Sensing of Replication Stress and Mec1 Activation Act through Two Independent Pathways Involving the 9-1-1 Complex and DNA Polymerase ε

English version České info

Following DNA damage or replication stress, budding yeast cells activate the Rad53 checkpoint kinase, promoting genome stability in these challenging conditions. The DNA damage and replication checkpoint pathways are partially overlapping, sharing several factors, but are also differentiated at various levels. The upstream kinase Mec1 is required to activate both signaling cascades together with the 9-1-1 PCNA-like complex and the Dpb11 (hTopBP1) protein. After DNA damage, Dpb11 is also needed to recruit the adaptor protein Rad9 (h53BP1). Here we analyzed the mechanisms leading to Mec1 activation in vivo after DNA damage and replication stress. We found that a ddc1Δdpb11-1 double mutant strain displays a synthetic defect in Rad53 and H2A phosphorylation and is extremely sensitive to hydroxyurea (HU), indicating that Dpb11 and the 9-1-1 complex independently promote Mec1 activation. A similar phenotype is observed when both the 9-1-1 complex and the Dpb4 non-essential subunit of DNA polymerase ε (Polε) are contemporarily absent, indicating that checkpoint activation in response to replication stress is achieved through two independent pathways, requiring the 9-1-1 complex and Polε.

Vyšlo v časopise: Sensing of Replication Stress and Mec1 Activation Act through Two Independent Pathways Involving the 9-1-1 Complex and DNA Polymerase ε. PLoS Genet 7(3): e32767. doi:10.1371/journal.pgen.1002022
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1002022

Souhrn

Zdroje

1. ChaRSKlecknerN 2002 ATR homolog Mec1 promotes fork progression, thus averting breaks in replication slow zones. Science 297 602 606

2. BrewerBJFangmanWL 1988 A replication fork barrier at the 3′ end of yeast ribosomal RNA genes. Cell 55 637 643

3. KrakoffIHBrownNCReichardP 1968 Inhibition of ribonucleoside diphosphate reductase by hydroxyurea. Cancer Res 28 1559 1565

4. BranzeiDFoianiM 2009 The checkpoint response to replication stress. DNA Repair (Amst) 8 1038 1046

5. SogoJMLopesMFoianiM 2002 Fork reversal and ssDNA accumulation at stalled replication forks owing to checkpoint defects. Science 297 599 602

6. DesanyBAAlcasabasAABachantJBElledgeSJ 1998 Recovery from DNA replicational stress is the essential function of the S-phase checkpoint pathway. Genes Dev 12 2956 2970

7. LopesMCotta-RamusinoCPellicioliALiberiGPlevaniP 2001 The DNA replication checkpoint response stabilizes stalled replication forks. Nature 412 557 561

8. LuccaCVanoliFCotta-RamusinoCPellicioliALiberiG 2004 Checkpoint-mediated control of replisome-fork association and signalling in response to replication pausing. Oncogene 23 1206 1213

9. HuangMZhouZElledgeSJ 1998 The DNA replication and damage checkpoint pathways induce transcription by inhibition of the Crt1 repressor. Cell 94 595 605

10. ZhaoXChabesADomkinVThelanderLRothsteinR 2001 The ribonucleotide reductase inhibitor Sml1 is a new target of the Mec1/Rad53 kinase cascade during growth and in response to DNA damage. EMBO J 20 3544 3553

11. SantocanaleCDiffleyJF 1998 A Mec1- and Rad53-dependent checkpoint controls late-firing origins of DNA replication. Nature 395 615 618

12. AllenJBZhouZSiedeWFriedbergECElledgeSJ 1994 The SAD1/RAD53 protein kinase controls multiple checkpoints and DNA damage-induced transcription in yeast. Genes Dev 8 2401 2415

13. BachantJJessenSRKavanaughSEFieldingCS 2005 The yeast S phase checkpoint enables replicating chromosomes to bi-orient and restrain spindle extension during S phase distress. J Cell Biol 168 999 1012

14. WeinertTAKiserGLHartwellLH 1994 Mitotic checkpoint genes in budding yeast and the dependence of mitosis on DNA replication and repair. Genes Dev 8 652 665

15. ZouLElledgeSJ 2003 Sensing DNA damage through ATRIP recognition of RPA-ssDNA complexes. Science 300 1542 1548

16. PudduFGranataMNolaLDBalestriniAPiergiovanniG 2008 Phosphorylation of the budding yeast 9-1-1 complex is required for Dpb11 function in the full activation of the UV-induced DNA damage checkpoint. Mol Cell Biol 28 4782 4793

