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A role for the yeast PCNA unloader Elg1 in eliciting the DNA damage checkpoint

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Abstract

During cell proliferation, the genome is constantly threatened by cellular and external factors. When the DNA is damaged, or when its faithful duplication is delayed by DNA polymerase stalling, the cells induce a coordinated response termed the DNA damage response (DDR) or checkpoint. Elg1 forms an RFC-like complex in charge of unloading the DNA polymerase processively factor PCNA during DNA replication and DNA repair. Using checkpoint-inducible strains, a recently published paper (Sau et al. in mBio 10(3):e01159-19. https://doi.org/10.1128/mbio.01159-19, 2019) uncovered a role for Elg1 in eliciting the DNA damage checkpoint (DC), one of the branches of the DDR. The apical kinase Mec1/ATR phosphorylates Elg1, as well as the adaptor proteins Rad9/53BP1 and Dpb11/TopBP1, which are recruited to the site of DNA damage to amplify the checkpoint signal. In the absence of Elg1, Rad9 and Dpb11 are recruited but fail to be phosphorylated and the signal is therefore not amplified. Thus, Elg1 appears to coordinate DNA repair and the induction of the DNA damage checkpoint.

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References

  1. Acharya N, Manohar K, Peroumal D, Khandagale P, Patel SK, Sahu SR, Kumari P (2018) Multifaceted activities of DNA polymerase eta: beyond translesion DNA synthesis. Curr Genet. https://doi.org/10.1007/s00294-018-0918-5

  2. Agmon N, Pur S, Liefshitz B, Kupiec M (2009) Analysis of repair mechanism choice during homologous recombination. Nucl Acids Res 37:5081–5092. https://doi.org/10.1093/nar/gkp495

  3. Agmon N, Liefshitz B, Zimmer C, Fabre E, Kupiec M (2013) Effect of nuclear architecture on the efficiency of double-strand break repair. Nat Cell Biol 15:694–699. https://doi.org/10.1038/ncb2745

  4. Aroya SB, Kupiec M (2005) The Elg1 replication factor C-like complex: a novel guardian of genome stability. DNA Repair (Amst) 4:409–417. https://doi.org/10.1016/j.dnarep.2004.08.003

  5. Ballew O, Lacefield S (2019) The DNA damage checkpoint and the spindle position checkpoint: guardians of meiotic commitment. Curr Genetics. https://doi.org/10.1007/s00294-019-00981-z

  6. Bantele SCS, Pfander B (2019) Quantitative mechanisms of DNA damage sensing and signaling. Curr Genetics. https://doi.org/10.1007/s00294-019-01007-4

  7. Bastos de Oliveira FM, Kim D, Cussiol JR, Das J, Jeong MC, Doerfler L, Schmidt KH, Yu H, Smolka MB (2015) Phosphoproteomics reveals distinct modes of Mec1/ATR signaling during DNA replication. Mol Cell 57:1124–1132. https://doi.org/10.1016/j.molcel.2015.01.043

  8. Bebenek A, Ziuzia-Graczyk I (2018) Fidelity of DNA replication-a matter of proofreading. Curr Genet 64:985–996. https://doi.org/10.1007/s00294-018-0820-1

  9. Bell DW, Sikdar N, Lee KY, Price JC, Chatterjee R, Park HD, Fox J, Ishiai M, Rudd ML, Pollock LM, Fogoros SK, Mohamed H, Hanigan CL, Zhang S, Cruz P, Renaud G, Hansen NF, Cherukuri PF, Borate B, McManus KJ, Stoepel J, Sipahimalani P, Godwin AK, Sgroi DC, Merino MJ, Elliot G, Elkahloun A, Vinson C, Takata M, Mullikin JC, Wolfsberg TG, Hieter P, Lim DS, Myung K (2011) Predisposition to cancer caused by genetic and functional defects of mammalian Atad5. PLoS Genet 7:e1002245. https://doi.org/10.1371/journal.pgen.1002245

  10. Bellaoui M, Chang M, Ou J, Xu H, Boone C, Brown GW (2003) Elg1 forms an alternative RFC complex important for DNA replication and genome integrity. EMBO J 22:4304–4313. https://doi.org/10.1093/emboj/cdg406

  11. Ben-Aroya S, Koren A, Liefshitz B, Steinlauf R, Kupiec M (2003) ELG1, a yeast gene required for genome stability, forms a complex related to replication factor C. Proc Natl Acad Sci USA 100:9906–9911. https://doi.org/10.1073/pnas.1633757100

