA damage checkpoint and homologous recombination genes were important for normal growth of rrm3 cells. However, the MUS81/MMS4 replication fork restart pathway did not affect growth of rrm3 cells. These data suggest a model in which the stalled and broken forks generated in rrm3 cells activate a checkpoint response that provides time for fork repair and restart. Stalled forks are converted by a Rad51p-mediated process to intermediates that are resolved by Sgs1p/Top3p. The rrm3 system provides a unique opportunity to learn the fate of forks whose progress is impaired by natural impediments rather than by exogenous DNA damage.

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Critical Role for Mouse Hus1 in an S-Phase DNA Damage Cell Cycle Checkpoint

Molecular and Cellular Biology ◽

10.1128/mcb.23.3.791-803.2003 ◽

2003 ◽

Vol 23 (3) ◽

pp. 791-803 ◽

Cited By ~ 50

Author(s):

Robert S. Weiss ◽

Philip Leder ◽

Cyrus Vaziri

Keyword(s):

Cell Cycle ◽

Dna Damage ◽

Dna Synthesis ◽

Critical Role ◽

S Phase ◽

Cell Cycle Checkpoint ◽

Dna Damage Checkpoint ◽

Null Mouse ◽

Cycle Checkpoint ◽

S Phase Checkpoint

ABSTRACT Mouse Hus1 encodes an evolutionarily conserved DNA damage response protein. In this study we examined how targeted deletion of Hus1 affects cell cycle checkpoint responses to genotoxic stress. Unlike hus1− fission yeast (Schizosaccharomyces pombe) cells, which are defective for the G2/M DNA damage checkpoint, Hus1-null mouse cells did not inappropriately enter mitosis following genotoxin treatment. However, Hus1-deficient cells displayed a striking S-phase DNA damage checkpoint defect. Whereas wild-type cells transiently repressed DNA replication in response to benzo(a)pyrene dihydrodiol epoxide (BPDE), a genotoxin that causes bulky DNA adducts, Hus1-null cells maintained relatively high levels of DNA synthesis following treatment with this agent. However, when treated with DNA strand break-inducing agents such as ionizing radiation (IR), Hus1-deficient cells showed intact S-phase checkpoint responses. Conversely, checkpoint-mediated inhibition of DNA synthesis in response to BPDE did not require NBS1, a component of the IR-responsive S-phase checkpoint pathway. Taken together, these results demonstrate that Hus1 is required specifically for one of two separable mammalian checkpoint pathways that respond to distinct forms of genome damage during S phase.

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S-Phase Checkpoint Pathways Stimulate the Mobility of the Retrovirus-Like Transposon Ty1

Molecular and Cellular Biology ◽

10.1128/mcb.01095-07 ◽

2007 ◽

Vol 27 (24) ◽

pp. 8874-8885 ◽

Cited By ~ 29

Author(s):

M. Joan Curcio ◽

Alison E. Kenny ◽

Sharon Moore ◽

David J. Garfinkel ◽

Matthew Weintraub ◽

...

Keyword(s):

Dna Damage ◽

Reverse Transcriptase ◽

Reverse Transcriptase Activity ◽

S Phase ◽

Dna Lesions ◽

Restriction Factors ◽

Transcriptase Activity ◽

Checkpoint Pathway ◽

Ty1 Mobility ◽

S Phase Checkpoint

ABSTRACT The mobility of the Ty1 retrotransposon in the yeast Saccharomyces cerevisiae is restricted by a large collection of proteins that preserve the integrity of the genome during replication. Several of these repressors of Ty1 transposition (Rtt)/genome caretakers are orthologs of mammalian retroviral restriction factors. In rtt/genome caretaker mutants, levels of Ty1 cDNA and mobility are increased; however, the mechanisms underlying Ty1 hypermobility in most rtt mutants are poorly characterized. Here, we show that either or both of two S-phase checkpoint pathways, the replication stress pathway and the DNA damage pathway, partially or strongly stimulate Ty1 mobility in 19 rtt/genome caretaker mutants. In contrast, neither checkpoint pathway is required for Ty1 hypermobility in two rtt mutants that are competent for genome maintenance. In rtt101Δ mutants, hypermobility is stimulated through the DNA damage pathway components Rad9, Rad24, Mec1, Rad53, and Dun1 but not Chk1. We provide evidence that Ty1 cDNA is not the direct target of the DNA damage pathway in rtt101Δ mutants; instead, levels of Ty1 integrase and reverse transcriptase proteins, as well as reverse transcriptase activity, are significantly elevated. We propose that DNA lesions created in the absence of Rtt/genome caretakers trigger S-phase checkpoint pathways to stimulate Ty1 reverse transcriptase activity.