17. HuyenYZgheibODitullioRAGorgoulisVGZacharatosP 2004 Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks. Nature 432 406 411

18. GiannattasioMLazzaroFPlevaniPMuzi-FalconiM 2005 The DNA damage checkpoint response requires histone H2B ubiquitination by Rad6-Bre1 and H3 methylation by Dot1. J Biol Chem 280 9879 9886

19. DuL-LNakamuraTMRussellP 2006 Histone modification-dependent and -independent pathways for recruitment of checkpoint protein Crb2 to double-strand breaks. Genes Dev 20 1583 1596

20. GranataMLazzaroFNovarinaDPanigadaDPudduF 2010 Dynamics of Rad9 Chromatin Binding and Checkpoint Function are Mediated by its Dimerization and are Cell Cycle-Regulated by CDK1 Activity. PLoS Genet 6 e1001047 doi:10.1371/journal.pgen.1001047

21. PellicioliALuccaCLiberiGMariniFLopesM 1999 Activation of Rad53 kinase in response to DNA damage and its effect in modulating phosphorylation of the lagging strand DNA polymerase. EMBO J 18 6561 6572

22. AlcasabasAAOsbornAJBachantJHuFWerlerPJ 2001 Mrc1 transduces signals of DNA replication stress to activate Rad53. Nat Cell Biol 3 958 965

23. ArakiHLeemSHPhongdaraASuginoA 1995 Dpb11, which interacts with DNA polymerase II(epsilon) in Saccharomyces cerevisiae, has a dual role in S-phase progression and at a cell cycle checkpoint. Proc Natl Acad Sci U S A 92 11791 11795

24. NavasTAZhouZElledgeSJ 1995 DNA polymerase epsilon links the DNA replication machinery to the S phase checkpoint. Cell 80 29 39

25. WangHElledgeSJ 1999 DRC1, DNA replication and checkpoint protein 1, functions with DPB11 to control DNA replication and the S-phase checkpoint in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 96 3824 3829

26. TanakaSUmemoriTHiraiKMuramatsuSKamimuraY 2007 CDK-dependent phosphorylation of Sld2 and Sld3 initiates DNA replication in budding yeast. Nature 445 328 332

27. ZegermanPDiffleyJFX 2007 Phosphorylation of Sld2 and Sld3 by cyclin-dependent kinases promotes DNA replication in budding yeast. Nature 445 281 285

28. OhyaTMakiSKawasakiYSuginoA 2000 Structure and function of the fourth subunit (Dpb4p) of DNA polymerase epsilon in Saccharomyces cerevisiae. Nucleic Acids Res 28 3846 3852

29. IidaTArakiH 2004 Noncompetitive counteractions of DNA polymerase epsilon and ISW2/yCHRAC for epigenetic inheritance of telomere position effect in Saccharomyces cerevisiae. Mol Cell Biol 24 217 227

30. AsturiasFJCheungIKSabouriNChilkovaOWepploD 2006 Structure of Saccharomyces cerevisiae DNA polymerase epsilon by cryo-electron microscopy. Nat Struct Mol Biol 13 35 43

31. DuaREdwardsSLevyDLCampbellJL 2000 Subunit interactions within the Saccharomyces cerevisiae DNA polymerase epsilon (pol epsilon) complex. Demonstration of a dimeric pol epsilon. J Biol Chem 275 28816 28825

32. KestiTFlickKKeränenSSyväojaJEWittenbergC 1999 DNA polymerase epsilon catalytic domains are dispensable for DNA replication, DNA repair, and cell viability. Mol Cell 3 679 685

33. ZouLLiuDElledgeSJ 2003 Replication protein A-mediated recruitment and activation of Rad17 complexes. Proc Natl Acad Sci U S A 100 13827 13832

34. MajkaJBinzSKWoldMSBurgersPM 2006 RPA directs loading of the DNA damage checkpoint clamp to 5′-DNA junctions. J Biol Chem 281 27855 27861

35. KumagaiALeeJYooHYDunphyWG 2006 TopBP1 activates the ATR-ATRIP complex. Cell 124 943 955

36. DelacroixSWagnerJMKobayashiMichi YamamotoKKarnitzLM 2007 The Rad9-Hus1-Rad1 (9-1-1) clamp activates checkpoint signaling via TopBP1. Genes Dev 21 1472 1477