  12. Berens TJ, Toczyski DP (2012) Colocalization of Mec1 and Mrc1 is sufficient for Rad53 phosphorylation in vivo. Mol Biol Cell 23:1058–1067. https://doi.org/10.1091/mbc.E11-10-0852

  13. Billon P, Li J, Lambert JP, Chen Y, Tremblay V, Brunzelle JS, Gingras AC, Verreault A, Sugiyama T, Couture JF, Cote J (2017) Acetylation of PCNA sliding surface by Eco1 promotes genome stability through homologous recombination. Mol Cell 65:78–90. https://doi.org/10.1016/j.molcel.2016.10.033

  14. Bonilla CY, Melo JA, Toczyski DP (2008) Colocalization of sensors is sufficient to activate the DNA damage checkpoint in the absence of damage. Mol Cell 30:267–276. https://doi.org/10.1016/j.molcel.2008.03.023

  15. Bordelet H, Dubrana K (2019) Keep moving and stay in a good shape to find your homologous recombination partner. Curr Genet 65:29–39. https://doi.org/10.1007/s00294-018-0873-1

  16. Botchkarev VV Jr, Haber JE (2018) Functions and regulation of the Polo-like kinase Cdc5 in the absence and presence of DNA damage. Curr Genet 64:87–96. https://doi.org/10.1007/s00294-017-0727-2

  17. Corcoles-Saez I, Dong K, Cha RS (2019) Versatility of the Mec1(ATM/ATR) signaling network in mediating resistance to replication, genotoxic, and proteotoxic stresses. Curr Genet 65:657–661. https://doi.org/10.1007/s00294-018-0920-y

  18. Fan Q, Xu X, Zhao X, Wang Q, Xiao W, Guo Y, Fu YV (2018) Rad5 coordinates translesion DNA synthesis pathway by recognizing specific DNA structures in saccharomyces cerevisiae. Curr Genet 64:889–899. https://doi.org/10.1007/s00294-018-0807-y

  19. Garcia-Blanco N, Moreno S (2019) Down-regulation of Cdk1 activity in G1 coordinates the G1/S gene expression programme with genome replication. Curr Genet 65:685–690. https://doi.org/10.1007/s00294-018-00926-y

  20. Garcia-Rodriguez N, Morawska M, Wong RP, Daigaku Y, Ulrich HD (2018) Spatial separation between replisome- and template-induced replication stress signaling. EMBO J. https://doi.org/10.15252/embj.201798369

  21. Gazy I, Kupiec M (2012) The importance of being modified: PCNA modification and DNA damage response. Cell Cycle 11:2620–2623. https://doi.org/10.4161/cc.20626

  22. Gilbert CS, Green CM, Lowndes NF (2001) Budding yeast Rad9 is an ATP-dependent Rad53 activating machine. Molecular Cell 8:129–136

  23. Harari Y, Kupiec M (2018) Mec1(ATR) is needed for extensive telomere elongation in response to ethanol in yeast. Curr Genet 64:223–234. https://doi.org/10.1007/s00294-017-0728-1

  24. Jakobsen KP, Andersen AH, Bjergbaek L (2019) Abortive activity of topoisomerase I: a challenge for genome integrity? Curr Genetics. https://doi.org/10.1007/s00294-019-00984-w

  25. Johnson C, Gali VK, Takahashi TS, Kubota T (2016) PCNA retention on DNA into G2/M phase causes genome instability in cells lacking Elg1. Cell Rep 16:684–695. https://doi.org/10.1016/j.celrep.2016.06.030

  26. Kanellis P, Agyei R, Durocher D (2003) Elg1 forms an alternative PCNA-interacting RFC complex required to maintain genome stability. Curr Biol CB 13:1583–1595

  27. Kee Y, D’Andrea AD (2010) Expanded roles of the Fanconi anemia pathway in preserving genomic stability. Genes Dev 24:1680–1694. https://doi.org/10.1101/gad.1955310

  28. Kuang Z, Ji H, Boeke JD (2018) Stress response factors drive regrowth of quiescent cells. Curr Genet 64:807–810. https://doi.org/10.1007/s00294-018-0813-0

  29. Kubota T, Stead DA, Hiraga S, ten Have S, Donaldson AD (2012) Quantitative proteomic analysis of yeast DNA replication proteins. Methods 57:196–202. https://doi.org/10.1016/j.ymeth.2012.03.012

  30. Kubota T, Nishimura K, Kanemaki MT, Donaldson AD (2013) The Elg1 replication factor C-like complex functions in PCNA unloading during DNA replication. Mol Cell 50:273–280. https://doi.org/10.1016/j.molcel.2013.02.012