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Activation of the DNA Damage Checkpoint in Mutants Defective in DNA Replication Initiation

Molecular Biology of the Cell ◽

10.1091/mbc.e08-01-0020 ◽

2008 ◽

Vol 19 (10) ◽

pp. 4374-4382 ◽

Cited By ~ 13

Author(s):

Ling Yin ◽

Alexandra Monica Locovei ◽

Gennaro D'Urso

Keyword(s):

Dna Damage ◽

Dna Replication ◽

Replication Fork ◽

S Phase ◽

Replication Initiation ◽

Dna Damage Checkpoint ◽

Origin Firing ◽

Dna Replication Initiation ◽

Fork Stalling ◽

S Phase Checkpoint

In the fission yeast, Schizosaccharomyces pombe, blocks to DNA replication elongation trigger the intra-S phase checkpoint that leads to the activation of the Cds1 kinase. Cds1 is required to both prevent premature entry into mitosis and to stabilize paused replication forks. Interestingly, although Cds1 is essential to maintain the viability of mutants defective in DNA replication elongation, mutants defective in DNA replication initiation require the Chk1 kinase. This suggests that defects in DNA replication initiation can lead to activation of the DNA damage checkpoint independent of the intra-S phase checkpoint. This might result from reduced origin firing that leads to an increase in replication fork stalling or replication fork collapse that activates the G2 DNA damage checkpoint. We refer to the Chk1-dependent, Cds1-independent phenotype as the rid phenotype (for replication initiation defective). Chk1 is active in rid mutants, and rid mutant viability is dependent on the DNA damage checkpoint, and surprisingly Mrc1, a protein required for activation of Cds1. Mutations in Mrc1 that prevent activation of Cds1 have no effect on its ability to support rid mutant viability, suggesting that Mrc1 has a checkpoint-independent role in maintaining the viability of mutants defective in DNA replication initiation.

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Surviving chromosome replication: the many roles of the S-phase checkpoint pathway

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2011.0071 ◽

2011 ◽

Vol 366 (1584) ◽

pp. 3554-3561 ◽

Cited By ~ 65

Author(s):

Karim Labib ◽

Giacomo De Piccoli

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Cell Cycle Progression ◽

Reductase Activity ◽

Critical Role ◽

Chromosome Replication ◽

S Phase ◽

Replication Forks ◽

Checkpoint Pathway ◽

S Phase Checkpoint

Checkpoints were originally identified as signalling pathways that delay mitosis in response to DNA damage or defects in chromosome replication, allowing time for DNA repair to occur. The ATR (ataxia- and rad-related) and ATM (ataxia-mutated) protein kinases are recruited to defective replication forks or to sites of DNA damage, and are thought to initiate the DNA damage response in all eukaryotes. In addition to delaying cell cycle progression, however, the S-phase checkpoint pathway also controls chromosome replication and DNA repair pathways in a highly complex fashion, in order to preserve genome integrity. Much of our understanding of this regulation has come from studies of yeasts, in which the best-characterized targets are the stimulation of ribonucleotide reductase activity by multiple mechanisms, and the inhibition of new initiation events at later origins of DNA replication. In addition, however, the S-phase checkpoint also plays a more enigmatic and apparently critical role in preserving the functional integrity of defective replication forks, by mechanisms that are still understood poorly. This review considers some of the key experiments that have led to our current understanding of this highly complex pathway.

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Role of Dot1-Dependent Histone H3 Methylation in G1 and S Phase DNA Damage Checkpoint Functions of Rad9

Molecular and Cellular Biology ◽

10.1128/mcb.25.19.8430-8443.2005 ◽

2005 ◽

Vol 25 (19) ◽

pp. 8430-8443 ◽

Cited By ~ 197

Author(s):

Robert Wysocki ◽

Ali Javaheri ◽

Stéphane Allard ◽

Fei Sha ◽

Jacques Côté ◽

...

Keyword(s):

Dna Damage ◽

Histone H3 ◽

S Phase ◽

Dna Damage Checkpoint ◽

Gene Deletions ◽

Dna Damage Signaling ◽

Pathway Gene ◽

Histone H3 Methylation ◽

Yeast Mutants ◽

S Phase Checkpoint

ABSTRACT We screened radiation-sensitive yeast mutants for DNA damage checkpoint defects and identified Dot1, the conserved histone H3 Lys 79 methyltransferase. DOT1 deletion mutants (dot1Δ) are G1 and intra-S phase checkpoint defective after ionizing radiation but remain competent for G2/M arrest. Mutations that affect Dot1 function such as Rad6-Bre1/Paf1 pathway gene deletions or mutation of H2B Lys 123 or H3 Lys 79 share dot1Δ checkpoint defects. Whereas dot1Δ alone confers minimal DNA damage sensitivity, combining dot1Δ with histone methyltransferase mutations set1Δ and set2Δ markedly enhances lethality. Interestingly, set1Δ and set2Δ mutants remain G1 checkpoint competent, but set1Δ displays a mild S phase checkpoint defect. In human cells, H3 Lys 79 methylation by hDOT1L likely mediates recruitment of the signaling protein 53BP1 via its paired tudor domains to double-strand breaks (DSBs). Consistent with this paradigm, loss of Dot1 prevents activation of the yeast 53BP1 ortholog Rad9 or Chk2 homolog Rad53 and decreases binding of Rad9 to DSBs after DNA damage. Mutation of Rad9 to alter tudor domain binding to methylated Lys 79 phenocopies the dot1Δ checkpoint defect and blocks Rad53 phosphorylation. These results indicate a key role for chromatin and methylation of histone H3 Lys 79 in yeast DNA damage signaling.

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