37. LeeJKumagaiADunphyWG 2007 The Rad9-Hus1-Rad1 checkpoint clamp regulates interaction of TopBP1 with ATR. J Biol Chem 282 28036 28044

38. MordesDAGlickGGZhaoRCortezD 2008 TopBP1 activates ATR through ATRIP and a PIKK regulatory domain. Genes Dev 22 1478 1489

39. Navadgi-PatilVMBurgersPM 2009 The unstructured C-terminal tail of the 9-1-1 clamp subunit Ddc1 activates Mec1/ATR via two distinct mechanisms. Mol Cell 36 743 753

40. MajkaJNiedziela-MajkaABurgersPMJ 2006 The Checkpoint Clamp Activates Mec1 Kinase during Initiation of the DNA Damage Checkpoint. Mol Cell 24 891 901

41. MordesDANamEACortezD 2008 Dpb11 activates the Mec1-Ddc2 complex. Proc Natl Acad Sci U S A 105 18730 18734

42. Navadgi-PatilVMBurgersPM 2008 Yeast DNA replication protein Dpb11 activates the Mec1/ATR checkpoint kinase. J Biol Chem 283 35853 35859

43. WangHElledgeSJ 2002 Genetic and physical interactions between DPB11 and DDC1 in the yeast DNA damage response pathway. Genetics 160 1295 1304

44. MuramatsuSHiraiKTakY-SKamimuraYArakiH 2010 CDK-dependent complex formation between replication proteins Dpb11, Sld2, Pol epsilon, and GINS in budding yeast. Genes Dev 24 602 612

45. EdwardsSLiCMLevyDLBrownJSnowPM 2003 Saccharomyces cerevisiae DNA polymerase epsilon and polymerase sigma interact physically and functionally, suggesting a role for polymerase epsilon in sister chromatid cohesion. Mol Cell Biol 23 2733 2748

46. FuruyaKPoiteleaMGuoLCaspariTCarrAM 2004 Chk1 activation requires Rad9 S/TQ-site phosphorylation to promote association with C-terminal BRCT domains of Rad4TOPBP1. Genes Dev 18 1154 1164

47. TaricaniLWangTSF 2006 Rad4TopBP1, a scaffold protein, plays separate roles in DNA damage and replication checkpoints and DNA replication. Mol Biol Cell 17 3456 3468

48. IraGPellicioliABalijjaAWangXFioraniS 2004 DNA end resection, homologous recombination and DNA damage checkpoint activation require CDK1. Nature 431 1011 1017

49. AylonYLiefshitzBKupiecM 2004 The CDK regulates repair of double-strand breaks by homologous recombination during the cell cycle. EMBO J 23 4868 4875

50. McElhinnySANGordeninDAStithCMBurgersPMJKunkelTA 2008 Division of labor at the eukaryotic replication fork. Mol Cell 30 137 144

51. DuaRLevyDLCampbellJL 1998 Role of the putative zinc finger domain of Saccharomyces cerevisiae DNA polymerase epsilon in DNA replication and the S/M checkpoint pathway. J Biol Chem 273 30046 30055

52. MasumotoHSuginoAArakiH 2000 Dpb11 controls the association between DNA polymerases alpha and epsilon and the autonomously replicating sequence region of budding yeast. Mol Cell Biol 20 2809 2817

53. KamimuraYMasumotoHSuginoAArakiH 1998 Sld2, which interacts with Dpb11 in Saccharomyces cerevisiae, is required for chromosomal DNA replication. Mol Cell Biol 18 6102 6109

54. BurgersPM 2008 Polymerase dynamics at the eukaryotic DNA replication fork. J Biol Chem 284 4041 4045

55. LongtineMSMcKenzieADemariniDJShahNGWachA 1998 Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14 953 961

56. FalconiMMPiseriAFerrariMLucchiniGPlevaniP 1993 De novo synthesis of budding yeast DNA polymerase alpha and POL1 transcription at the G1/S boundary are not required for entrance into S phase. Proc Natl Acad Sci U S A 90 10519 10523

57. LengronneAPaseroPBensimonASchwobE 2001 Monitoring S phase progression globally and locally using BrdU incorporation in TK(+) yeast strains. Nucleic Acids Res 29 1433 1442