  31. Kubota T, Katou Y, Nakato R, Shirahige K, Donaldson AD (2015) Replication-coupled PCNA unloading by the Elg1 complex occurs genome-wide and requires okazaki fragment ligation. Cell Rep 12:774–787. https://doi.org/10.1016/j.celrep.2015.06.066

  32. Lee KY, Yang K, Cohn MA, Sikdar N, D’Andrea AD, Myung K (2010) Human ELG1 regulates the level of ubiquitinated proliferating cell nuclear antigen (PCNA) through Its interactions with PCNA and USP1. J Biol Chem 285:10362–10369. https://doi.org/10.1074/jbc.M109.092544

  33. Lee KY, Fu H, Aladjem MI, Myung K (2013) ATAD5 regulates the lifespan of DNA replication factories by modulating PCNA level on the chromatin. J Cell Biol 200:31–44. https://doi.org/10.1083/jcb.201206084

  34. Leshets M, Ramamurthy D, Lisby M, Lehming N, Pines O (2018) Fumarase is involved in DNA double-strand break resection through a functional interaction with Sae2. Curr Genet 64:697–712. https://doi.org/10.1007/s00294-017-0786-4

  35. Li F, Ball LG, Fan L, Hanna M, Xiao W (2018) Sgs1 helicase is required for efficient PCNA monoubiquitination and translesion DNA synthesis in Saccharomyces cerevisiae. Curr Genet 64:459–468. https://doi.org/10.1007/s00294-017-0753-0

  36. Li S, Dong Z, Yang S, Feng J, Li Q (2019) Chaperoning RPA during DNA metabolism. Curr Genetics. https://doi.org/10.1007/s00294-019-00945-3

  37. Majka J, Burgers PM (2004) The PCNA-RFC families of DNA clamps and clamp loaders. Prog Nucl Acid Res Mol Biol 78:227–260. https://doi.org/10.1016/S0079-6603(04)78006-X

  38. Majka J, Binz SK, Wold MS, Burgers PM (2006) Replication protein A directs loading of the DNA damage checkpoint clamp to 5′-DNA junctions. J Biol Chem 281:27855–27861

  39. Maleva Kostovska I, Wang J, Bogdanova N, Schurmann P, Bhuju S, Geffers R, Durst M, Liebrich C, Klapdor R, Christiansen H, Park-Simon TW, Hillemanns P, Plaseska-Karanfilska D, Dork T (2016) Rare ATAD5 missense variants in breast and ovarian cancer patients. Cancer Lett 376:173–177. https://doi.org/10.1016/j.canlet.2016.03.048

  40. Marsella A, Cassani C, Casari E, Tisi R, Longhese MP (2019) Structure-function relationships of the Mre11 protein in the control of DNA end bridging and processing. Curr Genet 65:11–16. https://doi.org/10.1007/s00294-018-0861-5

  41. Mordes DA, Cortez D (2008) Activation of ATR and related PIKKs. Cell Cycle 7:2809–2812. https://doi.org/10.4161/cc.7.18.6689

  42. Moriel-Carretero M, Pasero P, Pardo B (2019) DDR Inc., one business, two associates. Curr Genet 65:445–451. https://doi.org/10.1007/s00294-018-0908-7

  43. Mosbach V, Poggi L, Richard GF (2019) Trinucleotide repeat instability during double-strand break repair: from mechanisms to gene therapy. Curr Genet 65:17–28. https://doi.org/10.1007/s00294-018-0865-1

  44. Offley SR, Schmidt MC (2019) Protein phosphatases of Saccharomyces cerevisiae. Curr Genet 65:41–55. https://doi.org/10.1007/s00294-018-0884-y

  45. Ogiwara H, Ui A, Enomoto T, Seki M (2007) Role of Elg1 protein in double strand break repair. Nucleic Acids Res 35:353–362. https://doi.org/10.1093/nar/gkl1027

  46. Osborn AJ, Elledge SJ (2003) Mrc1 is a replication fork component whose phosphorylation in response to DNA replication stress activates Rad53. Genes Dev 17:1755–1767. https://doi.org/10.1101/gad.1098303

  47. Parnas O, Zipin-Roitman A, Pfander B, Liefshitz B, Mazor Y, Ben-Aroya S, Jentsch S, Kupiec M (2010) Elg1, an alternative subunit of the RFC clamp loader, preferentially interacts with SUMOylated PCNA. EMBO J 29:2611–2622. https://doi.org/10.1038/emboj.20

  48. Pfander B, Diffley JF (2011) Dpb11 coordinates Mec1 kinase activation with cell cycle-regulated Rad9 recruitment. EMBO J 30:4897–4907. https://doi.org/10.1038/emboj.2011.345

  49. Sau S, Liefshitz B, Kupiec M (2019) The yeast PCNA unloader Elg1 RFC-like complex plays a role in eliciting the DNA damage checkpoint. mBio 10(3):e01159-19. https://doi.org/10.1128/mBio.01159-19

  50. Schwindt E, Paeschke K (2018) Mms1 is an assistant for regulating G-quadruplex DNA structures. Curr Genet 64:535–540. https://doi.org/10.1007/s00294-017-0773-9

  51. Shemesh K, Sebesta M, Pacesa M, Sau S, Bronstein A, Parnas O, Liefshitz B, Venclovas C, Krejci L, Kupiec M (2017) A structure-function analysis of the yeast Elg1 protein reveals the importance of PCNA unloading in genome stability maintenance. Nucleic Acids Res 10:100. https://doi.org/10.1093/nar/gkw1348

  52. Shiomi Y, Nishitani H (2013) Alternative replication factor C protein, Elg1, maintains chromosome stability by regulating PCNA levels on chromatin. Genes Cells 18:946–959. https://doi.org/10.1111/gtc.12087

  53. Shkedy D, Singh N, Shemesh K, Amir A, Geiger T, Liefshitz B, Harari Y, Kupiec M (2015) Regulation of Elg1 activity by phosphorylation. Cell Cycle. https://doi.org/10.1080/15384101.2015.1068475

  54. Singh B, Wu PJ (2019a) Linking the organization of DNA replication with genome maintenance. Curr Genet 65:677–683. https://doi.org/10.1007/s00294-018-0923-8

  55. Singh B, Wu PJ (2019b) Regulation of the program of DNA replication by CDK: new findings and perspectives. Curr Genet 65:79–85. https://doi.org/10.1007/s00294-018-0860-6

  56. Smith S, Hwang JY, Banerjee S, Majeed A, Gupta A, Myung K (2004) Mutator genes for suppression of gross chromosomal rearrangements identified by a genome-wide screening in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 101:9039–9044. https://doi.org/10.1073/pnas.0403093101

  57. Smolikov S, Mazor Y, Krauskopf A (2004) ELG1, a regulator of genome stability, has a role in telomere length regulation and in silencing. Proc Natl Acad Sci USA 101:1656–1661. https://doi.org/10.1073/pnas.0307796100

  58. Sugimoto K (2018) Branching the Tel2 pathway for exact fit on phosphatidylinositol 3-kinase-related kinases. Curr Genet 64:965–970. https://doi.org/10.1007/s00294-018-0817-9

  59. Szwajczak E, Fijalkowska IJ, Suski C (2018) The importance of an interaction network for proper DNA polymerase zeta heterotetramer activity. Curr Genet 64:575–580. https://doi.org/10.1007/s00294-017-0789-1

  60. Villa-Hernandez S, Bermejo R (2018) Cohesin dynamic association to chromatin and interfacing with replication forks in genome integrity maintenance. Curr Genet 64:1005–1013. https://doi.org/10.1007/s00294-018-0824-x

  61. Wani S, Maharshi N, Kothiwal D, Mahendrawada L, Kalaivani R, Laloraya S (2018) Interaction of the Saccharomyces cerevisiae RING-domain protein Nse1 with Nse3 and the Smc5/6 complex is required for chromosome replication and stability. Curr Genet 64:599–617. https://doi.org/10.1007/s00294-017-0776-6

  62. Zimmer C, Fabre E (2019) Chromatin mobility upon DNA damage: state of the art and remaining questions. Curr Genet 65:1–9. https://doi.org/10.1007/s00294-018-0852-6

  63. Zou L, Elledge SJ (2003) Sensing DNA damage through ATRIP recognition of RPA-ssDNA complexes. Science 300:1542–1548. https://doi.org/10.1126/science.1083430

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Acknowledgements

We thank all the members of the Kupiec lab for ideas and support. MK was supported by grants from the Israel Science Foundation, the Israel Cancer Research Fund and the Minerva Center. SS is a Ramalingaswami Fellow, supported by DBT, Govt. of India.

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Correspondence to Martin Kupiec.

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Sau, S., Kupiec, M. A role for the yeast PCNA unloader Elg1 in eliciting the DNA damage checkpoint. Curr Genet 66, 79–84 (2020). https://doi.org/10.1007/s00294-019-01020-7

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Keywords

  • PCNA unloading
  • DNA damage response
  • Replication checkpoint
  • DNA damage checkpoint
  • Mec1 (ATR)
  • RAD53 (CHK2)
  • Rad9 (53BP1)
  • Dpb11 (TopBP1)